Marine Genomics Working Group
US-EU Biotechnology Task Force Meeting
Washington D.C., 23-24 June 2011
Juli Trtanj, NOAAGarbiñe Guiu, EC
It is more than 20 years since marine biotechnology was designated an “area with great potential”
(R. R. Colwell, Oceanus and Science)
EU-US Task Force on biotechnology, 1996
Marine Biotechnology—Grasping the opportunity…at the right
time?
Marine Genomics Working Group Goal and Objectives
•To foster the collaboration of research and training in the EU and the US in the field of marine genomics
•To address key coordination bottle-necks and new developments in the science, through joint annual workshops
Goal: The Marine Genomics Working Group is designed to foster the evolution of marine genomics as a foundational underpinning for
understanding and knowledge across multiple disciplines
Current Working Group Members
Frank Oliver Glöckner, Bremen (EU Science Co-chair)Douglas Bartlett, University of California, San Diego (US Science Co-Chair)
The ad-hoc steering committees for the different activities are tailored according to the nature of the topic to be treated, with additional scientific expertise and institutional representatives added as appropriate
Garbiñe Guiu EC (formerly Maurice Lex)
Juli M. Trtanj NOAA (formerly Lita Proctor)
« 2006-2008 »
Continued efforts to reduce bioinformatics bottleneck (meta)genomics science:
Need for joint training course in bioinformatics
Include metagenomic scienceto address fundamentalquestions of microbial ecology
2009-2011 Activities
• Workshop “Marine Genomics: High throughput technologies, their application and influence on marine microbial genomics and biotechnology” October 10-12, 2010 in Washington D.C.
• New Directions--Five Year Strategic Plan
• Training Short Course in Marine Bioinformatics
• Finding Synergies and Partnerships
“Marine Genomics: High throughput technologies, their applicationand influence on marine microbial genomics and biotechnology”
October 10-12, 2010 in Washington D.C.
The workshop considered the ramifications of sequencing technology advances:
•the resulting bioinformatic bottlenecks, •the new biological questions that can be addressed,•the coupling between marine microbial genomics and functional and environmental studies .
A means to an end:Round table with industrial representatives Training of our next generation of marine scientists
Workshop GoalsDoug Bartlett (US, Scripps), Frank Oliver Glockner (EU, Max Plank)
“Marine Genomics: High throughput technologies, their applicationand influence on marine microbial genomics and biotechnology”
October 10-12, 2010 in Washington D.C.
In-depth focus on high throughput technologies and related opportunities and challenges in marine (meta) genomics:
•Optimize existing data utilization;
•Train the next generation of scientist to work across disciplines and have functional knowledge of basic marine bioinformatics
Expanded focus to:
• Address the application of the marine genomics tools for societal benefits (such as public health, seafood safety, conservation, natural products);
• Strengthen the link between marine biotechnology and environmental and ecological concerns
:
Workshop Outcomes
“MARINE GENOMICS WORKING GROUP”Strategic Plan 2011-2015
Two flagship areas:
• High throughput technologies: opportunities and challenges in marine (meta)genomics.
– Next generation scientist training– Optimisation of data utilisation
• Application of Marine Genomics to answer real world questions related to environment, ecology, conservation, human health
– Marine Natural products—conservation and models to move forward– Monitoring climate change and tracking diagnostics
How will we do this? Create Synergies across Working Groups and with new Partners
Cross-fertilize marine biotechnology, marine biodiversity, and oceanographic communities Stimulate innovative and transformative technologies
(What is your role?)
Other Ideas of Interest—(a.k.a. if we had more time and money)
• Marine sensors and ecosystem health--linking marine genomics with marine sensors/monitoring/observing systems);
• Indicators of ocean and coastal health--establishing and monitoring Ocean Health Indicators/Ocean environment indicators;
• Best Management Practices including pollution, toxicology, etc;
• Facilitating access to marine resources, biodiscovery and marine bioresource information.
• Collaborative Research Network model for marine genomics
MS4
Slide 10
MS4 I don't understand why these are 'future' ideas of interest (i.e., if we had time and money)....aren't these main foci with some members of the working group and/or at least in some areas ripe for collaboration?Mark S. Strom; 21/06/2011
MARINE GENOMICS WORKING GROUPStrategic Plan 2011-2015
Proposed activity June 2012--Training
Short Course: Next Generation Scientists for next generation sequencing: Making sense of marine omics data ,Bremen, 2012Convenors: F. O. Glöckner, MPI, Jacobs University overall organisation
D. Vaulot, Station Biologique de Roscoff,EU) J. Biddle (University of Delaware, US), (J.Gilbert Argoon National Laboratory, US)
Highly Comitted community: Outline and terms of reference ready
Aim: To bring together young scientists in a interdisciplinary forum that will set
the grounds for future overseas collaboration; Provide a resource for
graduate students and researchers to acquire the skills-set necessary for
proper experimental design, taking into account the diversity of analysis
tools and marine environment contextual data
Short Course: Next Generation Scientists for Next Generation sequencing: Making sense of marine Omics
data, Bremen June 2012
Short Course set up:14 days training course: Theoretical and hands on experience on bioinformaticsWill involve 24 students: 12 from each side of the AtlanticInterdisciplinary backgrounds: computer science, bioinformatics, marine microbial ecology, environmental science and oceanography:
« How to apply these technologies in a complementary way to best examine hypothesis driven research questions related to climate change, carbon cycling, environmental pollution, bioremediation, blue biotechnology.
« To obtain knowledge we need to combine data with experience »
Short Course: Next Generation Scientists for Next Generation sequencing: Making sense of marine
Omics data, Bremen June 2012
Open questions and synergies:• How do we make this a lasting effort; how to best use
online tools; what are the lessons learned from other Working Groups?
• Build synergies with other initiatives, universities, funding agencies priorities
MARINE GENOMICS WORKING GROUPStrategic Plan 2011-2015
Proposed activity June 2013—Application and Biotechnology
Workshop: Exploring the synergies between marine genomics in natural products research and conservation efforts, USA 2013
Convenors: NOAA, others TBD (New York Academy of Science)
Open questions and synergies:
• How can we best to enhance links between marine biotechnology and marine biodiversity and conservation efforts?
• What are innovative institutional models for moving forward?
• How do we usefully engage Industry?
Aim : The workshop goal will be to establish links and explore cross fertilization possibilities among
marine genomics, bioprospecting and conservation communities and industry; and link to ocean
exploration and global marine biodiversity efforts
MARINE GENOMICS WORKING GROUPStrategic Plan 2011-2015
Proposed activity June 2014— Data Utilisation
Workshop: Optimising the utilisation of sequence data in marine (meta) genomics, EU 2013
Convenors: Max Plank Institute, EBI, others TBD
Open questions and synergies:• There a need for this to be a continuous effort, what is the optimal and functional
model to serve this need?
Aim: To address key gaps and provide updates for marine biologists tobetter use sequence data. Topics include hypothesis formulation and experimental design, quality control, unknown gene characterization
(reference genomes), metabolic reconstruction, metagenome binning, and integration of metadata standards
Other Applications of Marine Genomics
Harmful algal species and toxins
GENOME
STIMULUS
PHYSIOLOGICALHormonal, metabolic
RESPONSE
Development,Differentiation
Infection orImmunity?
Stress ResponsePhysiology/Pathology
INFECTION
Gene Expression
ENVIRONMENTPhysical, chemical,
biological stress
And other of ‘omics technologiesProtected species and environmental health
-Microsatellite markers to identify toxic phytoplankton species -Transcriptomics to measure chronic HAB toxin exposure/marine mammal health assessments-Transcriptomics to identify gene markers of enviromental chemical contaminants in fish
Fish population restoration and aquaculture
-Microbial metagenomics of killer whale fecal samples to assess health-Metagenomics to measure microbial population abundance and diversity as an indicator of environmental health and change
-Transcriptome approaches to characterize genes that regulate reproduction and growth of Pacific Salmon -Genomics and transcriptomics to indentify genes that control sexual differentiation in sablefish-Fish gut microbiome analysis to assess dietary responses to alternative feeds
Blood Transcriptome Analysis of Disease Exposure in Sea Lions
Two major diseases cause morbidity and mortality of California Sea Lions on the California Coast
Leptospirosis
Domoic Acid Toxicosis
Refinement using Artificial Neural Networks (ANNs) showed 98% successful classification of Domoic acid versus Leptospirosis.
Lepto Other Healthy
DAT 0.986 0.853 1
Lepto 0.999 1
Other 1
Bioinformatic analysis of microarray data on whole blood showed promise for distinguishing the two disease states.
Blood transcriptomics is a promising approach for developing targeted tools for wildlife and human exposures
MARINE GENOMICS WORKING GROUPStrategic Plan 2011-2015
Proposed activity June 2014-15—Application: Environment and Health
Workshop: The role of marine genomics in monitoring, tracking and diagnosing climate related ocean, human and animal health impacts, USA 2014-15
Convenors: NOAA, others TBD
Open questions and synergies:
• Next steps are actively engaging the ocean observing and animal health communities
Aim: Explore the application of marine genomics in helping determine and monitor shifts in bacteria, viruses and pathogens of concern; and to
enhance the integration of biological factors into ocean observation and monitoring systems.
Genomics to aid develop of Health Early Warning Systems for Vibrios
Appropriate genetic markers on biosensors, linked to ocean observingNASA Aqua w/
MODIS
MLST analysis of Vp reveals diverse phylogeny
“Virulent” strains rare and less diverse
Genome sequencing of multiple strains to identify virulence markers
Pandemic isolates
PNW environmentalIsolates tdh+ (ST3)
PNW clinicalIsolates tdh+ (ST36)
PNW clinicalIsolates tdh- (ST65)
Oceanographic measurements and biogeographical linkages of pathogen to human illness
MARINE GENOMICS WORKING GROUPLooking Forward..Tapping the Untapped Potential
After 20 years marine genomics is still an area full of
potential…underpining understanding and innovation across multiple
disciplines ranging from oceanography, biomedicine, conservation, and health
to marine biotechnology industrial applications.
Questions, Comments, Ideas?