QuorumMarch 2016

SCELSESingapore Centre for Environmental Life Sciences Engineering

1Singapore Centre for Environmental Life Sciences Engineering, www.scelse.sg

Singapore’s National Research Foundation (NRF) has boosted

its long-term research funding pool to S$19 billion over five years in its sixth science and technology plan: Research Innovation and Enterprise 2020 plan (RIE2020).

This is a 19% increase in funding overall from the previous RIE2015 plan and includes a shift towards more

translational outcomes.RIE2020’s push for more translational

research complements the previous five-year plan, which had a proportionally larger provision for basic research, said Prof. Kjelleberg.

The translational focus will augment the outcomes of previous funding periods to develop a knowledge-based innovation-driven economy and society, he said.

One of RIE2020’s major thrusts involves promoting multidisciplinary, nationally coordinated collaborations and strategic investment in ‘curiosity driven and mission-oriented research’.

Overall, research centres can expect to benefit from the increased funding, but the focus will shift to applications rather than fundamentals. Similarly, we expect the number of post-graduate scholarships on offer might decrease, but the funding of post-

doctoral positions through competitive grants might increase, Prof. Kjelleberg said.

The RIE2020 framework promotes a strong research and innovation

community to build a core of innovative enterprises

with competitive translational

outcomes.Two of the four

technology domains directly relate to SCELSE:

Health and Biomedical Sciences, and Urban

Solutions and Sustainability, with allocated funding set

at $4 billion (21%) and $0.9 billion (5%) for each domain,

respectively.In addition, academic

research will be allocated $2.8 billion (15%) of the funding pool, slated for building a significant base of capabilities and to feed into translational research and drive the next phase of growth.

CalendarSCELSE Seminars

Thursdays 3:00 - 4:00pm, SBS-CR306 Apr: Dr Kiran Raosaheb Patil, EMBL Heidelberg, Germany.07 Apr: Prof. Grant Burgess, Newcastle University, UK.13 Apr: Assoc. Prof. Shauna Murray, University of Technology Sydney, Australia.20 Apr: Asst. Prof. Janelle Thompson, MIT, USA.

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.

15 Apr: SCELSE Cross-cluster Discussion Forum. 4:00pm - 5:00pm. B3 Meeting Room.

15 Apr: SCELSE Happy Hour. From 5:00pm. B2 Coffee Lounge.

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

10 - 20 Jul: Explorations in Data Analyses for Metagenomic Advances in Microbial Ecology (EDAMAME) Workshop, Kellogg Biological Station, Michigan, USA.

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

RIE2020 plan boosts Singapore’s long-term research funding

SCELSE’s new corporate identity

SCELSE’s new Corporate Identity was officially launched this month

with a bold new look that reflects the environmental focus and cutting edge research of the rapidly growing research centre.

The Corporate Identity is the culmination of many months of development and refinement by the communications and marketing team at SCELSE together with the professional design company Impetus.

These sleek and contemporary

designs have been incorporated into a new set of collaterals, such as powerpoint slides, poster templates, letterheads and envelopes. Attractive corporate gifts, which include SCELSE-

branded notebooks and pens, are also in the works for official events and meetings.

SCELSE members are kindly requested to use the collaterals without modifying them in order to achieve consistency in SCELSE’s

Corporate Identity for branding purposes.

SCELSE SAB2016

SCELSE’s annual Scientific Advisory Board meeting adopted a shift in

format when it convened earlier this month, with an increased focus on the centre’s research talent.

Faculty members and senior research fellows individually presented their research and discussed career development with the SAB.

This enabled the board members to assess SCELSE’s PIs and provide

advice on aspects crucial for career development.

The amended format required substantial input from participants and their efforts were very much appreciated, said Prof. Staffan Kjelleberg.

A more detailed account will be included in next month’s Quorum, once the SAB meeting outcomes have been reviewed by the Governing Board Chair.

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2 Singapore Centre for Environmental Life Sciences Engineering, www.scelse.sg

SCELSE staff profile

Ever since the dawn of human civilisation, microorganisms have

been playing an important role in the manufacture of many products, and yeasts – crucial to the production of bread, beer and wine – can be considered the oldest industrial microbes in history.

Rhodosporidium toruloides is an oil-producing yeast that can accumulate up to 60% of its dry weight in lipids, making it a potentially rich source of biofuels. In addition, it can produce carotenoids – for example beta-carotene that gives carrots their orange colour – which are valuable in the food and pharmaceutical industry.

However, lipids and carotenoids are hydrophobic compounds located in the lipid bilayer of the cell, and thus extraction and purification steps are necessary to liberate these compounds, which greatly drives up the cost of production. Furthermore, current extraction methods also require the use of organic solvents such as

chloroform, methanol or hexane, which are not friendly to the environment.

SCELSE researchers developed a novel approach to improve the extraction process by engineering a membrane transporter called “pleiotropic drug resistance 10” (Pdr10) into R. toruloides. In Saccharomyces cerevisiae, Pdr10 had previously been shown to export beta-carotene out of the cells.

The researchers transformed the gene encoding Pdr10 from S. cerevisiae into R. toruloides using a technology called Agrobacterium tumefaciens-mediated transformation (ATMT). Fungal colony PCR was used to confirm the positive transformants and Pdr10 protein expression was also checked using

immunofluorescence.This newly transformed Pdr10 strain

was then tested for carotenoid production using two-phase media. The Pdr10 strain exported 6 times as much carotenoids as the wild type strain into the oil phase of the media. Interestingly, the Pdr10 strain exported the carotenoid torulene with the greatest efficiency, instead of beta-carotene. There was also a small increase in total fatty acid production and change in the dominant type of fatty acids produced. The researchers explained that increased carotenoid and fatty acid production was due to the consumption of the oil in the two-phase culture media, which served as an additional carbon source.

In conclusion, SCELSE researchers report that this is the first study to provide a method for harvesting and separating lipids and carotenoids in R. toruloides by adding a transporter. Their approach is not only simpler but also more friendly to the environment, and may be applied to other similar organisms.

In scientific research, determination and collaboration are crucial ingredients

in a successful project. During her research journey so far, Dr Eliza Soh has demonstrated both in abundant measure. “Research is always a challenge! It is a good test of patience and perseverance,” she said.

At Asst. Prof. Kimberly Kline’s lab in SCELSE, Eliza is examining how Enterococcus faecalis contributes to mixed species biofilm-associated infections. Although Staphylococcus aureus, Enterococcus faecalis and Pseudomonas aeruginosa are common constituents of the wound environment, investigations in this niche have primarily focused on interactions between S. aureus and P. aeruginosa. “However, since E. faecalis and P. aeruginosa are found in as many as 71% of all polymicrobial wound infections, it greatly spurred my interest in understanding the mechanisms of pathogenesis that underlie the interaction between these two organisms,” she explained.

Eliza’s strategy is already producing promising results. “My experiments show that E. faecalis wound infection is more severe in the presence of the co-infecting P. aeruginosa. Interestingly, mixed infections results in significantly higher E. faecalis titre, and based on our latest findings, our working hypothesis is that both of these

organisms participate in a dynamic, niche-dependent synergy and antagonism that alters polymicrobial infection outcomes,” she elaborated.

“What I find most exciting is that this project exposes me to a myriad of new techniques, which serves to expand my repertoire. It is also wonderful to be working with a dynamic group of both friends and

colleagues whom I can bounce ideas off one another,” Eliza added. Aside from this work, she also collaborates with Asst. Prof. Yang Liang.

Eliza graduated from the University of Malaya (UM) in 2008 with a BSc (Hons) in Microbiology, and enrolled in UM’s MSc scholarship programme the following year. Six months into her MSc research, she was awarded a one-year attachment with University of

Nottingham (UoN) by the British Council’s 2nd Prime Minister’s Initiative (PMI-2) Scholarship Fund. She formally enrolled at UoN in 2011 and attained her PhD in 2014 under the guidance of Prof. Paul Williams, Prof. Miguel Cámara and Dr. Stephan Heeb.

“My thesis work focused on on three aspects of alkyl quinolone (AQ) signalling in P. aeruginosa, encompassing the design and development of a biosensor for agonists and antagonists of AQ signalling for novel therapeutics, a mechanistic study of Pseudomonas quinolone signal (PQS) inactivation by Achromobacter

and dysregulation of the quorum sensing cascade as a consequence of mutations in the Tat secretion pathway,” Eliza explained.

When asked about the highlight of her research career so far, she recalled: “Meeting and eventually collaborating with Prof. Susanne Fetzner from University of Münster in Germany. I met Suzanne at the 14th International Conference on Pseudomonas in 2013, where she expressed interest in my work on PQS inactivation during my poster presentation and proposed to collaborate. I had huge admiration in her work prior to that meeting especially since I often referred to her papers when I was encountering a big roadblock during the course of that project. I would never have imagined that we’d ultimately work and publish together!”

Eliza first came to SCELSE during the Summer Course in 2013 and was attracted to work here. “The research environment is highly international and robust, which makes it a great platform for forging collaborations on top of getting exposed to cutting edge research. There is also the added perk of a nice working environment in SCELSE,” she said. For students new to research, Eliza has this advice: “Always have an outline of your paper early. Projects are fluid and directions may change along the way, but it is always good to jot down a storyboard for your paper.”

Eliza said that she enjoys living in Singapore as it is safe here and has a fantastic performing arts scene. “I enjoy Yoga – a great way to unwind and recharge,” she added.

Eliza SohResearch Fellow

Engineered yeast for improved biofuel and carotenoid production

Publication profile

Latest SCELSE publications

3Singapore Centre for Environmental Life Sciences Engineering, www.scelse.sg

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SCELSE social

On 3rd of March PhD student Dan Roizman performed in the NTU Cultural Activities Club “Hourglass III” Jazz & Blues concert held at the National Library. SCELSE members attended the concert to enjoy the music and cheer Dan on!

NTU Jazz & Blues Concert

FOCUS Martial Arts conducted their Kenpo grading examination in March. New SCELSE members who earned their yellow belts from instructor Dr Damien Keogh include Dr Enrico Marsili, Dr James Houghton, Ezequiel Santillan and his wife Solange Elizabeth Astorga.

Dr Jamie Hinks, who already has a yellow belt, and recent participants Dr Sharon Longford and Dr Artur Matysik were also there for moral support.

Congratulations on their achievement!

SCELSE Kenpo Grading

NTU Open House 2016

Solar Eclipse 2016

SCELSE members participated in the NTU Open House in support of the Asian School of the Environment. There was a huge crowd and many prospective students enquired at the booth. Many thanks to PhD students Liu Xiaolin and Gayatri Chilambi for their help during the event!

SCELSE members stepped outdoors for a short while on 9th March to experience a partial solar eclipse – using a solar projector and eclipse viewers – right here on NTU campus. The next solar eclipse in Singapore will take place in 2019.

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4 Singapore Centre for Environmental Life Sciences Engineering, www.scelse.sg

Museum review Visiting Micropia museum in Amsterdam

SCELSE researcher Woo Yissue went to the Netherlands on vacation and

visited the Micropia museum there. Here is his review of the museum:

Micropia, which was dubbed a “Microbial zoo” – the first of its kind – recently opened in Artisplein or Artis Square (Artis is the oldest zoo in the Netherlands) in Amsterdam. This “zoo” aims to engage the public and expand their view of microbiology – highlighting the connection between the microbial world, the natural environment and the macroscopic world including ourselves. In addition, Micropia hopes to connect the scientific community and the general public.

The journey starts with an elevator ride, but not just any ride you’ve taken before. In the elevator box, the trip up transforms into a slow “zoom in” onto the surface of a cornea, ultimately arriving at a community of microbes living on the surface, which coincides with your arrival at the main exhibit.

The main exhibit is presented in a highly visual manner with a comfortable and dimly lit ambience, with well-placed spotlights highlighting the fixed exhibits.

Fixed microscopes are one of the main features, and you are free to control the viewing axis and focus using the joystick in front of the enclosure. A large viewing window affords you the pleasure of examining the live specimens in great detail without the discomfort of viewing through an eyepiece.

The microscope image is projected to an interactive touch screen, which also serves to provide the back story and description of the specimen being observed, often accompanied with eye-catching animations.

More than just a simple exhibition of miscellaneous microorganisms, the main message Micropia wants to tell is the relationship between microscopic and macroscopic organisms, and the environment they reside in. The

relationship between photosynthesis and life in general is highlighted in a

set up where oxygen generated from a culture of photosynthetic microbes is fed into a microcosm tank. Meanwhile, a demonstration of the connection between microbiotic and macrobiotic world is presented in an elaborate set up of an ant farm, complete with an ant colony in a tank of sand, connected to composting wastes and live vegetation.

Another special highlight of Micropia is a bigger-than-human

size interactive display, which allows you to explore the microbiota of the various parts of the human body. Simply stand on the indicated spot in front of the display, and a mock outline of your body appears to you, allowing you to select parts of the body by just gesturing.

Finally, you can’t have a microbial exhibit without cultures of microbes. All

the organisms exhibited in Micropia are live, which means that there is a need to constantly maintain and grow the organisms. This is why there is a dedicated laboratory within the museum itself, in full view of the public. It is staffed by a small group of employed technicians and volunteers. The laboratory

regularly conducts a seminar to the public, demonstrating how they keep the organisms in Micropia happy, in layman terms of course.

Visitors are given a small pamphlet and encouraged to collect all 30 stamps distributed among the various exhibits. Once you’ve collected the stamps,

scan it on the table located on the ground floor to see them “come alive”.

In conclusion, Micropia is a dedicated, highly visual “zoo” with a collection of more than 300 microorganisms, for the purpose of showing the public that no unit of life is on its own. All life, big or small, are connected to each other in one form or

the other. The marriage of biology and art, eases the communication of the science to the general public, and we could learn a few things from the Dutch.

Newsletter contactsFreddie: limlenghiong@ntu.edu.sg

Sharon: sharonlongford@ntu.edu.sg

Yissue in front of a statue of a Tardigrade – a highlight of

Micropia museum

SCELSE events

New format for SCELSE cross-cluster forum

The third monthly cross-cluster discussion forum took a

new format to encourage greater participation and engagement from attendees. The new format was geared towards a pure debate of an interesting theme instead of a more conventional focus on individual research papers.

The meeting discussed the topic “Does species matter?”, which was briefly overviewed by Dr Enzo Acerbi and Aditya Bandla prior to an open floor discussion.

The limitations of 16S rRNA sequencing, species vs operational taxonomic units (OTUs) vs strains,

and the importance of function in a microbial community analyses were

actively discussed by the participants.Other topics brought into the debate

included how research goals and environmental context impact on the significance of what a species means.

Prof. Yehuda Cohen, who facilitated the discourse, encouraged participants to consider the fundamental unit as a primordial “package” of organisms instead of distinct species.

“We now have the tools to investigate this. We have very potent technologies such as CRISPR-Cas9, which is a significant, maybe frightening step. A discussion like this

helps to provide a better understanding of what we are aiming for,” he said.