Colony size measurement of the yeast gene deletion strains for functional genomics

Abstract

Background: Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by gene mutations, chemicals or both. Manual inspection of the yeast colonies that are grown under different conditions is often used as a method to detect such growth differences.

Results: Here, we developed a computerized image analysis system called Growth Detector (GD), to automatically acquire quantitative and comparative information for yeast colony growth. GD offers great convenience and accuracy over the currently used manual growth measurement method. It distinguishes true yeast colonies in a digital image and provides an accurate coordinate oriented map of the colony areas. Some post-processing calculations are also conducted. Using GD, we successfully detected a genetic linkage between the molecular activity of the plant-derived antifungal compound berberine and gene expression components, among other cellular processes. A novel association for the yeast mek1 gene with DNA damage repair was also identified by GD and confirmed by a plasmid repair assay. The results demonstrate the usefulness of GD for yeast functional genomics research.

Conclusion: GD offers significant improvement over the manual inspection method to detect relative yeast colony size differences. The speed and accuracy associated with GD makes it an ideal choice for large-scale functional genomics investigations.

Figure 1

Spot Test analysis. Equal numbers of wild type or mutant yeast cells were spotted on media with or without 400 ug/ml of cobalt. The relative numbers of yeast cells spotted on the plates are indicated. In relation to wild type, the mutant strain did not produce as many colonies in the presence of cobalt. This suggests sensitivity to cobalt for the mutant cells. W/T is the wild type (normal) strain; Mut is the gene deletion mutant strain for the rox1 gene.

Figure 2

Sample input image. A sample input image to the system is shown in (a). Arrows show the red indicators. (b) Image in (a) is aligned using a linear conformal spatial transformation.

Figure 3

Segmentation threshold value acquired by three different methods. The values represent the data from 6 independent sets of plates. 96 plates of yeast arrays were used.

Figure 4

The automated system can detect colonies from other undesired objects. (a) Unwanted long entities and small blemishes are present in the image (arrows point to some instances). (b) The automated system correctly discards most of these objects as can be seen in the binary image after segmentation.

Figure 5

Missing rows. The bottom row of colonies is missing in (a). This is marked on the image by a white ellipse. (b) White rectangle showing position of distance checking limit. Each side of this rectangle is 100 pixels distant from the plate side parallel to it. Imposing the predefined periphery values (stars) compensates for the missing row.

Figure 6

Satellite effect around a colony. (a) Example of a colony, which is comprised of a main region and a few smaller islands (satellites). (b) Zoomed in version of (a).