From mhviegas from yahoo.com Sun Jul 5 13:57:21 2009 From: mhviegas from yahoo.com (Marcelo Viegas) Date: Sun Jul 5 20:32:38 2009 Subject: [Bioforum] biotinylated PCR stability Message-ID: <54985.60458.qm@web51412.mail.re2.yahoo.com> Hi, ? I am doing PCRs using biotin-dCTP.?Afterwards, I keep the?biotinylated product in the fridge. I noticed that if I use the labeled PCR the following day for my experiments, I get high signals (streptavidin development) but if I use it 3-4 days later instead, the signal is very weak. Does anyone know whether the biotin is that unstable bound to DNA? Thanks in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/bioforum/attachments/20090705/601e82fb/attachment.html From sqafyi from yahoo.com Tue Jul 21 14:48:07 2009 From: sqafyi from yahoo.com (biotech jobs) Date: Fri Jul 24 19:25:51 2009 Subject: [Bioforum] Bioinformatics Frequently Asked Question Message-ID: Bioinformatics Frequently Asked Question http://biotech.fyicenter.com/resource/bioinformatics_faq_2_table_of_contents.html A large collection of Frequently Asked Questions (FAQ) for Bioinformatics maintained by Damian Counsell, UK Medical Research Council Rosalind Franklin Centre for Genomic Research (the RFCGR) 1998-2004. Please visit: http://biotech.fyicenter.com/resource/bioinformatics_faq_2_table_of_contents.html Thank you, BioTech FYI Center http://biotech.fyicenter.com/ From editor from gene-quantification.info Mon Jul 27 02:14:22 2009 From: editor from gene-quantification.info (Editor www.Gene-Quantification.info) Date: Mon Jul 27 11:52:08 2009 Subject: [Bioforum] qPCR NEWS July 2009 - focus on single-cell qPCR Message-ID: <8f9548d1-52bb-4dca-a299-bc3bd3d3058e@g31g2000yqc.googlegroups.com> qPCR NEWS July 2009 - focus on single-cell qPCR ----------------------------------------------------------------- Dear researcher, dear Gene Quantification page reader, Our newsletter informs about the latest news in quantitative real-time PCR (qPCR and qRT-PCR), which are compiled and summarised on the Gene Quantification homepage. The focus of this newsletter issue is: - update in single-cell real-time PCR - qPCR / real-time PCR BLOG => http://real-time-pcr.blogspot.com/ - qPCR LinkedIN group - real-time PCR & qPCR => http://www.linkedin.com/groups?about=&gid=149835&trk=anet_ug_grppro - For better navigation we developed a TAG CLOUD => http://directory.gene-quantification.info/ - New qPCR events in autumn 2009: symposia & workshops => http://events.gene-quantification.info/ European wide qPCR application workshops => register now ! => course program spring - summer - autumn 2009 => http://www.gene-quantification.de/bioeps-courses-autumn-2009.pdf => http://www.gene-quantification.de/single-cell-qpcr-course-sept-2009.pdf -------------------------------------------------------------------------------- Single-cell molecular-biology is a relatively new scientific branch in biology. The first single-cell analysis were involved in the characterization of mitochondrial DNA in 1988. Single-cell DNA analysis, in particular genomic DNA, is important and may be informative in the analysis of genetics of cell clonality, genetic anticipation and single-cell DNA polymorphisms. Nowadays for most scientists the quantitative transcriptomics in a single-cell is much more important, and the analytical method of choice is the quantitative real-time RT-PCR. The relative abundance of single mRNAs and their up- or down-regulation in a single cell, compared to their neighbour cells, is the goal. The need for quantitative single-cell mRNA analysis is evident given the vast cellular heterogeneity of all tissue cells and the inability of conventional RNA methods, like northern blotting, RNAse protection assay or classical block RT-PCR, to distinguish individual cellular contributions to mRNA abundance differences. => http://singlecell.gene-quantification.info/ -------------------------------------------------------------------------------- new papers => http://www.gene-quantification.de/singlecell3.html - Imaging intracellular RNA distribution and dynamics in living cells. - mRNA-Seq whole-transcriptome analysis of a single cell. - Genomic expression analysis by single-cell mRNA differential display of quiescent CD8 T cells from tumour-infiltrating lymphocytes obtained from in vivo liver tumours. - Rac1 regulates pancreatic islet morphogenesis. - A novel single-cell quantitative real-time RT-PCR method for quantifying foot-and-mouth disease viral RNA. - Quantification of circulating endothelial and progenitor cells: comparison of quantitative PCR and four-channel flow cytometry. - Prognosis of non-small cell lung cancer patients by detecting circulating cancer cells in the peripheral blood with multiple marker genes. - Nanoliter reactors improve multiple displacement amplification of genomes from single cells. - Fluidigm Dynamic Arrays provide a platform for single-cell gene expression analysis. - Intracellular expression profiles measured by real-time PCR tomography in the Xenopus laevis oocyte. - Quantification of mRNA in single cells and modelling of RT-qPCR induced noise. - Intracellular Gene Expression Profi les Revealed with Real-time PCR Tomography -------------------------------------------------------------------------------- NEW blogs & groups qPCR / real-time PCR BLOG => http://real-time-pcr.blogspot.com/ qPCR LinkedIN group - real-time PCR & qPCR => http://www.linkedin.com/groups?about=&gid=149835&trk=anet_ug_grppro This group wants to join worldwide users in the field of real-time quantitative PCR. It offers a forum where new ideas can be exchanged, and allows networking with other people in this field. -------------------------------------------------------------------------------- Upcoming Events World-wide academic and commercial qPCR Events http://events.gene-quantification.info/ Symposia, Meetings, Conferences, Workshops, Seminars, Online-Seminars, qPCR Education Program, etc. Please submit your qPCR event here => events@gene- quantification.info -------------------------------------------------------------------------------- qPCR WORKSHOP BioEPS GmbH / TATAA Biocenter Germany - qPCR Application workshops At the TATAA Biocenter Germany we offer qPCR application workshops, a 3-day qPCR Core Module and a 2-day qPCR Biostatistics Module. All courses are held regularly in G?teborg, Sweden, in English and in Freising-Weihenstephan, Germany, in German and English, and in Prague, Czech Republic in English and Czech. Depending on the occasion the workshop language and the different prices may apply. Further customized workshops and specialized trainings will be held as well across Europe and world-wide. TATAA Biocenter Germany workshops are held in cooperation with BioEPS GmbH, located at the campus of the Technical University of Munich, in Freising-Weihenstephan, very close to the Munich Airport (MUC). For more information and registration, please see our web page: => http://TATAA.gene-quantification.info/ Course Occasions 2009: - 3-day qPCR Core Module (Mon. - Wed.) - 2-day BioStatistics Module (Thu. - Fri.) - 3-day single-cell qPCR Module (Mon. - Wed.) - 3-day microRNA Module (Mon. - Wed.) => http://site.bioeps.com/index.php?option=com_seminar&Itemid=6 14 - 16 September 2009 (E) NEW single-cell qPCR 19 - 23 September 2009 (E) 3-day microRNA Module (Mon. - Wed.) & 2-day BioStatistics (Thu. - Fri.) 26 - 28 October 2009 (E) 3-day qPCR Core Module (Mon. - Wed.) 16 - 20 November 2009 (E) 3-day microRNA Module (Mon. - Wed.) & 2-day BioStatistics (Thu. - Fri.) 7 - 11 December 2009 (E) 3-day qPCR Core Module (Mon. - Wed.) & 2-day BioStatistics (Thu. - Fri.) => http://www.gene-quantification.de/bioeps-courses-autumn-2009.pdf => http://www.gene-quantification.de/single-cell-qpcr-course-sept-2009.pdf -------------------------------------------------------------------------------- Forward Please send the qPCR NEWS to further scientists and friends who are interested in qPCR ! Best regards, Michael W. Pfaffl responsible Editor of the Gene Quantification Pages http://www.gene-quantification.info -------------------------------------------------------------------------------- If this newsletter is not displayed correctly by your email client, please use following link: http://qpcrnews.gene-quantification.info/ The qPCR NEWS and the Gene Quantification Pages are educational sites with the only purpose of facilitating access to qPCR related information on the internet. The qPCR NEWS and the Gene Quantification Pages are edited by Michael W. Pfaffl. Copyright ? 2005 - 2009 All rights reserved. Any unauthorized use, reproduction, or transfer of this message or its contents, in any medium, is strictly prohibited. Disclaimer & Copyrights are displayed on the homepage www.gene-quantification.com To subscribe or change your e-mail address in qPCR NEWS, and if you would like to receive future issues FREE of charge, please send an e- mail with the subject SUBSCRIBE to mailto:newsletter@gene- quantification.info?subject=SUBSCRIBE From ishunara from gmail.com Mon Jul 27 11:15:46 2009 From: ishunara from gmail.com (Lief Erikson) Date: Mon Jul 27 11:52:28 2009 Subject: [Bioforum] Ibuprofen Message-ID: <8e9a520a0907270915g66e836adt907449ad7519ea85@mail.gmail.com> Well, this is 14 years late, but... Ibuprofen's chemical makeup is C13H18O2. http://scripts.iucr.org/cgi-bin/paper?S0108270197003193 I just thought is would be fun to reply to a post fourteen years old. _____________________________________________ Hi! I'm not a med geek, I'm a computer geek. A friend of mine ( a med geek ) asked me to track down a list of chemicals that go into the manufacture of Ibuprofen. Does anyone know where to look? She's got a paper due tomorrow, has the molecular outline, etc... just not the base chemicals that go into its manufacture. She challenged me to find this information on the Net. I think I've done a good job just finding the chemical name ( Alpha-Methyl-4-(2-methylpropyl)benzeneacetic acid ) Please help! I'll owe you a computer geek favor :) Regards, Malcolm Mead ___________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/bioforum/attachments/20090727/4f2e75ab/attachment.html From riao2010_review from irit.fr Mon Jul 27 16:03:53 2009 From: riao2010_review from irit.fr (riao2010_review@irit.fr) Date: Mon Jul 27 16:29:12 2009 Subject: [Bioforum] 1st CFP RIAO 2010 Message-ID: <200907272103.n6RL3rRT018961@extra.irit.fr> --------------------------------- First Call for Papers RIAO 2010 - 9th RIAO Conference Adaptivity, Personalization and Fusion of Heterogeneous Information 28-30 April, 2010 Paris, France (Bibliotheque Nationale de France) http://www.riao2010.org/ Important dates: Paper submission deadline November 30, 2009 Notification to authors February 5, 2010 Camera-Ready copies due March 1, 2010 Conference dates April 28-30, 2010 --------------------------------------------- History The RIAO conference is a triennial conference, which addresses research topics related to the design of robust and large-scale scientific and industrial solutions to information processing. Previous RIAO editions were held at Grenoble (1985), MIT (1988), Barcelona (1991), Rockefeller University (1994), Montreal (1997), Paris (2000), and Avignon (2004), and Carnegie Mellon University (2007). Past RIAO conferences were constituted by both peer-reviewed scientific sessions and demonstrations of innovative industrial applications and advanced research prototypes. Scope of RIAO 2010 Submissions are invited which present recent, original and unpublished research on the theme of RIAO 2010: adapting, personalizing and merging heterogeneous information. Submissions may address one or more of the following subjects: Information filtering * Content based filtering * Collaborative filtering * Recommender systems * Spam, protection of minors Social networks * Folksonomies, tagging * Blogs * Social search * Communities * Opinion and sentiment Personalized IR and User modelling * Adaptive IR * Collaborative IR * Interfaces Information fusion * Mash Ups * Aggregated search * Systems for watch, business decision Formal models, theory Information extraction and natural language processing, multilinguality * Summarization * Question answering * Entity/relation extraction * Cross-Language IR, Machine translation for IR Multimedia Information Retrieval * Image IR * Video IR * Speech/audio IR * Music IR, analysis of multimedia content Web Search and Advertising * Adversial IR * Advertising * Link analysis Applications * Cultural heritage * Trademark search * Scientific media * Bio-computing and medical * Database offloading Evaluation, benchmarking Machine Learning for IR * Learning to rank * Probabilistic topic models * All kinds of learning techniques applied to IR Program Chairs Gabriella Pasi (Europe) Tie-Yan Liu (Asia) Prabhakar Raghavan (Americas) Paper Submission We welcome submissions from both research and industrial communities addressing the main conference theme. Submitted papers must describe an unpublished original work, emphasizing completed or advanced research, possibly with releted experiments. A parallel submission to other venues should be clearly indicated to the program committee. The submissions (which have to be blind) will be reviewed by at least three program committee members. The submissions will be evaluated on the basis of originality, relevance, technical quality, and presentation. Papers can be submitted in two categories: full papers and short papers, where full papers are appropriate for describing substantial research with related evaluations and short papers will typically describe ongoing research and preliminary results. All accepted papers in both categories will be published in the conference proceedings. At the conference, full papers will be presented as a talk and short papers will be presented as a poster. Long papers must not exceed 12 pages (5000 words), in one column format, starting with an abstract. Short papers must not exceed 6 pages (2500 words), in one column, starting with an abstract. Submissions should be in Microsoft Word format or in PDF. The conference proceedings will be available to conference attendees, and through the CID after the conference. From mhviegas from yahoo.com Tue Jul 28 10:10:24 2009 From: mhviegas from yahoo.com (Marcelo Viegas) Date: Tue Jul 28 11:15:38 2009 Subject: [Bioforum] (no subject) Message-ID: <862067.81627.qm@web51407.mail.re2.yahoo.com> Hello out there! I would like to ask whether anyone knows any easy test to verify thiolination of oligonucleotides. It turns out to be that I use thionilated oligos for my experiments and sometimes I have trouble and this seems to be a synthesis problem (i.e. the thionilation reaction?of the oligos was not complete). Thanks a lot in advance. ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/bioforum/attachments/20090728/ae433be3/attachment.html From Heather.Vincent from manchester.ac.uk Thu Jul 30 15:35:25 2009 From: Heather.Vincent from manchester.ac.uk (Heather Vincent) Date: Thu Jul 30 17:54:54 2009 Subject: [Bioforum] Professional development in bioinformatics and systems biology Message-ID: <4A72040D.5020700@manchester.ac.uk> Evidence of continuing professional development is increasingly important to scientists planning a career move, whether this is to be a promotion or a change in direction. The University of Manchester's online courses in computational biology and bioinformatics can help with your career development, being specifically designed for biologists needing to update their skills while remaining in the workplace. The courses are also very suitable for those interested home study, helping you to keep in touch with a research environment during a career break. The courses running next semester, starting in October 2009, include: Introduction to Bioinformatics Bioinformatics for Systems Biology Introduction to software development in Java Theory and Applications in Bioinformatics You will find further information, including fees and a link to the online application form, here : http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any questions, or need advice on the module options, please contact Heather.Vincent@manchester.ac.uk