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SDB-LASDB 2012 PASI Short Course Report

By Jennifer Fish

Jennifer Fish is a postdoc in the Department of Orthopaedic Surgery at the University of California, San Francisco in Richard Schneider's lab. She studies craniofacial development, in particular the jaw, with a focus on the role of variation in development, disease, and evolution. Jennifer was one of thirty students selected from a pool of 77 applicants from the United States and nine Latin American countries to attend the SDB-LASDB PASI short course.

The Satellite Short Course of the Sixth International Meeting of the Latin American Society for Developmental Biology was held at the Universidad de la Republica & Institut Pasteur de Montevideo in Montevideo, Uruguay from April 16-25, 2012. The 2012 course, A Systems Biology Approach to Understanding Mechanisms of Organismal Evolution, offered a combination of lectures with significant hands-on learning of important theories, concepts, and methods in evolutionary biology. Scientists at all levels of their careers came from around the world to participate in this course with instructors representing Argentina (Rolando Rivera Pomar), England (Andrea Streit and Claudio Stern), Germany (Detlev Arendt), Switzerland (Brigitte Galliot), the United States (Siobhan Brady, Yolanda Cruz, Katia Del Rio-Tsonis, Nipam Patel, Alejandro Sanchez-Alvarado, Billie Swalla, and Panagiotis Tsonis), local scientists Luis Acerenza, Nibia Berois, Maria Castello, Enrique Lessa, and Flavio Zolessi from Uruguay, and 30 students from 29 universities in 7 different countries throughout the American continents.

The aim of the 2012 short course was to teach young scientists novel methodological techniques in evolutionary biology and introduce them to a variety of model organisms in order to expand their knowledge base of evolutionary processes. Emerging approaches to investigating systems biology and gene regulatory networks were a particular emphasis of this year's course. Multiple bioinformatic tools, including Biotapestry, Cytoscape, and CellNetAnalyzer, were taught in hands-on computer based modules.  A focus of these modules was to integrate data from disparate sources to allow the investigator to generate testable hypotheses about biological processes. For example, in the Cytoscape lesson, we generated a gene regulatory network using published data of gene targets of the well-studied Drosophila Hox genes, Ultrabithorax and homothorax derived from ChIP analyses. Our Cytoscape-generated networks allowed us to predict the tissue-specific expression of spalt, a downstream target of Hox genes in this network. We subsequently tested hypotheses based on these bioinformatic predictions by investigating spalt expression in the Arthropod lab module.

The course also contained modules in standard developmental biological techniques, such as comparative development and morphology. A focus was placed on exposure to non-model systems, such as annual and electric fish, as well as multiple invertebrate species. There were several modules on molecular mechanisms of tissue regeneration, in which we investigated animals of differing levels of complexity and cuteness (planaria, hydra, and axolotl). In addition to comparative analyses, the wet lab modules covered many classical methods in gene expression and embryonic manipulation, including tissue transplantation and electroporation in chick embryos.

Beyond the lessons in the classroom, two important messages were re-enforced to me, as a participant in this course. First, although funding issues influence scientific progress in many ways, creativity and resourcefulness cannot be underestimated. In this regard, I was consistently impressed with the persistence and ingenuity of the local scientists to find solutions to technical challenges and devise alternative strategies to answer their scientific questions of interest. Second, science is a global discipline, undertaken by people of different backgrounds, cultures and worldviews. Yet the ethic of science, built around the pursuit of knowledge towards a greater understanding of the natural world, can be a unifying force across many boundaries. As we are all well aware, this does not mean scientists, or even participants in this course, always agree on everything. We are all chordates, but we still debate the origin of the first neuron ancestral to our dorsal nerve cord. Nonetheless, at the heart of this and other scientific debates is a common goal to understand the unknown. To accomplish this goal, open communication and exchange of knowledge is essential, and the 2012 LASDB mini-course provided an environment where the best aspects of the scientific community were manifested.

The course was structured so that students and faculty had concentrated research blocks spent together in a closed environment. Despite the long days and often rigorous schedule, the setting and atmosphere established by the course organizers encouraged all participants to interact equally, with no sense of hierarchy, creating a comfortable, amicable environment where students could freely ask questions about all aspects of science- from methods, to publishing strategies, to advice on post-doctoral applications. Impromptu discussions and spontaneous chalkboard explanations were commonly seen throughout the 10-day course. We worked together, ate together, and (sometimes) danced together. In the end, the 2012 course achieved its goal to be integrative, both methodologically, by combining techniques to answer biological questions, and personally, in building lasting relationships. For this unique experience, all the participants sincerely thank the organizers, Mike Levine (University of California, Berkeley), Ida Chow (Society for Developmental Biology), Flavio Zolessi (Universidad de la Republica, and Nibia Berois (Universidad de la Republica), as well as the local volunteers who made the 2012 LASDB mini-course possible.

2012 SDB-LASDB PASI Short Course students and faculty