A set of keys for biochemical identification of environmental Vibrio species

A set of biochemical keys which provide fast and presumptive identification for Vibrio spp. is presented. They have been specially designed for environmental isolates, and can be used for strains that are Gram-negative, give a positive oxidase test, grow on TCBS medium and are facultative anaerobes. The keys are constituted by 28 tests and a maximum of 10 tests are needed for the most complicated identification. They have been designed for routine purposes, especially for studies with a high number of isolates. Some tests are included in enzyme-activity based kits that could be used with these keys through certain results, principally for environmental isolates, should be confirmed by standard methods.     

Numerical Diagnostic Key for the Identification of Enterobacteriaceae

A numerical diagnostic key for enteric organisms is described which permits the identification of typical strains and of biochemical variants with high accuracy. Unknown strains are inoculated into a basic set of five media which permit the testing of eight biochemical reactions. The positive reactions are assigned points, and the score of a strain is added up, after which the identification of the strain is obtained from a table. In many instances, the final identification is obtained with this set of biochemical tests; and, in other instances, a small number of additional tests are required to distinguish between organisms giving the same score in the basic set of biochemical tests. The key permits an accurate, rapid, and economical differentiation of the typical and the more common atypical biotypes of enteric organisms in the clinical laboratory.     

Use of a computer for the purpose of identifying bacteria of the family Enterobacteriaceae and the determination of the minimal set of differential tests]

Algorhythm and a program for identification of bacteria of the Enterobacteriaceae family, based on Edwards and Ewing's diagnostic scheme, were worked out. Use of this program permitted to analyze different sets of abbreviated biochemical tests. To determine the genera and species of enterobacteria a minimal set of 11 tests is suggested, including indol formation, Voges-Proskauer's reaction, the presence of urease enzymes, gelatinase, lysine decraboxylase, phenylalanine deaminase, glucose fermentation (gas), or lactose, inosite, sorbit, arabinose, rhamnose. The program admits increase of both the biochemical tests, and toxonomic groups of bacteria, this permitting to consider several families. The presence of strains deviating by properties from this scheme points to the necessity of further improvement of diagnostic schemes for the enterobacteria identification.     

交互式检索表提升分类学研究与应用效率:以兰科植物为例

与传统的连续检索表相比,基于计算机等数字终端的多通道交互式检索表具有很多优势,如易于携带、实时更新、界面直观、使用方便、用户广泛、产生新数据集且便于研究以及能够推动分类学知识的普及等。本文以兰科植物为例介绍了交互式检索表的特点、程序建立和应用。兰科植物是生物多样性保育的旗舰类群,具有很强的观赏和药用价值,但中国兰科植物种类繁多,分类困难。我们在自主研发交互式检索表软件MagIden的基础上,以《中国植物志》和Flora of China的描述为依据,制作了中国兰科植物交互式电子检索表,为分类学研究者和爱好者提供了一个新的、鉴定中国兰科植物的中英文双语工具;同时,交互式检索表生成的MVSP和Bayes形态特征数据集可用于聚类分析和分支分类学研究。交互式检索表在数据积累、更新和分析利用等方面具有独特的优势,是提高传统植物分类学研究与应用效率的重要工具。     

Identification of Enterococcus spp. with a biochemical key.

A six-step biochemical key is presented for the identification of all recognized Enterococcus spp. The key consists of 12 tests, but no more than 6 are needed for the most complicated identification. The reliability of the key has been evaluated with collection type strains and clinical and environmental isolates. This key has fewer tests than those reported in previous studies. There is no commercial kit that includes the whole set of tests. However, some of the tests are included in enzyme activity-based kits that could be used with the proposed key. The key is designed for use in routine applications, especially in environmental and clinical studies with a high number of isolates.     

Identification of Enterococcus spp. with a Biochemical Key

A six-step biochemical key is presented for the identification of all recognized Enterococcus spp. The key consists of 12 tests, but no more than 6 are needed for the most complicated identification. The reliability of the key has been evaluated with collection type strains and clinical and environmental isolates. This key has fewer tests than those reported in previous studies. There is no commercial kit that includes the whole set of tests. However, some of the tests are included in enzyme activity-based kits that could be used with the proposed key. The key is designed for use in routine applications, especially in environmental and clinical studies with a high number of isolates.     

Usefulness of the diagnostic kit Enteroplast for identification of Enterobacteriaceae

Comparative evaluation of biochemical properties determined by ENTEROPLAST kit (P.P.Z. Plastomed) and biochemical set of tests (conventional method) of 140 strains representing 12 genera of Enterobacteriaceae family was undertaken. Consistent results positive or negative (in 12 biochemical tests) were obtained in 93%. The highest percentage of inconsistent results of biochemical reactions (positive in conventional method and negative in ENTEROPLAST kit) were observed in following tests: growth on Simmons medium--17.8%, MR--7.8%, fermentation of raffinose--7.2%. Significantly lower percentage of inconsistent results was found in the case of false positive reactions (negative in conventional method and positive in ENTEROPLAST kit). In summary, it seems that Enteroplast kit can be used for routine diagnostic examinations for identification of rods of Enterobacteriaceae family, basing on their biochemical properties.     

新版DELTA系统在植物分类学中的应用——以羊茅属研究为例

DELTA系统是针对分类学研究开发的综合性多功能软件包。新版DELTA系统在运行环境、程序、指令、界面、操作方式及中文字符处理等重要功能上比旧版本均有较大改进。作为国际分类学数据库数据交换标准,应用该系统可以规范分类学描述,对研究中所有常用性状进行识别和处理,自动生成各个研究对象分类学特征描述并对其进行详尽的相似性和差异性比较,对性状特征和分类单元进行注释和图像示例,将数据转换为数量分类学或分支分类学所需格式以生成树状图,自动生成检索表,建成基于本地和网络的交互式专家辅助鉴定系统等。DELTA系统作为植物分类学研究的常用手段和工具是非常适合及大有帮助的。     

Further development of simple tests to differentiate the legionellas

Current methods for the identification of the Legionellaceae to species level are suitable only for the specialist or research laboratory. As part of a continuing taxonomic study 42 simple biochemical tests were screened for their ability to differentiate species of Legionella. Only 23 of these were of practical use. These tests are able to differentiate 21 of 23 recognized species of Legionella and six new species. Phenotypic screening with these tests may prove useful to the routine microbiologist and be a viable alternative to identification techniques currently employed.     

Further development of simple tests to differentiate the legionellas

Current methods for the identification of the Legionellaceae to species level are suitable only for the specialist or research laboratory. As part of a continuing taxonomic study 42 simple biochemical tests were screened for their ability to differentiate species of Legionella. Only 23 of these were of practical use. These tests are able to differentiate 21 of 23 recognized species of Legionella and six new species. Phenotypic screening with these tests may prove useful to the routine microbiologist and be a viable alternative to identification techniques currently employed.     

Taxonomic identification of Amazonian tree crowns from aerial photography

Question: To what extent can aerial photography be used for taxonomic identification of Amazonian tree crowns? Objective: To investigate whether a combination of dichotomous keys and a web‐based interface is a suitable approach to identify tree crowns. Location: The fieldwork was conducted at Tiputini Biodiversity Station located in the Amazon, eastern Ecuador. Methods: High‐resolution imagery was taken from an airplane flying at a low altitude (600 m) above the ground. Imagery of the observable upper layer of the tree crowns was used for the analysis. Dichotomous identification keys for different types of crowns were produced and tested. The identification keys were designed to be web‐based interactive, using Google Earth as the main online platform. The taxa analysed were Iriartea, Astrocaryum, Inga, Parkia, Cecropia, Pourouma, Guarea, Otoba, Lauraceae and Pouteria. Results: This paper demonstrates that a combination of photo‐imagery, dichotomous keys and a web‐based interface can be useful for the taxonomic identification of Amazonian trees based on their crown characteristics. The keys tested with an overall identification accuracy of over 50% for five of the ten taxa with three of them showing accuracy greater than 70% (Iriartea, Astrocaryum and Cecropia). Conclusions: The application of dichotomous keys and a web‐based interface provides a new methodological approach for taxonomic identification of various Amazonian tree crowns. Overall, the study showed that crowns with a medium‐rough texture are less reliably identified than crowns with smoother or well‐defined surfaces.     

JellyWeb: an interactive information system on Scyphozoa,Cubozoa and Staurozoa

Identification of organisms is traditionally based on the use of “classic” identification keys, normally printed on paper. These keys have several drawbacks: they are mainly based on the systematics, requiring identification of orders, families and genera at first; they are written by experts for other experts, in a specific scientific jargon; they have a “frozen” structure (sequence of theses/antitheses); once published, they cannot be changed or updated without printing a new edition. Due to the use of computers, it is now possible to build new digital identification tools, which: 1) can be produced automatically, if the characters are stored in a database; 2) can be freed from the traditional systematics, giving priority to easy-to-observe characters, incl. those usually uncommon to the classical keys, such as ecology and distribution; 3) can be updated in real time once published on-line; 4) can be available on different media, and on mobile devices. An important feature of these new digital tools is their “collaborative” nature. They can be enriched by the contribution of several researchers, which can cooperate while maintaining rights and property of the resources and data they contribute to the system. JellyWeb, the information system on Scyphozoa, Cubozoa and Staurozoa has been developed in Trieste since 2010. The system was created with the aim of – potentially – becoming a starting point for a wide collaborative effort in developing a user-friendly worldwide digital identification system for jellyfishes.     

Identification of the enterobacteria isolated from patients by using the Enterotube test system]

The Enterotube test system intended for the accelerated identification of enterobacteria was used to study 319 strains isolated from patients with suppurative complications after surgical operations and traumatic lesions. The test system was found to allow a reliable identification of Enterobacteriaceae having characteristic biochemical properties. It was also found that the kit intended for 10 tests could prove insufficient for the identification of atypical bacteria. The Enterotube test system made it possible to differentiate 95% of enterobacterial strains; in the identification of bacteria by their genus and species and results obtained with the use of the Enterotube test system and common biochemical methods were found to be identical (in 96.4% of tests).     

Identification of Enterococcus spp. based on specific hybridisation with 16S rDNA probes

The conventional methods for routine enterococci species identification are usually based on phenotypic characteristics. However, in recent years, some studies have defined specific probes based on both 16S and 23S rRNA genes for the identification of some Enterococcus spp. A set of probes based on the 16S rRNA gene has been developed in order to evaluate the usefulness of a six-step biochemical key for species level identification of enterococci. Probe specificity has been evaluated with type collection and environmental strains by dot blot hybridisation. A high correlation was obtained between biochemical key and hybridisation identifications. This set of probes provides a confirmative method for phenotypic species identification.     

Optimization of Taxonomic Keys by Means of Probabilistic Modelling

At present biological systematics, i. e. classification and identification of organisms, is also a subject of the employment of mathematical methods. The topic of this paper is identification. One of the most important methods of identification is that by means of keys. Therefore a short review on the types of keys and their valuation is represented. Moreover there are discussed the essential properties of keys: reliability and velocity of identification. Further in connection with these two quantities probabilistic models are treated. The last part of the article deals with the optimization of keys concerning theory and practice of the problem.     

Understanding the enzymology of archaeal DNA replication: progress in form and function

The analysis of completed archaeal genome sequences led to the identification of a set of approximately 10-20 genes whose protein products were inferred to be involved in chromosomal DNA replication. Until recently, however, little was known of the biochemical properties of these proteins. Here, I review recent progress in this area brought about by biochemical and structural analysis. Aside from shedding considerable new light on the molecular machinery of DNA replication in the archaea, the results of these studies also present new opportunities for understanding the molecular events of chromosomal DNA replication in eukaryotic cells.     

Some ideas for activities involving the construction of computer-based identification keys

Conserving global biodiversity depends on public awareness, hence the vital role of education and the recent thinking that biodiversity conservation should form part of a new and general scientific literacy taught in schools. A crucial aspect of biodiversity conservation is species identification. Taxonomy in general, and identification keys in particular, are often seen as boring and outdated. Indeed, curricula focused on contemporary areas of biology tend to give a low priority to taxonomy or ignore it completely. However, concern for diminishing global biodiversity has provoked a renewed interest in both traditional and more innovative identification methods, including computer-aided taxonomy.

Some ideas for applying information and communication technology (ICT) to constructing identification keysare discussed. The use of linked web pages is proposed as the most easily used and readily accessible method for Year 8 pupils (ages 12 – 13). It is suggested that there is more educational value in pupils then testing and evaluating each other's keys rather than simply using them and that to facilitate this, web-based keys can easily be exchanged via a network.

It is concluded that this approach promotes a wide range of transferable ICT skills, but applies them in the context of a current problem facing real biologists, so illustrating how computer technology is assisting biodiversity research.     

神农架川金丝猴源肠道粪肠球菌的分离与鉴定

通过培养特征、形态观察、抑菌性实验,从神农架健康野生金丝猴肠道分离到8株抑菌效果明显的菌株;生理生化鉴定和16S rRNA基因序列同源性分析,该8株菌为粪肠球菌。毒力因子检测和动物急性毒性实验筛选出2株安全性良好的菌株,研究两菌株对胃肠道环境（低pH值、高胆盐）的耐受特性和生长情况。结果表明,粪肠球菌dlt7a和dlt7b株繁殖能力很强,无迟缓期,具有较强的耐受胃酸及肠道高胆盐环境的能力,且安全性好,具有较好的益生特性,可作为金丝猴微生态制剂的候选菌株。