From jlpeng from iastate.edu Fri Oct 3 18:42:58 2008 From: jlpeng from iastate.edu (Jianling Peng) Date: Fri Oct 3 19:35:50 2008 Subject: [Arabidopsis] cis element analysis Message-ID: <5842183910852761@webmail.iastate.edu> Hi, Is there anybody who can give me some suggestions how to analyze the cis- element in the promoter region? Any suggestions are appreciated. Thanks! Jianling > Send Arab-gen mailing list submissions to > arab-gen@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bio.net/biomail/listinfo/arab-gen > or, via email, send a message with subject or body 'help' to > arab-gen-request@net.bio.net > > You can reach the person managing the list at > arab-gen-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Arab-gen digest..." > > > Today's Topics: > > 1. ICAR 2009 - First Announcement (Ruth Bastow) > 2. CALL FOR ABSTRACTS - Plant & Animal Genome XVII Conference > (PAG-XVII Conference) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 04 Sep 2008 17:28:55 +0100 > From: Ruth Bastow > Subject: [Arabidopsis] ICAR 2009 - First Announcement > To: > Message-ID: > Content-Type: text/plain; charset="US-ASCII" > > Dear All > The 20th International Conference on Arabidopsis Research (ICAR) will be > held in Edinburgh, Scotland, UK from June 30th to 4th July 2009. > > To register your interest for the conference, which will ensure you get all > the latest updates and information, such as when registration and abstract > submission begin, please visit > https://registration.meetingmakers.co.uk/dev-cgi/ICAR_intent/begin?short_con > ference_name=ICAR_intent > > A preliminary website for the conference is available at > http://arabidopsis2009.com/ > > The conference will include plenary session on Systems Biology, Development, > Environmental responses, Natural Variation, Plant Defence, Cell Biology and > Genome Organisation. > Confirmed speakers included Sally Assmann, Enrico Coen, Caroline Dean, > Nicholas Harberd, Jiri Friml, Ben Scheres, and Mark Stitt. > > A full list of plenary sessions and chairs can be downloaded from the > website http://arabidopsis2009.com/ > > I hope you will be able to join us in Edinburgh next year. > Regards > Ruth > > > > > ------------------------------ > > Message: 2 > Date: Thu, 4 Sep 2008 20:16:07 -0400 (EDT) > From: PAG-XVII Conference > Subject: [Arabidopsis] CALL FOR ABSTRACTS - Plant & Animal Genome XVII > Conference > To: arab-gen@magpie.bio.indiana.edu > Message-ID: <200809050016.m850G70a000961@www.intl-pag.org> > > Dear Colleague: > > You are invited to attend the Plant & Animal Genome XVII Conference > (PAG-XVII), January 10-14, 2009 taking place at the Town & Country > Convention Center in San Diego, California. This is a call for > abstracts and pre-registration. > > Everyone who submits an abstract is required to pay the registration > fee prior to the meeting to be included in the Final Abstract Guide > and posted on the website. You must be registered by December 1, or > your abstract will NOT be printed or posted on the website. Please > update us if you cannot attend so we may free up poster space in the > Grand Exhibit Hall where exhibits and coffee breaks are just steps > from the Atlas Foyer. > > Don't forget to check out the Travel Grant Applications; the deadlines > are closing soon. > > The meeting will again offer the satellite sessions and workshops as > presented in earlier conferences. A couple of new workshops this time > are "Genomics of Plant Disease Resistance" and "Recombination". There > will be over 100 technical, industry, and computer training workshops. > The meeting draft for PAG-XVII and abstracts from PG-I through PAG-XVI > are available on the PAG website at: http://intl-pag.org/ > > We are requesting that all abstracts be submitted electronically. > Point your browser to the address below and click on the "Abstracts > Submission" link when ready to submit your abstract at: > > http://intl-pag.org/ > > Due to severe delays in getting VISAs to enter the US, we recommend > that you plan ahead and begin the process now. DO NOT WAIT! See > the information link at the web site as updates are provided. > > All researchers presenting posters must pre-register for the meeting to > have their abstract printed in the final meeting program. The abstract > DEADLINE is Friday, October 3, 2008. Registration is available via the > internet using our secure on-line registration form. > > Full Conference (Univ/Non-Profit/Govt) Registration for ALL attendees: > Pre-Registration (deadline November 1, 2008): $550 > Late Registration (after November 1, 2008): $650 > On-site Registration: $750 > > Full Conference (Industry) Registration for ALL attendees: > Pre-Registration (deadline November 1, 2008): $750 > Late Registration (after November 1, 2008): $850 > On-site Registration: $950 > > Weekend Only (Univ/Non-Profit/Govt) Registration (Fri/Sat/Sun) for ALL attendees: > Pre-Registration (deadline November 1, 2008): $375 > Late Registration (after November 1, 2008): $425 > On-site Registration: $475 > > Weekend Only (Industry) Registration (Fri/Sat/Sun) for ALL attendees: > Pre-Registration (deadline November 1, 2008): $475 > Late Registration (after November 1, 2008): $525 > On-site Registration: $575 > > Student Registration (proof required): > Pre-Registration (deadline November 1, 2008): $350 > Late Registration (after November 1, 2008): $400 > > All questions regarding Plant & Animal Genome XVII should be > directed to Scherago Int'l at Tel: 201-653-4777 ext. 20, > Fax: 201-653-5705 or Email: pag@scherago.com. > > Sincerely, > > Darrin Scherago - VP, Meeting Manager > Scherago International, Inc. > 525 Washington Blvd., Suite 3310, Jersy City, NJ 07310 > -------------------------------------------------------------------------- > Plant & Animal Genome XVII Conference ---------------- January 10-14, 2009 > -------------------------------------------------------------------------- > > > > ------------------------------ > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > > End of Arab-gen Digest, Vol 41, Issue 1 > *************************************** > ************************************************************* Jianling Peng http://www.public.iastate.edu/~mash/people.html Department of Genetics, Development and Cell Biology Iowa State University 433 Bessey Ames, IA 50011 ************************************************************* From Robert.H.Gross from Dartmouth.EDU Sat Oct 4 12:07:39 2008 From: Robert.H.Gross from Dartmouth.EDU (Robert H. Gross) Date: Sat Oct 4 14:09:26 2008 Subject: [Arabidopsis] cis element analysis Message-ID: <133665088@newdasher.Dartmouth.EDU> --- You wrote: Hi, Is there anybody who can give me some suggestions how to analyze the cis- element in the promoter region? Any suggestions are appreciated. Thanks! Jianling --- end of quote --- Hello Jianling - Your note was forwarded to me from a colleague. My lab has developed something to do exactly this called SCOPE. You can access it at: . It is designed to find common regulatory elements for any set of genes that you input to the server. There are references to papers on the genie server. Please let me know if you have any questions or would like to talk about your questions. I'm always open to new collaborations. Good luck. Bob Gross ----------------------------------------------------------------------------- Robert H. Gross, Ph.D. phone: 603-646-2059 Assoc. Prof., Dept. Biology email: robert.h.gross@dartmouth.edu Director, Ctr. for Biol. & Biomed. Computing Office: Remsen 210 Gilman Labs 104 URL: http://www.dartmouth.edu/~bglab/ Dartmouth College Hanover, NH 03755 USA From info from noster-it.com Mon Oct 6 05:05:10 2008 From: info from noster-it.com (Dokorek) Date: Mon Oct 6 12:04:42 2008 Subject: [Arabidopsis] Join the Fastest Growing Bio Community Message-ID: <4be176a2-5ae5-4e08-95ce-ac4b91b95d82@75g2000hso.googlegroups.com> Join the Fastest Growing Bio Community - you know Facebook, Xing or MySpace, LinkedIn. In biology it exists as well: Visit academic portal http://biospace.ethz.ch register, confirm registration in email - join group, institute, create own group of interesst and share data, contacts, micorscope images, build network. You can be first and can create a future scientific group of interests. ETH Zuerich Team From pooggin from yahoo.com Mon Oct 6 08:02:37 2008 From: pooggin from yahoo.com (Mikail Pooggin) Date: Mon Oct 6 12:04:48 2008 Subject: [Arabidopsis] Postdoc and PhD student positions available Message-ID: <621606.81041.qm@web32803.mail.mud.yahoo.com> Postdoc and PhD student positions are available at the Institute of Botany, University of Basel, Switzerland, to study the relationship between viruses and the plant RNA silencing machinery. The project is funded by Swiss National Science Foundation. We are looking for a motivated and hard working young scientist with a solid background in molecular plant virology, basic skills in biochemistry, experience with RNA work including small RNA blot hybridization, and a deep interest in RNA silencing and viruses. ? Send your motivation letter, CV and names of two referees by e-mail to Mikhail Pooggin (pooggin@yahoo.com) From jcsedbr from ilstu.edu Mon Oct 6 11:13:58 2008 From: jcsedbr from ilstu.edu (John Sedbrook) Date: Mon Oct 6 12:04:52 2008 Subject: [Arabidopsis] Faculty position available, Developmental Biology at Illinois State University Message-ID: ASSISTANT PROFESSOR, DEVELOPMENTAL BIOLOGY ILLINOIS STATE UNIVERSITY A tenure-track faculty position in DEVELOPMENTAL BIOLOGY is available in the Department of Biological Sciences at Illinois State University, Normal, IL (www.bio.ilstu.edu ). We seek a scientist using molecular, cellular, and genetic approaches to investigate fundamental mechanisms of development in multicellular organisms. The successful candidate will be part of a diverse department that is home to 25 faculty members, over 500 undergraduates, 85 M.S. and Ph.D. students and postdoctoral fellows. Candidates that enhance existing research strengths within the department are especially encouraged to apply. Those strengths include cell signaling, cytoskeleton, tissue patterning and morphogenesis, neurobiology, and plant biology/bioenergy. The successful candidate is expected to develop a competitive, extramurally funded research program. Teaching responsibilities will include a course in developmental biology. Ph.D. and postdoctoral experience are required. To assure full consideration, send the following as hard copies or as pdfs by email: cover letter, CV, three recommendation letters, 3-5 reprints, and a statement of research goals to: Dr. John Sedbrook, Developmental Biology Search Committee, Campus Box 4120, Illinois State University, Normal, IL 61790-4120; (jcsedbr@ilstu.edu). Review of applications will begin on Oct. 26, 2008. Preferred start date of Aug. 16, 2009. Illinois State University is an Equal Opportunity University encouraging diversity. From GCopenhaver from bio.unc.edu Mon Oct 6 12:26:36 2008 From: GCopenhaver from bio.unc.edu (Copenhaver, Gregory P (Biology)) Date: Mon Oct 6 14:59:30 2008 Subject: [Arabidopsis] UNC Assistant Professor Position Message-ID: <5805338EEBC6DB4AB6F96B9693F2ABDB04C86BCD@email.bio.unc.edu> ASSISTANT PROFESSOR QUANTITATIVE BIOLOGY OR BIOINFORMATICS DEPARTMENT OF BIOLOGY UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL The Department of Biology at the University of North Carolina at Chapel Hill invites applications for a tenure-track Assistant Professor in Quantitative Biology or Bioinformatics. We seek a researcher who is applying quantitative and/or computational methods to the study of molecular, cellular or developmental systems. Examples of appropriate specializations include, but are not limited to, the study of physical processes within the cell, developmental processes unfolding at multiple scales, and the use of genomic data to study the biology of microbial communities. Research may or may not be purely computational. The successful candidate will contribute to a new initiative in Quantitative Biology and be affiliated with the NIH-funded graduate Curriculum in Bioinformatics and Computational Biology (http://bcb.unc.edu). To apply, submit a cover letter, CV, research and teaching statements, and optionally one additional supporting document online at http://hr.unc.edu/jobseekers (recruitment ID 1001095). At least four letters of reference are required. Electronic copies should be sent to cpasternak@bio.unc.edu and signed hardcopies to: Quantitative Biology Search Committee, Campus Box 3280, Department of Biology, University of North Carolina, Chapel Hill, NC 27599. Review of applications will begin November 19, 2008. The position will be effective on or after July 1, 2009 and will remain open until filled. The successful candidate must have a Ph.D. in Biology, Applied Math, Computer Science, or related field by the effective date. The University of North Carolina is an equal opportunity employer. For inquiries, please contact Dr. Todd Vision (tjv@bio.unc.edu; 919-843-4507) or Dr. Jason Lieb (jlieb@bio.unc.edu; 919-843-3228). The Department of Biology (http://www.bio.unc.edu) consists of over 40 faculty engaged in basic research in the life sciences. The Carolina Center for Genome Sciences (http://genomics.unc.edu/) co-ordinates genomics research, training and outreach across campus, and a new Genome Sciences Building is currently under construction to house and foster collaboration between experimental, computational, and theoretical scientists. UNC faculty, postdocs and graduate students routinely interact with colleagues at nearby Duke and North Carolina State Universities, as well as other institutions in Research Triangle Park. The quality of life in North Carolina's Triangle area is consistently rated among the highest in the nation. From I.Manfield from leeds.ac.uk Mon Oct 6 12:29:50 2008 From: I.Manfield from leeds.ac.uk (Iain Manfield) Date: Mon Oct 6 14:59:36 2008 Subject: [Arabidopsis] cis element analysis - using co-expressed genes. In-Reply-To: <133665088@newdasher.Dartmouth.EDU> Message-ID: <1B314609ED89A2449037E67690426B236C436C@HERMES1.ds.leeds.ac.uk> Dear Jianling, If you're interested in promoters of Arabidopsis genes... we have developed a site calculating the correlation of expression patterns for Arabidopsis genes from a database of Affymetrix microarray experiments. Co-expressed genes are often co-regulated and therefore analysis of a set of promoters for strongly co-expressed genes (including the promoter you're most interested in) can help to predict significant motifs with better confidence than looking at a single sequence. http://www.arabidopsis.leeds.ac.uk/act/coexpanalyser.php#CO2 Use the "ID exchanger" to get the Affymetrix probe ID from an AGI code and put this into the "probe ID" box at the site with the above address. With a set of AGI codes from the returned list you can get the promoter sequences from TAIR and use the SCOPE tool as Robert Gross has suggested (amongst other tools). Best wishes, Iain. Dr Iain Manfield Centre for Plant Sciences Faculty of Biological Sciences University of Leeds Leeds LS2 9JT U.K. Tel. 00 44 (0)113 343 7279 --- You wrote: Hi, Is there anybody who can give me some suggestions how to analyze the cis- element in the promoter region? Any suggestions are appreciated. Thanks! Jianling --- end of quote --- Hello Jianling - Your note was forwarded to me from a colleague. My lab has developed something to do exactly this called SCOPE. You can access it at: . It is designed to find common regulatory elements for any set of genes that you input to the server. There are references to papers on the genie server. Please let me know if you have any questions or would like to talk about your questions. I'm always open to new collaborations. Good luck. Bob Gross ------------------------------------------------------------------------ ----- Robert H. Gross, Ph.D. phone: 603-646-2059 Assoc. Prof., Dept. Biology email: robert.h.gross@dartmouth.edu Director, Ctr. for Biol. & Biomed. Computing Office: Remsen 210 Gilman Labs 104 URL: http://www.dartmouth.edu/~bglab/ Dartmouth College Hanover, NH 03755 USA _______________________________________________ Arab-gen mailing list Arab-gen@net.bio.net http://www.bio.net/biomail/listinfo/arab-gen From evewurtele from gmail.com Tue Oct 7 10:12:40 2008 From: evewurtele from gmail.com (Eve Wurtele) Date: Tue Oct 7 11:39:14 2008 Subject: [Arabidopsis] cis element analysis - using co-expressed genes. In-Reply-To: <1B314609ED89A2449037E67690426B236C436C@HERMES1.ds.leeds.ac.uk> References: <133665088@newdasher.Dartmouth.EDU> <1B314609ED89A2449037E67690426B236C436C@HERMES1.ds.leeds.ac.uk> Message-ID: <7fdaa81b0810070812s458e6190uaa1746109d20e92b@mail.gmail.com> Hi Jianling, Expanding on this idea, MetaOmGraph (metnetdb.org) enables you to do correlations with very large datasets (thousands of chips) on either already-created files of data from Arabidopsis or several other organisms, or on your own microarray or metabolomic data files. Alternately, you can create files from ArrayExpress public microarray data. There are multiple options for visualization, ordering, and sorting the types of experimental conditions you want to include in the correlation. best, Eve On Mon, Oct 6, 2008 at 12:29 PM, Iain Manfield wrote: > Dear Jianling, > > If you're interested in promoters of Arabidopsis genes... we have > developed a site calculating the correlation of expression patterns for > Arabidopsis genes from a database of Affymetrix microarray experiments. > Co-expressed genes are often co-regulated and therefore analysis of a > set of promoters for strongly co-expressed genes (including the promoter > you're most interested in) can help to predict significant motifs with > better confidence than looking at a single sequence. > > http://www.arabidopsis.leeds.ac.uk/act/coexpanalyser.php#CO2 > > Use the "ID exchanger" to get the Affymetrix probe ID from an AGI code > and put this into the "probe ID" box at the site with the above address. > > > With a set of AGI codes from the returned list you can get the promoter > sequences from TAIR and use the SCOPE tool as Robert Gross has suggested > (amongst other tools). > > Best wishes, > > Iain. > > Dr Iain Manfield > Centre for Plant Sciences > Faculty of Biological Sciences > University of Leeds > Leeds > LS2 9JT > U.K. > > Tel. 00 44 (0)113 343 7279 > > --- You wrote: > Hi, > > Is there anybody who can give me some suggestions how to analyze the > cis- > element in the promoter region? > > Any suggestions are appreciated. > > Thanks! > > Jianling > --- end of quote --- > Hello Jianling - > > Your note was forwarded to me from a colleague. My lab has developed > something > to do exactly this called SCOPE. You can access it at: > . > > It is designed to find common regulatory elements for any set of genes > that you > input to the server. There are references to papers on the genie server. > > Please let me know if you have any questions or would like to talk about > your > questions. I'm always open to new collaborations. > > Good luck. > > Bob Gross > > ------------------------------------------------------------------------ > ----- > Robert H. Gross, Ph.D. phone: > 603-646-2059 > Assoc. Prof., Dept. Biology email: > robert.h.gross@dartmouth.edu > Director, Ctr. for Biol. & Biomed. Computing Office: > Remsen 210 > Gilman Labs 104 URL: > http://www.dartmouth.edu/~bglab/ > Dartmouth College > Hanover, NH 03755 USA > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > -- Eve Syrkin Wurtele, Professor Bioinformatics and Computational Biology Dept Genetics, Development, & Cell Biology 2624D Howe Hall Iowa State University, Ames IA 50011, USA 515-294-2023 515-708-3232 (cell) metnetdb.org metablast.org calendar at /embed?src=evewurtele%40gmail.com&ctz=America/Chicago From zhao.124 from osu.edu Wed Oct 8 10:00:33 2008 From: zhao.124 from osu.edu (QIAO ZHAO) Date: Wed Oct 8 22:34:19 2008 Subject: [Arabidopsis] developmental stage-specific promoters In-Reply-To: References: <000001c91e8a$a4da7470$c9c4ce84@MCGILLCEC1FBBD> Message-ID: Hi All, I am looking for developmental stage specific promoters and I need different stages not a particular one. Can anyone give me some suggestion? thank you Qiao Zhao The Ohio State University Department of Plant Cellular and Molecular Biology 244 Rightmire Hall laboratory 1060 Carmack Road Columbus, OH 43210 Tel:(614)-292-5623 From kongjixiang from yahoo.cn Wed Oct 8 10:10:03 2008 From: kongjixiang from yahoo.cn (Stone) Date: Wed Oct 8 22:34:26 2008 Subject: [Arabidopsis] help Message-ID: <882385.26542.qm@web92402.mail.cnh.yahoo.com> Dear all Now I come across with a problem about my study. When I overexpress the gene which i am interested in and get the transgenic plant.Then I find that some lines have the phenotype which is sterile. However I do not know why this overexpression can cause sterile. Then I analyze the expression pattern of the promoter. But it does not express neither in pollen nor pollen tube. It expresses in guard cells of stoma and style. According to the expression, I guess the gene may influence the style and cause sterile. But I do another experiment. I pollinate the line with other pollen and then it has the fertilities. Could someone tell me some possibilites?? Thanks a lot Regards Jixiang Kong --------------------------------- ÑÅ»¢ÓÊÏ䣬ÄúµÄÖÕÉúÓÊÏ䣡From jiangyqcn from hotmail.com Thu Oct 9 00:21:50 2008 From: jiangyqcn from hotmail.com (Jxy) Date: Thu Oct 9 02:01:45 2008 Subject: [Arabidopsis] pseudogene or not Message-ID: Hi collegues, I recently cloned some genes of Brassica napus by RT-PCR/RACE through mining ESTs in GenBank. The primers were designed based on ESTs. After sequencing more than 2 clones for each gene, I found, for quite a few genes, obviously, alleles exist. The most common is nucleotide substitution, next indel(insertion/deletion). An interesting phenomenon I found is for those alleles with a a long insertion compared to the other allele, the insertion is not 3-folds, i.e. the insertion leads to premature stop codon in the insertion or immedialtely after the insertion. The means that the translated amino acid sequence of one allele is normal (compared to At homolog), while the other is much shorter (premature stop codon). My question is why the insertion is not 3-folds and they are, for example 79bp, 100bp, etc? Are the alleles bearing the 79bp, 100bp insertion pseudogenes? BTW, I used high-fidelity polymerase when cloning those genes and, sequenced the clones from two ends with the same sequence, which excludes sequencing errors. Although RTase is error-prone, I have no way to predict this. >From Wikipedia, I know that: Pseudogenes are defunct relatives of known genes that have lost their protein-coding ability or are otherwise no longer expressed in the cell. Therefore, a pseudogene may be transcribed, but not translated into a functional protein as a results of "extra" premature stop codon. Could someone provide any explanation? Thanks. _________________________________________________________________ From jagreetk from yahoo.com Fri Oct 10 06:24:24 2008 From: jagreetk from yahoo.com (jagreet kaur) Date: Fri Oct 10 11:31:00 2008 Subject: [Arabidopsis] Cvi Cosmid library Message-ID: <389583.79588.qm@web36802.mail.mud.yahoo.com> Hello I am looking for a genomic library for Arabidopsis ecotype Cvi in a binary Cosmid vector. If someone somewhere has made it and can share it for research purpose it would be great. Otherwise any suggestion on which Binary Cosmid vector should I use? looking forward for responses thanks Jagreet? From kongjixiang from gmail.com Fri Oct 10 09:02:25 2008 From: kongjixiang from gmail.com (jixiang kong) Date: Fri Oct 10 11:31:34 2008 Subject: [Arabidopsis] software for scanning protein localization. Message-ID: <2633185e0810100702te19fbacm7db91cab66dbdddf@mail.gmail.com> Hello all Does someone know some software which could scan the exact localization of expression protein in protoplast of Arabidopsis? I have taken some pictures when I saw the expression within the protoplast, and the protein was expressing near the membrane of the cell. I heard that there is a soft ware which can scan the exact position of the expression, just as on the membrane or just near the membrane. Thanks a lot! Jixiang From jiangyqcn from hotmail.com Thu Oct 9 23:42:28 2008 From: jiangyqcn from hotmail.com (Jiang Yakim) Date: Fri Oct 10 11:33:29 2008 Subject: [Arabidopsis] At gene expression in E.coli Message-ID: Hello, I ever tried to express a few At transcription factor (TF) genes in E.coli using the Novagen pET32a(+) vector and BL21(DE3) as well as Rosetta-gami strain. Only one of them (aa shorter than the others) was successfully expressed in the Rosetta-gami strain, suggesting that codon bias is possibly a problem for plant TFs exp in E.coli. However, the sole expressed TF was not in the soluble fraction; it is in the form of inclusion body, although I induced it at 30C for only 3 h. It takes a lot effort to get it out from the inclusion body and then refold it. So far, I did not see much use of using E.coli to express a TF protein. Another lab mate also got an unknown protein gene expressed in the inclusion body. A friend saw a fungal gene expressed in the inclusion body too. I ever read a paper describing a strategy in E.coli(not too sure) that adds a tag to target protein and secrete the protein into the medium, is any company selling this type of vector? What made I very doubtful is I saw a published paper expressing one of the TF genes I failed to get exp in E.coli and they succeeded with BL21(DE3) strain. I checked their "Materials and methods" section and found that the IPTG concentration they used was also 1 mM, the same as I ever used. Other than this, no more detail was included in their paper; they just saw "according to the manufacturer's manual". No idea whether that TF was expressed in soluble form or in inclusion body. No info was included in the supplemental data. Were they cheating me? How about in yeast? What are the working yeast vector and strain (vendor?) for expressing At genes? Does anyone ever get an At gene expressed in the soluble form in yeast? How does yeast exp system compared to E.coli system? Thanks for your reply. _________________________________________________________________ From jiangyqcn from hotmail.com Fri Oct 10 13:40:36 2008 From: jiangyqcn from hotmail.com (Yakim Jiang) Date: Fri Oct 10 15:55:07 2008 Subject: [Arabidopsis] software for scanning protein localization. In-Reply-To: <2633185e0810100702te19fbacm7db91cab66dbdddf@mail.gmail.com> References: <2633185e0810100702te19fbacm7db91cab66dbdddf@mail.gmail.com> Message-ID: try WoLF PSORT http://wolfpsort.org/ or TargetP 1.1 Server http://www.cbs.dtu.dk/services/TargetP/ P.S. I don't think there is a software than can do the type of work you expected. The exact localization needs experimental evidence plus suitable positive controls. For example, if you find your protein in on the cell membrane (not at the edge of cytoplasm as result of vacuolar pushing), test a known membrane protein using GOI-GFP under the same procedures and assay conditions. > Date: Fri, 10 Oct 2008 22:02:25 +0800 > From: kongjixiang@gmail.com> To: arab-gen@magpie.bio.indiana.edu> CC: > Subject: [Arabidopsis] software for scanning protein localization.> > Hello all> > Does someone know some software which could scan the exact localization of> expression protein in protoplast of Arabidopsis?> > I have taken some pictures when I saw the expression within the protoplast,> and the protein was expressing near the membrane of the cell. I heard that> there is a soft ware which can scan the exact position of the expression,> just as on the membrane or just near the membrane.> > Thanks a lot!> Jixiang> _______________________________________________> Arab-gen mailing list> Arab-gen@net.bio.net> http://www.bio.net/biomail/listinfo/arab-gen _________________________________________________________________ From dsomers from crops.org Sun Oct 12 17:59:12 2008 From: dsomers from crops.org (David Somers) Date: Sun Oct 12 23:27:06 2008 Subject: [Arabidopsis] FW: The Plant Genome In-Reply-To: <1E763C55E318CD4CB6AD118FAE00ADB104F5366A60@mail.agronomy.org> References: <1E763C55E318CD4CB6AD118FAE00ADB12569CD58@mail.agronomy.org>, <1E763C55E318CD4CB6AD118FAE00ADB104F5366A60@mail.agronomy.org> Message-ID: <1E763C55E318CD4CB6AD118FAE00ADB104F5366A61@mail.agronomy.org> Please make this available the Arabnet community. Thanks Dave Somers Dear Plant Genomics Colleague: The Plant Genome is an international open-access electronic journal published by the Crop Science Society of America. The goal of The Plant Genome is to provide the readership with a short submission-to-online publication of the latest advances and breakthroughs in plant genomics research. The Plant Genome publishes original research investigating all aspects of plant genomics. Technical breakthroughs reporting improvements in the efficiency and speed of acquiring and interpreting plant genomics data are welcome. The editorial board will give preference to novel reports that use innovative genomic applications that advance our understanding of plant biology and that may have applications to crop improvement. The journal also publishes invited review articles and perspectives that offer insight and commentary on recent advances in genomics and their potential for agronomic improvement. The first issue of the journal was published in July 2008 and is available at http://plantgenome.scijournals.org/ Our next issue will be available in Novemeber 2008. For more information on The Plant Genome, including instructions to authors and the editorial board, please go to The Plant Genome. Papers may be submitted through The Plant Genome's online submission website at: http://mc.manuscriptcentral.com/plantgenome. We look forward to receiving your manuscripts for publication in The Plant Genome. Sincerely, David A. Somers Editor From sfrank from CeBiTec.Uni-Bielefeld.DE Mon Oct 13 06:35:22 2008 From: sfrank from CeBiTec.Uni-Bielefeld.DE (sfrank@CeBiTec.Uni-Bielefeld.DE) Date: Mon Oct 13 11:06:09 2008 Subject: [Arabidopsis] genomic Nd-0 (Niederzenz-0) and C24 binary fosmid (or cosmid) library Message-ID: <56320.129.70.160.91.1223897722.squirrel@www.CeBiTec.Uni-Bielefeld.DE> Please make this available the Arabnet community. Thanks Dear colleagues, I am searching for a genomic Nd-0 (Niederzenz-0) and C24 binary fosmid (or cosmid) library. Has anyone generated those libraries and would share them for research purposes? Thanks in advance for your replies, Sandra Frank -- Sandra Frank Bielefeld University Chair of Genome Research Universitaetsstr. 27 D-33594 Bielefeld From I.Manfield from leeds.ac.uk Mon Oct 13 11:53:18 2008 From: I.Manfield from leeds.ac.uk (Iain Manfield) Date: Mon Oct 13 17:16:04 2008 Subject: [Arabidopsis] Feedback on usefulness of the Arabidopsis Co-expression Tool (ACT) and suggestions for updates. Message-ID: <1B314609ED89A2449037E67690426B236C4391@HERMES1.ds.leeds.ac.uk> Dear Colleagues in Plant Science, Feedback on usefulness of the Arabidopsis Co-expression Tool (ACT) and suggestions for updates. We are updating our co-expression analysis website and would like some feedback and suggestions. What have you found useful, if you have used ACT? What tools would you like to have for co-expression analysis of microarray data? With thanks and best wishes, Iain. Dr Iain Manfield Centre for Plant Sciences Faculty of Biological Sciences University of Leeds Leeds LS2 9JT U.K. Tel. 00 44 (0)113 343 7279 To use the Arabidopsis Co-expression Tool, visit our web-site, http://www.arabidopsis.leeds.ac.uk/act/coexpanalyser.php For information on how co-expression analysis may be useful to you, look at our article in the Nucleic Acids Research Web-server special issue, http://nar.oxfordjournals.org/cgi/reprint/34/suppl_2/W504 From maria.siomos from gmi.oeaw.ac.at Wed Oct 15 05:02:08 2008 From: maria.siomos from gmi.oeaw.ac.at (Siomos, Maria) Date: Wed Oct 15 11:18:16 2008 Subject: [Arabidopsis] FEBS Workshop 'Adaptation Potential in Plants': 19-21 March 2009, VIenna, Austria Message-ID: <3ED3D285FFD58F41BDE657B18F548C0382170F@gmi-mail01.gmi.oeaw.ac.at> Dear all, I am writing to invite you to register for the FEBS Workshop 'Adaptation Potential in Plants', which will be held at the Gregor Mendel Institute of Molecular Plant Biology in Vienna, Austria from 19-21 March 2009. Confirmed Speakers: David Baulcombe Luca Comai Caroline Dean Bill Easterling Ueli Grossniklaus Andrzej Jerzmanowski Csaba Koncz Susan Lolle Ivan Matic Thomas Mitchell-Olds Jean Molinier Ferenc Nagy Eric Richards Ida Ruberti Michael Thomashow Elizabeth Vierling Eva Zazimalova Jian-Kang Zhu Detailed information about the Workshop and registration procedure are available on the Workshop website: www.gmi.oeaw.ac.at/febs2009 . A poster can be downloaded at http://www.gmi.oeaw.ac.at/fileadmin/gmi/FEBS_Conference_2009/Adaptation_ Potential_in_Plants.pdf. The registration deadline is 15 January 2009. There are 10 Youth Travel Fund awards available for attending the Workshop. The deadline for being considered for a Youth Travel Fund is 10 December 2009. For conditions of award, please consult: http://www.gmi.oeaw.ac.at/en/other-sites/febs/youth-travel-fund-awards/. Yours sincerely, Maria Siomos Dr. Maria Siomos Head of Science Support Unit maria.siomos@gmi.oeaw.ac.at Gregor Mendel Institute of Molecular Plant Biology GMI GmbH Dr. Bohrgasse 3 Vienna 1030 Austria T: +43 1 79044 9101 F: +43 1 79044 23 9101 W: www.gmi.oeaw.ac.at From pspringer from ucr.edu Wed Oct 15 17:02:35 2008 From: pspringer from ucr.edu (Patricia Springer) Date: Wed Oct 15 18:19:41 2008 Subject: [Arabidopsis] upcoming UC Riverside symposium - please post Message-ID: Greetings! The UC Riverside Botany and Plant Sciences department is pleased to announce our 25th Symposium in Plant Biology - "The Evolution of Plant Development" to be held January 29 - 31, 2009 at the Riverside Convention Center. Details about the Symposium can be found at http://cepceb.ucr.edu/Symp. A flyer detailing highlights of the program can be downloaded at http://cepceb.ucr.edu/Symp/flyer.pdf and a tentative program is below. We have reserved a number of openings in the schedule that we plan to fill by selecting speakers from submitted abstracts. Registration is now open and will be open until December 4, 2008. Please contact Patty Springer (patricia.springer@ucr.edu) if you have questions about the symposium. We look forward to seeing you in Riverside in January! Thursday, January 29, 2009 Session I Comparative Genomics and Speciation 1:15 - 1:45 pm Claude dePamphilis, Penn State University 1:45 - 2:15 pm Loren Rieseberg, University of British Columbia 2:15 - 2:45 pm Richard Clark, University of Utah 2:45 - 3:00 pm Speaker selected from those submitting abstracts 3:00 - 3:15 pm Speaker selected from those submitting abstracts 3:15 - 3:45 pm BREAK 3:45 - 4:15 pm John Willis, Duke University 4:15 - 4:45 pm Cris Kuhlemeier, University of Bern 4:45 - 5:15 pm TBA 5:15 - 5:30 pm Speaker selected from those submitting abstracts 6:00 - 7:30 pm RECEPTION 8:00 - 10:00 pm Poster Session and Reception Friday, January 30, 2009 9:00 - 10:00 am Keynote Address, Antonia Monteiro, Yale University 10:00 - 10:20 am BREAK Session II Leaves and Vascular Patterning 10:20 - 10:50 am Neelima Sinha, UC Davis 10:50 - 11:20 am John Bowman, Monash University 11:20 - 11:50 am Jane Langdale, Oxford University 11:50 am - 12:05 pm Speaker selected from those submitting abstracts 12:05 - 1:30 pm LUNCH Session III Evolution of Floral Form 1:30 - 2:00 pm Vivian Irish, Yale University 2:00 - 2:30 pm Elena Kramer, Harvard University 2:30 - 3:00 pm G?nter Theissen, Friedrich Schiller. University 3:00 - 3:15 pm Speaker selected from those submitting abstracts 3:15 - 3:45 pm BREAK 3:45 - 4:15 pm Sabine Zachgo, University of Osnabr?ck 4:15 - 4:45 pm Tom Gerats, Radboud University Nijmegen 4:45 - 5:00 pm Speaker selected from those submitting abstracts 5:00 - 5:15 pm Speaker selected from those submitting abstracts 5:15 - 5:30 pm Speaker selected from those submitting abstracts 7:30 - 10:00 pm Poster Session and Reception Saturday, January 31, 2009 Session IV Inflorescence Architecture 9:00 - 9:30 am David Baum, University of Wisconsin, Madison 9:30 - 10:00 am Elizabeth Kellogg, University of Missouri, St. Louis 10:00 - 10:30 am TBA 10:30 - 10:45 am Speaker selected from those submitting abstracts 10:45 - 11:15 am BREAK 11:15 - 11:45 am Clint Whipple, Cold Spring Harbor Lab 11:45 am- 12:15 pm Simon Malcomber, California State University, Long Beach 12:15 - 12:30 pm Speaker selected from those submitting abstracts 12:30 - 1:30 pm LUNCH Session V Ovules, Carpels, and Fruit Evolution 1:30 - 2:00 pm Chuck Gasser, UC Davis 2:00 - 2:30 pm William Friedman, University of Colorado 2:30 - 3:00 pm Esther van der Knapp, Ohio State University, Wooster 3:00 - 3:15 pm Speaker selected from those submitting abstracts 3:15 - 3:30 pm Speaker selected from those submitting abstracts 3:30 - 3:50 pm BREAK Session VI Early Land Plants 3:50 - 4:20 pm Jody Banks, Purdue University 4:20 - 4:50 pm Ralph Quatrano, Washington University 4:50 - 5:20 pm Mitsuyasu Hasebe, Laboratory of Evolutionary Biology, Okazaki, Japan 5:20 - 5:35 pm Speaker selected from those submitting abstracts 5:35 - 5:50 pm Speaker selected from those submitting abstracts 7:00 pm SYMPOSIUM BANQUET -- From csgasser from ucdavis.edu Wed Oct 15 19:01:39 2008 From: csgasser from ucdavis.edu (Charles S. Gasser) Date: Wed Oct 15 19:03:18 2008 Subject: [Arabidopsis] re: pseudogene or not Message-ID: Dear jiangyqcn, You wrote: >Hi collegues, > >I recently cloned some genes of Brassica napus by RT-PCR/RACE >through mining ESTs in GenBank. Note - if you did RT-PCR, you did not clone "genes", you cloned "cDNAs". This is a very important distinction that you should be careful to make. >The primers were designed based on ESTs. After sequencing more than >2 clones for each gene, I found, for quite a few genes, obviously, >alleles exist. The most common is nucleotide substitution, next >indel(insertion/deletion). An interesting phenomenon I found is for >those alleles with a a long insertion compared to the other allele, >the insertion is not 3-folds, i.e. the insertion leads to premature >stop codon in the insertion or immedialtely after the insertion. The >means that the translated amino acid sequence of one allele is >normal (compared to At homolog), while the other is much shorter >(premature stop codon). > >My question is why the insertion is not 3-folds and they are, for >example 79bp, 100bp, etc? Are the alleles bearing the 79bp, 100bp >insertion pseudogenes? BTW, I used high-fidelity polymerase when >cloning those genes and, sequenced the clones from two ends with the >same sequence, which excludes sequencing errors. Although RTase is >error-prone, I have no way to predict this. What you see is common, most of your data do not likely reflect either alleles or pseudogenes. The base substitutions you see could potentially represent alleles, or homeologous genes. There should be two different sequences because B. napus appears to be an allotetraploid of B. oleraceae and B. rapa, so you would get sequences from each. But is is also quite likely that some substitutions represent errors by RT-ase or resulting from PCR. The insertions are almost certainly retained introns. These can result from either the presence in your RNA samples of nuclear RNA precursors that have not yet been fully spliced (notably in many cases poly-A addition can happen prior to splicing - so oligo dT will still work to prime these transcripts for RT). In addition, it is not uncommon for partially spliced transcripts to erroneously leave the nucleus. If they have internal stop codons they should be subject to nonsense-mediated decay and should, in theory, be at relatively low frequency, but we and others see such partially spliced cDNA products for many different genes. You can check this theory by looking for "GT" at the start of the insert and "AG" at the end of the insert, consistent with their being introns. Also, your insert sized of >65 bases are consistent with their being introns. Thus, you can get multiple different partially spliced cDNAs from a single gene - with no need to invoke the existence of pseudogenes. For example, for one gene family, in one maize EST database we found nearly 90% of the cDNA sequences to include retained introns. > > >Could someone provide any explanation? See above. > >Thanks. You are welcome. Chuck Gasser U. C. Davis (and arab-gen moderator) From dee.rawsthorne from bbsrc.ac.uk Thu Oct 16 06:29:58 2008 From: dee.rawsthorne from bbsrc.ac.uk (dee rawsthorne (TOC)) Date: Thu Oct 16 13:10:27 2008 Subject: [Arabidopsis] Two-question survey on GM for the UKs Sense about Science organisation -- your help please Message-ID: Apologies if you get this more than once! Dear All We would be grateful if you could help with a two question survey as soon as you are able. You can access the survey here: http://www.surveymonkey.com/s.aspx?sm=8oI2WCuqD5BAdFZIMIvsvg_3d_3d We have put this survey to gather information for our forthcoming publication, Making Sense of GM. It would be extremely helpful if you would please send this link on to your colleagues who are scientists or retired scientists in the field of genetics. Many thanks for your help. Kindest Aarathi Aarathi Prasad, PhD Project Liaison Sense About Science 25 Shaftesbury Avenue London W1D 7EG Reg. Charity No. 1101114 Tel: +44 (0)20 7478 4380 Mob:+44 (0)7737 788 868 www.senseaboutscience.org Sense About Science is a small charity promoting good science and evidence for the public. We depend on donations, large and small, from people who support our work. You can donate, or find out more, at www.senseaboutscience.org/donate From marie-theres.hauser from boku.ac.at Thu Oct 16 12:19:58 2008 From: marie-theres.hauser from boku.ac.at (Marie-Theres Hauser) Date: Thu Oct 16 13:11:06 2008 Subject: [Arabidopsis] Search for the famous MM2d cells Message-ID: <48F793DE0200004600025E24@gwia2.boku.ac.at> Dear Arab-Gen-Netters, Recently our MM2d cell culture faded away and I was wondering if somebody would be willing to send us an aliquot? Our attempt to contact the creators of this cell line (Menges and Murray, TPJ 2002, 30, 203 Synchronous Arabidopsis suspension cultures for analysis of cell-cycle gene activity) was unfortunately unsuccessful. It is possible to send an aliquot in a falcon tube best per the fastest mail possible. We certainly would be willing to pay the transport fee. With the hope that somebody of this community is using this line and willing to share. Marie-Theres Hauser Dr. Marie-Theres Hauser Center of Applied Genetics and Cell Biology BOKU - University of Natural Resources and Applied Life Sciences, Vienna Muthgasse 18 A-1190 Vienna Austria/EUROPE Tel: +43-1-36006-6371 FAX: +43-1-36006-6392 e-mail: marie-theres.hauser@boku.ac.at http://www.boku.ac.at/zag/AG_hauser.htm From braam from rice.edu Fri Oct 17 17:20:53 2008 From: braam from rice.edu (Janet Braam) Date: Mon Oct 20 01:05:50 2008 Subject: [Arabidopsis] Faculty Position at Rice University Message-ID: FACULTY POSITION Rice University Biochemistry and Cell Biology http://www.rice.edu/ Applications are invited for a tenure-track Assistant Professor faculty position within broad areas of biological research, with particular emphasis in the physical properties of biological systems, structure and function of multi-component biomolecular systems, cell and developmental biology of model organisms, synthetic biology, biophysics, and molecular evolution. Applicants using experimental and/or theoretical biological approaches that are interdisciplinary with chemistry, physics, engineering, and computational methods are encouraged to apply. Candidates must have a Ph.D., postdoctoral training, and outstanding potential in research and teaching. Successful candidates are expected to develop and maintain a vigorous research program supported by extramural funding and participate in graduate and undergraduate education. Review of applications will commence Nov. 1, 2008 and continue until the position is filled. Please send letter of application, curriculum vitae, summary of past research, and statement of future research plans, and arrange for four letters of reference to be sent to: Dr. J. Braam, Chair Biochemistry and Cell Biology, MS140 Rice University PO Box 1892 Houston, TX 77251-1892 Rice University is an Equal Opportunity/Affirmative Action Employer; women and minority candidates are especially encouraged to apply. From procha_ac from yahoo.co.uk Fri Oct 17 04:27:10 2008 From: procha_ac from yahoo.co.uk (P. Rocha) Date: Mon Oct 20 01:09:07 2008 Subject: [Arabidopsis] Wanted Nicotiana benthamiana and N. tabacum seeds Message-ID: <303998.86570.qm@web28601.mail.ukl.yahoo.com> Dear Colleagues, I would be grateful to anyone willing to spare a few seeds of N. benthamiana and (or) N. tabacum. Plants will be used for stable and transient transformation experiments (and to get more seeds) and it would be useful if their "pedigree"/variety is known. Thank you, Pedro Rocha procha_ac@yahoo.co.uk Send instant messages to your online friends http://uk.messenger.yahoo.com From sanjaysingh765 from gmail.com Sat Oct 18 10:31:31 2008 From: sanjaysingh765 from gmail.com (chunnu) Date: Mon Oct 20 01:09:58 2008 Subject: [Arabidopsis] e-value Message-ID: <19600f6e-63d4-45ef-b58e-580dd05670fe@a3g2000prm.googlegroups.com> hi all, i have a set of arabidopsis genes ( approx. 100 ) and want to point out their orthologs from oryza sativa.Can anyone suggest me the best method to do this...I was thinking about reciprocal best Basic Local Alignment Search Tool hits (RBH) but I was confused about the parameters especially for e-value.Plz sugggest me the optimal e-value for oorthologs and homologs identification regards From dee.rawsthorne from bbsrc.ac.uk Mon Oct 20 01:18:31 2008 From: dee.rawsthorne from bbsrc.ac.uk (dee rawsthorne (TOC)) Date: Mon Oct 20 15:13:45 2008 Subject: [Arabidopsis] Two-question survey on GM for Sense about Science UK- your help please Message-ID: Apologies if you get this more than once. Dear All We would be grateful if you could help with a two question survey as soon as you are able. You can access the survey here: http://www.surveymonkey.com/s.aspx?sm=8oI2WCuqD5BAdFZIMIvsvg_3d_3d We have put this survey to gather information for our forthcoming publication, Making Sense of GM. It would be extremely helpful if you would please send this link on to your colleagues who are scientists or retired scientists in the field of genetics. Many thanks for your help. Kindest Aarathi Aarathi Prasad, PhD Project Liaison Sense About Science 25 Shaftesbury Avenue London W1D 7EG Reg. Charity No. 1101114 Tel: +44 (0)20 7478 4380 Mob:+44 (0)7737 788 868 www.senseaboutscience.org Sense About Science is a small charity promoting good science and evidence for the public. We depend on donations, large and small, from people who support our work. You can donate, or find out more, at www.senseaboutscience.org/donate From nikhilesh.dhar from gmail.com Mon Oct 20 22:07:17 2008 From: nikhilesh.dhar from gmail.com (Nikhilesh Dhar) Date: Tue Oct 21 15:37:39 2008 Subject: [Arabidopsis] How to identify these defense mutants. Message-ID: <7815a9150810202007m3a5da001of86846740a4dd002@mail.gmail.com> Hi Friends, I have some defense mutants which wwere handed to me by the outgoing post-doc a year back. I want to use them but can any one please suggest how to identify etr1-1/etr1-3/jar1/ndr1/eds1/pad4/npr1 mutants ( for example using PCR based methods). Thanks in advance. Nik On Mon, Oct 20, 2008 at 1:03 PM, wrote: > Send Arab-gen mailing list submissions to > arab-gen@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bio.net/biomail/listinfo/arab-gen > or, via email, send a message with subject or body 'help' to > arab-gen-request@net.bio.net > > You can reach the person managing the list at > arab-gen-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Arab-gen digest..." > > > Today's Topics: > > 1. Faculty Position at Rice University (Janet Braam) > 2. Wanted Nicotiana benthamiana and N. tabacum seeds (P. Rocha) > 3. e-value (chunnu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Oct 2008 17:20:53 -0500 > From: Janet Braam > Subject: [Arabidopsis] Faculty Position at Rice University > To: arab-gen@magpie.bio.indiana.edu > Message-ID: > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > FACULTY POSITION > Rice University > Biochemistry and Cell Biology > http://www.rice.edu/ > > Applications are invited for a tenure-track Assistant Professor > faculty position within broad areas of biological research, with > particular emphasis in the physical properties of biological systems, > structure and function of multi-component biomolecular systems, cell > and developmental biology of model organisms, synthetic biology, > biophysics, and molecular evolution. Applicants using experimental > and/or theoretical biological approaches that are interdisciplinary > with chemistry, physics, engineering, and computational methods are > encouraged to apply. > > Candidates must have a Ph.D., postdoctoral training, and outstanding > potential in research and teaching. Successful candidates are > expected to develop and maintain a vigorous research program > supported by extramural funding and participate in graduate and > undergraduate education. Review of applications will commence Nov. > 1, 2008 and continue until the position is filled. Please send > letter of application, curriculum vitae, summary of past research, > and statement of future research plans, and arrange for four letters > of reference to be sent to: > > Dr. J. Braam, Chair > Biochemistry and Cell Biology, MS140 > Rice University > PO Box 1892 > Houston, TX 77251-1892 > > Rice University is an Equal Opportunity/Affirmative Action Employer; > women and minority candidates are especially encouraged to apply. > > > > ------------------------------ > > Message: 2 > Date: Fri, 17 Oct 2008 09:27:10 +0000 (GMT) > From: "P. Rocha" > Subject: [Arabidopsis] Wanted Nicotiana benthamiana and N. tabacum > seeds > To: arab-gen@magpie.bio.indiana.edu > Message-ID: <303998.86570.qm@web28601.mail.ukl.yahoo.com> > Content-Type: text/plain; charset=utf-8 > > Dear Colleagues, > > I would be grateful to anyone willing to spare a few seeds of N. > benthamiana and (or) N. tabacum. Plants will be used for stable and > transient transformation experiments (and to get more seeds) and it would be > useful if their "pedigree"/variety is known. > > Thank you, > > Pedro Rocha > > procha_ac@yahoo.co.uk > > > > > Send instant messages to your online friends http://uk.messenger.yahoo.com > > ------------------------------ > > Message: 3 > Date: Sat, 18 Oct 2008 08:31:31 -0700 (PDT) > From: chunnu > Subject: [Arabidopsis] e-value > To: bionet-genome-arabidopsis@moderators.isc.org > Message-ID: > <19600f6e-63d4-45ef-b58e-580dd05670fe@a3g2000prm.googlegroups.com> > Content-Type: text/plain; charset=ISO-8859-1 > > hi all, > i have a set of arabidopsis genes ( approx. 100 ) and want to point > out their orthologs from oryza sativa.Can anyone suggest me the best > method to do this...I was thinking about reciprocal best Basic Local > Alignment Search Tool hits (RBH) but I was confused about the > parameters especially for e-value.Plz sugggest me the optimal e-value > for oorthologs and homologs identification > regards > > > > ------------------------------ > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > > End of Arab-gen Digest, Vol 42, Issue 13 > **************************************** > -- With Regards Nikhilesh Dhar From hairong from mtu.edu Wed Oct 22 08:12:22 2008 From: hairong from mtu.edu (Hairong Wei) Date: Wed Oct 22 11:57:55 2008 Subject: [Arabidopsis] Ph.D. Assistantship in Plant Boinformatics In-Reply-To: <361897367.1883341224680858838.JavaMail.root@shupac.merit.edu> Message-ID: <2024951676.1884751224681142210.JavaMail.root@shupac.merit.edu> Ph. D. Graduate Research Assistantship in Plant Bioinformatics A graduate research assistantship at the Ph.D. level is available in the laboratory of Dr. Hairong Wei at School of Forest Resources & Environmental Science, Michigan Technological University (MTU) to develop novel computational approaches for inferring gene function via network construction using gene expression data and other types of genomic data. Other research options like gene expression data analysis, software/database development are potentially available. The selected candidate will acquire training in bioinformatics, and data mining for biological knowledge discovery, and also have chance to learn some essential wetlab techniques for conducting research in molecular biology if he/she is interested in. Applicants should have interest in developing a career in bioinformatics/systems biology. Any of those who have a good background in statistics or computer science or both are encouraged to apply. Strong ability in data manipulation using at least one of programming language like R/SAS, perl, java, and C is anticipated. The candidate should possess the ability to work independently and the attitude to work cooperatively. A background in either machine learning or (molecular) biology will be a plus, though not a requirement. Additional information and requirements can be found at http://forest.mtu.edu/gradstudies/prospecitve.htm Expected starting date: January 2009 Interested candidates should send a resume highlighting their experience and interests, GRE scores (TOEFL is required for international students), names and email addresses of three references to Dr. Hairong Wei (hairong@mtu.edu). Hairong Wei, Ph.D. Assistant Professor of Plant Bioinformatics, and Molecular Biology School of Forest Resources and Environmental Science Michigan Technological University 1400 Townsend Drive, Houghton, MI 49931 Email: hairong@mtu.edu From jagreet.kaur from south.du.ac.in Wed Oct 22 00:03:45 2008 From: jagreet.kaur from south.du.ac.in (jagreet.kaur@south.du.ac.in) Date: Wed Oct 22 11:59:00 2008 Subject: [Arabidopsis] Cvi Cosmid library In-Reply-To: References: Message-ID: > Hello > I am looking for a genomic library for Arabidopsis "ecotype Cvi" in a > binary Cosmid or fosmid vector. If someone has made it and can > share it for research purpose it would be great. > > Otherwise any suggestion on which Binary Cosmid vector should I use > to get the best results? > > looking forward for responses > thanks in advance > > Jagreet jagreetk@yahoo.com From jixiangk from yahoo.com Wed Oct 22 10:08:05 2008 From: jixiangk from yahoo.com (Jixiang Kong) Date: Wed Oct 22 13:55:35 2008 Subject: [Arabidopsis] help Message-ID: <655515.33962.qm@web59805.mail.ac4.yahoo.com> Hi all Does anyone have ideas about root cap development of arabidopsis?? I have got some RNAi lines and find many of them have abnormal on root cap. In addition, I have several?overexpression lines show the abnormal cell division within endodermis. I want some information about it. Thanks a lot! Stone From cxde from iastate.edu Thu Oct 23 09:33:37 2008 From: cxde from iastate.edu (Xi Chen) Date: Thu Oct 23 19:49:11 2008 Subject: [Arabidopsis] did anyone find a mutant of Arabidopsis with the whole green flowers Message-ID: <8af797d40810230733v3b1946b3h4d3700a9e8da7507@mail.gmail.com> Hello researchers, Just like the tile. Any suggestion about this phenotype will be appreciated. Thanks! Best, Xi From Helene.Berges from toulouse.inra.fr Thu Oct 23 09:57:09 2008 From: Helene.Berges from toulouse.inra.fr (=?iso-8859-1?Q?H=E9l=E8ne_Berges?=) Date: Thu Oct 23 19:49:42 2008 Subject: [Arabidopsis] Technician position available at CNRGV France In-Reply-To: <68EE62A7AEFD478BB2C7EBADC30DDFAD@YOUR75A2502B97> References: <68EE62A7AEFD478BB2C7EBADC30DDFAD@YOUR75A2502B97> Message-ID: <009701c9351f$a051e630$1b676393@cnrgv.toulouse.inra.fr> Technician position at the FRENCH PLANT GENOMIC RESOURCE CENTER The French Plant Genomic Resource Centre (CNRGV) is a national platform responsible for preserving and maintaining plant genomic libraries produced in the context of major projects by internationally-renowned laboratories. A technician position is available to participate in the achievement of the main missions of this laboratory including genomic libraries management and screening. See description in the attached file. Applicants should send curriculum vitae, a cover letter describing research experience, interests, and the names and email addresses for at least one reference to: Dr. BERGES : +33 5 61 28 55 65 hberges@toulouse.inra.fr --------------------------------------------------------------------- Dr Helene BERGES Director of the French Plant Genomic Resource Center INRA - CNRGV Chemin de Borde Rouge BP 52627 31326 Castanet Tolosan FRANCE Tel : 33(0) 561 28 55 65 Fax : 33(0) 561 28 55 64 Port : 06 07 95 89 01 Email : hberges@toulouse.inra.fr http://cnrgv.toulouse.inra.fr/ --------------------------------------------------------------------- From huji from msu.edu Wed Oct 22 14:38:09 2008 From: huji from msu.edu (Jianping Hu) Date: Thu Oct 23 19:49:59 2008 Subject: [Arabidopsis] postdoctoral position at Michigan State Message-ID: <200810221937.m9MJbTV21529@net.bio.net> A postdoctoral position is available immediately in the laboratory of Jianping Hu at the MSU-DOE Plant Research Laboratory, Michigan State University. The successful candidate will use proteomics, bioinformatics, cell biology, and reverse genetics to study peroxisomal protein networks in Arabidopsis and follow up newly identified proteins with hypothesis-driven approaches. The applicant should have a PhD degree in biochemistry, molecular biology, genetics, or a related field, and publications in international journals. Prior experience with plant biochemistry and a background or interests in bioinformatics are preferred. Funding is available for two years with the possibility of extension. Interested applicants should email a CV, a brief statement of research experience, and names and contact information of three references to Jianping Hu (huji@msu.edu). From vkalavacharla from desu.edu Thu Oct 23 09:16:41 2008 From: vkalavacharla from desu.edu (Venugopal Kalavacharla) Date: Thu Oct 23 19:50:34 2008 Subject: [Arabidopsis] Postdoctoral position-Plant Molecular Genetics/Genomics/Proteomics-Delaware State University Message-ID: <68EE62A7AEFD478BB2C7EBADC30DDFAD@YOUR75A2502B97> Post Doctoral Research Associate -Plant Molecular Genetics/Plant Genomics/Plant Proteomics Currently accepting applications for a Post Doctoral Research Associate in the Dept. of Agriculture & Natural Resources, Delaware State University, Dover, DE starting in the end of 2008. Please send an email with a current CV/resume, and letter of interest to Dr. Venu Kalavacharla ( vkalavacharla@desu.edu, phone: 302-857-6492). General Description of the Job Applicants for this position will have a Ph.D. in molecular genetics/genomics/proteomics with advanced experience and interest in molecular genetics, genomics, proteomics and plant tissue culture. Experience working with the genetics of plant host-pathogen interactions, construction of genomic and cDNA libraries, RNA interference is an added plus. Essential Functions The following are the functions essential to performing this job. 1. Conduct plant molecular genetics/genomics/proteomics research and manage laboratory, greenhouse and growth room experiments. 2. Communicate effectively with faculty, students, DSU Administrators and professional groups. 3. Provide leadership by encouraging excellence in research, education and outreach activities that are undertaken by the Plant Molecular Genetics & Genomics group. 4. Mentor undergraduate and graduate students, technician, and other laboratory staff in research programs. 5. Serves as a representative for activities of the Plant Molecular Genetics & Genomics group and promote its best interests. Other Functions Individuals in this job may be assigned one or more of the following tasks on a rotating or as-needed basis. 1. Mentor laboratory research personnel including undergraduate and graduate students and technician. 2. High school and Community outreach. 3. Research in area(s) of expertise. Required Knowledge, Skills, and Abilities The individual in this job must possess these skills and abilities or be able to explain and demonstrate that they can perform the essential functions of the job, with or without reasonable accommodation, using some other combination of skills and abilities. 1. Research experience in molecular genetics and genomics 2. Ability to work successfully with diverse students and faculty. 3. Effective written and verbal communication skills. Qualification Standards 1. Earned Ph.D. level degree and work experience in Plant Molecular Biology, Plant Molecular Genetics/Proteomics/Genomics/Plant Pathology/Plant Biology 2. Experience in advanced molecular genetic, genomic and proteomic techniques 3. Not required but added plus: Prior experience in plant tissue culture, host-pathogen interactions and/or working with model or non-model plant species, management of laboratory, greenhouse, and growth room experiments and mentoring students. Performance Standards The criteria for evaluation in this position include, but are not limited to, the following: 1. Successful completion of the tasks listed as essential functions. 2. Publication and professional presentations. 3. Lab management and mentoring abilities. Delaware State University is an equal opportunity employer and does not discriminate because of race, creed, national or ethnic origin, sex or disability. Venu (Kal) Kalavacharla Ph.D. Plant Molecular Genetics & Genomics Department of Agriculture & Natural Resources Delaware State University Dover, DE 19901 Ph:(302) 857-6492 Fax:(302) 857-6402 Email: vkalavacharla@desu.edu From jaiswalp from science.oregonstate.edu Fri Oct 24 14:31:04 2008 From: jaiswalp from science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Fri Oct 24 15:43:56 2008 Subject: [Arabidopsis] Postdoctoral Fellow and Software Developer Positions in Comparative Genomics and Systems Biology Message-ID: <49022278.4030301@science.oregonstate.edu> Postdoctoral Fellow and Software developer positions in Comparative Genomics and Systems Biology Jaiswal lab at Oregon State University (http://www.oregonstste.edu) is seeking talented and motivated candidates for current and future job openings as postdoctoral fellows and software developers in the systems biology and bioinformatics. The successful candidates are expected to have either or both the experience of working in a biology wet lab and/or bioinformatics, computational biology lab. The successful candidate(s) will collaborate with researchers from Biochemistry, Molecular Biology, Plant Development, Genetics and Systems Biology programs. Postdoctoral applicants must have a Ph.D. (or equivalent degree) in biology, bioinformatics, molecular biology, biochemistry, genetics, computational biology or related fields, and some demonstrated experience in computer science/bioinformatics. For the computational biologists and software developer positions in addition to their experience and interest in biology, expertise in at least one scientific programming language and relational data management system is preferred. Candidates with experience in network analysis methods are encouraged to apply. Candidates with BS/MS degrees are also encouraged to apply for future positions in the lab. Interested individuals should send or email letter of intent/cover letter , CV/Resume with contact info of three references, and a 1-2 page description of previous accomplishments to the following address. E mail is preferred. Pankaj Jaiswal, Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA Email: jaiswalp@science.oregonstate.edu From pj37 from cornell.edu Fri Oct 24 12:40:55 2008 From: pj37 from cornell.edu (Pankaj Jaiswal) Date: Fri Oct 24 15:44:24 2008 Subject: [Arabidopsis] Pathway database curator position at Gramene Message-ID: <490208A7.5040401@cornell.edu> http://bivouac.cshl.edu/gramene-news/?p=44 A full time 3-year pathway database curator position at the Research Associate or Postdoctoral Associate level is available immediately in Dr. Pankaj Jaiswal’s group at the Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR (http://www.science.oregonstate.edu/bpp/). This position is required to develop a comprehensive catalog of rice and other cereal plant metabolic pathways and enzymes. The project expands the coverage of metabolic pathways from Rice (http://gramene.org/pathway/) to all known pathways in major cereal plants such as for maize, sorghum and wheat. The curator will be responsible for development, curation and maintenance of the Pathways section on Gramene Database (http://www.gramene.org) in following ways. i) Develop novel methods on annotating the metabolic and regulatory pathway associations to the genomic and genetic datasets. ii) Research new plant metabolic pathways and enzymes in the scientific literature, and to evaluate, extract, organize, and enter that information to the database; iii) Development /improvement of new or existing standard procedures and operation rules on curation methods and to the general development of the database, such as data integration, web page enhancement, and data exchange with database namely the www.reactome.org. iv) Communicating with the research community to improve the quality of the data, to train them in using the database and related tools, and to support user requests. The successful candidates will work with Gramene database team that includes highly trained PhD. level bioinformatics specialists and software developers. The person will also work with collaborator databases such as Rice Genome Annotation Project, MaizeGDB, GrainGenes, MetaCyc, PlantCyc, AraCyc, SolCyc, and a number of pioneering plant biochemists from around the world. Qualified candidates should have a Ph.D. degree or equivalent in biochemistry, biological chemistry, metabolomics, or related field preferably in plants, but not necessarily. The successful candidate should also have a demonstrated ability for independent and critical thinking, excellent communication skills and enjoy teamwork. Experience with Lynux and Windows operating system, Perl, Java and HTML editing is desirable. Please send an email with a current CV/resume, and letter of interest to Pankaj Jaiswal (jaiswalp@oregonstate.edu). Oregon State University is an equal opportunity employer (EOE). -- Pankaj Jaiswal Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA Ph.: +1-541-737-8471 Fax: +1-541-737-3573 Web: www.gramene.org www.plantontology.org From xiang.m.xu from uis.no Fri Oct 24 01:34:23 2008 From: xiang.m.xu from uis.no (xiang.m.xu@uis.no) Date: Fri Oct 24 15:44:50 2008 Subject: [Arabidopsis] Wanted Nicotiana benthamiana and N. tabacum seeds Message-ID: Tell me your address. I can send your some N.tabacum Havana seeds. From pj37 from cornell.edu Fri Oct 24 16:07:01 2008 From: pj37 from cornell.edu (Pankaj Jaiswal) Date: Fri Oct 24 16:18:15 2008 Subject: [Arabidopsis] Pathway database curator position at Gramene In-Reply-To: <490208A7.5040401@cornell.edu> References: <490208A7.5040401@cornell.edu> Message-ID: <490238F5.6060104@cornell.edu> e-mail address correction. Please send the application material at the following address jaiswalp@science.oregonstate.edu Thanks Pankaj Pankaj Jaiswal wrote: > http://bivouac.cshl.edu/gramene-news/?p=44 > > A full time 3-year pathway database curator position at the Research > Associate or Postdoctoral Associate level is available immediately in > Dr. Pankaj Jaiswal’s group at the Department of Botany and Plant > Pathology, Oregon State University, Corvallis, OR > (http://www.science.oregonstate.edu/bpp/). This position is required to > develop a comprehensive catalog of rice and other cereal plant metabolic > pathways and enzymes. The project expands the coverage of metabolic > pathways from Rice (http://gramene.org/pathway/) to all known pathways > in major cereal plants such as for maize, sorghum and wheat. The curator > will be responsible for development, curation and maintenance of the > Pathways section on Gramene Database (http://www.gramene.org) in > following ways. > > i) Develop novel methods on annotating the metabolic and regulatory > pathway associations to the genomic and genetic datasets. > ii) Research new plant metabolic pathways and enzymes in the > scientific literature, and to evaluate, extract, organize, and enter > that information to the database; > iii) Development /improvement of new or existing standard procedures > and operation rules on curation methods and to the general development > of the database, such as data integration, web page enhancement, and > data exchange with database namely the www.reactome.org. > iv) Communicating with the research community to improve the quality > of the data, to train them in using the database and related tools, and > to support user requests. > > The successful candidates will work with Gramene database team that > includes highly trained PhD. level bioinformatics specialists and > software developers. The person will also work with collaborator > databases such as Rice Genome Annotation Project, MaizeGDB, GrainGenes, > MetaCyc, PlantCyc, AraCyc, SolCyc, and a number of pioneering plant > biochemists from around the world. > > Qualified candidates should have a Ph.D. degree or equivalent in > biochemistry, biological chemistry, metabolomics, or related field > preferably in plants, but not necessarily. The successful candidate > should also have a demonstrated ability for independent and critical > thinking, excellent communication skills and enjoy teamwork. Experience > with Lynux and Windows operating system, Perl, Java and HTML editing is > desirable. Please send an email with a current CV/resume, and letter of > interest to Pankaj Jaiswal (jaiswalp@oregonstate.edu). Oregon State > University is an equal opportunity employer (EOE). > > From anirbanb from ncbs.res.in Mon Oct 27 03:46:11 2008 From: anirbanb from ncbs.res.in (Anirban Baral) Date: Mon Oct 27 11:19:45 2008 Subject: [Arabidopsis] Golgi specific dye. Message-ID: <42732.192.168.1.1.1225097171.squirrel@mail.ncbs.res.in> Hi Arabineters, I am looking for a dye/marker that specifically marks Golgi(the idea is to separate golgi & exosomes from endosomes). I shall be grateful if you please give some suggestions. Regards Anirban -- Anirban Baral JUNIOR SCHOLAR NATIONAL CENTRE FOR BIOLOGICAL SCIENCES TATA INSTITUTE OF FUNDAMENTAL RESEARCH UAS-GKVK CAMPUS,BELLARY ROAD BANGALORE-560065,INDIA From nikhilesh.dhar from gmail.com Mon Oct 27 14:18:27 2008 From: nikhilesh.dhar from gmail.com (Nick) Date: Mon Oct 27 21:31:19 2008 Subject: [Arabidopsis] Re: Arab-gen Digest, Vol 42, Issue 19 In-Reply-To: <200810271703.m9RH3ZV14836@net.bio.net> References: <200810271703.m9RH3ZV14836@net.bio.net> Message-ID: <7815a9150810271218t56afe112v5d07d4f9ad569f34@mail.gmail.com> Hi, Anirban look into invitrogen site.they have some golgi and ER marker for plants. Cheers, Nikhil On Mon, Oct 27, 2008 at 1:03 PM, wrote: > Send Arab-gen mailing list submissions to > arab-gen@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bio.net/biomail/listinfo/arab-gen > or, via email, send a message with subject or body 'help' to > arab-gen-request@net.bio.net > > You can reach the person managing the list at > arab-gen-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Arab-gen digest..." > > > Today's Topics: > > 1. Golgi specific dye. (Anirban Baral) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 27 Oct 2008 14:16:11 +0530 (IST) > From: "Anirban Baral" > Subject: [Arabidopsis] Golgi specific dye. > To: arab-gen@magpie.bio.indiana.edu > Message-ID: <42732.192.168.1.1.1225097171.squirrel@mail.ncbs.res.in> > Content-Type: text/plain;charset=iso-8859-1 > > Hi Arabineters, > > I am looking for a dye/marker that specifically marks Golgi(the idea is to > separate golgi & exosomes from endosomes). > I shall be grateful if you please give some suggestions. > > Regards > > Anirban > > > -- > Anirban Baral > JUNIOR SCHOLAR > NATIONAL CENTRE FOR BIOLOGICAL SCIENCES > TATA INSTITUTE OF FUNDAMENTAL RESEARCH > UAS-GKVK CAMPUS,BELLARY ROAD > BANGALORE-560065,INDIA > > > > ------------------------------ > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > > End of Arab-gen Digest, Vol 42, Issue 19 > **************************************** > -- With Regards Nikhilesh Dhar From adamisle from hotmail.com Tue Oct 28 10:14:14 2008 From: adamisle from hotmail.com (adamisle@hotmail.com) Date: Tue Oct 28 12:08:26 2008 Subject: [Arabidopsis] Plant Biologist (Bioinformatics) and Field Application Specialists jobs Message-ID: <435fe1e6-25f9-4390-a012-1a541be48c06@s9g2000prg.googlegroups.com> Dear bionet.genome.arabidopsis user group, My name is Adam Isle and I¡¦m the Director of Hudson Shribman Scientific Recruitment, based in London. I¡¦m not sure whether this user group is usually open to postings about job opportunities, but as I didn¡¦t see any guidance on this subject I thought I¡¦d make contact ¡V I hope that¡¦s okay. Hudson Shribman Scientific Recruitment is currently working with two companies who are seeking to recruit scientists with experience of working on array data. One of these positions is based in the United Kingdom in Cambridgeshire. The post is working for a plant biotech company who are looking to recruit a junior management grade microarray plant biologist. This position offers a competitive salary, great benefits package and international relocation support for those needing to move to take up the job. It's antry level management grade job with good career prospects. There is also a Field Applications Specialist role available for a Germany/ Netherlands based scientist. This post is working for a leading provider of computer based scientific solutions. Again, a decent salary and competitive benefits package is offered, but relocation support isn't on offer for this role. If someone involved in this user group is interested in finding out more about any of these positions I¡¦d be happy to provide additional information. Please contact me either by email (ideally including an up to date CV/ resume) me at: adam.isle@hs-scientific.co.uk Or, call me directly on: +44 (0)207 421 5232 or +44 (0)7875 686 226. In the event that these jobs aren¡¦t personally of interest but you might know of someone who would be keen to hear about them, please feel free to forward on my email/ contact details. Finally, if these jobs aren¡¦t of interest but you¡¦d be keen to hear about future positions that Hudson Shribman handle please get in touch and I¡¦d be happy to help. Once again, I hope that this email isn¡¦t unwelcome, or an intrusion. Kind regards, Adam Isle Director HUDSONSHRIBMAN s c i e n t i f i c r e c r u i t m e n t T: +44 (0)207 421 5232 (direct) M: +44 (0)7875 686 226 E: adam.isle@hs-scientific.co.uk W: www.hs-scientific.co.uk Vernon House, Sicilian Ave, London, WC1A 2QS ƒÀ Please consider the environment before printing this e-mail From eblancaflor from noble.org Tue Oct 28 10:26:42 2008 From: eblancaflor from noble.org (Blancaflor, Elison) Date: Tue Oct 28 12:09:56 2008 Subject: [Arabidopsis] RE: job posting In-Reply-To: 200810271703.m9RH3eV14849@net.bio.net References: 200810271703.m9RH3eV14849@net.bio.net Message-ID: <497D588A106806408FB0792E4E9A165801B2E4E1@mail2.noble.org> A colleague requested that I post the job opportunities below. Please contact Dr. Mary Fernandes at Monsanto directly if anyone has questions about the advertised positions. Dr. Mary Fernandes Model Systems Lead Monsanto Biotechnology Chesterfield, MO 63017 e-mail: mary.fernandes@monsanto.com MS position (microscopy)--# 8520 MONS - 00008520 Responsibilities: We are seeking a highly talented and experienced scientist with expertise in one or more of the following areas: Molecular Biology, Biochemistry, Cell Biology or Plant Biology/Development. The individual will be part of a larger multi-disciplinary effort aimed at developing methods for discovery and advancing the knowledge base around high priority leads in our crop pipeline. Successful applicants will work in a team based environment, manage individual project(s) and interact cross functionally within the organization. Required Skills: Applicants should have a degree in Plant Biology, Molecular Biology, Cell Biology, Biochemistry, or other related field with five plus years of laboratory experience (BS candidates) or a minimum of 1-2 years of laboratory experience (MS candidates). Proven expertise in molecular biology and/or cell biology is desired. Specific expertise in working with proteins and/or nucleic acids is required. Demonstrated skills in Cell Biology (eg. microscopy) or Plant Biology (eg. cell culture, transient systems, model systems, plant physiology) will be advantageous. Familiarity with routine bioinformatics tools used in the above fields is desirable. The successful candidate will be a highly motivated and results-oriented team player with excellent oral and written communication skills and project championship ability. PhD position Mol. Biologist - # 9321 Ph.D position Mol. Biology/Cell Biology Responsibilities: We are seeking a highly talented and experienced scientist with expertise in Molecular Biology and/or Cell Biology to be part of a larger multi-disciplinary effort aimed at developing methods for discovery and advancing the knowledge base around high priority leads in our crop pipeline. The individual will work in a team based environment while managing independent project(s) and interacting cross functionally within the organization. Required Skills: Successful candidates will have a PhD degree in Molecular Biology, Cell Biology or other related field with overall five plus years of laboratory experience. A solid background in imaging technologies including fluorescence/confocal microscopy and/or molecular biology technologies such as cloning is required. Preference will be given to candidates with strong computational/bioinformatics skills. The ideal candidate will also have excellent oral and written communication skills, project leadership ability and be highly motivated and results-oriented. From lcourtneysmith from gmail.com Tue Oct 28 13:21:25 2008 From: lcourtneysmith from gmail.com (L. Courtney Smith) Date: Wed Oct 29 00:38:44 2008 Subject: [Arabidopsis] Re: tenure track faculty position Message-ID: <660183310810281121v4df51981p11850c110bd985f7@mail.gmail.com> Please post the following advertisement. Thanks. ____________________________________________ TENURE TRACK FACULTY POSITION in MOLECULAR BIOLOGY The Department of Biological Sciences invites applications for a tenure track Assistant Professor for September, 2009. We are seeking a broadly trained scientist interested in the *molecular biology of organismal interactions*. Research could include, but is not limited to, immunology, parasitology, plant-microbe interactions, or symbiosis. Research conducted in an evolutionary context will be preferred. We seek a scientist who will strengthen and expand the research and teaching within the department (see www.gwu.edu/~biology). The successful candidate will develop or maintain an externally funded research program that involves graduate and undergraduate students. Teaching will include an undergraduate lab course in molecular biology and second course within the candidate's area of expertise. A completed PhD and postdoctoral experience is required. Review of applications will begin November 16, 2008 and will be ongoing until the position is filled. Application procedure: interested candidates should submit electronically 1) a letter of application, 2) a CV, 3) a brief description of research interests including past accomplishments and future plans, 4) a statement of teaching plans including a description of courses that could be taught, and 5) up to three publications. Candidates should arrange for three letters of recommendation to be sent to: Molecular Biology Search Chair Department of Biological Sciences 340 Lisner Hall 2023 G Street NW The George Washington University Washington DC 20052 e-mail: mbsearch@gwu.edu Phone: 202 994-6090 Only complete applications will be considered. GWU is an equal opportunity/affirmative action employer. The search committee seeks to attract an active, culturally and academically diverse faculty of the highest caliber. __________________________________________ -- L. Courtney Smith, PhD Professor 340 Lisner Hall (mailbox) 414 Lisner Hall (office) Department of Biological Sciences George Washington University 2023 G St NW Washington DC 20052 202-994-9211; office 202-994-6100; fax www.gwu.edu/~clade/faculty/smith/ From Andrew.T.Reid from studentmail.newcastle.edu.au Thu Oct 30 03:39:41 2008 From: Andrew.T.Reid from studentmail.newcastle.edu.au (Andrew.T.Reid@studentmail.newcastle.edu.au) Date: Thu Oct 30 13:57:47 2008 Subject: [Arabidopsis] Re: GFP Construct Message-ID: Dear Arabidopsis Researchers I am looking for help to locate a transgenic Arabidopsis line(s) espressing a GFP fusion with a known transmembrane protein (any will do) that places the the GFP on the outside of the plasma membrane (ie expoed to apoplasm), preferably driven by the 35S promoter. In the absence of transgenic lines, access to a construct with these characteristics would also be fine. I would be very grateful if anyone can point me on the direction of such materials. Many thanks in advance, yours sincerely Andrew Reid. From bahauser from botany.ufl.edu Wed Oct 29 11:43:32 2008 From: bahauser from botany.ufl.edu (Bernard Hauser) Date: Thu Oct 30 13:58:31 2008 Subject: [Arabidopsis] Evo-Devo. Faculty Position Message-ID: Search for a Plant Evolutionary Developmental Biologist The Department of Biology (comprising the newly merged departments of Botany and Zoology) at the University of Florida invites applications for a 9-month tenure-track faculty position in Plant Evolutionary Developmental Genetics at the level of Assistant Professor, effective fall semester, 2009. We offer a collegial environment that fosters collaborative, interdisciplinary research. Individuals examining plant developmental morphology and its genetic control in a comparative and/or evolutionary context are especially encouraged to apply. Instruction at both undergraduate and graduate levels is expected, including a course in plant anatomy/ morphology, and also genetics and/or involvement in introductory biology. Successful applicants must have a Ph.D. and postdoctoral experience. Our faculty enjoy strong ties with the Plant Molecular and Cellular Biology Program, UF Genetics Institute, UF Emerging Pathogens Institute, the Florida Museum of Natural History, and multiple University centers in biomedical, veterinary, environmental and agricultural sciences. Applicants should submit an electronic application consisting of a cover letter, curriculum vitae, statements of research and teaching interests, and three reprints; please go to http://www.biology.ufl.edu/search/. Applicants should also arrange to have three letters of reference mailed to Plant Evolutionary Developmental Genetics Search, PO Box 118525, University of Florida, Gainesville, FL USA, 32611-8525. Review of applications will begin on January 12th, 2008 and will continue until the position is filled. Our department is committed to diversity as a component of excellence. Women and members of under-represented groups are particularly encouraged to apply. The University of Florida is an equal opportunity institution. From jim_jianjunguo from yahoo.ca Wed Oct 29 23:24:06 2008 From: jim_jianjunguo from yahoo.ca (Jim GUO) Date: Thu Oct 30 13:59:29 2008 Subject: [Arabidopsis] Germination problem with Arabidopsis arenosa Message-ID: <981362.93323.qm@web56303.mail.re3.yahoo.com> Dear all, > > > In my lab, we tried to germinate *Arabidopsis arenosa* > recently. > > However, we couldn't get any germination so far. > > I was wondering if anyone has any idea about how to > germinate *A. arenosa*. > > We will be very appreciated for any information from you. > > > > Thanks a lot, > > Allen Liu > > Dept. Botany UBC __________________________________________________________________ Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark your favourite sites. Download it now at http://ca.toolbar.yahoo.com. From maria from acero.ca Wed Oct 29 13:01:58 2008 From: maria from acero.ca (Maria Acero) Date: Thu Oct 30 14:00:09 2008 Subject: [Arabidopsis] Looking for primers Message-ID: <2f1ae9160810291101if9fc0f9teda8081138c5c1f1@mail.gmail.com> Hello, I am a master student working on a mapping project. I am looking for markers in chromosome I between 12Mbp and the centromere. I have tried designing my own primers in this region using SNPs, but when I try them they show the same size for the Col and Ler bands. If someone could please give me information on markers that show differente band sizes for Col and Ler in this region, it would be greatly appreciated. Thanks, Maria Acero From rscholl from wowway.com Fri Oct 31 11:40:36 2008 From: rscholl from wowway.com (rscholl@wowway.com) Date: Fri Oct 31 12:28:35 2008 Subject: [Arabidopsis] Assistant Professor, two positions - Ohio State Univ. Message-ID: <20081031163629.M47932@wowway.com> Tenure-Track Faculty Positions, The Dept. of Plant Cellular and Molecular Biology and the Dept. of Molecular Genetics, Ohio State University The Department of Plant Cellular and Molecular Biology and the Department of Molecular Genetics, in conjunction with the Plant Molecular Biology/Biotechnology program (PMBB), invite applications for two full-time, tenure-track positions at the Assistant Professor level. These positions are part of the new Translational Plant Sciences emphasis within OSU?s Targeted Investment in Excellence initiative. Successful applicants are expected to develop an outstanding and novel research program and demonstrate a commitment to teaching at the undergraduate and graduate levels. Applicants with expertise in any area of plant molecular, cellular, and developmental biology are encouraged to apply. Potential areas of emphasis include plant biochemistry, genomics, systems biology, and biotechnology that focuses on fundamental processes related to bioenergy, bioproducts, and carbon sequestration. This research is intended to enhance fuel, food, human health and/or environmental quality through the use of eukaryotic photosynthetic organisms. Departmental faculty members participate in numerous campus-wide programs, centers, and focus groups including PMBB, the Plant Biotechnology Center, the Molecular Plant-Microbe Interaction Group, the Cell Biology Group, the Developmental Genetics Group, the Center for RNA Biology, the Institute for Energy and the Environment, the Arabidopsis Biological Resource Center, and the Mathematical Biosciences Institute. The Ohio State University is the flagship institution of the state's higher education system. It is located in Columbus, the state capital. Columbus is a rapidly growing and vibrant large city with a village flavor, and has been ranked as one of the country's best places to live and work. Further information about the departments, PMBB, the university, and Columbus can be obtained at http://www.biosci.ohio-state.edu/~plantbio/ (Plant Cellular and Molecular Biology), http://www.osumolgen.org (Molecular Genetics), and http://www.ag.ohio-state.edu/~pmbb/ (PMBB). Candidates with a Ph.D. and suitable postdoctoral experience can submit applications to pbsearch@biosci.osu.edu as a single PDF file that includes a curriculum vitae, a concise (3 pages or less) statement of research plans, a brief description of teaching experience and interests, and names of at least 3 professional references. A PDF is preferred, but paper copies may be sent to Search Committee Chair, Dept. of Plant Cellular and Molecular Biology, Ohio State University, 500 Aronoff Laboratory, 318 West 12th Ave., Columbus, OH 43210-1242. Review of applications will begin November 30, 2008 and will continue until a suitable candidate is identified. The Ohio State University is an EEO/AA Employer. To build a diverse workforce Ohio State encourages applications from individuals with disabilities, minorities, veterans, and women. Flexible work options available. From d-k.lee from utah.edu Fri Oct 31 12:57:43 2008 From: d-k.lee from utah.edu (Dong-Keun Lee) Date: Sat Nov 1 02:00:12 2008 Subject: [Arabidopsis] Asking whole mount in situ hybridization with seedling Message-ID: Hi I am doing whole mount in situ hybridization with 2 day old seedling. Every time, I got strong non-specific signals in mature regions of roots, hypocotyls, and cotyledons. I am wondering it is common or there is some tip to reduce the non-specific signals? Dk Lee