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August 2006 Newsletter



The release of Gramene V 22 is anticipated for late August. To receive email notification of updates to the Gramene website, you may join the Gramene-announce listserve at http://www.gramene.org/mailarch-announce/.

To submit items for this newsletter, contact the newsletter editor at: cer17@cornell.edu.

Gramene News:

Postdoctoral Associate - Job opportunity
Upcoming Gramene Outreach Activities
Recommended Reading from the Gramene Literature Database
Gramene FAQ

Community News:

Calls for Papers
Travel Award Available
Community News
Rice Outlook
Community Calendar

Gramene News

 
Job Opportunity - Postdoctoral Associate - 05677
Job Description

Gramene database (http://www.gramene.org), is seeking applicants for a full time position for a plant biology curator who will participate in the development and maintenance of structured vocabularies for describing plant morphology, anatomy, growth and development stages for its Plant Ontology Consortium (POC) project (http://www.plantontology.org). These vocabularies (ontologies) are necessary to provide the backbone for describing phenotypes and gene expression patterns, and allow database users to perform a set of common queries or searches across different plant databases. The Plant Ontology Consortium is a collaboration among plant genome databases related to rice, Arabidopsis, maize, legumes, Solanaceae, etc.

The successful candidate will work with a team of curators, software engineers, and database developers at Gramene and collaborating database projects, such as TAIR (http://www.arabidopsis.org) and MaizeGDB (http://maizegdb.org); contribute to annotation of phenotypes, germplasm and gene products by using the vocabularies developed in the project; participate in development and application of methods to improve consistency and to enhance the quality of annotations; promote the use of ontologies in comparative genomics and biology through active participation in workshops, seminars and scientific meetings.

Qualifications

Successful candidate will have a Ph.D. degree and training in Plant Biology and related fields (e.g. Systematics, Development, Physiology), a demonstrated ability for independent, critical thinking and excellent communication and teamwork skills. The curator must be able to travel to and attend 2-3 national and international meetings per year. Familiarity with biological data mining, basic UNIX/Linux commands, spreadsheets, and commonly used biological research tools is desired. A working knowledge of SQL would be an asset but not required. Qualified candidates should e-mail a cover letter and resume to Pankaj Jaiswal (pj37@cornell.edu).

 
Visit with Gramene at

 
Recommended Reading
  • Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa -- Londo et al.Proceedings of the National Academy of Science. June 20, 2006. 103 (25): 9578-9583 Sciences
  • Autophagic fungal cell death is necessary for infection by the rice blast fungus. Veneault-Fourrey, C. et. al. Science, 2006, 312, pp.580-583. ( More Info)
  • Os8N3 is a host disease-susceptibility gene for bacterial blight of rice. Yang, B. et al. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103, pp.10503-10508. ( More Info)
  • High Rate of Chimeric Gene Origination by Retroposition in Plant Genomes. Wang, W et al. The Plant cell. ( More Info)
  • Jekyll encodes a novel protein involved in the sexual reproduction of barley. Radchuk, V. et al. The Plant cell, 2006, 18, pp.1652-1666 ( More Info)

  •  
    Gramene FAQ. Gramene users are encouraged to contact Gramene for assistance in using the database. In addition to attending workshops, users contact Gramene through the "Feedback" link at the top of any page, or join the Gramene listserve. Here are some recent questions that have been answered.
    Q - Could you please tell me where in the current trait ontology I could find wheat quality trait / rheological trait. I've looked at the traits under the current quality category and it appears to be only for rice and does not seem to cover much of the wheat quality/rheological traits.

    A - We do not have the actual trait ontology term for rheological traits from wheat because we have not added the QTLs associated with them in Gramene database. As soon as we have the QTLs available for these traits from GrainGenes we will incorporate the traits in Gramene. The following papers have reported such traits: http://grain.jouy.inra.fr/cgi-bin/graingenes/report.cgi?class=reference;id=174 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15965651&dopt=Abstract. In the meantime if you simply need the trait ontology term for rheological trait and associated parameters such as dough extensibility and Rmax we can add them to the Trait Ontology. Please send us the appropriate definition of the terms and their assay method.
    Q - I am looking for leaf blast QTLs. There are 83 QTLs, all mapped in Moroberekan/CO39 RFLP map by Wang et al. 1994! There are only ten QTLs in the article. Could you provide me with more information about how these QTLs were submitted.

    A- All 83 QTL have been curated from the paper of Wang et al. (1994). We curated those following our standard curation procedure. According to our rule, QTL detected by different traits (in some cases, they could be parameters used for trait evaluation) or different environments are treated as different unique single QTL. While two single QTL have interaction, they will be also treated as two single QTLs, but the relationship of them will be explained by free text comments. So, for that paper:
    AQEN001-010: corresponding to all QTL in Table 1, and the QTL detected by lesion number in Fig 2.
    AQEN011-017: QTL detected with diseased leaf area in Fig 2.
    AQEN018-019: QTL detected with lesion size in Fig 2.
    AQEN020-59: QTL pairs with interaction effects in Table 2.
    AQEN060-082: QTL detected with diseased leaf area at other two sites in Table 3 (Cavinti, Sitiung).
    Q - I'd like to know if it is possible in some way to obtain from Gramene the information regarding QTL associated markers (best scored, positive, flanking) or the info is always to be seek "manually" on the map and in the references?

    A - Currently, we have only curated associated markers for a particular QTL (all markers located in a QTL region), but we didn't catch detail info such as best score and allele info. This more comprehensive info will occur when we do deep curation in the future.

    To get those associated markers for the QTLs, you can manually check qtl and associated markers nearby on the map using CMap. Yes, it will take time to go the process. Another alternative is, if you are only interested in a particular map set, you can go to our Maps Module to find that map set, (for instance http://www.gramene.org/db/cmap/map_set_info?map_set_acc=raj2003a) then download all related features (markers, qtl, etc) for that map set, and further using MS-excel or another computation to compare the qtl and marker position for that map set.

    Our developers are working actively on the issue and we hope we can provide an easier way for users to get those associated marker info in the near future.

    Community News

     
    Calls for Papers

    1) The Editoral Board of the International Journal of Plant Genomics (IJPG) has been established. It consists of associate editors from world-reconginized plant genomics scientists of 19 countries. There is now a call for papers. Get more information online at http://www.hindawi.com/GetJournal.aspx?journal=IJPG&page=guidelines.

    2) The January 2007 issue on "Genomics: moving towards gene revolution in rice" for "Physiology and Molecular Biology of Plants", an Indian journal is under review. I (Rajinder Kumar Jain) take this opportunity to call for the short review articles, research papers, notes, etc. for this special issue. For details you may visit www.phssfoundation.org. The last date of submitting the articles is August 31, 2006.

     
    Travel award available
    We are pleased to announce that the United State Department of Agriculture and the National Science Foundation have provided funds to help defray the cost of attending the "4th International Rice Functional Genomic Meeting" in France for up to seven graduate students and postdocs. Each awardee will be reimbursed for up to $2,250 of travel and meeting expenses.

    Graduate students/postdocs are encouraged to submit their title and abstract of what they plan to present at the meeting so that we can select those to receive the awards. Applicants must be US citizens due to Federal funding rules. For more info, please refer to http://www.irfgm2006.org/application/default.asp.

    Please submit titles/abstracts and contact information to sjackson@purdue.edu by 1 August 2006.

     
    Check out the latest news:

     
    US Rice Outlook (From 7/12/06 http://www.usda.gov/oce/commodity/wasde/latest.txt)

    Note: This WASDE report contains changes to global supply and use based on revisions made to the China supply and use, 1997/98-2006/07. See third paragraph of the rice section for more details.

    U.S. rice production in 2006/07 is projected at 200 million cwt, 2 percent below last month and 10 percent below 2005/06. Estimated harvested area of 2.895 million acres reported in the June 30 Acreage report is 2 percent below last month, and 14 percent below 2005/06. The yield for 2006/07 is projected at 6,908 pounds per acre, 39 pounds per acre below last month, and 272 pounds per acre below 2005/06. Long-grain rice production is projected at 154 million cwt, 2 percent below last month, and 13 percent below 2005/06. Combined medium- and short-grain rice production is projected at 46 million cwt, 4 percent below last month, but nearly 1 percent above 2005/06.

    Projected domestic and residual use of rice for 2006/07 is lowered slightly from a month ago. Exports for 2006/07 are projected at 100 million cwt down 3 million cwt from last month. Milled and brown rice exports are projected at 64 million cwt (rough basis), 3 million cwt below last month, while rough rice exports are projected at 36 million cwt, unchanged from last month. Ending stocks are projected at 22.8 million cwt, 7 percent below last month, and 34 percent below 2005/06. The season-average farm price range for 2006/07 is raised 15 cents per cwt on each end to $9.15 to $9.65 per cwt compared to a revised $7.60 to $7.65 per cwt for 2005/06.

    This month, USDA made revisions to global rice supply and use because of changes to China's stocks and domestic use estimates for 1997/98 to 2006/07. The revisions in China's supply and use estimates resulted in larger ending stocks from 2004/05-2006/07. While the upward revision in stocks is substantial, little, if any, impact on world trade and prices is expected. The July stocks revisions are primarily based on information from China's National Grain and Oilseeds Information Center indicating a substantial decline in feed use of rice in China since 2002/03. In addition, the combination of strong economic growth and increased urbanization have likely caused per capita food consumption of rice in China to slightly decline. The adjustment in the supply and use series for China beginning in 1997/98 resulted in an ending stocks estimate in 2006/07 of 37.4 million tons compared to last month's estimate of 18.8 million tons. A discussion of the revisions and a comparison of old and new estimates will be available at 8:45 a.m. on July 12 at: http://www.usda.gov/oce/commodity/wasde/revisions/historical.htm.

    Projected global 2006/07 production, and ending stocks are raised from a month ago, while consumption is lowered and trade is nearly unchanged. World production is projected at a record 418.3 million tons, 0.7 million above a month ago. The increase in global production is primarily due to a larger crop projected for Bangladesh, which is partially offset by lower U.S. production. Global consumption and ending stocks are changed primarily because of revisions made to the China rice supply and use balance. Global consumption is projected at 418.1 million tons, 6.7 million tons below last month, while ending stocks are projected at 79.1 million tons, 19 million tons above a month ago and nearly the same as the revised 2005/06 estimate.
    For more indepth information, see:

     
    Upcoming Meetings
    July 16-21, 2006. Plant Molecular Biology Gordon Conference, in New Hampshire, traditionally covering a wide range of topics: plant-microbe interactions, development, metabolism, epigenetics and hormones, using approaches ranging from cell biology and biochemistry to genetics and genomics.
    August 5-9, 2006. Joint Annual Meeting of the American Society of Plant Biologists and the Canadian Society of Plant Physiologists Société Canadienne de Physiologie Végétale. Hynes Convention Center, Boston, Massachusetts. The American Society of Plant Biologists was founded in 1924 to promote the growth and development of plant biology, to encourage and publish research in plant biology, and to promote the interests and growth of plant scientists in general. Over the decades the Society has evolved and expanded to provide a forum for molecular and cellular biology as well as to serve the basic interests of plant science. It publishes the highly cited and respected journals Plant Physiology and The Plant Cell. Membership spans six continents, and our members work in such diverse areas as academia, government laboratories, and industrial and commercial environments. The Society also has a large student membership. ASPB plays a key role in uniting the international plant science disciplines.
    August 6-10, 2006. ISMB 2006. Intelligent Systems for Molecular Biology (ISMB) is the annual meeting of the International Society for Computational Biology (ISCB). Over the past twelve years, the ISMB conference has grown to become the largest bioinformatics conference in the world. The ISMB conferences provide a multidisciplinary forum for disseminating the latest developments in bioinformatics. ISMB brings together scientists from computer science, molecular biology, mathematics, and statistics. Its principal focus is on the development and application of advanced computational methods for biological problems.
    August 16-19, 2006. Tropical Crop Biotechnology Conference 2006. Cairns, Australia. Tropical crops have enormous potential for the production of food, energy, industrial biomaterials and pharmaceutical products. Thehis conference is planned to address two critical research issues in the future development of tropical crops: 1) The potential for tropical crops as biofactories in the production of industrial biomaterials, renewable energy, functional foods and pharmaceuticals, and 2) Developing and using functional genomics in tropical crops to facilitate a quantum leap in the performance of tropical crop plants.
    August 20-25, 2006. 8th International Congress on Plant Molecular Biology. Adelaide, South Australia. Bringing together experts from a variety of fields to further knowledge and research in plant molecular biology.
    August 27, 2006. ACPFG Genomics Symposium and ITMI Workshop. McCracken Country Club, South Australia . The International Triticeae Mapping Initiative and the Australian Centre for Plant Functional Genomics are together hosting this years ITMI Workshop and Genomics Symposium. These programs both focus on research efforts in molecular genetics, genomics and genetic analysis in the Triticeae - wheat, barley, rye and their wild relatives. This event will bring together leading national and international researchers to exchange innovative ideas, discussion and debates.
    October 9-11, 2006. The 4th International Rice Functional Genomic Symposium will be held in Montpellier, France. This unformal consortium was created in 2000 with a goal to orientate, organise and coordinate rice functional genomic research worldwide and to share a number of resources created in various labs and countries (http://www.iris.irri.org/IRFGC/). An important purpose of this annual symposium is to focus on most recent results and to promote interactions between participants in an informal and friendly atmosphere.
    January 13-17, 2007. Plant and Animal Genome XV Conference
    March 23-27, 2007. 2nd International Conference on Plant Molecular Breeding. Sanya City, Hainan, P. R. China. This event will focus on Applied plant genomics and molecular plant breeding in view of the increasing need to use newl molecular approaches and mine novel gene resources. All important aspects of plant molecular breeding and related transgenic ecological risk and intellectual property right (IPR) will be covered in several sessions and satellite workshops.
    January 12-16, 2008. PAG-XVI
    See also:
  • Cold Spring Harbor Laboratory - Meetings and Courses
  • GrainGenes Calendar