19
News & Views Issue 7 January 2016 INDIA ALLIANCE

News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

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Page 1: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

News amp Views

Issue 7

January 2016

INDIA ALLIANCE

We at the India Alliance wish you a very happy and prosperous 2016 There were many highlights and events last year which we

tried to bring to you through these newsletters our brand new website social media and emails We hope to be able to do the same this

year

The first issue of 2016 has announcements of our Fellowship schemes updates on funded research and other IA activities It also

features interesting article interviews and event announcements

Apart from our Fellows who are making waves in their fields we are also very fortunate to have distinguished scientists on our

fellowship selection committee We wish to congratulate our committee member Dr Amit Sharma (ICGEB New Delhi) for being awarded

the Infosys Award 2015 for ldquofor his pioneering contributions to deciphering the molecular structure at atomic level of key proteins

involved in the biology of pathogenesis of the malarial parasiterdquo In a move to encourage and support women scientists Department of

Biotechnology Government of India along with Biotechnology and Biological Research Council (BBRC) Economic and Social Research

Council (ESRC) and the Royal Society announced a program for women in STEM at JNU New Delhi earlier this month Details of the

program will be announced Feb end 2016

Last year ended with 25 Fellowships being awarded at the November 2015 round of interviews for Clinical and Public Health

Research Margadarshi and Intermediate Research (basic) Fellowship schemes bringing the total number of awards to 202 at 64

different institutions We are happy to welcome the new awardees to the India Alliance Family We are now accepting preliminary

applications for the Clinical and Public Health Research Fellowships 2016 Please check our website for the call for applications for our

Research Training Fellowship Senior and Intermediate Fellowship (Basic scheme) and Margadrashi Fellowship early next month

On the Public Engagement front we are very pleased to announce our support for the Art amp Science Project at Khoj International

Artists Association details of which can be found in this newsletter and on the Khoj website It promises to be a great platform for

interdisciplinary dialogue and exchange between scientists and artists and we encourage anyone interested to apply (artists) or get

involved (scientists) In an effort to sensitize public about pressing health issues India Alliance along with Public Health Foundation of

India will be organizing a Health discussion series (Voices for Health) where the public thought leaders and experts will be engaged in

a series of panel discussions in multiple Indian cities across the year More information on this series will be posted on our website in a

couple of weeks This issue also includes reports on a Public Lecture given by renowned cancer researcher and Noble Laureate Dr

Harold Varmus in December at NII New Delhi and the first one-day Foldscope workshop organized by the Department of

Biotechnology

On the Science Communication front we will be holding our biannual two-day SciComm workshop in Hyderabad on 21-22 March

2016 Applications for this workshop are now closed and selected participants will be informed shortly Our SciComm team will be

visiting Maharaja Sayajirao University of Baroda to hold the one-day SciComm101 workshop in March In an attempt to strengthen and

diversify its Science Communication activities India Alliance has tied up with Nature India and Nature Jobs to launch a new workshop

format which would focus on science writing communication and alternate science careers Please write to us if you would like to know

more about this workshop

In this issue we feature interviews of our Clinical and Public Health Research Fellowship Selection Committee member and eminent

geneticist Dr Aravinda Chakravarti Senior Fellow Dr Roop Malik who is working on motor proteins at TIFR Mumbai and Dr Sujatha

Reddy our Grants Adviser Heartfelt gratitude to them for sharing interesting and useful insights on their work and life In the piece

titled ldquoA Sponge Against a Swordrdquo Intermediate Fellow Dr Partho Sarothi Ray writes about the molecular underpinnings of cancer and

inflammation and the crosstalk between the two in the backdrop of his recently published research on RNA-binding proteins bdquoAsk the

Scientist‟ section is an attempt to make science more accessible and understandable and includes simple questions from non-scientists who

are keen to know more about scientific principles underlying life processes the human body etc In this issue questions on brain and its

functions are answered by our Fellows- Dr Venkatasubramanian Ganesan Dr Urvakhsh Mehta Dr Supratim Ray and Dr Nixon Abraham

A big thank you to all of them

Last but not the least thank you to our Early Career Fellow Dr Srinivas Marmamula for sharing the image for the cover which shows a

vision technician assessing vision in a woman in a remote rural area as part of public research project in Telangana initiated by L V

Prasad Eye Institute in India

Here‟s to a year of new possibilities explorations and discoveries

Best wishes

Sarah Iqbal PhD

Public Engagement Officer

EDITORIAL

1

CONTENTS

3 INDIA ALLIANCE CALL FOR APPLICATIONS

Clinical and Public Health Research Fellowships 2016

4 INDIA ALLIANCE RECOMMENDED FELLOWSHIP AWARDEES

Clinical and Public Health Research Fellowship Intermediate (Basic) Fellowship

5 IN CONVERSATION WITH

Dr Aravinda Chakravarti Director Center for Complex Disease Genomics amp Professor of Medicine

at Johns Hopkins University School of Medicine

7 SCIENCE COMMUNICATION

New Nature India-India Alliance workshop SciComm Hyderabad SciComm101 workshop

announcements

8 PUBLIC ENGAGEMENT CORNER

Art amp Science project Harold Varmus Lecture report Ask the Scientist

12 INDIA ALLIANCE FELLOW IN SPOTLIGHT

Dr Roop Malik Senior Fellow TIFR Mumbai

13 FEATURE ARTICLE

ldquoA Sponge Against a Sword rdquo

by Dr Partho Sarothi Roy Intermediate Fellow IISER Kolkata

15 INDIA ALLIANCE STAFF CORNER

Dr Sujatha Reddy Grants Adviser India Alliance

16 EXTERNAL EVENTS

First Foldscope Workshop in India- report Medicine Corner Exhibition Trick or Treat workshop

2

Sarah Iqbal- IA
Text Box
Click on the titles to go directly to the pages

Eligibility

Eligibility limit covers the entire range of Clinical and Public

Health Research Fellowship schemes

bull No age or Nationality restrictions

bull The candidates need not be resident in India while

applying but should be willing to establish an

independent research career in India

bull Clinicians and Public health researchers do not require a

PhD to apply

bull This competition is open for clinicians and public health

researchers with up to 15 years of post-

MDMSMPHPhD or equivalent clinical public health

research experience

bull The Applicants are advised to choose the most

appropriate scheme suitable for them based on their

qualification research experience career trajectory and

track record Please refer to the guidance notes

provisions and mandate of the scheme for assessing your

eligibility on the website The Office reserves the right to

advice on the suitability of the scheme accordingly

Early Career Fellowship This scheme provides a unique

opportunity for those who have shown promise to pursue

research and wish to further their efforts to build a research

career under the supervision of a Fellowship

supervisor Guidance note Suitable for applicants in the final

year PhDMDMSMPH or have up to 4 years of relevant

experience

Intermediate Fellowship For those who have been

successful in building a track record of pursuing a cutting

edge research and wish to establish their own independent

clinicalpublic health research program in India Guidance

note Suitable for applicants with 4-7 years of relevant

experience

INDIA ALLIANCE FELLOWSHIP ANNOUNCEMENT

CALL FOR APPLICATIONS

Application forms are available on the India Alliance online

application System (IASys) at

httpsfellowshipswellcomedbtorgLoginaspx

Please visit our website for further information on the application process Please write to us with

queries to infowellcomedbtorg

3

CLINICAL AND PUBLIC HEALTH RESEARCH FELLOWSHIPS 2016

Preliminary Application Deadline 1 March 2016

India Alliance invites applications for three Fellowship schemes

Early Career Fellowships Intermediate Fellowships and Senior Fellowships

Senior Fellowship For those who have demonstrated their

potential to lead an independent research program and

want to expand it further to undertake pioneering research

Guidance note Suitable for applicants with 7-15 years of

relevant experience

Remit Full spectrum of biomedical science involving clinical

and public health research

Provisions

bull These Fellowships would encourage interested clinicians

to pursue their research goals in combination with their

clinical duties

bull Competitive personal support

bull Generous research support with flexibility to

accommodate requirements of clinical and public health

research

bull Flexibility to request additional support staff

bull Support training cost and research sabbatical

bull Funds for International training and travel

bull Opportunity to pursue a PhD on the India Alliance

funded research

Essentials on the application

bull A research proposal that seeks to answer an original

biomedical research question

bull A not-for-profit Host Institution in India that will

administer the Fellowship for the full duration of the

award A salaried position or commitment to a salaried

position at the Host Institution is not required

bull A Sponsor at the Host Institution who can guarantee

space and resources for the duration of the award

bull In case of an Early Career Fellowship a Fellowship

Supervisor who can guarantee access to laboratory

space and resources required for the project as well as

provide relevant scientific guidance for the tenure of the

Fellowship

CLINICAL AND PUBLIC HEALTH RESEARCH FELLOWSHIPS

Early Career Fellowships

Dr Jayanth Kumar Palanichamy All India Institute of Medical Sciences New Delhi

Dr Aparna Mukherjee All India Institute of Medical Sciences New Delhi

Dr Deepak Kamath St Johns National Academy Of Health Sciences Bangalore

Intermediate Fellowships

Dr Aparna Rao L V Prasad Eye Institute Bhubaneswar

Dr Abi Vanak Ashoka Trust for Research in Ecology and the Environment Bangalore

Dr Shivarama VaramballyNational Institute of Mental Health and Neurosciences Bangalore

Dr Rashmi Rodrigues St Johns National Academy Of Health Sciences Bangalore

Dr Mahesh Kate Christian Medical College Ludhiana

Research Training Fellowships

Ms Urvita Bhatia Sangath Porvorim

Dr Deepak Gautam All India Institute of Medical Sciences New Delhi

Dr Sumsum P Sunny Mazumdar Shaw Medical Center Bangalore

Dr Dhruva Ithal National Institute of Mental Health and Neurosciences Bangalore

Dr Rakshathi B National Institute of Mental Health and Neurosciences Bangalore

ANNOUNCEMENT

RECENTLY RECOMMENDED AWARDEES

BASIC RESEARCH FELLOWSHIPS

Intermediate Fellowships

Dr Sridharan Devarajan Indian Institute of Science Bangalore

Dr Nitin Gupta Indian Institute Of Technology Kanpur

Dr Sachin Kotak Indian Institute of Science Bangalore

Dr Aravind Penmatsa Indian Institute of Science Bangalore

Dr Siddhesh Shashikant Kamat Indian Institute of Science Education and Research Pune

Dr Mohan Joshi Centre for DNA Fingerprinting and Diagnostics Hyderabad

Dr Satish Khurana Indian Institute of Science Education and Research Thiruvananthapuram

Dr Pinky Kain Indian Institute of Technology Roorkee

Dr Santosh Chauhan Institute Of Life Sciences Bhubaneswar

India Alliance announced Fellowship Awardees of the Clinical and Public Health Research Fellowship

scheme and Intermediate Fellowship under the Basic Biomedical Research competition in December 2015

The interviews for these Fellowship schemes were held in November 2015

indicates institution that before this award did not have any India Alliance Fellow

4

MARGADARSHI FELLOWSHIP

Prof Satyajit Mayor National Centre for Biological Science Bangalore

IN CONVERSATION WITH

Dr Aravinda Chakravarti

Dr Aravinda Chakravarti is a Professor of Medicine Pediatrics Molecular Biology amp Genetics and Biostatistics and Director Center

for Complex Disease Genomics at the Johns Hopkins University School of Medicine and the Bloomberg School of Public Health He

also has a long association with the India Alliance as a member of its Clinical and Public Health Research Fellowship committee

What motivated you to become a scientist

I cannot say that it was any one person or one event or any one

point of time that led me to consider doing science Nor did I know

what being a scientist would entail or how one prepared to become

one I was not interested in science nor good at it or anything else for

that matter before the 9th grade But subsequently it was the

concreteness and logic of mathematics and the sciences that

appealed to me I also began reading material outside my textbooks

such as books in the Nuffield Science Series and others I came across

in the Calcutta British Council Library which began giving me a

broader look at the world of science But I was still clueless This was

evident in my applying for almost every conceivable program for

college (Engineering Medicine Geology Agriculture Physics and

Statistics) and being selected but not necessarily into the best schools

or programs Thus bdquosuccess‟ did not clarify my thinking any one bit

Finally I did choose to attend the Indian Statistical Institute (ISI)

outside Calcuttahellipa then beautiful oasis of calm in the politically

turbulent Calcutta of 1970‟s when being young well-read and aware

were enough to raise suspicions in the Calcutta Police (For those who

doubt the serious and mortal danger all young people in Calcutta

were under during this time read the daily newspaper reports from

the 70‟s)

For me Indian Statistical Institute (ISI) was

an escape from reality and an entry into a

synthetic artificial and manufactured world

of quantitative ideas

Our courses over 4 years in a US-style undergraduate were 50

Mathematics and Statistics and 50 an assortment of sciences and

economics (to learn the various domains in which quantitative

reasoning would be critical) where we were taught to ask bdquowhy‟ not

only bdquohow‟ something worked For the first time I found myself in an

atmosphere where understanding mattered more than knowledge

(dont worry knowledge did matter greatly) the pursuit of a job was

a side issue and we were encouraged to discover any area we

wished (or thats how I felt) I also had passionate teachers who were

the very best in the world For the first time I felt liberated learning

was fun and pursuing science as a life seemed like the only natural

thing to do It wasnt a one day transformationhellipby the time I left ISI I

knew that I could ask and answer at least some questions ISI was the

institution where the famed British polymath and geneticist J B S

Haldane came to in 1957 and became one of the architects of my

undergraduate program Although Haldane died in 1964 his ghost

was still around when I was a student at the ISI That I would do

genetics and be a scientist particularly in human genetics was

therefore a no brainer

Could you briefly take us through your scientific journey and

about your interest in genetics

My interest in genetics was established at the ISI but no less fueled by

my reading of Jim Watson‟s The Double Helix in 1970 and then as

credited by Watson and Crick Erwin Schrodinger‟s What is Life As a

student of the quantitative sciences at ISI the part of genetics that

appealed to me (simply because I could digest it) was Population

Genetics Also ISI had a Department of Human Genetics that

performed numerous studies of human genetic molecular diversity

across populations in India So my early training was in studies of

human population diversity Nevertheless Haldane‟s research (that I

was increasingly becoming aware of) was equally in family studies

that exemplified mechanisms not evident in population studies So as

a student I conducted and published research into the inheritance of

simply observable traits (bdquohand clasping‟ or the phenotype where you

classify individuals by whether they fold their left thumb over their

right or vice versahelliptry it only one way feels correct) just to learn

genetics and to attempt to combine the family and the population

methods that are so common today Fortunately by this time I had left

myself few opportunities to be interested in doing anything else but

human genetics

5

IN CONVERSATION WITH Dr Aravinda Chakravarti

Being rejected by several programs to study genetics in India

(because I was not a biology undergraduate) I chose to do graduate

work with the noted geneticist and molecular evolutionist Masatoshi

Nei at the University of Texas Houston where he had just moved I

arrived in Houston in 1974 and was immediately thrust into a small

intense center with brilliant people and expected to perform research

at a level I was surely unaccustomed to This group was the epicenter

of the then neutralist-selectionist debate in molecular evolution a

problem that was exciting but not my cup of tea I wanted to study

human genetics and finally fashioned a research project with Nei that

explored the theoretical consequences of improved genetic counseling

with linkage and association (linkage disequilibrium) markers and

graduated with a PhD in 1979 This research was not only far ahead

of its time coming before the proposal of creating a human linkage

map using RFLPs (restriction fragment length polymorphism) in 1980

but I was the only Nei student who worked outside molecular

evolution In many ways then my development in genetics became

very broad and haphazard since I often focused on areas that were

not my primary training grounds

By this time I was a geneticist but thought I needed further training in

genetic epidemiology to understand human disease better However

after an unsuccessful postdoc at Seattle I abandoned this idea to

take a non-tenured teaching position at the University of Pittsburgh

thinking that the bdquofree‟ time I would have would allow me to catch up

on the revolution in recombinant DNA technology that was underway I

am glad I did since this was one of the best

professional decisions I made by forgoing

the standard path

I taught at Pittsburgh for 5 years and subsequently obtained an NIH

Research Career Development Award to pursue a research career

That began my standard research career in human genetics

What according to you are the challenges in your field of

research

The field of human genetics is not the one I trained in since so much

has changed with the sequencing of the human genome Human

genetics has two distinct themes one descriptive as to the causes of

human variation be it molecular or phenotypic (the bdquohow‟ question)

and a second mechanistic as to how variation in molecular

mechanisms impact phenotype variation particularly disease (the

bdquowhy‟ question) The whole attraction of the human genome project to

me and others like me who spent more than a decade on building the

now available community resources (maps clones sequences variants

transcripts etc) was to move from the first set to the second set of

questions This transformation is difficult since it is not in the comfort

zone of conventional human genetics its hard and unpredictable

much more hypothesis-driven and much more experimental The

challenge in my field and in many associated medical specialties is

that it‟s far easier to do the first then the second Scientists are voting

with their feet Human geneticists are far more content in sequencing

human genomes finding associations with disease and doing facile

functional annotation than a serious investigation into why does this

gene causes type 2 diabetes and the next one congenital cataract

Or why mutations in the same gene cause a neuroendocrine tumor

when activating but congenital aganglionosis when loss-of-function

Or how come the same mutation can act as either activating or loss-

of-function

The biggest challenge in my field is to

overcome the inertia that molecular

description = etiological explanation

If you were not a scientist you would behellip

I really have no idea I presume the Bengali in me implicitly wants

or always wanted to be a writer but that would be a great leap of

faith and quite arrogant Even good scientific writing is hard very

hard indeed I have often read someone else‟s paper that I enjoyed

and thought that I could have done the same work a similar thought

has not appeared after reading someone else‟s creative work except

when it is quite bad

5 What is the best advice you have ever received

Unfortunately most advice that most people get and give is bad

More correctly its difficult to know (what‟s the test) when it is good

and when bad Each of us likely adapt a post-hoc explanation to our

stories all of which are likely revisionist Nevertheless two different

people (a brother and a family friend) at about the same time

(1979-1982) told me to abandon what I was doing (an unsuccessful

postdoc and forcing myself to complete reading a fairly racist

account of the Black Hole of Calcutta) because it was beyond my

enjoyment They both suggested that I drop it and do something else

One should not shoulder a burden that is great unless some higher

purpose is at stake One needs to learn how to apportion risk with

benefit

Your message for young students and researchers

Science is difficult but exhilarating in its rare moments of success

and it‟s usually followed by long periods of stasis It is a great but

frustrating life and there are many worse ways of making a living It

is like other types of creative endeavors where discovery is real but

rare If you wish to do it be sure you can enjoy its moods Science

today is also multidisciplinary and translational its application to

humans and other benefits can also be tangible sources of pride But

do it not for these benefits do it because the science gives you great

joy Yes joy Consider that you are one in an

unbroken intellectual chain from Johannes

Kepler and Isaac Newton If you choose

science you are special

Dr Chakravarti‟s laboratory focuses on the development and

applications of molecular genetic genomic and computational

methods for identification of human disease genes through

genetic dissectionldquo He has been a key participant and architect

of the Human Genome HapMap and 1000 Genomes project Find

out more about his research here

6

Workshop at a glance One-day workshop to equip young science

researchers with tools and strategies for effective communication of

their ideas experiments and scientific results from a science

communication perspective Help them to make science career choices

Vision Science communication plays an integral role in one‟s scientific

career Being able to effectively disseminate research findings within

the community and to consider collective opinions in prioritising

research needs is an important attribute of scientific maturity In

keeping with its mandate to empower future leaders of Indian science

the Wellcome TrustDBT India Alliance periodically conducts one-day

(SciComm101) and two-day (SciComm Hyderabad) science

communication workshops for the past four years This complements

seamlessly with Nature India‟s mandate to showcase India‟s science bdquoas

it happens‟ in laboratories and institutions across the country through

in-depth coverage and analysis of research and science policy The

proposed workshop would be part of Nature India‟s many

communication outreach activities as the one-stop media platform for

India‟s science

The Wellcome TrustDBT India Alliance and Nature India both

represent possibilities for young PhD scholars and postdoctoral

scientists to transition into academic as well as non-academic science

careers Information and advice on how to explore various career

options will form an important part of these workshops with

Naturejobs as the key organiser of the career session

Structure amp format

The workshop will be a one-day event preceding a biomedical (or

scientific) conference organised by reputed science

societiesorganisationsinstitutes and Universities in India A large

participation by PhD students postdoctoral fellows and junior

scientists will be a pre-requisite for holding this workshop Organising

this workshop as part of a conference will ensure participation from a

wide range of institutions across India The workshop will include 3

separate sessions

Session 1 Scientific Writing (moderated by WTDBT Alliance)

Topics to be covered

bull Ethics in research

bull Presentation skills

bull Manuscript writing

bull Grants writing

bull CVs and letters

Session 2 Science Communication (moderated by Nature India)

Topics to be covered

bull Science journalism

bull Popular science writing

bull Effective press releases

bull Hands-on skills on dejargonising science

Session 3 Alternate Science Career (moderated by Nature Jobs)

Topics to be covered

bull Career in the Industry

bull Career in Science PromotionIntellectual Property

bull Career in PolicyGrant organizations Journalism

Science Communication and Career Workshop Series (In partnership with Nature India amp Naturejobs )

Please contact us at workshopswellcomedbtorg to find out more about this series

INDIA ALLIANCE

SCIENCE COMMUNICATION

SciComm101 workshop

10 March 2016 MSU Baroda

Two-day SciComm workshop

21-22 March 2016 Hyderabad Applications under review

For more details visit SciComm Workshop under Quick Links on our website

Upcoming Workshops

5

ABOUT THE ART amp SCIENCE PROJECT

CALL FOR APPLICATIONS THE UNDIVIDED MIND |ART +

SCIENCE RESIDENCY AT KHOJ

Residency Dates March 2nd ndash April 2nd 2015

Application Deadline February 2nd 2015

Proposals are invited for bdquoThe Undivided Mind‟ a four-week

international residency for artists whose work explores the

intersection of art and science

At first it may seem that the pairing of Art amp Science is an atypical

choice as the two fields and methods of practice have almost

universally been represented as diametric opposites of each other

However on closer examination the similarities between artists and

scientists far outweigh their stereotypical differences Both are

dedicated to research and to asking the big question- what is true

Why does it matter How can we move society forward Moreover

both the lab and the studio are spaces that famously encourage

open-ended enquiry and emphasis on process In tune with Khoj‟s

commitment to cultivate an environment that allows for

experimentation and innovation the Art amp Science residency will be

a step towards furthering the explorations of interdisciplinary

practitioners This is the second edition of a Khoj residency focusing

on Art + Science to know more about the first edition please

click bdquohere‟

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

The following India Alliance Fellows will be participating in the

project

(NOTE If an applicant wishes to connect with any of the following

researchers in advance of submitting their proposal please contact

the Khoj team at bdquoapplicationskhojworkshoporg‟ for an

introduction please do the same if you are a scientist and would like

take part in this project )

Dr Venkatasubramanian Ganesan National Institute of Mental

Health and Neurosciences (NIMHANS) Bangalore

Dr Pallab K Maulik The George Institute for Global Health New

Delhi

Dr Anurag Agarwal CSIR-Institute of Genomics amp Integrative

Biology (IGIB) New Delhi

Dr Tavpritesh Sethi All India Institute of Medical Sciences (AIIMS)

New Delhi

Dr Lolitika Mandal Indian Institute of Science Education and

Research (IISER) Mohali

Dr Urvakhsh MehtaNIMHANS Bangalore

Dr Sheetal Gandotra IGIB New Delhi

Visit Khoj website to find out more about the residency and the application process

Apply by

2 February 2016

India Alliance is pleased to announce its support for Art amp Science Project at Khoj International Artists Association New Delhi details of

which can be found below and on the Khoj website It promises to be a great platform for interdisciplinary dialogue and exchange

between scientists and artists and we encourage anyone interested to apply (artists) and get involved (scientists)

THEME

The theme of the 2016 edition of The Undivided Mind is bdquoHealth‟

Within this broader framework three curatorial frameworks or

modes for exploration are suggested Terrestrial Health refers to

that which is on or related to the earth This sub ndash theme suggests an

investigation into the physical health and structure of the body (both

human and animal) the environment the community and the

interrelations between these spheres Mental Health refers to that

which is of or relating to the mind This sub ndash theme focuses on a

psychological investigation of what constitutes Health of the mind

and raises questions about the bdquosocially‟ defined state of well-being

where issues‟ surrounding the legal rights and entitlement of

personhood for those living with a mental disorder is open for

debate Finally Extraterrestrial Health may refer to any object

being or idea beyond the planet Earth This sub ndash theme opens up a

space where the relationship between Earth and other planetary

bodies can be studied What does it mean for human existence when

sending human life forms to Mars is projected to take place by

2020 What are the long term effects and solution to space debris

if life projects out beyond Earth This sub ndash theme also invites

applicants to consider the abstract and metaphorical imaginings of

health in contemporary and future societies

6

Nobel Laureate Dr Harold Varmus recognized for his research on

retroviruses and the genetic basis of cancer gave a lecture on ldquoRecent

Developments in Cancer Researchrdquo at National Institute of Immunology

(NII) New Delhi an event co-organised by NII Wellcome TrustDBT

India Alliance and Department of Biotechnology Government of

India His lecture largely gave an overview of the recent

developments challenges and the future directions in the field of

cancer research which included the current research of his group in

this area

Dr Varmus who had spent time in Bareilly as a young medical

student described cancer as a complex disease that requires

innovative research and treatment strategies At the outset Dr Varmus

introduced the key questions that drive the cancer research field- Is

cancer one disease or many diseases What makes the cancer cell

grow so stably in such an inappropriate manner How does a normal

cell become a cancer cell Providing answers to these questions

formed the backdrop of Dr Varmus‟s lecture which drew from his

research work till date and other advances in the field

Dr Varmus entered the field of cancer research in 1970s as a

postdoctoral scientist in the laboratory of Dr John J Michael Bishop at

University of California San Francisco USA the same year National

Cancer Act was signed in the country Dr Bishop and Dr Varmus

together received the Nobel Prize in Medicine and Physiology in

1989 ldquofor their discovery of the cellular origins of retroviral

oncogenesrdquo During his lecture Dr Varmus confessed standing on the

shoulders of giants of retroviral and cancer research such as Dr

Peyton Rous Dr Harry Rubin and Dr Howard Temin to ask the question

of how retroviruses transformed cells and cause tumours This question

led him to look for genes that make a normal cell behave like a

cancer cell which initially involved studying cancer-causing RNA

virusesretroviruses in animals The retrovirus that played a lead role

in Dr Varmus and his colleague‟s work was the Rous Sarcoma Virus

(RSV) discovered by Dr Peyton Rous in 1911 which he showed caused

a type of cancer in chickens Dr Varmus and colleagues set out to

prove the hypothesis that retroviruses enter host cells and capture

normal genes in that cell by inserting their DNA converting them into

cancer-causing genes or oncogenes Dr Varmus and his group

employed various cellular chemical as well as genetic tools to

establish that retroviruses can indeed act as mutagens by inserting

their DNA in host cells and turning them into cancer cells After this his

group went on to identify the cancer-causing genes present in the

virus and subsequently discovered many new oncogenes v-Src (a

gene of RSV) being the first one Following these discoveries and

subsequently many others led to the belief that the genetic basis of

cancer is highly heterogeneous Dr Varmus told us that in order to

catalogue these complexities the Cancer Genome Atlas was

established in 2005 which till today serves as a collection of the

genetic mutations responsible for different cancers

Apart from the complexity and vastness of the cancer genome

other challenges in the field according to Dr Varmus are genetic

heterogeneity and evolution of tumours due to various environmental

factors such as exposure to UV pollution tobacco use and other

environmental carcinogens that are on the rise He used the example

of renal tumor evolution which illustrates Darwin‟s theory of ldquoevolution

of speciesrdquo to show that this rapidly changing genetic repertoire can

have significant impact on diagnosis therapeutic interventions and

prognosis Another issue of concern highlighted by Dr Varmus was the

absence of suitable drugs against many common targets for cancer

such as cancer-causing RAS genes and many transcription factors

which have been shown to contribute towards cancer formation Dr

Varmus opined that lack of understanding of the underlying

complexity of resistance to cancer therapies is another roadblock in

cancer treatment He was also strongly of the opinion that there are

not enough public health interventions to prevent cancer- this he felt

needs to go hand in hand with finding cure for cancer

Dr Varmus also offered solutions to these problems He suggested

that research needs to ldquolook beyond genes and focus on patterns and

pathwaysrdquo and physiological changes taking place in cancer cells He

shared his group‟s current interest in studying ldquooncogene addictionrdquo

which is based on the premise that some oncogenes not only give rise

to cancer but also maintain the cancerous state of the cells

Interpreting the downstream effects of these cancer genes on the

pathways could be employed as a strategy to attack multiple targets

by drugs in different cancers Even though he hailed the successes of

many commonly used and extremely efficacious anti-cancer drugs

such as Gleevec Gefitinib Erlotinib but in light of growing

complexity of the disease proposed the need for adopting more

innovative drug discovery and treatment approaches Continuing on

the topic of therapeutics Dr Varmus mentioned the recent advances in

immunotherapeutic approaches to treat cancer which would require

us to understand why the otherwise combative immune system does

not kill cancer cells He suggested that gaining understanding of these

immune check points and accordingly targeting them by antibody

inhibitors could serve as one more effective treatment strategy-

another project his research group has undertaken In addition to

these therapeutic approaches Dr Varmus very strongly asserted that

ldquonot everything we talk about cancer should be about cancer therapy

but also about preventionrdquo and that this disease ought to be on the

global health agenda

Dr Varmus very eloquently concluded his talk by stating that

ldquoconfronting cancer needs a balance between grasping its complexity

and seeking simple solutionsrdquo As expected he received many

questions from the audience after his lecture on the genetics and

biology of various cancers potential use of vaccines in cancer

treatment crosstalk of cancer with other diseases and many others to

which he responded with prudence and an underlying sense of

optimism

Prior to his lecture Dr Varmus over an hour meeting with 10 young

cancer researchers discussed their work This group included the

following Wellcome TrustDBT India Alliance Fellows - Dr Reety Arora

(ECF InStem Bangalore) Dr Anjali Bajpai (ECF IIT Kanpur) Dr

Bushra Ateeq (Int Fellow IIT Kanpur) Dr Kundan Sengupta (Int Fellow

IISER Pune) and Dr Sandeep Singh (Int Fellow NIBMG Kalyani) Dr

Varmus also sought information on the India Alliance Fellowships and

was impressed by its funding model and reach

LECTURE REPORT

Recent Developments in Cancer Research By Dr Harold Varmus Nobel Prize in Medicine and Physiology Weill Cornell Medical College USA

at

National Institute of Immunology New Delhi

16 November 2015

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

7

ASK THE SCIENTIST about

The Human Brain

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

This section will bring to you answers to those burning scientific questions that you always wanted to ask the guys in the white

coat For this issue we asked some of our Fellows to shed light on the various operations of the brain

How can we measure attention

DR SUPRATIM RAY Indian Institute of Science Bangalore

Intermediate Fellow

Attention can be of different types such as sustained (vigilance)

selective (focusing at one stimulus in the presence of distractors) or

alternating (involves switching) which can be measured using a

variety of cognitive tests (such as test of everyday attention (TEA) or

Posner cuing task) For example in a classical Posner task a subject

is repeatedly shown two stimuli and cued to attend to one of them

and instructed to respond to a change in the stimulus (say by

pressing a button) The cue could be valid (change occurs at the cued

stimulus say for 80 of the trials) invalid (change occurs at the

uncued stimulus) or neutral (ambiguous) Selection attention can be

measured by comparing the accuracy and the time taken to press

the button after stimulus change (called reaction time) for different

cue types

Different components of attention such as orienting towards a

location detecting a target or maintaining vigilance are carried out

by distinct brain areas in the prefrontal and parietal lobes and some

sub-cortical structures (such as superior colliculus) Overall

performance depends not only on how these areas perform but also

how they communicate with each other and on the levels of

neuromodulators such as norepinephrine

How can we sense smell Is it possible to live without this

sense of smell

DR NIXON ABRAHAM Indian Institutes of Science Education amp

Research (IISER) Pune

Intermediate Fellow

Once Dr Lewis Thomas (1913-1993) the poet and a philosopher of

medicine who also served as the dean of the medical schools at the

New York University and Yale was asked to select seven wonders of

the modern world Olfaction (olfactory receptor cell) was fifth in his

list How does the modern fifth wonder that brings us the smell of our

surroundings ndash the good and bad work

The process of making sense of smell start by binding the odor

molecules to the olfactory receptors located in the olfactory sensory

neurons (OSNs) in the nose This binding triggers a series of signal

amplification steps which lead to electrical spikes (so called action

potentials) in OSNs This olfactory information whose intensity is

encoded by varying the number of action potentials is then passed

onto the projection neurons named mitral and tufted cells in the

olfactory bulb These projection neurons whose excitatory actions

are controlled by various inhibitory neurons carry the olfactory

information to the higher centers in the brain so that we perceive the

smell of spicy tasty food and putrid garbage ndash the good and bad

from the environment

Continued

9

Brain waves

measured by EEG

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

What is really happening inside the brain of a Schizophrenia

patient Does it look any different from a normal brain

DR VENKATASUBRAMANIAN GANESAN NIMHANS Bengaluru

Intermediate Fellow

The brain of a schizophrenia patient is reduced in overall volume

with increase in the size of the ventricles (parts of the brain that

contain cerebrospinal fluid) however certain parts like hippocampus

superior temporal gyrus and prefrontal cortex are more affected

than others Using certain advanced brain imaging research studies

(for example high resolution structural MRI functional MRI Magnetic

Resonance Spectroscopy Positron Emission Tomography and Diffusion

Tensor Imaging and similar others) subtle brain abnormalities in

structure function neurochemical profile as well as brain connectivity

have been demonstrated in several brain regions in schizophrenia

patients It is important to note that these findings are obtained

from advanced research studies that have compared brains of a

Why are the mirror neurons called the Minds mirror What do

they reflect

DR URVAKHSH MEHTA National Institute of Mental Health amp

Neurosciences (NIMHANS) Bengaluru

Early Career Fellow

Mirror neurons are specialized nerve cells that discharge when

we perform actions as well as when we observe others perform the

same action Rizzolatti and colleagues accidentally discovered them

in monkeys These neurons also get vicariously activated when we

perceive emotional states of others This unique bdquoexperience sharing‟

property of mirror neurons perhaps enables us to decipher goals

intentions and emotions of others

In several of our daily social interactions we need to take

perspectives of others decipher deception share feelings and

empathize with others The mirror neuron system is an important

brain network that helps us peek into the minds of others and try to

understand people They translate sensory information (eg

observation of an action) into a motor template which is similar to

the format an observer himself uses to perform that very action This

motor template can help us interpret the goals and feelings

underlying observed actions The definitive demonstration of mirror

neurons in humans was as recent as 2010 There is also growing

evidence of a dysfunctional mirror neuron system in psychiatric

disorders like autism and schizophrenia It is a long and exciting

future ahead to decipher spatiotemporal regulatory and genetic

underpinnings of this unique neuronal network ndash this will possibly

help understand and treat social brain disorders better

Schizophrenia

What happens if we loose our sense of smell Loss of olfaction can

be caused by many reasons ranging from viral infections to

neurodegenerative disorders As our emotions and memories are

strongly related to olfaction the loss of this sense can lead to

depressed state and even affect bonding with family members Just

imagine sipping from your morning coffee without sensing it‟s aroma

- our taste could be badly affected by losing sense of smell The

ongoing research at the nasal stem cell level might provide clinical

solutions for the disorders of the olfactory sensory neurons to regain

this wonderful sense

group of schizophrenia patients with that of healthy subjects thus

these are group averaged findings that are currently not applicable

for diagnosing schizophrenia in an individual patient in a regular

clinical setting In ldquoa specific patientrdquo one may not be able to find

any striking abnormality in the physical appearance of the brain (ie

a routine CT or MRI brain scan may not be able to identify any

obvious aberration) Several ongoing research studies are in pursuit

to identify clinically useful biomarker to diagnose schizophrenia

Find out more about Dr Ganesan‟s research on schizophrenia here

Do you have a burning scientific

question

Send them to

publicengagementwellcomedbtorg

Mirror neuron activity in the brain both when the monkey grasps an object

and when it observes the experimenter grasping the object Mirror neurons

were first discovered by Rizzolatti and colleagues when they were studying

motor actions in macque monkeys

10

INDIA ALLIANCE FELLOW

DR ROOP MALIK Senior Fellow TIFR Mumbai

Dr Roop Malik is a biophysicist based at Tata Institute of Fundamental Research Mumbai Dr Malikrsquos research focuses on nanoscale molecular motor proteins that transport material such as virus mitochondria endosomes etc inside living cells

What is your research group working on and what impact do you

hope it will have

We try to understand how the living cell achieves an organization that

is well defined yet dynamic Most of the components within a cell

have a lipid membrane boundary This boundary is fairly well

defined and visible under a microscope yet it undergoes constant

deformation to allow exchange of material between different parts

of a cell Motor proteins attach to the lipid membrane boundary and

act as transporters physically carrying cellular material from one

membrane to another in the form of a vesicular cargo How do the

motors and lipids collaborate to decide the fate of the cargo

We work on two such cargoes -- the Phagosome (may enclose

pathogens) and the Lipid droplet (encloses fat) We hope that our

research will help understand how pathogens infect us by modifying

the lipid membrane and the motors attached to it We also

investigate how fat stored inside the Lipid droplets in our liver is

circulated to different parts of the body There is a tremendous

change in the amount of fat stored in liver at every feedingfasting

cycle This is visible in the form of Lipid droplet accumulation in rat

liver sections after fasting How does the liver handle this flux of fat

What special mechanisms are required Answering these questions

may help understand the progression of fatty liver diseases

What inspired you to become a scientist

To be frank nothing in particular It was an acquired taste I started

doing experiments and gradually realised I was doing well I like the

planning that is involved in investigating the unknown and the

surprises that crop up inevitably These force you to change your

well-laid plans Thats when it gets really exciting

What role canshould scientists play in todays India

I think there is a lot of scientific freedom in India Granting agencies

are not as hawkish as in the western world This freedom is an

opportunity to do what drives you There are many young scientists in

the country who are keen to share ideas and resources We should

focus on solving difficult problems by taking advantage of this

environment If we do good science it will inspire the public

The primary job of a scientist is to do science and to do it well

Beyond that we also need to think about how science can be

propagated We have to mentor students and give them the

confidence and enthusiasm so that they go on to do better science

than we did We also have to communicate our science to common

man and facilitate them We must impress on students (and also on

their parents) that they should not look at studying Physics or Biology

or Chemistry in isolation Those who want to take up science as a

career should also understand that they must learn to deal with many

failures before something succeeds

How has Wellcome TrustDBT India Alliance Fellowship helped

you and your research (your IA experience)

I have been a Senior fellow with Wellcome Trust (UK) and then with

Wellcome Trust DBT India Alliance since 2006 The rigorous selection

process helped me fine-tune the questions that I wanted to ask The

subsequent evaluations and annual meetings helped in keeping my

research on track Last but not the least we were given a lot of

freedom in executing our science I thank the India Alliance for this

degree of trust in their Fellows This has helped me to focus on the

science

What keeps you going every day

Coffee tea and the excitement of planning and executing science

with my colleagues Regular breaks to get out into the hills for some

adventure

Find out more about

Dr Roop Malik‟s

work on motor

proteins on his

website In order to

make his research

understandable to

a wide range of

people he has put

up translation of his

research summary

in Hindi and

Marathi in addition

to Engalish on his

website

11

A Sponge Against a Sword An RNA-binding protein Prevents Chronic Inflammation and Cancer

By Dr Partho Sarothi Ray Intermediate Fellow

Anyone who has had a bruise is familiar with the redness

swelling warmth and pain that mark the site of the injury This

response known as inflammation has been recognized since ancient

times and its hallmarks were first described by the Greek physician

Galen 2000 years ago The process which is often set in motion by

specialized cells of the immune system occurs whenever tissue is

infected or damaged as for example when you have a pimple or

more seriously suffer a heart attack The latter condition is called

sterile inflammation which happens in absence of infection by a

pathogen and when it goes awry it contributes to a wide range of

seemingly unrelated diseases from Alzheimer‟s disease to diabetes to

cancer

Inflammation is the primary protective response of the body to any

infection or injury However as our common experience shows the

inflammation after being triggered goes away of its own a process

known as resolution However in certain cases the inflammation fails

to resolve and it‟s continuation known as chronic inflammation acts as

an underlying contributor to virtually every chronic disease- a list that

besides obvious culprits such as rheumatoid arthritis and

Crohn‟s disease includes diabetes and depression along with major

killers such as heart disease and stroke and especially cancer

Therefore inflammation is a double-edged sword it protects our

body but can also harm it when it occurs in an uncontrolled manner

Over the past decade and half this role of inflammation has come

under intense scrutiny and many research groups throughout the

world are attempting to discover the underlying mechanisms which

regulate the onset and resolution of inflammation

Connection between Cancer and Inflammation

The connection between cancer and inflammation was recognized a

long time ago In fact in 1863 the renowned German pathologist

Rudolf Virchow found the presence of white blood cells cells which

mediate inflammation in tumors In 1986 the cancer biologist Harold

Dvorak of Harvard Medical School remarked that tumors are

wounds that do not heal However it is only over the last two

decades that the connections between inflammation and cancer have

transformed our understanding of how cancers develop This

transformation recognizes that the chronic inflammatory state serves

as a key mediator of the middle stages of tumor development

Cancer begins with a series of genetic changes that prompt a group

of cells to proliferate and then invade surrounding tissue the point at

which true malignancy begins Eventually some tumor cells may break

off and establish new growths (metastases) at distant sites This has

been understood for a long time But cancer biologists and

immunologists have begun to realize that the progression from

diseased tissue to full-blown invasive cancer often requires cells that

normally participate in inflammation to be diverted to the pre-

malignant tissue where they are hijacked to become co-conspirators

that aid and abet carcinogenesis As described by researchers

genetic damage is the match that lights the fire and inflammation

is the fuel that feeds it Therefore the aim of our lab is to understand

the molecular processes and mechanisms that normally prevent chronic

inflammation and thereby prevent the transition from a pre-malignant

stage to a full-blown cancer Hopefully this understanding will allow in

not-so-distant future to detect and treat cancers at the pre-malignant

stage which will make cancer treatment much easier and affordable

In addition to that this understanding will possibly be helpful in the

treatment of all chronic inflammatory diseases as the basic cellular

mechanisms underlying chronic inflammation are thought to be the

same in all cases

Inflammation in cells

At the cellular level inflammation involves two types of cells the

cells of the tissue or organ that is injured that is the inflamed cells

and the cells that mediate the inflammation that is the inflammatory

cells The latter consist mainly of cells that are originally in the blood

such as monocytes and neutrophils which migrate to the site of the

inflammation and literally eat up (phagocytose) the infecting

microorganisms or the injured cells In many cases there are

monocytes present within the inflamed tissue itself called

macrophages or big eaters which form the first line of attack on the

invading pathogen or damaged tissue Now both the inflamed cells

and the inflammatory cells secrete special signalling chemicals called

cytokines which attract more inflammatory cells to the site of the

inflammation Together with the cytokines the inflammatory cells (the

macrophages and neutrophils) also produce a variety of other factors

that allow the cells to move through the wall of the blood vessels and

then into the tissue where they attack engulf and destroy the

invading pathogen or the damaged cells It is obvious that many of

these factors such as reactive oxygen species (ROS)

metalloproteases interleukins like IL6 and blood vessel growth factors

like VEGF are toxic and if continued to be produced will damage

the healthy tissue as well That is why the production of both the

cytokines which attract these cells to the site of inflammation and

these factors which cause the death and destruction of the pathogens

ceases when the cause of the inflammation is removed and allows the

inflammation to resolve Failure to stop the production of these

inflammatory factors therefore leads to chronic inflammation and the

chronic inflammatory diseases The inflammatory factors cytokines

and others are produced by genes which are called pro-

inflammatory genes Therefore the expression of these genes that is

the production of proteins from the genes have to be tightly

regulated both in space and time

12

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 2: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

We at the India Alliance wish you a very happy and prosperous 2016 There were many highlights and events last year which we

tried to bring to you through these newsletters our brand new website social media and emails We hope to be able to do the same this

year

The first issue of 2016 has announcements of our Fellowship schemes updates on funded research and other IA activities It also

features interesting article interviews and event announcements

Apart from our Fellows who are making waves in their fields we are also very fortunate to have distinguished scientists on our

fellowship selection committee We wish to congratulate our committee member Dr Amit Sharma (ICGEB New Delhi) for being awarded

the Infosys Award 2015 for ldquofor his pioneering contributions to deciphering the molecular structure at atomic level of key proteins

involved in the biology of pathogenesis of the malarial parasiterdquo In a move to encourage and support women scientists Department of

Biotechnology Government of India along with Biotechnology and Biological Research Council (BBRC) Economic and Social Research

Council (ESRC) and the Royal Society announced a program for women in STEM at JNU New Delhi earlier this month Details of the

program will be announced Feb end 2016

Last year ended with 25 Fellowships being awarded at the November 2015 round of interviews for Clinical and Public Health

Research Margadarshi and Intermediate Research (basic) Fellowship schemes bringing the total number of awards to 202 at 64

different institutions We are happy to welcome the new awardees to the India Alliance Family We are now accepting preliminary

applications for the Clinical and Public Health Research Fellowships 2016 Please check our website for the call for applications for our

Research Training Fellowship Senior and Intermediate Fellowship (Basic scheme) and Margadrashi Fellowship early next month

On the Public Engagement front we are very pleased to announce our support for the Art amp Science Project at Khoj International

Artists Association details of which can be found in this newsletter and on the Khoj website It promises to be a great platform for

interdisciplinary dialogue and exchange between scientists and artists and we encourage anyone interested to apply (artists) or get

involved (scientists) In an effort to sensitize public about pressing health issues India Alliance along with Public Health Foundation of

India will be organizing a Health discussion series (Voices for Health) where the public thought leaders and experts will be engaged in

a series of panel discussions in multiple Indian cities across the year More information on this series will be posted on our website in a

couple of weeks This issue also includes reports on a Public Lecture given by renowned cancer researcher and Noble Laureate Dr

Harold Varmus in December at NII New Delhi and the first one-day Foldscope workshop organized by the Department of

Biotechnology

On the Science Communication front we will be holding our biannual two-day SciComm workshop in Hyderabad on 21-22 March

2016 Applications for this workshop are now closed and selected participants will be informed shortly Our SciComm team will be

visiting Maharaja Sayajirao University of Baroda to hold the one-day SciComm101 workshop in March In an attempt to strengthen and

diversify its Science Communication activities India Alliance has tied up with Nature India and Nature Jobs to launch a new workshop

format which would focus on science writing communication and alternate science careers Please write to us if you would like to know

more about this workshop

In this issue we feature interviews of our Clinical and Public Health Research Fellowship Selection Committee member and eminent

geneticist Dr Aravinda Chakravarti Senior Fellow Dr Roop Malik who is working on motor proteins at TIFR Mumbai and Dr Sujatha

Reddy our Grants Adviser Heartfelt gratitude to them for sharing interesting and useful insights on their work and life In the piece

titled ldquoA Sponge Against a Swordrdquo Intermediate Fellow Dr Partho Sarothi Ray writes about the molecular underpinnings of cancer and

inflammation and the crosstalk between the two in the backdrop of his recently published research on RNA-binding proteins bdquoAsk the

Scientist‟ section is an attempt to make science more accessible and understandable and includes simple questions from non-scientists who

are keen to know more about scientific principles underlying life processes the human body etc In this issue questions on brain and its

functions are answered by our Fellows- Dr Venkatasubramanian Ganesan Dr Urvakhsh Mehta Dr Supratim Ray and Dr Nixon Abraham

A big thank you to all of them

Last but not the least thank you to our Early Career Fellow Dr Srinivas Marmamula for sharing the image for the cover which shows a

vision technician assessing vision in a woman in a remote rural area as part of public research project in Telangana initiated by L V

Prasad Eye Institute in India

Here‟s to a year of new possibilities explorations and discoveries

Best wishes

Sarah Iqbal PhD

Public Engagement Officer

EDITORIAL

1

CONTENTS

3 INDIA ALLIANCE CALL FOR APPLICATIONS

Clinical and Public Health Research Fellowships 2016

4 INDIA ALLIANCE RECOMMENDED FELLOWSHIP AWARDEES

Clinical and Public Health Research Fellowship Intermediate (Basic) Fellowship

5 IN CONVERSATION WITH

Dr Aravinda Chakravarti Director Center for Complex Disease Genomics amp Professor of Medicine

at Johns Hopkins University School of Medicine

7 SCIENCE COMMUNICATION

New Nature India-India Alliance workshop SciComm Hyderabad SciComm101 workshop

announcements

8 PUBLIC ENGAGEMENT CORNER

Art amp Science project Harold Varmus Lecture report Ask the Scientist

12 INDIA ALLIANCE FELLOW IN SPOTLIGHT

Dr Roop Malik Senior Fellow TIFR Mumbai

13 FEATURE ARTICLE

ldquoA Sponge Against a Sword rdquo

by Dr Partho Sarothi Roy Intermediate Fellow IISER Kolkata

15 INDIA ALLIANCE STAFF CORNER

Dr Sujatha Reddy Grants Adviser India Alliance

16 EXTERNAL EVENTS

First Foldscope Workshop in India- report Medicine Corner Exhibition Trick or Treat workshop

2

Sarah Iqbal- IA
Text Box
Click on the titles to go directly to the pages

Eligibility

Eligibility limit covers the entire range of Clinical and Public

Health Research Fellowship schemes

bull No age or Nationality restrictions

bull The candidates need not be resident in India while

applying but should be willing to establish an

independent research career in India

bull Clinicians and Public health researchers do not require a

PhD to apply

bull This competition is open for clinicians and public health

researchers with up to 15 years of post-

MDMSMPHPhD or equivalent clinical public health

research experience

bull The Applicants are advised to choose the most

appropriate scheme suitable for them based on their

qualification research experience career trajectory and

track record Please refer to the guidance notes

provisions and mandate of the scheme for assessing your

eligibility on the website The Office reserves the right to

advice on the suitability of the scheme accordingly

Early Career Fellowship This scheme provides a unique

opportunity for those who have shown promise to pursue

research and wish to further their efforts to build a research

career under the supervision of a Fellowship

supervisor Guidance note Suitable for applicants in the final

year PhDMDMSMPH or have up to 4 years of relevant

experience

Intermediate Fellowship For those who have been

successful in building a track record of pursuing a cutting

edge research and wish to establish their own independent

clinicalpublic health research program in India Guidance

note Suitable for applicants with 4-7 years of relevant

experience

INDIA ALLIANCE FELLOWSHIP ANNOUNCEMENT

CALL FOR APPLICATIONS

Application forms are available on the India Alliance online

application System (IASys) at

httpsfellowshipswellcomedbtorgLoginaspx

Please visit our website for further information on the application process Please write to us with

queries to infowellcomedbtorg

3

CLINICAL AND PUBLIC HEALTH RESEARCH FELLOWSHIPS 2016

Preliminary Application Deadline 1 March 2016

India Alliance invites applications for three Fellowship schemes

Early Career Fellowships Intermediate Fellowships and Senior Fellowships

Senior Fellowship For those who have demonstrated their

potential to lead an independent research program and

want to expand it further to undertake pioneering research

Guidance note Suitable for applicants with 7-15 years of

relevant experience

Remit Full spectrum of biomedical science involving clinical

and public health research

Provisions

bull These Fellowships would encourage interested clinicians

to pursue their research goals in combination with their

clinical duties

bull Competitive personal support

bull Generous research support with flexibility to

accommodate requirements of clinical and public health

research

bull Flexibility to request additional support staff

bull Support training cost and research sabbatical

bull Funds for International training and travel

bull Opportunity to pursue a PhD on the India Alliance

funded research

Essentials on the application

bull A research proposal that seeks to answer an original

biomedical research question

bull A not-for-profit Host Institution in India that will

administer the Fellowship for the full duration of the

award A salaried position or commitment to a salaried

position at the Host Institution is not required

bull A Sponsor at the Host Institution who can guarantee

space and resources for the duration of the award

bull In case of an Early Career Fellowship a Fellowship

Supervisor who can guarantee access to laboratory

space and resources required for the project as well as

provide relevant scientific guidance for the tenure of the

Fellowship

CLINICAL AND PUBLIC HEALTH RESEARCH FELLOWSHIPS

Early Career Fellowships

Dr Jayanth Kumar Palanichamy All India Institute of Medical Sciences New Delhi

Dr Aparna Mukherjee All India Institute of Medical Sciences New Delhi

Dr Deepak Kamath St Johns National Academy Of Health Sciences Bangalore

Intermediate Fellowships

Dr Aparna Rao L V Prasad Eye Institute Bhubaneswar

Dr Abi Vanak Ashoka Trust for Research in Ecology and the Environment Bangalore

Dr Shivarama VaramballyNational Institute of Mental Health and Neurosciences Bangalore

Dr Rashmi Rodrigues St Johns National Academy Of Health Sciences Bangalore

Dr Mahesh Kate Christian Medical College Ludhiana

Research Training Fellowships

Ms Urvita Bhatia Sangath Porvorim

Dr Deepak Gautam All India Institute of Medical Sciences New Delhi

Dr Sumsum P Sunny Mazumdar Shaw Medical Center Bangalore

Dr Dhruva Ithal National Institute of Mental Health and Neurosciences Bangalore

Dr Rakshathi B National Institute of Mental Health and Neurosciences Bangalore

ANNOUNCEMENT

RECENTLY RECOMMENDED AWARDEES

BASIC RESEARCH FELLOWSHIPS

Intermediate Fellowships

Dr Sridharan Devarajan Indian Institute of Science Bangalore

Dr Nitin Gupta Indian Institute Of Technology Kanpur

Dr Sachin Kotak Indian Institute of Science Bangalore

Dr Aravind Penmatsa Indian Institute of Science Bangalore

Dr Siddhesh Shashikant Kamat Indian Institute of Science Education and Research Pune

Dr Mohan Joshi Centre for DNA Fingerprinting and Diagnostics Hyderabad

Dr Satish Khurana Indian Institute of Science Education and Research Thiruvananthapuram

Dr Pinky Kain Indian Institute of Technology Roorkee

Dr Santosh Chauhan Institute Of Life Sciences Bhubaneswar

India Alliance announced Fellowship Awardees of the Clinical and Public Health Research Fellowship

scheme and Intermediate Fellowship under the Basic Biomedical Research competition in December 2015

The interviews for these Fellowship schemes were held in November 2015

indicates institution that before this award did not have any India Alliance Fellow

4

MARGADARSHI FELLOWSHIP

Prof Satyajit Mayor National Centre for Biological Science Bangalore

IN CONVERSATION WITH

Dr Aravinda Chakravarti

Dr Aravinda Chakravarti is a Professor of Medicine Pediatrics Molecular Biology amp Genetics and Biostatistics and Director Center

for Complex Disease Genomics at the Johns Hopkins University School of Medicine and the Bloomberg School of Public Health He

also has a long association with the India Alliance as a member of its Clinical and Public Health Research Fellowship committee

What motivated you to become a scientist

I cannot say that it was any one person or one event or any one

point of time that led me to consider doing science Nor did I know

what being a scientist would entail or how one prepared to become

one I was not interested in science nor good at it or anything else for

that matter before the 9th grade But subsequently it was the

concreteness and logic of mathematics and the sciences that

appealed to me I also began reading material outside my textbooks

such as books in the Nuffield Science Series and others I came across

in the Calcutta British Council Library which began giving me a

broader look at the world of science But I was still clueless This was

evident in my applying for almost every conceivable program for

college (Engineering Medicine Geology Agriculture Physics and

Statistics) and being selected but not necessarily into the best schools

or programs Thus bdquosuccess‟ did not clarify my thinking any one bit

Finally I did choose to attend the Indian Statistical Institute (ISI)

outside Calcuttahellipa then beautiful oasis of calm in the politically

turbulent Calcutta of 1970‟s when being young well-read and aware

were enough to raise suspicions in the Calcutta Police (For those who

doubt the serious and mortal danger all young people in Calcutta

were under during this time read the daily newspaper reports from

the 70‟s)

For me Indian Statistical Institute (ISI) was

an escape from reality and an entry into a

synthetic artificial and manufactured world

of quantitative ideas

Our courses over 4 years in a US-style undergraduate were 50

Mathematics and Statistics and 50 an assortment of sciences and

economics (to learn the various domains in which quantitative

reasoning would be critical) where we were taught to ask bdquowhy‟ not

only bdquohow‟ something worked For the first time I found myself in an

atmosphere where understanding mattered more than knowledge

(dont worry knowledge did matter greatly) the pursuit of a job was

a side issue and we were encouraged to discover any area we

wished (or thats how I felt) I also had passionate teachers who were

the very best in the world For the first time I felt liberated learning

was fun and pursuing science as a life seemed like the only natural

thing to do It wasnt a one day transformationhellipby the time I left ISI I

knew that I could ask and answer at least some questions ISI was the

institution where the famed British polymath and geneticist J B S

Haldane came to in 1957 and became one of the architects of my

undergraduate program Although Haldane died in 1964 his ghost

was still around when I was a student at the ISI That I would do

genetics and be a scientist particularly in human genetics was

therefore a no brainer

Could you briefly take us through your scientific journey and

about your interest in genetics

My interest in genetics was established at the ISI but no less fueled by

my reading of Jim Watson‟s The Double Helix in 1970 and then as

credited by Watson and Crick Erwin Schrodinger‟s What is Life As a

student of the quantitative sciences at ISI the part of genetics that

appealed to me (simply because I could digest it) was Population

Genetics Also ISI had a Department of Human Genetics that

performed numerous studies of human genetic molecular diversity

across populations in India So my early training was in studies of

human population diversity Nevertheless Haldane‟s research (that I

was increasingly becoming aware of) was equally in family studies

that exemplified mechanisms not evident in population studies So as

a student I conducted and published research into the inheritance of

simply observable traits (bdquohand clasping‟ or the phenotype where you

classify individuals by whether they fold their left thumb over their

right or vice versahelliptry it only one way feels correct) just to learn

genetics and to attempt to combine the family and the population

methods that are so common today Fortunately by this time I had left

myself few opportunities to be interested in doing anything else but

human genetics

5

IN CONVERSATION WITH Dr Aravinda Chakravarti

Being rejected by several programs to study genetics in India

(because I was not a biology undergraduate) I chose to do graduate

work with the noted geneticist and molecular evolutionist Masatoshi

Nei at the University of Texas Houston where he had just moved I

arrived in Houston in 1974 and was immediately thrust into a small

intense center with brilliant people and expected to perform research

at a level I was surely unaccustomed to This group was the epicenter

of the then neutralist-selectionist debate in molecular evolution a

problem that was exciting but not my cup of tea I wanted to study

human genetics and finally fashioned a research project with Nei that

explored the theoretical consequences of improved genetic counseling

with linkage and association (linkage disequilibrium) markers and

graduated with a PhD in 1979 This research was not only far ahead

of its time coming before the proposal of creating a human linkage

map using RFLPs (restriction fragment length polymorphism) in 1980

but I was the only Nei student who worked outside molecular

evolution In many ways then my development in genetics became

very broad and haphazard since I often focused on areas that were

not my primary training grounds

By this time I was a geneticist but thought I needed further training in

genetic epidemiology to understand human disease better However

after an unsuccessful postdoc at Seattle I abandoned this idea to

take a non-tenured teaching position at the University of Pittsburgh

thinking that the bdquofree‟ time I would have would allow me to catch up

on the revolution in recombinant DNA technology that was underway I

am glad I did since this was one of the best

professional decisions I made by forgoing

the standard path

I taught at Pittsburgh for 5 years and subsequently obtained an NIH

Research Career Development Award to pursue a research career

That began my standard research career in human genetics

What according to you are the challenges in your field of

research

The field of human genetics is not the one I trained in since so much

has changed with the sequencing of the human genome Human

genetics has two distinct themes one descriptive as to the causes of

human variation be it molecular or phenotypic (the bdquohow‟ question)

and a second mechanistic as to how variation in molecular

mechanisms impact phenotype variation particularly disease (the

bdquowhy‟ question) The whole attraction of the human genome project to

me and others like me who spent more than a decade on building the

now available community resources (maps clones sequences variants

transcripts etc) was to move from the first set to the second set of

questions This transformation is difficult since it is not in the comfort

zone of conventional human genetics its hard and unpredictable

much more hypothesis-driven and much more experimental The

challenge in my field and in many associated medical specialties is

that it‟s far easier to do the first then the second Scientists are voting

with their feet Human geneticists are far more content in sequencing

human genomes finding associations with disease and doing facile

functional annotation than a serious investigation into why does this

gene causes type 2 diabetes and the next one congenital cataract

Or why mutations in the same gene cause a neuroendocrine tumor

when activating but congenital aganglionosis when loss-of-function

Or how come the same mutation can act as either activating or loss-

of-function

The biggest challenge in my field is to

overcome the inertia that molecular

description = etiological explanation

If you were not a scientist you would behellip

I really have no idea I presume the Bengali in me implicitly wants

or always wanted to be a writer but that would be a great leap of

faith and quite arrogant Even good scientific writing is hard very

hard indeed I have often read someone else‟s paper that I enjoyed

and thought that I could have done the same work a similar thought

has not appeared after reading someone else‟s creative work except

when it is quite bad

5 What is the best advice you have ever received

Unfortunately most advice that most people get and give is bad

More correctly its difficult to know (what‟s the test) when it is good

and when bad Each of us likely adapt a post-hoc explanation to our

stories all of which are likely revisionist Nevertheless two different

people (a brother and a family friend) at about the same time

(1979-1982) told me to abandon what I was doing (an unsuccessful

postdoc and forcing myself to complete reading a fairly racist

account of the Black Hole of Calcutta) because it was beyond my

enjoyment They both suggested that I drop it and do something else

One should not shoulder a burden that is great unless some higher

purpose is at stake One needs to learn how to apportion risk with

benefit

Your message for young students and researchers

Science is difficult but exhilarating in its rare moments of success

and it‟s usually followed by long periods of stasis It is a great but

frustrating life and there are many worse ways of making a living It

is like other types of creative endeavors where discovery is real but

rare If you wish to do it be sure you can enjoy its moods Science

today is also multidisciplinary and translational its application to

humans and other benefits can also be tangible sources of pride But

do it not for these benefits do it because the science gives you great

joy Yes joy Consider that you are one in an

unbroken intellectual chain from Johannes

Kepler and Isaac Newton If you choose

science you are special

Dr Chakravarti‟s laboratory focuses on the development and

applications of molecular genetic genomic and computational

methods for identification of human disease genes through

genetic dissectionldquo He has been a key participant and architect

of the Human Genome HapMap and 1000 Genomes project Find

out more about his research here

6

Workshop at a glance One-day workshop to equip young science

researchers with tools and strategies for effective communication of

their ideas experiments and scientific results from a science

communication perspective Help them to make science career choices

Vision Science communication plays an integral role in one‟s scientific

career Being able to effectively disseminate research findings within

the community and to consider collective opinions in prioritising

research needs is an important attribute of scientific maturity In

keeping with its mandate to empower future leaders of Indian science

the Wellcome TrustDBT India Alliance periodically conducts one-day

(SciComm101) and two-day (SciComm Hyderabad) science

communication workshops for the past four years This complements

seamlessly with Nature India‟s mandate to showcase India‟s science bdquoas

it happens‟ in laboratories and institutions across the country through

in-depth coverage and analysis of research and science policy The

proposed workshop would be part of Nature India‟s many

communication outreach activities as the one-stop media platform for

India‟s science

The Wellcome TrustDBT India Alliance and Nature India both

represent possibilities for young PhD scholars and postdoctoral

scientists to transition into academic as well as non-academic science

careers Information and advice on how to explore various career

options will form an important part of these workshops with

Naturejobs as the key organiser of the career session

Structure amp format

The workshop will be a one-day event preceding a biomedical (or

scientific) conference organised by reputed science

societiesorganisationsinstitutes and Universities in India A large

participation by PhD students postdoctoral fellows and junior

scientists will be a pre-requisite for holding this workshop Organising

this workshop as part of a conference will ensure participation from a

wide range of institutions across India The workshop will include 3

separate sessions

Session 1 Scientific Writing (moderated by WTDBT Alliance)

Topics to be covered

bull Ethics in research

bull Presentation skills

bull Manuscript writing

bull Grants writing

bull CVs and letters

Session 2 Science Communication (moderated by Nature India)

Topics to be covered

bull Science journalism

bull Popular science writing

bull Effective press releases

bull Hands-on skills on dejargonising science

Session 3 Alternate Science Career (moderated by Nature Jobs)

Topics to be covered

bull Career in the Industry

bull Career in Science PromotionIntellectual Property

bull Career in PolicyGrant organizations Journalism

Science Communication and Career Workshop Series (In partnership with Nature India amp Naturejobs )

Please contact us at workshopswellcomedbtorg to find out more about this series

INDIA ALLIANCE

SCIENCE COMMUNICATION

SciComm101 workshop

10 March 2016 MSU Baroda

Two-day SciComm workshop

21-22 March 2016 Hyderabad Applications under review

For more details visit SciComm Workshop under Quick Links on our website

Upcoming Workshops

5

ABOUT THE ART amp SCIENCE PROJECT

CALL FOR APPLICATIONS THE UNDIVIDED MIND |ART +

SCIENCE RESIDENCY AT KHOJ

Residency Dates March 2nd ndash April 2nd 2015

Application Deadline February 2nd 2015

Proposals are invited for bdquoThe Undivided Mind‟ a four-week

international residency for artists whose work explores the

intersection of art and science

At first it may seem that the pairing of Art amp Science is an atypical

choice as the two fields and methods of practice have almost

universally been represented as diametric opposites of each other

However on closer examination the similarities between artists and

scientists far outweigh their stereotypical differences Both are

dedicated to research and to asking the big question- what is true

Why does it matter How can we move society forward Moreover

both the lab and the studio are spaces that famously encourage

open-ended enquiry and emphasis on process In tune with Khoj‟s

commitment to cultivate an environment that allows for

experimentation and innovation the Art amp Science residency will be

a step towards furthering the explorations of interdisciplinary

practitioners This is the second edition of a Khoj residency focusing

on Art + Science to know more about the first edition please

click bdquohere‟

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

The following India Alliance Fellows will be participating in the

project

(NOTE If an applicant wishes to connect with any of the following

researchers in advance of submitting their proposal please contact

the Khoj team at bdquoapplicationskhojworkshoporg‟ for an

introduction please do the same if you are a scientist and would like

take part in this project )

Dr Venkatasubramanian Ganesan National Institute of Mental

Health and Neurosciences (NIMHANS) Bangalore

Dr Pallab K Maulik The George Institute for Global Health New

Delhi

Dr Anurag Agarwal CSIR-Institute of Genomics amp Integrative

Biology (IGIB) New Delhi

Dr Tavpritesh Sethi All India Institute of Medical Sciences (AIIMS)

New Delhi

Dr Lolitika Mandal Indian Institute of Science Education and

Research (IISER) Mohali

Dr Urvakhsh MehtaNIMHANS Bangalore

Dr Sheetal Gandotra IGIB New Delhi

Visit Khoj website to find out more about the residency and the application process

Apply by

2 February 2016

India Alliance is pleased to announce its support for Art amp Science Project at Khoj International Artists Association New Delhi details of

which can be found below and on the Khoj website It promises to be a great platform for interdisciplinary dialogue and exchange

between scientists and artists and we encourage anyone interested to apply (artists) and get involved (scientists)

THEME

The theme of the 2016 edition of The Undivided Mind is bdquoHealth‟

Within this broader framework three curatorial frameworks or

modes for exploration are suggested Terrestrial Health refers to

that which is on or related to the earth This sub ndash theme suggests an

investigation into the physical health and structure of the body (both

human and animal) the environment the community and the

interrelations between these spheres Mental Health refers to that

which is of or relating to the mind This sub ndash theme focuses on a

psychological investigation of what constitutes Health of the mind

and raises questions about the bdquosocially‟ defined state of well-being

where issues‟ surrounding the legal rights and entitlement of

personhood for those living with a mental disorder is open for

debate Finally Extraterrestrial Health may refer to any object

being or idea beyond the planet Earth This sub ndash theme opens up a

space where the relationship between Earth and other planetary

bodies can be studied What does it mean for human existence when

sending human life forms to Mars is projected to take place by

2020 What are the long term effects and solution to space debris

if life projects out beyond Earth This sub ndash theme also invites

applicants to consider the abstract and metaphorical imaginings of

health in contemporary and future societies

6

Nobel Laureate Dr Harold Varmus recognized for his research on

retroviruses and the genetic basis of cancer gave a lecture on ldquoRecent

Developments in Cancer Researchrdquo at National Institute of Immunology

(NII) New Delhi an event co-organised by NII Wellcome TrustDBT

India Alliance and Department of Biotechnology Government of

India His lecture largely gave an overview of the recent

developments challenges and the future directions in the field of

cancer research which included the current research of his group in

this area

Dr Varmus who had spent time in Bareilly as a young medical

student described cancer as a complex disease that requires

innovative research and treatment strategies At the outset Dr Varmus

introduced the key questions that drive the cancer research field- Is

cancer one disease or many diseases What makes the cancer cell

grow so stably in such an inappropriate manner How does a normal

cell become a cancer cell Providing answers to these questions

formed the backdrop of Dr Varmus‟s lecture which drew from his

research work till date and other advances in the field

Dr Varmus entered the field of cancer research in 1970s as a

postdoctoral scientist in the laboratory of Dr John J Michael Bishop at

University of California San Francisco USA the same year National

Cancer Act was signed in the country Dr Bishop and Dr Varmus

together received the Nobel Prize in Medicine and Physiology in

1989 ldquofor their discovery of the cellular origins of retroviral

oncogenesrdquo During his lecture Dr Varmus confessed standing on the

shoulders of giants of retroviral and cancer research such as Dr

Peyton Rous Dr Harry Rubin and Dr Howard Temin to ask the question

of how retroviruses transformed cells and cause tumours This question

led him to look for genes that make a normal cell behave like a

cancer cell which initially involved studying cancer-causing RNA

virusesretroviruses in animals The retrovirus that played a lead role

in Dr Varmus and his colleague‟s work was the Rous Sarcoma Virus

(RSV) discovered by Dr Peyton Rous in 1911 which he showed caused

a type of cancer in chickens Dr Varmus and colleagues set out to

prove the hypothesis that retroviruses enter host cells and capture

normal genes in that cell by inserting their DNA converting them into

cancer-causing genes or oncogenes Dr Varmus and his group

employed various cellular chemical as well as genetic tools to

establish that retroviruses can indeed act as mutagens by inserting

their DNA in host cells and turning them into cancer cells After this his

group went on to identify the cancer-causing genes present in the

virus and subsequently discovered many new oncogenes v-Src (a

gene of RSV) being the first one Following these discoveries and

subsequently many others led to the belief that the genetic basis of

cancer is highly heterogeneous Dr Varmus told us that in order to

catalogue these complexities the Cancer Genome Atlas was

established in 2005 which till today serves as a collection of the

genetic mutations responsible for different cancers

Apart from the complexity and vastness of the cancer genome

other challenges in the field according to Dr Varmus are genetic

heterogeneity and evolution of tumours due to various environmental

factors such as exposure to UV pollution tobacco use and other

environmental carcinogens that are on the rise He used the example

of renal tumor evolution which illustrates Darwin‟s theory of ldquoevolution

of speciesrdquo to show that this rapidly changing genetic repertoire can

have significant impact on diagnosis therapeutic interventions and

prognosis Another issue of concern highlighted by Dr Varmus was the

absence of suitable drugs against many common targets for cancer

such as cancer-causing RAS genes and many transcription factors

which have been shown to contribute towards cancer formation Dr

Varmus opined that lack of understanding of the underlying

complexity of resistance to cancer therapies is another roadblock in

cancer treatment He was also strongly of the opinion that there are

not enough public health interventions to prevent cancer- this he felt

needs to go hand in hand with finding cure for cancer

Dr Varmus also offered solutions to these problems He suggested

that research needs to ldquolook beyond genes and focus on patterns and

pathwaysrdquo and physiological changes taking place in cancer cells He

shared his group‟s current interest in studying ldquooncogene addictionrdquo

which is based on the premise that some oncogenes not only give rise

to cancer but also maintain the cancerous state of the cells

Interpreting the downstream effects of these cancer genes on the

pathways could be employed as a strategy to attack multiple targets

by drugs in different cancers Even though he hailed the successes of

many commonly used and extremely efficacious anti-cancer drugs

such as Gleevec Gefitinib Erlotinib but in light of growing

complexity of the disease proposed the need for adopting more

innovative drug discovery and treatment approaches Continuing on

the topic of therapeutics Dr Varmus mentioned the recent advances in

immunotherapeutic approaches to treat cancer which would require

us to understand why the otherwise combative immune system does

not kill cancer cells He suggested that gaining understanding of these

immune check points and accordingly targeting them by antibody

inhibitors could serve as one more effective treatment strategy-

another project his research group has undertaken In addition to

these therapeutic approaches Dr Varmus very strongly asserted that

ldquonot everything we talk about cancer should be about cancer therapy

but also about preventionrdquo and that this disease ought to be on the

global health agenda

Dr Varmus very eloquently concluded his talk by stating that

ldquoconfronting cancer needs a balance between grasping its complexity

and seeking simple solutionsrdquo As expected he received many

questions from the audience after his lecture on the genetics and

biology of various cancers potential use of vaccines in cancer

treatment crosstalk of cancer with other diseases and many others to

which he responded with prudence and an underlying sense of

optimism

Prior to his lecture Dr Varmus over an hour meeting with 10 young

cancer researchers discussed their work This group included the

following Wellcome TrustDBT India Alliance Fellows - Dr Reety Arora

(ECF InStem Bangalore) Dr Anjali Bajpai (ECF IIT Kanpur) Dr

Bushra Ateeq (Int Fellow IIT Kanpur) Dr Kundan Sengupta (Int Fellow

IISER Pune) and Dr Sandeep Singh (Int Fellow NIBMG Kalyani) Dr

Varmus also sought information on the India Alliance Fellowships and

was impressed by its funding model and reach

LECTURE REPORT

Recent Developments in Cancer Research By Dr Harold Varmus Nobel Prize in Medicine and Physiology Weill Cornell Medical College USA

at

National Institute of Immunology New Delhi

16 November 2015

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

7

ASK THE SCIENTIST about

The Human Brain

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

This section will bring to you answers to those burning scientific questions that you always wanted to ask the guys in the white

coat For this issue we asked some of our Fellows to shed light on the various operations of the brain

How can we measure attention

DR SUPRATIM RAY Indian Institute of Science Bangalore

Intermediate Fellow

Attention can be of different types such as sustained (vigilance)

selective (focusing at one stimulus in the presence of distractors) or

alternating (involves switching) which can be measured using a

variety of cognitive tests (such as test of everyday attention (TEA) or

Posner cuing task) For example in a classical Posner task a subject

is repeatedly shown two stimuli and cued to attend to one of them

and instructed to respond to a change in the stimulus (say by

pressing a button) The cue could be valid (change occurs at the cued

stimulus say for 80 of the trials) invalid (change occurs at the

uncued stimulus) or neutral (ambiguous) Selection attention can be

measured by comparing the accuracy and the time taken to press

the button after stimulus change (called reaction time) for different

cue types

Different components of attention such as orienting towards a

location detecting a target or maintaining vigilance are carried out

by distinct brain areas in the prefrontal and parietal lobes and some

sub-cortical structures (such as superior colliculus) Overall

performance depends not only on how these areas perform but also

how they communicate with each other and on the levels of

neuromodulators such as norepinephrine

How can we sense smell Is it possible to live without this

sense of smell

DR NIXON ABRAHAM Indian Institutes of Science Education amp

Research (IISER) Pune

Intermediate Fellow

Once Dr Lewis Thomas (1913-1993) the poet and a philosopher of

medicine who also served as the dean of the medical schools at the

New York University and Yale was asked to select seven wonders of

the modern world Olfaction (olfactory receptor cell) was fifth in his

list How does the modern fifth wonder that brings us the smell of our

surroundings ndash the good and bad work

The process of making sense of smell start by binding the odor

molecules to the olfactory receptors located in the olfactory sensory

neurons (OSNs) in the nose This binding triggers a series of signal

amplification steps which lead to electrical spikes (so called action

potentials) in OSNs This olfactory information whose intensity is

encoded by varying the number of action potentials is then passed

onto the projection neurons named mitral and tufted cells in the

olfactory bulb These projection neurons whose excitatory actions

are controlled by various inhibitory neurons carry the olfactory

information to the higher centers in the brain so that we perceive the

smell of spicy tasty food and putrid garbage ndash the good and bad

from the environment

Continued

9

Brain waves

measured by EEG

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

What is really happening inside the brain of a Schizophrenia

patient Does it look any different from a normal brain

DR VENKATASUBRAMANIAN GANESAN NIMHANS Bengaluru

Intermediate Fellow

The brain of a schizophrenia patient is reduced in overall volume

with increase in the size of the ventricles (parts of the brain that

contain cerebrospinal fluid) however certain parts like hippocampus

superior temporal gyrus and prefrontal cortex are more affected

than others Using certain advanced brain imaging research studies

(for example high resolution structural MRI functional MRI Magnetic

Resonance Spectroscopy Positron Emission Tomography and Diffusion

Tensor Imaging and similar others) subtle brain abnormalities in

structure function neurochemical profile as well as brain connectivity

have been demonstrated in several brain regions in schizophrenia

patients It is important to note that these findings are obtained

from advanced research studies that have compared brains of a

Why are the mirror neurons called the Minds mirror What do

they reflect

DR URVAKHSH MEHTA National Institute of Mental Health amp

Neurosciences (NIMHANS) Bengaluru

Early Career Fellow

Mirror neurons are specialized nerve cells that discharge when

we perform actions as well as when we observe others perform the

same action Rizzolatti and colleagues accidentally discovered them

in monkeys These neurons also get vicariously activated when we

perceive emotional states of others This unique bdquoexperience sharing‟

property of mirror neurons perhaps enables us to decipher goals

intentions and emotions of others

In several of our daily social interactions we need to take

perspectives of others decipher deception share feelings and

empathize with others The mirror neuron system is an important

brain network that helps us peek into the minds of others and try to

understand people They translate sensory information (eg

observation of an action) into a motor template which is similar to

the format an observer himself uses to perform that very action This

motor template can help us interpret the goals and feelings

underlying observed actions The definitive demonstration of mirror

neurons in humans was as recent as 2010 There is also growing

evidence of a dysfunctional mirror neuron system in psychiatric

disorders like autism and schizophrenia It is a long and exciting

future ahead to decipher spatiotemporal regulatory and genetic

underpinnings of this unique neuronal network ndash this will possibly

help understand and treat social brain disorders better

Schizophrenia

What happens if we loose our sense of smell Loss of olfaction can

be caused by many reasons ranging from viral infections to

neurodegenerative disorders As our emotions and memories are

strongly related to olfaction the loss of this sense can lead to

depressed state and even affect bonding with family members Just

imagine sipping from your morning coffee without sensing it‟s aroma

- our taste could be badly affected by losing sense of smell The

ongoing research at the nasal stem cell level might provide clinical

solutions for the disorders of the olfactory sensory neurons to regain

this wonderful sense

group of schizophrenia patients with that of healthy subjects thus

these are group averaged findings that are currently not applicable

for diagnosing schizophrenia in an individual patient in a regular

clinical setting In ldquoa specific patientrdquo one may not be able to find

any striking abnormality in the physical appearance of the brain (ie

a routine CT or MRI brain scan may not be able to identify any

obvious aberration) Several ongoing research studies are in pursuit

to identify clinically useful biomarker to diagnose schizophrenia

Find out more about Dr Ganesan‟s research on schizophrenia here

Do you have a burning scientific

question

Send them to

publicengagementwellcomedbtorg

Mirror neuron activity in the brain both when the monkey grasps an object

and when it observes the experimenter grasping the object Mirror neurons

were first discovered by Rizzolatti and colleagues when they were studying

motor actions in macque monkeys

10

INDIA ALLIANCE FELLOW

DR ROOP MALIK Senior Fellow TIFR Mumbai

Dr Roop Malik is a biophysicist based at Tata Institute of Fundamental Research Mumbai Dr Malikrsquos research focuses on nanoscale molecular motor proteins that transport material such as virus mitochondria endosomes etc inside living cells

What is your research group working on and what impact do you

hope it will have

We try to understand how the living cell achieves an organization that

is well defined yet dynamic Most of the components within a cell

have a lipid membrane boundary This boundary is fairly well

defined and visible under a microscope yet it undergoes constant

deformation to allow exchange of material between different parts

of a cell Motor proteins attach to the lipid membrane boundary and

act as transporters physically carrying cellular material from one

membrane to another in the form of a vesicular cargo How do the

motors and lipids collaborate to decide the fate of the cargo

We work on two such cargoes -- the Phagosome (may enclose

pathogens) and the Lipid droplet (encloses fat) We hope that our

research will help understand how pathogens infect us by modifying

the lipid membrane and the motors attached to it We also

investigate how fat stored inside the Lipid droplets in our liver is

circulated to different parts of the body There is a tremendous

change in the amount of fat stored in liver at every feedingfasting

cycle This is visible in the form of Lipid droplet accumulation in rat

liver sections after fasting How does the liver handle this flux of fat

What special mechanisms are required Answering these questions

may help understand the progression of fatty liver diseases

What inspired you to become a scientist

To be frank nothing in particular It was an acquired taste I started

doing experiments and gradually realised I was doing well I like the

planning that is involved in investigating the unknown and the

surprises that crop up inevitably These force you to change your

well-laid plans Thats when it gets really exciting

What role canshould scientists play in todays India

I think there is a lot of scientific freedom in India Granting agencies

are not as hawkish as in the western world This freedom is an

opportunity to do what drives you There are many young scientists in

the country who are keen to share ideas and resources We should

focus on solving difficult problems by taking advantage of this

environment If we do good science it will inspire the public

The primary job of a scientist is to do science and to do it well

Beyond that we also need to think about how science can be

propagated We have to mentor students and give them the

confidence and enthusiasm so that they go on to do better science

than we did We also have to communicate our science to common

man and facilitate them We must impress on students (and also on

their parents) that they should not look at studying Physics or Biology

or Chemistry in isolation Those who want to take up science as a

career should also understand that they must learn to deal with many

failures before something succeeds

How has Wellcome TrustDBT India Alliance Fellowship helped

you and your research (your IA experience)

I have been a Senior fellow with Wellcome Trust (UK) and then with

Wellcome Trust DBT India Alliance since 2006 The rigorous selection

process helped me fine-tune the questions that I wanted to ask The

subsequent evaluations and annual meetings helped in keeping my

research on track Last but not the least we were given a lot of

freedom in executing our science I thank the India Alliance for this

degree of trust in their Fellows This has helped me to focus on the

science

What keeps you going every day

Coffee tea and the excitement of planning and executing science

with my colleagues Regular breaks to get out into the hills for some

adventure

Find out more about

Dr Roop Malik‟s

work on motor

proteins on his

website In order to

make his research

understandable to

a wide range of

people he has put

up translation of his

research summary

in Hindi and

Marathi in addition

to Engalish on his

website

11

A Sponge Against a Sword An RNA-binding protein Prevents Chronic Inflammation and Cancer

By Dr Partho Sarothi Ray Intermediate Fellow

Anyone who has had a bruise is familiar with the redness

swelling warmth and pain that mark the site of the injury This

response known as inflammation has been recognized since ancient

times and its hallmarks were first described by the Greek physician

Galen 2000 years ago The process which is often set in motion by

specialized cells of the immune system occurs whenever tissue is

infected or damaged as for example when you have a pimple or

more seriously suffer a heart attack The latter condition is called

sterile inflammation which happens in absence of infection by a

pathogen and when it goes awry it contributes to a wide range of

seemingly unrelated diseases from Alzheimer‟s disease to diabetes to

cancer

Inflammation is the primary protective response of the body to any

infection or injury However as our common experience shows the

inflammation after being triggered goes away of its own a process

known as resolution However in certain cases the inflammation fails

to resolve and it‟s continuation known as chronic inflammation acts as

an underlying contributor to virtually every chronic disease- a list that

besides obvious culprits such as rheumatoid arthritis and

Crohn‟s disease includes diabetes and depression along with major

killers such as heart disease and stroke and especially cancer

Therefore inflammation is a double-edged sword it protects our

body but can also harm it when it occurs in an uncontrolled manner

Over the past decade and half this role of inflammation has come

under intense scrutiny and many research groups throughout the

world are attempting to discover the underlying mechanisms which

regulate the onset and resolution of inflammation

Connection between Cancer and Inflammation

The connection between cancer and inflammation was recognized a

long time ago In fact in 1863 the renowned German pathologist

Rudolf Virchow found the presence of white blood cells cells which

mediate inflammation in tumors In 1986 the cancer biologist Harold

Dvorak of Harvard Medical School remarked that tumors are

wounds that do not heal However it is only over the last two

decades that the connections between inflammation and cancer have

transformed our understanding of how cancers develop This

transformation recognizes that the chronic inflammatory state serves

as a key mediator of the middle stages of tumor development

Cancer begins with a series of genetic changes that prompt a group

of cells to proliferate and then invade surrounding tissue the point at

which true malignancy begins Eventually some tumor cells may break

off and establish new growths (metastases) at distant sites This has

been understood for a long time But cancer biologists and

immunologists have begun to realize that the progression from

diseased tissue to full-blown invasive cancer often requires cells that

normally participate in inflammation to be diverted to the pre-

malignant tissue where they are hijacked to become co-conspirators

that aid and abet carcinogenesis As described by researchers

genetic damage is the match that lights the fire and inflammation

is the fuel that feeds it Therefore the aim of our lab is to understand

the molecular processes and mechanisms that normally prevent chronic

inflammation and thereby prevent the transition from a pre-malignant

stage to a full-blown cancer Hopefully this understanding will allow in

not-so-distant future to detect and treat cancers at the pre-malignant

stage which will make cancer treatment much easier and affordable

In addition to that this understanding will possibly be helpful in the

treatment of all chronic inflammatory diseases as the basic cellular

mechanisms underlying chronic inflammation are thought to be the

same in all cases

Inflammation in cells

At the cellular level inflammation involves two types of cells the

cells of the tissue or organ that is injured that is the inflamed cells

and the cells that mediate the inflammation that is the inflammatory

cells The latter consist mainly of cells that are originally in the blood

such as monocytes and neutrophils which migrate to the site of the

inflammation and literally eat up (phagocytose) the infecting

microorganisms or the injured cells In many cases there are

monocytes present within the inflamed tissue itself called

macrophages or big eaters which form the first line of attack on the

invading pathogen or damaged tissue Now both the inflamed cells

and the inflammatory cells secrete special signalling chemicals called

cytokines which attract more inflammatory cells to the site of the

inflammation Together with the cytokines the inflammatory cells (the

macrophages and neutrophils) also produce a variety of other factors

that allow the cells to move through the wall of the blood vessels and

then into the tissue where they attack engulf and destroy the

invading pathogen or the damaged cells It is obvious that many of

these factors such as reactive oxygen species (ROS)

metalloproteases interleukins like IL6 and blood vessel growth factors

like VEGF are toxic and if continued to be produced will damage

the healthy tissue as well That is why the production of both the

cytokines which attract these cells to the site of inflammation and

these factors which cause the death and destruction of the pathogens

ceases when the cause of the inflammation is removed and allows the

inflammation to resolve Failure to stop the production of these

inflammatory factors therefore leads to chronic inflammation and the

chronic inflammatory diseases The inflammatory factors cytokines

and others are produced by genes which are called pro-

inflammatory genes Therefore the expression of these genes that is

the production of proteins from the genes have to be tightly

regulated both in space and time

12

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 3: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

CONTENTS

3 INDIA ALLIANCE CALL FOR APPLICATIONS

Clinical and Public Health Research Fellowships 2016

4 INDIA ALLIANCE RECOMMENDED FELLOWSHIP AWARDEES

Clinical and Public Health Research Fellowship Intermediate (Basic) Fellowship

5 IN CONVERSATION WITH

Dr Aravinda Chakravarti Director Center for Complex Disease Genomics amp Professor of Medicine

at Johns Hopkins University School of Medicine

7 SCIENCE COMMUNICATION

New Nature India-India Alliance workshop SciComm Hyderabad SciComm101 workshop

announcements

8 PUBLIC ENGAGEMENT CORNER

Art amp Science project Harold Varmus Lecture report Ask the Scientist

12 INDIA ALLIANCE FELLOW IN SPOTLIGHT

Dr Roop Malik Senior Fellow TIFR Mumbai

13 FEATURE ARTICLE

ldquoA Sponge Against a Sword rdquo

by Dr Partho Sarothi Roy Intermediate Fellow IISER Kolkata

15 INDIA ALLIANCE STAFF CORNER

Dr Sujatha Reddy Grants Adviser India Alliance

16 EXTERNAL EVENTS

First Foldscope Workshop in India- report Medicine Corner Exhibition Trick or Treat workshop

2

Sarah Iqbal- IA
Text Box
Click on the titles to go directly to the pages

Eligibility

Eligibility limit covers the entire range of Clinical and Public

Health Research Fellowship schemes

bull No age or Nationality restrictions

bull The candidates need not be resident in India while

applying but should be willing to establish an

independent research career in India

bull Clinicians and Public health researchers do not require a

PhD to apply

bull This competition is open for clinicians and public health

researchers with up to 15 years of post-

MDMSMPHPhD or equivalent clinical public health

research experience

bull The Applicants are advised to choose the most

appropriate scheme suitable for them based on their

qualification research experience career trajectory and

track record Please refer to the guidance notes

provisions and mandate of the scheme for assessing your

eligibility on the website The Office reserves the right to

advice on the suitability of the scheme accordingly

Early Career Fellowship This scheme provides a unique

opportunity for those who have shown promise to pursue

research and wish to further their efforts to build a research

career under the supervision of a Fellowship

supervisor Guidance note Suitable for applicants in the final

year PhDMDMSMPH or have up to 4 years of relevant

experience

Intermediate Fellowship For those who have been

successful in building a track record of pursuing a cutting

edge research and wish to establish their own independent

clinicalpublic health research program in India Guidance

note Suitable for applicants with 4-7 years of relevant

experience

INDIA ALLIANCE FELLOWSHIP ANNOUNCEMENT

CALL FOR APPLICATIONS

Application forms are available on the India Alliance online

application System (IASys) at

httpsfellowshipswellcomedbtorgLoginaspx

Please visit our website for further information on the application process Please write to us with

queries to infowellcomedbtorg

3

CLINICAL AND PUBLIC HEALTH RESEARCH FELLOWSHIPS 2016

Preliminary Application Deadline 1 March 2016

India Alliance invites applications for three Fellowship schemes

Early Career Fellowships Intermediate Fellowships and Senior Fellowships

Senior Fellowship For those who have demonstrated their

potential to lead an independent research program and

want to expand it further to undertake pioneering research

Guidance note Suitable for applicants with 7-15 years of

relevant experience

Remit Full spectrum of biomedical science involving clinical

and public health research

Provisions

bull These Fellowships would encourage interested clinicians

to pursue their research goals in combination with their

clinical duties

bull Competitive personal support

bull Generous research support with flexibility to

accommodate requirements of clinical and public health

research

bull Flexibility to request additional support staff

bull Support training cost and research sabbatical

bull Funds for International training and travel

bull Opportunity to pursue a PhD on the India Alliance

funded research

Essentials on the application

bull A research proposal that seeks to answer an original

biomedical research question

bull A not-for-profit Host Institution in India that will

administer the Fellowship for the full duration of the

award A salaried position or commitment to a salaried

position at the Host Institution is not required

bull A Sponsor at the Host Institution who can guarantee

space and resources for the duration of the award

bull In case of an Early Career Fellowship a Fellowship

Supervisor who can guarantee access to laboratory

space and resources required for the project as well as

provide relevant scientific guidance for the tenure of the

Fellowship

CLINICAL AND PUBLIC HEALTH RESEARCH FELLOWSHIPS

Early Career Fellowships

Dr Jayanth Kumar Palanichamy All India Institute of Medical Sciences New Delhi

Dr Aparna Mukherjee All India Institute of Medical Sciences New Delhi

Dr Deepak Kamath St Johns National Academy Of Health Sciences Bangalore

Intermediate Fellowships

Dr Aparna Rao L V Prasad Eye Institute Bhubaneswar

Dr Abi Vanak Ashoka Trust for Research in Ecology and the Environment Bangalore

Dr Shivarama VaramballyNational Institute of Mental Health and Neurosciences Bangalore

Dr Rashmi Rodrigues St Johns National Academy Of Health Sciences Bangalore

Dr Mahesh Kate Christian Medical College Ludhiana

Research Training Fellowships

Ms Urvita Bhatia Sangath Porvorim

Dr Deepak Gautam All India Institute of Medical Sciences New Delhi

Dr Sumsum P Sunny Mazumdar Shaw Medical Center Bangalore

Dr Dhruva Ithal National Institute of Mental Health and Neurosciences Bangalore

Dr Rakshathi B National Institute of Mental Health and Neurosciences Bangalore

ANNOUNCEMENT

RECENTLY RECOMMENDED AWARDEES

BASIC RESEARCH FELLOWSHIPS

Intermediate Fellowships

Dr Sridharan Devarajan Indian Institute of Science Bangalore

Dr Nitin Gupta Indian Institute Of Technology Kanpur

Dr Sachin Kotak Indian Institute of Science Bangalore

Dr Aravind Penmatsa Indian Institute of Science Bangalore

Dr Siddhesh Shashikant Kamat Indian Institute of Science Education and Research Pune

Dr Mohan Joshi Centre for DNA Fingerprinting and Diagnostics Hyderabad

Dr Satish Khurana Indian Institute of Science Education and Research Thiruvananthapuram

Dr Pinky Kain Indian Institute of Technology Roorkee

Dr Santosh Chauhan Institute Of Life Sciences Bhubaneswar

India Alliance announced Fellowship Awardees of the Clinical and Public Health Research Fellowship

scheme and Intermediate Fellowship under the Basic Biomedical Research competition in December 2015

The interviews for these Fellowship schemes were held in November 2015

indicates institution that before this award did not have any India Alliance Fellow

4

MARGADARSHI FELLOWSHIP

Prof Satyajit Mayor National Centre for Biological Science Bangalore

IN CONVERSATION WITH

Dr Aravinda Chakravarti

Dr Aravinda Chakravarti is a Professor of Medicine Pediatrics Molecular Biology amp Genetics and Biostatistics and Director Center

for Complex Disease Genomics at the Johns Hopkins University School of Medicine and the Bloomberg School of Public Health He

also has a long association with the India Alliance as a member of its Clinical and Public Health Research Fellowship committee

What motivated you to become a scientist

I cannot say that it was any one person or one event or any one

point of time that led me to consider doing science Nor did I know

what being a scientist would entail or how one prepared to become

one I was not interested in science nor good at it or anything else for

that matter before the 9th grade But subsequently it was the

concreteness and logic of mathematics and the sciences that

appealed to me I also began reading material outside my textbooks

such as books in the Nuffield Science Series and others I came across

in the Calcutta British Council Library which began giving me a

broader look at the world of science But I was still clueless This was

evident in my applying for almost every conceivable program for

college (Engineering Medicine Geology Agriculture Physics and

Statistics) and being selected but not necessarily into the best schools

or programs Thus bdquosuccess‟ did not clarify my thinking any one bit

Finally I did choose to attend the Indian Statistical Institute (ISI)

outside Calcuttahellipa then beautiful oasis of calm in the politically

turbulent Calcutta of 1970‟s when being young well-read and aware

were enough to raise suspicions in the Calcutta Police (For those who

doubt the serious and mortal danger all young people in Calcutta

were under during this time read the daily newspaper reports from

the 70‟s)

For me Indian Statistical Institute (ISI) was

an escape from reality and an entry into a

synthetic artificial and manufactured world

of quantitative ideas

Our courses over 4 years in a US-style undergraduate were 50

Mathematics and Statistics and 50 an assortment of sciences and

economics (to learn the various domains in which quantitative

reasoning would be critical) where we were taught to ask bdquowhy‟ not

only bdquohow‟ something worked For the first time I found myself in an

atmosphere where understanding mattered more than knowledge

(dont worry knowledge did matter greatly) the pursuit of a job was

a side issue and we were encouraged to discover any area we

wished (or thats how I felt) I also had passionate teachers who were

the very best in the world For the first time I felt liberated learning

was fun and pursuing science as a life seemed like the only natural

thing to do It wasnt a one day transformationhellipby the time I left ISI I

knew that I could ask and answer at least some questions ISI was the

institution where the famed British polymath and geneticist J B S

Haldane came to in 1957 and became one of the architects of my

undergraduate program Although Haldane died in 1964 his ghost

was still around when I was a student at the ISI That I would do

genetics and be a scientist particularly in human genetics was

therefore a no brainer

Could you briefly take us through your scientific journey and

about your interest in genetics

My interest in genetics was established at the ISI but no less fueled by

my reading of Jim Watson‟s The Double Helix in 1970 and then as

credited by Watson and Crick Erwin Schrodinger‟s What is Life As a

student of the quantitative sciences at ISI the part of genetics that

appealed to me (simply because I could digest it) was Population

Genetics Also ISI had a Department of Human Genetics that

performed numerous studies of human genetic molecular diversity

across populations in India So my early training was in studies of

human population diversity Nevertheless Haldane‟s research (that I

was increasingly becoming aware of) was equally in family studies

that exemplified mechanisms not evident in population studies So as

a student I conducted and published research into the inheritance of

simply observable traits (bdquohand clasping‟ or the phenotype where you

classify individuals by whether they fold their left thumb over their

right or vice versahelliptry it only one way feels correct) just to learn

genetics and to attempt to combine the family and the population

methods that are so common today Fortunately by this time I had left

myself few opportunities to be interested in doing anything else but

human genetics

5

IN CONVERSATION WITH Dr Aravinda Chakravarti

Being rejected by several programs to study genetics in India

(because I was not a biology undergraduate) I chose to do graduate

work with the noted geneticist and molecular evolutionist Masatoshi

Nei at the University of Texas Houston where he had just moved I

arrived in Houston in 1974 and was immediately thrust into a small

intense center with brilliant people and expected to perform research

at a level I was surely unaccustomed to This group was the epicenter

of the then neutralist-selectionist debate in molecular evolution a

problem that was exciting but not my cup of tea I wanted to study

human genetics and finally fashioned a research project with Nei that

explored the theoretical consequences of improved genetic counseling

with linkage and association (linkage disequilibrium) markers and

graduated with a PhD in 1979 This research was not only far ahead

of its time coming before the proposal of creating a human linkage

map using RFLPs (restriction fragment length polymorphism) in 1980

but I was the only Nei student who worked outside molecular

evolution In many ways then my development in genetics became

very broad and haphazard since I often focused on areas that were

not my primary training grounds

By this time I was a geneticist but thought I needed further training in

genetic epidemiology to understand human disease better However

after an unsuccessful postdoc at Seattle I abandoned this idea to

take a non-tenured teaching position at the University of Pittsburgh

thinking that the bdquofree‟ time I would have would allow me to catch up

on the revolution in recombinant DNA technology that was underway I

am glad I did since this was one of the best

professional decisions I made by forgoing

the standard path

I taught at Pittsburgh for 5 years and subsequently obtained an NIH

Research Career Development Award to pursue a research career

That began my standard research career in human genetics

What according to you are the challenges in your field of

research

The field of human genetics is not the one I trained in since so much

has changed with the sequencing of the human genome Human

genetics has two distinct themes one descriptive as to the causes of

human variation be it molecular or phenotypic (the bdquohow‟ question)

and a second mechanistic as to how variation in molecular

mechanisms impact phenotype variation particularly disease (the

bdquowhy‟ question) The whole attraction of the human genome project to

me and others like me who spent more than a decade on building the

now available community resources (maps clones sequences variants

transcripts etc) was to move from the first set to the second set of

questions This transformation is difficult since it is not in the comfort

zone of conventional human genetics its hard and unpredictable

much more hypothesis-driven and much more experimental The

challenge in my field and in many associated medical specialties is

that it‟s far easier to do the first then the second Scientists are voting

with their feet Human geneticists are far more content in sequencing

human genomes finding associations with disease and doing facile

functional annotation than a serious investigation into why does this

gene causes type 2 diabetes and the next one congenital cataract

Or why mutations in the same gene cause a neuroendocrine tumor

when activating but congenital aganglionosis when loss-of-function

Or how come the same mutation can act as either activating or loss-

of-function

The biggest challenge in my field is to

overcome the inertia that molecular

description = etiological explanation

If you were not a scientist you would behellip

I really have no idea I presume the Bengali in me implicitly wants

or always wanted to be a writer but that would be a great leap of

faith and quite arrogant Even good scientific writing is hard very

hard indeed I have often read someone else‟s paper that I enjoyed

and thought that I could have done the same work a similar thought

has not appeared after reading someone else‟s creative work except

when it is quite bad

5 What is the best advice you have ever received

Unfortunately most advice that most people get and give is bad

More correctly its difficult to know (what‟s the test) when it is good

and when bad Each of us likely adapt a post-hoc explanation to our

stories all of which are likely revisionist Nevertheless two different

people (a brother and a family friend) at about the same time

(1979-1982) told me to abandon what I was doing (an unsuccessful

postdoc and forcing myself to complete reading a fairly racist

account of the Black Hole of Calcutta) because it was beyond my

enjoyment They both suggested that I drop it and do something else

One should not shoulder a burden that is great unless some higher

purpose is at stake One needs to learn how to apportion risk with

benefit

Your message for young students and researchers

Science is difficult but exhilarating in its rare moments of success

and it‟s usually followed by long periods of stasis It is a great but

frustrating life and there are many worse ways of making a living It

is like other types of creative endeavors where discovery is real but

rare If you wish to do it be sure you can enjoy its moods Science

today is also multidisciplinary and translational its application to

humans and other benefits can also be tangible sources of pride But

do it not for these benefits do it because the science gives you great

joy Yes joy Consider that you are one in an

unbroken intellectual chain from Johannes

Kepler and Isaac Newton If you choose

science you are special

Dr Chakravarti‟s laboratory focuses on the development and

applications of molecular genetic genomic and computational

methods for identification of human disease genes through

genetic dissectionldquo He has been a key participant and architect

of the Human Genome HapMap and 1000 Genomes project Find

out more about his research here

6

Workshop at a glance One-day workshop to equip young science

researchers with tools and strategies for effective communication of

their ideas experiments and scientific results from a science

communication perspective Help them to make science career choices

Vision Science communication plays an integral role in one‟s scientific

career Being able to effectively disseminate research findings within

the community and to consider collective opinions in prioritising

research needs is an important attribute of scientific maturity In

keeping with its mandate to empower future leaders of Indian science

the Wellcome TrustDBT India Alliance periodically conducts one-day

(SciComm101) and two-day (SciComm Hyderabad) science

communication workshops for the past four years This complements

seamlessly with Nature India‟s mandate to showcase India‟s science bdquoas

it happens‟ in laboratories and institutions across the country through

in-depth coverage and analysis of research and science policy The

proposed workshop would be part of Nature India‟s many

communication outreach activities as the one-stop media platform for

India‟s science

The Wellcome TrustDBT India Alliance and Nature India both

represent possibilities for young PhD scholars and postdoctoral

scientists to transition into academic as well as non-academic science

careers Information and advice on how to explore various career

options will form an important part of these workshops with

Naturejobs as the key organiser of the career session

Structure amp format

The workshop will be a one-day event preceding a biomedical (or

scientific) conference organised by reputed science

societiesorganisationsinstitutes and Universities in India A large

participation by PhD students postdoctoral fellows and junior

scientists will be a pre-requisite for holding this workshop Organising

this workshop as part of a conference will ensure participation from a

wide range of institutions across India The workshop will include 3

separate sessions

Session 1 Scientific Writing (moderated by WTDBT Alliance)

Topics to be covered

bull Ethics in research

bull Presentation skills

bull Manuscript writing

bull Grants writing

bull CVs and letters

Session 2 Science Communication (moderated by Nature India)

Topics to be covered

bull Science journalism

bull Popular science writing

bull Effective press releases

bull Hands-on skills on dejargonising science

Session 3 Alternate Science Career (moderated by Nature Jobs)

Topics to be covered

bull Career in the Industry

bull Career in Science PromotionIntellectual Property

bull Career in PolicyGrant organizations Journalism

Science Communication and Career Workshop Series (In partnership with Nature India amp Naturejobs )

Please contact us at workshopswellcomedbtorg to find out more about this series

INDIA ALLIANCE

SCIENCE COMMUNICATION

SciComm101 workshop

10 March 2016 MSU Baroda

Two-day SciComm workshop

21-22 March 2016 Hyderabad Applications under review

For more details visit SciComm Workshop under Quick Links on our website

Upcoming Workshops

5

ABOUT THE ART amp SCIENCE PROJECT

CALL FOR APPLICATIONS THE UNDIVIDED MIND |ART +

SCIENCE RESIDENCY AT KHOJ

Residency Dates March 2nd ndash April 2nd 2015

Application Deadline February 2nd 2015

Proposals are invited for bdquoThe Undivided Mind‟ a four-week

international residency for artists whose work explores the

intersection of art and science

At first it may seem that the pairing of Art amp Science is an atypical

choice as the two fields and methods of practice have almost

universally been represented as diametric opposites of each other

However on closer examination the similarities between artists and

scientists far outweigh their stereotypical differences Both are

dedicated to research and to asking the big question- what is true

Why does it matter How can we move society forward Moreover

both the lab and the studio are spaces that famously encourage

open-ended enquiry and emphasis on process In tune with Khoj‟s

commitment to cultivate an environment that allows for

experimentation and innovation the Art amp Science residency will be

a step towards furthering the explorations of interdisciplinary

practitioners This is the second edition of a Khoj residency focusing

on Art + Science to know more about the first edition please

click bdquohere‟

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

The following India Alliance Fellows will be participating in the

project

(NOTE If an applicant wishes to connect with any of the following

researchers in advance of submitting their proposal please contact

the Khoj team at bdquoapplicationskhojworkshoporg‟ for an

introduction please do the same if you are a scientist and would like

take part in this project )

Dr Venkatasubramanian Ganesan National Institute of Mental

Health and Neurosciences (NIMHANS) Bangalore

Dr Pallab K Maulik The George Institute for Global Health New

Delhi

Dr Anurag Agarwal CSIR-Institute of Genomics amp Integrative

Biology (IGIB) New Delhi

Dr Tavpritesh Sethi All India Institute of Medical Sciences (AIIMS)

New Delhi

Dr Lolitika Mandal Indian Institute of Science Education and

Research (IISER) Mohali

Dr Urvakhsh MehtaNIMHANS Bangalore

Dr Sheetal Gandotra IGIB New Delhi

Visit Khoj website to find out more about the residency and the application process

Apply by

2 February 2016

India Alliance is pleased to announce its support for Art amp Science Project at Khoj International Artists Association New Delhi details of

which can be found below and on the Khoj website It promises to be a great platform for interdisciplinary dialogue and exchange

between scientists and artists and we encourage anyone interested to apply (artists) and get involved (scientists)

THEME

The theme of the 2016 edition of The Undivided Mind is bdquoHealth‟

Within this broader framework three curatorial frameworks or

modes for exploration are suggested Terrestrial Health refers to

that which is on or related to the earth This sub ndash theme suggests an

investigation into the physical health and structure of the body (both

human and animal) the environment the community and the

interrelations between these spheres Mental Health refers to that

which is of or relating to the mind This sub ndash theme focuses on a

psychological investigation of what constitutes Health of the mind

and raises questions about the bdquosocially‟ defined state of well-being

where issues‟ surrounding the legal rights and entitlement of

personhood for those living with a mental disorder is open for

debate Finally Extraterrestrial Health may refer to any object

being or idea beyond the planet Earth This sub ndash theme opens up a

space where the relationship between Earth and other planetary

bodies can be studied What does it mean for human existence when

sending human life forms to Mars is projected to take place by

2020 What are the long term effects and solution to space debris

if life projects out beyond Earth This sub ndash theme also invites

applicants to consider the abstract and metaphorical imaginings of

health in contemporary and future societies

6

Nobel Laureate Dr Harold Varmus recognized for his research on

retroviruses and the genetic basis of cancer gave a lecture on ldquoRecent

Developments in Cancer Researchrdquo at National Institute of Immunology

(NII) New Delhi an event co-organised by NII Wellcome TrustDBT

India Alliance and Department of Biotechnology Government of

India His lecture largely gave an overview of the recent

developments challenges and the future directions in the field of

cancer research which included the current research of his group in

this area

Dr Varmus who had spent time in Bareilly as a young medical

student described cancer as a complex disease that requires

innovative research and treatment strategies At the outset Dr Varmus

introduced the key questions that drive the cancer research field- Is

cancer one disease or many diseases What makes the cancer cell

grow so stably in such an inappropriate manner How does a normal

cell become a cancer cell Providing answers to these questions

formed the backdrop of Dr Varmus‟s lecture which drew from his

research work till date and other advances in the field

Dr Varmus entered the field of cancer research in 1970s as a

postdoctoral scientist in the laboratory of Dr John J Michael Bishop at

University of California San Francisco USA the same year National

Cancer Act was signed in the country Dr Bishop and Dr Varmus

together received the Nobel Prize in Medicine and Physiology in

1989 ldquofor their discovery of the cellular origins of retroviral

oncogenesrdquo During his lecture Dr Varmus confessed standing on the

shoulders of giants of retroviral and cancer research such as Dr

Peyton Rous Dr Harry Rubin and Dr Howard Temin to ask the question

of how retroviruses transformed cells and cause tumours This question

led him to look for genes that make a normal cell behave like a

cancer cell which initially involved studying cancer-causing RNA

virusesretroviruses in animals The retrovirus that played a lead role

in Dr Varmus and his colleague‟s work was the Rous Sarcoma Virus

(RSV) discovered by Dr Peyton Rous in 1911 which he showed caused

a type of cancer in chickens Dr Varmus and colleagues set out to

prove the hypothesis that retroviruses enter host cells and capture

normal genes in that cell by inserting their DNA converting them into

cancer-causing genes or oncogenes Dr Varmus and his group

employed various cellular chemical as well as genetic tools to

establish that retroviruses can indeed act as mutagens by inserting

their DNA in host cells and turning them into cancer cells After this his

group went on to identify the cancer-causing genes present in the

virus and subsequently discovered many new oncogenes v-Src (a

gene of RSV) being the first one Following these discoveries and

subsequently many others led to the belief that the genetic basis of

cancer is highly heterogeneous Dr Varmus told us that in order to

catalogue these complexities the Cancer Genome Atlas was

established in 2005 which till today serves as a collection of the

genetic mutations responsible for different cancers

Apart from the complexity and vastness of the cancer genome

other challenges in the field according to Dr Varmus are genetic

heterogeneity and evolution of tumours due to various environmental

factors such as exposure to UV pollution tobacco use and other

environmental carcinogens that are on the rise He used the example

of renal tumor evolution which illustrates Darwin‟s theory of ldquoevolution

of speciesrdquo to show that this rapidly changing genetic repertoire can

have significant impact on diagnosis therapeutic interventions and

prognosis Another issue of concern highlighted by Dr Varmus was the

absence of suitable drugs against many common targets for cancer

such as cancer-causing RAS genes and many transcription factors

which have been shown to contribute towards cancer formation Dr

Varmus opined that lack of understanding of the underlying

complexity of resistance to cancer therapies is another roadblock in

cancer treatment He was also strongly of the opinion that there are

not enough public health interventions to prevent cancer- this he felt

needs to go hand in hand with finding cure for cancer

Dr Varmus also offered solutions to these problems He suggested

that research needs to ldquolook beyond genes and focus on patterns and

pathwaysrdquo and physiological changes taking place in cancer cells He

shared his group‟s current interest in studying ldquooncogene addictionrdquo

which is based on the premise that some oncogenes not only give rise

to cancer but also maintain the cancerous state of the cells

Interpreting the downstream effects of these cancer genes on the

pathways could be employed as a strategy to attack multiple targets

by drugs in different cancers Even though he hailed the successes of

many commonly used and extremely efficacious anti-cancer drugs

such as Gleevec Gefitinib Erlotinib but in light of growing

complexity of the disease proposed the need for adopting more

innovative drug discovery and treatment approaches Continuing on

the topic of therapeutics Dr Varmus mentioned the recent advances in

immunotherapeutic approaches to treat cancer which would require

us to understand why the otherwise combative immune system does

not kill cancer cells He suggested that gaining understanding of these

immune check points and accordingly targeting them by antibody

inhibitors could serve as one more effective treatment strategy-

another project his research group has undertaken In addition to

these therapeutic approaches Dr Varmus very strongly asserted that

ldquonot everything we talk about cancer should be about cancer therapy

but also about preventionrdquo and that this disease ought to be on the

global health agenda

Dr Varmus very eloquently concluded his talk by stating that

ldquoconfronting cancer needs a balance between grasping its complexity

and seeking simple solutionsrdquo As expected he received many

questions from the audience after his lecture on the genetics and

biology of various cancers potential use of vaccines in cancer

treatment crosstalk of cancer with other diseases and many others to

which he responded with prudence and an underlying sense of

optimism

Prior to his lecture Dr Varmus over an hour meeting with 10 young

cancer researchers discussed their work This group included the

following Wellcome TrustDBT India Alliance Fellows - Dr Reety Arora

(ECF InStem Bangalore) Dr Anjali Bajpai (ECF IIT Kanpur) Dr

Bushra Ateeq (Int Fellow IIT Kanpur) Dr Kundan Sengupta (Int Fellow

IISER Pune) and Dr Sandeep Singh (Int Fellow NIBMG Kalyani) Dr

Varmus also sought information on the India Alliance Fellowships and

was impressed by its funding model and reach

LECTURE REPORT

Recent Developments in Cancer Research By Dr Harold Varmus Nobel Prize in Medicine and Physiology Weill Cornell Medical College USA

at

National Institute of Immunology New Delhi

16 November 2015

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

7

ASK THE SCIENTIST about

The Human Brain

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

This section will bring to you answers to those burning scientific questions that you always wanted to ask the guys in the white

coat For this issue we asked some of our Fellows to shed light on the various operations of the brain

How can we measure attention

DR SUPRATIM RAY Indian Institute of Science Bangalore

Intermediate Fellow

Attention can be of different types such as sustained (vigilance)

selective (focusing at one stimulus in the presence of distractors) or

alternating (involves switching) which can be measured using a

variety of cognitive tests (such as test of everyday attention (TEA) or

Posner cuing task) For example in a classical Posner task a subject

is repeatedly shown two stimuli and cued to attend to one of them

and instructed to respond to a change in the stimulus (say by

pressing a button) The cue could be valid (change occurs at the cued

stimulus say for 80 of the trials) invalid (change occurs at the

uncued stimulus) or neutral (ambiguous) Selection attention can be

measured by comparing the accuracy and the time taken to press

the button after stimulus change (called reaction time) for different

cue types

Different components of attention such as orienting towards a

location detecting a target or maintaining vigilance are carried out

by distinct brain areas in the prefrontal and parietal lobes and some

sub-cortical structures (such as superior colliculus) Overall

performance depends not only on how these areas perform but also

how they communicate with each other and on the levels of

neuromodulators such as norepinephrine

How can we sense smell Is it possible to live without this

sense of smell

DR NIXON ABRAHAM Indian Institutes of Science Education amp

Research (IISER) Pune

Intermediate Fellow

Once Dr Lewis Thomas (1913-1993) the poet and a philosopher of

medicine who also served as the dean of the medical schools at the

New York University and Yale was asked to select seven wonders of

the modern world Olfaction (olfactory receptor cell) was fifth in his

list How does the modern fifth wonder that brings us the smell of our

surroundings ndash the good and bad work

The process of making sense of smell start by binding the odor

molecules to the olfactory receptors located in the olfactory sensory

neurons (OSNs) in the nose This binding triggers a series of signal

amplification steps which lead to electrical spikes (so called action

potentials) in OSNs This olfactory information whose intensity is

encoded by varying the number of action potentials is then passed

onto the projection neurons named mitral and tufted cells in the

olfactory bulb These projection neurons whose excitatory actions

are controlled by various inhibitory neurons carry the olfactory

information to the higher centers in the brain so that we perceive the

smell of spicy tasty food and putrid garbage ndash the good and bad

from the environment

Continued

9

Brain waves

measured by EEG

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

What is really happening inside the brain of a Schizophrenia

patient Does it look any different from a normal brain

DR VENKATASUBRAMANIAN GANESAN NIMHANS Bengaluru

Intermediate Fellow

The brain of a schizophrenia patient is reduced in overall volume

with increase in the size of the ventricles (parts of the brain that

contain cerebrospinal fluid) however certain parts like hippocampus

superior temporal gyrus and prefrontal cortex are more affected

than others Using certain advanced brain imaging research studies

(for example high resolution structural MRI functional MRI Magnetic

Resonance Spectroscopy Positron Emission Tomography and Diffusion

Tensor Imaging and similar others) subtle brain abnormalities in

structure function neurochemical profile as well as brain connectivity

have been demonstrated in several brain regions in schizophrenia

patients It is important to note that these findings are obtained

from advanced research studies that have compared brains of a

Why are the mirror neurons called the Minds mirror What do

they reflect

DR URVAKHSH MEHTA National Institute of Mental Health amp

Neurosciences (NIMHANS) Bengaluru

Early Career Fellow

Mirror neurons are specialized nerve cells that discharge when

we perform actions as well as when we observe others perform the

same action Rizzolatti and colleagues accidentally discovered them

in monkeys These neurons also get vicariously activated when we

perceive emotional states of others This unique bdquoexperience sharing‟

property of mirror neurons perhaps enables us to decipher goals

intentions and emotions of others

In several of our daily social interactions we need to take

perspectives of others decipher deception share feelings and

empathize with others The mirror neuron system is an important

brain network that helps us peek into the minds of others and try to

understand people They translate sensory information (eg

observation of an action) into a motor template which is similar to

the format an observer himself uses to perform that very action This

motor template can help us interpret the goals and feelings

underlying observed actions The definitive demonstration of mirror

neurons in humans was as recent as 2010 There is also growing

evidence of a dysfunctional mirror neuron system in psychiatric

disorders like autism and schizophrenia It is a long and exciting

future ahead to decipher spatiotemporal regulatory and genetic

underpinnings of this unique neuronal network ndash this will possibly

help understand and treat social brain disorders better

Schizophrenia

What happens if we loose our sense of smell Loss of olfaction can

be caused by many reasons ranging from viral infections to

neurodegenerative disorders As our emotions and memories are

strongly related to olfaction the loss of this sense can lead to

depressed state and even affect bonding with family members Just

imagine sipping from your morning coffee without sensing it‟s aroma

- our taste could be badly affected by losing sense of smell The

ongoing research at the nasal stem cell level might provide clinical

solutions for the disorders of the olfactory sensory neurons to regain

this wonderful sense

group of schizophrenia patients with that of healthy subjects thus

these are group averaged findings that are currently not applicable

for diagnosing schizophrenia in an individual patient in a regular

clinical setting In ldquoa specific patientrdquo one may not be able to find

any striking abnormality in the physical appearance of the brain (ie

a routine CT or MRI brain scan may not be able to identify any

obvious aberration) Several ongoing research studies are in pursuit

to identify clinically useful biomarker to diagnose schizophrenia

Find out more about Dr Ganesan‟s research on schizophrenia here

Do you have a burning scientific

question

Send them to

publicengagementwellcomedbtorg

Mirror neuron activity in the brain both when the monkey grasps an object

and when it observes the experimenter grasping the object Mirror neurons

were first discovered by Rizzolatti and colleagues when they were studying

motor actions in macque monkeys

10

INDIA ALLIANCE FELLOW

DR ROOP MALIK Senior Fellow TIFR Mumbai

Dr Roop Malik is a biophysicist based at Tata Institute of Fundamental Research Mumbai Dr Malikrsquos research focuses on nanoscale molecular motor proteins that transport material such as virus mitochondria endosomes etc inside living cells

What is your research group working on and what impact do you

hope it will have

We try to understand how the living cell achieves an organization that

is well defined yet dynamic Most of the components within a cell

have a lipid membrane boundary This boundary is fairly well

defined and visible under a microscope yet it undergoes constant

deformation to allow exchange of material between different parts

of a cell Motor proteins attach to the lipid membrane boundary and

act as transporters physically carrying cellular material from one

membrane to another in the form of a vesicular cargo How do the

motors and lipids collaborate to decide the fate of the cargo

We work on two such cargoes -- the Phagosome (may enclose

pathogens) and the Lipid droplet (encloses fat) We hope that our

research will help understand how pathogens infect us by modifying

the lipid membrane and the motors attached to it We also

investigate how fat stored inside the Lipid droplets in our liver is

circulated to different parts of the body There is a tremendous

change in the amount of fat stored in liver at every feedingfasting

cycle This is visible in the form of Lipid droplet accumulation in rat

liver sections after fasting How does the liver handle this flux of fat

What special mechanisms are required Answering these questions

may help understand the progression of fatty liver diseases

What inspired you to become a scientist

To be frank nothing in particular It was an acquired taste I started

doing experiments and gradually realised I was doing well I like the

planning that is involved in investigating the unknown and the

surprises that crop up inevitably These force you to change your

well-laid plans Thats when it gets really exciting

What role canshould scientists play in todays India

I think there is a lot of scientific freedom in India Granting agencies

are not as hawkish as in the western world This freedom is an

opportunity to do what drives you There are many young scientists in

the country who are keen to share ideas and resources We should

focus on solving difficult problems by taking advantage of this

environment If we do good science it will inspire the public

The primary job of a scientist is to do science and to do it well

Beyond that we also need to think about how science can be

propagated We have to mentor students and give them the

confidence and enthusiasm so that they go on to do better science

than we did We also have to communicate our science to common

man and facilitate them We must impress on students (and also on

their parents) that they should not look at studying Physics or Biology

or Chemistry in isolation Those who want to take up science as a

career should also understand that they must learn to deal with many

failures before something succeeds

How has Wellcome TrustDBT India Alliance Fellowship helped

you and your research (your IA experience)

I have been a Senior fellow with Wellcome Trust (UK) and then with

Wellcome Trust DBT India Alliance since 2006 The rigorous selection

process helped me fine-tune the questions that I wanted to ask The

subsequent evaluations and annual meetings helped in keeping my

research on track Last but not the least we were given a lot of

freedom in executing our science I thank the India Alliance for this

degree of trust in their Fellows This has helped me to focus on the

science

What keeps you going every day

Coffee tea and the excitement of planning and executing science

with my colleagues Regular breaks to get out into the hills for some

adventure

Find out more about

Dr Roop Malik‟s

work on motor

proteins on his

website In order to

make his research

understandable to

a wide range of

people he has put

up translation of his

research summary

in Hindi and

Marathi in addition

to Engalish on his

website

11

A Sponge Against a Sword An RNA-binding protein Prevents Chronic Inflammation and Cancer

By Dr Partho Sarothi Ray Intermediate Fellow

Anyone who has had a bruise is familiar with the redness

swelling warmth and pain that mark the site of the injury This

response known as inflammation has been recognized since ancient

times and its hallmarks were first described by the Greek physician

Galen 2000 years ago The process which is often set in motion by

specialized cells of the immune system occurs whenever tissue is

infected or damaged as for example when you have a pimple or

more seriously suffer a heart attack The latter condition is called

sterile inflammation which happens in absence of infection by a

pathogen and when it goes awry it contributes to a wide range of

seemingly unrelated diseases from Alzheimer‟s disease to diabetes to

cancer

Inflammation is the primary protective response of the body to any

infection or injury However as our common experience shows the

inflammation after being triggered goes away of its own a process

known as resolution However in certain cases the inflammation fails

to resolve and it‟s continuation known as chronic inflammation acts as

an underlying contributor to virtually every chronic disease- a list that

besides obvious culprits such as rheumatoid arthritis and

Crohn‟s disease includes diabetes and depression along with major

killers such as heart disease and stroke and especially cancer

Therefore inflammation is a double-edged sword it protects our

body but can also harm it when it occurs in an uncontrolled manner

Over the past decade and half this role of inflammation has come

under intense scrutiny and many research groups throughout the

world are attempting to discover the underlying mechanisms which

regulate the onset and resolution of inflammation

Connection between Cancer and Inflammation

The connection between cancer and inflammation was recognized a

long time ago In fact in 1863 the renowned German pathologist

Rudolf Virchow found the presence of white blood cells cells which

mediate inflammation in tumors In 1986 the cancer biologist Harold

Dvorak of Harvard Medical School remarked that tumors are

wounds that do not heal However it is only over the last two

decades that the connections between inflammation and cancer have

transformed our understanding of how cancers develop This

transformation recognizes that the chronic inflammatory state serves

as a key mediator of the middle stages of tumor development

Cancer begins with a series of genetic changes that prompt a group

of cells to proliferate and then invade surrounding tissue the point at

which true malignancy begins Eventually some tumor cells may break

off and establish new growths (metastases) at distant sites This has

been understood for a long time But cancer biologists and

immunologists have begun to realize that the progression from

diseased tissue to full-blown invasive cancer often requires cells that

normally participate in inflammation to be diverted to the pre-

malignant tissue where they are hijacked to become co-conspirators

that aid and abet carcinogenesis As described by researchers

genetic damage is the match that lights the fire and inflammation

is the fuel that feeds it Therefore the aim of our lab is to understand

the molecular processes and mechanisms that normally prevent chronic

inflammation and thereby prevent the transition from a pre-malignant

stage to a full-blown cancer Hopefully this understanding will allow in

not-so-distant future to detect and treat cancers at the pre-malignant

stage which will make cancer treatment much easier and affordable

In addition to that this understanding will possibly be helpful in the

treatment of all chronic inflammatory diseases as the basic cellular

mechanisms underlying chronic inflammation are thought to be the

same in all cases

Inflammation in cells

At the cellular level inflammation involves two types of cells the

cells of the tissue or organ that is injured that is the inflamed cells

and the cells that mediate the inflammation that is the inflammatory

cells The latter consist mainly of cells that are originally in the blood

such as monocytes and neutrophils which migrate to the site of the

inflammation and literally eat up (phagocytose) the infecting

microorganisms or the injured cells In many cases there are

monocytes present within the inflamed tissue itself called

macrophages or big eaters which form the first line of attack on the

invading pathogen or damaged tissue Now both the inflamed cells

and the inflammatory cells secrete special signalling chemicals called

cytokines which attract more inflammatory cells to the site of the

inflammation Together with the cytokines the inflammatory cells (the

macrophages and neutrophils) also produce a variety of other factors

that allow the cells to move through the wall of the blood vessels and

then into the tissue where they attack engulf and destroy the

invading pathogen or the damaged cells It is obvious that many of

these factors such as reactive oxygen species (ROS)

metalloproteases interleukins like IL6 and blood vessel growth factors

like VEGF are toxic and if continued to be produced will damage

the healthy tissue as well That is why the production of both the

cytokines which attract these cells to the site of inflammation and

these factors which cause the death and destruction of the pathogens

ceases when the cause of the inflammation is removed and allows the

inflammation to resolve Failure to stop the production of these

inflammatory factors therefore leads to chronic inflammation and the

chronic inflammatory diseases The inflammatory factors cytokines

and others are produced by genes which are called pro-

inflammatory genes Therefore the expression of these genes that is

the production of proteins from the genes have to be tightly

regulated both in space and time

12

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 4: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

Eligibility

Eligibility limit covers the entire range of Clinical and Public

Health Research Fellowship schemes

bull No age or Nationality restrictions

bull The candidates need not be resident in India while

applying but should be willing to establish an

independent research career in India

bull Clinicians and Public health researchers do not require a

PhD to apply

bull This competition is open for clinicians and public health

researchers with up to 15 years of post-

MDMSMPHPhD or equivalent clinical public health

research experience

bull The Applicants are advised to choose the most

appropriate scheme suitable for them based on their

qualification research experience career trajectory and

track record Please refer to the guidance notes

provisions and mandate of the scheme for assessing your

eligibility on the website The Office reserves the right to

advice on the suitability of the scheme accordingly

Early Career Fellowship This scheme provides a unique

opportunity for those who have shown promise to pursue

research and wish to further their efforts to build a research

career under the supervision of a Fellowship

supervisor Guidance note Suitable for applicants in the final

year PhDMDMSMPH or have up to 4 years of relevant

experience

Intermediate Fellowship For those who have been

successful in building a track record of pursuing a cutting

edge research and wish to establish their own independent

clinicalpublic health research program in India Guidance

note Suitable for applicants with 4-7 years of relevant

experience

INDIA ALLIANCE FELLOWSHIP ANNOUNCEMENT

CALL FOR APPLICATIONS

Application forms are available on the India Alliance online

application System (IASys) at

httpsfellowshipswellcomedbtorgLoginaspx

Please visit our website for further information on the application process Please write to us with

queries to infowellcomedbtorg

3

CLINICAL AND PUBLIC HEALTH RESEARCH FELLOWSHIPS 2016

Preliminary Application Deadline 1 March 2016

India Alliance invites applications for three Fellowship schemes

Early Career Fellowships Intermediate Fellowships and Senior Fellowships

Senior Fellowship For those who have demonstrated their

potential to lead an independent research program and

want to expand it further to undertake pioneering research

Guidance note Suitable for applicants with 7-15 years of

relevant experience

Remit Full spectrum of biomedical science involving clinical

and public health research

Provisions

bull These Fellowships would encourage interested clinicians

to pursue their research goals in combination with their

clinical duties

bull Competitive personal support

bull Generous research support with flexibility to

accommodate requirements of clinical and public health

research

bull Flexibility to request additional support staff

bull Support training cost and research sabbatical

bull Funds for International training and travel

bull Opportunity to pursue a PhD on the India Alliance

funded research

Essentials on the application

bull A research proposal that seeks to answer an original

biomedical research question

bull A not-for-profit Host Institution in India that will

administer the Fellowship for the full duration of the

award A salaried position or commitment to a salaried

position at the Host Institution is not required

bull A Sponsor at the Host Institution who can guarantee

space and resources for the duration of the award

bull In case of an Early Career Fellowship a Fellowship

Supervisor who can guarantee access to laboratory

space and resources required for the project as well as

provide relevant scientific guidance for the tenure of the

Fellowship

CLINICAL AND PUBLIC HEALTH RESEARCH FELLOWSHIPS

Early Career Fellowships

Dr Jayanth Kumar Palanichamy All India Institute of Medical Sciences New Delhi

Dr Aparna Mukherjee All India Institute of Medical Sciences New Delhi

Dr Deepak Kamath St Johns National Academy Of Health Sciences Bangalore

Intermediate Fellowships

Dr Aparna Rao L V Prasad Eye Institute Bhubaneswar

Dr Abi Vanak Ashoka Trust for Research in Ecology and the Environment Bangalore

Dr Shivarama VaramballyNational Institute of Mental Health and Neurosciences Bangalore

Dr Rashmi Rodrigues St Johns National Academy Of Health Sciences Bangalore

Dr Mahesh Kate Christian Medical College Ludhiana

Research Training Fellowships

Ms Urvita Bhatia Sangath Porvorim

Dr Deepak Gautam All India Institute of Medical Sciences New Delhi

Dr Sumsum P Sunny Mazumdar Shaw Medical Center Bangalore

Dr Dhruva Ithal National Institute of Mental Health and Neurosciences Bangalore

Dr Rakshathi B National Institute of Mental Health and Neurosciences Bangalore

ANNOUNCEMENT

RECENTLY RECOMMENDED AWARDEES

BASIC RESEARCH FELLOWSHIPS

Intermediate Fellowships

Dr Sridharan Devarajan Indian Institute of Science Bangalore

Dr Nitin Gupta Indian Institute Of Technology Kanpur

Dr Sachin Kotak Indian Institute of Science Bangalore

Dr Aravind Penmatsa Indian Institute of Science Bangalore

Dr Siddhesh Shashikant Kamat Indian Institute of Science Education and Research Pune

Dr Mohan Joshi Centre for DNA Fingerprinting and Diagnostics Hyderabad

Dr Satish Khurana Indian Institute of Science Education and Research Thiruvananthapuram

Dr Pinky Kain Indian Institute of Technology Roorkee

Dr Santosh Chauhan Institute Of Life Sciences Bhubaneswar

India Alliance announced Fellowship Awardees of the Clinical and Public Health Research Fellowship

scheme and Intermediate Fellowship under the Basic Biomedical Research competition in December 2015

The interviews for these Fellowship schemes were held in November 2015

indicates institution that before this award did not have any India Alliance Fellow

4

MARGADARSHI FELLOWSHIP

Prof Satyajit Mayor National Centre for Biological Science Bangalore

IN CONVERSATION WITH

Dr Aravinda Chakravarti

Dr Aravinda Chakravarti is a Professor of Medicine Pediatrics Molecular Biology amp Genetics and Biostatistics and Director Center

for Complex Disease Genomics at the Johns Hopkins University School of Medicine and the Bloomberg School of Public Health He

also has a long association with the India Alliance as a member of its Clinical and Public Health Research Fellowship committee

What motivated you to become a scientist

I cannot say that it was any one person or one event or any one

point of time that led me to consider doing science Nor did I know

what being a scientist would entail or how one prepared to become

one I was not interested in science nor good at it or anything else for

that matter before the 9th grade But subsequently it was the

concreteness and logic of mathematics and the sciences that

appealed to me I also began reading material outside my textbooks

such as books in the Nuffield Science Series and others I came across

in the Calcutta British Council Library which began giving me a

broader look at the world of science But I was still clueless This was

evident in my applying for almost every conceivable program for

college (Engineering Medicine Geology Agriculture Physics and

Statistics) and being selected but not necessarily into the best schools

or programs Thus bdquosuccess‟ did not clarify my thinking any one bit

Finally I did choose to attend the Indian Statistical Institute (ISI)

outside Calcuttahellipa then beautiful oasis of calm in the politically

turbulent Calcutta of 1970‟s when being young well-read and aware

were enough to raise suspicions in the Calcutta Police (For those who

doubt the serious and mortal danger all young people in Calcutta

were under during this time read the daily newspaper reports from

the 70‟s)

For me Indian Statistical Institute (ISI) was

an escape from reality and an entry into a

synthetic artificial and manufactured world

of quantitative ideas

Our courses over 4 years in a US-style undergraduate were 50

Mathematics and Statistics and 50 an assortment of sciences and

economics (to learn the various domains in which quantitative

reasoning would be critical) where we were taught to ask bdquowhy‟ not

only bdquohow‟ something worked For the first time I found myself in an

atmosphere where understanding mattered more than knowledge

(dont worry knowledge did matter greatly) the pursuit of a job was

a side issue and we were encouraged to discover any area we

wished (or thats how I felt) I also had passionate teachers who were

the very best in the world For the first time I felt liberated learning

was fun and pursuing science as a life seemed like the only natural

thing to do It wasnt a one day transformationhellipby the time I left ISI I

knew that I could ask and answer at least some questions ISI was the

institution where the famed British polymath and geneticist J B S

Haldane came to in 1957 and became one of the architects of my

undergraduate program Although Haldane died in 1964 his ghost

was still around when I was a student at the ISI That I would do

genetics and be a scientist particularly in human genetics was

therefore a no brainer

Could you briefly take us through your scientific journey and

about your interest in genetics

My interest in genetics was established at the ISI but no less fueled by

my reading of Jim Watson‟s The Double Helix in 1970 and then as

credited by Watson and Crick Erwin Schrodinger‟s What is Life As a

student of the quantitative sciences at ISI the part of genetics that

appealed to me (simply because I could digest it) was Population

Genetics Also ISI had a Department of Human Genetics that

performed numerous studies of human genetic molecular diversity

across populations in India So my early training was in studies of

human population diversity Nevertheless Haldane‟s research (that I

was increasingly becoming aware of) was equally in family studies

that exemplified mechanisms not evident in population studies So as

a student I conducted and published research into the inheritance of

simply observable traits (bdquohand clasping‟ or the phenotype where you

classify individuals by whether they fold their left thumb over their

right or vice versahelliptry it only one way feels correct) just to learn

genetics and to attempt to combine the family and the population

methods that are so common today Fortunately by this time I had left

myself few opportunities to be interested in doing anything else but

human genetics

5

IN CONVERSATION WITH Dr Aravinda Chakravarti

Being rejected by several programs to study genetics in India

(because I was not a biology undergraduate) I chose to do graduate

work with the noted geneticist and molecular evolutionist Masatoshi

Nei at the University of Texas Houston where he had just moved I

arrived in Houston in 1974 and was immediately thrust into a small

intense center with brilliant people and expected to perform research

at a level I was surely unaccustomed to This group was the epicenter

of the then neutralist-selectionist debate in molecular evolution a

problem that was exciting but not my cup of tea I wanted to study

human genetics and finally fashioned a research project with Nei that

explored the theoretical consequences of improved genetic counseling

with linkage and association (linkage disequilibrium) markers and

graduated with a PhD in 1979 This research was not only far ahead

of its time coming before the proposal of creating a human linkage

map using RFLPs (restriction fragment length polymorphism) in 1980

but I was the only Nei student who worked outside molecular

evolution In many ways then my development in genetics became

very broad and haphazard since I often focused on areas that were

not my primary training grounds

By this time I was a geneticist but thought I needed further training in

genetic epidemiology to understand human disease better However

after an unsuccessful postdoc at Seattle I abandoned this idea to

take a non-tenured teaching position at the University of Pittsburgh

thinking that the bdquofree‟ time I would have would allow me to catch up

on the revolution in recombinant DNA technology that was underway I

am glad I did since this was one of the best

professional decisions I made by forgoing

the standard path

I taught at Pittsburgh for 5 years and subsequently obtained an NIH

Research Career Development Award to pursue a research career

That began my standard research career in human genetics

What according to you are the challenges in your field of

research

The field of human genetics is not the one I trained in since so much

has changed with the sequencing of the human genome Human

genetics has two distinct themes one descriptive as to the causes of

human variation be it molecular or phenotypic (the bdquohow‟ question)

and a second mechanistic as to how variation in molecular

mechanisms impact phenotype variation particularly disease (the

bdquowhy‟ question) The whole attraction of the human genome project to

me and others like me who spent more than a decade on building the

now available community resources (maps clones sequences variants

transcripts etc) was to move from the first set to the second set of

questions This transformation is difficult since it is not in the comfort

zone of conventional human genetics its hard and unpredictable

much more hypothesis-driven and much more experimental The

challenge in my field and in many associated medical specialties is

that it‟s far easier to do the first then the second Scientists are voting

with their feet Human geneticists are far more content in sequencing

human genomes finding associations with disease and doing facile

functional annotation than a serious investigation into why does this

gene causes type 2 diabetes and the next one congenital cataract

Or why mutations in the same gene cause a neuroendocrine tumor

when activating but congenital aganglionosis when loss-of-function

Or how come the same mutation can act as either activating or loss-

of-function

The biggest challenge in my field is to

overcome the inertia that molecular

description = etiological explanation

If you were not a scientist you would behellip

I really have no idea I presume the Bengali in me implicitly wants

or always wanted to be a writer but that would be a great leap of

faith and quite arrogant Even good scientific writing is hard very

hard indeed I have often read someone else‟s paper that I enjoyed

and thought that I could have done the same work a similar thought

has not appeared after reading someone else‟s creative work except

when it is quite bad

5 What is the best advice you have ever received

Unfortunately most advice that most people get and give is bad

More correctly its difficult to know (what‟s the test) when it is good

and when bad Each of us likely adapt a post-hoc explanation to our

stories all of which are likely revisionist Nevertheless two different

people (a brother and a family friend) at about the same time

(1979-1982) told me to abandon what I was doing (an unsuccessful

postdoc and forcing myself to complete reading a fairly racist

account of the Black Hole of Calcutta) because it was beyond my

enjoyment They both suggested that I drop it and do something else

One should not shoulder a burden that is great unless some higher

purpose is at stake One needs to learn how to apportion risk with

benefit

Your message for young students and researchers

Science is difficult but exhilarating in its rare moments of success

and it‟s usually followed by long periods of stasis It is a great but

frustrating life and there are many worse ways of making a living It

is like other types of creative endeavors where discovery is real but

rare If you wish to do it be sure you can enjoy its moods Science

today is also multidisciplinary and translational its application to

humans and other benefits can also be tangible sources of pride But

do it not for these benefits do it because the science gives you great

joy Yes joy Consider that you are one in an

unbroken intellectual chain from Johannes

Kepler and Isaac Newton If you choose

science you are special

Dr Chakravarti‟s laboratory focuses on the development and

applications of molecular genetic genomic and computational

methods for identification of human disease genes through

genetic dissectionldquo He has been a key participant and architect

of the Human Genome HapMap and 1000 Genomes project Find

out more about his research here

6

Workshop at a glance One-day workshop to equip young science

researchers with tools and strategies for effective communication of

their ideas experiments and scientific results from a science

communication perspective Help them to make science career choices

Vision Science communication plays an integral role in one‟s scientific

career Being able to effectively disseminate research findings within

the community and to consider collective opinions in prioritising

research needs is an important attribute of scientific maturity In

keeping with its mandate to empower future leaders of Indian science

the Wellcome TrustDBT India Alliance periodically conducts one-day

(SciComm101) and two-day (SciComm Hyderabad) science

communication workshops for the past four years This complements

seamlessly with Nature India‟s mandate to showcase India‟s science bdquoas

it happens‟ in laboratories and institutions across the country through

in-depth coverage and analysis of research and science policy The

proposed workshop would be part of Nature India‟s many

communication outreach activities as the one-stop media platform for

India‟s science

The Wellcome TrustDBT India Alliance and Nature India both

represent possibilities for young PhD scholars and postdoctoral

scientists to transition into academic as well as non-academic science

careers Information and advice on how to explore various career

options will form an important part of these workshops with

Naturejobs as the key organiser of the career session

Structure amp format

The workshop will be a one-day event preceding a biomedical (or

scientific) conference organised by reputed science

societiesorganisationsinstitutes and Universities in India A large

participation by PhD students postdoctoral fellows and junior

scientists will be a pre-requisite for holding this workshop Organising

this workshop as part of a conference will ensure participation from a

wide range of institutions across India The workshop will include 3

separate sessions

Session 1 Scientific Writing (moderated by WTDBT Alliance)

Topics to be covered

bull Ethics in research

bull Presentation skills

bull Manuscript writing

bull Grants writing

bull CVs and letters

Session 2 Science Communication (moderated by Nature India)

Topics to be covered

bull Science journalism

bull Popular science writing

bull Effective press releases

bull Hands-on skills on dejargonising science

Session 3 Alternate Science Career (moderated by Nature Jobs)

Topics to be covered

bull Career in the Industry

bull Career in Science PromotionIntellectual Property

bull Career in PolicyGrant organizations Journalism

Science Communication and Career Workshop Series (In partnership with Nature India amp Naturejobs )

Please contact us at workshopswellcomedbtorg to find out more about this series

INDIA ALLIANCE

SCIENCE COMMUNICATION

SciComm101 workshop

10 March 2016 MSU Baroda

Two-day SciComm workshop

21-22 March 2016 Hyderabad Applications under review

For more details visit SciComm Workshop under Quick Links on our website

Upcoming Workshops

5

ABOUT THE ART amp SCIENCE PROJECT

CALL FOR APPLICATIONS THE UNDIVIDED MIND |ART +

SCIENCE RESIDENCY AT KHOJ

Residency Dates March 2nd ndash April 2nd 2015

Application Deadline February 2nd 2015

Proposals are invited for bdquoThe Undivided Mind‟ a four-week

international residency for artists whose work explores the

intersection of art and science

At first it may seem that the pairing of Art amp Science is an atypical

choice as the two fields and methods of practice have almost

universally been represented as diametric opposites of each other

However on closer examination the similarities between artists and

scientists far outweigh their stereotypical differences Both are

dedicated to research and to asking the big question- what is true

Why does it matter How can we move society forward Moreover

both the lab and the studio are spaces that famously encourage

open-ended enquiry and emphasis on process In tune with Khoj‟s

commitment to cultivate an environment that allows for

experimentation and innovation the Art amp Science residency will be

a step towards furthering the explorations of interdisciplinary

practitioners This is the second edition of a Khoj residency focusing

on Art + Science to know more about the first edition please

click bdquohere‟

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

The following India Alliance Fellows will be participating in the

project

(NOTE If an applicant wishes to connect with any of the following

researchers in advance of submitting their proposal please contact

the Khoj team at bdquoapplicationskhojworkshoporg‟ for an

introduction please do the same if you are a scientist and would like

take part in this project )

Dr Venkatasubramanian Ganesan National Institute of Mental

Health and Neurosciences (NIMHANS) Bangalore

Dr Pallab K Maulik The George Institute for Global Health New

Delhi

Dr Anurag Agarwal CSIR-Institute of Genomics amp Integrative

Biology (IGIB) New Delhi

Dr Tavpritesh Sethi All India Institute of Medical Sciences (AIIMS)

New Delhi

Dr Lolitika Mandal Indian Institute of Science Education and

Research (IISER) Mohali

Dr Urvakhsh MehtaNIMHANS Bangalore

Dr Sheetal Gandotra IGIB New Delhi

Visit Khoj website to find out more about the residency and the application process

Apply by

2 February 2016

India Alliance is pleased to announce its support for Art amp Science Project at Khoj International Artists Association New Delhi details of

which can be found below and on the Khoj website It promises to be a great platform for interdisciplinary dialogue and exchange

between scientists and artists and we encourage anyone interested to apply (artists) and get involved (scientists)

THEME

The theme of the 2016 edition of The Undivided Mind is bdquoHealth‟

Within this broader framework three curatorial frameworks or

modes for exploration are suggested Terrestrial Health refers to

that which is on or related to the earth This sub ndash theme suggests an

investigation into the physical health and structure of the body (both

human and animal) the environment the community and the

interrelations between these spheres Mental Health refers to that

which is of or relating to the mind This sub ndash theme focuses on a

psychological investigation of what constitutes Health of the mind

and raises questions about the bdquosocially‟ defined state of well-being

where issues‟ surrounding the legal rights and entitlement of

personhood for those living with a mental disorder is open for

debate Finally Extraterrestrial Health may refer to any object

being or idea beyond the planet Earth This sub ndash theme opens up a

space where the relationship between Earth and other planetary

bodies can be studied What does it mean for human existence when

sending human life forms to Mars is projected to take place by

2020 What are the long term effects and solution to space debris

if life projects out beyond Earth This sub ndash theme also invites

applicants to consider the abstract and metaphorical imaginings of

health in contemporary and future societies

6

Nobel Laureate Dr Harold Varmus recognized for his research on

retroviruses and the genetic basis of cancer gave a lecture on ldquoRecent

Developments in Cancer Researchrdquo at National Institute of Immunology

(NII) New Delhi an event co-organised by NII Wellcome TrustDBT

India Alliance and Department of Biotechnology Government of

India His lecture largely gave an overview of the recent

developments challenges and the future directions in the field of

cancer research which included the current research of his group in

this area

Dr Varmus who had spent time in Bareilly as a young medical

student described cancer as a complex disease that requires

innovative research and treatment strategies At the outset Dr Varmus

introduced the key questions that drive the cancer research field- Is

cancer one disease or many diseases What makes the cancer cell

grow so stably in such an inappropriate manner How does a normal

cell become a cancer cell Providing answers to these questions

formed the backdrop of Dr Varmus‟s lecture which drew from his

research work till date and other advances in the field

Dr Varmus entered the field of cancer research in 1970s as a

postdoctoral scientist in the laboratory of Dr John J Michael Bishop at

University of California San Francisco USA the same year National

Cancer Act was signed in the country Dr Bishop and Dr Varmus

together received the Nobel Prize in Medicine and Physiology in

1989 ldquofor their discovery of the cellular origins of retroviral

oncogenesrdquo During his lecture Dr Varmus confessed standing on the

shoulders of giants of retroviral and cancer research such as Dr

Peyton Rous Dr Harry Rubin and Dr Howard Temin to ask the question

of how retroviruses transformed cells and cause tumours This question

led him to look for genes that make a normal cell behave like a

cancer cell which initially involved studying cancer-causing RNA

virusesretroviruses in animals The retrovirus that played a lead role

in Dr Varmus and his colleague‟s work was the Rous Sarcoma Virus

(RSV) discovered by Dr Peyton Rous in 1911 which he showed caused

a type of cancer in chickens Dr Varmus and colleagues set out to

prove the hypothesis that retroviruses enter host cells and capture

normal genes in that cell by inserting their DNA converting them into

cancer-causing genes or oncogenes Dr Varmus and his group

employed various cellular chemical as well as genetic tools to

establish that retroviruses can indeed act as mutagens by inserting

their DNA in host cells and turning them into cancer cells After this his

group went on to identify the cancer-causing genes present in the

virus and subsequently discovered many new oncogenes v-Src (a

gene of RSV) being the first one Following these discoveries and

subsequently many others led to the belief that the genetic basis of

cancer is highly heterogeneous Dr Varmus told us that in order to

catalogue these complexities the Cancer Genome Atlas was

established in 2005 which till today serves as a collection of the

genetic mutations responsible for different cancers

Apart from the complexity and vastness of the cancer genome

other challenges in the field according to Dr Varmus are genetic

heterogeneity and evolution of tumours due to various environmental

factors such as exposure to UV pollution tobacco use and other

environmental carcinogens that are on the rise He used the example

of renal tumor evolution which illustrates Darwin‟s theory of ldquoevolution

of speciesrdquo to show that this rapidly changing genetic repertoire can

have significant impact on diagnosis therapeutic interventions and

prognosis Another issue of concern highlighted by Dr Varmus was the

absence of suitable drugs against many common targets for cancer

such as cancer-causing RAS genes and many transcription factors

which have been shown to contribute towards cancer formation Dr

Varmus opined that lack of understanding of the underlying

complexity of resistance to cancer therapies is another roadblock in

cancer treatment He was also strongly of the opinion that there are

not enough public health interventions to prevent cancer- this he felt

needs to go hand in hand with finding cure for cancer

Dr Varmus also offered solutions to these problems He suggested

that research needs to ldquolook beyond genes and focus on patterns and

pathwaysrdquo and physiological changes taking place in cancer cells He

shared his group‟s current interest in studying ldquooncogene addictionrdquo

which is based on the premise that some oncogenes not only give rise

to cancer but also maintain the cancerous state of the cells

Interpreting the downstream effects of these cancer genes on the

pathways could be employed as a strategy to attack multiple targets

by drugs in different cancers Even though he hailed the successes of

many commonly used and extremely efficacious anti-cancer drugs

such as Gleevec Gefitinib Erlotinib but in light of growing

complexity of the disease proposed the need for adopting more

innovative drug discovery and treatment approaches Continuing on

the topic of therapeutics Dr Varmus mentioned the recent advances in

immunotherapeutic approaches to treat cancer which would require

us to understand why the otherwise combative immune system does

not kill cancer cells He suggested that gaining understanding of these

immune check points and accordingly targeting them by antibody

inhibitors could serve as one more effective treatment strategy-

another project his research group has undertaken In addition to

these therapeutic approaches Dr Varmus very strongly asserted that

ldquonot everything we talk about cancer should be about cancer therapy

but also about preventionrdquo and that this disease ought to be on the

global health agenda

Dr Varmus very eloquently concluded his talk by stating that

ldquoconfronting cancer needs a balance between grasping its complexity

and seeking simple solutionsrdquo As expected he received many

questions from the audience after his lecture on the genetics and

biology of various cancers potential use of vaccines in cancer

treatment crosstalk of cancer with other diseases and many others to

which he responded with prudence and an underlying sense of

optimism

Prior to his lecture Dr Varmus over an hour meeting with 10 young

cancer researchers discussed their work This group included the

following Wellcome TrustDBT India Alliance Fellows - Dr Reety Arora

(ECF InStem Bangalore) Dr Anjali Bajpai (ECF IIT Kanpur) Dr

Bushra Ateeq (Int Fellow IIT Kanpur) Dr Kundan Sengupta (Int Fellow

IISER Pune) and Dr Sandeep Singh (Int Fellow NIBMG Kalyani) Dr

Varmus also sought information on the India Alliance Fellowships and

was impressed by its funding model and reach

LECTURE REPORT

Recent Developments in Cancer Research By Dr Harold Varmus Nobel Prize in Medicine and Physiology Weill Cornell Medical College USA

at

National Institute of Immunology New Delhi

16 November 2015

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

7

ASK THE SCIENTIST about

The Human Brain

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

This section will bring to you answers to those burning scientific questions that you always wanted to ask the guys in the white

coat For this issue we asked some of our Fellows to shed light on the various operations of the brain

How can we measure attention

DR SUPRATIM RAY Indian Institute of Science Bangalore

Intermediate Fellow

Attention can be of different types such as sustained (vigilance)

selective (focusing at one stimulus in the presence of distractors) or

alternating (involves switching) which can be measured using a

variety of cognitive tests (such as test of everyday attention (TEA) or

Posner cuing task) For example in a classical Posner task a subject

is repeatedly shown two stimuli and cued to attend to one of them

and instructed to respond to a change in the stimulus (say by

pressing a button) The cue could be valid (change occurs at the cued

stimulus say for 80 of the trials) invalid (change occurs at the

uncued stimulus) or neutral (ambiguous) Selection attention can be

measured by comparing the accuracy and the time taken to press

the button after stimulus change (called reaction time) for different

cue types

Different components of attention such as orienting towards a

location detecting a target or maintaining vigilance are carried out

by distinct brain areas in the prefrontal and parietal lobes and some

sub-cortical structures (such as superior colliculus) Overall

performance depends not only on how these areas perform but also

how they communicate with each other and on the levels of

neuromodulators such as norepinephrine

How can we sense smell Is it possible to live without this

sense of smell

DR NIXON ABRAHAM Indian Institutes of Science Education amp

Research (IISER) Pune

Intermediate Fellow

Once Dr Lewis Thomas (1913-1993) the poet and a philosopher of

medicine who also served as the dean of the medical schools at the

New York University and Yale was asked to select seven wonders of

the modern world Olfaction (olfactory receptor cell) was fifth in his

list How does the modern fifth wonder that brings us the smell of our

surroundings ndash the good and bad work

The process of making sense of smell start by binding the odor

molecules to the olfactory receptors located in the olfactory sensory

neurons (OSNs) in the nose This binding triggers a series of signal

amplification steps which lead to electrical spikes (so called action

potentials) in OSNs This olfactory information whose intensity is

encoded by varying the number of action potentials is then passed

onto the projection neurons named mitral and tufted cells in the

olfactory bulb These projection neurons whose excitatory actions

are controlled by various inhibitory neurons carry the olfactory

information to the higher centers in the brain so that we perceive the

smell of spicy tasty food and putrid garbage ndash the good and bad

from the environment

Continued

9

Brain waves

measured by EEG

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

What is really happening inside the brain of a Schizophrenia

patient Does it look any different from a normal brain

DR VENKATASUBRAMANIAN GANESAN NIMHANS Bengaluru

Intermediate Fellow

The brain of a schizophrenia patient is reduced in overall volume

with increase in the size of the ventricles (parts of the brain that

contain cerebrospinal fluid) however certain parts like hippocampus

superior temporal gyrus and prefrontal cortex are more affected

than others Using certain advanced brain imaging research studies

(for example high resolution structural MRI functional MRI Magnetic

Resonance Spectroscopy Positron Emission Tomography and Diffusion

Tensor Imaging and similar others) subtle brain abnormalities in

structure function neurochemical profile as well as brain connectivity

have been demonstrated in several brain regions in schizophrenia

patients It is important to note that these findings are obtained

from advanced research studies that have compared brains of a

Why are the mirror neurons called the Minds mirror What do

they reflect

DR URVAKHSH MEHTA National Institute of Mental Health amp

Neurosciences (NIMHANS) Bengaluru

Early Career Fellow

Mirror neurons are specialized nerve cells that discharge when

we perform actions as well as when we observe others perform the

same action Rizzolatti and colleagues accidentally discovered them

in monkeys These neurons also get vicariously activated when we

perceive emotional states of others This unique bdquoexperience sharing‟

property of mirror neurons perhaps enables us to decipher goals

intentions and emotions of others

In several of our daily social interactions we need to take

perspectives of others decipher deception share feelings and

empathize with others The mirror neuron system is an important

brain network that helps us peek into the minds of others and try to

understand people They translate sensory information (eg

observation of an action) into a motor template which is similar to

the format an observer himself uses to perform that very action This

motor template can help us interpret the goals and feelings

underlying observed actions The definitive demonstration of mirror

neurons in humans was as recent as 2010 There is also growing

evidence of a dysfunctional mirror neuron system in psychiatric

disorders like autism and schizophrenia It is a long and exciting

future ahead to decipher spatiotemporal regulatory and genetic

underpinnings of this unique neuronal network ndash this will possibly

help understand and treat social brain disorders better

Schizophrenia

What happens if we loose our sense of smell Loss of olfaction can

be caused by many reasons ranging from viral infections to

neurodegenerative disorders As our emotions and memories are

strongly related to olfaction the loss of this sense can lead to

depressed state and even affect bonding with family members Just

imagine sipping from your morning coffee without sensing it‟s aroma

- our taste could be badly affected by losing sense of smell The

ongoing research at the nasal stem cell level might provide clinical

solutions for the disorders of the olfactory sensory neurons to regain

this wonderful sense

group of schizophrenia patients with that of healthy subjects thus

these are group averaged findings that are currently not applicable

for diagnosing schizophrenia in an individual patient in a regular

clinical setting In ldquoa specific patientrdquo one may not be able to find

any striking abnormality in the physical appearance of the brain (ie

a routine CT or MRI brain scan may not be able to identify any

obvious aberration) Several ongoing research studies are in pursuit

to identify clinically useful biomarker to diagnose schizophrenia

Find out more about Dr Ganesan‟s research on schizophrenia here

Do you have a burning scientific

question

Send them to

publicengagementwellcomedbtorg

Mirror neuron activity in the brain both when the monkey grasps an object

and when it observes the experimenter grasping the object Mirror neurons

were first discovered by Rizzolatti and colleagues when they were studying

motor actions in macque monkeys

10

INDIA ALLIANCE FELLOW

DR ROOP MALIK Senior Fellow TIFR Mumbai

Dr Roop Malik is a biophysicist based at Tata Institute of Fundamental Research Mumbai Dr Malikrsquos research focuses on nanoscale molecular motor proteins that transport material such as virus mitochondria endosomes etc inside living cells

What is your research group working on and what impact do you

hope it will have

We try to understand how the living cell achieves an organization that

is well defined yet dynamic Most of the components within a cell

have a lipid membrane boundary This boundary is fairly well

defined and visible under a microscope yet it undergoes constant

deformation to allow exchange of material between different parts

of a cell Motor proteins attach to the lipid membrane boundary and

act as transporters physically carrying cellular material from one

membrane to another in the form of a vesicular cargo How do the

motors and lipids collaborate to decide the fate of the cargo

We work on two such cargoes -- the Phagosome (may enclose

pathogens) and the Lipid droplet (encloses fat) We hope that our

research will help understand how pathogens infect us by modifying

the lipid membrane and the motors attached to it We also

investigate how fat stored inside the Lipid droplets in our liver is

circulated to different parts of the body There is a tremendous

change in the amount of fat stored in liver at every feedingfasting

cycle This is visible in the form of Lipid droplet accumulation in rat

liver sections after fasting How does the liver handle this flux of fat

What special mechanisms are required Answering these questions

may help understand the progression of fatty liver diseases

What inspired you to become a scientist

To be frank nothing in particular It was an acquired taste I started

doing experiments and gradually realised I was doing well I like the

planning that is involved in investigating the unknown and the

surprises that crop up inevitably These force you to change your

well-laid plans Thats when it gets really exciting

What role canshould scientists play in todays India

I think there is a lot of scientific freedom in India Granting agencies

are not as hawkish as in the western world This freedom is an

opportunity to do what drives you There are many young scientists in

the country who are keen to share ideas and resources We should

focus on solving difficult problems by taking advantage of this

environment If we do good science it will inspire the public

The primary job of a scientist is to do science and to do it well

Beyond that we also need to think about how science can be

propagated We have to mentor students and give them the

confidence and enthusiasm so that they go on to do better science

than we did We also have to communicate our science to common

man and facilitate them We must impress on students (and also on

their parents) that they should not look at studying Physics or Biology

or Chemistry in isolation Those who want to take up science as a

career should also understand that they must learn to deal with many

failures before something succeeds

How has Wellcome TrustDBT India Alliance Fellowship helped

you and your research (your IA experience)

I have been a Senior fellow with Wellcome Trust (UK) and then with

Wellcome Trust DBT India Alliance since 2006 The rigorous selection

process helped me fine-tune the questions that I wanted to ask The

subsequent evaluations and annual meetings helped in keeping my

research on track Last but not the least we were given a lot of

freedom in executing our science I thank the India Alliance for this

degree of trust in their Fellows This has helped me to focus on the

science

What keeps you going every day

Coffee tea and the excitement of planning and executing science

with my colleagues Regular breaks to get out into the hills for some

adventure

Find out more about

Dr Roop Malik‟s

work on motor

proteins on his

website In order to

make his research

understandable to

a wide range of

people he has put

up translation of his

research summary

in Hindi and

Marathi in addition

to Engalish on his

website

11

A Sponge Against a Sword An RNA-binding protein Prevents Chronic Inflammation and Cancer

By Dr Partho Sarothi Ray Intermediate Fellow

Anyone who has had a bruise is familiar with the redness

swelling warmth and pain that mark the site of the injury This

response known as inflammation has been recognized since ancient

times and its hallmarks were first described by the Greek physician

Galen 2000 years ago The process which is often set in motion by

specialized cells of the immune system occurs whenever tissue is

infected or damaged as for example when you have a pimple or

more seriously suffer a heart attack The latter condition is called

sterile inflammation which happens in absence of infection by a

pathogen and when it goes awry it contributes to a wide range of

seemingly unrelated diseases from Alzheimer‟s disease to diabetes to

cancer

Inflammation is the primary protective response of the body to any

infection or injury However as our common experience shows the

inflammation after being triggered goes away of its own a process

known as resolution However in certain cases the inflammation fails

to resolve and it‟s continuation known as chronic inflammation acts as

an underlying contributor to virtually every chronic disease- a list that

besides obvious culprits such as rheumatoid arthritis and

Crohn‟s disease includes diabetes and depression along with major

killers such as heart disease and stroke and especially cancer

Therefore inflammation is a double-edged sword it protects our

body but can also harm it when it occurs in an uncontrolled manner

Over the past decade and half this role of inflammation has come

under intense scrutiny and many research groups throughout the

world are attempting to discover the underlying mechanisms which

regulate the onset and resolution of inflammation

Connection between Cancer and Inflammation

The connection between cancer and inflammation was recognized a

long time ago In fact in 1863 the renowned German pathologist

Rudolf Virchow found the presence of white blood cells cells which

mediate inflammation in tumors In 1986 the cancer biologist Harold

Dvorak of Harvard Medical School remarked that tumors are

wounds that do not heal However it is only over the last two

decades that the connections between inflammation and cancer have

transformed our understanding of how cancers develop This

transformation recognizes that the chronic inflammatory state serves

as a key mediator of the middle stages of tumor development

Cancer begins with a series of genetic changes that prompt a group

of cells to proliferate and then invade surrounding tissue the point at

which true malignancy begins Eventually some tumor cells may break

off and establish new growths (metastases) at distant sites This has

been understood for a long time But cancer biologists and

immunologists have begun to realize that the progression from

diseased tissue to full-blown invasive cancer often requires cells that

normally participate in inflammation to be diverted to the pre-

malignant tissue where they are hijacked to become co-conspirators

that aid and abet carcinogenesis As described by researchers

genetic damage is the match that lights the fire and inflammation

is the fuel that feeds it Therefore the aim of our lab is to understand

the molecular processes and mechanisms that normally prevent chronic

inflammation and thereby prevent the transition from a pre-malignant

stage to a full-blown cancer Hopefully this understanding will allow in

not-so-distant future to detect and treat cancers at the pre-malignant

stage which will make cancer treatment much easier and affordable

In addition to that this understanding will possibly be helpful in the

treatment of all chronic inflammatory diseases as the basic cellular

mechanisms underlying chronic inflammation are thought to be the

same in all cases

Inflammation in cells

At the cellular level inflammation involves two types of cells the

cells of the tissue or organ that is injured that is the inflamed cells

and the cells that mediate the inflammation that is the inflammatory

cells The latter consist mainly of cells that are originally in the blood

such as monocytes and neutrophils which migrate to the site of the

inflammation and literally eat up (phagocytose) the infecting

microorganisms or the injured cells In many cases there are

monocytes present within the inflamed tissue itself called

macrophages or big eaters which form the first line of attack on the

invading pathogen or damaged tissue Now both the inflamed cells

and the inflammatory cells secrete special signalling chemicals called

cytokines which attract more inflammatory cells to the site of the

inflammation Together with the cytokines the inflammatory cells (the

macrophages and neutrophils) also produce a variety of other factors

that allow the cells to move through the wall of the blood vessels and

then into the tissue where they attack engulf and destroy the

invading pathogen or the damaged cells It is obvious that many of

these factors such as reactive oxygen species (ROS)

metalloproteases interleukins like IL6 and blood vessel growth factors

like VEGF are toxic and if continued to be produced will damage

the healthy tissue as well That is why the production of both the

cytokines which attract these cells to the site of inflammation and

these factors which cause the death and destruction of the pathogens

ceases when the cause of the inflammation is removed and allows the

inflammation to resolve Failure to stop the production of these

inflammatory factors therefore leads to chronic inflammation and the

chronic inflammatory diseases The inflammatory factors cytokines

and others are produced by genes which are called pro-

inflammatory genes Therefore the expression of these genes that is

the production of proteins from the genes have to be tightly

regulated both in space and time

12

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 5: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

CLINICAL AND PUBLIC HEALTH RESEARCH FELLOWSHIPS

Early Career Fellowships

Dr Jayanth Kumar Palanichamy All India Institute of Medical Sciences New Delhi

Dr Aparna Mukherjee All India Institute of Medical Sciences New Delhi

Dr Deepak Kamath St Johns National Academy Of Health Sciences Bangalore

Intermediate Fellowships

Dr Aparna Rao L V Prasad Eye Institute Bhubaneswar

Dr Abi Vanak Ashoka Trust for Research in Ecology and the Environment Bangalore

Dr Shivarama VaramballyNational Institute of Mental Health and Neurosciences Bangalore

Dr Rashmi Rodrigues St Johns National Academy Of Health Sciences Bangalore

Dr Mahesh Kate Christian Medical College Ludhiana

Research Training Fellowships

Ms Urvita Bhatia Sangath Porvorim

Dr Deepak Gautam All India Institute of Medical Sciences New Delhi

Dr Sumsum P Sunny Mazumdar Shaw Medical Center Bangalore

Dr Dhruva Ithal National Institute of Mental Health and Neurosciences Bangalore

Dr Rakshathi B National Institute of Mental Health and Neurosciences Bangalore

ANNOUNCEMENT

RECENTLY RECOMMENDED AWARDEES

BASIC RESEARCH FELLOWSHIPS

Intermediate Fellowships

Dr Sridharan Devarajan Indian Institute of Science Bangalore

Dr Nitin Gupta Indian Institute Of Technology Kanpur

Dr Sachin Kotak Indian Institute of Science Bangalore

Dr Aravind Penmatsa Indian Institute of Science Bangalore

Dr Siddhesh Shashikant Kamat Indian Institute of Science Education and Research Pune

Dr Mohan Joshi Centre for DNA Fingerprinting and Diagnostics Hyderabad

Dr Satish Khurana Indian Institute of Science Education and Research Thiruvananthapuram

Dr Pinky Kain Indian Institute of Technology Roorkee

Dr Santosh Chauhan Institute Of Life Sciences Bhubaneswar

India Alliance announced Fellowship Awardees of the Clinical and Public Health Research Fellowship

scheme and Intermediate Fellowship under the Basic Biomedical Research competition in December 2015

The interviews for these Fellowship schemes were held in November 2015

indicates institution that before this award did not have any India Alliance Fellow

4

MARGADARSHI FELLOWSHIP

Prof Satyajit Mayor National Centre for Biological Science Bangalore

IN CONVERSATION WITH

Dr Aravinda Chakravarti

Dr Aravinda Chakravarti is a Professor of Medicine Pediatrics Molecular Biology amp Genetics and Biostatistics and Director Center

for Complex Disease Genomics at the Johns Hopkins University School of Medicine and the Bloomberg School of Public Health He

also has a long association with the India Alliance as a member of its Clinical and Public Health Research Fellowship committee

What motivated you to become a scientist

I cannot say that it was any one person or one event or any one

point of time that led me to consider doing science Nor did I know

what being a scientist would entail or how one prepared to become

one I was not interested in science nor good at it or anything else for

that matter before the 9th grade But subsequently it was the

concreteness and logic of mathematics and the sciences that

appealed to me I also began reading material outside my textbooks

such as books in the Nuffield Science Series and others I came across

in the Calcutta British Council Library which began giving me a

broader look at the world of science But I was still clueless This was

evident in my applying for almost every conceivable program for

college (Engineering Medicine Geology Agriculture Physics and

Statistics) and being selected but not necessarily into the best schools

or programs Thus bdquosuccess‟ did not clarify my thinking any one bit

Finally I did choose to attend the Indian Statistical Institute (ISI)

outside Calcuttahellipa then beautiful oasis of calm in the politically

turbulent Calcutta of 1970‟s when being young well-read and aware

were enough to raise suspicions in the Calcutta Police (For those who

doubt the serious and mortal danger all young people in Calcutta

were under during this time read the daily newspaper reports from

the 70‟s)

For me Indian Statistical Institute (ISI) was

an escape from reality and an entry into a

synthetic artificial and manufactured world

of quantitative ideas

Our courses over 4 years in a US-style undergraduate were 50

Mathematics and Statistics and 50 an assortment of sciences and

economics (to learn the various domains in which quantitative

reasoning would be critical) where we were taught to ask bdquowhy‟ not

only bdquohow‟ something worked For the first time I found myself in an

atmosphere where understanding mattered more than knowledge

(dont worry knowledge did matter greatly) the pursuit of a job was

a side issue and we were encouraged to discover any area we

wished (or thats how I felt) I also had passionate teachers who were

the very best in the world For the first time I felt liberated learning

was fun and pursuing science as a life seemed like the only natural

thing to do It wasnt a one day transformationhellipby the time I left ISI I

knew that I could ask and answer at least some questions ISI was the

institution where the famed British polymath and geneticist J B S

Haldane came to in 1957 and became one of the architects of my

undergraduate program Although Haldane died in 1964 his ghost

was still around when I was a student at the ISI That I would do

genetics and be a scientist particularly in human genetics was

therefore a no brainer

Could you briefly take us through your scientific journey and

about your interest in genetics

My interest in genetics was established at the ISI but no less fueled by

my reading of Jim Watson‟s The Double Helix in 1970 and then as

credited by Watson and Crick Erwin Schrodinger‟s What is Life As a

student of the quantitative sciences at ISI the part of genetics that

appealed to me (simply because I could digest it) was Population

Genetics Also ISI had a Department of Human Genetics that

performed numerous studies of human genetic molecular diversity

across populations in India So my early training was in studies of

human population diversity Nevertheless Haldane‟s research (that I

was increasingly becoming aware of) was equally in family studies

that exemplified mechanisms not evident in population studies So as

a student I conducted and published research into the inheritance of

simply observable traits (bdquohand clasping‟ or the phenotype where you

classify individuals by whether they fold their left thumb over their

right or vice versahelliptry it only one way feels correct) just to learn

genetics and to attempt to combine the family and the population

methods that are so common today Fortunately by this time I had left

myself few opportunities to be interested in doing anything else but

human genetics

5

IN CONVERSATION WITH Dr Aravinda Chakravarti

Being rejected by several programs to study genetics in India

(because I was not a biology undergraduate) I chose to do graduate

work with the noted geneticist and molecular evolutionist Masatoshi

Nei at the University of Texas Houston where he had just moved I

arrived in Houston in 1974 and was immediately thrust into a small

intense center with brilliant people and expected to perform research

at a level I was surely unaccustomed to This group was the epicenter

of the then neutralist-selectionist debate in molecular evolution a

problem that was exciting but not my cup of tea I wanted to study

human genetics and finally fashioned a research project with Nei that

explored the theoretical consequences of improved genetic counseling

with linkage and association (linkage disequilibrium) markers and

graduated with a PhD in 1979 This research was not only far ahead

of its time coming before the proposal of creating a human linkage

map using RFLPs (restriction fragment length polymorphism) in 1980

but I was the only Nei student who worked outside molecular

evolution In many ways then my development in genetics became

very broad and haphazard since I often focused on areas that were

not my primary training grounds

By this time I was a geneticist but thought I needed further training in

genetic epidemiology to understand human disease better However

after an unsuccessful postdoc at Seattle I abandoned this idea to

take a non-tenured teaching position at the University of Pittsburgh

thinking that the bdquofree‟ time I would have would allow me to catch up

on the revolution in recombinant DNA technology that was underway I

am glad I did since this was one of the best

professional decisions I made by forgoing

the standard path

I taught at Pittsburgh for 5 years and subsequently obtained an NIH

Research Career Development Award to pursue a research career

That began my standard research career in human genetics

What according to you are the challenges in your field of

research

The field of human genetics is not the one I trained in since so much

has changed with the sequencing of the human genome Human

genetics has two distinct themes one descriptive as to the causes of

human variation be it molecular or phenotypic (the bdquohow‟ question)

and a second mechanistic as to how variation in molecular

mechanisms impact phenotype variation particularly disease (the

bdquowhy‟ question) The whole attraction of the human genome project to

me and others like me who spent more than a decade on building the

now available community resources (maps clones sequences variants

transcripts etc) was to move from the first set to the second set of

questions This transformation is difficult since it is not in the comfort

zone of conventional human genetics its hard and unpredictable

much more hypothesis-driven and much more experimental The

challenge in my field and in many associated medical specialties is

that it‟s far easier to do the first then the second Scientists are voting

with their feet Human geneticists are far more content in sequencing

human genomes finding associations with disease and doing facile

functional annotation than a serious investigation into why does this

gene causes type 2 diabetes and the next one congenital cataract

Or why mutations in the same gene cause a neuroendocrine tumor

when activating but congenital aganglionosis when loss-of-function

Or how come the same mutation can act as either activating or loss-

of-function

The biggest challenge in my field is to

overcome the inertia that molecular

description = etiological explanation

If you were not a scientist you would behellip

I really have no idea I presume the Bengali in me implicitly wants

or always wanted to be a writer but that would be a great leap of

faith and quite arrogant Even good scientific writing is hard very

hard indeed I have often read someone else‟s paper that I enjoyed

and thought that I could have done the same work a similar thought

has not appeared after reading someone else‟s creative work except

when it is quite bad

5 What is the best advice you have ever received

Unfortunately most advice that most people get and give is bad

More correctly its difficult to know (what‟s the test) when it is good

and when bad Each of us likely adapt a post-hoc explanation to our

stories all of which are likely revisionist Nevertheless two different

people (a brother and a family friend) at about the same time

(1979-1982) told me to abandon what I was doing (an unsuccessful

postdoc and forcing myself to complete reading a fairly racist

account of the Black Hole of Calcutta) because it was beyond my

enjoyment They both suggested that I drop it and do something else

One should not shoulder a burden that is great unless some higher

purpose is at stake One needs to learn how to apportion risk with

benefit

Your message for young students and researchers

Science is difficult but exhilarating in its rare moments of success

and it‟s usually followed by long periods of stasis It is a great but

frustrating life and there are many worse ways of making a living It

is like other types of creative endeavors where discovery is real but

rare If you wish to do it be sure you can enjoy its moods Science

today is also multidisciplinary and translational its application to

humans and other benefits can also be tangible sources of pride But

do it not for these benefits do it because the science gives you great

joy Yes joy Consider that you are one in an

unbroken intellectual chain from Johannes

Kepler and Isaac Newton If you choose

science you are special

Dr Chakravarti‟s laboratory focuses on the development and

applications of molecular genetic genomic and computational

methods for identification of human disease genes through

genetic dissectionldquo He has been a key participant and architect

of the Human Genome HapMap and 1000 Genomes project Find

out more about his research here

6

Workshop at a glance One-day workshop to equip young science

researchers with tools and strategies for effective communication of

their ideas experiments and scientific results from a science

communication perspective Help them to make science career choices

Vision Science communication plays an integral role in one‟s scientific

career Being able to effectively disseminate research findings within

the community and to consider collective opinions in prioritising

research needs is an important attribute of scientific maturity In

keeping with its mandate to empower future leaders of Indian science

the Wellcome TrustDBT India Alliance periodically conducts one-day

(SciComm101) and two-day (SciComm Hyderabad) science

communication workshops for the past four years This complements

seamlessly with Nature India‟s mandate to showcase India‟s science bdquoas

it happens‟ in laboratories and institutions across the country through

in-depth coverage and analysis of research and science policy The

proposed workshop would be part of Nature India‟s many

communication outreach activities as the one-stop media platform for

India‟s science

The Wellcome TrustDBT India Alliance and Nature India both

represent possibilities for young PhD scholars and postdoctoral

scientists to transition into academic as well as non-academic science

careers Information and advice on how to explore various career

options will form an important part of these workshops with

Naturejobs as the key organiser of the career session

Structure amp format

The workshop will be a one-day event preceding a biomedical (or

scientific) conference organised by reputed science

societiesorganisationsinstitutes and Universities in India A large

participation by PhD students postdoctoral fellows and junior

scientists will be a pre-requisite for holding this workshop Organising

this workshop as part of a conference will ensure participation from a

wide range of institutions across India The workshop will include 3

separate sessions

Session 1 Scientific Writing (moderated by WTDBT Alliance)

Topics to be covered

bull Ethics in research

bull Presentation skills

bull Manuscript writing

bull Grants writing

bull CVs and letters

Session 2 Science Communication (moderated by Nature India)

Topics to be covered

bull Science journalism

bull Popular science writing

bull Effective press releases

bull Hands-on skills on dejargonising science

Session 3 Alternate Science Career (moderated by Nature Jobs)

Topics to be covered

bull Career in the Industry

bull Career in Science PromotionIntellectual Property

bull Career in PolicyGrant organizations Journalism

Science Communication and Career Workshop Series (In partnership with Nature India amp Naturejobs )

Please contact us at workshopswellcomedbtorg to find out more about this series

INDIA ALLIANCE

SCIENCE COMMUNICATION

SciComm101 workshop

10 March 2016 MSU Baroda

Two-day SciComm workshop

21-22 March 2016 Hyderabad Applications under review

For more details visit SciComm Workshop under Quick Links on our website

Upcoming Workshops

5

ABOUT THE ART amp SCIENCE PROJECT

CALL FOR APPLICATIONS THE UNDIVIDED MIND |ART +

SCIENCE RESIDENCY AT KHOJ

Residency Dates March 2nd ndash April 2nd 2015

Application Deadline February 2nd 2015

Proposals are invited for bdquoThe Undivided Mind‟ a four-week

international residency for artists whose work explores the

intersection of art and science

At first it may seem that the pairing of Art amp Science is an atypical

choice as the two fields and methods of practice have almost

universally been represented as diametric opposites of each other

However on closer examination the similarities between artists and

scientists far outweigh their stereotypical differences Both are

dedicated to research and to asking the big question- what is true

Why does it matter How can we move society forward Moreover

both the lab and the studio are spaces that famously encourage

open-ended enquiry and emphasis on process In tune with Khoj‟s

commitment to cultivate an environment that allows for

experimentation and innovation the Art amp Science residency will be

a step towards furthering the explorations of interdisciplinary

practitioners This is the second edition of a Khoj residency focusing

on Art + Science to know more about the first edition please

click bdquohere‟

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

The following India Alliance Fellows will be participating in the

project

(NOTE If an applicant wishes to connect with any of the following

researchers in advance of submitting their proposal please contact

the Khoj team at bdquoapplicationskhojworkshoporg‟ for an

introduction please do the same if you are a scientist and would like

take part in this project )

Dr Venkatasubramanian Ganesan National Institute of Mental

Health and Neurosciences (NIMHANS) Bangalore

Dr Pallab K Maulik The George Institute for Global Health New

Delhi

Dr Anurag Agarwal CSIR-Institute of Genomics amp Integrative

Biology (IGIB) New Delhi

Dr Tavpritesh Sethi All India Institute of Medical Sciences (AIIMS)

New Delhi

Dr Lolitika Mandal Indian Institute of Science Education and

Research (IISER) Mohali

Dr Urvakhsh MehtaNIMHANS Bangalore

Dr Sheetal Gandotra IGIB New Delhi

Visit Khoj website to find out more about the residency and the application process

Apply by

2 February 2016

India Alliance is pleased to announce its support for Art amp Science Project at Khoj International Artists Association New Delhi details of

which can be found below and on the Khoj website It promises to be a great platform for interdisciplinary dialogue and exchange

between scientists and artists and we encourage anyone interested to apply (artists) and get involved (scientists)

THEME

The theme of the 2016 edition of The Undivided Mind is bdquoHealth‟

Within this broader framework three curatorial frameworks or

modes for exploration are suggested Terrestrial Health refers to

that which is on or related to the earth This sub ndash theme suggests an

investigation into the physical health and structure of the body (both

human and animal) the environment the community and the

interrelations between these spheres Mental Health refers to that

which is of or relating to the mind This sub ndash theme focuses on a

psychological investigation of what constitutes Health of the mind

and raises questions about the bdquosocially‟ defined state of well-being

where issues‟ surrounding the legal rights and entitlement of

personhood for those living with a mental disorder is open for

debate Finally Extraterrestrial Health may refer to any object

being or idea beyond the planet Earth This sub ndash theme opens up a

space where the relationship between Earth and other planetary

bodies can be studied What does it mean for human existence when

sending human life forms to Mars is projected to take place by

2020 What are the long term effects and solution to space debris

if life projects out beyond Earth This sub ndash theme also invites

applicants to consider the abstract and metaphorical imaginings of

health in contemporary and future societies

6

Nobel Laureate Dr Harold Varmus recognized for his research on

retroviruses and the genetic basis of cancer gave a lecture on ldquoRecent

Developments in Cancer Researchrdquo at National Institute of Immunology

(NII) New Delhi an event co-organised by NII Wellcome TrustDBT

India Alliance and Department of Biotechnology Government of

India His lecture largely gave an overview of the recent

developments challenges and the future directions in the field of

cancer research which included the current research of his group in

this area

Dr Varmus who had spent time in Bareilly as a young medical

student described cancer as a complex disease that requires

innovative research and treatment strategies At the outset Dr Varmus

introduced the key questions that drive the cancer research field- Is

cancer one disease or many diseases What makes the cancer cell

grow so stably in such an inappropriate manner How does a normal

cell become a cancer cell Providing answers to these questions

formed the backdrop of Dr Varmus‟s lecture which drew from his

research work till date and other advances in the field

Dr Varmus entered the field of cancer research in 1970s as a

postdoctoral scientist in the laboratory of Dr John J Michael Bishop at

University of California San Francisco USA the same year National

Cancer Act was signed in the country Dr Bishop and Dr Varmus

together received the Nobel Prize in Medicine and Physiology in

1989 ldquofor their discovery of the cellular origins of retroviral

oncogenesrdquo During his lecture Dr Varmus confessed standing on the

shoulders of giants of retroviral and cancer research such as Dr

Peyton Rous Dr Harry Rubin and Dr Howard Temin to ask the question

of how retroviruses transformed cells and cause tumours This question

led him to look for genes that make a normal cell behave like a

cancer cell which initially involved studying cancer-causing RNA

virusesretroviruses in animals The retrovirus that played a lead role

in Dr Varmus and his colleague‟s work was the Rous Sarcoma Virus

(RSV) discovered by Dr Peyton Rous in 1911 which he showed caused

a type of cancer in chickens Dr Varmus and colleagues set out to

prove the hypothesis that retroviruses enter host cells and capture

normal genes in that cell by inserting their DNA converting them into

cancer-causing genes or oncogenes Dr Varmus and his group

employed various cellular chemical as well as genetic tools to

establish that retroviruses can indeed act as mutagens by inserting

their DNA in host cells and turning them into cancer cells After this his

group went on to identify the cancer-causing genes present in the

virus and subsequently discovered many new oncogenes v-Src (a

gene of RSV) being the first one Following these discoveries and

subsequently many others led to the belief that the genetic basis of

cancer is highly heterogeneous Dr Varmus told us that in order to

catalogue these complexities the Cancer Genome Atlas was

established in 2005 which till today serves as a collection of the

genetic mutations responsible for different cancers

Apart from the complexity and vastness of the cancer genome

other challenges in the field according to Dr Varmus are genetic

heterogeneity and evolution of tumours due to various environmental

factors such as exposure to UV pollution tobacco use and other

environmental carcinogens that are on the rise He used the example

of renal tumor evolution which illustrates Darwin‟s theory of ldquoevolution

of speciesrdquo to show that this rapidly changing genetic repertoire can

have significant impact on diagnosis therapeutic interventions and

prognosis Another issue of concern highlighted by Dr Varmus was the

absence of suitable drugs against many common targets for cancer

such as cancer-causing RAS genes and many transcription factors

which have been shown to contribute towards cancer formation Dr

Varmus opined that lack of understanding of the underlying

complexity of resistance to cancer therapies is another roadblock in

cancer treatment He was also strongly of the opinion that there are

not enough public health interventions to prevent cancer- this he felt

needs to go hand in hand with finding cure for cancer

Dr Varmus also offered solutions to these problems He suggested

that research needs to ldquolook beyond genes and focus on patterns and

pathwaysrdquo and physiological changes taking place in cancer cells He

shared his group‟s current interest in studying ldquooncogene addictionrdquo

which is based on the premise that some oncogenes not only give rise

to cancer but also maintain the cancerous state of the cells

Interpreting the downstream effects of these cancer genes on the

pathways could be employed as a strategy to attack multiple targets

by drugs in different cancers Even though he hailed the successes of

many commonly used and extremely efficacious anti-cancer drugs

such as Gleevec Gefitinib Erlotinib but in light of growing

complexity of the disease proposed the need for adopting more

innovative drug discovery and treatment approaches Continuing on

the topic of therapeutics Dr Varmus mentioned the recent advances in

immunotherapeutic approaches to treat cancer which would require

us to understand why the otherwise combative immune system does

not kill cancer cells He suggested that gaining understanding of these

immune check points and accordingly targeting them by antibody

inhibitors could serve as one more effective treatment strategy-

another project his research group has undertaken In addition to

these therapeutic approaches Dr Varmus very strongly asserted that

ldquonot everything we talk about cancer should be about cancer therapy

but also about preventionrdquo and that this disease ought to be on the

global health agenda

Dr Varmus very eloquently concluded his talk by stating that

ldquoconfronting cancer needs a balance between grasping its complexity

and seeking simple solutionsrdquo As expected he received many

questions from the audience after his lecture on the genetics and

biology of various cancers potential use of vaccines in cancer

treatment crosstalk of cancer with other diseases and many others to

which he responded with prudence and an underlying sense of

optimism

Prior to his lecture Dr Varmus over an hour meeting with 10 young

cancer researchers discussed their work This group included the

following Wellcome TrustDBT India Alliance Fellows - Dr Reety Arora

(ECF InStem Bangalore) Dr Anjali Bajpai (ECF IIT Kanpur) Dr

Bushra Ateeq (Int Fellow IIT Kanpur) Dr Kundan Sengupta (Int Fellow

IISER Pune) and Dr Sandeep Singh (Int Fellow NIBMG Kalyani) Dr

Varmus also sought information on the India Alliance Fellowships and

was impressed by its funding model and reach

LECTURE REPORT

Recent Developments in Cancer Research By Dr Harold Varmus Nobel Prize in Medicine and Physiology Weill Cornell Medical College USA

at

National Institute of Immunology New Delhi

16 November 2015

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

7

ASK THE SCIENTIST about

The Human Brain

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

This section will bring to you answers to those burning scientific questions that you always wanted to ask the guys in the white

coat For this issue we asked some of our Fellows to shed light on the various operations of the brain

How can we measure attention

DR SUPRATIM RAY Indian Institute of Science Bangalore

Intermediate Fellow

Attention can be of different types such as sustained (vigilance)

selective (focusing at one stimulus in the presence of distractors) or

alternating (involves switching) which can be measured using a

variety of cognitive tests (such as test of everyday attention (TEA) or

Posner cuing task) For example in a classical Posner task a subject

is repeatedly shown two stimuli and cued to attend to one of them

and instructed to respond to a change in the stimulus (say by

pressing a button) The cue could be valid (change occurs at the cued

stimulus say for 80 of the trials) invalid (change occurs at the

uncued stimulus) or neutral (ambiguous) Selection attention can be

measured by comparing the accuracy and the time taken to press

the button after stimulus change (called reaction time) for different

cue types

Different components of attention such as orienting towards a

location detecting a target or maintaining vigilance are carried out

by distinct brain areas in the prefrontal and parietal lobes and some

sub-cortical structures (such as superior colliculus) Overall

performance depends not only on how these areas perform but also

how they communicate with each other and on the levels of

neuromodulators such as norepinephrine

How can we sense smell Is it possible to live without this

sense of smell

DR NIXON ABRAHAM Indian Institutes of Science Education amp

Research (IISER) Pune

Intermediate Fellow

Once Dr Lewis Thomas (1913-1993) the poet and a philosopher of

medicine who also served as the dean of the medical schools at the

New York University and Yale was asked to select seven wonders of

the modern world Olfaction (olfactory receptor cell) was fifth in his

list How does the modern fifth wonder that brings us the smell of our

surroundings ndash the good and bad work

The process of making sense of smell start by binding the odor

molecules to the olfactory receptors located in the olfactory sensory

neurons (OSNs) in the nose This binding triggers a series of signal

amplification steps which lead to electrical spikes (so called action

potentials) in OSNs This olfactory information whose intensity is

encoded by varying the number of action potentials is then passed

onto the projection neurons named mitral and tufted cells in the

olfactory bulb These projection neurons whose excitatory actions

are controlled by various inhibitory neurons carry the olfactory

information to the higher centers in the brain so that we perceive the

smell of spicy tasty food and putrid garbage ndash the good and bad

from the environment

Continued

9

Brain waves

measured by EEG

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

What is really happening inside the brain of a Schizophrenia

patient Does it look any different from a normal brain

DR VENKATASUBRAMANIAN GANESAN NIMHANS Bengaluru

Intermediate Fellow

The brain of a schizophrenia patient is reduced in overall volume

with increase in the size of the ventricles (parts of the brain that

contain cerebrospinal fluid) however certain parts like hippocampus

superior temporal gyrus and prefrontal cortex are more affected

than others Using certain advanced brain imaging research studies

(for example high resolution structural MRI functional MRI Magnetic

Resonance Spectroscopy Positron Emission Tomography and Diffusion

Tensor Imaging and similar others) subtle brain abnormalities in

structure function neurochemical profile as well as brain connectivity

have been demonstrated in several brain regions in schizophrenia

patients It is important to note that these findings are obtained

from advanced research studies that have compared brains of a

Why are the mirror neurons called the Minds mirror What do

they reflect

DR URVAKHSH MEHTA National Institute of Mental Health amp

Neurosciences (NIMHANS) Bengaluru

Early Career Fellow

Mirror neurons are specialized nerve cells that discharge when

we perform actions as well as when we observe others perform the

same action Rizzolatti and colleagues accidentally discovered them

in monkeys These neurons also get vicariously activated when we

perceive emotional states of others This unique bdquoexperience sharing‟

property of mirror neurons perhaps enables us to decipher goals

intentions and emotions of others

In several of our daily social interactions we need to take

perspectives of others decipher deception share feelings and

empathize with others The mirror neuron system is an important

brain network that helps us peek into the minds of others and try to

understand people They translate sensory information (eg

observation of an action) into a motor template which is similar to

the format an observer himself uses to perform that very action This

motor template can help us interpret the goals and feelings

underlying observed actions The definitive demonstration of mirror

neurons in humans was as recent as 2010 There is also growing

evidence of a dysfunctional mirror neuron system in psychiatric

disorders like autism and schizophrenia It is a long and exciting

future ahead to decipher spatiotemporal regulatory and genetic

underpinnings of this unique neuronal network ndash this will possibly

help understand and treat social brain disorders better

Schizophrenia

What happens if we loose our sense of smell Loss of olfaction can

be caused by many reasons ranging from viral infections to

neurodegenerative disorders As our emotions and memories are

strongly related to olfaction the loss of this sense can lead to

depressed state and even affect bonding with family members Just

imagine sipping from your morning coffee without sensing it‟s aroma

- our taste could be badly affected by losing sense of smell The

ongoing research at the nasal stem cell level might provide clinical

solutions for the disorders of the olfactory sensory neurons to regain

this wonderful sense

group of schizophrenia patients with that of healthy subjects thus

these are group averaged findings that are currently not applicable

for diagnosing schizophrenia in an individual patient in a regular

clinical setting In ldquoa specific patientrdquo one may not be able to find

any striking abnormality in the physical appearance of the brain (ie

a routine CT or MRI brain scan may not be able to identify any

obvious aberration) Several ongoing research studies are in pursuit

to identify clinically useful biomarker to diagnose schizophrenia

Find out more about Dr Ganesan‟s research on schizophrenia here

Do you have a burning scientific

question

Send them to

publicengagementwellcomedbtorg

Mirror neuron activity in the brain both when the monkey grasps an object

and when it observes the experimenter grasping the object Mirror neurons

were first discovered by Rizzolatti and colleagues when they were studying

motor actions in macque monkeys

10

INDIA ALLIANCE FELLOW

DR ROOP MALIK Senior Fellow TIFR Mumbai

Dr Roop Malik is a biophysicist based at Tata Institute of Fundamental Research Mumbai Dr Malikrsquos research focuses on nanoscale molecular motor proteins that transport material such as virus mitochondria endosomes etc inside living cells

What is your research group working on and what impact do you

hope it will have

We try to understand how the living cell achieves an organization that

is well defined yet dynamic Most of the components within a cell

have a lipid membrane boundary This boundary is fairly well

defined and visible under a microscope yet it undergoes constant

deformation to allow exchange of material between different parts

of a cell Motor proteins attach to the lipid membrane boundary and

act as transporters physically carrying cellular material from one

membrane to another in the form of a vesicular cargo How do the

motors and lipids collaborate to decide the fate of the cargo

We work on two such cargoes -- the Phagosome (may enclose

pathogens) and the Lipid droplet (encloses fat) We hope that our

research will help understand how pathogens infect us by modifying

the lipid membrane and the motors attached to it We also

investigate how fat stored inside the Lipid droplets in our liver is

circulated to different parts of the body There is a tremendous

change in the amount of fat stored in liver at every feedingfasting

cycle This is visible in the form of Lipid droplet accumulation in rat

liver sections after fasting How does the liver handle this flux of fat

What special mechanisms are required Answering these questions

may help understand the progression of fatty liver diseases

What inspired you to become a scientist

To be frank nothing in particular It was an acquired taste I started

doing experiments and gradually realised I was doing well I like the

planning that is involved in investigating the unknown and the

surprises that crop up inevitably These force you to change your

well-laid plans Thats when it gets really exciting

What role canshould scientists play in todays India

I think there is a lot of scientific freedom in India Granting agencies

are not as hawkish as in the western world This freedom is an

opportunity to do what drives you There are many young scientists in

the country who are keen to share ideas and resources We should

focus on solving difficult problems by taking advantage of this

environment If we do good science it will inspire the public

The primary job of a scientist is to do science and to do it well

Beyond that we also need to think about how science can be

propagated We have to mentor students and give them the

confidence and enthusiasm so that they go on to do better science

than we did We also have to communicate our science to common

man and facilitate them We must impress on students (and also on

their parents) that they should not look at studying Physics or Biology

or Chemistry in isolation Those who want to take up science as a

career should also understand that they must learn to deal with many

failures before something succeeds

How has Wellcome TrustDBT India Alliance Fellowship helped

you and your research (your IA experience)

I have been a Senior fellow with Wellcome Trust (UK) and then with

Wellcome Trust DBT India Alliance since 2006 The rigorous selection

process helped me fine-tune the questions that I wanted to ask The

subsequent evaluations and annual meetings helped in keeping my

research on track Last but not the least we were given a lot of

freedom in executing our science I thank the India Alliance for this

degree of trust in their Fellows This has helped me to focus on the

science

What keeps you going every day

Coffee tea and the excitement of planning and executing science

with my colleagues Regular breaks to get out into the hills for some

adventure

Find out more about

Dr Roop Malik‟s

work on motor

proteins on his

website In order to

make his research

understandable to

a wide range of

people he has put

up translation of his

research summary

in Hindi and

Marathi in addition

to Engalish on his

website

11

A Sponge Against a Sword An RNA-binding protein Prevents Chronic Inflammation and Cancer

By Dr Partho Sarothi Ray Intermediate Fellow

Anyone who has had a bruise is familiar with the redness

swelling warmth and pain that mark the site of the injury This

response known as inflammation has been recognized since ancient

times and its hallmarks were first described by the Greek physician

Galen 2000 years ago The process which is often set in motion by

specialized cells of the immune system occurs whenever tissue is

infected or damaged as for example when you have a pimple or

more seriously suffer a heart attack The latter condition is called

sterile inflammation which happens in absence of infection by a

pathogen and when it goes awry it contributes to a wide range of

seemingly unrelated diseases from Alzheimer‟s disease to diabetes to

cancer

Inflammation is the primary protective response of the body to any

infection or injury However as our common experience shows the

inflammation after being triggered goes away of its own a process

known as resolution However in certain cases the inflammation fails

to resolve and it‟s continuation known as chronic inflammation acts as

an underlying contributor to virtually every chronic disease- a list that

besides obvious culprits such as rheumatoid arthritis and

Crohn‟s disease includes diabetes and depression along with major

killers such as heart disease and stroke and especially cancer

Therefore inflammation is a double-edged sword it protects our

body but can also harm it when it occurs in an uncontrolled manner

Over the past decade and half this role of inflammation has come

under intense scrutiny and many research groups throughout the

world are attempting to discover the underlying mechanisms which

regulate the onset and resolution of inflammation

Connection between Cancer and Inflammation

The connection between cancer and inflammation was recognized a

long time ago In fact in 1863 the renowned German pathologist

Rudolf Virchow found the presence of white blood cells cells which

mediate inflammation in tumors In 1986 the cancer biologist Harold

Dvorak of Harvard Medical School remarked that tumors are

wounds that do not heal However it is only over the last two

decades that the connections between inflammation and cancer have

transformed our understanding of how cancers develop This

transformation recognizes that the chronic inflammatory state serves

as a key mediator of the middle stages of tumor development

Cancer begins with a series of genetic changes that prompt a group

of cells to proliferate and then invade surrounding tissue the point at

which true malignancy begins Eventually some tumor cells may break

off and establish new growths (metastases) at distant sites This has

been understood for a long time But cancer biologists and

immunologists have begun to realize that the progression from

diseased tissue to full-blown invasive cancer often requires cells that

normally participate in inflammation to be diverted to the pre-

malignant tissue where they are hijacked to become co-conspirators

that aid and abet carcinogenesis As described by researchers

genetic damage is the match that lights the fire and inflammation

is the fuel that feeds it Therefore the aim of our lab is to understand

the molecular processes and mechanisms that normally prevent chronic

inflammation and thereby prevent the transition from a pre-malignant

stage to a full-blown cancer Hopefully this understanding will allow in

not-so-distant future to detect and treat cancers at the pre-malignant

stage which will make cancer treatment much easier and affordable

In addition to that this understanding will possibly be helpful in the

treatment of all chronic inflammatory diseases as the basic cellular

mechanisms underlying chronic inflammation are thought to be the

same in all cases

Inflammation in cells

At the cellular level inflammation involves two types of cells the

cells of the tissue or organ that is injured that is the inflamed cells

and the cells that mediate the inflammation that is the inflammatory

cells The latter consist mainly of cells that are originally in the blood

such as monocytes and neutrophils which migrate to the site of the

inflammation and literally eat up (phagocytose) the infecting

microorganisms or the injured cells In many cases there are

monocytes present within the inflamed tissue itself called

macrophages or big eaters which form the first line of attack on the

invading pathogen or damaged tissue Now both the inflamed cells

and the inflammatory cells secrete special signalling chemicals called

cytokines which attract more inflammatory cells to the site of the

inflammation Together with the cytokines the inflammatory cells (the

macrophages and neutrophils) also produce a variety of other factors

that allow the cells to move through the wall of the blood vessels and

then into the tissue where they attack engulf and destroy the

invading pathogen or the damaged cells It is obvious that many of

these factors such as reactive oxygen species (ROS)

metalloproteases interleukins like IL6 and blood vessel growth factors

like VEGF are toxic and if continued to be produced will damage

the healthy tissue as well That is why the production of both the

cytokines which attract these cells to the site of inflammation and

these factors which cause the death and destruction of the pathogens

ceases when the cause of the inflammation is removed and allows the

inflammation to resolve Failure to stop the production of these

inflammatory factors therefore leads to chronic inflammation and the

chronic inflammatory diseases The inflammatory factors cytokines

and others are produced by genes which are called pro-

inflammatory genes Therefore the expression of these genes that is

the production of proteins from the genes have to be tightly

regulated both in space and time

12

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 6: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

IN CONVERSATION WITH

Dr Aravinda Chakravarti

Dr Aravinda Chakravarti is a Professor of Medicine Pediatrics Molecular Biology amp Genetics and Biostatistics and Director Center

for Complex Disease Genomics at the Johns Hopkins University School of Medicine and the Bloomberg School of Public Health He

also has a long association with the India Alliance as a member of its Clinical and Public Health Research Fellowship committee

What motivated you to become a scientist

I cannot say that it was any one person or one event or any one

point of time that led me to consider doing science Nor did I know

what being a scientist would entail or how one prepared to become

one I was not interested in science nor good at it or anything else for

that matter before the 9th grade But subsequently it was the

concreteness and logic of mathematics and the sciences that

appealed to me I also began reading material outside my textbooks

such as books in the Nuffield Science Series and others I came across

in the Calcutta British Council Library which began giving me a

broader look at the world of science But I was still clueless This was

evident in my applying for almost every conceivable program for

college (Engineering Medicine Geology Agriculture Physics and

Statistics) and being selected but not necessarily into the best schools

or programs Thus bdquosuccess‟ did not clarify my thinking any one bit

Finally I did choose to attend the Indian Statistical Institute (ISI)

outside Calcuttahellipa then beautiful oasis of calm in the politically

turbulent Calcutta of 1970‟s when being young well-read and aware

were enough to raise suspicions in the Calcutta Police (For those who

doubt the serious and mortal danger all young people in Calcutta

were under during this time read the daily newspaper reports from

the 70‟s)

For me Indian Statistical Institute (ISI) was

an escape from reality and an entry into a

synthetic artificial and manufactured world

of quantitative ideas

Our courses over 4 years in a US-style undergraduate were 50

Mathematics and Statistics and 50 an assortment of sciences and

economics (to learn the various domains in which quantitative

reasoning would be critical) where we were taught to ask bdquowhy‟ not

only bdquohow‟ something worked For the first time I found myself in an

atmosphere where understanding mattered more than knowledge

(dont worry knowledge did matter greatly) the pursuit of a job was

a side issue and we were encouraged to discover any area we

wished (or thats how I felt) I also had passionate teachers who were

the very best in the world For the first time I felt liberated learning

was fun and pursuing science as a life seemed like the only natural

thing to do It wasnt a one day transformationhellipby the time I left ISI I

knew that I could ask and answer at least some questions ISI was the

institution where the famed British polymath and geneticist J B S

Haldane came to in 1957 and became one of the architects of my

undergraduate program Although Haldane died in 1964 his ghost

was still around when I was a student at the ISI That I would do

genetics and be a scientist particularly in human genetics was

therefore a no brainer

Could you briefly take us through your scientific journey and

about your interest in genetics

My interest in genetics was established at the ISI but no less fueled by

my reading of Jim Watson‟s The Double Helix in 1970 and then as

credited by Watson and Crick Erwin Schrodinger‟s What is Life As a

student of the quantitative sciences at ISI the part of genetics that

appealed to me (simply because I could digest it) was Population

Genetics Also ISI had a Department of Human Genetics that

performed numerous studies of human genetic molecular diversity

across populations in India So my early training was in studies of

human population diversity Nevertheless Haldane‟s research (that I

was increasingly becoming aware of) was equally in family studies

that exemplified mechanisms not evident in population studies So as

a student I conducted and published research into the inheritance of

simply observable traits (bdquohand clasping‟ or the phenotype where you

classify individuals by whether they fold their left thumb over their

right or vice versahelliptry it only one way feels correct) just to learn

genetics and to attempt to combine the family and the population

methods that are so common today Fortunately by this time I had left

myself few opportunities to be interested in doing anything else but

human genetics

5

IN CONVERSATION WITH Dr Aravinda Chakravarti

Being rejected by several programs to study genetics in India

(because I was not a biology undergraduate) I chose to do graduate

work with the noted geneticist and molecular evolutionist Masatoshi

Nei at the University of Texas Houston where he had just moved I

arrived in Houston in 1974 and was immediately thrust into a small

intense center with brilliant people and expected to perform research

at a level I was surely unaccustomed to This group was the epicenter

of the then neutralist-selectionist debate in molecular evolution a

problem that was exciting but not my cup of tea I wanted to study

human genetics and finally fashioned a research project with Nei that

explored the theoretical consequences of improved genetic counseling

with linkage and association (linkage disequilibrium) markers and

graduated with a PhD in 1979 This research was not only far ahead

of its time coming before the proposal of creating a human linkage

map using RFLPs (restriction fragment length polymorphism) in 1980

but I was the only Nei student who worked outside molecular

evolution In many ways then my development in genetics became

very broad and haphazard since I often focused on areas that were

not my primary training grounds

By this time I was a geneticist but thought I needed further training in

genetic epidemiology to understand human disease better However

after an unsuccessful postdoc at Seattle I abandoned this idea to

take a non-tenured teaching position at the University of Pittsburgh

thinking that the bdquofree‟ time I would have would allow me to catch up

on the revolution in recombinant DNA technology that was underway I

am glad I did since this was one of the best

professional decisions I made by forgoing

the standard path

I taught at Pittsburgh for 5 years and subsequently obtained an NIH

Research Career Development Award to pursue a research career

That began my standard research career in human genetics

What according to you are the challenges in your field of

research

The field of human genetics is not the one I trained in since so much

has changed with the sequencing of the human genome Human

genetics has two distinct themes one descriptive as to the causes of

human variation be it molecular or phenotypic (the bdquohow‟ question)

and a second mechanistic as to how variation in molecular

mechanisms impact phenotype variation particularly disease (the

bdquowhy‟ question) The whole attraction of the human genome project to

me and others like me who spent more than a decade on building the

now available community resources (maps clones sequences variants

transcripts etc) was to move from the first set to the second set of

questions This transformation is difficult since it is not in the comfort

zone of conventional human genetics its hard and unpredictable

much more hypothesis-driven and much more experimental The

challenge in my field and in many associated medical specialties is

that it‟s far easier to do the first then the second Scientists are voting

with their feet Human geneticists are far more content in sequencing

human genomes finding associations with disease and doing facile

functional annotation than a serious investigation into why does this

gene causes type 2 diabetes and the next one congenital cataract

Or why mutations in the same gene cause a neuroendocrine tumor

when activating but congenital aganglionosis when loss-of-function

Or how come the same mutation can act as either activating or loss-

of-function

The biggest challenge in my field is to

overcome the inertia that molecular

description = etiological explanation

If you were not a scientist you would behellip

I really have no idea I presume the Bengali in me implicitly wants

or always wanted to be a writer but that would be a great leap of

faith and quite arrogant Even good scientific writing is hard very

hard indeed I have often read someone else‟s paper that I enjoyed

and thought that I could have done the same work a similar thought

has not appeared after reading someone else‟s creative work except

when it is quite bad

5 What is the best advice you have ever received

Unfortunately most advice that most people get and give is bad

More correctly its difficult to know (what‟s the test) when it is good

and when bad Each of us likely adapt a post-hoc explanation to our

stories all of which are likely revisionist Nevertheless two different

people (a brother and a family friend) at about the same time

(1979-1982) told me to abandon what I was doing (an unsuccessful

postdoc and forcing myself to complete reading a fairly racist

account of the Black Hole of Calcutta) because it was beyond my

enjoyment They both suggested that I drop it and do something else

One should not shoulder a burden that is great unless some higher

purpose is at stake One needs to learn how to apportion risk with

benefit

Your message for young students and researchers

Science is difficult but exhilarating in its rare moments of success

and it‟s usually followed by long periods of stasis It is a great but

frustrating life and there are many worse ways of making a living It

is like other types of creative endeavors where discovery is real but

rare If you wish to do it be sure you can enjoy its moods Science

today is also multidisciplinary and translational its application to

humans and other benefits can also be tangible sources of pride But

do it not for these benefits do it because the science gives you great

joy Yes joy Consider that you are one in an

unbroken intellectual chain from Johannes

Kepler and Isaac Newton If you choose

science you are special

Dr Chakravarti‟s laboratory focuses on the development and

applications of molecular genetic genomic and computational

methods for identification of human disease genes through

genetic dissectionldquo He has been a key participant and architect

of the Human Genome HapMap and 1000 Genomes project Find

out more about his research here

6

Workshop at a glance One-day workshop to equip young science

researchers with tools and strategies for effective communication of

their ideas experiments and scientific results from a science

communication perspective Help them to make science career choices

Vision Science communication plays an integral role in one‟s scientific

career Being able to effectively disseminate research findings within

the community and to consider collective opinions in prioritising

research needs is an important attribute of scientific maturity In

keeping with its mandate to empower future leaders of Indian science

the Wellcome TrustDBT India Alliance periodically conducts one-day

(SciComm101) and two-day (SciComm Hyderabad) science

communication workshops for the past four years This complements

seamlessly with Nature India‟s mandate to showcase India‟s science bdquoas

it happens‟ in laboratories and institutions across the country through

in-depth coverage and analysis of research and science policy The

proposed workshop would be part of Nature India‟s many

communication outreach activities as the one-stop media platform for

India‟s science

The Wellcome TrustDBT India Alliance and Nature India both

represent possibilities for young PhD scholars and postdoctoral

scientists to transition into academic as well as non-academic science

careers Information and advice on how to explore various career

options will form an important part of these workshops with

Naturejobs as the key organiser of the career session

Structure amp format

The workshop will be a one-day event preceding a biomedical (or

scientific) conference organised by reputed science

societiesorganisationsinstitutes and Universities in India A large

participation by PhD students postdoctoral fellows and junior

scientists will be a pre-requisite for holding this workshop Organising

this workshop as part of a conference will ensure participation from a

wide range of institutions across India The workshop will include 3

separate sessions

Session 1 Scientific Writing (moderated by WTDBT Alliance)

Topics to be covered

bull Ethics in research

bull Presentation skills

bull Manuscript writing

bull Grants writing

bull CVs and letters

Session 2 Science Communication (moderated by Nature India)

Topics to be covered

bull Science journalism

bull Popular science writing

bull Effective press releases

bull Hands-on skills on dejargonising science

Session 3 Alternate Science Career (moderated by Nature Jobs)

Topics to be covered

bull Career in the Industry

bull Career in Science PromotionIntellectual Property

bull Career in PolicyGrant organizations Journalism

Science Communication and Career Workshop Series (In partnership with Nature India amp Naturejobs )

Please contact us at workshopswellcomedbtorg to find out more about this series

INDIA ALLIANCE

SCIENCE COMMUNICATION

SciComm101 workshop

10 March 2016 MSU Baroda

Two-day SciComm workshop

21-22 March 2016 Hyderabad Applications under review

For more details visit SciComm Workshop under Quick Links on our website

Upcoming Workshops

5

ABOUT THE ART amp SCIENCE PROJECT

CALL FOR APPLICATIONS THE UNDIVIDED MIND |ART +

SCIENCE RESIDENCY AT KHOJ

Residency Dates March 2nd ndash April 2nd 2015

Application Deadline February 2nd 2015

Proposals are invited for bdquoThe Undivided Mind‟ a four-week

international residency for artists whose work explores the

intersection of art and science

At first it may seem that the pairing of Art amp Science is an atypical

choice as the two fields and methods of practice have almost

universally been represented as diametric opposites of each other

However on closer examination the similarities between artists and

scientists far outweigh their stereotypical differences Both are

dedicated to research and to asking the big question- what is true

Why does it matter How can we move society forward Moreover

both the lab and the studio are spaces that famously encourage

open-ended enquiry and emphasis on process In tune with Khoj‟s

commitment to cultivate an environment that allows for

experimentation and innovation the Art amp Science residency will be

a step towards furthering the explorations of interdisciplinary

practitioners This is the second edition of a Khoj residency focusing

on Art + Science to know more about the first edition please

click bdquohere‟

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

The following India Alliance Fellows will be participating in the

project

(NOTE If an applicant wishes to connect with any of the following

researchers in advance of submitting their proposal please contact

the Khoj team at bdquoapplicationskhojworkshoporg‟ for an

introduction please do the same if you are a scientist and would like

take part in this project )

Dr Venkatasubramanian Ganesan National Institute of Mental

Health and Neurosciences (NIMHANS) Bangalore

Dr Pallab K Maulik The George Institute for Global Health New

Delhi

Dr Anurag Agarwal CSIR-Institute of Genomics amp Integrative

Biology (IGIB) New Delhi

Dr Tavpritesh Sethi All India Institute of Medical Sciences (AIIMS)

New Delhi

Dr Lolitika Mandal Indian Institute of Science Education and

Research (IISER) Mohali

Dr Urvakhsh MehtaNIMHANS Bangalore

Dr Sheetal Gandotra IGIB New Delhi

Visit Khoj website to find out more about the residency and the application process

Apply by

2 February 2016

India Alliance is pleased to announce its support for Art amp Science Project at Khoj International Artists Association New Delhi details of

which can be found below and on the Khoj website It promises to be a great platform for interdisciplinary dialogue and exchange

between scientists and artists and we encourage anyone interested to apply (artists) and get involved (scientists)

THEME

The theme of the 2016 edition of The Undivided Mind is bdquoHealth‟

Within this broader framework three curatorial frameworks or

modes for exploration are suggested Terrestrial Health refers to

that which is on or related to the earth This sub ndash theme suggests an

investigation into the physical health and structure of the body (both

human and animal) the environment the community and the

interrelations between these spheres Mental Health refers to that

which is of or relating to the mind This sub ndash theme focuses on a

psychological investigation of what constitutes Health of the mind

and raises questions about the bdquosocially‟ defined state of well-being

where issues‟ surrounding the legal rights and entitlement of

personhood for those living with a mental disorder is open for

debate Finally Extraterrestrial Health may refer to any object

being or idea beyond the planet Earth This sub ndash theme opens up a

space where the relationship between Earth and other planetary

bodies can be studied What does it mean for human existence when

sending human life forms to Mars is projected to take place by

2020 What are the long term effects and solution to space debris

if life projects out beyond Earth This sub ndash theme also invites

applicants to consider the abstract and metaphorical imaginings of

health in contemporary and future societies

6

Nobel Laureate Dr Harold Varmus recognized for his research on

retroviruses and the genetic basis of cancer gave a lecture on ldquoRecent

Developments in Cancer Researchrdquo at National Institute of Immunology

(NII) New Delhi an event co-organised by NII Wellcome TrustDBT

India Alliance and Department of Biotechnology Government of

India His lecture largely gave an overview of the recent

developments challenges and the future directions in the field of

cancer research which included the current research of his group in

this area

Dr Varmus who had spent time in Bareilly as a young medical

student described cancer as a complex disease that requires

innovative research and treatment strategies At the outset Dr Varmus

introduced the key questions that drive the cancer research field- Is

cancer one disease or many diseases What makes the cancer cell

grow so stably in such an inappropriate manner How does a normal

cell become a cancer cell Providing answers to these questions

formed the backdrop of Dr Varmus‟s lecture which drew from his

research work till date and other advances in the field

Dr Varmus entered the field of cancer research in 1970s as a

postdoctoral scientist in the laboratory of Dr John J Michael Bishop at

University of California San Francisco USA the same year National

Cancer Act was signed in the country Dr Bishop and Dr Varmus

together received the Nobel Prize in Medicine and Physiology in

1989 ldquofor their discovery of the cellular origins of retroviral

oncogenesrdquo During his lecture Dr Varmus confessed standing on the

shoulders of giants of retroviral and cancer research such as Dr

Peyton Rous Dr Harry Rubin and Dr Howard Temin to ask the question

of how retroviruses transformed cells and cause tumours This question

led him to look for genes that make a normal cell behave like a

cancer cell which initially involved studying cancer-causing RNA

virusesretroviruses in animals The retrovirus that played a lead role

in Dr Varmus and his colleague‟s work was the Rous Sarcoma Virus

(RSV) discovered by Dr Peyton Rous in 1911 which he showed caused

a type of cancer in chickens Dr Varmus and colleagues set out to

prove the hypothesis that retroviruses enter host cells and capture

normal genes in that cell by inserting their DNA converting them into

cancer-causing genes or oncogenes Dr Varmus and his group

employed various cellular chemical as well as genetic tools to

establish that retroviruses can indeed act as mutagens by inserting

their DNA in host cells and turning them into cancer cells After this his

group went on to identify the cancer-causing genes present in the

virus and subsequently discovered many new oncogenes v-Src (a

gene of RSV) being the first one Following these discoveries and

subsequently many others led to the belief that the genetic basis of

cancer is highly heterogeneous Dr Varmus told us that in order to

catalogue these complexities the Cancer Genome Atlas was

established in 2005 which till today serves as a collection of the

genetic mutations responsible for different cancers

Apart from the complexity and vastness of the cancer genome

other challenges in the field according to Dr Varmus are genetic

heterogeneity and evolution of tumours due to various environmental

factors such as exposure to UV pollution tobacco use and other

environmental carcinogens that are on the rise He used the example

of renal tumor evolution which illustrates Darwin‟s theory of ldquoevolution

of speciesrdquo to show that this rapidly changing genetic repertoire can

have significant impact on diagnosis therapeutic interventions and

prognosis Another issue of concern highlighted by Dr Varmus was the

absence of suitable drugs against many common targets for cancer

such as cancer-causing RAS genes and many transcription factors

which have been shown to contribute towards cancer formation Dr

Varmus opined that lack of understanding of the underlying

complexity of resistance to cancer therapies is another roadblock in

cancer treatment He was also strongly of the opinion that there are

not enough public health interventions to prevent cancer- this he felt

needs to go hand in hand with finding cure for cancer

Dr Varmus also offered solutions to these problems He suggested

that research needs to ldquolook beyond genes and focus on patterns and

pathwaysrdquo and physiological changes taking place in cancer cells He

shared his group‟s current interest in studying ldquooncogene addictionrdquo

which is based on the premise that some oncogenes not only give rise

to cancer but also maintain the cancerous state of the cells

Interpreting the downstream effects of these cancer genes on the

pathways could be employed as a strategy to attack multiple targets

by drugs in different cancers Even though he hailed the successes of

many commonly used and extremely efficacious anti-cancer drugs

such as Gleevec Gefitinib Erlotinib but in light of growing

complexity of the disease proposed the need for adopting more

innovative drug discovery and treatment approaches Continuing on

the topic of therapeutics Dr Varmus mentioned the recent advances in

immunotherapeutic approaches to treat cancer which would require

us to understand why the otherwise combative immune system does

not kill cancer cells He suggested that gaining understanding of these

immune check points and accordingly targeting them by antibody

inhibitors could serve as one more effective treatment strategy-

another project his research group has undertaken In addition to

these therapeutic approaches Dr Varmus very strongly asserted that

ldquonot everything we talk about cancer should be about cancer therapy

but also about preventionrdquo and that this disease ought to be on the

global health agenda

Dr Varmus very eloquently concluded his talk by stating that

ldquoconfronting cancer needs a balance between grasping its complexity

and seeking simple solutionsrdquo As expected he received many

questions from the audience after his lecture on the genetics and

biology of various cancers potential use of vaccines in cancer

treatment crosstalk of cancer with other diseases and many others to

which he responded with prudence and an underlying sense of

optimism

Prior to his lecture Dr Varmus over an hour meeting with 10 young

cancer researchers discussed their work This group included the

following Wellcome TrustDBT India Alliance Fellows - Dr Reety Arora

(ECF InStem Bangalore) Dr Anjali Bajpai (ECF IIT Kanpur) Dr

Bushra Ateeq (Int Fellow IIT Kanpur) Dr Kundan Sengupta (Int Fellow

IISER Pune) and Dr Sandeep Singh (Int Fellow NIBMG Kalyani) Dr

Varmus also sought information on the India Alliance Fellowships and

was impressed by its funding model and reach

LECTURE REPORT

Recent Developments in Cancer Research By Dr Harold Varmus Nobel Prize in Medicine and Physiology Weill Cornell Medical College USA

at

National Institute of Immunology New Delhi

16 November 2015

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

7

ASK THE SCIENTIST about

The Human Brain

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

This section will bring to you answers to those burning scientific questions that you always wanted to ask the guys in the white

coat For this issue we asked some of our Fellows to shed light on the various operations of the brain

How can we measure attention

DR SUPRATIM RAY Indian Institute of Science Bangalore

Intermediate Fellow

Attention can be of different types such as sustained (vigilance)

selective (focusing at one stimulus in the presence of distractors) or

alternating (involves switching) which can be measured using a

variety of cognitive tests (such as test of everyday attention (TEA) or

Posner cuing task) For example in a classical Posner task a subject

is repeatedly shown two stimuli and cued to attend to one of them

and instructed to respond to a change in the stimulus (say by

pressing a button) The cue could be valid (change occurs at the cued

stimulus say for 80 of the trials) invalid (change occurs at the

uncued stimulus) or neutral (ambiguous) Selection attention can be

measured by comparing the accuracy and the time taken to press

the button after stimulus change (called reaction time) for different

cue types

Different components of attention such as orienting towards a

location detecting a target or maintaining vigilance are carried out

by distinct brain areas in the prefrontal and parietal lobes and some

sub-cortical structures (such as superior colliculus) Overall

performance depends not only on how these areas perform but also

how they communicate with each other and on the levels of

neuromodulators such as norepinephrine

How can we sense smell Is it possible to live without this

sense of smell

DR NIXON ABRAHAM Indian Institutes of Science Education amp

Research (IISER) Pune

Intermediate Fellow

Once Dr Lewis Thomas (1913-1993) the poet and a philosopher of

medicine who also served as the dean of the medical schools at the

New York University and Yale was asked to select seven wonders of

the modern world Olfaction (olfactory receptor cell) was fifth in his

list How does the modern fifth wonder that brings us the smell of our

surroundings ndash the good and bad work

The process of making sense of smell start by binding the odor

molecules to the olfactory receptors located in the olfactory sensory

neurons (OSNs) in the nose This binding triggers a series of signal

amplification steps which lead to electrical spikes (so called action

potentials) in OSNs This olfactory information whose intensity is

encoded by varying the number of action potentials is then passed

onto the projection neurons named mitral and tufted cells in the

olfactory bulb These projection neurons whose excitatory actions

are controlled by various inhibitory neurons carry the olfactory

information to the higher centers in the brain so that we perceive the

smell of spicy tasty food and putrid garbage ndash the good and bad

from the environment

Continued

9

Brain waves

measured by EEG

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

What is really happening inside the brain of a Schizophrenia

patient Does it look any different from a normal brain

DR VENKATASUBRAMANIAN GANESAN NIMHANS Bengaluru

Intermediate Fellow

The brain of a schizophrenia patient is reduced in overall volume

with increase in the size of the ventricles (parts of the brain that

contain cerebrospinal fluid) however certain parts like hippocampus

superior temporal gyrus and prefrontal cortex are more affected

than others Using certain advanced brain imaging research studies

(for example high resolution structural MRI functional MRI Magnetic

Resonance Spectroscopy Positron Emission Tomography and Diffusion

Tensor Imaging and similar others) subtle brain abnormalities in

structure function neurochemical profile as well as brain connectivity

have been demonstrated in several brain regions in schizophrenia

patients It is important to note that these findings are obtained

from advanced research studies that have compared brains of a

Why are the mirror neurons called the Minds mirror What do

they reflect

DR URVAKHSH MEHTA National Institute of Mental Health amp

Neurosciences (NIMHANS) Bengaluru

Early Career Fellow

Mirror neurons are specialized nerve cells that discharge when

we perform actions as well as when we observe others perform the

same action Rizzolatti and colleagues accidentally discovered them

in monkeys These neurons also get vicariously activated when we

perceive emotional states of others This unique bdquoexperience sharing‟

property of mirror neurons perhaps enables us to decipher goals

intentions and emotions of others

In several of our daily social interactions we need to take

perspectives of others decipher deception share feelings and

empathize with others The mirror neuron system is an important

brain network that helps us peek into the minds of others and try to

understand people They translate sensory information (eg

observation of an action) into a motor template which is similar to

the format an observer himself uses to perform that very action This

motor template can help us interpret the goals and feelings

underlying observed actions The definitive demonstration of mirror

neurons in humans was as recent as 2010 There is also growing

evidence of a dysfunctional mirror neuron system in psychiatric

disorders like autism and schizophrenia It is a long and exciting

future ahead to decipher spatiotemporal regulatory and genetic

underpinnings of this unique neuronal network ndash this will possibly

help understand and treat social brain disorders better

Schizophrenia

What happens if we loose our sense of smell Loss of olfaction can

be caused by many reasons ranging from viral infections to

neurodegenerative disorders As our emotions and memories are

strongly related to olfaction the loss of this sense can lead to

depressed state and even affect bonding with family members Just

imagine sipping from your morning coffee without sensing it‟s aroma

- our taste could be badly affected by losing sense of smell The

ongoing research at the nasal stem cell level might provide clinical

solutions for the disorders of the olfactory sensory neurons to regain

this wonderful sense

group of schizophrenia patients with that of healthy subjects thus

these are group averaged findings that are currently not applicable

for diagnosing schizophrenia in an individual patient in a regular

clinical setting In ldquoa specific patientrdquo one may not be able to find

any striking abnormality in the physical appearance of the brain (ie

a routine CT or MRI brain scan may not be able to identify any

obvious aberration) Several ongoing research studies are in pursuit

to identify clinically useful biomarker to diagnose schizophrenia

Find out more about Dr Ganesan‟s research on schizophrenia here

Do you have a burning scientific

question

Send them to

publicengagementwellcomedbtorg

Mirror neuron activity in the brain both when the monkey grasps an object

and when it observes the experimenter grasping the object Mirror neurons

were first discovered by Rizzolatti and colleagues when they were studying

motor actions in macque monkeys

10

INDIA ALLIANCE FELLOW

DR ROOP MALIK Senior Fellow TIFR Mumbai

Dr Roop Malik is a biophysicist based at Tata Institute of Fundamental Research Mumbai Dr Malikrsquos research focuses on nanoscale molecular motor proteins that transport material such as virus mitochondria endosomes etc inside living cells

What is your research group working on and what impact do you

hope it will have

We try to understand how the living cell achieves an organization that

is well defined yet dynamic Most of the components within a cell

have a lipid membrane boundary This boundary is fairly well

defined and visible under a microscope yet it undergoes constant

deformation to allow exchange of material between different parts

of a cell Motor proteins attach to the lipid membrane boundary and

act as transporters physically carrying cellular material from one

membrane to another in the form of a vesicular cargo How do the

motors and lipids collaborate to decide the fate of the cargo

We work on two such cargoes -- the Phagosome (may enclose

pathogens) and the Lipid droplet (encloses fat) We hope that our

research will help understand how pathogens infect us by modifying

the lipid membrane and the motors attached to it We also

investigate how fat stored inside the Lipid droplets in our liver is

circulated to different parts of the body There is a tremendous

change in the amount of fat stored in liver at every feedingfasting

cycle This is visible in the form of Lipid droplet accumulation in rat

liver sections after fasting How does the liver handle this flux of fat

What special mechanisms are required Answering these questions

may help understand the progression of fatty liver diseases

What inspired you to become a scientist

To be frank nothing in particular It was an acquired taste I started

doing experiments and gradually realised I was doing well I like the

planning that is involved in investigating the unknown and the

surprises that crop up inevitably These force you to change your

well-laid plans Thats when it gets really exciting

What role canshould scientists play in todays India

I think there is a lot of scientific freedom in India Granting agencies

are not as hawkish as in the western world This freedom is an

opportunity to do what drives you There are many young scientists in

the country who are keen to share ideas and resources We should

focus on solving difficult problems by taking advantage of this

environment If we do good science it will inspire the public

The primary job of a scientist is to do science and to do it well

Beyond that we also need to think about how science can be

propagated We have to mentor students and give them the

confidence and enthusiasm so that they go on to do better science

than we did We also have to communicate our science to common

man and facilitate them We must impress on students (and also on

their parents) that they should not look at studying Physics or Biology

or Chemistry in isolation Those who want to take up science as a

career should also understand that they must learn to deal with many

failures before something succeeds

How has Wellcome TrustDBT India Alliance Fellowship helped

you and your research (your IA experience)

I have been a Senior fellow with Wellcome Trust (UK) and then with

Wellcome Trust DBT India Alliance since 2006 The rigorous selection

process helped me fine-tune the questions that I wanted to ask The

subsequent evaluations and annual meetings helped in keeping my

research on track Last but not the least we were given a lot of

freedom in executing our science I thank the India Alliance for this

degree of trust in their Fellows This has helped me to focus on the

science

What keeps you going every day

Coffee tea and the excitement of planning and executing science

with my colleagues Regular breaks to get out into the hills for some

adventure

Find out more about

Dr Roop Malik‟s

work on motor

proteins on his

website In order to

make his research

understandable to

a wide range of

people he has put

up translation of his

research summary

in Hindi and

Marathi in addition

to Engalish on his

website

11

A Sponge Against a Sword An RNA-binding protein Prevents Chronic Inflammation and Cancer

By Dr Partho Sarothi Ray Intermediate Fellow

Anyone who has had a bruise is familiar with the redness

swelling warmth and pain that mark the site of the injury This

response known as inflammation has been recognized since ancient

times and its hallmarks were first described by the Greek physician

Galen 2000 years ago The process which is often set in motion by

specialized cells of the immune system occurs whenever tissue is

infected or damaged as for example when you have a pimple or

more seriously suffer a heart attack The latter condition is called

sterile inflammation which happens in absence of infection by a

pathogen and when it goes awry it contributes to a wide range of

seemingly unrelated diseases from Alzheimer‟s disease to diabetes to

cancer

Inflammation is the primary protective response of the body to any

infection or injury However as our common experience shows the

inflammation after being triggered goes away of its own a process

known as resolution However in certain cases the inflammation fails

to resolve and it‟s continuation known as chronic inflammation acts as

an underlying contributor to virtually every chronic disease- a list that

besides obvious culprits such as rheumatoid arthritis and

Crohn‟s disease includes diabetes and depression along with major

killers such as heart disease and stroke and especially cancer

Therefore inflammation is a double-edged sword it protects our

body but can also harm it when it occurs in an uncontrolled manner

Over the past decade and half this role of inflammation has come

under intense scrutiny and many research groups throughout the

world are attempting to discover the underlying mechanisms which

regulate the onset and resolution of inflammation

Connection between Cancer and Inflammation

The connection between cancer and inflammation was recognized a

long time ago In fact in 1863 the renowned German pathologist

Rudolf Virchow found the presence of white blood cells cells which

mediate inflammation in tumors In 1986 the cancer biologist Harold

Dvorak of Harvard Medical School remarked that tumors are

wounds that do not heal However it is only over the last two

decades that the connections between inflammation and cancer have

transformed our understanding of how cancers develop This

transformation recognizes that the chronic inflammatory state serves

as a key mediator of the middle stages of tumor development

Cancer begins with a series of genetic changes that prompt a group

of cells to proliferate and then invade surrounding tissue the point at

which true malignancy begins Eventually some tumor cells may break

off and establish new growths (metastases) at distant sites This has

been understood for a long time But cancer biologists and

immunologists have begun to realize that the progression from

diseased tissue to full-blown invasive cancer often requires cells that

normally participate in inflammation to be diverted to the pre-

malignant tissue where they are hijacked to become co-conspirators

that aid and abet carcinogenesis As described by researchers

genetic damage is the match that lights the fire and inflammation

is the fuel that feeds it Therefore the aim of our lab is to understand

the molecular processes and mechanisms that normally prevent chronic

inflammation and thereby prevent the transition from a pre-malignant

stage to a full-blown cancer Hopefully this understanding will allow in

not-so-distant future to detect and treat cancers at the pre-malignant

stage which will make cancer treatment much easier and affordable

In addition to that this understanding will possibly be helpful in the

treatment of all chronic inflammatory diseases as the basic cellular

mechanisms underlying chronic inflammation are thought to be the

same in all cases

Inflammation in cells

At the cellular level inflammation involves two types of cells the

cells of the tissue or organ that is injured that is the inflamed cells

and the cells that mediate the inflammation that is the inflammatory

cells The latter consist mainly of cells that are originally in the blood

such as monocytes and neutrophils which migrate to the site of the

inflammation and literally eat up (phagocytose) the infecting

microorganisms or the injured cells In many cases there are

monocytes present within the inflamed tissue itself called

macrophages or big eaters which form the first line of attack on the

invading pathogen or damaged tissue Now both the inflamed cells

and the inflammatory cells secrete special signalling chemicals called

cytokines which attract more inflammatory cells to the site of the

inflammation Together with the cytokines the inflammatory cells (the

macrophages and neutrophils) also produce a variety of other factors

that allow the cells to move through the wall of the blood vessels and

then into the tissue where they attack engulf and destroy the

invading pathogen or the damaged cells It is obvious that many of

these factors such as reactive oxygen species (ROS)

metalloproteases interleukins like IL6 and blood vessel growth factors

like VEGF are toxic and if continued to be produced will damage

the healthy tissue as well That is why the production of both the

cytokines which attract these cells to the site of inflammation and

these factors which cause the death and destruction of the pathogens

ceases when the cause of the inflammation is removed and allows the

inflammation to resolve Failure to stop the production of these

inflammatory factors therefore leads to chronic inflammation and the

chronic inflammatory diseases The inflammatory factors cytokines

and others are produced by genes which are called pro-

inflammatory genes Therefore the expression of these genes that is

the production of proteins from the genes have to be tightly

regulated both in space and time

12

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 7: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

IN CONVERSATION WITH Dr Aravinda Chakravarti

Being rejected by several programs to study genetics in India

(because I was not a biology undergraduate) I chose to do graduate

work with the noted geneticist and molecular evolutionist Masatoshi

Nei at the University of Texas Houston where he had just moved I

arrived in Houston in 1974 and was immediately thrust into a small

intense center with brilliant people and expected to perform research

at a level I was surely unaccustomed to This group was the epicenter

of the then neutralist-selectionist debate in molecular evolution a

problem that was exciting but not my cup of tea I wanted to study

human genetics and finally fashioned a research project with Nei that

explored the theoretical consequences of improved genetic counseling

with linkage and association (linkage disequilibrium) markers and

graduated with a PhD in 1979 This research was not only far ahead

of its time coming before the proposal of creating a human linkage

map using RFLPs (restriction fragment length polymorphism) in 1980

but I was the only Nei student who worked outside molecular

evolution In many ways then my development in genetics became

very broad and haphazard since I often focused on areas that were

not my primary training grounds

By this time I was a geneticist but thought I needed further training in

genetic epidemiology to understand human disease better However

after an unsuccessful postdoc at Seattle I abandoned this idea to

take a non-tenured teaching position at the University of Pittsburgh

thinking that the bdquofree‟ time I would have would allow me to catch up

on the revolution in recombinant DNA technology that was underway I

am glad I did since this was one of the best

professional decisions I made by forgoing

the standard path

I taught at Pittsburgh for 5 years and subsequently obtained an NIH

Research Career Development Award to pursue a research career

That began my standard research career in human genetics

What according to you are the challenges in your field of

research

The field of human genetics is not the one I trained in since so much

has changed with the sequencing of the human genome Human

genetics has two distinct themes one descriptive as to the causes of

human variation be it molecular or phenotypic (the bdquohow‟ question)

and a second mechanistic as to how variation in molecular

mechanisms impact phenotype variation particularly disease (the

bdquowhy‟ question) The whole attraction of the human genome project to

me and others like me who spent more than a decade on building the

now available community resources (maps clones sequences variants

transcripts etc) was to move from the first set to the second set of

questions This transformation is difficult since it is not in the comfort

zone of conventional human genetics its hard and unpredictable

much more hypothesis-driven and much more experimental The

challenge in my field and in many associated medical specialties is

that it‟s far easier to do the first then the second Scientists are voting

with their feet Human geneticists are far more content in sequencing

human genomes finding associations with disease and doing facile

functional annotation than a serious investigation into why does this

gene causes type 2 diabetes and the next one congenital cataract

Or why mutations in the same gene cause a neuroendocrine tumor

when activating but congenital aganglionosis when loss-of-function

Or how come the same mutation can act as either activating or loss-

of-function

The biggest challenge in my field is to

overcome the inertia that molecular

description = etiological explanation

If you were not a scientist you would behellip

I really have no idea I presume the Bengali in me implicitly wants

or always wanted to be a writer but that would be a great leap of

faith and quite arrogant Even good scientific writing is hard very

hard indeed I have often read someone else‟s paper that I enjoyed

and thought that I could have done the same work a similar thought

has not appeared after reading someone else‟s creative work except

when it is quite bad

5 What is the best advice you have ever received

Unfortunately most advice that most people get and give is bad

More correctly its difficult to know (what‟s the test) when it is good

and when bad Each of us likely adapt a post-hoc explanation to our

stories all of which are likely revisionist Nevertheless two different

people (a brother and a family friend) at about the same time

(1979-1982) told me to abandon what I was doing (an unsuccessful

postdoc and forcing myself to complete reading a fairly racist

account of the Black Hole of Calcutta) because it was beyond my

enjoyment They both suggested that I drop it and do something else

One should not shoulder a burden that is great unless some higher

purpose is at stake One needs to learn how to apportion risk with

benefit

Your message for young students and researchers

Science is difficult but exhilarating in its rare moments of success

and it‟s usually followed by long periods of stasis It is a great but

frustrating life and there are many worse ways of making a living It

is like other types of creative endeavors where discovery is real but

rare If you wish to do it be sure you can enjoy its moods Science

today is also multidisciplinary and translational its application to

humans and other benefits can also be tangible sources of pride But

do it not for these benefits do it because the science gives you great

joy Yes joy Consider that you are one in an

unbroken intellectual chain from Johannes

Kepler and Isaac Newton If you choose

science you are special

Dr Chakravarti‟s laboratory focuses on the development and

applications of molecular genetic genomic and computational

methods for identification of human disease genes through

genetic dissectionldquo He has been a key participant and architect

of the Human Genome HapMap and 1000 Genomes project Find

out more about his research here

6

Workshop at a glance One-day workshop to equip young science

researchers with tools and strategies for effective communication of

their ideas experiments and scientific results from a science

communication perspective Help them to make science career choices

Vision Science communication plays an integral role in one‟s scientific

career Being able to effectively disseminate research findings within

the community and to consider collective opinions in prioritising

research needs is an important attribute of scientific maturity In

keeping with its mandate to empower future leaders of Indian science

the Wellcome TrustDBT India Alliance periodically conducts one-day

(SciComm101) and two-day (SciComm Hyderabad) science

communication workshops for the past four years This complements

seamlessly with Nature India‟s mandate to showcase India‟s science bdquoas

it happens‟ in laboratories and institutions across the country through

in-depth coverage and analysis of research and science policy The

proposed workshop would be part of Nature India‟s many

communication outreach activities as the one-stop media platform for

India‟s science

The Wellcome TrustDBT India Alliance and Nature India both

represent possibilities for young PhD scholars and postdoctoral

scientists to transition into academic as well as non-academic science

careers Information and advice on how to explore various career

options will form an important part of these workshops with

Naturejobs as the key organiser of the career session

Structure amp format

The workshop will be a one-day event preceding a biomedical (or

scientific) conference organised by reputed science

societiesorganisationsinstitutes and Universities in India A large

participation by PhD students postdoctoral fellows and junior

scientists will be a pre-requisite for holding this workshop Organising

this workshop as part of a conference will ensure participation from a

wide range of institutions across India The workshop will include 3

separate sessions

Session 1 Scientific Writing (moderated by WTDBT Alliance)

Topics to be covered

bull Ethics in research

bull Presentation skills

bull Manuscript writing

bull Grants writing

bull CVs and letters

Session 2 Science Communication (moderated by Nature India)

Topics to be covered

bull Science journalism

bull Popular science writing

bull Effective press releases

bull Hands-on skills on dejargonising science

Session 3 Alternate Science Career (moderated by Nature Jobs)

Topics to be covered

bull Career in the Industry

bull Career in Science PromotionIntellectual Property

bull Career in PolicyGrant organizations Journalism

Science Communication and Career Workshop Series (In partnership with Nature India amp Naturejobs )

Please contact us at workshopswellcomedbtorg to find out more about this series

INDIA ALLIANCE

SCIENCE COMMUNICATION

SciComm101 workshop

10 March 2016 MSU Baroda

Two-day SciComm workshop

21-22 March 2016 Hyderabad Applications under review

For more details visit SciComm Workshop under Quick Links on our website

Upcoming Workshops

5

ABOUT THE ART amp SCIENCE PROJECT

CALL FOR APPLICATIONS THE UNDIVIDED MIND |ART +

SCIENCE RESIDENCY AT KHOJ

Residency Dates March 2nd ndash April 2nd 2015

Application Deadline February 2nd 2015

Proposals are invited for bdquoThe Undivided Mind‟ a four-week

international residency for artists whose work explores the

intersection of art and science

At first it may seem that the pairing of Art amp Science is an atypical

choice as the two fields and methods of practice have almost

universally been represented as diametric opposites of each other

However on closer examination the similarities between artists and

scientists far outweigh their stereotypical differences Both are

dedicated to research and to asking the big question- what is true

Why does it matter How can we move society forward Moreover

both the lab and the studio are spaces that famously encourage

open-ended enquiry and emphasis on process In tune with Khoj‟s

commitment to cultivate an environment that allows for

experimentation and innovation the Art amp Science residency will be

a step towards furthering the explorations of interdisciplinary

practitioners This is the second edition of a Khoj residency focusing

on Art + Science to know more about the first edition please

click bdquohere‟

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

The following India Alliance Fellows will be participating in the

project

(NOTE If an applicant wishes to connect with any of the following

researchers in advance of submitting their proposal please contact

the Khoj team at bdquoapplicationskhojworkshoporg‟ for an

introduction please do the same if you are a scientist and would like

take part in this project )

Dr Venkatasubramanian Ganesan National Institute of Mental

Health and Neurosciences (NIMHANS) Bangalore

Dr Pallab K Maulik The George Institute for Global Health New

Delhi

Dr Anurag Agarwal CSIR-Institute of Genomics amp Integrative

Biology (IGIB) New Delhi

Dr Tavpritesh Sethi All India Institute of Medical Sciences (AIIMS)

New Delhi

Dr Lolitika Mandal Indian Institute of Science Education and

Research (IISER) Mohali

Dr Urvakhsh MehtaNIMHANS Bangalore

Dr Sheetal Gandotra IGIB New Delhi

Visit Khoj website to find out more about the residency and the application process

Apply by

2 February 2016

India Alliance is pleased to announce its support for Art amp Science Project at Khoj International Artists Association New Delhi details of

which can be found below and on the Khoj website It promises to be a great platform for interdisciplinary dialogue and exchange

between scientists and artists and we encourage anyone interested to apply (artists) and get involved (scientists)

THEME

The theme of the 2016 edition of The Undivided Mind is bdquoHealth‟

Within this broader framework three curatorial frameworks or

modes for exploration are suggested Terrestrial Health refers to

that which is on or related to the earth This sub ndash theme suggests an

investigation into the physical health and structure of the body (both

human and animal) the environment the community and the

interrelations between these spheres Mental Health refers to that

which is of or relating to the mind This sub ndash theme focuses on a

psychological investigation of what constitutes Health of the mind

and raises questions about the bdquosocially‟ defined state of well-being

where issues‟ surrounding the legal rights and entitlement of

personhood for those living with a mental disorder is open for

debate Finally Extraterrestrial Health may refer to any object

being or idea beyond the planet Earth This sub ndash theme opens up a

space where the relationship between Earth and other planetary

bodies can be studied What does it mean for human existence when

sending human life forms to Mars is projected to take place by

2020 What are the long term effects and solution to space debris

if life projects out beyond Earth This sub ndash theme also invites

applicants to consider the abstract and metaphorical imaginings of

health in contemporary and future societies

6

Nobel Laureate Dr Harold Varmus recognized for his research on

retroviruses and the genetic basis of cancer gave a lecture on ldquoRecent

Developments in Cancer Researchrdquo at National Institute of Immunology

(NII) New Delhi an event co-organised by NII Wellcome TrustDBT

India Alliance and Department of Biotechnology Government of

India His lecture largely gave an overview of the recent

developments challenges and the future directions in the field of

cancer research which included the current research of his group in

this area

Dr Varmus who had spent time in Bareilly as a young medical

student described cancer as a complex disease that requires

innovative research and treatment strategies At the outset Dr Varmus

introduced the key questions that drive the cancer research field- Is

cancer one disease or many diseases What makes the cancer cell

grow so stably in such an inappropriate manner How does a normal

cell become a cancer cell Providing answers to these questions

formed the backdrop of Dr Varmus‟s lecture which drew from his

research work till date and other advances in the field

Dr Varmus entered the field of cancer research in 1970s as a

postdoctoral scientist in the laboratory of Dr John J Michael Bishop at

University of California San Francisco USA the same year National

Cancer Act was signed in the country Dr Bishop and Dr Varmus

together received the Nobel Prize in Medicine and Physiology in

1989 ldquofor their discovery of the cellular origins of retroviral

oncogenesrdquo During his lecture Dr Varmus confessed standing on the

shoulders of giants of retroviral and cancer research such as Dr

Peyton Rous Dr Harry Rubin and Dr Howard Temin to ask the question

of how retroviruses transformed cells and cause tumours This question

led him to look for genes that make a normal cell behave like a

cancer cell which initially involved studying cancer-causing RNA

virusesretroviruses in animals The retrovirus that played a lead role

in Dr Varmus and his colleague‟s work was the Rous Sarcoma Virus

(RSV) discovered by Dr Peyton Rous in 1911 which he showed caused

a type of cancer in chickens Dr Varmus and colleagues set out to

prove the hypothesis that retroviruses enter host cells and capture

normal genes in that cell by inserting their DNA converting them into

cancer-causing genes or oncogenes Dr Varmus and his group

employed various cellular chemical as well as genetic tools to

establish that retroviruses can indeed act as mutagens by inserting

their DNA in host cells and turning them into cancer cells After this his

group went on to identify the cancer-causing genes present in the

virus and subsequently discovered many new oncogenes v-Src (a

gene of RSV) being the first one Following these discoveries and

subsequently many others led to the belief that the genetic basis of

cancer is highly heterogeneous Dr Varmus told us that in order to

catalogue these complexities the Cancer Genome Atlas was

established in 2005 which till today serves as a collection of the

genetic mutations responsible for different cancers

Apart from the complexity and vastness of the cancer genome

other challenges in the field according to Dr Varmus are genetic

heterogeneity and evolution of tumours due to various environmental

factors such as exposure to UV pollution tobacco use and other

environmental carcinogens that are on the rise He used the example

of renal tumor evolution which illustrates Darwin‟s theory of ldquoevolution

of speciesrdquo to show that this rapidly changing genetic repertoire can

have significant impact on diagnosis therapeutic interventions and

prognosis Another issue of concern highlighted by Dr Varmus was the

absence of suitable drugs against many common targets for cancer

such as cancer-causing RAS genes and many transcription factors

which have been shown to contribute towards cancer formation Dr

Varmus opined that lack of understanding of the underlying

complexity of resistance to cancer therapies is another roadblock in

cancer treatment He was also strongly of the opinion that there are

not enough public health interventions to prevent cancer- this he felt

needs to go hand in hand with finding cure for cancer

Dr Varmus also offered solutions to these problems He suggested

that research needs to ldquolook beyond genes and focus on patterns and

pathwaysrdquo and physiological changes taking place in cancer cells He

shared his group‟s current interest in studying ldquooncogene addictionrdquo

which is based on the premise that some oncogenes not only give rise

to cancer but also maintain the cancerous state of the cells

Interpreting the downstream effects of these cancer genes on the

pathways could be employed as a strategy to attack multiple targets

by drugs in different cancers Even though he hailed the successes of

many commonly used and extremely efficacious anti-cancer drugs

such as Gleevec Gefitinib Erlotinib but in light of growing

complexity of the disease proposed the need for adopting more

innovative drug discovery and treatment approaches Continuing on

the topic of therapeutics Dr Varmus mentioned the recent advances in

immunotherapeutic approaches to treat cancer which would require

us to understand why the otherwise combative immune system does

not kill cancer cells He suggested that gaining understanding of these

immune check points and accordingly targeting them by antibody

inhibitors could serve as one more effective treatment strategy-

another project his research group has undertaken In addition to

these therapeutic approaches Dr Varmus very strongly asserted that

ldquonot everything we talk about cancer should be about cancer therapy

but also about preventionrdquo and that this disease ought to be on the

global health agenda

Dr Varmus very eloquently concluded his talk by stating that

ldquoconfronting cancer needs a balance between grasping its complexity

and seeking simple solutionsrdquo As expected he received many

questions from the audience after his lecture on the genetics and

biology of various cancers potential use of vaccines in cancer

treatment crosstalk of cancer with other diseases and many others to

which he responded with prudence and an underlying sense of

optimism

Prior to his lecture Dr Varmus over an hour meeting with 10 young

cancer researchers discussed their work This group included the

following Wellcome TrustDBT India Alliance Fellows - Dr Reety Arora

(ECF InStem Bangalore) Dr Anjali Bajpai (ECF IIT Kanpur) Dr

Bushra Ateeq (Int Fellow IIT Kanpur) Dr Kundan Sengupta (Int Fellow

IISER Pune) and Dr Sandeep Singh (Int Fellow NIBMG Kalyani) Dr

Varmus also sought information on the India Alliance Fellowships and

was impressed by its funding model and reach

LECTURE REPORT

Recent Developments in Cancer Research By Dr Harold Varmus Nobel Prize in Medicine and Physiology Weill Cornell Medical College USA

at

National Institute of Immunology New Delhi

16 November 2015

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

7

ASK THE SCIENTIST about

The Human Brain

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

This section will bring to you answers to those burning scientific questions that you always wanted to ask the guys in the white

coat For this issue we asked some of our Fellows to shed light on the various operations of the brain

How can we measure attention

DR SUPRATIM RAY Indian Institute of Science Bangalore

Intermediate Fellow

Attention can be of different types such as sustained (vigilance)

selective (focusing at one stimulus in the presence of distractors) or

alternating (involves switching) which can be measured using a

variety of cognitive tests (such as test of everyday attention (TEA) or

Posner cuing task) For example in a classical Posner task a subject

is repeatedly shown two stimuli and cued to attend to one of them

and instructed to respond to a change in the stimulus (say by

pressing a button) The cue could be valid (change occurs at the cued

stimulus say for 80 of the trials) invalid (change occurs at the

uncued stimulus) or neutral (ambiguous) Selection attention can be

measured by comparing the accuracy and the time taken to press

the button after stimulus change (called reaction time) for different

cue types

Different components of attention such as orienting towards a

location detecting a target or maintaining vigilance are carried out

by distinct brain areas in the prefrontal and parietal lobes and some

sub-cortical structures (such as superior colliculus) Overall

performance depends not only on how these areas perform but also

how they communicate with each other and on the levels of

neuromodulators such as norepinephrine

How can we sense smell Is it possible to live without this

sense of smell

DR NIXON ABRAHAM Indian Institutes of Science Education amp

Research (IISER) Pune

Intermediate Fellow

Once Dr Lewis Thomas (1913-1993) the poet and a philosopher of

medicine who also served as the dean of the medical schools at the

New York University and Yale was asked to select seven wonders of

the modern world Olfaction (olfactory receptor cell) was fifth in his

list How does the modern fifth wonder that brings us the smell of our

surroundings ndash the good and bad work

The process of making sense of smell start by binding the odor

molecules to the olfactory receptors located in the olfactory sensory

neurons (OSNs) in the nose This binding triggers a series of signal

amplification steps which lead to electrical spikes (so called action

potentials) in OSNs This olfactory information whose intensity is

encoded by varying the number of action potentials is then passed

onto the projection neurons named mitral and tufted cells in the

olfactory bulb These projection neurons whose excitatory actions

are controlled by various inhibitory neurons carry the olfactory

information to the higher centers in the brain so that we perceive the

smell of spicy tasty food and putrid garbage ndash the good and bad

from the environment

Continued

9

Brain waves

measured by EEG

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

What is really happening inside the brain of a Schizophrenia

patient Does it look any different from a normal brain

DR VENKATASUBRAMANIAN GANESAN NIMHANS Bengaluru

Intermediate Fellow

The brain of a schizophrenia patient is reduced in overall volume

with increase in the size of the ventricles (parts of the brain that

contain cerebrospinal fluid) however certain parts like hippocampus

superior temporal gyrus and prefrontal cortex are more affected

than others Using certain advanced brain imaging research studies

(for example high resolution structural MRI functional MRI Magnetic

Resonance Spectroscopy Positron Emission Tomography and Diffusion

Tensor Imaging and similar others) subtle brain abnormalities in

structure function neurochemical profile as well as brain connectivity

have been demonstrated in several brain regions in schizophrenia

patients It is important to note that these findings are obtained

from advanced research studies that have compared brains of a

Why are the mirror neurons called the Minds mirror What do

they reflect

DR URVAKHSH MEHTA National Institute of Mental Health amp

Neurosciences (NIMHANS) Bengaluru

Early Career Fellow

Mirror neurons are specialized nerve cells that discharge when

we perform actions as well as when we observe others perform the

same action Rizzolatti and colleagues accidentally discovered them

in monkeys These neurons also get vicariously activated when we

perceive emotional states of others This unique bdquoexperience sharing‟

property of mirror neurons perhaps enables us to decipher goals

intentions and emotions of others

In several of our daily social interactions we need to take

perspectives of others decipher deception share feelings and

empathize with others The mirror neuron system is an important

brain network that helps us peek into the minds of others and try to

understand people They translate sensory information (eg

observation of an action) into a motor template which is similar to

the format an observer himself uses to perform that very action This

motor template can help us interpret the goals and feelings

underlying observed actions The definitive demonstration of mirror

neurons in humans was as recent as 2010 There is also growing

evidence of a dysfunctional mirror neuron system in psychiatric

disorders like autism and schizophrenia It is a long and exciting

future ahead to decipher spatiotemporal regulatory and genetic

underpinnings of this unique neuronal network ndash this will possibly

help understand and treat social brain disorders better

Schizophrenia

What happens if we loose our sense of smell Loss of olfaction can

be caused by many reasons ranging from viral infections to

neurodegenerative disorders As our emotions and memories are

strongly related to olfaction the loss of this sense can lead to

depressed state and even affect bonding with family members Just

imagine sipping from your morning coffee without sensing it‟s aroma

- our taste could be badly affected by losing sense of smell The

ongoing research at the nasal stem cell level might provide clinical

solutions for the disorders of the olfactory sensory neurons to regain

this wonderful sense

group of schizophrenia patients with that of healthy subjects thus

these are group averaged findings that are currently not applicable

for diagnosing schizophrenia in an individual patient in a regular

clinical setting In ldquoa specific patientrdquo one may not be able to find

any striking abnormality in the physical appearance of the brain (ie

a routine CT or MRI brain scan may not be able to identify any

obvious aberration) Several ongoing research studies are in pursuit

to identify clinically useful biomarker to diagnose schizophrenia

Find out more about Dr Ganesan‟s research on schizophrenia here

Do you have a burning scientific

question

Send them to

publicengagementwellcomedbtorg

Mirror neuron activity in the brain both when the monkey grasps an object

and when it observes the experimenter grasping the object Mirror neurons

were first discovered by Rizzolatti and colleagues when they were studying

motor actions in macque monkeys

10

INDIA ALLIANCE FELLOW

DR ROOP MALIK Senior Fellow TIFR Mumbai

Dr Roop Malik is a biophysicist based at Tata Institute of Fundamental Research Mumbai Dr Malikrsquos research focuses on nanoscale molecular motor proteins that transport material such as virus mitochondria endosomes etc inside living cells

What is your research group working on and what impact do you

hope it will have

We try to understand how the living cell achieves an organization that

is well defined yet dynamic Most of the components within a cell

have a lipid membrane boundary This boundary is fairly well

defined and visible under a microscope yet it undergoes constant

deformation to allow exchange of material between different parts

of a cell Motor proteins attach to the lipid membrane boundary and

act as transporters physically carrying cellular material from one

membrane to another in the form of a vesicular cargo How do the

motors and lipids collaborate to decide the fate of the cargo

We work on two such cargoes -- the Phagosome (may enclose

pathogens) and the Lipid droplet (encloses fat) We hope that our

research will help understand how pathogens infect us by modifying

the lipid membrane and the motors attached to it We also

investigate how fat stored inside the Lipid droplets in our liver is

circulated to different parts of the body There is a tremendous

change in the amount of fat stored in liver at every feedingfasting

cycle This is visible in the form of Lipid droplet accumulation in rat

liver sections after fasting How does the liver handle this flux of fat

What special mechanisms are required Answering these questions

may help understand the progression of fatty liver diseases

What inspired you to become a scientist

To be frank nothing in particular It was an acquired taste I started

doing experiments and gradually realised I was doing well I like the

planning that is involved in investigating the unknown and the

surprises that crop up inevitably These force you to change your

well-laid plans Thats when it gets really exciting

What role canshould scientists play in todays India

I think there is a lot of scientific freedom in India Granting agencies

are not as hawkish as in the western world This freedom is an

opportunity to do what drives you There are many young scientists in

the country who are keen to share ideas and resources We should

focus on solving difficult problems by taking advantage of this

environment If we do good science it will inspire the public

The primary job of a scientist is to do science and to do it well

Beyond that we also need to think about how science can be

propagated We have to mentor students and give them the

confidence and enthusiasm so that they go on to do better science

than we did We also have to communicate our science to common

man and facilitate them We must impress on students (and also on

their parents) that they should not look at studying Physics or Biology

or Chemistry in isolation Those who want to take up science as a

career should also understand that they must learn to deal with many

failures before something succeeds

How has Wellcome TrustDBT India Alliance Fellowship helped

you and your research (your IA experience)

I have been a Senior fellow with Wellcome Trust (UK) and then with

Wellcome Trust DBT India Alliance since 2006 The rigorous selection

process helped me fine-tune the questions that I wanted to ask The

subsequent evaluations and annual meetings helped in keeping my

research on track Last but not the least we were given a lot of

freedom in executing our science I thank the India Alliance for this

degree of trust in their Fellows This has helped me to focus on the

science

What keeps you going every day

Coffee tea and the excitement of planning and executing science

with my colleagues Regular breaks to get out into the hills for some

adventure

Find out more about

Dr Roop Malik‟s

work on motor

proteins on his

website In order to

make his research

understandable to

a wide range of

people he has put

up translation of his

research summary

in Hindi and

Marathi in addition

to Engalish on his

website

11

A Sponge Against a Sword An RNA-binding protein Prevents Chronic Inflammation and Cancer

By Dr Partho Sarothi Ray Intermediate Fellow

Anyone who has had a bruise is familiar with the redness

swelling warmth and pain that mark the site of the injury This

response known as inflammation has been recognized since ancient

times and its hallmarks were first described by the Greek physician

Galen 2000 years ago The process which is often set in motion by

specialized cells of the immune system occurs whenever tissue is

infected or damaged as for example when you have a pimple or

more seriously suffer a heart attack The latter condition is called

sterile inflammation which happens in absence of infection by a

pathogen and when it goes awry it contributes to a wide range of

seemingly unrelated diseases from Alzheimer‟s disease to diabetes to

cancer

Inflammation is the primary protective response of the body to any

infection or injury However as our common experience shows the

inflammation after being triggered goes away of its own a process

known as resolution However in certain cases the inflammation fails

to resolve and it‟s continuation known as chronic inflammation acts as

an underlying contributor to virtually every chronic disease- a list that

besides obvious culprits such as rheumatoid arthritis and

Crohn‟s disease includes diabetes and depression along with major

killers such as heart disease and stroke and especially cancer

Therefore inflammation is a double-edged sword it protects our

body but can also harm it when it occurs in an uncontrolled manner

Over the past decade and half this role of inflammation has come

under intense scrutiny and many research groups throughout the

world are attempting to discover the underlying mechanisms which

regulate the onset and resolution of inflammation

Connection between Cancer and Inflammation

The connection between cancer and inflammation was recognized a

long time ago In fact in 1863 the renowned German pathologist

Rudolf Virchow found the presence of white blood cells cells which

mediate inflammation in tumors In 1986 the cancer biologist Harold

Dvorak of Harvard Medical School remarked that tumors are

wounds that do not heal However it is only over the last two

decades that the connections between inflammation and cancer have

transformed our understanding of how cancers develop This

transformation recognizes that the chronic inflammatory state serves

as a key mediator of the middle stages of tumor development

Cancer begins with a series of genetic changes that prompt a group

of cells to proliferate and then invade surrounding tissue the point at

which true malignancy begins Eventually some tumor cells may break

off and establish new growths (metastases) at distant sites This has

been understood for a long time But cancer biologists and

immunologists have begun to realize that the progression from

diseased tissue to full-blown invasive cancer often requires cells that

normally participate in inflammation to be diverted to the pre-

malignant tissue where they are hijacked to become co-conspirators

that aid and abet carcinogenesis As described by researchers

genetic damage is the match that lights the fire and inflammation

is the fuel that feeds it Therefore the aim of our lab is to understand

the molecular processes and mechanisms that normally prevent chronic

inflammation and thereby prevent the transition from a pre-malignant

stage to a full-blown cancer Hopefully this understanding will allow in

not-so-distant future to detect and treat cancers at the pre-malignant

stage which will make cancer treatment much easier and affordable

In addition to that this understanding will possibly be helpful in the

treatment of all chronic inflammatory diseases as the basic cellular

mechanisms underlying chronic inflammation are thought to be the

same in all cases

Inflammation in cells

At the cellular level inflammation involves two types of cells the

cells of the tissue or organ that is injured that is the inflamed cells

and the cells that mediate the inflammation that is the inflammatory

cells The latter consist mainly of cells that are originally in the blood

such as monocytes and neutrophils which migrate to the site of the

inflammation and literally eat up (phagocytose) the infecting

microorganisms or the injured cells In many cases there are

monocytes present within the inflamed tissue itself called

macrophages or big eaters which form the first line of attack on the

invading pathogen or damaged tissue Now both the inflamed cells

and the inflammatory cells secrete special signalling chemicals called

cytokines which attract more inflammatory cells to the site of the

inflammation Together with the cytokines the inflammatory cells (the

macrophages and neutrophils) also produce a variety of other factors

that allow the cells to move through the wall of the blood vessels and

then into the tissue where they attack engulf and destroy the

invading pathogen or the damaged cells It is obvious that many of

these factors such as reactive oxygen species (ROS)

metalloproteases interleukins like IL6 and blood vessel growth factors

like VEGF are toxic and if continued to be produced will damage

the healthy tissue as well That is why the production of both the

cytokines which attract these cells to the site of inflammation and

these factors which cause the death and destruction of the pathogens

ceases when the cause of the inflammation is removed and allows the

inflammation to resolve Failure to stop the production of these

inflammatory factors therefore leads to chronic inflammation and the

chronic inflammatory diseases The inflammatory factors cytokines

and others are produced by genes which are called pro-

inflammatory genes Therefore the expression of these genes that is

the production of proteins from the genes have to be tightly

regulated both in space and time

12

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 8: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

Workshop at a glance One-day workshop to equip young science

researchers with tools and strategies for effective communication of

their ideas experiments and scientific results from a science

communication perspective Help them to make science career choices

Vision Science communication plays an integral role in one‟s scientific

career Being able to effectively disseminate research findings within

the community and to consider collective opinions in prioritising

research needs is an important attribute of scientific maturity In

keeping with its mandate to empower future leaders of Indian science

the Wellcome TrustDBT India Alliance periodically conducts one-day

(SciComm101) and two-day (SciComm Hyderabad) science

communication workshops for the past four years This complements

seamlessly with Nature India‟s mandate to showcase India‟s science bdquoas

it happens‟ in laboratories and institutions across the country through

in-depth coverage and analysis of research and science policy The

proposed workshop would be part of Nature India‟s many

communication outreach activities as the one-stop media platform for

India‟s science

The Wellcome TrustDBT India Alliance and Nature India both

represent possibilities for young PhD scholars and postdoctoral

scientists to transition into academic as well as non-academic science

careers Information and advice on how to explore various career

options will form an important part of these workshops with

Naturejobs as the key organiser of the career session

Structure amp format

The workshop will be a one-day event preceding a biomedical (or

scientific) conference organised by reputed science

societiesorganisationsinstitutes and Universities in India A large

participation by PhD students postdoctoral fellows and junior

scientists will be a pre-requisite for holding this workshop Organising

this workshop as part of a conference will ensure participation from a

wide range of institutions across India The workshop will include 3

separate sessions

Session 1 Scientific Writing (moderated by WTDBT Alliance)

Topics to be covered

bull Ethics in research

bull Presentation skills

bull Manuscript writing

bull Grants writing

bull CVs and letters

Session 2 Science Communication (moderated by Nature India)

Topics to be covered

bull Science journalism

bull Popular science writing

bull Effective press releases

bull Hands-on skills on dejargonising science

Session 3 Alternate Science Career (moderated by Nature Jobs)

Topics to be covered

bull Career in the Industry

bull Career in Science PromotionIntellectual Property

bull Career in PolicyGrant organizations Journalism

Science Communication and Career Workshop Series (In partnership with Nature India amp Naturejobs )

Please contact us at workshopswellcomedbtorg to find out more about this series

INDIA ALLIANCE

SCIENCE COMMUNICATION

SciComm101 workshop

10 March 2016 MSU Baroda

Two-day SciComm workshop

21-22 March 2016 Hyderabad Applications under review

For more details visit SciComm Workshop under Quick Links on our website

Upcoming Workshops

5

ABOUT THE ART amp SCIENCE PROJECT

CALL FOR APPLICATIONS THE UNDIVIDED MIND |ART +

SCIENCE RESIDENCY AT KHOJ

Residency Dates March 2nd ndash April 2nd 2015

Application Deadline February 2nd 2015

Proposals are invited for bdquoThe Undivided Mind‟ a four-week

international residency for artists whose work explores the

intersection of art and science

At first it may seem that the pairing of Art amp Science is an atypical

choice as the two fields and methods of practice have almost

universally been represented as diametric opposites of each other

However on closer examination the similarities between artists and

scientists far outweigh their stereotypical differences Both are

dedicated to research and to asking the big question- what is true

Why does it matter How can we move society forward Moreover

both the lab and the studio are spaces that famously encourage

open-ended enquiry and emphasis on process In tune with Khoj‟s

commitment to cultivate an environment that allows for

experimentation and innovation the Art amp Science residency will be

a step towards furthering the explorations of interdisciplinary

practitioners This is the second edition of a Khoj residency focusing

on Art + Science to know more about the first edition please

click bdquohere‟

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

The following India Alliance Fellows will be participating in the

project

(NOTE If an applicant wishes to connect with any of the following

researchers in advance of submitting their proposal please contact

the Khoj team at bdquoapplicationskhojworkshoporg‟ for an

introduction please do the same if you are a scientist and would like

take part in this project )

Dr Venkatasubramanian Ganesan National Institute of Mental

Health and Neurosciences (NIMHANS) Bangalore

Dr Pallab K Maulik The George Institute for Global Health New

Delhi

Dr Anurag Agarwal CSIR-Institute of Genomics amp Integrative

Biology (IGIB) New Delhi

Dr Tavpritesh Sethi All India Institute of Medical Sciences (AIIMS)

New Delhi

Dr Lolitika Mandal Indian Institute of Science Education and

Research (IISER) Mohali

Dr Urvakhsh MehtaNIMHANS Bangalore

Dr Sheetal Gandotra IGIB New Delhi

Visit Khoj website to find out more about the residency and the application process

Apply by

2 February 2016

India Alliance is pleased to announce its support for Art amp Science Project at Khoj International Artists Association New Delhi details of

which can be found below and on the Khoj website It promises to be a great platform for interdisciplinary dialogue and exchange

between scientists and artists and we encourage anyone interested to apply (artists) and get involved (scientists)

THEME

The theme of the 2016 edition of The Undivided Mind is bdquoHealth‟

Within this broader framework three curatorial frameworks or

modes for exploration are suggested Terrestrial Health refers to

that which is on or related to the earth This sub ndash theme suggests an

investigation into the physical health and structure of the body (both

human and animal) the environment the community and the

interrelations between these spheres Mental Health refers to that

which is of or relating to the mind This sub ndash theme focuses on a

psychological investigation of what constitutes Health of the mind

and raises questions about the bdquosocially‟ defined state of well-being

where issues‟ surrounding the legal rights and entitlement of

personhood for those living with a mental disorder is open for

debate Finally Extraterrestrial Health may refer to any object

being or idea beyond the planet Earth This sub ndash theme opens up a

space where the relationship between Earth and other planetary

bodies can be studied What does it mean for human existence when

sending human life forms to Mars is projected to take place by

2020 What are the long term effects and solution to space debris

if life projects out beyond Earth This sub ndash theme also invites

applicants to consider the abstract and metaphorical imaginings of

health in contemporary and future societies

6

Nobel Laureate Dr Harold Varmus recognized for his research on

retroviruses and the genetic basis of cancer gave a lecture on ldquoRecent

Developments in Cancer Researchrdquo at National Institute of Immunology

(NII) New Delhi an event co-organised by NII Wellcome TrustDBT

India Alliance and Department of Biotechnology Government of

India His lecture largely gave an overview of the recent

developments challenges and the future directions in the field of

cancer research which included the current research of his group in

this area

Dr Varmus who had spent time in Bareilly as a young medical

student described cancer as a complex disease that requires

innovative research and treatment strategies At the outset Dr Varmus

introduced the key questions that drive the cancer research field- Is

cancer one disease or many diseases What makes the cancer cell

grow so stably in such an inappropriate manner How does a normal

cell become a cancer cell Providing answers to these questions

formed the backdrop of Dr Varmus‟s lecture which drew from his

research work till date and other advances in the field

Dr Varmus entered the field of cancer research in 1970s as a

postdoctoral scientist in the laboratory of Dr John J Michael Bishop at

University of California San Francisco USA the same year National

Cancer Act was signed in the country Dr Bishop and Dr Varmus

together received the Nobel Prize in Medicine and Physiology in

1989 ldquofor their discovery of the cellular origins of retroviral

oncogenesrdquo During his lecture Dr Varmus confessed standing on the

shoulders of giants of retroviral and cancer research such as Dr

Peyton Rous Dr Harry Rubin and Dr Howard Temin to ask the question

of how retroviruses transformed cells and cause tumours This question

led him to look for genes that make a normal cell behave like a

cancer cell which initially involved studying cancer-causing RNA

virusesretroviruses in animals The retrovirus that played a lead role

in Dr Varmus and his colleague‟s work was the Rous Sarcoma Virus

(RSV) discovered by Dr Peyton Rous in 1911 which he showed caused

a type of cancer in chickens Dr Varmus and colleagues set out to

prove the hypothesis that retroviruses enter host cells and capture

normal genes in that cell by inserting their DNA converting them into

cancer-causing genes or oncogenes Dr Varmus and his group

employed various cellular chemical as well as genetic tools to

establish that retroviruses can indeed act as mutagens by inserting

their DNA in host cells and turning them into cancer cells After this his

group went on to identify the cancer-causing genes present in the

virus and subsequently discovered many new oncogenes v-Src (a

gene of RSV) being the first one Following these discoveries and

subsequently many others led to the belief that the genetic basis of

cancer is highly heterogeneous Dr Varmus told us that in order to

catalogue these complexities the Cancer Genome Atlas was

established in 2005 which till today serves as a collection of the

genetic mutations responsible for different cancers

Apart from the complexity and vastness of the cancer genome

other challenges in the field according to Dr Varmus are genetic

heterogeneity and evolution of tumours due to various environmental

factors such as exposure to UV pollution tobacco use and other

environmental carcinogens that are on the rise He used the example

of renal tumor evolution which illustrates Darwin‟s theory of ldquoevolution

of speciesrdquo to show that this rapidly changing genetic repertoire can

have significant impact on diagnosis therapeutic interventions and

prognosis Another issue of concern highlighted by Dr Varmus was the

absence of suitable drugs against many common targets for cancer

such as cancer-causing RAS genes and many transcription factors

which have been shown to contribute towards cancer formation Dr

Varmus opined that lack of understanding of the underlying

complexity of resistance to cancer therapies is another roadblock in

cancer treatment He was also strongly of the opinion that there are

not enough public health interventions to prevent cancer- this he felt

needs to go hand in hand with finding cure for cancer

Dr Varmus also offered solutions to these problems He suggested

that research needs to ldquolook beyond genes and focus on patterns and

pathwaysrdquo and physiological changes taking place in cancer cells He

shared his group‟s current interest in studying ldquooncogene addictionrdquo

which is based on the premise that some oncogenes not only give rise

to cancer but also maintain the cancerous state of the cells

Interpreting the downstream effects of these cancer genes on the

pathways could be employed as a strategy to attack multiple targets

by drugs in different cancers Even though he hailed the successes of

many commonly used and extremely efficacious anti-cancer drugs

such as Gleevec Gefitinib Erlotinib but in light of growing

complexity of the disease proposed the need for adopting more

innovative drug discovery and treatment approaches Continuing on

the topic of therapeutics Dr Varmus mentioned the recent advances in

immunotherapeutic approaches to treat cancer which would require

us to understand why the otherwise combative immune system does

not kill cancer cells He suggested that gaining understanding of these

immune check points and accordingly targeting them by antibody

inhibitors could serve as one more effective treatment strategy-

another project his research group has undertaken In addition to

these therapeutic approaches Dr Varmus very strongly asserted that

ldquonot everything we talk about cancer should be about cancer therapy

but also about preventionrdquo and that this disease ought to be on the

global health agenda

Dr Varmus very eloquently concluded his talk by stating that

ldquoconfronting cancer needs a balance between grasping its complexity

and seeking simple solutionsrdquo As expected he received many

questions from the audience after his lecture on the genetics and

biology of various cancers potential use of vaccines in cancer

treatment crosstalk of cancer with other diseases and many others to

which he responded with prudence and an underlying sense of

optimism

Prior to his lecture Dr Varmus over an hour meeting with 10 young

cancer researchers discussed their work This group included the

following Wellcome TrustDBT India Alliance Fellows - Dr Reety Arora

(ECF InStem Bangalore) Dr Anjali Bajpai (ECF IIT Kanpur) Dr

Bushra Ateeq (Int Fellow IIT Kanpur) Dr Kundan Sengupta (Int Fellow

IISER Pune) and Dr Sandeep Singh (Int Fellow NIBMG Kalyani) Dr

Varmus also sought information on the India Alliance Fellowships and

was impressed by its funding model and reach

LECTURE REPORT

Recent Developments in Cancer Research By Dr Harold Varmus Nobel Prize in Medicine and Physiology Weill Cornell Medical College USA

at

National Institute of Immunology New Delhi

16 November 2015

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

7

ASK THE SCIENTIST about

The Human Brain

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

This section will bring to you answers to those burning scientific questions that you always wanted to ask the guys in the white

coat For this issue we asked some of our Fellows to shed light on the various operations of the brain

How can we measure attention

DR SUPRATIM RAY Indian Institute of Science Bangalore

Intermediate Fellow

Attention can be of different types such as sustained (vigilance)

selective (focusing at one stimulus in the presence of distractors) or

alternating (involves switching) which can be measured using a

variety of cognitive tests (such as test of everyday attention (TEA) or

Posner cuing task) For example in a classical Posner task a subject

is repeatedly shown two stimuli and cued to attend to one of them

and instructed to respond to a change in the stimulus (say by

pressing a button) The cue could be valid (change occurs at the cued

stimulus say for 80 of the trials) invalid (change occurs at the

uncued stimulus) or neutral (ambiguous) Selection attention can be

measured by comparing the accuracy and the time taken to press

the button after stimulus change (called reaction time) for different

cue types

Different components of attention such as orienting towards a

location detecting a target or maintaining vigilance are carried out

by distinct brain areas in the prefrontal and parietal lobes and some

sub-cortical structures (such as superior colliculus) Overall

performance depends not only on how these areas perform but also

how they communicate with each other and on the levels of

neuromodulators such as norepinephrine

How can we sense smell Is it possible to live without this

sense of smell

DR NIXON ABRAHAM Indian Institutes of Science Education amp

Research (IISER) Pune

Intermediate Fellow

Once Dr Lewis Thomas (1913-1993) the poet and a philosopher of

medicine who also served as the dean of the medical schools at the

New York University and Yale was asked to select seven wonders of

the modern world Olfaction (olfactory receptor cell) was fifth in his

list How does the modern fifth wonder that brings us the smell of our

surroundings ndash the good and bad work

The process of making sense of smell start by binding the odor

molecules to the olfactory receptors located in the olfactory sensory

neurons (OSNs) in the nose This binding triggers a series of signal

amplification steps which lead to electrical spikes (so called action

potentials) in OSNs This olfactory information whose intensity is

encoded by varying the number of action potentials is then passed

onto the projection neurons named mitral and tufted cells in the

olfactory bulb These projection neurons whose excitatory actions

are controlled by various inhibitory neurons carry the olfactory

information to the higher centers in the brain so that we perceive the

smell of spicy tasty food and putrid garbage ndash the good and bad

from the environment

Continued

9

Brain waves

measured by EEG

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

What is really happening inside the brain of a Schizophrenia

patient Does it look any different from a normal brain

DR VENKATASUBRAMANIAN GANESAN NIMHANS Bengaluru

Intermediate Fellow

The brain of a schizophrenia patient is reduced in overall volume

with increase in the size of the ventricles (parts of the brain that

contain cerebrospinal fluid) however certain parts like hippocampus

superior temporal gyrus and prefrontal cortex are more affected

than others Using certain advanced brain imaging research studies

(for example high resolution structural MRI functional MRI Magnetic

Resonance Spectroscopy Positron Emission Tomography and Diffusion

Tensor Imaging and similar others) subtle brain abnormalities in

structure function neurochemical profile as well as brain connectivity

have been demonstrated in several brain regions in schizophrenia

patients It is important to note that these findings are obtained

from advanced research studies that have compared brains of a

Why are the mirror neurons called the Minds mirror What do

they reflect

DR URVAKHSH MEHTA National Institute of Mental Health amp

Neurosciences (NIMHANS) Bengaluru

Early Career Fellow

Mirror neurons are specialized nerve cells that discharge when

we perform actions as well as when we observe others perform the

same action Rizzolatti and colleagues accidentally discovered them

in monkeys These neurons also get vicariously activated when we

perceive emotional states of others This unique bdquoexperience sharing‟

property of mirror neurons perhaps enables us to decipher goals

intentions and emotions of others

In several of our daily social interactions we need to take

perspectives of others decipher deception share feelings and

empathize with others The mirror neuron system is an important

brain network that helps us peek into the minds of others and try to

understand people They translate sensory information (eg

observation of an action) into a motor template which is similar to

the format an observer himself uses to perform that very action This

motor template can help us interpret the goals and feelings

underlying observed actions The definitive demonstration of mirror

neurons in humans was as recent as 2010 There is also growing

evidence of a dysfunctional mirror neuron system in psychiatric

disorders like autism and schizophrenia It is a long and exciting

future ahead to decipher spatiotemporal regulatory and genetic

underpinnings of this unique neuronal network ndash this will possibly

help understand and treat social brain disorders better

Schizophrenia

What happens if we loose our sense of smell Loss of olfaction can

be caused by many reasons ranging from viral infections to

neurodegenerative disorders As our emotions and memories are

strongly related to olfaction the loss of this sense can lead to

depressed state and even affect bonding with family members Just

imagine sipping from your morning coffee without sensing it‟s aroma

- our taste could be badly affected by losing sense of smell The

ongoing research at the nasal stem cell level might provide clinical

solutions for the disorders of the olfactory sensory neurons to regain

this wonderful sense

group of schizophrenia patients with that of healthy subjects thus

these are group averaged findings that are currently not applicable

for diagnosing schizophrenia in an individual patient in a regular

clinical setting In ldquoa specific patientrdquo one may not be able to find

any striking abnormality in the physical appearance of the brain (ie

a routine CT or MRI brain scan may not be able to identify any

obvious aberration) Several ongoing research studies are in pursuit

to identify clinically useful biomarker to diagnose schizophrenia

Find out more about Dr Ganesan‟s research on schizophrenia here

Do you have a burning scientific

question

Send them to

publicengagementwellcomedbtorg

Mirror neuron activity in the brain both when the monkey grasps an object

and when it observes the experimenter grasping the object Mirror neurons

were first discovered by Rizzolatti and colleagues when they were studying

motor actions in macque monkeys

10

INDIA ALLIANCE FELLOW

DR ROOP MALIK Senior Fellow TIFR Mumbai

Dr Roop Malik is a biophysicist based at Tata Institute of Fundamental Research Mumbai Dr Malikrsquos research focuses on nanoscale molecular motor proteins that transport material such as virus mitochondria endosomes etc inside living cells

What is your research group working on and what impact do you

hope it will have

We try to understand how the living cell achieves an organization that

is well defined yet dynamic Most of the components within a cell

have a lipid membrane boundary This boundary is fairly well

defined and visible under a microscope yet it undergoes constant

deformation to allow exchange of material between different parts

of a cell Motor proteins attach to the lipid membrane boundary and

act as transporters physically carrying cellular material from one

membrane to another in the form of a vesicular cargo How do the

motors and lipids collaborate to decide the fate of the cargo

We work on two such cargoes -- the Phagosome (may enclose

pathogens) and the Lipid droplet (encloses fat) We hope that our

research will help understand how pathogens infect us by modifying

the lipid membrane and the motors attached to it We also

investigate how fat stored inside the Lipid droplets in our liver is

circulated to different parts of the body There is a tremendous

change in the amount of fat stored in liver at every feedingfasting

cycle This is visible in the form of Lipid droplet accumulation in rat

liver sections after fasting How does the liver handle this flux of fat

What special mechanisms are required Answering these questions

may help understand the progression of fatty liver diseases

What inspired you to become a scientist

To be frank nothing in particular It was an acquired taste I started

doing experiments and gradually realised I was doing well I like the

planning that is involved in investigating the unknown and the

surprises that crop up inevitably These force you to change your

well-laid plans Thats when it gets really exciting

What role canshould scientists play in todays India

I think there is a lot of scientific freedom in India Granting agencies

are not as hawkish as in the western world This freedom is an

opportunity to do what drives you There are many young scientists in

the country who are keen to share ideas and resources We should

focus on solving difficult problems by taking advantage of this

environment If we do good science it will inspire the public

The primary job of a scientist is to do science and to do it well

Beyond that we also need to think about how science can be

propagated We have to mentor students and give them the

confidence and enthusiasm so that they go on to do better science

than we did We also have to communicate our science to common

man and facilitate them We must impress on students (and also on

their parents) that they should not look at studying Physics or Biology

or Chemistry in isolation Those who want to take up science as a

career should also understand that they must learn to deal with many

failures before something succeeds

How has Wellcome TrustDBT India Alliance Fellowship helped

you and your research (your IA experience)

I have been a Senior fellow with Wellcome Trust (UK) and then with

Wellcome Trust DBT India Alliance since 2006 The rigorous selection

process helped me fine-tune the questions that I wanted to ask The

subsequent evaluations and annual meetings helped in keeping my

research on track Last but not the least we were given a lot of

freedom in executing our science I thank the India Alliance for this

degree of trust in their Fellows This has helped me to focus on the

science

What keeps you going every day

Coffee tea and the excitement of planning and executing science

with my colleagues Regular breaks to get out into the hills for some

adventure

Find out more about

Dr Roop Malik‟s

work on motor

proteins on his

website In order to

make his research

understandable to

a wide range of

people he has put

up translation of his

research summary

in Hindi and

Marathi in addition

to Engalish on his

website

11

A Sponge Against a Sword An RNA-binding protein Prevents Chronic Inflammation and Cancer

By Dr Partho Sarothi Ray Intermediate Fellow

Anyone who has had a bruise is familiar with the redness

swelling warmth and pain that mark the site of the injury This

response known as inflammation has been recognized since ancient

times and its hallmarks were first described by the Greek physician

Galen 2000 years ago The process which is often set in motion by

specialized cells of the immune system occurs whenever tissue is

infected or damaged as for example when you have a pimple or

more seriously suffer a heart attack The latter condition is called

sterile inflammation which happens in absence of infection by a

pathogen and when it goes awry it contributes to a wide range of

seemingly unrelated diseases from Alzheimer‟s disease to diabetes to

cancer

Inflammation is the primary protective response of the body to any

infection or injury However as our common experience shows the

inflammation after being triggered goes away of its own a process

known as resolution However in certain cases the inflammation fails

to resolve and it‟s continuation known as chronic inflammation acts as

an underlying contributor to virtually every chronic disease- a list that

besides obvious culprits such as rheumatoid arthritis and

Crohn‟s disease includes diabetes and depression along with major

killers such as heart disease and stroke and especially cancer

Therefore inflammation is a double-edged sword it protects our

body but can also harm it when it occurs in an uncontrolled manner

Over the past decade and half this role of inflammation has come

under intense scrutiny and many research groups throughout the

world are attempting to discover the underlying mechanisms which

regulate the onset and resolution of inflammation

Connection between Cancer and Inflammation

The connection between cancer and inflammation was recognized a

long time ago In fact in 1863 the renowned German pathologist

Rudolf Virchow found the presence of white blood cells cells which

mediate inflammation in tumors In 1986 the cancer biologist Harold

Dvorak of Harvard Medical School remarked that tumors are

wounds that do not heal However it is only over the last two

decades that the connections between inflammation and cancer have

transformed our understanding of how cancers develop This

transformation recognizes that the chronic inflammatory state serves

as a key mediator of the middle stages of tumor development

Cancer begins with a series of genetic changes that prompt a group

of cells to proliferate and then invade surrounding tissue the point at

which true malignancy begins Eventually some tumor cells may break

off and establish new growths (metastases) at distant sites This has

been understood for a long time But cancer biologists and

immunologists have begun to realize that the progression from

diseased tissue to full-blown invasive cancer often requires cells that

normally participate in inflammation to be diverted to the pre-

malignant tissue where they are hijacked to become co-conspirators

that aid and abet carcinogenesis As described by researchers

genetic damage is the match that lights the fire and inflammation

is the fuel that feeds it Therefore the aim of our lab is to understand

the molecular processes and mechanisms that normally prevent chronic

inflammation and thereby prevent the transition from a pre-malignant

stage to a full-blown cancer Hopefully this understanding will allow in

not-so-distant future to detect and treat cancers at the pre-malignant

stage which will make cancer treatment much easier and affordable

In addition to that this understanding will possibly be helpful in the

treatment of all chronic inflammatory diseases as the basic cellular

mechanisms underlying chronic inflammation are thought to be the

same in all cases

Inflammation in cells

At the cellular level inflammation involves two types of cells the

cells of the tissue or organ that is injured that is the inflamed cells

and the cells that mediate the inflammation that is the inflammatory

cells The latter consist mainly of cells that are originally in the blood

such as monocytes and neutrophils which migrate to the site of the

inflammation and literally eat up (phagocytose) the infecting

microorganisms or the injured cells In many cases there are

monocytes present within the inflamed tissue itself called

macrophages or big eaters which form the first line of attack on the

invading pathogen or damaged tissue Now both the inflamed cells

and the inflammatory cells secrete special signalling chemicals called

cytokines which attract more inflammatory cells to the site of the

inflammation Together with the cytokines the inflammatory cells (the

macrophages and neutrophils) also produce a variety of other factors

that allow the cells to move through the wall of the blood vessels and

then into the tissue where they attack engulf and destroy the

invading pathogen or the damaged cells It is obvious that many of

these factors such as reactive oxygen species (ROS)

metalloproteases interleukins like IL6 and blood vessel growth factors

like VEGF are toxic and if continued to be produced will damage

the healthy tissue as well That is why the production of both the

cytokines which attract these cells to the site of inflammation and

these factors which cause the death and destruction of the pathogens

ceases when the cause of the inflammation is removed and allows the

inflammation to resolve Failure to stop the production of these

inflammatory factors therefore leads to chronic inflammation and the

chronic inflammatory diseases The inflammatory factors cytokines

and others are produced by genes which are called pro-

inflammatory genes Therefore the expression of these genes that is

the production of proteins from the genes have to be tightly

regulated both in space and time

12

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 9: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

ABOUT THE ART amp SCIENCE PROJECT

CALL FOR APPLICATIONS THE UNDIVIDED MIND |ART +

SCIENCE RESIDENCY AT KHOJ

Residency Dates March 2nd ndash April 2nd 2015

Application Deadline February 2nd 2015

Proposals are invited for bdquoThe Undivided Mind‟ a four-week

international residency for artists whose work explores the

intersection of art and science

At first it may seem that the pairing of Art amp Science is an atypical

choice as the two fields and methods of practice have almost

universally been represented as diametric opposites of each other

However on closer examination the similarities between artists and

scientists far outweigh their stereotypical differences Both are

dedicated to research and to asking the big question- what is true

Why does it matter How can we move society forward Moreover

both the lab and the studio are spaces that famously encourage

open-ended enquiry and emphasis on process In tune with Khoj‟s

commitment to cultivate an environment that allows for

experimentation and innovation the Art amp Science residency will be

a step towards furthering the explorations of interdisciplinary

practitioners This is the second edition of a Khoj residency focusing

on Art + Science to know more about the first edition please

click bdquohere‟

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

The following India Alliance Fellows will be participating in the

project

(NOTE If an applicant wishes to connect with any of the following

researchers in advance of submitting their proposal please contact

the Khoj team at bdquoapplicationskhojworkshoporg‟ for an

introduction please do the same if you are a scientist and would like

take part in this project )

Dr Venkatasubramanian Ganesan National Institute of Mental

Health and Neurosciences (NIMHANS) Bangalore

Dr Pallab K Maulik The George Institute for Global Health New

Delhi

Dr Anurag Agarwal CSIR-Institute of Genomics amp Integrative

Biology (IGIB) New Delhi

Dr Tavpritesh Sethi All India Institute of Medical Sciences (AIIMS)

New Delhi

Dr Lolitika Mandal Indian Institute of Science Education and

Research (IISER) Mohali

Dr Urvakhsh MehtaNIMHANS Bangalore

Dr Sheetal Gandotra IGIB New Delhi

Visit Khoj website to find out more about the residency and the application process

Apply by

2 February 2016

India Alliance is pleased to announce its support for Art amp Science Project at Khoj International Artists Association New Delhi details of

which can be found below and on the Khoj website It promises to be a great platform for interdisciplinary dialogue and exchange

between scientists and artists and we encourage anyone interested to apply (artists) and get involved (scientists)

THEME

The theme of the 2016 edition of The Undivided Mind is bdquoHealth‟

Within this broader framework three curatorial frameworks or

modes for exploration are suggested Terrestrial Health refers to

that which is on or related to the earth This sub ndash theme suggests an

investigation into the physical health and structure of the body (both

human and animal) the environment the community and the

interrelations between these spheres Mental Health refers to that

which is of or relating to the mind This sub ndash theme focuses on a

psychological investigation of what constitutes Health of the mind

and raises questions about the bdquosocially‟ defined state of well-being

where issues‟ surrounding the legal rights and entitlement of

personhood for those living with a mental disorder is open for

debate Finally Extraterrestrial Health may refer to any object

being or idea beyond the planet Earth This sub ndash theme opens up a

space where the relationship between Earth and other planetary

bodies can be studied What does it mean for human existence when

sending human life forms to Mars is projected to take place by

2020 What are the long term effects and solution to space debris

if life projects out beyond Earth This sub ndash theme also invites

applicants to consider the abstract and metaphorical imaginings of

health in contemporary and future societies

6

Nobel Laureate Dr Harold Varmus recognized for his research on

retroviruses and the genetic basis of cancer gave a lecture on ldquoRecent

Developments in Cancer Researchrdquo at National Institute of Immunology

(NII) New Delhi an event co-organised by NII Wellcome TrustDBT

India Alliance and Department of Biotechnology Government of

India His lecture largely gave an overview of the recent

developments challenges and the future directions in the field of

cancer research which included the current research of his group in

this area

Dr Varmus who had spent time in Bareilly as a young medical

student described cancer as a complex disease that requires

innovative research and treatment strategies At the outset Dr Varmus

introduced the key questions that drive the cancer research field- Is

cancer one disease or many diseases What makes the cancer cell

grow so stably in such an inappropriate manner How does a normal

cell become a cancer cell Providing answers to these questions

formed the backdrop of Dr Varmus‟s lecture which drew from his

research work till date and other advances in the field

Dr Varmus entered the field of cancer research in 1970s as a

postdoctoral scientist in the laboratory of Dr John J Michael Bishop at

University of California San Francisco USA the same year National

Cancer Act was signed in the country Dr Bishop and Dr Varmus

together received the Nobel Prize in Medicine and Physiology in

1989 ldquofor their discovery of the cellular origins of retroviral

oncogenesrdquo During his lecture Dr Varmus confessed standing on the

shoulders of giants of retroviral and cancer research such as Dr

Peyton Rous Dr Harry Rubin and Dr Howard Temin to ask the question

of how retroviruses transformed cells and cause tumours This question

led him to look for genes that make a normal cell behave like a

cancer cell which initially involved studying cancer-causing RNA

virusesretroviruses in animals The retrovirus that played a lead role

in Dr Varmus and his colleague‟s work was the Rous Sarcoma Virus

(RSV) discovered by Dr Peyton Rous in 1911 which he showed caused

a type of cancer in chickens Dr Varmus and colleagues set out to

prove the hypothesis that retroviruses enter host cells and capture

normal genes in that cell by inserting their DNA converting them into

cancer-causing genes or oncogenes Dr Varmus and his group

employed various cellular chemical as well as genetic tools to

establish that retroviruses can indeed act as mutagens by inserting

their DNA in host cells and turning them into cancer cells After this his

group went on to identify the cancer-causing genes present in the

virus and subsequently discovered many new oncogenes v-Src (a

gene of RSV) being the first one Following these discoveries and

subsequently many others led to the belief that the genetic basis of

cancer is highly heterogeneous Dr Varmus told us that in order to

catalogue these complexities the Cancer Genome Atlas was

established in 2005 which till today serves as a collection of the

genetic mutations responsible for different cancers

Apart from the complexity and vastness of the cancer genome

other challenges in the field according to Dr Varmus are genetic

heterogeneity and evolution of tumours due to various environmental

factors such as exposure to UV pollution tobacco use and other

environmental carcinogens that are on the rise He used the example

of renal tumor evolution which illustrates Darwin‟s theory of ldquoevolution

of speciesrdquo to show that this rapidly changing genetic repertoire can

have significant impact on diagnosis therapeutic interventions and

prognosis Another issue of concern highlighted by Dr Varmus was the

absence of suitable drugs against many common targets for cancer

such as cancer-causing RAS genes and many transcription factors

which have been shown to contribute towards cancer formation Dr

Varmus opined that lack of understanding of the underlying

complexity of resistance to cancer therapies is another roadblock in

cancer treatment He was also strongly of the opinion that there are

not enough public health interventions to prevent cancer- this he felt

needs to go hand in hand with finding cure for cancer

Dr Varmus also offered solutions to these problems He suggested

that research needs to ldquolook beyond genes and focus on patterns and

pathwaysrdquo and physiological changes taking place in cancer cells He

shared his group‟s current interest in studying ldquooncogene addictionrdquo

which is based on the premise that some oncogenes not only give rise

to cancer but also maintain the cancerous state of the cells

Interpreting the downstream effects of these cancer genes on the

pathways could be employed as a strategy to attack multiple targets

by drugs in different cancers Even though he hailed the successes of

many commonly used and extremely efficacious anti-cancer drugs

such as Gleevec Gefitinib Erlotinib but in light of growing

complexity of the disease proposed the need for adopting more

innovative drug discovery and treatment approaches Continuing on

the topic of therapeutics Dr Varmus mentioned the recent advances in

immunotherapeutic approaches to treat cancer which would require

us to understand why the otherwise combative immune system does

not kill cancer cells He suggested that gaining understanding of these

immune check points and accordingly targeting them by antibody

inhibitors could serve as one more effective treatment strategy-

another project his research group has undertaken In addition to

these therapeutic approaches Dr Varmus very strongly asserted that

ldquonot everything we talk about cancer should be about cancer therapy

but also about preventionrdquo and that this disease ought to be on the

global health agenda

Dr Varmus very eloquently concluded his talk by stating that

ldquoconfronting cancer needs a balance between grasping its complexity

and seeking simple solutionsrdquo As expected he received many

questions from the audience after his lecture on the genetics and

biology of various cancers potential use of vaccines in cancer

treatment crosstalk of cancer with other diseases and many others to

which he responded with prudence and an underlying sense of

optimism

Prior to his lecture Dr Varmus over an hour meeting with 10 young

cancer researchers discussed their work This group included the

following Wellcome TrustDBT India Alliance Fellows - Dr Reety Arora

(ECF InStem Bangalore) Dr Anjali Bajpai (ECF IIT Kanpur) Dr

Bushra Ateeq (Int Fellow IIT Kanpur) Dr Kundan Sengupta (Int Fellow

IISER Pune) and Dr Sandeep Singh (Int Fellow NIBMG Kalyani) Dr

Varmus also sought information on the India Alliance Fellowships and

was impressed by its funding model and reach

LECTURE REPORT

Recent Developments in Cancer Research By Dr Harold Varmus Nobel Prize in Medicine and Physiology Weill Cornell Medical College USA

at

National Institute of Immunology New Delhi

16 November 2015

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

7

ASK THE SCIENTIST about

The Human Brain

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

This section will bring to you answers to those burning scientific questions that you always wanted to ask the guys in the white

coat For this issue we asked some of our Fellows to shed light on the various operations of the brain

How can we measure attention

DR SUPRATIM RAY Indian Institute of Science Bangalore

Intermediate Fellow

Attention can be of different types such as sustained (vigilance)

selective (focusing at one stimulus in the presence of distractors) or

alternating (involves switching) which can be measured using a

variety of cognitive tests (such as test of everyday attention (TEA) or

Posner cuing task) For example in a classical Posner task a subject

is repeatedly shown two stimuli and cued to attend to one of them

and instructed to respond to a change in the stimulus (say by

pressing a button) The cue could be valid (change occurs at the cued

stimulus say for 80 of the trials) invalid (change occurs at the

uncued stimulus) or neutral (ambiguous) Selection attention can be

measured by comparing the accuracy and the time taken to press

the button after stimulus change (called reaction time) for different

cue types

Different components of attention such as orienting towards a

location detecting a target or maintaining vigilance are carried out

by distinct brain areas in the prefrontal and parietal lobes and some

sub-cortical structures (such as superior colliculus) Overall

performance depends not only on how these areas perform but also

how they communicate with each other and on the levels of

neuromodulators such as norepinephrine

How can we sense smell Is it possible to live without this

sense of smell

DR NIXON ABRAHAM Indian Institutes of Science Education amp

Research (IISER) Pune

Intermediate Fellow

Once Dr Lewis Thomas (1913-1993) the poet and a philosopher of

medicine who also served as the dean of the medical schools at the

New York University and Yale was asked to select seven wonders of

the modern world Olfaction (olfactory receptor cell) was fifth in his

list How does the modern fifth wonder that brings us the smell of our

surroundings ndash the good and bad work

The process of making sense of smell start by binding the odor

molecules to the olfactory receptors located in the olfactory sensory

neurons (OSNs) in the nose This binding triggers a series of signal

amplification steps which lead to electrical spikes (so called action

potentials) in OSNs This olfactory information whose intensity is

encoded by varying the number of action potentials is then passed

onto the projection neurons named mitral and tufted cells in the

olfactory bulb These projection neurons whose excitatory actions

are controlled by various inhibitory neurons carry the olfactory

information to the higher centers in the brain so that we perceive the

smell of spicy tasty food and putrid garbage ndash the good and bad

from the environment

Continued

9

Brain waves

measured by EEG

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

What is really happening inside the brain of a Schizophrenia

patient Does it look any different from a normal brain

DR VENKATASUBRAMANIAN GANESAN NIMHANS Bengaluru

Intermediate Fellow

The brain of a schizophrenia patient is reduced in overall volume

with increase in the size of the ventricles (parts of the brain that

contain cerebrospinal fluid) however certain parts like hippocampus

superior temporal gyrus and prefrontal cortex are more affected

than others Using certain advanced brain imaging research studies

(for example high resolution structural MRI functional MRI Magnetic

Resonance Spectroscopy Positron Emission Tomography and Diffusion

Tensor Imaging and similar others) subtle brain abnormalities in

structure function neurochemical profile as well as brain connectivity

have been demonstrated in several brain regions in schizophrenia

patients It is important to note that these findings are obtained

from advanced research studies that have compared brains of a

Why are the mirror neurons called the Minds mirror What do

they reflect

DR URVAKHSH MEHTA National Institute of Mental Health amp

Neurosciences (NIMHANS) Bengaluru

Early Career Fellow

Mirror neurons are specialized nerve cells that discharge when

we perform actions as well as when we observe others perform the

same action Rizzolatti and colleagues accidentally discovered them

in monkeys These neurons also get vicariously activated when we

perceive emotional states of others This unique bdquoexperience sharing‟

property of mirror neurons perhaps enables us to decipher goals

intentions and emotions of others

In several of our daily social interactions we need to take

perspectives of others decipher deception share feelings and

empathize with others The mirror neuron system is an important

brain network that helps us peek into the minds of others and try to

understand people They translate sensory information (eg

observation of an action) into a motor template which is similar to

the format an observer himself uses to perform that very action This

motor template can help us interpret the goals and feelings

underlying observed actions The definitive demonstration of mirror

neurons in humans was as recent as 2010 There is also growing

evidence of a dysfunctional mirror neuron system in psychiatric

disorders like autism and schizophrenia It is a long and exciting

future ahead to decipher spatiotemporal regulatory and genetic

underpinnings of this unique neuronal network ndash this will possibly

help understand and treat social brain disorders better

Schizophrenia

What happens if we loose our sense of smell Loss of olfaction can

be caused by many reasons ranging from viral infections to

neurodegenerative disorders As our emotions and memories are

strongly related to olfaction the loss of this sense can lead to

depressed state and even affect bonding with family members Just

imagine sipping from your morning coffee without sensing it‟s aroma

- our taste could be badly affected by losing sense of smell The

ongoing research at the nasal stem cell level might provide clinical

solutions for the disorders of the olfactory sensory neurons to regain

this wonderful sense

group of schizophrenia patients with that of healthy subjects thus

these are group averaged findings that are currently not applicable

for diagnosing schizophrenia in an individual patient in a regular

clinical setting In ldquoa specific patientrdquo one may not be able to find

any striking abnormality in the physical appearance of the brain (ie

a routine CT or MRI brain scan may not be able to identify any

obvious aberration) Several ongoing research studies are in pursuit

to identify clinically useful biomarker to diagnose schizophrenia

Find out more about Dr Ganesan‟s research on schizophrenia here

Do you have a burning scientific

question

Send them to

publicengagementwellcomedbtorg

Mirror neuron activity in the brain both when the monkey grasps an object

and when it observes the experimenter grasping the object Mirror neurons

were first discovered by Rizzolatti and colleagues when they were studying

motor actions in macque monkeys

10

INDIA ALLIANCE FELLOW

DR ROOP MALIK Senior Fellow TIFR Mumbai

Dr Roop Malik is a biophysicist based at Tata Institute of Fundamental Research Mumbai Dr Malikrsquos research focuses on nanoscale molecular motor proteins that transport material such as virus mitochondria endosomes etc inside living cells

What is your research group working on and what impact do you

hope it will have

We try to understand how the living cell achieves an organization that

is well defined yet dynamic Most of the components within a cell

have a lipid membrane boundary This boundary is fairly well

defined and visible under a microscope yet it undergoes constant

deformation to allow exchange of material between different parts

of a cell Motor proteins attach to the lipid membrane boundary and

act as transporters physically carrying cellular material from one

membrane to another in the form of a vesicular cargo How do the

motors and lipids collaborate to decide the fate of the cargo

We work on two such cargoes -- the Phagosome (may enclose

pathogens) and the Lipid droplet (encloses fat) We hope that our

research will help understand how pathogens infect us by modifying

the lipid membrane and the motors attached to it We also

investigate how fat stored inside the Lipid droplets in our liver is

circulated to different parts of the body There is a tremendous

change in the amount of fat stored in liver at every feedingfasting

cycle This is visible in the form of Lipid droplet accumulation in rat

liver sections after fasting How does the liver handle this flux of fat

What special mechanisms are required Answering these questions

may help understand the progression of fatty liver diseases

What inspired you to become a scientist

To be frank nothing in particular It was an acquired taste I started

doing experiments and gradually realised I was doing well I like the

planning that is involved in investigating the unknown and the

surprises that crop up inevitably These force you to change your

well-laid plans Thats when it gets really exciting

What role canshould scientists play in todays India

I think there is a lot of scientific freedom in India Granting agencies

are not as hawkish as in the western world This freedom is an

opportunity to do what drives you There are many young scientists in

the country who are keen to share ideas and resources We should

focus on solving difficult problems by taking advantage of this

environment If we do good science it will inspire the public

The primary job of a scientist is to do science and to do it well

Beyond that we also need to think about how science can be

propagated We have to mentor students and give them the

confidence and enthusiasm so that they go on to do better science

than we did We also have to communicate our science to common

man and facilitate them We must impress on students (and also on

their parents) that they should not look at studying Physics or Biology

or Chemistry in isolation Those who want to take up science as a

career should also understand that they must learn to deal with many

failures before something succeeds

How has Wellcome TrustDBT India Alliance Fellowship helped

you and your research (your IA experience)

I have been a Senior fellow with Wellcome Trust (UK) and then with

Wellcome Trust DBT India Alliance since 2006 The rigorous selection

process helped me fine-tune the questions that I wanted to ask The

subsequent evaluations and annual meetings helped in keeping my

research on track Last but not the least we were given a lot of

freedom in executing our science I thank the India Alliance for this

degree of trust in their Fellows This has helped me to focus on the

science

What keeps you going every day

Coffee tea and the excitement of planning and executing science

with my colleagues Regular breaks to get out into the hills for some

adventure

Find out more about

Dr Roop Malik‟s

work on motor

proteins on his

website In order to

make his research

understandable to

a wide range of

people he has put

up translation of his

research summary

in Hindi and

Marathi in addition

to Engalish on his

website

11

A Sponge Against a Sword An RNA-binding protein Prevents Chronic Inflammation and Cancer

By Dr Partho Sarothi Ray Intermediate Fellow

Anyone who has had a bruise is familiar with the redness

swelling warmth and pain that mark the site of the injury This

response known as inflammation has been recognized since ancient

times and its hallmarks were first described by the Greek physician

Galen 2000 years ago The process which is often set in motion by

specialized cells of the immune system occurs whenever tissue is

infected or damaged as for example when you have a pimple or

more seriously suffer a heart attack The latter condition is called

sterile inflammation which happens in absence of infection by a

pathogen and when it goes awry it contributes to a wide range of

seemingly unrelated diseases from Alzheimer‟s disease to diabetes to

cancer

Inflammation is the primary protective response of the body to any

infection or injury However as our common experience shows the

inflammation after being triggered goes away of its own a process

known as resolution However in certain cases the inflammation fails

to resolve and it‟s continuation known as chronic inflammation acts as

an underlying contributor to virtually every chronic disease- a list that

besides obvious culprits such as rheumatoid arthritis and

Crohn‟s disease includes diabetes and depression along with major

killers such as heart disease and stroke and especially cancer

Therefore inflammation is a double-edged sword it protects our

body but can also harm it when it occurs in an uncontrolled manner

Over the past decade and half this role of inflammation has come

under intense scrutiny and many research groups throughout the

world are attempting to discover the underlying mechanisms which

regulate the onset and resolution of inflammation

Connection between Cancer and Inflammation

The connection between cancer and inflammation was recognized a

long time ago In fact in 1863 the renowned German pathologist

Rudolf Virchow found the presence of white blood cells cells which

mediate inflammation in tumors In 1986 the cancer biologist Harold

Dvorak of Harvard Medical School remarked that tumors are

wounds that do not heal However it is only over the last two

decades that the connections between inflammation and cancer have

transformed our understanding of how cancers develop This

transformation recognizes that the chronic inflammatory state serves

as a key mediator of the middle stages of tumor development

Cancer begins with a series of genetic changes that prompt a group

of cells to proliferate and then invade surrounding tissue the point at

which true malignancy begins Eventually some tumor cells may break

off and establish new growths (metastases) at distant sites This has

been understood for a long time But cancer biologists and

immunologists have begun to realize that the progression from

diseased tissue to full-blown invasive cancer often requires cells that

normally participate in inflammation to be diverted to the pre-

malignant tissue where they are hijacked to become co-conspirators

that aid and abet carcinogenesis As described by researchers

genetic damage is the match that lights the fire and inflammation

is the fuel that feeds it Therefore the aim of our lab is to understand

the molecular processes and mechanisms that normally prevent chronic

inflammation and thereby prevent the transition from a pre-malignant

stage to a full-blown cancer Hopefully this understanding will allow in

not-so-distant future to detect and treat cancers at the pre-malignant

stage which will make cancer treatment much easier and affordable

In addition to that this understanding will possibly be helpful in the

treatment of all chronic inflammatory diseases as the basic cellular

mechanisms underlying chronic inflammation are thought to be the

same in all cases

Inflammation in cells

At the cellular level inflammation involves two types of cells the

cells of the tissue or organ that is injured that is the inflamed cells

and the cells that mediate the inflammation that is the inflammatory

cells The latter consist mainly of cells that are originally in the blood

such as monocytes and neutrophils which migrate to the site of the

inflammation and literally eat up (phagocytose) the infecting

microorganisms or the injured cells In many cases there are

monocytes present within the inflamed tissue itself called

macrophages or big eaters which form the first line of attack on the

invading pathogen or damaged tissue Now both the inflamed cells

and the inflammatory cells secrete special signalling chemicals called

cytokines which attract more inflammatory cells to the site of the

inflammation Together with the cytokines the inflammatory cells (the

macrophages and neutrophils) also produce a variety of other factors

that allow the cells to move through the wall of the blood vessels and

then into the tissue where they attack engulf and destroy the

invading pathogen or the damaged cells It is obvious that many of

these factors such as reactive oxygen species (ROS)

metalloproteases interleukins like IL6 and blood vessel growth factors

like VEGF are toxic and if continued to be produced will damage

the healthy tissue as well That is why the production of both the

cytokines which attract these cells to the site of inflammation and

these factors which cause the death and destruction of the pathogens

ceases when the cause of the inflammation is removed and allows the

inflammation to resolve Failure to stop the production of these

inflammatory factors therefore leads to chronic inflammation and the

chronic inflammatory diseases The inflammatory factors cytokines

and others are produced by genes which are called pro-

inflammatory genes Therefore the expression of these genes that is

the production of proteins from the genes have to be tightly

regulated both in space and time

12

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 10: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

Nobel Laureate Dr Harold Varmus recognized for his research on

retroviruses and the genetic basis of cancer gave a lecture on ldquoRecent

Developments in Cancer Researchrdquo at National Institute of Immunology

(NII) New Delhi an event co-organised by NII Wellcome TrustDBT

India Alliance and Department of Biotechnology Government of

India His lecture largely gave an overview of the recent

developments challenges and the future directions in the field of

cancer research which included the current research of his group in

this area

Dr Varmus who had spent time in Bareilly as a young medical

student described cancer as a complex disease that requires

innovative research and treatment strategies At the outset Dr Varmus

introduced the key questions that drive the cancer research field- Is

cancer one disease or many diseases What makes the cancer cell

grow so stably in such an inappropriate manner How does a normal

cell become a cancer cell Providing answers to these questions

formed the backdrop of Dr Varmus‟s lecture which drew from his

research work till date and other advances in the field

Dr Varmus entered the field of cancer research in 1970s as a

postdoctoral scientist in the laboratory of Dr John J Michael Bishop at

University of California San Francisco USA the same year National

Cancer Act was signed in the country Dr Bishop and Dr Varmus

together received the Nobel Prize in Medicine and Physiology in

1989 ldquofor their discovery of the cellular origins of retroviral

oncogenesrdquo During his lecture Dr Varmus confessed standing on the

shoulders of giants of retroviral and cancer research such as Dr

Peyton Rous Dr Harry Rubin and Dr Howard Temin to ask the question

of how retroviruses transformed cells and cause tumours This question

led him to look for genes that make a normal cell behave like a

cancer cell which initially involved studying cancer-causing RNA

virusesretroviruses in animals The retrovirus that played a lead role

in Dr Varmus and his colleague‟s work was the Rous Sarcoma Virus

(RSV) discovered by Dr Peyton Rous in 1911 which he showed caused

a type of cancer in chickens Dr Varmus and colleagues set out to

prove the hypothesis that retroviruses enter host cells and capture

normal genes in that cell by inserting their DNA converting them into

cancer-causing genes or oncogenes Dr Varmus and his group

employed various cellular chemical as well as genetic tools to

establish that retroviruses can indeed act as mutagens by inserting

their DNA in host cells and turning them into cancer cells After this his

group went on to identify the cancer-causing genes present in the

virus and subsequently discovered many new oncogenes v-Src (a

gene of RSV) being the first one Following these discoveries and

subsequently many others led to the belief that the genetic basis of

cancer is highly heterogeneous Dr Varmus told us that in order to

catalogue these complexities the Cancer Genome Atlas was

established in 2005 which till today serves as a collection of the

genetic mutations responsible for different cancers

Apart from the complexity and vastness of the cancer genome

other challenges in the field according to Dr Varmus are genetic

heterogeneity and evolution of tumours due to various environmental

factors such as exposure to UV pollution tobacco use and other

environmental carcinogens that are on the rise He used the example

of renal tumor evolution which illustrates Darwin‟s theory of ldquoevolution

of speciesrdquo to show that this rapidly changing genetic repertoire can

have significant impact on diagnosis therapeutic interventions and

prognosis Another issue of concern highlighted by Dr Varmus was the

absence of suitable drugs against many common targets for cancer

such as cancer-causing RAS genes and many transcription factors

which have been shown to contribute towards cancer formation Dr

Varmus opined that lack of understanding of the underlying

complexity of resistance to cancer therapies is another roadblock in

cancer treatment He was also strongly of the opinion that there are

not enough public health interventions to prevent cancer- this he felt

needs to go hand in hand with finding cure for cancer

Dr Varmus also offered solutions to these problems He suggested

that research needs to ldquolook beyond genes and focus on patterns and

pathwaysrdquo and physiological changes taking place in cancer cells He

shared his group‟s current interest in studying ldquooncogene addictionrdquo

which is based on the premise that some oncogenes not only give rise

to cancer but also maintain the cancerous state of the cells

Interpreting the downstream effects of these cancer genes on the

pathways could be employed as a strategy to attack multiple targets

by drugs in different cancers Even though he hailed the successes of

many commonly used and extremely efficacious anti-cancer drugs

such as Gleevec Gefitinib Erlotinib but in light of growing

complexity of the disease proposed the need for adopting more

innovative drug discovery and treatment approaches Continuing on

the topic of therapeutics Dr Varmus mentioned the recent advances in

immunotherapeutic approaches to treat cancer which would require

us to understand why the otherwise combative immune system does

not kill cancer cells He suggested that gaining understanding of these

immune check points and accordingly targeting them by antibody

inhibitors could serve as one more effective treatment strategy-

another project his research group has undertaken In addition to

these therapeutic approaches Dr Varmus very strongly asserted that

ldquonot everything we talk about cancer should be about cancer therapy

but also about preventionrdquo and that this disease ought to be on the

global health agenda

Dr Varmus very eloquently concluded his talk by stating that

ldquoconfronting cancer needs a balance between grasping its complexity

and seeking simple solutionsrdquo As expected he received many

questions from the audience after his lecture on the genetics and

biology of various cancers potential use of vaccines in cancer

treatment crosstalk of cancer with other diseases and many others to

which he responded with prudence and an underlying sense of

optimism

Prior to his lecture Dr Varmus over an hour meeting with 10 young

cancer researchers discussed their work This group included the

following Wellcome TrustDBT India Alliance Fellows - Dr Reety Arora

(ECF InStem Bangalore) Dr Anjali Bajpai (ECF IIT Kanpur) Dr

Bushra Ateeq (Int Fellow IIT Kanpur) Dr Kundan Sengupta (Int Fellow

IISER Pune) and Dr Sandeep Singh (Int Fellow NIBMG Kalyani) Dr

Varmus also sought information on the India Alliance Fellowships and

was impressed by its funding model and reach

LECTURE REPORT

Recent Developments in Cancer Research By Dr Harold Varmus Nobel Prize in Medicine and Physiology Weill Cornell Medical College USA

at

National Institute of Immunology New Delhi

16 November 2015

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

7

ASK THE SCIENTIST about

The Human Brain

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

This section will bring to you answers to those burning scientific questions that you always wanted to ask the guys in the white

coat For this issue we asked some of our Fellows to shed light on the various operations of the brain

How can we measure attention

DR SUPRATIM RAY Indian Institute of Science Bangalore

Intermediate Fellow

Attention can be of different types such as sustained (vigilance)

selective (focusing at one stimulus in the presence of distractors) or

alternating (involves switching) which can be measured using a

variety of cognitive tests (such as test of everyday attention (TEA) or

Posner cuing task) For example in a classical Posner task a subject

is repeatedly shown two stimuli and cued to attend to one of them

and instructed to respond to a change in the stimulus (say by

pressing a button) The cue could be valid (change occurs at the cued

stimulus say for 80 of the trials) invalid (change occurs at the

uncued stimulus) or neutral (ambiguous) Selection attention can be

measured by comparing the accuracy and the time taken to press

the button after stimulus change (called reaction time) for different

cue types

Different components of attention such as orienting towards a

location detecting a target or maintaining vigilance are carried out

by distinct brain areas in the prefrontal and parietal lobes and some

sub-cortical structures (such as superior colliculus) Overall

performance depends not only on how these areas perform but also

how they communicate with each other and on the levels of

neuromodulators such as norepinephrine

How can we sense smell Is it possible to live without this

sense of smell

DR NIXON ABRAHAM Indian Institutes of Science Education amp

Research (IISER) Pune

Intermediate Fellow

Once Dr Lewis Thomas (1913-1993) the poet and a philosopher of

medicine who also served as the dean of the medical schools at the

New York University and Yale was asked to select seven wonders of

the modern world Olfaction (olfactory receptor cell) was fifth in his

list How does the modern fifth wonder that brings us the smell of our

surroundings ndash the good and bad work

The process of making sense of smell start by binding the odor

molecules to the olfactory receptors located in the olfactory sensory

neurons (OSNs) in the nose This binding triggers a series of signal

amplification steps which lead to electrical spikes (so called action

potentials) in OSNs This olfactory information whose intensity is

encoded by varying the number of action potentials is then passed

onto the projection neurons named mitral and tufted cells in the

olfactory bulb These projection neurons whose excitatory actions

are controlled by various inhibitory neurons carry the olfactory

information to the higher centers in the brain so that we perceive the

smell of spicy tasty food and putrid garbage ndash the good and bad

from the environment

Continued

9

Brain waves

measured by EEG

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

What is really happening inside the brain of a Schizophrenia

patient Does it look any different from a normal brain

DR VENKATASUBRAMANIAN GANESAN NIMHANS Bengaluru

Intermediate Fellow

The brain of a schizophrenia patient is reduced in overall volume

with increase in the size of the ventricles (parts of the brain that

contain cerebrospinal fluid) however certain parts like hippocampus

superior temporal gyrus and prefrontal cortex are more affected

than others Using certain advanced brain imaging research studies

(for example high resolution structural MRI functional MRI Magnetic

Resonance Spectroscopy Positron Emission Tomography and Diffusion

Tensor Imaging and similar others) subtle brain abnormalities in

structure function neurochemical profile as well as brain connectivity

have been demonstrated in several brain regions in schizophrenia

patients It is important to note that these findings are obtained

from advanced research studies that have compared brains of a

Why are the mirror neurons called the Minds mirror What do

they reflect

DR URVAKHSH MEHTA National Institute of Mental Health amp

Neurosciences (NIMHANS) Bengaluru

Early Career Fellow

Mirror neurons are specialized nerve cells that discharge when

we perform actions as well as when we observe others perform the

same action Rizzolatti and colleagues accidentally discovered them

in monkeys These neurons also get vicariously activated when we

perceive emotional states of others This unique bdquoexperience sharing‟

property of mirror neurons perhaps enables us to decipher goals

intentions and emotions of others

In several of our daily social interactions we need to take

perspectives of others decipher deception share feelings and

empathize with others The mirror neuron system is an important

brain network that helps us peek into the minds of others and try to

understand people They translate sensory information (eg

observation of an action) into a motor template which is similar to

the format an observer himself uses to perform that very action This

motor template can help us interpret the goals and feelings

underlying observed actions The definitive demonstration of mirror

neurons in humans was as recent as 2010 There is also growing

evidence of a dysfunctional mirror neuron system in psychiatric

disorders like autism and schizophrenia It is a long and exciting

future ahead to decipher spatiotemporal regulatory and genetic

underpinnings of this unique neuronal network ndash this will possibly

help understand and treat social brain disorders better

Schizophrenia

What happens if we loose our sense of smell Loss of olfaction can

be caused by many reasons ranging from viral infections to

neurodegenerative disorders As our emotions and memories are

strongly related to olfaction the loss of this sense can lead to

depressed state and even affect bonding with family members Just

imagine sipping from your morning coffee without sensing it‟s aroma

- our taste could be badly affected by losing sense of smell The

ongoing research at the nasal stem cell level might provide clinical

solutions for the disorders of the olfactory sensory neurons to regain

this wonderful sense

group of schizophrenia patients with that of healthy subjects thus

these are group averaged findings that are currently not applicable

for diagnosing schizophrenia in an individual patient in a regular

clinical setting In ldquoa specific patientrdquo one may not be able to find

any striking abnormality in the physical appearance of the brain (ie

a routine CT or MRI brain scan may not be able to identify any

obvious aberration) Several ongoing research studies are in pursuit

to identify clinically useful biomarker to diagnose schizophrenia

Find out more about Dr Ganesan‟s research on schizophrenia here

Do you have a burning scientific

question

Send them to

publicengagementwellcomedbtorg

Mirror neuron activity in the brain both when the monkey grasps an object

and when it observes the experimenter grasping the object Mirror neurons

were first discovered by Rizzolatti and colleagues when they were studying

motor actions in macque monkeys

10

INDIA ALLIANCE FELLOW

DR ROOP MALIK Senior Fellow TIFR Mumbai

Dr Roop Malik is a biophysicist based at Tata Institute of Fundamental Research Mumbai Dr Malikrsquos research focuses on nanoscale molecular motor proteins that transport material such as virus mitochondria endosomes etc inside living cells

What is your research group working on and what impact do you

hope it will have

We try to understand how the living cell achieves an organization that

is well defined yet dynamic Most of the components within a cell

have a lipid membrane boundary This boundary is fairly well

defined and visible under a microscope yet it undergoes constant

deformation to allow exchange of material between different parts

of a cell Motor proteins attach to the lipid membrane boundary and

act as transporters physically carrying cellular material from one

membrane to another in the form of a vesicular cargo How do the

motors and lipids collaborate to decide the fate of the cargo

We work on two such cargoes -- the Phagosome (may enclose

pathogens) and the Lipid droplet (encloses fat) We hope that our

research will help understand how pathogens infect us by modifying

the lipid membrane and the motors attached to it We also

investigate how fat stored inside the Lipid droplets in our liver is

circulated to different parts of the body There is a tremendous

change in the amount of fat stored in liver at every feedingfasting

cycle This is visible in the form of Lipid droplet accumulation in rat

liver sections after fasting How does the liver handle this flux of fat

What special mechanisms are required Answering these questions

may help understand the progression of fatty liver diseases

What inspired you to become a scientist

To be frank nothing in particular It was an acquired taste I started

doing experiments and gradually realised I was doing well I like the

planning that is involved in investigating the unknown and the

surprises that crop up inevitably These force you to change your

well-laid plans Thats when it gets really exciting

What role canshould scientists play in todays India

I think there is a lot of scientific freedom in India Granting agencies

are not as hawkish as in the western world This freedom is an

opportunity to do what drives you There are many young scientists in

the country who are keen to share ideas and resources We should

focus on solving difficult problems by taking advantage of this

environment If we do good science it will inspire the public

The primary job of a scientist is to do science and to do it well

Beyond that we also need to think about how science can be

propagated We have to mentor students and give them the

confidence and enthusiasm so that they go on to do better science

than we did We also have to communicate our science to common

man and facilitate them We must impress on students (and also on

their parents) that they should not look at studying Physics or Biology

or Chemistry in isolation Those who want to take up science as a

career should also understand that they must learn to deal with many

failures before something succeeds

How has Wellcome TrustDBT India Alliance Fellowship helped

you and your research (your IA experience)

I have been a Senior fellow with Wellcome Trust (UK) and then with

Wellcome Trust DBT India Alliance since 2006 The rigorous selection

process helped me fine-tune the questions that I wanted to ask The

subsequent evaluations and annual meetings helped in keeping my

research on track Last but not the least we were given a lot of

freedom in executing our science I thank the India Alliance for this

degree of trust in their Fellows This has helped me to focus on the

science

What keeps you going every day

Coffee tea and the excitement of planning and executing science

with my colleagues Regular breaks to get out into the hills for some

adventure

Find out more about

Dr Roop Malik‟s

work on motor

proteins on his

website In order to

make his research

understandable to

a wide range of

people he has put

up translation of his

research summary

in Hindi and

Marathi in addition

to Engalish on his

website

11

A Sponge Against a Sword An RNA-binding protein Prevents Chronic Inflammation and Cancer

By Dr Partho Sarothi Ray Intermediate Fellow

Anyone who has had a bruise is familiar with the redness

swelling warmth and pain that mark the site of the injury This

response known as inflammation has been recognized since ancient

times and its hallmarks were first described by the Greek physician

Galen 2000 years ago The process which is often set in motion by

specialized cells of the immune system occurs whenever tissue is

infected or damaged as for example when you have a pimple or

more seriously suffer a heart attack The latter condition is called

sterile inflammation which happens in absence of infection by a

pathogen and when it goes awry it contributes to a wide range of

seemingly unrelated diseases from Alzheimer‟s disease to diabetes to

cancer

Inflammation is the primary protective response of the body to any

infection or injury However as our common experience shows the

inflammation after being triggered goes away of its own a process

known as resolution However in certain cases the inflammation fails

to resolve and it‟s continuation known as chronic inflammation acts as

an underlying contributor to virtually every chronic disease- a list that

besides obvious culprits such as rheumatoid arthritis and

Crohn‟s disease includes diabetes and depression along with major

killers such as heart disease and stroke and especially cancer

Therefore inflammation is a double-edged sword it protects our

body but can also harm it when it occurs in an uncontrolled manner

Over the past decade and half this role of inflammation has come

under intense scrutiny and many research groups throughout the

world are attempting to discover the underlying mechanisms which

regulate the onset and resolution of inflammation

Connection between Cancer and Inflammation

The connection between cancer and inflammation was recognized a

long time ago In fact in 1863 the renowned German pathologist

Rudolf Virchow found the presence of white blood cells cells which

mediate inflammation in tumors In 1986 the cancer biologist Harold

Dvorak of Harvard Medical School remarked that tumors are

wounds that do not heal However it is only over the last two

decades that the connections between inflammation and cancer have

transformed our understanding of how cancers develop This

transformation recognizes that the chronic inflammatory state serves

as a key mediator of the middle stages of tumor development

Cancer begins with a series of genetic changes that prompt a group

of cells to proliferate and then invade surrounding tissue the point at

which true malignancy begins Eventually some tumor cells may break

off and establish new growths (metastases) at distant sites This has

been understood for a long time But cancer biologists and

immunologists have begun to realize that the progression from

diseased tissue to full-blown invasive cancer often requires cells that

normally participate in inflammation to be diverted to the pre-

malignant tissue where they are hijacked to become co-conspirators

that aid and abet carcinogenesis As described by researchers

genetic damage is the match that lights the fire and inflammation

is the fuel that feeds it Therefore the aim of our lab is to understand

the molecular processes and mechanisms that normally prevent chronic

inflammation and thereby prevent the transition from a pre-malignant

stage to a full-blown cancer Hopefully this understanding will allow in

not-so-distant future to detect and treat cancers at the pre-malignant

stage which will make cancer treatment much easier and affordable

In addition to that this understanding will possibly be helpful in the

treatment of all chronic inflammatory diseases as the basic cellular

mechanisms underlying chronic inflammation are thought to be the

same in all cases

Inflammation in cells

At the cellular level inflammation involves two types of cells the

cells of the tissue or organ that is injured that is the inflamed cells

and the cells that mediate the inflammation that is the inflammatory

cells The latter consist mainly of cells that are originally in the blood

such as monocytes and neutrophils which migrate to the site of the

inflammation and literally eat up (phagocytose) the infecting

microorganisms or the injured cells In many cases there are

monocytes present within the inflamed tissue itself called

macrophages or big eaters which form the first line of attack on the

invading pathogen or damaged tissue Now both the inflamed cells

and the inflammatory cells secrete special signalling chemicals called

cytokines which attract more inflammatory cells to the site of the

inflammation Together with the cytokines the inflammatory cells (the

macrophages and neutrophils) also produce a variety of other factors

that allow the cells to move through the wall of the blood vessels and

then into the tissue where they attack engulf and destroy the

invading pathogen or the damaged cells It is obvious that many of

these factors such as reactive oxygen species (ROS)

metalloproteases interleukins like IL6 and blood vessel growth factors

like VEGF are toxic and if continued to be produced will damage

the healthy tissue as well That is why the production of both the

cytokines which attract these cells to the site of inflammation and

these factors which cause the death and destruction of the pathogens

ceases when the cause of the inflammation is removed and allows the

inflammation to resolve Failure to stop the production of these

inflammatory factors therefore leads to chronic inflammation and the

chronic inflammatory diseases The inflammatory factors cytokines

and others are produced by genes which are called pro-

inflammatory genes Therefore the expression of these genes that is

the production of proteins from the genes have to be tightly

regulated both in space and time

12

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 11: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

ASK THE SCIENTIST about

The Human Brain

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

This section will bring to you answers to those burning scientific questions that you always wanted to ask the guys in the white

coat For this issue we asked some of our Fellows to shed light on the various operations of the brain

How can we measure attention

DR SUPRATIM RAY Indian Institute of Science Bangalore

Intermediate Fellow

Attention can be of different types such as sustained (vigilance)

selective (focusing at one stimulus in the presence of distractors) or

alternating (involves switching) which can be measured using a

variety of cognitive tests (such as test of everyday attention (TEA) or

Posner cuing task) For example in a classical Posner task a subject

is repeatedly shown two stimuli and cued to attend to one of them

and instructed to respond to a change in the stimulus (say by

pressing a button) The cue could be valid (change occurs at the cued

stimulus say for 80 of the trials) invalid (change occurs at the

uncued stimulus) or neutral (ambiguous) Selection attention can be

measured by comparing the accuracy and the time taken to press

the button after stimulus change (called reaction time) for different

cue types

Different components of attention such as orienting towards a

location detecting a target or maintaining vigilance are carried out

by distinct brain areas in the prefrontal and parietal lobes and some

sub-cortical structures (such as superior colliculus) Overall

performance depends not only on how these areas perform but also

how they communicate with each other and on the levels of

neuromodulators such as norepinephrine

How can we sense smell Is it possible to live without this

sense of smell

DR NIXON ABRAHAM Indian Institutes of Science Education amp

Research (IISER) Pune

Intermediate Fellow

Once Dr Lewis Thomas (1913-1993) the poet and a philosopher of

medicine who also served as the dean of the medical schools at the

New York University and Yale was asked to select seven wonders of

the modern world Olfaction (olfactory receptor cell) was fifth in his

list How does the modern fifth wonder that brings us the smell of our

surroundings ndash the good and bad work

The process of making sense of smell start by binding the odor

molecules to the olfactory receptors located in the olfactory sensory

neurons (OSNs) in the nose This binding triggers a series of signal

amplification steps which lead to electrical spikes (so called action

potentials) in OSNs This olfactory information whose intensity is

encoded by varying the number of action potentials is then passed

onto the projection neurons named mitral and tufted cells in the

olfactory bulb These projection neurons whose excitatory actions

are controlled by various inhibitory neurons carry the olfactory

information to the higher centers in the brain so that we perceive the

smell of spicy tasty food and putrid garbage ndash the good and bad

from the environment

Continued

9

Brain waves

measured by EEG

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

What is really happening inside the brain of a Schizophrenia

patient Does it look any different from a normal brain

DR VENKATASUBRAMANIAN GANESAN NIMHANS Bengaluru

Intermediate Fellow

The brain of a schizophrenia patient is reduced in overall volume

with increase in the size of the ventricles (parts of the brain that

contain cerebrospinal fluid) however certain parts like hippocampus

superior temporal gyrus and prefrontal cortex are more affected

than others Using certain advanced brain imaging research studies

(for example high resolution structural MRI functional MRI Magnetic

Resonance Spectroscopy Positron Emission Tomography and Diffusion

Tensor Imaging and similar others) subtle brain abnormalities in

structure function neurochemical profile as well as brain connectivity

have been demonstrated in several brain regions in schizophrenia

patients It is important to note that these findings are obtained

from advanced research studies that have compared brains of a

Why are the mirror neurons called the Minds mirror What do

they reflect

DR URVAKHSH MEHTA National Institute of Mental Health amp

Neurosciences (NIMHANS) Bengaluru

Early Career Fellow

Mirror neurons are specialized nerve cells that discharge when

we perform actions as well as when we observe others perform the

same action Rizzolatti and colleagues accidentally discovered them

in monkeys These neurons also get vicariously activated when we

perceive emotional states of others This unique bdquoexperience sharing‟

property of mirror neurons perhaps enables us to decipher goals

intentions and emotions of others

In several of our daily social interactions we need to take

perspectives of others decipher deception share feelings and

empathize with others The mirror neuron system is an important

brain network that helps us peek into the minds of others and try to

understand people They translate sensory information (eg

observation of an action) into a motor template which is similar to

the format an observer himself uses to perform that very action This

motor template can help us interpret the goals and feelings

underlying observed actions The definitive demonstration of mirror

neurons in humans was as recent as 2010 There is also growing

evidence of a dysfunctional mirror neuron system in psychiatric

disorders like autism and schizophrenia It is a long and exciting

future ahead to decipher spatiotemporal regulatory and genetic

underpinnings of this unique neuronal network ndash this will possibly

help understand and treat social brain disorders better

Schizophrenia

What happens if we loose our sense of smell Loss of olfaction can

be caused by many reasons ranging from viral infections to

neurodegenerative disorders As our emotions and memories are

strongly related to olfaction the loss of this sense can lead to

depressed state and even affect bonding with family members Just

imagine sipping from your morning coffee without sensing it‟s aroma

- our taste could be badly affected by losing sense of smell The

ongoing research at the nasal stem cell level might provide clinical

solutions for the disorders of the olfactory sensory neurons to regain

this wonderful sense

group of schizophrenia patients with that of healthy subjects thus

these are group averaged findings that are currently not applicable

for diagnosing schizophrenia in an individual patient in a regular

clinical setting In ldquoa specific patientrdquo one may not be able to find

any striking abnormality in the physical appearance of the brain (ie

a routine CT or MRI brain scan may not be able to identify any

obvious aberration) Several ongoing research studies are in pursuit

to identify clinically useful biomarker to diagnose schizophrenia

Find out more about Dr Ganesan‟s research on schizophrenia here

Do you have a burning scientific

question

Send them to

publicengagementwellcomedbtorg

Mirror neuron activity in the brain both when the monkey grasps an object

and when it observes the experimenter grasping the object Mirror neurons

were first discovered by Rizzolatti and colleagues when they were studying

motor actions in macque monkeys

10

INDIA ALLIANCE FELLOW

DR ROOP MALIK Senior Fellow TIFR Mumbai

Dr Roop Malik is a biophysicist based at Tata Institute of Fundamental Research Mumbai Dr Malikrsquos research focuses on nanoscale molecular motor proteins that transport material such as virus mitochondria endosomes etc inside living cells

What is your research group working on and what impact do you

hope it will have

We try to understand how the living cell achieves an organization that

is well defined yet dynamic Most of the components within a cell

have a lipid membrane boundary This boundary is fairly well

defined and visible under a microscope yet it undergoes constant

deformation to allow exchange of material between different parts

of a cell Motor proteins attach to the lipid membrane boundary and

act as transporters physically carrying cellular material from one

membrane to another in the form of a vesicular cargo How do the

motors and lipids collaborate to decide the fate of the cargo

We work on two such cargoes -- the Phagosome (may enclose

pathogens) and the Lipid droplet (encloses fat) We hope that our

research will help understand how pathogens infect us by modifying

the lipid membrane and the motors attached to it We also

investigate how fat stored inside the Lipid droplets in our liver is

circulated to different parts of the body There is a tremendous

change in the amount of fat stored in liver at every feedingfasting

cycle This is visible in the form of Lipid droplet accumulation in rat

liver sections after fasting How does the liver handle this flux of fat

What special mechanisms are required Answering these questions

may help understand the progression of fatty liver diseases

What inspired you to become a scientist

To be frank nothing in particular It was an acquired taste I started

doing experiments and gradually realised I was doing well I like the

planning that is involved in investigating the unknown and the

surprises that crop up inevitably These force you to change your

well-laid plans Thats when it gets really exciting

What role canshould scientists play in todays India

I think there is a lot of scientific freedom in India Granting agencies

are not as hawkish as in the western world This freedom is an

opportunity to do what drives you There are many young scientists in

the country who are keen to share ideas and resources We should

focus on solving difficult problems by taking advantage of this

environment If we do good science it will inspire the public

The primary job of a scientist is to do science and to do it well

Beyond that we also need to think about how science can be

propagated We have to mentor students and give them the

confidence and enthusiasm so that they go on to do better science

than we did We also have to communicate our science to common

man and facilitate them We must impress on students (and also on

their parents) that they should not look at studying Physics or Biology

or Chemistry in isolation Those who want to take up science as a

career should also understand that they must learn to deal with many

failures before something succeeds

How has Wellcome TrustDBT India Alliance Fellowship helped

you and your research (your IA experience)

I have been a Senior fellow with Wellcome Trust (UK) and then with

Wellcome Trust DBT India Alliance since 2006 The rigorous selection

process helped me fine-tune the questions that I wanted to ask The

subsequent evaluations and annual meetings helped in keeping my

research on track Last but not the least we were given a lot of

freedom in executing our science I thank the India Alliance for this

degree of trust in their Fellows This has helped me to focus on the

science

What keeps you going every day

Coffee tea and the excitement of planning and executing science

with my colleagues Regular breaks to get out into the hills for some

adventure

Find out more about

Dr Roop Malik‟s

work on motor

proteins on his

website In order to

make his research

understandable to

a wide range of

people he has put

up translation of his

research summary

in Hindi and

Marathi in addition

to Engalish on his

website

11

A Sponge Against a Sword An RNA-binding protein Prevents Chronic Inflammation and Cancer

By Dr Partho Sarothi Ray Intermediate Fellow

Anyone who has had a bruise is familiar with the redness

swelling warmth and pain that mark the site of the injury This

response known as inflammation has been recognized since ancient

times and its hallmarks were first described by the Greek physician

Galen 2000 years ago The process which is often set in motion by

specialized cells of the immune system occurs whenever tissue is

infected or damaged as for example when you have a pimple or

more seriously suffer a heart attack The latter condition is called

sterile inflammation which happens in absence of infection by a

pathogen and when it goes awry it contributes to a wide range of

seemingly unrelated diseases from Alzheimer‟s disease to diabetes to

cancer

Inflammation is the primary protective response of the body to any

infection or injury However as our common experience shows the

inflammation after being triggered goes away of its own a process

known as resolution However in certain cases the inflammation fails

to resolve and it‟s continuation known as chronic inflammation acts as

an underlying contributor to virtually every chronic disease- a list that

besides obvious culprits such as rheumatoid arthritis and

Crohn‟s disease includes diabetes and depression along with major

killers such as heart disease and stroke and especially cancer

Therefore inflammation is a double-edged sword it protects our

body but can also harm it when it occurs in an uncontrolled manner

Over the past decade and half this role of inflammation has come

under intense scrutiny and many research groups throughout the

world are attempting to discover the underlying mechanisms which

regulate the onset and resolution of inflammation

Connection between Cancer and Inflammation

The connection between cancer and inflammation was recognized a

long time ago In fact in 1863 the renowned German pathologist

Rudolf Virchow found the presence of white blood cells cells which

mediate inflammation in tumors In 1986 the cancer biologist Harold

Dvorak of Harvard Medical School remarked that tumors are

wounds that do not heal However it is only over the last two

decades that the connections between inflammation and cancer have

transformed our understanding of how cancers develop This

transformation recognizes that the chronic inflammatory state serves

as a key mediator of the middle stages of tumor development

Cancer begins with a series of genetic changes that prompt a group

of cells to proliferate and then invade surrounding tissue the point at

which true malignancy begins Eventually some tumor cells may break

off and establish new growths (metastases) at distant sites This has

been understood for a long time But cancer biologists and

immunologists have begun to realize that the progression from

diseased tissue to full-blown invasive cancer often requires cells that

normally participate in inflammation to be diverted to the pre-

malignant tissue where they are hijacked to become co-conspirators

that aid and abet carcinogenesis As described by researchers

genetic damage is the match that lights the fire and inflammation

is the fuel that feeds it Therefore the aim of our lab is to understand

the molecular processes and mechanisms that normally prevent chronic

inflammation and thereby prevent the transition from a pre-malignant

stage to a full-blown cancer Hopefully this understanding will allow in

not-so-distant future to detect and treat cancers at the pre-malignant

stage which will make cancer treatment much easier and affordable

In addition to that this understanding will possibly be helpful in the

treatment of all chronic inflammatory diseases as the basic cellular

mechanisms underlying chronic inflammation are thought to be the

same in all cases

Inflammation in cells

At the cellular level inflammation involves two types of cells the

cells of the tissue or organ that is injured that is the inflamed cells

and the cells that mediate the inflammation that is the inflammatory

cells The latter consist mainly of cells that are originally in the blood

such as monocytes and neutrophils which migrate to the site of the

inflammation and literally eat up (phagocytose) the infecting

microorganisms or the injured cells In many cases there are

monocytes present within the inflamed tissue itself called

macrophages or big eaters which form the first line of attack on the

invading pathogen or damaged tissue Now both the inflamed cells

and the inflammatory cells secrete special signalling chemicals called

cytokines which attract more inflammatory cells to the site of the

inflammation Together with the cytokines the inflammatory cells (the

macrophages and neutrophils) also produce a variety of other factors

that allow the cells to move through the wall of the blood vessels and

then into the tissue where they attack engulf and destroy the

invading pathogen or the damaged cells It is obvious that many of

these factors such as reactive oxygen species (ROS)

metalloproteases interleukins like IL6 and blood vessel growth factors

like VEGF are toxic and if continued to be produced will damage

the healthy tissue as well That is why the production of both the

cytokines which attract these cells to the site of inflammation and

these factors which cause the death and destruction of the pathogens

ceases when the cause of the inflammation is removed and allows the

inflammation to resolve Failure to stop the production of these

inflammatory factors therefore leads to chronic inflammation and the

chronic inflammatory diseases The inflammatory factors cytokines

and others are produced by genes which are called pro-

inflammatory genes Therefore the expression of these genes that is

the production of proteins from the genes have to be tightly

regulated both in space and time

12

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 12: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

INDIA ALLIANCE

PUBLIC ENGAGEMENT CORNER

What is really happening inside the brain of a Schizophrenia

patient Does it look any different from a normal brain

DR VENKATASUBRAMANIAN GANESAN NIMHANS Bengaluru

Intermediate Fellow

The brain of a schizophrenia patient is reduced in overall volume

with increase in the size of the ventricles (parts of the brain that

contain cerebrospinal fluid) however certain parts like hippocampus

superior temporal gyrus and prefrontal cortex are more affected

than others Using certain advanced brain imaging research studies

(for example high resolution structural MRI functional MRI Magnetic

Resonance Spectroscopy Positron Emission Tomography and Diffusion

Tensor Imaging and similar others) subtle brain abnormalities in

structure function neurochemical profile as well as brain connectivity

have been demonstrated in several brain regions in schizophrenia

patients It is important to note that these findings are obtained

from advanced research studies that have compared brains of a

Why are the mirror neurons called the Minds mirror What do

they reflect

DR URVAKHSH MEHTA National Institute of Mental Health amp

Neurosciences (NIMHANS) Bengaluru

Early Career Fellow

Mirror neurons are specialized nerve cells that discharge when

we perform actions as well as when we observe others perform the

same action Rizzolatti and colleagues accidentally discovered them

in monkeys These neurons also get vicariously activated when we

perceive emotional states of others This unique bdquoexperience sharing‟

property of mirror neurons perhaps enables us to decipher goals

intentions and emotions of others

In several of our daily social interactions we need to take

perspectives of others decipher deception share feelings and

empathize with others The mirror neuron system is an important

brain network that helps us peek into the minds of others and try to

understand people They translate sensory information (eg

observation of an action) into a motor template which is similar to

the format an observer himself uses to perform that very action This

motor template can help us interpret the goals and feelings

underlying observed actions The definitive demonstration of mirror

neurons in humans was as recent as 2010 There is also growing

evidence of a dysfunctional mirror neuron system in psychiatric

disorders like autism and schizophrenia It is a long and exciting

future ahead to decipher spatiotemporal regulatory and genetic

underpinnings of this unique neuronal network ndash this will possibly

help understand and treat social brain disorders better

Schizophrenia

What happens if we loose our sense of smell Loss of olfaction can

be caused by many reasons ranging from viral infections to

neurodegenerative disorders As our emotions and memories are

strongly related to olfaction the loss of this sense can lead to

depressed state and even affect bonding with family members Just

imagine sipping from your morning coffee without sensing it‟s aroma

- our taste could be badly affected by losing sense of smell The

ongoing research at the nasal stem cell level might provide clinical

solutions for the disorders of the olfactory sensory neurons to regain

this wonderful sense

group of schizophrenia patients with that of healthy subjects thus

these are group averaged findings that are currently not applicable

for diagnosing schizophrenia in an individual patient in a regular

clinical setting In ldquoa specific patientrdquo one may not be able to find

any striking abnormality in the physical appearance of the brain (ie

a routine CT or MRI brain scan may not be able to identify any

obvious aberration) Several ongoing research studies are in pursuit

to identify clinically useful biomarker to diagnose schizophrenia

Find out more about Dr Ganesan‟s research on schizophrenia here

Do you have a burning scientific

question

Send them to

publicengagementwellcomedbtorg

Mirror neuron activity in the brain both when the monkey grasps an object

and when it observes the experimenter grasping the object Mirror neurons

were first discovered by Rizzolatti and colleagues when they were studying

motor actions in macque monkeys

10

INDIA ALLIANCE FELLOW

DR ROOP MALIK Senior Fellow TIFR Mumbai

Dr Roop Malik is a biophysicist based at Tata Institute of Fundamental Research Mumbai Dr Malikrsquos research focuses on nanoscale molecular motor proteins that transport material such as virus mitochondria endosomes etc inside living cells

What is your research group working on and what impact do you

hope it will have

We try to understand how the living cell achieves an organization that

is well defined yet dynamic Most of the components within a cell

have a lipid membrane boundary This boundary is fairly well

defined and visible under a microscope yet it undergoes constant

deformation to allow exchange of material between different parts

of a cell Motor proteins attach to the lipid membrane boundary and

act as transporters physically carrying cellular material from one

membrane to another in the form of a vesicular cargo How do the

motors and lipids collaborate to decide the fate of the cargo

We work on two such cargoes -- the Phagosome (may enclose

pathogens) and the Lipid droplet (encloses fat) We hope that our

research will help understand how pathogens infect us by modifying

the lipid membrane and the motors attached to it We also

investigate how fat stored inside the Lipid droplets in our liver is

circulated to different parts of the body There is a tremendous

change in the amount of fat stored in liver at every feedingfasting

cycle This is visible in the form of Lipid droplet accumulation in rat

liver sections after fasting How does the liver handle this flux of fat

What special mechanisms are required Answering these questions

may help understand the progression of fatty liver diseases

What inspired you to become a scientist

To be frank nothing in particular It was an acquired taste I started

doing experiments and gradually realised I was doing well I like the

planning that is involved in investigating the unknown and the

surprises that crop up inevitably These force you to change your

well-laid plans Thats when it gets really exciting

What role canshould scientists play in todays India

I think there is a lot of scientific freedom in India Granting agencies

are not as hawkish as in the western world This freedom is an

opportunity to do what drives you There are many young scientists in

the country who are keen to share ideas and resources We should

focus on solving difficult problems by taking advantage of this

environment If we do good science it will inspire the public

The primary job of a scientist is to do science and to do it well

Beyond that we also need to think about how science can be

propagated We have to mentor students and give them the

confidence and enthusiasm so that they go on to do better science

than we did We also have to communicate our science to common

man and facilitate them We must impress on students (and also on

their parents) that they should not look at studying Physics or Biology

or Chemistry in isolation Those who want to take up science as a

career should also understand that they must learn to deal with many

failures before something succeeds

How has Wellcome TrustDBT India Alliance Fellowship helped

you and your research (your IA experience)

I have been a Senior fellow with Wellcome Trust (UK) and then with

Wellcome Trust DBT India Alliance since 2006 The rigorous selection

process helped me fine-tune the questions that I wanted to ask The

subsequent evaluations and annual meetings helped in keeping my

research on track Last but not the least we were given a lot of

freedom in executing our science I thank the India Alliance for this

degree of trust in their Fellows This has helped me to focus on the

science

What keeps you going every day

Coffee tea and the excitement of planning and executing science

with my colleagues Regular breaks to get out into the hills for some

adventure

Find out more about

Dr Roop Malik‟s

work on motor

proteins on his

website In order to

make his research

understandable to

a wide range of

people he has put

up translation of his

research summary

in Hindi and

Marathi in addition

to Engalish on his

website

11

A Sponge Against a Sword An RNA-binding protein Prevents Chronic Inflammation and Cancer

By Dr Partho Sarothi Ray Intermediate Fellow

Anyone who has had a bruise is familiar with the redness

swelling warmth and pain that mark the site of the injury This

response known as inflammation has been recognized since ancient

times and its hallmarks were first described by the Greek physician

Galen 2000 years ago The process which is often set in motion by

specialized cells of the immune system occurs whenever tissue is

infected or damaged as for example when you have a pimple or

more seriously suffer a heart attack The latter condition is called

sterile inflammation which happens in absence of infection by a

pathogen and when it goes awry it contributes to a wide range of

seemingly unrelated diseases from Alzheimer‟s disease to diabetes to

cancer

Inflammation is the primary protective response of the body to any

infection or injury However as our common experience shows the

inflammation after being triggered goes away of its own a process

known as resolution However in certain cases the inflammation fails

to resolve and it‟s continuation known as chronic inflammation acts as

an underlying contributor to virtually every chronic disease- a list that

besides obvious culprits such as rheumatoid arthritis and

Crohn‟s disease includes diabetes and depression along with major

killers such as heart disease and stroke and especially cancer

Therefore inflammation is a double-edged sword it protects our

body but can also harm it when it occurs in an uncontrolled manner

Over the past decade and half this role of inflammation has come

under intense scrutiny and many research groups throughout the

world are attempting to discover the underlying mechanisms which

regulate the onset and resolution of inflammation

Connection between Cancer and Inflammation

The connection between cancer and inflammation was recognized a

long time ago In fact in 1863 the renowned German pathologist

Rudolf Virchow found the presence of white blood cells cells which

mediate inflammation in tumors In 1986 the cancer biologist Harold

Dvorak of Harvard Medical School remarked that tumors are

wounds that do not heal However it is only over the last two

decades that the connections between inflammation and cancer have

transformed our understanding of how cancers develop This

transformation recognizes that the chronic inflammatory state serves

as a key mediator of the middle stages of tumor development

Cancer begins with a series of genetic changes that prompt a group

of cells to proliferate and then invade surrounding tissue the point at

which true malignancy begins Eventually some tumor cells may break

off and establish new growths (metastases) at distant sites This has

been understood for a long time But cancer biologists and

immunologists have begun to realize that the progression from

diseased tissue to full-blown invasive cancer often requires cells that

normally participate in inflammation to be diverted to the pre-

malignant tissue where they are hijacked to become co-conspirators

that aid and abet carcinogenesis As described by researchers

genetic damage is the match that lights the fire and inflammation

is the fuel that feeds it Therefore the aim of our lab is to understand

the molecular processes and mechanisms that normally prevent chronic

inflammation and thereby prevent the transition from a pre-malignant

stage to a full-blown cancer Hopefully this understanding will allow in

not-so-distant future to detect and treat cancers at the pre-malignant

stage which will make cancer treatment much easier and affordable

In addition to that this understanding will possibly be helpful in the

treatment of all chronic inflammatory diseases as the basic cellular

mechanisms underlying chronic inflammation are thought to be the

same in all cases

Inflammation in cells

At the cellular level inflammation involves two types of cells the

cells of the tissue or organ that is injured that is the inflamed cells

and the cells that mediate the inflammation that is the inflammatory

cells The latter consist mainly of cells that are originally in the blood

such as monocytes and neutrophils which migrate to the site of the

inflammation and literally eat up (phagocytose) the infecting

microorganisms or the injured cells In many cases there are

monocytes present within the inflamed tissue itself called

macrophages or big eaters which form the first line of attack on the

invading pathogen or damaged tissue Now both the inflamed cells

and the inflammatory cells secrete special signalling chemicals called

cytokines which attract more inflammatory cells to the site of the

inflammation Together with the cytokines the inflammatory cells (the

macrophages and neutrophils) also produce a variety of other factors

that allow the cells to move through the wall of the blood vessels and

then into the tissue where they attack engulf and destroy the

invading pathogen or the damaged cells It is obvious that many of

these factors such as reactive oxygen species (ROS)

metalloproteases interleukins like IL6 and blood vessel growth factors

like VEGF are toxic and if continued to be produced will damage

the healthy tissue as well That is why the production of both the

cytokines which attract these cells to the site of inflammation and

these factors which cause the death and destruction of the pathogens

ceases when the cause of the inflammation is removed and allows the

inflammation to resolve Failure to stop the production of these

inflammatory factors therefore leads to chronic inflammation and the

chronic inflammatory diseases The inflammatory factors cytokines

and others are produced by genes which are called pro-

inflammatory genes Therefore the expression of these genes that is

the production of proteins from the genes have to be tightly

regulated both in space and time

12

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 13: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

INDIA ALLIANCE FELLOW

DR ROOP MALIK Senior Fellow TIFR Mumbai

Dr Roop Malik is a biophysicist based at Tata Institute of Fundamental Research Mumbai Dr Malikrsquos research focuses on nanoscale molecular motor proteins that transport material such as virus mitochondria endosomes etc inside living cells

What is your research group working on and what impact do you

hope it will have

We try to understand how the living cell achieves an organization that

is well defined yet dynamic Most of the components within a cell

have a lipid membrane boundary This boundary is fairly well

defined and visible under a microscope yet it undergoes constant

deformation to allow exchange of material between different parts

of a cell Motor proteins attach to the lipid membrane boundary and

act as transporters physically carrying cellular material from one

membrane to another in the form of a vesicular cargo How do the

motors and lipids collaborate to decide the fate of the cargo

We work on two such cargoes -- the Phagosome (may enclose

pathogens) and the Lipid droplet (encloses fat) We hope that our

research will help understand how pathogens infect us by modifying

the lipid membrane and the motors attached to it We also

investigate how fat stored inside the Lipid droplets in our liver is

circulated to different parts of the body There is a tremendous

change in the amount of fat stored in liver at every feedingfasting

cycle This is visible in the form of Lipid droplet accumulation in rat

liver sections after fasting How does the liver handle this flux of fat

What special mechanisms are required Answering these questions

may help understand the progression of fatty liver diseases

What inspired you to become a scientist

To be frank nothing in particular It was an acquired taste I started

doing experiments and gradually realised I was doing well I like the

planning that is involved in investigating the unknown and the

surprises that crop up inevitably These force you to change your

well-laid plans Thats when it gets really exciting

What role canshould scientists play in todays India

I think there is a lot of scientific freedom in India Granting agencies

are not as hawkish as in the western world This freedom is an

opportunity to do what drives you There are many young scientists in

the country who are keen to share ideas and resources We should

focus on solving difficult problems by taking advantage of this

environment If we do good science it will inspire the public

The primary job of a scientist is to do science and to do it well

Beyond that we also need to think about how science can be

propagated We have to mentor students and give them the

confidence and enthusiasm so that they go on to do better science

than we did We also have to communicate our science to common

man and facilitate them We must impress on students (and also on

their parents) that they should not look at studying Physics or Biology

or Chemistry in isolation Those who want to take up science as a

career should also understand that they must learn to deal with many

failures before something succeeds

How has Wellcome TrustDBT India Alliance Fellowship helped

you and your research (your IA experience)

I have been a Senior fellow with Wellcome Trust (UK) and then with

Wellcome Trust DBT India Alliance since 2006 The rigorous selection

process helped me fine-tune the questions that I wanted to ask The

subsequent evaluations and annual meetings helped in keeping my

research on track Last but not the least we were given a lot of

freedom in executing our science I thank the India Alliance for this

degree of trust in their Fellows This has helped me to focus on the

science

What keeps you going every day

Coffee tea and the excitement of planning and executing science

with my colleagues Regular breaks to get out into the hills for some

adventure

Find out more about

Dr Roop Malik‟s

work on motor

proteins on his

website In order to

make his research

understandable to

a wide range of

people he has put

up translation of his

research summary

in Hindi and

Marathi in addition

to Engalish on his

website

11

A Sponge Against a Sword An RNA-binding protein Prevents Chronic Inflammation and Cancer

By Dr Partho Sarothi Ray Intermediate Fellow

Anyone who has had a bruise is familiar with the redness

swelling warmth and pain that mark the site of the injury This

response known as inflammation has been recognized since ancient

times and its hallmarks were first described by the Greek physician

Galen 2000 years ago The process which is often set in motion by

specialized cells of the immune system occurs whenever tissue is

infected or damaged as for example when you have a pimple or

more seriously suffer a heart attack The latter condition is called

sterile inflammation which happens in absence of infection by a

pathogen and when it goes awry it contributes to a wide range of

seemingly unrelated diseases from Alzheimer‟s disease to diabetes to

cancer

Inflammation is the primary protective response of the body to any

infection or injury However as our common experience shows the

inflammation after being triggered goes away of its own a process

known as resolution However in certain cases the inflammation fails

to resolve and it‟s continuation known as chronic inflammation acts as

an underlying contributor to virtually every chronic disease- a list that

besides obvious culprits such as rheumatoid arthritis and

Crohn‟s disease includes diabetes and depression along with major

killers such as heart disease and stroke and especially cancer

Therefore inflammation is a double-edged sword it protects our

body but can also harm it when it occurs in an uncontrolled manner

Over the past decade and half this role of inflammation has come

under intense scrutiny and many research groups throughout the

world are attempting to discover the underlying mechanisms which

regulate the onset and resolution of inflammation

Connection between Cancer and Inflammation

The connection between cancer and inflammation was recognized a

long time ago In fact in 1863 the renowned German pathologist

Rudolf Virchow found the presence of white blood cells cells which

mediate inflammation in tumors In 1986 the cancer biologist Harold

Dvorak of Harvard Medical School remarked that tumors are

wounds that do not heal However it is only over the last two

decades that the connections between inflammation and cancer have

transformed our understanding of how cancers develop This

transformation recognizes that the chronic inflammatory state serves

as a key mediator of the middle stages of tumor development

Cancer begins with a series of genetic changes that prompt a group

of cells to proliferate and then invade surrounding tissue the point at

which true malignancy begins Eventually some tumor cells may break

off and establish new growths (metastases) at distant sites This has

been understood for a long time But cancer biologists and

immunologists have begun to realize that the progression from

diseased tissue to full-blown invasive cancer often requires cells that

normally participate in inflammation to be diverted to the pre-

malignant tissue where they are hijacked to become co-conspirators

that aid and abet carcinogenesis As described by researchers

genetic damage is the match that lights the fire and inflammation

is the fuel that feeds it Therefore the aim of our lab is to understand

the molecular processes and mechanisms that normally prevent chronic

inflammation and thereby prevent the transition from a pre-malignant

stage to a full-blown cancer Hopefully this understanding will allow in

not-so-distant future to detect and treat cancers at the pre-malignant

stage which will make cancer treatment much easier and affordable

In addition to that this understanding will possibly be helpful in the

treatment of all chronic inflammatory diseases as the basic cellular

mechanisms underlying chronic inflammation are thought to be the

same in all cases

Inflammation in cells

At the cellular level inflammation involves two types of cells the

cells of the tissue or organ that is injured that is the inflamed cells

and the cells that mediate the inflammation that is the inflammatory

cells The latter consist mainly of cells that are originally in the blood

such as monocytes and neutrophils which migrate to the site of the

inflammation and literally eat up (phagocytose) the infecting

microorganisms or the injured cells In many cases there are

monocytes present within the inflamed tissue itself called

macrophages or big eaters which form the first line of attack on the

invading pathogen or damaged tissue Now both the inflamed cells

and the inflammatory cells secrete special signalling chemicals called

cytokines which attract more inflammatory cells to the site of the

inflammation Together with the cytokines the inflammatory cells (the

macrophages and neutrophils) also produce a variety of other factors

that allow the cells to move through the wall of the blood vessels and

then into the tissue where they attack engulf and destroy the

invading pathogen or the damaged cells It is obvious that many of

these factors such as reactive oxygen species (ROS)

metalloproteases interleukins like IL6 and blood vessel growth factors

like VEGF are toxic and if continued to be produced will damage

the healthy tissue as well That is why the production of both the

cytokines which attract these cells to the site of inflammation and

these factors which cause the death and destruction of the pathogens

ceases when the cause of the inflammation is removed and allows the

inflammation to resolve Failure to stop the production of these

inflammatory factors therefore leads to chronic inflammation and the

chronic inflammatory diseases The inflammatory factors cytokines

and others are produced by genes which are called pro-

inflammatory genes Therefore the expression of these genes that is

the production of proteins from the genes have to be tightly

regulated both in space and time

12

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 14: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

A Sponge Against a Sword An RNA-binding protein Prevents Chronic Inflammation and Cancer

By Dr Partho Sarothi Ray Intermediate Fellow

Anyone who has had a bruise is familiar with the redness

swelling warmth and pain that mark the site of the injury This

response known as inflammation has been recognized since ancient

times and its hallmarks were first described by the Greek physician

Galen 2000 years ago The process which is often set in motion by

specialized cells of the immune system occurs whenever tissue is

infected or damaged as for example when you have a pimple or

more seriously suffer a heart attack The latter condition is called

sterile inflammation which happens in absence of infection by a

pathogen and when it goes awry it contributes to a wide range of

seemingly unrelated diseases from Alzheimer‟s disease to diabetes to

cancer

Inflammation is the primary protective response of the body to any

infection or injury However as our common experience shows the

inflammation after being triggered goes away of its own a process

known as resolution However in certain cases the inflammation fails

to resolve and it‟s continuation known as chronic inflammation acts as

an underlying contributor to virtually every chronic disease- a list that

besides obvious culprits such as rheumatoid arthritis and

Crohn‟s disease includes diabetes and depression along with major

killers such as heart disease and stroke and especially cancer

Therefore inflammation is a double-edged sword it protects our

body but can also harm it when it occurs in an uncontrolled manner

Over the past decade and half this role of inflammation has come

under intense scrutiny and many research groups throughout the

world are attempting to discover the underlying mechanisms which

regulate the onset and resolution of inflammation

Connection between Cancer and Inflammation

The connection between cancer and inflammation was recognized a

long time ago In fact in 1863 the renowned German pathologist

Rudolf Virchow found the presence of white blood cells cells which

mediate inflammation in tumors In 1986 the cancer biologist Harold

Dvorak of Harvard Medical School remarked that tumors are

wounds that do not heal However it is only over the last two

decades that the connections between inflammation and cancer have

transformed our understanding of how cancers develop This

transformation recognizes that the chronic inflammatory state serves

as a key mediator of the middle stages of tumor development

Cancer begins with a series of genetic changes that prompt a group

of cells to proliferate and then invade surrounding tissue the point at

which true malignancy begins Eventually some tumor cells may break

off and establish new growths (metastases) at distant sites This has

been understood for a long time But cancer biologists and

immunologists have begun to realize that the progression from

diseased tissue to full-blown invasive cancer often requires cells that

normally participate in inflammation to be diverted to the pre-

malignant tissue where they are hijacked to become co-conspirators

that aid and abet carcinogenesis As described by researchers

genetic damage is the match that lights the fire and inflammation

is the fuel that feeds it Therefore the aim of our lab is to understand

the molecular processes and mechanisms that normally prevent chronic

inflammation and thereby prevent the transition from a pre-malignant

stage to a full-blown cancer Hopefully this understanding will allow in

not-so-distant future to detect and treat cancers at the pre-malignant

stage which will make cancer treatment much easier and affordable

In addition to that this understanding will possibly be helpful in the

treatment of all chronic inflammatory diseases as the basic cellular

mechanisms underlying chronic inflammation are thought to be the

same in all cases

Inflammation in cells

At the cellular level inflammation involves two types of cells the

cells of the tissue or organ that is injured that is the inflamed cells

and the cells that mediate the inflammation that is the inflammatory

cells The latter consist mainly of cells that are originally in the blood

such as monocytes and neutrophils which migrate to the site of the

inflammation and literally eat up (phagocytose) the infecting

microorganisms or the injured cells In many cases there are

monocytes present within the inflamed tissue itself called

macrophages or big eaters which form the first line of attack on the

invading pathogen or damaged tissue Now both the inflamed cells

and the inflammatory cells secrete special signalling chemicals called

cytokines which attract more inflammatory cells to the site of the

inflammation Together with the cytokines the inflammatory cells (the

macrophages and neutrophils) also produce a variety of other factors

that allow the cells to move through the wall of the blood vessels and

then into the tissue where they attack engulf and destroy the

invading pathogen or the damaged cells It is obvious that many of

these factors such as reactive oxygen species (ROS)

metalloproteases interleukins like IL6 and blood vessel growth factors

like VEGF are toxic and if continued to be produced will damage

the healthy tissue as well That is why the production of both the

cytokines which attract these cells to the site of inflammation and

these factors which cause the death and destruction of the pathogens

ceases when the cause of the inflammation is removed and allows the

inflammation to resolve Failure to stop the production of these

inflammatory factors therefore leads to chronic inflammation and the

chronic inflammatory diseases The inflammatory factors cytokines

and others are produced by genes which are called pro-

inflammatory genes Therefore the expression of these genes that is

the production of proteins from the genes have to be tightly

regulated both in space and time

12

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 15: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

A Sponge Against a Sword By Dr Partho Sarothi Ray

They should express as long as the cause of the inflammation is there

and at the site of inflammation only and then stop to allow the

resolution of inflammation Gene expression is regulated in many

ways and of particular importance in the case of pro-inflammatory

genes is the regulation of protein synthesis what is called as

translation Our lab therefore studies the regulation of translation

of pro-inflammatory genes and attempts to understand how such

regulation might fail under certain circumstances which could lead

to sustained expression of pro-inflammatory genes giving rise to

chronic inflammation

The process of translation involves the binding of various proteins

called translation initiation factors to the messenger RNA (mRNA)

which ultimately recruits the mRNA into the translation factory the

ribosome to synthesize the protein encoded by that particular mRNA

This process is regulated mainly by two types of molecules a set of

proteins called RNA-binding proteins and a set of small RNAs called

microRNAs The concentration of both these proteins and microRNAs in

cells and how they function will therefore determine how translation

is regulated The concentration of many of these proteins and

microRNAs are known to change in chronic inflammatory conditions

and cancers thereby affecting the regulation of proinflammatory

genes and ultimately the process of inflammation resolution Our lab

therefore studies the cross-talk between these RNA-binding proteins

and microRNAs to understand their role in the regulation of pro-

inflammatory genes

Recently our work has focused on the regulation of translation of a

particular pro-inflammatory gene called Programmed Cell Death 4 or

PDCD4 This gene plays a crucial role in preventing chronic

inflammation from turning into cancer It is produced by cells when

they are inflamed but then it prevents the uncontrolled multiplication

of these cells to avert the transition to cancer Therefore it acts as a

tumor-suppressor gene It has been found that it is absent or fails to

function in various cancers One major reason it is absent in many

cancers is that its translation is stopped by a microRNA called miR-

21 This microRNA is well known to be highly present in a variety of

cancers and therefore acts as an oncogene This type of microRNAs

which are highly expressed in tumors and prevent the expression of

tumor-suppressor genes are therefore called as oncomiRs

Interestingly we found that an RNA-binding protein known as HuR

can counteract the effect of miR-21 and thereby prevent the

concentration of PDCD4 from going down This means that in a

condition such as a chronic inflammatory state when miR-21 level is

high then high level of HuR can prevent the stoppage in the

production of PDCD4 and thereby help in preventing the transition to

malignancy Now how do cells achieve the high level of HuR

Interestingly we found that under inflammatory conditions cells just

dont produce more HuR rather they transfer the HuR which is

normally present within the nucleus of cells into the cytoplasm where

translation actually happens and where it counteracts the effect of

miR-21

Now when we tried to find the mechanism by which HuR counteracts

miR-21 we found a surprising new phenomenon HuR on one hand

binds to the mRNA of PDCD4 and prevents the binding of miR-21 On

the other hand it directly binds to miR-21 and prevents its interaction

with the PDCD4 mRNA These RNA-binding proteins are known to bind

to mRNAs but their binding to microRNAs was not well known

Therefore HuRs ability to bind to and sequester miR-21 and

preventing its repressive action on PDCD4 translation suggests a

novel way in which HuR can function like a microRNA sponge (Fig 1)

This microRNA sponging function of HuR is therefore a mechanism

which will prevent the level of PDCD4 from going down in

inflammatory conditions and thereby prevent the uncontrolled cell

division which is the hallmark of the transition from chronic

inflammation to cancer This novel function has been described in a

paper from our lab which was published in the journal Oncogene

(Poria DK et al Oncogene 2015) This phenomenon now tells us that

when genetic mutations or some other stress might increase the level

of miR-21 and thereby induce a pre-malignant condition HuR will

move out from the cell nucleus into the cytoplasm sponge up the miR-

21 and prevent the level of tumor suppressors like PDCD4 from going

down This will be a major way in which the cells will be prevented

from transitioning from the pre-malignant to the malignant condition

and thereby prevent carcinogenesis

Fig 1 The microRNA Sponge HuR is a RNA binding protein which is normally present within the

nucleus of cells When the cells are exposed to an inflammatory stimulus HuR moves out from

the nucleus to the cytoplasm and binds to both the PDCD4 mRNA and to miR-21 acting as a

ldquomiRNA spongerdquo

These exciting observations tell us quite a few things about how

cells prevent the transition from chronic inflammation to cancer

Moreover they tell us what might contribute to this transition If HuR

fails to sponge miR-21 because of defects in HuR production or

translocation to the cytoplasm then miR-21 would suppress the

translation of PDCD4 and other tumor suppressor genes like PDCD4

and thereby contribute to the development of cancer On the other

hand it also tells us that in conditions where miR-21 is high some

therapeutic agent which will cause the translocation of HuR to the

cytoplasm and sponging of miR-21 might prevent its action and

thereby prevent the transition to malignancy Therefore the sponge

of HuR might be used to fight the double-edged sword of chronic

inflammation and cancer

Discovery of such processes that regulate inflammation improves

our understanding of the process of chronic inflammation and its role

in cancer development This will allow the development of anti-

inflammatory agents as part of anti-cancer therapy Anti-

inflammatory cancer therapy will prevent premalignant cells from

turning fully cancerous or impede an existing tumor from spreading to

distant sites in the body thereby making it much easier to detect

treat and cure cancer

DK Poria A Guha I Nandi and PS Ray RNA-binding protein HuR

sequesters microRNA-21 to prevent translation repression of

proinflammatory tumor suppressor gene programmed cell death 4

Oncogene 2015

13

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 16: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

INDIA ALLIANCE STAFF CORNER

DR SUJATHA REDDY Grants Adviser

Dr Sujatha Reddy joined the grants team in 2013 after finishing her

Postdoc stint at CCMB Hyderabad Sujatha has been involved with

many activities at India Alliance and is currently looking after India

Alliance‟s Grants Management System IASys along with her grant

advising duties

What is your background

I am from Hyderabad and I hold a PhD in Genetics My postdoc was

in Tissue Engineering and my second postdoc was to study the

epigenetics of adult neurogenesis I joined India Alliance in 2013

after spending a considerable amount of time at the Centre for

Cellular and Molecular Biology Hyderabad

Tell us about your India Alliance journey so far

Like any other researcher I too was occupied with my bench work and

have my share of experience of applying for funding submitting

progress reports expecting fund release etc Moving into science

administration was a carefully thought-out decision and I was well

aware that I would no longer wake up anxiously to look at the Ct

values of my overnight run Real time PCR or the growth of my cultures

Nevertheless at IA I get to read science across the spectrum which

was otherwise restricted to my focus area I certainly feel that

scientific training and experience have been very handy at almost

every aspect of my job profile as bdquoGrants Adviser‟ at IA as we need

to understand projects and related requirements have knowledge of

ethical issues and understanding of the policies and liaise with

eminent international experts Many a times the experience of being

a researcher has helped me to closely comprehend the issues faced

by candidates and Fellows

As a grants adviser I get to facilitate important processes of grants

management provide the necessary support to candidates and

contribute to problem solving at several instances Working at IA has

not only helped me hone my existing set of skills but also develop

several new ones Some of the important skills that the job

continuously teaches are multitasking prioritizing and time

management With six rounds of competitions launched each year

and several existing Fellowships awardees to manage and other

crucial responsibilities within the organization the grants advisers

handle multiple tasks at any given time point Since all the activities

are time bound and require high levels of attention and commitment

the experience has substantially contributed to develop my abilities to

simultaneously perform multiple duties with efficiency

The culture of Team work at IA is yet another thing which I feel good

about The grants team comprises of people from different specialties

and the office has been a great place for knowledge exchange and

some interesting discussions Each member has unique expertise and

experience thus bringing in multiple outlooks and varied views on

every aspect during our discussions As a team we share

responsibilities and support each other on an everyday basis which

has grounded a healthy atmosphere within the organization

Being a grants adviser with IA has not only given me a rich

experience to manage grants along the lines of international

standards but also benefit immensely from the experience which came

with varied responsibilities that I was entrusted with The job also

requires us to provide necessary guidance to candidates and timely

support to Fellows which I personally have a liking too as I consider it

as a unique approach to help researchers towards their effort to

progress further In this regard I am happy to have several good

memories to cherish at IA I would say that managing science from the

other side of the bench by facilitating funding process is indeed

interesting and more so if one has the fervor to contribute in some

way to the growth of science

When not busy on the job what do you enjoy doing

I enjoy music of all kinds and I grew up listening to MS

Subbalakshmi and also the melodies of the 70‟s and 80‟s My mother

was a Veena teacher and I learnt Carnatic music as a child I enjoy

singing light classical and bhajans I find a lot of pleasure in painting

mostly seascapes and landscapes with acrylic medium Going on a

holiday with my family is also something I always look forward to

Who inspires you (living or dead)

Several people have been a source of inspiration for different

reasons My father however remains as one of the important

individuals to have inspired me enormously He was a self-made man

with high moral standards and had touched several lives with his

benevolence Quite often I recollect his words and ways of living In

the recent times I found Nick Vujicic to be highly inspiring His

confidence and determination are simply amazing

16

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 17: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

OTHER EVENTS

FIRST FOLDSCOPE WORKSHOP IN INDIA

Stanford researchers urged Indian students to bdquolook at the world more closely‟ at the first Foldscope

Workshop held in New Delhi

Stanford University based Assistant Professor Dr Manu Prakash and

his team conducted the first one-day Foldscope workshop in India at

Sri Venkateshwara College which was followed by a Public Lecture

by Manu at Gargi College in New Delhi on 16th December 2015 This

workshop was jointly organised by Department of Biotechnology

(DBT) Government of India and Stanford University USA and was

part of DBT‟s celebratory events leading up to February 2016 that

marks 30 years since its foundation

Manu‟s wish to bdquomake the world a more curious place‟ along with his

deep-rooted interest in providing solutions for global health problems

led him to develop the $1 microscope dubbed Foldscope along with

his PhD student Jim Cybulski Foldscope is an origami based print and

fold paper microscope with magnification capabilities of up to 2000

times and weighs about 8 grams which makes it one of the lightest

and the cheapest basic field microscope available today One can

explore the biodiversity around or the bdquomicrocosmos‟ as Manu likes to

refer to it with this scope by simply attaching it to a camera phone A

typical Foldscope kit contains a sheet of foldable paper lens an LED

light and instructions During the morning session of the workshop

Manu and his team guided groups of students from various colleges

of Delhi University on how to assemble and use this paper microscope

to view samples on a slide In the second half of the workshop

students were encouraged to go outside explore and pick up samples

to observe under the Foldscope they had assembled and the best

image was given a prize and microcertificate which as the name

suggests could only be viewed under the Foldscope

Apart from serving as an ideal tool to educate students about

microscopes and their use to view the diverse bdquomicrocosmos‟ around

them Manu and his group have developed different Foldscopes to

diagnose different diseases The Foldscope can have different

imaging capabilities depending on the light source and lens which

includes bright-field reflected light dark-field polarisation

fluorescence and projection microscopy The examples of these

imaging capabilities can be seen online where Foldscope users from

around the world have uploaded their images

Manu‟s public lecture at Gargi College after the workshop lucidly

summarised his scientific work and journey inspiration behind the

Foldscope and his other research endeavours In his talk he shared

five lessons with the students which were learn to make original

observations value of stupidity in science find your own taste in

science importance of frugal science and amoeba (a pun on

elephant) in the room- the microcosmos These lessons were shared in

form of Manu‟s own experiences in the lab and the field For instance

he recounted how his interest in entomology as a kid led him to

develop a very simple and cost-effective assay which could be used

to genetically identify mosquitoes The data from this assay he hopes

can be useful for developing therapeutic tools against malaria and

other infectious diseases Manu stressed on the importance of doing

frugal science his favourite of the five lessons and its deep impact on

the global community Apart from drawing in from his own work on

the Foldscope and other projects he further supported the case of

frugal science by giving examples of other successful models- one

such was that of an American startup company Tribogenics that

developed a portable X-ray source from scotch tape Manu opined

that frugal science is not merely about bringing the costs down but

intellectually it is about exploring completely different approaches of

achieving what we set out to achieve Throughout his talk Manu

repeatedly urged the students to make their own observations and

not just rely on books to seek answers for their scientific curiosities

Manu concluded his lecture by saying ldquoit is not just for the scientists to

know the world curiosity needs to be nurtured and kept aliverdquo

In the QampA session Manu enthusiastically answered questions related

to Foldscope applications limitations effectiveness in controlling

disease outbreaks in a country like India it‟s availability in a store

and many others Foldscopes are not available commercially yet but

Manu and his group have dispatched 10000 Foldscopes to interested

individuals in 130 different countries in the hope that this citizen

science initiative will help us in gaining a much wider understanding of

the world around us The active participation and questioning by the

students at the workshop and lecture clearly suggests the need and

importance of such workshops and experiences in igniting interest in

scientific explorations at a very young age One student at the

workshop remarked ldquothis is has been my favourite kind of classroomrdquo

a sentiment shared by many students both young and old at this

event

Following the Delhi event Manu and his group conducted two other

workshops at Guwahati and Kaziranga which were facilitated by

DBT The novel findings of the microcosmos by the new users of the

Foldscope in India will be uploaded here

8

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 18: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

OTHER EVENTS

Trick or Treat is a year long project of discovery and synthesis of diverse practice and practitioners of healthcare systems

in India Sweeping through urban and rural contexts as well as researching a wide spectrum of healing approaches the

project pitches the use of digital art and techniques to create various public engagement experiences

The intention of the project is to raise an awareness and engagement with the plurality of health-related experiences in

the country with intended audiences from the public and scientific community Some of the key media outputs from the

project include a microsite a publication a workshopseminar a performance and a pop-up exhibition

If you would like to know more about Trick or Treat project and their upcoming Seminar amp Workshop at British Council

click here

ldquobdquoTabiyat Medicine and Healing in India‟ examines the history and contemporary practice of sustaining human health

in one of the world‟s great civilisations The exhibition will feature dazzling antiquities and modern vernacular art in an

aesthetically seductive intellectually rich mix of art science history and the ordinary made extraordinary

Find out more about Medicine Corner and this Exhibition here

rdquo

rdquo

ldquo

17

Please send your feedback suggestions and contributions to publicengagementwellcomedbtorg

Follow us on

18

Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph

Page 19: News & Views - India Alliance · Dr Siddhesh Shashikant Kamat, Indian Institute of Science Education and Research Pune Dr Mohan Joshi, Centre for DNA Fingerprinting and Diagnostics

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Images in this issue

Credit S Gschmeissner K Hodivala-Dilke amp M Stone Wellcome Images

Blood vessel in a melanoma Scanning electron micrograph

Credit Annie Cavanagh Wellcome Images

Breast cancer cells A cluster of breast cancer cells showing visual evidence of

programmed cell death (apoptosis) Scanning electron micrograph