SGD Quarterly Newsletter, Fall 2008

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About this newsletter:

This is the November 2008 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can also subscribe to SGD's RSS feed to receive updates on SGD news - http://www.yeastgenome.org/feed

Contents

Curation Focus: Autophagy

Autophagy is a highly conserved eukaryotic pathway for sequestering and transporting bulk cytoplasm to the lysosome for degradation and eventual re-use in biosynthesis (reviewed in Yorimitsu and Klionsky, 2005). Information in SGD about 28 genes involved in autophagy has been reviewed and updated, including their descriptions, GO annotations, and mutant phenotypes, and Gene Summary Paragraphs have been added to their Locus Summary pages. We greatly appreciate Dan Klionsky's assistance in reviewing the work and for providing a summary diagram that is available for download from the Gene Summary paragraphs.

New and Improved Textpresso

The SGD full-text literature search capability (powered by Textpresso) has been upgraded and expanded to include publications from 2008. The full-text literature search can be accessed via the Full-text search link on the home page, from a link on the SGD Search Options contents page, and from any Search results page where the search form is prefilled with your search query. The new Textpresso is installed on the first of a series of new servers that are being rolled out at SGD over the next few weeks

New links to FitDB

Links to the Yeast Fitness Database (FitDB), a website to view fitness defects in mutant yeast strains in the presence of various chemicals, as described in Hillenmeyer et al., 2008, have been added to the "Phenotype" pull-down menu on the Locus Summary and Phentoype Details pages. Thanks to Maureen Hillenmeyer, Larry Heisler, and Guri Giaever for helping to set up these links.

Biochemical Pathways Wall Poster

The Biochemical Pathways poster on display at the 2008 YGMB meeting in Toronto can be downloaded from theBiochemical Pathways page. The poster can be printed for easy viewing as a wall chart. In addition, the Yeast Biochemical Pathways have been upgraded to Pathway Tools version 12.0. The yeastcyc12.0 data files that can be used with version 12.0 and the biochemical_pathways.tab file are available for download from SGD's Download Data Files page.

Summary Paragraphs Progress, 35 new since July 2008

Summary paragraphs summarize published biological information for a gene/feature and are designed to familiarize both yeast and non-yeast researchers with the general facts and important subtleties regarding a locus. During the last quarter (July 2008 - October 2008), new summary paragraphs for the following 35 features have been added to their respective Locus Summary pages:


List of Summary Paragraphs Added During the Last Quarter
YCR102C YLR460C YML131W YNL134C ADH1/YOL086C ADH2/YMR303C
ADH3/YMR083W ADH5/YBR145W ADH6/YMR318C ADH7/YCR105W AST1/YBL069W AST2/YER101C
BDH1/YAL060W BDH2/YAL061W ETR1/YBR026C MDH1/YKL085W MET13/YGL125W SCR1
SEC65/YML105C SEN2/YLR105C SEN15/YMR059W SEN34/YAR008W SEN54/YPL083C SFA1/YDL168W
SOR1/YJR159W SOR2/YDL246C SRP14/YDL092W SRP21/YKL122C SRP54/YPR088C SRP68/YPL243W
SRP72/YPL210C XYL2/YLR070C YFH1/YDL120W YIM1/YMR152W ZTA1/YBR046C

Community News

  • Classic Yeast Book Reprinted

The Early Days of Yeast Genetics, which was originally published in 1993 but has been out of print for many years, has been reprinted by the Cold Spring Harbor Laboratory press. This classic book contains a series of illustrated essays written by pioneers of yeast biology, including H. Roman, D. Botstein, L. Hartwell, E. Jones, F. Sherman, G. Fink, and others. These informal essays chronicle the development of yeast as a research system prior to 1975 and include reminiscences on the science, the events, and the personalities associated with these early studies.

Upcoming Conferences and Meetings

Information on registration and abstract deadlines for the following conferences is available at: http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses

  • 25th Fungal Genetics Conference
Asilomar, CA
March 17-22, 2009
  • XXIV International Conference on Yeast Genetics and Molecular Biology
University of Manchester
Manchester, United Kingdom
July 19 - 24, 2009
Poster in PDF format
  • 11th Biannual International Meeting on Yeast Cell Biology
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY
August 11 - 15, 2009


asterisks indicate attendance by SGD.*

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