From kerstin.kaufmann from wur.nl Mon Aug 3 10:55:18 2009 From: kerstin.kaufmann from wur.nl (Kaufmann, Kerstin) Date: Mon Aug 3 12:06:35 2009 Subject: [Arabidopsis] PhD-position Arabidopsis flower development, Netherlands Message-ID: <9C00C2F0ECEC594580FCF26CA09DFF52011E38AA@scomp0040.wurnet.nl> POSITION: PhD-position Arabidopsis flower development as part of the EU-Marie Curie Research training network SYSFLO (Systems biology of Flowering) Organization: Wageningen University and Research Centre (Wageningen UR) is an international renowned knowledge institute in the fields of life sciences and sustainability. SYSFLO: One of the major current challenges in biology is to understand the networks of gene expression that orchestrate development and cell differentiation. To achieve this goal, it is necessary to identify key regulatory genes and their target genes, how regulatory sequences within target genes integrate inputs from multiple regulatory proteins, and how chromatin changes may restrict the access of regulatory proteins to parts of the genome in different cells and developmental stages. These tasks require a combination of sophisticated molecular and bioinformatics approaches: genome-wide analysis of gene expression and protein-DNA interactions, recognition of patterns within large datasets of regulatory sequences and in silico simulations to model and predict the behaviour of the regulatory network. The EU-training network SYSFLO offers young European researchers training in a combination of skills required for the type of challenge outlined above. Besides the training offered by the SYSFLO consortium, the PhD student will have access to courses and training opportunities offered by the Wageningen University. Each of the 9 participating labs will focus on different aspects of the same biological system: plant reproductive development. The project: The fellow that will be appointed by Wageningen UR will study the temporal regulation of target genes of several Arabidopsis MADS domain transcription factor complexes during floral organ development. Subsequently, the biological role of some selected target genes in establishing the flower will be studied using genetic and molecular approaches. Techniques that will be used are: Chromatin Immunoprecipitation (ChIP), expression studies using micro arrays, in vitro DNA-protein interaction studies, Fluorescence protein imaging using microscopy and mutant analyses. Requirements: We are looking for and enthusiastic result-driven European scientist with ? a university degree at MSc or equivalent level in (plant) molecular biology ? Non-Dutch nationality and no longer than 1 year residence in The Netherlands ? an interest in regulation of plant development and in multidisciplinary approaches ? preferred experience with Arabidopsis ? proficiency in English ? willing to visit and perform experiments in labs of the other SYSFLO partners ? team player with excellent communication skills Conditions of employment: Start: second half 2009 Estimated maximum gross salary per month: ? 2042 in the first year rising to ? 2612 in the fourth year. Duration of the contract: for a period of 18 months and extension for an additional 30 months pending a positive performance evaluation. Additional information about this position and SYSFLO can be obtained from: Prof Dr Gerco Angenent, telephone: + 317-480953; E-mail address: gerco.angenent@wur.nl Application: You can apply for this by sending your application, including two references to: Wageningen UR, Plant Sciences Group, Mrs A.M.D. Bikker, P.O. Box 16, 6700 AA Wageningen, The Netherlands, e-mail address: vacaturemeldingen.psg@wur.nl When applying for this job always mention the vacancy number 09.Biosc.09 Review of applications will start immediately, and will continue until the position has been filled. From jdfriesner from ucdavis.edu Mon Aug 3 19:20:08 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Mon Aug 3 23:48:02 2009 Subject: [Arabidopsis] More funding for US grad students and postdocs Message-ID: <000301ca1499$53864260$fa92c720$@edu> There is still some funding left to send US grad students and postdocs from NSF-funded Arabidopsis labs to German Arabidopsis labs for short-term research visits. Final upcoming application deadlines: Sept. 15, 2008 Jan. 15, 2010 All travel must be completed by May 31, 2010. See this site for complete application directions: http://arabidopsis.org/portals/masc/funding.jsp From debouba77 from yahoo.fr Wed Aug 5 07:06:19 2009 From: debouba77 from yahoo.fr (Mohamed Debouba) Date: Wed Aug 5 12:17:41 2009 Subject: [Arabidopsis] looking for Training on Microarray Message-ID: <65908.93757.qm@web24504.mail.ird.yahoo.com> Hi, I have same results on transcripts changes of nitrogen assimilating enzymes in Arabidopsis (Columbia ecotype) by using RT-PCR on prepared cDNA. But this technique seems?insufficient to?discuss?the results. Currently, I try to master the microarray to better characterize the effects of salt stress on the expression of certain genes. I'm looking for a training on microarray in a laboratory using this technique.? Can any one give me informations, ?--------------------------------------------------------------- Dr. Mohamed Debouba E-mail : mohamed.debouba@gmail.com Institut Sup?rieur de Biologie Appliqu?e de M?denine Route El Jorf - Km 22.5 - 4119 Medenine, Tunisie. Phone : 75 633 919 - Fax : 75 633 918 From sabine.mueller from zmbp.uni-tuebingen.de Wed Aug 5 07:37:33 2009 From: sabine.mueller from zmbp.uni-tuebingen.de (Sabine Mueller) Date: Wed Aug 5 12:18:00 2009 Subject: [Arabidopsis] PhD student position in Plant Sciences Message-ID: <20090805143733.12112u2hz8ni73t9@webmail.uni-tuebingen.de> PhD student position available at the Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tuebingen, Germany starting September/October 2009. The laboratory of Dr. Sabine M?ller is interested in molecular mechanism governing plant cell division and morphogenesis in the model plant Arabidopsis thaliana using molecular and cell biological approaches. For further information see M?ller et al. (2009) Cell Biol. 19:180-188, Walker et al.(2007) Current Biol. 17:1827-1836, M?ller et al. (2006) Current Biol. 16, 888-894. The successful candidate holds a diploma/masters degree in Biology, is experienced in molecular biology, genetics or cell biology and proficient in English. The position is offered according to German E 13 TV-L (50%, PhD). Please send applications including, Curriculum vitae, motivation letter and contact information of two referees. Contact: Dr. Sabine M?ller (sabine.mueller@zmbp.uni-tuebingen.de) -- Dr. Sabine M?ller Center for Plant Molecular Biology - ZMBP Developmental Genetics University of T?bingen Auf der Morgenstelle 3 D - 72076 T?bingen, Germany Phone: +49 (0)7071 - 29 78888 Fax: +49 (0)7071 - 29 5797 Email: sabine.mueller@zmbp.uni-tuebingen.de From stefanie.debodt from psb.vib-ugent.be Thu Aug 6 10:15:25 2009 From: stefanie.debodt from psb.vib-ugent.be (Stefanie De Bodt) Date: Thu Aug 6 11:19:01 2009 Subject: [Arabidopsis] PhD in Gent Message-ID: <4A7AF38D.5010106@psb.vib-ugent.be> -- PhD student Systems Biology of Yield -- Job description: For our group, we are looking for enthusiastic PhD students in bioinformatics/systems biology. You will be involved in a project which is highly complementary to ongoing research in the group, where microarray, proteomics and interaction data related to growth control is generated. You will be responsible for the application and development of computational methods to analyze and integrate these data. You will collaborate with both experimental and computational biologists to obtain a systems-level understanding of leaf growth (http://www.psb.ugent.be/groups/systems-biology-of-yield-group). . Profile: • You have a degree in Bioinformatics, Informatics or in Biotechnology/ Biochemistry/Bioengineering. • You have a good knowledge/experience in programming (Perl, R, Java and/or C++). • You have knowledge or experience with databases (mySQL). • You have an interest in web design (PHP). • You speak English fluently. • You have good communication skills. You are a team player. You are independent and like to take initiative. You are flexible. We offer a contract of 2 years, within University Gent, with the possibility of prolongation. We offer a diverse job in a young team, an open and informal work atmosphere and in modern facilities. The Department of Plant Systems Biology, VIB, University Gent (www.psb.ugent.be) is an internationally renowned and dynamic research institute that employs molecular genetics, genomics and bioinformatics to unravel developmental processes in plants and is led by Prof. Dirk Inzι. Start date: as soon as possible, the position remains vacant until a suitable candidate is found. Information: Further information can be obtained by contacting Stefanie De Bodt (stefanie.debodt@psb.vib-ugent.be) Application: Send your letter of motivation, your CV and if possible references to: Stefanie De Bodt Department of Plant Systems Biology Technologiepark 927 9052 Gent Tel: +32 93313806 or through email to stefanie.debodt@psb.vib-ugent.be -- ================================================================== Stefanie De Bodt, PhD VIB Department of Plant Systems Biology, UGent Technologiepark 927 B-9052 Gent Belgium Tel: 32 (0)9 3313692 Website: http://www.psb.ugent.be ================================================================== From mizhang118 from gmail.com Thu Aug 6 13:28:58 2009 From: mizhang118 from gmail.com (mini) Date: Thu Aug 6 14:04:00 2009 Subject: [Arabidopsis] Re: looking for Training on Microarray References: Message-ID: On Aug 5, 5:06?am, Mohamed Debouba wrote: > Hi, > > I have same results on transcripts changes of nitrogen assimilating enzymes in Arabidopsis (Columbia ecotype) by using RT-PCR on prepared cDNA. But this technique seems?insufficient to?discuss?the results. Currently, I try to master the microarray to better characterize the effects of salt stress on the expression of certain genes. I'm looking for a training on microarray in a laboratory using this technique.? > > Can any one give me informations, > > ?--------------------------------------------------------------- > Dr. Mohamed Debouba > E-mail : mohamed.debo...@gmail.com > Institut Sup?rieur de Biologie Appliqu?e de M?denine > Route El Jorf - Km 22.5 - 4119 Medenine, Tunisie. > Phone : 75 633 919 - Fax : 75 633 918 Hi, You may try www.ExpressionBrowser.com. This site is built with hundreds of Arabidopsis microarray experiments. You can search Arabidopsis gene expression information. Many salt stress experiments had been included in this site. From abhikarve from gmail.com Thu Aug 6 16:35:06 2009 From: abhikarve from gmail.com (ABHIJIT KARVE) Date: Fri Aug 7 13:14:01 2009 Subject: [Arabidopsis] Arabidopsis Ecotype seeds Message-ID: Hi, I am looking for the seeds of Arabidopsis ecotype: Finland (Fl-1) ( ABRC germplasm # CS6706). I ordered the seeds originally from ABRC to bulk, but did not get enough because of the differences in the growth conditions required for this ecotype. I would really appreciate if anyone can spare 300-500 seeds of this ecotype. Thanks Abhijit Karve Post doctoral research associate Oak Ridge National Lab karveaa@ornl.gov From liling from iastate.edu Thu Aug 6 21:49:11 2009 From: liling from iastate.edu (Ling Li) Date: Fri Aug 7 13:17:04 2009 Subject: [Arabidopsis] Look for a real time-PCR Facility that will do real time-PCR analysis for the expression of an Arabidopsis gene to RNA samples provided by customers. Message-ID: <200908070249.n772nAF0016755@despam-10.iastate.edu> Hi Arabidopsis researchers, I am looking for a real time-PCR Facility that is experienced in doing real time-PCR analysis for the expression of an Arabidopsis gene to RNA samples provided by customers. That is, I provide Arabidopsis leaf RNA samples (more than 100 samples, of time series or of different genotypes), and hope to get sensitive, accurate, and reproducible measurements of levels of expression of a gene that I am interested in. Any information regarding such facility providing such kind of service would be highly appreciated! Ling From randall_k from yahoo.com Thu Aug 6 17:25:46 2009 From: randall_k from yahoo.com (Randy Kerstetter) Date: Fri Aug 7 13:17:26 2009 Subject: [Arabidopsis] Bioinformatics Postdoc in High Throughput Sequencing Message-ID: <27869.99678.qm@web38908.mail.mud.yahoo.com> Bioinformatics Postdoc in High Throughput Sequencing http://waksman.rutgers.edu/postdoc.php The Waksman Institute of Microbiology located on the New Brunswick campus of Rutgers University is seeking applicants for a bioinformatics postdoc appointment to develop bioinformatic tools and analyze genome, transcriptome and epigenome data generated on the 454, Illumina and SOLiD high-throughput sequencing platforms. The qualified candidate will develop methods to extract biological meaning from DNA sequence information and should have a strong background in biology, bioinformatics and scripting languages with experience building and maintaining biological databases. The qualified candidate should be able to process information from sequencing machines and solve long term genomics questions that high-throughput sequencing can address. It is expected that research will lead to publication in top tier journals and presentation at National and International conferences. Requirements: * Ph.D. in molecular biology, genetics, bioinformatics, systems biology or other related fields; ?candidates with a Ph.D. in physics, mathematics or computer science that have some practical ?biology knowledge and experience are also encouraged to apply. * Strong publication record and demonstrated scientific track record. * Strong computational and statistical skills. * Programming and database experience; Perl, python or Ruby expertise required. * Experience with next generation sequencing, microarrays or other high-throughput biology is ?desirable. * Willingness to supervise graduate students and undergraduates is desirable. How to apply: >Send a cover letter stating why you are interested in this position and how your skill set > complements this position, curriculum vitae, and the names of three references that we > will contact if you are chosen for an interview to: hr@waksman.rutgers.edu with > ?Genomics and Bioinformatics Postdoctoral Fellow? in the subject line. Rutgers is an equal opportunity employer. For more information about this position please contact: >> Dr. Joachim Messing (messing@waksman.rutgers.edu) >or visit the website - http://waksman.rutgers.edu/postdoc.php > >Posted for Dr. Messing by: >Randall A. Kerstetter, PhD >Assistant Professor, Plant Biology >Rutgers, The State University of New Jersey >Waksman Institute of Microbiology >190 Frelinghuysen Road >Piscataway, NJ 08854 >http://waksman.rutgers.edu > > From raraina from syr.edu Fri Aug 7 13:04:26 2009 From: raraina from syr.edu (Ramesh Raina) Date: Fri Aug 7 13:18:02 2009 Subject: [Arabidopsis] manuals for an ISCO SR spectroradiometer Message-ID: <93F4C2F3D19A03439EAC16D47C591DDE225130D2@suex07-mbx-08.ad.syr.edu> Dear Arabidopsis community, A collague of mine, Ed Lipson, in the Physics department is looking for the manuals for an ISCO SR spectroradiometer, and an ISCO SRC spectroradiometer calibrator (standard lamp). This is an old instrument and ISCO doesn't have these manuals. He also check at NIH instrumentation museum and they do have some ISCO manuals, but not these ones. I know from literature that several plant biologists have used this instrument. So if you have these manuals, please let me or Ed (edlipson@syr.edu) know. Thanks very much for your help. Regards, Ramesh ----------------------------------------------------------- Ramesh Raina, Ph.D. Associate Professor Co-Director, Biology Graduate Program Biology Department 464 Life Sciences Complex 107 College Place Syracuse University Syracuse, NY 13244 USA Tel: 315-443-4546 (office) Tel: 315-443-4750 (lab) Fax: 315-443-2012 http://biology.syr.edu/raina/index.html From walk2iron from gmail.com Thu Aug 6 15:28:12 2009 From: walk2iron from gmail.com (Elsbeth Walker) Date: Fri Aug 7 13:18:34 2009 Subject: [Arabidopsis] Postdoctoral Positions, University of Massachusetts, Amherst Message-ID: Two postdoctoral positions are open in the Walker Lab in the Biology Department at the University of Massachusetts, Amherst (see http://www.bio.umass.edu/biology/faculty/ewalker.phtml for a brief overview). The first position will be to investigate the *Yellow Stripe-Like * family of genes in maize. The second is to perform transcription profiling experiments to identify key genes for the production of the chemotherapeutic drug taxol. Each uses a combination of genetics, bioinformatics, and biochemistry. Applicants with previous plant molecular biology experience are preferred. To apply, please send the following materials to ewalker@bio.umass.edu: 1. A cover letter explaining specifically why you are interested in joining the group, what skills and knowledge you would contribute, and what you think we could offer in terms of training. In addition, please describe your career goals. 2. A CV with three or more references and their full contact information. 3. A brief proposal (a few paragraphs is enough) for a possible project in the lab. This need not be detailed, but should indicate that you have read enough of the literature to be sincerely interested in some aspect of our research, and that you can think independently and creatively about your work. This can be part of the cover letter. -- Elsbeth L Walker Director, Plant Biology Graduate Program Associate Professor, Biology UMass, Amherst Amherst, MA 01003 413 545-0861 (voice) 413 545-3243 (fax) From vonarnim from utk.edu Fri Aug 7 16:19:55 2009 From: vonarnim from utk.edu (Albrecht Von Arnim) Date: Sun Aug 9 20:45:44 2009 Subject: [Arabidopsis] Postdoctoral position - RNA Biology Message-ID: Postdoctoral Position ? Arabidopsis RNA Biology A Postdoctoral position is available in the laboratory of Albrecht von Arnim in the Department of Biochemistry Cell & Molecular Biology at the University of Tennessee at Knoxville. The research will elaborate, by combining genome-scale analysis and molecular biochemistry, how gene regulation at the level of translation contributes to Arabidopsis growth and development. This is an open field with many fundamental questions remaining to be solved. Recent discoveries in the lab have been on the role of the eIF3 complex in supporting translation of regulatory mRNAs harboring upstream open reading frames. For related papers see Kim et al., Plant Cell 16, 3341-3356 (2004); Kim et al., Genome Biology 8: R60 (2007); Yahalom et al., Plant Journal 53: 300-311 (2008); and Kim and von Arnim, Plant Journal 58:208-219 (2009). Applicants must have a PhD in plant molecular genetics or a related discipline, a solid record of productivity, and good communication skills. As evident from our publications, experience with Arabidopsis genetics, RNA biology, and bioinformatics are additional assets. Salary will be commensurate with experience. The application should be submitted as a single pdf file including: a) Curriculum vitae and list of publications. b) Cover letter outlining the significance of your previous research and how you might contribute to this project. c) Names and contact information of three references. Applications should be sent to vonarnim@utk.edu, preferably by August 31, 2009. For more orientation about the lab see http://www.bio.utk.edu/vonarnim/. Knoxville harbors the flagship campus of the UT system. Its residents (pop. 380,000) enjoy living here and can take advantage of numerous cultural attractions and the surrounding natural beauty. -- Albrecht von Arnim Associate Professor University of Tennessee Dept. of Biochemistry, Cellular and Molecular Biology Associate Director, Genome Science and Technology Walters Life Science Room M407 Knoxville, TN 37996-0840, USA Phone: (865) 974-6206 http://www.bio.utk.edu/vonarnim/default.html ************************* From dee.rawsthorne from bbsrc.ac.uk Wed Aug 12 12:07:10 2009 From: dee.rawsthorne from bbsrc.ac.uk (dee rawsthorne (TOC)) Date: Fri Aug 14 23:30:58 2009 Subject: [Arabidopsis] REMINDER - Genetics 100 Years On - Norwich, UK - 9th-11th September 2009 Message-ID: <92C274E2DE278B4EBAAF9DA3CB0DE290032C261EA7@nbiexch1.nbi.bbsrc.ac.uk> Late booking fee will be applied for registrations received post August! Genetics 100 Years On John Innes Centre, Norwich, UK, 9-11 September, 2009 http://www.jic.ac.uk/centenary/events/Genetics100YearsOn/ To help celebrate 100 years of genetics at John Innes, join us for a very special symposium. Paul Nurse will open with the Bateson Lecture and Sydney Brenner will open the main Conference proceedings with "Genetics 100 Years On". Sandwiched in between will be reflections on areas of human interest that have been transformed by a genetic approach, examining where they are now, and where they might be in the next 100 years. Come and listen to David Stern, Stewart Cole, Jonathan Hodgkin, John Doebley, Walter Bodmer, Linda Partridge, Michael Stratton, Chris Tyler-Smith, Leena Peltonen-Palotie, Rico Coen, Eric Wieschaus, Rich Losick, Mark Patshne, Daniel St Johnson, David Baulcombe and Caroline Dean. If you are interested in the history of genetics there is a one day meeting immediately preceding the symposium http://www.jic.ac.uk/centenary/events/historyofgenetics/programme.htm, and if you have ever worked at JI there is an Alumni Day following the symposium where you can meet up with old friends. http://www.jic.ac.uk/centenary/events/alumniday/programme.htm We would be very grateful if you could please forward to all your colleagues - thank you. on behalf of the Organising Committee Professor Keith Roberts (Chair, JIC Emeritus Professor), Professor Chris Lamb (Director JIC), Professor Sir David Hopwood (JIC Emeritus Professor), Professor Enrico Coen, (JIC), Dr Sarah Wilmot (JIC), Professor Sir Paul Nurse (Rockefeller, NY, USA), Sir Walter Bodmer (Oxford, UK). Dee Rawsthorne, PhD Outreach Coordinator Norwich BioScience Institutes Norwich Research Park Colney Norwich NR4 7UA Direct Line: 44 (0)1603 251457 Fax: 44 (0)1603 255168 E mail: dee.rawsthorne@bbsrc.ac.uk www.ifr.ac.uk www.jic.ac.uk http://www.tsl.ac.uk Need a meeting venue? Visit www.venue-norwich.info Want to find out first hand what's going on in world leading science research centres then join for free Friends of the John Innes Centre and IFR in the City http://www.jic.ac.uk/corporate/friends/index.htm Are you a former employee, student, post-doc or project leader? If so, make sure we have your details on our Alumni Database and keep up to date with news from John Innes http://www.jic.ac.uk/corporate/friends/alumni-association.htm www.plantsandus.org.uk - Plants and Us - an innovative new charity devoted to promoting understanding about plants and plant science From Dylan.Edwards from uea.ac.uk Thu Aug 13 10:10:44 2009 From: Dylan.Edwards from uea.ac.uk (Edwards Dylan Prof (BIO)) Date: Fri Aug 14 23:31:38 2009 Subject: FW: [Arabidopsis] Look for a real time-PCR Facility that will do real time-PCR analysis for the expression of an Arabidopsis gene to RNA samples provided by customers. Message-ID: Dear Ling Your email came to me via Prof. John Turner. Caroline Pennington in my lab is an expert in TaqMan real-time PCR and has just set up a new commercial venture (Gen-ID) http://www.uea.ac.uk/bio/enterprise/genid She can offer a commercial gene expression analysis service. She is presently away on vacation (hence the delay in responding to this message) but will be able to contact you and discuss quotes etc on Monday Aug 17 Best wishes Dylan Edwards Prof. Dylan Edwards Head of School School of Biological Sciences University of East Anglia Norwich NR4 7TJ Phone 44 (0)1603 592184 FAX 44 (0)1603 592250 Please visit our webpages: http://www.uea.ac.uk/bio From: Turner John Prof (BIO) Sent: Friday, August 07, 2009 9:04 PM To: Pennington Caroline Dr (BIO) Subject: FW: [Arabidopsis] Look for a real time-PCR Facility that will do real time-PCR analysis for the expression of an Arabidopsis gene to RNA samples provided by customers. For info John John Turner Professor of Plant Science School of Biological Sciences University of East Anglia Norwich Research Park Norwich NR4 7TJ England email: j.g.turner@uea.ac.uk Telephone: 0 1603 592192 FAX: 0 1603 592250 URL: http://www.uea.ac.uk/bio ________________________________ From: arab-gen-bounces@oat.bio.indiana.edu on behalf of Ling Li Sent: Fri 07/08/2009 03:49 To: arab-gen@magpie.bio.indiana.edu Subject: [Arabidopsis] Look for a real time-PCR Facility that will do real time-PCR analysis for the expression of an Arabidopsis gene to RNA samples provided by customers. Hi Arabidopsis researchers, I am looking for a real time-PCR Facility that is experienced in doing real time-PCR analysis for the expression of an Arabidopsis gene to RNA samples provided by customers. That is, I provide Arabidopsis leaf RNA samples (more than 100 samples, of time series or of different genotypes), and hope to get sensitive, accurate, and reproducible measurements of levels of expression of a gene that I am interested in. Any information regarding such facility providing such kind of service would be highly appreciated! Ling _______________________________________________ Arab-gen mailing list Arab-gen@net.bio.net http://www.bio.net/biomail/listinfo/arab-gen From ehaswell from wustl.edu Fri Aug 14 09:17:11 2009 From: ehaswell from wustl.edu (Elizabeth Haswell) Date: Fri Aug 14 23:31:55 2009 Subject: [Arabidopsis] Research Technician Position, St. Louis, MO Message-ID: A Lab Technician position is available for an enthusiastic individual in a plant molecular biology lab at Washington University. For information about our research, see the Haswell Lab website at http://biology4.wustl.edu/faculty/haswell/ . Major responsibilities will include i) laboratory management, ordering, and database maintenance; and ii) media preparation, subcloning, PCR-genotyping, and plant care. If appropriately skilled and motivated, the successful candidate will also have the opportunity to work on an independent research project in the area of plant mechanotransduction (see website for additional information). The ideal candidate will be highly organized, technically proficient, and able to learn new techniques and approaches quickly. Good communication and interpersonal skills are also necessary. MS level or BS with appropriate experience are required, but previous experience in plant molecular biology is preferred. Salary will be competitive and commensurate with experience. To apply for this position, go to http://www.wustlcareers.com/applicants/Central?quickFind=59444. _____________________________ Elizabeth Haswell Assistant Professor Dept. of Biology, Box 1137 Washington University in St. Louis One Brookings Drive St. Louis, MO 63130 ph (314) 935-9223 email: ehaswell@wustl.edu http://biology4.wustl.edu/faculty/haswell/ From gleon from unab.cl Fri Aug 14 18:40:03 2009 From: gleon from unab.cl (=?iso-8859-1?Q?Gabriel_Le=F3n?=) Date: Fri Aug 14 23:32:34 2009 Subject: [Arabidopsis] Is possible to splice out a T-DNA with different levels of efficiency? Message-ID: <3C54A83BE6F391439CDA648C95DEACA604211B@exchange.UAB.local> Hi Arabidopsis researchers, We recently identified two allelic mutants in Arabidopsis, both displaying the same phenotype. One of the mutants has a T-DNA insertion in the first intron of the gene, and initially we identified a single homozygous mutant plant of this line. As expected, 100% of the F1 was homozygous mutant, but many of the analyzed plants do not display the phenotype. Since the allelic mutant show the same phenotype is not likely that a second insertion could explain the presence of a phenotype in some plants. Interestingly, by RT-PCR analysis we have found a strong correlation between the expression of the gene and the phenotype. Those plants without phenotype show expression levels similar to wild type plants, whereas plants that show the phenotype have a very strong reduction in the mRNA (almost undetectable in a 35 cycles PCR). In many papers is described that some intron-located T-DNAs can be removed by splicing, with different level of efficiency. However, none of these reports mention differences in the splicing efficiency between different individuals with the same genotype. Has anybody ear/seen something like these before? Any suggestions are welcome. Thank you, Gabriel __ Gabriel Leon, PhD Laboratory of Plant Reproduction & Development Center of Plant Biotechnology Andres Bello University Santiago | Chile Phone: +56-02-7703035 (office) | +56-02-7703034 (lab) gleon@unab.cl From Jean-Luc.Gallois from avignon.inra.fr Thu Aug 13 08:16:19 2009 From: Jean-Luc.Gallois from avignon.inra.fr (Gallois) Date: Fri Aug 14 23:32:52 2009 Subject: [Arabidopsis] Silwet L77 in France Message-ID: <4A841223.3040501@avignon.inra.fr> Dear colleagues, Does anyone know where I could order some Silwet L77 in France/Europe? Are all Silwet L77 OK for arabidopsis transformation, whoever the supplier is? Thanks Jean-luc -- Jean-Luc GALLOIS INRA-UR 1052 G?n?tique et Am?lioration des Fruits et L?gumes Domaine St Maurice, BP94 84143 Montfavet cedex, France tel : +00 33 (0)4 32 72 27 96 e-mail : jlgallois@avignon.inra.fr From O.Berkowitz from murdoch.edu.au Mon Aug 10 03:40:57 2009 From: O.Berkowitz from murdoch.edu.au (Oliver Berkowitz) Date: Fri Aug 14 23:33:12 2009 Subject: [Arabidopsis] PhD position Message-ID: PhD position (Perth, Australia) - Phosphite Induced Resistance to Phytophthora cinnamomi. The oomycete pathogen Phytophthora cinnamomi is causing a devastating pandemic of native Australian plant species which threatens the sustainability of many native ecosystems with consequent effects on fauna. Many of the threatened plant species are on the verge of extinction as they are unique to Australia. The disease can be managed using the chemical phosphite, an analogue of phosphate. Application of phosphite makes plants to resistant to infection. A position is available for a postgraduate student with interests in plant molecular biology and plant pathology to investigate how phosphite induces resistance in plants. The focus will be on the use of Arabidopsis thaliana as a model system. The project will involve the use of transcriptomic, metabolomic, or proteomic approaches and the construction of transgenic plants to investigate how resistance develops. The project is a joint Murdoch University / University of Western Australia project funded by the Australian Research Council in partnership with Dept. of Environment and Conservation, Minerals and Energy Research Institute of Western Australia, Alcoa World Alumina, and TiWest. The student will be based with the Phytophthora research team at Murdoch University in Perth but will be working with a multidisciplinary team including plant ecophysiologists, plant molecular biologists, and plant pathologists from the University of Western Australia, and the industry partners. A tax free stipend of $25,118 and a generous operating allowance will apply. In addition there will be opportunities for travel to national and international conferences as well as additional funding opportunities and interaction with other scientists and students. The successful applicant should hold a First Class or Upper 2A Honours, Postgraduate Diploma or Masters degree (or equivalent) and must have a basic understanding of molecular biology, plant pathology or microbiology, and, or the willingness, interest and ability to acquire these skills. They should also be an Australian Citizen or Permanent Resident. For further information regarding the position please contact: Prof Giles Hardy, 08 9497 9385, email G.Hardy@murdoch.edu.au or Dr Philip O'Brien, 08 9360 2785, email: P.Obrien@murdoch.edu.au Applicants are requested to submit an application in writing together with their CV, a copy of their academic transcript and the names and contact details for two referees (including at least one university referee). Please send applications to Dr P. O'Brien, School of Biological Sciences and Biotechnology, Murdoch University, Murdoch, WA 6150 (: P.Obrien@murdoch.edu.au ______________________________________ Dr. Oliver Berkowitz Murdoch University School of Biological Sciences and Biotechnology Centre for Phytophthora Science and Management South Street Murdoch WA 6150 Perth, Australia P: +61 - (0)8 9360 7537 F: +61 - (0)8 9310 7084 E: o.berkowitz@murdoch.edu.au From xux from cshl.edu Mon Aug 10 21:20:10 2009 From: xux from cshl.edu (Xu, Xianfeng) Date: Fri Aug 14 23:33:46 2009 Subject: [Arabidopsis] Fertility and germination problems during EMS mutagenesis. References: <200908101704.n7AH4Gp08400@net.bio.net> Message-ID: <2A4882406F6D47428E41C649BC54C8D85C5CD4@mailbox11.cshl.edu> Dear All, I am writing to seek suggestions on dealing with EMS-induced sterility in Arabidopsis. I have been doing EMS mutagenesis with Arabidopsis seeds and found fertility of the M1 plants severely dropped. Fertility problems persisted into subsequent generations as well. A seed germination problem was also spotted. There are various protocols for Arabidopsis seed EMS mutagenesis, differing in the EMS concentration and the length of EMS incubation. I followed one which pre-soaks the seeds in water @4C for 2 days and then soaks in 0.3% fresh EMS diluted in water overnight. A report from Euphytica 17 (1968): 363-370 suggested that sterility and compromised germination may be simply considered as the price one has to pay for the high mutant frequency after EMS. I am wondering anyone might have or might be having similar problems. Any suggestions or sharing will be greatly appreciated! Thanks, Morgan (Xianfeng) Xu Postdoc Fellow Cold Spring Harbor Laboratory Delbruck Building 1 Bungtown Rd Cold Spring Harbor, NY, 11724, USA 516-367-8827 From sgillmor from sas.upenn.edu Sun Aug 16 10:14:38 2009 From: sgillmor from sas.upenn.edu (Stewart Gillmor) Date: Sun Aug 16 14:38:41 2009 Subject: [Arabidopsis] EMS mutagenesis protocol In-Reply-To: <2A4882406F6D47428E41C649BC54C8D85C5CD4@mailbox11.cshl.edu> References: <200908101704.n7AH4Gp08400@net.bio.net> <2A4882406F6D47428E41C649BC54C8D85C5CD4@mailbox11.cshl.edu> Message-ID: Dear Xianfeng, Here is a protocol that I worked out for ems mutagenesis of Arabidopsis seeds. It has worked well for me many times. This protocol was gives heavy mutagenesis (50% of siliques of M1 plants were segregating at least one embryo defective), but little or no sterility. I think the key thing is the extensive rinsing after the ems treatment. 1) Agitate 100mg of seed in 25mL water with 3uL Tween20 for 15 minutes. Then rinse with dH2O until there are no more Tween20 bubbles. 2) Leave seed overnight at 4C on a rocker in 40mL dH2O. 3) The next day, pour off the water and add 10mLs of 0.4% EMS in 100mM Sodium Phosphate buffer, pH 7. Leave in hood for 9 hours on a rocker or rotator so that seed are gently agitated. 4) After 9 hours, rinse the seed 10 times (this is very important) with 25 mLs of water each time. 5) Sow the seed on soil. To do this I resuspend them in 0.1% Agar and sow them out with a 25mL pipet. What I have done is sow out about 20 flats of seed, leave them in the cold room, and put out 5 flats per week (Seeds will start to germinate in the cold room after about 3 weeks). That way you don't need to look at all of the flats at the same time. best wishes, Stewart Stewart Gillmor Department of Biology University of Pennsylvania 433 S University Ave. Philadelphia PA 19104 USA tel 215 898 8916 fax 215 898 8780 On Aug 10, 2009, at 10:20 PM, Xu, Xianfeng wrote: > Dear All, > > I am writing to seek suggestions on dealing with EMS-induced > sterility in Arabidopsis. I have been doing EMS mutagenesis with > Arabidopsis seeds and found fertility of the M1 plants severely > dropped. Fertility problems persisted into subsequent generations as > well. A seed germination problem was also spotted. > > There are various protocols for Arabidopsis seed EMS mutagenesis, > differing in the EMS concentration and the length of EMS incubation. > I followed one which pre-soaks the seeds in water @4C for 2 days and > then soaks in 0.3% fresh EMS diluted in water overnight. > > A report from Euphytica 17 (1968): 363-370 suggested that sterility > and compromised germination may be simply considered as the price > one has to pay for the high mutant frequency after EMS. > > I am wondering anyone might have or might be having similar > problems. Any suggestions or sharing will be greatly appreciated! > Thanks, > > > Morgan (Xianfeng) Xu > > Postdoc Fellow > Cold Spring Harbor Laboratory > Delbruck Building > 1 Bungtown Rd > Cold Spring Harbor, NY, 11724, USA > 516-367-8827 From O.Berkowitz from murdoch.edu.au Sun Aug 16 20:53:41 2009 From: O.Berkowitz from murdoch.edu.au (Oliver Berkowitz) Date: Mon Aug 17 01:01:27 2009 Subject: [Arabidopsis] PhD position, Murdoch University, Perth Message-ID: Please post on the newsgroup: PhD position (Perth, Australia) - Phosphite Induced Resistance to Phytophthora cinnamomi. The oomycete pathogen Phytophthora cinnamomi is causing a devastating pandemic of native Australian plant species which threatens the sustainability of many native ecosystems with consequent effects on fauna. Many of the threatened plant species are on the verge of extinction as they are unique to Australia. The disease can be managed using the chemical phosphite, an analogue of phosphate. Application of phosphite makes plants to resistant to infection. A position is available for a postgraduate student with interests in plant molecular biology and plant pathology to investigate how phosphite induces resistance in plants. The focus will be on the use of Arabidopsis thaliana as a model system. The project will involve the use of transcriptomic, metabolomic, or proteomic approaches and the construction of transgenic plants to investigate how resistance develops. The project is a joint Murdoch University / University of Western Australia project funded by the Australian Research Council in partnership with Dept. of Environment and Conservation, Minerals and Energy Research Institute of Western Australia, Alcoa World Alumina, and TiWest. The student will be based with the Phytophthora research team at Murdoch University in Perth but will be working with a multidisciplinary team including plant ecophysiologists, plant molecular biologists, and plant pathologists from the University of Western Australia, and the industry partners. A tax free stipend of $25,118 and a generous operating allowance will apply. In addition there will be opportunities for travel to national and international conferences as well as additional funding opportunities and interaction with other scientists and students. The successful applicant should hold a First Class or Upper 2A Honours, Postgraduate Diploma or Masters degree (or equivalent) and must have a basic understanding of molecular biology, plant pathology or microbiology, and, or the willingness, interest and ability to acquire these skills. They should also be an Australian Citizen or Permanent Resident. For further information regarding the position please contact: Prof Giles Hardy, 08 9497 9385, email G.Hardy@murdoch.edu.au or Dr Philip O'Brien, 08 9360 2785, email: P.Obrien@murdoch.edu.au Applicants are requested to submit an application in writing together with their CV, a copy of their academic transcript and the names and contact details for two referees (including at least one university referee). Please send applications to Dr P. O'Brien, School of Biological Sciences and Biotechnology, Murdoch University, Murdoch, WA 6150 ( P.Obrien@murdoch.edu.au ) ______________________________________ Dr. Oliver Berkowitz Murdoch University School of Biological Sciences and Biotechnology Centre for Phytophthora Science and Management South Street Murdoch WA 6150 Perth, Australia P: +61 - (0)8 9360 7537 F: +61 - (0)8 9310 7084 E: o.berkowitz@murdoch.edu.au From ijf from mole.bio.cam.ac.uk Mon Aug 17 08:46:13 2009 From: ijf from mole.bio.cam.ac.uk (Ian Furner) Date: Mon Aug 17 11:20:50 2009 Subject: [Arabidopsis] Fertility and germination problems during EMS mutagenesis. Message-ID: Dear Morgan I have quite a lot of experience with EMS and Arabidopsis. If you are getting a large decrease in viability and problems with sterility you are probably giving too high a dose or treating for too long a time. Typically I use 0.25% to 1% W/V EMS for 3 hours. The use of 2% EMS for 3 hours gives sterile plants. There is an old protocol written by Ottoline Leyser and I in the compleate guide (http://www.arabidopsis.org/comguide/ table_of_contents.html) Kind Regards Ian Furner From carl.h.johnson from vanderbilt.edu Mon Aug 17 15:01:34 2009 From: carl.h.johnson from vanderbilt.edu (Carl Johnson) Date: Mon Aug 17 18:10:20 2009 Subject: [Arabidopsis] Open-rank position in plant development, Vanderbilt University Message-ID: FACULTY POSITION DEVELOPMENTAL GENETICS The Department of Biological Sciences at Vanderbilt University seeks candidates to fill an open rank faculty position in developmental genetics. Research of candidates will be considered in all areas of development, with emphasis on early development in vertebrates (including stem cell research) or plant developmental genetics. We desire candidates whose interests broadly overlap the interests of our current faculty. Central criteria for the position are excellence in research and the ability to teach undergraduate and graduate students with a high level of effectiveness. Women and under-represented minority candidates are especially encouraged to apply. For information about the Department, visit our website: http://sitemason.vanderbilt.edu/biosci. For information about developmental biology at Vanderbilt, see http://www.mc.vanderbilt.edu/devbio/. Applicants should send a letter of application together with a curriculum vitae, a statement of current and future research interests, three letters of recommendation, teaching evaluations, if available, and selected reprints to: Developmental Genetics Search Committee, Department of Biological Sciences, Vanderbilt University, VU Station B 351634, Nashville, TN 37235-1634 U.S.A. Review of applicants will begin October 1, 2009, and will continue until the position has been filled. Vanderbilt University is an Affirmative Action / Equal Opportunity Employer. We are very interested in hiring an excellent plant developmental biologist, especially someone who will interact productively with existing faculty in our department and with the larger developmental biology community at Vanderbilt. Our department has excellent greenhouse and other types of research facilities. If you have any questions, do not hesitate to email or call me for further information. Best wishes, Carl Johnson Carl Johnson, Ph.D., Professor Dept. of Biological Sciences, U-8211 BSB/MRB III VU Station B, Box 35-1634 Vanderbilt University Nashville, TN 37235 USA TEL: 615-322-2384 FAX: 615-936-0205 Email: carl.h.johnson@vanderbilt.edu Website: http://www.cas.vanderbilt.edu/johnsonlab/ From jdfriesner from ucdavis.edu Mon Aug 17 16:26:48 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Mon Aug 17 18:10:35 2009 Subject: [Arabidopsis] MASC reports available Message-ID: <000101ca1f81$6e1bac30$4a530490$@edu> Dear all, I have a limited number of 2009 annual reports of the Multinational Arabidopsis Steering Committee remaining. The report describes the progress in Arabidopsis research regarding functional genomics in the global community over the past year. In addition to MASC progress and recommendations and reports from MASC countries and subcommittees, the report includes descriptions of how basic research in Arabidopsis is being translated to products in industry and other areas and summaries of recent research efforts by Arabidopsis researchers. It also contains information on Arabidopsis publication and patent rates as compared to the rice and corn communities. If you are located in the U.S. and would like a copy, please email your complete mailing address directly to jdfriesner@ucdavis.edu. Otherwise, digital versions of this and past reports are available at: http://arabidopsis.org/portals/masc/masc_docs/masc_reports.jsp and http://arabidopsis.info/progreports.html yours, Joanna ? Joanna Friesner, PhD MASC Coordinator 1 Shields Ave. Section of Molecular and Cellular Biology UC Davis Davis, CA 95616 ? From toomajia from k-state.edu Tue Aug 18 09:16:40 2009 From: toomajia from k-state.edu (Chris Toomajian) Date: Tue Aug 18 11:46:07 2009 Subject: [Arabidopsis] PhD position - bioinformatics - Kansas State University Message-ID: PhD student position available in the laboratory of Chris Toomajian (sites.google.com/site/=20= toomajianlab) at Kansas State University to pursue projects in plant =20 population genetics and functional genomics. Looking for a student =20 with a bachelor=92s or master=92s degree in bioinformatics, biology, or = a =20 related quantitative discipline such as computational biology, =20 computer science, or statistics. Applicants should have some computer =20= programming experience and a working knowledge of molecular evolution =20= or population genetics, ideally with some coursework in statistics. =20 Prior work on a project combining these fields is advantageous. The =20 student=92s projects will likely involve the statistical and population =20= genetic analysis of DNA sequence and polymorphism data-sets. This may =20= include collaborations with molecular biologists, bioinformaticians, =20 and statistical geneticists. Please contact me for further information =20= about potential projects. Research will emphasize bioinformatics, though additional wet-lab or =20 bioinformatics components may be added depending on shared interests =20 and funding opportunities. The expected starting date is flexible, anywhere between January and =20 August 2010, though earlier start dates are preferred. To apply: For all email correspondence, please use =93PhD student =20 recruitment=94 as your subject. Send a letter describing your interests =20= and qualifications for the position, specifying how your skills match =20= the position requirements, your CV, and contact information for 3 =20 academic/professional references. Please include your GPA and GRE =20 scores (if available) in your application. The selected student is =20 expected to enroll either in the Interdepartmental Genetics program = (www.oznet.ksu.edu/genetics)=20 or the Department of Plant Pathology (www.plantpath.k-state.edu). =20 Further information about policies and entrance requirements =20 pertaining to university admission are found at the Kansas State =20 University Graduate School website (www.k-state.edu/grad/). Current stipends for Ph.D. students in either program are $22,300. The =20= KSU Department of Plant Pathology is a diverse and nurturing graduate =20= training environment, and little or no teaching assistant duties are =20 required for the degree. The lab also participates in K-State=92s =20 Ecological Genomics Institute, a vibrant community composed of =20 faculty, post-docs, and graduate students from a number of disciplines. for more information, contact: Christopher Toomajian Assistant Professor Kansas State University Department of Plant Pathology 4024 Throckmorton Plant Sciences Center Manhattan, KS 66506 office: (785) 532-0879 fax: (785) 532-5692 toomajia@ksu.edu http://sites.google.com/site/toomajianlab/ iChat A/V: christoomajian@AIM From jdfriesner from ucdavis.edu Wed Aug 19 16:52:58 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Wed Aug 19 19:09:12 2009 Subject: [Arabidopsis] New Online List of 2010 Projects and Resources Message-ID: <000301ca2117$6a4f0b50$3eed21f0$@edu> A new resource listing all the Arabidopsis 2010 projects funded by NSF (up to 2007), including project websites, PI contact, and whether and where resources are deposited for public use has been launched at TAIR. A list of relevant community databases is also included. Updates from the community are requested and all information can be found at this URL: http://arabidopsis.org/portals/masc/2010_resources.jsp The resource was compiled by the MASC Coordinator on behalf of the community. Joanna Friesner MASC Coordinator From jdfriesner from ucdavis.edu Wed Aug 19 16:56:09 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Wed Aug 19 19:09:24 2009 Subject: [Arabidopsis] Results of YouTube Plant Videos Contest Message-ID: <000401ca2117$dc53bc00$94fb3400$@edu> The first ChloroFilms contest for plant videos on YouTube has announced the winners. There are some very cool videos ranging from technical to artistic, basic to advanced. http://chlorofilms.org/index.php?module=Pages&func=display&pageid=13 Just a few winning titles: # Fantastic vesicle traffic- 1st prize technical - vesicle movement through Arabidopsis root hairs in germinating seeds # La Bloomba- 1st prize artistic- Nice time-lapse photography of flowers opening # Photosynthesis 101: presented by Dr. Undergrad- Basic intro to photosynthesis starting with a cartoon about the 'Model' Arabidopsis # Measuring Leaf Area with Adobe Photoshop CS3- technical teaching video to analyze growth of Arabidopsis leaves # "Sweet Home Apparatus" - the ultimate Golgi music video- a music video for Golgi lovers- or for those who just like saying the word 'golgi!' # And many more including lots of other kinds of plants (switchgrass, corn, artichokes, oats, pines, christmas trees, and the elusive Foil Flower) Contest 2 opens soon for new entries. From simonnea from supagro.inra.fr Thu Aug 20 09:42:00 2009 From: simonnea from supagro.inra.fr (Simonneau Thierry) Date: Thu Aug 20 12:22:24 2009 Subject: [Arabidopsis] Seeking 2 candidates for 3-year doctoral positions in France Message-ID: <4A8D60B8.2060207@supagro.inra.fr> Dear Colleagues, I seek you help in finding suitable candidates with a master dergree or equivalent for two 3-year doctoral (funded) positions that are now open in my lab in South France. position 1 : Analysis and modelling of ovary abortion in water-stressed maize plants. position 2 : Effects of natural allelic variability on the sensitivities of leaf growth and water use in maize. Research environment. The student will interact with a dynamic group with diverse skills in environmental plant physiology. The LEPSE (Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, http://www1.montpellier.inra.fr/ibip/lepse/english/teams/mage.htm) is located within the Ecole Nationale Superieure d'Agronomie (http://www.supagro.fr/web/?idl=20) and the Institut National de la Recherche Agronomique (http://www.montpellier.inra.fr/montpellier_eng/) that is equipped with state-of-art facilities in plant physiology and molecular biology. Requirements. For the position, a master degree or equivalent with strong background in (environmental) plant physiology is required. Motivated candidates with skills in data analysis and good knowledge of environmental plant physiology/genetics are encouraged to apply. Salary. We can offer a monthly payment of about Euros 1200 after taxes. Contact. Please send your application, including CV and references to Dr T. Simonneau, LEPSE, 2 place Viala, 34060 Montpellier cedex 1, France. Phone +33 4 99 61 27 52 or fax +33 67 52 21 16. Email: simonneau@supagro.inra.fr Thank you for your help in bringing these positions to the attention of qualified candidates. All the best, Thierry -- Thierry Simonneau Head of Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE) UMR759 INRA-SupAgro Institut de Biologie Int?grative des Plantes (IBIP, bat. 7) 2, place Viala, F-34060 Montpellier Cedex 1 tel 33 4 99 61 27 52 fax 33 4 67 52 21 16 http://www1.montpellier.inra.fr/ibip/lepse/ From nicholas.provart from utoronto.ca Fri Aug 21 16:37:05 2009 From: nicholas.provart from utoronto.ca (Nicholas Provart) Date: Sat Aug 22 23:06:35 2009 Subject: [Arabidopsis] BAR News: eFP Browser for At-TAX data sets, ePlant, and call for views Message-ID: <200908212137.n7LLbRp05853@net.bio.net> Hello Arabidopsis Researchers, The Bio-Array Resource is happy to announce the inclusion of At-TAX data sets from Detlef Weigel's group/s in Tuebingen (Laubinger et al. 2008 and Zeller et al. 2009) in our Arabidopsis eFP Browser. This inclusion is made possible through the use of JSON-based webservices developed by Christian Widmer and Stefan Henz, whereby the eFP Browser retrieves At-TAX data directly from Tuebingen for display. Thanks also to Sascha Laubinger for information regarding the samples. The inclusion of At-TAX data means that expression information for several thousand more Arabidopsis genes not included on the ATH1 chip is now available within the eFP Browser system. The dual view At-TAX/ATH1 eFP view was implemented by Yuan Ji in my lab. The BAR is also pleased to introduce a conceptual implementation of a "Google Earth" for plant biology, called ePlant. Try it at bar.utoronto.ca/eplant! ePlant permits or will soon permit easy 3D viewing of large plant biology data sets from the km to nm scale (sequence variation, gene expression, subcellular localisation, protein interactors and protein structure for now). ePlant was implemented by Geoff Fucile, David Di Biase, Shokoufeh Khodabandeh and Hardeep Nahal, and makes extensive use of data from the Arabidopsis community: Schmid et al. 2005, Geisler-Lee et al. 2007, the SUBA database from A. Harvey Millar's lab via webservice, and soon sequence polymorphism data from Joe Ecker and others. A new, much faster version based on Google's O3D 3D rendering engine will be available shortly. The ePlant system uses 3D models of the type used in the video games and the computer generated imagery industry. We've also set up the 3D Data Display Initiative at 3ddi.org to further these kind of developments. Finally, we're expanding our cell-type-specific views in the eFP Browser with the inclusion of several new cell-type-specific data sets, such as a floral meristem set from Venu Reddy's lab at UCR, pollen germination data from Mark Johnson (Brown) and Ravishankar Palanivelu (Arizona), and salt and nitrogen root cell-type-responses from the Benfey (Duke) and Birnbaum (NYU) labs. If you're aware of any other cell-type-specific data sets, let us know and we'll add them this Fall! Best regards and, as always, we welcome any feedback. Nick ......................................... Nicholas Provart, PhD Assistant Professor, Plant Cyberinfrastructure & 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 The Bio-Array Resource. http://www.BAR.utoronto.ca email. nicholas.provart@utoronto.ca TTC. Spadina LRT, Willcocks St. From jupin from ijm.univ-paris-diderot.fr Mon Aug 24 02:53:57 2009 From: jupin from ijm.univ-paris-diderot.fr (Isabelle Jupin) Date: Mon Aug 24 10:58:17 2009 Subject: [Arabidopsis] Postdoctoral position, Paris Message-ID: <06f03d486fbc730d23e62a2afc99a4a2.squirrel@webmail.ijm.univ-paris-diderot.fr> Postdoctoral Position Institut Jacques Monod CNRS - University Paris Diderot Paris, France A postdoctoral position is available at the Institut Jacques Monod in the field of host/virus interactions. The postdoc will investigate the cellular trafficking of viral replication complexes in Arabidopsis cells using biochemical, molecular and cellular approaches. Applicants should have a PhD with strong background in molecular and cellular biology. Previous research experience in plant virology is a plus but is not mandatory. The position is available as soon as November 2009. The Institut Jacques-Monod is one of the main centres for basic research in biology in the Paris area. It has recently moved to a new building on the Paris left-bank and offers state-of-the-art core facilities. http://mimas.ijm.univ-paris-diderot.fr/ijm/the-institut/overview The application should be submitted as a single pdf file including: a) Curriculum vitae and list of publications. b) a cover letter outlining your research interests and date of availability c) The names and contact information of three references. Applications should be sent to jupin@ijm.univ-paris-diderot.fr From chiangscn from gmail.com Wed Aug 26 18:37:31 2009 From: chiangscn from gmail.com (smith Chiang) Date: Thu Aug 27 11:26:11 2009 Subject: [Arabidopsis] complementation Message-ID: <40a6ed990908261637j5b93b97dg53c19d553ba7f653@mail.gmail.com> Hi researchers, Could anyone help me on designing a complementation construct to complement an Arabidopsis mutant? The genomic sequence of my gene in TAIR has a short 5'UTR and also a short 3'UTR. The vector-pCAMBIA1300 has no promoter or terminator sequence, so I am going to PCR the promoter-5'UTR-coding region-3'UTR (based on the genomic sequence) and clone a ~5kb fragment into this vector. My question is: how to decide how long I should clone after 3'UTR? How can I determine if the 3' part sequence has the terminator sequence that, after transformed into the mutant, the gene can be properly transcribed? I am going to use a 2kb promoter region, but do not know how long I should clone the 3'UTR/terminator sequence. I checked a few papers and found that someones even did not include any 3'UTR (reverse primer just around the stop codon) when using pCAMBIA1300 for complementation, and this could lead to non-stop during the transcription, am I right? Thanks for your reply. Smith From dee.rawsthorne from bbsrc.ac.uk Thu Aug 27 04:06:19 2009 From: dee.rawsthorne from bbsrc.ac.uk (dee rawsthorne (TOC)) Date: Thu Aug 27 11:26:32 2009 Subject: [Arabidopsis] REMINDER - Genetics 100 Years On - Norwich, UK - 9th-11th September 2009 In-Reply-To: <92C274E2DE278B4EBAAF9DA3CB0DE290032C261EA7@nbiexch1.nbi.bbsrc.ac.uk> References: <92C274E2DE278B4EBAAF9DA3CB0DE290032C261EA7@nbiexch1.nbi.bbsrc.ac.uk> Message-ID: <92C274E2DE278B4EBAAF9DA3CB0DE290042F1BD150@nbiexch1.nbi.bbsrc.ac.uk> Late booking fee will be applied for registrations received post August! Genetics 100 Years On John Innes Centre, Norwich, UK, 9-11 September, 2009 http://www.jic.ac.uk/centenary/events/Genetics100YearsOn/ To help celebrate 100 years of genetics at John Innes, join us for a very special symposium. Paul Nurse will open with the Bateson Lecture and Sydney Brenner will open the main Conference proceedings with "Genetics 100 Years On". Sandwiched in between will be reflections on areas of human interest that have been transformed by a genetic approach, examining where they are now, and where they might be in the next 100 years. Come and listen to David Stern, Stewart Cole, Jonathan Hodgkin, John Doebley, Walter Bodmer, Linda Partridge, Michael Stratton, Jane Rogers, Chris Tyler-Smith, Leena Peltonen-Palotie, Rico Coen, Eric Wieschaus, Rich Losick, Mark Patshne, Daniel St Johnson, David Baulcombe and Caroline Dean. If you are interested in the history of genetics there is a one day meeting immediately preceding the symposium http://www.jic.ac.uk/centenary/events/historyofgenetics/programme.htm, and if you have ever worked at JI there is an Alumni Day following the symposium where you can meet up with old friends. http://www.jic.ac.uk/centenary/events/alumniday/programme.htm We would be very grateful if you could please forward to all your colleagues - thank you. on behalf of the Organising Committee Professor Keith Roberts (Chair, JIC Emeritus Professor), the late Professor Chris Lamb (Director JIC), Professor Sir David Hopwood (JIC Emeritus Professor), Professor Enrico Coen, (JIC), Dr Sarah Wilmot (JIC), Professor Sir Paul Nurse (Rockefeller, NY, USA), Sir Walter Bodmer (Oxford, UK). Dee Rawsthorne, PhD Outreach Coordinator Norwich BioScience Institutes Norwich Research Park Colney Norwich NR4 7UA Direct Line: 44 (0)1603 251457 Fax: 44 (0)1603 255168 E mail: dee.rawsthorne@bbsrc.ac.uk www.ifr.ac.uk www.jic.ac.uk http://www.tsl.ac.uk Need a meeting venue? Visit www.venue-norwich.info Want to find out first hand what's going on in world leading science research centres then join for free Friends of the John Innes Centre and IFR in the City http://www.jic.ac.uk/corporate/friends/index.htm Are you a former employee, student, post-doc or project leader? If so, make sure we have your details on our Alumni Database and keep up to date with news from John Innes http://www.jic.ac.uk/corporate/friends/alumni-association.htm www.plantsandus.org.uk - Plants and Us - an innovative new charity devoted to promoting understanding about plants and plant science _______________________________________________ Arab-gen mailing list Arab-gen@net.bio.net http://www.bio.net/biomail/listinfo/arab-gen From kv35 from cornell.edu Thu Aug 27 07:49:49 2009 From: kv35 from cornell.edu (Klaas van Wijk) Date: Fri Aug 28 12:48:57 2009 Subject: [Arabidopsis] Postdoctoral Position for a Plant Biochemist in Systems biology of Maize/Rice C3-C4 leaf development and cell differentiation Message-ID: <6.2.1.2.2.20090827084842.031c3410@postoffice6.mail.cornell.edu> Postdoctoral Position for a Plant Biochemist in Systems biology of Maize/Rice C3-C4 leaf development and cell differentiation van Wijk lab, Cornell University, Ithaca, NY, USA [1]http://cbsu.tc.cornell.edu/vanwijk/ A postdoctoral position for a Plant Biochemist is available in the van Wijk lab to contribute to a collaborative project sponsored by the NSF-Genome program. This project concerns a cell-type specific comparative analysis of C3 and C4 leaf development in Rice, Sorghum and Maize. In leaves of such C4 grasses photosynthetic activities are partitioned between two morphologically and biochemically distinct bundle sheath (BS) and mesophyll (M) cells. The overall objectives are to compare the quantitative and qualitative patterns of transcripts, proteins, metabolic activities and anatomy at discrete stages and in specific cell types in rice (C3), maize and sorghum (C4), and to develop a model of the regulatory networks governing C4 anatomy and function. These experimental datasets will be linked by new informatics tools for comparative transcriptional and proteome analysis, to provide the foundation for a systems biology approach to understanding C4 biology. The responsibilities of the postdoc include isolation of specific subsets of leaf proteomes (e.g. Bundle strands) for proteome analysis, as well as biological interpretation of large scale proteome (and other) datasets. In particular, a strong effort is needed on extracting biological conclusions and hypotheses from these large scale datasets. Experience in plant protein biochemistry and a strong interest in plant metabolism and systems biology is required. The postdoc will work closely together with other team members, including mass spectrometry specialists and bioinformaticians. Salary will be commensurate with experience with generous employee benefits according the Cornell Human Resource Office. Review of applications will begin immediately, and continue until the position is filled. Application Instructions: Send your curriculum vitae, a statement of research interests and career goals, and three letters of reference by email to: [2]kv35@cornell.edu Klaas J. van Wijk, Associate Professor, Dept of Plant Biology, Cornell University, Ithaca, NY 14853, USA; tel +1-607-255-3664; Relevant papers: Majeran, W., and van Wijk, K.J. (2009) Cell-type specific differentiation of chloroplasts in C4 plants. Trends in Plant Science 14(2):100-9 Majeran W., Zybailov B., Ytterberg A.J., Dunsmore J., Sun Q., and van Wijk K.J. (2008) Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells. Mol Cell Proteomics 2008 7: 1609-1638 Covshoff S., Majeran W., Liu P., Kolkman J.M., van Wijk K.J.and Brutnell T.P. (2008) Deregulation of maize c4 photosynthetic development in a mesophyll cell-defective mutant. Plant Physiol 146: 1469-1481. Majeran W., Cai Y., Sun Q.and van Wijk K.J. (2005) Functional Differentiation of Bundle Sheath and Mesophyll Maize Chloroplasts Determined by Comparative Proteomics. The Plant Cell 17: 3111-3140. Klaas J. van Wijk Associate Professor Director of Graduate Studies (DGS) for the Field of Plant Biology Dept of Plant Biology 332 Emerson Hall Cornell University Ithaca, NY 14853, USA tel +1-607-255-3664 [3]http://cbsu.tc.cornell.edu/vanwijk/ References 1. http://cbsu.tc.cornell.edu/vanwijk/ 2. mailto:kv35@cornell.edu 3. http://cbsu.tc.cornell.edu/vanwijk/ From aloraine from gmail.com Fri Aug 28 18:26:40 2009 From: aloraine from gmail.com (Ann Loraine) Date: Sat Aug 29 17:36:48 2009 Subject: [Arabidopsis] Bioinformatics Postdoc Loraine Lab UNC Charlotte Message-ID: <83722dde0908281626w672d108aqfd8980bfb973bba5@mail.gmail.com> *Bioinformatics Postdoc* The Loraine lab at UNC Charlotte seeks a postdoctoral researcher for primarily computational projects, with possibility for experimental work. Available projects include: Analysis and annotation of blueberry transcriptomes and next-generation sequencing data; Developing methods, tools, and Web services for mining expression data in plants; and developing visualization software for bioinformatics and genomics (IGB, Genoviz SDK, TableView, etc.). *General qualifications:* Ph.D. in one of: computer science, applied math, physics, chemistry, biology. *Qualifications, by project:* *Analysis and annotation of blueberry NGS data*: Familiarity with molecular biology and gene expression regulation; research experience using bioinformatics programs; excellent cross-disciplinary communication and writing skills; scripting experience and some command-line programming. *Co-expression*: Java Web programming (or similar); familiarity with DNA expression microarray design and analysis methods, especially R and Bioconductor; and sufficient lab training to design expression measurement experiments at the bench. *Visualization*: User interface development in Java; knowledge of software engineering principles; excellent communication skills; experience supervising or training junior colleagues; and a track record of high productivity and quality in software development. The position is at the North Carolina Research Campus in Kannapolis, NC, located 15 miles north of the UNC Charlotte main campus. Fringe benefits: Vacation and health insurance coverage with additional spousal or dependent coverage available for purchase. To apply: Email aloraine@uncc.edu with (1) cover letter describing your interests and qualifications for the position, (2) a CV, (3) the names and contact information for 3 references. For further information about the lab, please visit http://www.transvar.org. For information about postdoctoral positions at UNC Charlotte, visit: http://www.research.uncc.edu/rs/postdoctoral.cfm From mocliamgtoh from hotmail.com Sun Aug 30 18:45:46 2009 From: mocliamgtoh from hotmail.com (liamgtoh moc) Date: Sun Aug 30 23:49:11 2009 Subject: [Arabidopsis] Binary BAC transformation Message-ID: Dear All=2C =20 I am writing to seek suggestions on transforming Binary BAC (BiBAC or TAC) = into Arabidopsis. I need to transform a few BiBAC clones into Arabidospis = C24 and Col ecotypes hopefully by flower dipping. Can anyone share with me= a detailed protocol for BiBAC transformation? In addition=2C it will be h= elpful to know the efficiency of BiBAC transformation comparing with routin= e binary vectors. Are there any special strains preferred instead of regul= ar GV3101 Agrobacteria? =20 For BAC handling=2C can tri-parental mating be used to introduce BiBAC into= Agrobacteria. If so=2C can I have this protocol as well? Any suggestions or sharing will be greatly appreciated! =20 Thanks=2C =20 Morgan Gordon =20 Assistant Professor Department of Biological Science California State University=2C Fullerton _________________________________________________________________ Windows Live: Make it easier for your friends to see what you=92re up to on= Facebook. http://windowslive.com/Campaign/SocialNetworking?ocid=3DPID23285::T:WLMTAGL= :ON:WL:en-US:SI_SB_facebook:082009=