Mining gene expression data by interpreting principal components

Background  

There are many methods for analyzing microarray data that group together genes having similar patterns of expression over all conditions tested. However, in many instances the biologically important goal is to identify relatively small sets of genes that share coherent expression across only some conditions, rather than all or most conditions as required in traditional clustering; e.g. genes that are highly up-regulated and/or down-regulated similarly across only a subset of conditions. Equally important is the need to learn which conditions are the decisive ones in forming such gene sets of interest, and how they relate to diverse conditional covariates, such as disease diagnosis or prognosis.     

Vegetation and hydrology stratification as proxies to estimate methane emission from tidal marshes

Biogeochemistry - Direct measurement of methane emissions is cost-prohibitive for greenhouse gas offset projects, necessitating the development of alternative accounting methods such as proxies....     

Lights,Rhythms, Infection: The Role of Light and the Circadian Clock in Determining the Outcome of Plant–Pathogen Interactions

The importance of light with respect to the outcome of plant–pathogen interactions is becoming increasingly evident: light affects both the host response and the virulence of some pathogens. The response of plants to environmental signals and stresses is modulated by the circadian clock, and it is apparent that this may include immune responses. Photo and temporal regulation of immune responses may allow plants to anticipate and react more effectively to particular pathogen infections. These aspects of regulation are sometimes overlooked when designing experiments to understand plant–pathogen interactions, complicating the interpretation of the outcomes and the direct comparisons of studies. We review recent key findings in these areas and discuss the implications for experimental design and analyses.     

Dodecyl-{beta}-D-maltoside as a substrate for glucosyl and xylosyl transfer by glycogenin

Glycogenin is the core protein of glycogen proteoglycan andis, at the same time, a self-glucosylating enzyme which catalysesearly glucosyl transfer steps in the biosynthesis of glycogen.In the course of this process, glycogenin is glucosylated progressivelyuntil an oligosaccharide containing 8–11 glucose residueshas been formed. Although glycogenin, under physiological conditions,is both enzyme and acceptor in the glucosyl transfer reactions,it is also capable of utilizing p-nitrophenyl-linked malto-oligosaccharidesas exogenous acceptors. In view of the potential usefulnessof exogenous acceptors in the study of the mechanism of theglycogenin reaction, we have expanded the search for such compoundsand report here that several alkyl glucosides and alkyl maltosidesmay serve as acceptors in glucosyl transfer by beef kidney glycogenin.Dodecyl-ß-D-maltoside (K_m {small tilde}100 µM)was the most effective acceptor among the compounds tested andyielded 30 times as much product as p-nitrophenyl-