一株微囊藻毒素降解辅助菌的分离和鉴定

以从太湖蓝藻中提取的微囊藻毒素作为微囊藻毒素降解菌的筛选物质, 通过稀释平板涂布法从腐烂的蓝藻中富集分离到一菌株, 经形态特征、生理生化特征和16S rDNA 序列分析将该菌株(GenBank 序列登录号为GQ143751)鉴定为藤黄微球菌(Micrococcus luteus); 微囊藻毒素降解实验结果表明该菌株几乎不能降解微囊藻毒素, 但可以明显促进一株微囊藻毒素降解菌微嗜酸寡养单胞菌(Stenotrophomonas acidaminiphila)对微囊藻毒素的降解能力, 将筛选菌株与微嗜酸寡养单胞菌混合培养, 混合菌对微囊藻毒素的降解能力比微嗜酸寡养单胞菌单独培养时提高66.7%。     

一种基于MeSH主题词的临床?鄄组学关系挖掘方法

癌症的发生发展与机体内基因的改变有密切联系,在临床上表现为症状或检测指标的异常．通过挖掘分析临床表现与基因改变之间的关系,可为癌症早期诊断和精准治疗提供临床决策支持．从文献数据出发,利用结论性数据挖掘基因与临床表现的关系具有重要意义．本文提出一种基于医学主题词(Medical Subject Headings,MeSH)的生物医学实体关系挖掘方法．该方法利用PubMed中提供的文献信息,借用向量空间模型思想,使用MeSH主题词矢量表达待研究实体,引入文献相互引用因素对结果进行修正,将关系挖掘转化为矢量间的数学运算,实现定量分析．本文将该方法应用于结直肠癌临床表现和基因关系的研究中,得到与结直肠癌相关的203个基因和对应的临床-基因462个关系．通过结合使用基因功能和通路分析工具g:Profiler和KEGG等,对结果进行分析验证．结果表明,基于MeSH主题词的文献挖掘方法,避免传统“共现”方法对发现潜在关系的限制和复杂语义分析带来的大量计算,为生物实体之间潜在关系的挖掘提供一种新的思路和方法．     

Identification and Phylogenetic Relationships of Microsporidia by Riboprinting

ABSTRACT. The SSUrDNA and the ITS of different microsporidia from eight fishes, four insects and a shrimp were amplified and digested with restriction enzymes. The generated riboprints suggest a close evolutionary relationship between Glugea americanus and Spraguea lophii suggesting that Glugea americanus should be renamed Spraguea americanus and that the tissue infected and host origin should be considered of greater taxonomic importance for defining a genus than previously considered. Phylogenetic analysis of the riboprints demonstrates an unidentified microsporidium from a bumper fish ( Chloroscombrus chrysurus ) is related although not identical to Microgemma oviodea , a parasite from red band fish. We were also able to distinguish between Glugea anomala and Glugea atherinae and Glugea stephani but were not able to differenciate among the latter two. Insects isolates, Nosema costelytrae, N. bombycis, N. trichoplusiae, Nosema sp. and a shrimp isolate, Agmasoma penaei , are not related to the fish isolates.     

Molecular Identification and Genetic Relationships of Palestinian Grapevine Cultivars

Palestine has a wide range of agro-ecological concerns and hosts a large variety of plants. Grapes are part of the cultural heritage and provide an indispensable food ingredient. Local cultivars have been traditionally identified on the basis of morphological traits, geographical origin, or names of the vineyard owner; therefore, the occurrence of homonymy, synonymy, and misnaming significantly prevents their valorization. DNA profiling by 22 common SSR markers was used to characterize 43 putative cultivars grown mainly for local table grape consumption at the southern highland regions of West-Bank, to further evaluate genetic diversity and relationships of the population. Consistent matching of SSR markers with grapevines cultivated in neighboring countries or maintained in European germplasm collections was found for 8 of the 21 different non-redundant genotypes discovered, suggesting possible synonyms as well as the occurrence of breeding selections formerly developed in the USA. Genetic relationships inferred from SSR markers clearly assigned Palestinian cultivars to the Proles orientalis subpr. Antasiatica ancestral population, and they even remarked the connection between local resources and cultivars generated from international table grape breeding. This study supports the value of collection and conservation of vines endemic to a region of immense historical importance for viticulture.     

裸盖菇属的真菌鉴定及分子系统学初探

裸盖菇属(Psilocybe)的许多真菌含有神经致幻型毒素,这些毒素被中国卫生部列为A类管制药品。在药检时,这些真菌样品通常是粉末。因此,仅依靠形态分类鉴定该类真菌非常困难。研究采用ITS序列分析的方法鉴定该类真菌并初步探讨了该属种间的系统发育关系。由系统发育树推断Psilocybe属可能是多源进化的。通过序列分析可以鉴定真菌样品为Psilocybe属。     

Terms for Kith and Kin

Scheffler and Needham give alternative interpretations of Karo Batak terminology, the former describing it as a kinship terminology, the latter as a terminology of social/symbolic classification. Both these points of view prove useful in understanding the way Karo use kinship terms and behave as kin. The organization of ritual, the etiquette of reference and address, and the way Karo forge kinlike ties illustrate how both genealogy and alliance categories operate in Karo kinship.     

Phylogenetic Relationships Among Colletotrichum Pathogens of Strawberry and Design of PCR Primers for their Identification

Isolates of Colletotrichum acutatum, C. fragariae and C. gloeosporioides pathogenic to strawberry plants were examined by sequence analysis of the 5.8S‐ITS region. Phylogenetic relationships among isolates of Colletotrichum are, for the most part, congruent with the molecular groups established in earlier works. 5.8S‐ITS sequence analysis showed a high level of genetic divergence within C. acutatum. Isolates of this species clustered into two very distinct clusters with further subdivision. The divergences between C. fragariae and C. gloeosporioides were too low to distinguish them as separate species. On the basis of the sequence data, specific primers were designed both to identify isolates belonging to the genus Colletotrichum, and to distinguish isolates of the species C. acutatum. The specificity of these primers was validated by testing a wide range of strawberry isolates of Colletotrichum, non‐strawberry isolates of Colletotrichum and other fungi used as controls. Although the 5.8S‐ITS sequences were not polymorphic enough to allow the construction of C. gloeosporioides‐specific primers, specific PCR amplification followed by an MvnI digestion provides a tool to specifically identify strawberry isolates of C. gloeosporioides.     

Quantitative Structure-Activity Relationships for Antifungal 3-(3,5-Dichloropheny)-2,4-imidazolidinediones

The antifungal activity of 441-acyl derivatives of 3-(3,5-dichlorophenyl)-2,4-imidazol- idinedione against Botrytis cinerea, and of 10 1-sulfonyl compounds against Aiternaria kikuchi- ana were assayed by the agar medium dilution method. The structure-activity relationships for the substituents of the acyl and sulfonyl moieties were analyzed with such physicochemical parameters as hydrophobic π, inductive electronic σ₁, and steric E′^c_s and B₁ values by multiple regression. The activity of the acyl derivatives against B. cinerea was related parabolically to the hydrophobicity of the substituents. The stronger the electron-donating power, the larger the overall steric bulkiness, and the smaller the minimum width in the direction perpendicular to the bond axis of the substituents, the greater was the activity. The activity of the sulfonyl derivatives against A. kikuciana was related only to the hydrophobicity of the substituents.     

Identification of Logic Relationships between Genes and Subtypes of Non-Small Cell Lung Cancer

Non-small cell lung cancer (NSCLC) has two major subtypes: adenocarcinoma (AC) and squamous cell carcinoma (SCC). The diagnosis and treatment of NSCLC are hindered by the limited knowledge about the pathogenesis mechanisms of subtypes of NSCLC. It is necessary to research the molecular mechanisms related with AC and SCC. In this work, we improved the logic analysis algorithm to mine the sufficient and necessary conditions for the presence states (presence or absence) of phenotypes. We applied our method to AC and SCC specimens, and identified lower and higher logic relationships between genes and two subtypes of NSCLC. The discovered relationships were independent of specimens selected, and their significance was validated by statistic test. Compared with the two earlier methods (the non-negative matrix factorization method and the relevance analysis method), the current method outperformed these methods in the recall rate and classification accuracy on NSCLC and normal specimens. We obtained biomarkers. Among biomarkers, genes have been used to distinguish AC from SCC in practice, and other six genes were newly discovered biomarkers for distinguishing subtypes. Furthermore, NKX2-1 has been considered as a molecular target for the targeted therapy of AC, and other genes may be novel molecular targets. By gene ontology analysis, we found that two biological processes (‘epidermis development’ and ‘cell adhesion’) were closely related with the tumorigenesis of subtypes of NSCLC. More generally, the current method could be extended to other complex diseases for distinguishing subtypes and detecting the molecular targets for targeted therapy.     

Lakota Sioux Terms for White and Negro

Abstract

The primary concern herein is to expose the suggested etymologies and meanings of the terms the Sioux employ to discuss members of the white and black races. This paper deals with the Oglala Sioux Indians of South Dakota, primarily current Lakota speakers of Pine Ridge and their ancestors over the past three hundred years.     

Biochemical Identification and Phylogenetic Relationships in Free-Living Amoebas of the Genus Naegleria1

Using isoelectric focusing, the zymograms of 23 pathogenic and nonpathogenic Naegleria strains were studied for the activity of 16 enzymes. Certain enzymes (lactate dehydrogenase, L-threonine dehydrogenase, superoxide dismutase, acid phosphatase, malic enzyme, and leucine aminopeptidase) proved particularly useful from a practical point of view as they allow easy and reliable identification of pathogenic N. fowleri and N. australiensis as well as nonpathogenic N. lovaniensis strains. Genetic interpretation of these zymograms gave estimates of genetic distances that largely confirmed the taxonomic position of the Naegleria species. In addition, the genetic data suggest that there are two main phylogenetic groups in the genus Naegleria.     

Lineage Identification and Genealogical Relationships Among Captive Galápagos Tortoises

Genetic tools have become a critical complement to traditional approaches for meeting short‐ and long‐term goals of ex situ conservation programs. The San Diego Zoo (SDZ) harbors a collection of wild‐born and captive‐born Galápagos giant tortoises (n = 22) of uncertain species designation and unknown genealogical relationships. Here, we used mitochondrial DNA haplotypic data and nuclear microsatellite genotypic data to identify the evolutionary lineage of wild‐born and captive‐born tortoises of unknown ancestry, to infer levels of relatedness among founders and captive‐born tortoises, and assess putative pedigree relationships assigned by the SDZ studbook. Assignment tests revealed that 12 wild‐born and five captive‐born tortoises represent five different species from Isabela Island and one species from Santa Cruz Island, only five of which were consistent with current studbook designations. Three wild‐born and one captive‐born tortoise were of mixed ancestry. In addition, kinship analyses revealed two significant first‐order relationship pairs between wild‐born and captive‐born tortoises, four second‐order relationships (half‐sibling) between wild‐born and captive tortoises (full‐sibs or parent‐offspring), and one second‐order relationship between two captive‐born tortoises. Of particular note, we also reconstructed a first‐order relationship between two wild‐born individuals, violating the founder assumption. Overall, our results contribute to a worldwide effort in identifying genetically important Galápagos tortoises currently in captivity while revealing closely related founders, reconstructing genealogical relationships, and providing detailed management recommendations for the SDZ tortoises. Zoo Biol 31:107;–120, 2012. © 2011 Wiley Periodicals, Inc.     

Cultivar Identification and Relationships in Pisum Sativum L. Based on RAPD and Isoenzymes

Two approaches were used to detect variability within 23 pea cultivars. Eight random amplified polymorphic DNA (RAPD) primers produced 163 bands (114 polymorphic), whereas five isoenzyme systems produced 25 bands (20 polymorphic). Both methods provided good results in finger-printing and identified all cultivars tested. Genetic similarity analysis (UPGMA) gave different results from RAPD and isoenzyme data. This could reflect different properties of both marker types. These data were also analysed using the bootstrap method, which supported the idea of one common progenitor of cultivated peas. This revised version was published online in July 2006 with corrections to the Cover Date.     

遗传学专业术语不规范化的现象探研—I.同名异义现象

对现行的遗传学教材中存在的专业术语同名异义现象进行探研,针对Y连锁遗传、限性遗传、从性遗传、单倍体、多倍性和累加作用等专业术语存在的表达不清,相互矛盾,同名异义等问题,进行分析探讨,并提出Y连锁遗传不能与限性遗传相混淆,限性遗传和从性遗传的基因是位于常染色体上,但二者存在区别。单倍体是指具有配子染色体数目的个体,但并不等同于一倍体。建议多倍体用染色体基数来表达,如三倍体用3X表示。 累加作用是指数量性状遗传基因间的相互累加作用。     

Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves,Mammalia, and Actinopterygii

The coalescence of next-generation DNA sequencing methods, ecological perspectives, and bioinformatics analysis tools is rapidly advancing our understanding of the evolution and function of vertebrate-associated bacterial communities. Delineation of host-microbe associations has applied benefits ranging from clinical treatments to protecting our natural waters. Microbial communities follow some broad-scale patterns observed for macroorganisms, but it remains unclear how the specialization of intestinal vertebrate-associated communities to a particular host environment influences broad-scale patterns in microbial abundance and distribution. We analyzed the V6 region of 16S rRNA genes amplified from 106 fecal samples spanning Aves, Mammalia, and Actinopterygii (ray-finned fish). We investigated the interspecific abundance-occupancy relationship, where widespread taxa tend to be more abundant than narrowly distributed taxa, among operational taxonomic units (OTUs) within and among host species. In a separate analysis, we identified specialist OTUs that were highly abundant in a single host and rare in all other hosts by using a multinomial model without excluding undersampled OTUs a priori. We show that intestinal microbes in humans and other vertebrates display abundance-occupancy relationships, but because intestinal host-associated communities have undergone intense specialization, this trend is violated by a disproportionately large number of specialist taxa. Although it is difficult to distinguish the effects of dispersal limitations, host selection, historical contingency, and stochastic processes on community assembly, results suggest that intestinal bacteria can be shared among diverse hosts in ways that resemble the distribution of “free-living” bacteria in the extraintestinal environment.