Environment Canada Environmental Biotechnology Applications Div by tyndale

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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.


                                                1
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

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What is Environmental Genomics?


s   Environmental Genomics (EG)bridges the gap between
    genetics, physiology, and ecology

s   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

s   EG can pinpoint potentially novel interactions between
    environmental stressors and expression of specific human,
    animal and plant genes


                                                                   3
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

                                                   4
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


                                                                5
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

                                                             6
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



                                                               7
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

                                                              8
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




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  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)
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     Environment Canada’s Genomics
     Program – Research Focus
1.    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.

2.    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.
4.    Conservation Biology and Wildlife Management
      •   The Canadian Wildlife Service (CWS) is developing and applying genetic markers towards
          the resolution of conservation issues.

6.    Improved Enforcement & Compliance
      •   The PESC has completed a Pulp and Paper study that positively identifies mill effluents that
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          are causing endocrine disruptor effects to fish.
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

Functional/Metabolic:
   • Targeting catabolic, biogeochemical cycling,
     metal resistance
   • Pollutant transformation processes
   • Ecosystem health

Taxonomic
   • Targeting 16S rDNA
   • Microbial community profiling
   • Phylogenetic identification

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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

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


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


„ 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?



                                                        17
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)

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  Barcoding Products and Life




  10                15
11 = 100 Billion   4 = 1 Billion19
The Microgenomics Network




                            20
Identifying Life




                   21
DNA Barcode:
short sequence enabling species discrimination




                                            22
        Concordia University / Genome Quebec
       Enzyme Systems for Pulp and Paper Industry



                           White-rot fungi:
                           • Phanerochaete
                           chrysosporium
                           • Trametes versicolor
                           • Lentinula edodes
Other lignin and pitch
                                        Pollutant degrading fungi:
degrading fungi:
                                        • Aureobasidium pullulans
• Gloeophyllum trabeum
                                        • Amorphotheca resinae
• Ophiostoma piliferum
                                        • Leucosporidium scottii
• Corpinus cinereus
                                        • Cunninghamella elegans

Freeze-tolerant fungi:            Thermophilic composters:
• Chrysosporium                   • Thermomyces lanuginosa (600C)
pannorum                          • Chaetomium thermophile (500C)
• Cryptococcus laurentii
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
                                                           24
•   NOPP – Pollution Detection, Monitoring, Surveillance
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:

•   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

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

    Whole Range Of Priority Areas We Could Be Involved In:
Interim Genomics R & D                    Potential Future
Activities                                Genomics R & D Priorities

•    Identification
                                         • Contaminated sites
•    Risk Assessment / Management          remediation / restoration
         Test method Development
                                         • Bioprospecting
         Environmental Monitoring

                                         • Industrial ecology and green
•    Conservation Biology and Wildlife     “chemistry”
     Management
                                         • Climate change/Bioenergy
•    Improved Enforcement &
     Compliance                          • Biobarcoding                27
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


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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

                                                                   29
Canadian Genomics Research in the
Environment Network- A Concept




                                    30
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?



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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




                                              32
USEPA Genomics Research
and Development 2003-04

Computational Toxicology




                           33
 Research Focus Areas

Chemical transformation
Metabonomics
Molecular indicators
Dose metrics
Toxicity pathways
Systems biology
Computational infrastructure




                               34
USDOE GENOMES TO LIFE PROGRAM




                                35
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

                                                               36
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???



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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
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