ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration

SUMMARY: ESS++ is a C++ implementation of a fully Bayesian variable selection approach for single and multiple response linear regression. ESS++ works well both when the number of observations is larger than the number of predictors and in the 'large p, small n' case. In the current version, ESS++ can handle several hundred observations, thousands of predictors and a few responses simultaneously. The core engine of ESS++ for the selection of relevant predictors is based on Evolutionary Monte Carlo. Our implementation is open source, allowing community-based alterations and improvements. AVAILABILITY: C++ source code and documentation including compilation instructions are available under GNU licence at http://bgx.org.uk/software/ESS.html.     

Enhanced proliferation of cultured human vascular smooth muscle cells linked to increased function of RNA-binding protein HuR

In dividing cells, the RNA-binding protein HuR associates with and stabilizes labile mRNAs encoding proliferative proteins, events that are linked to the increased cytoplasmic presence of HuR. Here, assessment of HuR levels in various vascular pathologies (intimal hyperplasia, atherosclerosis and neointimal proliferation, sclerosis of arterialized saphenous venous graft, and fibromuscular dysplasia) revealed a distinct increase in HuR expression and cytoplasmic abundance within the intima and neointima layers. On the basis of these observations, we postulated a role for HuR in promoting the proliferation of vascular smooth muscle cells. To test this hypothesis directly, we investigated the expression, subcellular localization, and proliferative influence of HuR in human vascular smooth muscle cells (hVSMCs). Treatment of hVSMCs with platelet-derived growth factor increased HuR levels in the cytoplasm, thereby influencing the expression of metabolic, proliferative, and structural genes. Importantly, knockdown of HuR expression by using RNA interference caused a reduction of hVSMC proliferation, both basally and following platelet-derived growth factor treatment. We propose that HuR contributes to regulating hVSMC growth and homeostasis in pathologies associated with vascular smooth muscle proliferation.     

Lack of enhanced spinal regeneration in Nogo-deficient mice

The failure of regeneration of severed axons in the adult mammalian central nervous system is thought to be due partly to the presence of endogenous inhibitors of axon regeneration. The nogo gene encodes three proteins (Nogo-A, -B, and -C) that have been proposed to contribute to this inhibition. To determine whether deletion of nogo enhances regenerative ability, we generated two lines of mutant mice, one lacking Nogo-A and -B but not -C (Nogo-A/B mutant), and one deficient in all three isoforms (Nogo-A/B/C mutant). Although Nogo-A/B-deficient myelin has reduced inhibitory activity in a neurite outgrowth assay in vitro, tracing of corticospinal tract fibers after dorsal hemisection of the spinal cord did not reveal an obvious increase in regeneration or sprouting of these fibers in either mouse line, suggesting that elimination of Nogo alone is not sufficient to induce extensive axon regeneration.     

Effects of supercritical CO2 exposure and depressurization on immobilized lipase activity

Lipozyme IM20 from Novo Nordisk (Denmark) was examined after various treatments. Conditions were chosen to reflect those that would be considered in the design of an industrial process. A two-level factorial design was employed to assess the effects of pressurization/depressurization cycles, rate of depressurization and exposure length. A significant three-factor interaction was observed. Lowest residual activity was observed for runs in which the depressurization rate was 86–89 bar min^–1. Incubation for 12 h also yielded low residual activity but only when exposing the immobilized enzyme to one cycle. The highest residual activity was obtained for immobilized enzymes repeatedly exposed for periods of 12 h (5 times) with a depressurization rate of 4.3 to 4.45 bar min^–1. This effect may be due to the extraction of an inhibiting compound. Tuning process parameters can lead to a seven-fold change in residual activity.     

Prevalence and seasonal variations of six bee viruses in Apis mellifera L. and Varroa destructor mite populations in France

A survey of six bee viruses on a large geographic scale was undertaken by using seemingly healthy bee colonies and the PCR technique. Samples of adult bees and pupae were collected from 36 apiaries in the spring, summer, and autumn during 2002. Varroa destructor samples were collected at the end of summer following acaricide treatment. In adult bees, during the year deformed wing virus (DWV) was found at least once in 97% of the apiaries, sacbrood virus (SBV) was found in 86% of the apiaries, chronic bee paralysis virus (CBPV) was found in 28% of the apiaries, acute bee paralysis virus (ABPV) was found in 58% of the apiaries, black queen cell virus (BQCV) was found in 86% of the apiaries, and Kashmir bee virus (KBV) was found in 17% of the apiaries. For pupae, the following frequencies were obtained: DWV, 94% of the apiaries; SBV, 80% of the apiaries; CBPV, none of the apiaries; ABPV, 23% of the apiaries; BQCV, 23% of the apiaries; and KBV, 6% of the apiaries. In Varroa samples, the following four viruses were identified: DWV (100% of the apiaries), SBV (45% of the apiaries), ABPV (36% of the apiaries), and KBV (5% of the apiaries). The latter findings support the putative role of mites in transmitting these viruses. Taken together, these data indicate that bee virus infections occur persistently in bee populations despite the lack of clinical signs, suggesting that colony disease outbreaks might result from environmental factors that lead to activation of viral replication in bees.     

K2P18.1 translates T cell receptor signals into thymic regulatory T cell development

It remains largely unclear how thymocytes translate relative differences in T cell receptor (TCR) signal strength into distinct developmental programs that driv...     

Evolutionary analysis of life span, competition, and adaptive radiation, motivated by the Pacific rockfishes (Sebastes)

The Pacific rockfishes (Sebastes spp) are remarkable for both their diversity (on the order of 100 species) and range of maximum life span ( approximately 10 years for Calico rockfish to approximately 200 years for Rougheye rockfish). We describe the natural history and patterns of diversity and life span in these species and then use independent contrasts to explore correlates of these. When phylogenetic history is taken into account, maximum life span is explained by age at maturity, size at maturity, and the interaction of these two. We introduce a life-history model that allows insight into the origin of these correlations. We then describe a variety of mechanisms that may increase lifepans and diversity. These include fluctuating environments (in which organisms basically have to "wait out" bad periods to reproduce successfully), diversity, and longevity inspired by interspecific competition and physiological complexity in growth and accumulation of cellular damage. All of the results point toward the importance of flat or "indifferent" fitness surfaces as a key element in the evolution of diversity. We conclude that further development of the theory of flat or indifferent fitness surfaces as applied to diversity and life span is clearly warranted.