News


March 2017: Academy-industry day on Business Opportunities in Biological Frontiers organised at Warwick

We were delighted to be involved in hosting this important meeting to bring academics and industry together to explore the science and potential of new technologies for biotech, agri-tech and biomedicine. The mini-workshop featured 19 'flash' talks, with attendees spanning four universities and 15 companies.

February 2017: OSSlab and sLoLa teams visit SIAM

Many of the OSS Lab and sLola groups travelled to Nijmegen, in the Netherlands, for a research exchange workshop with members of the SIAM (The Soehngen Institute of Anaerobic Microbiology) research program, hosted by Prof. Mike Jetten. The two days of activities included scientific talks, posters, lab tour, pub quiz! and round table discussions on 'natural vs sythetic communities', 'new techniques' and 'future collaborations'. Thank you to our hosts for organising this fantastic event. Please visit the SIAM website to find out more about their research, training and events: http://anaerobic-microbiology.eu/scientists/

July 2017: Andrea makes it to the top list of best teachers award!

The winners and commendees from the 2017 Warwick Awards for Teaching Excellence (WATE) PGR have recently been announced and we were delighted to see that Andrea Martinez from the OSS Lab had not only been nominated for her excellent contribution to 'enhancing the student learning experience' but that she had also been shortlisted for an award. Well done Andrea for your hard work inspiring and motivating students at Warwick.

Dec 2016 - Anaerodynamics is online

The home page of our 1-year monitoring project of industrial anaerobic digesters is now online. This 1 year project, funded by BBSRC focuses on furthering our understanding of anaerobic digestion, particularly on how the complex microbial communities affect and are affected by operational conditions. 16 UK AD reactors are taking part in the project, where both genetic and meta-data are collected weekly. The large amounts of genetic data will allow us to characterise which species of microbes inhabit the digesters, what their functions are and, importantly, how they change over time. The meta-data will allow us to monitor changes in response to their environment. The datasets will be made available through the project website at http://anaerodynamics.com, providing an unbiased and transparent source of information on the performance of industrial AD reactors in real time, which we hope will help to enhance and expand this technology in the UK.

Aug 2016 - evoFBA is published

After a long development process, evoFBA, a computational tool that combines cell-level metabolic models with evolutionary and ecological dynamics is finally published in BMC Evolutionary Biology. The paper describes the evoFBA approach in the context of an application to the famous Lenski experiment of long-term evolution of Escherichia coli. We find that the combined modeling of cellular metabolism and evolutionary/ecological dynamics allows prediction of diversification involving niche construction and character displacement through differential nutrient uptake and metabolic regulation. Read more details by downloading the paper, and check evoFBA for yourself through downloading the source code.

Aug 2016 - Welcome to Fred Farrell

Fred Farrell joins the lab on a collaborative project with Chris Quince (Warwick Medical School). This is a pilot project that will monitor industrial scale anaerobic digesters for a year, on a weekly basis, using new generation sequencing. We will be developing analysis tools to make sense of this data, as well predictive models that can explain the data. The resulting data set and associated digester meta-data will be available publicly through a dedicated website.

June 2016 - Postdoc position

We are looking for a postdoctoral researcher to lead our effort to create an unprecedented, temporal dataset of microbiomes found in industrial-scale anaerobic digesters. We will sample such reactors on a weekly basis for over a year and analyze the resulting data set, towards developing better models of community structure and function. See "open positions" for more details and application link.

March 2016_ community papers out

In the last month we have got three papers out on microbial communities; two original articles from our own work and one review/opinion piece as part of a large consortia. All three papers are significant in their own right. The consortia paper makes a call for more and better integration of theoretical and experimental work in the field of microbial ecology and development of model experimental systems. The two other papers present our own work in this direction. In one paper, we develop a thermodynamical theory for microbial co-existence. This paper presents a fresh view on the analysis of microbial co-existence and shows that under a thermodynamic regime, species can co-exist even under the presence of a single growth-supporting substrate. This suggest that thermodynamic considerations can be key for understanding microbial diversity in many environments, but particularly those with low energy reactions. The final paper presents an experimental analysis of a syntrophic co-culture between a sulfate reducing bacteria and a methanogen. We report identification of a genetic polymorphism in the sulfate reducer, that underpins its ability to engage in syntrophy. It turns out that this genetic change directly relates to the thermodynamic basis of metabolism in the sulfate reducer, emphasizing the importance of thermodynamics again in the study of microbial communities.

June 2015. Best Presentation Award

Tobias Grosskopf from OSS lab received the "best presentation award" at the Anaerobic Digestion Early Career Researcher event organized by BBSRC Anerobic Digestion Network. Tobi presented his work on "Mutational Reshaping of Metabolism facilitates Microbial Syntrophy", which was highly well received by the panel of judges and the audience alike. The event was attended by over 40 participants from 17 Universities, who presented their research on aerobic digestion and associated microbial communities.

March 2015. Fellowship at the Wissenschaftskolleg zu Berlin (WIKO)

The WIKO was founded in 1981 with the purpose to offer scholars and scientists the opportunity to concentrate on projects of their own choice for one academic year, free from administrative duties. OSS lab head Orkun Soyer experienced this privileged position as a short term WIKO fellow this year. During his time at WIKO, Orkun concentrated on developing theories on thermodynamic basis of microbial interactions and ideas on how to better analyze and engineer microbial communities. The latter work has culminated in a research proposal, while the former will underpin two upcoming papers (together with from Tobias Grosskopf who joined Orkun at WIKO as visiting fellow). Being at Berlin for an extended time has also allowed formation of links with researchers from Humboldt University, leading to organization of a one day workshop attended by the OSS Lab members. Overall, the fellowship was an unforgettable and highly rewarding experience. Interested parties should consider applying at WIKO's junior fellows program .

January 2015. Warwick Integrative Synthetic Biology Centre (WISB) receives major funding

The WISB, the recently established interdisciplinary centre for advancing synthetic biology research is announced as one of the six EPSRC/BBSRC funded synthetic biology research centers in the UK. The unique vision of WISB is to develop new engineering and experimental approaches that will facilitate improved understanding, control and exploitation of the unique features of biological systems through synthetic biology. Our lab was heavily involved in the establishment of WISB and is leading one of its research themes, the one on engineering synthetic microbial communities.

July 2014. Research on Microbial Communities Explained

This is a nice, 3-minute video explaining our research on microbial communities. The video is directed by Conal Reid and acted/implemented by Henry, Tobias and Kalesh.

June 2014. Research Programme on Microbial Communites Ready To Kick Off

About a year ago, together with several colleagues from around the UK, Denmark and New Zealand, we have received funding from the Isaac Newton Institute to organise a 4-month residential research program on "understanding microbial communities". The broad idea was to bring together empricial and theoretical scientists to discuss and develop new approaches to studying and understanding the sturcture and function of microbial communities. With this vision in our heads, we have been working on organising the program for almost a year now and the kick off is only a month away, scheduled for mid-August. Hosting well over 60 scientists over the 4-months, the research program will feature several public talks, three 3-day workshops, one student training event, and one academia/industry linking event. All aspects of the program will also be open to external participatns. If you are interested to learn more or apply for a place, please visit the program website.

May 2014. Anaerobic Digestion Network

Through our research on "engineering microbial communities for biomethane production", we got to lead development of a research/industry network on anaerobic digestion. Funded by the BBSRC, this network is now active and will be helping to develop the research on anaerobic digestion and mcirobial communities. In particular, the network will be organising several events and handing out pump prime funding. For more information and to join visit the AD Network

December 2013. UK's First Doctoral Training Centre in Synthetic Biology!

UK's first and only doctoral training centre in synthetic biology, which we have played a key role in developing and where Orkun takes an associate directorship role, is jointly funded by EPSRC and BBSRC. The centre will be known as SynBioCDT and will provide a doctoral training program that combines the fundamental understanding of biological systems with the principles of engineering, so as to create the next generation of industrial and academic leaders in synthetic biology. SynBioCDT builds on the multi-disciplinary expertise offered by the research environment at the Universities of Oxford, Bristol and Warwick to provide training that covers all parts of this extremely broad remit, including not only individual cells but self-assembled biomimetic systems, engineered microbial communities and multicellular organisms. Such coverage is vital in the emerging area of Synthetic Biology. SynBioCDT is now accepting applications from motivated students!

September 2013. University of Warwick launches Warwick Centre for Integrative Synthetic Biology!

Warwick Centre for Integrative Synthetic Biology, WISB for short, is a new interdicsiplinary centre for advancing synthetic biology research. The unique vision of WISB is to develop new engineering and experimental approaches that will facilitate improved understanding, control and exploitation of the unique features of biological systems through synthetic biology. In particular, research at WISB will focus on the role and exploitation of noise in gene circutis, evolutionarily inspired approaches to pathway engineering, and development of engineering toolkits for synthetic multi-cell, multi-compartment systems.

May 2013. OSS Lab is now part of University of Warwick, School of Life Sciences!

After three exciting and productive years at the University of Exeter, in which we played a key role in establishing systems biology approaches to biological problems, the OSS Lab has now moved to the University of Warwick, School of Life Sciences. The move sees us embarking on experimental work in our own labs and also engaging fully with the emerging field of synthetic biology. This is bound to be an exciting development for all of us at the OSS Lab, and hopefully for the larger scientific community both at Warwick and beyond.

Feb 2013. Biotechnology, Biomedicine and Microbial Communities

Most, not all, of industrial biotechnology deals with microbes in one way or the other. And when it comes to microbes the conventional thinking seem to rely on two concepts; make it simple, make it big. Thus, many industrial applications involve large reactors of clonal cultures of a single species, which usually performs some metabolic conversion. In nature, however, bacteria almost never is found in isolation but rather in heterogenous communities. Such communities are believed to kept together via structural and functional associations such as metabolic dependencies. The study of microbial communities is an emerging field, boosted by the emergence of -omics technologies. Most -omics studies are descriptive at the moment, focusing on identifying the species composition of communities. There are a plethora of other questions though. What makes a stable microbial community for example? What are the species abundance dynamics? Can one define a "function" for communities? If the function is metabolism-based, how can we understand/manipulate metabolic connections in a community? Can we de-complex natural communities? Can we create complex communities from bottom-up, starting from co-cultures? The answers to these and many other questions in microbial communities are unanswered at the moment, creating an highly fertile resaerch ground. The answers emerging from this research can make significant impact in industrial biotechnology and biomedicine.
Targeting a BBSRC call on "networks in industrial biotechnology", we are in the process of developing a research&industry network that should facilitate the "evolution" of research on microbial communities. If you want to get involved, please visit the online discussion platform BBSRC has set up for this call, or check out the outline of the idea.

Nov 2012. The Chancellor George Osborne announces our new project!

It was a big excitement for us today as the Chancellor has announced our project along with 5 others in a speech at the Royal Society. The six grants constitute a move by BBSRC towards revolutionising major industries in biotechnology and bioenergy through funding in synthetic biology. You can see the full press release by BBSRC on their web site. The grant that we're leading is on understanding natural microbial communities for biomethane production through directed evolution and engineering synthetic communities through synthetic biology. Including scientists from University of Exeter, Newcastle University, Imperial College and TGAC, this interdisciplinary project promises to make a big impact on our understanding and control of complex microbial communities. To follow our progress please keep an eye on the project web site.

Oct 2012. Metabolic Tinker.

We have just released a computational tool on "guiding" synthetic design of metabolism called Metabolic Tinker, or Tinker for short. In a nutshell, the tool allows searching the entire universe of known reactions (which we call URN :) for paths between two user given compounds. It is based on graph theory and does take into account thermodynamic feasibility of reactions. It is capable of finding both natural paths and potential alternatives, with results returned in a rank order based on total deltaG over the path. While these are novel features, Tinker is not yet the perfect design tool (e.g. it does not take into account substrate availability) but rather something that could potentially help identifying interesting solutions to a given chemical conversion problem. In case you (or your students) want to check it out, please visit the Tinker web site.

Sept 2012. Evolution in action!

As our own projects relating to better characterising microbial pathogens' behaviour and the evolution of underlying molecular systems start to mature, we were recently glued to TV to watch the beautifully made BBC documentary on evolution on antibiotic resistance. If you haven't seen it, you must catch it on the web. Among other things, it features the "morbidistat" developed in the Kishony lab and a super simple/nice experiment inspired by it. It involves growing bacteria on a large petri dish embedding a drug gradient. As bacteria grow, they evolve increasing drug resistance and leave a visible and temporally segregated colony trace on the dish. The experiment is not only a visual demonstration of evolution in action, but it also inspires several interesting follow up ideas.

July 2012. Evolutionary Systems Biology book is out!

Evolutionary Systems Biology is an emerging synthesis between evolutionary and systems biology. I've been editing the first book on this emerging field, which is just published from Springer as part of their Advances in Experimental Medicine and Biology series. The hope is for more such volumes to follow as the field matures. I would like to thank again to all contributors and Melanie Tucker from Springer for a seamless publication experience. You can order the book here or access the individual chapters via PubMed. I hope they will provide you with thought provoking reading.

March 2012. Robustness workshop

This one day workshop organised together with Sabine Leonelli from Egenis brought together a diverse set of speakers and participants for a discussion about the role of the engineering concepts such as robustness in biology. With the attendance of social scientists, engineers and biologists, the forum gave rise to very interesting and fruitful discussions. The invited speakers' presentations (see poster workshop here) provided the perfect setting for these discussions.

January 2012. Evolution of evolvability!

The result of a long collaboration with Hiroyuki Kuwahara at Carnegie Mellon, our latest paper on the evolution of bistablity is now online at Nature MSB web site. This has been a most exciting and interesting work that will hopefully lead to several follow up studies both from us and others. It is exciting, because it is (I believe) the first demonstration that systems dynamics can evolve in such a way to increase evolvability (e.g. shorten adaptation time to a new environment) of a biological system. It will be even more exciting to see how generally applicable these results will turn out to be. This will require more theoretical and experimental work. It was interesting, because we ended up with results that we didn't even think of at the beginning of this project. Our initial ideas were revolving around exploring the evolution of noise under fluctuating environments, but we gradually moved to (or I should say the data pushed us to) analysing the evolution of bistability and the link of this to evolvability. In sum, it was a great journey and I'm very glad the paper finally saw daylight!

September 2011. Introduction to systems biology and a documentary.

As part of a new MSc program , I'm designing a new course, which will act as an introduction to systems biology. Besides discussing some of the basic tools and approaches in the field, I would also like to use the course to make students aware of the history and philosophy of systems biology. More material from the course will be available on this web site soon, but if you are thinking what "systems" is about, I highly recommend a recent Adam Curtis documentary; All Watched Over By Machines of Loving Grace. The second episode is particularly dealing with the emergence of ideas around systems in ecology and engineering and their effects in other areas. It also provides an interesting and personal take on how scientists/people can get carried away with their own ideas.

August 2011. Functional change in structural continuity.

A new article, co-written with my long time collaborator and previous mentor Richard Goldstein, titled "Evolution of response dynamics underlying bacterial chemotaxis" has just come out in BMC Evolutionary Biology. I'm quite excited about this work because in it we describe a potential evolutionary route for the response dynamics as seen in bacterial chemotaxis. This dynamics and the underlying networks have been deemed "complex" previously, but our analysis provides a straightforward, incremental route to it at least in terms of response dynamics. Most interestingly, this route turns out to be an example for the "functional change in structural continuity" principle first proposed by Darwin.

May 2011. Philosophy of Science.

The interest at OSS Lab into the philosophy of science and related discussions with Maureen O'Malley are slowly bearing fruit. Together, we explore in a recent publication (see publications section) how integration takes place at various levels in the general field of systems biology and how it makes an impact on knowledge generation.

The fundamental question behind this (and similar) analyses/investigations is how science as an activity differs from other forms of human activity.

March 2011. Exeter Synthetic Biology Sandpit.

Together with John Dupre (director of EGENIS), I'm organizing an internal sandpit event at the University of Exeter to increase awareness of synthetic biology research and its many facets and to foster internal collaborations in this field.

Synthetic biology aims to engineer controlled functionalities using biological systems by combining a variety of approaches and techniques from mathematics, engineering, molecular biology and genetics. Besides their clear objectives in the applied/industrial domain, such constructs are highly useful for gaining basic understanding into natural systems, allowing synthetic biology to act as a bridge between applied and basic research.

Exeter Synthetic Biology Sandpit will open with a public talk by Mark Bedau (Reed College, USA) at 6pm on 2nd June. On 3rd June, selected participants will attend a full day sandpit, with talks from four external facilitators leading into open discussion and brainstorming. Participants will interact, discuss and form research project during the day, which will be presented to facilitators and peers for feedback. We expect the emerging research projects to evolve into short proposals; those submitted by 10th June will be evaluated by a selection panel and succesful projects will be allocated a moderate sum of seed funding.

External facilitators for this event will be: Mark Bedau (Reed College); Stuart Dunbar (Syngenta); Antonis Papachristodoulou (Oxford University), Paul Freemont (Imperial College) and Jane Calvert (University of Edinburgh)

The event is sponsored by the Bridging the Gaps project, the four Colleges of the University of Exeter and the Research Knowledge Transfer unit.

January 2011. Watch top scientists present

The presentations from the Frontiers workshop, for which I was the lead organiser for, is now available online. You can watch and listen to presentations from the Frontiers of multidisciplinary research: mathematics, engineering, and biology .

December 2010. Editing a book!

OSS lab head Orkun Soyer will be editing a book titled "Evolutionary Systems Biology" to be published by Springer. Evolutionary systems biology is an emerging field that draws on systems biology, laboratory evolution, population genetics and comparative genomics to answer system level biological questions within an evolutionary framework. To cover this broad definition the book will feature a diverse array of chapters touching on the different methodologies and approaches employed in the field and the questions asked.

December 2010. Review process revealed.

The Publications section of this web site will from now on feature excerpts from reviews of OSS Lab publications. I decided to have this feature in an attempt to provide insight into the reviewing process, mainly as a training-experience for upcoming scientists. If you find this useful or have any other comments please get in touch. Do also get in touch if you would like to share excerpts from reviews you received.

November 2010. Varun and Al joins the lab!

OSS Lab welcomes Varun Bhaskar Kothamachu and Nihat Al Sayar, PhD. Al will explore ideas in synthetic and systems biology of metabolic networks, while Varun starts his PhD as a receipient of the prestigious Dorothy Hodgkin Award.

September 2010. Assoc. Editor at BMC!

OSS lab head Orkun Soyer is appointed as Associate Editor at BMC Evolutionary Biology, Evolutionary Systems Biology Section. BMC Evolutionary Biology is an Open Access, peer-reviewed journal that considers articles on all aspects of molecular and non-molecular evolution of all organisms, as well as phylogenetics and palaeontology. The journal is included in Thomson Reuters Web of Science and other products. It's latest Impact Factor is 4.29.

August 2010. Phil of Science!

OSS lab head Orkun Soyer is appointed as Senior Fellow at the ESRC Centre for Genomics in Society (Egenis). This honorary appointment acknowledges Orkun's ongoing support and contributions to research done at Egenis, in particular at the interface where public engagement, philosophy of science, systems and synthetic biology meet. For more information, visit the centre web site:
Egenis

June 2010. New MSc course.

Applications are now open for an MSc program in systems biology at the University of Exeter. One of the two core modules for this program is developed by Ozgur Akman and Orkun Soyer and will focus on the Dynamics and Evolution of Biological Systems. For applications and more information, visit the course web site:
MSc Systems Biology

April 2010. A unique workshop!

Abstract submission opens for a unique workshop co-organised by Orkun Soyer. Aiming to foster interdisciplinary thought and approaches at the interface of engineering, biology and mathematics this workshop brings together leading figures and students from a variety of disciplines. For abstract submission and more information, visit the event web site:
Frontiers of multidisciplinary research: mathematics, engineering, and biology

March 2010. A good start.

OSS Lab receives two grants over the course of February and March. More details are provided in the "Funded Projects" section.

March 2015. Fellowship at the Wissenschaftskolleg zu Berlin (WIKO)

The WIKO was founded in 1981 with the purpose to offer scholars and scientists the opportunity to concentrate on projects of their own choice for one academic year, free from administrative duties. OSS lab head Orkun Soyer experienced this privileged position as a short term WIKO fellow this year. During his time at WIKO, Orkun concentrated on developing theories on thermodynamic basis of microbial interactions and ideas on how to better analyze and engineer microbial communities. The latter work has culminated in a research proposal, while the former will underpin two upcoming papers (together with from Tobias Grosskopf who joined Orkun at WIKO as visiting fellow). Being at Berlin for an extended time has also allowed formation of links with researchers from Humboldt University, leading to organization of a one day workshop attended by the OSS Lab members. Overall, the fellowship was an unforgettable and highly rewarding experience. Interested parties should consider applying at WIKO's junior fellows program.

June 2015. Best Presentation Award

Tobias Grosskopf from OSS lab received the "best presentation award" at the Anaerobic Digestion Early Career Researcher event organized by BBSRC Anerobic Digestion Network. Tobi presented his work on "Mutational Reshaping of Metabolism facilitates Microbial Syntrophy", which was highly well received by the panel of judges and the audience alike. The event was attended by over 40 participants from 17 Universities, who presented their research on aerobic digestion and associated microbial communities.

Updated Design

We have updated our website and design.