Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis

Background  

Concerns are often raised about the accuracy of microarray technologies and the degree of cross-platform agreement, but there are yet no methods which can unambiguously evaluate precision and sensitivity for these technologies on a whole-array basis.     

Seasonal habitat use and selection by grizzly bears in Northern British Columbia

We defined patterns of habitat use and selection by female grizzly bears (Ursus arctos) in the Besa-Prophet watershed of northern British Columbia. We fitted 13 adult females with Geographic Positioning System (GPS) radio-collars and monitored them between 2001 and 2004. We examined patterns of habitat selection by grizzly bears relative to topographical attributes and 3 potential surrogates of food availability: land-cover class, vegetation biomass or quality (as measured by the Normalized Difference Vegetation Index), and selection value for prey species themselves (moose [Alces alces], elk [Cervus elaphus], woodland caribou [Rangifer tarandus], Stone's sheep [Ovis dalli stonei]). Although vegetation biomass and quality, and selection values for prey were important in seasonal selection by some individual bears, land-cover class, elevation, aspect, and vegetation diversity most influenced patterns of habitat selection across grizzly bears, which rely on availability of plant foods and encounters with ungulate prey. Grizzly bears as a group avoided conifer stands and areas of low vegetation diversity, and selected for burned land-cover classes and high vegetation diversity across seasons. They also selected mid elevations from what was available within seasonal ranges. Quantifying relative use of different attributes helped place selection patterns within the context of the landscape. Grizzly bears used higher elevations (1,595 ± 31 m SE) in spring and lower elevations (1,436 ± 27 m) in fall; the range of average elevations used among individuals was highest (500 m) during the summer. During all seasons, grizzly bears most frequented aspects with high solar gain. Use was distributed across 10 land-cover classes and depended on season. Management and conservation actions must maintain a diverse habitat matrix distributed across a large elevational gradient to ensure persistence of grizzly bears as levels of human access increase in the northern Rocky Mountains. © 2011 The Wildlife Society.     

From burned slopes to streams: how wildfire affects nitrogen cycling and retention in forests and fire-prone watersheds

Biogeochemistry - Wildfire is a major driver of nitrogen (N) cycling and export from terrestrial to aquatic systems. While fire is a natural process in many watersheds, it can still degrade water...     

Developmental changes in microheterogeneity of foetal plasma glycoproteins of mice

Changes in microheterogeneity of foetal plasma glycoproteins during development of mouse embryos were investigated. Analysis of foetal plasma by polyacrylamide-gel electrophoresis indicated three major zones of proteins: (1) transferrins, (2) alpha-foetoproteins and (3) albumin. Three transferrins (Tr1, Tr2, Tr3) and five alpha-foetoproteins (Fp1, Fp2, Fp3, Fp4, Fp5) were resolved. Evidence for the presence of transferrins was the binding of (59)Fe to the three electrophoretic variants. By day 15.5 of gestation, there was a marked increase in the more-acidic components (Tr3, Fp4, Fp5) and a decrease in the less-acidic ones (Tr1, Tr2, Fp1, Fp2, Fp3). Treatment of foetal plasma with neuraminidase at this time of development converted the more acidic components into Tr1 and Tr2 and Fp1, Fp2 and Fp3. Furthermore, it was shown that early in development (day 12.5) only the less-acidic components of transferrin and alpha-foetoprotein were synthesized; at the later time in development (day 14.5) new synthesis of the acidic components of both groups occurred. That these more-acidic components of alpha-foetoprotein (Fp4, Fp5) were in fact electrophoretic variants of the less-acidic alpha-foetoproteins was shown by the immunoprecipitation of labelled Fp4 and Fp5 with anti-Fp1, anti-Fp2 and anti-Fp3. From these results it is postulated that the plasma glycoproteins that are synthesized later in development contain increased amounts of sialic acid and that the observed changes in microheterogeneity of these proteins represent regulation of glycoprotein biosynthesis at the level of carbohydrate attachment.     

EDC3 phosphorylation regulates growth and invasion through controlling P‐body formation and dynamics

Regulation of mRNA stability and translation plays a critical role in determining protein abundance within cells. Processing bodies (P‐bodies) are critical regulators of these processes. Here, we report that the Pim1 and 3 protein kinases bind to the P‐body protein enhancer of mRNA decapping 3 (EDC3) and phosphorylate EDC3 on serine (S)161, thereby modifying P‐body assembly. EDC3 phosphorylation is highly elevated in many tumor types, is reduced upon treatment of cells with kinase inhibitors, and blocks the localization of EDC3 to P‐bodies. Prostate cancer cells harboring an EDC3 S161A mutation show markedly decreased growth, migration, and invasion in tissue culture and in xenograft models. Consistent with these phenotypic changes, the expression of integrin β1 and α6 mRNA and protein is reduced in these mutated cells. These results demonstrate that EDC3 phosphorylation regulates multiple cancer‐relevant functions and suggest that modulation of P‐body activity may represent a new paradigm for cancer treatment.