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PUTTING A “ GREEN THUMB” ON THE “ GENOMICS HAND” Canadian Research Efforts in Environmental Genomics Presented to : . “eGenomics: Genomes and the Environment NIEeS Workshop Cambridge University September 5-6 / 2005. . Purpose of Presentation.

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PUTTING A “GREEN THUMB” ON THE “GENOMICS HAND” Canadian Research Efforts in Environmental GenomicsPresented to:

“eGenomics: Genomes and the Environment

NIEeS Workshop

Cambridge University

September 5-6 / 2005.

purpose of presentation
Purpose of Presentation
  • Introduce importance of environmental genomics to Canada
  • Outline how Canadian federal government and selected universities are organizing themselves in support of environmental genomics research and development
  • Identify some research elements of the current opportunity / challenge agenda for selected environmental genomics research activities
  • Introduce evolving North American / International efforts at environmental genomics research capacity building
  • Set the stage for discussion with you on how we can collaborate more fulsomely on complementary future environmental genomics research initiatives
what is environmental genomics
What is Environmental Genomics?
  • Environmental Genomics (EG)bridges the gap between genetics, physiology, and ecology
  • It involves utilization of a broad range of modern molecular techniques such as gene arrays and single nucleotide polymorphism (SNP) screens to monitor variation in gene structure and expression
  • EG can pinpoint potentially novel interactions between environmental stressors and expression of specific human, animal and plant genes
what is environmental genomics4
What is Environmental Genomics?
  • Applies knowledge gained on gene identification, structure and expression to environmental protection & management:
    • Can rapidly identify species in complex environments
    • Can indicate how environmental stressors affect gene expression in humans, animals & plants
    • Can demonstrate deleterious effects at molecular level before organism-level effects are shown
importance of environmental genomics i
Importance of Environmental Genomics (I)
  • Genomics builds upon and enhances traditional approaches to environmental toxicology determination
  • Genomics provides an understanding of organisms and biological systems that is a prerequisite for understanding environmental change
  • A key objective for environmental science is improved understanding, identification, and prevention of environmental problems
  • The behaviour and response of an organism / groups of organisms to environmental stressors is ultimately controlled by genes and the products they encode
importance of environmental genomics ii
Importance of Environmental Genomics (II)
  • Genomics can provide the next generation tools to help protect and manage the environment:
    • Environmental remediation & restoration (e.g. plants that can clean up contaminated sites)
    • Pollution abatement, prevention & detection (e.g. identification of soil / water pathogens, toxicants)
    • Wildlife management & conservation biology techniques (e.g. genetic ‘barcoding’ for species identification)
    • High throughput analysis and identification of soil / freshwater / marine microbial community
importance of environmental genomics iii
Importance of Environmental Genomics (III)
  • Genomics could be critical to examining biotechnology’s potential impacts on the environment, such as:
    • Unintended properties of genetically modified organisms (toxicity, allergenicity)
    • Emergence of invasive species
    • Displacement of native species
    • Spread of new ‘pest’ species
    • Gene transfer occurrence and mechanisms from genetically modified organisms to other organisms
why environmental genomics and why now
Why Environmental Genomics and Why Now?
  • “In the environment, virtually all microorganisms exist in complex communities whose function as a whole is far greater than the sum of what their individual members can achieve.. Understanding these interactions – the ways in which microorganisms work together to achieve complex tasks – will provide insights that can be used to address global challenges of energy production, improved human and animal nutrition, understanding infectious disease mechanisms, and furthering environmental remediation and restoration”
  • Source Jay Short – President and CEO Diversa 2004
why environmental genomics and why now9
Why Environmental Genomics and Why Now?
  • “The growth and survival of microorganisms drives biogeochemical cycling of elements, detoxifies many organic compounds, sequesters many inorganic compounds, produces a wide range of valuable and renewable industrial compounds, makes essential nutrients present in the biomass of one generation available to the next generation, and maintains the conditions critical to all life on earth”
  • Source ASM 2003
canadian federal government genomics platform a tale of two cities
CANADIAN FEDERAL GOVERNMENT GENOMICS PLATFORM – A “TALE OF TWO CITIES”
  • Extramural Funding - Genome Canada:
  • Funding: (2002-2005) - $ 375M (2005-2007) - $165M
  • Obligation: Build national technical capacity in industry and
  • university (health, GE3LS agriculture, forestry,
  • environment)
  • Delivery: Five regional nodes supporting university /
  • industry collaboration
  • Intramural Funding – (HC, NRC, AAFC, DFO, NRCan, EC)

Funding: (1999-2005) (2005-2007) - $20 M/yr ($1 M to Environment

Canada)

Obligation: To establish initial genomics R & D capabilities

ECDelivery Mechanism: Several EC Regional Nodes Under Strategic Technology Applications of Genomics in the Environment Program (STAGE)

environment canada s genomics program research focus
Environment Canada’s Genomics Program – Research Focus
  • Identification
    • Risk Identification
      • The National Water Research Institute (NWRI) is developing and applying methods that will use DNA microarrays to answer questions about the effects of environmental contaminants on the biodiversity and function of microbial communities.
  • Risk Assessment / Management
    • Test Method Development
      • TheEnvironmental Technology Centre (ETC) is developing & standardizing genomic-based procedures to ensure more accurate data for submission under the New Substances Notifications Regulations.
    • Environmental Monitoring
      • The Pacific Environmental Science Centre (PESC) & National Wildlife Research Centre (NWRC) are using toxicogenomic techniques to link observed effects of toxics to specific environmental exposures & providing improved “early warning” signals to industry regulators.
  • Conservation Biology and Wildlife Management
    • The Canadian Wildlife Service (CWS) is developing and applying genetic markers towards the resolution of conservation issues.
  • Improved Enforcement & Compliance
    • The PESC has completed a Pulp and Paper study that positively identifies mill effluents that are causing endocrine disruptor effects to fish.
toxicogenomic applications
Toxicogenomic Applications
  • Environment Canada BC Labs have created internal capacity for all phases of genomic testing, with the exception of gene array spotting.
  • Focus to use EC existing aquatic toxicological methods as platform (Rainbow trout test fry and early stage test, new amphibian methods in works)
  • Application to chronic endpoint; traditional methods not sensitive enough to detect molecular level toxicity. Good predicator to “real world” effects
development of microarrays
Development of Microarrays
  • Functional/Metabolic:
    • Targeting catabolic, biogeochemical cycling, metal resistance
    • Pollutant transformation processes
    • Ecosystem health
  • Taxonomic
    • Targeting 16S rDNA
    • Microbial community profiling
    • Phylogenetic identification
current toxicogenomic projects
Current Toxicogenomic Projects
  • Arrays have been used extensively on testing effects of:
    • Pure chemical testing
    • Agricultural runoff
    • MWWE
    • Pulp & Paper effluent, 9 mill survey
    • Georgia Basin Action Plan-5 year study EDC effects using in-house fish and amphibian gene arrays.
wildlife management using genomic tools
Wildlife Management Using Genomic Tools
  • Focus on the following conservation issues:
  • How can we delineate discrete population units for migratory species?
  • What is the effect of selective harvesting of males on subsequent population growth?
  • What is the conservation significance of peripheral populations?
population genetics for wildlife management
Population Genetics for Wildlife Management
  • Information obtained from population genetics
  • studies can be used to determine:
  • Population structure and size
  • Parentage – social structure
  • Identification – subspecies, sex, individual (e.g. forensics)
  • Distribution – genetic diversity
  • Gene flow
  • Hybridization
  • Population viability
  • Evolutionary history
  • All information that is important in the design of
  • effective conservation programs.
toxicogenomics wildlife toxicology
Toxicogenomics & Wildlife Toxicology
  • How and why do species differ in sensitivity to the effects of environmental contaminants?
  • Can we determine which species might be most affected by existing & new environmental contaminants?
  • Can we develop better biomarkers?
microbial test methods for assessing environmental fate using genomic tools
Microbial Test Methods for Assessing Environmental Fate using Genomic Tools
  • Objectives:
  • To develop in-house expertise and laboratory capability for developing genomic-based soil testing methods for assessing the potential environmental risk of domestic or new microbial substances
  • To develop & standardize genomic-based procedures to ensure that notifiers generate more reliable & accurate data on environmental fate for their submissions
  • To generate risk assessment data on the 29 microbial substances listed on the CEPA 1999 Domestic Substances List (DSL)
slide19

Barcoding Products and Life

1110 = 100 Billion

415 = 1 Billion

slide22

DNA Barcode:

short sequence enabling species discrimination

slide23

Concordia University / Genome Quebec Enzyme Systems for Pulp and Paper Industry

  • White-rot fungi:
  • Phanerochaete chrysosporium
  • Trametes versicolor
  • Lentinula edodes
  • Other lignin and pitch degrading fungi:
  • Gloeophyllum trabeum
  • Ophiostoma piliferum
  • Corpinus cinereus
  • Pollutant degrading fungi:
  • Aureobasidium pullulans
  • Amorphotheca resinae
  • Leucosporidium scottii
  • Cunninghamella elegans
  • Freeze-tolerant fungi:
  • Chrysosporium pannorum
  • Cryptococcus laurentii
  • Thermophilic composters:
  • Thermomyces lanuginosa (600C)
  • Chaetomium thermophile (500C)
environment canada genomics research end users conservation and protection
Environment Canada - Genomics Research End Users – Conservation and Protection
  • CEPA New Substances – Biotechnology
    • enumeration, detection, monitoring
  • EC Alien / Invasives Initiative
    • identification, detection
  • Ecosystem Effects of Novel Living Organisms (EENLO)
    • fate and effects
  • CWS – Species at Risk and CITES
  • Access and Benefit Sharing (ABS)
  • Enforcement – both ECS and EPS
  • NOPP – Pollution Detection, Monitoring, Surveillance
environmental genomics and new stewardship regulatory challenges
Environmental Genomics and New Stewardship / Regulatory Challenges
  • cohort specific regulations?
  • bioavailability vs. total pollutant loading?
  • cell lines vs. whole animal testing?
  • genetic tests for “screening” CEPA backlog
  • greater specificity for non target organism testing?
  • “fur, feather, feces” analysis vs. live capture?
  • basis for enforcement efficiency of CITES and SARA
synopsis of environmental genomics research experiences 1999 2005
Synopsis of Environmental Genomics Research Experiences 1999-2005:
  • Potential environmental impacts from applied genomics in agroforestry, fisheries, mining, and industry
  • Low prominence / priority ascribed to environmental genomics writ large until recently
  • Little recognition outside EC given to stewardship issues (regulatory, ethics, IP, biodiversity)
  • Increasing importance being ascribed to environmental genomics & “smart regulations”
  • Sub-critical masses of environmental genomics capacity across Canada
  • Limited current EC capacity in environmental genomics against all research areas
  • Evidence of tremendous interest for green genomics on the horizon and attendant funding mechanisms to support basic and applied R & D
establishing future genomics r d priorities environment canada work in progress
Contaminated sites remediation / restoration

Bioprospecting

Industrial ecology and green “chemistry”

Climate change/Bioenergy

Biobarcoding

Identification

Risk Assessment / Management

Test method Development

Environmental Monitoring

Conservation Biology and Wildlife Management

Improved Enforcement & Compliance

ESTABLISHING FUTURE GENOMICS R & D PRIORITIES ENVIRONMENT CANADA-WORK IN PROGRESS

Whole Range Of Priority Areas We Could Be Involved In:

Potential Future Genomics R & D Priorities

Interim Genomics R & D Activities

pursuit of future environment canada environmental genomics partnerships
Pursuit of Future Environment Canada Environmental Genomics “Partnerships”
  • Organized Canadian Environmental Genomics Network Meeting in 1999
  • Supported 20+ NSERC / CFI Submissions
  • Ongoing collaboration and support to several provincial government / university genomics labs
  • Environment Canada / Genome Canada Environmental Genomics workshop 2003
  • Canada / US / UK Environmental Genomics Workshop – Ottawa 2004
proposed environment canada strategy for 2005 ff alliance and convergence
Proposed Environment Canada Strategy for 2005 ff – Alliance andConvergence
  • Continue collaboration with Canadian environmental genomics community in calibration of long term R & D Agenda and federal government genomics architecture
  • Convene EC intramural STAGE community Nov 05/ January / 06.
  • Enhance EC/ USEPA / USDOE / NIEHS / NERC / NIEeS collaboration
  • “Harvest the results from SETAC, OECD, and NIEeS workshops
  • Explore establishment of CanGreen
  • Begin to calibrate R & D Agenda and co-operative mechanisms necessary for sustained environmental genomics research agenda for Canada
pursuit of future environment canada green genomics partnerships
Pursuit of Future Environment Canada Green Genomics Partnerships
  • NIEeS Genomes and the Environment UK Workshop 2005
  • SETAC Session on “Omics” November 2005(Maryland)
  • SETAC Pelleston Workshop on “Toxicogenomics”(Michigan)
  • OECD Toxicogenomics Workshop November 2005
  • Environment Canada CANGREEN workshop 2006?
potential for future international green genomics r d alliances
Potential for Future International “Green Genomics” R & D Alliances
  • USEPA Environmental Genomics Program
  • US Department of Energy Genomes to Life Program
  • UK BBSRC / NERC Environmental Genomics Program
slide34

ResearchFocusAreas

  • Chemical transformation
  • Metabonomics
  • Molecular indicators
  • Dose metrics
  • Toxicity pathways
  • Systems biology
  • Computational infrastructure
scientific goals of usdoe genomes to life program
Scientific Goals of USDOE Genomes to Life Program
  • Identify the protein machines that carry out critical life functions
  • Characterize the gene regulatory networks that control these machines
  • Explore the functional repertoire of complex microbial communities in their natural environments as a prelude to their use against DOE priorities
  • Develop the computational capabilities to integrate and understand this data
developing uk canada linkages in genomics
Developing UK-Canada Linkages in Genomics
  • Brassica genomics – collaborative agreement between Canadian and UK genomic networks (BBSRC/NRC/AAFC); joint fund for travel, meetings and short exchanges for post-doctoral researchers
  • Stem cells – major UK mission to Canada and the USA in 2003 (Canadian stem cells network currently advising BBSRC on establishing similar activity in the UK
  • Environment Canada – BBSRC / NERC / NIEeS Future Collaboration???
for further contact
FOR FURTHER CONTACT
  • Terry McIntyre Ph.D. P.Ag.
  • Chief Environmental Biotechnology
  • Applications Division
  • Technology and Industry Branch
  • Environment Canada
  • 18th Floor, P.V.M.,
  • 351 St. Joseph Blvd.,
  • Gatineau, Quebec, CANADA
  • Tel (8l9) 994-1105
  • e-mail terry.mcintyre@ec.gc.ca