肿瘤微阵列数据统计分析概述

微阵列技术已广泛应用于生物学和医学研究领域,如肿瘤的诊断和分型、预测和治疗,理解肿瘤的发生机制、生物学通路和基因网络。统计学方法在这一科学挑战中的地位至关重要。我们综述了微阵列实验数据分析的统计学方法最新发展,主要描述了微阵列数据的标准化、差异表达基因的统计学检验及微阵列技术在肿瘤治疗中的应用,重点介绍了时间序列微阵列数据分析方法和基因调控网络在肿瘤研究中的最新发展。     

基于MaxEnt模型的生态系统服务需求及其簇的空间分异——以陕西省米脂县为例

从微观土地利用主体视角量化并明确生态系统服务需求的空间格局对于改善资源依赖地区农户福祉具有重要意义。以地处黄土丘陵沟壑区的米脂县为例,基于参与式制图与MaxEnt模型实现10类生态系统服务需求空间评估;同时,采用K-means聚类识别村域服务需求簇,并探究环境变量对服务需求及其簇空间分布的影响。结果如下：(1)各类服务需求空间分异明显。供给服务中粮食和肉类供给均呈现中部高东西低的空间格局,水果供给空间分布规律相反;调节服务中土壤保持和空气净化高需求区均分布于高海拔区域,水源涵养高需求区分布于无定河流域;4类文化服务均呈现高、中、低需求区相间分布的空间格局但各等级需求区面积占比差异明显。(2)研究区有食物供给需求簇、文化娱乐需求簇和生态保育需求簇等3类。其中,食物供给需求簇是当地主导的需求簇,主要分布在研究区北部和南部;文化娱乐需求簇主要集中在无定河两岸;生态保育需求簇在研究区南部紧邻文化娱乐需求簇,在北部则较为分散。(3)影响各类服务需求空间分布的主导环境因子各不相同;影响食物供给需求簇的环境变量排序为：土地利用>海拔>距水体距离,影响文化娱乐需求簇的环境变量排序为：距居民...     

1 067例不同年龄及地域人群肠道菌群特征

目的 探索不同人群在不同年龄阶段的菌群结构特点,了解环境因素对肠道菌群组成及发展的影响。方法 收集65例中国健康儿童粪便样本并进行16S rRNA检测,同时从已发表文献中获取来自亚洲、非洲、欧洲、北美洲及南美洲国家的1 002例健康人群肠道菌群数据,分析来自不同年龄阶段健康人群肠道菌群的特征。结果 3岁以下全球各地儿童肠道菌群的种类较为一致：拟杆菌属和双歧杆菌属在儿童肠道菌群中占据主导地位,且它们在免疫调节上有重要作用。3岁以上健康人群的肠道菌群则展示出了地域性特征：亚洲健康人群的肠道代表菌属为考拉杆菌属和巨单胞菌属,非洲健康人群的肠道代表菌属为粪杆菌属,欧洲健康人群的肠道代表菌属也是粪杆菌属,北美洲健康人群的肠道代表菌属为拟杆菌属,南美洲健康人群的肠道代表菌属为普氏菌属。另外,经济较发达的欧洲及北美洲健康人群的肠道菌群多样性显著高于其他经济较落后地区。结论 本研究加深了对不同地域人群肠道菌群特点以及它们随年龄增长而发展变化的认识。     

生态斑块重要性综合评价方法研究——以四川省为例

生态斑块为生物提供生存和发展的场所,城市化的推进引发生态斑块面积锐减且趋于破碎化,严重威胁生态系统服务。通过对生态斑块重要性的分析,可识别对保持景观连接度有关键作用的区域,是优化有限资金配置、实现高效生态保护和分级管理的有效途径。以2015年的四川省为例,从景观连接度出发,基于网络建模和拓扑指标计算,结合逼近理想点排序法(TOPSIS)和有序样品聚类进行了斑块重要性的综合评估和排序。研究结果表明,四川省内生态斑块呈现西北部相对连续,南部和东部零散而稀疏的分布特点,在此基础上构建的生态基础设施网络具有无标度性;所选拓扑指标结合综合评价方法后可有效评估斑块重要性,所有斑块可分为5个重要性层级,高层级斑块主要位于相对核心的位置,低层级斑块分布于全省边缘。针对不同层级斑块的特点提出了相应规划建议,从整体角度出发引导局部生态规划,以期为有限资源下省域尺度复合种群保护工作提供参考与借鉴。     

Trends in genome dynamics among major orders of insects revealed through variations in protein families

Background

Insects belong to a class that accounts for the majority of animals on earth. With over one million identified species, insects display a huge diversity and occupy extreme environments. At present, there are dozens of fully sequenced insect genomes that cover a range of habitats, social behavior and morphologies. In view of such diverse collection of genomes, revealing evolutionary trends and charting functional relationships of proteins remain challenging.

Results

We analyzed the relatedness of 17 complete proteomes representative of proteomes from insects including louse, bee, beetle, ants, flies and mosquitoes, as well as an out-group from the crustaceans. The analyzed proteomes mostly represented the orders of Hymenoptera and Diptera. The 287,405 protein sequences from the 18 proteomes were automatically clustered into 20,933 families, including 799 singletons. A comprehensive analysis based on statistical considerations identified the families that were significantly expanded or reduced in any of the studied organisms. Among all the tested species, ants are characterized by an exceptionally high rate of family gain and loss. By assigning annotations to hundreds of species-specific families, the functional diversity among species and between the major clades (Diptera and Hymenoptera) is revealed. We found that many species-specific families are associated with receptor signaling, stress-related functions and proteases. The highest variability among insects associates with the function of transposition and nucleic acids processes (collectively coined TNAP). Specifically, the wasp and ants have an order of magnitude more TNAP families and proteins relative to species that belong to Diptera (mosquitoes and flies).

Conclusions

An unsupervised clustering methodology combined with a comparative functional analysis unveiled proteomic signatures in the major clades of winged insects. We propose that the expansion of TNAP families in Hymenoptera potentially contributes to the accelerated genome dynamics that characterize the wasp and ants.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1771-2) contains supplementary material, which is available to authorized users.     

Atg23 and Atg27 Act at the Early Stages of Atg9 Trafficking in S. cerevisiae

Atg9 is a conserved multipass transmembrane protein with an essential role in autophagy. In Saccharomyces cerevisiae, it travels through the secretory pathway to a unique compartment, the Atg9 peripheral structures. These structures are then targeted to the phagophore assembly site (PAS), where they are proposed to help deliver membrane to the forming autophagosome. We used ‘in vivo reconstitution’ of this process in a multiple‐knockout strain to define four proteins, Atg11, Atg19, Atg23 and Atg27, as the core minimal machinery necessary and sufficient for the trafficking of Atg9 to the PAS. Atg23 and Atg27 function in the formation of the Atg9 peripheral structures. Overexpression of Atg9 can bypass the need for Atg23, suggesting that the amount of Atg9 in each peripheral structure is a critical factor in their targeting to the PAS. In contrast, overexpression of Atg23 or Atg27 interferes with Atg9 trafficking, suggesting that these proteins must be present in the appropriate stoichiometry in order to function properly. These data allow us to resolve existing controversies regarding the role of Atg23 and Atg27, and propose a model that ties together previous observations regarding the role of Atg9 in autophagosome formation.      

Estimation of Toxicity Equivalency and Probabilistic Health Risk on Lifetime Daily Intake of Polycyclic Aromatic Hydrocarbons from Urban Residential Soils

In this study, toxicity equivalents and health risks, based on concentration of 16 priority polycyclic aromatic hydrocarbons (PAHs) in urban residential soils were estimated for the human population in Gwalior, India. Benzo(a)pyrene total potency equivalents (BaP TPE) were estimated for assessment of human health risk from direct contact with PAH-contaminated soil. Potential risk to contaminated groundwater from leaching of carcinogenic PAHs was assessed by estimating the index of additive cancer risk (IACR). On the basis of lifetime average daily intake of 16 PAHs through ingestion of PAH-contaminated soils, lifetime cancer risk to human adults and children was estimated. The concentration of probable human carcinogenic PAHs in soils accounted for 38% of ∑16PAHs. BaP TPE and index of additive cancer risk (IACR) were lower than guideline values of 0.6 mg kg^?1 and <1, respectively. Estimated lifetime average daily intakes of PAHs via soil ingestion were lower than recommended dose. However, the ILCR for human adults was within acceptable limits recommended by regulatory agencies, but may need action for children in Gwalior, India.     

Slope-related variations in twig and leaf traits of Robinia pseudoacacia in the northern mountains of Lanzhou

 枝叶生长关系是植物在环境胁迫条件下提高空间资源利用能力的一种策略, 弄清枝叶生长关系对理解植物应对环境异质性的表型可塑性具有重要意义。该文利用ArcGIS建立研究区域的数字高程模型, 研究了兰州市北山不同坡向人工林刺槐(Robinia pseudoacacia)小枝茎截面积-总叶面积和出叶强度-单叶面积的生长关系。结果表明: 随着坡向由北坡向东坡、南坡和西坡转变, 刺槐林群落的郁闭度、高度和土壤含水量呈现先减小后增大的趋势, 刺槐小枝茎截面积、总叶面积和单叶面积呈现先减小后增大的趋势, 出叶强度呈现先增大后减小的趋势; 北坡、东坡、南坡和西坡4个坡向的刺槐小枝的茎截面积和总叶面积均呈显著的正相关关系(p < 0.05), 并存在显著大于1的共同斜率, 刺槐的出叶强度与单叶面积均呈显著的负相关关系(p < 0.05), 并存在接近于–1的共同斜率; 随着坡向由北坡向东坡、南坡和西坡转变, 茎截面积-总叶面积和出叶强度-单叶面积两组关系的回归方程截距呈现先减小后增大的趋势。刺槐枝叶在不同坡向上的异速生长关系反映了植物功能性状对生长环境的响应和适应, 以及植物构型构建的投资权衡机制。