PRACTICAL APPROACH TO ECOTOXICOGENOMICS

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1 ANNOUNCEMENT PRACTICAL APPROACH TO ECOTOXICOGENOMICS Advanced Workshop Studies in Biology and Applied Biosciences Department of Biology University of Aveiro, 30 April- 4 May 2007 This one-week post-graduate workshop aims to provide knowledge on the development of molecular markers of stress using molecular biology techniques. This includes among others the following: RNA extraction, cdna synthesis, basic cloning techniques, PCR reaction development and optimisation, real time PCR, DNA sequencing, and development of microarrays (cdna arrays), their hybridization and analysis. The course is addressed to scientists and PhD and M.Sc. students with a background in Biology, Natural and Environmental Sciences, Chemistry, Environmental engineering or related fields, members of consulting companies and of private and public institutions responsible for environmental management. This course is being held within the NoMiracle project consortium (http://nomiracle.jrc.it/default.aspx).

2 Course Coordinators: Mónica Amorim, Manuel Santos and Amadeu Soares - Department of Biology, University of Aveiro, Aveiro, Portugal. Main Themes - Basics of ecotoxicogenomics: strategies and designs; - RNA extraction, cdna synthesis; - Basic cloning techniques; - PCR reaction development and optimisation; - Real time PCR - Development of microarrays: spotting arrays (cdna arrays, oligo s); - Hybridization techniques - Microarray analysis; - DNA sequencing; This course will comprise a combination of lectures and practical work in which hands-on experience will be gained.

3 Lecturers: Dr Dick Roelofs holds an MSc degree in Agricultural Sciences at the Wageningen University, where he specialized in plant molecular genetics and plant biotechnology. After conducting a research project at the Colorado State University (USA) on molecular cytogenetics he started his PhD project at the University of Amsterdam. During this project he studied the molecular evolutionary consequences of cytoplasmatic introgression in plants. After graduating for his PhD project in 1996 he conducted a post-doc project at the Genetics department of the Vrije Universiteit Amsterdam, to study the molecular mechanism of RNA interference. In 1999 he started to work as a Technical Services Scientist for the US based company Promega life sciences. During this period he conducted the development of new technologies for the life science industry, specifically for high throughput screening. In 2002 he switched back to the academic environment as lecturer at the department of Animal Ecology, Vrije Universiteit Amsterdam. Currently, he is project leader of the Ecogenomics team participating in the Dutch Ecogenomics consortium trying to assess and unlock life support functions of the soil. He teaches courses in Evolutionary Genetics, Evolutionary Biology and Environmental Genomics. Dr Wim De Coen is a molecular biologist with a PhD in environmental toxicology. Is the head of the research group dealing with biochemical and molecular aspects of toxicology. His research focused on the development and evaluation of biochemical and molecular markers to detect adverse effects of pollutants on aquatic organisms. He studied effects of toxicants on the energy metabolism and DNA damage and developed criteria for the prediction of chronic population level effects in aquatic and terrestrial organisms. During his post-doctoral fellowship at the Michigan State University he specialized in the use of cellular assays with human, fish, rat and other mammalian cell systems for the detection of endocrine disruption of xenobiotics. At the same university he got familiar with recent developments in the field of differential gene expression analysis and the potential of DNA arrays. At present, he is responsible for the development and evaluation of molecular and cellular environmental toxicology studies at the University of Antwerp, Laboratory for Ecophysiology, Biochemistry and Toxicology, Belgium. Dr. Mónica Amorim is an Assistant Researcher at the University of Aveiro, Portugal. She has done her PhD on ecotoxicology focusing on the study of the effect of different soils properties in organisms and its interaction with toxic substances. Main research area has been ecotoxicology, where several years were devoted to the development of an active research programme, mostly terrestrial, field and laboratory, addressing a series of both fundamental and prenormative research questions. Ecotoxicogenomics has been the latest research area. Progresses have already taken place, such as the development of a new micro-array for a relevant test species. Dr. Amorim has been involved in several research projects and in the standardisation of new guidelines, having published several papers in the area. - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Portugal. Dr Adelaide Freitas is a Statistician at the Department of Mathematics of the University of Aveiro, Portugal. She is a member of the Bioinformatics group created at the University of Aveiro which is involved in the implementation of a National Facility for DNA Microarrays. One of her current research interests is the development of biclustering techniques for large data sets (microarray data, data mining) as well as the study of statistical methodologies associated to contingency tables for building genome wide codon context maps for identification of potencial error prone mrna. UIMA-Research Unit Mathematics and Applications, Department of Mathematics, University of Aveiro.

4 Dr. Karlijn van der Ven is a postdoctoral researcher at the University of Antwerp. During her Phd at the laboratory for Ecophysiology, Biochemistry and Ecotoxicology (www.ecotox.be) she optimised the use of microarrays to investigate effects of exposure of aquatic organisms to toxicants on gene expression. Her current research involves transcriptoom and proteoom analysis to elucidate PPAR-mediated pathways in fish, both in in vitro and in vivo testsystems. She is involved in several reseach projects in the area of (eco)toxicogenomics and was one of the instructors of the toxicogenomics short course in SETAC The Hague and Montreal. Tine Vandenbrouck is a PhD student at the Ecophysiology, Biochemisty and Toxicology lab at University of Antwerp, Belgium (www.ecotox.be). She mainly focuses on molecular responses of Daphnia magna after toxicant exposures, more specific mixture exposures. Therefore, a custom microarray is used to unravel more mechanistic information regarding mixture toxicity in this model organism. This project fits in the framework of the EU NoMiracle project. At EB&T, experience with different molecular techniques such as SSH, microarray analysis, RT-PCR, was gained. She was also one of the instructors of the toxicogenomics short course at SETAC Montreal Dr Laura Carreto is a Post-Doctoral Fellow at the University of Aveiro. Her current research interests include the use of DNA microarray technology for the comprehensive monitoring of gene expression during alcoholic fermentation in wine yeast isolated in Portugal, as well as the characterization of the karyotype rearrangements which often occur in strains adapted to oenological environments, with the aim of elucidating the key metabolic pathways activated in the process, while looking for molecular markers that correlate metabolic properties and wine production performance of the isolates. She is part of a multidisciplinary team involved in the implementation of a National Facility for DNA Microarrays (NFDM), were she is responsible for the in-house production, processing and analysis of DNA-oligonucleotide Microarrays targeting Saccharomyces cerevisiae ORFeome. -, Department of Biology, University of Aveiro, Portugal. Dr Patrícia M. Pereira is a Post-Doctoral Fellow at the University of Aveiro. Her recent research interests include the study of micrornas expression profiling in vertebrate organisms using DNA microarray technology, as well as study the role of micrornas in zebrafish biology. She is part of a multidisciplinary team involved in the implementation of a National Facility for DNA Microarrays (NFDM), were she is responsible for the in-house production, processing and analysis of DNA-oligonucleotide Microarrays targeting micrornas from vertebrate organisms. -, Department of Biology, University of Aveiro, Portugal. Joel Arrais, after finishing the degree in computer science in 2004 at the University of Aveiro joined the bioinformatics group in the same institution. In 2006 started a PhD program that aims to produce a contribution to the microarray community by improving the workflow of the laboratory data. The main research topics are microarray data standards, ontology s, information retrieval as also microarray data analysis tools. One of the main achievements has been the development of a Microarray Information Database (Mind) that aims to be an all-inone web application that contain tools to store, analyse and publish the results of microarray studies.

5 Course Fees Normal course fee- 500 Euros Discount fee Euros (members of Ordem dos Biólogos, SICTA, SETAC and members of the NoMiracle project) For updated information on this course, please go to:

6 REGISTRATION FORM (send by fax ( ) or to Mónica Amorim till the 23 rd of March) Name: Institution: Address: Country: Course Fee: Normal Fee: 500 Discount Fee: 400 (please provide confirmation of eligibility for the discount fee) Accommodation: Yes, I am interested in booking a room Arrival date: /04/2007 Departure date: /05/2007

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