Genetics April 2006

genetics@lists.oulu.fi

9 participants
13 discussions

FW: Sybr safe
by Minna Ruokonen 14 Jul '06

14 Jul '06

Hi, Finnzymes has given us a small amount of Sybr Safe dye, which can be used instead of ethidium bromide on agarose gels. Sybr Safe should be less toxic compared to EtBr, but we are still trying to find out what kind of precautions and waste disposal are necessary (an email from Finnzymes below). Soile tried Sybr Safe and it worked nicely, also photos were OK with the camera we have now (no specific instruments or even filters necessary). If you want to try it yourself, ask Soile. The price for 400 microliters is 67 eur (November 2005), 1 microliter of dye / 10 ml of gel solution is needed. Minna ---------- Forwarded message ---------- Date: Wed, 29 Mar 2006 09:16:59 +0300 From: Katja Mäntylä <katja.mantyla(a)finnzymes.fi> To: 'Minna Ruokonen' <mruokone(a)sun3.oulu.fi> Subject: FW: Sybr safe -jätteenkäsittely Euroopassa Hei Minna, Alla vielä Invitrogenilta saamani vastaus koskien Sybr Safe geelivärijätteen käsittelyä Euroopassa. Vastaus on melko ylimalkainen johtuen siitä että paikallisten viranomaisten ohjeet vaihtelevat maakohtaisesti. Toivottavasti tästä on kuitenkin jotain apua! Ystävällisin terveisin, Katja ************************** Katja Mäntylä, M.Sc. Product Manager Finnzymes Oy Keilaranta 16 A 02150 Espoo Finland Tel. +358 9 5841 2246 Fax +358 9 5841 2200 Katja.mantyla(a)finnzymes.fi -----Original Message----- From: Yamaoka, Larry [mailto:larry.yamaoka@invitrogen.com] Sent: 22. helmikuuta 2006 1:31 To: Finnzymes Oy (Katya); !EUG-Sybrsafe Subject: RE: Sybr safe waste handling in Europe Dear Katja: We do not have any specific suggestions (for Europe) for disposal of SYBR Safe DNA gel stain. Because local rules may differ from Federal (USA) guidelines, the suggestion from our environmental safety office is: -characterize the material you want to dispose -go to the local authority that has jurisdiction over route(s) of disposal (e.g., landfill, wastewater, etc.) -show them what you know about your waste (i.e., the information provided in the SYBR Safe product manual) -ask them if they approve the disposal. Please contact me if you have other questions or require additional information. Sincerely, Larry Yamaoka, Ph.D. Invitrogen Corporation Molecular Probes Detection Technologies Technical Support Scientist Phone: 541 335 0353 Fax: 541 335 0238 larry.yamaoka(a)invitrogen.com _____ From: Katja Mäntylä [mailto:katja.mantyla@finnzymes.fi] Sent: Tuesday, February 21, 2006 4:27 AM To: !EUG-Sybrsafe Subject: Sybr safe waste handling in Europe Dear Receiver, Have you got any European guidelines for the waste handling of Sybr safe DNA gel stain? Thanks and kind regards, Katja ************************** Katja Mäntylä, M.Sc. Product Manager Finnzymes Oy Keilaranta 16 A 02150 Espoo Finland Tel. +358 9 5841 2246 Fax +358 9 5841 2200 Katja.mantyla(a)finnzymes.fi

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[BioClients] Basic R / Bioconductor course at CSC, 22.-24.5.2006 (fwd)
by Minna Ruokonen 25 Apr '06

25 Apr '06

---------- Forwarded message ---------- Date: Tue, 25 Apr 2006 13:48:07 +0300 (EEST) From: Jarno Tuimala <jtuimala(a)csc.fi> To: bioclients(a)postit.csc.fi Subject: [BioClients] Basic R / Bioconductor course at CSC, 22.-24.5.2006 Dear Bioscientist, A new course on DNA microarray data analysis using R / Bioconductor is arranged at CSC on 22.-24.5.2006. The course registration is currently open. This course will cover the basics of R and Bioconductor. Participants are expected to have some background knowledge on DNA microarrays, although the basic datatypes and concepts are introduced on the course. No previous knowledge of R or Bioconductor is expected. The course consists of lectures and hands-on exercises, the emphasis being on the exercises. For more detailed schedule and registration, see http://www.csc.fi/suomi/koulutus/kurssi.phtml.fi?id=281 . Best Regards, Jarno Tuimala ----------------------------------------------------------------------------- Jarno Tuimala, FT, bioinformatiikan asiantuntija, CSC, PL 405, 02101 Espoo puh.: (09) 457 2226, fax: (09) 457 2302, s-posti: jarno.tuimala(a)csc.fi CSC on tieteen tietotekniikan keskus, http://www.csc.fi/molbio Jarno Tuimala, PhD, bioinformatics, CSC, P.O.Box 405, FI-02101 Espoo, Finland tel.: +358 9 457 2226, fax: +358 9 457 2302, e-mail: jarno.tuimala(a)csc.fi CSC is the Finnish IT Center for Science, http://www.csc.fi/molbio -----------------------------------------------------------------------------

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19 Apr '06

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FW: Course: PortoPortugal PopSizeEstimation Aug30-Sep2
by Jouni Aspi 19 Apr '06

19 Apr '06

Subject: Course: PortoPortugal PopSizeEstimation Aug30-Sep2 *Conservation Genetics Data Analysis Course: * *Recent Approaches for Estimation of Population Size, * *Structure, Gene flow, Parentage, & Selection Detection* */30 August to 2 September, 2006, Porto, Portugal/* * * *Objective:* To provide training in conceptual and practical aspects of data analysis for the conservation genetics of natural and managed populations. Emphasis will be on interpretation of output from recent novel statistical approaches and software programs. The course also will allow daily discussions among young researchers and top-researchers to help develop the next generation of conservation geneticists, and to identify developments needed to improve data analysis approaches. This course will mainly cover analysis of allele frequency data (not DNA sequence data), including coalescent, Bayesian, approximate Bayesian, and likelihood-based approaches. * * *Who should apply:* Ph.D. students, post-docs, and population biologists with a background of at least one semester university-level course in population genetics and a course in population ecology. Applicants must have a basic background in population genetic data analysis, including testing for Hardy-Weinberg proportions and gametic disequilibrium. Participation will be limited to 25 people allowing efficient instruction with hands-on computer exercises during the course. Priority will be given to persons with their own data to analyze (for example graduate students near the end of their degree program). * * *Course/Workshop Format:* For each subject, we provide 30-45 minutes of background, theory, discussion and introduction to concepts. Immediately following, we will conduct data analyses together for 30-45 minutes using relevant software programs and real data sets. Evening hands-on computer sessions and housing together of instructors and students in the same location will allow for extensive exchange and facilitate learning. *Instructors/Speakers:* Fred Allendorf, Mark Beaumont, Peter Beerli, Albano Beja-Pereira, Daniel Falush, Adam Jones, Gordon Luikart, Karen Martien, Mark Miller, Scott Mills, Mike Schwartz, David Tallmon, and Robin Waples. * * *Location: *The course will be held in the facilities at CIBIO (Center for Investigation of Biodiversity and Genetic Resources; http://cibio.up.pt/ ) on the Campus for Agricultural Sciences in the rural village of Vairão, just north of Porto, and a few kilometres from the Atlantic coast and the airport. Vairão is an ancient village whose origins can be traced back to the Roman Period (the Roman village Valeriani). *Registration and cost:* For detailed information see http:\\cibio.fc.up.pt\congen (webpage will be available on 30 April; in the meantime for enquiries contact albanobp(a)mail.icav.up.pt <mailto:albanobp@mail.icav.up.pt> or gordon.luikart(a)mso.umt.edu). Accommodations and meals are included in the registration fee. Cost: $US 1,000 per person will cover all meals, lodging, transportation to and from the airport, and a visit to Gerês National Park and the World Heritage City of Porto. Up to two reduced-cost scholarships will be available for candidates with no funding. *Application and criteria for acceptance:* /Deadline/ for application is */15 June/, 2006*. Applicants must provide a brief description of their research interests, career goals, and what they would like to learn from this course. Priority will be given to persons with their own data to analyze (for example graduate students near the end of their degree program). The applicants should submit a brief summary (<200 words) about the current state of their work, the hypotheses or questions addressed, the genetic markers used, and study species. To apply for scholarship support, candidates should also send their CV, a cover letter explaining why they should receive the scholarship, a cost estimate for their flight (round trip) to Porto, and a phone number where they can be reached for a brief interview. ** Albano Beja-Pereira <albanobp(a)fc.up.pt> --ZPt4rx8FFjLCG7dd Content-Type: text/html; charset=ISO-8859-1 Content-Disposition: inline <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type"> <title></title> </head> <body bgcolor="#ffffff" text="#000000"> Conservation Genetics Data Analysis Course:  <o:p></o:p> Recent Approaches for Estimation of Population Size, <o:p></o:p> Structure, Gene flow, Parentage, & Selection Detection<o:p></o:p> 30 August to 2 September, 2006, <st1:place w:st="on"><st1:City w:st="on">Porto</st1:City>, <st1:country-region w:st="on">Portugal</st1:country-region></st1:place><o:p></o:p> <o:p> </o:p> Objective: To provide training in conceptual and practical aspects of data analysis for the conservation genetics of natural and managed populations.  Emphasis will be on interpretation of output from recent novel statistical approaches and software programs.  The course also will allow daily discussions among young researchers and top-researchers to help develop the next generation of conservation geneticists, and to identify developments needed to improve data analysis approaches.  This course will mainly cover analysis of allele frequency data (not DNA sequence data), including coalescent, Bayesian, approximate Bayesian, and likelihood-based approaches.<o:p></o:p> <o:p> </o:p> Who should apply:  Ph.D. students, post-docs, and population biologists with a background of at least one semester university-level course in population genetics and a course in population ecology.  Applicants must have a basic background in population genetic data analysis, including testing for Hardy-Weinberg proportions and gametic disequilibrium.  Participation will be limited to 25 people allowing efficient instruction with hands-on computer exercises during the course.  Priority will be given to persons with their own data to analyze (for example graduate students near the end of their degree program).  <o:p></o:p> <o:p> </o:p> Course/Workshop Format:  For each subject, we provide 30-45 minutes of background, theory, discussion and introduction to concepts. Immediately following, we will conduct data analyses together for 30-45 minutes using relevant software programs and real data sets.  Evening hands-on computer sessions and housing together of instructors and students in the same location will allow for extensive exchange and facilitate learning.<o:p></o:p> <o:p></o:p> Instructors/Speakers:  Fred Allendorf, Mark Beaumont, Peter Beerli, Albano Beja-Pereira, Daniel Falush, Adam Jones, Gordon Luikart, Karen Martien, Mark Miller, Scott Mills, Mike Schwartz, David Tallmon, and Robin Waples.<o:p></o:p> <o:p> </o:p> Location:  The course will be held in the facilities at CIBIO (Center for Investigation of Biodiversity and Genetic Resources; <a href="http://cibio.up.pt/">http://cibio.up.pt/</a> ) on the <big><big><big><big><big><big>Campus for Agricultural Sciences</big></big></big></big></big></big> in the rural <st1:PlaceType w:st="on">village</st1:PlaceType> of <st1:PlaceName w:st="on">Vairão</st1:PlaceName>, just north of <st1:place w:st="on">Porto</st1:place>, and a few kilometres from the Atlantic coast and the airport.  Vairão is an ancient village whose origins can be traced back to the Roman Period (the Roman village Valeriani).  <o:p></o:p> <o:p> </o:p> Registration and cost: For detailed information see <a class="moz-txt-link-freetext" href="http:\\cibio.fc.up.pt\congen">http:\\cibio.fc.up.pt\congen</a> (webpage will be available on 30 April; in the meantime for enquiries contact <a href="mailto:albanobp@mail.icav.up.pt">albanobp(a)mail.icav.up.pt</a> or <a class="moz-txt-link-abbreviated" href="mailto:gordon.luikart@mso.umt.edu">gordon.luikart(a)mso.umt.edu</a>).<sp an style="">  Accommodations and meals are included in the registration fee.  Cost:  $US 1,000 per person will cover all meals, lodging, transportation to and from the airport, and a visit to Gerês National Park and the World Heritage City of Porto.  Up to two reduced-cost scholarships will be available for candidates with no funding. <o:p></o:p> <o:p> </o:p> Application and criteria for acceptance:  Deadline for application is 15 June, 2006.  Applicants must provide a brief description of their research interests, career goals, and what they would like to learn from this course.  Priority will be given to persons with their own data to analyze (for example graduate students near the end of their degree program).  The applicants should submit a brief summary (<200 words) about the current state of their work, the hypotheses or questions addressed, the genetic markers used, and study species.  To apply for scholarship support, candidates should also send their CV, a cover letter explaining why they should receive the scholarship, a cost estimate for their flight (round trip) to Porto, and a phone number where they can be reached for a brief interview. <o:p></o:p> <pre class="moz-signature" cols="72"> </pre> </body> </html> --ZPt4rx8FFjLCG7dd--

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Invitation to Genomics 2006-Nov-Cuba (fwd)
by Minna Ruokonen 13 Apr '06

13 Apr '06

Second Announcement November 4-10, 2006 Dr. Minna Ruokonen Dear Colleague, We are delighted to extend you a cordial invitation to Genomics 2006 which will be held in Varadero (Hotel: Playa Varadero 1920) and Havana (CIGB) - from Nov 4 to 10, 2006. Genomics 2006 should be a fruitful source of scientific exchange and discussion among researchers from all over the world. The program will include state-of-the-art lectures, discussions and short report presentations from worldwide authorities in genomics and genetics. The lectures will be delivered at the famous health resort of Varadero 4-8 Nov2006. More than 40 top-level speakers from 18 countries have confirmed their attendance and will deliver lectures at Genomics 2006 in an intense program. See below the list of confirmed speakers. For a weekly updated list of confirmed speakers, countries and affiliations, as well as the last version of the scientific program please visit the "speakers" and "program" pages at our web site http://eventogenomica.cigb.edu.cu There will also be a series of practical demonstrations which will be organized in the days following the Theoretical Lectures (9-10 Nov) at the CIGB lab facilities. Participants are encouraged to send an abstract of their work. As a novelty and in an attempt of extending the possibility of knowing the work of these groups by all the attendees selected works will be delivered as 10 min short-report presentations November is one of the most beautiful months in Cuba. We wish to achieve a perfect mix of art and science, research, culture, and paradisiacal beach. We sincerely hope you will be part of the challenge. We look forward to see you in Cuba in 2006 for what we expect to be a stimulating and exciting meeting. Yours sincerely, Lidia Ines Novoa and Annia Ferrer Organizing Committee Scope Genomics 2006 follows the tradition of the CIGB International Workshops on Genomic Research and comprises this year two important workshops: the 3rd Workshop on Genomic Reseach and the 1st Cuban Workshop on Genomics. The 1st Cuban Workshop on Genomics is an International Workshop, organized and sponsored by the INTERNATIONAL CENTRE FOR GENETIC ENGINEERING (ICGEB), Trieste, Italy an international organization dedicated to advanced research and training in molecular biology and biotechnology, with special regard to the needs of the developing world. The 3rd International Workshop on Genomic Reseach is organized this year as a Satellite Meeting for the International Congress Biotechnology Havana 2006 . Genomics 2006 is organized to review the state of the art on Genetics and Genomic of Complex Traits (High Blood Pressure, Schizophrenia, Autoimmune Diseases), Study Design for Complex Traits, HLA typing and Disease Association, SNPs, Haplotyping and Pharmacogenomics, Databases, Bioinformatics and Statistical Analysis. Genomics 2006 is aimed to teach the participants both theoretical basis and practical applications of genomic research, genetics and molecular biology methods. The main goal is to stimulate basic research in these fields in Central and South American and the Caribbean countries. The workshop also intends to encourage the development of local and regional laboratories where different human samples will be collected and analysed for genomic and genetic studies. The workshop has been planned as an international forum for scientific exchange on all major areas of genomics and human genetics, with an opportunity for each of the participants to exchange views on the present state of knowledge, the emergence of new concepts and the development of innovative techniques relevant to regional problems. Genomics 2006 will include a series of lectures, a range of tutorials and a practical course embodying cutting-edge technology. The workshop is intended for students and researchers with limited experience in using different tools for genomic research and bioinformatics methods. Main Topics Lecture topics have been selected that have an emphasis on genomics appropriate to the region. These will include: 1. Human population genetic structure/substructure, founder effect, drift, endogamy, consanguinity 2. Immunogenetics, HLA Typing and Disease Association 3. Genetic and Genomic of Complex Traits 4. Statistical Methods for Population Genetic and Genomic 5. Genetic Admixture methodology and application to complex diseases 6. Pharmacogenomics 7. Cancer genetics 8. Genetic predisposition to disease (hypertension, diabetes, Schizophrenia, etc) 9. Molecular cytogenetics 10. Single gene defects, especially the haemoglobinpathies/ thalassaemias 11. Host susceptibility to infectious disease (SARS, AIDS, TB, Leprosy, etc) 12. Diseases of adult-onset 13. The design of community-based education and counseling programs/community involvement in the prevention of genetic disease 14. Establishment of disease registers/screening programs for diseases of high local/regional/community prevalence. 15. Ethical issues of human genetics. Practical demonstrations will include: 1. Pedigree creation using PROGENY and Cyrillic software. 2. Genome and population data analysis: introduction to population structure and differentiation, migration inference and genetic distance matrix (ARLEQUIN software and others 3. Linkage analysis including - parametric methods (two-point and multipoint analysis); allele sharing (nonparametric) methods for sib-pairs and extended families (two-point and multipoint analysis), fine mapping, linkage admixture, association studies (trios and case control, sample size estimation (extended families [simulation studies], sib-pairs and case-control data) and estimating empirical p-values. Introduction to GENEHUNTER/ALLEGRO and LINKAGE/FASTLINK software 4. Medical diagnosis, questionnaires and blood sample collection and witness preservation. 5. Genomic DNA purification, evaluation, amplification and preservation. 6. HLA genotyping by SSP, SSO - PCR and sequencing. 7. SNP analysis by sequencing 8. Bioinformatics and data handling Confirmed Speakers Name Country Affiliation Alarcon, Marta Sweeden Unit for Medical Genetics, Uppsala University Baralle, Francisco Italy General Director, ICGEB Baralle, Diana UK Addenbrookes Hospital, Cambridge Barreiro, Luis France Pasteur Institute Bittles, Alan Australia Centre for Human Genetic Bodmer, Sir Walter UK Weatherall Institute of Molecular Medicine, Oxford Bontrop, Ronald Netherlands Biomedical Primate Research Center Borevitz, Justin USA University of Chicago Burchard, Esteban USA University of California, San Francisco Carin, Mahmut Turkey Head of the Medical Biology Department, Istanbul University Charron, Dominique France Director, Unité Rech. Immunog. Hum. INSERM U396 Collins, Andrew UK University of Southampton Cooper, Richard USA Loyola University Stritch School of Medicine Cordeiro, Quirino Brazil Universidade de São Paulo (USP), São Paulo, SP, Brazil. Chakraborty, Ranajit USA Center for Genome Information, University of Cincinnati Darvasi Ariel Israel Institute Of Life Sciences the Hebrew University Of Jerusalem Divers, Jasmine USA Section on Statistical Genetics, Dep. Biostatistics, UAB Dopazo, Joaquin Spain Centro de Inv Principe Felipe, Valencia Fernández Jose USA University, Alabama at Birmingham Froguel Philippe UK Genome Centre, Imperial College, London Garrido, Federico Spain President, European Federation of Immunogenetics (EFI) Garvey, Timothy USA Chair, Nutrition Science Dept., UAB Gervais, Thibaut Belgium UCL-Cliniques St Luc Immunohaematology. Brussels Goldstein, David USA Director, Ctr. Pop. Genomics & Pharmacog., Durham, NC Herrera, Luis Cuba General Director, CIGB Kittles, Rick USA Comprehensive Cancer Center, Ohio State University Kurland, Lisa Sweden Uppsala University Labuda, Damian Canada Pediatrics Department, Montreal University Lakowski, Bernard France Pasteur Institute Landegren Ulf Sweeden Uppsala University Mancheco, Beatriz Cuba Director, National Center for Medical Genetics McElreavy, Ken France Pasteur Institute McLeod, Howard USA Washington University School of Medicine. St Louis Middleton, Derek UK Director, N. Ireland Histocomp. Immunog. Lab., Belfast Mytilineos, Joannis Germany University of Heidelberg Munroe, Patricia UK Clinical Pharmacology and The Genome Centre, London Oglesbee, Steve USA UNC Lineberger Comprehensive Cancer Center Ott, Jurg USA Rockefeller University Parra, Esteban Canada Universidad de Toronto Patrinos, George Netherland Erasmus Medical Center, Rotterdam Patton, Michael UK St George's Hospital Medical School Phillip, Avner France Pasteur Institute Quintana-Murci, Luis France Pasteur Institute Reinhardt, Richard Germany MPI Molecular Genetics. Berlin. Risch, Neil USA Ctr. Hum. Gen. Univ. California. San Francisco Ruiz-Linares, Andres UK Head, Galton Lab, University College London Saggar, Anand Canada St George's Hospital Medical School Schmidt, Wolfgang M. Austria University of Viena Sperling, Silke Germany Max Planck Institute for Molecular Genetics, Berlin Stankovic, Aleksandra Serbia/Mngro Institute of Nuclear Sciences. Belgrade Terwilliger, Joseph USA Genome Center, Columbia University Thorsby, Erik Norway Head, Institute Immunol. Rikshospitalet Univ. Hospital, Oslo Tilanus, Marcel G.J Netherlands Dept. of Pathology, Utrech Zoellner, Sebastian USA Biostatistics Department. Michigan University Registration Registration Fees: Genomics 2006 Due to lab limitations, practical demonstrations are limited to 30 participants. There is a fellowship program for 14 undergraduate and postgraduate students mainly from Caribbean and Latin American countries. There are different variants in the fellowship program covering either accommodation assistance + registration fees or accommodation assistance. Only students from ICGEB member countries can apply for this program. Advance Registration Fees: (until August 15, 2006) * Commercial Institution: 450 CUC * University / NonProfit Institution: 350 CUC * Accompanying Person: 80 CUC Remarks Due to venue capacity restrictions, Genomics 2006 registration is limited to 50 places. Applications will be processed on a "first come, first served" basis. * It is not required to present a paper in order to participate in the workshop. Even when we are encourage to all participants to present a short report that will be published in a Proceeding as an official publication. The design of this forum grants outstanding importance to the presence of persons who are interested in the topics in discussion and to their participation in the debates during the work sessions. In this respect, all participants are considered as delegates. * All prices given are in CUC (Cuban Convertible Pesos). * For more details, please contact the Organizing Committee at: Calle 134 e/ 23 y 25, Cubanacan, Playa. POBox 6996, Havana 10600, Cuba (53-7) 208 7465 (53-7) 208 7421 (53-7) 271 4764 (53-7) 208 0553 genomic(a)cigb.edu.cu Or visit our Web Site at http://eventogenomica.cigb.edu.cu/

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Genetics April 2006