CalendarSCELSE Seminars

Wednesdays 3:00 - 4:00pm, SBS-CR303 Feb: Tan Shi Ming (ARB course sharing session), SCELSE.15 Feb: Prof. Per Nielsen, Aalborg University, Denmark.17 Feb: Dr Ashlee Earl, Broad Institute MIT & Harvard, USA.24 Feb: Prof. Paul del Giorgio, Université du Québec à Montréal, Canada.

Group MeetingsEnvironmental Engineering meeting:Tuesdays 9am, B3 Meeting Room.

Kline Group meeting: Mondays 9:30am, B3 Meeting Room (please check with Kimberly prior to joining).

EventsWednesdays: Focus Martial Arts. 6:30pm - 8:30pm. NTU Nanyang Auditorium Annex.

Fridays: Shut Up and Write. 9:00am. B3 Meeting Room.

03 Feb: SCELSE Cross-cluster Discussion Forum. 10:00 - 11:30 am, SBS-CR3.

16 - 18 Feb: Experimental Design and Data Analysis Workshop conducted by Dr Ezequiel “Ziggy” Marzinelli. Centre for Life Sciences (CeLS), NUS.

19 Feb: SCELSE Happy Hour. From 5:00pm. B2 Coffee Lounge.

Conferences 201617 - 21 Apr: Gut Microbiota, Metabolic Disorders and Beyond. Rhode Island, USA.

24 - 28 Jul: 2016 Society for Industrial Microbiology and Biotechnology (SIMB) Annual Meeting. New Orleans, Louisiana, USA.

16 - 19 Sep: Managing Environmental Quality in the Asia Century. Society of Environmental Toxicology and Chemistry Conference. Singapore.

Quorum JANUARY 2016www.scelse.sg

New SCELSE appointments

This month, we feature the “Shut Up and Write” weekly meeting, headed

by Dr Rohan Williams and Asst. Prof. Kimberly Kline. “Shut Up and Write” is a means of providing protected time for writing manuscripts, theses or other work-related documents. “It uses the ‘Pomodoro Technique’, in which an activity is organised in set blocks of time,” Dr Williams explained. Each Friday session runs over 2 hours and consists of four 30-minute blocks

of time. Everyone in the room writes for 25 min in silence and then takes a five minute break where you can talk and walk around. Then, this 30-minute block is repeated four times. People can bring coffee or tea but not food, and are requested to turn mobile devices to silent mode. “You can also use this approach by yourself, but the activity of writing with other people really helps in focusing attention,” he said.

SCELSE begins the new year with two new appointments and a new

organisational unit. We congratulate Prof. Sven Pettersson on his new appointment as Deputy Research Director of the Meta-’omics & Systems Biology cluster. Prof. Pettersson is a professor at NTU Lee Kong

Chian School of Medicine and had a fractional appointment at SCELSE in the past three years. He is a world leader on host–microbiome interactions and has been a strong proponent for implementing the holobiont concept in SCELSE’s research portfolio. We look forward to increased research collaboration with Prof. Pettersson. A new organisational unit has been formed within SCELSE, named the

“Integrative Analysis Unit” (IAU). Dr Rohan Williams, who served as Deputy Research Director of Meta-’omics &

Systems Biology cluster, will move to head the new unit. The objectives of the IAU are: to act as a hub for the provision of appropriate bioinformatics and systems biology services, to conduct research on major

problems relating to the structure and function of complex microbial biofilm communities, and to improve knowledge, skills and standards related to the areas of its expertise, within SCELSE and its partner institutions via the conduct of focused workshops. We thank Dr Williams for his fine contributions as Deputy Research Director and congratulate him on his new appointment.

SCELSE collaboration with BioSyMSCELSE has been formally

collaborating with BioSyM for two years now and together have achieved significant research progress. SCELSE senior research fellow Dr Thomas Seviour is a co-principal investigator in this collaboration and helps to provide BioSyM researchers with a biological context for their work. We asked Dr Seviour to give us an overview of this joint effort. “BioSyM is made up of researchers

from MIT and Singapore institutes, and develops technologies to address medical and biological questions, with a strong emphasis on meeting the industrial and scientific needs of Singapore. Specifically, these technologies focus on the interaction between mechanics and biology,” he said. “SCELSE wants to better understand biofilm mechanics within an ecological context, which is the basis of ‘Biofilm Ecomechanics’. This involves understanding how the biofilm mechanics respond to environmental conditions, the interplay with extracellular matrix content, and how biofilm mechanics in turn affect biofilm

Meeting synopsis: Shut Up and Writecont. p. 4

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SCELSE Staff Profile

No matter which area of life sciences you work in, nucleic acids are the

common thread that links everything together. Dr Daniela Moses embodies in-depth knowledge and mastery of the next-generation DNA sequencing pipeline, empowering SCELSE researchers to make exciting new biofilm discoveries. “I am leading SCELSE’s sequencing facility and I work with pretty much anybody who has sequencing needs,” Daniela said. “Sequencing is such a rapidly evolving field. Many of the sequencing projects that we are working on today would have been impossible to accomplish just a few years ago. The first human genome took more than 10 years to complete and cost a fortune; today, sequencing is so fast and cheap that pretty much everybody can afford to have their genome sequenced. Likewise, metagenomics and metatranscriptomics of complex communities would not be possible without the massive throughput of today’s sequencing platforms. Having been in part of this journey has been a lot of fun!” she explained enthusiastically. Daniela is a microbiologist by training and she started her career investigating predator-prey interactions between Bdellovibrio

bacteriovorus and its hosts. She attained her doctorate degree from Eberhard Karls Universität in Tübingen, Germany in 2009 while performing all the experimental work for her thesis in Prof. Stephan Schuster’s lab at Pennsylvania State University in the USA. “Even early on in my career, I was exposed

to different sequencing technologies: first Sanger sequencing and soon after, next-generation sequencing. Our lab at Penn State was one of the first labs worldwide to have ventured into this new field. That was the time when I left the microbial world and focused more on the genome sequencing of extinct and endangered species such as the woolly mammoth, Tasmanian tiger and Tasmanian devil,” she recalled. In her daily work, the

sensitivity of the sequencing process to the condition of the sample material presents some unique challenges. “As a PhD student, I could not imagine that there could be anything more challenging than working with ancient samples. Therefore, the moment when clusters started lighting up on the sequencer display was always a moment of joy. But I must admit that some of the environmental samples we are working with here at SCELSE are equally challenging!” she conceded.

Daniela is one of the SCELSE pioneers who has been here since the beginning in 2011. “As I was completing my PhD, I learned that there was a plan to build a next-generation sequencing facility within SCELSE. It took very little convincing and no hesitation to jump on this opportunity! Having worked in the next-gen sequencing field for several years by that point and having established the Illumina sequencing pipeline at the Penn State lab, I was eager to take on the challenge of setting up a brand-new sequencing facility. Also, I spent part of my teenage life in Hong Kong and I was very excited to get the chance to move back to this part of the world!” she recalled. When asked about what she likes in Singapore, Daniela replied, “The people, the food and the weather! Yes, I am one of those folks who would choose heat and humidity over snow and cold any time!” Outside of the lab, Daniela is deeply attracted by the splendour of the sea. “I am a passionate scuba diver and photographer and whenever possible, I like to combine the two hobbies! Before moving to Singapore, I worked in the Philippines as a Divemaster for a while and I later became an Assistant Instructor and helped teach scuba courses for students at Penn State. I love underwater macro and supermacro photography. The smaller the object, the better! I often joke that this passion for the small is the last remnant of my previous life as a microbiologist!” she laughed.

Publication Profile

Daniela Moses Senior Research Fellow

Latest SCELSE Publications

Identifying biofilms with CDy11According to the US National

Institutes of Health, more than 80% of all infections are associated with biofilms. In addition, bacteria in biofilms are up to 1,000 times more resistant to antibiotics than free-living bacteria and are often non-culturable. Thus it is important to have a rapid and reliable way to identify biofilm-associated infections in order to choose the correct treatment strategy at the clinic. Currently, biofilm detection methods include the use of DNA staining dyes to detect biofilm extracellular DNA, Amaryllis lectin that binds to Psl polysaccharide in biofilms, ligand targeted ultrasound contrast agents and fluorescence in situ hybridization (FISH). These have different levels of effectiveness in vitro but there is no established method for in vivo biofilm imaging so far. Focusing on the opportunistic

pathogen Pseudomonas aeruginosa, SCELSE researchers chose functional amyloids in Pseudomonas (Fap) as their molecular target for biofilm imaging. They used their in house “Diversity Oriented Fluorescent Library” (DOFL), screened thousands of dye compounds for clear and reproducible fluorescence in the selective staining of P. aeruginosa PAO1 biofilms, and picked the best, called “CDy11”. They then tested CDy11 for generality to other biofilms such as E. coli and S. typhimurium, for sensitivity via serial dilution of bacteria,

and validated the binding target by the colocalisation of CDy11 with Fap antibody staining. The next step was to test CDy11 in animal models of infection. SCELSE researchers used a mouse corneal infection model and found that P. aeruginosa biofilms in an infected eye could be detected in vivo by simply using CDy11 eyedrops, without needing further surgery or culture process. To test for biofilm detection in a surgical format, they used a mouse implant model and found that

biofilm-coated silicone tubes were specifically stained by CDy11. In conclusion, SCELSE researchers have developed CDy11, a novel biofilm imaging probe, and demonstrated its potential as an in vivo diagnostic tool for detecting biofilms.

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SCELSE Social

Conference Report Computational Metabolomics at Leibniz Center for Informatics

Last December, Dr Rohan Williams attended a workshop

on Computational Metabolomics at the Leibniz Center for Informatics at Schloss Dagsthul in Germany. The Leibniz Center is a 50-year-old research centre in computing which runs a year round series of invitation-only workshops. “The format for these meetings is quite different from a normal conference. There are no formal talks, and the organisers are expected to organise attendees into open discussion sessions. The number of participants is limited to 45 or 50 people, from across all career levels, including a number of PhD students,” Dr Williams explained. The location was a small castle (“Schloss” in German) in Saarland at the western part of Germany. The facility houses a resident scientific director, his staff and includes an extensive technical

library, a music room, dining room and a beer cellar among a large number of small meeting rooms. “The attendees

were mostly a mix of machine learning types and analytical chemists, along with some people from systems biology and several application domains, including the environmental sciences. The discussion sessions, including some

held outdoors, ranged across a range of topics in experimental and computational metabolomics, largely focused on the challenges of compound identification of MS2 data, as well as

discussions on data integration, artefacts and data sharing culture within the field,” he recalled. “This format was a welcome relief from the standard conference format of days full of talks. The entire experience was rejuvenating and has inspired me to experiment with similar formats in Asia. I would highly recommend attending such a meeting if you get the opportunity,” Dr Williams added. Another highlight of the meeting was a visit to the small city of Trier (previously Treves), which contains a number of ancient ruins from the

Roman period, but is also where philosopher Karl Marx was born and spent his formative years. Dr Williams also spent several days in Tubingen working with Prof. Daniel Huson on an ongoing collaboration on the development of new methods for metagenome analysis, visualisation and interpretation.

Leibniz Center for Informatics at Schloss Dagsthul in Germany

SCELSE Happy Hour

SCELSE Charity Activity

The first SCELSE Happy Hour of 2016 was held on 15th January and there was much to celebrate. Congratulations to Dr Feng Shugeng who successfully passed his PhD defence! Special thanks to A/Prof. Scott Rice and Dr Jamie Hinks for sponsoring the pizzas during the celebration.

A group of SCELSE members volunteered their time and effort for a charity activity on 17th January. “We helped with the cooking and packaging of meals for ‘Willing Hearts’, a charity organisation that prepares thousands of meals daily for needy people in Singapore, such as low income families and the elderly,” said Dr Enzo Acerbi who coordinated the activity. Many thanks to SCELSE volunteers with their hearts of gold!

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SCELSE Student Profile Anee Mohanty PhD Student

Course Report

This month’s student profile features Anee Mohanty!

Tell us a bit about your work in SCELSE (what do you do and who do you work with?) I am currently in my final year of PhD. I must say it has been an incredible learning experience so far. I am especially thankful to my supervisor Asst. Prof. Cao Bin for giving me this opportunity to work here. His passion and dedication for work inspires me all the time. My research focuses on studying the “sublethal” effect of nanomaterials on bacterial functions. Specifically, the objective of my study is to elucidate the impact of nanomaterials on social behaviors e.g. production of communal resources, cell-cell interactions. Just like most microorganisms exist as multi-species communities in nature and their interactions are key to their function, I got the opportunity to interact with many researchers in SCELSE. We actively collaborate with my co-supervisor Asst. Prof. Liang Yang and his group. Apart from that,

I work closely with Dr Grant Tan and did have the opportunity to briefly work with Dr Damien Keogh. Any interesting findings or experiences so far?

Majority of the toxicological studies of nanomaterials have focused on their bactericidal (killing) and bacteriostatic (growth-inhibiting) effects. Little is known about the influences of nanomaterials at sub-lethal concentrations on critical functions of microorganisms. We have shown that certain nanomaterials significantly inhibit siderophore

(pyoverdine) in our model environmental bacterium P. aeruginosa. Siderophores facilitate iron uptake and it is an important communal resource in environmental microbial communities. We also investigated the effect of nanomaterials on quorum sensing signals and found that interestingly the effect is very specific in terms of type of signal and bacterial species. We hope that our study will provide a novel insight into ecotoxicity of

nanomaterials.What excites you and what makes you go zzzzzz?Knowing new people and getting to learn from their experiences in life excites me the most and working alone in lab on weekends make me sad especially when experiments don’t work.If you were stranded on a deserted island, what would you want to bring with you?A good camera to capture the beauty of nature, comfortable shoes to explore the island, and drinking water.Fill in the blanks: When _____ , I _____. When I am with my family, I am the happiest.Anything you would like to say to fellow students?I would like to say from my own experience nobody is an expert in everything so whenever you feel somebody is good at a particular thing don’t shy away from asking them because it’s always better to learn from a person than from textbooks. So in my opinion “collaboration” is the key. Similarly share your expertise with others when they need it, in this way we all grow and prosper.

phenotype,” Dr Seviour added. This common focus in mechanics helped to drive interest towards a formal collaboration with BioSyM. “Some of the specific questions we have relate to antibiotic resistance and to what extent intermicrobial organisation and interactions depend on the physical properties of the matrix. We need to understand this at micro scale, and while we’re well equipped at observing cells through our Zeiss affiliation, we’re not so good at understanding the mechanics of these system at the required resolution, which is why we sought a collaboration with BioSyM,” he

explained. In these two years, SCELSE researchers developed a platform to investigate the mechanical properties of biofilms, resulting in a series of excellent publications in this field of research. “We’ve made quite good progress and have developed techniques for manipulating biofilms in a number of different ways and directions. This includes stretching biofilms over large length scales, which is relevant for understanding how biofilms are deformed by flow; probing the surface properties of biofilms, which is important for understanding

how biofilms interact with their physical and chemical environment; and understanding mechanical heterogeneity within biofilms. So we’ve laid the foundations for this concept of Biofilm Ecomechanics and have a very good platform for better understanding the interplay between the properties of biofilm extracellular polymeric substances (EPS) and phenotype,” Dr Seviour summarised.

SCELSE collaboration with BioSyM (from p. 1)

Newsletter contactsFreddie: limlenghiong@ntu.edu.sg

Sharon: sharonlongford@ntu.edu.sg

On 3rd of February, SCELSE PhD

student Tan Shi Ming will be presenting his report on an ARB course he attended in December last year. The course was held at the Max Planck Institute for Marine Microbiology in Bremen, Germany. He briefly shared with us his goals for going on the trip and his experiences there.“I wanted to learn more about pipelines for processing 16S rRNA data and the classical approach for FISH probe

design,” Shi Ming explained. ARB – short for “arbor” or tree in Latin – is a software package consisting of tools that allow for sequence database handling

and data analysis. Software features include comparative sequence alignment of 16S rRNA gene sequences,

construction of phylogenetic trees, taxonomic classification, and probe design and matching. Shi Ming had a surprising encounter during the course. “I met some of my supervisor’s old colleagues and students when he was part of the Scientific Advisory Board 15 years ago in Bremen!” he recalled excitedly.

All SCELSE personnel who are interested in the classical methodology of FISH probe design and the SILVA database are encouraged to attend Shi Ming’s sharing session.

ARB Course at Max Planck Institute for Marine Microbiology

Shi Ming (3rd from right) and other ARB course participants

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