A catalogue of Clostridium thermocellum endoglucanase, β-glucosidase and xylanase genes cloned in Escherichia coli

Abstract Two independent collections of clones containing Clostridium thermocellum genes involved in cellulose have been previously obtained at IAPGR, Cambridge, and at the Pasteur Institute, Paris. The two collections were compared for cross-hybridization, restriction maps and enzyme phenotypes. Truly distinct genes were one β-glucosidase gene, two xylanase genes, and fifteen endogluconase genes. Two of the cloned fragments contained extraneous DNA which was absent from their respective counterparts isolated in the other collection. The dicrepancies resulted from in vivo rearrangements which had occurred in either of the C. thermocellum NCIB 10682 stocks used to generate the two gene banks.     

Catalogue et affinités géographiques des Odonata des îles voisines de Madagascar (Insecta: Pterygota)

Une analyse bibliographique exhaustive révèle que 71 espèces et sous-espèces d’Odonates sont présentes sur l’ensemble des îles voisines de Madagascar appartenant aux archipels des Mascareignes, des Comores et des Seychelles. Le taux d’endémisme maximal pour l’ensemble des îles voisines de Madagascar est de 34 %. Le taux d’endémisme est sensiblement plus important dans les Mascareignes (34 %) qu’aux Comores (23 %) ou aux Seychelles (19 %). Le peuplement odonatologique y est dominé par les Libellulidae (36 taxons) et les Coenagrionidae (18 taxons). Chaque archipel possède au moins un des 23 taxons endémiques présents sur ces îles. Les Seychelles comptent deux genres monospécifiques endémiques: Allolestes et Leptocnemis. Les Mascareignes abritent deux genres endémiques: Thalassothemis et Coenagriocnemis. Ce dernier a subi une radiation évolutive au sein de l’archipel. Les îles voisines de Madagascar se caractérisent par une radiation évolutive des genres Hemicordulia et Gynacantha à l’échelle de la région. Les affinités géographiques sont principalement afro-tropicales. La colonisation à partir de l’Afrique est le fait de taxons particuliers qui ne sont pas un échantillon aléatoire de l’ensemble du pool continental. Sur l’ensemble des îles voisines de Madagascar, la richesse spécifique des peuplements d’Odonates d’affinité africaine est maximale sur les îles proches du continent.     

Domain-Based and Family-Specific Sequence Identity Thresholds Increase the Levels of Reliable Protein Function Transfer

Divergence in function of homologous proteins is based on both sequence and structural changes. Overall enzyme function has been reported to diverge earlier (50% sequence identity) than overall structure (35%). We herein study the functional conservation of enzymes and non-enzyme sequences using the protein domain families in CATH-Gene3D. Despite the rapid increase in sequence data since the last comprehensive study by Tian and Skolnick, our findings suggest that generic thresholds of 40% and 60% aligned sequence identity are still sufficient to safely inherit third-level and full Enzyme Commission numbers, respectively. This increases to 50% and 70% on the domain level, unless the multi-domain architecture matches. Assignments from the Kyoto Encyclopedia of Genes and Genomes and the Munich Information Center for Protein Sequences Functional Catalogue seem to be less conserved with sequence, probably due to a more pathway-centric view: 80% domain sequence identity is required for safe function transfer. Comparing domains (more pairwise relationships) and the use of family-specific thresholds (varying evolutionary speeds) yields the highest coverage rates when transferring functions to model proteomes. An average twofold increase in enzyme annotations is seen for 523 proteomes in Gene3D. As simple ‘rules of thumb’, sequence identity thresholds do not require a bioinformatics background. We will provide and update this information with future releases of CATH-Gene3D.     

中国兽类名录(2021版)

中国是全球兽类物种多样性最高的国家之一,掌握我国兽类物种多样性和分类地位是兽类学研究的基础前提,也是科学保护野生种群的前提。为厘清中国兽类的物种数量及分类地位等关键分类学信息,中国动物学会兽类学分会组织国内长期致力于兽类各类群分类的科学研究人员,在总结前人研究的基础上,根据最新的形态学和分子遗传学证据,综合现代兽类分类学家意见,经编委会充分讨论,形成了最新的中国兽类名录,包括我国现阶段兽类12目59科254属686种。该中国兽类名录使用基于系统发生关系的分类系统,并对物种有效性进行了充分慎重的确认和讨论。     

安徽省茶园蜘蛛名录

报道了安徽省茶园蜘蛛的部分种类,计有22科68属118种。     

某省级医院执行《江苏省医保药品目录》

目的 分析某省级三甲医院对《江苏省基本医疗保险药品目录》的执行效果。方法 选取江苏省某省级三级医院为研究对象,比较分析城镇职工医保患者和自费患者的药品使用情况。结果 新版《医保药品目录》能基本满足该院临床治疗需求;对门诊医保患者费用控制具有显著作用,但对住院医保患者的药品费用控制效果不明显,对不同疾病药品费用控制效果不一。结论 建立和完善严格的用药考核制度,需加强中高档药物使用的监管,并增加相应的适应症限制,应考虑将临床治疗可供选择、药价适应的药品纳入目录。     

Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism

Elementary modes analysis allows one to reveal whether a set of known enzymes is sufficient to sustain functionality of the cell. Moreover, it is helpful in detecting missing reactions and predicting which enzymes could fill these gaps. Here, we perform a comprehensive elementary modes analysis and a genomic context analysis of Mycoplasma pneumoniae nucleotide metabolism, and search for new enzyme activities. The purine and pyrimidine networks are reconstructed by assembling enzymes annotated in the genome or found experimentally. We show that these reaction sets are sufficient for enabling synthesis of DNA and RNA in M. pneumoniae. Special focus is on the key modes for growth. Moreover, we make an educated guess on the nutritional requirements of this micro-organism. For the case that M. pneumoniae does not require adenine as a substrate, we suggest adenylosuccinate synthetase (EC 6.3.4.4), adenylosuccinate lyase (EC 4.3.2.2) and GMP reductase (EC 1.7.1.7) to be operative. GMP reductase activity is putatively assigned to the NRDI_MYCPN gene on the basis of the genomic context analysis. For the pyrimidine network, we suggest CTP synthase (EC 6.3.4.2) to be active. Further experiments on the nutritional requirements are needed to make a decision. Pyrimidine metabolism appears to be more appropriate as a drug target than purine metabolism since it shows lower plasticity.     

Review of the Capitellidae (Annelida, Polychaeta) from the Eastern Tropical Pacific region, with notes on selected species

The main objective of this work is to contribute to the taxonomic knowledge of the species of Capitellidae reported for the Eastern Tropical Pacific. This catalogue includes the original name of each species, new names, synonymies, type localities, the museum or institution where the type material is deposited, revision of the material reported for the region by different authors, new examined material, previous reports from other regions of the world, and comments on systematics and distributions. The catalogue lists 43 species in 19 genera. Of these, 6 species were erroneously recorded for the region (Decamastus gracilis Hartman, 1963; Decamastus nudus Thomassin, 1970; Mastobranchus variabilis Edwing, 1984; Notomastus aberans Day, 1957; Notomastus americanus Day, 1973; Notomastus latericeus Sars, 1851) and 5 species are found here to be questionable records for the Eastern Tropical Pacific (Capitella capitata (Fabricius, 1780); Dasybranchus glabrus Moore, 1909; Decamastus lumbricoides Grube, 1878; Notomastus lineatus Claparède, 1870 and Notomastus tenuis Moore, 1909).     

国际葡萄品种目录数据库的使用与分析

葡萄是世界上最重要的果树之一,在世界范围内拥有上万份的种质资源,其遗传多样性非常丰富。近年来,随着葡萄产业与计算机信息通信技术的飞速发展,建立葡萄种质资源网络数据库显得尤为重要。1984年,德国Geilweilerhof葡萄育种研究所在国际植物遗传资源委员会(IPGRI,现更名Bioversity International)与国际葡萄和葡萄酒组织(OIV)支持下,建立了世界上最丰富的葡萄种质数据库——国际葡萄品种目录(VIVC,Vitis International Variety Catalogue)。为了让广大葡萄育种者和科研人员更好地认识VIVC的功能及其所登录的大量葡萄种质的特点,达到促进对葡萄种质资源的利用与创新,本研究介绍了VIVC的主要功能与数据库中登录的葡萄种质资源的情况,并对这些葡萄种质的育种地区、用途、果皮色泽、花器类型、种子有无等性状以及SSR标记在葡萄种质鉴定中的利用等进行了分析。