Accounting for Redundancy when Integrating Gene Interaction Databases

During the last years gene interaction networks are increasingly being used for the assessment and interpretation of biological measurements. Knowledge of the interaction partners of an unknown protein allows scientists to understand the complex relationships between genetic products, helps to reveal unknown biological functions and pathways, and get a more detailed picture of an organism''s complexity. Being able to measure all protein interactions under all relevant conditions is virtually impossible. Hence, computational methods integrating different datasets for predicting gene interactions are needed. However, when integrating different sources one has to account for the fact that some parts of the information may be redundant, which may lead to an overestimation of the true likelihood of an interaction. Our method integrates information derived from three different databases (Bioverse, HiMAP and STRING) for predicting human gene interactions. A Bayesian approach was implemented in order to integrate the different data sources on a common quantitative scale. An important assumption of the Bayesian integration is independence of the input data (features). Our study shows that the conditional dependency cannot be ignored when combining gene interaction databases that rely on partially overlapping input data. In addition, we show how the correlation structure between the databases can be detected and we propose a linear model to correct for this bias. Benchmarking the results against two independent reference data sets shows that the integrated model outperforms the individual datasets. Our method provides an intuitive strategy for weighting the different features while accounting for their conditional dependencies.     

斑点嗜蓝孢孔菌化学成分、生物活性及水提物荧光猝灭研究

对斑点嗜蓝孢孔菌乙醇提取物进行分级萃取,利用柱层析技术得到6个单体化合物。经核磁数据比对为β-谷甾醇(1)、麦角甾醇(2)、麦角甾-7,22-二烯-3β-醇(3)、5,8-过氧麦角甾-6,22-二烯-3β-醇(4)、3-乙酰齐墩果酸(5)、白桦脂醇(6)。采用Alamar Blue法检测各有机相及单体化合物对NCI-H460人非小细胞肺癌细胞增殖的影响,用DPPH自由基清除法检测其抗氧化活性。利用荧光光谱及紫外-可见光光谱研究方法在模拟人体生理条件下,研究了斑点嗜蓝孢孔菌水提物与人纤维蛋白原的相互作用,实     

小麦细胞增殖核抗原基因启动子的克隆及活性分析

细胞增殖核抗原（proliferating cell nuclear antigen,PCNA）基因是DNA聚合酶δ的辅助因子,在真核细胞DNA复制及其损伤修复中发挥着重要的作用.采用高效热不对称交互PCR法（high-efficiency thermal asymmetric interlaced PCR,hiTAIL PCR）从小麦西农1 376基因组中扩增得到小麦PCNA基因启动子片段,并命名为TaPCNA启动子. PlantCARE启动子在线分析软件预测含有光应答调控元件（Box I）、脱落酸应答元件（ABRE）、花粉发育应答元件（GGTT motif,GTGA motif）及细胞周期转换结合位点（E2F-binding site）等.为了分析其启动子活性, 通过替换pBI121载体上的CaMV35S启动子,构建了TaPCNA启动子与β-葡糖醛酸酶（GUS）基因的融合表达载体,通过农杆菌介导法在烟草叶片中进行瞬时表达. GUS组织化学染色结果表明,TaPCNA基因启动子能够驱动GUS基因在烟草叶片中表达,证实了所获得的启动子序列具有启动活性.本研究通过hiTAIL-PCR法克隆得到TaPCNA基因的启动子,为深入研究该基因的功能奠定了基础.     

生产力调控对翌年苹果园土壤水分和苹果叶片光合特性的影响

以盛果期‘长枝富士’为试验材料, 以生产力调控翌年苹果(Malus pumila)树坐果期为主要观测期, 对不同生产力水平下果园土壤水分状况及苹果叶片光合特性进行了研究。结果表明: 在生产力调控范围内, 土壤剖面各个层次土壤含水量均随着生产力水平的减小而增加, 其中在60 cm处达到最大增量, 为31.02%; 而在600 cm范围内土壤贮水量最大能够提高15.41%。随着生产力水平的降低, “光合午休”现象减弱, 净光合速率(P_n)增加, 最大增幅为25.71%, 下午时段的蒸腾速率(T_r)下降迅速, 水分利用效率(WUE)最大提高34.12%。通过相关分析表明, 土壤贮水量(WSC)与P_n、T_r、WUE之间均达到显著相关, 其相关系数分别为: 0.973^**、-0.543^*和0.992^**。土壤贮水量(x)与水分利用效率(y)之间符合y = 0.002 3x - 1.480 6, R²= 0.984 4^**的回归模型。通过生产力调控可以改善土壤水分状况和果树光合能力, 提高WUE。     

D-氨基酸氧化酶研究进展

D-氨基酸氧化酶(D-amino acid oxidase:oxidoreductase, DAAO, EC 1.4.3.3)是一种以黄素腺嘌呤(FAD)为辅基的典型黄素蛋白酶类,可氧化D-氨基酸的氨基生成相应的酮酸和氨。在体内D-氨基酸的代谢中起着重要作用。主要介绍了D-氨基酸氧化酶的生理功能和应用、表达条件优化及通过定点突变对酶学性质的研究。     

Morphological Variation in Wild Marmosets (Callithrix penicillata and C. geoffroyi) and Their Hybrids

Evolutionary theory and observation predict wider phenotypic variation in hybrids than parental species. Emergent phenotypic novelty in hybrids may in turn drive new adaptations or speciation by breaking parental phenotypic constraints. Primate hybridization is often documented through genetic evidence, but knowledge about the primate hybrid phenotype remains limited due to a small number of available studies on hybrid primate morphology. Here, we examine pelage and morphometric variation in two Brazilian marmoset species (Callithrix penicillata and C. geoffroyi) and their hybrids. Hybrids were sampled in an anthropogenic hybrid zone in the municipality of Viçosa, Minas Gerais state, Brazil. We analyzed hybrid facial and body pelage color variation, and compared 13 morphometric measures between hybrids and parental species. Five different hybrid facial morphotypes were observed, varying from intermediate to parental-like. Hybrid facial morphotypes were biased towards C. penicillata, suggesting that the pelage of this species may be dominant to that of C. geoffroyi in this context, and indicating that mate preference, and therefore gene flow/introgression, may be biased towards C. penicillata within the hybrid zone. Hybrid morphometric features were on average intermediate to parental species traits, but transgressive hybrids were also observed, suggesting that morphometric variation for the studied traits is consistent with Rieseberg’s complementary allele model. Finally, we observed a decoupling of facial patterning and size/shape in hybrids, relative to parent phenotypes, suggesting that an important factor driving phenotypic novelty within the Viçosa marmoset hybrid zone might be the loosening of evolutionary constraints on phenotypic trait integration.     

Pole age affects cell size and the timing of cell division in Methylobacterium extorquens AM1

A number of recent experiments at the single-cell level have shown that genetically identical bacteria that live in homogeneous environments often show a substantial degree of phenotypic variation between cells. Often, this variation is attributed to stochastic aspects of biology-the fact that many biological processes involve small numbers of molecules and are thus inherently variable. However, not all variation between cells needs to be stochastic in nature; one deterministic process that could be important for cell variability in some bacterial species is the age of the cell poles. Working with the alphaproteobacterium Methylobacterium extorquens, we monitored individuals in clonally growing populations over several divisions and determined the pole age, cell size, and interdivision intervals of individual cells. We observed the high levels of variation in cell size and the timing of cell division that have been reported before. A substantial fraction of this variation could be explained by each cell's pole age and the pole age of its mother: cell size increased with increasing pole age, and the interval between cell divisions decreased. A theoretical model predicted that populations governed by such processes will quickly reach a stable distribution of different age and size classes. These results show that the pole age distribution in bacterial populations can contribute substantially to cellular individuality. In addition, they raise questions about functional differences between cells of different ages and the coupling of cell division to cell size.     

Orthoglymma wangapeka gen.n., sp.n. (Coleoptera: Carabidae: Broscini): a newly discovered relict from the Buller Terrane,north‐western South Island,New Zealand,corroborates a general pattern of Gondwanan endemism

Orthoglymma Liebherr, Marris, Emberson, Syrett & Roig‐Juñent gen.n. (Coleoptera: Carabidae: Broscini) is described to accommodate the single type species Orthoglymma wangapeka Liebherr, Marris, Emberson, Syrett & Roig‐Juñent sp.n., known from the Wangapeka Track, Kahurangi National Park, north‐western South Island, New Zealand. Orthoglymma wangapeka sp.n. is analysed cladistically along with a comprehensive array of 42 other broscine generic terminals and four out‐group taxa, using information obtained from 73 morphological characters, and placed as adelphotaxon to the remainder of subtribe Nothobroscina, a clade distributed in New Zealand, southern South America and Australia. Based on fossil evidence for Carabidae, the occurrence of Orthoglymma wangapeka sp.n. on the Buller Terrane, a geological feature once situated on the eastern margin of Gondwana, and early cladistic divergence of Orthoglymma from the remaining Nothobroscina, Orthoglymma wangapeka sp.n. is interpreted as a Gondwanan relict. The New Zealand arthropod fauna is reviewed to identify other taxa in existence at the time of Cretaceous vicariance of New Zealand and Australia. These candidate Gondwanan taxa, all of which are specified using fossil data or molecular divergence‐based estimates, are analysed biogeographically. Where phylogenetic hypotheses are available, primordial distributions are optimized using event‐based, dispersal‐vicariance (DIVA) analysis. The hypothesized Gondwanan‐aged taxa demonstrate inordinate fidelity to the Gondwanan‐aged geological terranes that constitute the western portions of New Zealand, especially in the South Island. Persistence of these relicts through a hypothesized ‘Oligocene drowning’ event is the most parsimonious explanation for the concentration of Gondwanan relicts in the Nelson, Buller and Fiordland districts of the South Island. Geographic patterns of Gondwanan‐aged taxa are compared with distributions of taxa hypothesized to have colonized New Zealand across the Tasman Sea from Australia and New Caledonia, subsequent to Cretaceous vicariance. These post‐Gondwanan taxa exhibit very different patterns of distribution and diversification in New Zealand, including: (i) abundant endemism in Northland, and the islands and peninsulas of the North Island; (ii) species geographically restricted to areas underlain by the youngest Rakaia and Pahau geological terranes; and (iii) species exhibiting exceedingly widespread geographic distributions spanning geological terranes of disparate ages.

相似文献   

Reduced clearance of respiratory syncytial virus infection in a preterm lamb model

Respiratory syncytial virus (RSV) causes significant respiratory disease in children worldwide. For the study of severe RSV disease seen in preterm infants, a suitable animal model is lacking. The novel hypothesis of this study was that preterm lambs are susceptible to bovine RSV (bRSV) infection, an analogous pneumovirus with ruminant host specificity, and that there would be age-dependent differences in select RSV disease parameters. During RSV infection, preterm lambs had elevated temperatures and respiration rates with mild anorexia and cough compared to controls. Gross lesions included multifocal consolidation and atelectasis with foci of hyperinflation. Microscopic lesions included multifocal alveolar septal thickening and bronchiolitis. Immunohistochemistry localized the RSV antigen to all layers of bronchiolar epithelium from a few basal cells to numerous sloughing epithelia. A few mononuclear cells were also immunoreactive. To assess for age-dependent differences in RSV infection, neonatal lambs were infected similarly to the preterm lambs or with a high-titer viral inoculum. Using morphometry at day 7 of infection, preterm lambs had significantly more cellular immunoreactivity for RSV antigen (P <0.05) and syncytial cell formation (P <0.05) than either group of neonatal lambs. This work suggests that perinatal RSV clearance is age-dependent, which may explain the severity of RSV infection in preterm infants. The preterm lamb model is useful for assessing age-dependent mechanisms of severe RSV infection.