In a liquid, bacteria swim around seeking nutrients with the aid of a polar flagellum. On a surface, however, certain species of bacteria can reorganize their cellular structure on a massive scale, growing large numbers of lateral flagella and allowing the bacteria to swarm over the surface. The basic question of interest in this study is how exactly some bacteria species recognize that they are on a surface.
To eliminate confounding effects from the environmental background (liquid vs surface), the researchers employed a mechanism that forced the bacteria into swimmer and swarmer states – i.e., to grow swarmer cells in a liquid and swimmer cells on a plate. The study consisted of measuring gene expression under four experimental conditions: swimmer cells grown on a plate, swimmer cells grown in a liquid, swarmer cells grown on a plate, and swarmer cells grown in a liquid. The primary goal is to find genes that are specifically turned on (or off) in response to a swarmer cell growing on a plate – not just growing on a plate or just the swarmer cell type, but when the two are combined.
The species of bacteria in this study is called Vibrio parahaemolyticus.
Y: Gene expression measurements, normalized and on the log2 scale. Here, each row represents a gene.expCond: A data frame listing the experimental conditions in each sample with respect to Environment (plate, liquid) and Celltype (swimmer, swarmer)geneInfo: A named vector corresponding to the rows of Y providing information about the function of each gene, if it is known (the V. parahaemolyticus genome is less well-annotated than the human genome).Gode-Potratz C, Kustusch R, Breheny P, Weiss D and McCarter L (2011). Surface sensing in Vibrio parahaemolyticus triggers a programme of gene expression that promotes colonization and virulence. Molecular Microbiology, 79: 240-263.