基于分块主成分分析的太行山猕猴面部相似性

2012 年4 ～8 月,在太行山猕猴国家级自然保护区济源管理局天坛山管护区(北纬35°05′ ～ 35°15′,东经112°12′ ～ 112°22′),对太行山猕猴王屋1 群(WW - 1)内的3 个母系单元(matrilineal unit) 中大于(等于)3 岁龄的26 只个体进行面部拍照,获取其面部特写照片,进而利用分块主成分分析(modular principal component analysis,MPCA)法,对个体进行面部识别分析,旨在探讨个体间面部相似度与亲缘关系的相关性。结果表明:(1)太行山猕猴个体间的面部相似度与亲缘类型有关,母亲与大于3 岁龄子代间的面部相似度为0.93 ±0. 00,显著高于单元内(0. 89 ± 0. 00)和单元间(0.84 ±0.01)的面部相似度;(2)太行山猕猴个体的面部特征随年龄增长而变化,4 岁(含4 岁)龄以上个体与母亲间的面部相似度较高(0.88 ～ 0. 95),依此值可准确地识别母子关系。本研究采用量化方法对非人灵长类个体间面部相似度进行分析,发现太行山猕猴个体间的面部相似度与亲缘关系密切相关;研究结果可为非人灵长类的个体识别提供较为客观的手段和方法。     

An unexpected similarity between antibiotic-resistant NDM-1 and beta-lactamase II from Erythrobacter litoralis

NDM-1 (New Delhi metallo-beta-lactamase) gene encodes a metallo-beta-lactamase (MBL) with high carbapenemase activity, which makes the host bacterial strain easily dispatch the last-resort antibiotics known as carbapenems and cause global concern. Here we present the bioinformatics data showing an unexpected similarity between NDM-1 and beta-lactamase II from Erythrobacter litoralis, a marine microbial isolate. We have further expressed these two mature proteins in E. coli cells, both of which present as a monomer with a molecular mass of 25 kDa. Antimicrobial susceptibility assay reveals that they share similar substrate specificities and are sensitive to aztreonam and tigecycline. The conformational change accompanied with the zinc binding visualized by nuclear magnetic resonance, Zn²⁺-bound NDM-1, adopts at least some stable tertiary structure in contrast to the metal-free protein. Our work implies a close evolutionary relationship between antibiotic resistance genes in environmental reservoir and in the clinic, challenging the antimicrobial resistance monitoring.     

生物信息学电子文档收编及优化检索的实现

生物信息学涉及生物、化学、物理、数学、计算机和互联网应用等多方面知识,要从事这个领域的研究工作,必须掌握更多的各方面知识。目前该领域的很多资料和文献在网上以电子文档的形式存在。电子文档能够包含比常规的文档包含更广泛,更丰富的内容,对电子文档的收编整理发能大大节省文档的搜索时间,并能提供更专业,更有效的检索结果,为科研工作服务。本文论述了建立包括电子文档的收集,标注,优化检索的一个方案,检索结果按照文档和检索条件的相似程度分级列出。实践证明,该系统能够有效的提供生物信息学专业信息的管理和检索。     

Spatial similarity of urban bird communities: a multiscale approach

Aim Human land use, especially urbanization, might homogenize the world's biota. The objective of this study is to find out if urbanization homogenizes wintering bird communities, and if habitat type affects the spatial variation of urban bird communities across spatial scales. Location We compared the quantitative similarity of winter bird communities between town centres, apartment block areas and single‐family house areas across regional and local scales in five towns in northern Finland. Methods The wintering birds were surveyed using a single‐visit study plot (30 ha) method in January and February 2001. The validity of single‐visit and single‐year data was confirmed by using data from several‐visit surveys and multi‐year data set. The level of urbanization was measured according to the number of inhabitants and general structure of the habitat. Results Temporal variability in species richness and total number of individuals was low, both between winters and within winter. Bird community similarity between different habitat types within a single town was about the same as that in similar habitats in different towns. At the regional scale, bird community similarity between town centres (30%) was lower than between areas of apartment blocks (54%) or between areas of single‐family houses (54%). We detected a threshold point between towns of 35,000 and 105,000 inhabitants and between town sizes of 5.0–8.5 km in diameter where human impact causes marked changes in bird community structure. At the local scale, bird community similarity level between apartment block areas (49%) and single‐family house areas (62%) were about the same. Passer domesticus, Parus major and Pica pica dominated the bird communities in residential areas. Different habitat factors affected bird species abundances on the local and regional scales. Conclusions Urbanization cannot be seen as a process that monotonically increases the similarity of bird communities. Our results indicate that the similarity between urban bird communities is dependent on the size of the town, location of the study site within the town and especially the local habitat structure. Because different habitat factors affected bird species abundances, it is difficult to extrapolate bird–habitat relationships derived from one scale to other scales. In wintertime, single‐family house areas are important biodiversity hotspots in cities. Therefore, it is especially important to understand the factors affecting the occurrence of birds in the single‐family house area in order to maintain or even increase diversity on winter birds in other urban habitats.     

湖北烟区烤烟气候适生性评价及与国外烟区的相似性分析

分析了湖北烟区不同移栽期条件下的气候状况,通过定量估算气候适生性指数(CFI),合理评价了烤烟种植的气候适生性,并对各植烟县(市)建议移栽期下的气候条件与国外优质烟区进行了相似性分析,结果表明:(1)当气温稳定通过15℃、18℃、20℃和22℃分别进行移栽时,CFI值依次为0.863±0.06、0.848±0.06、0.855±0.07和0.890±0.05,表明移栽期是影响烟叶品质形成的重要因素.(2)确定了24个植烟县(市)的烤烟建议移栽期,即利川、五峰、老河口、兴山、郧西、房县、竹山和长阳等8个植烟县(市)适宜于当气温稳定通过18℃时移栽;宣恩适宜于气温稳定通过20℃时移栽;其余15个植烟县(市)适宜于低温移栽(气温稳定通过15℃移栽).(3)湖北烟区在烤烟建议移栽期的气候条件与巴西、津巴布韦的相似程度较美国高,相似性分析为充分利用湖北烟区自然资源提供了参考依据.     

基于支持向量机分类的RNA共同二级结构预测

比较序列分析作为RNA二级结构预测的最可靠途径, 已经发展出许多算法。将基于此方法的结构预测视为一个二值分类问题: 根据序列比对给出的可用信息, 判断比对中任意两列能否构成碱基对。分类器采用支持向量机方法, 特征向量包括共变信息、热力学信息和碱基互补比例。考虑到共变信息对序列相似性的要求, 通过引入一个序列相似度影响因子, 来调整不同序列相似度情况下共变信息和热力学信息对预测过程的影响, 提高了预测精度。通过49组Rfam-seed比对的验证, 显示了该方法的有效性, 算法的预测精度优于多数同类算法, 并且可以预测简单的假节。     

Modern humans are not (quite) isometric

Allometric relationships are important sources of information for many types of anthropological and biological research. The baseline for all allometric relationships is isometry (or geometric similarity), the principal that shape is invariant of size. Here, we formally test for geometric similarity in modern humans, looking at the maximum lengths of four long bones (humerus, radius, femur, and tibia). We use Jolicoeur's multivariate allometry method to examine globally distributed samples of human populations, both collectively and individually. Results indicate that humans are not geometrically similar, although morphological deviations from isometry are small.     

Relationships among <Emphasis Type="Italic">Leymus</Emphasis> species assessed by RAPD markers

The DNA genetic diversity of 40 accessions of genus Leymus was analyzed by random amplified polymorphic DNA (RAPD) markers. A total of 352 products were amplified by 34 10-mer arbitrary primers, among which 337 products (95.74 %) were found to be polymorphic. 5–14 polymorphic bands were amplified by each polymorphic primer, with an average of 9.91 bands. The data of 352 RAPD bands were used to generate Jaccard’s similarity coefficients and to construct a dendrogram by means of UPGMA. Great genetic diversity in genus Leymus was observed, the genetic diversity among the different species more abundant than that of the different accessions, and the different accessions in a species or the species from the same areas were clustered together.