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PUTTING A GREEN THUMB ON THE GENOMICS HAND Canadian Research Efforts in Environmental Genomics Prese

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Title: PUTTING A GREEN THUMB ON THE GENOMICS HAND Canadian Research Efforts in Environmental Genomics Prese


1
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.

2
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

3
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

4
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

5
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

6
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

7
Importance of Environmental Genomics (III)
  • Genomics could be critical to examining
    biotechnologys 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

8
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

9
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

10
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
  • EC Delivery Mechanism Several EC Regional Nodes
    Under Strategic Technology
    Applications of Genomics in the
    Environment Program (STAGE)

11
Environment Canadas 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
  • The Environmental 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.

12
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

13
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

14
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.

15
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?

16
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.

17
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?

18
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)

19
Barcoding Products and Life
415 1 Billion
1110 100 Billion
20
The Microgenomics Network
21
Identifying Life
22
DNA Barcode
short sequence enabling species discrimination
23
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)

24
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

25
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

26
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

27
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
  • Identification
  • Risk Assessment / Management
  • Test method Development
  • Environmental Monitoring
  • Conservation Biology and Wildlife Management
  • Improved Enforcement Compliance
  • Contaminated sites remediation / restoration
  • Bioprospecting
  • Industrial ecology and green chemistry
  • Climate change/Bioenergy
  • Biobarcoding

28
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

29
Proposed Environment Canada Strategy for 2005 ff
Alliance and Convergence
  • 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

30
Canadian Genomics Research in the Environment
Network- A Concept
31
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(Michi
    gan)
  • OECD Toxicogenomics Workshop November 2005
  • Environment Canada CANGREEN workshop 2006?

32
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

33
USEPA Genomics Research and Development 2003-04
Computational Toxicology
34
Research Focus Areas
Chemical transformation Metabonomics Molecular
indicators Dose metrics Toxicity pathways Systems
biology Computational infrastructure
35
USDOE GENOMES TO LIFE PROGRAM
36
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

37
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???

38
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_at_ec.gc.ca
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