US-EC Task Force Five-Year Strategic Plan · Five-Year Strategic Plan 2011-2015 6 SUMMARY It is anticipated that the work of the Task Force will be carried out initially under the

US-EU Task Force on Biotechnology Research

Five-Year Strategic Plan 2011-2015

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US-EU Task Force on

Biotechnology Research Five-Year Strategic Plan

2011-2015

June 23. 2011



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TABLE OF CONTENTS CO-CHAIRS' FORWARD 5 SUMMARY 6 ANIMAL BIOTECHNOLOGY WORKING GROUP 9 Membership 10 Programming Priorities for 2011 to 2016 11 Action Plan 11 BIOENERGY AND BIOBASED PRODUCTS WORKING GROUP 13 Topics 14 Activities in the next years 14 ENVIRONMENTAL BIOTECHNOLOGY WORKING GROUP 16 Activities planned for 2011 17 MARINE GENOMICS BIOTECHNOLOGY WORKING GROUP 19 Structure 19 Planned activites 20 PLANT BIOTECHNOLOGY WORKING GROUP 23 Structure 23 Planned activites 24 SYNTHETIC BIOLOGY WORKING GROUP 25 Structure 25 Planned activites 26 OBESITY AND NUTRITIONAL SCIENCES FOCUS AREA 28



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Website:

http://ec.europa.eu/research/biotechnology/ec-us/index_en.html



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US-EU Task Force on Biotechnology Research Five-Year Strategic Plan

2011-2015

CO-CHAIRS' FORWARD

Established 20 years ago the EU US Task Force on Biotechnology research aims to promote information exchange and coordination in biotechnology research between programmes funded by the European Commission and the US Government funding agencies (USDA, DOE, NIH, NSF and NOAA). Over the years the task force has become a successful think tank on Biotechnology Research with a strong forward looking approach and with concrete examples of successful coordination in the areas of: environmental biotechnology, plant biotechnology, biobased products, marine genomics etc. The need for this transatlantic collaboration within this unique forum will certainly be maintained, and is expected to be even deepened, in the near future.

This "Strategic Plan: 2011-2015" presents what the Task Force and the different working groups want to deliver over the next 5 years. This is a result-oriented strategy that takes into account all working group goals and major overarching aims. These include future collaboration on a series of important research areas, key to enhance transatlantic biotechnology innovation potential, and in which the need for international coordination has been highlighted by scientific community and task force members.

US CO-CHAIR EU CO-CHAIR

Judith ST. JOHN Maive RUTE Associate Administrator Director Biotechnologies, Agriculture, Food Agricultural Research Service DG Research and Innovation U.S. Department of Agriculture European Commission



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SUMMARY

It is anticipated that the work of the Task Force will be carried out initially under the auspices of six working groups with the following charges:

The mission of Animal Biotechnology working group, established in 2009, is to foster collaboration to best address challenges and opportunities linked to the scientific and technological progress on genomics and bioinformatics in the fields of "animal health": understanding the links between the genetic code and diseases; and "animal production": gen discovery, validation and epigenetic research on animal breeding. Over the next five years the working group intends to concentrate its efforts on the enhancement of genomic data visualization; physical database coordination and genome assisted selection. Calls to encourage coordinate research projects are also envisaged.

Bioenergy and Biobased Products working group was established in 2004 to facilitate and coordinate research on bio-based products and on the potential for plants to become an expanded source of industrial feedstock, reducing dependence on petrochemicals and creating new markets for farmers. In the past the working group combined activities in training, dissemination of outcomes and collaborative projects in three key flagship areas: Oils for Novel Chemicals, Biopolymers and Plant-Cell Walls. Topics of particular importance for the working group over the next 5 years include: Methods for assessing sustainability of bioenergy/bioproducts; added-value bioproducts from plants; and novel sources of biomass.

The Environmental Biotechnology working group was establish in 1994 to foster collaboration and exchange ideas on using emerging biotechnology capabilities to address environmental problems. At the heart of the working group mission is the establishment of collaborative ties among US and European scientist, particularly early career scientist. Over the next 5 years, efforts will be stepped-up identifying research areas and topics of mutual interest that can provide key understanding to some of the most globally significant and challenging environmental problems such as climate change effects, environmental contamination and bioenergy production. At the heart of the working group's activities is the desire to explore the remarkable metabolic abilities of microorganisms. The possibility of cooperative EU/US research, based on agreed funding mechanisms and parties involved is envisaged.

The aim of the Marine Genomics Working Group, establish 1998, is to foster collaboration in emerging areas of marine ecology and biotechnology. Over the next 5 years Marine genomics working group will focus in two key flagship areas. First flagship area includes high throughput technologies and related opportunities and challenges in



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marine (meta) genomics. Activities on optimization of data utilization and next generation scientist training, are been considered. The second key flagship area of this working group will be driven by how better link marine biotechnology development to environmental and ecological concerns. At the core of this area activities is the cross fertilization between marine biotechnology and marine biodiversity efforts which promises to result in a series of innovative and transformative technologies.

The Plant Biotechnology working group was established in 2006 to help develop a joint vision and suggestions for research cooperation between the US and the EU in the area of molecular plant sciences and biotechnology. Work has resulted in recommendations for collaboration in the wider area of plant bioinformatics, addressing aspects of training, standards, infrastructures and stewardship of data resources. Work over the next five years will build on these recommendations with the aim of establishing a platform for regular discussions, events (e.g. training courses, technical workshops) and scientific partnerships in the interface between plant sciences and bioinformatics. This area is seen as crucial to exploit the wealth of genomic and other 'omics resources with the aim to translate these into knowledge and applications, such as plant breeding.

The Synthetic Biology working group was established in 2010 to foster exchange of views and collaboration on scientific and technical progress in implementing synthetic biology principles in such areas as standards, orthogonality, minimal genomes, ethics, biosafety (including environmental safety), biosecurity, and education. Over the next 5 years the working group will focus on standardisation needs not met or realized yet via current practice; it will follow Ethical, legal and social issues in relationship to the scientific and technical progress of synthetic biology; and will pay special attention to the contribution of synthetic biology to the different domains of Biotechnology. Calls encouraging coordinated research projects on synthetic biology standardization of biological parts have recently been launched.

Plant, animal and marine working groups will also concentrate their efforts on a number of clear opportunities for synergy across working group activities. Specific areas include:

• Enhancing genomic data visualization and management through improved bioinformatic infrastructure and tools,

• Coordinate physical databases to integrate genomic and genotypic information with phenotypic data

• Apply tools and databases to broadly stimulate research and technology development for genomics

• Coordinated calls for research proposals, announced on the appropriate US and EC funding web pages, to encourage coordinated research projects in animal biotechnology and bioinformatics.



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• Development of eLearning tools to expand the impact of training courses beyond the meeting and to leverage investment in US and EU projects in biotechnology

Working groups will be terminated and/or new groups established in response to scientific needs and the clear potential for fostering cooperation among US and EU agencies.

Over the next five years the Task force will also continue its activities in the focus area of Obesity: The aim will be to identify opportunities most amendable to transatlantic cooperation, catalyze further interaction across US agencies, and to consider engagement with US and European scientific societies on implementation of the “New Technologies and Innovations to Tackle Obesity” workshop (Brussels, November 2010) recommendations.

During the next five year period, EU and US have agreed that the "EU US Task Force on Biotechnology Research" will emphasize the bioeconomy priorities on both sides of the Atlantic. For this period the Task Force will also aim to use new opportunities for collaboration, for example, with the Transatlantic Innovation Action Partnership, which through its bio-based products priority area will complement work on this topic already under way in the EU-US Task Force.



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ANIMAL BIOTECHNOLOGY WORKING GROUP

While it took 13 years to sequence the human genome, significant technological and computational breakthroughs have commoditized DNA sequencing and animal whole genome sequences of animals can now be delivered inexpensively in only a few weeks. Although it is abundantly clear that animal genome sequences alone are insufficient to impact animal health and production, much needs to be done in developing the genomic tools and infrastructure for animal genomic research. Today we are at a crossroads where we can begin to harvest the fruits of scientific and technological progress moving animal health and production research to new dimensions, by addressing previously intractable challenges in animal health and breeding.

The development of whole genome selection and genome wide association studies within the animal agriculture community has significantly improved our understanding and appreciation of the value of genomics. The reduced costs of sequence data and the growing need for resequencing of additional individual genomes is also significantly impacting genome science and increasing the need for computing and bioinformatic support. In addition to progress in DNA sequencing and gene annotation, understanding the complexity of gene expression, gene regulation and genome methylation is progressing faster than ever before. However, the increasing need for data storage and data analysis tools (bioinformatics) is profound and is a critical need to continue the rapid progress currently being achieved in genomic research. These tools are needed to provide improved biological understanding at cell, tissue, individual, and population levels. Storing, curating and retrieving the structured information resulting from genomic and population studies, which is core to these challenges are just beginning to be addressed.

Recent advances in genomics are now providing unprecedented opportunities for animal health in understanding the links between the genetic code and diseases. Gene discovery and validation, selection studies and epigenetic analyses are priorities for the animal production industries and promise to continue to create significant value for animal industry stakeholders. Technologies such as whole genome selection (already initiated in commercial dairy cattle) will enhance genetic progress even on traits of low heritability. However, it is paramount to understand that this kind of research requires large and accurate health and production phenotypic databases with comprehensive trait coverage from large pedigreed populations, which are not available for many animals, and thus must be developed for continued academic and commercial development of genomic tools and technologies.



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Agricultural animals can also play an important role in comparative genomics for humans and other species of academic and natural resource importance. The ability to make desired breeding decisions and test hypotheses requiring specific matings among animals, with well-known and accurate pedigrees and well-defined phenotypes, is an important attribute of animal agriculture. Furthermore, illuminating the effects of selection on gene frequencies and whole physiological pathways has already yielded insights on the relative importance of genes and their expression, illustrating that agricultural animal genomes serve well as models for understanding the human genome. For example the genes and organization of genes involved in both immunity and lactation biology in cows provides a closer model to human biology than typical rodent models.

Membership:

Coordination for the ABWG:

Jean-Charles Cavitte, Scientific Officer, Directorate General of European Commission. Steve Kappes, Deputy Administrator of the USDA- ARS, Beltsville, MD. Additional administrative support for the ABWG:

Anne-Sophie Lequarré, Stamatios Varsamos, EU Commission, Brussels, Belgium Muquarrab Qureshi, USDA-National Institutes of Food and Agriculture Jeff Silverstein, Mark Boggess and Cyril Gay, USDA-ARS all Beltsville, MD

ABWG scientific members for the EC:

Michel Georges, University of Liège, Liège, Belgium Martien Groenen, Wageningen University, Wageningen, Netherlands Elisabetta Giuffra, of Parco Tecnologico Padano, and currently at INRA, Jouy-en-Josas, France Johan Vanhemelrijck, former Secretary General of EuropaBio and FEDESA (tbc) Helen Sang, Biotechnology and Biological Sciences Research Council, Roslin Institute (tbc) Elena Sarropoulou, Hellenic Centre of Marine Research, Heraklion, Greece (tbc)



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ABWG scientific members for the US:

Shane Burgess, Mississippi State University, Starkville, MS Gary Rohrer, USDA-ARS Meat Animal Research Center , Clay Center, NE Christine Elsik, Georgetown University, Georgetown, Washington, D.C. Marcus Kehrli, USDA-ARS National Animal Disease Center, Ames, IA Greg Wiens, USDA-ARS National Center for Cool and Cold Water Aquaculture, Leetown, WV

Programming Priorities for 2011 to 2016:

The Animal Biotechnology Working Group on has set out broad goals to develop workshops and foster collaborative research including:

• Enhancing genomic data visualization and management through improved bioinformatic infrastructure and tools,

• Coordinate physical databases to integrate genomic and genotypic information with phenotypic data, and

• Apply the tools and databases to broadly stimulate research and technology development for genomics and to enhance genome assisted selection and prediction of phenotype from genomic information.

• Coordinated calls for research proposals, announced on the appropriate US and EC funding web pages, to encourage coordinated research projects in animal biotechnology and bioinformatics.

Equally important, this working group recognizes, and will continue to develop, opportunities to engage with other Working Groups such as Plant Biotechnology, and Marine Biotechnology, which have similar priorities in information processing and utilization and considerable common interests. Additional priorities will focus on training and developing young scientists and strengthening ties with biomedical and life science communities.

Action Plan

The ABWG met in San Diego, CA in January 2011. This meeting was held to review and recommend membership for the ABWG, review ABWG mission and objectives and initiate development of a 5 year vision for programming. The US roster for the ABWG has been completed. The EC roster will be expanded in 2011 to balance membership numbers and ABWG expertise.



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• Quarterly conference calls with the EU-US ABWG will be facilitated via phone, Skype or other interactive media to facilitate better communication and enhance working group dynamics, and to update the ABWG regarding progress and opportunity, etc.

• Annual meetings for the ABWG will be scheduled at the Plant and Animal Genome meeting, held each January in San Diego, CA as well as in conjunction with other international meeting opportunities. This meeting(s) will focus on programming progress reporting and program planning.

• Coordinated calls, which will be announced on the appropriate US and EU funding web pages, to encourage coordinated proposals in animal biotechnology and bioinformatics.

• Exploitation of synergies with other Task Force Working Groups, especially in common areas such as genomics, bioinformatics and training that arise in marine genomics, plant genomics and bioinformatics.

• Exploration of virtual meeting approaches to facilitate more nimble discussions of scientific topics that are urgent and/or might not require a formal meeting or workshop.

• Training courses will be discussed, developed and implemented as priority arises.

Workshops or planning sessions for 2011: • Two workshops are planned for Animal Health in 2011. The first on African Swine

Fever in Europe or the U.S. The second on Foot and Mouth Disease to be held in Argentina.

• A planning session is being developed to explore the feasibility of a 2011 international workshop on the development of comprehensive genomic and phenotypic databases.

Workshops or planning sessions for 2012: • A workshop is being planned for alternatives to antibiotics (Jean-Charles Cavitte

and Cyril Gay).

Workshops or planning sessions for 2013 and beyond: • Workshop schedules for these years will be planned in 2011-2012 pending the full

appointment of the ABWG roster and summary reports from the workshops planned for 2011.



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BIOENERGY AND BIOBASED PRODUCTS WORKING GROUP

The WG on Biobased Products and Bioenergy continues to build on the success of the Biobased Products working group which organized a EU-U£S Workshop on “Applications of Molecular Biology for the Production of Plants for Biobased Products and Bioenergy in April 2004. Subsequently, an international project EPOBIO was supported through the EU’s 6th Framework Research Programme with the participation of the USDA, that identified the subject of three key flagship projects: Oils for Novel Chemicals, Biopolymers and Plant-Cell Walls. More recently, the 2008 "Biotechnology for the Development of Sustainable Bioenergy" workshop reported valuable suggestions for transatlantic collaboration with a focus beyond bioethanol and its associated processes, including diverse fuel types and conversion technologies. Life cycle analysis continues to be important and there are notable gaps in this area. An important focus is on biomass quantity and quality but there are also important issues at the other end of scale-up that need to be considered. In 2009, the Task Force has combined its working groups on Biobased Products and Bioenergy into a single working group. Biobased products may make biofuel production more economical. Bioproducts have considerably higher added value than biofuels and could save substantial energy in processing to the final product compared to products made from fossil oil. There is a growing urgency internationally to develop and use clean energy and green products. This working group is poised to continue the exchange of fundamental scientific information needed for the successful development and use of bioenergy and biobased products. The working group will continue its focus on topics of common interest to both the US and EC with an emphasis on topics at the leading edge of technology and scientific development. By engaging leading experts from the EC and the US, the working group will support workshops that lead to the identification of critical new areas for discovery and trans Atlantic collaboration. By including and mentoring promising students or early career scientists in these workshops, the working group will help foster the training and development of scientists who will make tomorrow’s discoveries in bioenergy and biobased products.



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Topics of particular importance for the working group include:

• Biomass and Biofuels

o Sustainability, with an emphasis on feedstocks.

o Increasing biomass production, in particular on marginal lands.

o Characterization of where the biomass goes in different use sectors around the world.

o Methodologies for assessing sustainability and Life Cycle Analysis for both cost and the environment since don’t currently have unified methodologies.

o Greater focus on agricultural processes.

• Biobased products

o Recognizing that plants are terrific organic chemists, additional research is needed on the extraction of valuable compounds from plants, especially added value products that can be produced and extracted jointly with biomass feedstock production.

o Simple monomeric molecules (e.g., glycerol, ethanol) from biorefineries may not have added value for product production compared to fossil oil monomers. Research regarding added value bioproducts produced in plants should be prioritized.

o Long or medium chain hydrocarbons needed as transportation fuels. Renewable sources most efficiently met by plant oils (including waxes). Research to increase oil content in plants, including lipids in plant tissues normally not accumulating lipids should be prioritized.

Activities in the next years

The following Workshops are planned for 2011 and 2012: a) Method for assessing sustainability of bioenergy/bioproducts – 25-26 October 2011. Organizer: Prof: Steve Long; co-chairs: Dr Guido Reinhardt; Prof Steve Long



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The workshop will be hosted in Champaign-Urbana, Illinois, by the University of Illinois. Main points of discussion will be: The Economics of LCAs ; Using LCAs to Improve Bioenergy Systems; Making LCAs Better

b) Added-value products from plants – Spring 2012 (tbd) – Sweden, Europe Organizer: Prof. Sten Stymne Purpose of the Workshop: i) to identify target molecules that on a big scale can economically compete with fossil oil as feedstock for the chemical and material industry. Ii) To review the progress of optimizing the structure and quantity of the added value product. iii) To identify barriers for the development of a bio-based industry. iv) to identify uses of rest-products to improve overall economy (e.g. bioenergy).



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ENVIRONMENTAL BIOTECHNOLOGY WORKING GROUP

Environmental Biotechnology continues to be a rapidly changing area of science for US-EU collaborative activities. For the past 16 years the Environmental Biotechnology Working Group has explored the latest biotechnology techniques and approaches to address environmental problems common to the US and Europe. Through workshops, short courses and exchange fellowships the Working Group has endeavored to create opportunities for young US and European scientists to discuss the latest biotechnology ideas for the environment with established researchers and with each other. Establishing collaborative ties among US and European scientists, particularly early career scientists, is one aim of the Working Group’s mission with the underlying philosophy that collaborations beginning early in a scientific career can last a lifetime.

However, today's main challenges of climate change, dwindling fossil resources and need to improve sustainability of agricultural, industrial and household activities, affect both sides of the Atlantic. Consequently, over the next five years the Working Group's strategic aim will be to identify and verify key technologies and approaches which will contribute to providing solutions to these challenges. For achieving this ambitious goal, the working group needs to create opportunities to advance direct collaboration among US and European researchers in programs of mutual interest and benefit. The EU-US coordinators will support this by working-out the possible modalities in terms of the necessary funding mechanisms and instruments. A planned workshop in 2011 is envisaged providing an opportunity for an initial discussion on a road-map to future research collaboration in this regard. It is foreseen that by 2014 at the latest the first collaborative EU-US research project on environmental biotechnology will be launched. In addition, the promotion of collaboration among US and European early career and established scientists via workshops and short courses will be continued.

Key to these activities will be promoting and developing biotechnological approaches to merge/leverage the latest “omics” techniques with process science via computation to understand microbial processes in environmental systems of concern. As solutions to environmental problems become more multidisciplinary there is a need to establish closer linkages between a wider range of scientific disciplines including microbiologists, geoscientists and computational scientists. Integrated, multi-disciplinary approaches to environmental challenges are of interest in both the US and the European research community. The Working Group will promote activities that connect disciplines and approach environmental challenges from new perspectives.



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Two activities are planned for 2011:

Short Course Microbial Catalysts for the Environment (Univ. Lausanne, Switzerland) (J. van der Meer, G. Zylstra Workshop Microbial Community dynamics: Cooperation and Competition (St. Louis, MO) (J. Wall, K. Bender) Concerning the arrangements for the organization of workshops and short courses the Working Group will continue to alternate these activities between US and European locations with at least one planned activity per year. The workshop topics will align with common science themes within US and EU research programs to maximize the potential for mutual collaboration. The format for each activity will follow a previously successful strategy of pairing established scientists with early career scientists in a collaborative setting where the latest technological advances and scientific approaches in environmental biotechnology can be discussed and/or demonstrated. Discussion of scientific topics will be combined with mentoring opportunities for early career scientists. A tentative schedule for these activities is: 2012 – Workshop (EU location) 2013 – Short Course (US location) 2014 – Workshop (US location) 2015 – Short Course (EU Location) 2016 – Workshop (EU Location) Science themes to be explored: Interdisciplinary Applications of Environmental Biotechnology Integrated “Omics” Approaches to Understand and Predict Environmental Processes Connecting Computational Science and Biotechnology in Environmental Applications



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Environmental biotechnology issues to be discussed in the context of the science themes include:

• Approaches that advance an understanding of microbial ecosystem function in response to climate change.

• New approaches for and new insights of bioremediation processes and long term monitoring of environmental impacts of contamination.

• Exploring new computational approaches for modeling and predicting microbial processes under changing environmental conditions.

• New methods to assess the spatial distribution and impact of microbial processes across larger scales of observations (i.e. changing landscape usage).

• Metagenomics – Bioexploration for industrial applications (e.g. extremophilic enzymes).

• Environmental biotechnology as applied sciences in waste water treatment and for the decontamination of emerging pollutants and for nutrient recovery.



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MARINE GENOMICS WORKING GROUP

The working group on Marine Genomics was established in 2005 with the objective 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 in this area.

During this period (2005-2010) four very successful US/EU workshops in the wider context of "Marine Genomics" were held. The workshops had the clear objective of moving forward and coordinating trans-Atlantic research in this important area of emerging science that underpin many different aspects of marine ecology and biotechnology.

• EU-US Workshop on Marine Genomics: High throughput technologies and their application/influence on marine microbial genomics and biotechnology, Washington D.C., October 10-12, 2010

• Marine Genomics: "The Interface of Marine Microbial Ecology and Biotechnological Applications" - 12 - 14 October 2008 in Principality of Monaco

• US-EU Workshop on Cyber infrastructure Resources for Genome-Enabled Research on Microbial Life and the Marine Environment, September 9-11, 2007, Arlington VA, US ‘

• Genomic approaches for studying marine environment and resources, May12-13,

2005, Bremen, Germany

Structure

The working group on Marine Genomics comprises a US Task Force representative Juli Trtanj (NOAA) and an EC Task Force representative Garbiñe Guiu (DG Research and innovation) who serve as Executive Secretaries of the Working Group and prepare and provide regular reports to the Task Force on the activities of the Working Group. Frank Oliver Glocker (EU) and Doug Bartlett (US) are identified as scientific co-chairs of the working group. One or two other scientists each from the US and the EU will be identified to act as punctual working group members for specific activities depending on needed expertise (e.g .depending on the kind of activity: workshop or short course, and the topic).



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Funding for the activities will be sought and promoted by the members of the WG on both sides. Funding opportunities for more demanding actions such as short courses are actually being explored.

The working group will submit proposed topics for each workshop to the Task Force prior to their funding being approved by the respective funding agencies. The proceedings of the workshops and any developments arising from them will be reported back to the Task Force each year. Planned activities

For the next 5 years the working group intends follow up actions on two different areas:

First it intends to explore as much as possible the latest workshop conclusions and recommended actions concerning high throughput technologies and opportunities/ challenges in marine (meta)genomics. From these conclusions (i) a short course on "Next Generation Scientist for next generation sequencing: Making sense of marine omics data" and (ii) a workshop action covering some of the aspects of the "Optimization of the utilization of sequence data in marine (meta)genomics" are of special relevant.

A second objective of the working group during this 5 years period will be to expand the scope of the work to more applied oriented topics driven by how to answer ecological questions and better link marine biotechnology development to environmental/ecological concerns in areas such as: Monitoring climate change and tracking diagnostics; and Marine Natural Products and conservation – The role of scientific exploration for marine natural products in leading conservation efforts. All five years:

• Plan regular tele/video conferences at least every two months, more frequently when workshops or other activities with deadlines are planned to facilitate better communications and enhance working group dynamics, and to update regarding progress and opportunities.

• Exploration of synergies with other Task Force Working Groups, especially in common areas such as bioinformatics and training that arise in animal biotechnology and plant genomics working group. As opportunities arise, joint workshops and training courses may be contemplated.

• Exchange of information for opportunities of international collaboration on topics of mutual interests on Marine Genomics e.g. Explore opportunities for Webinar to highlight Marine Genomics funding opportunities from both sides of the Atlantic - to



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be organized in accordance with the schedule of the EU and US call for proposals in this field; OECD work on marine biotechnology etc.

Face-to-face workshops:

• Monitoring climate change and tracking diagnostics Monitoring, Early Warning, and Vulnerability assessments for tracking climate impacts on ocean and coastal ecosystems, and related human and animal health effects. Changes in climate across time scales, from seasonal variation to decadal changes, is already affecting coastal and marine ecosystems and resources, and related marine and human health. We see changes in the distribution of certain marine algae, and the role of climate and marine virus/zoonotics is really not well understood. Marine Genomics plays a role in helping determine and monitor shifts in bacteria, viruses and other pathogens of concerns, as part of a larger early warning system of ocean monitoring and satellites or in a diagnostic capacity. Planned date 2012.

• Optimizing the utilization of sequence data in marine (meta)genomics. The opportunities and challenges in marine (meta)genomics are being greatly amplified as a result of the continuing dramatic improvements in the cost and yield of nucleic acid sequencing. To allow marine biologists to make best use of this data continued advances in the utilization of sequence data are needed including: experimental design, better quality control, unknown gene characterization (reference genomes), metabolic reconstruction, metagenome binning, and the integration of metadata (metadata standard). (This workshop has strong links with the short training course planned 2013). Planned date: 2013

• Marine Natural Products and conservation – The role of scientific exploration for marine natural products in leading conservation efforts. A comprehensive knowledge of marine life through marine genomics is essential for the preservation and sustainable management of marine environments /ecosystems /resources and for lying the foundation for new biotechnological applications and exploitation of marine natural products. The workshop should aim establishing links and exploring cross fertilisation possibilities among these communities. I should highlight the role of marine genomics scientific exploration for marine natural products in leading conservation efforts. Link to ocean exploration and to global marine biodiversity efforts such as the Census of Marine Life should be highlighted. Planned date: 2014



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Other topics of common interest the working group may consider developing during the next five years include (i) Genomics of marine sensors and ecosystems health. Linking Marine Genomics with marine sensors/monitoring/observing systems); (ii) Indicators of ocean and coastal health. Establish and monitor Ocean Health Indicators/Ocean environment indicators; (iii). Best Management Practices including pollution, toxicology, etc (iv) Facilitating access to marine resources, biodiscovery and marine bioresource information.

Training courses:

• Short joint course on "Next Generation Scientist for next generation sequencing technologies: Making sense of marine omics data" This training activity which is already in the planning stage will aim at a 5-10 day short course to provide for a forum through which to disseminate the skills required to allow marine biologists to access, make best use and finally "make sense" of the huge amount of data been generated by high throughput technologies. EU scientific Co-chair Frank Oliver Glocker has preliminarily agreed to be the leader in the organisation of the course. Possible locations for the course include Argonne National Laboratory and the European Bioinformatics Institute. The aim is that the proposed workshop will be complimented by an on-line training resource for each of the main data analysis portals (MG-RAST, CAMERA, VAMPS, QIIME GALAXY, IMG, VIROME, ARB/SILVA etc). Planned date: 2012



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PLANT BIOTECHNOLOGY WORKING GROUP

The Working Group on Plant Biotechnology (WGPB) was established in 2006 to develop joint research cooperation between the US and EU in the broader area of molecular plant sciences and biotechnology. Prior to the formation of the WGPB, the Task Force held two workshops addressing plant research, including the workshops on "Plant and Animal Bioinformatics" (Arlington, VA, 1999) and "Biotechnological Approaches to Disease Resistance in Plants and Animals" (Washington, DC, 2003). However, it was at the Conference on the "Future of Plant Biotechnology", which was held in Arlington in 2003, that a concrete recommendation was made by the scientific experts to establish a dedicated forum for discussion of transatlantic cooperation on plant genomics and biotechnology. The experts considered that the time was ripe to develop a common vision for plant sciences for the next 10 - 20 years, building on the impressive advances in genomic and post-genomic sciences. While highlighting the different approaches to research funding in the EU and US (for example, more fundamental work on Arabidopsis versus research in various crops), they concluded that fundamental and applied approaches could complement one other and be an asset for setting up joint activities.

In its first five years, the WGPB has held two scientific meetings and based on the recommendations of the second meeting, organized a workshop on plant bioinformatics, held in Hinxton, United Kingdom, December 2009. The activities proposed for the next five years will focus on the key recommendations from the workshop report.

Structure Initially, the WGPB comprised a US Task Force representative, an EU Task Force representative, and four additional scientists, two each from the US and EU, with two serving as the US and EU Co-Chairs. While this fixed structure was useful in the initial scientific meetings defining broad areas of potential cooperation, it is proposed to move to a structure in which only the co-chairs are fixed and the other members are appointed for specific activities, depending on needed expertise. The co-chairs proposed are Doreen Ware (USDA-ARS, Cold Spring Harbor Laboratory) and Klaus Mayer (MIPS, Germany), who organized the Hinxton workshop.



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Planned activities

• All five years

o Coordinated calls, which will be announced on the appropriate US and EU funding web pages, to encourage coordinated proposals in plant biotechnology and plant bioinformatics.

o Exploitation of synergies with other Task Force Working Groups, especially in common areas such as genomics, bioinformatics and training that arise in marine genomics, animal genomics and environmental biotechnology. As opportunities arise, joint workshops and training courses are contemplated.

o Exploration of virtual meeting approaches to facilitate more nimble discussions of scientific topics that are urgent and/or might not require a formal workshop

Use of a Second Life meeting space for virtual meetings and workshops

Skype meetings and workshops

o "Stock Taking": Assembling information on successful initiatives which can be used for planned workshops or courses, e.g. in the area of e-learning tools for bioinformatics training

• Face-to-face workshops

o Workshop on phenotyping and data integration, and linking genotype to phenotype that includes database PIs, to be held in the US. Organization could include the US iPlant Collaborative. Planned date in early 2012, perhaps before or after the Plant and Animal Genome meeting in San Diego, CA or a similar international meeting.

• Training courses

o A course focused on standards and ontologies, using the systems database as a model to be held at the European Bioinformatics Institute, Hinxton, UK. Planned date late 2012 or early 2013

o A course focused on analysis of next generation sequence data and integration with other genomics datasets to be held in the US, summer 2014



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SYNTHETIC BIOLOGY WORKING GROUP

Synthetic Biology is rapidly consolidating as one of the important fields with significant potential applications and implications in biotechnology. There have been a number of efforts throughout the world to identify the barriers and realize the potential of the Synthetic Biology. There is complementary as well as overlapping expertise in the area in the US and the EU. There is an underlying need to enable sharing and cooperation across national and regional boundaries in order to make progress. As with all new and emerging technologies, there are also some unknowns with respect to the environmental and health impacts of synthetic biology. Given the potential of synthetic biology to change the way we do molecular biology or metabolic engineering, there is compelling need to work together to overcome barriers to practice and implementation in the field along with the safety, biosecurity, ethics and education issues.

Following the background and stated needs the group already organized a successful workshop in Segovia in June 2010. In this workshop it was agreed that as initial direction the working group should be looking to standards to allow communication and material exchange, and technique development. Finally a "formal" working group on Synthetic Biology was established during the EU US Task Force video conference December 2010.

Structure

Christina Naneva (EU) and Sohi Rastegar (US) will serve as Executive Secretaries of the Working Group who will prepare and provide regular reports to the Task Force on the activities of the Working Group. Because of his background experience in the field and in bilateral activities, Ioannis Economidis will serve in advisory capacity to the Working Group. Lino Paula (EU) following ethical and governance aspects of Synthetic biology will complete the group of officials. Victor de Lorenzo (EU-Spain) and Drew Endy (US) are identified as preliminary members. Two or three other scientists each from the US and the EU will still need to be identified. Funding for the activities will be sought and promoted by the members of the WG on both sides. Funding opportunities for international collaboration will be specifically sought to allow exchange of scientists and students both for learning and for conduct of collaborative research.



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Planned activities

All five years:

• Plan regular tele/video conferences at least quarterly, more frequently when workshops or other activities with deadlines are planned. The WG will also plan to meet in person at least once every two years as a group, most likely in conjunction with a sponsored workshop. If opportunities raised members of the Working Group will organize planning meetings in conjunction to International scientific relevant events. (congresses, Symposia etc. ) For 2011 a meeting held in conjunction with the Synthetic Biology meeting at Stanford is under consideration.

• Exchange of information for opportunities of international collaboration on topics of mutual interests on Synthetic Biology e.g. Explore opportunities for Webinar to highlight Synthetic Biology funding opportunities. Action starting 2012- To be organised in accordance with the schedule of the EU and US call for proposals in this field.

Face-to-face workshop:

• Follow up workshops on "standards" drawn from Segovia meeting. The workshops should focus on top standardization “needs” not met or realized yet via current practice; a set of fresh scientific research areas that might be strategically coupled to support current engineering goals in synthetic biology; and third, a working list of now unmet programmatic or facility needs necessary to see such work carried out in a timely fashion. Possible ideas currently considered as next possible workshops include "Orthogonality and orthogonal systems in Biology", “Cell operative systems” and “Deep metabolic engineering” Planned date 2012 for the first workshop; a second workshop on this issue could be held end of this 5 years period, 2014.



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Questions to be answered by these workshops and follow up discussions:

Standarization

Define accurately the nature and boundaries of biological functions

Formalization and non-ambiguous representation of biological information is a major bottleneck for the development of SB

Development of consensus criteria for Biological Standards

What is a biological part? Is it possible to convert a natural, context-dependent module into an autonomous component?

One of the outcomes and issues of discussion during the workshops should be also the establishment of an US-EU Group on Biological Standards which will act as both as an observatory of bottom-up initiatives and as a think tank on research topics with a prenormative value.

• Workshop on Ethical, Legal, and Social issues in relationship (or in juxtaposition) to the scientific and technical progress of Synthetic Biology. Discussion of ELSA issues drawn from the European Group on Ethics (EGE) Opinion on the ethical, legal and social implications raised by synthetic biology and the US Presidential Commission for the Study of Bioethical Issues reports on Synthetic Biology. Planned date 2013-2014

• Workshop on relevant contribution of Synthetic Biology to different domains of

Biotechnology. Which could be also coupled with the previous workshop on ELSA Planed date 2012-2013

Training courses:

• Short term courses with theoretical and practical (laboratory) sessions focused on basic techniques and principles of synthetic biology. The focus of the course will be identified according to the development of the domain. Planned date on 2013.

• Exploration of funding possibilities for short term exchanges of US young scholars

to EU research institutions with reciprocity of short term exchanges of EU young scholars to US research establishments.



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OBESITY AND NUTRITIONAL SCIENCES FOCUS AREA The aim will be to identify opportunities most beneficial from transatlantic cooperation, catalyse further interaction with US agencies, and to consider engagement with US and European scientific societies in implementation of the recommendations emerging from the workshop entitled, “New Technologies and Innovations to Tackle Obesity”, held in November 2010 in Brussels. Specific areas of research were suggested for the future:

• To explore the foetal programming as a major long-term impact factor for obesity and diet related diseases.

• To analyze the long term effects of chemical toxicants on diet related diseases.

• To develop knowledge on systemic inflammatory cytokines and inflammatory cell infiltration associated with obesity in adipose tissue.

• To define a "healthy“ gut microbiome, its ability to utilize or metabolize macronutrients, influence energy expenditure as well as study the lifestyle factors influencing it.

• To develop and investigate genotype-specific diets in weight loss/ maintenance => personalized nutrition.

• To emphasize research on social determinants of diet related diseases to help address social and health disparities.

• To study the effect of behavior change from the perinatal period, including role of mother& father regarding habits and taste/determinants and process of decision making by families.

New and cutting edge common research topics where clear synergies would be brought to light will be considered. Program staff from both US and EC have agreed to informally share plans for the development of respective initiatives, to seek one another's input as relevant as relevant workshop are planned in either Europe or the US, and to further encourage US and EC investigators to have dialogue and develop collaborations

Documents

US-EC Task Force Five-Year Strategic Plan · Five-Year Strategic Plan 2011-2015 6 SUMMARY It is anticipated that the work of the Task Force will be carried out initially under the