From conferences from embl.de Tue May 5 03:54:33 2009 From: conferences from embl.de (EMBL Courses & Conferences) Date: Tue May 5 17:40:25 2009 Subject: [Arabidopsis] EMBO Conference Series on Protein Synthesis and Translational Control Message-ID: <200905050852.n458qfb14353@net.bio.net> Dear Colleagues, EMBO Conference Series on Protein Synthesis and Translational Control Partnered with the "CSHL Meeting on Translational Control" EMBL Heidelberg, Germany, 9 - 13 September 2009 This is to alert you of the upcoming registration and abstract deadline 1 June 2009, which is less than 1 month away. There will be no deadline extension possible, because the organizers meet soon after the deadline to discuss the session allocations of the submitted abstracts. From the registrations that we have had already and based on the success of the 2005 and 2007 meetings here in Heidelberg, this will be a very popular meeting for which we will need to limit participation to a maximum of 300 attendees. The time of registration will be an admission criterium in case that the meeting is oversubscribed. We invite you to register and submit your abstract as soon as possible via http://www.embl.de/conferences/TransControl/2009 Looking forward to welcoming you in September! Anne, Marina, Nahum and Matt For further inquiries, please contact: EMBL Course and Conference Office Bettina Schaefer Meyerhofstr. 1 69117 Heidelberg email: schaefer@embl.de phone: +49-6221-387-8836 If you do not wish to receive any further information about events taking place at EMBL, please reply with "unsubscribe" in the subject. From jaiswalp from science.oregonstate.edu Thu May 7 02:21:16 2009 From: jaiswalp from science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Thu May 7 12:05:53 2009 Subject: [Arabidopsis] PlantGeneWiki Beta release Message-ID: <4A028BEC.6080803@science.oregonstate.edu> From http://news.gramene.org/?p=220 PlantGeneWiki Beta release Posted on May 6, 2009, 5:40 PM, by pankaj, under Community news, Database release, Gramene, Gramene news. The Gramene database project team is happy to announce beta release of the PlantGeneWiki. It is designed as an online community portal on plant genes and their annotations. Our goal for PlantGeneWiki is to generate community curated/annotated pages where the researchers can browse, search, read and manage the content by editing. Yes, the biggest advantage of them all is that researchers now have the ability to update and edit the information known about the genes identified in plants on their own without any delays. If you don’t find a gene of your interest in the PlantGeneWiki, you can add it as well. Any content you add/edit on PlantGeneWiki is released for instant online access and cites your contribution. Therefore a good starting place is to add/edit information on known genes. PlantGeneWiki is freely accessible to everyone and you can help us make it better in following ways: * Share your knowledge by EDITING existing and/or ADDING new information to the existing gene pages. * Adding NEW GENE PAGES. * Adding links. * Correct and report our errors. We encourage first time users to get familiarized with the portal and user/contributor functions by taking the Guided Tours/Tutorials. The PlantGeneWiki website can be accessed from any of the following URL’s. http://plantgenewiki.gramene.org/ http://plantgenewiki.org/ Pankaj Jaiswal Web: www.gramene.org www.plantontology.org -- 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 sujata from unipune.ernet.in Thu May 7 12:03:42 2009 From: sujata from unipune.ernet.in (Dr. Sujata Bhargava (Faculty@Botany)) Date: Thu May 7 12:06:16 2009 Subject: [Arabidopsis] (no subject) Message-ID: <2147.59.95.29.112.1241715822.squirrel@unipune.ernet.in> Dear Colleagues, I wish to know how I can derive the sequence of mature miRNA (~20nt) from pre-miRNA sequence (70-100nt). Thanks, Sujata From csgasser from ucdavis.edu Thu May 7 12:14:18 2009 From: csgasser from ucdavis.edu (Charles S. Gasser) Date: Thu May 7 12:17:56 2009 Subject: [Arabidopsis] Optimal germination of older Arabidopsis seeds Message-ID: Dear Arabidopsis community, We have some quite old Arabidopsis seed that appears to have largely lost viability - i. e. when sown on pots or plates they fail to germinate even when first stratified. Does anyone have suggestions for optimal/improved conditions for germination of such seeds? Workers on other species have suggested soaking in a GA solution or scratching the seed (I was thinking this might be accomplished by shaking them briefly with carborundum powder). Does anyone have experience with these or other methods to allow perhaps weaked survivors to germinate? Post to the group or e-mail me directly and if I get multiple answers I will post a summary. -- ======================================= Charles S. Gasser Professor Dept. of Molecular and Cellular Biology University of California, Davis 1 Shields Ave. Davis, CA 95616 104 Briggs Hall csgasser@ucdavis.edu http://www.mcb.ucdavis.edu/faculty-labs/gasser/gasser-lab.html Tel. 530 752-1013 FAX 530 752-3085 From cohen047 from umn.edu Thu May 7 12:53:12 2009 From: cohen047 from umn.edu (Jerry D. Cohen) Date: Thu May 7 14:26:24 2009 Subject: [Arabidopsis] Optimal germination of older Arabidopsis seeds In-Reply-To: References: Message-ID: <4A032008.9010006@umn.edu> I am not sure about the scratching working with older seeds, but here my colleagues use GA4 to induce germination with Arabidopsis in total darkness (works better than GA3). From our work years ago with long dormant seeds, I would guess that would be your best bet. Regards, Jerry Charles S. Gasser wrote: > Dear Arabidopsis community, > We have some quite old Arabidopsis seed that appears to have largely > lost viability - i. e. when sown on pots or plates they fail to > germinate even when first stratified. > > Does anyone have suggestions for optimal/improved conditions for > germination of such seeds? Workers on other species have suggested > soaking in a GA solution or scratching the seed (I was thinking this > might be accomplished by shaking them briefly with carborundum > powder). Does anyone have experience with these or other methods to > allow perhaps weaked survivors to germinate? > > Post to the group or e-mail me directly and if I get multiple answers > I will post a summary. -- ==================================================== Dr. Jerry D. Cohen, Professor, Bailey Endowed Chair University of Minnesota Department of Horticultural Science and Microbial and Plant Genomics Institute 1970 Folwell Ave., 305 Alderman Hall Saint Paul, MN 55108 Phone 612.624.9212; FAX 612.624.4941 Lab phone 612.624.1218 Email cohen047@tc.umn.edu Web: http://horticulture.cfans.umn.edu/Jerry_Cohen.html ===================================================== "By three methods we may learn wisdom: First by reflection, which is noblest; second by imitation, which is easiest; and third by experience, which is the bitterest. - Confucius From huq from mail.utexas.edu Thu May 7 12:57:12 2009 From: huq from mail.utexas.edu (Enamul Huq) Date: Thu May 7 14:27:07 2009 Subject: [Arabidopsis] POSTDOCTORAL POSITION AT UT AUSTIN Message-ID: A postdoctoral position is available for two years to work on the phytochrome-interacting basic helix-loop-helix (bHLH) transcription factor (PIF1) that is involved in controlling photomorphogenesis in Arabidopsis. The research involves understanding the mechanisms of regulation of PIF1 by light using biochemical, genetic and genomic approaches. Applicants should have a recent Ph.D. in molecular genetics or biochemistry. Prior experience in Arabidopsis is advantageous but not essential. Salary and benefits will be competitive and commensurate with experience. Interested applicants should send a CV, brief summary of research experience, and names and email addresses of at least three referees preferably by email to huq@mail.utexas.edu. The University of Texas at Austin is an affirmative action, equal opportunity employer committed to excellence through diversity. Interested applicants are encouraged to look at recent papers from our lab: 1. Castillon, A., Shen, H. and Huq, E. (2009) Blue light induces degradation of the negative regulator Phytochrome Interacting Factor 1 to promote photomorphogenic development of Arabidopsis seedlings. Genetics 182:161-171. 2. Leivar, P., Monte, E., Oka, Y., Liu, T., Carle, C., Castillon, A., Huq, E. and Quail, P.H. (2008) Multiple phytochrome-interacting bHLH transcription factors repress premature seedling photomorphogenesis in darkness. Current Biology 18:1815-1823. 3. Shen, H., Ling, Z., Castillon, A., Majee, M., Downie, B. and Huq, E. (2008) Light-induced phosphorylation and degradation of the negative regulator PIF1 depends upon its direct physical interactions with photoactivated phytochromes. Plant Cell 20:1586-1602. 4. Moon, J., Zhu, L., Shen, H. and Huq, E. (2008) PIF1 directly and indirectly regulates chlorophyll biosynthesis to optimize the greening process in Arabidopsis. Proc. Natl. Acad. Sci. USA 105: 9433-9438. 5. Shen, H., Luong, P. and Huq, E. (2007) The F-box protein MAX2 functions as a positive regulator of photomorphogenesis in Arabidopsis. Plant Physiology 145: 1471-1483. 6. Castillon, A., Shen, H. and Huq, E. (2007) Phytochrome Interacting Factors: central players in phytochrome-mediated light signaling networks. Trends Plant Sci. 12: 514-521. *********************************************** Enamul Huq Assistant Professor Molecular Cell and Developmental Biology University of Texas at Austin 1 University Station, A6700 Austin, TX 78712. Phone: 512-471-9848 Fax: 512-232-3402 http://www.sbs.utexas.edu/huq/lab For express mail: Enamul Huq Molecular Cell and Developmental Biology University of Texas at Austin Bio Labs #311 205 W. 24th St. Austin, TX 78712. ********************************************** From cohen047 from umn.edu Thu May 7 15:51:32 2009 From: cohen047 from umn.edu (Jerry D. Cohen) Date: Thu May 7 18:06:51 2009 Subject: [Arabidopsis] Optimal germination of older Arabidopsis seeds In-Reply-To: References: <4A032008.9010006@umn.edu> Message-ID: <4A0349D4.9040900@umn.edu> Yes, of course, I should have said 'my colleagues who wish to germinate seeds in darkness' use GA4. Light + GA is better. I will add that GA4 is also preferred over the 4+7 mixture, but either is choice is better than GA3. Thanks for the chance for clarification, Jerry PEETAMBAR DAHAL wrote: > Light should be better than total darkness to enable germination of the > viable fraction of seeds in the presence of GA4+7. > > Peetambar Dahal > > -----Original Message----- > From: arab-gen-bounces@oat.bio.indiana.edu > [mailto:arab-gen-bounces@oat.bio.indiana.edu] On Behalf Of Jerry D. > Cohen > Sent: Thursday, May 07, 2009 10:53 AM > To: Charles S. Gasser > Cc: arab-gen@magpie.bio.indiana.edu > Subject: Re: [Arabidopsis] Optimal germination of older Arabidopsis > seeds > > I am not sure about the scratching working with older seeds, but here my > > colleagues use GA4 to induce germination with Arabidopsis in total > darkness (works better than GA3). From our work years ago with long > dormant seeds, I would guess that would be your best bet. Regards, Jerry > > Charles S. Gasser wrote: > >> Dear Arabidopsis community, >> We have some quite old Arabidopsis seed that appears to have largely >> lost viability - i. e. when sown on pots or plates they fail to >> germinate even when first stratified. >> >> Does anyone have suggestions for optimal/improved conditions for >> germination of such seeds? Workers on other species have suggested >> soaking in a GA solution or scratching the seed (I was thinking this >> might be accomplished by shaking them briefly with carborundum >> powder). Does anyone have experience with these or other methods to >> allow perhaps weaked survivors to germinate? >> >> Post to the group or e-mail me directly and if I get multiple answers >> I will post a summary. >> > > PEETAMBAR DAHAL wrote: > Light should be better than total darkness to enable germination of the > viable fraction of seeds in the presence of GA4+7. > > Peetambar Dahal > > -----Original Message----- > From: arab-gen-bounces@oat.bio.indiana.edu > [mailto:arab-gen-bounces@oat.bio.indiana.edu] On Behalf Of Jerry D. > Cohen > Sent: Thursday, May 07, 2009 10:53 AM > To: Charles S. Gasser > Cc: arab-gen@magpie.bio.indiana.edu > Subject: Re: [Arabidopsis] Optimal germination of older Arabidopsis > seeds > > I am not sure about the scratching working with older seeds, but here my > > colleagues use GA4 to induce germination with Arabidopsis in total > darkness (works better than GA3). From our work years ago with long > dormant seeds, I would guess that would be your best bet. Regards, Jerry > > Charles S. Gasser wrote: > >> Dear Arabidopsis community, >> We have some quite old Arabidopsis seed that appears to have largely >> lost viability - i. e. when sown on pots or plates they fail to >> germinate even when first stratified. >> >> Does anyone have suggestions for optimal/improved conditions for >> germination of such seeds? Workers on other species have suggested >> soaking in a GA solution or scratching the seed (I was thinking this >> might be accomplished by shaking them briefly with carborundum >> powder). Does anyone have experience with these or other methods to >> allow perhaps weaked survivors to germinate? >> >> Post to the group or e-mail me directly and if I get multiple answers >> I will post a summary. >> > > -- ==================================================== Dr. Jerry D. Cohen, Professor, Bailey Endowed Chair University of Minnesota Department of Horticultural Science and Microbial and Plant Genomics Institute 1970 Folwell Ave., 305 Alderman Hall Saint Paul, MN 55108 Phone 612.624.9212; FAX 612.624.4941 Lab phone 612.624.1218 Email cohen047@tc.umn.edu Web: http://horticulture.cfans.umn.edu/Jerry_Cohen.html ===================================================== "By three methods we may learn wisdom: First by reflection, which is noblest; second by imitation, which is easiest; and third by experience, which is the bitterest. - Confucius From jiangyqcn from hotmail.com Wed May 13 00:23:13 2009 From: jiangyqcn from hotmail.com (Y Jiang) Date: Thu May 14 17:14:00 2009 Subject: [Arabidopsis] homeoallele In-Reply-To: References: Message-ID: Hi colleagues, Could you provide a definition of homeoallele in plants like Brassica napus (AACC genome)? Thanks, Jiang > Date: Thu, 7 May 2009 12:57:12 -0500 > From: huq@mail.utexas.edu > To: arab-gen@magpie.bio.indiana.edu > CC: > Subject: [Arabidopsis] POSTDOCTORAL POSITION AT UT AUSTIN > > A postdoctoral position is available for two years to work on the > phytochrome-interacting basic helix-loop-helix (bHLH) transcription factor > (PIF1) that is involved in controlling photomorphogenesis in Arabidopsis. > The research involves understanding the mechanisms of regulation of PIF1 by > light using biochemical, genetic and genomic approaches. Applicants should > have a recent Ph.D. in molecular genetics or biochemistry. Prior experience > in Arabidopsis is advantageous but not essential. Salary and benefits will > be competitive and commensurate with experience. Interested applicants > should send a CV, brief summary of research experience, and names and email > addresses of at least three referees preferably by email to > huq@mail.utexas.edu. > > The University of Texas at Austin is an affirmative action, equal > opportunity employer committed to excellence through diversity. > > Interested applicants are encouraged to look at recent papers from our lab: > > 1. Castillon, A., Shen, H. and Huq, E. (2009) Blue light induces degradation > of the negative regulator Phytochrome Interacting Factor 1 to promote > photomorphogenic development of Arabidopsis seedlings. Genetics 182:161-171. > > 2. Leivar, P., Monte, E., Oka, Y., Liu, T., Carle, C., Castillon, A., Huq, > E. and Quail, P.H. (2008) Multiple phytochrome-interacting bHLH > transcription factors repress premature seedling photomorphogenesis in > darkness. Current Biology 18:1815-1823. > > 3. Shen, H., Ling, Z., Castillon, A., Majee, M., Downie, B. and Huq, E. > (2008) Light-induced phosphorylation and degradation of the negative > regulator PIF1 depends upon its direct physical interactions with > photoactivated phytochromes. Plant Cell 20:1586-1602. > > 4. Moon, J., Zhu, L., Shen, H. and Huq, E. (2008) PIF1 directly and > indirectly regulates chlorophyll biosynthesis to optimize the greening > process in Arabidopsis. Proc. Natl. Acad. Sci. USA 105: 9433-9438. > > 5. Shen, H., Luong, P. and Huq, E. (2007) The F-box protein MAX2 functions > as a positive regulator of photomorphogenesis in Arabidopsis. Plant > Physiology 145: 1471-1483. > > 6. Castillon, A., Shen, H. and Huq, E. (2007) Phytochrome Interacting > Factors: central players in phytochrome-mediated light signaling networks. > Trends Plant Sci. 12: 514-521. > > *********************************************** > Enamul Huq > Assistant Professor > Molecular Cell and Developmental Biology > University of Texas at Austin > 1 University Station, A6700 > Austin, TX 78712. > Phone: 512-471-9848 > Fax: 512-232-3402 > http://www.sbs.utexas.edu/huq/lab > > For express mail: > Enamul Huq > Molecular Cell and Developmental Biology > University of Texas at Austin > Bio Labs #311 > 205 W. 24th St. > Austin, TX 78712. > ********************************************** > > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen _________________________________________________________________ One at a time or all at once? Get updates from your friends in one place. http://go.microsoft.com/?linkid=9660827 From sanjaysingh765 from gmail.com Fri May 15 05:57:42 2009 From: sanjaysingh765 from gmail.com (chunnu) Date: Fri May 15 14:39:17 2009 Subject: [Arabidopsis] gene expression study Message-ID: <18573ee5-73a4-4491-8cc1-1ff73cecd297@18g2000prx.googlegroups.com> Hi all, I am interested to study the expression of a set of genes from rice and arabidopsis.Can any one tell me the simplest server/site to perform this analysis for me. regards chunnu From susie from cpib.ac.uk Fri May 15 09:55:53 2009 From: susie from cpib.ac.uk (Susannah Lydon) Date: Fri May 15 14:39:44 2009 Subject: [Arabidopsis] Plant Growth Biology and Modeling Workshop - October 2009, Spain Message-ID: <4A0D8279.9010604@cpib.ac.uk> Plant Growth Biology and Modeling Workshop 14-16 October, 2009 - Elche (Spain) This workshop covers the latest advances in the biology, modelling and automated phenotyping of leaf and root development. Speakers include: Tobias Baskin, University of Massachusetts (USA) Malcolm Bennett, CPIB, Nottingham (UK) Thomas Berleth, Toronto University (Canada) Enrico Coen, John Innes Centre (UK) Yuval Eshed, Weizmann Institute of Science (Israel) Mark Estelle, University of California, San Diego (USA) Christine Granier, INRA Montpellier (France) Robert Last, Michigan State University (USA) Timothy Nelson, Yale University (USA) Uli Schurr, Research Centre J?lich (Germany) Miltos Tsiantis, University of Oxford (UK) Hirokazu Tsukaya, Tokyo University (Japan) Deadline for abstract submission is September 1st, 2009. For more information and registration please visit the workshop website: http://www.agron-omics.eu/index.php/workshop This workshop is sponsored by the Agron-Omics consortium, the Centre for Plant Integrative Biology (UK) and Universidad Miguel Hern?ndez de Elche (Spain). Best wishes Susie -- Dr Susannah Lydon Outreach Officer Centre for Plant Integrative Biology School of Biosciences University of Nottingham Sutton Bonington Campus Loughborough, LE12 5RD, UK http://www.cpib.ac.uk email: susie@cpib.ac.uk tel: +44 (0)1159 516289 This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. From csgasser from ucdavis.edu Fri May 15 16:46:30 2009 From: csgasser from ucdavis.edu (Charles S. Gasser) Date: Fri May 15 16:51:26 2009 Subject: [Arabidopsis] Optimal germination of older Arabidopsis seeds Message-ID: Thanks very much to all who replied to my request for information on ways to aid older Arabidopsis seeds in germination. I asked if anyone had suggestions for helping us as some samples of seed were failing to germinate on either soil or plates. Some replied to both me and the group, but I summarize them all here. June Medford pointed out that the plates (media) was the better of the two methods we were using since "you can at least see if the seed swells and the radicle protrudes but I don't know how well this works (e.g., no quantitative data)." Jim Tokuhisa provided a useful reference: >Here is a relevant citation. I have not looked at the article nor have >I tried the protocol but the abstract covers the important bits. > >Usmanov,P.D. (1999). Aging of Arabidopsis thaliana seeds and its >overcoming. Russian Journal of Plant Physiology 46, 423-425. >Ref ID: 18276 >Keywords: nail/Arabidopsis/seed/viability/cytokinin/Lazarus >Reprint: Not in File >Abstract: The viability of seeds of Arabidopsis thaliana (L.) Heynh >seeds (race Enkhein) declined in the course of their storage at room >temperature. In the eighth year of storage, the germination percentage >of Arabidopsis thaliana seeds collected from plants grown in soil was >50%, and for plants grown on agar medium in tubes, 22%. In both cases, >seeds fully lost their capacity for germination by the ninth or tenth >year of storage. Fertile plants were obtained after the treatment of >such seeds with 1 mg/l. kinetin or after the addition of 1% yeast >extract to the agar medium. A. thaliana seeds stored for 11 years or >longer did not regain their capacity for germination even after >treatment with kinetin, yeast extract, a mixture of amino acids, >vitamins, and purine and pyrimidine bases. Thus, during long-term >storage, irreversible loss of seed viability takes place. > >Jim Tokuhisa, Ph.D. >Assistant Professor >Horticulture Department >Virginia Tech (0390) Jyoti Shah and Eva Huala suggested physical assistance: >In the past I have had moderate success with >using flat tweezers to gently break open the >seed after it has been sitting on MS plates for >3-4 days. > >Jyoti > >Dr. Jyoti Shah >Associate Professor >University of North Texas >Department of Biological Sciences > >In a former life when I was working with GA >mutant seed and I wanted to germinate them >without GA treatment I would sterilize them, >imbibe them and then carefully remove the seed >coat with tweezers and leave them on an agar >plate where they would begin to grow. I don't >know if this would work for old seeds though, >maybe it would be too stressful. > >Eva A number of people suggested various means for use of GA to promote germination: Jerry D. Cohen >I am not sure about the scratching working with >older seeds, but here my colleagues use GA4 to >induce germination with Arabidopsis in total >darkness (works better than GA3). From our work >years ago with long dormant seeds, I would guess >that would be your best bet. Regards, Jerry >Yes, of course, I should have said 'my >colleagues who wish to germinate seeds in >darkness' use GA4. Light + GA is better. I >will add that GA4 is also preferred over the 4+7 >mixture, but either is choice is better than GA3. >Thanks for the chance for clarification, Jerry >Typically 100 uM is what they are using here. >That is the level that gets good germination of >new seeds even without light. For older seeds I >would use that amount with light treatment as >well. Hope this works, Jerry Peetambar Dahal >This would be quite an achievement if someone could make seed(s) that >might have lost viability. Since germination phenomenon of normal >distribution has been described in mathematical terms, it is possible >some of the seeds in the population may still be viable and might >respond to 1-100 uM GA(4+7) treatment after cold stratification. If >there are enough seeds, treatment with ACC, careful incision at the >micropylar end might help. I have not tried this in Arabidopsis but hope >that our experience with tomato and lettuce might to Arabidopsis as >well. > >Light should be better than total darkness to >enable germination of the viable fraction of >seeds in the presence of GA4+7. Luis Lopez-Molina provided the most detailed response suggesting GA, and possibly the addition of sucrose and norflurazon as well. >Dear Dr. Gasser, > >Everything you say is fine. >Avoid pots if you have a delicate seed batch. >I would recommend that you don't drown the seeds >in a GA solution. Rather, have the GA in the >plate (10?M is plenty). 1% sucrose helps. > >GA should obliterate the need of scratching the >seed coat. However, if they still don't >germinate it makes sense to try to mechanically >remove the seed coat: dissect them yourself >with fine forceps (instead of the carborundum >powder). We perform dissection experiments >routinely, if you have some seeds we can try to >help you with pleasure. > >A last thing you may try is to add norflurazon >to the medium (100?M). If you dissect the seed >and have it in a medium with GA and >norflurazon....then your embryo is most likely >dead. > >I can't think of anything else. We store the >seeds at 4C and they last years.....some people >store them at -20C (I have never tried). >Best wishes > >Luis Lopez-Molina We will likely try the GA4 in plates first I and pick at the seeds if they appear to swell but not split the seed coat. Best wishes, Chuck Gasser -- ======================================= Charles S. Gasser Professor Section of Molecular and Cellular Biology University of California 1 Shields Ave. Davis, CA 95616 csgasser@ucdavis.edu http://www.mcb.ucdavis.edu/faculty-labs/gasser/gasser-lab.html Tel. 530 752-1013 FAX 530 752-3085 From conferences from embl.de Wed May 20 05:05:24 2009 From: conferences from embl.de (EMBL Courses & Conferences) Date: Wed May 20 11:40:49 2009 Subject: [Arabidopsis] Last Announcement: EMBO Conference Series on Protein Synthesis and Translational Control Message-ID: <200905201004.n4KA4up25146@net.bio.net> Dear Colleagues, EMBO Conference Series on Protein Synthesis and Translational Control Partnered with the "CSHL Meeting on Translational Control" EMBL Heidelberg, Germany, 9 - 13 September 2009 This is to alert you of the upcoming registration and abstract deadline 1 June 2009. There will be no deadline extension possible, because the organizers meet soon after the deadline to discuss the session allocations of the submitted abstracts. From the registrations that we have had already and based on the success of the 2005 and 2007 meetings here in Heidelberg, this will be a very popular meeting for which we will need to limit participation to a maximum of 300 attendees. The time of registration will be an admission criterium in case that the meeting is oversubscribed. We invite you to register and submit your abstract as soon as possible via http://www.embl.de/conferences/TransControl/2009 Looking forward to welcoming you in September! Anne, Marina, Nahum and Matt For further inquiries, please contact: EMBL Course and Conference Office Bettina Schaefer Meyerhofstr. 1 69117 Heidelberg email: schaefer@embl.de phone: +49-6221-387-8836 If you do not wish to receive any further information about events taking place at EMBL, please reply with "unsubscribe" in the subject. From sayanti_mandal from yahoo.com Thu May 21 08:00:18 2009 From: sayanti_mandal from yahoo.com (sayanti mandal) Date: Thu May 21 12:39:05 2009 Subject: [Arabidopsis] Re: Arab-gen Digest, Vol 49, Issue 3 Message-ID: <537847.58287.qm@web35106.mail.mud.yahoo.com> hello friends, i am working on hoste pathogen interaction, on arabidopsis and alternaria brassicae.i always face a problem after infection, that their is fungal growth in the dead leaves that touch the soil,pzl give solution to avoid this fungal growth, room has a humidity of 77% and temp 22c. next problem is that the marked? leaves dry out aafter infection.pzl help me out as my infections fail every time. --- On Fri, 15/5/09, arab-gen-request@oat.bio.indiana.edu wrote: From: arab-gen-request@oat.bio.indiana.edu Subject: Arab-gen Digest, Vol 49, Issue 3 To: arab-gen@magpie.bio.indiana.edu Date: Friday, 15 May, 2009, 10:36 PM 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. homeoallele (Y Jiang) ---------------------------------------------------------------------- Message: 1 Date: Tue, 12 May 2009 23:23:13 -0600 From: Y Jiang Subject: [Arabidopsis] homeoallele To: , Arabidopsis newsgroup ??? Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi colleagues, Could you provide a definition of homeoallele in plants like Brassica napus (AACC genome)? Thanks, Jiang > Date: Thu, 7 May 2009 12:57:12 -0500 > From: huq@mail.utexas.edu > To: arab-gen@magpie.bio.indiana.edu > CC: > Subject: [Arabidopsis] POSTDOCTORAL POSITION AT UT AUSTIN > > A postdoctoral position is available for two years to work on the > phytochrome-interacting basic helix-loop-helix (bHLH) transcription factor > (PIF1) that is involved in controlling photomorphogenesis in Arabidopsis. > The research involves understanding the mechanisms of regulation of PIF1 by > light using biochemical, genetic and genomic approaches. Applicants should > have a recent Ph.D. in molecular genetics or biochemistry. Prior experience > in Arabidopsis is advantageous but not essential. Salary and benefits will > be competitive and commensurate with experience. Interested applicants > should send a CV, brief summary of research experience, and names and email > addresses of at least three referees preferably by email to > huq@mail.utexas.edu. > > The University of Texas at Austin is an affirmative action, equal > opportunity employer committed to excellence through diversity. > > Interested applicants are encouraged to look at recent papers from our lab: > > 1. Castillon, A., Shen, H. and Huq, E. (2009) Blue light induces degradation > of the negative regulator Phytochrome Interacting Factor 1 to promote > photomorphogenic development of Arabidopsis seedlings. Genetics 182:161-171. > > 2. Leivar, P., Monte, E., Oka, Y., Liu, T., Carle, C., Castillon, A., Huq, > E. and Quail, P.H. (2008) Multiple phytochrome-interacting bHLH > transcription factors repress premature seedling photomorphogenesis in > darkness. Current Biology 18:1815-1823. > > 3. Shen, H., Ling, Z., Castillon, A., Majee, M., Downie, B. and Huq, E. > (2008) Light-induced phosphorylation and degradation of the negative > regulator PIF1 depends upon its direct physical interactions with > photoactivated phytochromes. Plant Cell 20:1586-1602. > > 4. Moon, J., Zhu, L., Shen, H. and Huq, E. (2008) PIF1 directly and > indirectly regulates chlorophyll biosynthesis to optimize the greening > process in Arabidopsis. Proc. Natl. Acad. Sci. USA 105: 9433-9438. > > 5. Shen, H., Luong, P. and Huq, E. (2007) The F-box protein MAX2 functions > as a positive regulator of photomorphogenesis in Arabidopsis. Plant > Physiology 145: 1471-1483. > > 6. Castillon, A., Shen, H. and Huq, E. (2007) Phytochrome Interacting > Factors: central players in phytochrome-mediated light signaling networks= From nixxx008 from tc.umn.edu Sat May 23 17:30:14 2009 From: nixxx008 from tc.umn.edu (Min Ni) Date: Sun May 24 00:02:37 2009 Subject: [Arabidopsis] Opening position Message-ID: <12A2F821-30AA-4C93-AB22-C24989708AF1@tc.umn.edu> Applicants are invited for a postdoctoral position in the laboratory =20 of Dr. Min Ni at the University of Minnesota, starting soon or date =20 negotiable. Experience in molecular and cellular biology, genetics, =20 and biochemistry will be a plus. Our lab is currently focused on two =20 separate research areas: light-regulated de-etiolation and stomatal =20 opening response and Arabidopsis seed development. We have identified =20= a few T-DNA-tagged mutants and characterized a few key regulators =20 involved in these processes. We aim to study their actions and =20 interactions with other components in these signaling pathways by =20 using a variety of tools in molecular genetics, molecular biology, and =20= biochemistry. The successful applicant will also have an opportunity =20 to characterize existing mutants and to clone the mutated gene from =20 these mutants. For further information, please visit our web site = (http://www.cbs.umn.edu/plantbio/faculty/NiMin/=20 ). The University of Minnesota at twin cities provides excellent =20 research facilities and educational opportunities = (http://www.cbs.umn.edu/biodale/=20 ). Diverse cultural and recreational activities are easily accessible =20= around the Minneapolis/St. Paul =93Twin Cities=94 area = (http://www.exploreminnesota.com/home.aspx=20 ). To apply, please send, by e-mail, letter of application, curriculum =20= vitae, and names of three references (including address, phone, and =20 email address) to nixxx008@tc.umn.edu. Min Ni, Department of Plant =20 Biology, 250 Biosci Center, 1445 Gortner Avenue, University of =20 Minnesota, St. Paul, MN 55108 (Phone: 612-625-3702). The University of =20= Minnesota is an equal opportunities employer.= From clchiham from ucdavis.edu Sun May 24 09:32:24 2009 From: clchiham from ucdavis.edu (CECILIA CHI-HAM) Date: Sun May 24 16:51:09 2009 Subject: [Arabidopsis] (no subject) Message-ID: Please post, Postdoctoral Position Opened Immediately The Public Intellectual Property Resource for Agriculture (PIPRA) at the University of California Davis is seeking a highly motivated post-doctoral fellow to join its Biotechnology Resources Group immediately. The incumbent will contribute to a multi-year project aimed at developing a plant transformation system that addresses legal, regulatory, and consumer concerns. The successful applicant must have a Ph.D in plant molecular biology or related field and practical experience in molecular biology techniques, characterization of transgenic plants, analysis of gene expression, and plant transformation. Familiarity with alfalfa is highly desirable. This postdoctoral position offers a competitive salary determined by the successful candidate's experience and full health benefits. Please send a statement describing your interests, detailed curriculum vitae, and 2-3 letters of references to Alan B. Bennett abbennett@ucdavis.edu. From hnbjed from yahoo.com Mon May 25 02:04:37 2009 From: hnbjed from yahoo.com (hnbjed) Date: Mon May 25 12:17:56 2009 Subject: [Arabidopsis] PEG8000 use for water deficit Message-ID: <164934.51734.qm@web110502.mail.gq1.yahoo.com> Hi colleagues, ? I want to use PEG8000 to introduce water deficit stress to Arabidopsis roots. What is the suitable concentration of it to induce mild dehydration stress, eg. in 1/2x MS medium? I do not like high concentration as it may cause plasmolysis (I personally do not like 200 or 300 mM NaCl used by so many Arabidopsis researchers in salt stress study). However, a too low concentration of PEG8000 may have slow effect in a short time. Is there anyone knowing a reasonable concentration of it in hydroponics system of Arabidopsis? I want to harvest the tissue in a few hours (less then half a day). How about 10% or 15%?? Low concentration stimulates root elongation while high concentration won't, according to some references. ? Thanks for your input. From Veronique.Ziegler-Graff from ibmp-ulp.u-strasbg.fr Tue May 26 09:53:22 2009 From: Veronique.Ziegler-Graff from ibmp-ulp.u-strasbg.fr (Veronique Ziegler-Graff) Date: Tue May 26 14:42:42 2009 Subject: [Arabidopsis] post-doc position France Message-ID: Postdoctoral Opportunity A Postdoctoral Researcher Position is available in the area of RNA silencing and viruses. Location : IBMP, Strasbourg, France The successful candidate will join an ongoing programme of work aimed at functional dissection of the role of small RNA in tissue tropism of plant viruses. The objective is to unravel a potential link between RNA silencing and confinement of poleroviruses to vascular tissues (where these viruses are naturally present). To this purpose cell-type specific siRNA profiling of healthy and infected Arabidopsis thaliana wild-type will be undertaken and analysed to identify siRNA that may target host genes and contribute to viral partitioning and pathogenicity. Essential scientific skills required are in the fields of molecular biology, plant genetics and bioinformatics. Strong motivation, good organisational skills and ability to work in a team are requested. Important: the candidate should hold his/her PhD from a non French University, come to work to Strasbourg for the first time and be aged of less than 35 years old. The starting date is between the 1st of september and the 31st of october 2009. For further details of this project, please contact : Veronique Ziegler-Graff Veronique.Ziegler-Graff@ibmp-ulp.u-strasbg.fr To apply, applicants should send (as e-mail attachments) a cover letter, a complete CV including the names, titles and addresses of two professional references. -- V?ronique ZIEGLER-GRAFF D?partement de Virologie Int?grative Institut de Biologie Mol?culaire des Plantes 12 rue du G?n?ral Zimmer, 67084 STRASBOURG Cedex, France Email: Veronique.Ziegler-Graff@ibmp-ulp.u-strasbg.fr From debouba77 from yahoo.fr Wed May 27 02:27:31 2009 From: debouba77 from yahoo.fr (Mohamed Debouba) Date: Thu May 28 12:20:49 2009 Subject: [Arabidopsis] Water stress Message-ID: <709102.78121.qm@web24504.mail.ird.yahoo.com> Hi, ? I'm working on plants (Tomato, Arabidopsis) response to salt stress, and i recommand to use 100 mM NaCl for Arabidopsis or it equivalent in PEG. If it is Colombia ecotype, you can get enough shoot fresh matter, while root growth will be very affected. So, you can grow up?a high number of plants per treatment to get enough root matter. ? Good luck, --------------------------------------------------------------- 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 --- En date de?: Mar 26.5.09, arab-gen-request@oat.bio.indiana.edu a ?crit?: De: arab-gen-request@oat.bio.indiana.edu Objet: Arab-gen Digest, Vol 49, Issue 9 ?: arab-gen@magpie.bio.indiana.edu Date: Mardi 26 Mai 2009, 19h03 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. PEG8000 use for water deficit (hnbjed) ---------------------------------------------------------------------- Message: 1 Date: Mon, 25 May 2009 00:04:37 -0700 (PDT) From: hnbjed Subject: [Arabidopsis] PEG8000 use for water deficit To: arab-gen@magpie.bio.indiana.edu Message-ID: <164934.51734.qm@web110502.mail.gq1.yahoo.com> Content-Type: text/plain; charset=iso-8859-1 Hi colleagues, ? I want to use PEG8000 to introduce water deficit stress to Arabidopsis roots. What is the suitable concentration of it to induce mild dehydration stress, eg. in 1/2x MS medium? I do not like high concentration as it may cause plasmolysis (I personally do not like 200 or 300 mM NaCl used by so many Arabidopsis researchers in salt stress study). However, a too low concentration of PEG8000 may have slow effect in a short time. Is there anyone knowing a reasonable concentration of it in hydroponics system of Arabidopsis? I want to harvest the tissue in a few hours (less then half a day). How about 10% or 15%?? Low concentration stimulates root elongation while high concentration won't, according to some references. ? Thanks for your input. ------------------------------ _______________________________________________ Arab-gen mailing list Arab-gen@net.bio.net http://www.bio.net/biomail/listinfo/arab-gen End of Arab-gen Digest, Vol 49, Issue 9 *************************************** From liat.avrahami from mail.huji.ac.il Thu May 28 16:43:51 2009 From: liat.avrahami from mail.huji.ac.il (Liat Avrahami) Date: Fri May 29 00:34:57 2009 Subject: [Arabidopsis] plant cDNA expression library to express in yeast Message-ID: Hello, My name is Liat Avrahami. I am a PhD student under the supervision of Profs. S. Braun and D. Engelberg at the Hebrew University of Jerusalem. I'm looking for a plant cDNA expression library in a yeast vector (not a 2-hybrid) to use for rescue of different yeast strain ( S.cerevisiae). Do you know how can I found one? Thanks in advance, All the best, Liat. Liat Avrahami. Department of Biological Chemistry Institute of Life Sciences The Hebrew University of Jerusalem Jerusalem 91904, Israel Phone: ++972 2 6586525 Fax: ++972 2 658 6448 E-mail: liat.avrahami@mail.huji.ac.il From wfrommer from stanford.edu Thu May 28 13:12:29 2009 From: wfrommer from stanford.edu (Wolf Frommer) Date: Fri May 29 00:35:45 2009 Subject: [Arabidopsis] Faculty position at the Carnegie Institution, Plant Biology, Stanford Message-ID: <28A866F8-D1FE-4280-9649-0D246FB648CC@stanford.edu> Faculty Position in Plant Biology The Department of Plant Biology of the Carnegie Institution seeks a faculty member with an innovative and exciting research program in any aspect of plant biology and will consider investigators at all career stages. The Department of Plant Biology is part of the nonprofit research institution (Carnegie Institution for Science) and is affiliated with and is situated on the campus of Stanford University, California. Additional information about the department and its faculty may be found at http://carnegiedpb.stanford.edu/. Applicants should send a curriculum vitae, statement of research interest, and have three names of contacts willing to write letters of recommendation sent to: Director, Department of Plant Biology, Carnegie Institution, 260 Panama St., Stanford, CA 94305 (w12frommer@stanford.edu ). An Equal Opportunity/Affirmative Action Employer. P.S. please do not apply if you look for a postdoc position, this is equivalent to an assistant/associate/full professor position. ************************************** Wolf B. Frommer Carnegie Institution for Science Department of Plant Biology 260 Panama St Stanford CA 94305 Tel. 650 325 1521 x208 www.plantbiology.ciw.edu *************************************** From jkieber from bio.unc.edu Fri May 29 20:01:22 2009 From: jkieber from bio.unc.edu (Kieber, Joe J. (Biology)) Date: Fri May 29 23:47:44 2009 Subject: [Arabidopsis] Urgent: TAIR Funding in Jeopardy! Message-ID: <5805338EEBC6DB4AB6F96B9693F2ABDB05DA521B@email.bio.unc.edu> Dear Arabidopsis community, I am writing on behalf of the Multinational Arabidopsis Steering Committee (MASC) to bring to your attention an important matter regarding the funding of TAIR (The Arabidopsis Information Resource: http://www.arabidopsis.org/ ) . The TAIR board of directors (Joe Ecker, Chuck Gasser and Mary Lou Guerinot) have brought to my attention the fact that the funding of TAIR is currently in jeopardy. TAIR funding is due to expire at the end of August this year (3.5 months from now). Although a proposal for continued support was submitted to NSF in August 2008, NSF has not yet made a decision and TAIR staff have gotten early indications that NSF doesn't want to provide ongoing long term support for TAIR but would prefer that TAIR find other sources of funding (subscription fees, other granting agencies). If you value TAIR as a free, open resource to the Arabidopsis community (and beyond), it is imperative that the NSF be made aware of the widespread strong support for TAIR in the community. I am writing to ask that if you agree that an open, freely accessible TAIR is an essential tool for the future of Arabidopsis research, you write a letter of support. The TAIR board has asked that you address your letter to the "TAIR Board of Directors" and send it by e-mail to any of the following: csgasser@ucdavis.edu ecker@salk.edu Mary.Lou.Guerinot@Dartmouth.edu or send it to me at: jkieber@unc.edu Below is a letter that I wrote in case you need help getting started, but your own words would be even more effective. If you're very pressed for time but still want to help, I also include another letter at the bottom for multiple signatures. If you prefer this option, let Chuck Gasser (csgasser@ucdavis.edu ) know that you agree to have your name added to the list of signatories. Please act on this quickly as the decision regarding the future of TAIR will be made very soon. Cheers, Joseph Kieber Chair, Multinational Arabidopsis Steering Committee Professor and Associate Chair Department of Biology University of North Carolina Coker Hall, CB#3280 Chapel Hill, NC 27599-3280 919-962-2144 http://www.bio.unc.edu/faculty/kieber/lab/ My letter: To: TAIR Board of Directors: I just became aware that TAIR's current funding will end on August 31st of this year and that a proposal to continue support of this resource is currently under consideration at NSF. Please convey my strong support of this proposal to the NSF for continued funding of TAIR. It is absolutely essential to the Arabidopsis community that TAIR continues to function. TAIR has been an invaluable resource not only for Arabidopsis researchers because it provides the ONLY reliable entry portal to plant gene structure, transcriptome information, and it is connected to the most important other freely available analysis tools. . TAIR provides easy access to many non-Arabidopsis data and biological resources through search interfaces and web-based data analysis tools. Rather than considering termination of support, TAIR should receive substantially more support. TAIRs mission will continue to grow in importance as large new datasets continue to be generated, such as the interactome, proteome, importantly also the epigenome, and the large scale sequencing of many Arabidopsis accessions, and soon of Arabidopsis relatives. Notwithstanding the importance of crop-centered databases, TAIR is equally essential as a check for information that is obtained with crop species because it includes the information on fundamental biological and evolutionary processes in plants that is referenced in other plant databases. TAIR access which is currently free to all should remain free to all. Requiring TAIR to become self-supporting through subscriptions would be problematic for many reasons. The most important consideration is that fees would eliminate the participation of many researchers. This would be discrimination based on wealth. Also, a number of other fee-based databases would emerge inevitably resulting in the fragmentation of knowledge, and the generation of privileged knowledge, which would in essence countermand the attempts made by NSF to foster integration, for example through the iPlant initiative. Arguments against a subscription model for TAIR support (please alter wording if you use these): TAIR shares its data freely with other organizations such as NCBI (providing new genome releases), GO, BioGRID, and the Plant Ontology Consortium. Future iPlant projects are also likely to need access to TAIR data. Charging a fee for access would work against the concept of free data sharing and motivate TAIR to stop sharing their data with other groups. It could also result in large institutions setting up an internal copy of TAIR after paying for a single subscription or developing a similar resource for storing their own data. ABRC depends on the TAIR database to provide access to Arabidopsis seed and DNA stocks. These biological tools have leveled the playing field for plant researchers all over the world, making it possible for researchers in labs that are not well funded to do cutting edge science without a huge monetary investment. A subscription fee to use TAIR will discourage researchers from exploring these resources and finding the materials they need. Also, high school and college teachers who use these resources for teaching purposes will find it difficult to pay a fee. If TAIR charges a subscription fee for database access, I would be less motivated to provide my data to them. It's not clear to me why should I pay to access data that was freely provided by the community. If TAIR receives less community data it will become a less valuable resource and the motivation to pay a subscription fee will decrease even further. TAIR collects data from Plant Physiology authors at the time of publication and I've heard they're planning to expand this to other journals. However, journals are struggling with open access and may not like it if TAIR begins to charge a subscription fee for displaying data from their articles when they're providing free access to the article. It's possible that journals would reconsider their participation or would ask for a portion of the subscription fees if TAIR began to charge for access. Community Letter for common signatures: Dear TAIR Advisory Board, I'm writing to express my concern about the imminent expiration of funding for TAIR at the end of August 2009. TAIR serves as the central repository for data on the model plant Arabidopsis and I consider it essential for my research. Important aspects of TAIR's work include generating new genome releases yearly with updated gene structure and function information, gathering new data from the literature and community submissions and adding it to the database, and providing easy and convenient access to Arabidopsis data and biological resources through search interfaces and web-based data analysis tools. TAIR is essential to a wide range of biological research ranging from development of new crops to increasing our understanding of fundamental biological and evolutionary processes in plants and other organisms. Please let NSF know that I support continued funding for this project so that the amount and types of data housed by TAIR will continue to grow and will remain freely accessible to all without restriction. Sincerely, Name / Affiliation / Research area From jpbcs from acadjourn.org Mon May 4 02:58:49 2009 From: jpbcs from acadjourn.org (Journal of Plant Breeding and Crop Science) Date: Wed Sep 30 17:18:17 2009 Subject: [Arabidopsis] (no subject) Message-ID: *Journal of Plant Breeding and Crop Science* www.academicjournals.org/JPBCS * * Dear Colleague, The *Journal of Plant Breeding and Crop ** **Science** * *(JPBCS) *is a* *multidisciplinary peer-reviewed journal published monthly by Academic Journals ( www.academicjournals.org/JPBCS dedicated to increasing the depth of Crop Science across disciplines with the ultimate aim of improving plant research. *Call for Papers* *JPBCS* will cover all areas of plant breeding and crop science. The journal welcomes he submission of manuscripts that meet the general criteria of significance and scientific excellence, and will publish: ? Original articles in basic and applied research ? Case studies ? Critical reviews, surveys, opinions, commentaries and essays We invite you to submit your manuscript(s) to jpbcs@acadjourn.orgfor publication in the Maiden Issue (January 2009). Our objective is to inform authors of the decision on their manuscript(s) within four weeks of submission. Following acceptance, a paper will normally be published in the next issue. Instruction for authors and other details are available on our website; http://www.academicjournals.org/JPBCS/Instruction.htm JPBCS is an Open Access Journal One key request of researchers across the world is unrestricted access to research publications. Open access gives a worldwide audience larger than that of any subscription-based journal ad thus increases the visibility and impact of published work. It also enhances indexing, retrieval power and eliminates the need for permissions to reproduce and distribute content.JPBCS is fully committed to the Open Access Initiative and will provide free access to all articles as soon as they are published. Best regards, *Anighoro Clementina* Editorial Assistant Journal of Plant Breeding and Crop Science (JPBCS) E-mail: jpbcs@acadjourn.org, www.academicjournals.org/JPBCS