Marine Genomics working group EU US Task Force on ...ec.europa.eu/research/biotechnology/eu-us-task... · better use sequence data. Topics include hypothesis formulation and experimental

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?