From rochus.franke from uni-bonn.de Fri May 2 09:55:43 2008 From: rochus.franke from uni-bonn.de (Rochus Benni Franke) Date: Fri May 2 10:51:27 2008 Subject: [Arabidopsis] group leader position at Bonn University Message-ID: The Institute of Cellular and Molecular Botany (IZMB, http://izmb.de) University of Bonn, Germany, invites applications for the position as Postdoc/ Junior Group Leader in Molecular Plant Sciences (wissenschaftlicher Mitarbeiter, paid according to E 13 TVL) starting at October 1, 2008. Applicants must hold a PhD degree (Dr. rer. nat.) in Botany/Plant Sciences, should have some post doc experience (1-3 years), a good publication record and teaching experiences. We seek a highly motivated and qualified person with a research focus in either plant-microbe interaction, molecular plant physiology, plant cell biology, or plant biotechnology. The successful candidate is expected to participate in the M.Sc. Plant Sciences degree programme with a teaching obligation of 4SWS. A laboratory with basic equipment for plant molecular and cell biological work is available and additional equipment may be shared with the other research groups in the institute. The junior group leader will be supported by a part time technician, a student teaching assistant, and a moderate budget to cover the most basic expenses. Additional third-party fund sources will have to be developed by the successful candidate. The initial contract runs for 3 years with the possibility of renewal for maximally 3 more years. The jobholder will be entitled to a local commuter "Job-Ticket" available from the public utility company, Bonn. The University of Bonn is an equal opportunities employer. Preference will be given to suitably qualified women or handicapped people, all other considerations being equal. Applicants for the academic position are expected to submit a cover letter, CV, list of publications, description of research activities/projects and teaching experience, final grade certificates and names of three referees. Please address your application to: Managing Director Institute of Cellular and Molecular Botany University of Bonn Kirschallee 1, D-53115 Bonn Germany The deadline for applications is July 1, 2008. From xu.161 from osu.edu Wed May 7 09:40:36 2008 From: xu.161 from osu.edu (Morgan Xu) Date: Thu May 8 13:22:08 2008 Subject: [Arabidopsis] For gl1 (glabrous1) mutant in Ler background. Message-ID: Dear All, We are looking for a gl1 (glabrous1) mutant in Ler background. I've searched ABRC and didn't find one. It will be greatly appreciated if you can share with us some seeds or give us some infomation on where to find it. Thanks, Morgan From G.G.Simpson from dundee.ac.uk Thu May 8 03:23:13 2008 From: G.G.Simpson from dundee.ac.uk (Gordon Simpson) Date: Thu May 8 13:22:15 2008 Subject: [Arabidopsis] Plant Science PI positions, Dundee, Scotland Message-ID: <4822C681.C7F2.0008.0@dundee.ac.uk> UNIVERSITY OF DUNDEE DIVISION OF PLANT SCIENCES COLLEGE OF LIFE SCIENCES PRINCIPAL INVESTIGATORS We invite applications from outstanding candidates, at any stage in their career, for Principal Investigator positions in the newly-formed Division of Plant Sciences at Dundee University. Candidates working in any area of plant science will be considered, but we particularly welcome applications from those taking molecular, genetic and biochemical approaches to explore and explain important features of plant biology. This is an excellent opportunity for plant scientists who already have, or who would apply for, a research fellowship to establish their laboratory in a new and dynamic research division. Successful candidates will benefit from advantageous contractual arrangements: research fellows may receive up to two years of additional salary support beyond the tenure of their fellowship. Dundee combines quality of life with quality of science and offers: ? Collaboration with a wider community of plant scientists through co-location of the Plant Sciences Division at the Scottish Crop Research Institute (SCRI), the largest plant and crop research institute in Scotland. ? State-of-the-art facilities in plant growth, cell biology, microscopy, transcriptomics, genomics, proteomics, metabolomics and other core facilities in the College of Life Sciences and at SCRI. ? A vibrant and collegiate research environment. ? A highly successful PhD programme. A few facts about The College of Life Sciences at Dundee: ? Over 760 research and support staff from 53 countries and an annual research turnover of more than ?25 million. ? The top University in Europe in ?Biology and Biochemistry? and 2nd in Europe in ?Molecular Biology and Genetics? according to citations per paper over the last 10 years (Thomson Scientific, Philadelphia). ? Named ?the best place to work in Europe? in a poll of scientists conducted by The Scientist magazine in 2003 and 2004. ? Achieved the highest possible ?5-star? rating in the most recent UK Research Assessment Exercise. ? Prof. David Baulcombe is the Plant Sciences member of the College Scientific Advisory Committee Please visit our web site www.lifesci.dundee.ac.uk/ps to learn more about us. Applications in the form of a CV, an outline of past achievements and future research plans together with a covering letter should be sent to HR-LifeSciences@dundee.ac.uk quoting LS/2203. Alternatively, please send 2 copies of your application to Human Resources, College of Life Sciences, MSI/WTB/JBC Complex, University of Dundee, DD1 5EH. Closing Date: 31 August 2008 The University of Dundee is committed to equal opportunities and welcomes applications from all sections of the community. The University of Dundee is a registered Scottish charity, No: SCO15096 Gordon Simpson Division of Plant Sciences College of Life Sciences Dundee University at SCRI DD2 5DA Scotland g.g.simpson@dundee.ac.uk Direct Dial 44 1382 568572 Fax: 44 1382 562426 http://www.lifesci.dundee.ac.uk/people/gordon_simpson/ The University of Dundee is a registered Scottish charity, No: SC015096 From leszek.kleczkowski from plantphys.umu.se Fri May 9 06:29:46 2008 From: leszek.kleczkowski from plantphys.umu.se (leszek.kleczkowski@plantphys.umu.se) Date: Fri May 9 11:34:28 2008 Subject: [Arabidopsis] Ph.D. student position (UPSC, Umea, SWEDEN) Message-ID: <79670c83-1ee8-4ee8-9835-b2a40beddbf5@l42g2000hsc.googlegroups.com> A Ph.D. student position is currently available in my laboratory at the Department of Plant Physiology, Umea Plant Science Centre, Umea University, Sweden. The position will generally be focused on regulation of gene expression and protein activities involved in carbohydrate metabolism in plants. Specific focus will be on posttranscriptional (e.g. gene splicing) and posttranslational regulation (e.g. phosphorylation) (see Plant Physiology 134: 912-918, 2004; Gene 389: 186-195, 2007). Other part will concern identification and verification of cis regulatory elements (CREs) responsible for sugar signaling in Arabidopsis, using synthetic promoters based on specific CREs (see Plant Journal 45: 384-398, 2006). The successful candidate must be highly motivated and have a Master’s degree, or equivalent, and have a strong background in molecular and cell biology or related fields. The application should include a letter of interest, a curriculum vitae, and names and e-mail addresses of two references familiar with the candidate´s qualifications. For more information, please contact: Leszek.Kleczkowski@plantphys.umu.se The UPSC provides a thriving environment for scientific advancement, with over 170 researchers from over 30 countries having combined skills in molecular biology, gene technology, plant physiology and biochemistry. For more information on research activities at UPSC please consult our web page at http://www.upsc.se/ From anirbanb from ncbs.res.in Fri May 9 03:34:01 2008 From: anirbanb from ncbs.res.in (Anirban Baral) Date: Fri May 9 11:35:40 2008 Subject: [Arabidopsis] Imaging in Arabidopsis suspension cell culture Message-ID: <54742.192.168.1.1.1210322041.squirrel@mail.ncbs.res.in> Dear Arabineters, I am a freshly joined graduate student intending to work in plant endocytosis. In genetic aspects,Arabidopsis is good for my study, but I am not sure wheather fluorescence imaging at subcellular level is possible in Arabidopsis suspension cell culture or not. I shall be very grateful if you please give me some suggestions about the feasibility of working with the mentioned system & please suggest me some alternatives also ,which you think will be good to work with. Regards -- Anirban Baral JUNIOR SCHOLAR NATIONAL CENTRE FOR BIOLOGICAL SCIENCES TATA INSTITUTE OF FUNDAMENTAL RESEARCH UAS-GKVK CAMPUS,BELLARY ROAD BANGALORE-560065,INDIA From nicholas.provart from utoronto.ca Fri May 9 12:30:31 2008 From: nicholas.provart from utoronto.ca (Nicholas Provart) Date: Fri May 9 15:30:48 2008 Subject: [Arabidopsis] Arabidopsis eFP Browser webservices from the BAR In-Reply-To: <200805091703.m49H3eO06098@net.bio.net> Message-ID: <004c01c8b1fa$61b6cf10$5bd6968e@uic00o3tkmejay> Hello everyone, Two webservices are now available from the Bio-Array Resouce: getAGI_SubCellLocalisationImage, and getAGI_eFPImage. getAGI_SubCellLocalisationImage will return a Cell eFP Browser image for the predicted and documented subcellular localizations of any one of more than 24000 Arabidopsis genes, as documented in Heazlewood et al.'s (2007) SUBA database (NAR 35:D213-8). getAGI_eFPImage will return an eFP Browser image showing where your gene of interest is being expressed in gene expression compendia from the AtGenExpress Consortium and from other labs worldwide: there are Chemical, Hormone, Developmental Map, Tissue Specific, Natural Variation, Seed, Biotic Stress, Abiotic Stress, and Light Series compendia encompassing more than 2000 Affymetrix data sets across ~24k genes. You can access BAR webservice through BioMOBY at http://moby.ucalgary.ca/gbrowse_moby Namespace: AGI_LocusCode ID: enter any AGI authority: bar.utoronto.ca Semantics Enabled Many thanks to Chris Town and colleagues at TIGR/JCVI for a workshop on how to set up webservices, and to Hardeep Nahal for her programming efforts to enable webservices for the BAR. Best regards, Nick ......................................... Nicholas Provart, PhD Assistant Professor, Plant Bioinformatics & Systems Biology Director, Graduate Program in Genome Biology and Bioinformatics Member, Centre for the Analysis of Genome Evolution and Function Rm 3051, Dept. of Cell and Systems Biology, Uni. Toronto 25 Willcocks St., Toronto, ON. M5S 3B2. CANADA Tel. (+1) (416) 978-7141, Fax. (+1) (416) 978-5878 URL. http://www.csb.utoronto.ca/faculty/provart-nicholas Arabidopsis Tools. http://www.bar.utoronto.ca email. nicholas.provart@utoronto.ca TTC. Spadina LRT, Willcocks St. From indibwa from yahoo.com Mon May 12 07:33:55 2008 From: indibwa from yahoo.com (Indieka Abwao) Date: Mon May 12 13:24:43 2008 Subject: [Arabidopsis] GCN2 knockout line(s) Message-ID: <867349.87880.qm@web36903.mail.mud.yahoo.com> Hello everyone, I am looking for Arabidopsis GCN2 knockout mutants line(s). If you have some, or you can advice where I can source from, please let me know. Best Regards, A.S. Indieka ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From pj37 from cornell.edu Mon May 12 12:39:55 2008 From: pj37 from cornell.edu (Pankaj Jaiswal) Date: Mon May 12 13:25:11 2008 Subject: [Arabidopsis] Gramene Database build 27 released Message-ID: <482880EB.5050605@cornell.edu> Dear Gramene users, We are happy to announce the release of our 27th build of the Gramene database and website [www.gramene.org]. Some of the highlights for this release include: - Four new species added to the genome browser: -- Oryza glaberrima short arm -- Sorghum bicolor (Sorghum) -- Vitis vinifera (grape) -- Populus trichocarpain (poplar) - The markers database contains a total of 30M markers including up-to- date nucleotide sequences of all Viridiplantae contained in the NCBI Genbank Core Nucleotide, dbEST, and dbGSS division. - Introduced Gazetteer (GAZ) ontology to describe places, place names and the relations between them to annotate the source site of germplasm collection - New SorghumCyc 1.0 metabolic pathways beta release - New RiceCyc 2.0 metabolic pathways release - New sorghum genetic diversity database For the complete release notes, please see here: http://www.gramene.org/db/help?state=current_release_notes This is our first release since moving to our 6-month cycle, so you can expect to see build 28 in the fall. Thank you for your continued use and support of Gramene, and please let us know of any problems, concerns or suggestions you have: http://www.gramene.org/db/feedback/send_feedback The Gramene team gramene@gramene.org www.gramene.org From pablojenik from aya.yale.edu Mon May 12 16:35:34 2008 From: pablojenik from aya.yale.edu (Pablo JENIK) Date: Mon May 12 22:52:19 2008 Subject: [Arabidopsis] Problems with sterility Message-ID: <446fce520805121435j1d7fc706i7ea0554ac7401588@mail.gmail.com> Dear colleagues, I have sometimes encountered fertility problems with my plants, and maybe somebody can tell me the causes and how to avoid them. Plants are growing in the greenhouse just fine and then, from what seems from one day to the next, carpels turn yellow and are very small and sterile. Pollen does not do very well either, and production of new flowers ceases. It seems to be environmental, because some times the plants recover and start making good flowers. Looking at the greenhouse logs I can not find any obvious culprit. In any case, it is very frustrating, when one's subject of study are embryos. Any ideas or suggestions would be welcome. Yours, Pablo -- Pablo Jenik, Ph.D. Visiting Assistant Professor Department of Biology Franklin and Marshall College P.O. Box 3003 Lancaster, PA 17604-3003 (717) 358-4431 From vinodh from uab.edu Wed May 14 16:41:21 2008 From: vinodh from uab.edu (Vinodh Srinivasasainagendra) Date: Wed May 14 18:02:42 2008 Subject: [Arabidopsis] CressExpress - Co-expression analysis for Arabidopsis, Message-ID: <9A596E4B31E3C64C8B087DFA7AED155ADCEF05@phealth1.soph.local> Hi all, We are pleased to announce our tool "CressExpress - Co-expression analysis for Arabidopsis" is launched and can be accessed at http://www.cressexpress.org/ . For more information on CressExpress, please refer to http://www.plantphysiol.org/cgi/rapidpdf/pp.107.115535v1 . CressExpress Team From gregory from salk.edu Thu May 15 09:49:30 2008 From: gregory from salk.edu (Brian D. Gregory) Date: Thu May 15 11:24:12 2008 Subject: [Arabidopsis] Arabidopsis Uncapped and Cleaved Transcript Database Message-ID: To the Arabidopsis Community, The sequencing data presented in our paper “A link between RNA metabolism and silencing affecting Arabidopsis development”, Developmental Cell (2008) 10.1016/j.devcel.2008.04.005, is freely accessible in a dynamic Web2.0 based genomic browser called AnnoJ, which is designed to effectively handle both current and emerging genomic data-types. The browser displays (from the megabase down to the single base) our new deep sequencing data sets of Col-0, abh1-1, ein5-6, and ein5-6 abh1-1 mutant plants, including: - smRNA-seq: deep sequencing of the smRNA component of the transcriptome. - GMUCT-seq: deep sequencing of uncapped and cleaved transcripts. These data sets are all open access, and to view them in this browser just go to the URL below with Firefox or Safari: http://neomorph.salk.edu/aj/pages/smRNAome.html Brian D. Gregory Damon Runyon Postdoctoral Fellow Plant Biology Laboratory (Ecker) The Salk Institute for Biological Studies 10010 North Torrey Pines Rd. LaJolla, CA 92037 Phone (858) 453-4100 x1533 From hscheller from lbl.gov Thu May 15 04:30:19 2008 From: hscheller from lbl.gov (Henrik Vibe Scheller) Date: Thu May 15 11:24:54 2008 Subject: [Arabidopsis] Post doc positions in cell wall biosynthesis - Joint Bioenergy Institute, California Message-ID: <482C02AB.4000308@lbl.gov> Cell wall biosynthesis - Post doc positions Molecular & Cell Biologist, Chemist: Three post doc positions are available at Joint Bioenergy Institute. The incumbent shall be responsible for developing new methods and using existing methods for investigating enzymes involved in biosynthesis of plant cell walls and characterizing plants with mutations in the genes encoding these enzymes. Candidates for the positions should have experience with biochemistry and molecular biology. Candidates should also have experence in one or more of the following areas and techniques: HPLC, characterization of complex carbohydrates, plant genetics, heterologous expression of proteins, and animal cell culture. Position 1: Heterologous expression of glycosyltransferases in insect cells Position 2: Development of high through put methods for assaying cell wall biosynthetic enzymes. Position 3: Biochemistry of polysaccharide modifications, particularly feruloylation of hemicelluloses Duties: • Develop methods to analyze function of glycosyltransferases and other cell wall biosynthetic enzymes. Cultivate and transform animal cells. • Reverse genetics in Arabidopsis. Bioimaging. • Collect and analyze data and prepare results for publication in scientific journals and presentations at seminars. • Assist with the development of funding proposals. Assist PI with training and managing the workflow of technical staff and students. Participate in group meetings and seminars. • Maintain an accurate and detailed scientific logbook of all experiments performed. Ensure that others could duplicate results. Qualifications: • Ph.D in Biochemistry, Molecular Biology or related areas. • Knowledge of biological systems. Experience with characterization of complex carbohydrates. • Experience with enzyme assays. • Demonstrated ability to conduct experiments independently, maintain appropriate records and manage data. Strong collaborative skills and ability to work in a team environment. The Joint BioEnergy Institute (JBEI) is a new multi-organizational research center comprising world-class resources and expertise located in one facility at Emeryville, California. The goal of JBEI is to use rapidly advancing scientific techniques, such as systems and synthetic biology, to accelerate development of the nation's biofuels industry. JBEI is a U.S. Department of Energy funded Bioenergy Research Center, managed by Lawrence Berkeley National Laboratory (LBNL) with partners from 5 internationally recognized scientific institutions: Sandia National Laboratories (SNL), Lawrence Livermore National Laboratory (LLNL), University of California-Davis (UCD), University of California-Berkeley (UCB), and the Carnegie Institution for Science Notes: These are one year Term appointments, renewable under the same conditions, contingent upon the continued availability of funding and work. For consideration apply online at: http://jobs.lbl.gov, select “Search Jobs”, and enter jobnumber 21752 in the keyword search field. For additional information please refer questions to Dr. Henrik V. Scheller at hscheller@lbl.gov. For more information about JBEI Feedstocks go to: www.jbei.org/feedstocks -- Henrik Vibe Scheller Program Director of Cell Wall Biosynthesis, Dr. scient. Joint BioEnergy Institute Feedstocks Division Lawrence Berkeley National Laboratory 717 Potter St. Berkeley, CA 94720 Tel.: 510-486-7371 (office) 510-207-0283 (cell) Fax: 510-486-4252