Dicty News Electronic Edition Volume 23, number 8 August 27, 2004 Please submit abstracts of your papers as soon as they have been accepted for publication by sending them to dicty@northwestern.edu or by using the form at http://dictybase.org/db/cgi-bin/dictyBase/abstract_submit. Back issues of Dicty-News, the Dicty Reference database and other useful information is available at dictyBase - http://dictybase.org. ============= Abstracts ============= Microarray Data Mining with Visual Programming Tomaz Curk (1), Janez Demsar (1), Qikai Xu (3,4), Gregor Leban (1), Uros Petrovic (2), Ivan Bratko (1,2), Gad Shaulsky (3,4) and Blaz Zupan (1,3,*) 1 University of Ljubljana, Faculty of Computer and Information Science, 2 Jozef Stefan Institute, Ljubljana, Slovenia, 3 Department of Molecular and Human Genetics, 4 Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA. * corresponding author Bioinformatics, in press. Summary: Visual programming offers an intuitive means of combining known analysis and visualization methods into powerful applications. The system presented here enables users who are not programmers to manage microarray and genomic data flow and to customize their analysis by combining common data analysis tools to fit their needs. Availability: magix.fri.uni-lj.si/bi-visprog Contact: blaz.zupan@fri.uni-lj.si Supplementary information: magix.fri.uni-lj.si/bi-visprog Submitted by: Gad Shaulsky [gadi@bcm.tmc.edu] ----------------------------------------------------------------------------- Calmodulin Binds to and Inhibits the Activity of Phosphoglycerate Kinase Michael A. Myre1,2 Danton H. OâDay1,3 1Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Rd. Mississauga, ON, L5L 1C6 Canada 2Current address: Harvard Medical School, Massachusetts General Hospital, Building 114--114 16th Street, Charlestown MA 02129-9142 3Corresponding author: Phone: 905-828-3896; Fax: 905-828-3792; Email: doday@utm.utoronto.ca Biochimica Biophysica Acta÷Molecular Cell Research, in press Phosphoglycerate kinase functions as a cytoplasmic ATP-generating glycolytic enzyme, a nuclear mediator in DNA replication and repair, a stimulator of Sendai virus transcription and an extracellular disulphide reductase in angiogenesis. Probing of a developmental expression library from Dictyostelium discoideum with radiolabelled calmodulin led to the isolation of a cDNA encoding a putative calmodulin-binding protein (DdPGK) with 68% sequence similarity to human PGK. Dictyostelium, rabbit and yeast PGKs bound to calmodulin-agarose in a calcium-dependent manner while DdPGK constructs lacking the calmodulin-binding domain (209KPFLAILGGAKVSDKIKLIE228) failed to bind. The calmodulin-binding domain shows 80% identity between diverse organisms and is situated beside the hinge and within the ATP binding domain adjacent to nine mutations associated with phosphoglycerate kinase deficiency. Calmodulin addition inhibits yeast PGK activity in vitro while the calmodulin antagonist W-7 abrogates this inhibition. Together these data suggest that PGK activity may be negatively regulated by calcium and calmodulin signalling in eukaryotic cells. Submitted by: Danton O'Day [doday@utm.utoronto.ca] ----------------------------------------------------------------------------- Dictyostelium Nucleomorphin is a member of the BRCT-domain family of cell cycle checkpoint proteins Michael A. Myre1,2 Danton H. OâDay1,3 1Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Rd. Mississauga, ON, L5L 1C6 Canada 2Current address: Harvard Medical School, Massachusetts General Hospital, Building 114--114 16th Street, Charlestown MA 02129-9142 3Corresponding author: Phone: 905-828-3896; Fax: 905-828-3792; Email: doday@utm.utoronto.ca Biochimica Biophysica Acta÷General Subjects, in press A search of the Dictyostelium genome project database (http://dictybase.org/db/cgi-bin/blast.pl) with NumA, a protein that regulates nuclear number, predicted it to be encoded by a larger gene containing a putative breast cancer carboxy- terminus domain (BRCT). Using RT-PCR, northern and western blotting we have identified a differentially expressed, 2318 bp cDNA encoding a protein isoform of Dictyostelium NumA with an apparent molecular weight of 70 kDa that we have called NumB. It contains a single amino-terminal BRCT-domain spanning residueâs 125-201. Starvation of shaking cultures reduces NumA expression by ~ 88 ± 5.6 %, whereas NumB expression increases ~ 35 ± 3.5 % from vegetative levels. NumC, a third isoform that is also expressed during development but not growth, remains to be characterized. These findings suggest DdNumA is a member of the BRCT-domain containing cell cycle checkpoint proteins. Submitted by: Danton O'Day [doday@utm.utoronto.ca] ============================================================================== [End Dicty News, volume 23, number 8]