From amovil from gmail.com Wed Jul 1 10:59:45 2009 From: amovil from gmail.com (Adrian) Date: Wed Jul 1 18:48:09 2009 Subject: [Arabidopsis] Re: Could anyone help me on Arabidopsis genomic DNA cloning? References: Message-ID: On Jun 29, 8:21?pm, ??? wrote: > 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.) First at all, I would recommend to use 35 or 40 PCR cycles instead 20. Second, I will use a hot start Taq an use 10 min. of initial denaturation at 95 ?C, then the following denaturation steps should be 1 min. at 95 ?C. As tip I recommend to pipette several times the DNA before add it to the PCR reaction. Hope this help! Adrian Moreno, M.Sc. Centro de Biotecnologia Vegetal Universidad Andres Bello Republica 217, Santiago 837-0146 CHILE From cmmcmichael from wisc.edu Wed Jul 1 10:10:30 2009 From: cmmcmichael from wisc.edu (COLLEEN M MCMICHAEL) Date: Wed Jul 1 18:49:09 2009 Subject: [Arabidopsis] Reply to "Could anyone help me on Arabidopsis genomic DNA" (Arab-gen Digest, Vol 50, Issue 15) In-Reply-To: <200906301704.n5UH4Tp02408@net.bio.net> References: <200906301704.n5UH4Tp02408@net.bio.net> Message-ID: Hi Chunmei, I have often had problems with PCR using genomic DNA as a template. For the most part, using the CTAB DNA preparation versus other faster, yet dirtier, preparations has helped tremendously. Since you are already using this preparation method, you might now want to try using additives that will help melt your DNA/primers, stabilize the polymerase, etc (for example add DMSO, glycerol, glycine betaine or BSA). BSA has helped more than any other additive for me. Also, increasing the buffer (complete with Mg2+) concentration can also help (up to 1.6 X final). Finally, have you tried varying the annealing temperature for your primer set? I suggest using a gradient machine to test a rangeof tmperatures. Please keep in mind that all PCR products are unique in their needs, and that the best conditions for your reaction must be determined empirically. Here is a link to a website that helped guide me toward possible PCR variations to try: http://www.med.yale.edu/genetics/ward/tavi/PCR. html. Good Luck! Colleen McMichael Bednarek Lab 219 Biochemistry Addition (608) 263-0314 x3237 > Message: 3 > Date: Mon, 29 Jun 2009 19:21:15 -0500 > From: =?GB2312?B?88O0q8PA?= > 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=ISO-8859-1 > > 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.) > > > ------------------------------ > > _______________________________________________ > 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 > **************************************** > From jaiswalp from science.oregonstate.edu Thu Jul 2 15:02:11 2009 From: jaiswalp from science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Thu Jul 2 23:44:22 2009 Subject: [Arabidopsis] Job Opening: Plant Ontology Project Coordinator Message-ID: <4A4D1243.906@science.oregonstate.edu> Deadline extended until July 31st. Also, if you are attending the following meetings please feel free to contact us to learn more about this position and the project: ASPB-Plant Biology 2009 : Contact Pankaj Jaiswal BSA Botany & Mycology 2009: Contact Aaron Liston Position Title: Research Associate (Senior Postdoc) / Research Associate (Postdoc) Working Title: Plant Ontology Project Coordinator 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 project is funded by the National Science Foundation. The Consortium also collaborates with the curators of many model organism databases including rice, Arabidopsis, maize, grasses, legumes, Solanaceae, Bryophytes, Rosaceae 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) How to Apply: To review the position description in detail 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 7/31/09. 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. -- 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 phoebe.chen from deakin.edu.au Thu Jul 2 21:33:40 2009 From: phoebe.chen from deakin.edu.au (Phoebe Chen) Date: Thu Jul 2 23:45:04 2009 Subject: [Arabidopsis] Deadline Approaching - CFP - APBC2010 Message-ID: <096466DE3CBF11439436E7B189DC44090874A4AA@mirzam-1.du.deakin.edu.au> =============================================================== Deadline Approaching 20 July ! - Call for Papers - APBC2010 The Eighth Asia-Pacific Bioinformatics Conference (APBC2010) Bangalore, India, 18-21 January 2010 http://cs.nyu.edu/parida/APBC2010/index.html =============================================================== The Asia Pacific Bioinformatics Conference (APBC) series, founded in 2003, (Previous APBC meetings APBC2009 (13-16 January 2009, Beijing, China) APBC2008 (14-17 January 2008, Kyoto, Japan) APBC2007 (14-17 January 2007, Hong Kong) APBC2006 (13-16 February 2006, Taipei, Taiwan) APBC2005 (17-21 January 2005, Singapore) APBC2004 (18-22 January 2004, Dunedin, New Zealand) APBC2003 (4-7 February 2003, Adelaide, Australia)) is an annual international forum for exploring research, development and applications of Bioinformatics and Computational Biology. The Eighth Asia-Pacific Bioinformatics Conference, APBC2010 will be held in Bangalore, India. The aim of the conference is to bring together researchers, professionals, and industrial practitioners from all over the world for interaction and exchange of knowledge and ideas in all areas of bioinformatics and computational biology. ---------------------------------------------------------------- Important Dates Paper submission open May 1, 2009 Paper submission deadline July 20, 2009 Paper acceptance decision Sep 14, 2009 Camera-ready copy of papers and Author registration Oct 9, 2009 Poster submission open July 21, 2009 Poster submission deadline Sep 25, 2009 Poster acceptance decision Oct 9, 2009 Registration open Sept 20, 2009 Early-bird registration Nov 20, 2009 Conference Jan 18-21, 2010 ---------------------------------------------------------- Conference chairs: Laxmi Parida, IBM T.J. Watson Research Center, USA Ramanathan Sowdhamini, National Centre for Biological Sciences, India Program committee chairs: Gene Myers, HHMI, Janelia Farm, USA Laxmi Parida, IBM T.J. Watson Research Center, USA APBC Steering Committee Phoebe Chen (Chair), Deakin University, Australia Sang Yup Lee, KAIST, Korea Satoru Miyano, University of Tokyo, Japan Mark Ragan, University of Queensland, Australia Limsoon Wong, National University of Singapore Michael Q. Zhang, CHSL, USA and Tsinghua University, China ----------------------------------------------------------------- Topics of Interest Papers are solicited on, but not limited to, the following topics: - Sequence Analysis - Motif Finding - Recognition of Genes and Functional Elements - RNA Analysis - Physical and Genetic Mapping - Molecular Evolution and Phylogeny - Protein Structure Analysis - Microarray Design and Data Analysis - Deep Sequencing Data Processing - Transcriptome, Gene Expression - Epigenomics - Proteomics and Post-Translational Modifications - Pathways, Networks and Systems - Ontologies - Databases and Data Integration - Biomedical Literature Mining and Understanding - Population Genetics, SNP and Haplotyping - Comparative Genomics --------------------------------------------------------------- Program committee (Confirmed): Srinivas Aluru, Iowa State University, USA Tatsuya Akutsu, Kyoto University, Japan Joel Bader, Johns Hopkins University, USA Chitta Baral, Arizona State University, USA Upinder Bhalla, National Center for Biological Sciences, India Alok Bhattacharya, Jawaharlal Nehru University, India Harmen Bussemaker, Columbia University, USA Francis Chin, Hong Kong University, Hong Kong Nadia El-Mabrouk, University of Montreal, Canada Mikhail Gelfand, Institute for Information Transmission Problems RAS, Russia Roderic Guigo, Centre de Regulacio Genomica, Barcelona, Spain Wen-Lian Hsu, Academia Sinica, Taiwan Daniel Huson, University of Tubingen, Germany Jenn-Kang Hwang, National Chiao Tung University, Taiwan Uri Keich, University of Sydney, Australia Tak Wah Lam, University of Hong Kong, Hong Kong Doheon Lee, KAIST, Korea Sang Yup Lee, KAIST, Korea Ming Li, University of Waterloo, Canada Wentian Li, Feinstein Institute for Medical Research, USA Jingchu Luo, Peking University, China Bin Ma, University of Waterloo, Canada Hiroshi Mamitsuka, Kyoto University, Japan Sharmila Mande, TCS, India Shekhar Mande, CDFD, India Bud Mishra, New York University, USA Satoru Miyano, University of Tokyo, Japan Debasisa Mohanty, National Institute of Immunology, India Kenta Nakai, University of Tokyo, Japan Gajendra Raghava, Institute of Microbial Technology, India Mark Ragan, The University of Queensland, Australia Naren Ramakrishnan, Virginia Tech, USA Marie-France Sagot, INRIA and University Claude Bernard Lyon, France R. Sankararamakrishnan, IIT Kanpur, India David Sankoff, University of Ottawa, Canada Rahul Siddharthan, The Institute of Mathematical Sciences, India Steven Skiena, Stony Brook University, USA Paul Spellman, Lawrence Berkeley National Laboratory, USA Fengzhu Sun, University of Southern California, USA Lusheng Wang, City University of Hong Kong, Hong Kong Pramod Wangikar, IIT Bombay, India Limsoon Wong, National University of Singapore, Singapore Eric Xing, Carnegie Mellon University, USA Louxin Zhang, National University of Singapore, Singapore Michael Zhang, Cold Spring Harbor Laboratory, USA Xuegong Zhang, Tsinghua University, China Hongyu Zhao, Yale University, USA Local organizing chair Narayanaswamy Srinivasan, IISc, India Local organizing committee Alok Bhattacharya, JNU, Delhi, India Nagasuma Chandra, IISc, Bangalore, India P. Gautam, Anna University, Chennai, India S. Krishnaswamy, Madurai Kamaraj University, Madurai, India S. Ramakumar, Bioinformatics Centre, IISc, India Ram Ramaswamy, JNU, India D.N. Rao, IISc, Bangalore, India Veronica Rodrigues, NCBS, Bangalore, India Rahul Siddharthan, Institute of Mathematical Sciences, Chennai, India Tutorial chair Nagasuma Chandra, Bioinformatics Centre, IISc, India Tutorial committee K. Sekar, Bioinformatics Centre, IISC, India Ramanathan Sowdhamini, National Centre for Biological Sciences, India Industry Track M Vidyasagar, TCS, Hyderabad, India Publication and web chair Asif Javed, IBM T.J. Watson Research Center, USA ----------------------------------------------------------------- APBC2010 invites high-quality original papers and posters on any topic related to Bioinformatics and Computational Biology. Accepted papers will be invited to be published in the journal: BMC Bioinformatics. ------------------------------------------------------------------- Call for Papers APBC2010 invites high-quality original full papers on any topic related to Bioinformatics and Computational Biology. The submitted papers must have not been published or under the consideration for publication in any other journal or conference with formal proceedings. All accepted papers will have to be presented by one on the authors at the conference. Accepted papers will be invited to be published in the journal BMC Bioinformatics, following the journals publication policy. Papers should not be more than 10 pages in length, including the title, authors and addresses, abstract, text, figures and tables, and references. Authors can provide supplementary materials at their own website if necessary. The format of the files must follow BMC Bioinformatics guidelines. Please note that your submission risks not being considered for the review process if it does not meet these format requirements. Please check http://cs.nyu.edu/parida/APBC2010/CFP.html for submission guideline. The online submission system will be open from May 1 to July 20, 2009. From baskin from bio.umass.edu Mon Jul 6 17:41:35 2009 From: baskin from bio.umass.edu (Tobias Baskin) Date: Tue Jul 7 00:20:21 2009 Subject: [Arabidopsis] postdoc position open Message-ID: Arabidobsters -- don't be shocked -- this position is for work on Brachypodium distachyon. Universality through diversity! Thanks. TB A postdoctoral position is available to study the relation between cell wall structure and morphogenesis. The project uses the emerging model grass, Brachypodium distachyon, and both forward and reverse genetic approaches. The forward genetic approach will be a screen for mutants with aberrant root morphology; the reverse genetic approach will be to inactivate genes that are known to be important in other species. The position requires a Ph.D. in a relevant area of biology and preference will be given to candidates having experience with any of the following: developmental genetics; cell wall analysis; microscopy. The Baskin lab participates actively in the University of Massachusetts-Amherst Interdisciplinary Program in Plant Biology and also in a new cluster of scientists on campus working on B. distachyon. The University of Massachusetts is an Equal Opportunity Employer and I encourage all qualified persons to apply. To apply, please send your cv to baskin@bio.umass.edu. Check http://www.bio.umass.edu/biology/baskin/ for (somewhat outdated) information about my lab and feel free to contact me for more information. -- _ ____ __ ____ / \ / / \ / \ \ Tobias I. Baskin / / / / \ \ \ Biology Department /_ / __ /__ \ \ \__ 611 N. Pleasant St. / / / \ \ \ University of Massachusetts / / / \ \ \ Amherst, MA, 01003 / / ___ / \ \__/ \ ____ www.bio.umass.edu/biology/baskin Voice: 413 - 545 - 1533 Fax: 413 - 545 - 3243 From omar from ibt.unam.mx Tue Jul 7 21:53:08 2009 From: omar from ibt.unam.mx (Omar Pantoja) Date: Wed Jul 8 12:31:57 2009 Subject: [Arabidopsis] constitutive genes in rice Message-ID: <1247021588.4a540a142a819@webmail.ibt.unam.mx> Hi, I will appreciate your help in identifying a database that may contain information on consitutively expressed genes in rice. Thank you! -- Omar Pantoja (PhD) Instituto de Biotecnolog?a UNAM Apdo. Postal 510-3 Cuernavaca, Morelos 62250 M?xico Phone: (52) 5556 227656 Fax: (52) 7773 114691 e-mail: omar@ibt.unam.mx opantoja@gmail.com ---------------------------------------------------------------- Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. From sayanti_mandal from yahoo.com Sat Jul 11 04:03:52 2009 From: sayanti_mandal from yahoo.com (sayanti mandal) Date: Sun Jul 12 00:58:31 2009 Subject: [Arabidopsis] help!!!!!!!!!!! Message-ID: <241910.85705.qm@web35107.mail.mud.yahoo.com> hi I am a student from India,Delhi.doing PhD from University of Delhi South Campus,i am working in host-pathogen interactions,using arabidopsis as a model plant.But the problem is that my arabidopsi plant aren't grow well, they are still stunt, after one month of their transfer from the germination plate.They are grow in a temp of 22c,12 hrs day /night light with proper watering + nutrient also. After 2 months of growth they look thin and skeleton like. So every experiment is a failure, as the pathogen is opportunistic one,grows well on stressed tissue.My work is also suffering because of it. I hope to look froward for a reply. Sayanti Mandal Genetics Lab South Campus University of Delhi South Delhi,India-110021 Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com From Atef.Abo-Ogiala from forst.uni-goettingen.de Tue Jul 14 04:14:26 2009 From: Atef.Abo-Ogiala from forst.uni-goettingen.de (Abo-Ogiala, Atef) Date: Tue Jul 14 12:08:00 2009 Subject: [Arabidopsis] At5g02020 Message-ID: <99392551BB49ED458ACFE796416D3189E1DBD3@VS3.exc.top.gwdg.de> Hello, We ordered SALK_040413 of the gene At5g02020. We have problem with this line. The whole plants that we get from the seeds are wild type. Please if you have homozygous line for At5g02020 gene except Salk_146631 tell me from which source I can get it. 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 barragan from salk.edu Wed Jul 15 14:17:44 2009 From: barragan from salk.edu (Cesar Barragan) Date: Wed Jul 15 16:01:30 2009 Subject: [Arabidopsis] Re: Arab-gen Digest, Vol 51, Issue 7 In-Reply-To: <59adb7f80907151111m4f45f693o690cc920b0af7862@mail.gmail.com> References: <200907151703.n6FH3sp23299@net.bio.net> <59adb7f80907151111m4f45f693o690cc920b0af7862@mail.gmail.com> Message-ID: Mr, Abo-Ogiala You were targeting seeds for segregated lines. Do you have any PCR pictures we could see? How did you genotype these lines? A homozygous line has being already isolated for gene At5g02020, you can request SALK_064028C to ABRC. Thanks Cesar Barragan The Salk Institute for Biological Studies Genomic Analysis Laboratory 10010 North Torrey Pines Road La Jolla, CA 92037 Tel 858-453-4100 ext 1108 barragan@salk.edu On Jul 15, 2009, at 11:11 AM, Ronan OMalley wrote: > ---------- Forwarded message ---------- > From: > Date: Wed, Jul 15, 2009 at 9:03 AM > Subject: Arab-gen Digest, Vol 51, Issue 7 > To: arab-gen@magpie.bio.indiana.edu > > > 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. At5g02020 (Abo-Ogiala, Atef) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 14 Jul 2009 11:14:26 +0200 > From: "Abo-Ogiala, Atef" > Subject: [Arabidopsis] At5g02020 > To: > Message-ID: > <99392551BB49ED458ACFE796416D3189E1DBD3@VS3.exc.top.gwdg.de> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > We ordered SALK_040413 of the gene At5g02020. We have problem with > this line. > The whole plants that we get from the seeds are wild type. Please > if you have > homozygous line for At5g02020 gene except Salk_146631 tell me from > which > source I can get it. > > 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 > > > > > > ------------------------------ > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > > End of Arab-gen Digest, Vol 51, Issue 7 > *************************************** > From jaiswalp from science.oregonstate.edu Wed Jul 15 13:25:21 2009 From: jaiswalp from science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Wed Jul 15 16:02:00 2009 Subject: [Arabidopsis] Research Associate (Post Doc) at Oregon State Univ. Message-ID: <4A5E1F11.4070400@science.oregonstate.edu> Please post. Position Title: Research Associate (Post Doc) The Department of Botany and Plant Pathology has an immediate opening for a Research Associate (Post Doc) to work on a cereal plant genome wide gene expression analysis. This is a full-time, (1.0 FTE), 12-month, fixed-term position working in Dr. Pankaj Jaiswal's lab (http://www.science.oregonstate.edu/bpp/). How to Apply: To review the position description and apply, go to posting #0004455 at http://oregonstate.edu/jobs. When applying, you will be required to electronically submit your application, a Letter of Intent, and a Curriculum Vitae (including 3 references). For full consideration, apply by 07/31/09 when review of applications will begin. This position is required to develop a comprehensive gene expression catalog of rice and other cereal plant genes in various the plant development stages. The project includes histological studies, whole genome transcriptome and proteome data generation and analysis. The incumbent will be responsible for designing microarray and whole genome transcriptome/digital gene expression experiment(s) using newer high throughput sequencing technologies developed by Illumina, 454-LifeSciences, etc. Development of methods suitable to the experimental conditions and plant material being investigated, carrying out the experiments on analysis of anatomical samples using microscopy and whole genome transcriptome, data analysis and publication of the results in peer reviewed journals and submission to major data repositories. Besides this, the incumbent will also participate in lab's outreach activities, help in mentoring undergraduates and graduate students. Successful candidate will work with existing lab personnel and various collaborators that includes project PIs, faculty, highly trained PhD. level bioinformatics specialists, software developers and the department's fellow postdoc and graduate students. Required qualifications: - PhD in Plant Biology, Molecular Biology, Genetics, Biochemistry, Biological Chemistry, Metabolomics, or related field. - Worked previously on gene expression data generation and analysis in their PhD studies or postdoctoral training. Demonstrated expertise in studying plant development, anatomy, histology, microarrays, gene expression, proteomics, genetics and general understanding of plant biochemistry and gene regulation. - Demonstrated ability for independent and critical thinking, excellent communication skills in oral and written presentations in English and ability to work in teams. Pankaj Jaiswal Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA From barragan from salk.edu Wed Jul 15 17:47:29 2009 From: barragan from salk.edu (Cesar Barragan) Date: Wed Jul 15 18:36:42 2009 Subject: [Arabidopsis] Re: Arab-gen Digest, Vol 51, Issue 7 In-Reply-To: <1BE48506-35BC-4569-B98B-085B3FE78DB9@salk.edu> References: <6005D0F4-B30F-4F0C-800C-5FBCF684BC9F@salk.edu> <1BE48506-35BC-4569-B98B-085B3FE78DB9@salk.edu> Message-ID: Hello Abo-Ogiala Another source you might want to check is our website (http:// signal.salk.edu), here you can find more information about these lines or any other you may be interested. As an example, you will find that line SALK_146631 is a contaminated line so you could try instead SALK_139052 or SALK_127904 (http://signal.salk.edu/cgi-bin/ tdnaexpress). Information about this problem can be found in the FAQ section (http://signal.salk.edu/tdna_FAQs.html) as follow: 16. Q: On the T-DNA Express website, some insertion lines are very close in number or have the same number. For example SALK_005299, 005300, 005301, and 005305) have the same sequence. How can this be? A: We have found that the ABI 384-well sequence precipitation method can lead to cross-contamination of samples. A new protocol was devised to reduce the number of contaminating sequences. When verifying insertions of interest you should order and test all lines listed for that gene. The most definitive test to determining if the line contains the expected gene insertion is to use Southern blotting. Often times PCR can give a false negative result. We strongly suggest that you carry out Southern blotting and hybridization with the labeled gene as a probe to determine if the line you received contains an insertion in the expected gene. We hope these information and links can be useful for you and the community. Best Wishes. Cesar Barragan The Salk Institute for Biological Studies Genomic Analysis Laboratory 10010 North Torrey Pines Road La Jolla, CA 92037 Tel 858-453-4100 ext 1796 barragan@salk.edu >> Mr, Abo-Ogiala >> >> You were targeting seeds for segregated lines. Do you have any >> PCR pictures we could see? How did you genotype these lines? >> A homozygous line has being already isolated for gene At5g02020, >> you can request SALK_064028C to ABRC. >> Thanks >> >> Cesar Barragan >> The Salk Institute for Biological Studies >> Genomic Analysis Laboratory >> 10010 North Torrey Pines Road >> La Jolla, CA 92037 >> Tel 858-453-4100 ext 1796 >> barragan@salk.edu >> >> On Jul 15, 2009, at 11:11 AM, Ronan OMalley wrote: >> >>> ---------- Forwarded message ---------- >>> From: >>> Date: Wed, Jul 15, 2009 at 9:03 AM >>> Subject: Arab-gen Digest, Vol 51, Issue 7 >>> To: arab-gen@magpie.bio.indiana.edu >>> >>> >>> 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. At5g02020 (Abo-Ogiala, Atef) >>> >>> >>> -------------------------------------------------------------------- >>> -- >>> >>> Message: 1 >>> Date: Tue, 14 Jul 2009 11:14:26 +0200 >>> From: "Abo-Ogiala, Atef" >>> Subject: [Arabidopsis] At5g02020 >>> To: >>> Message-ID: >>> <99392551BB49ED458ACFE796416D3189E1DBD3@VS3.exc.top.gwdg.de> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> Hello, >>> >>> We ordered SALK_040413 of the geneSALK_040413. We have problem >>> with this line. >>> The whole plants that we get from the seeds are wild type. Please >>> if you have >>> homozygous line for At5g02020 gene except Salk_146631 tell me >>> from which >>> source I can get it. >>> >>> 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 >>> >>> >>> >>> >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> Arab-gen mailing list >>> Arab-gen@net.bio.net >>> http://www.bio.net/biomail/listinfo/arab-gen >>> >>> End of Arab-gen Digest, Vol 51, Issue 7 >>> *************************************** >>> >> > > Joseph R. Ecker > Professor, The Salk Institute for Biological Studies > Plant Biology/Genomic Analysis Laboratories > 10010 North Torrey Pines Road > La Jolla, CA 92037 > Phone (858) 453-4100 x1752 > FAX (858) 558-6379 > > Web addresses: > http://www.salk.edu > http://signal.salk.edu > http://pbio.salk.edu/pbioe/finaleckerhomepage.html > http://www.salk.edu/faculty/ecker.html > > Administrative Assistant: > > Nancy Benson > Phone (858) 453-4100 x1106 > Fax (858) 558-6379 > email: nbenson@salk.edu > > > > From jdfriesner from ucdavis.edu Wed Jul 15 18:19:17 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Wed Jul 15 18:37:11 2009 Subject: [Arabidopsis] Arabidopsis-2010: Website Open Message-ID: <002a01ca05a2$acd547e0$067fd7a0$@edu> The ICAR is coming to Yokohama, Japan and the new website has been launched. See the program listed, and the invited plenary speakers. Keynote speakers include Maarten Koorneef and Elliot Meyerowitz. http://arabidopsis2010.psc.riken.jp/ Also, the 2011 ICAR is scheduled to return to Madison, Wisconsin! With best regards, Joanna Friesner MASC Coordinator UC Davis From zjchen from mail.utexas.edu Wed Jul 15 16:50:21 2009 From: zjchen from mail.utexas.edu (Chen, Z. Jeffrey) Date: Wed Jul 15 18:37:50 2009 Subject: [Arabidopsis] Postdoctoral Fellow in Computational Biology In-Reply-To: References: Message-ID: Postdoctoral Fellow in Computational Biology The University of Texas at Austin We seek a highly motivated scientist to work in a plant molecular genetics and genomics laboratory. Our recent work on polyploidy, hybrid vigor, and epigenetics has led to the publications in Nature and PNAS http://polyploidy.biosci.utexas.edu/publications.php. The position is available immediately, and salary is competitive with experience. Successful candidates should have a Ph.D. in Computational Biology, Statistics or Computer Science with interest and experience in analyzing genome sequence and gene expression data. Training and skills in computer programming (perl/C/C++/shell script/linux), mathematical modeling, statistic tests, genome browser, and DNA sequence analysis are desirable. Experience with data structure of plant genomes, microarrays, small RNAs, microRNAs, and next-generation sequencing data are helpful. In addition to hypothesis testing using genomic and expression data, the postdoctoral fellow will work with a dynamic team of experimental biologists to analyze RNA-seq, ChIP-seq, and small RNA-seq data. The Chen lab http://polyploidy.biosci.utexas.edu/ is located in the section of Molecular Cell and Developmental Biology (http://www.biosci.utexas.edu/MCDB/) in the School of Biological Sciences (http://www.biosci.utexas.edu/) and the Institute for Cellular and Molecular Biology (http://www.icmb.utexas.edu/) at The University of Texas at Austin. There will be excellent opportunities for the postdoctoral fellows and graduate students to interact with faculty and students within MCDB as well as research groups in the Integrative Biology (http://www.biosci.utexas.edu/IB/) and the Center for Computational Biology and Bioinformatics (http://ccbb.biosci.utexas.edu/). Please visit http://www.utexas.edu for more information about the university and living in Austin. The University of Texas at Austin is an Affirmative Action/Equal Opportunity employer. Interested candidates should send a statement of career goals and a copy of curriculum vitae including names and addresses of three references via email . Z. Jeffrey Chen, Ph. D. D. J. Sibley Centennial Professor of Plant Molecular Genetics The University of Texas at Austin Institute for Cellular and Molecular Biology (ICMB) 1 University Station A-4800 Austin, TX 78712-0159 http://polyploidy.biosci.utexas.edu/ E-mail: zjchen@mail.utexas.edu Office: 512-475-9327 Lab: 512-475-9335 Fax: 512-471-2149 From akhilsr from gmail.com Wed Jul 15 20:07:29 2009 From: akhilsr from gmail.com (Akhil S.) Date: Thu Jul 16 12:13:34 2009 Subject: [Arabidopsis] Re: help!!!!!!!!!!! References: Message-ID: <3bdabd07-89aa-4012-80f2-5d121ff82a7a@i4g2000prm.googlegroups.com> On Jul 11, 2:03?am, sayanti mandal wrote: > hi > > I am a student from India,Delhi.doing PhD from University of Delhi South > Campus,i am working in host-pathogen interactions,using arabidopsis as a model > plant.But the problem is that my arabidopsi plant aren't grow well, they are > still stunt, after one month of their transfer from the germination plate.They are > grow in a temp of 22c,12 hrs day /night light with proper watering + nutrient also. After > 2 months of growth they look thin and skeleton like. So every experiment is a failure, as the > pathogen is opportunistic one,grows well on stressed tissue.My work is also > suffering because of it. I hope to look froward for a reply. > > Sayanti Mandal > > Genetics Lab > > South Campus > > University of Delhi South > > Delhi,India-110021 > > ? ? ? Love Cricket? Check out live scores, photos, video highlights and more. Click herehttp://cricket.yahoo.com Hi, on which pathogen you are working on. From conferences from embl.de Thu Jul 16 06:45:22 2009 From: conferences from embl.de (EMBL Courses & Conferences) Date: Thu Jul 16 12:13:58 2009 Subject: [Arabidopsis] EMBO Conference Series on Morphogenesis and Dynamics of Multicellular Systems, EMBL Germany Message-ID: <124774461479118430@lxmail02-vm> EMBL Conference Announcement Dear Colleagues, Please be informed that the programme for the EMBO Conference Series on Morphogenesis and Dynamics of Multicellular Systems 2 - 6 October 2009, European Molecular Biology Laboratory, Heidelberg, Germany is available online. Please check the conference website for more information: http://www.embl.de/conferences/morphogenesis/2009 Registration and abstract deadline: 31 July 2009 The aim of this meeting is to bring together researchers addressing the role of collective cell behaviour in generating complex biological form. The number of researchers investigating such issues is rapidly increasing and we feel that there is a need to exchange knowledge in a specialised meeting. We are particularly keen to incorporate cutting-edge, imaging, biophysical and computational approaches that will drive the field in new directions. We have a reduced registration fee for PhD students. Please circulate this announcement to interested members and groups within your institute. The poster you can download at: http://www.embl.de/conferences/morphogenesis/2009/poster.pdf If you wish to receive more information about courses and conferences at EMBL, please sign up for our newsletter. If you do not wish to receive further announcements of EMBL events, please reply to this message with "unsubscribe" in the subject line. ************************************************ Best wishes, Adela Valceanu Conference Officer European Molecular Biology Laboratory Meyerhofstr. 1 D-69117 Heidelberg Tel: +49-6221-387 8625 Fax: +49-6221-387 8158 For full event listings please visit our website: www.embl.org/events or sign up for our newsletter. ************************************************ From ehaswell from wustl.edu Thu Jul 16 09:36:19 2009 From: ehaswell from wustl.edu (Elizabeth Haswell) Date: Thu Jul 16 12:14:23 2009 Subject: [Arabidopsis] Arab-gen mailing list submission Message-ID: A postdoctoral position is open in the Haswell Lab in the Biology Department at Washington University in St. Louis (see http://biology4.wustl.edu/faculty/haswell/ for a research description). Several projects are available; each uses a combination of genetic, cell biological, biochemical, and/or electrophysiological techniques to study the structure and function of a family of mechanosensitive ion channels in the model plant Arabidopsis thaliana. Applicants with previous plant biology or electrophysiology experience are preferred. To apply, please submit to ehaswell@wustl.edu: 1. A cover letter explaining specifically why you are interested in joining the group, what skills and knowledge you would contribute, and what you think we could offer in terms of training. In addition, please describe your career goals. 2. A CV with three or more references and their full contact information. 3. A short proposal for a possible project in the lab. This need not be detailed, but should indicate that you have read enough of the literature to be sincerely interested in some aspect of our research, and that you can think independently and creatively about your work. This can be part of the cover letter. _____________________________ Elizabeth Haswell Assistant Professor Dept. of Biology, Box 1137 Washington University in St. Louis One Brookings Drive St. Louis, MO 63130 ph (314) 935-9223 email: ehaswell@wustl.edu http://biology4.wustl.edu/faculty/haswell/ From aakash.chawade from gmail.com Thu Jul 16 14:52:47 2009 From: aakash.chawade from gmail.com (Aakash Chawade) Date: Fri Jul 17 13:03:11 2009 Subject: [Arabidopsis] Re: help!!!!!!!!!!! Message-ID: <3e081bb50907161252q6f9fcf0dvbe771a3bc3cf636d@mail.gmail.com> Do you mean the plants won't grow properly even without any applied biotic stress? From bastiaan76 from gmail.com Fri Jul 17 10:16:32 2009 From: bastiaan76 from gmail.com (bastiaan76@gmail.com) Date: Fri Jul 17 13:03:42 2009 Subject: [Arabidopsis] GenBank ID to AGI number Message-ID: <0016e642d710f80cde046ee84552@google.com> Hello all, I am looking for a way to convert a list of GenBank Gen Info Identifier numbers (eg gi:5123694) to AGI IDs (eg At4g34770) and have unfortunately been unsuccessful so far. I am able to convert them one at a time by using the NCBI search and following a link in the resulting hit but would really like to be able to do this for large genelists. Thank you, -Bas ************************************************************ Bastiaan Bargmann, Ph.D. Plant Genomics and Networks Center for Genomics and Systems Biology Biology Department New York University 100 Washington Square East 1009 Silver Building New York, NY 10003 phone: +1 212 992 9560 fax: +1 212 995 3691 email: bob1@nyu.edu ************************************************************ From soheil.mahmoud from ubc.ca Thu Jul 16 18:40:51 2009 From: soheil.mahmoud from ubc.ca (Mahmoud, Soheil) Date: Fri Jul 17 13:04:42 2009 Subject: [Arabidopsis] Technician or Postdoc position Message-ID: <6EEA43D22289484890D119821101B1DF48918F@exchange20.mercury.ad.ubc.ca> A full time position for a highly motivated technician or postdoctoral fellow is immediately available in the laboratory of Dr. Soheil Mahmoud at the Okanagan campus of the University of British Columbia in Kelowna, British Columbia, Canada (http://www.kelowna.ca/cm/site3.aspx). The project involves investigating the molecular basis of aroma formation in lavender flowers using modern molecular approaches. This exciting project is funded in part by Genome British Colombia and offers exceptional opportunities for the right candidate. Qualifications include strong background in plant molecular biology and/ or biochemistry (MSc or PhD), experience with transcript profiling, real time PCR, and with transformation of bacteria and plants. Please forward current CV and contact information for three referees by email to Soheil.Mahmoud@ubc.ca. This position is for one year, with possibility of renewal pending availability of funds. Soheil S. Mahmoud Irving K. Barber School of Arts and Sciences University of British Columbia Okanagan 3333 University Way Kelowna, B.C. Canada V1V 1V7 Tel: 250.807.8752 Fax: 250.807.8005 soheil.mahmoud@ubc.ca http://people.ok.ubc.ca/smahmoud/soheilhome.htm From anirbanb from ncbs.res.in Sun Jul 19 23:43:41 2009 From: anirbanb from ncbs.res.in (Anirban Baral) Date: Mon Jul 20 13:05:44 2009 Subject: [Arabidopsis] Arabidopsis RNAi lines. Message-ID: <58085.192.168.1.1.1248065021.squirrel@mail.ncbs.res.in> Hi everyone, I am looking for RNAi lines in Arabidopsis against specific genes.So far I have come across only Agricola(ASCB).Can someone please suggest me an alternative source as some of the genes I wish to silence are not availble in their resources. Thanks in advance. Anirban. -- Anirban Baral JUNIOR SCHOLAR NATIONAL CENTRE FOR BIOLOGICAL SCIENCES TATA INSTITUTE OF FUNDAMENTAL RESEARCH UAS-GKVK CAMPUS,BELLARY ROAD BANGALORE-560065,INDIA From dcoman from ethz.ch Sat Jul 18 12:43:24 2009 From: dcoman from ethz.ch (Diana Coman) Date: Mon Jul 20 13:11:42 2009 Subject: [Arabidopsis] Re: Arab-gen Digest, Vol 51, Issue 10 In-Reply-To: <200907181703.n6IH3Gp18392@net.bio.net> References: <200907181703.n6IH3Gp18392@net.bio.net> Message-ID: Dear Bas, Here is a useful link : http://bar.utoronto.ca/ntools/cgi-bin/ntools_agi_converter.cgi Good luck! Diana Sent from my iPhone On 18.07.2009, at 19:03, 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. Re: help!!!!!!!!!!! (Aakash Chawade) > 2. GenBank ID to AGI number (bastiaan76@gmail.com) > 3. Technician or Postdoc position (Mahmoud, Soheil) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 16 Jul 2009 21:52:47 +0200 > From: Aakash Chawade > Subject: [Arabidopsis] Re: help!!!!!!!!!!! > To: arab-gen@magpie.bio.indiana.edu > Message-ID: > <3e081bb50907161252q6f9fcf0dvbe771a3bc3cf636d@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Do you mean the plants won't grow properly even without any applied > biotic > stress? > > > ------------------------------ > > Message: 2 > Date: Fri, 17 Jul 2009 15:16:32 +0000 > From: bastiaan76@gmail.com > Subject: [Arabidopsis] GenBank ID to AGI number > To: arab-gen@magpie.bio.indiana.edu > Message-ID: <0016e642d710f80cde046ee84552@google.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes > > Hello all, > > I am looking for a way to convert a list of GenBank Gen Info > Identifier > numbers (eg gi:5123694) to AGI IDs (eg At4g34770) and have > unfortunately > been unsuccessful so far. > > I am able to convert them one at a time by using the NCBI search and > following a link in the resulting hit but would really like to be > able to > do this for large genelists. > > Thank you, > > -Bas > > ************************************************************ > Bastiaan Bargmann, Ph.D. > > Plant Genomics and Networks > Center for Genomics and Systems Biology > Biology Department > New York University > 100 Washington Square East > 1009 Silver Building > New York, NY 10003 > phone: +1 212 992 9560 > fax: +1 212 995 3691 > email: bob1@nyu.edu > ************************************************************ > > > ------------------------------ > > Message: 3 > Date: Thu, 16 Jul 2009 16:40:51 -0700 > From: "Mahmoud, Soheil" > Subject: [Arabidopsis] Technician or Postdoc position > To: > Message-ID: > <6EEA43D22289484890D119821101B1DF48918F@exchange20.mercury.ad.ubc.ca > > > Content-Type: text/plain; charset="us-ascii" > > A full time position for a highly motivated technician or postdoctoral > fellow is immediately available in the laboratory of Dr. Soheil > Mahmoud > at the Okanagan campus of the University of British Columbia in > Kelowna, > British Columbia, Canada (http://www.kelowna.ca/cm/site3.aspx). The > project involves investigating the molecular basis of aroma > formation in > lavender flowers using modern molecular approaches. This exciting > project is funded in part by Genome British Colombia and offers > exceptional opportunities for the right candidate. Qualifications > include strong background in plant molecular biology and/ or > biochemistry (MSc or PhD), experience with transcript profiling, real > time PCR, and with transformation of bacteria and plants. Please > forward current CV and contact information for three referees by email > to Soheil.Mahmoud@ubc.ca. This position is for one year, with > possibility of renewal pending availability of funds. > > > > > > Soheil S. Mahmoud > > Irving K. Barber School of Arts and Sciences > > University of British Columbia Okanagan > > 3333 University Way > > Kelowna, B.C. Canada V1V 1V7 > > Tel: 250.807.8752 Fax: 250.807.8005 > > soheil.mahmoud@ubc.ca > > http://people.ok.ubc.ca/smahmoud/soheilhome.htm > > > > > > ------------------------------ > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > > End of Arab-gen Digest, Vol 51, Issue 10 > **************************************** From phoebe.chen from deakin.edu.au Sun Jul 19 22:17:16 2009 From: phoebe.chen from deakin.edu.au (Phoebe Chen) Date: Mon Jul 20 13:12:38 2009 Subject: [Arabidopsis] Deadline Extended - APBC2010 Message-ID: <096466DE3CBF11439436E7B189DC44092C296587@mirzam-1.du.deakin.edu.au> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Due to many requests, the paper submission deadline is extended to August 15, 2009. The Eighth Asia-Pacific Bioinformatics Conference (APBC2010) Bangalore, India, 18-21 January 2010 http://cs.nyu.edu/parida/APBC2010/index.html =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D The Asia Pacific Bioinformatics Conference (APBC) series, founded in 2003, (Previous APBC meetings APBC2009 (13-16 January 2009, Beijing, China) APBC2008 (14-17 January 2008, Kyoto, Japan) APBC2007 (14-17 January 2007, Hong Kong) APBC2006 (13-16 February 2006, Taipei, Taiwan) APBC2005 (17-21 January 2005, Singapore) APBC2004 (18-22 January 2004, Dunedin, New Zealand) APBC2003 (4-7 February 2003, Adelaide, Australia)) is an annual international forum for exploring research, development and applications of Bioinformatics and Computational Biology. The Eighth Asia-Pacific Bioinformatics Conference, APBC2010 will be held in Bangalore, India. The aim of the conference is to bring together researchers, professionals, and industrial practitioners from all over the world for interaction and exchange of knowledge and ideas in all areas of bioinformatics and computational biology. ---------------------------------------------------------------- Important Dates Paper submission deadline (extended) August 15, 2009 Paper acceptance decision Sep 14, 2009 Camera-ready copy of papers and Author registration Oct 9, 2009 Poster submission open July 21, 2009 Poster submission deadline Sep 25, 2009 Poster acceptance decision Oct 9, 2009 Registration open Sept 20, 2009 Early-bird registration Nov 20, 2009 Conference Jan 18-21, 2010 ---------------------------------------------------------- Conference chairs: Laxmi Parida, IBM T.J. Watson Research Center, USA Ramanathan Sowdhamini, National Centre for Biological Sciences, India Program committee chairs: Gene Myers, HHMI, Janelia Farm, USA Laxmi Parida, IBM T.J. Watson Research Center, USA APBC Steering Committee Phoebe Chen (Chair), Deakin University, Australia Sang Yup Lee, KAIST, Korea Satoru Miyano, University of Tokyo, Japan Mark Ragan, University of Queensland, Australia Limsoon Wong, National University of Singapore Michael Q. Zhang, CHSL, USA and Tsinghua University, China ----------------------------------------------------------------- Topics of Interest Papers are solicited on, but not limited to, the following topics: =95 Sequence Analysis =95 Motif Finding =95 Recognition of Genes and Functional Elements =95 RNA Analysis =95 Physical and Genetic Mapping =95 Molecular Evolution and Phylogeny =95 Protein Structure Analysis =95 Microarray Design and Data Analysis =95 Deep Sequencing Data Processing =95 Transcriptome, Gene Expression =95 Epigenomics =95 Proteomics and Post-Translational Modifications =95 Pathways, Networks and Systems =95 Ontologies =95 Databases and Data Integration =95 Biomedical Literature Mining and Understanding =95 Population Genetics, SNP and Haplotyping =95 Comparative Genomics --------------------------------------------------------------- Program committee (Confirmed): Srinivas Aluru, Iowa State University, USA Tatsuya Akutsu, Kyoto University, Japan Joel Bader, Johns Hopkins University, USA Chitta Baral, Arizona State University, USA Upinder Bhalla, National Center for Biological Sciences, India Alok Bhattacharya, Jawaharlal Nehru University, India Harmen Bussemaker, Columbia University, USA Francis Chin, Hong Kong University, Hong Kong Nadia El-Mabrouk, University of Montreal, Canada Mikhail Gelfand, Institute for Information Transmission Problems RAS, Russi= a Roderic Guigo, Centre de Regulacio Genomica, Barcelona, Spain Wen-Lian Hsu, Academia Sinica, Taiwan Daniel Huson, University of Tubingen, Germany Jenn-Kang Hwang, National Chiao Tung University, Taiwan Uri Keich, University of Sydney, Australia Tak Wah Lam, University of Hong Kong, Hong Kong Doheon Lee, KAIST, Korea Sang Yup Lee, KAIST, Korea Ming Li, University of Waterloo, Canada Wentian Li, Feinstein Institute for Medical Research, USA Jingchu Luo, Peking University, China Bin Ma, University of Waterloo, Canada Hiroshi Mamitsuka, Kyoto University, Japan Sharmila Mande, TCS, India Shekhar Mande, CDFD, India Bud Mishra, New York University, USA Satoru Miyano, University of Tokyo, Japan Debasisa Mohanty, National Institute of Immunology, India Kenta Nakai, University of Tokyo, Japan Gajendra Raghava, Institute of Microbial Technology, India Mark Ragan, The University of Queensland, Australia Naren Ramakrishnan, Virginia Tech, USA Marie-France Sagot, INRIA and University Claude Bernard Lyon, France R. Sankararamakrishnan, IIT Kanpur, India David Sankoff, University of Ottawa, Canada Rahul Siddharthan, The Institute of Mathematical Sciences, India Steven Skiena, Stony Brook University, USA Paul Spellman, Lawrence Berkeley National Laboratory, USA Fengzhu Sun, University of Southern California, USA Lusheng Wang, City University of Hong Kong, Hong Kong Pramod Wangikar, IIT Bombay, India Limsoon Wong, National University of Singapore, Singapore Eric Xing, Carnegie Mellon University, USA Louxin Zhang, National University of Singapore, Singapore Michael Zhang, Cold Spring Harbor Laboratory, USA Xuegong Zhang, Tsinghua University, China Hongyu Zhao, Yale University, USA Local organizing chair Narayanaswamy Srinivasan, IISc, India Local organizing committee Alok Bhattacharya, JNU, Delhi, India Nagasuma Chandra, IISc, Bangalore, India P. Gautam, Anna University, Chennai, India S. Krishnaswamy, Madurai Kamaraj University, Madurai, India S. Ramakumar, Bioinformatics Centre, IISc, India Ram Ramaswamy, JNU, India D.N. Rao, IISc, Bangalore, India Veronica Rodrigues, NCBS, Bangalore, India Rahul Siddharthan, Institute of Mathematical Sciences, Chennai, India Tutorial chair Nagasuma Chandra, Bioinformatics Centre, IISc, India Tutorial committee K. Sekar, Bioinformatics Centre, IISC, India Ramanathan Sowdhamini, National Centre for Biological Sciences, India Industry Track M Vidyasagar, TCS, Hyderabad, India Publication and web chair Asif Javed, IBM T.J. Watson Research Center, USA ----------------------------------------------------------------- APBC2010 invites high-quality original papers and posters on any topic related to Bioinformatics and Computational Biology. Accepted papers will be invited to be published in the journal BMC Bioinformatics. ------------------------------------------------------------------- Call for Papers APBC2010 invites high-quality original full papers on any topic related to Bioinformatics and Computational Biology. The submitted papers must have not been published or under the consideration for publication in any other journal or conference with formal proceedings. All accepted papers will have to be presented by one on the authors at the conference. Accepted papers will be invited to be published in the journal BMC Bioinformatics, following the journals publication polic= y. Papers should not be more than 10 pages in length, including the title, authors and addresses, abstract, text, figures and tables, and references. Authors can provide supplementary materials at their own website if necessa= ry. The format of the files must follow BMC Bioinformatics guidelines. Please note that your submission risks not being considered for the review process if it does not meet these format requirements. Please check http://cs.nyu.edu/parida/APBC2010/CFP.html for submission guideline. The online submission system will be open from May 1 to July 20, 2009. --------------------------------------------------------------- From gl242 from cornell.edu Wed Jul 22 16:12:17 2009 From: gl242 from cornell.edu (gl242) Date: Thu Jul 23 11:28:12 2009 Subject: [Arabidopsis] the problem of protein degradation Message-ID: <000601ca0b11$1860ff40$4922fdc0$@edu> Hello everyone, I am working on one of transposase proteins. When I tried to extract the endogenous protein, I found a very strange problem. I can only get the truncated form of this protein if without SDS in the extraction buffer. If I added SDS in the protein extraction buffer, it will inhibit the protein degradation. Triton X-100 has no any effect on the protein degradation. High concentration of protease inhibitors cocktail (Sigma; for plant tissue extraction) also failed to inhibit the protein degradation. Can someone please suggest me how to prevent the protein degradation in the extraction process? Any comments are welcome! Thanks in advance. Gang From ijf from mole.bio.cam.ac.uk Mon Jul 27 07:45:07 2009 From: ijf from mole.bio.cam.ac.uk (Ian Furner) Date: Mon Jul 27 11:55:11 2009 Subject: [Arabidopsis] Re Arabidopsis RNAi lines Message-ID: <45953767-FE37-4B24-A17E-0E4C9786E436@mole.bio.cam.ac.uk> Dear All to the best of my knowledge the Agrikola lines are by far the single largest collection of RNAi lines (http:// www.agrikola.org/index.php?o=/agrikola/main) . A smaller collection of lines was made by the ChromDB (http://www.chromdb.org/) but these are directed against genes involved in chromatin. You can order these lines from NASC(http://arabidopsis.info/). Ian Furner Dept of Genetics, University of Cambridge From vnunes from igc.gulbenkian.pt Mon Jul 27 11:31:57 2009 From: vnunes from igc.gulbenkian.pt (Vera Nunes) Date: Mon Jul 27 11:57:24 2009 Subject: [Arabidopsis] Fungus gnats treatment and prevention Message-ID: <1248712317.4a6dd67d5538d@webmail.igc.gulbenkian.pt> Hello, Our growth chambers have been shown a continuous increase of the fungus gnats population. We always do the first watering, as well as the subsequent ones, with the biological insecticide Vectobac (an equivalent to Gnatrol, Bacillus thuringiensis var. israelensis). However, we continue to have larvae infestations in some inserts as well as an increase of adult insects captures, although we don't overwater. Can someone please tell me insecticides (active ingredient, concentration, formulation) that we can use to control the adult flies and also larvae not only in a curative but also preventive way (to apply in the future), that wont interfere with Arabidopsis physiology? Thanks a lot! Vera From cashandy from gmail.com Mon Jul 27 22:10:24 2009 From: cashandy from gmail.com (=?GB2312?B?8eO5+tPC?=) Date: Tue Jul 28 12:20:42 2009 Subject: [Arabidopsis] HelP: ion leakage assay In-Reply-To: <967b5ae60907271958k38d58d0cqa426d85c7b277570@mail.gmail.com> References: <967b5ae60907271958k38d58d0cqa426d85c7b277570@mail.gmail.com> Message-ID: <967b5ae60907272010r4c61b273r961dd5469a52dbef@mail.gmail.com> Dear all, Recently I needed to perform ion leakage assay, and referred to one cell paper on autophagy. But I am confused with this method about eaf disc collection: how long after pathogen infection to collect the discs? Whether the method means leaf disc is collected once and conductivity is measureed ove time or collecting leaf at different infection time points and measuring once? If the former is used in your lab, I doubt whether HR is still induced ex vivo. If you deliver me the detailed protocol your lab follow routinely, the help will do me a great favor. Thank you very much! From kkvinodh from gmail.com Tue Jul 28 01:02:11 2009 From: kkvinodh from gmail.com (K.K.Vinod) Date: Tue Jul 28 12:21:37 2009 Subject: [Arabidopsis] A global search for a classic work Message-ID: <63d480890907272302j4b57a8ecu2a2d7ec971ba166d@mail.gmail.com> *Dear Colleagues,* * * *I am recirculating this request, because my earlier request had a (gross) typographic mistake.... Regret for that ** * *Kosambi's mapping function (Kosambi, 1944) had almost become synonymous to marker based linkage mapping studies world wide. Akin to most of the classical geneticists, Kosambi's work also perhaps remained unpopular for quite a long time till the transition decade of the 20th century. To know more about D D Kosambi please check **http://plant-breeding.**blogspot.com* *. * *D D Kosambi, basically a mathematician, worked on this classical mapping function when he was a mathematics Professor at Ferguson College, Pune, India. The circumstances leading to this work is not found recorded anywhere. * *To start with this endeavour, I was looking for the basic material - the paper itself. Unfortunately I could not get it so far. This is a global request for the paper D D Kosambi had published in Annals of Eugenics. The citation is, * * * *Kosambi DD (1944) The estimation of map distance from recombination values, Annals of Eugenics, 12(3): 172-175* * * *This paper may be available in your library. Please send me a scanned / photocopy.* * * *With kind regards,* * * *Dr K K Vinod* * * *Senior Scientist (Plant Breeding) Indian Agricultural Research Institute Rice Breeding and Genetics Research Centre Aduthurai 612101 Tanjavur District Tamil Nadu INDIA ============================== Phone: +91 435 2470308 Fax: +91 435 2471195 Cell: +91 94430 81539 ============================== Alternate E-mail: **kkvinod@hotmail.com* * Web Address: **http://kkvinod.webs.com* * ==============================* From Madlen.Schiller from mailbox.tu-dresden.de Tue Jul 28 03:25:54 2009 From: Madlen.Schiller from mailbox.tu-dresden.de (Madlen Schiller) Date: Tue Jul 28 12:22:18 2009 Subject: [Arabidopsis] differential centrifugation of Arabidopsis In-Reply-To: <200907231703.n6NH39p20914@net.bio.net> References: <200907231703.n6NH39p20914@net.bio.net> Message-ID: <20090728102554.p2z7j4eus8ww0w0s@mail.zih.tu-dresden.de> Hello everyone, I'm doing differential centrifugation to isolate proteins of Arabidopsis. But unfortunatelly I am not sure what is in fraction P1 (1000 g, cell fragments, nucleus?), P8 (8000 g, ER-bodies, plasmamembran?) and P12 (12 000 g, mitochondria, chloroplasts?). Does anyone knows what is in the fractions or a paper? Thanks a lot Madlen From rmitra from carleton.edu Wed Jul 29 11:02:37 2009 From: rmitra from carleton.edu (Raka Mitra) Date: Wed Jul 29 13:36:22 2009 Subject: [Arabidopsis] Gateway-compatible GFP fusion vector Message-ID: <3E45AE22-5947-4CBF-A279-8DD72D6ECD57@carleton.edu> Hi Arabidopsis researchers, I am looking for a binary Gateway-compatible destination vector with these characteristics: 1. Creates C-terminal GFP fusions, driven by the 35S (or 2x35S) promoter, such as the pMDC 83, 84, 85 set developed by Mark Curtis and Ueli Grossniklaus: http://www.plantphysiol.org/cgi/content/full/133/2/462/ 2. Confers Kanamycin resistance in the plant 3. Confers something OTHER than Kanamycin resistance in bacteria (as we are using Invitrogen's pENTR Gateway entry vectors). Thus far, my searches of published vectors has proven unsuccessful. Is anyone aware of such a vector, and if so, how can I get it? Thank you! - Raka -------------------------------------- Raka M. Mitra, PhD Assistant Professor, Biology Carleton College One North College Street Northfield, MN 55057 U.S.A. https://apps.carleton.edu/people/rmitra/ From kkvinodh from gmail.com Wed Jul 29 06:48:14 2009 From: kkvinodh from gmail.com (K.K.Vinod) Date: Wed Jul 29 13:37:02 2009 Subject: [Arabidopsis] A global search for a classic work - A success Message-ID: <63d480890907290448o63333a88qaacc268bc99aa441@mail.gmail.com> *Dear Colleagues,* * * *I am happy to announce that my search for DD Kosambi's work on recombination values (Kosambi, 1944) has been successful. I am very thankful to Dr Bernhard Kaupe of Germany for sending me a copy of the paper. I wish to share this with everyone, who are interested in this work.* * * *With kind regards,* * * *Dr K K Vinod* * * *Senior Scientist (Plant Breeding) Indian Agricultural Research Institute Rice Breeding and Genetics Research Centre Aduthurai 612101 Tanjavur District Tamil Nadu INDIA ============================== Phone: +91 435 2470308 Fax: +91 435 2471195 Cell: +91 94430 81539 ============================== E-mail: kkvinodh@gmail.com* *Alternate E-mail: **kkvinod@hotmail.com* * Web Address: **http://kkvinod.webs.com* * ==============================* From simonmi1 from post.tau.ac.il Wed Jul 29 02:49:45 2009 From: simonmi1 from post.tau.ac.il (simonmi1@post.tau.ac.il) Date: Wed Jul 29 13:37:29 2009 Subject: [Arabidopsis] differential centrifugation of Arabidopsis In-Reply-To: <20090728102554.p2z7j4eus8ww0w0s@mail.zih.tu-dresden.de> References: <200907231703.n6NH39p20914@net.bio.net> <20090728102554.p2z7j4eus8ww0w0s@mail.zih.tu-dresden.de> Message-ID: <20090729104945.16214po2eleogxsp@webmail.tau.ac.il> Hi Madlen, I don't know about P8, but in P1 you should have starch, nuclei and cell debris and in P12 you should have mitochondria, some plastids and peroxisomes. Obviously each fraction is contaminated with all other organelles, its just that each fraction should be enriched with the organelles you look for. If you need to isolate a particular organelle such as mitochondria you should spin the P12 in a density gradient such as percoll. Hope this helps a bit and good luck Simon Quoting "Madlen Schiller" : > Hello everyone, > > I'm doing differential centrifugation to isolate proteins of > Arabidopsis. But unfortunatelly I am not sure what is in fraction P1 > (1000 g, cell fragments, nucleus?), P8 (8000 g, ER-bodies, > plasmamembran?) and P12 (12 000 g, mitochondria, chloroplasts?). > Does anyone knows what is in the fractions or a paper? > > Thanks a lot > > Madlen > > > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > From Roberta.Galletti from uniroma1.it Thu Jul 30 10:07:47 2009 From: Roberta.Galletti from uniroma1.it (Roberta.Galletti@uniroma1.it) Date: Thu Jul 30 12:08:51 2009 Subject: [Arabidopsis] Vector for DEX-dependent transgene expression in Arabidopsis Message-ID: I would be very grateful to anyone who could provide a vector for DEXAMETHASONE-inducible transgene expression in Arabidopsis with resistance in plant to whatever antibiotic or herbicide, but NOT hygromycin! Roberta Galletti, PhD Department of Plant Biology University of Rome ?La Sapienza? P.le Aldo Moro 5, 00185 Rome (Italy) Phone : + 39-06-49912459 Fax : +39-06-49912446 ------------------------------------- ..A lab is just another place to play.... >From ?Dancing naked in the mind field? Kary B. Mullis, Nobel Prize in Chemistry 1993. From paulslpool from yahoo.co.uk Fri Jul 31 02:11:22 2009 From: paulslpool from yahoo.co.uk (Paul smith) Date: Fri Jul 31 12:20:21 2009 Subject: [Arabidopsis] Seeking protocol for seed & seedling fatty acid analysis Message-ID: <787676.61109.qm@web26402.mail.ukl.yahoo.com> Hello, Not being a chemist, I am seeking a detailed protocol for extraction and GC analysis of "free" fatty acids and fatty acids in triglycerides (TGAs) in Arabidopsis seeds and seedlings (time-course experiments). This is to look quantitatively and qualitatively at the amount and composition of TGAs in seeds of a mutant vs. wildtype and their changes during germination and seedling establishment. None of the methods I have seen in the literature is detailed enough for someone inexperienced to follow without assistance of an expert (none available where I work). I am also concerned about the safety aspects with all the dangerous organic chemicals involved. I would be very grateful to any expert that may provide me with a detailed protocol that can safely be followed. I would also appreciate that details are included for special glassware & equipment that is required for the procedures. Please note that I do have access to a Agilent 6890N GC machine with an automatic injector and a 30 m HP-5 30 m column, suitable for FAs. Thank you! Paul Smith paulslpool@yahoo.co.uk From benholt from ou.edu Fri Jul 31 13:07:42 2009 From: benholt from ou.edu (Holt, Ben F. III) Date: Fri Jul 31 18:26:59 2009 Subject: [Arabidopsis] RE:Ion Leakage Message-ID: I haven't done this assay in a long time, but you can look at Figure 2C in Cell 108, 743-754 for an example measuring HR and/or disease related cell death after bacterial infiltration. If my history is correct, I think C.J. Baker's lab originally reported this in the early 90's and we started using it in the Dangl lab at UNC-Chapel Hill about 10 years later. Since then a number of other papers have reported the use of conductance/ion leakage as a proxy for dell death measurement. You will have to test it in your own system, but I can say that cell death and disease symptoms do proceed ex vivo. In fact, the curves of increasing ion conductivity in water containing these infiltrated leaf disks would look pretty much identical to a "curve" of visual symptoms for HR or disease related cell death symptoms. The general protocol is straightforward: 1. Infiltrate leaf with bacteria (and don't be going crazy with the syringe - if you can't infiltrate 1/2 the leaf by touching the leaf and infiltrating in ONE spot, you need to practice that technique first) 2. Perhaps wait 1/2 hour to hour 3. Cut out uniform leaf disks with a sharp cork borer - avoid syringe damaged area if they exist and try to take samples in the same area on each leaf 4. Wash in distilled water in weigh boats to remove ions released by cutting the disks - I think we originally did 1/2 hour wash, but that's probably overkill 5. While the disks are washing, measure out identical, small volumes of distilled water into tubes (conductivity probe must fit!) or weigh boats. I can't remember the ratios, but I want to say roughly 6-8 disks in 20ml water - play with it. 6. Take a zero measurement of the water to make sure your water and tubes are ion free upfront 7. Moving quickly, move disks to paper towels to remove wash water (very gently dab with with kimwipe) and place in prepared tubes 8. Measure conductivity changes over time as a proxy for ion leakage/cell death Notes: If you use tubes, be careful not to touch (crush) leaf disks when inserting the probe to make measurements. Also, as with all proxy measurements, at a minimum, you had best be sure that the ion leakage measurements correlate with known visual symptoms. Finally, don't expect the leaf disks to show typical HR symptoms (visually) while floating in the water, but if you remove them from the water (and compare to controls), they will show real obvious HR collapse as soon as they dry up a bit. If you want to know the latest method and/or corrections for ion leaks in my memory, try writing Jeff Dangl (UNC) or Dave Mackey (OSU). Good luck Ben ======== Ben Holt Assistant Professor University of Oklahoma Department of Botany and Microbiology GLCH Rm 219 770 Van Vleet Oval Norman, OK 73019 Phone (405)325-9018 FAX (405)325-7619 http://www.ou.edu/cas/botany-micro/faculty/holt.html From jwe.journal from gmail.com Mon Jul 20 04:44:08 2009 From: jwe.journal from gmail.com (jwe journal) Date: Wed Sep 30 17:18:29 2009 Subject: [Arabidopsis] (no subject) Message-ID: <24ee84b20907200152y5455a4f9q13068125a8d0a0b0@mail.gmail.com> *Journal of Wood Engineering* www.academicjournals.org/JWE * * Dear Colleague, The *Journal of Wood Engineering(JWE)* is a multidisciplinary peer-reviewed journal published monthly by Academic Journals (www.academicjournals.org/JWE ). *JWE* is dedicated to increasing the depth of research across all areas of this subject. *Editors and reviewers* JWE* *is seeking qualified researchers to join its editorial team as editors, subeditors or reviewers. Kindly send your resume to * jwe.journal@gmail.com *. *Call for Papers* JWE will cover all areas of English and Literature. The journal welcomes the submission of manuscripts that meet the general criteria of significance and scientific excellence in this subject area, 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 *jwe.journal@gmail.com * for publication in the Maiden Issue (October 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/JWE/Instruction.htm *JWE *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. JWEis fully committed to the Open Access Initiative and will provide free access to all articles as soon as they are published. Best regards, *Yore Daniel* Editorial Assistant Journal of Wood Engineering (JWE) E-mail: *jwe.journal@gmail.com * www.academicjournals.org/*JWE* From jpap.journal from gmail.com Thu Jul 23 11:46:27 2009 From: jpap.journal from gmail.com (jpap journal) Date: Wed Sep 30 17:18:35 2009 Subject: [Arabidopsis] (no subject) Message-ID: <124d52af0907230920wc7d74fay6bf75e7691d2d0e1@mail.gmail.com> *Journal of Physiology and Pathophysiology * *www.academicjournals.org/JPAP* Dear Colleague, The *Journal of Physiology and Pathophysiology** **(**JPAP)* is a multidisciplinary peer-reviewed journal published monthly by Academic Journals (www.academicjournals.org/JPAP). JPAP has an ultimate aim of improving research in Physiology and Pathophysiology to meet the general criteria of significance and academic excellence across related disciplines* *of Physiology and Pathology. *Editors and reviewers* * * JPAP* *is seeking qualified researchers to join its editorial team as editors, subeditors or reviewers. Kindly send your resume to * jpap.journal@gmail.com*. *Call for Papers* JPAP will cover all areas of living organisms, organic functions, endocrinology, kinesiology, enzymology, nutrition, immunology, cytology, hemodynamics, neurophysiology, diseases and abnormalities. The journal welcomes the submission of manuscripts that meet the general criteria of significance and scientific excellence in this subject area, 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 *jpap.journal@gmail.com* for publication in the Maiden Issue (October 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/JPAP/Instruction.htm JPAP* *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. JPAP 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 Physiology and Pathophysiology* *(JPAP) E-mail: *jpap.journal@gmail.com* www.academicjournals.org/JPAP From manuscript.jpbcs from acadjourn.org Fri Jul 31 03:32:26 2009 From: manuscript.jpbcs from acadjourn.org (Journal of Plant Breeding and Crop Science) Date: Wed Sep 30 17:18:41 2009 Subject: [Arabidopsis] (no subject) Message-ID: <1546cee10907310132q3d1372b8seb28c2697f32695a@mail.gmail.com> *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 For Dr. Munir Turk Editor Journal of Plant Breeding and Crop Science (JPBCS) E-mail: jpbcs@acadjourn.org, www.academicjournals.org/JPBCS