From nicholas.provart from utoronto.ca Sun Feb 3 17:31:24 2008 From: nicholas.provart from utoronto.ca (Nicholas Provart) Date: Mon Feb 4 12:03:39 2008 Subject: [Arabidopsis] New eFP Browser Light and Natural Variation views and tissue-specific data sets Message-ID: <003801c866b4$823e0c30$5bd6968e@uic00o3tkmejay> Hi everyone, We are happy to announce the addition of 2 new views and several new tissue-specific expression microarray data sets to our eFP Browser, at http://bar.utoronto.ca/efp/. 1. eFP Light Series: Several microarray datasets are displayed describing diurnal, thermocycling, circadian and light treatment experiments generated by researchers around the world including Todd Michael (Michael et al., PLoS Genetics, 2008), Mark Stitt (Blaesing et al, 2005), Steve Kay, Joanne Chory, Stacey Harmer (Covington & Harmer, 2007), Alison Smith (Smith et al., 2004), Andrew Millar (Edwards & Millar, 2007) as well as the AtGenExpress Consortium. See diurnal and circadian cycling of CCA1 (At2g46830) here: http://At2g46830.notlong.com 2. Natural Variation Series: See the expression of your gene of interest across 34 Arabidopsis ecotypes, in data generated by the Weigel Laboratory. For example, see the reduced expression of PHYC in the Fr-2 ecotype, described in Balasubramanian et al. (2006, Nature Genetics), here: http://At5g35840.notlong.com 3. Additional tissue-specific data sets from the Schroeder, Ohlrogge and Preuss labs. The data described in the guard cell set from the Schroeder lab will be published shortly in Plant Methods, and epidermal and stigma and ovary expression data from the Ohlrogge and Preuss labs are published. You can check out epidermal-specific expression of CUT1, a wax biosynthetic enzyme for the epidermis, here: http://At1g68530.notlong.com or guard-cell-specific expression of a potassium channel, KAT1, here: http://At5g46240.notlong.com or a stigma-specific gene, S-locus related 1 (AtS1), here: http://At3g12000.notlong.com Thanks to Todd Michael, Julian Schroeder, Yingzhen Yang, John Ohlrogge, Owen Rowland, and Detlef Weigel for feedback in putting these views together, and to Hardeep Nahal for database assistance. Any other feedback or comments are welcome. The eFP Browser is described in Winter et al., PLoS One 2(8):e718, see http://dx.doi.org/10.1371/journal.pone.0000718. Best regards, Nick ......................................... Nicholas Provart, PhD Assistant Professor, Plant Bioinformatics & Systems Biology Director, Graduate Program in Genome Biology and Bioinformatics Member, Centre for the Analysis of Genome Evolution and Function Rm 3051, Dept. of Cell and Systems Biology, Uni. Toronto 25 Willcocks St., Toronto, ON. M5S 3B2. CANADA Tel. (+1) (416) 978-7141, Fax. (+1) (416) 978-5878 URL. http://www.csb.utoronto.ca/faculty/provart/ Arabidopsis Tools. http://www.bar.utoronto.ca email. nicholas.provart@utoronto.ca From jdfriesner from ucdavis.edu Mon Feb 4 16:20:35 2008 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Tue Feb 5 00:27:05 2008 Subject: [Arabidopsis] Funding, Registration, T-shirts, Workshops for the 2008 Arabidopsis meeting Message-ID: <002f01c86773$c8f616d0$6500a8c0@mcb.ucdavis.edu> Registration for the 19th International Conference on Arabidopsis Research is now open at: http://www.plantconferences.org/Arabidopsis2008/ -Reduced Fee Deadline: April 30, 2008 (lower fee for students and postdocs) -Conference Funding: ALL applications are due by APRIL 4, 2008 (1) Plant Biologists in the US- accepting applications for Registration Fee Awards AND for full funding of under-represented minorities (2) Plant Biologists in Canada- accepting applications for Registration Fee Awards (3) Plant Biologists outside of the US and Canada- accepting applications for Registration Fee Awards (Full information is available at the conference website under the 'Funding' link.) -Workshops: Proposals are due by MAY 19, 2008 6 slots for community-proposed and organized workshops are available. A brief application is required and the conference committee will select and approve up to 6 workshop proposals. (Full information is available at the conference website under the 'Workshops' link.) -Conference t-shirt: designed this year by Vishwanath Sollapura, a PhD student at Carleton University in Ottawa, Canada. The t-shirt design is shown on the registration page, and shirts can be pre-ordered during registration. Shirts will also be sold at the conference but quantities may be limited so order during registration to guarantee the color and size you want. -Abstract submission for ORAL consideration (for Concurrent Sessions) MUST BE submitted by April 30, 2008. After that date, all submissions will be for POSTERS only. (Full information on the website under the 'Abstracts' link.) -Housing Reservation is open online- A recently-renovated hotel is McGill University's newest dorm and we have reserved this for graduate student and postdoc housing. Regular attendees can reserve rooms at the Hyatt Regency, the conference site. (Full information on the website under the 'Housing' link.) We look forward to seeing you all in Montreal this July! Joanna Friesner, PhD MASC Coordinator jdfriesner@ucdavis.edu 19th International Conference on Arabidopsis Research July 23-37, 2008 Montreal, Canada http://www.plantconferences.org/Arabidopsis2008/ From imtechnology from gmail.com Mon Feb 4 17:36:32 2008 From: imtechnology from gmail.com (ims) Date: Tue Feb 5 00:27:12 2008 Subject: [Arabidopsis] Re: Barcode/tracking system for seeds, plants References: Message-ID: On Feb 1, 11:54 am, Michael Steinwand wrote: > Hi All, > > I am seeking advice about any software that can be used for creating > and tracking seeds, plant specimens etc using a barcoding system. Our > lab will have a large population of Brachypodium, and we'd like to > figure out a way to improve our cataloging/tracking system before > we're flooded with samples. I'm really interested in using software > that can print sample-specific labels in various sizes and can also > be used with a mobile scanning unit like a PDA. I've done some > research and found asset tracking software like that fromwww.redbeam.comand label-making software like Bar Tender, but I'm > wondering if there are better options that other labs use to track > seeds, etc. Any ideas or helpful tips on barcoding? > > Thanks, > > Michael Steinwand > > USDA ARS > 800 Buchanan St. > Albany, CA 94710 Hi Michael! I started a website for pretty much this reason and also to keep track of our oligos glycerols and chemicals!!! Its located here: http://www.yourlabdata.com It's a work in progress but it's already quite functional although i haven't added the barcode functionality for seeds, and other items, yet but it is on my to do list (that's the trouble when you are doing a PhD you're always strapped for time). I will also be introducing a backup system shortly as well so that the lab group owner is emailed a backup of all of their database content on a weekly basis... just have a few kinks to work out. Anyway have a look... our lab is using it very successfully to keep track of our oligos and a number of other labs are now using it as well. I would be interested in hearing about improvements I could make to the system so please don't hesitate to let me know. (if you find a bug or have a suggestion you should post it in this forum... http://www.yourlabdata.com/index.php?option=com_fireboard&Itemid=29&func=showcat&catid=17) Cheers, Edwin. From belostotskyd from umkc.edu Mon Feb 4 17:41:18 2008 From: belostotskyd from umkc.edu (Belostotsky, Dmitry) Date: Tue Feb 5 00:27:17 2008 Subject: [Arabidopsis] medium-throughout Arabidopsis genotyping solution? Message-ID: <5C13F286F3DAE649BFF21749E3DEE0960623D5CA@KC-MSX1.kc.umkc.edu> Anyone can recommend a method that can be used in 96 well plate or similar format WITHOUT robotics - and produce reliable shorty quality PCRable stuff? Thanks much Dmitry Dmitry A. Belostotsky, Ph.D. Associate Professor Division of Molecular Biology and Biochemistry School of Biological Sciences University of Missouri Kansas City, MO 64110 From mrunning from danforthcenter.org Mon Feb 4 18:44:28 2008 From: mrunning from danforthcenter.org (Mark Running) Date: Tue Feb 5 00:27:23 2008 Subject: [Arabidopsis] Postdoctoral Position in Plant Development Message-ID: Description A postdoctoral position is available in the Running Laboratory at the Donald Danforth Plant Science Center. The Running Laboratory studies the mechanisms of lipid modification of plant proteins, as well as the role of these proteins in plant development and environmental response. Successful candidates must be highly motivated and have a Ph.D. in biology or a related field. A strong background in biochemistry or molecular biology is preferred. To apply, please send a cover letter, C.V., and 2-3 letters of references to: Donald Danforth Plant Science Center Billie Broeker, Human Resources REF: Running Lab/PostDoc 975 North Warson Road St. Louis, Missouri 63132 or by email with RunningLab/PostDoc in the subject line to bcbroeker@danforthcenter.org. The Donald Danforth Plant Science Center is an equal opportunity/affirmative action employer and encourages applications from underrepresented groups, including minorities, women, and people with disabilities. -- Mark P. Running, Ph.D. Assistant Member, Principal Investigator Donald Danforth Plant Science Center 975 N Warson Rd Saint Louis MO 63132 Phone(314) 587-1641 Cell(314)359-9344 Fax(314) 587-1741 mrunning@danforthcenter.org From b.g.forde from lancaster.ac.uk Tue Feb 5 05:06:05 2008 From: b.g.forde from lancaster.ac.uk (Forde, Brian) Date: Tue Feb 5 20:00:22 2008 Subject: [Arabidopsis] Re: Barcode/tracking system for seeds, plants In-Reply-To: Message-ID: <199A8D531E24DF47ADCC977CE0E94AFC0221A4BA@exchange-be6.lancs.local> Hi Michael A very useful and versatile system has just been published in Plant Methods by Exner and colleagues, although it doesn't incorporate barcoding.... This is the link: http://www.plantmethods.com/content/4/1/1 Hope this helps Brian ===================================== Brian G. Forde Prof. of Environmental Plant Biotechnology Department of Biological Sciences Lancaster Environment Centre Lancaster University Bailrigg Lancaster LA1 4YQ tel. +44 (0)1524 510207 (direct line) email b.g.forde@lancaster.ac.uk http://biol.lancs.ac.uk/bs/research/plants/bgf.htm Editor-in-Chief Plant Methods email plantmethods@lancaster.ac.uk http://www.plantmethods.com ===================================== -----Original Message----- From: arab-gen-bounces@oat.bio.indiana.edu [mailto:arab-gen-bounces@oat.bio.indiana.edu] On Behalf Of ims Sent: 04 February 2008 22:37 To: bionet-genome-arabidopsis@moderators.isc.org Subject: [Arabidopsis] Re: Barcode/tracking system for seeds, plants On Feb 1, 11:54 am, Michael Steinwand wrote: > Hi All, > > I am seeking advice about any software that can be used for creating > and tracking seeds, plant specimens etc using a barcoding system. Our > lab will have a large population of Brachypodium, and we'd like to > figure out a way to improve our cataloging/tracking system before > we're flooded with samples. I'm really interested in using software > that can print sample-specific labels in various sizes and can also be > used with a mobile scanning unit like a PDA. I've done some research > and found asset tracking software like that fromwww.redbeam.comand > label-making software like Bar Tender, but I'm wondering if there are > better options that other labs use to track seeds, etc. Any ideas or > helpful tips on barcoding? > > Thanks, > > Michael Steinwand > > USDA ARS > 800 Buchanan St. > Albany, CA 94710 Hi Michael! I started a website for pretty much this reason and also to keep track of our oligos glycerols and chemicals!!! Its located here: http://www.yourlabdata.com It's a work in progress but it's already quite functional although i haven't added the barcode functionality for seeds, and other items, yet but it is on my to do list (that's the trouble when you are doing a PhD you're always strapped for time). I will also be introducing a backup system shortly as well so that the lab group owner is emailed a backup of all of their database content on a weekly basis... just have a few kinks to work out. Anyway have a look... our lab is using it very successfully to keep track of our oligos and a number of other labs are now using it as well. I would be interested in hearing about improvements I could make to the system so please don't hesitate to let me know. (if you find a bug or have a suggestion you should post it in this forum... http://www.yourlabdata.com/index.php?option=com_fireboard&Itemid=29&func =showcat&catid=17) Cheers, Edwin. _______________________________________________ Arab-gen mailing list Arab-gen@net.bio.net http://www.bio.net/biomail/listinfo/arab-gen From James.Hartwell from liverpool.ac.uk Tue Feb 5 07:39:22 2008 From: James.Hartwell from liverpool.ac.uk (James Hartwell) Date: Tue Feb 5 20:00:27 2008 Subject: [Arabidopsis] Postdoctoral position - 454 transcriptome sequencing of Kalanchoe fedtschenkoi Message-ID: UNIVERSITY OF LIVERPOOL, UK PLANT SCIENCES RESEARCH GROUP SCHOOL OF BIOLOGICAL SCIENCES You will join a 3-year BBSRC-funded project =93Sequencing the =20 trancriptome of Kalanchoe fedtschenkoi: a model for Crassulacean acid =20= metabolism (CAM), embryogenic plantlet formation and the =20 Saxifragales=94. This is a ground-breaking project that will employ the =20= latest ultra high-throughput pyrosequencing technology (Roche/454 GS =20 Leonardo) to achieve deep sequencing of the transcribed portion of =20 the K. fedtschenkoi genome. POSTDOCTORAL RESEARCHER =A328,289 - =A329,139 pa You will generate cDNA samples for 454 sequencing and undertake =20 digital northern analysis of the 454 data to identify the genes =20 required for the circadian control of CAM, plantlet formation and =20 other unique aspects of K. fedtschenkoi's biology. You will =20 collaborate with a second bioinformatics postdoc to build contigs =20 from the 454 reads, and develop a K. fedtschenkoi EST database to =20 provide access to the ~15 billion base pairs of K. fedtschenkoi DNA =20 sequence that you will be involved in generating. For the CAM-=20 associated genes identified through the 454 sequencing, you will =20 perform detailed circadian transcriptome analysis using a Beckman-=20 Coulter GeXP system to profile the transcript abundance of groups of =20 30 genes simultaneously. CAM-associated regulatory genes will be =20 manipulated by generating transgenic K. fedtschenkoi lines, and you =20 will perform detailed phenotypic analysis to study the ability of =20 these lines to perform CAM. You will also coordinate the production =20 of a K. fedtschenkoi BAC library, clone BACs for CAM-associated =20 genes, and sequence the BACs using the Roche/454 GS Leonardo. You should have (or be about to obtain) a PhD with experience in =20 plant molecular biology, biochemistry and/or physiology with =20 preference being given to individuals with experience of analysis of =20 large genomics data sets. Ideally, you will also have experience of =20 generating plant binary constructs for RNAi and overexpression, and =20 working with non-model plant species. Job Ref: R-567182 RESEARCH TECHNICIAN GRADE 5 =A320,458 - =A322,332 pa You will be responsible for the growth and maintenance of K. =20 fedtschenkoi, isolation of RNA and DNA samples, generating transgenic =20= lines to manipulate key CAM genes, and the study of the phenotypes of =20= these lines. You should be qualified to BTEC Higher level (or equivalent) with =20 experience in plant molecular biology, biochemistry and/or physiology =20= with preference being given to individuals with experience of tissue =20 culture based plant transformation. Ideally, you will also have =20 experience of PCR, RT-PCR, and enzyme and metabolite assays. Job Ref: =20= S-567180 Closing date for both posts: 22 February 2008 For informal enquiries, please contact Dr. James Hartwell, e-mail: =20 hartwell@liv.ac.uk Weblink for Hartwell lab research interests: http://www.liv.ac.uk/=20 biolsci/people/academic/hartwell_j/index.html For full details, or to request an application pack, visit www.liv.ac.uk/working/job_vacancies/ or e-mail jobs@liv.ac.uk Tel 0151 794 2210 (24 hr answerphone), please quote Ref: in all enquiries Dr. James Hartwell, Lecturer in Plant Metabolism, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB United Kingdom Tel: +44 (0)151 795 4561 Fax: +44 (0)151 795 4410 E-mail: hartwell@liv.ac.uk Web: http://www.liv.ac.uk/biolsci/people/academic/hartwell_j/index.html From jsr22 from psu.edu Tue Feb 5 09:56:51 2008 From: jsr22 from psu.edu (Jai S Rohila) Date: Tue Feb 5 20:00:32 2008 Subject: [Arabidopsis] medium-throughout Arabidopsis genotyping solution? In-Reply-To: <5C13F286F3DAE649BFF21749E3DEE0960623D5CA@KC-MSX1.kc.umkc.e du> References: <5C13F286F3DAE649BFF21749E3DEE0960623D5CA@KC-MSX1.kc.umkc.edu> Message-ID: <7.0.1.0.2.20080205095458.02291a10@psu.edu> Hi Dmitry, Try the following protocol. High-Throughput DNA Extraction Method Suitable for PCR Zhanguo Xin, Jeff P. Velten, Melvin J. Oliver, and John J. Burke BioTechniques Vol. 34, No. 4: pp 820-826 (Apr 2003) Full text Best, Jai At 05:41 PM 2/4/2008, Belostotsky, Dmitry wrote: >Anyone can recommend a method that can be used in 96 well plate or >similar format WITHOUT robotics - and produce reliable shorty >quality PCRable stuff? >Thanks much > >Dmitry > >Dmitry A. Belostotsky, Ph.D. > >Associate Professor > >Division of Molecular Biology and Biochemistry >School of Biological Sciences >University of Missouri >Kansas City, MO 64110 > > > >_______________________________________________ >Arab-gen mailing list >Arab-gen@net.bio.net >http://www.bio.net/biomail/listinfo/arab-gen From imtechnology from gmail.com Tue Feb 5 16:58:46 2008 From: imtechnology from gmail.com (ims) Date: Tue Feb 5 20:00:57 2008 Subject: [Arabidopsis] Re: Barcode/tracking system for seeds, plants References: Message-ID: <057810bb-e757-4986-aa46-c72c85512afa@v46g2000hsv.googlegroups.com> On Feb 5, 9:36 am, ims wrote: > On Feb 1, 11:54 am, Michael Steinwand wrote: > > > > > Hi All, > > > I am seeking advice about any software that can be used for creating > > and tracking seeds, plant specimens etc using a barcoding system. Our > > lab will have a large population of Brachypodium, and we'd like to > > figure out a way to improve our cataloging/tracking system before > > we're flooded with samples. I'm really interested in using software > > that can print sample-specific labels in various sizes and can also > > be used with a mobile scanning unit like a PDA. I've done some > > research and found asset tracking software like that fromwww.redbeam.comandlabel-making software like Bar Tender, but I'm > > wondering if there are better options that other labs use to track > > seeds, etc. Any ideas or helpful tips on barcoding? > > > Thanks, > > > Michael Steinwand > > > USDA ARS > > 800 Buchanan St. > > Albany, CA 94710 > > Hi Michael! > > I started a website for pretty much this reason and also to keep track > of our oligos glycerols and chemicals!!! Its located here:http://www.yourlabdata.com > > It's a work in progress but it's already quite functional although i > haven't added the barcode functionality for seeds, and other items, > yet but it is on my to do list (that's the trouble when you are doing > a PhD you're always strapped for time). I will also be introducing a > backup system shortly as well so that the lab group owner is emailed a > backup of all of their database content on a weekly basis... just have > a few kinks to work out. > > Anyway have a look... our lab is using it very successfully to keep > track of our oligos and a number of other labs are now using it as > well. > > I would be interested in hearing about improvements I could make to > the system so please don't hesitate to let me know. > (if you find a bug or have a suggestion you should post it in this > forum...http://www.yourlabdata.com/index.php?option=com_fireboard&Itemid=29&f...) > > Cheers, > > Edwin. I should probably add that I am aware that there are some small problems in internet explorer 6 so if you are using this browser you will need to upgrade to version 7... which you really should do for safety reasons or use firefox! Cheers, Edwin. From zrsung from nature.berkeley.edu Tue Feb 5 17:40:44 2008 From: zrsung from nature.berkeley.edu (Renee Sung) Date: Tue Feb 5 20:01:01 2008 Subject: [Arabidopsis] Postdoctoral position in brassica epigenetics in IPMB, Taiwan Message-ID: A postdoctoral fellow position is available at the Institute of Plant and Microbial Biology, Academia Sinica (IPMB-AS), to study the role of Polycomb Group proteins in plant (broccoli) development, a collaborative effort between Dr. Z. Renee Sung, UC Berkeley, California and Dr. L. Oliver Chen in IPMB-AS, Taiwan. Polycomb group proteins play major roles in embryogenesis, cancer and stem cell renewal. They encode chromatin proteins that form multi-protein complexes, functioning to maintain gene silencing via histone modifications. In Arabidopsis, PcG proteins are required to regulate major developmental processes such as seed development and flowering. Dr. Sung's laboratory has been studying the molecular mechanism of PcG proteins in silencing flower MADS-box genes and maintain vegetative development. Dr. Chen's laboratory focuses on transgenics and functional gene analyses on broccoli (Brassica oleracea. Var. italica) The collaborative project investigates the role of PcG proteins in broccoli development with 2 emphases-- the evolution of PcG protein genes and the isolation of the PcG protein complexes. Despite the importance of the PcG protein genes in Arabidopsis development, little is known of the role of these genes in other plant species. Broccoli, being a close relative of Arabidopsis, is an ideal organism for investigating the functional conservation of these genes during evolution. Moreover, tools developed in Arabidopsis can be readily applied to broccoli. Due to its large plant size, broccoli is also excellent for protein purification and protein complex isolation studies. Candidates should have a PhD and experiences in plant molecular biology and protein biochemistry with skills in gene cloning, DNA and RNA analysis, protein purification, immunoprecipitation, western analysis. Experiences in Chromatin immunoprecipitation, microarray, transgenic plants and plant genetic analyses are desirable. Reasonable levels of writing and verbal communicating skills in English are required. Successful applicants will be one who is capable of independent research and experimental designs. A self-motivated, creative individual with communication skills are required. The appointee will lead a small group of Chinese graduates and research assistants. For additional information, candidate should access Dr. Sung's website through the Department of Plant and Microbial Biology, UC Berkeley, http://pmb.berkeley.edu, and Dr. Chen's website through the Institute of Plant and Microbial Biology, Academia Sinica, http://ipmb.sinica.edu.tw. The salary will be between US$1,700.00~2,600.00 per month depending on experience. The positions can start as early as February 2008. IPMB-AS is well-equipped with five nice core facilities for cell biology, microarray analysis, proteomics, transgenic plant generation and bioinformatics studies. For your interest, you are welcome to visit our web site as indicated previously. There are seven other Life Science Research Centers or Institutes -- Institutes of Molecular Biology, Biological Chemistry, Biomedical Sciences, Cellular and Organismic Biology and Genomic Research Center, Agricultural Biotechnology Research Center and Research Center for Biodiversity all in the walking distance providing an excellent research environment for collaborative studies. Rental apartments and housings are available in the neighborhood. Minimal level of living costs is around US$700.00~800.00/month. Convenient transportation system to downtown Taipei as well as travel around the island is also available. If you have any other question, please contact us at zrsung@nature, or ochenlf@gate.sinica.edu.tw From brasiu from yahoo.com Wed Feb 6 06:00:05 2008 From: brasiu from yahoo.com (Wojciech Strzalka) Date: Wed Feb 6 15:44:31 2008 Subject: [Arabidopsis] BY2 transformation protocol Message-ID: <487559.1298.qm@web60718.mail.yahoo.com> Hi, I am looking for working BY2 transformation protocol. Anybody can help me? Bests, Wojciech ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping From b.g.forde from lancaster.ac.uk Wed Feb 6 06:15:53 2008 From: b.g.forde from lancaster.ac.uk (Forde, Brian) Date: Wed Feb 6 15:44:37 2008 Subject: [Arabidopsis] medium-throughout Arabidopsis genotyping solution? In-Reply-To: <7.0.1.0.2.20080205095458.02291a10@psu.edu> Message-ID: <199A8D531E24DF47ADCC977CE0E94AFC0221A4C4@exchange-be6.lancs.local> Hi Dimitry The following paper by Katie Clark and Patrick Krysan is Open Access and describes a protocol that might be suitable for your purposes: Protocol: An improved high-throughput method for generating tissue samples in 96-well format for plant genotyping (Ice-Cap 2.0) http://www.plantmethods.com/content/3/1/8 Hope this helps Brian -----Original Message----- From: arab-gen-bounces@oat.bio.indiana.edu [mailto:arab-gen-bounces@oat.bio.indiana.edu] On Behalf Of Jai S Rohila Sent: 05 February 2008 14:57 To: Belostotsky, Dmitry Cc: arab-gen@magpie.bio.indiana.edu Subject: Re: [Arabidopsis] medium-throughout Arabidopsis genotyping solution? Hi Dmitry, Try the following protocol. High-Throughput DNA Extraction Method Suitable for PCR Zhanguo Xin, Jeff P. Velten, Melvin J. Oliver, and John J. Burke BioTechniques Vol. 34, No. 4: pp 820-826 (Apr 2003) Full text Best, Jai At 05:41 PM 2/4/2008, Belostotsky, Dmitry wrote: >Anyone can recommend a method that can be used in 96 well plate or >similar format WITHOUT robotics - and produce reliable shorty >quality PCRable stuff? >Thanks much > >Dmitry > >Dmitry A. Belostotsky, Ph.D. > >Associate Professor > >Division of Molecular Biology and Biochemistry >School of Biological Sciences >University of Missouri >Kansas City, MO 64110 > > > >_______________________________________________ >Arab-gen mailing list >Arab-gen@net.bio.net http://www.bio.net/biomail/listinfo/arab-gen _______________________________________________ Arab-gen mailing list Arab-gen@net.bio.net http://www.bio.net/biomail/listinfo/arab-gen From thomas.greb from gmi.oeaw.ac.at Wed Feb 6 09:39:04 2008 From: thomas.greb from gmi.oeaw.ac.at (Greb, Thomas) Date: Wed Feb 6 15:44:42 2008 Subject: [Arabidopsis] pBIN19 Message-ID: <3ED3D285FFD58F41BDE657B18F548C034542AC@gmi-mail01.gmi.oeaw.ac.at> Hi, we would like to use the pBIN19 vector for transient expression experiments. Could anybody supply us with an aliquot of DNA? Many thanks! Thomas ------------------------------------------------ Thomas Greb, JPI Gregor Mendel Institute of Molecular Plant Biology Dr. Bohr-Gasse 3 A-1030 Vienna Austria From jeedward from yahoo.com Wed Feb 6 10:28:40 2008 From: jeedward from yahoo.com (John Edward) Date: Wed Feb 6 15:44:47 2008 Subject: [Arabidopsis] Draft paper submission deadline is extended: BCBGC-08 Message-ID: <726027.71498.qm@web45906.mail.sp1.yahoo.com> Dear Professors, Colleagues and Friends Kindly share the announcement below with those who may be interested: thank you in advance. Sincerely John Edward BCBGC-08 Draft paper submission deadline is extended. The 2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) (website: www.PromoteResearch.org ) will be held during July 7-10 2008 in Orlando, FL, USA. The draft paper submission deadline is extended until February 19 2008 due to several requests from the authors. The conference will be held at the same time and location where several major events (see below) will be taking place. BCBGC brings together both academic and industrial scientists and developers from a diverse range of disciplines including bioinformatics, computer science, computational biology, genomics, proteomics and chemoinformatics. One of the main goals of the conference is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers in different fields. Papers that demonstrate applications of existing techniques or developments of new methods are equally welcomed to the conference. Sincerely John Edward ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-08) ? International Conference on Automation, Robotics and Control Systems (ARCS-08) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-08) ? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-08) ? International Conference on Software Engineering Theory and Practice (SETP-08) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-08) --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. From mlsulliv from wisc.edu Wed Feb 6 15:59:09 2008 From: mlsulliv from wisc.edu (Michael Sullivan) Date: Wed Feb 6 18:31:56 2008 Subject: [Arabidopsis] BY2 transformation protocol In-Reply-To: <487559.1298.qm@web60718.mail.yahoo.com> References: <487559.1298.qm@web60718.mail.yahoo.com> Message-ID: See the following link. This worked very well for me back in my Green Lab days. http://ag.udel.edu/plsc/faculty/pamgreen/by2.htm Mike Sullivan US Dairy Forage Research Center, ARS-USDA On Feb 6, 2008, at 5:00 AM, Wojciech Strzalka wrote: > Hi, > > I am looking for working BY2 transformation protocol. > Anybody can help me? > > Bests, > > Wojciech > > > > ______________________________________________________________________ > ______________ > Looking for last minute shopping deals? > Find them fast with Yahoo! Search. http://tools.search.yahoo.com/ > newsearch/category.php?category=shopping > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen From wenxian16 from yahoo.com Wed Feb 6 11:24:27 2008 From: wenxian16 from yahoo.com (Wenxian Sun) Date: Thu Feb 7 16:22:22 2008 Subject: [Arabidopsis] Question about CoIP Message-ID: <940014.94937.qm@web58708.mail.re1.yahoo.com> Hi Colleagues, I am trying to use CoIP to study the protein-protein interaction in Arabidopsis seedlings. The proteins are tagged by HA and cMyc-GFP, respectively. When I use anti-cMyc antibody to do immunoprecipitation, I can detect the HA-tagged protein in the pulldown pretty well. However, if I use anti-HA antibody to do IP, I can not detect any cMyc-GFP tagged protein with anti-cMyc or GFP antibodies. The results are highly repeatable. The anti-GFP antibody is from Invitrogen. The anti-HA, cMyc antibodies are from Covance. I have tried protein A (Amersham), protein A/G (Pierce) beads and HA.11 affinity matrix (Covance) and have no luck. Anyone has the similar problem or any suggestion? Thanks a lot, Wenxian --------------------------------- Never miss a thing. Make Yahoo your homepage. From younesi from informatik.uni-bonn.de Thu Feb 7 11:03:39 2008 From: younesi from informatik.uni-bonn.de (Erfan Younesi) Date: Thu Feb 7 16:22:56 2008 Subject: [Arabidopsis] Nicotiana gene families Message-ID: <55289.129.26.132.8.1202400219.squirrel@webmail.iai.uni-bonn.de> Dear all, I'm a bioinformatician searching for a "gene family classification" schema in the Solanaceae family generally and Nicotiana species particularly. It would be even better if these genes have been already annotated, for example in a database. I should be very grateful if someone could help me in this regard. Thank you in advance, Erfan Younesi -- Group of Life Science Informatics, B-IT,University of Bonn, Pariserstra?e 54, PoBox 347,53117 Bonn Germany From jrunions from brookes.ac.uk Fri Feb 8 11:09:18 2008 From: jrunions from brookes.ac.uk (John Runions) Date: Fri Feb 8 12:29:10 2008 Subject: [Arabidopsis] Nicotiana gene families In-Reply-To: <55289.129.26.132.8.1202400219.squirrel@webmail.iai.uni-bonn.de> References: <55289.129.26.132.8.1202400219.squirrel@webmail.iai.uni-bonn.de> Message-ID: <47AC7EAE.80609@brookes.ac.uk> Hi Erfan, there is the Tobacco Genome Initiative at North Carolina State University: [1]http://www.tobaccogenome.org/index.html John Erfan Younesi wrote: Dear all, I'm a bioinformatician searching for a "gene family classification" schema in the Solanaceae family generally and Nicotiana species particularly. It would be even better if these genes have been already annotated, for example in a database. I should be very grateful if someone could help me in this regard. Thank you in advance, Erfan Younesi -- ********************************* C. John Runions, Ph.D. School of Life Sciences Oxford Brookes University Oxford, UK OX3 0BP email: [2]jrunions@brookes.ac.uk phone: +44 (0) 1865 483 964 [3]Runions' lab web site Visit [4]The Illuminated Plant Cell dot com Oxford Brookes Master's in [5]Bioimaging with Molecular Technology References 1. http://www.tobaccogenome.org/index.html 2. mailto:jrunions@brookes.ac.uk 3. http://www.brookes.ac.uk/lifesci/runions/HTMLpages/index.html%21 4. http://www.illuminatedcell.com/ER.html 5. http://www.brookes.ac.uk/studying/courses/postgraduate/2007/bmt From msteinwand from pw.usda.gov Fri Feb 8 13:17:49 2008 From: msteinwand from pw.usda.gov (Michael Steinwand) Date: Sat Feb 9 01:42:22 2008 Subject: [Arabidopsis] Barcode software information Message-ID: <200802081817.m18IHuKC014852@aggie.pw.usda.gov> Hello everyone, Last week I sent an e-mail about suggestions for software for a barcoding system for our project, specifically to help track and catalog plants, stems and seeds. I've received requests for me to share any suggestions that I received. One of the software systems recommended to me by several people is LabCollector, which can be found at www.labcollector.com This program operates in an Internet browser, like Explorer, and has a number of different categories for items, including antibodies, sequences and samples. The program allows you to print barcodes for samples, and that information can be imported from text files (You can't import right from Excel, the software needs delimited data). LabCollector prints labels one at a time, so I think you'll need a barcode printer as well. The company offers a PDA barcode scanner, so this is mobile software that can be used outside the lab, if needed. The link has a free 30-day demo. Another program that I have heard of but not really used is Bar Tender, which is software that can be used to make very versatile labels. Information for labels can be imported from Excel, but I don't believe that it has any ability to maintain a database. It offers a large variety of barcode fonts and possible label designs. More information can be found at http://www.seagullscientific.com/aspx/btw_down.aspx. For information on databases that can be used for tracking plants and seeds, although they are currently without a barcode feature, see http://www.plantmethods.com/content/4/1/1/abstract and http://www.yourlabdata.com. Thank you to those who responded and I'm still seeking suggestions, so please let me know if you come across anything. Thanks, Michael USDA ARS 800 Buchanan St Albany, CA 94710 From hw75 from cornell.edu Fri Feb 8 16:19:58 2008 From: hw75 from cornell.edu (Haiyang Wang) Date: Sat Feb 9 01:42:28 2008 Subject: [Arabidopsis] Postdoc position available Message-ID: A postdoctoral position is available in Haiyang Wang's Laboratory at the Boyce Thompson Institute for Plant Research, Cornell University. The Wang Laboratory studies the molecular mechanisms of phytochrome signaling in Arabidopsis and crop species. Projects include studying two novel transposase-derived transcription factors in regulating phyA signaling (Lin et al., 2007, Science, 318:1302-1305) and regulation of HFR1 (a bHLH transcription factor) function by posttranslational modifications (ubiquitination and phosphorylation) (Yang et al., Plant Cell 17:804-821; Yang et al., Plant J. 43:131-141; Yang and Wang, Plant J. 47:564-576). Successful candidates should have a Ph.D. in molecular genetics or biochemistry, be self-motivated and capable of independent research and experimental designs. A strong background in cell biology or bioinformatics will be a plus. Reasonable levels of writing and verbal communicating skills in English are required. To apply, send cover letter detailing research experience and achievements, curriculum vitae (including course highlights and technical skills), and the names of three references. Please indicate the job code BTI #2008-06 in your application. For more information or to apply, please contact Haiyang Wang, Boyce Thompson Institute, Ithaca, NY 14853; email: hw75@cornell.edu. -- Haiyang Wang Tower Road Boyce Thompson Institute Cornell University Ithaca, NY, 14853 phone: 607-254-7476 fax: 607-254-1242 From FALBELTG from uwec.edu Sat Feb 9 16:10:53 2008 From: FALBELTG from uwec.edu (Falbel, Tanya G.) Date: Sun Feb 10 00:47:47 2008 Subject: [Arabidopsis] brands of agar Message-ID: Colleagues: Over the years, I've used several brands of agar for growing Arabidopsis seedlings on MS medium, from Gibco, Sigma, and others. I've heard that some groups use Noble agar, others, bacto-agar, others in the past have washed their own agar, used phytagel or other gelling agents. I have two questions: 1) What brands of agar are most commonly in use now by groups? I've found something similar to Gibco's Phytagar that is now available through Caisson labs. Other groups seem to like Sigma's A1296. But besides those, what do most groups use? I'm especially interested in the opinion of groups that measure root length or root branching - growing roots vertically on plates for more than just a couple of days. (as opposed to just antibiotic selection) 2) Does anyone know what inhibitors are washed away? Are micronutrient ions or other toxic compounds bound to the crude agar? Has anyone looked into this? This may have been a question that came up among researchers 10 years ago, but I couldn't find any record in the archives. Here's why I'm asking. I made up a batch of medium with a brand of 'purified agar for microbial use', and got a very strong inhibition of root meristems. Seed germination was good, but roots failed to elongate any further after about 4 days of growth. The root meristems became a swollen mess, reminiscent of what happens in weak gnom alleles. I'm trying to decide if this is something worth looking into. I know that for regeneration of plants in tissue culture, folks are very fussy about particular brands of agar. Please let me know what brands you have used with success or failure. I'd be especially interested in other similar experiences - where a brand wreaked havoc on root meristems. Thanks Tanya Falbel Department of Biology 105 Garfield Avenue University of Wisconsin-Eau Claire Eau Claire, WI 54702-4004, USA Tel: 715-836-5087 Fax: 715-836-5089 From b.g.forde from lancaster.ac.uk Mon Feb 11 05:04:43 2008 From: b.g.forde from lancaster.ac.uk (Forde, Brian) Date: Tue Feb 12 18:54:36 2008 Subject: [Arabidopsis] brands of agar In-Reply-To: Message-ID: <199A8D531E24DF47ADCC977CE0E94AFC0221A501@exchange-be6.lancs.local> Hi Tanya For the last 15 years or so we have been routinely studying Arabidopsis root growth and branching on vertical 'agar' plates, for up to two weeks after germination. We have used 0.8% agar-agar in the past with reasonable results, but found that batches were variable and sometimes root growth would be inhibited. We now choose to use PhytagelTM, which is purer and gives a clearer gel, and we have had no problems with different batches (note that you have to make sure that the divalent cation concentration in the medium is at least 2 mM, otherwise it won't set!). As an important aside, I would strongly recommend that you *don't* use MS (or even 1/2 MS) for anything other than tissue culture or antibiotic selection. It is an extremely rich medium with non-physiological N concentrations that far exceed anything that plants are ever likely to have experienced in nature (40 mM nitrate + 20 mM ammonium)and root growth in this medium is also very slow. We use a dilute form of B5 medium that allows much faster root growth. We have done direct comparisons with Ler and Col-0 growing in MS, 1/2 MS and in our modified B5 medium at different rates of N supply and found that all growth parameters (lateral roots, primary roots, shoots) are faster on the modified B5 medium. The modified B5 medium also allows you to vary individual components of the nutrient supply without creating severe nutrient imbalances that cause plant stress. The composition of our medium was originally published in Zhang & Forde (1998) Science 279, 407-409, but I can give you more details if you wish to email me. Good luck! Brian ===================================== Brian G. Forde Prof. of Environmental Plant Biotechnology Department of Biological Sciences Lancaster Environment Centre Lancaster University Bailrigg Lancaster LA1 4YQ tel. +44 (0)1524 510207 (direct line) email b.g.forde@lancaster.ac.uk http://biol.lancs.ac.uk/bs/research/plants/bgf.htm Editor-in-Chief Plant Methods email plantmethods@lancaster.ac.uk http://www.plantmethods.com ===================================== -----Original Message----- From: arab-gen-bounces@oat.bio.indiana.edu [mailto:arab-gen-bounces@oat.bio.indiana.edu] On Behalf Of Falbel, Tanya G. Sent: 09 February 2008 21:11 To: arab-gen@net.bio.net Subject: [Arabidopsis] brands of agar Colleagues: Over the years, I've used several brands of agar for growing Arabidopsis seedlings on MS medium, from Gibco, Sigma, and others. I've heard that some groups use Noble agar, others, bacto-agar, others in the past have washed their own agar, used phytagel or other gelling agents. I have two questions: 1) What brands of agar are most commonly in use now by groups? I've found something similar to Gibco's Phytagar that is now available through Caisson labs. Other groups seem to like Sigma's A1296. But besides those, what do most groups use? I'm especially interested in the opinion of groups that measure root length or root branching - growing roots vertically on plates for more than just a couple of days. (as opposed to just antibiotic selection) 2) Does anyone know what inhibitors are washed away? Are micronutrient ions or other toxic compounds bound to the crude agar? Has anyone looked into this? This may have been a question that came up among researchers 10 years ago, but I couldn't find any record in the archives. Here's why I'm asking. I made up a batch of medium with a brand of 'purified agar for microbial use', and got a very strong inhibition of root meristems. Seed germination was good, but roots failed to elongate any further after about 4 days of growth. The root meristems became a swollen mess, reminiscent of what happens in weak gnom alleles. I'm trying to decide if this is something worth looking into. I know that for regeneration of plants in tissue culture, folks are very fussy about particular brands of agar. Please let me know what brands you have used with success or failure. I'd be especially interested in other similar experiences - where a brand wreaked havoc on root meristems. Thanks Tanya Falbel Department of Biology 105 Garfield Avenue University of Wisconsin-Eau Claire Eau Claire, WI 54702-4004, USA Tel: 715-836-5087 Fax: 715-836-5089 _______________________________________________ Arab-gen mailing list Arab-gen@net.bio.net http://www.bio.net/biomail/listinfo/arab-gen From baskin from bio.umass.edu Mon Feb 11 09:33:17 2008 From: baskin from bio.umass.edu (Tobias Baskin) Date: Tue Feb 12 18:54:42 2008 Subject: [Arabidopsis] brands of agar In-Reply-To: References: Message-ID: Dear Tanya, Some years ago, we investigated a variety of different agars (some of which you mention). We found reproducible differences in root elongation rate but perhaps on the order of 10 to 20 %. Clearly the roots liked some agar better than others. We also found a little bit later when using phytagel that root elongation rate depended on the temperature the molten mix was held at before pouring, or might have simply been quite irreproducible. But again I am talking about differences on the order of 20%. Big enough to readily measure but not monstrous. On no agar did we see the kind of developmental change you are mentioning. On some conditions I have seen (and read) that severely salt stressed or water deficit stressed roots will swell so I'd guess what you are describing goes way beyond what can be expected from different brands/formulations of agar. Hope this helps, Tobias At 3:10 PM -0600 2/9/08, Falbel, Tanya G. wrote: >Colleagues: > >Over the years, I've used several brands of agar for growing >Arabidopsis seedlings on MS medium, >from Gibco, Sigma, and others. I've heard that some groups use Noble agar, >others, bacto-agar, others in the past have washed their own agar, >used phytagel or other >gelling agents. I have two questions: > >1) What brands of agar are most commonly in use now by groups? I've >found something similar >to Gibco's Phytagar that is now available through Caisson labs. >Other groups seem to like Sigma's >A1296. But besides those, what do most groups use? I'm especially >interested in the opinion of >groups that measure root length or root branching - growing roots >vertically on plates >for more than just a couple of days. (as opposed to just antibiotic selection) > >2) Does anyone know what inhibitors are washed away? Are >micronutrient ions or other toxic >compounds bound to the crude agar? Has anyone looked into this? >This may have been a question >that came up among researchers 10 years ago, but I couldn't find any >record in the archives. > >Here's why I'm asking. I made up a batch of medium with a brand of >'purified agar for microbial use', >and got a very strong inhibition of root meristems. Seed >germination was good, but roots failed to elongate >any further after about 4 days of growth. The root meristems became >a swollen mess, reminiscent of what >happens in weak gnom alleles. I'm trying to decide if this is >something worth looking into. > >I know that for regeneration of plants in tissue culture, folks are >very fussy about particular brands of agar. > >Please let me know what brands you have used with success or failure. >I'd be especially interested in other similar experiences - where a brand >wreaked havoc on root meristems. > >Thanks > >Tanya Falbel >Department of Biology >105 Garfield Avenue >University of Wisconsin-Eau Claire >Eau Claire, WI 54702-4004, USA > >Tel: 715-836-5087 >Fax: 715-836-5089 > > >_______________________________________________ >Arab-gen mailing list >Arab-gen@net.bio.net >http://www.bio.net/biomail/listinfo/arab-gen -- _ ____ __ ____ / \ / / \ / \ \ Tobias I. Baskin / / / / \ \ \ Biology Department /_ / __ /__ \ \ \__ 611 N. Pleasant St. / / / \ \ \ University of Massachusetts / / / \ \ \ Amherst, MA, 01003 / / ___ / \ \__/ \ ____ http://www.bio.umass.edu/biology/baskin/ Voice: 413 - 545 - 1533 Fax: 413 - 545 - 3243 From norman from warthmann.com Mon Feb 11 11:10:11 2008 From: norman from warthmann.com (Norman Warthmann) Date: Tue Feb 12 19:19:25 2008 Subject: [Arabidopsis] group leader position at IRRI Message-ID: To assist the International Rice research Institute (IRRI) in identifying a suitable candidate I would be happy if you considered circulating this vacancy announcement. more details also at: http://www.irri.org/jobs/international.asp -------------------------- Plant Breeding, Genetics and Biotechnology Molecular Biologist IRRI is seeking a molecular biologist to join its internationally recruited staff to lead research on rice transformation. The position will be based in the Institute’s Plant Breeding, Genetics and Biotechnology Division with an initial appointment of 3 years and renewable for subsequent multi-year contracts. Responsibilities The primary responsibilities will be to 1) apply innovative molecular tools and approaches for the development of transgenic products carrying agronomically and nutritionally important genes and other value-added traits; 2) establish high-throughput transformation systems; 3) work with breeders and other teams to link the above research outputs to breeding and gene discovery programs; 4) collaborate with national agricultural research and extension systems (NARES) for training in rice transformation and in developing, evaluating, and sharing transgenic products; and 5) establish collaborations with advanced research institutes for applying current advances in molecular biology in transformation research. Qualifications Applicants should have a PhD in genetics, molecular biology, or a related field, with at least 5 years of post-PhD experience. Candidates should have a strong background in molecular biology and transformation, and with a proven record of innovative contributions. Also required are: 1) experience working with governmental institutions in field testing of GM crops, 2) sound interpersonal and communication skills, and 3) demonstrated ability to work in a multi- disciplinary environment and with colleagues in NARES. Perquisites and IRRI environment IRRI, located at Los Baños, 70 kilometers south of Manila, Philippines, offers salary and perquisites that are internationally competitive including support for education of children, car and housing at reasonable rental rates, and medical and retirement benefits. IRRI provides a gender-sensitive environment and welcomes women applicants. Citizens of developing countries, particularly rice- producing countries, are encouraged to apply. The Institute is committed to assisting families in making personal and, to the extent possible, professional adjustments to the local environment. IRRI has an accredited international school (pre-K to grade 5) and, excellent preparatory schools for younger children are available locally. Applications Applications will be received up until 15 February 2008. Please submit your application online at www.irri.org/jobs/adda.asp or send (preferably via e-mail) a comprehensive curriculum vitae and names and email addresses of three referees to: Ms. Selene M. Ocampo Officer-HR Coordination International Rice Research Institute DAPO Box 7777, Metro Manila, Philippines Tel: (63-2) 891-1292/580-5600 Fax: (63-2) 580-5699 Email: IRRIRecruitment@cgiar.org Only short-listed candidates will be notified ----------------------- From cramer from unr.edu Tue Feb 12 19:40:19 2008 From: cramer from unr.edu (Grant Cramer) Date: Wed Feb 13 12:52:27 2008 Subject: [Arabidopsis] brands of agar In-Reply-To: References: Message-ID: I have found very negative effects on root growth using BactoAgar both from batches in the United States and Australia. I have NEVER had a problem with PhytoAgar on root growth in root length assays up to a week. After that they are in the dish for too long and will suffer. One can supplement with sucrose in a standard quarter strength Hoaglands solution without problem. I agree you should not use MS medium or you will suffer from osmotic stress and perhaps other things that are out of balance for roots. The roots will grow without the sucrose but slower. It depends on your experiment, but those shaded cotyledons in a plastic petri dish can only do so much in the dark or dim light. I always grow them in the dark, as light inhibits root growth. Grant R. Cramer Professor Department of Biochemistry and Molecular Biology, MS 200 University of Nevada, Reno Reno, NV 89557 (775) 784-4204 cramer@unr.edu http://www.ag.unr.edu/cramer/ On Feb 11, 2008, at 6:33 AM, Tobias Baskin wrote: > Dear Tanya, > Some years ago, we investigated a variety of different agars (some > of which you mention). We found reproducible differences in root > elongation rate but perhaps on the order of 10 to 20 %. Clearly the > roots liked some agar better than others. We also found a little > bit later when using phytagel that root elongation rate depended on > the temperature the molten mix was held at before pouring, or might > have simply been quite irreproducible. But again I am talking about > differences on the order of 20%. Big enough to readily measure but > not monstrous. On no agar did we see the kind of developmental > change you are mentioning. On some conditions I have seen (and > read) that severely salt stressed or water deficit stressed roots > will swell so I'd guess what you are describing goes way beyond > what can be expected from different brands/formulations of agar. > > Hope this helps, > Tobias > > At 3:10 PM -0600 2/9/08, Falbel, Tanya G. wrote: >> Colleagues: >> >> Over the years, I've used several brands of agar for growing >> Arabidopsis seedlings on MS medium, >> from Gibco, Sigma, and others. I've heard that some groups use >> Noble agar, >> others, bacto-agar, others in the past have washed their own agar, >> used phytagel or other >> gelling agents. I have two questions: >> >> 1) What brands of agar are most commonly in use now by groups? >> I've found something similar >> to Gibco's Phytagar that is now available through Caisson labs. >> Other groups seem to like Sigma's >> A1296. But besides those, what do most groups use? I'm >> especially interested in the opinion of >> groups that measure root length or root branching - growing roots >> vertically on plates >> for more than just a couple of days. (as opposed to just >> antibiotic selection) >> >> 2) Does anyone know what inhibitors are washed away? Are >> micronutrient ions or other toxic >> compounds bound to the crude agar? Has anyone looked into this? >> This may have been a question >> that came up among researchers 10 years ago, but I couldn't find >> any record in the archives. >> >> Here's why I'm asking. I made up a batch of medium with a brand of >> 'purified agar for microbial use', >> and got a very strong inhibition of root meristems. Seed >> germination was good, but roots failed to elongate >> any further after about 4 days of growth. The root meristems >> became a swollen mess, reminiscent of what >> happens in weak gnom alleles. I'm trying to decide if this is >> something worth looking into. >> >> I know that for regeneration of plants in tissue culture, folks >> are very fussy about particular brands of agar. >> >> Please let me know what brands you have used with success or failure. >> I'd be especially interested in other similar experiences - where >> a brand >> wreaked havoc on root meristems. >> >> Thanks >> >> Tanya Falbel >> Department of Biology >> 105 Garfield Avenue >> University of Wisconsin-Eau Claire >> Eau Claire, WI 54702-4004, USA >> >> Tel: 715-836-5087 >> Fax: 715-836-5089 >> >> >> _______________________________________________ >> Arab-gen mailing list >> Arab-gen@net.bio.net >> http://www.bio.net/biomail/listinfo/arab-gen > > > -- > _ ____ __ ____ / \ / / > \ / \ \ Tobias I. Baskin > / / / / \ \ \ Biology Department > /_ / __ /__ \ \ \__ 611 N. Pleasant St. > / / / \ \ \ University of > Massachusetts > / / / \ \ \ Amherst, MA, 01003 > / / ___ / \ \__/ \ ____ > http://www.bio.umass.edu/biology/baskin/ > Voice: 413 - 545 - 1533 Fax: 413 - 545 - 3243 > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen From baskin from bio.umass.edu Wed Feb 13 09:29:26 2008 From: baskin from bio.umass.edu (Tobias Baskin) Date: Wed Feb 13 12:52:37 2008 Subject: [Arabidopsis] brands of agar In-Reply-To: References: Message-ID: Greetings, In replies to this thread, Grant Cramer mentions "PhytoAgar" and Brian Forde mentions "PhytagelTM" which I think is the same phytagel we used awhile back too. But is PhytoAgar the same stuff as Phytagel? or are they different? Do you know? Thanks, Tobias At 4:40 PM -0800 2/12/08, Grant Cramer wrote: >I have found very negative effects on root growth using BactoAgar >both from batches in the United States and Australia. I have NEVER >had a problem with PhytoAgar on root growth in root length assays up >to a week. After that they are in the dish for too long and will >suffer. One can supplement with sucrose in a standard quarter >strength Hoaglands solution without problem. I agree you should not >use MS medium or you will suffer from osmotic stress and perhaps >other things that are out of balance for roots. The roots will grow >without the sucrose but slower. It depends on your experiment, but >those shaded cotyledons in a plastic petri dish can only do so much >in the dark or dim light. I always grow them in the dark, as light >inhibits root growth. > >Grant R. Cramer >Professor >Department of Biochemistry and Molecular Biology, MS 200 >University of Nevada, Reno >Reno, NV 89557 >(775) 784-4204 >cramer@unr.edu >http://www.ag.unr.edu/cramer/ > > > >On Feb 11, 2008, at 6:33 AM, Tobias Baskin wrote: > >>Dear Tanya, >> Some years ago, we investigated a variety of different agars >>(some of which you mention). We found reproducible differences in >>root elongation rate but perhaps on the order of 10 to 20 %. >>Clearly the roots liked some agar better than others. We also found >>a little bit later when using phytagel that root elongation rate >>depended on the temperature the molten mix was held at before >>pouring, or might have simply been quite irreproducible. But again >>I am talking about differences on the order of 20%. Big enough to >>readily measure but not monstrous. On no agar did we see the kind >>of developmental change you are mentioning. On some conditions I >>have seen (and read) that severely salt stressed or water deficit >>stressed roots will swell so I'd guess what you are describing goes >>way beyond what can be expected from different brands/formulations >>of agar. >> >> Hope this helps, >> Tobias >> >>At 3:10 PM -0600 2/9/08, Falbel, Tanya G. wrote: >> >>>Colleagues: >>> >>>Over the years, I've used several brands of agar for growing >>>Arabidopsis seedlings on MS medium, >>>from Gibco, Sigma, and others. I've heard that some groups use Noble agar, >>>others, bacto-agar, others in the past have washed their own agar, >>>used phytagel or other >>>gelling agents. I have two questions: >>> >>>1) What brands of agar are most commonly in use now by groups? >>>I've found something similar >>>to Gibco's Phytagar that is now available through Caisson labs. >>>Other groups seem to like Sigma's >>>A1296. But besides those, what do most groups use? I'm >>>especially interested in the opinion of >>>groups that measure root length or root branching - growing roots >>>vertically on plates >>>for more than just a couple of days. (as opposed to just >>>antibiotic selection) >>> >>>2) Does anyone know what inhibitors are washed away? Are >>>micronutrient ions or other toxic >>>compounds bound to the crude agar? Has anyone looked into this? >>>This may have been a question >>>that came up among researchers 10 years ago, but I couldn't find >>>any record in the archives. >>> >>>Here's why I'm asking. I made up a batch of medium with a brand of >>>'purified agar for microbial use', >>>and got a very strong inhibition of root meristems. Seed >>>germination was good, but roots failed to elongate >>>any further after about 4 days of growth. The root meristems >>>became a swollen mess, reminiscent of what >>>happens in weak gnom alleles. I'm trying to decide if this is >>>something worth looking into. >>> >>>I know that for regeneration of plants in tissue culture, folks >>>are very fussy about particular brands of agar. >>> >>>Please let me know what brands you have used with success or failure. >>>I'd be especially interested in other similar experiences - where a brand >>>wreaked havoc on root meristems. >>> >>>Thanks >>> >>>Tanya Falbel >>>Department of Biology >>>105 Garfield Avenue >>>University of Wisconsin-Eau Claire >>>Eau Claire, WI 54702-4004, USA >>> >>>Tel: 715-836-5087 >>>Fax: 715-836-5089 >>> >>> >>>_______________________________________________ >>>Arab-gen mailing list >>>Arab-gen@net.bio.net >>>http://www.bio.net/biomail/listinfo/arab-gen >>> >> >> >>-- >> _ ____ __ ____ / \ / / \ >>/ \ \ Tobias I. Baskin >> / / / / \ \ \ Biology Department >> /_ / __ /__ \ \ \__ 611 N. Pleasant St. >> / / / \ \ \ University of Massachusetts >> / / / \ \ \ Amherst, MA, 01003 >>/ / ___ / \ \__/ \ ____ >>http://www.bio.umass.edu/biology/baskin/ >>Voice: 413 - 545 - 1533 Fax: 413 - 545 - 3243 >> >>_______________________________________________ >>Arab-gen mailing list >>Arab-gen@net.bio.net >>http://www.bio.net/biomail/listinfo/arab-gen From Witt from mpimp-golm.mpg.de Wed Feb 13 12:12:18 2008 From: Witt from mpimp-golm.mpg.de (Isabell Witt) Date: Wed Feb 13 12:52:43 2008 Subject: [Arabidopsis] doctoral fellowships IMPRS Message-ID: <2103FFF56D64D64CBC81B1B5A2AAD439322AF34B86@MAIL01.mpimp-golm.mpg.de> Doctoral fellowships We are seeking students who are highly motivated to tackle scientific problems in modern plant biology. We offer cutting-edge interdisciplinary training spanning genetics, genomics, physiology, high-end analytical techniques, and bioinformatics. Doctoral studies will focus on systems-oriented approaches using the model plant Arabidopsis thaliana with an emphasis on molecular phenotyping ('omics') technologies, data integration, and modelling. Individual career development plans will be configured with the students. The IMPRS-PMPG is a joint initiative of the Max Planck Institute of Molecular Plant Physiology and the University of Potsdam with internationally renowned faculty, strong research groups, and vibrant doctoral students. The entire programme is in English and no tuition fees apply. For further information about the programme and the online application procedure, please visit our web site at: http://www-en.mpimp-golm.mpg.de/IMPRS_GoFORSYS/index.html The Max Planck Institute of Molecular Plant Physiology is one of the largest plant research centres in Europe. Three Max Planck Institutes, two Fraunhofer Institutes, the University of Potsdam, and a new centre for start-up companies provide an excellent infrastructure for modern cross-disciplinary training. The campus is located in close proximity to the many research and educational facilities in Berlin. Further information about the institute can be found at: www.mpimp-golm.mpg.de. Applications by February 29, 2008 Dr. Isabell Witt Scientific Coordinator Doctoral Program IMPRS-PMPG MPI-MP Am Muehlenberg 1 D-14476 Potsdam +49 (0) 331 5678 444 Witt@mpimp-golm.mpg.de From b.g.forde from lancaster.ac.uk Wed Feb 13 12:13:34 2008 From: b.g.forde from lancaster.ac.uk (Forde, Brian) Date: Wed Feb 13 12:52:48 2008 Subject: [Arabidopsis] brands of agar In-Reply-To: Message-ID: <199A8D531E24DF47ADCC977CE0E94AFC0221A536@exchange-be6.lancs.local> Hi Tobias, and Arabidopsis colleagues Phytagel and Phytagar are definitely different. Phytagar is a genuine agar (or, I believe, a blend of agars, presumably of algal origin), while Phytagel is an agar subsitute (other names Gellan gum, Kelcogel, Gelrite, Gel-Gro) that is produced as a fermentation product by a pure culture of the bacterium Sphingomonas elodea. Chemically, agar is a galactose polymer, while Phytagel consists of four linked monosaccharides, including one molecule of rhamnose, one molecule of glucuronic acid and two molecules of glucose. The physical properties of the two gels definitely differ and some people use mixtures of the two. A different behaviour of root hairs on the two substrates was reported in this paper from Rich Meagher's lab: http://www.ncbi.nlm.nih.gov/pubmed/12481103. I'm not sure if Invitrogen still supply Phytagel - I just looked and couldn't find it. There is another product called Phytoblend supplied by Caisson Laboratories Inc and which they say is similar. all the best Brian ===================================== Brian G. Forde Prof. of Environmental Plant Biotechnology Department of Biological Sciences Lancaster Environment Centre Lancaster University Bailrigg Lancaster LA1 4YQ tel. +44 (0)1524 510207 (direct line) email b.g.forde@lancaster.ac.uk http://biol.lancs.ac.uk/bs/research/plants/bgf.htm Editor-in-Chief Plant Methods email plantmethods@lancaster.ac.uk http://www.plantmethods.com ===================================== -----Original Message----- From: Tobias Baskin [mailto:baskin@bio.umass.edu] Sent: 13 February 2008 14:29 To: Grant Cramer; Forde, Brian Cc: Falbel, Tanya G.; arab-gen@net.bio.net Subject: Re: [Arabidopsis] brands of agar Greetings, In replies to this thread, Grant Cramer mentions "PhytoAgar" and Brian Forde mentions "PhytagelTM" which I think is the same phytagel we used awhile back too. But is PhytoAgar the same stuff as Phytagel? or are they different? Do you know? Thanks, Tobias At 4:40 PM -0800 2/12/08, Grant Cramer wrote: I have found very negative effects on root growth using BactoAgar both from batches in the United States and Australia. I have NEVER had a problem with PhytoAgar on root growth in root length assays up to a week. After that they are in the dish for too long and will suffer. One can supplement with sucrose in a standard quarter strength Hoaglands solution without problem. I agree you should not use MS medium or you will suffer from osmotic stress and perhaps other things that are out of balance for roots. The roots will grow without the sucrose but slower. It depends on your experiment, but those shaded cotyledons in a plastic petri dish can only do so much in the dark or dim light. I always grow them in the dark, as light inhibits root growth. Grant R. Cramer Professor Department of Biochemistry and Molecular Biology, MS 200 University of Nevada, Reno Reno, NV 89557 (775) 784-4204 cramer@unr.edu http://www.ag.unr.edu/cramer/ On Feb 11, 2008, at 6:33 AM, Tobias Baskin wrote: Dear Tanya, Some years ago, we investigated a variety of different agars (some of which you mention). We found reproducible differences in root elongation rate but perhaps on the order of 10 to 20 %. Clearly the roots liked some agar better than others. We also found a little bit later when using phytagel that root elongation rate depended on the temperature the molten mix was held at before pouring, or might have simply been quite irreproducible. But again I am talking about differences on the order of 20%. Big enough to readily measure but not monstrous. On no agar did we see the kind of developmental change you are mentioning. On some conditions I have seen (and read) that severely salt stressed or water deficit stressed roots will swell so I'd guess what you are describing goes way beyond what can be expected from different brands/formulations of agar. Hope this helps, Tobias At 3:10 PM -0600 2/9/08, Falbel, Tanya G. wrote: Colleagues: Over the years, I've used several brands of agar for growing Arabidopsis seedlings on MS medium, from Gibco, Sigma, and others. I've heard that some groups use Noble agar, others, bacto-agar, others in the past have washed their own agar, used phytagel or other gelling agents. I have two questions: 1) What brands of agar are most commonly in use now by groups? I've found something similar to Gibco's Phytagar that is now available through Caisson labs. Other groups seem to like Sigma's A1296. But besides those, what do most groups use? I'm especially interested in the opinion of groups that measure root length or root branching - growing roots vertically on plates for more than just a couple of days. (as opposed to just antibiotic selection) 2) Does anyone know what inhibitors are washed away? Are micronutrient ions or other toxic compounds bound to the crude agar? Has anyone looked into this? This may have been a question that came up among researchers 10 years ago, but I couldn't find any record in the archives. Here's why I'm asking. I made up a batch of medium with a brand of 'purified agar for microbial use', and got a very strong inhibition of root meristems. Seed germination was good, but roots failed to elongate any further after about 4 days of growth. The root meristems became a swollen mess, reminiscent of what happens in weak gnom alleles. I'm trying to decide if this is something worth looking into. I know that for regeneration of plants in tissue culture, folks are very fussy about particular brands of agar. Please let me know what brands you have used with success or failure. I'd be especially interested in other similar experiences - where a brand wreaked havoc on root meristems. Thanks Tanya Falbel Department of Biology 105 Garfield Avenue University of Wisconsin-Eau Claire Eau Claire, WI 54702-4004, USA Tel: 715-836-5087 Fax: 715-836-5089 _______________________________________________ Arab-gen mailing list Arab-gen@net.bio.net http://www.bio.net/biomail/listinfo/arab-gen -- _ ____ __ ____ / \ / / \ / \ \ Tobias I. Baskin / / / / \ \ \ Biology Department /_ / __ /__ \ \ \__ 611 N. Pleasant St. / / / \ \ \ University of Massachusetts / / / \ \ \ Amherst, MA, 01003 / / ___ / \ \__/ \ ____ http://www.bio.umass.edu/biology/baskin/ Voice: 413 - 545 - 1533 Fax: 413 - 545 - 3243 _______________________________________________ Arab-gen mailing list Arab-gen@net.bio.net http://www.bio.net/biomail/listinfo/arab-gen From cramer from unr.edu Wed Feb 13 14:15:32 2008 From: cramer from unr.edu (Grant Cramer) Date: Wed Feb 13 18:02:18 2008 Subject: [Arabidopsis] brands of agar In-Reply-To: References: Message-ID: <94617511-AA97-4B39-944D-6124A5FBC607@unr.edu> Sorry for the confusion. I miswrote. I meant Phytagel not PhytoAgar. That was a brain short circuit! Grant R. Cramer Professor Department of Biochemistry and Molecular Biology, MS 200 University of Nevada, Reno Reno, NV 89557 (775) 784-4204 cramer@unr.edu http://www.ag.unr.edu/cramer/ On Feb 13, 2008, at 6:29 AM, Tobias Baskin wrote: > Greetings, > In replies to this thread, Grant Cramer mentions > "PhytoAgar" and Brian Forde mentions "PhytagelTM" which I think is > the same phytagel we used awhile back too. But is PhytoAgar the > same stuff as Phytagel? or are they different? Do you know? > > Thanks, > Tobias > > At 4:40 PM -0800 2/12/08, Grant Cramer wrote: >> I have found very negative effects on root growth using BactoAgar >> both from batches in the United States and Australia. I have NEVER >> had a problem with PhytoAgar on root growth in root length assays >> up to a week. After that they are in the dish for too long and >> will suffer. One can supplement with sucrose in a standard quarter >> strength Hoaglands solution without problem. I agree you should >> not use MS medium or you will suffer from osmotic stress and >> perhaps other things that are out of balance for roots. The roots >> will grow without the sucrose but slower. It depends on your >> experiment, but those shaded cotyledons in a plastic petri dish >> can only do so much in the dark or dim light. I always grow them >> in the dark, as light inhibits root growth. >> Grant R. Cramer >> Professor >> Department of Biochemistry and Molecular Biology, MS 200 >> University of Nevada, Reno >> Reno, NV 89557 >> (775) 784-4204 >> cramer@unr.edu >> http://www.ag.unr.edu/cramer/ >> >> >> >> On Feb 11, 2008, at 6:33 AM, Tobias Baskin wrote: >> >>> Dear Tanya, >>> Some years ago, we investigated a variety of different >>> agars (some of which you mention). We found reproducible >>> differences in root elongation rate but perhaps on the order of >>> 10 to 20 %. Clearly the roots liked some agar better than others. >>> We also found a little bit later when using phytagel that root >>> elongation rate depended on the temperature the molten mix was >>> held at before pouring, or might have simply been quite >>> irreproducible. But again I am talking about differences on the >>> order of 20%. Big enough to readily measure but not monstrous. On >>> no agar did we see the kind of developmental change you are >>> mentioning. On some conditions I have seen (and read) that >>> severely salt stressed or water deficit stressed roots will swell >>> so I'd guess what you are describing goes way beyond what can be >>> expected from different brands/formulations of agar. >>> >>> Hope this helps, >>> Tobias >>> >>> At 3:10 PM -0600 2/9/08, Falbel, Tanya G. wrote: >>>> Colleagues: >>>> >>>> Over the years, I've used several brands of agar for growing >>>> Arabidopsis seedlings on MS medium, >>>> from Gibco, Sigma, and others. I've heard that some groups use >>>> Noble agar, >>>> others, bacto-agar, others in the past have washed their own >>>> agar, used phytagel or other >>>> gelling agents. I have two questions: >>>> >>>> 1) What brands of agar are most commonly in use now by groups? >>>> I've found something similar >>>> to Gibco's Phytagar that is now available through Caisson labs. >>>> Other groups seem to like Sigma's >>>> A1296. But besides those, what do most groups use? I'm >>>> especially interested in the opinion of >>>> groups that measure root length or root branching - growing >>>> roots vertically on plates >>>> for more than just a couple of days. (as opposed to just >>>> antibiotic selection) >>>> >>>> 2) Does anyone know what inhibitors are washed away? Are >>>> micronutrient ions or other toxic >>>> compounds bound to the crude agar? Has anyone looked into this? >>>> This may have been a question >>>> that came up among researchers 10 years ago, but I couldn't find >>>> any record in the archives. >>>> >>>> Here's why I'm asking. I made up a batch of medium with a brand >>>> of 'purified agar for microbial use', >>>> and got a very strong inhibition of root meristems. Seed >>>> germination was good, but roots failed to elongate >>>> any further after about 4 days of growth. The root meristems >>>> became a swollen mess, reminiscent of what >>>> happens in weak gnom alleles. I'm trying to decide if this is >>>> something worth looking into. >>>> >>>> I know that for regeneration of plants in tissue culture, folks >>>> are very fussy about particular brands of agar. >>>> >>>> Please let me know what brands you have used with success or >>>> failure. >>>> I'd be especially interested in other similar experiences - >>>> where a brand >>>> wreaked havoc on root meristems. >>>> >>>> Thanks >>>> >>>> Tanya Falbel >>>> Department of Biology >>>> 105 Garfield Avenue >>>> University of Wisconsin-Eau Claire >>>> Eau Claire, WI 54702-4004, USA >>>> >>>> Tel: 715-836-5087 >>>> Fax: 715-836-5089 >>>> >>>> >>>> _______________________________________________ >>>> Arab-gen mailing list >>>> Arab-gen@net.bio.net >>>> http://www.bio.net/biomail/listinfo/arab-gen >>> >>> >>> -- >>> _ ____ __ ____ / \ / / >>> \ / \ \ Tobias I. Baskin >>> / / / / \ \ \ Biology Department >>> /_ / __ /__ \ \ \__ 611 N. Pleasant St. >>> / / / \ \ \ University of >>> Massachusetts >>> / / / \ \ \ Amherst, MA, >>> 01003 >>> / / ___ / \ \__/ \ ____ >>> http://www.bio.umass.edu/biology/baskin/ >>> Voice: 413 - 545 - 1533 Fax: 413 - 545 - 3243 >>> >>> _______________________________________________ >>> Arab-gen mailing list >>> Arab-gen@net.bio.net >>> http://www.bio.net/biomail/listinfo/arab-gen > > > From jsmalle from uky.edu Fri Feb 15 10:58:19 2008 From: jsmalle from uky.edu (Smalle, Jan A) Date: Fri Feb 15 14:59:04 2008 Subject: [Arabidopsis] brands of agar Message-ID: Hi Tanya, we had a similar experience using agar from ACROS (code: 400400010). Root elongation was severely inhibited and root tips appeared swollen. -- Jan Smalle Dept. Plant and Soil Sciences University of Kentucky KTRDC bldg, 104A Cooper and University drives Lexington, KY 40546 USA From jstone2 from unlnotes.unl.edu Fri Feb 15 11:19:59 2008 From: jstone2 from unlnotes.unl.edu (Julie M. Stone) Date: Fri Feb 15 14:59:09 2008 Subject: [Arabidopsis] University of Nebraska Molecular Fungal-Plant Interactions position Message-ID: A tenure-track Assistant Professor position with a focus on Molecular Fungal-Plant Interactions is available in Plant Pathology. Please bring this to the attention of suitable candidates. Thanks, Julie The Department of Plant Pathology at the University of Nebraska-Lincoln invites applications for a 9-month tenure-track faculty position at the Assistant Professor level. This position is 80% research and 20% teaching. We are seeking candidates interested in research that is focused on elucidating fungal/oomycete-plant interactions using molecular genetics/genomic approaches or other cutting-edge technologies. The successful candidate is expected to have a strong commitment to undergraduate and graduate education and the ability to teach courses within a broad microbiology curriculum, including mycology. Candidates must have a demonstrated research record consisting of publications in high profile journals and the ability to attract external grant funds. A Ph.D. in plant pathology, microbiology, or other relevant areas of biological sciences is required. To apply, go to http://employment.unl.edu and complete the faculty/administrative form (Requisition #080055) and attach a letter of application, curriculum vitae, a 2-3 page description of research interests, and a brief statement of teaching philosophy. In addition, arrange to have 3 letters of recommendation sent to: Search Committee Chair, Department of Plant Pathology, Rm. 406 Plant Science Hall, University of Nebraska-Lincoln, Lincoln, NE 68583-0722. Review of applications will commence on 4-15-08 and will continue until the position is filled or the search is closed. UNL is committed to a pluralistic campus community through affirmative action and equal opportunity and is responsive to the needs of dual career couples. We assure reasonable accommodation under the Americans with Disabilities Act; contact Dr. James Steadman at 402-472-2858 or jsteadman1@unl.edu for assistance. Julie M. Stone, Ph.D. Assistant Professor Biochemistry & Plant Science Initiative University of Nebraska - Lincoln N230 Beadle Center 1901 Vine Street Lincoln, NE 68588-0660 office 402 472 4902 lab 402 472 3028 fax 402 472 3139 email: jstone2@unl.edu From jacobsen from ucla.edu Sun Feb 17 16:00:52 2008 From: jacobsen from ucla.edu (Steve Jacobsen) Date: Sun Feb 17 21:57:03 2008 Subject: [Arabidopsis] Single nucleotide resolution DNA methylation browser Message-ID: To accompany our manuscript "Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning". Nature 10.1038/nature06745, we have created a browser that allows community access to detailed patterns of DNA methylation. http://epigenomics.mcdb.ucla.edu/BS-Seq/ click "Browser "and type in the name or AtID of your favorite gene in the position/search box. A quick tutorial on using the site is at http://epigenomics.mcdb.ucla.edu/BS-Seq/Guide/ Happy hunting Steve Jacobsen Department of MCD Biology University of California, Los Angeles P. O. Box 951606 Los Angeles, CA 90095-1606 Office: 310 825-0182 Lab: 310 206-3336 Lab Home page http://www.mcdb.ucla.edu/Research/Jacobsen/index.html -- ______________________________________________________________________ From SVemuri12 from gmail.com Mon Feb 18 11:08:42 2008 From: SVemuri12 from gmail.com (SV) Date: Mon Feb 18 15:55:04 2008 Subject: [Arabidopsis] arabidopsis genome - urgent Message-ID: <634f7060-4f4a-4b62-a504-cca639fbe7cc@d4g2000prg.googlegroups.com> Does anyone have the latest information in literature on these about Arabidopsis: - size of genome in kb or Mbp - number of chromosomes -total number of genes to date I have been browsing through scientific articles and am not hitting on any articles in the past two years to give me the most updated answers. Can anyone point me in the right direction, even better if they can send the pdfs? Thanks. From jdfriesner from ucdavis.edu Mon Feb 18 13:59:14 2008 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Mon Feb 18 15:55:10 2008 Subject: [Arabidopsis] Feb. 28 deadline to register for new NAASC nominations Message-ID: <001601c87260$5b679100$6600a8c0@mcb.ucdavis.edu> Dear North American Arabidopsis Researchers, As in previous years, we will soon solicit nominations for the election of two new members to the North American Arabidopsis Steering Committee (NAASC). Committee members are YOUR representatives for relevant Arabidopsis issues in North America. In order to nominate and/or vote for the new NAASCers you must first register with TAIR. Please register by February 28 if you have not already: http://www.arabidopsis.org/servlets/Community?action=login. NAASC officers currently are (listed in order of most to least seniority): Xing Wang Deng (Yale University, MASC chair), Judith Bender (Brown University), Joe Kieber (UNC-Chapel Hill, MASC co-chair, ICAR 2008 co-organizer), Xuemei Chen (UC Riverside, ICAR 2008 co-organizer), Julian Schroeder (UC San Diego, ICAR 2008 fund-raiser), Caren Chang (Univ. of Maryland, ICAR 2008 fund-raiser), George Haughn (Univ. of British Columbia, ICAR 2008 fund-raiser), and Scott Poethig (Univ. of PA-Philadelphia). Procedure: -An email asking for nominations will be sent to *registered North American TAIR members* on or around February 29, 2008. -The nomination deadline is March 31, 2008. Once nominees are contacted and their willingness to stand for election is verified, a second email will be sent asking members to vote for up to 2 names on the list (via a secure website). -The voting deadline is May 5, 2008. -The top 2 candidates will be contacted and their willingness to serve confirmed. Winners will be announced around the end of May. Without the efforts of the NAASC, the Arabidopsis Conference and funding for young scientists, including underrepresented minorities, would be jeopardized. Service on the NAASC is important to the community and highly appreciated. We need to replace 2 members who rotate off this year and we need community members to first nominate good Arabidopsis community candidates and then vote for those who agree to stand. One example of the importance of the NAASC to the community is the effort they've spent over the last few months working on aspects of the 19th International Conference on Arabidopsis Research (July 23-27, Montreal, Canada), including developing the scientific program, writing grant proposals to provide funding to help community members attend the meeting, and soliciting sponsorship. NAASC members will review and select the awardees of conference funding. The NAASC also participates in the Multinational Arabidopsis Steering Committee to communicate with Arabidopsis researchers around the world and funding bodies such as the NSF. Currently, NAASC members are both chair and co-chair of the MASC. About serving on NAASC: Members serve for four full calendar years, beginning around the date of the Annual International Conference on Arabidopsis Research, and rotating off following the Conference held in their fourth year of service. - Originally established in 1992 in response to the need for elected North American representatives to the Multinational Arabidopsis Steering Committee, NAASC has evolved into the main organizing and fundraising body for the International Conference on Arabidopsis Research when it is held in North America. - The NAASC also helps ensure solicitation and choice of the conference site for meetings held outside of North America. The NAASC solicits funds to help North American junior scientists travel to these international meetings. Additionally, the NAASC serves as a liaison between members of the community and government and not-for-profit granting agencies and provides representation of the community to service facilities such as ABRC and TAIR. More information about the roles, history, and past members of the NAASC can be found at: http://www.arabidopsis.org/portals/masc/countries/NAASC_Info.jsp. From FVigneault from nrcan.gc.ca Mon Feb 18 16:46:39 2008 From: FVigneault from nrcan.gc.ca (=?iso-8859-1?Q?Vigneault=2C_Fr=E9d=E9ric?=) Date: Mon Feb 18 18:33:28 2008 Subject: [Arabidopsis] arabidopsis genome - urgent Message-ID: <8C16DEDEF6DE8B418A724B298297A5300205F7DB@S0-OTT-X3.nrn.nrcan.gc.ca> http://arabidopsis.org/portals/genAnnotation/genome_snapshot.jsp 115,409,949 bp (source unkown, but sometime in 2005) 119,186,497 bp (TIGR 2007) 134, 634,692 bp (TAIR 2007) 5 chromosomes 26,819 protein coding genes (on these 5 chr, according to TAIR 7.0) These numbers only take into account the nuclear chromosomes. Fred From mhudson from uiuc.edu Mon Feb 18 19:06:04 2008 From: mhudson from uiuc.edu (Matthew Hudson) Date: Mon Feb 18 22:35:24 2008 Subject: [Arabidopsis] Faculty position in biofuel genomics Message-ID: <200802190005.m1J05DSw024019@expredir6.cites.uiuc.edu> University of Illinois at Urbana-Champaign Department of Crop Sciences Assistant/Associate/Full Professor of Genomics of Perennial Biofuel Feedstocks A faculty position in genomics with an emphasis on the improvement of perennial grasses as ligno-cellulosic(LC) feedstocks for the emerging biofuels industry. This is a 9-month tenured or tenure track position with opportunity for summer appointment. Responsibilities will be allocated as 75% research and 25% teaching in the Department of Crop Sciences, University of Illinois at Urbana-Champaign. Candidate will also be an integral part of the Urbana branch of the Energy Biosciences Institute (EBI), a joint institute funded by the energy company BP between the University of Illinois, University of California, Berkeley and Lawrence Berkeley National Laboratory (www.energybiosciencesinstitute.org). The successful applicant is expected to develop an internationally-recognized, externally-funded research program that will utilize and develop emerging structural and functional genomics approaches for the improvement of perennial LC fuel feedstock crops. Candidate will initially be expected to conduct at least 50% of their research on LC crops within the EBI housed within the Institute for Genomic Biology, funding for this research effort will be provided by the EBI. The candidate is expected to specialize in perennial crops, for example grasses (such as switchgrass, Miscanthus or sugarcane) or tree species (such as Populus). The successful candidate will utilize functional and/or structural genomic tools to advance perennial crop biology employing knowledge from current model and agronomic plant systems. Approaches may include genetic and physical mapping, quantitative and association genetics, and the analysis of polymorphisms or pathways on a genome scale toward improvement of LC perennial crops as biofuel feedstocks. The successful candidate will be expected to participate in the development of curricula for student education in bioenergy training. Candidates must have a Ph.D. and experience beyond the Ph.D. is preferable. The candidate must have research experience in molecular biology, genomics, crop science, or related disciplines. Prior experience preferred with structural and functional genomic analyses, ideally with perennials. The candidate must demonstrate outstanding potential to conduct and publish high-impact research, both independently and as part of the EBI team, attract extramural research funding, and develop an excellent teaching program. For appointment at the Associate or Full Professor rank, the candidate must exhibit a very strong record of independent scholarship that includes credentials meeting the standards required to attain that level at the University of Illinois. Such credentials include national and/or international recognition and impact in research and teaching in a related area, with clear evidence of obtaining competitive funding, initiating, completing, and publishing the results of successful projects. Salary will be commensurate with qualifications and experience with a comprehensive benefits package for eligible employees. The position is available as soon as possible thereafter that the candidate is available. To assure full consideration, a cover letter including a detailed statement of research and teaching goals, curriculum vitae, a valid e-mail address, certified undergraduate and graduate transcripts, and three letters of reference must be submitted by March 15, 2008 to the address below. Please cite announcement number 01/08A-11653 when applying. The packet should be sent to: Professor Robert Hoeft, Head, Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1102 South Goodwin Avenue, Urbana, Illinois 61801. Telephone (217) 333-9480. For additional information please contact: Dr. Lila Vodkin, Search Committee Chair, Department of Crop Sciences, University of Illinois at Urbana-Champaign. Telephone: (217) 244-6147; FAX (217) 244-333-4582, email: l-vodkin@uiuc.edu. Additional information about the Department of Crop Sciences, is available at http://www.cropsci.uiuc.edu THE UNIVERSITY OF ILLINOIS IS AN AFFIRMATIVE ACTION/EQUAL OPPORTUNITY EMPLOYER. Matthew Hudson Assistant Professor Department of Crop Sciences 334 NSRC, 1101 W. Peabody Urbana, IL 61801, United States. Phone 217 244 8096, email mhudson@uiuc.edu From JanW.Vos from wur.nl Tue Feb 19 03:16:54 2008 From: JanW.Vos from wur.nl (Vos, Jan (PCB)) Date: Tue Feb 19 12:04:12 2008 Subject: [Arabidopsis] PhD positions at Wageningen University Message-ID: <7DB62732493999499BD9117BFAD39E17B1DF1A@scomp0041.wurnet.nl> Dear Colleague, Currently, there are 11 vacancies for PhD students at Wageningen University. These are open exclusively to candidates from non-EU member states. Amongst these is a project in our laboratory on microtubule organization that has both cell biological and biophysical aspects (Project 07: Microtubules Alone and in Bundles). We would be grateful if you could bring the attached information to the attention of qualified students at your institute, or to those whom might be interested. Best wishes, Jan Vos and Marcel Janson ---------------------------------------------------------------------------------------------------------------------------------------- EPS International PhD Programme 2008: 4-year PhD projects in Experimental Plant Sciences The Graduate school "Experimental Plant Sciences" offers eleven 4-year PhD positions in Biochemistry, Biophysics, Entomology, Genetics, Molecular Biology, Plant Cell Biology, Plant-Microbe Interactions and Plant Physiology. The selected candidates will be fully funded with a fellowship of ? 1300 per month, a traveling allowance and reimbursement of visa costs. Location: Wageningen University, the Netherlands Who can apply? PhD candidates from non-EU member states Deadline for application: 15 April 2008 Start of the Programme: September-October 2008 The Graduate School 'Experimental Plant Sciences' (EPS) is a collaborative research and teaching institution of Wageningen University (WU), Radboud University (RU), Vrije Universiteit Amsterdam (VU), Leiden University (LU), University of Amsterdam (UvA) and Utrecht University (UU). EPS was founded in 1992 in order to organize and coordinate the fundamental and strategic plant research of the collaborating universities. EPS also facilitates the training and teaching of PhD students in these fields by organizing PhD courses, seminars and summer schools. All information about the EPS International PhD Programme 2008 can be found at www.graduateschool-eps.info. ---------------------------------------------------------------------------------------------------------------------------------------- Dr. Jan W. Vos Assistant professor Laboratory of Plant Cell Biology (building 352) Wageningen University Arboretumlaan 4, 6703 BD Wageningen The Netherlands Tel: +31-317-484321 Fax: +31-317-485005 Email: janw.vos@wur.nl Website: http://www.pcb.wur.nl/UK/ From tine.beunens from psb.ugent.be Tue Feb 19 07:54:58 2008 From: tine.beunens from psb.ugent.be (Tine Beunens) Date: Tue Feb 19 12:04:19 2008 Subject: [Arabidopsis] double selection: sulfadiazine and kanamycin Message-ID: <47BAD1A2.2070600@psb.ugent.be> I was wondering if anyone had positive experience's with selecting for sulfadiazine and kanamycin resistant plants at the same time (adding both to the medium simultaneously) Thx! Tine tibeu@psb.ugent.be From twe from leicester.ac.uk Tue Feb 19 11:07:36 2008 From: twe from leicester.ac.uk (Twell, Professor D.) Date: Tue Feb 19 12:04:25 2008 Subject: [Arabidopsis] Epigenetic Postdoctoral RA Message-ID: Description: THE EPIGENETIC CONTROL OF PLANT MALE GAMETOPHYTE AND GERMLINE DEVELOPMENT Postdoctoral Research Associate Salary Grade 7 - ?28,289 to ?32,796 per annum Available immediately for 36 months. Ref: R3640 Applications are invited for a 3-year BBSRC-funded postdoctoral position to investigate the role and diversity of small RNA (sRNA) pathways that operate in the epigenetic control of gene expression during male gametophyte and male germline development. The project forms part of a collaboration with the University of Oxford (Prof. Hugh Dickinson) and offers the opportunity to join a leading research group working on the mechanisms regulating cell division and cell fate determination during male reproductive development in Arabidopsis. Applicants should have a PhD in molecular genetics, biochemistry or a related discipline. Experience in molecular techniques, bioinformatics and cell imaging would be of particular value. Applications Downloadable application forms and further particulars are available from www.le.ac.uk/personnel/jobs. If you require a hard copy, please contact Personnel Services - tel: 0116 252 2435, fax: 0116 252 5140, email: recruitment4@le.ac.uk. Please note that CVs will only be accepted in support of a fully completed application form. Informal enquiries may be directed to Prof. David Twell, twe@le.ac.uk Closing Date: 6 March 2008 ********************************************************************* David Twell, PhD Professor of Plant Biology Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom _________________________________________________________________ E-mail: twe@le.ac.uk Tel: +44-116-2522281 Fax: +44-116-2522791 Personal Homepage: http://www.le.ac.uk/bl/staff/bltwe.htm TWELL LAB Homepage: http://www.le.ac.uk/biology/research/pollen/pollen.html Department of Biology Homepage: http://www.le.ac.uk/biology/bl.htm ********************************************************************* From eblancaflor from noble.org Wed Feb 20 12:10:13 2008 From: eblancaflor from noble.org (Blancaflor, Elison) Date: Wed Feb 20 12:33:45 2008 Subject: [Arabidopsis] RE: Postdoctoral Position at the Noble Foundation In-Reply-To: 200802201703.m1KH3uL14996@net.bio.net Message-ID: <497D588A106806408FB0792E4E9A1658015EF5A4@mail2.noble.org> Position ID: PB-S095-373 The Samuel Roberts Noble Foundation is seeking a postdoctoral fellow to work on the molecular and cellular mechanisms underlying polarity establishment and directional growth control in plants. Studies will focus on characterizing root developmental mutants in Arabidopsis using multidisciplinary approaches including live cell imaging, molecular biology, genetics and biochemistry. Research will be conducted in the laboratory of Dr. Elison Blancaflor in the Plant Biology Division. A Ph.D. in Plant Biology or Cell/Molecular Biology is required. The Samuel Roberts Noble Foundation has state-of-the-art research, greenhouse facilities, modern laboratory and office areas and excellent benefits. Application Instructions: Applicants are requested to apply online by completing the application and submitting a resume, contact information for three references (excluding relatives), and a cover letter explaining interest in the position and career goals. If applicant does not have the ability to upload the additional documents they can be faxed to (580) 224-6240 (please include position number), but the application should be completed and submitted online. Applications will be accepted until a candidate is hired. Interested applicants should apply immediately. The Samuel Roberts Noble Foundation, Inc. Human Resources Department Position Number: PB-S095-373 P.O. Box 2180 Ardmore, OK 73402 Website: http://www.noble.org/ The Samuel Roberts Noble Foundation, Inc., is an Equal Opportunity Employer and will consider all qualified applicants for employment, regardless of their race, color, creed, gender, national origin, age, disability, or veteran status. From l.hunt from sheffield.ac.uk Wed Feb 20 12:15:27 2008 From: l.hunt from sheffield.ac.uk (Lee Hunt) Date: Wed Feb 20 12:33:52 2008 Subject: [Arabidopsis] double selection: sulfadiazine and kanamycin In-Reply-To: <47BAD1A2.2070600@psb.ugent.be> References: <47BAD1A2.2070600@psb.ugent.be> Message-ID: <1203527727.47bc602f13b12@webmail.shef.ac.uk> Hi Tine I've not had any problem doing this, as long as the kanamycin isn't silenced in one of the parents (I assume this is a result of crossing). I used 5mg/L sulf, 50mg/L kan. The plants do struggle and take much longer than normal to recover as they would whichever two antibiotics you used Lee From dolzblasz from biologie.uni-freiburg.de Wed Feb 20 05:06:58 2008 From: dolzblasz from biologie.uni-freiburg.de (Alicja Dolzblasz) Date: Wed Feb 20 16:14:57 2008 Subject: [Arabidopsis] pkl-1 genotyping primers Message-ID: Dear all Does anyone knows properly working genotyping for pkl-1 allele? Thanks a lot, Alicja From huala from acoma.stanford.edu Wed Feb 20 13:09:19 2008 From: huala from acoma.stanford.edu (Eva Huala) Date: Wed Feb 20 16:15:04 2008 Subject: [Arabidopsis] arabidopsis genome - urgent In-Reply-To: <8C16DEDEF6DE8B418A724B298297A5300205F7DB@S0-OTT-X3.nrn.nrcan.gc.ca> References: <8C16DEDEF6DE8B418A724B298297A5300205F7DB@S0-OTT-X3.nrn.nrcan.gc.ca> Message-ID: <47BC6CCF.8050906@acoma.stanford.edu> Hi Fr?d?ric, The TAIR7 release contains a total of 32,041 genes including 26,819 nuclear-encoded protein-coding genes, 1054 nuclear genes encoding RNAs, 3,889 nuclear pseudogenes and transposon genes and 279 genes encoded by the chloroplast and mitochondrial genomes. Here's a citation for the TAIR7 genome release: Swarbreck et al. (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Research 36:D1009-D1014 You can download it from http://arabidopsis.org/about/D1009.pdf For the TAIR6 and TAIR7 releases there was no change to the assembly so the size of the genome remains the same as for TIGR5. The 5 nuclear chromosomes have a total size of 118,998 Mb as described for the TIGR5 release: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15784138 Eva Vigneault wrote: > http://arabidopsis.org/portals/genAnnotation/genome_snapshot.jsp > > 115,409,949 bp (source unkown, but sometime in 2005) > 119,186,497 bp (TIGR 2007) > 134, 634,692 bp (TAIR 2007) > 5 chromosomes > 26,819 protein coding genes (on these 5 chr, according to TAIR 7.0) > > These numbers only take into account the nuclear chromosomes. > > Fred > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen From ureddy from wvstateu.edu Wed Feb 20 20:10:35 2008 From: ureddy from wvstateu.edu (umesh reddy) Date: Thu Feb 21 12:35:39 2008 Subject: [Arabidopsis] Postdoctoral position Message-ID: <000601c87426$907c65b0$4500a8c0@H133UR> We are looking for a PhD in biology/life sciences with at least one year experience in resolving markers using ABI 3130XL. Interested can send their CV, three names of reference to Dr.Padma Nimmakayala at padma@wvstateu.edu Full Description: West Virginia State University (WVSU) Gus R. Douglass Institute invites applications for the Post Doctorial Associate. This position is supported from a USDA-CSREES funded grant for sweet potato genomics. From bioinformatics from null.nil Thu Feb 21 15:52:44 2008 From: bioinformatics from null.nil (bioinformatics@null.nil) Date: Fri Feb 22 12:58:20 2008 Subject: [Arabidopsis] Bioinformatics Scientist Position Message-ID: Bioinformatics Scientist Mendel Biotechnology, Inc. is looking for an individual to lead an important project to collect, organize and analyze data with the goal of improving traits in Miscanthus and other plants for use as biofeedstocks. You will work with biologists, agronomists, business people, and computer scientists in an interdisciplinary environment. This is a well-funded, full-time position in our Hayward, California offices. Knowledge in these areas is helpful: o Genomics and gene databases; o Standard bioinformatics tools; o Plant traits and QTLs; o Plant breeding and pedigree databases; o SNPs; o Illumina Beadstation; o Oracle, Linux, Perl, Apache interactions; To apply for this job, please read carefully: 1. Do not send attachments or HTML-formatted mail; 2. Send plain-text ASCII mail with highlights of your c.v. or resume in the body of the e-mail; 3. You may include relevant URLs in your e-mail; 4. Send e-mail to job107@mendelbio.com For more information on Mendel Biotechnology see http://www.mendelbio.com/ From ulrich.eckhardt from rz.hu-berlin.de Fri Feb 22 08:43:58 2008 From: ulrich.eckhardt from rz.hu-berlin.de (ulrich eckhardt) Date: Fri Feb 22 12:58:27 2008 Subject: [Arabidopsis] GFP seeds wanted Message-ID: Dear newsgroup, does any of you have seeds from Arabidopsis plants that strongly express GFP (cytosol or ER). I need them as a control for gene silencing studies. They must not be resistant to Basta or Hygromycin. Thank you very much in advance Uli Dr. Ulrich Eckhardt Humboldt University Plant Physiology Philippstr. 13, Haus 12 10115 Berlin Germany From thron from mpiz-koeln.mpg.de Wed Feb 27 09:50:53 2008 From: thron from mpiz-koeln.mpg.de (Birgit Thron) Date: Wed Feb 27 12:21:14 2008 Subject: [Arabidopsis] Post-doc advertisement, MPIZ Cologne/Germany Message-ID: <20080227143135.D960F1368289@mpizmail.mpiz-koeln.mpg.de> Dear Madam/Sir, Please see our advertisement below for a post-doc position at the Max Planck Institute for Plant Breeding Research in Cologne, Germany. Could you please forward the announcement to contacts who might be interested in this position. Thank you. Kind regards Birgit Thron Secretary to Prof Maarten Koornneef Director, Plant Breeding and Genetics Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne/Germany Tel: 0049-221-5062-401 Fax: 0049-221-5062-413 E-mail: thron@mpiz-koeln.mpg.de www.mpiz-koeln.mpg.de The Max Planck Institute for Plant Breeding Research (MPIZ) seeks a post-doctoral scientist to establish Affymetrix chip hybridizations for different types of array. In addition the successful applicant will work closely with research groups to prepare hybridization experiments and analyze the data. The position will be based in the DNA core facility which houses a DNA sequencing service, robots for array construction and an Affymetrix chip hybridization station. Extension of the facility to include massively parallel sequencing approaches is planned for the next year. We seek a candidate with a PhD in biology, genetics or a related field. Previous experience with array hybridizations or other genomics-based approaches would be an advantage. Very good English skills are required and German language skills would be advantageous. Payment and benefits are according to the German TV?D. The position will initially be limited to two years with the possibility of a further extension depending on performance. The Max Planck Institute for Plant Breeding Research (MPIZ) in Cologne (www.mpiz-koeln.mpg.de) is one of the world?s premier sites committed to basic research and training in plant science. The institute consists of four scientific departments, three independent research groups and specialist support, totalling about 400 staff, including externally funded positions. The Max Planck Society is an equal opportunity employer. Please send your detailed application by 28 March 2008 to: Max Planck Institute for Plant Breeding Research Personalverwaltung Carl-von-Linn?-Weg 10 50829 Cologne Germany From mukim.iitkgp from gmail.com Wed Feb 27 10:50:45 2008 From: mukim.iitkgp from gmail.com (Mukem) Date: Wed Feb 27 12:21:21 2008 Subject: [Arabidopsis] GENESIS- annual festival of Dept. of Biochnology, IIT Kharagpur Message-ID: GENESIS - The annual fest of Department of Biotechnology, IITKharagpur will be organized from 4th to 6th of April 2008 in IIT Kharagpur Campus.It will provide a platform to people interested in biotechnology from all over the country to explore there interest through various events. Following events will be held during the fest 1) BIOTECHNNOVATION - Paper and Poster Presentation competition 2) BIOSTANCE - Debate Competition 3) BIOLUMINESENCE - Panel Discussion 4) BIOSCOPE - Guest Lectures in varied fields of Biotechnology 5) BIOCASO - Case Study Competition. 6) SYMBIOTEK - well known as icebreaker (Funzone). 7) BIOQUEST - BIOQuiz Competition. 8) BIONETICS - Bioinformatics Competition. 9) BIZWIZ - Business Plan Competition. Registration and Event submission has already started. All the information regarding registration and events details is available at GENESIS website (www.genesisiitkgp.in).The fest is open to all strata of students (Undergrads and Postgrads). Participation certificates will be given to each and every participant. All of you are requested to take this opportunity and learn about your interest. For any query, please contact Mukim Pathan(mukim@genesisiitkgp.in)/ Suma Jaini(suma@genesisiitkgp.in). Please pass this message to all of your friends so that everyone can take this opportunity. From bambusa from gmail.com Thu Feb 28 08:57:11 2008 From: bambusa from gmail.com (bambusa@gmail.com) Date: Thu Feb 28 12:37:27 2008 Subject: [Arabidopsis] ap1 cal1 with petals Message-ID: Dear all, I am growing ap1-1 cal1-1 double mutants from seeds ordered from ABRC (CS6161), of which ap1-1 is homozygous and cal1-1 is heterozygous. However, I saw some white petals from some of the plants. Could anyone please help me to understand this, or give me some suggestions what I should do with those plants having petals? Thank you so much. SL From rpj3 from leicester.ac.uk Thu Feb 28 14:06:56 2008 From: rpj3 from leicester.ac.uk (Jarvis, Dr R.P.) Date: Thu Feb 28 19:34:53 2008 Subject: [Arabidopsis] Postdoc position in chloroplast protein import, Leicester, UK Message-ID: <7722595275A4DD4FA225B92CDBF174A1020997BE@EXC-MBX3.cfs.le.ac.uk> Postdoctoral Research Associate Department of Biology, University of Leicester Salary Grade 7 - GBP 28,289 to 32,796 per annum Available immediately for 18 months Ref: R3654 A BBSRC-funded postdoctoral position is available immediately for a strongly motivated individual to study novel nuclear mutations that affect the efficiency of chloroplast protein import in the model plant, Arabidopsis thaliana. The mutations were identified in forward-genetic screens for extragenic suppressors of the well-characterised chloroplast protein import mutants, ppi1 and tic40. Applicants should have a PhD and a strong background in a relevant discipline. Experience of molecular biology research will be essential, and experience of research on Arabidopsis and/or organelle biology will be highly desirable. Downloadable application forms and further particulars are available from http://www.le.ac.uk/personnel/jobs/r3654a.html. If you require a hard copy, please contact Personnel Services - tel: +44 116 252 2435, fax: +44 116 252 5140, email: recruitment4@le.ac.uk. Please note that CVs will only be accepted in support of a fully completed application form. Closing Date: 18 March 2008 ----------------------------------------------------------- Dr R. Paul Jarvis, Group Leader, Royal Society Rosenheim Research Fellow, Biology Department, University of Leicester, Leicester LE1 7RH, United Kingdom. ----------------------------------------------------------- Tel: +44-116-223-1296; Fax: +44-116-252-3330 E-mail: rpj3@le.ac.uk Web: ----------------------------------------------------------- From dawn.barrett from BBSRC.AC.UK Fri Feb 29 05:21:58 2008 From: dawn.barrett from BBSRC.AC.UK (dawn barrett (TOC)) Date: Fri Feb 29 12:51:08 2008 Subject: [Arabidopsis] independent research fellowships available at John Innes Centre Message-ID: Dear Colleagues Please can you circulate the information below to all interested parties Many thanks Independent Research Fellowships The John Innes Centre (JIC), Norwich, UK is a world leading centre of excellence in plant and microbial sciences based on the Norwich Research Park. We are inviting applications from outstanding researchers who either hold, or wish to apply for Independent Research Fellowships, to attend a Conference at the JIC on 2/3 June 2008. At the meeting you will be able to present a talk about your proposed area of research and to discuss your proposals, the development of your group and your future career plans in depth with senior JIC Scientists. After the Conference we will select and mentor outstanding candidates in writing Fellowship applications and/or offer the opportunity to move existing Fellowships to the JIC. Further details and particulars can be found at http://www.jic.ac.uk/corporate/opportunities/vacancies/fellows.htm Please e-mail a 2-page summary of your research plan, a copy of your CV and arrange for three letters of recommendation to be emailed to dawn.barrett@bbsrc.ac.uk by Friday 18th April 2008. The John Innes Centre is a registered charity (No223852) grant-aided by the Biotechnology and Biological Sciences Research Council and is an Equal Opportunities Employer. Yours ------------------------------------------------ Dawn Barrett AInstAM(Dip), Communications Officer The Operations Centre Norwich Bioscience Institutes Tel: +44 (0) 1603 255 328 Fax: +44 (0) 1603 255 168 e-mail: dawn.barrett@bbsrc.ac.uk www.ifr.ac.uk www.jic.ac.uk www.tsl.ac.uk email disclaimer: www.ifr.ac.uk/edisclaimer From hailing.jin from ucr.edu Fri Feb 29 14:43:34 2008 From: hailing.jin from ucr.edu (Hailing Jin) Date: Fri Feb 29 16:41:16 2008 Subject: [Arabidopsis] (no subject) Message-ID: A postdoctoral researcher position is available immediately at University of California, Riverside A postdoctoral researcher position is available immediately to study the regulatory mechanism of pathogen-induced small RNAs in plant immunity. Endogenous small RNAs have emerged as important players in gene expression reprogramming during disease responses. The candidate will establish and conduct the genetic screening to identify new components in this pathway in Arabidopsis. The candidate will be also involved in identification and functional characterization of the pathogen-induced small RNAs. Applicants should have a Ph.D. degree and a strong background in genetics, molecular biology and biochemistry. Experience in Arabidopsis genetic screening is highly desirable. We are part of the Center for Plant Cell Biology (CEPCEB), Institute for Integrative Genome Biology that equipped with state of art genomics, proteomics, and bioinformatics facilities. Please send a letter of interest, CV, names and addresses of three references to: Dr. Hailing Jin Department of Plant Pathology and Microbiology Center for Plant Cell Biology Institute for Integrative Genome Biology University of California Riverside, CA92521 Email: hailingj@ucr.edu Phone: 951-8277995 --