From dbird from mtroyal.ca Mon Jun 1 12:51:33 2009 From: dbird from mtroyal.ca (David Bird) Date: Mon Jun 1 14:05:34 2009 Subject: [Arabidopsis] source for Fast Neutron M2 seeds Message-ID: Hello Arab community, I am looking for a source of Fast neutron M2 seeds to do genetic screening by PCR. I have ordered from Lehle seeds in the US, but they seem to be having some (significant) delays in delivering. Does anyone know of another source for FN seeds? Thanks very much, David Bird Chemical and Biological Sciences Mount Royal College 4825 Mount Royal Gate S.W. Calgary, AB T3E 6K6 Ph: 403- 440-8750 Fx: 403-440-6095 ------------------------------------------------------------------------------------------------------------------------ This communication is intended for the use of the recipient to which it is addressed, and may contain confidential, personal, and or privileged information. Please contact the sender immediately if you are not the intended recipient of this communication, and do not copy, distribute, or take action relying on it. Any communication received in error, or subsequent reply, should be deleted or destroyed. From jdfriesner from ucdavis.edu Tue Jun 2 15:11:44 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Tue Jun 2 19:04:24 2009 Subject: [Arabidopsis] Closing in 12 days! Online Registration for ICAR 2009 Message-ID: <002f01c9e3be$59ab4de0$0d01e9a0$@edu> Dear All The 20th International Conference on Arabidopsis Research will take place 30th June - 4th July 2009 in the historic and vibrant city of Edinburgh, Scotland, UK. http://arabidopsis2009.com/ Online registration for the conference closes on the 15th June, so if you have not yet registered for the meeting please make sure you register soon by visiting http://arabidopsis2009.com/registernow.html **************************************************************************** The keynote speaker at ICAR 2009 will be the Lasker Prize winning scientist Prof. David Baulcombe We have a great programme of world-renowned speaker confirmed including Enrico Coen, Caroline Dean, Joe Ecker, Jiri Firml, Nicholas Harberd, Alistair Hetherington, Andrew Millar, Ben Scheres, Mark Stitt and Jian-Kang Zhu. For a full programme visit http://arabidopsis2009.com/programme.html and http://arabidopsis2009.com/speakers.html The conference will consist of two plenary sessions each morning and four concurrent sessions each afternoon, which will include presentations chosen from submitted abstracts. The conference will feature a number of community-led workshops that will provide opportunities for focused discussion, whilst three poster sessions will provide ample time for research discussion. Delegates will also have a free afternoon between the Friday morning sessions and evening poster session to engage in networking, scientific discussion and to explore Edinburgh and it?s surroundings. We look forward to seeing you in Edinburgh. Ruth Bastow From lehle from lehleseeds.com Fri Jun 5 13:41:46 2009 From: lehle from lehleseeds.com (lehle@lehleseeds.com) Date: Sat Jun 6 23:52:30 2009 Subject: [Arabidopsis] Book Wanted - John Bowen 1994 Arabidopsis An Atlas of Morphology and Development Message-ID: Dear Arabidopsis Community, A university librarian (USA) contacted me recently looking for a copy of John Bowman (ed) 1994 Arabidopsis An Atlas of Morphology and Development. Springer-Verlag New York 450 pp. The library had a copy, but it was checked out and not returned. Now they would like to replace it, but cannot find a commercial copy for sale at an attractive price. If you have a personal copy you are willing to donate or sell to this library, let me know and I will pass your interest along to them. Similarly, if you know of a commerical book dealer who is selling a copy, I will pass this information along to them as well. Thanks in advance. Fred Lehle From jdfriesner from ucdavis.edu Thu Jun 11 11:35:29 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Thu Jun 11 12:21:19 2009 Subject: [Arabidopsis] 4 days left to register online for the International Arabidopsis Conference Message-ID: <000901c9eab2$a241a860$e6c4f920$@edu> Dear All The 20th International Conference on Arabidopsis Research will take place 30th June - 4th July 2009 in the historic and vibrant city of Edinburgh, Scotland, UK. http://arabidopsis2009.com/ Online registration for the conference closes on the 15th June, so if you have not yet registered for the meeting please make sure you register today by visiting http://arabidopsis2009.com/registernow.html **************************************************************************** The keynote speaker at ICAR 2009 will be the Lasker Prize winning scientist Prof. David Baulcombe We have a great programme of world-renowned speaker confirmed including Enrico Coen, Caroline Dean, Joe Ecker, Jiri Firml, Nicholas Harberd, Alistair Hetherington, Andrew Millar, Ben Scheres, Mark Stitt and Jian-Kang Zhu. For a full programme visit http://arabidopsis2009.com/programme.html and http://arabidopsis2009.com/speakers.html The conference will consist of two plenary sessions each morning and four concurrent sessions each afternoon, which will include presentations chosen from submitted abstracts. The conference will feature a number of community-led workshops that will provide opportunities for focused discussion, whilst three poster sessions will provide ample time for research discussion. Delegates will also have a free afternoon between the Friday morning sessions and evening poster session to engage in networking, scientific discussion and to explore Edinburgh and it?s surroundings. We look forward to seeing you in Edinburgh. Ruth Bastow -------------- next part -------------- _______________________________________________ Arabuk mailing list Arabuk@lists.bbsrc.ac.uk https://www.lists.bbsrc.ac.uk/mailman/listinfo/arabuk From fttfl1 from gmail.com Thu Jun 11 21:02:40 2009 From: fttfl1 from gmail.com (JH Ahn) Date: Fri Jun 12 15:12:07 2009 Subject: [Arabidopsis] Is overexpression driven by the Gateway vectors weaker? Message-ID: <55013fbe-c6db-4edd-be74-dca163f84b87@d7g2000prl.googlegroups.com> Dear Arabidopsis netters, Several experiences in my group suggested that overexpression driven by the Gateway vectors did not lead to strong effects, comparing to ones by other vectors, including pCHF3 and pSKI015 (activation tagging vector). Transcript levels were not greatly increased in transgenic plants generated by using the Gateway system and in turn only a small portion among transgenic plants showed the strong phenotype, seen in pCHF3-driven or pSKI015-driven plants. Does anyone have similar experience? Any comments would be much appreciated. Best regards, Ji Hoon Ahn Professor National Creative Initiative (Lab of Floral Biology) School of Life Sciences and Biotechnology, Korea University Anam dong 5 ga, Seongbuk-Gu, Seoul 136-701, Korea Phone: 82-2-3290-3451; Fax: 82-2-927-9028 Homepage : http://biotech.korea.ac.kr/lab/PDMG From Atef.Abo-Ogiala from forst.uni-goettingen.de Mon Jun 15 06:40:26 2009 From: Atef.Abo-Ogiala from forst.uni-goettingen.de (Abo-Ogiala, Atef) Date: Mon Jun 15 17:54:53 2009 Subject: [Arabidopsis] request for info on T-DNA orientation Message-ID: <99392551BB49ED458ACFE796416D3189CD7921@VS3.exc.top.gwdg.de> Please I need answer for the same question: I want to find the orientation of T-DNA insertion in some mutants of Arabidopsis. Best regards Atef Abo-Ogiala PhD student B?sgen-Institut Forstbotanik und Baumphysiologie Georg-August Universit?t B?sgenweg 2 37077 Goettingen Germany Tel: +49 (0)551 - 39 9362 Fax: +49 (0)551 - 39 22705 From kikubh from gmail.com Tue Jun 16 01:04:14 2009 From: kikubh from gmail.com (KKB) Date: Tue Jun 16 11:41:52 2009 Subject: [Arabidopsis] How to identify a specific metabolic pathway from a list of genes. Message-ID: <4A3735DE.4040001@gmail.com> Hi, I have a list of Arabidopsis genes identified from microarray studies. I want to find out if these genes are part of any specific metabolic pathways. I have been exploring AraCyc of TAIR, but I am not able find a platform where I can input any genes that will tell me the related pathway. I will really appreciate if you have a suggestion on how to find if any of these genes are involved in or are regulating any specific metabolic pathways. Thanks, Kumar From Atef.Abo-Ogiala from forst.uni-goettingen.de Tue Jun 16 06:34:45 2009 From: Atef.Abo-Ogiala from forst.uni-goettingen.de (Abo-Ogiala, Atef) Date: Tue Jun 16 11:42:38 2009 Subject: [Arabidopsis] (no subject) Message-ID: <99392551BB49ED458ACFE796416D3189D881A0@VS3.exc.top.gwdg.de> Please, I need to know how I can check the orientation of Arab. mutants using web sites before PCR reaction. I mean to short the time and to avoid to do the three primers compinations (Lp+Rp), (Rp+LBa), (Lp+LBa). I mean how I can know that the T-DNA insertion inverted or not before the PCR reactions. Best regards Atef Abo-Ogiala From Atef.Abo-Ogiala from forst.uni-goettingen.de Tue Jun 16 06:35:32 2009 From: Atef.Abo-Ogiala from forst.uni-goettingen.de (Abo-Ogiala, Atef) Date: Tue Jun 16 11:42:52 2009 Subject: [Arabidopsis] (no subject) Message-ID: <99392551BB49ED458ACFE796416D3189D881A1@VS3.exc.top.gwdg.de> I did the PCR reaction for one of Arabidopsis mutants to verify the T-DNA insertion and the results are a bit strange. I mean I should get from the first generation of the mutant at least one hetero plant but that is not happened. The whole plants were wild type. So it could be there is no T-DNA insertion or what? Another question concerning cDNA, I tested the cDNA with the specific primers of my gene (Lp+Rp) and also with (Rp+LB) and I got results in both reactions, however I got the RNA from wildtype plants. For that I have a doubt that cDNA could be contaminated or I have no idea? Best regards Atef Abo-Ogiala From evewurtele from gmail.com Tue Jun 16 12:00:37 2009 From: evewurtele from gmail.com (Eve Wurtele) Date: Tue Jun 16 14:38:54 2009 Subject: [Arabidopsis] How to identify a specific metabolic pathway from a list of genes. In-Reply-To: <4A3735DE.4040001@gmail.com> References: <4A3735DE.4040001@gmail.com> Message-ID: <7fdaa81b0906161000k5fa7c357wa86b770fca95fb1a@mail.gmail.com> Hi Kumar, Go to AtGeneSearch at MetNet metnetdb.org Paste in your gene list, you will get a table with info about pathways, GO terms, regulons membership and more for each gene, plus clickable links to more info. Of course, for the many Arabidopsis genes of unknown function, there will be no pathway listed. best, Eve On Tue, Jun 16, 2009 at 1:04 AM, KKB wrote: > Hi, > I have a list of Arabidopsis genes identified from microarray studies. I > want to find out if these genes are part of any specific metabolic pathways. > I have been exploring AraCyc of TAIR, but I am not able find a platform > where I can input any genes that will tell me the related pathway. I will > really appreciate if you have a suggestion on how to find if any of these > genes are involved in or are regulating any specific metabolic pathways. > > Thanks, > Kumar > > _______________________________________________ > 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 2624D Howe Hall, VRAC, Iowa State University, Ames IA 50011, USA 515-708-3232 (cell) https://www.metnetdb.org https://www.metablast.org A neutron goes into a bar and asks the bartender, "How much for a beer?" The bartender replies, "For you, no charge." From jaiswalp from science.oregonstate.edu Tue Jun 16 12:44:40 2009 From: jaiswalp from science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Tue Jun 16 14:39:12 2009 Subject: [Arabidopsis] Job Opening: Plant Ontology Project Coordinator Message-ID: <4A37DA08.4080904@science.oregonstate.edu> Position Title: Research Associate (Senior Postdoc) / Research Associate (Postdoc) Working Title: Plant Ontology Project Coordinator How to Apply: -------------- To review the position description and apply, go to posting #0004322 at http://oregonstate.edu/jobs. When applying, you will be required to electronically submit your application, a cover letter citing your interest in the position and your experience, and a CV/resume including 3 references. Closing date 7/15/09. Position description: --------------------- The Plant Ontology Consortium (www.plantontology.org) is seeking applicants for a full-time position of scientific curator who will coordinate the Consortium’s efforts. The Plant Ontology Consortium is a collaboration among researchers at Oregon State University, Cornell University and New York Botanical Garden. The Consortium also collaborates with the curators of many model organism databases including rice, Arabidopsis, maize, grasses, legumes, Solanaceae, bryophytes and plant phylogenomics. The project aims to develop shared vocabularies on plant anatomy and growth and developmental stages, to describe patterns of phenotype(s) and gene expression. For more details on the project please see the publications (PubMed IDs:18194960, 17142475, 16905665, 18629207) Duties / Responsibilities: -------------------------- Develop and refine the ontologies with the PO curators in participating databases and core labs, annotate gene products and stocks with the vocabularies in the ontologies, participate in the development and application of methods to streamline and enhance the quality of annotations, manage website content, set project milestones, organize and moderate project meetings, and work with the project members to deliver the database releases and project reports on strict timelines. Required qualifications: ------------------------ Ph.D. in an aspect of plant biology (e.g. Development, Physiology, Biochemistry, Genetics, Plant Pathology, Systematics) and/or genomics, Phylogenomics, Systematics, Plant Biology and Plant Anatomy. Available immediately to start working on the project. Demonstrated ability for independent, critical thinking and excellent communication, networking and teamwork skills. Previous work in any one or more areas of Plant Development, Plant Physiology, Plant Biochemistry, Plant Genetics and/or genomics, Plant Pathology, Museum specimen curation, Phylogenomics, Systematics, Plant Biology and Plant Anatomy. Excellent communication skills in English is a must. Experience in teaching and outreach. Familiarity with Plant Development and Anatomy. Able to travel and attend 3-4 meetings/year of the PO consortium. In order to be considered for the Research Associate (senior Postdoc) position, the candidate must have 3 or more years of postdoctoral/scientist research experience and supporting publications in peer reviewed international journals. The selection committee will judge the candidate based on the qualifications below; in addition, to showing the ability to lead on a scientific project as an independent researcher. Preferred qualifications: ------------------------- Past experience in project coordination, large scale gene expression and phenotype evaluation, familiarity with basic UNIX commands, spreadsheets, and commonly used biological research tools such as BLAST and Literature Database search is desired. A working knowledge of PERL and/or SQL will be considered an asset but not required. From aloraine from uncc.edu Tue Jun 16 17:26:58 2009 From: aloraine from uncc.edu (Loraine, Ann) Date: Tue Jun 16 17:40:53 2009 Subject: [Arabidopsis] New version of IGB viewer available for Arabidopsis systems biology, genomics researchers Message-ID: Dear Colleagues, We are pleased to announce that a new version of the Integrated Genome Browser (IGB, pronounced "ig-bee") is available from http://igb.bioviz.org. IGB is an open source, freely-available graphical display tool implemented in Java that supports real-time zooming and panning through a genome; layout of genomic features and data sets in moveable, adjustable tracks; incremental or genome-scale data loading from remote Web servers or local files; and dynamic manipulation of quantitative data via genome graphs. Many of you may have been using the version available from the Affymetrix Web site to view data from Affymetrix tiling arrays. As of July 2008, my lab has taken on the lead role of supporting and developing the software for the Arabidopsis research community. (This work is supported by NSF award 0820371 titled "Arabidopsis 2010: Visualization Software and Data Server for Arabidopsis.") Please note that the new version (5.5) available from http://igb.bioviz.org is very different from the version currently hosted on the Affymetrix site. The new version includes many bug fixes as well as a streamlined mechanism for data loading. We are working with the team at Affymetrix to update their copy of the software, pending further testing to make sure the IGB 5.5 is still compatible with their systems. We have also set up IGB-compatible back end data servers (Bioviz Quickload and Bioviz DAS2) that support loading sequence and annotations data from the TAIR8 and January 2004 genome and annotations releases. We welcome any feedback about the software, the data, or anything else. Also, if you are interested in setting up data server sites to distribute your own data sets via Quickload or DAS, please let us know. It is not difficult and we would be happy to help if you run into problems. Sincerely, Ann Loraine (PI) John Nicol (Programming) Archana Raja (Testing and Documentation) Steven Blanchard (Systems Administration) ____________________ Ann Loraine Associate Professor Department of Bioinformatics and Genomics University of North Carolina, Charlotte North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28083 704-250-5750 (Kannapolis) 704-687-5451 (Charlotte) www.transvar.org From peifenz from acoma.stanford.edu Tue Jun 16 15:20:23 2009 From: peifenz from acoma.stanford.edu (Peifen Zhang) Date: Tue Jun 16 17:41:32 2009 Subject: [Arabidopsis] How to identify a specific metabolic pathway from a list of genes. In-Reply-To: <4A3735DE.4040001@gmail.com> References: <4A3735DE.4040001@gmail.com> Message-ID: <4A37FE87.3000407@acoma.stanford.edu> Hi Kumar, Have you tried the "Omics Viewers" tool from AraCyc, http://www.plantcyc.org:1555/ARA/expression.html. The tool is ideal for displaying quantitative large-scale omics data, such as gene expression, on Arabidopsis metabolic pathways. For example, reaction steps of pathways will be color-coded with up or down- regulated enzyme-coding genes. It allows you visualize and quickly spot areas of metabolism responding to a particular experimental condition. A tutorial on the tool is at http://www.plantcyc.org/tutorials/omics_viewer_tutorial.faces. You can also use the tool to display a list of genes without quantitative data, by simply making up/providing any data value (i.e 2) for all the genes on your input file. There is also a flat file of AraCyc that you can use to look up pair-wise info about genes and pathways, ftp://ftp.arabidopsis.org/home/tair/Pathways/aracyc_dump.20090311. Please write back to us (curator@plantcyc.org) for any questions using AraCyc. Regards, Peifen KKB wrote: > Hi, > I have a list of Arabidopsis genes identified from microarray studies. I > want to find out if these genes are part of any specific metabolic > pathways. I have been exploring AraCyc of TAIR, but I am not able find a > platform where I can input any genes that will tell me the related > pathway. I will really appreciate if you have a suggestion on how to > find if any of these genes are involved in or are regulating any > specific metabolic pathways. > > Thanks, > Kumar > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen From amovil from gmail.com Wed Jun 17 15:15:07 2009 From: amovil from gmail.com (Adrian) Date: Thu Jun 18 11:59:08 2009 Subject: [Arabidopsis] Re: request for info on T-DNA orientation References: Message-ID: <57913ce9-8990-4504-b4b0-7e54141f1a6c@x5g2000yqk.googlegroups.com> On Jun 15, 7:40?am, "Abo-Ogiala, Atef" wrote: > Please I need answer for the same question: > > I want to find the orientation of T-DNA insertion in some mutants of > Arabidopsis. > > Best regards > > Atef Abo-Ogiala > > PhD student > > B?sgen-Institut > > Forstbotanik und Baumphysiologie > > Georg-August Universit?t > > B?sgenweg 2 > > 37077 Goettingen > > Germany > > Tel: ?+49 (0)551 - 39 9362 > > Fax: +49 (0)551 - 39 22705 Depending from which mutant bank you request the mutants is possible to see the orientation of the insertion on the SIGnAL T-DNA Express tool (http://signal.salk.edu/cgi-bin/tdnaexpress), just need the AGI number of the interrupted gene and the code of the mutant. The page will display the gene orientation on the genome and the orientation of all T-DNA insertion mapped to that gene. If you have your own mutant bank generated by T-DNA insertion, to find the T-DNA orientation you should perform a TAIL-PCR using the T-DNA that you prefer. I hope this help... From amovil from gmail.com Wed Jun 17 15:22:04 2009 From: amovil from gmail.com (Adrian) Date: Thu Jun 18 11:59:40 2009 Subject: [Arabidopsis] Re: (no subject) References: Message-ID: On Jun 16, 7:35?am, "Abo-Ogiala, Atef" wrote: > I did the PCR reaction for one of Arabidopsis mutants to verify the T-DNA > insertion and the results are a bit strange. I mean I should get from the > first generation of the mutant at least one hetero plant but that is not > happened. The whole plants were wild type. So it could be there is no T-DNA > insertion or what? Another question concerning cDNA, I tested the cDNA with > the specific primers of my gene (Lp+Rp) and also with (Rp+LB) and I got > results in both reactions, however I got the RNA from wildtype plants. For > that I have a doubt that cDNA could be contaminated or I have no idea? > > Best regards > > Atef Abo-Ogiala Use the SIGnAL T-DNA Express tool to find the T-DNA orientation for your mutants. (http://signal.salk.edu/cgi-bin/tdnaexpress). As recommendation avoid the use of LBb1 primer for Salk mutants, instead use the LBb1.3 or LBa1 primer. Regarding to your PCR on cDNA just repeat it but extract RNA from Arabidopsis WT plants grow up by another person, if no possible grow a new batch of WT plants. Hope this help! From jdfriesner from ucdavis.edu Wed Jun 17 12:19:40 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Thu Jun 18 12:00:12 2009 Subject: [Arabidopsis] 'Mothers in Science'- Free online book Message-ID: <000001c9ef6f$cc99a740$65ccf5c0$@edu> As part of her Royal Society Rosalind Franklin award, Professor Ottoline Leyser (University of York) has produced a book entitled Mothers in Science. The aim of this book is to illustrate, graphically, that it is perfectly possible to combine a successful and fulfilling career in research science with motherhood, and that there are no rules about how to do this. On each page you will find a timeline showing on one side, the career path of a research group leader in academic science, and on the other side, important events in her family life. Each of the 64 contributors has also provided a brief text about their research and about how they have combined their career and family commitments. The book is available for free download at: http://bioltfws1.york.ac.uk/biostaff/staffdetail.php?id=hmol (text reference: June issue of the UK's GARNet newsletter) From jh299 from cornell.edu Sat Jun 20 11:16:34 2009 From: jh299 from cornell.edu (Jian Hua) Date: Sat Jun 20 13:35:48 2009 Subject: [Arabidopsis] postdoc position Message-ID: <000301c9f1c2$7b301d30$71905790$@edu> Postdoctoral Position Laboratory of Dr. Jian Hua Department of Plant Biology Cornell University, Ithaca, NY 14853 http://www.plantbio.cornell.edu/people658e.html?netID=jh299 A postdoctoral position is available in the Department of Plant Biology at Cornell University to study molecular mechanisms by which plant defense responses are modulated by genetic repressors and temperature in Arabidopsis. The postdoc will investigate how the Arabidopsis BON1 and BAP1 genes negatively regulate disease resistance genes at the molecular and biochemical level. Applicants should have a Ph D with strong background in biochemistry, molecular biology, and genetics. Research experience in plant pathogen interaction is a plus. Applicant should send a letter of intent, a CV, and contact information of three references to Dr. Jian Hua via email (jh299@cornell.edu). From marketing from embl.de Mon Jun 22 03:32:35 2009 From: marketing from embl.de (EMBL Courses & Conferences) Date: Mon Jun 22 19:57:44 2009 Subject: [Arabidopsis] EMBL Events - Please subscribe Message-ID: <124565956379113530@lxmail03.embl.de> Dear Colleagues, we would like to invite you to join our mailing list to receive information about events taking place at the European Molecular Biology Laboratory. Please use the following link to subscribe to our mailing list to receive our newsletter, event posters or e-announcements: http://www.embl.de/training/courses_conferences/cco/contact/information/index.html If you do not wish to receive any information from EMBL, please reply with the subject "unsubscribe". Thanks for your interest in our events. Best wishes, the Team of the EMBL Course & Conference Office ......................................................................................................... European Molecular Biology Laboratory Course & Conference Office Meyerhofstr. 2 69117 Heidelberg Germany Email: conferences@embl.de From HorvathDP from gmail.com Tue Jun 23 11:15:50 2009 From: HorvathDP from gmail.com (Dave Horvath) Date: Tue Jun 23 21:27:41 2009 Subject: [Arabidopsis] measuring flowering time? Message-ID: <878538d3-b5de-4033-8003-0d9633fe69e1@f16g2000vbf.googlegroups.com> Hi, I am in the novel position of having to look for altered flowering time in a transgenic arabidopsis carrying a gene from leafy spurge. There seems to be multiple ways this has been done in the literature, and I am wondering if any particular method has been more accepted than others. Any advice on the best way to do this, as well as any possible things I should be careful of would be greatly appreciated. Thanks! Dave Horvath USDA/ARS Fargo ND From vgrbic from uwo.ca Wed Jun 24 15:49:13 2009 From: vgrbic from uwo.ca (Vojislava Grbic) Date: Wed Jun 24 19:00:41 2009 Subject: [Arabidopsis] postdoctoral and PhD positions Message-ID: FOUR POSTDOCTORAL POSITIONS AND TWO PhD POSITIONS for work on PLANT-SPIDER MITE INTERACTION are available beginning September 1, 2009, in the labs of Miodrag and Vojislava Grbic at the Dept. of Biology, The University of Western Ontario, Canada (http://www.uwo.ca/). A joint multidisciplinary effort funded by Genome Canada that combines genomics, bioinformatics, genetics, biochemistry, population biology, plant biotechnology and plant breeding will open new opportunities to dissect interactions between plants and herbivores on the whole genome level. This work builds on the whole genome sequencing project of the spider mite Tetranychus urticae (JGI: http://www.jgi.doe.gov/sequencing/why/50028.html) and is part of the international collaboration with the groups of Prof. Yves Van de Peer (VIB, Flanders Institute for Biotechnology, Gent, Belgium), Prof. Maria Navajas (INRA, Montpellier, France), and Prof. Isabel Diaz and Dr F?lix Ortego (CSIC, Institute and Universidad Polit?cnica de Madrid, Spain), Prof. Jos? Miguel Mart?nez-Zapater (CNB, Madrid, Spain) and Prof. Richard Clark (University of Utah, USA) (OGI: http://www.ontariogenomics.ca/research/project/334). Strongly motivated candidates with demonstrated expertise in genetics, molecular biology, bioinformatics, genomics and/or plant-pest interactions, who are willing to be engaged in international collaboration, are encouraged to apply. Funding for this position is secured for four years. Please forward applications including a curriculum vitae and contact information of two senior scientist referees by e-mail to vgrbic@uwo.ca. Please, put "Genome Canada-funded positions" in the subject line. Contact information: Vojislava Grbic Department of Biology WSC 341 University of Western Ontario London, Ontario, N6A 5B7 Canada e-mail: vgrbic@uwo.ca Phone: 1- 519- 661-2111 x 86898 Fax: 1- 519- 661- 3935 From hcallahan from barnard.edu Thu Jun 25 09:12:09 2009 From: hcallahan from barnard.edu (Hilary S. Callahan) Date: Thu Jun 25 11:20:13 2009 Subject: [Arabidopsis] protein extraction from cambium Message-ID: <4A4385B9.3060009@barnard.edu> Hello, Here is a question from one of my students. It's not about Arabidopsis, but I would imagine that some readers of thi list have ideas about extracting from very low protein concentration? QUOTE: I am in Finland right now working as a trainee for 4 months (well 2 months left to go). My project is looking at telomerase activity in different aged trees and also in different tissues of the same trees. I've been trying to iron out the protocol for the past few weeks... We are taking protein extracts from needles, buds and cambium tissue types for this experiment by grinding tissues in liquid nitrogen and then resuspending in lysis buffer. The problem is, trying to collect protein from cambium yields extremely low quantities and we think this is because there is so much water content in the cambium compared to other tissue types. I have tried increasing the homogenized tissue-to-buffer ratio as much as possible and still barely manage 0.1 ?g/?l (target is 1.0 ?g/?l) which means I need to either attempt to concentrate the protein or use a large quantity of this protein extract in my TRAP/PCR. I've tried both ways - concentrating the protein causes the lysis buffer also to become concentrated, which then causes issues with protein concentration assay as well as PCR, because lysis buffer has all these different noxious components in it... and with the second option, having large quantity of lysis buffer in the PCR also may have interfered with the results because when I ran the PCR there were no bands in the cambium lanes even though theoretically the amount of protein in the cambium lanes was approximate to the amount of needle and bud protein in adjacent lanes. So now I am sort of stuck. My mentor and I both think that the best path forward is to look for ways to extract a higher initial concentration of cambium protein so that we don't have to deal with lysis buffer concentration issues in later steps, but I am not sure how to do this. So I am asking everyone scientific-minded that I know for suggestions! Do you know of any protocols that allow extraction of very low protein concentrations? From b.g.forde from lancaster.ac.uk Fri Jun 26 08:51:43 2009 From: b.g.forde from lancaster.ac.uk (Forde, Brian) Date: Fri Jun 26 13:17:23 2009 Subject: [Arabidopsis] dexamethasone and microarrays Message-ID: <199A8D531E24DF47ADCC977CE0E94AFC062589D0@exchange-be6.lancs.local> Hi there Can anyone point me to Arabidopsis microarray experiments where the effect of dexamethasone on gene expression in *control* lines (preferably in roots) has been reported? This would have been done for comparison with transgenic lines expressing a Dex-inducible gene. Many thanks Brian ===================================== Brian G. Forde Prof. of Environmental Plant Biotechnology Centre for Sustainable Agriculture Lancaster Environment Centre Lancaster University Lancaster LA1 4YQ tel. +44 (0)1524 510207 (direct line) email b.g.forde@lancaster.ac.uk http://biol.lancs.ac.uk/bs/people/teach/bgf.html Editor-in-Chief Plant Methods email plantmethods@lancaster.ac.uk http://www.plantmethods.com ===================================== From puna459 from hotmail.com Mon Jun 29 06:28:20 2009 From: puna459 from hotmail.com (punamaya Maharjan) Date: Mon Jun 29 11:48:31 2009 Subject: [Arabidopsis] Embryogenic culture Message-ID: Dear Sir/ madam I would like to post my query in this page .=20 Thank you . Puna "Query" Dear=20 arab-gen users=2C=20 I am posting a query related to the problem of contamination in embryogenic cultures. If anybody has idea t= o overcome it=2C I highly appreciate any kind of your comments.=20 I followed the method described in the paper by Mordhorst et al.=2C 1998. As= mentioned in the Mordhorst et al.=2C 1998=2C seeds were surface sterilized for 10 sec in 70% ethanol followed by a 10- min incubati= on in commercial bleach (final concentration 2% sodium hypochlorite=2C contain= ing 0.3% Tween 20)=2C washed 9 times with sterile water=2C dried on filter pape= r=2C and stored at room temperature before use. Then 30 seeds were incubated in 20 m= l MS-4 (pH 5.8) induction medium [Murashige and Skoog salts containing 2% (w/v) Sucrose =2C= 4.5 uM 2=2C4-D=2C and 10 mm MES [2-(N-morpholino)-ethanesulonic acid]. After a cold treatment of 4 d at 4=B0C=2C cultures were kept on a ro= tary shaker (100 rpm) at 25=B0C in the light or darkness. For seed incubation=2C= I used the 250 ml flasks instead of 190-ml Greiner plastic Containers (Alphen a/d = Rijn=2C The Netherlands) mentioned in Mordhorst et al.=2C 1998. I have tried with different sterilization buffers like 1) 5 % Clorax=2C 1% SDS 2) 0.05 % Trit= onX-100 followed by absolute ethanol washing. Still I am getting the contamination= problem just 1 week after transferring the flasks from cold room. Does anyone have the idea to overcome the problem? Does this experiment need specific 190-ml Greiner plastic Containers (Alphen a/d Rijn=2C The Netherlands). I tried to find this container also b= ut I could not get the information about it. Would you please give me suggestion? I thank you in advance for your reply.=20 =20 Puna=20 _________________________________________________________________ More than messages=96check out the rest of the Windows Live=99. http://www.microsoft.com/windows/windowslive/= From dbird from mtroyal.ca Mon Jun 29 12:31:11 2009 From: dbird from mtroyal.ca (David Bird) Date: Mon Jun 29 15:14:03 2009 Subject: [Arabidopsis] M.Sc. Position available: ABC transporters in plant secondary metabolism Message-ID: M.Sc. Position available: ABC transporters in plant secondary metabolism. A graduate student is sought for a(n) MSc/PhD project under the joint supervision of David Bird and Peter Facchini in the Department of Biological Sciences at the University of Calgary. The goal of this research program is to identify and characterize ABC transporters involved in the transport of cuticular lipids and alkaloids in the model plants Arabidopsis thaliana and Papaver somniferum, respectively. The goal of the Masters project is to identify candidate transporters using comparative genomics, bioinformatics, and gene silencing analysis. To be considered, the candidate should hold a B.Sc. in Biology, with an emphasis on molecular biology or biochemistry. The ideal candidate will hold an excellent academic record meeting the requirements for external scholarships and will have laboratory experience in biochemistry or molecular biology. Interested candidates should contact David Bird (dabird@ucalgary.ca) and provide a CV, academic transcripts, and the names of two references. ------------------------------------------------------------------------------------------------------------------------ This communication is intended for the use of the recipient to which it is addressed, and may contain confidential, personal, and or privileged information. Please contact the sender immediately if you are not the intended recipient of this communication, and do not copy, distribute, or take action relying on it. Any communication received in error, or subsequent reply, should be deleted or destroyed. From evewurtele from gmail.com Mon Jun 29 13:00:27 2009 From: evewurtele from gmail.com (Eve Wurtele) Date: Mon Jun 29 15:14:52 2009 Subject: [Arabidopsis] Embryogenic culture In-Reply-To: References: Message-ID: <7fdaa81b0906291100s4f453a7bg95a5aeb73d22574d@mail.gmail.com> it might help to reduce the number of seeds you are using in each flask. one bad seed contaminates the whole flask. also, have you tried controls in which you do the same protocol, but do not add ANY seeds- and then put on shaker. this will help you rule out something to do with flasks, media, etc. On Mon, Jun 29, 2009 at 6:28 AM, punamaya Maharjan wro= te: > > Dear Sir/ madam > I would like to post my query in this page . > > Thank you . > Puna > > "Query" > > > > Dear > arab-gen users, > > I am posting a query related to > the problem of contamination in embryogenic cultures. If anybody has idea > to overcome it, I highly appreciate any kind of your comments. > > I > followed the method described in the paper by Mordhorst et al., 1998. As > mentioned in the Mordhorst et al., 1998, seeds were > surface sterilized for 10 sec in 70% ethanol followed by a 10- min > incubation > in commercial bleach (final concentration 2% sodium hypochlorite, > containing > 0.3% Tween 20), washed 9 times with sterile water, dried on filter paper, > and > stored at room temperature before use. Then 30 seeds were incubated in 20 > ml MS-4 (pH 5.8) > induction medium [Murashige and Skoog salts containing 2% (w/v) Sucrose , > 4.5 uM 2,4-D, > and 10 mm MES > [2-(N-morpholino)-ethanesulonic > acid]. After a cold treatment of 4 d at 4=B0C, cultures were kept on a ro= tary > shaker (100 rpm) at 25=B0C in the light or darkness. For seed incubation,= I > used > the 250 ml flasks instead of 190-ml Greiner plastic Containers (Alphen a/= d > Rijn, The > Netherlands) mentioned in Mordhorst et al., 1998. I have tried with > different sterilization buffers like 1) 5 % Clorax, 1% SDS 2) 0.05 % > TritonX-100 > followed by absolute ethanol washing. Still I am getting the contaminati= on > problem > just 1 week after transferring the flasks from cold room. > > Does anyone have the idea to overcome the > problem? Does this experiment need > specific 190-ml Greiner plastic Containers > (Alphen a/d Rijn, The Netherlands). I tried to find this container also b= ut > I > could not get the information about it. Would you please give me > suggestion? I thank you in advance for > your reply. > > > > Puna > > > > > _________________________________________________________________ > More than messages=96check out the rest of the Windows Live=99. > > http://www.microsoft.com/windows/windowslive/____________________________= ___________________ > Arab-genmailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > --=20 Eve Syrkin Wurtele, Professor Bioinformatics and Computational Biology 2624D Howe Hall, VRAC, Iowa State University, Ames IA 50011, USA 515-708-3232 (cell) https://www.metnetdb.org https://www.metablast.org A neutron goes into a bar and asks the bartender, "How much for a beer?" Th= e bartender replies, "For you, no charge." From zhuchuanmei04 from gmail.com Mon Jun 29 19:21:15 2009 From: zhuchuanmei04 from gmail.com (=?GB2312?B?88O0q8PA?=) Date: Mon Jun 29 22:49:51 2009 Subject: [Arabidopsis] Could anyone help me on Arabidopsis genomic DNA cloning? Message-ID: Hi, I am a graduate student in Washington University. I have trouble in cloning a ~1.9 kb DNA fragment from Arabidopsis genomic DNA recently. The genomic DNA was prepared by CTAB method and was dissolved in H2O. For 25ul PCR reaction, I use DNA ~500ng, MgCl2 1.5mM, dNTP 160uM, Taq 2.5U, primer each 0.2uM, buffer 1x. The PCR program was 94' 5min; 94' 45s, 54' 45s, 72' 2min, 20cycle; 72' 5min, 4' for ever. I tried several times, including trying different concentration of DNA, MgCl2... However, I never got the expected 1.9kb band? This was my first time to clone gene from genomic DNA, I have no idea why it turns out to be so difficult. Did you have any suggestions? Thanks in advance. Best, -- Chuanmei Zhu DBBS(plant biology), Washington University, St.Louis, MO,USA. 63130. Tsinghua U (B.S.) From anbuarun12345 from gmail.com Tue Jun 30 07:43:51 2009 From: anbuarun12345 from gmail.com (Anbu) Date: Tue Jun 30 12:04:54 2009 Subject: [Arabidopsis] Re: Embryogenic culture References: Message-ID: <7d6c1b6d-33df-40fc-b710-120e2cb6457e@r36g2000vbn.googlegroups.com> On Jun 29, 4:28 pm, punamaya Maharjan wrote: >   Dear Sir/ madam >  I would like to post my query in this page . > > Thank you . > Puna > >  "Query" > >     Dear > arab-gen users, > > I am posting a query related to > the problem of contamination in embryogenic cultures. If anybody has idea to overcome it, I highly appreciate any kind of your comments. > > I > followed the method described in the paper by Mordhorst et al., 1998.  As mentioned in the Mordhorst et al., 1998, seeds were > surface sterilized for 10 sec in 70% ethanol followed by a 10- min incubation > in commercial bleach (final concentration 2% sodium hypochlorite, containing > 0.3% Tween 20), washed 9 times with sterile water, dried on filter paper, and > stored at room temperature before use. Then 30 seeds were incubated in 20 ml  MS-4 (pH 5.8) > induction medium [Murashige and Skoog salts containing 2% (w/v) Sucrose , 4.5 uM 2,4-D, > and 10 mm MES > [2-(N-morpholino)-ethanesulonic > acid]. After a cold treatment of 4 d at 4°C, cultures were kept on a rotary > shaker (100 rpm) at 25°C in the light or darkness. For seed incubation, I used > the 250 ml flasks instead of 190-ml Greiner plastic Containers (Alphen a/d Rijn, The > Netherlands) mentioned in Mordhorst et al., 1998. I have tried with > different sterilization buffers like 1) 5 % Clorax, 1% SDS 2) 0.05 % TritonX-100 > followed by absolute ethanol washing.  Still I am getting the contamination problem > just 1 week after transferring the flasks from cold room. > >  Does anyone have the idea to overcome the > problem?  Does this experiment need > specific 190-ml Greiner plastic Containers > (Alphen a/d Rijn, The Netherlands). I tried to find this container also but I > could not get the information about it. Would you please give me > suggestion?  I thank you in advance for > your reply. > >  Puna > > _________________________________________________________________ > More than messages–check out the rest of the Windows Live™.http://www.microsoft.com/windows/windowslive/ Dear Puna, I am suggesting you the following, 1. Remove infected seeds before starting sterilization procedure. 2. Use autoclaved filter paper 3. Use minimal amount of seeds I hope this will be very helpful to you. looking forward to hear from you From shah from unt.edu Tue Jun 30 14:47:45 2009 From: shah from unt.edu (Shah, Jyoti) Date: Tue Jun 30 15:54:59 2009 Subject: [Arabidopsis] Twp postdoctoral positions at the University of North Texas Message-ID: Two postdoctoral positions are available in the Department of Biological Sc= iences at the University of North Texas, which is located in Denton near Da= llas (Texas). Position 1 (Requisition #090681): Postdoctoral position in Plant =96Insect= Interaction University of North Texas is seeking a full time postdoctoral research asso= ciate to study plant defense response. The research emphasis will be on st= udying Arabidopsis defense responses to the green peach aphid. We seek cand= idates with a Ph.D. in molecular biology, entomology or a related field. A= pplicants should have expertise in plant molecular biology. Candidates wit= h expertise working with aphids are preferred. The successful candidate mus= t be able to design and conduct independent experiments. Excellent oral and= written communication skills and the ability to work well in a team-based/= collaborative research atmosphere are essential. The Postdoctoral Research= Associate will work under the direction of Dr. Jyoti Shah in the Departmen= t of Biological Sciences. Position 2 (Requisition #090679): Postdoctoral position in Plant Biochemis= try and Molecular Biology University of North Texas is seeking a full time postdoctoral research asso= ciate to study oxylipin metabolism in plants. The research emphasis will b= e on studying Arabidopsis genes involved in oxidized lipid metabolism and t= heir contribution to oxylipins in plant stress response. We seek candidates= with a Ph.D. in biochemistry and/or molecular biology or a related field. = Applicants should have expertise in plant molecular biology. Candidates w= ith expertise working with lipids are preferred. The successful candidate m= ust be able to design and conduct independent experiments. Excellent oral a= nd written communication skills and the ability to work well in a team-base= d/collaborative research atmosphere are essential. The Postdoctoral Resear= ch Associate will work under the direction of Dr. Jyoti Shah in the Departm= ent of Biological Sciences. For both positions (Requisition # 090681 and 090679) complete applications = must be submitted online at https://jobs.unt.edu. A complete application m= ust consist of 1) a cover letter detailing your qualifications and how they= relate to the advertised position, 2) a professional resume, 3) names and = contact information for three references. Screening of application begins J= uly 15 2009, and will continue until the positions are filled. University of North Texas is an equal opportunity employer and actively see= ks diversity among its employees. ---------------------------------------------------------------------------= ---------------------------------------------------- Dr. Jyoti Shah Associate Professor University of North Texas Department of Biological Sciences 1155 Union Circle, #305220 Denton, TX 76203-5017 Phone (940) 565-3535 Fax: (940) 565-4136 Email: shah@unt.edu For Courier Delivery: Science and Research Building # 124 1504 West Mulberry Street Denton, TX 76203-5017 From ramu.tiger123 from gmail.com Tue Jun 30 22:33:55 2009 From: ramu.tiger123 from gmail.com (Ramu gowda) Date: Wed Jul 1 02:09:47 2009 Subject: [Arabidopsis] Re: Arab-gen Digest, Vol 50, Issue 15 In-Reply-To: <200906301704.n5UH4Op02356@net.bio.net> References: <200906301704.n5UH4Op02356@net.bio.net> Message-ID: Dear Chuanmei Zhu DBBS(plant biology), Washington University, St.Louis, MO,USA. 63130 the genomic DNA of arabidopsis has the introns,UTRS,etc thats why you may not be able to amplify the expected amplicon, so its better to amplify from CDNA, if you have plant tissue prepare RNA , from that prepare CDNA using superscript or effecient MMLV(RTenzyme). so that you may amplify exact amplicon then try to clone to cloning vector and subsequently sequencing an= d binary vector or interaction studies etc . hope this may give you some idea= . take care On 6/30/09, arab-gen-request@oat.bio.indiana.edu < arab-gen-request@oat.bio.indiana.edu> 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. M.Sc. Position available: ABC transporters in plant secondary > metabolism (David Bird) > 2. Re: Embryogenic culture (Eve Wurtele) > 3. Could anyone help me on Arabidopsis genomic DNA cloning? > (=3D?GB2312?B?88O0q8PA?=3D) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 29 Jun 2009 11:31:11 -0600 > From: David Bird > Subject: [Arabidopsis] M.Sc. Position available: ABC transporters in > plant secondary metabolism > To: arab-gen@magpie.bio.indiana.edu > Message-ID: > < > OF873D8FB6.FB20BA9E-ON872575E4.00602464-872575E4.00603C51@mtroyal.ca> > Content-Type: text/plain; charset=3D"US-ASCII" > > M.Sc. Position available: ABC transporters in plant secondary metabolism. > > A graduate student is sought for a(n) MSc/PhD project under the joint > supervision of David Bird and Peter Facchini in the Department of > Biological Sciences at the University of Calgary. The goal of this > research program is to identify and characterize ABC transporters involve= d > in the transport of cuticular lipids and alkaloids in the model plants > Arabidopsis thaliana and Papaver somniferum, respectively. The goal of th= e > Masters project is to identify candidate transporters using comparative > genomics, bioinformatics, and gene silencing analysis. To be considered, > the candidate should hold a B.Sc. in Biology, with an emphasis on > molecular biology or biochemistry. The ideal candidate will hold an > excellent academic record meeting the requirements for external > scholarships and will have laboratory experience in biochemistry or > molecular biology. Interested candidates should contact David Bird > (dabird@ucalgary.ca) and provide a CV, academic transcripts, and the name= s > of two references. > > > > -------------------------------------------------------------------------= ----------------------------------------------- > > This communication is intended for the use of the recipient to which it i= s > addressed, and may > contain confidential, personal, and or privileged information. Please > contact the sender > immediately if you are not the intended recipient of this communication, > and do not copy, > distribute, or take action relying on it. Any communication received in > error, or subsequent > reply, should be deleted or destroyed. > > ------------------------------ > > Message: 2 > Date: Mon, 29 Jun 2009 13:00:27 -0500 > From: Eve Wurtele > Subject: Re: [Arabidopsis] Embryogenic culture > To: punamaya Maharjan > Cc: arab-gen@magpie.bio.indiana.edu > Message-ID: > <7fdaa81b0906291100s4f453a7bg95a5aeb73d22574d@mail.gmail.com> > Content-Type: text/plain; charset=3Dwindows-1252 > > it might help to reduce the number of seeds you are using in each flask. > one bad seed contaminates the whole flask. > > also, have you tried controls in which you do the same protocol, but do n= ot > add ANY seeds- and then put on shaker. > > this will help you rule out something to do with flasks, media, etc. > > On Mon, Jun 29, 2009 at 6:28 AM, punamaya Maharjan >wrote: > > > > > Dear Sir/ madam > > I would like to post my query in this page . > > > > Thank you . > > Puna > > > > "Query" > > > > > > > > Dear > > arab-gen users, > > > > I am posting a query related to > > the problem of contamination in embryogenic cultures. If anybody has id= ea > > to overcome it, I highly appreciate any kind of your comments. > > > > I > > followed the method described in the paper by Mordhorst et al., 1998. = As > > mentioned in the Mordhorst et al., 1998, seeds were > > surface sterilized for 10 sec in 70% ethanol followed by a 10- min > > incubation > > in commercial bleach (final concentration 2% sodium hypochlorite, > > containing > > 0.3% Tween 20), washed 9 times with sterile water, dried on filter pape= r, > > and > > stored at room temperature before use. Then 30 seeds were incubated in = 20 > > ml MS-4 (pH 5.8) > > induction medium [Murashige and Skoog salts containing 2% (w/v) Sucrose= , > > 4.5 uM 2,4-D, > > and 10 mm MES > > [2-(N-morpholino)-ethanesulonic > > acid]. After a cold treatment of 4 d at 4=B0C, cultures were kept on a > rotary > > shaker (100 rpm) at 25=B0C in the light or darkness. For seed incubatio= n, I > > used > > the 250 ml flasks instead of 190-ml Greiner plastic Containers (Alphen > a/d > > Rijn, The > > Netherlands) mentioned in Mordhorst et al., 1998. I have tried with > > different sterilization buffers like 1) 5 % Clorax, 1% SDS 2) 0.05 % > > TritonX-100 > > followed by absolute ethanol washing. Still I am getting the > contamination > > problem > > just 1 week after transferring the flasks from cold room. > > > > Does anyone have the idea to overcome the > > problem? Does this experiment need > > specific 190-ml Greiner plastic Containers > > (Alphen a/d Rijn, The Netherlands). I tried to find this container also > but > > I > > could not get the information about it. Would you please give me > > suggestion? I thank you in advance for > > your reply. > > > > > > > > Puna > > > > > > > > > > _________________________________________________________________ > > More than messages=96check out the rest of the Windows Live=99. > > > > > http://www.microsoft.com/windows/windowslive/____________________________= ___________________ > > Arab-gen< > http://www.microsoft.com/windows/windowslive/____________________________= ___________________%0AArab-gen>mailing > list > > Arab-gen@net.bio.net > > http://www.bio.net/biomail/listinfo/arab-gen > > > > > > -- > Eve Syrkin Wurtele, Professor > Bioinformatics and Computational Biology > 2624D Howe Hall, VRAC, Iowa State University, > Ames IA 50011, USA > 515-708-3232 (cell) > https://www.metnetdb.org > https://www.metablast.org > > A neutron goes into a bar and asks the bartender, "How much for a beer?" > The > bartender replies, "For you, no charge." > > > ------------------------------ > > Message: 3 > Date: Mon, 29 Jun 2009 19:21:15 -0500 > From: =3D?GB2312?B?88O0q8PA?=3D > Subject: [Arabidopsis] Could anyone help me on Arabidopsis genomic DNA > cloning? > To: arab-gen@magpie.bio.indiana.edu > Message-ID: > > Content-Type: text/plain; charset=3DISO-8859-1 > > Hi, > I am a graduate student in Washington University. I have trouble in cloni= ng > a ~1.9 kb DNA fragment from Arabidopsis genomic DNA recently. The genomic > DNA was prepared by CTAB method and was dissolved in H2O. For 25ul PCR > reaction, I use DNA ~500ng, MgCl2 1.5mM, dNTP 160uM, Taq 2.5U, primer eac= h > 0.2uM, buffer 1x. The PCR program was 94' 5min; 94' 45s, 54' 45s, 72' > 2min, 20cycle; 72' 5min, 4' for ever. > > I tried several times, including trying different concentration of DNA, > MgCl2... However, I never got the expected 1.9kb band? This was my first > time to clone gene from genomic DNA, I have no idea why it turns out to b= e > so difficult. Did you have any suggestions? Thanks in advance. > > Best, > > -- > Chuanmei Zhu > DBBS(plant biology), > Washington University, St.Louis, MO,USA. 63130. > > Tsinghua U (B.S.) > > > ------------------------------ > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > > End of Arab-gen Digest, Vol 50, Issue 15 > **************************************** > --=20 Ramu.S.V Senior research fellow dept of crop physiology, Molecular plant physiology lab, UAS, GKVK, Bangalore