The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression

High-throughput analyses that are central to microbial systems biology and ecophysiology research benefit from highly homogeneous and physiologically well-defined cell cultures. While attention has focused on the technical variation associated with high-throughput technologies, biological variation introduced as a function of cell cultivation methods has been largely overlooked. This study evaluated the impact of cultivation methods, controlled batch or continuous culture in bioreactors versus shake flasks, on the reproducibility of global proteome measurements in Shewanellaoneidensis MR-1. Variability in dissolved oxygen concentration and consumption rate, metabolite profiles, and proteome was greater in shake flask than controlled batch or chemostat cultures. Proteins indicative of suboxic and anaerobic growth (e.g., fumarate reductase and decaheme c-type cytochromes) were more abundant in cells from shake flasks compared to bioreactor cultures, a finding consistent with data demonstrating that “aerobic” flask cultures were O2 deficient due to poor mass transfer kinetics. The work described herein establishes the necessity of controlled cultivation for ensuring highly reproducible and homogenous microbial cultures. By decreasing cell to cell variability, higher quality samples will allow for the interpretive accuracy necessary for drawing conclusions relevant to microbial systems biology research

The nature and identification of quantitative trait loci: A community's view

This white paper by eighty members of the Complex Trait Consortium presents a community’s view on the approaches and statistical analyses that are needed for the identification of genetic loci that determine quantitative traits. Quantitative trait loci (QTLs) can be identified in several ways, but is there a definitive test of whether a candidate locus actually corresponds to a specific QTL? Much of the genetic variation that underlies disease susceptibility and morphology is complex and is governed by loci that have quantitative effects on the phenotype. Gene–gene and gene–environment interactions are common and make these loci difficult to analyse. Here, we present a community’s view on the steps that are necessary to identify genetic loci that govern quantitative traits, along with a set of interpretive guidelines. This community mostly represents interests in the analyses of rodent quantitative trait loci (QTLs), although many of the same principles apply to other species. With the development of new genetic techniques and with more information about the mammalian genome, we are confident that QTLs will become easier to identify and will provide valuable information about normal development and disease processes

Differences in dietary habits, serum fatty acid compositions and other coronary risk characteristics between freshmen and fourth-year male university students

Westernization of lifestyles among Japanese, in particular among young generations, is a matter of concern for future increase in coronary heart disease. We surveyed a total of 349 male university students to examine changes in lifestyles and coronary risk factors in campus life. We compared dietary habits and serum fatty acid compositions as well as other coronary risk characteristics between freshmen (n=171) and fourth-year (senior) students (n=178). Serum fatty acid compositions and dietary intakes of selected foods as well as serum lipids, blood pressures and physical characteristics were examined at the 1996 and 1997 annual health examinations