Systems Biology at Washington University

FIBR


Synechocystis 6803 : Exposure to High Light and High CO2

In this experiment cells were subjected to high light conditions while providing excess CO2 ( 1%). A co-expression netwok was generated using time series microarray data in order to identify the main expression patterns and group genes based on behavioral similarity.

Key Findings: Co-expression network contained twelve subnetworks with hub-and-spoke architecture. ( more : Aurora Lab ) The core subnetwork was enriched in proteins that (putatively) bind Fe-S clusters and proteins that mediate iron and sulfate homeostasis Center of this core is a sulfate permease, suggesting sulfate is rate limiting for cells grown in high light, with excess CO2 supply This was verified experimentally, by demonstrating the limited ability of cell growth in sulfate-depleted medium under high light





Co-expression Network

By Rajeev Aurora

The topology of the 782-node coexpression network and the distribution of edges: There are 38,418 edges for the 782 vertices. The mapping between the Cyanobase identifiers and Gene Ontology (GO; http://www.geneontology.org) identifiers was generated in two steps: first the Cyanobase identifiers were mapped to Swiss Prot identifiers using the table provided by Expasy (ftp://ftp.expasy.org/databases/swiss-prot/release/syny3.txt). In the second step the Swiss Prot identifiers were mapped to the Gene Ontology terms using the gene ontology association tables (GOA; (Camon et al., 2003); downloaded from http://www.ebi.ac.uk/GOA/). Finally the GO terms with statistical significance (P< 0.05) for the biological process are shown in this table. Of the 207 ORFs, 25% could be mapped across all the tables (80 of the ORFs are annotated as hypothetical or unknown). Within each sub-network the number of vertices, and the molecular function (based on the GO categories) of the genes are shown. The number of unknown or hypothetical genes is also shown.
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Core Subnetwork

By Rajeev Aurora

Topology of the 336-node coexpression network: The core sub-network consists of 336 nodes and 30,753 edges. The 207 core genes and their first neighbors are rendered for this subnetwork.
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Cell Growth in Sulfate-depleted Medium under High Light

Growth curves of Synechocystis 6803 cells in complete medium, or iron, sulfate, iron and sulfate depleted media under either low light (top) or high light (bottom). This growth experiment was repeated three times with nearly identical doubling times observed. The experiment shown is representative of the three independent growth experiments. Cells were grown to a cell density (OD730) of 0.45, spun down and washed once in either complete or depleted media. Cells used for iron and iron plus sulfate starvation were incubated in 10 mM EDTA, 20 mM MES, pH 5.0 for 15 min, spun down and resuspended in Fe or Fe+S depleted BG11 media. After washing, cells were inoculated in fresh media and cell density was adjusted to OD at 730 nm of 0.1 and split into two tubes. One tube was incubated at low light and the other at high light. The growth of cells was assayed by measuring light scattering at 730 nm over time. Back
By Abhay Singh