Accounting for biological variation in differential display two-dimensional electrophoresis experiments

Proteomic Analysis of Normal Expression Differences Exist in Bacillus Subtilis 168 Cultivation

Biological science discovery often involves comparing conditions to a normal state, but little is known about "normal." Therefore, we used proteomic strategy to compare data from replicate samples of Bacillus subtilis 168 which were grown under identical condition. The results show that 294 differentially expressed proteins were annotated in 88 Gene Ontology functional groups and enriched in 13 KEGG pathways. We assume that normal expression differences are associated with adaptation to diverse environments. Moreover, five proteins (CotY, ThiG, SspA, SspB, and SspE) and their related genes were identified as having significantly different expressions at translational and transcriptional levels. Most of them are related to stress resistance and germination, indicating that normal expression differences can be regarded as a rapid response mechanism for survival. However, unstable protein expression may cause some fermentative problems that were observed in histidine and sulfur metabolism pathways. Our study facilitates dissection of the influence of biological variance on cultivation safety and stability.

Sources of Experimental Variation in 2-D Maps: The Importance of Experimental Design in Gel-Based Proteomics

The success of proteomic studies employing 2-D maps largely depends on the way surveys and experiments have been organized and performed. Planning gel-based proteomic experiments involves the selection of equipment, methodology, treatments, types and number of samples, experimental layout, and methods for data analysis. A good experimental design will maximize the output of the experiment while taking into account the biological and technical resources available. In this chapter we provide guidelines to assist proteomics researchers in all these choices and help them to design quantitative 2-DE experiments.