anaerobic digestion lola

 
 
 







Group Leaders 
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 Researchers 
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 Technicians 
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 PhD Students
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Orkun
S. Soyer (University of Warwick), PI
Expertise: Soyer is an expert in the theoretical analysis of structure and dynamics of biological networks. His research in systems biology has elucidated evolutionary paths and factors leading to current day features of cellular networks and as such is linked to minimal, and evolutionarily stable design in synthetic biology. Role: Soyer's lab will focus on developing the theoretical and experimental approaches for synthetic community design and contribute to directed evolution and modelling of natural communities. Soyer Lab




Angus Buckling (University of Exeter), Co-I
Expertise: Buckling is an expert in experimental microbial evolution and ecology. 
He has worked extensively on host-parasite (bacteria-phage) coevolution, social evolution and evolutionary diversification. 
He has recently started to carry out experimental evolution in natural environments to achieve more applied aims. 
Role: Buckling's lab will focus on directed evolution of microbial communities and will contribute to 
design and analysis of synthetic communities. 
Buckling Lab




Tom Curtis (Newcastle University), Co-I
Expertise: Curtis is an expert in the engineering of biological treatment systems. His core interest is the engineering of real open microbial systems and he has become particularly well known for his work on the engineering of the diversity and community assembly of microbial communities. Role: Curtis' lab will focus on scale-up of synthetic communities to large scale reactors and implementation of developed insights from natural communities. He will also heavily contribute to modelling, synthetic design, and directed evolution experiments. Curtis Lab




Phil Hobbs, consultant
Expertise:Hobbs is an expert in 
microbial systems used in waste treatment and biomethane production. Recently, his 
research led to the design of a commercial high technology small scale digester. This and 
his work on benchmarking commercial biomethane plants in the EU has led to a focus on process 
control for optimisation using microbial approaches. Role:Hobbs will contribute to the design 
of directed evolution experiments in serial batch reactors and experimental design of synthetic communities. 
Anaerobic Analytics




David Swarbreck (TGAC), Co-I
Expertise: Swarbreck is an expert on computational approaches to analyse next generation sequence data for a wide variety of applications including gene prediction, transcriptomics and epigenetics. He has contributed to the analysis of human and mouse genomes for (in particular human chromosome one) and played a key role in the development of the TAIR resource as major international plant genomics database.Role: Swarbreck lab will focus on the metagenomic and metatranscriptomic analyses of samples collected from directed evolution experiments. Swarbreck Lab



Richard Titball (University of Exeter), Co-I
Expertise: Titball is an expert in molecular microbiology and intracellular pathogens. He has worked extensively determining the molecular basis of virulence and has significant expertise on the construction of mutants and the overexpression of genes in environmental bacteria. Role: Titball lab will focus on the design and experimental development of synthetic microbial communities. Titball Lab



David Stuckey (Imperial College London), Co-I
Expertise: Stuckey is a expert on anaerobic digestion and has developed both the novel Anaerobic 
Baffled Reactor (ABR), and the Submerged Anaerobic Membrane Bioreactor (SAMBR). The latter was awarded the Royal Society Brian Mercer 
Award for Innovation in 2008. Over the years he has developed the standard bioassay techniques used in the field and is internationally 
leading in the production and characterisation of Soluble Microbial Products (SMPs) in anaerobic systems. Role: Stuckey lab will 
focus on the scaling up of developed synthetic communities and transfer of insights from natural communities to applications in 
industrial reactors. Stuckey Lab




Declan Bates (University of Warwick), Co-I
Expertise: Bates is an expert in the development and application of techniques for the modelling, analysis, control and optimisation of complex dynamical systems. He has pioneered application of tools and ideas from control theory to biological systemsRole: Bates lab will contribute to the development of theoretical approaches to the study of natural communities and design of synthetic ones. Bates Lab




Jan Dolfing (Newcastle University), Co-I
Expertise: Dolfing is an expert on anaerobic bioreactors, syntrophic interactions and the degradation of halogenated compounds. The recurring theme in his work is the use of thermodynamics to delineate the limits and logic of anaerobic microbial processes. Role: Dolfing lab will focus on the development of mathematical models for the study of natural and synthetic communities. Dolfing Lab




David Studholme (University of Exeter), Co-I
Expertise: Studholme is an expert on comparative genomics and bioinformatics approaches to microbes and the evolution of emerging diseases. He contributed to the development of, now widely used, Pfam and InterPro databases. He also played a key role in establishing methods and pipelines for handling step-change in sequencing data when Illumina GA sequencing facilities first became available. Role: Studholme lab will contribute to the analysis of genomic and transcriptomic data from directed evolution experiments and synthetic communities. Studholme Lab




Russell Davenport (Newcastle University), Co-I
Expertise: Davenport is an expert in the development and application of molecular tools to understand relationships between microorganisms and the processes that they mediate. His work has focussed on specific bacterial functional groups and overall diversity using quantitative, and recently, next-generation sequencing tools. Role: Davenport lab will contribute to the analysis of genomic and transcriptomic data from directed evolution experiments and synthetic communities. Davenport Lab




Mary Coates, Project manager
sLola Project Manager since Summer 2013 (30% FTE); Project facilitator (2008-2014) for the BBSRC systems biology PRESTA project 'Plant Responses to Environmental STress in Arabidopsis'; PhD, Warwick HRI, The University of Warwick (2007) 'Defining Downy Mildew (Hyaloperonospora parasitica) Avirulence Loci'. BSc (Hons) Biological Sciences, The University of Exeter (2001). Off-work hobbies: Spending time with my children, crochet, reading, cocktails, snowboarding, enjoying the countyside.





Tobias Grosskopf, PDRA
Born in Munich in 1981. Diploma in Biological Oceanography from the University of Kiel, Germany (2008). Dr. rer. nat. (PhD) in Marine Biogeochemistry from the University of Kiel (2012), working in the Molecular Biology Lab of Prof. Julie LaRoche in the Helmholtz Centre for Ocean Research (GEOMAR). Worked on the project April 2013 to June 2016. Research Area: Engineering Synthetic Microbial Communities, Biomethane Production.
Off work: Sailing, playing guitar, skiing






Matthew Wade, PDRA
MsC in Environmental Engineering from the Newcastle University (2000). PhD in Electronic and Electrical Engineering from the University of Strathclyde (2004). Worked on the project April 2013 to June 2016. Research Area: Knowledge extraction for improving process understanding and operation, primarily through advanced data analysis techniques and biological modelling.





Pawel Sierocinski, PDRA
Born in 1981 in Warsaw in Poland. Did his MSc in Biotechnology in Wageningen University, where he worked 2007-2011 researching transcriptome of hyperthermophillic Archaea. 2012-2013 researched influence of sex-like bacterial behaviour on evolution of bacteria under pressure from parasites and pharmaceuticals. In the sLoLa team since May 2013. Research area: Elucidating the impacts of community mixing, species sorting and evolution on methane production using natural and commercial microbial communities. Off-work: Cooking; Blogging.





Yu Tao, PDRA
Born in Harbin, China in 1985. MSc and Dr in Environmental Science and Engineering from Harbin Institute of Technology in 2010 and 2015, respectively. PhD study in the Lab of Urban Water Resource and Environment with Prof. Dawen Gao (2008-2015, HIT) and in Sanitary Engineering with Prof. Jules van Lier (2011-2013, TU Delft). Started on the project in February 2015. Research Area: Bioaugmenting methane production from evolved and synthetic microbial communities. Off work: travelling.






Jing Chen, PDRA
Born in Chongqing, China in 1985. BEng in Bioengineering (2008) and MEng in Biochemical Engineering (2011) from Sichuan University, China. PhD in Environmental Microbiology from The University of Hong Kong (2016), supervised by Dr. Ji-Dong Gu on the topic of molecular detection of denitrifying anaerobic methane oxidation bacteria in coastal and ocean sediments. Started on the project in February, 2016. Research area: Engineering synthetic microbial communities, quantitatively characterizing their dynamics and stability. Off work: Hiking, reading and cooking.






Mark Alston, PDRA
A computational biologist specialising in the analysis of metagenomic and metatranscriptomic data from environmental samples, I provide insight into complex communities of microbes. Working closely with ‘wet-lab’ scientists I put these data into a biological context. I joined the sLOLA team in 2015 and applying my skills to studying microbial communities for biomethane production. Prior to joining EI, I gained an MSc in Computer Science before joining the Foodborne Bacterial Pathogens group at the Institute of Food Research analysing and interpreting transcriptomic and regulatory network data. With a first degree and PhD in biochemistry, my previous roles in academia and industry applied novel biocatalysts to challenges in the synthesis of natural compounds, drug intermediates and microemulsions.





Evangelos Petropoulos, PDRA
B.Eng. in Civil Engineering from the Technological Institute of Thessaloniki (2008). Masters and Ph.D. in Environmental Engineering from Newcastle University (2010 and 2015 respectively - supervised by Prof. Thomas P. Curtis). Rich experience in engineering projects related to the construction of water and wastewater treatment plants (Greece, 2007-2009). Marie Curie Research Fellowship in AD-WINE project (2014-2015) hosted at AEMA (SP) and at Newcastle University (UK). Research Associate in the sLoLa project since February ’15 (Newcastle University (UK). Research area: Investigation of the hypothesis that acclimation to low temperatures assists the synthesis of a stable, highly active methanogenic community. Off work: Finance..





Florian Bayer, Technican
Born in Bavaria, Germany (1977). Background in emergency medicine. Intern at IEB, University of Edinburgh (2008). Research Technician in Frank Jiggins lab, Department of Genetics, University of Cambridge (2009-2010). Research technician at IEB, University of Edinburg in the Pemberton and Hadfield labs (2011 -2012). Volunteer at Genomic Diversity Centre, ETH Zurich, Switzerland in the Wilfert lab (2012). Consultant for large-scale genotyping and gene expression studies (2012 – 2013). Started on the project in April 2013. Off-work: Hiking and brewing.




 


Xue Jiang, PhD student, University of Warwick
Born in Chongqing, China. Undergraduate in Bioscience from Sichuan University, China (2010). MPhil in Chemistry from University of St Andrews (2012). Started PhD at OSS lab on September 2013. Phd project title: Biomethane communities optimization. Off-work hobbies: Cooking, animations and badminton.





Henry Porter, PhD student, University of Warwick
Born in New Jersey in 1989. Acquired a BSc in Biomedical Science at Lancaster University (2010) and an MSc in Molecular Medicine at Imperial College London (2012). Work experiences at Vancouver General Hospital, the Agribusiness Syngenta and the African Health Policy Network. I am interested in basic questions regarding microbial ecology and hope to generate stable, synthetic methanogenic communities.






Melchior Du Lac, PhD student, University of Warwick
Melchior du Lac was born in Toulouse France, but was educated at EABJM Paris with an IB diploma. He received his Bsc in Biotechnology from the University of Glasgow, in 2011. Although a biologist at heart, he is very interested in the computer science side of biology and is particularly interested in systems biology and modeling of biological systems. He subsequently received his Msc in Bioinformatics from the same University in 2012. He did his Masters project in developing an extension of the sleeping sickness (t.brucei) parasite glycolytic model. More prescicely looking at the possible routes of L-Pyruvate consumption by the enzyme Alanine Aminotranstransferase and other enzymes. 





Peter Stilwell, PhD student, University of Exeter
Born in Devon, England. Undergraduate degree in Evolutionary Biology from University of Edinburgh (2005-2009). Research Technician in molecular virology in the Barclay Lab, Imperial College (2010-2012). Master's Degree in Evolutionary and Behavioural Ecology from University of Exeter (2012-2013). PhD with Angus Buckling investigating evolution of microbial communities. Off-work: Guitar, piano, motorcycling. 





Barbara Shannon, PhD student, University of Exeter
Born in South Yorkshire, England. Undergraduate degree: Biochemistry with Molecular Biology (Leeds University 2013). Placement year: Mayo Clinic, Jacksonville Florida, USA (2011-2012); research field: Genetics of Parkinson’s disease. I am currently a first year PhD student at the University of Exeter, Biosciences (2013). Area of research: Engineering synthetic microbial communities for biomethane production. PhD title: Genome analysis and mutagenesis of Methanococcus. Off work: Walking, Irish dancing, cooking.





Katy Jones, PhD student, University of Exeter
I obtained a BSc in Medical Imaging from the University of Exeter in 2012 and an MSc in Bioinformatics, also from the University of Exeter, in 2013. My MSc project used bioinformatic methods to identify and analyse the genomes of several bacteria found in consortia with the hydrocarbon-producing alga Botryococcus braunii. My current PhD research involves using both bioinformatic and laboratory methods to investigate interactions amongst microbial communities. Off work I like walking and visiting the beach in Exmouth, where I live, with my daughter.




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