海洋鱼类肠道微生物研究进展及应用前景

肠道微生物在动物体内数量庞大、结构复杂,在宿主生长发育过程中发挥着重要作用.淡水鱼类肠道微生物的研究主要集中于其对鱼类生长代谢、营养吸收及免疫调节等方面的影响,海洋鱼类则研究相对较少,且多集中于肠道微生物多样性及其变动影响因素分析.本文在归纳总结鱼类肠道微生物功能及其研究方法的基础上,着重分析肠道微生物在海洋鱼类生长发...     

膜蛋白ATAD3A在线粒体质量控制中的作用

线粒体质量控制对于线粒体网络的稳态和线粒体功能的正常发挥具有重要意义。三磷酸腺苷酶家族蛋白3A(ATAD3A)是同时参与调节线粒体结构功能、线粒体动力学和线粒体自噬等重要生物学过程的线粒体膜蛋白之一。近期研究表明,ATAD3A既可与Mic60/Mitofilin和线粒体转录因子A (TFAM)等因子相互作用以维持线粒体嵴的形态和氧化磷酸化功能,又能与发动蛋白相关蛋白1 (Drp1)结合而正性/负性调节线粒体分裂,还可作为线粒体外膜转位酶（TOM）复合物和线粒体内膜转位酶（TIM）复合物之间的桥接因子而介导PTEN诱导激酶（PINK1）输入线粒体进行加工,显示出促自噬或抗自噬活性。本文对ATAD3A在调控线粒体质量控制中的作用及其机制进行了综述。     

西藏色季拉山垂直植被带土壤细菌群落组成及功能潜势

研究青藏高原土壤微生物群落组成和功能的空间分布特征有助于深入理解典型高寒生态系统中土壤微生物的重要生态功能.本研究采用16S rDNA高通量测序方法,分析了西藏色季拉山4个不同海拔土壤细菌群落物种组成和功能潜势的变化特征及其驱动因子.结果 表明:随着海拔的升高,土壤细菌的丰富度和Shannon多样性指数显著降低;酸杆菌...     

Effects of sampling protocol on the shapes of species richness curves

Aim Scheiner (Journal of Biogeography, 2009, 36 , 2005–2008) criticized several issues regarding the typology and analysis of species richness curves that were brought forward by Dengler (Journal of Biogeography, 2009, 36 , 728–744). In order to test these two sets of views in greater detail, we used a simulation model of ecological communities to demonstrate the effects of different sampling schemes on the shapes of species richness curves and their extrapolation capability. Methods We simulated five random communities with 100 species on a 64 × 64 grid using random fields. Then we sampled species–area relationships (SARs, contiguous plots) as well as species–sampling relationships (SSRs, non‐contiguous plots) from these communities, both for the full extent and the central quarter of the grid. Finally, we fitted different functions (power, quadratic power, logarithmic, Michaelis–Menten, Lomolino) to the obtained data and assessed their goodness‐of‐fit (Akaike weights) and their extrapolation capability (deviation of the predicted value from the true value). Results We found that power functions gave the best fit for SARs, while for SSRs saturation functions performed better. Curves constructed from data of 32² grid cells gave reasonable extrapolations for 64² grid cells for SARs, irrespective of whether samples were gathered from the full extent or the centre only. By contrast, SSRs worked well for extrapolation only in the latter case. Main conclusions SARs and SSRs have fundamentally different curve shapes. Both sampling strategies can be used for extrapolation of species richness to a target area, but only SARs allow for extrapolation to a larger area than that sampled. These results confirm a fundamental difference between SARs and area‐based SSRs and thus support their typological differentiation.     

Modeling continuous auxiliary covariate data in generalized linear mixed models using the kernel smoother

Auxiliary covariate data are often collected in biomedical studies when the primary exposure variable is only assessed on a subset of the study subjects. In this study, we investigate a semiparametric‐estimated likelihood estimation for the generalized linear mixed models (GLMM) in the presence of a continuous auxiliary variable. We use a kernel smoother to handle continuous auxiliary data. The method can be used to deal with missing or mismeasured covariate data problems in a variety of applications when an auxiliary variable is available and cluster sizes are not too small. Simulation study results show that the proposed method performs better than that which ignores the random effects in GLMM and that which only uses data in the validation data set. We illustrate the proposed method with a real data set from a recent environmental epidemiology study on the maternal serum 1,1‐dichloro‐2,2‐bis(p‐chlorophenyl) ethylene level in relationship to preterm births.     

An Efficient Timer and Sizer of Biomacromolecular Motions

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Identification and in silico prediction of metabolites of tebufenozide derivatives by major human cytochrome P450 isoforms

Cytochrome P450 (CYP) enzymes constitute a superfamily of heme-containing monooxygenases. CYPs are involved in the metabolism of many chemicals such as drugs and agrochemicals. Therefore, examining the metabolic reactions by each CYP isoform is important to elucidate their substrate recognition mechanisms. The clarification of these mechanisms may be useful not only for the development of new drugs and agrochemicals, but also for risk assessment of chemicals. In our previous study, we identified the metabolites of tebufenozide, an insect growth regulator, formed by two human CYP isoforms: CYP3A4 and CYP2C19. The accessibility of each site of tebufenozide to the reaction center of CYP enzymes and the susceptibility of each hydrogen atom for metabolism by CYP enzymes were evaluated by a docking simulation and hydrogen atom abstraction energy estimation at the density functional theory level, respectively. In this study, the same in silico prediction method was applied to the metabolites of tebufenozide derivatives by major human CYPs (CYP1A2, 2C9, 2C19, 2D6, and 3A4). In addition, the production rate of the metabolites by CYP3A4 was quantitively analyzed by frequency based on docking simulation and hydrogen atom abstraction energy using the classical QSAR approach. Then, the obtained QSAR model was applied to predict the sites of metabolism and the metabolite production order by each CYP isoform.