From G.G.Simpson from dundee.ac.uk Wed Sep 2 03:52:03 2009 From: G.G.Simpson from dundee.ac.uk (Gordon Simpson) Date: Wed Sep 2 11:06:22 2009 Subject: [Arabidopsis] 2 Post-Doc Positions, RNA Biology and Bioinformatics Message-ID: <4A9E4043.C7A6.0008.0@dundee.ac.uk> 2 x Postdoctoral Research Assistants College of Life Sciences, Dundee University Alternative Polyadenylation: RNA Biology and Bioinformatics Grade 7 (Starting Salary ?28,839 ? ?31,513 pa) An exciting opportunity to join a ?1million BBSRC funded project that will combine cutting-edge technology for DNA sequencing and computational analysis with molecular genetics to answer fundamental questions in gene regulation. We have discovered genetically independent regulators of alternative polyadenylation while studying Arabidopsis flower development. Although this mode of gene regulation is common in eukaryotes, it is surprisingly poorly understood. This project will dissect the mechanisms and roles of alternative polyadenylation. Our programme addresses the molecular mechanisms involved and uses next generation sequencing to reveal and quantify genome-wide shifts in poly(A) site selection. The project fuses the extensive experience of Dr Gordon Simpson in Arabidopsis RNA biology, who will lead the molecular aspects of the work, with the computational skills of Prof Geoff Barton, who will lead the bioinformatics analysis. The Barton group has long-standing expertise in developing computational techniques that are widely applied and has had recent successful experience in studying RNA processing and expression by analysis of next generation sequencing data. The integrated nature of this programme offers the opportunity for the molecular and bioinformatics analyses to be iteratively validated and refined. The first post (LS/2917) requires a Molecular Biologist and previous experience with the molecular analysis of either RNA processing or genetic analysis of Arabidopsis would be an advantage. The second post (LS/2918) requires an individual with strong data analysis and software development expertise. These skills may have been gained in bioinformatics, or in related scientific fields such as Physics. Dundee is a centre of excellence in life sciences research and combines quality of life with quality of science. Consistently topping polls in The Scientist magazine of best places to work, staff of more than 50 different nationalities create a vibrant international working environment, with a particularly active Post-Doc Association. Gordon Simpson?s lab web site: www.lifesci.dundee.ac.uk/groups/gordon_simpson/ Geoff Barton?s lab web site: www.compbio.dundee.ac.uk/ Both positions are full-time for 3 years. HOW TO APPLY: Applications in the form of a CV and covering letter, including the names and addresses of 3 referees and a list of publications, should be sent to email address ( http://mini.dundee.ac.uk/locate/?2009733650hu250711 ) . Alternatively, please send 2 hard copies of your CV and covering letter to Human Resources, College of Life Sciences, MSI/WTB/JBC Complex, University of Dundee, DD1 5EH. Applicants will only be contacted if invited for interview. The University of Dundee is committed to equal opportunities and welcomes applications from all sections of the community. The University of Dundee is a Scottish Registered Charity, No. SC015096 How to apply: Apply by Curriculum Vitae (CV) and covering letter. You must also return the Supplementary Information Forms ( http://www.dundee.ac.uk/hr/recruitment/_lib/docs/job_supplementary_information_form.pdf ) (PDF) 36KB with your application. Please remember to quote the job reference. Please return your application to: (use postal or email address from the advert itself above) About: The University of Dundee and the City of Dundee ( http://www.dundee.ac.uk/main/about.htm ) Gordon Simpson Principal Investigator Division of Plant Sciences College of Life Sciences University of Dundee Scotland g.g.simpson@dundee.ac.uk Direct Dial: 44 1382 568572 http://www.lifesci.dundee.ac.uk/groups/gordon_simpson/ The University of Dundee is a registered Scottish charity, No: SC015096 From Urs.Fischer from forst.uni-goettingen.de Wed Sep 2 07:09:44 2009 From: Urs.Fischer from forst.uni-goettingen.de (Fischer, Urs) Date: Wed Sep 2 11:06:41 2009 Subject: [Arabidopsis] Open PhD position Message-ID: <496AACD85991444AA5AFABD263EE3FAB065F1A76@VS2.exc.top.gwdg.de> Applications are invited for the post of a PhD student in the Department of Forest Botany and Tree Physiology, University of Goettingen, Germany, to investigate the function of auxin transport in leaf abscission. Our group is interested in seasonal leaf abscission; a process which relies on highly coordinated cell separation. While down-stream events, as the activation and secretion of hydrolytic enzymes, are rather well studied; the hormonal signaling leading from the perception of decreasing photoperiod in the leaf blade to the induction of the separation process in the petiole is only poorly understood. We recently established an experimental model system in poplar in order to study leaf abscission and could show that polar auxin transport is involved in the early signaling. The successful candidate will identify and localize auxin transporters in the abscission zone of poplar. She/he will be trained in immunolocalization, confocal microscopy and other relevant techniques. Mechanisms of hormonal cross-talk will be studied in Arabidopsis. Hands-on experience with basic techniques of molecular biology and a Master's or equal degree in Biology or Life Sciences are required. The position is funded for 36 months and the salary will be based on Bat IIa/E13 (50%). Informal enquiries should be directed to Urs Fischer, ufische@gwdg.de. Applications including CV, cover letter and names and addresses of two references should be submitted to Urs Fischer, Buesgen-Institute, Department of Forest Botany and Tree Physiology, Buesgenweg 2, 37077 Goettingen, Germany or preferably via email to ufische@gwdg.de. Closing date: 15th of October 2009. Funding is available immediately. The University of Goettingen is committed to equality of opportunity. Dr. Urs Fischer Georg-August Universit?t G?ttingen Forstbotanik und Baumphysiologie B?sgenweg 2 37077 G?ttingen Germany Fax: +49 551-3922705 Tel: + 49 551-393372 ufische@gwdg.de From jdfriesner from ucdavis.edu Wed Sep 2 14:01:33 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Fri Sep 4 14:43:36 2009 Subject: [Arabidopsis] Sept. 15th deadline for U.S. funding opportunity Message-ID: <000001ca2bff$c9edcc20$5dc96460$@edu> Reminder: deadline coming up Sept. 15th: There is still some funding left to send U.S. graduate students and postdocs from NSF-funded Arabidopsis labs to German Arabidopsis labs for short-term research visits. Final upcoming application deadlines for the program: Sept. 15, 2008 Jan. 15, 2010 All travel must be completed by May 31, 2010. See this site for complete application directions: http://arabidopsis.org/portals/masc/funding.jsp From ruhal.manoj from gmail.com Wed Sep 2 14:43:11 2009 From: ruhal.manoj from gmail.com (manoj ruhal) Date: Fri Sep 4 14:43:54 2009 Subject: [Arabidopsis] endogenous control for ABI Taqman and SYBR green dyes Message-ID: <1b240be80909021243w6780ed08p36d733afdea62b8b@mail.gmail.com> Hello everyone, I am trying to get relative standard curve of plant myosin gene. So in real-time PCR I am using SYBR green PCR master mix to get fluorescence.I have ABI Taqman human GAPDH control as an endogenous control in place of SYBR .For endogenous control, Is it possible to use ABI Taqman human GAPDH assay mix with SYBR chemistry?- Kumar, Manoj Research Assistant Microscopy Center Department of Biology University of Louisiana at Lafayette Lafayette, LA 70504 USA From eblumwald from ucdavis.edu Fri Sep 4 22:24:41 2009 From: eblumwald from ucdavis.edu (EDUARDO BLUMWALD) Date: Fri Sep 4 23:31:58 2009 Subject: [Arabidopsis] Postdoctoral position in Plant Stress Biology at the University of California, Davis. Message-ID: <89D18526411C1B49B32BFB2F64AD3C72FCED82@EXCHANGE.plantsciences.ucdavis.edu> Can you please post this ad? Thank you in advance Ed Postdoctoral position in Plant Stress Biology at the University of California, Davis. A Postdoctoral position is available immediately in the Laboratory of Dr. Eduardo Blumwald at the Dept of Plant Sciences, University of California, Davis. The successful candidate will participate in ongoing multidisciplinary research projects aimed at the identification and characterization of regulatory networks and isolation of genes associated with the tolerance of crop plants to drought stress (see Rivero et al. 2007, PNAS 104:19631-19636; Rivero et al. 2009, Plant Physiology 150:1380-1393). Applicants should have a Ph.D. with strong background in molecular biology and physiology/biochemistry. Additional experience in genetics, genomics and/or bioinformatics would be valuable. Strong written and oral communication skills and ability to work in a team-oriented environment are required. The position is for two years with possibility of extension. Initial appointment is for one year and is renewable depending on satisfactory performance. Salaries are competitive and include benefits. Interested applicants should send via email a cover letter detailing experience, CV, and names, telephone numbers and e-mail addresses of three references to Dr. Eduardo Blumwald at eblumwald@ucdavis.edu. Dr. Eduardo Blumwald Professor of Cell Biology and Will W. Lester Chair Department of Plant Sciences - Mail Stop 5 University of California 1 Shields Ave, Davis, CA 95616 phone:530-752-4640; FAX:530-752-2278 email:eblumwald@ucdavis.edu P Before printing this email, think about the environment From eblumwald from ucdavis.edu Fri Sep 4 22:25:25 2009 From: eblumwald from ucdavis.edu (EDUARDO BLUMWALD) Date: Fri Sep 4 23:32:15 2009 Subject: [Arabidopsis] Postdoctoral position in Plant Transformation and Tissue Culture at the University of California, Davis. Message-ID: <89D18526411C1B49B32BFB2F64AD3C72FCED83@EXCHANGE.plantsciences.ucdavis.edu> Postdoctoral position in Plant Transformation and Tissue Culture at the University of California, Davis. A Postdoctoral or Research Associate position is available immediately in the Laboratory of Dr. Eduardo Blumwald at the Dept of Plant Sciences, University of California, Davis. The successful candidate will conduct research leading to the genetic transformation and regeneration of desert tree species. A solid experience in plant tissue culture, tissue propagation, embryogenesis, Agrobacterium-mediated plant transformation and molecular biology techniques is essential. Excellent written and oral communication skills and the ability to work and interact in a collaborative research environment are required. The position is for two years with possibility of extension. Initial appointment is for one year and is renewable depending on satisfactory performance. Salaries are competitive and include benefits. Interested applicants should send via email a cover letter detailing experience, CV, and names, telephone numbers and e-mail addresses of three references to Dr. Eduardo Blumwald at eblumwald@ucdavis.edu. Dr. Eduardo Blumwald Professor of Cell Biology and Will W. Lester Chair Department of Plant Sciences - Mail Stop 5 University of California 1 Shields Ave, Davis, CA 95616 phone:530-752-4640; FAX:530-752-2278 email:eblumwald@ucdavis.edu P Before printing this email, think about the environment From chiangscn from gmail.com Mon Sep 7 19:08:59 2009 From: chiangscn from gmail.com (smith Chiang) Date: Mon Sep 7 19:21:06 2009 Subject: [Arabidopsis] At accessions for T-DNA mutants Message-ID: <40a6ed990909071708y2c906692kd13ec554d3af712b@mail.gmail.com> Hi researchers, I thought that all Syngenta lines (SAIL_xxx) were in the background of Col-0, which is the same as SALK lines. But recently, I saw from ABRC website that some SAIL lines are in the background of Col-3. could anyone inform me the difference between Col-0 and Col-3? Why Syngenta used different accesions of At T-DNA insertion population? I want to make double mutants using single mutants, and so hope to get single mutants in the same genetic background. Thanks for your reply. Good luck in your research. From detlef.weigel from tuebingen.mpg.de Mon Sep 7 04:24:03 2009 From: detlef.weigel from tuebingen.mpg.de (Detlef Weigel) Date: Mon Sep 7 19:21:51 2009 Subject: [Arabidopsis] Postdoc and PhD positions in genetic incompatibility/hybrid necrosis Message-ID: Several years ago, the Weigel lab discovered that hybrid necrosis, a type of genetic incompatibility found in many different plants, also occurs in Arabidopsis thaliana. Even though the underlying genetic basis appears to be heterogeneous, a collaboration with the Dangl lab established autoimmunity as the common cause. Since our first publication on hybrid necrosis in 2007 (Bomblies, Lempe et al., PLoS Biology 5, e236), we have cloned several additional causal loci. Interesting patterns are emerging for their molecular nature and allelic diversity, and we are expanding our biochemical and population genomic analyses of this interesting phenomenon. We are looking for additional postdocs and PhD students to join an active team of five postdocs and PhD students already working in this exciting area. Postdoc applicants need to have published at least one first-author paper in an international journal. PhD students must have a Masters degree in a relevant discipline and need to document practical experience in molecular genetics, biochemistry, population genetics and/or bioinformatics. Apart from members of the Weigel lab, you will interact with colleagues on a joint international HFSP grant (with Jeff Dangl [UNC]; Jonathan Jones [Sainsbury Laboratory]; and Michael Doebeli [UBC]). You will also benefit from the 1001 Genomes (http://1001genomes.org) resources we are generating. Additional information on the group, the institute, and T?bingen can be found on our website (http://weigelworld.org ). Please send applications, with a statement of purpose, at least three names of references, and the subject line to Detlef Weigel Director, MPI for Developmental Biology weigel@weigelworld.org From hhchou from iastate.edu Mon Sep 7 14:38:38 2009 From: hhchou from iastate.edu (Hui-Hsien Chou) Date: Mon Sep 7 19:22:11 2009 Subject: [Arabidopsis] Postdoctoral Research Associate on RNA Interference Technology Message-ID: <0705F778BC0246D6BC502EC1E4657A77@gdcb.iastate.edu> Postdoctoral Research Associate on RNA Interference Technology One to two postdoctoral research associate positions are available immediately for energetic individuals with a firm background training in molecular biology or biochemistry and a prior PhD research work on Arabidopsis, C. elegans or other related model species. Special preferences are given to candidates who have performed RNA interference (RNAi) experiments on these model species. The annual salary will be no less than $40K and commensurate with candidate qualification. These positions are expected to last four years until August 2013, subject to the continuous funding support from National Science Foundation (NSF). The successful candidates will be given the resource and guidance to conduct research on RNAi transfection technologies. The candidates will devise more controllable, economical and efficient RNAi delivery procedures for various model species, and to design and perform experiments involving RNAi transfections, microarray hybridizations and qRT-PCRs to validate the newly developed RNAi transfection procedures. The new postdocs will be members of our new NSF sponsored project team to develop optimal siRNA design software based on whole genome thermodynamic analysis. This project will use the novel RNAi transfection procedures to validate the designed siRNAs in vivo. For these postdoc positions, applicants must hold a Ph.D. degree in related fields with the preferred expertise as stated above. Use of computers in solving biological research problems will be an essential part of the project. Nevertheless, prior experience in bioinformatics is helpful but not essential - we will train the new postdocs on the job for using computational biology techniques. To apply, please send a letter of intent stating your future research interest and also a curriculum vitae documenting your past experience to Dr. Chou's email address below. Upon request from us, applicants may be asked to solicit three reference letters to be sent directly to the same email address below. Our laboratory conducts interdisciplinary research, taking advantage of expertises from both computational and biological sciences, We are a member of the Iowa State bioinformatics research community and are affiliated with the Laurence H. Baker Center for Bioinformatics and Biological Statistics, the Center for Plant Genomes, the Center for Integrated Animal Genomics and the Plant Sciences Institute. We are also affiliated with the Bioinformatics and Computational Biology Interdepartmental Graduate Major and the Bioinformatics and Computational Biology Undergraduate Major at Iowa State University. Dr. Hui-Hsien Chou Complex Computation Lab Department of Genetics, Development and Cell Biology Department of Computer Science Iowa State University Ames, IA 50011-3223 Email: hhchou at iastate dot edu From isabell.witt from uni-koeln.de Mon Sep 7 12:46:20 2009 From: isabell.witt from uni-koeln.de (Isabell Witt) Date: Mon Sep 7 19:22:38 2009 Subject: [Arabidopsis] PhD fellowships Message-ID: <007c01ca2fe3$1ba350d0$52e9f270$@witt@uni-koeln.de> Cologne International Graduate School >From Embryo to old Age, Development, Health and Disease 6 Fellowships 3-year Ph.D. programme starting spring 2010 The University of Cologne has a long-standing tradition and world-wide reputation of top-level molecular biological research. Beginning in spring 2010 the Research School in Biology ?From embryo to old age: the cell biology and genetics of health and disease? will be offering a high-level Ph.D. programme for students with excellent qualifications. The participating research groups use today's microbial, plant and animal model systems to investigate cell biological and genetic mechanisms whose perturbation during the life cycle of an organism results in disease. The three-year programme starts with a six-month rotation and course period, followed by a PhD project in one of the participating groups. Seminars and training courses complement the research work. Comprehensive support is provided throughout the programme. The programme language is English. Accepted students get a laptop computer and 500 EUR to get started in Cologne. No tuition fees apply. Six competitive three-year fellowships (initially 1000 EUR, then 1300 EUR per month) are available. We invite you to apply to the IGSDHD in Cologne, the exciting city in the heart of Europe. To obtain further information please visit our website at: http://www.uni-koeln.de/bio-graduateschool/ Submission deadline of complete applications is October 31, 2009 Contact: Dr. Isabell Witt, IGSDHD, Z?lpicher Strasse 47, D-50674 Cologne, Phone: +49(0)221 4701683, Fax: +49(0) 470 1632, isabell.witt@uni-koeln.de Dr. Isabell Witt Graduate School for Biological Sciences Z?lpicher Strasse 47 D-50674 Cologne +49 (0) 221 4701683 fax: +49 (0) 221 4701632 isabell.witt@uni-koeln.de From jdfriesner from ucdavis.edu Tue Sep 8 11:42:05 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Tue Sep 8 11:45:16 2009 Subject: [Arabidopsis] 2008 awards added to AT2010 project resource Message-ID: <002601ca30a3$4d3916f0$e7ab44d0$@edu> The recently listed 2008 AT2010 project awards have been added to the online 2010 project resource (see below). A new resource listing all the Arabidopsis 2010 projects funded by NSF (up to 2007), including project websites, PI contact, and whether and where resources are deposited for public use has been launched at TAIR. A list of relevant community databases is also included. Updates from the community are requested and all information can be found at this URL: http://arabidopsis.org/portals/masc/2010_resources.jsp The resource was compiled by the MASC Coordinator on behalf of the community. Joanna Friesner UC Davis From schen from ufl.edu Wed Sep 9 08:03:09 2009 From: schen from ufl.edu (Sixue Chen) Date: Wed Sep 9 11:27:11 2009 Subject: [Arabidopsis] Postdoctoral position available immediately in functional genomics Message-ID: <4AA7A78D.7040802@ufl.edu> POSTDOCTORAL POSITION in Functional Genomics of Glucosinolate Metabolism A postdoctoral position is open to study the molecular networks that regulate glucosinolate metabolism in model plant Arabidopsis thaliana. This project is funded by the National Science Foundation (NSF) to study key aspects of molecular networks regulating glucosinolate metabolism using multidisciplinary approaches including reverse genetics, molecular biology, biochemistry, proteomics, metabolomics and bioinformatics. The postdoctoral associates will be responsible for testing perturbation of glucosinolate metabolism, investigating molecular changes at protein and metabolite levels, correlating the changes and constructing networks using bioinformatics tools. The associate is expected to receive multidisciplinary training, work closely with collaborators in different areas, and be involved in the outreach activities of the project, such as educating high school teachers in the area of functional genomics. Applicants are expected to have a strong publication record and demonstrated expertise in one or more of these areas: gel- and/or liquid chromatography-based proteomics, plant molecular biology, functional genomics, metabolite profiling and metabolomics, and/or systems biology. Experience with protein or metabolite separation/purification and mass spectrometry would be an advantage. Applicants should send a cover letter, a statement of research interests and a CV including the names and contact information of three references to: Dr. Sixue Chen, Department of Biology, University of Florida, PO Box 118526, Gainesville, FL 32610, Email: schen@ufl.edu. More information about Chen lab research and education activities can be found at the following websites: http://www.biology.ufl.edu, http://www.moleculardetective.org, http://www.icbr.ufl.edu, http://proteomics.centers.ufl.edu. Positions will remain open until filled. We encourage applications from individuals of diverse backgrounds. University of Florida is committed to affirmative action, equal opportunity and the diversity of its workforce. -- Sixue Chen, Ph.D. Assistant Professor of Biology Cancer & Genetics Research Complex, Room 438 University of Florida 1376 Mowry Road Gainesville, FL 32610, USA Tel: +1 (352) 273-8330 Fax: +1 (352) 273-8284 Email: schen@ufl.edu Web page: http://www.botany.ufl.edu/people/index.html http://pmcb.ifas.ufl.edu/faculty.htm http://www.ufgi.ufl.edu/ Director of Proteomics Facility Interdisciplinary Center for Biotechnology Research (ICBR) Cancer & Genetics Research Complex, Room 169 University of Florida, PO Box 103622 Gainesville, FL 32610, USA Tel: +1 (352) 273-8057 (ICBR office) Fax: +1 (352) 273-8284 Email: schen@ufl.edu Web page: http://www.biotech.ufl.edu/proteomics/ Service Contacts: Peptide Synthesis: Alfred Chung, Tel: (352) 273-8058 2D gel and Biacore: Marjorie Chow, Tel: (352) 273-8059 Mass Spectrometry: Carolyn Diaz, Tel: (352) 273-8061 From Thomas.P.Jack from Dartmouth.EDU Wed Sep 9 08:03:08 2009 From: Thomas.P.Jack from Dartmouth.EDU (Thomas P. Jack) Date: Wed Sep 9 11:27:31 2009 Subject: [Arabidopsis] Postdoc Position Available Message-ID: <154152410@newdasher.Dartmouth.EDU> Postdoctoral Position in Arabidopsis Flower Development A postdoctoral position is currently available in the laboratory of Dr. Tom Jack (Dartmouth College) to work on an NSF-funded project on genes that control the growth of the floral organs in Arabidopsis. Specifically, we are studying the role of two genes that are necessary for proper growth of petals and stamens. The first is DORNR?SCHEN-LIKE, which encodes an AP2-domain transcription factor. The second is microRNA319a, which is necessary for proper growth of both petals and stamens. The successful applicant will become a member of vibrant group of researchers at Dartmouth that focus on plant biology and developmental biology. The successful applicant should be highly motivated and be capable of working independently. Experience in some or all of the following disciplines is desirable: genetics in model systems, molecular biology, developmental biology, and/or biochemistry. Application Instructions: Please send a letter of application describing research background, a CV, and the names and contact information for three references to Tom Jack at Dartmouth College, Dept. of Biology, Hanover, NH 03755 or by email to thomas.p.jack@dartmouth.edu. From sugimoto from psc.riken.jp Thu Sep 10 00:39:33 2009 From: sugimoto from psc.riken.jp (Keiko Sugimoto) Date: Thu Sep 10 12:17:15 2009 Subject: [Arabidopsis] =?iso-2022-jp?b?U2VuaW9yIHNjaWVudGlzdCBvciBwb3N0?= =?iso-2022-jp?b?ZG9jdG9yYWwgcG9zaXRpb24bJEIhIRsoQmF0IHRoZSBSSUtF?= =?iso-2022-jp?b?TiBQbGFudCBTY2llbmNlIENlbnRlcg==?= Message-ID: <007001ca31d9$137eecf0$3a7cc6d0$@riken.jp> Senior scientist or postdoctoral position in plant development at the RIKEN Plant Science Center A senior scientist or postdoctoral position is available immediately in the laboratory of Dr Keiko Sugimoto at the RIKEN Plant Science Center, Yokohama, Japan. The Sugimoto Lab has recently identified a novel SUMO E3 ligase HIGH PLOIDY 2 and a trihelix transcription factor GTL1 as a key regulator of plant cell growth (see Ishida et al 2009, Plant Cell online published; Breuer et al 2009, Plant Cell online published). The successful candidate will join the multidisciplinary research programme to elucidate how these regulatory proteins mediate plant growth and development using Arabidopsis as a model system. For further information on our research programme, please see our lab website (http://labs2.psc.riken.jp/cfru/English/index.html). Applications should have a PhD with a strong background in molecular biology, genetics and cell biology/biochemistry. Special preferences are given to candidates with a prior research experience in plant developmental biology. A senior scientist should have 5-year-research experience as a postdoctoral scientist in related disciplines. Initial appointment is until March 2010 and the position is renewable up to 2013 depending on satisfactory performance. For further information on these posts, please see the RIKEN website (http://www.riken.jp/engn/r-world/info/recruit/index.html). RIKEN Plant Science Center is one of the leading research institutes in plant biology in Japan. The Center is part of the RIKEN Yokohama Institute (http://www.yokohama.riken.jp/english/index.html) which offers state-of-the-art core facilities in transcriptome, proteome and metabolome analyses. To apply for the post, please send by email (a) cover letter describing your research interests and previous research experiences, (b) CV, (c) list of publications, (d) a reference letter to Keiko Sugimoto (sugimoto@psc.riken.jp). ------------------------------------------------------------------ Keiko Sugimoto Group Leader Plant Science Center RIKEN Yokohama Institute 1-7-22 Tsurumi, Yokohama, Kanagawa, 230-0045, Japan Tel: +81-45-503-9575 Fax: +81-45-503-9591 http://www.psc.riken.jp/eng/group/index.html ------------------------------------------------------------------- From G.G.Simpson from dundee.ac.uk Fri Sep 11 10:11:20 2009 From: G.G.Simpson from dundee.ac.uk (Gordon Simpson) Date: Fri Sep 11 13:50:02 2009 Subject: [Arabidopsis] Post Doc Alternative RNA Polyadenylation Message-ID: <4AAA76A7.C7A6.0008.0@dundee.ac.uk> Postdoctoral Research Assistant College of Life Sciences, Dundee University GRADE 7 (?28,839 - ?35,469) SUBJECT AREA: ALTERNATIVE RNA POLYADENYLATION A postdoc position is available immediately in the group of Gordon Simpson at the College of Life Sciences in Dundee, Scotland. The aim of this position is to dissect the mechanism by which alternative polyadenylation (APA) is controlled. You will be working in a highly international research group that is passionate about working with RNA. We combine questions on plant development with state-of-the-art analysis of RNA processing and collaborate with other research groups in Dundee focused on computational biology and human RNA biology. For more information about the group see: http://www.lifesci.dundee.ac.uk/groups/gordon_simpson/ The post-holder will take molecular genetic approaches to dissect mechanisms of APA control. As part of a ?1 million BBSRC-funded research programme, the post-holder will work closely with a computational biologist, who will analyse next generation sequence data for APA. This aspect of the project is a collaboration with Geoff Barton?s group: http://www.compbio.dundee.ac.uk/ therefore an ability to work well in a team is an important requirement of this post and a basic feature of Gordon Simpson?s group. Training, as required, will be provided in a well-equipped, well-funded and supportive environment enabling the successful candidate to extend skills and expertise. The College has excellent facilities for all aspects of research, including in-house and easily accessible services, such as cloning, proteomics, microscopy, DNA sequencing, oligo synthesis and preparation of growth media. State-of-the-art plant growth facilities are provided by SCRI. This position is suited for a candidate with a recent PhD and a strong background in RNA or Arabidopsis research, with first author publications in good scientific journals. The candidate should be able to demonstrate an aspiration to move on to an independent faculty position after their postdoctoral work. The position is available immediately and is for 3-years. The starting salary is a minimum of Grade 7, point 29 (?28,839). Dundee is a centre of excellence in life sciences research and combines quality of life with quality of science. It lies close to areas of outstanding natural beauty, including large sandy beaches and island and mountain wilderness. The culturally rich cities of Glasgow and Edinburgh can be reached in little over an hour. Rainfall charts show that Dundee is one of the most sunny & dry places in the UK, see: http://www.metoffice.gov.uk/climate/uk/averages/19712000/mapped.html Informal enquiries may be made to Gordon Simpson g.g.simpson@dundee.ac.uk ( mailto:dmfvanaalten@dundee.ac.uk ) (Applications sent to this address alone will not be considered - see below). HOW TO APPLY: Applications in the form of a CV and covering letter, including the names and addresses of 3 referees and a list of publications, should be sent to email address ( http://mini.dundee.ac.uk/locate/?2009733650hu250711 ). Alternatively, please send 2 hard copies of your CV and covering letter to Human Resources, College of Life Sciences, MSI/WTB/JBC Complex, University of Dundee, DD1 5EH. You must also return the Supplementary Information Forms ( http://www.dundee.ac.uk/hr/recruitment/_lib/docs/job_supplementary_information_form.pdf ) (PDF) 36KB with your application. Please remember to quote the job reference. About: The University of Dundee and the City of Dundee ( http://www.dundee.ac.uk/main/about.htm ) Closing date: 1st October 2009 Applicants will only be contacted if invited for interview. The University of Dundee is committed to equal opportunities and welcomes applications from all sections of the community. The University of Dundee is a Scottish Registered Charity, No. SC015096 Gordon Simpson Principal Investigator Division of Plant Sciences College of L ife Sciences University of Dundee Scotland g.g.simpson@dundee.ac.uk Direct Dial: 44 1382 568572 http://www.lifesci.dundee.ac.uk/groups/gordon_simpson/ The University of Dundee is a registered Scottish charity, No: SC015096 From ndhar from syr.edu Fri Sep 11 19:40:19 2009 From: ndhar from syr.edu (Nik) Date: Fri Sep 11 23:37:41 2009 Subject: [Arabidopsis] RNA silencing mutants Message-ID: <7815a9150909111740i478cc4d8x6d24c85f2957a49f@mail.gmail.com> Hi, I am trying to identify homozygous lines for the following (EMS) mutant lines to use in my experiments. Can anyone please shed light on how to identify these mutants from the community stock seeds - dcl1-7 CS3089 rdr6-11 CS24285 hyl1-2 CS859864 Thanks in advance, Nik From lilynn.xu from gmail.com Sun Sep 13 08:33:45 2009 From: lilynn.xu from gmail.com (Lynn) Date: Sun Sep 13 22:32:43 2009 Subject: [Arabidopsis] Does anyone here know how to download the absolute expression value via Genevestigator? Message-ID: Hi, all, Does anybody in this community know how to download the absolute expression value via Genevestigator? I remembered it can be done before... Thanks in advance, :P Lynn From george.e.schaller from dartmouth.edu Tue Sep 15 13:22:03 2009 From: george.e.schaller from dartmouth.edu (Eric Schaller) Date: Wed Sep 16 01:03:59 2009 Subject: [Arabidopsis] Postdoctoral position in ethylene signaling Message-ID: <2A33D619-3815-48EF-BEEC-EF2E7CDF0003@dartmouth.edu> Postdoctoral Position in Ethylene Signal Transduction A postdoctoral position is currently available in the laboratory of Dr. G. Eric Schaller (Dartmouth College) to work on a DOE-funded project to examine the roles of post-transcriptional regulation in ethylene signaling. One focus of this project is on how physical interactions among the ethylene receptors coordinate signal output (Gao et al., 2008, J. Biol. Chem. 283:23081-23810). In addition, we are characterizing how a small family of novel proteins modulates signaling by the receptors. Successful applicants should be highly motivated, be capable of working independently, and have a relevant PhD. Experience in some or all of the following disciplines is desirable: genetics in model systems, molecular biology, and/or biochemistry. Application Instructions: Please send a letter of application describing research background, a CV, and the names and contact information for three references to G. Eric Schaller at Dartmouth College, Dept. of Biology, Hanover, NH 03755 or by email to george.e.schaller@dartmouth.edu. From mpggm1 from cid.csic.es Thu Sep 17 03:08:06 2009 From: mpggm1 from cid.csic.es (=?ISO-8859-1?Q?Mary_Paz_Gonz=E1lez_Garc=EDa?=) Date: Thu Sep 17 11:27:09 2009 Subject: [Arabidopsis] question about alexa 405 Message-ID: <497A86DD-69B5-4C34-80CC-EE9967B4AA87@cid.csic.es> Hello, I am trying to analyze a whole mount Imunolocalization hybridized with Alexa 405 antibody and also stained with DAPI, Does anybody know how to separated emission peaks without having crosstalk? (I am using a Olympus FV1000 confocal system) thanks in advance MaryPaz From galbraith from arizona.edu Thu Sep 17 12:25:04 2009 From: galbraith from arizona.edu (David Galbraith) Date: Thu Sep 17 15:05:13 2009 Subject: [Arabidopsis] Microarray Workshop in Tucson, Arizona Message-ID: <6.2.3.4.2.20090917102342.03efceb0@ag.arizona.edu> TENTH INTERNATIONAL LONG-OLIGONUCLEOTIDE MICROARRAY WORKSHOP January 3-8, 2010 The University of Arizona Tucson, Arizona This workshop will comprise a combination of lectures and hand-on laboratory sessions. The participants will primarily employ Arabidopsis and maize (plant side) and human, bovine and porcine (animal side) whole genome 70-mer oligonucleotide microarrays in their laboratory work (for details of the plant arrays see http://www.ag.arizona.edu/microarray and http://www.maizearray.org/. The workshop will be divided into two parts: Part I (Sunday 4PM to Wednesday 5PM) will cover wet-lab aspects of microarray target production and amplification, microarray hybridization, and scanning. Part II (all day, Thursday and Friday) will concentrate on data extraction, statistical analysis, and experimental design. Together these topics are aimed at the goal of the participants obtaining optimal results using oligonucleotide-based microarrays. Part II may be taken separately. Specific topics to be covered include: * Experimental design. * Probe preparation and microarray printing. * Microarray rehydration and probe immobilization. * Target preparation, including RNA extraction, direct and indirect labeling, and amplification techniques. * Microarray hybridization. * Array scanning and data extraction. * Data analysis and archiving. Registration (Part I plus Part II) is $700, which includes costs of the microarrays and other supplies that you will use. Part II registration only is $300. Part I participants will be limited to 40 on a first-come, first-serve basis. Overall participation will be limited to 60 individuals. Note: There are a number of airline connections from Tucson to San Diego on Friday evening, allowing workshop participants convenient access to the Plant and Animal Genome XVIII Meeting (January 9-13). For further details and to register, please contact David Galbraith (galbraith@arizona.edu) or Georgina Lambert (georgina@cals.arizona.edu) David W. Galbraith Professor of Plant Sciences & Professor, Bio5 Institute University of Arizona Office: 341 Keating Building Mailing address: BIO5 Institute The University of Arizona 1657 E. Helen St. Tucson, AZ 85721-0240 Tel: (520) 621-9153 Fax: (520) 626-4824 Email: galbraith@arizona.edu http://cals.arizona.edu/galbraith From aloraine from gmail.com Thu Sep 17 17:30:32 2009 From: aloraine from gmail.com (Ann Loraine) Date: Thu Sep 17 17:56:37 2009 Subject: [Arabidopsis] seeking TAIR9 bpmap file for Arabidopsis tiling array 1.0R Message-ID: <83722dde0909171530w6bd02b7do197669db757274cd@mail.gmail.com> Dear Colleagues, I'm looking for a "bpmap" file that maps Affymetrix Arabidopsis tiling array 1.0R probes onto the TAIR9 or TAIR8 genome sequence. (This is for setting up a demonstration server that will show labs how they can easily visualize and share tiling array and RNA-Seq data via the Integrated Genome Browser (igb.bioviz.org) and DAS, one of the deliverables for an NSF 2010 award, which started a year ago.) The array corresponds to GEO platform accession GPL1980. (If this is wrong, please let me know...the Web page for it is here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1980) The Web page for GPL1980 at GEO links to a bpmap file, but we are not yet sure which genome it references. Probably it is the TAIR7 genome, but we haven't tested it as yet. The bpmap file that Affymetrix distributes references TAIR7 (what they call Jan 2004) and the company has no immediate plans to update it because their tiling array support relies on a genome being supported by the UCSC Genome Bioinformatics group, which only supports animal and some fungal genomes. If you know of anyone who has a bpmap file for the Arabidopsis Tiling 1.0R Array for TAIR9, or even TAIR8, I would be very grateful if you would give me their contact information or send me a link to the file. Also, if you are looking for such a file, please let me know, and I'll get in touch as soon as I find one...or as soon as we create it, if one cannot be found. Thank you very much for your time, Ann Loraine Associate Professor Dept. of Bioinformatics and Genomics UNC Charlotte From chiangscn from gmail.com Tue Sep 22 12:08:46 2009 From: chiangscn from gmail.com (smith Chiang) Date: Tue Sep 22 16:46:31 2009 Subject: [Arabidopsis] recommend bioinformatics books Message-ID: <40a6ed990909221008g41aee5adwb72efa20a9cdf64f@mail.gmail.com> Hi, I want to learn something about bioinformatics, can anyone recommend a few bioinformatics books? I know how to use BLAST, also know how to use a few softwares like Clustal, DNASTAR, DNAMAN, MEGA, PAUP, etc, and used quite a few online plant databases (like Genevestigator, Smart, ACT, AtGenExpress, TAIR, TIGR, etc) for the research, and some basics on R program. I heard Perl is important for bioinformatics, so it is necearray to master Perl first? I want to learn bioinformatics so as to utilize so many sequenced genome info for my own research, not major in in evolutional biology though. Thanks for your reply. From pmgnair from gmail.com Mon Sep 21 22:48:38 2009 From: pmgnair from gmail.com (Prakash M G) Date: Tue Sep 22 16:47:09 2009 Subject: [Arabidopsis] genomic and proteomic data not matching Message-ID: <18918d970909212048y106dc35p607a0c814b1cfc6d@mail.gmail.com> Dear all, I have a problem on matching or correlating the gene expression data with proteomic data. The micro array data for the treatments are not matching with the proteomic data for the same treatments. Charecterisation of differentially expressed proteins are not matching with the differentially expressed genes. May I know why this problem and how to overcome this problem? Thanking you all with regards Prakash On Mon, Sep 21, 2009 at 2:20 AM, 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. Microarray Workshop in Tucson, Arizona (David Galbraith) > 2. seeking TAIR9 bpmap file for Arabidopsis tiling array 1.0R > (Ann Loraine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Sep 2009 10:25:04 -0700 > From: David Galbraith > Subject: [Arabidopsis] Microarray Workshop in Tucson, Arizona > To: arab-gen@magpie.bio.indiana.edu > Message-ID: <6.2.3.4.2.20090917102342.03efceb0@ag.arizona.edu> > Content-Type: text/plain; charset="us-ascii"; format=flowed > > TENTH INTERNATIONAL LONG-OLIGONUCLEOTIDE > MICROARRAY WORKSHOP > > January 3-8, 2010 > The University of Arizona > Tucson, Arizona > > This workshop will comprise a combination of lectures and hand-on > laboratory sessions. The participants will primarily employ > Arabidopsis and maize (plant side) and human, bovine and > porcine (animal side) whole genome 70-mer oligonucleotide > microarrays in their laboratory work (for details of the plant arrays see > http://www.ag.arizona.edu/microarray and > http://www.maizearray.org/. > > The workshop will be divided into two parts: Part I (Sunday 4PM to > Wednesday 5PM) will cover wet-lab aspects of microarray target > production and amplification, microarray hybridization, and scanning. > Part II (all day, Thursday and Friday) will concentrate on data extraction, > statistical analysis, and experimental design. Together these topics > are aimed at the goal of the participants obtaining optimal results using > oligonucleotide-based microarrays. Part II may be taken separately. > > Specific topics to be covered include: > > * Experimental design. > * Probe preparation and microarray printing. > * Microarray rehydration and probe immobilization. > * Target preparation, including RNA extraction, direct and indirect > labeling, and amplification techniques. > * Microarray hybridization. > * Array scanning and data extraction. > * Data analysis and archiving. > > Registration (Part I plus Part II) is $700, which includes costs of > the microarrays and other supplies that you will use. > Part II registration only is $300. Part I participants will be > limited to 40 on a first-come, first-serve basis. Overall > participation will be limited to 60 individuals. > > Note: There are a number of airline connections from > Tucson to San Diego on Friday evening, allowing > workshop participants convenient access to the Plant > and Animal Genome XVIII Meeting (January 9-13). > > For further details and to register, please contact > David Galbraith (galbraith@arizona.edu) or Georgina Lambert > (georgina@cals.arizona.edu) > > > > David W. Galbraith > Professor of Plant Sciences > & Professor, Bio5 Institute > University of Arizona > Office: 341 Keating Building > > Mailing address: > BIO5 Institute > The University of Arizona > 1657 E. Helen St. > Tucson, AZ 85721-0240 > > > Tel: (520) 621-9153 > Fax: (520) 626-4824 > Email: galbraith@arizona.edu > http://cals.arizona.edu/galbraith > > > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Sep 2009 18:30:32 -0400 > From: Ann Loraine > Subject: [Arabidopsis] seeking TAIR9 bpmap file for Arabidopsis tiling > array 1.0R > To: arab-gen@magpie.bio.indiana.edu > Message-ID: > <83722dde0909171530w6bd02b7do197669db757274cd@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Colleagues, > > I'm looking for a "bpmap" file that maps Affymetrix Arabidopsis tiling > array > 1.0R probes onto the TAIR9 or TAIR8 genome sequence. > > (This is for setting up a demonstration server that will show labs how they > can easily visualize and share tiling array and RNA-Seq data via the > Integrated Genome Browser (igb.bioviz.org) and DAS, one of the > deliverables > for an NSF 2010 award, which started a year ago.) > > The array corresponds to GEO platform accession GPL1980. (If this is wrong, > please let me know...the Web page for it is here: > http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1980) > > The Web page for GPL1980 at GEO links to a bpmap file, but we are not yet > sure which genome it references. Probably it is the TAIR7 genome, but we > haven't tested it as yet. The bpmap file that Affymetrix distributes > references TAIR7 (what they call Jan 2004) and the company has no immediate > plans to update it because their tiling array support relies on a genome > being supported by the UCSC Genome Bioinformatics group, which only > supports > animal and some fungal genomes. > > If you know of anyone who has a bpmap file for the Arabidopsis Tiling 1.0R > Array for TAIR9, or even TAIR8, I would be very grateful if you would give > me their contact information or send me a link to the file. > > Also, if you are looking for such a file, please let me know, and I'll get > in touch as soon as I find one...or as soon as we create it, if one cannot > be found. > > Thank you very much for your time, > > Ann Loraine > Associate Professor > Dept. of Bioinformatics and Genomics > UNC Charlotte > > > ------------------------------ > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > > End of Arab-gen Digest, Vol 53, Issue 10 > **************************************** > From rrodriguez from ibr.gov.ar Wed Sep 23 09:37:53 2009 From: rrodriguez from ibr.gov.ar (=?ISO-8859-1?Q?Ramiro_Rodr=EDguez?=) Date: Wed Sep 23 17:33:24 2009 Subject: [Arabidopsis] ChiP Message-ID: <4ABA32C1.5080809@ibr.gov.ar> Dear all, I?m starting a project to do ChromatinIP experiments of the transcription factors I?m working with. From all the options to tag them (GFP, HA, etc), wich option would be the best? I already have nice fusion protein between my TF and GUS. Does anybody had use anti-GUS (if it exists) for ChiP? Thanks, Ramiro. -- Dr. Ramiro E. Rodriguez Investigador Asistente de CONICET Instituto de Biolog?a Molecular y Celular de Rosario (IBR) - CONICET Suipacha 531 - S2002LRK - Rosario, Santa Fe ARGENTINA TEL: 54-341-4351235 (Ext. 147) Fax: 54-341-4390465 E-mail: rrodriguez@ibr.gov.ar From staceyg from missouri.edu Tue Sep 22 17:32:34 2009 From: staceyg from missouri.edu (Stacey, Gary) Date: Wed Sep 23 17:34:08 2009 Subject: [Arabidopsis] genomic and proteomic data not matching In-Reply-To: <18918d970909212048y106dc35p607a0c814b1cfc6d@mail.gmail.com> References: <18918d970909212048y106dc35p607a0c814b1cfc6d@mail.gmail.com> Message-ID: <964681C84DC6E34F96D993D3717487A707E02F587C@UM-EMAIL05.um.umsystem.edu> This is what one would expect. Transcriptomic and proteomic data have very low correlation. Check the literature and you will find numerous examples of this. Gary Stacey, Ph.D. Director, Center for Sustainable Energy Assoc. Director, National Center for Soybean Biotechnology Divisions of Plant Sciences and Biochemistry Department of Molecular Microbiology and Immunology 271E Christopher S. Bond Life Sciences Center University of Missouri Columbia, MO? 65211 Office phone: 573-884-4752 Lab Phone: 573-884-4799 FAX: 573-884-9676 email: staceyg@missouri.edu NEW LAB WEBSITE: http://www.staceylab.missouri.edu/ MU CSE site: http://www.energy.missouri.edu/ NCSB site: http://www.soybiotechcenter.org NSF Project site: http://www.soybeangenome.org ? -----Original Message----- From: arab-gen-bounces@oat.bio.indiana.edu [mailto:arab-gen-bounces@oat.bio.indiana.edu] On Behalf Of Prakash M G Sent: Monday, September 21, 2009 10:49 PM To: arab-gen@oat.bio.indiana.edu Subject: [Arabidopsis] genomic and proteomic data not matching Dear all, I have a problem on matching or correlating the gene expression data with proteomic data. The micro array data for the treatments are not matching with the proteomic data for the same treatments. Charecterisation of differentially expressed proteins are not matching with the differentially expressed genes. May I know why this problem and how to overcome this problem? Thanking you all with regards Prakash On Mon, Sep 21, 2009 at 2:20 AM, 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. Microarray Workshop in Tucson, Arizona (David Galbraith) > 2. seeking TAIR9 bpmap file for Arabidopsis tiling array 1.0R > (Ann Loraine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Sep 2009 10:25:04 -0700 > From: David Galbraith > Subject: [Arabidopsis] Microarray Workshop in Tucson, Arizona > To: arab-gen@magpie.bio.indiana.edu > Message-ID: <6.2.3.4.2.20090917102342.03efceb0@ag.arizona.edu> > Content-Type: text/plain; charset="us-ascii"; format=flowed > > TENTH INTERNATIONAL LONG-OLIGONUCLEOTIDE > MICROARRAY WORKSHOP > > January 3-8, 2010 > The University of Arizona > Tucson, Arizona > > This workshop will comprise a combination of lectures and hand-on > laboratory sessions. The participants will primarily employ > Arabidopsis and maize (plant side) and human, bovine and > porcine (animal side) whole genome 70-mer oligonucleotide > microarrays in their laboratory work (for details of the plant arrays see > http://www.ag.arizona.edu/microarray and > http://www.maizearray.org/. > > The workshop will be divided into two parts: Part I (Sunday 4PM to > Wednesday 5PM) will cover wet-lab aspects of microarray target > production and amplification, microarray hybridization, and scanning. > Part II (all day, Thursday and Friday) will concentrate on data extraction, > statistical analysis, and experimental design. Together these topics > are aimed at the goal of the participants obtaining optimal results using > oligonucleotide-based microarrays. Part II may be taken separately. > > Specific topics to be covered include: > > * Experimental design. > * Probe preparation and microarray printing. > * Microarray rehydration and probe immobilization. > * Target preparation, including RNA extraction, direct and indirect > labeling, and amplification techniques. > * Microarray hybridization. > * Array scanning and data extraction. > * Data analysis and archiving. > > Registration (Part I plus Part II) is $700, which includes costs of > the microarrays and other supplies that you will use. > Part II registration only is $300. Part I participants will be > limited to 40 on a first-come, first-serve basis. Overall > participation will be limited to 60 individuals. > > Note: There are a number of airline connections from > Tucson to San Diego on Friday evening, allowing > workshop participants convenient access to the Plant > and Animal Genome XVIII Meeting (January 9-13). > > For further details and to register, please contact > David Galbraith (galbraith@arizona.edu) or Georgina Lambert > (georgina@cals.arizona.edu) > > > > David W. Galbraith > Professor of Plant Sciences > & Professor, Bio5 Institute > University of Arizona > Office: 341 Keating Building > > Mailing address: > BIO5 Institute > The University of Arizona > 1657 E. Helen St. > Tucson, AZ 85721-0240 > > > Tel: (520) 621-9153 > Fax: (520) 626-4824 > Email: galbraith@arizona.edu > http://cals.arizona.edu/galbraith > > > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Sep 2009 18:30:32 -0400 > From: Ann Loraine > Subject: [Arabidopsis] seeking TAIR9 bpmap file for Arabidopsis tiling > array 1.0R > To: arab-gen@magpie.bio.indiana.edu > Message-ID: > <83722dde0909171530w6bd02b7do197669db757274cd@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Colleagues, > > I'm looking for a "bpmap" file that maps Affymetrix Arabidopsis tiling > array > 1.0R probes onto the TAIR9 or TAIR8 genome sequence. > > (This is for setting up a demonstration server that will show labs how they > can easily visualize and share tiling array and RNA-Seq data via the > Integrated Genome Browser (igb.bioviz.org) and DAS, one of the > deliverables > for an NSF 2010 award, which started a year ago.) > > The array corresponds to GEO platform accession GPL1980. (If this is wrong, > please let me know...the Web page for it is here: > http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1980) > > The Web page for GPL1980 at GEO links to a bpmap file, but we are not yet > sure which genome it references. Probably it is the TAIR7 genome, but we > haven't tested it as yet. The bpmap file that Affymetrix distributes > references TAIR7 (what they call Jan 2004) and the company has no immediate > plans to update it because their tiling array support relies on a genome > being supported by the UCSC Genome Bioinformatics group, which only > supports > animal and some fungal genomes. > > If you know of anyone who has a bpmap file for the Arabidopsis Tiling 1.0R > Array for TAIR9, or even TAIR8, I would be very grateful if you would give > me their contact information or send me a link to the file. > > Also, if you are looking for such a file, please let me know, and I'll get > in touch as soon as I find one...or as soon as we create it, if one cannot > be found. > > Thank you very much for your time, > > Ann Loraine > Associate Professor > Dept. of Bioinformatics and Genomics > UNC Charlotte > > > ------------------------------ > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > > End of Arab-gen Digest, Vol 53, Issue 10 > **************************************** > _______________________________________________ Arab-gen mailing list Arab-gen@net.bio.net http://www.bio.net/biomail/listinfo/arab-gen From h.poorter from gmail.com Fri Sep 25 04:43:49 2009 From: h.poorter from gmail.com (Hendrik Poorter) Date: Fri Sep 25 11:33:09 2009 Subject: [Arabidopsis] Workshop and school on (high-throughput) phenotyping Message-ID: EPSO Workshop and ETNA school on Plant Phenotyping. Dear All, In November 2009 there will be a workshop on phenotyping in J?lich, Germany EPSO Workshop High-throughput phenotyping now becomes essential in screening large number of genotypes in a (semi)-automated way. The Phytosphere Institute at the Forschungszentrum J?lich organizes on behalf of the European Plant Science Organization (EPSO) a two-day workshop on the state of the art in medium to high-throughput plant phenotyping, A range of international experts from Universities, Institutes as well as industry will discuss the progresses made in plant imaging, but also various other techniques used to quantify key plant structure, composition and function. A detailed program of the workshop as well as the subscription costs can be found at http://www.plantphenomics.com/phenotyping_workshop. ETNA school The EPSO workshop is also part of an ETNA school for PhD students and PostDocs. The school allows to get both a theoretical basis and hands-on experience on plant phenotyping. Including the workshop it lasts 10 days and covers a wide range of aspects, starting with attention for the best way to grow plants, a range of non-invasive imaging techniques, the relation between photosynthesis and chlorophyll fluorescence, hyperspectral imaging, microwave resonance and remote sensing of crops and vegetations, as well as tomographic techniques such as NMR, and positron emission tomography to visualize short-lived isotope transport. A number of these techniques will be applied by the participants in their own dedicated experiments. The weekend will be used to organize various activities for and with the participants. A program of the ETNA school as well as other details can be found at http://www.plantphenomics.com/ETNA. -- Dr. Hendrik Poorter ICG-3; Research Institute J?lich D-52428 J?lich; Germany From pag from intl-pag.org Mon Sep 28 02:41:22 2009 From: pag from intl-pag.org (PAG-XVIII Conference) Date: Mon Sep 28 13:05:49 2009 Subject: [Arabidopsis] CALL FOR ABSTRACTS - Plant & Animal Genome XVIII Conference Message-ID: <200909280741.n8S7fMlv006488@www.intl-pag.org> Dear Colleague: You are invited to attend the Plant & Animal Genome XVIII Conference (PAG-XVIII), January 9-13, 2010 taking place at the Town & Country Convention Center in San Diego, California. To view the pre-registration brochure please download the PDF file: http://www.scherago.com/pag/RegBrochure.pdf The meeting will again offer the satellite sessions and workshops which took place at Plant & Animal Genome XVII. The meeting draft for PAG-XVIII and abstracts from PG-I through PAG-XVII are available on the PAG website listed below. The exhibits and posters will now take place in the Grand Exhibit Hall, adjacent to the California room. We are no longer using the lower level parking facility. We are requesting that all abstracts be submitted electronically. The abstract deadline is MONDAY, November 2, 2009; extended to allow for the new registration process. The abstract submission website is now open. All attendees looking to submit an abstract will be required to pay the registration fee PRIOR to submitting their abstract. You will be assigned an attendee ID# which will be issued once you complete the on-line registration process. You can look up your ID# on the PAG website at: http://intl-pag.org You will be required to provide your attendee ID# to complete the on-line abstract submission process. Due to severe delays in getting VISAs to enter the United States, we recommend that you plan ahead and do NOT wait for your abstract acceptance to begin the process. DO NOT WAIT. All researchers presenting posters must pre-register for the meeting to have their abstract printed in the final meeting program. Tha abstract deadline is MONDAY, November 2, 2009. Registration is available via the Internet using our secure on-line registration form listed below. https://www.pagregistration.com/pag18reg.shtml Full Conference (Univ/Non-Profit/Govt) Registration for ALL attendees: Pre-Registration (deadline November 2, 2009): $550 Late Registration (after November 2, 2009): $650 On-site Registration: $750 Full Conference (Industry) Registration for ALL attendees: Pre-Registration (deadline November 2, 2009): $775 Late Registration (after November 2, 2009): $875 On-site Registration: $975 Weekend Only (Univ/Non-Profit/Govt) Registration (Fri/Sat/Sun) for ALL attendees: Pre-Registration (deadline November 2, 2009): $400 Late Registration (after November 2, 2009): $450 On-site Registration: $500 Weekend Only (Industry) Registration (Fri/Sat/Sun) for ALL attendees: Pre-Registration (deadline November 2, 2009): $500 Late Registration (after November 2, 2009): $550 On-site Registration: $600 Student Registration (proof required): Pre-Registration (deadline November 1, 2009): $375 Late Registration (after November 1, 2009): $425 On-site Registration: $475 All questions regarding Plant & Animal Genome XVIII should be directed to Scherago Int'l at Tel: 201-653-4777 ext. 20, Fax: 201-653-5705 or or Email: pag@scherago.com. Sincerely, Darrin Scherago - VP, Meeting Manager Scherago International, Inc. 525 Washington Blvd., Suite 3310, Jersy City, NJ 07310 -------------------------------------------------------------------------- Plant & Animal Genome XVIII Conference ---------------- January 9-13, 2007 -------------------------------------------------------------------------- From jaiswalp from science.oregonstate.edu Wed Sep 30 14:12:35 2009 From: jaiswalp from science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Wed Sep 30 14:18:34 2009 Subject: [Arabidopsis] (Bio)Informatics openings at Oregon State University Message-ID: <4AC3ADA3.8010902@science.oregonstate.edu> http://news.gramene.org/?p=392 Bioinformatics and software programmer openings at the rank of Faculty Research Assistant are available in the Jaiswal lab at the Department of Botany and Plant Pathology to work on the Computational Biology and Bioinformatics projects. This is a full-time, (1.0 FTE), 12-month, fixed-term position working in the Jaiswal lab (http://www.science.oregonstate.edu/bpp/faculty/jaiswal/). The positions are renewable annually. The projects involve development and maintenance of the databases, software and analysis pipelines necessary for development of the Plant Gene Expression, biochemical and regulatory pathway networks, comparative genomics, text mining and biological ontology projects. The incumbent will have the necessary skills on developing the software in C, C++, Java, Perl, BioPerl, R, MATLAB, Shell, any other scientific programming language, etc.; and development of MySQL database driven web accessible applications, website coding in HTML, XML, JSP, PHP and computer science applications. To review the position description and apply, go to posting #0004776 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). Applications will be considered throughout the 2009-2010 fiscal year. The closing date is subject to change without notice to applicants. Oregon State University is an Affirmative Action/Equal Opportunity Employer and has a policy of being responsive to dual-career needs. -- Pankaj Jaiswal Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA Web: www.gramene.org www.plantontology.org From kbrowning from mail.utexas.edu Tue Sep 29 14:13:44 2009 From: kbrowning from mail.utexas.edu (Karen Browning) Date: Wed Sep 30 14:19:02 2009 Subject: [Arabidopsis] good set of "housekeeping" genes in AT? Message-ID: <4AC25C68.6000707@mail.utexas.edu> What would be a good set of housekeeping genes to use for "standards" for comparing expression data in Arabidopsis? Anyone have a standard list of At gene numbers that they use, e.g. actin, tubulin, etc.? -- *********************************************************** Dr. Karen S. Browning Associate Professor Department of Chemistry and Biochemistry The University of Texas at Austin Welch Hall 5.248, 24th and Speedway (Overnight Deliveries) 1 University Station A5300 (Regular Mail) Austin TX 78712-0165 kbrowning@mail.utexas.edu http://research.cm.utexas.edu/kbrowning/ 512-471-4562 512-471-8696 FAX From ruohe.yin from helmholtz-muenchen.de Wed Sep 30 03:42:19 2009 From: ruohe.yin from helmholtz-muenchen.de (Yin, Ruohe) Date: Wed Sep 30 14:19:56 2009 Subject: [Arabidopsis] linkage inheritance Message-ID: <3ECE124EF4197A45A9EC80574B0BEA0154690D7986@XCH11.scidom.de> Dear all, I have two T-DAN insertion Arabidopsis lines. The two knock-out loci are about 1Mb in distance on chromosome V. After genetic cross of the two single mutants, F1 plants were self-pollinated and seeds were harvested. My question is how many F2 individuals I would need to ensure one expected double mutant. Thanks a lot for your help. Yin