From jdfriesner from ucdavis.edu Tue Feb 3 11:35:08 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Tue Feb 3 12:37:45 2009 Subject: [Arabidopsis] NAASC election participation Message-ID: <200902031635.n13GZ82E023458@phaenicia.ucdavis.edu> Dear North American Arabidopsis Researchers, We are requesting your participation in nominating two new members of the North American Arabidopsis Steering Committee (NAASC). To participate, first register with TAIR (if you haven’t already): http://www.arabidopsis.org/servlets/Community?action=login (Forgot if you are registered with TAIR? Go to http://www.arabidopsis.org/servlets/Community?action=remind, type in your last and/or first name, hit search. Choose your name from the list and log-in to verify your current email address on file. You can have also your information emailed to you, or register as a new user.) Election Procedure: -An email asking for nominations will be sent to registered North American TAIR members on or around February 16, 2009. -The nomination deadline is March 17, 2009. Once nominees are confirmed an email will be sent on 4/1/2009 asking you to vote for up to 2 names on the nomination list (via a secure TAIR webpage). -The voting deadline is May 1, 2009. -The top 2 candidates will be contacted and their willingness to serve confirmed. Winners will be announced around the middle of May. Without the efforts of the NAASC, organization of the Arabidopsis Conference and funding to attend the annual Arabidopsis conference for young scientists and underrepresented minorities would be jeopardized. NAASC also represents North America to the international community. Service on the NAASC is important and highly appreciated. Two members that rotate off NAASC this year need to be replaced and we need community members to first nominate good Arabidopsis community candidates and then vote for those who agree to stand. NAASC officers currently are (listed in order of most to least seniority): Joe Kieber (UNC-Chapel Hill), Xuemei Chen (UC Riverside), Julian Schroeder (UC San Diego), Caren Chang (Univ. of Maryland), George Haughn (Univ. of British Columbia, Scott Poethig (Univ. of PA-Philadelphia), Jane Glazebrook (University of Minnesota-St. Paul), and Mark Estelle (UC San Diego). Their service to the community is much appreciated. 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 solicits funds to help North American junior scientists and minorities 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. -The NAASC contributes to the annual progress report on international Arabidopsis research efforts. 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. Best regards, Joanna Friesner MASC/NAASC Coordinator UC Davis From walterjackson91 from gmail.com Tue Feb 3 11:23:36 2009 From: walterjackson91 from gmail.com (Walter Jackson) Date: Tue Feb 3 12:38:30 2009 Subject: [Arabidopsis] Paper submission deadline extended: MULTICONF-09 Message-ID: <2508df7d0902030823g13e97f82x886a0391ffe05b4@mail.gmail.com> Paper submission deadline extended: MULTICONF-09 The deadline for draft paper submission at the 2009 Multi Conference in Computer Science, Information Technology and Control systems and Computational Science and Computer Engineering (MULTICONF-09) (website: http://www.PromoteResearch.org ) is extended due to numerous requests from the authors. The conference will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. The event consists of the following conferences: ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ? International Conference on Automation, Robotics and Control Systems (ARCS-09) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ? International Conference on Information Security and Privacy (ISP-09) ? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ? International Conference on Software Engineering Theory and Practice (SETP-09) ? International Conference on Theory and Applications of Computational Science (TACS-09) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) The website http://www.PromoteResearch.org contains more details. Sincerely Walter Jackson Publicity committee From zleblanc from uoguelph.ca Tue Feb 3 18:47:58 2009 From: zleblanc from uoguelph.ca (Zacharie LeBlanc) Date: Tue Feb 3 19:38:14 2009 Subject: [Arabidopsis] RNA extraction from dry seed Message-ID: Hi all, I'm trying to extract RNA from dry Arabidopsis seeds in order to do some expression profiling. I'm currently using a homogenizer in order to grind 0.1 grams of seeds then use the protocol given along with Plant RNA Reagent by Invitrogen. verification of my product on a 0.1% agarose gel hasn't yielded any positive results yet. any thoughts? -Zach LeBlanc From yuanqing from ualberta.ca Tue Feb 3 19:50:59 2009 From: yuanqing from ualberta.ca (yuanqing@ualberta.ca) Date: Tue Feb 3 19:56:57 2009 Subject: [Arabidopsis] RNA extraction from dry seed In-Reply-To: References: Message-ID: <20090203175059.66353x6ezt0k1y0w@webmail.ualberta.ca> Hi, Most kits do not work with dry seeds, in my view. I ever extracted total RNA from dry At seeds using the following protocol and got RNA comparable to young tissue RNA extracted using Qiagen Plant RNeasy mini kit. Good luck! Suzuki Y, Kawazu T, Koyama H (2004) RNA isolation from siliques, dry seeds, and other tissues of Arabidopsis thaliana. Biotechniques 37:542?544 Quoting "Zacharie LeBlanc" : > Hi all, I'm trying to extract RNA from dry Arabidopsis seeds in order to do > some expression profiling. I'm currently using a homogenizer in order to > grind 0.1 grams of seeds then use the protocol given along with Plant RNA > Reagent by Invitrogen. verification of my product on a 0.1% agarose gel > hasn't yielded any positive results yet. any thoughts? > -Zach LeBlanc > _______________________________________________ > Arab-gen mailing list > Arab-gen@net.bio.net > http://www.bio.net/biomail/listinfo/arab-gen > > From edwin.reidel from nunhems.com Wed Feb 4 13:33:35 2009 From: edwin.reidel from nunhems.com (Edwin Reidel) Date: Wed Feb 4 14:17:20 2009 Subject: [Arabidopsis] RE: RNA extraction from dry seed Message-ID: It's hard to beat the modified hot borate buffer developed for RNA extraction from cotton seeds by Wan & Wilkins: Analytical Biochemistry: 223(1): 7-12. Also check the citing papers for further modifications significantly simplifying their protocol, especially Wu et al. (Plant Molecular Biology Reporter. 20(3): 213-218) I routinely extracted intact, high-purity RNA from various plant tissues with the hot borate buffer. Regards, Edwin J. Reidel Scientist, Seed Production Research Nunhems USA, Inc. _______________________________________________________________________________________________ The information contained in this e-mail is for the exclusive use of the intended recipient(s) and may be confidential, proprietary, and/or legally privileged. Inadvertent disclosure of this message does not constitute a waiver of any privilege. If you receive this message in error, please do not directly or indirectly use, print, copy, forward, or disclose any part of this message. Please also delete this e-mail and all copies and notify the sender. Thank you. For alternate languages please go to http://bayerdisclaimer.bayerweb.com _______________________________________________________________________________________________ From jdfriesner from ucdavis.edu Wed Feb 4 13:24:55 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Wed Feb 4 14:17:43 2009 Subject: [Arabidopsis] 2009 Arabidopsis Conference - Keynote Announced and Abstract Submission Open Message-ID: <200902041824.n14IOt4r007001@xylocopa.ucdavis.edu> Dear All We are pleased to announce that abstract submission for the 20th International Conference on Arabidopsis Research is now open at http://arabidopsis2009.com/ The 20th Anniversary meeting will take place 30th June - 4th July 2009 in the historic and vibrant city of Edinburgh, Scotland, UK. The keynote speaker at ICAR 2009 will be the Lasker Prize winning scientist Prof. David Baulcombe. We also have a great programme of world-renowned speaker confirmed including Enrico Coen, Caroline Dean, Joe Ecker, Jiri Friml, Nicholas Harberd, Alistair Hetherington, Andrew Millar, Ben Scheres, Mark Stitt and Jian-Kang Zhu. For a full programme visit http://arabidopsis2009.com/programme.html and http://arabidopsis2009.com/speakers.html The conference will consist of two plenary sessions each morning and four concurrent sessions each afternoon, which will include presentations chosen from submitted abstracts. As in the past, the conference will feature a number of community-led workshops that will provide opportunities for focused discussion, whilst three poster sessions will provide ample time for research discussion. Delegates will also have a free afternoon between the Friday morning sessions and evening poster session to engage in networking, scientific discussion and to explore Edinburgh and its surroundings. If you would like to hold a community workshop please see the instructions at http://arabidopsis2009.com/workshops.html Important Deadlines Discounted Early Registration Fee Closes 27th March 2009 Oral Abstract Submission Closes 1st April 2009 Poster Abstract Submission Closes 1st May 2009 Regular Registration Closes 15th June 2009 We look forward to seeing you in Edinburgh. Ruth Bastow On Behalf of the UK Organising Committee From marie-theres.hauser from boku.ac.at Wed Feb 4 11:17:45 2009 From: marie-theres.hauser from boku.ac.at (Marie-Theres Hauser) Date: Wed Feb 4 14:18:10 2009 Subject: [Arabidopsis] Use of different LUC systems in Arabidopsis? Message-ID: <4989CDB9020000460002A069@gwia1.boku.ac.at> Dear Arabidopsis newsgroup members, I am wondering if anyone has experience with different luciferase systems. I am particularly interested in the Renilla and the novel secreted Metridia luciferase which was optimized for animal systems. Thanks for your help Marie-Theres Dr. Marie-Theres Hauser Department of Applied Genetics and Cell Biology BOKU - University of Natural Resources and Applied Life Sciences, Vienna Muthgasse 18 A-1190 Vienna Austria/EUROPE Tel: +43-1-36006-6371 FAX: +43-1-36006-6392 e-mail: marie-theres.hauser@boku.ac.at http://www.boku.ac.at/zag/AG_hauser.htm From procha_ac from yahoo.co.uk Wed Feb 4 04:54:40 2009 From: procha_ac from yahoo.co.uk (P. Rocha) Date: Wed Feb 4 14:18:42 2009 Subject: [Arabidopsis] Wanted info on electrical drill for homogenisation in 1.5 ml tubes Message-ID: <978889.193.qm@web28608.mail.ukl.yahoo.com> Dear colleagues, I am seeking recommendations for purchasing an electrical drill (or similar device) that can be used with plastic "disposable" pestles for homogenisation of soft plant material (usually Arabidopsis leaves) in 1.5 ml tubes. Ideally the machine should: a. Be light enough to be used by hand or that can be safely held on a lab stand b. Allow easy and quick replacement of the pestles (keyless chuck perhaps?) c. Sufficient torque to do the job (and not easily get stuck as it happens with lesser machines) If you have personal successful experience with such wonderful tool I would be grateful if you could let me know its manufacturer and model. Thank you, Pedro Rocha procha_ac@yahoo.co.uk From pdahal from ucdavis.edu Wed Feb 4 14:26:36 2009 From: pdahal from ucdavis.edu (PEETAMBAR DAHAL) Date: Wed Feb 4 14:27:43 2009 Subject: [Arabidopsis] RNA extraction from dry seed In-Reply-To: <20090203175059.66353x6ezt0k1y0w@webmail.ualberta.ca> References: <20090203175059.66353x6ezt0k1y0w@webmail.ualberta.ca> Message-ID: Seeds are special as these carry life to the next generation. So, we have to be extra careful to get RNA out of seeds. Below is our protocol. RNA extraction protocol for seeds 1. Pulverize the seed tissue in LN. Add 7 mL Grinding buffer with 105 ul Beta-mercaptoethanol to 500 mg of seed tissue quickly (without thawing) and vortex well. Can add tiny bit of sea sand from Fisher to help grinding (too much will damage your probe) 2. Homogenize at the highest speed, 1 min each 3 times (Immerse the tube in ice bucket while homogenizing in the hood. Use double gloves, goggles). Pause 1 min between each grinding. 3. Shake the sample for 10-20 minutes at 300 rpm and centrifuge the sample for 20-30 minutes in table top-centrifuge or microplate centrifuge (RT, max speed ) or 6000-8000 g at 4.C (using swinging rotors only). 4. Collect the supernatant (Take out as much supernatant as possible without disturbing the interphase) and add equal volume of phenol : cholorform : isoamyl alcohol (25:24:1)?mix the solution by vortexing for 1 min?then spin for 20-30 min. (RT oK) 5. Collect the supernatant, note the volume, and add equal volume of 4 M LiCl for seeds (1/3 volume of 8M LiCl for other plant parts), mix thoroughly using clean side of parafilm and incubate the sample at ?20C ON. 6. Spin 11,000 g for 30-40 min (4 C). 7. For carbohydrate contamination: Add 0.5 mL of 10 mM Tris pH 8.0 and 50 ?l of 2M KOAc to the pellet. Incubate in ice for 20-30 min min. Spin 11,000 g for 10 min (4 C). Pipet out the supernatant and add 1.3 mL 100% ETOH to the supernatant in 2 mL eppies and incubate at -20 for ON or -80 C for at least 1 h. 8. Spin at 11,000 rpm (14,000Xg) at 4C and wash the pellet with 0.2-0.5mL 80% ETOH. (volume of ETOH should be adjusted based on pellet size). Spin @ 11,000 RPM for 5-10 min at 4 C. Dry the pellet for 20- 25 min at RT in laminar flow hood or use Vacuum for 5-7 min. (ETOH must be removed completely). 9. Dissolve in 50-200 ul DEPC treated water. 10. DNase treatment: (for RT and RT PCR): Follow Turbo DNAse Free (including DNAse inactivating reagent) from Ambion. Grinding Buffer = 15mL of TLE Buffer + 1.2mL of 2M NaOAc, pH 4.0, 15mL of phenol, 3mL chloroform. TLE : 0.18 M Tris,, 0.09 M LiCl, 4.5 mM EDTA, 1% SDS, pH 8.2 with HCl (Current Protocols in Mol Biol, pp 4.3.3) Phenol equilibration.: Melt phenol at 60 C. Transfer onto a clear DEPC treated 1 L bottle and wrap with aluminum foil. Add 0.1% 8-hydroxyquinoline and mix well (anti-oxidant as well as a coloring marker). Add equal volume of 1 M Tris (Make Tris in DEPC water and filter (0.22 ?M) and mix thoroughly. Let it stand in cold and try to remove as much of I M Tris as possible. Then wash 3-4 times with 0.1 M pH 7.0 Tris similarly. (pH of the supn. is around 7.2). pH meter: Immerse pH probe in 7 M GuHCl for 5 min and rinse the probe with room temperature DEPC treated water before checking pH of TLE buffer. Do not immerse the probe into phenol directly, rather check pH of supernatant. Any base or acid more than 1 M is regarded as RNAse free. Notes: I have scaled down the protocol for lettuce seeds and used 7 mL Grinding Buffer for 0.5 g seed in 15 mL polypropylene falcon tubes (do not use polystyrene tubes). Peetambar Dahal -----Original Message----- From: arab-gen-bounces@oat.bio.indiana.edu [mailto:arab-gen-bounces@oat.bio.indiana.edu] On Behalf Of yuanqing@ualberta.ca Sent: Tuesday, February 03, 2009 4:51 PM To: Zacharie LeBlanc Cc: arab-gen@magpie.bio.indiana.edu Subject: Re: [Arabidopsis] RNA extraction from dry seed Hi, Most kits do not work with dry seeds, in my view. I ever extracted total RNA from dry At seeds using the following protocol and got RNA comparable to young tissue RNA extracted using Qiagen Plant RNeasy mini kit. Good luck! Suzuki Y, Kawazu T, Koyama H (2004) RNA isolation from siliques, dry seeds, and other tissues of Arabidopsis thaliana. Biotechniques 37:542?544 Quoting "Zacharie LeBlanc" : > Hi all, I'm trying to extract RNA from dry Arabidopsis seeds in order to do > some expression profiling. I'm currently using a homogenizer in order to > grind 0.1 grams of seeds then use the protocol given along with Plant RNA > Reagent by Invitrogen. verification of my product on a 0.1% agarose gel > hasn't yielded any positive results yet. any thoughts? > -Zach LeBlanc > _______________________________________________ > 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 June.Medford from ColoState.EDU Wed Feb 4 18:18:15 2009 From: June.Medford from ColoState.EDU (Medford,June) Date: Wed Feb 4 19:34:16 2009 Subject: [Arabidopsis] Plant Synthetic Biology Post Doctoral Positions Message-ID: <1614CC49B128F3428A42BD11A67E466B75A39A87DD@EVS3.ColoState.EDU> Plant Synthetic Biology Post-doc Positions Three post-doctoral positions are available in the Medford Lab in the Department of Biology at Colorado State University. Projects include work on the cutting edge field of plant synthetic biology with a focus on synthetic signal transduction, gene circuits for detector plants and sustainable plant-made biofuels. The Medford lab is one of just a few labs, world-wide, to apply synthetic biology to plants. Synthetic biology allows plant biologists to both probe our understanding of natural systems and re-design or re-wire plants systems to produce innovative biotechnological tools (see Bowen et al. 2008, Cultivating plant synthetic biology from systems biology. New Phytol. 178: 583-587). One group has defined synthetic biology as "the engineering of biology: the synthesis of complex, biologically based (or inspired) systems, which display functions that do not exist in nature. This engineering perspective may be applied at all levels of the hierarchy of biological structures-from individual molecules to whole cells, tissues and organisms". Examples of synthetic biology's accomplishments include reprogramming cell morphology, synthetic multi-cellular pattern formation and novel biological functions. In plants, for example, we have used synthetic biology to produce a synthetic signal transduction system and linked rationally designed components so that input from computationally re-designed receptors produces a highly specific detector plants for substances like environmental pollutants or explosives. The synthetic signal transduction system is being used to dissect complex eukaryotic signaling and is being improved to control biological input and output (e.g., perception and response). Also, using computationally re-designed proteins we have, along with a new biotech company, produced the means to removed unwanted DNA sequences such as antibiotic and herbicide resistance genes from plants. A Ph.D. in molecular biology, plant molecular biology or a related field is required. Ideal applicants will have experience in molecular biology, gene cloning and analysis of transgenic plants. Experience in transgene expression and signal transduction in plant systems as well as skills in written and verbal communication are desirable. The incumbents are expected to interact with other post-docs, graduate students, and part-time undergraduate students. Duties include a variety of molecular biology techniques including 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 positions will start as soon as possible. Colorado State University is located in Fort Collins, Colorado a city of 120,000 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 send your curriculum vitae indicating publications, a brief statement of research experience, and names and telephone numbers of three references to Dr. June Medford via email (June.Medford@colostate.edu). For further information, please contact Dr. Medford. For full consideration applications must be received by February 27, 2009 by 5 p.m (local time). Contact Information: Dr. June Medford Department of Biology Colorado State University Fort Collins, CO 80523-1878 Phone: 970-491-7865 FAX: 970-491-0649 Email: June.Medford@colostate.edu Colorado State University is an equal opportunity/affirmative action employer and complies with all federal and Colorado laws, regulations, and executive orders regarding affirmative action requirements in all programs. To assist Colorado State University in meeting its affirmative action responsibilities, ethnic minorities, women and other protected class members are encouraged to apply and to so identify themselves. Colorado State University is committed to providing a safe and productive learning and living community. To achieve that goal, we conduct background investigations for all final candidates being considered for employment. Background checks may include, but are not limited to, criminal history, national sex offender search and motor vehicle history. From pyo6n from virginia.edu Wed Feb 4 15:17:30 2009 From: pyo6n from virginia.edu (Patricia Oikawa) Date: Wed Feb 4 19:34:39 2009 Subject: [Arabidopsis] In need of transgenic Arabidopsis with altered root:shoot ratio Message-ID: Hello, I am a graduate student in need of an Arabidopsis with expression of isopentenyl transferase (IPT) gene in the roots. I need the plants to exhibit drastically reduced root:shoot ratios, or significantly reduced root mass. Does anyone have suggestions? Thank you, Patty Oikawa University of Virginia From Isabelle.Damiani from sophia.inra.fr Fri Feb 6 04:11:26 2009 From: Isabelle.Damiani from sophia.inra.fr (Damiani) Date: Fri Feb 6 12:43:19 2009 Subject: [Arabidopsis] avoiding sample movement in confocal microscope Message-ID: <498BFEBE.4040708@sophia.inra.fr> Dear members, Using confocal microscopy I want to see fluorescence appear after treatment of roots with various solutions. The problem is that the treatment makes the sample move on the slide. Thus, I cannot follow the fluorescence on the same focal plan. Is anybody know how to fix a sample on a slide to avoid all the movements of the sample? Thank you. Isabelle From benholt from ou.edu Fri Feb 6 15:57:23 2009 From: benholt from ou.edu (Holt, Ben F. III) Date: Sat Feb 7 20:01:30 2009 Subject: [Arabidopsis] Wanted info on electrical drill for homogenisation in 1.5 ml tubes In-Reply-To: <978889.193.qm@web28608.mail.ukl.yahoo.com> Message-ID: Hi Pedro, We have had good luck with the Heidolph Overhead Stirrers - they have some pretty fancy models, but we find the stripped down RZR1 model works great for what you want to do. It isn't a keyless chuck, but we do have people that use the plastic pestles all the time and it has tons of torque. I personally prefer to use a stainless steel bit that is cut to the interior shape (bit smaller for buffer and sample) of a 1.5ml Eppendorf tube. For proteins, a quick wipe down is enough between samples. For DNA that will be amplified, we clean the pestle with a kimwipe and water and just make sure we wipe if off while the bit spins with plenty of water and a couple of wipes with clean parts of the kimwipe. Works great. http://www.brinkmann.com/products/stirrer_OH_mechanical_de.asp Good luck, Ben On 2/4/09 3:54 AM, "P. Rocha" wrote: Dear colleagues, I am seeking recommendations for purchasing an electrical drill (or similar device) that can be used with plastic "disposable" pestles for homogenisation of soft plant material (usually Arabidopsis leaves) in 1.5 ml tubes. Ideally the machine should: a. Be light enough to be used by hand or that can be safely held on a lab stand b. Allow easy and quick replacement of the pestles (keyless chuck perhaps?) c. Sufficient torque to do the job (and not easily get stuck as it happens with lesser machines) If you have personal successful experience with such wonderful tool I would be grateful if you could let me know its manufacturer and model. Thank you, Pedro Rocha procha_ac@yahoo.co.uk _______________________________________________ Arab-gen mailing list Arab-gen@net.bio.net http://www.bio.net/biomail/listinfo/arab-gen ======== Ben Holt Assistant Professor University of Oklahoma Department of Botany and Microbiology GLCH Rm 219 770 Van Vleet Oval Norman, OK 73019 Phone (405)325-9018 FAX (405)325-7619 http://www.ou.edu/cas/botany-micro/faculty/holt.html From chatterjee.29 from osu.edu Fri Feb 6 16:18:53 2009 From: chatterjee.29 from osu.edu (Jayanta Chatterjee) Date: Sat Feb 7 20:02:09 2009 Subject: [Arabidopsis] anti-His antibody for plant expressed proteins Message-ID: <200902062118.n16LIsCe011206@defang6.it.ohio-state.edu> Dear all, Can anyone please suggest a decent anti-His antibody to detect His tagged proteins, expressed in plants (mainly tobacco and arabidopsis)? I have tried a few Anti-His antibody from different sources (e.g rabbit anti-His antibody from Invitrogen and Santa Cruz Biotech and mouse anti-His antibody from Agrisera) but could not get specific any signal for my His-tagged proteins in western blots. All antibodies, I tried, were giving a strong signal around 37kDa and a weaker signal around 27 kDa; even in wild type, untransformed plants. Any suggestion will be highly appreciated. Thanks and regards, Jay From hnbjed from yahoo.com Mon Feb 9 01:17:53 2009 From: hnbjed from yahoo.com (hnbjed) Date: Mon Feb 9 16:46:07 2009 Subject: [Arabidopsis] technical replicates vs biological replicates Message-ID: <799163.81904.qm@web111115.mail.gq1.yahoo.com> Hi, =A0 I often saw many research papers, including those in Plant Cell, Plant Phys= iol and Plant J, published results with only 2-3 technical replicates, NO b= iological replicates at all. Obviously, one would get very small standard e= rror with only tech reps. Many, not just some, reseachers even did not perf= orm strict tech rep at all. For example, for quantitative RT-PCR, they just= extracted RNA from one boil rep (they only prepared tissue once) only, and= then ran three parallel rxns, and then say =93data from three replicates..= =94. No body knows what are values of their data. I will certainly doubt th= is and challenge them if I am one of the reviewers. After statistical analy= sis, data from only tech reps are usually significant, cause the SE is smal= l. But if running bio reps, you may find that your data is no longer useful= , cause SE is large and thus p>0.05, then you may not dare to say "under xx= x condition, one gene/mutant is significantly different from the other/wt...". In our lab, we have been performing 3 independent biol reps = (3x3=3D9 measurements), and therefore, I found out that the SE is large eve= n if I tried my best to decrease the variance (judged by eyes) between reps= ...... Our way, of course, put our papers under a rather disadvantageous conditi= on. Everyone want to publish papers in a high-impact journal, but we should= play fairly. =A0 Another thing confusing me is why data with T1 generation (overexpression, = RNAi, and promoter-GUS fusion) was accepted by a recent paper on cell wall = in Plant Cell? I checked a few earlier papers from the same group in a Geor= gia university and was astonished to find out they have been using data fro= m only T1 transgenic plants for their papers in the past years.=A0Is this a= cceptable? In our group, we at least used T2 generation, usually homozygous= T3 generation. =A0 I=A0am afraid to irritate some researchers, but want to=A0expose some pract= ices that I do not agree with to every researcher.=A0 I think for biologica= l experiment, a strict boil reps (at least 2) should be followed.=20 =A0 =0A=0A=0A From procha_ac from yahoo.co.uk Sun Feb 8 23:05:59 2009 From: procha_ac from yahoo.co.uk (P. Rocha) Date: Mon Feb 9 16:46:42 2009 Subject: [Arabidopsis] Summary of replies on electrical drill for homogenisation in 1.5 ml tubes Message-ID: <521584.42090.qm@web28607.mail.ukl.yahoo.com> Hello, Many thanks to those who have sent useful information regarding their choice of and experience with electrical drills for homogenisation of soft plant tissue in 1.5 ml tubes. As several people have asked me to share any replies, here is a summary of them: 1) from Ketan Patel ? I have used this in the past.? The speed is a bit hard to control and you have to be careful about having too much liquid in your 1.5ml eppendorpf tube (liquid can splash out if there is too much).? Once you get the hang of it it is great for grinding tissue frozen in liquid nitrogen in a epp tube.? It worth a try as it is not very expensive.? You might be able to find it online through someone else other than fisher/vwr. Let me know i you have any questions. Fisherbrand* Disposable Pestle System Low-cost alternative to mechanical or metal and glass tissue grinders ?Pestle Grinder System? 03-392-106? Go to fisher's website and search with the catalog number listed above. ? ? ? 2) from Kelly Zimm ? I have used the "pellet pestle" to grind liquid-nitrogen frozen root samples for protein extractions for MUG assays.? It works well and has all the features you're looking for - small, simple pestle replacement, doesn't get stuck... Here's a link from sigma: http://www.sigmaaldrich.com/catalog/ProductDetail.do?N4=Z359971|SIGMA&N5=Product%20No.|BRAND_KEY&F=SPEC ? ? 3) from Deane Falcone ? Hi Pedro:? Although it sounds like you want something smaller, my experience is that, in the end, you might want to go for an inexpensive "bench top" drill.? I've found that smaller portables, which I have mounted to a ringstand, work okay but when using them for long periods at the lower speeds for macerating tissue, the motors can burn out! Thus, I now use a Ryobi "drill press" in which the drill speeds are set by a belt position and the motor speed stays constant. It is a little on the large side but it does fit on the lab bench and it quite useful. Anyway, just my input from my experience with this. ? ? 4) from Thomas Martin We use handheld, rechargeable power drills from a hardware store. We did not spend a great deal of money on those and they work fine for fresh and powdered plant tissue. ? 5) from Ben Holt We have had good luck with the Heidolph Overhead Stirrers ? they have some pretty fancy models, but we find the stripped down RZR1 model works great for what you want to do. It isn?t a keyless chuck, but we do have people that use the plastic pestles all the time and it has tons of torque. I personally prefer to use a stainless steel bit that is cut to the interior shape (bit smaller for buffer and sample) of a 1.5ml Eppendorf tube. For proteins, a quick wipe down is enough between samples. For DNA that will be amplified, we clean the pestle with a kimwipe and water and just make sure we wipe if off while the bit spins with plenty of water and a couple of wipes with clean parts of the kimwipe. Works great. http://www.brinkmann.com/products/stirrer_OH_mechanical_de.asp ? ? 6) from Zhang Xiaoyu????? [same as 2.] ? Hi Pedro - we use these battery-powered pestles and moter from Sigma: Sigma Aldrich??? Z359947-100EA Sigma Aldrich??? Z359971-1EA --------- Happy grinding, Pedro Rocha From sanjaysingh765 from gmail.com Tue Feb 10 04:24:48 2009 From: sanjaysingh765 from gmail.com (chunnu) Date: Tue Feb 10 12:51:39 2009 Subject: [Arabidopsis] need pBI101 Message-ID: <6860d486-f8c3-4704-9fb0-71560c1f60d5@w39g2000prb.googlegroups.com> Hi there, I am graduate student and looking for the pBI101.Is there anyone kind enough to share his/her pBI101 with me. regards sanjay From jrunions from brookes.ac.uk Tue Feb 10 08:50:28 2009 From: jrunions from brookes.ac.uk (John Runions) Date: Tue Feb 10 16:13:00 2009 Subject: [Arabidopsis] PhD positions available in Oxford UK Message-ID: <49918624.1040705@brookes.ac.uk> Hi Everyone, greetings from Brookes, We have three PhD positions open for next September in our group at Oxford Brookes University. They come with a bursary of ?13,000 which is a good deal considering the value of the pound, and fees are paid by the University. Please could you bring them to the attention of any of your students who may be interested. Our group is Plant Cell Biology: [1]http://www.brookes.ac.uk/lifesci/research/groups/cellandmolebio/pla ntcellbiology/ Specific information about each of the three positions can be found by following the links below: 1) Three dimensional organisation of endomembranes during the cell division cycle. [2]http://www.brookes.ac.uk/lifesci/research/studentships_2009/hawes-e vans.doc Supervisors: Prof. Chris Hawes and Dr David Evans [a great chance to carry out some tomography on our new TEM] 2) Cell biology of plant reticulons. [3]http://www.brookes.ac.uk/lifesci/research/studentships_2009/hawes.d oc Supervisor: Prof. Chris Hawes (collaborating with Lorenzo Frigerio at University of Warwick) [we are getting great data lately on this fundamental group of ER-shaping proteins] 3) Exploring the plant nuclear envelope and nucleo-cytoskeletal bridging complexes. [4]http://www.brookes.ac.uk/lifesci/research/studentships_2009/evans.d oc Supervisor: Dr David Evans [an exciting new area for plant cell biology] -- (Sent from my cra%#y non-Blackberry electronic device that still has wires) ********************************* John Runions, Ph.D. School of Life Sciences Oxford Brookes University Oxford, UK OX3 0BP email: [5]jrunions@brookes.ac.uk phone: +44 (0) 1865 483 964 [6]Runions' lab web site Visit [7]The Illuminated Plant Cell dot com Oxford Brookes Master's in [8]Bioimaging with Molecular Technology References 1. http://www.brookes.ac.uk/lifesci/research/groups/cellandmolebio/plantcellbiology/ 2. http://www.brookes.ac.uk/lifesci/research/studentships_2009/hawes-evans.doc 3. http://www.brookes.ac.uk/lifesci/research/studentships_2009/hawes.doc 4. http://www.brookes.ac.uk/lifesci/research/studentships_2009/evans.doc 5. mailto:jrunions@brookes.ac.uk 6. http://www.brookes.ac.uk/lifesci/runions/HTMLpages/index.html%21 7. http://www.illuminatedcell.com/ER.html 8. http://www.brookes.ac.uk/studying/courses/postgraduate/2007/bmt From b.g.forde from lancaster.ac.uk Tue Feb 10 17:27:43 2009 From: b.g.forde from lancaster.ac.uk (Forde, Brian) Date: Wed Feb 11 02:21:13 2009 Subject: [Arabidopsis] PhD Studentship at Lancaster, UK Message-ID: <199A8D531E24DF47ADCC977CE0E94AFC0221AB4C@exchange-be6.lancs.local> Applications are invited for a BBSRC-funded multidisciplinary PhD studentship entitled: "Developing a computational model to predict nutritional effects on root system architecture". The project supervisors are Prof. Brian G. Forde and Prof Ian Marshall who are both in the Lancaster Environment Centre, Lancaster University. The project will be in collaboration with Dr Lionel Dupuy (SCRI, Dundee) and represents an exceptional opportunity to receive training in both computational modelling and plant physiology/molecular genetics. The BBSRC studentships provide funding for 4 years support; UK candidates are eligible for full awards, covering the cost of tuition fees and stipend (currently ?13000/annum), while EU candidates are eligible for tuition fees only. The deadline for applications is Thursday 26th February and interviews will take place in late March. For further project information and information on how to apply please see http://www.lec.lancs.ac.uk/postgraduate/phd/ or email lec.pg@lancaster.ac.uk. More details can be found on http://www.findaphd.com From jdfriesner from ucdavis.edu Tue Feb 10 22:50:17 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Wed Feb 11 02:22:31 2009 Subject: [Arabidopsis] Upcoming Funding Deadline for Arabidopsis Conference Message-ID: <200902110350.n1B3oHs1026609@phaenicia.ucdavis.edu> Funding Opportunities to attend the 2009 Arabidopsis Conference in Edinburgh, Scotland (1) US Scientists (2) Non-US Scientists (1) US Scientist Application Deadline- March 2, 2009 - Minority funding for US scientists: Full conference funding for qualifying under-represented minorities and faculty at designated US minority-serving institutions. - Travel awards for young US scientists: Awards up to $1,000 for travel to the conference. For graduate students, postdocs and junior faculty within 2 years of first academic appointment. US Citizenship is required for most awards (see funding URL for details). Funding URL: http://www.arabidopsis.org/portals/masc/funding.jsp (2) Funding for non-US scientists: http://www.arabidopsis2009.com/information.html Important information: Early Registration Fee (reduced cost) Deadline: March 27, 2009 Conference URL: http://www.arabidopsis2009.com/ From Claire.Grierson from bristol.ac.uk Fri Feb 13 05:37:45 2009 From: Claire.Grierson from bristol.ac.uk (Claire Grierson, School Biological Sciences) Date: Fri Feb 13 15:00:37 2009 Subject: [Arabidopsis] 100 Questions for Plant Science Research Message-ID: <4F6E041DEBFE72A2CC9A7D7E@bio-clairetab.bio.bris.ac.uk> Dear Colleague, What are the most important questions in plant science that can be addressed by the current generation of researchers? We are collecting suggestions. An expert panel will condense these to a final list of 100 questions for publication in a peer reviewed journal. Please go to: http://www.100plantsciencequestions.org.uk/index.php to see proposed questions and submit your own. A selection of questions from the web site is at the end of this email. Questions are credited or you can choose to be anonymous. We look forward to seeing your suggestions. With very best wishes, Ruth Bastow, Keith Edwards, and Claire Grierson ___________________________ Submitted Questions include: "How can global yields of stable food crops be substantially increased at the same time as non-renewable inputs and greenhouse gas emissions are substantially reduced?" Ian Crute "What controls/regulates the total mitochondrial number/mass in a plant cell during cellular differentiation and development?" Chris Leaver "What are the best ways to convince school and university students that plant science is exciting?" Helen Ougham "Is bio-ethanol from plants actually a sustainable agricultural practice?" Sean May "How can we use our knowledge of plants to design efficient solar energy converters?" Julie Gray "How do plants integrate different types of information to make a "decision"?" Marc Knight "How can we translate molecular systems biology into food security?" Anonymous ---------------------- Dr C S Grierson, http://openwetware.org/wiki/Grierson_Lab School of Biological Sciences, University of Bristol, BS8 1UG, UK. Tel: +44 (0)117 928 7480 e-mail: Claire.Grierson@bristol.ac.uk From James.Stark from umb.edu Tue Feb 17 01:08:31 2009 From: James.Stark from umb.edu (James Stark) Date: Tue Feb 17 13:11:04 2009 Subject: [Arabidopsis] Gateway-adapted 35S vectors for transient expression Message-ID: <5ACB5AED488C2F44A5B4B8FEA0B0F12203A4EB40@ebe3.umassb.net> I am hoping to find one or more Gateway-adapted 35S vectors to use as effector plasmids in protoplast transient expression assays (PEG transfection). There are many vectors available for Agrobacterium-mediated transformation, but since most are fairly large, smaller plasmids lacking plant selection markers and T-DNA left and right borders would be preferable. Does anyone know of a such a plain 35S-Gateway cassette vector, or perhaps even versions that add epitope tags to the genes inserted in the Gateway sites? Any information or leads would be very much appreciated. Thanks, Jim Stark UMass Boston USA From jiangyqcn from hotmail.com Tue Feb 17 16:09:24 2009 From: jiangyqcn from hotmail.com (Y Jiang) Date: Tue Feb 17 19:59:59 2009 Subject: [Arabidopsis] how to check ROS level in plants? Message-ID: Hi, plant researchers, Does anyone know a way to measure ROS levels in plants? i.e. to compare ROS levels between WT and mutants under some stress condition? if you know, could you please tell me the references and/or kit source? Thanks for your input. _________________________________________________________________ From nicholas.provart from utoronto.ca Tue Feb 17 17:06:39 2009 From: nicholas.provart from utoronto.ca (Nicholas Provart) Date: Tue Feb 17 20:00:36 2009 Subject: [Arabidopsis] BAR news, Feb. 2009: new interaction data sets and promoter tools Message-ID: <200902172207.n1HM71823260@net.bio.net> Hello Arabidopsis Researchers, A couple of news items for the Bio-Array Resource (BAR) at http://BAR.utoronto.ca. 1. We have updated our Arabidopsis Interactions Viewer (AIV) to include Dr. Matt Geisler's updated Interactome 2.0, which more than triples the number of predicted interactions in Arabidopsis to 70,944 by incorporating interaction data sets from many more organisms to compute Arabidopsis interologs. We have also added 1,276 MAP Kinase/target interactions determined using protein microarrays by Sorina Popescu and colleagues in Dinesh-Kumar's lab at Yale and published recently in Genes and Development, for a total of 2,779 literature-supported interactions. The AIV images now link to SVG graphic format files for high quality visualizations. 2. Two new tools, Cistome and Cistome Map, are now available. Cistome permits cis-element prediction using a variety of 3rd party packages, as well as with a new version of Promomer, Promomer2, which is an enumerative program that allows for degeneracy in potential cis-elements. Additionally, known cis-elements from PLACE may be mapped onto promoter sets. Cistome Map allows consensus sequences or PSSMs to be mapped onto diagrammatic representations of TAIR8 promoter sequences with defined transcriptional starts. Feedback, as always, is welcome. Keep an eye out in the coming months for a Medicago truncatula eFP Browser, as well as for the Affymetrix Whole Genome Tiling Array At-TAX data sets from the Weigel laboratory in our existing Arabidopsis eFP Browser. Best, 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-nicholas The Bio-Array Resource. http://www.BAR.utoronto.ca email. nicholas.provart@utoronto.ca TTC. Spadina LRT, Willcocks St. From xux from cshl.edu Wed Feb 18 14:14:44 2009 From: xux from cshl.edu (Xu, Xianfeng) Date: Wed Feb 18 14:55:08 2009 Subject: [Arabidopsis] RE: Gateway-adapted 35S vectors for transient expression References: <200902181704.n1IH43820818@net.bio.net> Message-ID: <2A4882406F6D47428E41C649BC54C8D85C5B14@mailbox11.cshl.edu> Please check out pSAT vectors: a modular series of plasmids for autofluorescent protein tagging and expression of multiple genes in plants Journal Plant Molecular Biology Publisher Springer Netherlands ISSN 0167-4412 (Print) 1573-5028 (Online) Issue Volume 57, Number 4 / March, 2005 Or there is a pAM PAT GW(35s) vector floating around our lab. It doesn't have any epitope tag. And I've never used it. It's about 7.5kb including the Gateway cassette. Let me know if you are interested. Morgan (Xianfeng) Postdoc Fellow Cold Spring Harbor Laboratory -----Original Message----- From: arab-gen-bounces@oat.bio.indiana.edu on behalf of arab-gen-request@oat.bio.indiana.edu Sent: Wed 2/18/2009 12:04 PM To: arab-gen@magpie.bio.indiana.edu Subject: Arab-gen Digest, Vol 46, Issue 8 Send Arab-gen mailing list submissions to arab-gen@net.bio.net To subscribe or unsubscribe via the World Wide Web, visit http://www.bio.net/biomail/listinfo/arab-gen or, via email, send a message with subject or body 'help' to arab-gen-request@net.bio.net You can reach the person managing the list at arab-gen-owner@net.bio.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Arab-gen digest..." Today's Topics: 1. Gateway-adapted 35S vectors for transient expression (James Stark) 2. how to check ROS level in plants? (Y Jiang) 3. BAR news, Feb. 2009: new interaction data sets and promoter tools (Nicholas Provart) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 Feb 2009 01:08:31 -0500 From: "James Stark" Subject: [Arabidopsis] Gateway-adapted 35S vectors for transient expression To: Message-ID: <5ACB5AED488C2F44A5B4B8FEA0B0F12203A4EB40@ebe3.umassb.net> Content-Type: text/plain; charset="iso-8859-1" I am hoping to find one or more Gateway-adapted 35S vectors to use as effector plasmids in protoplast transient expression assays (PEG transfection). There are many vectors available for Agrobacterium-mediated transformation, but since most are fairly large, smaller plasmids lacking plant selection markers and T-DNA left and right borders would be preferable. Does anyone know of a such a plain 35S-Gateway cassette vector, or perhaps even versions that add epitope tags to the genes inserted in the Gateway sites? Any information or leads would be very much appreciated. Thanks, Jim Stark UMass Boston USA From justinwilliams9 from gmail.com Sat Feb 21 14:19:47 2009 From: justinwilliams9 from gmail.com (Justin Williams) Date: Sat Feb 21 15:16:53 2009 Subject: [Arabidopsis] Last call for papers: MULTICONF-09 (deadline will not be extended further) Message-ID: *Apologies for cross posting. Kindly share with interested people* Last call for papers: MULTICONF-09 (deadline will not be extended further) The deadline for draft paper submission at the 2009 Multi Conference in Computer Science, Information Technology and Control systems and Computational Science and Computer Engineering (MULTICONF-09) (website: http://www.PromoteResearch.org ) is extended due to numerous requests from the authors and it will not be extedned further. The conference will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. The event consists of the following conferences: ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ? International Conference on Automation, Robotics and Control Systems (ARCS-09) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ? International Conference on Information Security and Privacy (ISP-09) ? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ? International Conference on Software Engineering Theory and Practice (SETP-09) ? International Conference on Theory and Applications of Computational Science (TACS-09) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) The website http://www.PromoteResearch.org contains more details. Sincerely Justin Williams Publicity committee From jean-pierre.metraux from unifr.ch Mon Feb 23 01:52:55 2009 From: jean-pierre.metraux from unifr.ch (METRAUX Jean-Pierre) Date: Mon Feb 23 12:53:23 2009 Subject: [Arabidopsis] (no subject) Message-ID: <5E12AB1D-7FFA-40FA-839E-66E1B783038B@unifr.ch> Hello: I am interested in the variegated mutants listed in the NASC library under N221 and N222 (in the En-T background). These lines have been donated in 1992 by Igor Vizir. Does anybody happen to have more information on these lines? Thanks! JP Jean-Pierre M?traux Department of biology University of Fribourg Chemin du Mus?e 10 CH-1700 Fribourg, Switzerland Tel: ++41 26 300 8811 FAX: ++41 26 300 9740 http://www.unifr.ch/plantbio From jdfriesner from ucdavis.edu Tue Feb 24 16:30:04 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Wed Feb 25 00:57:07 2009 Subject: [Arabidopsis] Last chance: Funding deadline- Monday, March 2nd Message-ID: <200902242130.n1OLU4YZ000686@melipona.ucdavis.edu> Funding Opportunities to attend the 2009 Arabidopsis Conference in Edinburgh, Scotland Applications and all supporting documents for US scientists must be received via email by March 2nd, 2009 for consideration. Please send 1 pdf or word document (advisor's letter of recommendation may be sent separately). (1) US Scientists (2) Non-US Scientists (1) US Scientist Application Deadline- March 2, 2009 - Minority funding for US scientists: Full conference funding for qualifying under-represented minorities and faculty at designated US minority-serving institutions. - Travel awards for young US scientists: Awards up to $1,000 for travel to the conference. For graduate students, postdocs and junior faculty within 2 years of first academic appointment. US Citizenship is required for most awards (see funding URL for details). Funding URL: http://www.arabidopsis.org/portals/masc/funding.jsp (2) Funding for non-US scientists: http://www.arabidopsis2009.com/information.html Important information: Early Registration Fee (reduced cost) Deadline: March 27, 2009 Conference URL: http://www.arabidopsis2009.com/ From Yinghua.Huang from ARS.USDA.GOV Tue Feb 24 13:05:35 2009 From: Yinghua.Huang from ARS.USDA.GOV (Huang, Yinghua) Date: Wed Feb 25 00:57:32 2009 Subject: [Arabidopsis] A Postdoctoral Position in Wheat Genetics Message-ID: Please help me announce a postdoctoral job as described below. Thanks. Dr. Yinghua Huang ________________________________________________________________________ _________________ A Postdoctoral Position in Wheat Genetics Oklahoma State University, Stillwater, Oklahoma, USA Cereal aphids such as greenbug and Russian wheat aphid are the two major pests of wheat worldwide, and they cause millions of dollars of losses to this important food crop each year. We have been identifying sources of aphid resistance and developing high-performance wheat germplasm/cultivars with genetic resistance to the aphid pests. It is important to develop a better understanding the mechanisms underlying host-plant resistance. Thus, a postdoctoral position is available immediately to a person to join a cooperative research project under Dr. Yinghua Huang of the USDA-ARS in collaboration with Dr. Brett Carver of Oklahoma State University. The incumbent will conduct experiments to analyze genetic diversity of aphid resistance and characterize genetic mechanisms of aphid resistance in winter wheat through genetic and genomic approaches. Research would involve developing molecular markers, genotyping and QTL mapping, and using genetic and breeding methodologies to identify genes controlling aphid resistance and to incorporate them into advanced breeding lines. Candidates should have a strong background in genetics, plant breeding, or related discipline. Experience in molecular marker technology, statistical/bioinformatic analysis of data, and germplasm enhancement research are desirable. Documented ability to communicate effectively in English both writing research publication and spoken language. The position is initially for two years and may be extended up to three years. Closing data: March 1, 2009, or continue until the position is filled. Please send a letter of research interest and professional goals, curriculum vitae, and contact information for three references by email to: yinghua.huang@ars.usda.gov. For additional information, please contact: Dr. Yinghua Huang USDA-ARS Plant Science Research Lab 1301 N. Western Road Stillwater, OK 74075 (405) 624-4141, ext. 230 yinghua.huang@ars.usda.gov From b.g.forde from lancaster.ac.uk Wed Feb 25 10:20:33 2009 From: b.g.forde from lancaster.ac.uk (Forde, Brian) Date: Wed Feb 25 12:07:56 2009 Subject: [Arabidopsis] fully funded PhD studentships open to students from any country Message-ID: <199A8D531E24DF47ADCC977CE0E94AFC0221ABD5@exchange-be6.lancs.local> Hi there Hi there This is to let you know that Lancaster University is offering up to 10 PhD Studentships that are open to students from any country (see http://www.lancaster.ac.uk/pgfunding/science.htm). Lancaster University Research Studentships are for up to four years. They exempt the recipient from paying tuition fees and include an annual living stipend at UK Research Council rates (?13,290 in 2009/10). Each year, recipients will also benefit from a personal research support account of ?1500, to use for training and skills enhancement. The closing date for consideration under this studentship scheme is Friday, 17 April 2009. If you have any highly motivated students who might be interested in applying for a studentship to work on a topic of their choosing, but in the general area of the regulation of root development or nutrient signalling, they should contact me at b.g.forde@lancaster.ac.uk as soon as possible. With best regards Brian Forde ===================================== Brian G. Forde Prof. of Environmental Plant Biotechnology 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 ===================================== From jaiswalp from science.oregonstate.edu Wed Feb 25 14:16:01 2009 From: jaiswalp from science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Wed Feb 25 20:46:02 2009 Subject: [Arabidopsis] Research Associate (Post Doc) Opening Message-ID: <49A598F1.20200@science.oregonstate.edu> --------------- Oregon State University Research Associate (Post Doc) To review the position description and apply, go to posting #0003896 at http://oregonstate.edu/jobs. When applying, you will be required to electronically submit your application, a Letter of Intent, and a Curriculum Vitae (including 3 references). Closing date 03/16/09. This is a full-time, (1.0 FTE), 12-month, fixed-term position working in Dr. Pankaj Jaiswal's lab (http://www.science.oregonstate.edu/bpp/). Research Associate (Post Doc), Department of Botany and Plant Pathology, Oregon State University, to work on a cereal plant genome wide gene expression analysis. Full-time (1.0 FTE), 12-month, fixed-term position. This position is required to develop a comprehensive gene expression catalog of rice and other cereal plant genes in various the plant development stages. The project includes histological studies, whole genome transcriptome and proteome data generation and analysis. Required qualifications include PhD in Plant Biology, Molecular Biology, Genetics, Biochemistry, Biological Chemistry, Metabolomics, or related field. Worked previously on gene expression data generation and analysis in their PhD studies or postdoctoral training. Has demonstrated expertise in studying plant development, anatomy, histology, microarrays, gene expression, proteomics, genetics and general understanding of plant biochemistry and gene regulation. Incumbent must have a demonstrated ability for independent and critical thinking, excellent communication skills in oral and written presentations in English and ability to work in teams. Preferred qualifications include a demonstrated commitment to promote and enhance diversity; experience working in wet lab research specializing in microarray, high throughput genome and whole genome transcription and/or Digital gene expression using newer sequencing and microarray technologies susch as those sequencing technologies developed by Illumina, 454-LifeSciences, etc, ; and biochemical and/or regulatory pathways, enzyme kinetics, gene regulation. Experience with Linux and Windows operating system, programming in Perl, Java, C++ and HTML editing. Oregon State University is an Affirmative Action/Equal Opportunity Employer and has a policy of being responsive to dual-career needs. -- Pankaj Jaiswal Oregon State University Corvallis, OR, 97331-2902, USA From Yves.Poirier from unil.ch Wed Feb 25 21:57:15 2009 From: Yves.Poirier from unil.ch (Yves.Poirier@unil.ch) Date: Thu Feb 26 12:26:16 2009 Subject: [Arabidopsis] postdoc on rice phosphate transport, Lausanne, Switzerland Message-ID: <49a6050b.31a.4ee4.664162248@unil.ch> A two-year postdoc position is available in the group of Yves Poirier at the Department of Plant Biology of the University of Lausanne, Switzerland. The project aims at studying the control of phosphate transport and homeostasis in rice, and to develop a strategy to diminish the level of phosphorus and phytic acid accumulating in seeds. An overview of the research projects of the laboratory can be found on the web site http://www.unil.ch/dbmv/page8008_en.html The position is available starting September 2009 or soon thereafter. Candidates should send their CV along with a motivation letter, list of publications and the name and address of at least 2 references to Yves.Poirier@unil.ch. From jdfriesner from ucdavis.edu Thu Feb 26 13:37:32 2009 From: jdfriesner from ucdavis.edu (Joanna Friesner) Date: Thu Feb 26 20:08:50 2009 Subject: [Arabidopsis] Young Researchers: Tansley Award Applications Now Accepted Message-ID: <200902261837.n1QIbWeV014873@biglossa.ucdavis.edu> The New Phytologist Tansley Medal for excellence in plant science is awarded annually in recognition of an outstanding contribution to research in Plant Science by an individual in the early stages of their career. The winner will receive a prize of prize of £2000 GBP and an article published in New Phytologist. Applications should be received by 15 June 2009. This is a global competition open to all plant scientists in the early stages of their career and includes both student and post-doctoral researchers with up to five years experience since gaining their PhD. For more information and rules, please see: http://www.newphytologist.org/tansleymedal.htm. From pj37 from cornell.edu Thu Feb 26 14:24:50 2009 From: pj37 from cornell.edu (Pankaj Jaiswal) Date: Thu Feb 26 20:09:59 2009 Subject: [Arabidopsis] Research Associate (Post Doc) Opening Message-ID: <49A6EC82.5030901@cornell.edu> --------------- Oregon State University Research Associate (Post Doc) To review the position description and apply, go to posting #0003896 at http://oregonstate.edu/jobs. When applying, you will be required to electronically submit your application, a Letter of Intent, and a Curriculum Vitae (including 3 references). Closing date 03/16/09. This is a full-time, (1.0 FTE), 12-month, fixed-term position working in Dr. Pankaj Jaiswal's lab (http://www.science.oregonstate.edu/bpp/). Research Associate (Post Doc), Department of Botany and Plant Pathology, Oregon State University, to work on model plant genome wide gene expression analysis. Full-time (1.0 FTE), 12-month, fixed-term position. The project includes histological studies, whole genome transcriptome and proteome data generation and analysis. Required qualifications include PhD in Plant Biology, Molecular Biology, Genetics, Biochemistry, Biological Chemistry, Metabolomics, or related field. Worked previously on gene expression data generation and analysis in their PhD studies or postdoctoral training. Has demonstrated expertise in studying plant development, anatomy, histology, microarrays, gene expression, proteomics, genetics and general understanding of plant biochemistry and gene regulation. Incumbent must have a demonstrated ability for independent and critical thinking, excellent communication skills in oral and written presentations in English and ability to work in teams. Preferred qualifications include a demonstrated commitment to promote and enhance diversity; experience working in wet lab research specializing in microarray, high throughput genome and whole genome transcription and/or Digital gene expression using newer sequencing and microarray technologies such as those sequencing technologies developed by Illumina, 454-LifeSciences, etc, ; and biochemical and/or regulatory pathways, enzyme kinetics, gene regulation. Experience with Linux and Windows operating system, programming in Perl, Java, C++ and HTML editing. Oregon State University is an Affirmative Action/Equal Opportunity Employer and has a policy of being responsive to dual-career needs. -- Pankaj Jaiswal Assistant Professor Oregon State University Corvallis, OR, 97331-2902, USA email: jaiswalp@science.oregonstate.edu From G.G.Simpson from dundee.ac.uk Fri Feb 27 07:09:00 2009 From: G.G.Simpson from dundee.ac.uk (Gordon Simpson) Date: Fri Feb 27 12:53:37 2009 Subject: [Arabidopsis] 2 Arabidopsis post-doc positions, Dundee, Scotland Message-ID: <49A7D7DC02000008002899ED@gw-out.dundee.ac.uk> Molecular genetics of Arabidopsis lignin biosynthesis Division of Plant Sciences, College of Life Sciences, University of Dundee, Scotland. Job Reference: LS/2554 Closing Date: 31st March 2009 2 Postdoctoral Research Assistants Grade 7 (?28,839 - ?35,469) Two post-doc positions are available in the newly formed Plant Sciences Division at Dundee University, Scotland. The positions are funded through a programme grant (US $2 million) from the Global Climate and Energy Project (GCEP), Stanford, USA, that also provides support for two technicians to join the team. The aim of the project is to use Arabidopsis as a model to better understand how to optimize the saccharification yield of plant lignocellulose for biofuel production. The research involves novel screens to identify mutants that affect lignin biosynthesis. The project is a collaboration between the neighbouring labs of Prof. Claire Halpin and Dr Gordon Simpson (University of Dundee). Prof. Claire Halpin?s lab is extremely well supported, with additional recent funding from the EU and programme grants from the BBSRC. Therefore, the successful applicants will join a vibrant group of researchers focused on plant biofuels. Dundee University Plant Science Faculty have their research labs at the nearby Scottish Crop Research Institute (SCRI), and benefit from expertise and state-of-the art resources at both organizations. The College of Life Sciences has a particularly vibrant post-doc association and in recent years has regularly been voted one of the best places to work in Europe by readers of The Scientist magazine. Located in a beautiful part of Scotland, Dundee combines quality of life with quality of science. An interest in lignin and previous experience of Arabidopsis molecular genetics would be an advantage. Applications in the form of a CV and covering letter, including the names and addresses of 3 referees, should be sent to email address quoting LS/2554. Alternatively, please send 2 hard copies of your CV and covering letter to Human Resources, College of Life Sciences, MSI/WTB/JBC Complex, University of Dundee, DD1 5EH. Applicants will only be contacted if invited for interview. The University of Dundee is committed to equal opportunities and welcomes applications from all sections of the community. The University of Dundee is a registered Scottish charity, No: SCO15096. www.dundee.ac.uk/jobs Gordon Simpson Division of Plant Sciences College of Life Sciences Dundee University at SCRI Invergowrie Scotland DD2 5DA direct dial: 44 (0)1382 568572 email: g.g.simpson@dundee.ac.uk web: http://www.lifesci.dundee.ac.uk/people/gordon_simpson/ The University of Dundee is a registered Scottish charity, No: SC015096 From jpbcs from acadjourn.org Fri Feb 27 08:30:44 2009 From: jpbcs from acadjourn.org (Journal of Plant Breeding and Crop Science) Date: Wed Sep 30 17:16:57 2009 Subject: [Arabidopsis] (no subject) Message-ID: *Journal of Plant Breeding and Crop Science* www.academicjournals.org/JPBCS * * Dear Colleague, The *Journal of Plant Breeding and Crop ** **Science** * *(JPBCS) *is a* *multidisciplinary peer-reviewed journal published monthly by Academic Journals ( www.academicjournals.org/JPBCS dedicated to increasing the depth of Crop Science across disciplines with the ultimate aim of improving plant research. *Call for Papers* *JPBCS* will cover all areas of plant breeding and crop science. The journal welcomes he submission of manuscripts that meet the general criteria of significance and scientific excellence, and will publish: ? Original articles in basic and applied research ? Case studies ? Critical reviews, surveys, opinions, commentaries and essays We invite you to submit your manuscript(s) to jpbcs@acadjourn.orgfor publication in the Maiden Issue (January 2009). Our objective is to inform authors of the decision on their manuscript(s) within four weeks of submission. Following acceptance, a paper will normally be published in the next issue. Instruction for authors and other details are available on our website; http://www.academicjournals.org/JPBCS/Instruction.htm JPBCS is an Open Access Journal One key request of researchers across the world is unrestricted access to research publications. Open access gives a worldwide audience larger than that of any subscription-based journal ad thus increases the visibility and impact of published work. It also enhances indexing, retrieval power and eliminates the need for permissions to reproduce and distribute content.JPBCS is fully committed to the Open Access Initiative and will provide free access to all articles as soon as they are published. Best regards, *Anighoro Clementina* Editorial Assistant Journal of Plant Breeding and Crop Science (JPBCS) E-mail: jpbcs@acadjourn.org, www.academicjournals.org/JPBCS