International CEMarin Omics Workshop: Omics Techniques for the Study of Marine Organisms and Ecosystems

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1 International CEMarin Omics Workshop: Omics Techniques for the Study of Marine Organisms and Ecosystems Genomics, proteomics and metabolomics, used alone, in combination with each other and/or with more traditional methods, are fields of study that are rapidly transforming many areas of biological and biomedical research. Stewart C. Johnson and Howard I. Browman Title of the course: Omics techniques for the study of marine organisms and ecosystems. Place: Universidad de los Andes, Bogotá, Colombia. Organizers: Center of Excellence in Marine Science (CEMarin). Coordinators of the course: Dr. Carmenza Duque, Dr. Thomas Wilke, Dr. Susana Caballero and Dr. Luis Fernando Cadavid. Schedule: The workshop will be held from September 28th to October 4 th, 2016, at Universidad de los Andes. Introduction and justification of the course: Coral reefs are among the most important marine ecosystems on earth. They are hotspots of biodiversity, and fundamental to the prosperity of many countries by providing important ecosystem functions and coastal protection against natural disasters. However, about one third of coral species and other living organisms in the reefs are endangered, approximately 19% of coral reefs have been effectively destroyed without immediate prospects of recovery, an additional 15% are at imminent risk of collapse under human pressure in the next years, and another 20% are under threat of collapsing in the longer term (Wilkinson, 2008). Among the most important animal species of these reefs are the sessile marine invertebrates, which have developed unique metabolic and physiological capabilities to survive in challenging and complex marine environments, allowing them to become structural and functional key components in coral reefs. One of the most important reasons for their success is the interaction with associated organisms. This complex biological assemblage is known as holobiont, a

2 collective term referring to the totality of an animal, its endolithic algae, and the associated community of microorganisms including bacteria, archaea, viruses and fungi. Microorganisms are also involved in metabolic and functional relationships with both invertebrates and vertebrates, and in such relationships these microorganisms are known as the microbiome. During the past decades, the holobiont and microbiome have been subject to numerous multidisciplinary scientific studies. Though the holobiont is not yet well understood, the development and application of omics techniques, e.g., genomics, transcriptomics, proteomics, and metabolomics, have strongly promoted holobiont research in particular and marine organism research in general. These technologies and methods are now used to address fundamental questions in areas such as marine ecology, biodiversity, evolution, and natural products. They also have allowed the transition from individual studies of single genes, proteins or metabolites to holistic studies of the macro and microorganism, and their interactions with the environment (systems biology). However, many of the new omics approaches that are currently being established have not yet found their way in marine sciences. Thus, the major goal of the current workshop is to provide a general overview of omics approaches (genomics, transcriptomics, metabolomics, proteomics) in general and in reef-building organisms in particular, and to discuss emerging methods and techniques as well as their challenges in the application to marine sciences. Specific Objectives: a) To promote state-of-the-art omics approaches in Colombia. b) To provide a critical view at modern omics tools. c) To introduce young researchers to various omics techniques and to enable them discussing their projects with international specialists in the field. d) To promote relationships between researchers and to establish an international omics research network. e) To stimulate new research ideas in the area of marine sciences. Directed to: Master and Doctoral students (CEMarin Early Stage Researchers ESR), postdocs and senior scientists (CEMarin Researchers) and other professionals working in marine sciences, omics, or related areas, as well as science administrators interested in establishing omics platforms at their institutions. Content of the course: Genomics, transcriptomics, proteomics and metabolomics.

3 Keynote lecturers: Jörn Kalinowski, PhD, Center for Biotechnology - CeBiTec / Technology Platforms / Technology Platform Genomics Daniel Wibberg, PhD, Center for Biotechnology - CeBiTec / German Network for Bioinformatics Infrastructure Alexander Goesmann, PhD Systems Biology, Justus-Liebig- of Applied Microbiology, Justus-Liebig-University Gießen, Germany David Overy, PhD. Adjunct Professor, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island. Marine Natural Products Lab Young Hae Choi, PhD. Associate Professor at Leiden University (Leiden, The Netherlands) Natural Products Laboratory, Institute of Biology Leiden, Alejandro Reyes, Universidad de los Andes, PhD, Washington University in Saint Louis Computational and Systems Biology, with over 10 years of research experience in molecular biology and microbiology involved in development projects of technologies and computational methods for the identification and characterization of microorganisms using latest technology. Poster session: course participants will have a two hour session to present posters showing their current research related with molecular biology-omic techniques. Lecturers will be able to understand the research being developed by the participants and provide initial advice for their work. Day 1 (28 September-Wednesday) 8:00-10:00 Course introduction 10:30-12:30 The future of natural products research with metabolomics Susana Caballero, PhD. Ecology and Evolution. Executive director CEMarin. Associate Professor Universidad de los Andes. Thomas Wilke, PhD. Professor and Head of the Systematics and Biodiversity Group at Justus Liebig University in Giessen. Young Hae Choi, PhD. Associate Professor at Leiden University (Leiden, The Netherlands) Natural Products Laboratory, Institute of Biology Leiden.

4 14:00-16:00 Metabolomics David Overy, PhD. Adjunct Professor, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island. Marine Natural Products Lab 16:00-17:00 Results of day 1-Discussion Day 2 (29 September-Thursday) 8:00-10:00 Workshop Metabolomics Young Hae Choi & David Overy 10:30-12:30 Workshop Metabolomics Young Hae Choi & David Overy 14:00-16:00 Poster session Course participants 16:00-17:00 Results of day 2-Discussion Day 3 (30 September-Friday) 8:00-10:00 Title of the talk pending Jörn Kalinowski, PhD, Center for Biotechnology - CeBiTec / Technology Platforms / Technology Platform Genomics 10:30-12:30 Title of the talk pending Daniel Wibberg, PhD, Center for Biotechnology - CeBiTec / German Network for Bioinformatics Infrastructure 14:00-16:00 Workshop pending Jörn Kalinowska & Daniel Wibberg 16:00-17:00 Results of day 3-Discussion Day 4 (1 October-Saturday) 8:00-10:00 Introduction to microbial genome annotation Alexander Goesmann, PhD Systems Biology, Justus-Liebig-University Gießen, Germany 10:30-12:30 Workshop Bacterial Holobiont Alexander Goesmann, PhD Systems Biology, Justus-Liebig-University Gießen, Germany Day 5 (3 October-Monday) 8:00-10:00 Title of the talk pending of Applied Microbiology, Justus-Liebig- 10:30-12:30 Workshop Bacterial Holobiont of Applied Microbiology, Justus-Liebig-

5 14:00-16:00 Workshop Bacterial Holobiont of Applied Microbiology, Justus-Liebig- 16:00-17:00 Results of day 5-Discussion Day 6 (4 October-Tuesday) 8:00-10:00 Introduction to genomics 10:30-12:30 Workshop Bioinformatics 14:00-16:00 Workshop Bioinformatics Alejandro Reyes, PhD, Doctorado Washington University in Saint Louis Computational and Systems Biology, With over 10 years of research experience in molecular biology and microbiology involved in development projects of technologies and computational methods for the identification and characterization of microorganisms using latest technology. 16:00-17:00 Results of day 6-Discussion Credit points: The total workload of the workshop is 48 hours. For active and successful participation, doctoral students may receive Colombian credit points or 1.5 ECTS credit points. Course fees: CEMarin ESR 100 USD CEMarin Univertities Students 110 USD Student from Non-CEMarin University: 125 USD CEMarin Researcher: 150 USD Independent Professional: 200 USD