QuorumMay 2017

SCELSESingapore Centre for Environmental Life Sciences Engineering

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

New teachers with new subjects are gearing up for the students at

this year’s SCELSE Summer Course.“This is the first time that we have

a session on synthetic biology by A/Prof. Poh Chueh Loo from NUS. We have also increased the number of experienced research fellows, such as Dr Law Yingyu and Dr Caroline Chénard, who will be teaching their areas of expertise at the course,” said Prof. Stefan Wuertz, who is heading the organisation of the upcoming Summer Course for the first time.

The annual course, which is in its seventh year, was first offered in 2011 and has seen a steady increase in the number of applicants from all over the world.

“It continues to be very diverse and this year there are many Singapore-based students,” Prof. Wuertz said.

The intensive three-week course brings together world-renowned scientists and engineers, and is well regarded by previous students.

“Through interactive sessions and discussions, we learn to ask the

right questions as we share lunch and coffee with the experts,” said Vincent Scholz from the University of Duisburg-Essen in Germany who attended the course last year.

SCELSE’s Summer Course will be held from 27th June to 15th July and successful applicants will be notified by the 31st of May.

SCELSE has been awarded four new Marine Science Research &

Development Programme (MSRDP) grants worth more than S$1.5 million, focusing on the fate of pathogens in the marine environment, antifouling coatings for tropical marine systems and antimicrobial drug discovery from micro-algae.

This latest funding was granted in the second and final round of current MSRDP funding and complements

existing SCELSE projects on marine microbial ecology/engineering, biocorrosion and virus/phytoplankton interactions awarded last year (November Quorum, 2016).

“SCELSE’s success in both rounds of MSRDP has established new exciting collaborations in Singapore and consolidated our marine science research,” said Prof. Staffan Kjelleberg.

He said that this further integrates and drives excellence in interdisciplinary life science and environmental research in SCELSE, and the MSRDP is now a truly inter-institutional and comprehensive marine research platform at the national level.

Prof. Stefan Wuertz is at the helm of a two-year S$733k project on the fate of pathogens in the marine environment investigating the interactions of disease-causing

organisms in the water column with marine sediments colonised by biofilms. The study will use long-term flume experiments to predict the fate and transport of these pathogens, to improve safety in aquaculture farming practices. SCELSE researchers including Nandini Shome will collaborate with Dr Maria Yung at the St. John’s Island National Marine Laboratory (SJINML), Mr Graham McBride at the National Institute of Water and Atmospheric Research (NIWA), New Zealand and Prof. Krassimira Hristova from Marquette University, USA.

“We expect to kick off activities in September and look forward to many fruitful interactions with marine researchers on St. John’s Island,” Prof. Wuertz said.

A/Prof. Ali Miserez at the NTU School of Materials Science and Engineering and A/Prof. Scott Rice at SCELSE are collaborating on a three-and-a-half-year S$665k project to study liquid infused coatings that can prevent marine biofouling in the tropical environment. These coatings are made by infusing a nanostructure or gel with a lubricant which stays in place due to its high chemical affinity for the substrate, thus making the surface very slippery. Previous work by A/Prof. Miserez has shown the effectiveness of these coatings in

Marine research towards fundamental science and practical goals

cont. p. 4

New teachers and subjects at the SCELSE Summer Course

CalendarSCELSE Seminars

01 Jun: Dr Stuart Stephen, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia. 2:00pm - 3:00pm. SBS-CR2

07 Jun: A/Prof. Hsu Li Yang, NUS Saw Swee Hock School of Public Health. 3:00pm - 4:00pm. SBS-CR3

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).

EventsFridays: Shut Up and Write! 10:00am. Please see teamsites for location.

16 Jun: SCELSE Happy Hour. 5:00pm onwards. B2 Coffee Lounge.

Jul: NIMBELS Grant Call 2017. Call for proposals.

Conferences and Courses01 - 05 Jun: American Society for Microbiology (ASM) Microbe 2017. New Orleans, Louisiana, USA.

17 - 21 Jul: International Union of Microbiological Societies (IUMS) Congresses 2017. Marina Bay Sands Convention Centre, Singapore.

24 - 26 Oct: Asian Conference on Energy, Power and Transportation Electrification (ACEPT 2017). Marina Bay Sands Convention Centre, Singapore.

06 - 14 Dec: EMBO Global Exchange Lecture Course. Structural and biophysical methods for biological macromolecules in solution. NTU School of Biological Sciences, Singapore.

The coast of St. John’s Island (Photo: Ria Tan)

Asian Conference on Energy, Power and Transportation Electrification (ACEPT)

24 - 26 Oct 2017 The second ACEPT brings together

world-leading experts to present emerging topics on energy, power and transportation electrification.

Deadline for submission of full paper has been extended to: 16 June 2017

For details, please visit:

http://acept.asia

QUORUM

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

SCELSE staff profile

Water quality is highlighted by United Nations Educational,

Scientific and Cultural Organization (UNESCO) as one of the main global challenges during the 21st century that impacts human health, food production, ecosystem function and economic growth. SCELSE researchers have validated the use of a water quality test based on host-associated Bacteroidales assays, conducted in Singapore as a model for tropical urban environments.

A serious threat to water quality is contamination by human sewage discharge, which may contain pathogens that cause diseases. Currently, the measurement of faecal indicator bacteria (FIB) is commonly used as a way to detect faecal contaminations in a water supply. However this method does not discriminate human from other animal faecal sources.

A new molecular-based technology using host-associated Bacteroidales 16S rRNA gene markers is currently being developed for specifically distinguishing human faecal contamination.

So far, most of the validation work has been done in temperate climates, and previous work showed that there is regional variability in the specificity of human-associated Bacteroidales markers. SCELSE researchers validated the test in Singapore as a model tropical urban environment for the Southeast Asia region.

They selected seven host-associated Bacteroidales assays, including one universal, five human and one canine assay, and evaluated the assays’ performance against 295 faecal samples from humans, sewage and eight relevant domesticated and wild animals selected in consultation with Singapore National Parks Board (NParks). Genomic DNA was then extracted from the samples and quantitative PCR (qPCR) performed

to detect the presence of the target sequences.

The researchers found that the candidate universal assay BacUni detected all samples except bird droppings (accuracy of 0.97), while the dog assay BacCan had an accuracy of 0.96 with a small percentage of cross-reaction with other animals, confirming the suitability of both assays. Interestingly, the human marker HF183-SYBR Green, which was the best performing assay of studies in India and Bangladesh, was not the best performer in Singapore. Instead, the B. theta marker had the highest accuracy (0.90) followed by BacHum (0.85). HF183-SYBR Green also had lower specificity (0.88) compared to B. theta (0.98) due to more cross-reaction with samples from other animals.

Based on these results, the researchers emphasised the importance of doing similar validation studies in a specific geographical location before relying on the technology. Findings from this study can be useful to other high population density cities in Southeast Asia for the detection of sewer leakage and protection of water resources.

Compared to human beings, microbes are very tiny organisms,

but together they exert a huge influence over global biogeochemical processes. Dr Viduthalai Rasheedkhan Regina is fascinated by the collective behaviour of microbes and what we can learn from them.

“As humans, we are living in a critical point of time when we are confronted with problems such as antibiotic resistance, emergence of pathogenesis and climate change. Ideally, as an intelligent big-brained civilisation, we should have taken collective action against these problems, but we clearly have not. Most people don’t even recognise that these are problems,” he said.

In contrast, microbes may be simple single-celled organisms, but they are very sophisticated in dealing with their environment, peers, rivals, and hosts. They have evolved to be the most successful entities on Earth, and perhaps on other planets too, Viduthalai said.

“Microbes have shown that they are more fit as a community. They also share public goods and deal with cooperation and conflicts, as we do. I try to think and understand how such traits could have evolved in a system that does not have a brain and if we could learn something from them,” he explained.

At SCELSE, Viduthalai works in the Microbial Biofilms cluster with A/Prof. Scott Rice on a mixed species biofilm that is relevant to human skin microbiota,

in collaboration with the French skin care and cosmetics company L’Oréal.

Viduthalai’s academic background is in classical biology. During his higher secondary school days in India, his teacher inspired him to choose zoology as the major for his bachelor’s degree.

He became fascinated by the idea of studying and manipulating genetic material and graduated with a Master’s degree in Biotechnology in 2004. At the time, he wanted to work on microbes because they are simple systems for studying biological processes and genetics. He started his research career at the National Institute of Ocean Technology (NIOT) where he had the first opportunity to study biofilms formed by

marine bacteria.In 2007, he went to the National

Center for Cell Sciences (NCCS) where he worked on the microbial ecology of a wastewater treatment plant and dissemination of antibiotic resistance genes among bacteria from pharmaceutical waste. Later, Viduthalai moved to the Interdisciplinary Nanoscience Center (iNANO) at Aarhus University (AU) in Denmark for his PhD, studying the critical role of eDNA in aiding bacteria to form biofilms and developing coatings that can prevent biofilm formation. He graduated in 2012 and did his first postdoc working on microbiota and biofilms that are relevant to the dairy industry.

He arrived at SCELSE in 2016, which he had considered since its inception as a world-class biofilm centre with top people in the field. In daily work, Viduthalai felt that challenges and failures are unavoidable in research life, and it is important to be persistent and work towards a solution.

“I spent more than a year of my PhD with negative results in an attempt to develop a nanoparticle-functionalised coating for biofilm prevention. Even though a year of my data went unpublished, the whole experience of discovering why the method didn’t work was rewarding, and I learned a lot from it,” he said.

For new research students, Viduthalai said that science progresses by communicating results and building up on each other’s findings. Therefore publishing, by writing good papers, is an important part of being a scientist.

“I am not an accomplished scientist to offer advice, but I can share this: academic English or scientific English is a language by itself, and like learning any other language it comes in handy with practice,” he said. He recommended students to watch Professor Roberto Kolter’s YouTube videos on ‘Why Write? How to Communicate Your Science Research’ for inspiration.

Viduthalai said that Singapore is a great place where one gets to see and work with talented people from all over the world. He loves the food and weather here. Outside science, he likes literature and history, and to be outdoors for a hike, a road trip, or just gazing at stars in a clear night sky.

Validating molecular-based water quality test in Singapore’s tropical urban environment

Publication profile

Viduthalai Rasheedkhan ReginaResearch Fellow

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

QUORUM QUORUM

Latest SCELSE publications

New SCELSE PhDsCongratulations to

SCELSE students Joey Yam (left) and Calvin Ng (right) who successfully completed their oral defences in May!

In short

SCELSE social

Systems biology approach to fight antibiotic resistance in biofilms

Antibiotic resistance is a serious global healthcare problem that

threatens to undo the life-saving success of antibiotics enjoyed over the past seven decades.

According to a recent UK government-commissioned “Review on Antimicrobial Resistance” by Jim O’Neill, currently at least 700,000 people die each year worldwide because of antibiotic resistance - a figure which may rise to 10 million a year by 2050 unless there is a concerted effort to combat the problem.

In addition, an estimated 65% of infectious diseases involve biofilms, especially persistent infections such as chronic lung and urinary tract infections.

In SCELSE’s Public Health & Medical Biofilms cluster, a team of researchers led by Asst Prof. Yang Liang is working

on a project entitled “Systems biology analysis of antibiotic resistance of pathogenic biofilms” to study the mechanism of resistance and find a

way to fight it.“Previously, people used to focus

on the extracellular polymeric substances (EPS) of the biofilms when it comes to antibiotic resistance. However, we now know that it is not the only consideration because some antibiotics can penetrate the matrix,” Asst Prof. Yang explained. He added that the specific biofilm-associated regulatory pathways are also potential drug targets.

“We are currently focusing on Pseudomonas aeruginosa as our model organism, but in future we can expand to other pathogenic bacteria such as Acinetobacter baumannii and Klebsiella pneumonia,” Asst Prof. Yang said.

Research director Prof. Mike Givskov heads the team, which

consists of core members Asst Prof. Yang, Dr Cheng Yingying, Dr Chew Su Chuen, Dr Gurjeet Singh Kohli,

Movement trajectories of live colistin-tolerant Pseudomonas aeruginosa PAO1

cell aggregates moving onto dead biofilm (Chua et al (2016) Nat. Comm. 7:10750)

SBS Happy Hour

Farewell gathering

The NTU School of Biological Science (SBS) Happy Hour in May was jointly organised by Prof. David Becker’s lab (LKCMedicine) and Asst Prof. Kimberly Kline’s lab. The turnout was excellent, with many attendees participating in the games and activities. (Photos: Tay Wei Hong, SCELSE)

The Kline Lab held a farewell gathering for three of their members who are leaving SCELSE.

Standing next to Kimberly, they are (from left): Dr Kishore Reddy Venkata Thappeta, Benny Wang and Dr Sharon Goh.

We wish them all the best for their future endeavours!

cont. p. 4

QUORUM

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

SCELSE student profile

This month’s student profile features Ee Yong Liang!

Tell us a bit about your work in SCELSE.

I study how plants and microbes interact at the roots and my current research seeks to understand how plant roots and their associated microbes improve plant growth under the holobiont (host and associated microbes) concept. There are changes in plant metabolites and their root microbiome that provide clues for me to elucidate metabolic pathways involved in their symbiosis.

In A/Prof. Sanjay’s lab, I work with Yong Jian and Johanan on the plants and Aditya on understanding the microbiome changes around and within plant roots. I also work with Shruti and Shivshankar on the metabolites involved between plants and microbes.

Any interesting findings or experiences so far?

It took me many repeats of my

experiment as well as consulting Ziggy (Dr Ezequiel Marzinelli) on analysing the data with a mixed effects model to get my first positive results.

It really gave me a sense of achievement and made me feel that

my efforts paid off.

What excites you and what makes you go zzzzzz?

It excites me to talk to others, especially juniors and undergrads, about science and research. The gleam of fascination in their eyes and their dreams to uncover places different from mine give me different perspectives.

It makes me go zzzzzz to label hundreds of sample

tubes, with numberings to remember and slight variation in labels so that I can identify samples within and between experiments. I tend to prepare them in advance, so that I am all ready to harvest plants and collect microbes without having to pause to label everything.

If you were stranded on a deserted island, what would you want to bring with you?

My fountain pen and some water-resistant notepads.

Comfy trousers. These are so hard to find.

Fill in the blanks: When _____ , I _____.

When I feel tired, I frag aliens and zombies on my gaming rig mindlessly (like a zombie) to unwind and recharge.

Anything you would like to say to fellow students?

“Science involves confronting our ‘absolute stupidity’. That kind of stupidity is an existential fact, inherent in our efforts to push our way into the unknown.”

Schwartz, M.A., 2008. The importance of stupidity in scientific research. Journal of Cell Science, 121(11), pp.1771-1771.

This is a gem of a one-pager I read in my undergrad years. It gave me the assurance that stupidity is acceptable, and one of the steps to finding the unknown and undiscovered.

Ee Yong LiangPhD Student

Dan Roizman, Joey Yam, July Fong, May Salido and Thet Tun Aung. In addition, the team includes external collaborators such as Dr Chua Song Lin from LKCMedicine NTU, A/Prof. Newman Sze at SBS NTU and Prof. Roger Beuerman from the Singapore Eye Research Institute (SERI).

Broadly, the research strategy is to combine systems biology - including proteomics, genomics and transcriptomics - and molecular biology to identify candidate genes involved in antibiotic resistance, which can

Systems biology approach to fight antibiotic resistance in

biofilms (from p. 3)

Newsletter contactsFreddie: limlenghiong@ntu.edu.sg

Sharon: sharonlongford@ntu.edu.sg

serve as novel drug targets. The project, which is supported by

a Ministry of Education (MOE) Tier 2 grant awarded in April 2015, is progressing very well and has already yielded seven research papers, one review article and two patent filings to date.

However, there are still tough challenges ahead. “We are trying to establish a modified version of transposon sequencing technology for the project. In our hands, the published methods are not working well and our team is developing a novel approach to resolve this,” Asst Prof. Yang said.

In addition to this project, the group is also working on novel antimicrobial solutions using chemical biology to target existing pathways that confer antibiotic tolerance, and working closely with local and international clinicians to study other aspects of antibiotic resistance, such as the evolution and spreading of mobile genetic elements.

“We are using a comprehensive approach of pursuing basic, applied and translational research - all three of them together to find solutions to the antibiotic resistance problem,” Asst Prof. Yang said.

Marine research towards fundamental science and practical goals (from p. 1)

preventing attachment by mussels – one of the most opportunistic marine biofouling organisms – and the team is planning to expand its work with A/Prof. Rice’s expertise in bacterial biofilms.

“Biofouling is a problem which is truly interdisciplinary in its scope, requiring the contribution of physics, chemistry, engineering, microbiology and field studies. Its global economic impact is about US$50 billion a year, for example due to increased hydrodynamic drag of ships, resulting in fuel wastage and elevated greenhouse gas emissions. It also contributes to the translocation of invasive species around the globe,” A/Prof. Miserez said.

He said biofouling research is scientifically very interesting because it has both fundamental science and practical goals. The team plans to quantify the adhesion strength of different biofilm types on different substrates and lubricants.

Asst Prof. Yang Liang leads a two-year S$200k project to discover novel antimicrobials from marine micro-algae and bacteria that can fight biofilm infections. His team usually uses a library of synthetic compounds as the starting point, but he also

intends to investigate nature-derived compounds by the identification and molecular characterisation of various marine microorganisms.

“Currently, most of the antimicrobial drugs approved for treatment of human diseases are actually derived from natural sources. This project is an extension of our antimicrobial research, with a different source,” Asst Prof. Yang said.

The fourth project is led by Asst Prof. Cao Bin and focuses on the diversity and prospecting of magnetotactic bacteria in the tropical marine environment, which can potentially become a resource for future biotechnological applications.