Investigators
Specialization: computational tools for bioinformatics, comparative genomics
Dr. Beiko is Assistant Professor and Canada Research Chair in Bioinformatics at Dalhousie University in Nova Scotia, where he specializes in comparative and evolutionary genomics. His research involves the development and use of sophisticated computational tools for the comparative analysis of DNA and protein sequences between micro-organisms to help determine the role of genes and proteins in the environment.
Dr. Beiko has expertise in the development of novel methods to tackle large and challenging data sets, and published the first detailed map of lateral gene transfer in PNAS in 2005. While continuing to mine the relationship between genome content, evolution, and function, he has also shifted his attention to the analysis of metagenomic data. He led the development of GenGIS, which combines microbial biodiversity information with phylogeny, geography and ecology, and has been applied to discover biogeographic patterns in the immense Global Ocean Sampling dataset, study the emergence of HIV, and model pathways of human migration. Dr. Beiko's other research achievements include the creation of the Microbial Online Analysis Database and work on enhanced biological phosphorous removal, a commonly used waste water treatment that uses microbes.
Within the BEEM project, Dr. Beiko works on the development, application and validation of methods for automatic annotation, metabolic network reconstruction and comparative analysis of metagenomes.
Tel: +1 902-494-8043
Specialization: transcriptional regulation, forest biotechnology
Dr. Campbell is a Professor in the Dept. of Cell and Systems Biology and Vice-Principal of Research at the University of Toronto Scarborough Campus. He is a renowned expert on the transcriptional regulation of plant cell wall biosynthesis and forest biotechnology. His research has focused on understanding the molecular mechanisms that control plant architecture, in particular those mechanisms involved in lignin biosynthesis. Dr. Campbell is extensively involved in the forest biotechnology community and was founder and coordinator of the European Forest Genomics Network. He is a member of the editorial board of Plant Biotechnology Journal and a member of the Board of Directors of the Institute for Forest Biotechnology in the USA.
As part of the BEEM project, Dr. Campbell's focus is on the discovery and use of microbial enzymes for the modification of industrially-relevant biomass, particularly forest products.
Tel: +1 416-208-4835
Specialization: anaerobic bioremediation, metagenomic data analysis, commercialization
Project Leader
Dr. Edwards is a Professor in the Dept. of Chemical Engineering and Applied Chemistry at the University of Toronto and is the Director of BioZone, a Centre for Applied Bioengineering Research. She is an internationally renowned expert in bioremediation and environmental biotechnology who has spent over 20 years developing techniques that use bacteria to clean up sites with groundwater contamination. The focus of her work is to harness and enhance the innate ability of soil micro-organisms to biologically transform common toxic pollutants, such as gasoline and industrial solvents, to render them less harmful to the environment and human health. Her research involves the characterization of microbial communities that degrade these compounds, and the use of molecular tools to detect gene and protein expression.
Dr. Edwards brings expertise in engineering scale-up and commercial application of bioproducts to the BEEM project, and was recently recognized with the 2009 NSERC Synergy Award for her highly successful partnership with Geosyntec, an international environmental consulting firm with whom she developed a microbial consortium called KB-1®. This commercially successful bioproduct biodegrades two of the world's most common and persistent groundwater pollutants, PCE (a common dry-cleaning agent) and TCE (a degreasing solvent), more quickly and at a lower cost than conventional methods. It has been used at over 200 sites around the world.
Dr. Edwards' research accomplishments have been recognized with several prestigious awards, including an NSERC Women's Faculty Award, a Premier's Research Excellence Award (PREA) and a Killam Research Fellowship (Canada Council for the Arts). She has authored over 60 peer-reviewed journal publications, and as many government and industrial reports, book chapters and conference papers. She is also a collaborator in Innovative Technologies for Groundwater Remediation (INTEGRATE).
As Project Leader, Dr. Edwards is responsible for the overall technical and administrative coordination of research activities, as well as providing particular guidance to activities related to enrichment of anaerobic consortia and technology transfer.
Tel: +1 416 946 3506
Specialization: microbial metagenomics in extreme environments, metagenomic libraries
Dr. Golyshin is a Professor and Chair in Environmental Genomics at Bangor University in the UK. He is a world-renowned expert in the environmental genomics of extremophilic bacteria and archaea, including Alcanivorax borkuimensis, a key player in marine oil degradation and the first marine oil-degrading bacterium ever sequenced. Dr. Golyshin has published over 80 papers and generated eight patents. He serves as coordinator for one of the BEEM project's partners, the large MAMBA project (Marine Metagenomics for New Biotechnological Applications), which aims to mine various environmental metagenomes for novel enzymes. MAMBA is in the process of creating one of the first large-scale metagenomic collections in the academic world and is specifically designed for the discovery of new industrial enzymes, especially those useful for the production of chemicals, antioxidants and anti-cancer drugs.
Dr. Golyshin helps to coordinate the exchange of environmental samples and genomic data between BEEM and MAMBA, and works on activity screens for metagenomic libraries.
Tel: +44 1248 38 3629
Specialization: environmental microbiology
Dr. Löffler is a Governor’s Chair at the University of Tennessee and Oak Ridge National Laboratory with appointments in the Department of Microbiology and the Department of Civil and Environmental Engineering. He has earned international recognition for his innovative research at the interface of biology, chemistry and engineering to understand and manage environmental processes and safeguard natural ecosystems. Discoveries in the Löffler lab have contributed to the advancement of bioremediation around the world, and have focused on how naturally occurring bacteria break down pollutants like chlorinated solvents, immobilize radioactive waste and control greenhouse gas emissions. His research accomplishments have been recognized with an NSF Career Award in 2001 and the SERDP Project of the Year award in 2004 and 2006. He was endowed with the Carlton Wilder Professorship in Environmental Engineering at the Georgia Institute of Technology in 2006 and received the Shimizu Visiting Professorship from Stanford University in 2009.
Dr. Löffler brings expertise in microbial physiology, enrichment and isolation procedures of anaerobes, and the design and application of molecular tools to the BEEM project.
Tel: +1 865-974-4933
Specialization: Environmental and economic life cycle analysis, public policy, GE3LS
Dr. MacLean is an Associate Professor in the Dept. of Civil Engineering at the University of Toronto and also has a joint appointment in the Dept. of Chemical Engineering and Applied Chemistry and the School of Public Policy and Governance. She is an internationally recognized expert in the field of energy systems analysis, with a particular focus on life cycle assessment of alternative energy and infrastructure systems for bioenergy and bioproducts. Over the last decade, she has worked closely with the automotive, biofuels and electricity industries, as well as federal and provincial governments. Her work on evaluating alternative bioenergy systems garnered her an Early Researcher Award from the Government of Ontario.
Dr. MacLean provides expertise to the policy analysis team for BEEM's GE3LS component, and will be a major contributor to the evaluation of bio-based products and their associated public policy implications.
Tel: +1 416 946 5056
Specialization: bioinformatics, metabolic modeling
Dr. Mahadevan is an Assistant Professor in the Dept. of Chemical Engineering and Applied Chemistry at the University of Toronto and brings essential expertise in the emerging field of systems biology and contraint-based models of metabolic networks to the BEEM project. Dr. Mahadevan is a pioneer in this new computational field that has arisen from a need to make sense of the vast amount of genomic information now available. Using computational and experimental methods, he was the first to model the unique metabolism of Geobacter sulfurreducens, an anaerobic metal-reducing bacterium with applications in bioremediation of toxic metals and bioelectricity generation. Dr. Mahadevan's compuational expertise is critical to the develpment of organism-independent metabolic models based on the metagenome sequence data generated in the BEEM project. Modeling results will help to direct and focus microbial and enzyme screens, as well as integrate knowledge gained from all project activities.
Dr. Mahadevan serves as leader for BEEM's bioinformatics research and heads the metabolic modeling and sequence analysis efforts.
Tel: +1 416 946 0996
Specialization: biodegradation of groundwater contaminants, technology transfer and commercialization
Project Leader
Dr. Major is a principal environmental scientist at Geosyntec Consultants Inc. in Guelph, Ontario, where he oversees the development and deployment of effective remediation strategies for sites with contaminated groundwater for clients such as Fortune 500 companies, the U.S. Departments of Energy and Defense and NASA. Dr. Major's area of expertise is the application of in-situ biodegradation of chlorinated industrial solvents, that is the use of micro-organisms that are able to biologically degrade these common groundwater contaminants. He was a pioneer in the development and use of monitored natural attenuation and enhanced in-situ bioremediation, and has worked with researchers at Dupont and Stanford University on molecular tools to identify genes of key dechlorinating microorganisms in the environment.
Geosyntec and Dr. Major were honoured recently with the 2010 NSERC Synergy Award for their collaboration with Dr. Elizabeth Edwards at the University of Toronto (BEEM Project Leader), with whom they developed and brought to market the microbial consortium KB-1®, which has been used at over 200 sites around the world to treat persistent groundwater pollutants.
Dr. Major serves on various national scientific and regulatory advisory boards and is a member of the Remediation Technologies Development Forum (RTDF), a public-private organization dedicated to developing, demonstrating, and evaluating technologies for high priority environmental problems. He has served on a U.S. EPA Expert Panel, and on the U.S. National Reserch Council Committee on Geological and Geotechnical Engineering in the New Millenium. Dr. Major is the author or co-author of over 50 peer-reviewed technical publications on environmental remediation topics, and over 45 conference publications, presentations and posters.
As Project Co-Leader, Dr. Major is responsible for overseeing and advising on activities related to bioproduct commercialization. He also serves as Co-Chair of the of the Commercialization Committee (CCOM).
Tel: 519-822-2230 ext 232
Specialization: enrichment of cultures from environmental samples, enzyme characterization, forest biotechnology
Dr. Master is an Assistant Professor in the Dept. of Chemical Engineering and Applied Chemistry at the University of Toronto and brings expertise in enzymology, applied functional genomics, proteomics and lignocellulose chemistry to the BEEM project. Her work focuses on advances in biotechnology that facilitate the extraction and alteration of materials from renewable resources, with a particular focus on the forest industry and the range of products that can be derived from wood fibres. By searching for enzymes that transform ligoncellulosic substrates, Dr. Master is working toward the production of biomaterials from currently underutilized sources such as mill wastes. In previous projects, she has been involved in the analysis and annotation of transcripts induced in wood-degrading fungi under defined conditions, and the evaluation and use of encoded gene products in industrial applications.
Dr. Master is the leader of BEEM's research activities in the enrichment of cultures and enzymes from environmental samples, and provides particular expertise in the enrichment of microbial consortia from forest product waste sources.
Tel: +1 416 946 7861
Specialization: ToFSIMS, characterization of enzyme activity on solids
Dr. Mims is a Professor in the Dept. of Chemical Engineering and Applied Chemistry at the University of Toronto and Director of Surface Interface Ontario, a multi-user surface analytical facility that is home to a Time-of-Flight Secondary Ion Mass Spectrometry (ToFSIMS) instrument facility with unique sample preparation capabilities. For the past 30 years, Dr. Mims has studied the fundamentals of surface reactions of interest in the energy, chemical and environmental fields. ToFSIMS is a technique that does not require a priori knowledge of reaction products and is suitable for high throughput analyses. It allows for a broader search of the enzyme space than most enzyme screens, thus greatly increasing the chance of ground-breaking discoveries.
As part of the BEEM project, Dr. Mims will design novel enzyme assays for solid substrates using his ToFSIMS facility.
Tel: +1 416 978 4575
Specialization: technology transfer, public policy
Dr. Reeve is a Professor in the Dept. of Chemical Engineering and Applied Chemistry at the University of Toronto, where he served as Department Chair from 2001 to 2011. He is appointed to the University of Toronto School of Public Policy and Governance and is internationally recognized for his expertise in pulp and paper research. He has authored over 90 publications and generated 18 patents.
Dr. Reeve brings tremendous expertise in technology transfer, public policy and sustainability issues to the BEEM project. Numerous awards have recognized his research achievements, most recently the RS Jane Memorial Award from the Canadian Society for Chemical Engineering in 2010, the John S. Bates Memorial Gold Medal from the Pulp and Paper Technical Association of Canada in 2007. He was named Fellow of the Canadian Academy of Engineering in 2006, and is co-author of the book "Current Affairs: Perspectives on Electricity Policy for Ontario", 2010.
As part of the BEEM project, Dr. Reeve leads activities related to policy analysis and GE3LS, co-chairs the Commercialization Committee, and provides leadership and guidance for technology transfer and industrial liaison.
Tel: +1 416 978 2543
Specialization: structural biology and biochemistry
Dr. Savchenko is a Group Leader at Structural Proteomics in Toronto (SPiT) and is an Assistant Professor at the Banting and Best Dept of Medical Research at the University of Toronto. He is also an Associate Professor at the Dept of Chemical Engineering and Applied Chemistry at the same university.
Dr. Savchenko's work focuses on characterization of protein function using a combination of structural (primarly X-ray crystallography), biochemical and in vivo methodologies. His Structural Genomics group is working on large-scale structural characterization of protein families whose 3-D shape cannot be predicted from existing protein structure data. Dr. Savchenko and his team developed the high-throughput protein crystallization pipeline that is central to SPiT as well as to two major Structural Genomics Centres (MCSG and CSGID) in the US. This pipeline produces more than 80 novel protein structures per year and is one of the most efficient in the field of structural biology. Dr. Savchenko has published over 100 papers and reviews, and his research has been funded by NIH, Genome Canada and NSERC.
As part of the BEEM project, Dr. Savchenko leads the protein cloning, expression, purification and structure determination research, and provides guidance for gene analysis.
Tel: +1 416 978 3925
Specialization: public policy, life cycle analysis, GE3LS
Dr. Saville is a Professor in the Dept. of Chemical Engineering and Applied Chemistry at the University of Toronto and is an expert in biofuels and bioenergy benchmarking. He has been involved in the biofuels area from bench scale R&D to commercialization, economics and policy. Technology derived from his research and patents related to novel hydrolytic enzymes has been field tested in seven North American fuel ethanol plants, and has been used in the production of more than 200 million US gallons of ethanol since 2004. Dr. Saville brings a wealth of knowledge about industrial production of bio-based products to the BEEM project, and has collaborated with BBI, Natural Resources Canada, Environment Canada and the North American Energy Working Group.
Dr. Saville is the BEEM project lead for research to evaluate bioproducts and their associated public policy implications.
Tel: +1 416 978 7745
Specialization: bioinformatics, annotation, genomics data analysis
Dr. Tillier is a Professor in the Dept. of Medical Biophysics at the University of Toronto and is Canada Research Chair in Analytical Genomics. Her expertise lies in the analysis of genomics data, annotation, bioinformatics and microarray design. The focus of her research is on biology and evolution on a genomic and metagenomic scale, and involves the development and optimization of tools to analyse large amounts of varied data accumulated by the technologies in the field. Dr. Tillier has developed several pioneering tools for the design of oligonucleotide probes for gene families, identification of interacting proteins, simulation of protein evolution, as well as tools to detect interactions between amino acids in proteins.
As part of BEEM, Dr. Tillier is responsible for the design of analytical tools and statistical data interpretation of metagenomic and genomic data.
Tel: +1 416 581 7534
Specialization: enzymology, high throughput screening
Dr. Yakunin is an Associate Professor in the Dept. of Chemical Engineering and Applied Chemistry at the University of Toronto. He is also Senior Research Associate and Assistant Professor in the the Banting and Best Dept. of Medical Research and Enzymology Group Leader at Structural Proteomics in Toronto (SPiT). His research is focused on enzyme discovery and functional annotation of unknown proteins. As an experimental approach, his group is using general enzymatic assays to screen purified unknown proteins for catalytic activity. Using these assays, unknown proteins can be quickly tested for diverse activities and identified to the sub- or sub-sub-class level, greatly streamlining the number of classical substrate profiling experiments needed for characterization. In addition, he has several projects involving biochemical characterization of novel microbial enzymes including nucleases, phosphotases, esterases, dehalogenases, and various industrial enzymes. Dr. Yakunin also has unique expertise in techniques for characterizing enzymes that function in anaerobic environments, and has published over 80 articles.
In the BEEM project, Dr. Yakunin oversees research activities related to activity screens for clones and purified proteins, and is responsible for the high-throughput enzyme screens of existing and new large-insert metagenome libraries.
Tel: +1 416 978 4013
