75 Integrating Membrane Transport with Male Gametophyte ... - TAIR

105 "MobyMan" a Light Weight Biomobyed MapMan Server Application
Bjorn Usadel 1 , Axel Nagel 2 , Dirk Steinhauser 1 , Henning Redestig 1 , Oliver Blaesing 1, 3 , Mark Stitt 1
1
Max-Planck Institute of Molecular Plant Physiology, System Regulation, Am Muhlenberg 1, D-14476 Golm,
2
RZPD Deutsches Ressourcenzentrum fur Genomforschung GmbH, Heubnerweg 6, D-14059 Berlin, 3 Present
Address: Metanomics, Tegeler Weg 33, 10589 Berlin
MapMan is a stand alone java application for the visualization of large datasets that arise from various profiling
experiments (see Abstract #9317). These datasets are visualized on pre-drawn maps which represent biological pathways
or overview pictures.
Even though a webversion of MapMan exists (http://www.gabi.rzpd.de/projects/MapMan/) this is based on the JAVA
technology, and thus requires a more potent platform when installing it on a web server.
However, since most small web servers are scripting enabled by default, we present here a completely new
implementation of MapMan in Perl which can be easily plugged into existing server sided analysis platforms for data
visualization. This implementation allows uploading of data which is then immediately displayed by the server. To further
facilitate interoperability of this new tool it has been equipped with a BioMoby interface for communication with other
biological databases.
The Biomoby interface allows both to access other third-party databases and to move data from these databases for
display into this “biomobyed” MapMan version.
As an exemplary case a novel microarray database extension to CSB.DB / MapMan and its interplay with the new
MapMan version will be discussed in detail.
Special thanks are due to Dr. Heiko Schoof for promoting and advocating the Biomoby interface.
106 Combinatorial Analysis of Cis-elements and Gene Expression to Identify Co-chaperones for
A. thaliana HSP90 Genes
Cecilia Vasquez-Robinet 1 , Amrita Pati 2 , T. Murali 2 , Lenwood Heath 2 , Hans Bohnert 3 , Ruth Grene 1
1
Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA, 2 Computer Sciences, Virginia
Tech, Blacksburg, VA, 3 Plant Biology, UIUC, Urbana-Champaign, IL
Exposure to mild drought stress can "pre-condition" the plant photosynthetic machinery, "acclimating" it to more successfully
defend itself against subsequent drought stresses. We have shown that specific expression patterns of genes encoding several heat
shock proteins (HSPs) are correlated with photosynthetic acclimation under mild drought stress in loblolly pine (1,2). The experiments
showed that a homolog of Arabidopsis HSP90-7 was up-regulated after rehydration coincident with acclimation (2). HSP90-7 is
a member of the HSP90 gene family that in mammals forms a complex with co-chaperones involved in activation, processing or
trafficking of signaling proteins. We found that the HSP90-7 homolog was co-expressed with candidate co-chaperones such as
HSP70-3, and a HSP40 homolog. Homologs of these proposed co-chaperone genes are present in A. thaliana as large multigene
families. The evolution of these large gene families in plants can be rationalized by the necessity of adaptation to a range of stresses,
since HSPs are induced not only under heat but also under other abiotic stresses, such as drought, as we observed in loblolly pine.
Therefore, adaptation might involve the formation of specific chaperone complexes for different stresses but a demonstration of their
existence in plant systems is still lacking.
Should plants produce specific chaperone complexes to signal and defend against abiotic stress, we would expect similar
arrangements of cis-elements in the upstream regions of plant HSP90s and their particular co-chaperones to guarantee stress-dependent
co-expression. Analysis of the promoter region of A. thaliana HSP90s and their putative co-chaperones with XcisClique (3) resulted in
the identification of candidate co-chaperones for each HSP90. Some of the candidate co-chaperones found in the Arabidopsis genome
for HSP90-1 and HSP90-7 are homologs of the pine genes that were co-expressed in our drought experiment. We are performing
yeast two hybrid experiments with candidate co-chaperones to confirm the predictions found by XcisClique.
(1)Watkinson, J.I., Sioson, A.A., Vasquez-Robinet, C., Shukla, M., Kumar, D., Ellis, M., Heath, L.S., Ramakrishnan, N., Chevone, B., Watson,
L.T., van Zyl, L., Egertsdotter, U., Sederoff, R.R. and Grene, R. (2003) Photosynthetic acclimation is reflected in specific patterns of gene
expression in drought-stressed loblolly pine. Plant Physiol, 133, 1702-1716.
(2)Vasquez-Robinet, C., Watkinson, J. I., Heath,L.,Ramakrishnan,N., Singhal,V., Moura,C., Sioson,A., Shuckla,M., Grene,R. (2004) Differential
expression of chaperone genes in preconditioning for photosynthetic acclimation in drought-stressed Loblolly pine. ASPB 2004, Orlando,Fl.
(3)Pati A, Vasquez-Robinet C, Heath L, Grene R, Murali TM (2006) XcisClique: Analyzing regulatory bicliques. BMC bioinformatics, 7: 218