From cdtown from jcvi.org Thu Oct 1 11:15:11 2009 From: cdtown from jcvi.org (Town, Christopher D.) Date: Thu Oct 1 11:54:09 2009 Subject: [Arabidopsis] good set of "housekeeping" genes in AT? In-Reply-To: <4AC25C68.6000707@mail.utexas.edu> References: <4AC25C68.6000707@mail.utexas.edu> Message-ID: <9F9FBD4CF09A1446BE3EDFA1F3A49E8702E90240@EXCHANGE.TIGR.ORG> See Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis by: Tomasz Czechowski, Mark Stitt, Thomas Altmann, Michael K. Udvardi, Wolf-Rudiger Scheible Plant Physiol., Vol. 139, No. 1. (1 September 2005), pp. 5-17. ___________________________ Chris Town Professor The J. Craig Venter Institute 9704 Medical Center Drive Rockville, MD 20850 Office Phone: 301-795-7523 Fax: 301-838-9142 Home Phone: 301-990-0878 Cell Phone: 301-204-6300 -----Original Message----- From: arab-gen-bounces@oat.bio.indiana.edu [mailto:arab-gen-bounces@oat.bio.indiana.edu] On Behalf Of Karen Browning Sent: Tuesday, September 29, 2009 3:14 PM To: Arab-gen@magpie.bio.indiana.edu Subject: [Arabidopsis] good set of "housekeeping" genes in AT? What would be a good set of housekeeping genes to use for "standards" for comparing expression data in Arabidopsis? Anyone have a standard list of At gene numbers that they use, e.g. actin, tubulin, etc.? -- *********************************************************** Dr. Karen S. Browning Associate Professor Department of Chemistry and Biochemistry The University of Texas at Austin Welch Hall 5.248, 24th and Speedway (Overnight Deliveries) 1 University Station A5300 (Regular Mail) Austin TX 78712-0165 kbrowning@mail.utexas.edu http://research.cm.utexas.edu/kbrowning/ 512-471-4562 512-471-8696 FAX _______________________________________________ Arab-gen mailing list Arab-gen@net.bio.net http://www.bio.net/biomail/listinfo/arab-gen From jdfriesner from ucdavis.edu Thu Oct 1 19:08:07 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Fri Oct 2 12:38:55 2009 Subject: [Arabidopsis] 10 iPlant Postdoc Openings Message-ID: <000e01ca42f4$6c25a3e0$4470eba0$@edu> (Sent on behalf of iPlant- please contact the indicated names for more information) 5 postdocs in each section: (1) Postdoctoral Research Positions-Computational Phylogenetics/Phyloinformatics Multiple postdoctoral positions are available for research and cyberinfrastructure development associated with reconstructing the green plant tree of life. Positions are sponsored by the iPlant Collaborative (http://iplantcollaborative.org), which is supporting cyberinfrastructure across the plant sciences. Individuals would work with one of a number of identified investigators focusing on specific issues in phylogenetic cyberinfrastructure development. These include high performance computing and scalable tree construction (Alexandros Stamatakis-Technical University, Munich; email: stamatak@cs.tum.edu), data set assembly (Doug Soltis-U Florida; email: dsoltis@botany.ufl.edu, Pam Soltis-U Florida; email: psoltis@flmnh.ufl.edu; Michael Donoghue-Yale; email: michael.donoghue@yale.edu), gene tree reconciliation (Todd Vision-UNC; email: tjv@bio.unc.edu), character evolution (Brian O'Meara-U Tennessee; email: bomeara@utk.edu), and tree visualization (Michael Sanderson, UC-Davis; email: sanderm@email.arizona.edu). Fellows can anticipate working in a highly collaborative, multi-institutional context, with some travel between working groups encouraged. In addition to undertaking basic research in phylogenetic methods, postdocs will be expected to provide advice on and work in collaboration with cyberinfastructure developers in the iPlant team. Qualifications include familiarity with the data, methods, and software of phylogenetic analysis, and programming experience at least at the level of a scripting language such as PERL. Individual PIs may have additional requirements. Inquiries should be directed to any of the Grand Challenge Team members listed above. Positions are available immediately. A full description of the iPToL (iPlant Tree of Life) project can be found online at http://iptol.iplantcollaborative.org. The institutions involved in this program may be Affirmative Action and/or Equal Opportunity Employers. (2) Program Announcement-Connecting Genotypes to Phenotypes in Complex Environments Multiple postdoctoral positions will be available for research and cyberinfrastructure development associated with elucidating the relationship between plant genotypes and the resultant phenotypes (G2P) in changing environments. The program is sponsored by the iPlant Collaborative (http://iplantcollaborative.org), which develops and enables cyberinfrastructure support for Grand Challenge research across the plant sciences. Individuals will be work in a team setting with one of a number of specific investigators having key roles in issues related to G2P cyberinfrastructure development. These include pipelining and analysis of Next Generation sequence data (Tom Brutnell-Boyce Thompson Institute, Cornell University; email: tpb8@cornell.edu), data integration (Matthew Vaughn email: vaughn@cshl.edu, and Doreen Ware email: ware@cshl.edu, - both at Cold Spring Harbor Laboratory), statistical inference for genome-wide association mapping (Dan Kliebenstein- University of California, Davis; email: kliebenstein@ucdavis.edu), visualization/analysis (Ruth Grene-Virginia Tech; email: grene@vt.edu), modeling tools (Stephen Welch-Kansas State University; email: welchsm@ksu.edu). The work setting will be a highly collaborative, multi-institutional context, with some travel between working groups encouraged. In addition to undertaking basic G2P research, individuals will be expected to provide advice on and work in collaboration with iPlant cyberinfastructure developers. Qualifications include familiarity with one (or preferably more) of the following areas: functional-, quantitative-, or computational genetics/genomics; bioinformatics; programming experience (either scripting languages like PERL or compiled languages like C/C++); modeling (systems biological, ecophysiological, or statistical); database use; current topics in plant biology (especially stress, photosynthesis, or phenology); or high performance computing. Individual investigators may have additional requirements. Inquiries should be directed to any of the individuals listed above. A full description of the iPlant G2P program, including specific position descriptions as they become available, can be found online at http://ipg2p.iplantcollaborative.org. The institutions involved in this program may be Affirmative Action and/or Equal Opportunity Employers. From neil from arabidopsis.info Fri Oct 2 04:05:24 2009 From: neil from arabidopsis.info (Neil Graham) Date: Fri Oct 2 12:39:48 2009 Subject: [Arabidopsis] Re: good set of "housekeeping" genes in AT? In-Reply-To: References: Message-ID: Hi Have a look at: Czechowsli et al 2005. Genome-wide identification of superior reference genes for transcript normalisation in Arabidopsis. Plant Physiology. 139:5-17. These genes were identified by finding genes with a low %CV across the AtGenExpress developmental series. Thanks Neil Graham -------------------------------------- http://arabidopsis.info Nottingham Arabidopsis Stock Centre Plant and Crop Sciences Division University of Nottingham Loughborough UK -------------------------------------- Karen Browning wrote: > What would be a good set of housekeeping genes to use for "standards" > for comparing expression data in Arabidopsis? > > Anyone have a standard list of At gene numbers that they use, e.g. > actin, tubulin, etc.? This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. From evewurtele from gmail.com Sat Oct 3 18:30:38 2009 From: evewurtele from gmail.com (Eve Wurtele) Date: Mon Oct 5 00:46:10 2009 Subject: [Arabidopsis] Re: good set of "housekeeping" genes in AT? In-Reply-To: <7fdaa81b0910031623o5c90d994m6ddd998b19196cd7@mail.gmail.com> References: <7fdaa81b0910031623o5c90d994m6ddd998b19196cd7@mail.gmail.com> Message-ID: <7fdaa81b0910031630w3554d6c0y7ed2f354c3bfee6b@mail.gmail.com> If you are concerned with more than developmental expression, 100 genes that vary least across about 1000 Affy chips (500 samples) from AtGenExpress are described in Mentzen 2008. (The chips include the developmental series, plus a variety of environmental and genetic perturbations). The reference as well as the actual "steady" gene list are below. BMC Plant Biol. 2008 Sep 30;8:99. Regulon organization of Arabidopsis. *Mentzen WI*, *Wurtele ES*. Listed at supplementary "*Additional file 5.* Genes with the most steady expression" Two quite steady transcripts with a high overall level of accumulation are : AT3G56460 and AT4G34110 (These transcripts have about 5-fold and 7-fold, respectively, higher accumulation than the mean value of the genes on the chips, which is set to 100) The genes with most steady expression comprise a fairly uniform mixture of metabolism, regulation, transport, and "unknown" functions. However, no "steady" "housekeeping" genes on the affy chip are completely steady. Thus, it makes sense to be sure the particular conditions you are testing (say "heat stress") are not the ones under which the "housekeeping gene" varies. For each gene, there are a couple conditions/in a couple chips out of the 500 in which there is variation (say 2-fold greater or less than the mean). You can use MetaOmGraphto visualize the conditions where there is a bit more variation. Download (free- funded by NSF-Arabidopsis 2010), a window will open. download Affy.ath1.data1 project, clicking the blue +to create a new gene list, and paste the locus IDs shown below into a the gene list after clicking import. (that's what I did to get the particular three genes listed above, its quick once you've learned the software) *Locus ID- Most steady expression- Mentzen and Wurtele, BMC Plant Biology 2008* AT5G12370 AT4G15415 AT4G15475 AT4G17430 AT1G73440 AT5G11040 AT5G28850; AT5G28900 AT5G21040 AT4G37130 AT3G56830 AT1G16570 AT5G16280 AT5G24830 AT5G65540 AT5G64830 AT5G64813 AT5G61840 AT5G48520 AT5G46190 AT5G45300 AT5G41480 AT5G38380 AT5G38360 AT5G37310 AT5G24360 AT5G18190 AT5G11490 AT5G11640 AT5G11380 AT5G07270 AT5G05920 AT5G05820 AT5G04070 AT5G02850 AT3G56460 AT3G55480 AT3G53090 AT3G52610 AT3G51040 AT3G51050 AT3G49850 AT3G47390 AT3G42050 AT4G39920 AT4G38040 AT4G38500 AT4G38180 AT4G35530 AT4G34110 AT4G31150 AT4G26410 AT4G11970 AT4G00420 AT3G28670 AT3G27320 AT3G17430 AT3G17450 AT1G53770 AT3G17750 AT3G20870 AT3G29010 AT3G04470 AT3G05040 AT3G04970 AT3G33520 AT3G05090; AT3G05080 AT1G13320 AT1G68980 AT1G73840 AT1G73970 AT1G34550 AT1G79810 AT1G01910 AT1G76340 AT1G80950 AT1G79975 AT1G54390 AT1G54150 AT1G05500 AT2G40410 AT2G36240 AT1G78810 AT1G08960 AT1G08750 AT2G17390 AT1G76940 AT1G30970 AT2G28390 AT2G38950 AT2G27600 AT2G27110 AT2G41350 AT2G35100 AT2G35360 AT2G40980 AT2G19280 AT2G39910 AT2G41960 > On Fri, Oct 2, 2009 at 4:05 AM, Neil Graham wrote: > >> Hi >> >> Have a look at: >> >> Czechowsli et al 2005. Genome-wide identification of superior reference >> genes for transcript normalisation in Arabidopsis. Plant Physiology. >> 139:5-17. >> >> These genes were identified by finding genes with a low %CV across the >> AtGenExpress developmental series. >> >> Thanks >> >> Neil Graham >> >> -------------------------------------- >> http://arabidopsis.info >> >> Nottingham Arabidopsis Stock Centre >> Plant and Crop Sciences Division >> University of Nottingham >> Loughborough >> UK >> -------------------------------------- >> >> Karen Browning wrote: >> >>> What would be a good set of housekeeping genes to use for "standards" for >>> comparing expression data in Arabidopsis? >>> >>> Anyone have a standard list of At gene numbers that they use, e.g. actin, >>> tubulin, etc.? >>> >> >> This message has been checked for viruses but the contents of an >> attachment >> may still contain software viruses, which could damage your computer >> system: >> you are advised to perform your own checks. Email communications with the >> University of Nottingham may be monitored as permitted by UK legislation. >> >> _______________________________________________ >> Arab-gen mailing list >> Arab-gen@net.bio.net >> http://www.bio.net/biomail/listinfo/arab-gen >> > > > > -- > Eve Syrkin Wurtele, Professor > Bioinformatics and Computational Biology > 2624D Howe Hall, VRAC, > Iowa State University, Ames IA 50011, USA > metnetdb.org > metablast.org 515-708-3232 (cell) > > -- Eve Syrkin Wurtele, Professor Bioinformatics and Computational Biology 2624D Howe Hall, VRAC, Iowa State University, Ames IA 50011, USA metnetdb.org metablast.org 515-708-3232 (cell) From george.e.schaller from dartmouth.edu Fri Oct 2 12:56:26 2009 From: george.e.schaller from dartmouth.edu (Eric Schaller) Date: Mon Oct 5 00:47:07 2009 Subject: [Arabidopsis] Postdoctoral Positions in Plant Molecular Biology at Dartmouth College Message-ID: Postdoctoral Positions in Plant Molecular Biology at Dartmouth College Postdoctoral positions are currently available in the laboratories of =20= Dr. Mary Lou Guerinot, Dr. Tom Jack, and Dr. G. Eric Schaller to work =20= on federally funded research projects. Guerinot: The research in Dr. Guerinot=92s laboratory involves the =20 study of metal ion homeostasis in Arabidopsis and rice with a special =20= emphasis on iron and zinc. We are continuing our studies on =20 localization of metals using synchrotron X-ray fluorescence =20 spectroscopy. In addition, we have been using high throughput =20 elemental profiling via ICP-MS to define a plant=92s ionome and have =20 used this information for functional characterization of various =20 mutants, for gene discovery, for developing ionomic signatures of =20 different physiological states and for exploring natural variation. Jack: The research in Dr. Jack=92s lab involves the elucidation of the =20= role of two genes necessary for proper growth of petals and stamens. =20= The first is DORNROSCHEN-LIKE, which encodes a AP2-domain =20 transcription factor. The second is microRNA319a, which functions to =20 regulate a subset of TCP transcription factor genes. Schaller: The research in Dr. Schaller=92s laboratory involves the =20 study of post-transcriptional regulation in ethylene signaling, with =20 a focus on action of the ethylene receptors. To this end we are =20 determining how physical interactions among the ethylene receptors =20 coordinate signal output. We are also determining the role played by =20 a small family of novel proteins in modulating receptor signaling. Additional information on each PI=92s research interests can be =20 accessed through their individual faculty web pages at http://=20 www.dartmouth.edu/~biology/biofaculty.html Successful applicants should be highly motivated, be capable of =20 working independently, and have a relevant PhD. Experience in some or =20= all of the following disciplines is desirable: genetics in model =20 systems, molecular biology, and/or biochemistry. Application Instructions: Please send a letter of application =20 describing research background, a CV, and the names and contact =20 information for three references by email to the faculty member(s) of =20= your choice: Mary Lou Guerinot (Mary.Lou.Guerinot@Dartmouth.edu), Tom =20= Jack (Thomas.P.Jack@Dartmouth.edu), G. Eric Schaller =20 (George.E.Schaller@Dartmouth.edu). This is a good opportunity if you =20 and a partner are both looking for postdoctoral positions at the same =20= institution, and it may be helpful to indicate if this is the case in =20= your cover letter. =20= From aloraine from gmail.com Mon Oct 5 07:42:18 2009 From: aloraine from gmail.com (Ann Loraine) Date: Mon Oct 5 13:05:37 2009 Subject: comparisons with NGS dat? Re: [Arabidopsis] Re: good set of "housekeeping" genes in AT? Message-ID: <83722dde0910050542l342e2ed2u303d4f79b564f266@mail.gmail.com> Thank you for this excellent advice! I've been following this thread with great interest in hopes of finding good controls for expression experiments. Has anyone assessed the behavior of "invariant" (in quotes because they may still vary under some treatments) genes using next-gen sequencing data? There are a several new Illumina data sets available in the short-read archive (from Oregon State) and my lab has a data set from a 454 sequencing experiment (longer reads) comparing a treatment and control. We were thinking of using the "invariant" genes to calculate a normalization factor across the data sets so that we could more confidently estimate differential expression, and then, of course, follow up with another gene measurement method (e.g., qRT-PCR) to confirm the results. Knowing which genes really do not vary (much) under our conditions of interest will be critical. Best, Ann Loraine On Sat, Oct 3, 2009 at 7:30 PM, Eve Wurtele wrote: > If you are concerned with more than developmental expression, 100 genes > that > vary least across about 1000 Affy chips (500 samples) from AtGenExpress are > described in Mentzen 2008. (The chips include the developmental series, > plus > a variety of environmental and genetic perturbations). The reference as > well as the actual "steady" gene list are below. BMC Plant Biol. 2008 Sep > 30;8:99. Regulon organization of > Arabidopsis.< > http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18826618 > > > *Mentzen WI*< > http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18826618 > >, > *Wurtele > ES*< > http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18826618 > >. > Listed at supplementary "*Additional file 5.* Genes with the most steady > expression"< > http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18826618 > > > Two quite steady transcripts with a high overall level of accumulation are > : > AT3G56460 and AT4G34110 (These transcripts have about 5-fold and 7-fold, > respectively, higher accumulation than the mean value of the genes on the > chips, which is set to 100) > The genes with most steady expression comprise a fairly uniform mixture of > metabolism, regulation, transport, and "unknown" functions. > > However, no "steady" "housekeeping" genes on the affy chip are completely > steady. Thus, it makes sense to be sure the particular conditions you are > testing (say "heat stress") are not the ones under which the "housekeeping > gene" varies. For each gene, there are a couple conditions/in a couple > chips > out of the 500 in which there is variation (say 2-fold greater or less than > the mean). You can use > MetaOmGraphto visualize > the conditions where there is a bit more variation. Download > (free- funded by NSF-Arabidopsis 2010), a window will open. download > Affy.ath1.data1 project, clicking the blue +to create a new gene list, and > paste the locus IDs shown below into a the gene list after clicking import. > > (that's what I did to get the particular three genes listed above, its > quick > once you've learned the software) > > *Locus ID- Most steady expression- Mentzen and Wurtele, BMC Plant Biology > 2008* > AT5G12370 > AT4G15415 > AT4G15475 > AT4G17430 > AT1G73440 > AT5G11040 > AT5G28850; AT5G28900 > AT5G21040 > AT4G37130 > AT3G56830 > AT1G16570 > AT5G16280 > AT5G24830 > AT5G65540 > AT5G64830 > AT5G64813 > AT5G61840 > AT5G48520 > AT5G46190 > AT5G45300 > AT5G41480 > AT5G38380 > AT5G38360 > AT5G37310 > AT5G24360 > AT5G18190 > AT5G11490 > AT5G11640 > AT5G11380 > AT5G07270 > AT5G05920 > AT5G05820 > AT5G04070 > AT5G02850 > AT3G56460 > AT3G55480 > AT3G53090 > AT3G52610 > AT3G51040 > AT3G51050 > AT3G49850 > AT3G47390 > AT3G42050 > AT4G39920 > AT4G38040 > AT4G38500 > AT4G38180 > AT4G35530 > AT4G34110 > AT4G31150 > AT4G26410 > AT4G11970 > AT4G00420 > AT3G28670 > AT3G27320 > AT3G17430 > AT3G17450 > AT1G53770 > AT3G17750 > AT3G20870 > AT3G29010 > AT3G04470 > AT3G05040 > AT3G04970 > AT3G33520 > AT3G05090; AT3G05080 > AT1G13320 > AT1G68980 > AT1G73840 > AT1G73970 > AT1G34550 > AT1G79810 > AT1G01910 > AT1G76340 > AT1G80950 > AT1G79975 > AT1G54390 > AT1G54150 > AT1G05500 > AT2G40410 > AT2G36240 > AT1G78810 > AT1G08960 > AT1G08750 > AT2G17390 > AT1G76940 > AT1G30970 > AT2G28390 > AT2G38950 > AT2G27600 > AT2G27110 > AT2G41350 > AT2G35100 > AT2G35360 > AT2G40980 > AT2G19280 > AT2G39910 > AT2G41960 > > > > On Fri, Oct 2, 2009 at 4:05 AM, Neil Graham > wrote: > > > >> Hi > >> > >> Have a look at: > >> > >> Czechowsli et al 2005. Genome-wide identification of superior reference > >> genes for transcript normalisation in Arabidopsis. Plant Physiology. > >> 139:5-17. > >> > >> These genes were identified by finding genes with a low %CV across the > >> AtGenExpress developmental series. > >> > >> Thanks > >> > >> Neil Graham > >> > >> -------------------------------------- > >> http://arabidopsis.info > >> > >> Nottingham Arabidopsis Stock Centre > >> Plant and Crop Sciences Division > >> University of Nottingham > >> Loughborough > >> UK > >> -------------------------------------- > >> > >> Karen Browning wrote: > >> > >>> What would be a good set of housekeeping genes to use for "standards" > for > >>> comparing expression data in Arabidopsis? > >>> > >>> Anyone have a standard list of At gene numbers that they use, e.g. > actin, > >>> tubulin, etc.? > >>> > >> > >> This message has been checked for viruses but the contents of an > >> attachment > >> may still contain software viruses, which could damage your computer > >> system: > >> you are advised to perform your own checks. Email communications with > the > >> University of Nottingham may be monitored as permitted by UK > legislation. > >> > >> _______________________________________________ > >> Arab-gen mailing list > >> Arab-gen@net.bio.net > >> http://www.bio.net/biomail/listinfo/arab-gen > >> > > > > > > > > -- > > Eve Syrkin Wurtele, Professor > > Bioinformatics and Computational Biology > > 2624D Howe Hall, VRAC, > > Iowa State University, Ames IA 50011, USA > > metnetdb.org > > metablast.org 515-708-3232 (cell) > > > > > > > -- > Eve Syrkin Wurtele, Professor > Bioinformatics and Computational Biology > 2624D Howe Hall, VRAC, > Iowa State University, Ames IA 50011, USA > metnetdb.org > metablast.org 515-708-3232 (cell) > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > From jdfriesner from ucdavis.edu Mon Oct 5 12:23:41 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Mon Oct 5 13:05:59 2009 Subject: [Arabidopsis] ICAR 2010- Japan- Important dates Message-ID: <000901ca45e0$95ddc390$c1994ab0$@edu> Please check this page (http://arabidopsis2010.psc.riken.jp/i_dates.html) for important dates on the 2010 Arabidopsis Conference. The meeting comes to Japan for the first time. From Scheible from mpimp-golm.mpg.de Mon Oct 5 01:11:23 2009 From: Scheible from mpimp-golm.mpg.de (Wolf-Ruediger Scheible) Date: Mon Oct 5 13:06:22 2009 Subject: AW: [Arabidopsis] Re: good set of "housekeeping" genes in AT? In-Reply-To: <7fdaa81b0910031630w3554d6c0y7ed2f354c3bfee6b@mail.gmail.com> References: <7fdaa81b0910031623o5c90d994m6ddd998b19196cd7@mail.gmail.com> <7fdaa81b0910031630w3554d6c0y7ed2f354c3bfee6b@mail.gmail.com> Message-ID: <3C6529856AC10C4E843BE21F6B9356DA9862E41E52@MAIL01.mpimp-golm.mpg.de> For clarification: the paper by Czechowski et al. (2005) identified novel reference genes not just from the AtGE developmental series but also from - a large abiotic stress series - hormone treatments - a biotic stress treatments - nutrient stress/re-addition experiments and a diurnal series The genes we finally proposed performed well in all these experimental conditions. Regards, Wolf Dr. Wolf Scheible Max-Planck Institute of Molecular Plant Physiology Science Park Golm Am M?hlenberg 1 14476 Potsdam, Germany phone +49-331-5678155 fax +49-331-5678134 _____________________ -----Urspr?ngliche Nachricht----- Von: arab-gen-bounces@oat.bio.indiana.edu [mailto:arab-gen-bounces@oat.bio.indiana.edu] Im Auftrag von Eve Wurtele Gesendet: Sunday, October 04, 2009 1:31 AM An: bionet-genome-arabidopsis@moderators.isc.org Betreff: Re: [Arabidopsis] Re: good set of "housekeeping" genes in AT? If you are concerned with more than developmental expression, 100 genes that vary least across about 1000 Affy chips (500 samples) from AtGenExpress are described in Mentzen 2008. (The chips include the developmental series, plus a variety of environmental and genetic perturbations). The reference as well as the actual "steady" gene list are below. BMC Plant Biol. 2008 Sep 30;8:99. Regulon organization of Arabidopsis. *Mentzen WI*, *Wurtele ES*. Listed at supplementary "*Additional file 5.* Genes with the most steady expression" Two quite steady transcripts with a high overall level of accumulation are : AT3G56460 and AT4G34110 (These transcripts have about 5-fold and 7-fold, respectively, higher accumulation than the mean value of the genes on the chips, which is set to 100) The genes with most steady expression comprise a fairly uniform mixture of metabolism, regulation, transport, and "unknown" functions. However, no "steady" "housekeeping" genes on the affy chip are completely steady. Thus, it makes sense to be sure the particular conditions you are testing (say "heat stress") are not the ones under which the "housekeeping gene" varies. For each gene, there are a couple conditions/in a couple chips out of the 500 in which there is variation (say 2-fold greater or less than the mean). You can use MetaOmGraphto visualize the conditions where there is a bit more variation. Download (free- funded by NSF-Arabidopsis 2010), a window will open. download Affy.ath1.data1 project, clicking the blue +to create a new gene list, and paste the locus IDs shown below into a the gene list after clicking import. (that's what I did to get the particular three genes listed above, its quick once you've learned the software) > On Fri, Oct 2, 2009 at 4:05 AM, Neil Graham wrote: > >> Hi >> >> Have a look at: >> >> Czechowsli et al 2005. Genome-wide identification of superior >> reference genes for transcript normalisation in Arabidopsis. Plant Physiology. >> 139:5-17. >> >> These genes were identified by finding genes with a low %CV across >> the AtGenExpress developmental series. >> >> Thanks >> >> Neil Graham >> >> -------------------------------------- >> http://arabidopsis.info >> >> Nottingham Arabidopsis Stock Centre >> Plant and Crop Sciences Division >> University of Nottingham >> Loughborough >> UK >> -------------------------------------- >> >> Karen Browning wrote: >> >>> What would be a good set of housekeeping genes to use for >>> "standards" for comparing expression data in Arabidopsis? >>> >>> Anyone have a standard list of At gene numbers that they use, e.g. >>> actin, tubulin, etc.? >>> >> >> This message has been checked for viruses but the contents of an >> attachment may still contain software viruses, which could damage >> your computer >> system: >> you are advised to perform your own checks. Email communications with >> the University of Nottingham may be monitored as permitted by UK legislation. >> >> _______________________________________________ >> Arab-gen mailing list >> Arab-gen@net.bio.net >> http://www.bio.net/biomail/listinfo/arab-gen >> > > > > -- > Eve Syrkin Wurtele, Professor > Bioinformatics and Computational Biology 2624D Howe Hall, VRAC, Iowa > State University, Ames IA 50011, USA metnetdb.org > metablast.org 515-708-3232 (cell) > > -- Eve Syrkin Wurtele, Professor Bioinformatics and Computational Biology 2624D Howe Hall, VRAC, Iowa State University, Ames IA 50011, USA metnetdb.org metablast.org 515-708-3232 (cell) _______________________________________________ Arab-gen mailing list Arab-gen@net.bio.net http://www.bio.net/biomail/listinfo/arab-gen From wfrommer from stanford.edu Mon Oct 5 16:57:56 2009 From: wfrommer from stanford.edu (Wolf Frommer) Date: Tue Oct 6 01:21:44 2009 Subject: [Arabidopsis] postdoctoral position Message-ID: <0C669201-FD4C-4BA9-A253-144F8A745FF4@stanford.edu> Postdoctoral position in Plant Cell Biology at the Carnegie Institution for Science, Stanford, California. A postdoctoral position is available immediately in the lab of Dr. Wolf B. Frommer at the Department of Plant Biology, Carnegie Institution for Science, Stanford, California. The successful candidate will participate in ongoing multi- disciplinary research projects aimed at the identification and the characterization of regulatory networks involved in controlling nutrient/metabolite uptake and allocation (Loqu? et al., 2007 Nature 446:195-8; 2008 J. Biol. Chem. 284:24988-95; Chaudhuri et al., 2008 Plant J. 56:948-62). Applicants should have a Ph.D. and a strong background in biochemistry and in cell and molecular biology. Experience in genetics, genomics and/or bioinformatics would be valuable. Strong written and oral communication skills and the ability to work in a team-oriented environment are important. The position is for two years with the possibility of an extension. The initial appointment is for one year and is renewable depending on satisfactory performance and fund availability. Salaries are competitive and include benefits. Interested applicants should send via email: a cover letter detailing experience as well as interest in the topic, resume, and names, addresses and e-mail of three references to pinarm@stanford.edu. ************************************** Wolf B. Frommer Carnegie Institution for Science Department of Plant Biology 260 Panama St Stanford CA 94305 Tel. 650 325 1521 x208 http://carnegiedpb.stanford.edu/ *************************************** From lmkoch from wisc.edu Wed Oct 7 15:12:51 2009 From: lmkoch from wisc.edu (LISA M KOCH) Date: Wed Oct 7 22:50:46 2009 Subject: [Arabidopsis] GUS staining in Alfalfa Message-ID: <6f60ce0488ce6.4accaff3@wiscmail.wisc.edu> We've been trying to do GUS staining in mature Alfalfa plants using a standard protocol of acetone fix / phosphate buffer &FeCNs & Xgluc / incubate at 37 / EtOH clear if necessary. This always worked very well for me in arabidopsis, but in alfalfa, the stain does not seem to permeate - even in constitutive GUS plants, only the blade-cut-edges will stain, leading me to believe this is a permeability issue. We tried the X-gulc method with cycling vacuum infiltration (which didn't work either) but I'm not sure what level of low pressure we achieved (we just used our speedvac). We've also attempted a fluorometric assay with MUG, which didn't give great results, and may return to that idea, but visualizing the stain would be much more convenient for us. Does anyone have any helpful suggestions on GUS staining permeability (besides looking at younger plants - this is not an option for this project)? Thanks! Lisa Koch From staceyg from missouri.edu Thu Oct 8 13:02:50 2009 From: staceyg from missouri.edu (Stacey, Gary) Date: Thu Oct 8 17:37:14 2009 Subject: [Arabidopsis] 21st North American Symbiotic Nitrogen Fixation Conference Message-ID: <964681C84DC6E34F96D993D3717487A707E02F59EC@UM-EMAIL05.um.umsystem.edu> We would like your help in publicizing the 21st North American Nitrogen Fixation Conference, which will be held in Columbia, MO from June 13-18, 2010. The scientific program is now under development and will be announced soon. Additional details are available at http://muconf.missouri.edu/nasnfc/ Please let any of your colleagues or others who may be interested in this topic area know about this upcoming conference. Thanks. Gary Gary Stacey, Ph.D. Director, Center for Sustainable Energy Assoc. Director, National Center for Soybean Biotechnology Divisions of Plant Sciences and Biochemistry Department of Molecular Microbiology and Immunology 271E Christopher S. Bond Life Sciences Center University of Missouri Columbia, MO 65211 Office phone: 573-884-4752 Lab Phone: 573-884-4799 FAX: 573-884-9676 email: staceyg@missouri.edu NEW LAB WEBSITE: http://www.staceylab.missouri.edu/ MU CSE site: http://www.energy.missouri.edu/ NCSB site: http://www.soybiotechcenter.org NSF Project site: http://www.soybeangenome.org From yadegari from email.arizona.edu Thu Oct 8 16:04:01 2009 From: yadegari from email.arizona.edu (Ramin Yadegari) Date: Thu Oct 8 17:37:37 2009 Subject: [Arabidopsis] Postdoctoral position Message-ID: <005101ca485a$dd528630$97f79290$@arizona.edu> Postdoctoral Associate Position in Arabidopsis and maize Developmental Genetics A postdoctoral associate position is available at the University of Arizona to study early endosperm development in Arabidopsis and maize. We are looking for a highly motivated individual with a Ph.D. degree and with demonstrated ability to carry out outstanding research in the fields of plant biology, genetics, or related disciplines. Proven experience with molecular biology techniques and demonstrated skills in written and oral communication are essential qualifications. Ability to interact and work collaboratively with others is also critical as this is a collaborative effort involving multiple laboratories. Previous experience with Arabidopsis, maize or knowledge of functional genomics and/or bioinformatics is desirable but not essential. Position is available immediately. To apply, send curriculum vitae and the names and contact information (address, phone, fax and e-mail) for three references to Ramin Yadegari, Ph.D. (yadegari@email.arizona.edu), School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036, United States. FAX 520-621-7186. The University of Arizona is an EEO/AA Employer-M/W/D/V. From zepedrof from gmail.com Thu Oct 8 10:17:01 2009 From: zepedrof from gmail.com (JP Fonseca) Date: Thu Oct 8 17:38:21 2009 Subject: [Arabidopsis] GUS staining in Alfalfa In-Reply-To: <6f60ce0488ce6.4accaff3@wiscmail.wisc.edu> References: <6f60ce0488ce6.4accaff3@wiscmail.wisc.edu> Message-ID: <774498f60910080817t4cde430enf24558ede6187ca8@mail.gmail.com> Hi Lisa, Not very familiar with Alfafa. I have observed GUS staining in Arabidopsis before by Agroinfiltrating leaves with a needleless syringe containing my GUS reporter constructs. Then allow transformed samples to rest for ~ 2 days to allow GUS expression and then incubate samples in GUS staining solution overnight at 37 C. Next day washed several times with ethanol 70% to remove clorophyll and... "voila!"...blue GUS spots observed. Hope it works in Alfafa. JP Fonseca On Wed, Oct 7, 2009 at 5:12 PM, LISA M KOCH wrote: > We've been trying to do GUS staining in mature Alfalfa plants using a > standard protocol of acetone fix / phosphate buffer &FeCNs & Xgluc / > incubate at 37 / EtOH clear if necessary. This always worked very well for > me in arabidopsis, but in alfalfa, the stain does not seem to permeate - > even in constitutive GUS plants, only the blade-cut-edges will stain, > leading me to believe this is a permeability issue. > > We tried the X-gulc method with cycling vacuum infiltration (which didn't > work either) but I'm not sure what level of low pressure we achieved (we > just used our speedvac). We've also attempted a fluorometric assay with > MUG, which didn't give great results, and may return to that idea, but > visualizing the stain would be much more convenient for us. > > Does anyone have any helpful suggestions on GUS staining permeability > (besides looking at younger plants - this is not an option for this > project)? > Thanks! > Lisa Koch > > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > From alperyilmaz from gmail.com Sat Oct 10 17:24:22 2009 From: alperyilmaz from gmail.com (alperyilmaz) Date: Mon Oct 12 21:37:09 2009 Subject: [Arabidopsis] Re: seeking TAIR9 bpmap file for Arabidopsis tiling array 1.0R References: Message-ID: I just found TAIR8 bpmap in this location: http://www.biostat.jhsph.edu/~hji/cisgenome/index_files/download.htm thanks, alper On Sep 17, 6:30?pm, Ann Loraine wrote: > Dear Colleagues, > > I'm looking for a "bpmap" file that maps Affymetrix Arabidopsis tiling array > 1.0R probes onto the TAIR9 or TAIR8 genome sequence. > > (This is for setting up a demonstration server that will show labs how they > can easily visualize and share tiling array and RNA-Seq data via the > Integrated Genome Browser (igb.bioviz.org) and DAS, one of the deliverables > for an NSF 2010 award, which started a year ago.) > > The array corresponds to GEO platform accession GPL1980. (If this is wrong, > please let me know...the Web page for it is here:http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1980) > > The Web page for GPL1980 at GEO links to a bpmap file, but we are not yet > sure which genome it references. Probably it is the TAIR7 genome, but we > haven't tested it as yet. The bpmap file that Affymetrix distributes > references TAIR7 (what they call Jan 2004) and the company has no immediate > plans to update it because their tiling array support relies on a genome > being supported by the UCSC Genome Bioinformatics group, which only supports > animal and some fungal genomes. > > If you know of anyone who has a bpmap file for the Arabidopsis Tiling 1.0R > Array for TAIR9, or even TAIR8, I would be very grateful if you would give > me their contact information or send me a link to the file. > > Also, if you are looking for such a file, please let me know, and I'll get > in touch as soon as I find one...or as soon as we create it, if one cannot > be found. > > Thank you very much for your time, > > Ann Loraine > Associate Professor > Dept. of Bioinformatics and ?Genomics > UNC Charlotte From meier.56 from osu.edu Sun Oct 11 20:25:24 2009 From: meier.56 from osu.edu (IRIS MEIER) Date: Mon Oct 12 21:37:28 2009 Subject: [Arabidopsis] Faculty Position Ohio State University Message-ID: Tenure Track Faculty Position in Plant Biology, Ohio State University The merging Departments of Plant Cellular & Molecular Biology and Molecular Genetics at The Ohio State University, in conjunction with the interdisciplinary Plant Molecular Biology/Biotechnology (PMBB) program, invite applications for a full-time, tenure-track faculty position. Appointment at the Assistant Professor level is preferred, but outstanding candidates at senior levels will also be considered. Successful applicants are expected to develop an outstanding research program and to participate in teaching at the undergraduate and graduate levels. Applicants with expertise in any areas of plant molecular, cellular, biochemical, developmental, genomics and systems biology are encouraged to apply. Research programs addressing fundamental problems of bioenergy, bioproducts, carbon sequestration or plant-microbe interactions are of particular interest. Candidates with a Ph.D. and suitable postdoctoral experience should submit applications including curriculum vitae, a 3 page or less research plan and a brief description of teaching experience and interests. Candidates for the Assistant Professor level should arrange to have at least 3 reference letters submitted. Electronic applications and reference letters to pbsearch@biosci.osu.edu are preferred, but paper copies may also be sent to Search Committee Chair, Dept. of Plant Cellular and Molecular Biology, Ohio State University, 500 Aronoff Laboratory, 318 West 12th Ave., Columbus, OH? 43210-1242. Review of applications will begin November 15, 2009 and continue until a suitable candidate is identified. To build a diverse workforce Ohio State encourages applications from individuals with disabilities, minorities, veterans, and women. EEO/AA Employer. Ohio State is an NSF Advance institution. _____________________________________ Iris Meier, Ph.D. Professor PCMB and Plant Biotechnology Center Ohio State University 500 Aronoff Laboratory 318 W. 12th Avenue Columbus, OH 43210 Phone:614-292-8323 Fax: 614-292-6345 meier.56@osu.edu http://www.biosci.ohio-state.edu/pcmb/osu_pcmb/people_faculty_meierIris.php From somers.24 from osu.edu Sun Oct 11 20:37:32 2009 From: somers.24 from osu.edu (David Somers) Date: Mon Oct 12 21:37:47 2009 Subject: [Arabidopsis] Postdoctoral/Technician Positions: Arabidopsis circadian clock Message-ID: <4AD2885C.8000202@osu.edu> *Post-doctoral and research technician positions* (2-3) are available to investigate the plant circadian clock in the new Division of Integrative Biosciences and Biotechnology at Pohang University of Science and Technology (POSTECH) in Pohang, South Korea. http://ibb.mpstation.net/m2/index3.html The successful applicants for these positions will be involved the establishment of a new laboratory in newly renovated research space with research opportunities to study post-translational processes, in particular phosphorylation, controlling the circadian system in Arabidopsis. There will also be the opportunity to initiate new genetic screens probing into the fundamental properties of the circadian clock. The lab will be housed in a building sharing growth facilities and other resources with excellent, well-established plant molecular groups at POSTECH, along with newly established labs in membrane biophysics and chemical biology of protein-protein and lipid-protein interactions. This is an excellent opportunity for Korean nationals interested in initiating a career path in plant science in South Korea, but is not limited to such individuals. Expertise in biochemistry, proteomics and molecular biology is highly desirable. Previous experience with Arabidopsis research is not a requirement, but very useful. Ability to work independently and coordinately will be an important asset. Highly motivated individuals with excellent English and Korean language and communication skills are strongly encouraged to apply. These positions are available in early March 2010, but there is the possibility of preliminary training and orientation at Ohio State University prior to positioning at POSTECH. Starting yearly salary for post-docs will be 25,000,000 KRW to 35,000,000KRW depending on experience; 20,000,000 to 25,000,000 KRW for technicians. Interested applicants should send inquires and their CV, a statement of research interests and career goals to the below address. Email attachments are preferred. Dr. David E. Somers Department of Plant Cellular and Molecular Biology Ohio State University/ Division of Integrative Biosciences and Biotechnology Pohang University of Science and Technology (POSTECH) somers.24@osu.edu http://www.biosci.ohio-state.edu/pcmb/osu_pcmb/people_faculty_somersDavid.php From acn from stowers.org Wed Oct 14 09:49:36 2009 From: acn from stowers.org (Noll, Aaron) Date: Wed Oct 14 11:41:11 2009 Subject: [Arabidopsis] Specific centromeric genomic coordinates for Arabidopsis Thaliana In-Reply-To: <000e01ca42f4$6c25a3e0$4470eba0$@edu> Message-ID: Hello, I haven't been able to find a source for the specific coordinates of the centromeric regions for Arabidopsis Thaliana. I have found the regions CEN1,CEN2,CEN3 PT.2OF3, CEN3 PT.30F3, CEN3 PT.10F3, CEN4 and CEN5. I am not certain if these are the true centromere regions for the five chromosomes however. Could anyone advise or point me in the right direction? I am a newbie to the Arabidopsis community so I apologize if this is an absurd question. Thanks, Aaron Noll Stowers Institute for Medical Research Programmer Analyst III From brachypodium from gmail.com Tue Oct 13 14:40:19 2009 From: brachypodium from gmail.com (John Vogel) Date: Wed Oct 14 11:41:40 2009 Subject: [Arabidopsis] Brachypodium positions with CSIRO and the USDA-ARS Message-ID: <742C778D3FD14F14B54AEE4A31E0B026@pcanderson1> Brachypodium positions with CSIRO and the USDA-ARS CSIRO in collaboration with the USDA-ARS is offering three positions- two Postdoctoral Fellowships and a PhD scholarship- to join an international team applying the recently sequenced grass genetic model Brachypodium to developing more efficient food and biofuel crops. Successful candidates will be based at the Black Mountain Laboratories in Canberra, Australia, and have access to state-of-the-art plant measurement technologies at the High Resolution Plant Phenomics Centre in Canberra. They will be part of an international team with Dr. John Vogel and the USDA-ARS in Albany, California. The positions are well-resourced with technical support and funding from the Australian Grains Research and Development Corporation and the US Department of Energy. The research team has access to a diverse collection of natural, mutagenised and transformed genotypes of Brachypodium, and has conducted a detailed analysis of Brachypodium sequenced line Bd21 shoot and root system development to provide the baseline for identifying genotypic variation. See http://www.brachypodium.org/ for information on Brachypodium. 1) Postdoctoral Fellow - Plant Biologist or Root Biologist The successful applicant will use Brachypodium to identify genomic regions associated with root architecture traits that increase water and nutrient uptake in wheat. Wheat lines with diverse architectures have already been identified. (International applicants) Contact: Michelle.Watt@csiro.au Apply online: https://recruitment.csiro.au/asp/job_details.asp?RefNo=2009%2F805 Position reference: 2009/806 2) Postdoctoral fellow - Plant physiology or molecular biology The role of this person is to phenotype diverse genotypes of Brachypodium for variation in traits valuable for biofuel and food crops. These include rapid shoot growth, high tillering, high photosynthetic rates and good water and nutrient use efficiency. (International applicants) Contact: Robert.Furbank@csiro.au Apply online at: https://recruitment.csiro.au/asp/job_details.asp?RefNo=2009%2F803 Position reference: 2009/803 3) PhD Student - Plant Biologist/ Plant Pathologist The goal of this PhD studentship is to apply Brachypodium to identify tolerance or resistance mechanisms to key root diseases of wheat. (Australian applicants only) Contact: Michelle.Watt@csiro.au Apply online: https://recruitment.csiro.au/asp/job_details.asp?RefNo=2009%2F805 Position reference: 2009/805 These three positions provide strong career development, high chance for novel discovery for publications, and opportunities to attend international conferences. Deadline for all applications: November 8 2009. John Vogel, Ph.D. Research Molecular Biologist Western Regional Research Center U.S. Department of Agriculture 800 Buchanan Street Albany, CA 94710 USA Voice: (510) 559 6117 FAX: (510) 559-5818 From phoebe from deakin.edu.au Thu Oct 15 18:35:40 2009 From: phoebe from deakin.edu.au (PHOEBE CHEN) Date: Thu Oct 15 19:35:23 2009 Subject: [Arabidopsis] APBC2010 Call for Posters - Tue 20 Oct 2009 Message-ID: <000a01ca4df0$3582ba10$a0882e30$@edu.au> Dear Colleagues, We apologize if you receive multiple copies of this call for posters. Please distribute it to your colleagues. Regards, Organizing Committee of APBC2010 ------------ CALL FOR POSTERS (APBC 2010) The Eighth Asia Pacific Bioinformatics Conference (APBC2010) 18-21 Jan, 2010, Bangalore, India http://cs.nyu.edu/parida/APBC2010/index.html Please consider to submit a poster in the conference. The deadline for Posters submission is 20 Oct, 2009 The details of the call for posters can be found here: http://cs.nyu.edu/parida/APBC2010/posters.html We are looking forward to meeting you in Bangalore. Organizing Committee of APBC2010 Conference chairs Laxmi Parida, IBM T.J. Watson Research Center, USA Ramanathan Sowdhamini, National Centre for Biological Sciences, India Program committee chairs Gene Myers, HHMI, Janelia Farm, USA Laxmi Parida, IBM T.J. Watson Research Center, USA From josette.masle from anu.edu.au Fri Oct 16 06:49:51 2009 From: josette.masle from anu.edu.au (Josette Masle) Date: Fri Oct 16 12:31:14 2009 Subject: [Arabidopsis] 2 Postdoctoral positions at ANU, Research School of Biology, Canberra Message-ID: <960876F2A519489E9A0F34BA862E2150@rsbsjosette> 2 Postdoctoral positions at ANU, Research School of Biology Two post-doctoral positions are available immediately in the laboratory of Dr Josette Masle, at the Research School of Biology, The Australian National University, Canberra. The successful candidates will join a grant funded research program aimed at identifying and characterising regulatory networks controlling plant growth and the plasticity of root development. POSITION 1- The successful applicant will investigate the function of the plant TCTP protein in the regulation of cellular growth and proliferation and the coordinated development of roots and shoot, using both Arabidopsis and cereals as model systems. We are particularly interested in elucidating the role of TCTP in the interplay between endogenous and exogenous signals during development under changing environmental conditions. The project follows from our recent work in Arabidopsis (Berkowitz et al.2008, Plant Cell, 20:3430-3447) where TCTP was identified as a controller of seedling growth, root development and tip growth and a likely mediator of TOR activity as in non-plant eukaryotes. The ideal candidate should have a strong background and demonstrated experience in the area of gene regulation, signal transduction and cell/developmental biology. Experience in genetics and bioinformatics would be valuable. POSITION 2 relates to the role of phospholipids and lipid signalling in plant development and root function. We are specifically interested in phosphoethanolamine N-methyltransferase (PEAMT) enzymes which in plants is thought to exert a major control on the de novo synthesis of phosphatidylcholine, the dominant membrane phospholipid as in most eukaryotes. We have identified a novel PEAMT isoform in wheat and demonstrated specificity within the family as well as novel regulatory processes of PEAMTs (Jost et al. 2009, JBC in press). The successful applicant will further investigate the function and regulation of plant PEAMTs using a combination of genetic, biochemical and physiological tools and genetic material readily available in my lab, including for a comparative genomic approach between cereals and model organisms. Strong background and demonstrated experience in biochemistry and in molecular genetics, including protein biochemistry are required. Experience in research related to stress signalling and/or cell biology would be an advantage. Both positions are for 3 years. Enquiries: Josette Masle, Tel: +61 2 6125 4410, Email: Josette.Masle@anu.edu.au Interested applicants should apply on line. Further information on the positions and selection criteria are also available on line: http://jobs.anu.edu.au/PositionDetail.aspx?p=921 for position 1, reference # A395-09TG http://jobs.anu.edu.au/PositionDetail.aspx?p=922 for position 2, reference # A394-09TG Josette Masle Research School of Biology College of Medicine, Biology and the Environment The Australian National University GPO Box 475 Canberra ACT2601 Australia Tel +61 2 6125 4410 http://www.rsbs.anu.edu.au/Profiles/Josette_Masle/ From SSubramanian from danforthcenter.org Fri Oct 16 12:30:32 2009 From: SSubramanian from danforthcenter.org (Subramanian, Senthil) Date: Fri Oct 16 12:31:57 2009 Subject: [Arabidopsis] Post-Doctoral Associate position to study miRNAs and nodule development (@ SDSU, Brookings, SD) Message-ID: <2EADE1E4101A0A4C8C0FC7212071A9F868502F68@mail2.ddpsc.org> Post Doctoral Associate - miRNAs in nodulation A post doctoral associate position to study the role of miRNAs and auxin si= gnaling during symbiotic nodule development is available in the Department = of Plant Science at South Dakota State University, Brookings, SD. Species-s= pecific association between legumes and rhizobia bacteria leads to the deve= lopment of nitrogen-fixing root nodules. The role of miRNA-regulated auxin = signaling in nodule development is largely unknown (See Subramanian et al. = 2008 BMC Genomics 9: 160; Simon et al. 2009 Plant Physiol). Dr. Subramanian= =92s lab is interested in understanding this process using a combination of= genomic and molecular approaches. The position offers excellent opportunities for training in plant-symbiont = interactions, hormone physiology, molecular biology, microscopy and genomic= s. The ideal candidate would possess a recent Ph.D. degree in plant science= or related area, be self-motivated with a desire to learn novel research t= echniques, have the ability to perform laboratory experiments in an organiz= ed manner, be efficient in proper documentation of results and be able to c= ommunicate well in English. Expertise in plant and bacterial DNA/RNA isolat= ion, gene expression assays (Northern analysis and qRTPCR), molecular cloni= ng, bacterial and plant culture techniques and fluorescence microscopy is d= esired but not essential. SDSU=92s research facilities include a functional= genomics core, micro-imaging facility with confocal and laser micro-dissec= tion scopes and a mass-spectrometry facility capable of analyzing both prot= eins and small molecules. Other opportunities available for career enhancem= ent include training in undergraduate/graduate teaching, scientific writing= and research presentations. Interested applicants please send a cover letter stating your research inte= rests and a detailed CV that includes list of publications, brief descripti= on of Ph.D. and/or post-doctoral research projects and contact information = for at least three references to Dr. Sen Subramanian (Senthil.Subramanian@s= dstate,edu; Phone: 605-688-5623). A= pplications will be accepted until a suitable candidate is found. Senthil Subramanian, Assistant Professor, Plant Science Department, Office: NPB245D, Lab: NPB137 South Dakota State University, Brookings, SD, 57007 Phone: 605-688-5623 Fax: 605-688-4452 From danabar1 from gmail.com Wed Oct 21 10:26:44 2009 From: danabar1 from gmail.com (Dana Bar) Date: Wed Oct 21 14:12:05 2009 Subject: [Arabidopsis] looking for a ler-o gene sequence Message-ID: I want to compare gene sequences of ler-o and col-o at a specific locus- At2g01170. i couldn't find ler-o sequences at TAIR, NCBI or TIGR. any suggestions? From whairong from gmail.com Tue Oct 20 18:41:44 2009 From: whairong from gmail.com (hairong wei) Date: Wed Oct 21 14:12:26 2009 Subject: [Arabidopsis] MS. assistantship in Bioinformatics Message-ID: <673936200910201641w5989445di3a6446447bb76183@mail.gmail.com> A graduate research assistantship at the MS level is available in the laboratory of Dr. Hairong Wei (http://forest.mtu.edu/faculty/wei/) at School of Forest Resources & Environmental Science, Michigan Technological University (MTU) to develop novel computational approaches for inferring gene function with microarray data from poplar. In addition, the candidate will develop web applications (tools) using JSP, or PHP, and MySQL. Applicants should have interest in developing a career in bioinformatics/systems biology. Those who have skills and experience in at least one of the following two areas are encouraged to apply: Computer programming (web application), gene expression data analysis. Strong ability in data manipulation using programming languages like R/SAS, perl, java, and C is anticipated. The candidate should possess the ability to work independently and the attitude to work cooperatively in a team environment. A background in either machine learning or molecular biology will be a plus, though not a requirement. *Expected start date: January, 2010 * Interested candidates should send a resume highlighting their experience and interests, GRE scores (TOEFL is required for international students), and names and email addresses of three references to Dr. Hairong Wei ( hairong@mtu.edu) From June.Medford from ColoState.EDU Thu Oct 22 10:42:27 2009 From: June.Medford from ColoState.EDU (Medford,June) Date: Thu Oct 22 12:06:33 2009 Subject: [Arabidopsis] Post Doctoral Positions Message-ID: <1614CC49B128F3428A42BD11A67E466B7725DE4AC0@EVS3.ColoState.EDU> POST-DOCTORAL POSITIONS Multiple positions in the areas of: ? Plant Cell Biology ? Protein Stability ? Signal Transduction ? Synthetic Biology ? Protein Structure and Function Join a dynamic group working on cutting-edge approaches in Plant Molecular Biology and Synthetic Biology. Synthetic Biology is an exciting and broad approach using rational and computational design of genes, proteins and genetic systems for a specific purpose (Basu et al., 2005; Bio et al., 2006; Bowen et al., 2008; Das and Baker, 2008). Synthetic Biology brings the accuracy of electrical and computer engineering to plant molecular biology and design of new plant traits. One example, it is possible to control what is sensed in plants with computer designed receptors. Synthetic Biology work has produced programmable three- dimensional pattern formation and spatiotemporal control of cell signaling. We have been using synthetic biology to re-design plants with useful traits and understand fundamental question about natural processes. We are expanding plant synthetic biology to broader areas such as those described for yeast and bacteria. For example, we provide input with computer designed receptors that activates a plant synthetic signal transduction pathway. Normal signal transduction is not a linear process but instead involves interactions with numerous components and pathways allowing fine-tuning of a response to a specific cell, tissue, developmental stage or environment. To begin to dissect complex signal transduction processes we built a synthetic system (Antunes et al., 2009b; Antunes et al., 2009a) and are using the tools of synthetic biology to further the approach. Because our system is constructed of modular and standardized parts we can re-assemble the system to ask how native molecules work. For details please see: http://rydberg.biology.colostate.edu/sites/medfordlab/ . The synthetic signal transduction system or biological input-output pathway is directed to producing a specific output. The output could accumulation of biofuels, flowering or a visual response. Our system is modular and by making chimeric molecules (e.g., synthetic::natural) we are able dissect fundamental processes normally used by plants. These are competitive positions for Post-doctoral Associates and Research Associates and offer generous salaries. Applicants must be U.S. citizens. The successful candidate will join a dynamic group applying synthetic biology to plants. In addition to the above, because we believe any new technology should have a positive impact on the environment we collaborated with PrecisionBiosciences (http://www.precisionbiosciences.com/) , and computationally re-designed proteins to produce a means to target T-DNAs and remove unwanted DNA (e.g., herbicide and antibiotic resistant genes). For post-doctoral positions, a Ph.D. in molecular biology, cell biology plant molecular biology or a related field is required. Ideal applicants will have experience in molecular biology, plant cell biology or gene cloning. Experience with transgenic plants is helpful but not essential. Well developed skills in written and verbal communication are desirable. The incumbents are expected to interact with other post-docs, graduate students, and undergraduate students. Duties include a variety, molecular biology techniques, cell biology studies, synthetic gene construction, bacterial expression, production and analysis of transgenic plants, planning experimental approaches based on research literature, and interpreting results. The successful individuals will be self-motivated and capable of independent thought and research. The Medford lab is located in the Biology Department at Colorado State University in Fort Collins, Colorado. Fort Collins is a city of 130,000 located at the base of the Rocky Mountains about an hour north of Denver. Colorado boasts 300+ sunny days a year and numerous recreational activities exist from the nearby mountains such as world class skiing and hiking. Please apply at: http://www.biology.colostate.edu/employment.html Click on the link for Post-Doctoral Associate or Research Associate Open pool. Indicate attention to Dr. June Medford. Antunes, M.S., Morey, K.J., Tewari-Singh, N., Bowen, T.A., Smith, J.J., Webb, C.T., Hellinga, H.W., and Medford, J.I. (2009a). Engineering key components in a synthetic eukaryotic signal transduction pathway. Mol Syst Biol 5, 270. Antunes, M.S., Morey, K.J., Smith, J.J., Albrecht, K.D., Bowen, T.A., Zdunek, J.K., Troupe, J.F., Cuneo, M.J., Webb, C.T., Hellinga, H.W., and Medford, J.I. (2009b). Computationally-designed receptors and synthetic signal transduction allow plants to serve as detectors for human and environmental use. (in review). Basu, S., Gerchman, Y., Collins, C.H., Arnold, F.H., and Weiss, R. (2005). A synthetic multicellular system for programmed pattern formation. Nature 434, 1130-1134. Bio, F.A.B.G., Baker, D., Church, G., Collins, J., Endy, D., Jacobson, J., Keasling, J., Modrich, P., Smolke, C., and Weiss, R. (2006). Engineering life: building a fab for biology. Sci Am 294, 44-51. Bowen, T.A., Zdunek, J.K., and Medford, J.I. (2008). Cultivating plant synthetic biology from systems biology. New Phytol 178, 583-587. Das, R., and Baker, D. (2008). Macromolecular modeling with rosetta. Annu Rev Biochem 77, 363-382. From mja18 from psu.edu Wed Oct 21 15:30:55 2009 From: mja18 from psu.edu (Michael Axtell) Date: Thu Oct 22 12:06:43 2009 Subject: [Arabidopsis] Faculty Position in Plant Biology at Penn State University Message-ID: The Department of Biology at The Pennsylvania State University invites applications for tenure-track faculty positions at the Assistant, Associate, or Full Professor level in Plant Biology, with research programs in molecular, cellular, and/or developmental aspects of plant biology. We particularly encourage applications from individuals whose work is related to energy storage in plants (including carbon partitioning; synthesis of cell walls, starch and lipids; and genetic control of these metabolic pathways) as well as other areas related to the physiology and development of land plants. Penn State is an international center for plant biology research, with particular emphases in cell biology, development, genomics, ecology, and evolution. Penn State has an outstanding interdisciplinary plant biology graduate program (http://www.huck.psu.edu/education/plant-biology ), excellent plant growth facilities, and a number of core resources that provide research support (http://www.huck.psu.edu/facilities), including bioimaging, molecular biology, genomics, and proteomics. Interaction with existing research programs is particularly encouraged. Prospective candidates should have a strong record of research accomplishments, ability to secure extramural grants, and a commitment to teaching undergraduates. Candidates should email a letter of application, curriculum vitae, research prospectus, statement of teaching interests, and names and contact information of at least three references, all as a single PDF document, to plantenergy4@bio.psu.edu . Publications and manuscripts (not more than three) may also be submitted as separate PDF documents along with the application. Review of completed applications will begin November 23, 2009. Penn State is committed to affirmative action, equal opportunity and the diversity of its workforce. Michael J. Axtell, Ph.D. Assistant Professor of Biology 410 Life Sciences Bldg. Pennsylvania State University University Park, PA 16802 USA PH: 814-867-0241 http://www.bio.psu.edu/people/faculty/Axtell/AxtellLab/ From Antony.Martin from newcastle.edu.au Wed Oct 21 19:53:09 2009 From: Antony.Martin from newcastle.edu.au (Antony Martin) Date: Thu Oct 22 12:06:49 2009 Subject: [Arabidopsis] Removal of the lower epidermal layer from mature rosette leaves? Message-ID: <4AE047A902000086000391AC@WINDOMPRD00.newcastle.edu.au> Dear Arabidopsis community, We are looking for a method to conveniently remove the lower epidermal layer (and preferably mesophyll) from mature rosette leaves. This is for a high throughput screen so the procedure needs to be relatively simple. We have tried floating leaves o/n on pectinase or physically peel away the epidermis, but the latter is way too tedious for the numbers of leaves we need to process. Scraping on fine sandpaper has not worked for us either. If anyone has ideas or proven methods we would be glad to hear. Thanks, Antony From jaiswalp from science.oregonstate.edu Thu Oct 22 14:10:34 2009 From: jaiswalp from science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Thu Oct 22 17:37:20 2009 Subject: [Arabidopsis] IPMB Gramene and Plant Ontology workshop Message-ID: <4AE0AE2A.1020501@science.oregonstate.edu> Dear IPMB Congress participants, We would like to invite the attendees of the 9th International Plant Molecular Biology (IPMB) Congress (http://www.ipmb2009.org/) to be held from October 25-30, 2009 in St. Louis, MO, USA to the Gramene Database and Plant Ontology Workshop. The workshop is free and open to everyone. Time: Monday October 26, 6-9pm Location: Room # 104/105 @ the meeting venue Workshop Title: Comparative Plant Genomics with the Gramene database and Plant Ontology project Schedule: 6-7pm: GRAMENE (www.gramene.org) -Get familiar with Gramene Database -How Gramene can help in your research -Questions and Answers 7-8pm: PLANT ONTOLOGY (www.plantontology.org) -Get familiar with Plant Ontology (PO) resource -How can PO resource help you -Questions and Answers 8-9pm: Discussion with the community of interested researchers and their participation in building community based curation network. - Plant Gene Wiki - Metabolic and regulatory Networks - Your feedback and interests. -- Pankaj Jaiswal Web: www.gramene.org www.plantontology.org From libra from qatar.net.qa Thu Oct 22 08:12:57 2009 From: libra from qatar.net.qa (Abdul Aziz) Date: Thu Oct 22 17:38:10 2009 Subject: [Arabidopsis] Plant culture vessels for arabidopsis Message-ID: <0KRX002MX3JD4600@nile.qatar.net.qa> I am looking for Plant cell culture vessels with specific dimensions to grow Arabidopsis plants. They were available with SIGMA as Phytacon Vessel with lid (product number P5557), clear polypropylene, Autoclavable with dimensions as Rim approx. 116 mm diam. (approx. 4-1/2 in.) Base 86 mm diam. (3-3/8 Size: H 140 mm. However, Sigma has discontinued this particular product. Please suggest me an equally good product (which stands repeated autoclaving) from other companies in US. Thank you. Surekha Dear Surekha I refer back to your above stated requirements.Please advise if you got the products are not.If still interested..I can provide you further details. Abdul Aziz M.Yousuf From gj32 from cornell.edu Sat Oct 24 21:08:50 2009 From: gj32 from cornell.edu (Georg Jander) Date: Sun Oct 25 13:47:20 2009 Subject: [Arabidopsis] Postdoc position: plant-insect interactions Message-ID: <6.2.5.6.2.20091024215939.04eeb848@cornell.edu> A postdoctoral position is available to study plant-insect interactions in Georg Jander's lab at the Boyce Thompson Institute. Genetic, biochemical, and insect behavior research approaches will be used to study natural variation in maize resistance to aphids and rootworms. Responsibilities of the successful applicant will include the design and implementation of laboratory and field experiments related to maize-insect interactions. Development of additional areas of interest within the scope of the project is encouraged. The research will also involve close interactions with engineers at Cornell University who are developing automated insect detection systems for laboratory and agricultural applications. The position will be filled as early as January, 2010, and funding is available for three years. Candidates with backgrounds in genetic mapping and quantitative genetics are particularly encouraged to apply. The Boyce Thompson Institute is a private not for profit research organization located on the campus of Cornell University in the scenic Finger Lakes region of upstate New York. Information about the institute and its facilities can be found at http://bti.cornell.edu. BTI is an equal opportunity employer. If interested, please send a description of prior research experience, career goals, curriculum vitae, and contact information for three references to: Georg Jander, Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA; email: gj32@cornell.edu; phone: (607) 254-1365. ********************************************************* Georg Jander Boyce Thompson Institute for Plant Research Tower Road Ithaca, NY 14853 gj32@cornell.edu Phone: 607-254-1365 FAX: 607-254-1502 http://bti.cornell.edu/jander/ From nuria from email.unc.edu Sat Oct 24 11:01:35 2009 From: nuria from email.unc.edu (Nuria Sanchez Coll) Date: Sun Oct 25 13:47:52 2009 Subject: [Arabidopsis] fluorescent protein vectors Message-ID: <4AE324DF.3080902@email.unc.edu> Hi, I'm looking for a pDONR P2R-P3 vector or a binary vector without promoter containing a C-terminal fluorescent tag other than YFP or GFP. Thanks Nuria -- ************************** Nuria Sanchez Coll, PhD. Dangl Lab Dept. of Biology, CB#3280 Coker Hall Rm. 108 Univ of North Carolina Chapel Hill, NC 27599-3280 Phone 919-962-5838 Fax 919-962-1625 From ekatz from ucdavis.edu Fri Oct 23 22:30:02 2009 From: ekatz from ucdavis.edu (Ehud Katz) Date: Sun Oct 25 13:48:33 2009 Subject: [Arabidopsis] Arabidopsis cDNA expression library for yeast needed Message-ID: Hi all, We are looking for Arabidopsis cDNA expression library for yeast driven by GAL promoter (or any other inducible promoter), preferably one enriched with low abundant cDNAs . If anyone knows where I can find it or if you have one, please drop me a line. Any help will be appreciated. Thank you, udi ------------------------------------------------- Ehud Katz Postdoctoral fellow Department of Plant Sciences, Plant Reproductive Biology, Mail Stop 5 University of California One Shields Ave, Davis, CA 95616 e-mail: ekatz@ucdavis.edu From carolina.mueller from tuebingen.mpg.de Tue Oct 27 06:31:24 2009 From: carolina.mueller from tuebingen.mpg.de (Carolina Mueller) Date: Wed Oct 28 10:48:30 2009 Subject: [Arabidopsis] Job posting Message-ID: To whom it corresponds, Find below the description of our job offer with kindly request to post it in the Arabidopsis Bionet: International PhD Program Tuebingen, Spring 2010 The Max Planck Institute for Developmental Biology and the Friedrich Miescher Laboratory in Tuebingen, Germany, invite applications for PhD positions in: Evolutionary Biology, Ecological Genomics, Developmental Genetics, Animal Development , Plant Development, Quantitative Genetics, Molecular & Cell Biology, Biochemistry, Structural Biology and Bioinformatics Highly qualified applicants from all countries are invited to apply. All applicants must hold or anticipate receiving a Diploma or Masters degree by the time of their start as a PhD student at our institutes. Candidates have to be fluent in written and spoken English. The positions are funded by Max Planck Fellowships. Application form, evaluation forms (2 needed) and all details about our online registration are available at www.eb.mpg.de/phd-program Application deadline is November 25, 2009. After the review of completed applications selected candidates will be invited for personal interviews in Tuebingen during February 10-12, 2010. Thanking you for the posting in advance! With kind regards, Carolina M?ller Dr. Carolina M?ller, PhD Program Coordinator Tel: +49 7071 601 1354 Fax: +49 7071 601 1353 E-mail: carolina.mueller@tuebingen.mpg.de PhD Program Office Max Planck Institute for Developmental Biology Spemannstr. 35; 72076 T?bingen http://www.eb.tuebingen.mpg.de/phd-program Dr. Carolina M?ller, PhD Program Coordinator Tel: +49 7071 601 1354 Fax: +49 7071 601 1353 E-mail: carolina.mueller@tuebingen.mpg.de PhD Program Office Max Planck Institute for Developmental Biology Spemannstr. 35; 72076 T?bingen http://www.eb.tuebingen.mpg.de/phd-program From gj32 from cornell.edu Tue Oct 27 00:05:00 2009 From: gj32 from cornell.edu (Georg Jander) Date: Wed Oct 28 10:48:58 2009 Subject: [Arabidopsis] postdoc position: Arabidopsis-aphid interactions Message-ID: <50152.96.35.128.57.1256619900.squirrel@webmail.cornell.edu> A postdoctoral position is available to study interactions between Arabidopsis and Myzus persicae (green peach aphid) in Georg Jander?s lab at the Boyce Thompson Institute. The focus of this research is the functional analysis of aphid saliva, with particular emphasis placed on identifying salivary effectors that either facilitate insect feeding or elicit plant defense responses. Other research will include analysis of mutants and natural variation in Arabidopsis aphid resistance. Development of additional areas of interest within the scope of the project is encouraged. The position will be filled as early as January, 2010, and funding is available for two years. Candidates with backgrounds in molecular biology, insect behavior assays, or small molecule analysis are particularly encouraged to apply. The Boyce Thompson Institute is a private not for profit research organization located on the campus of Cornell University in the scenic Finger Lakes region of upstate New York. Information about the institute and its facilities can be found at http://bti.cornell.edu. BTI is an equal opportunity employer. Please send a description of prior research experience, career goals, curriculum vitae, and contact information for three references to: Georg Jander, Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA; email: gj32@cornell.edu; phone: (607) 254-1365. From yuval.kaye from mail.huji.ac.il Mon Oct 26 04:44:06 2009 From: yuval.kaye from mail.huji.ac.il (Yuval Kaye) Date: Wed Oct 28 10:49:30 2009 Subject: [Arabidopsis] LR Gateway reaction pENTR223.1-Sfi-ORF in to pK7WGF2- problem Message-ID: <27e1240f0910260244gdcdb3d7k2a7cabd5e90dec7f@mail.gmail.com> My question is did any of you had a problem doing the LR reaction (gateway recombination) with the* *pENTR223.1 Sfi-ORF (from ABRC) and the* *pK7WGF2 (or any other Gateway Destination vector). If you had this problem how did you solve it? Thanks -- Yuval Kaye Department of Plant & environmental Sciences Institute of Life Sciences The Hebrew University of Jerusalem Givat Ram, Jerusalem, 91904, Israel E-Mail:yuval.kaye@mail.huji.ac.il