Linking microarray reporters with protein functions

Background  

The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways.     

基于最大熵生态位模型的中华穿山甲潜在适宜生境预测

中华穿山甲（Manis pentadactyla）属于全球极度濒危物种,也是我国一级保护动物。对中华穿山甲的非法捕杀曾导致其种群数量锐减。但是,近年来相关研究报道较少,穿山甲分布状况不明,极大地制约了对该物种的有效保护。搜集了近年来国内中华穿山甲的救护记录和救护新闻,甄别出67个记录分布点,利用最大熵模型软件（MaxEnt）进行因子筛选,结果表明最冷季度降水量、人口密度、年降水量、坡度、坡向、海拔等6个环境变量是与中华穿山甲分布显著相关的影响因子。基于6个主导环境变量构建的MaxEnt模型AUC平均值为0.961±0.014,预测结果达到极好标准。刀切法（Jackknife）表明,其中最冷季度降水量、年降水量、人口密度和海拔是影响中华穿山甲分布的主要因素。中华穿山甲适宜生境（出现概率大于0.498）具有以下特点：最冷季度降水量141.22-439.46 mm,年降水量1471.67-2386.56 mm,人口密度≥390人/km²,海拔<316.98 m。该模型预测中华穿山甲在我国的潜在分布适宜区主要位于我国长江以南地区,总面积约为74.27×10⁴ km²,占国土面积的7.73%,主要集中在江西、广东、湖南和广西省,面积分别占该区域的97.58%,89.65%,76.90%和73.08%;其次是浙江、福建、台湾和安徽省。湖北、江苏、四川、云南、贵州等省份也有中华穿山甲的零星分布。湖北东南部、江苏南部、浙江西南部和福建西北部等与江西接壤的区域也是中华穿山甲的重要潜在分布适宜区。明确中华穿山甲的潜在分布适宜区,可为该物种的种群保护和栖息地管理提供科技支撑。     

Prevention of postoperative bleeding after complex pediatric cardiac surgery by early administration of fibrinogen,prothrombin complex and platelets: a prospective observational study

Some retrospective and in vitro studies suggest that general anesthetics influence breast cancer recurrence and metastasis. We compared the effects of general anesthetics sevoflurane versus propofol on breast cancer cell survival, proliferation and invasion in vitro. The investigation focused on effects in intracellular Ca2+ homeostasis as a mechanism for general anesthetic-mediated effects on breast cancer cell survival and metastasis. Estrogen receptor-positive (MCF7) and estrogen receptor-negative (MDA-MB-436) human breast cancer cell lines along with normal breast tissue (MCF10A) were used. Cells were exposed to sevoflurane or propofol at clinically relevant and extreme doses and durations for dose- and time-dependence studies. Cell survival, proliferation and migration following anesthetic exposure were assessed. Intracellular and extracellular Ca2+ concentrations were modulated using Ca2+ chelation and a TRPV1 Ca2+ channel antagonist to examine the role of Ca2+ in mediating anesthetic effects. Sevoflurane affected breast cancer cell survival in dose-, time- and cell type-dependent manners. Sevoflurane, but not propofol, at equipotent and clinically relevant doses (2% vs. 2 μM) for 6 h significantly promoted breast cell survival in all three types of cells. Paradoxically, extreme exposure to sevoflurane (4%, 24 h) decreased survival in all three cell lines. Chelation of cytosolic Ca2+ dramatically decreased cell survival in both breast cancer lines but not control cells. Inhibition of TRPV1 receptors significantly reduced cell survival in all cell types, an effect that was partially reversed by equipotent sevoflurane but not propofol. Six-hour exposure to sevoflurane or propofol did not affect cell proliferation, metastasis or TRPV1 protein expression in any type of cell. Sevoflurane, but not propofol, at clinically relevant concentrations and durations, increased survival of breast cancer cells in vitro but had no effect on cell proliferation, migration or TRPV1 expression. Breast cancer cells require higher cytoplasmic Ca2+ levels for survival than normal breast tissue. Sevoflurane affects breast cancer cell survival via modulation of intracellular Ca2+ homeostasis.     

Predictions of Taylor's power law, density dependence and pink noise from a neutrally modeled time series

There has recently been increasing interest in neutral models of biodiversity and their ability to reproduce the patterns observed in nature, such as species abundance distributions. Here we investigate the ability of a neutral model to predict phenomena observed in single-population time series, a study complementary to most existing work that concentrates on snapshots in time of the whole community. We consider tests for density dependence, the dominant frequencies of population fluctuation (spectral density) and a relationship between the mean and variance of a fluctuating population (Taylor's power law). We simulated an archipelago model of a set of interconnected local communities with variable mortality rate, migration rate, speciation rate, size of local community and number of local communities. Our spectral analysis showed ‘pink noise’: a departure from a standard random walk dynamics in favor of the higher frequency fluctuations which is partly consistent with empirical data. We detected density dependence in local community time series but not in metacommunity time series. The slope of the Taylor's power law in the model was similar to the slopes observed in natural populations, but the fit to the power law was worse. Our observations of pink noise and density dependence can be attributed to the presence of an upper limit to community sizes and to the effect of migration which distorts temporal autocorrelation in local time series. We conclude that some of the phenomena observed in natural time series can emerge from neutral processes, as a result of random zero-sum birth, death and migration. This suggests the neutral model would be a parsimonious null model for future studies of time series data.     

Dopamine receptor genetic polymorphisms and body composition in undernourished pastoralists: An exploration of nutrition indices among nomadic and recently settled Ariaal men of northern Kenya

Background  

Minor alleles of the human dopamine receptor polymorphisms, DRD2/TaqI A and DRD4/48 bp, are related to decreased functioning and/or numbers of their respective receptors and have been shown to be correlated with body mass, height and food craving. In addition, the 7R minor allele of the DRD4 gene is at a higher frequency in nomadic compared to sedentary populations. Here we examine polymorphisms in the DRD2 and DRD4 genes with respect to body mass index (BMI) and height among men in two populations of Ariaal pastoralists, one recently settled (n = 87) and the other still nomadic (n = 65). The Ariaal live in northern Kenya, are chronically undernourished and are divided socially among age-sets.     

Subunit structure of Achromobacter collagenase.

The highly active form of collagenase (EC 3.4.24.3) from Achromobacter iophagus (specific activity 2 microkat/mg) has a molecular weight of 70,000 and the sedimentation coefficient s20,2 = 4.4 S. It is composed of two subunits of molecular weight 35,000 and s20,w of 2.9 S. The dissociation of the dimer under different conditions resulted in the complete and irreversible loss of enzymic activity. A unique N-terminal sequence Thr-Ala-Ala-Asp-Leu-Glu-Ala-Leu-Val- indicates that the two subunits are identical, at least in the N-terminal part of the polypeptide chain. Reduction and pyridylethylation of the subunit change neither molecular weight nor amino acid composition: therefore each subunit of molecular weight 35,000 consists of a single polypeptide chain. Another active and homogeneous form of Achromobacter collagenase (specific activity 1.64 microkat/mg) gives a value for the apparent molecular weight of 80,000 on sodium dodecyl sulphate-polyacrylamide electrophoresis. It is also a dimer in which each of the two subunits of molecular weight 35,000 binds non-covalently a peptide of molecular weight 5000. The dissociation of this form of collagenase is also accompanied by irreversible loss of enzymic activity. The amino acid composition of the subunits which were isolated from both 70,000 and 80,000 collagenases is the same. The role of dimer-monometer equilibrium in the biological function of collagenase is discussed.