A decoy set for the thermostable subdomain from chicken villin headpiece,comparison of different free energy estimators

Background  

Estimators of free energies are routinely used to judge the quality of protein structural models. As these estimators still present inaccuracies, they are frequently evaluated by discriminating native or native-like conformations from large ensembles of so-called decoy structures.     

HistoChoice® as an alternative to formalin fixation of undecalcified bone specimens

We compared histochemical and immunohistochemical staining as well as fluorochrome labeling in murine bone specimens that were fixed with 10% neutral buffered formalin to those fixed with HistoChoice®. We showed that sections from undecalcified tibiae fixed for 4 h in HistoChoice® resulted in enhanced toluidine blue and Von Kossa histochemical staining compared to formalin fixation. HistoChoice® produced comparable or improved staining for alkaline phosphatase. Acid phosphatase localization was better in formalin fixed specimens, but osteoclasts were visuralized more easily in HistoChoice® fixed specimens. As expected, immunohistochemical labeling was antibody dependent; some antibodies labeled better in HistoChoice® fixed specimens while others were better in formalin fixed specimens. Toluidine blue, Von Kossa, and alkaline phosphatase staining of sections fixed for 12 h produced sections that were similar to 4 h fixed sections. Fixation for 12 h preserved acid phosphatase activity better. Increasing fixation to 12 h affected immunolocalization differentially. Bone sialoprotein labeling in HistoChoice® fixed specimens was comparable to formalin fixed samples. On the other hand, after 12 h formalin fixation, osteocalcin labeling was comparable to HistoChoice®. For most histochemical applications, fixing murine bone specimens for 4 h with HistoChoice® yielded superior staining compared to formalin fixation. If immunohistochemical localization is desired, however, individual antibodies must be tested to determine which fixation process retains antigenicity better. In addition, there was no detectable difference in the intensity of fluorochrome labeling using either fixative. Finally, fixation duration did not alter the intensity of labeling.     

大型无脊椎动物群落指数和群落数量指数在河流水质评价中的应用

本文介绍了新西兰常用的大型无脊椎动物群落指数(MCI)和大型无脊椎动物群落数量指数(QMCI)的原理及使用方法,并利用MCI和QMCI对新西兰惠灵顿地区40条河流53个监测点进行评价.结果表明:MCI和QMCI均与河流营养指标呈极显著相关关系,可用来监测和评价水体的营养污染状况;二者快速准确地监测出惠灵顿地区河流水质总体良好,但部分河流污染严重,并分析了污染的原因.MCI与QMCI存在极显著相关关系,但MCI与营养指标间的相关关系大于QMCI,可以准确地反映出水体中营养元素的富集状况.     

Local and landscape scale determinants of macroinvertebrate assemblages and their conservation value in ponds across an urban land-use gradient

Urbanisation represents a growing threat to natural communities across the globe. Small aquatic habitats such as ponds are especially vulnerable and are often poorly protected by legislation. Many ponds are threatened by development and pollution from the surrounding landscape, yet their biodiversity and conservation value remain poorly described. Here we report the results of a survey of 30 ponds along an urban land-use gradient in the West Midlands, UK. We outline the environmental conditions of these urban ponds to identify which local and landscape scale environmental variables determine the biodiversity and conservation value of the macroinvertebrate assemblages in the ponds. Cluster analysis identified four groups of ponds with contrasting macroinvertebrate assemblages reflecting differences in macrophyte cover, nutrient status, riparian shading, the nature of the pond edge, surrounding land-use and the availability of other wetland habitats. Pond conservation status varied markedly across the sites. The richest macroinvertebrate assemblages with high conservation value were found in ponds with complex macrophyte stands and floating vegetation with low nutrient concentrations and little surrounding urban land. The most impoverished assemblages were found in highly urban ponds with hard-engineered edges, heavy shading and nutrient rich waters. A random forest classification model revealed that local factors usually had primacy over landscape scale factors in determining pond conservation value, and constitute a priority focus for management.     

TAP score: torsion angle propensity normalization applied to local protein structure evaluation

Background  

Experimentally determined protein structures may contain errors and require validation. Conformational criteria based on the Ramachandran plot are mainly used to distinguish bet ween distorted and adequately refined models. While the readily available criteria are sufficient to detect totally wrong structures, establishing the more subtle differences between plausible structures remains more challenging.     

Stream invertebrate communities of Campbell Island

Invertebrates at 20 sites on 19 Campbell Island streams were sampled over the Austral summer of 1996/97. Twelve of the 16 benthic invertebrate taxa known from the island were collected. The most abundant group was the Crustacea, which included an isopod (Notidotea lacustris) and two amphipods, one belonging to the family Eusiridae and one to the suborder Gammaridea. Five species of Diptera were found (three chironomids; Orthocladiinae sp., Chironominae sp. and Maoridiamesa insularis, as well as an empidid and a simuliid Austrosimulium campbellense). One trichopteran, the hydroptilid caddis Oxyethira albiceps and two plecopteran species Rungaperla campbelli and R. longicauda and unidentified Oligochaetes were also collected. In general, Campbell Island streams are stable, deeply incised, have unusually high salinity from wind-blown sea spray and a unique benthic invertebrate fauna. With the exception of high altitude streams with large boulders which had invertebrate communities dominated by Crustacea and the endemic stonefly of the genus Rungaperla, none of the measured environmental variables or geographic location could explain the distinctive communities found. The species-poor stream fauna and the absence of many invertebrate families commonly found on mainland New Zealand appears to be related to the extreme isolation and geological history of the island.     

The role of the mesangial cell and its matrix in the pathogenesis of diabetic nephropathy.

Mesangial cells are pericyte-like cells which are found the glomeruli of the kidney. It is well known that they have important contractile and synthetic properties regulating the function of the glomerulus. During diabetes the synthesis of various extracellular matrix (ECM) components by mesangial cells are increased. In recent years it has been recognized that degradation of ECM may also be decreased in diabetes, contributing to the process of mesangium accumulation. The major enzymes responsible for ECM degradation are a large group of enzymes collectively known as matrix metalloproteinases (MMPs). The physiology of MMPs is complex and their activity is tightly regulated at many levels. The MMPs are synthesized as proenzymes and require activation via catalytic cleavage to become fully active. In this regard it is of importance that the mesangial cell and its pericellular matrix have a very active plasminogen cascade that can liberate plasmin locally to mediate matrix degradation both directly and indirectly, by activating the MMPs. In addition, the MMPs are regulated by transforming growth factor beta (TGF-beta). There is evidence that each of these pathways regulating the matrix degradation is affected by the diabetic environment and this will be the subject of this contribution.     

The effect of patch disturbance on stream invertebrate community structure: the influence of disturbance history

The effect of disturbance history on the recovery of benthic invertebrate communities following disturbance was investigated in four streams in the Southern Alps of New Zealand. Two of the streams had a history of fluctuating discharge and temperature while the others did not. Recovery from disturbance was tested experimentally using baskets of cobbles, a third of which were disturbed every week for 9 weeks, a further third every 3 weeks and the final third left undisturbed. Algal biiomass, number of invertebrate taxa and total number of invertebrates all declined in baskets disturbed more frequently. Although the relative abundance of some taxa declined with time since the last disturbance, no taxa showed a significant decline in absolute abundance. However, several taxa showed marked increases in relative abundance in the less disturbed treatments particularly at the more stable sites. In contrast to the predictions of ecological theory, numbers of taxa and total invertebrates appeared to recover more quickly in the more complex communities at the stable sites. However, if these communities are considered to represent only stable communities, they do support the view that more complex communities will be more resilient. Community structure at the stable sites was also more similar between baskets in the undisturbed treatment than at the unstable sites, suggesting communities had reached a constant state more quickly. The more rapid recovery of communities measured at the stable sites may have been a consequence of experimental scale; disturbed patches were only 0.045 m² in area and the higher densities of invertebrates at the stable sites meant a larger pool of colonists was available following each experimental disturbance. Nevertheless, ideas of stability in ecological theory and the scale of most spate events suggest this is the appropriate scale for examining community recovery. Furthermore, the larger pool of available colonists could not explain all the differences in community response, as patterns of change in community structure at the stable sites differed considerably more from those expected by purely random colonisation processes than at the unstable sites.     

Productivity–diversity relationships for stream invertebrates differ geographically

More productive environments typically have more species, although the specific form of this relationship is unclear and can vary with spatial scale. This relationship has received little direct attention in lotic systems, and thus the nature of the relationship is unclear, as is any effect of spatial scale. We examined the link between stream primary productivity and macroinvertebrate diversity in Spain and New Zealand and hypothesized that macroinvertebrate diversity would increase log-linearly with increasing productivity in both regions. We sampled 24 streams in Cantabria, Spain, and 24 in the central North Island, New Zealand. Algal primary productivity was approximately three times higher in Spanish streams, but taxonomic richness of invertebrates did not differ between the regions. Richness and Shannon diversity only responded to productivity in the New Zealand streams, exhibiting the predicted log-linear increase. In the Spanish streams, only the total number of individuals increased with productivity. However, when plotted on the same axes, richness in the Spanish streams simply occurred on the linear portion of the graph to the right of the New Zealand streams. We speculate that productivity in the Spanish streams never became low enough to constrain diversity, but did in the New Zealand streams. Combining results from the two regions, there is no evidence of a decline in diversity with higher productivity.