Genus Pseudonocardia: What we know about its biological properties,abilities and current application in biotechnology

The genus Pseudonocardia belongs to a group of Actinomycetes, and is a member of the family Pseudonocardiacea. The members of this genus are aerobic, Gram-positive, non-motile bacteria that are commonly found in soil, plant and environment. Although this genus has a low clinical significance; however, it has an important role in biotechnology due to the production of secondary metabolites, some of which have anti-bacterial, anti-fungal and anti-tumour effects. The use of phenotypic tests, such as gelatinase activity, starch hydrolysis, catalase and oxidase tests, as well as molecular methods, such as polymerase chain reaction, are necessary for Pseudonocardia identification at the genus and species levels.     

对叶榕榕果内生细菌分离鉴定及抑菌活性的研究

【目的】为植物-内生细菌的生态关系研究, 以及植物内生细菌资源的利用提供一定的依据。【方法】采用微生物学传统分离培养的方法从对叶榕果实中分离到内生细菌54株, 通过限制性酶切分析(ARDRA)共有16个操作分类单元(Operational taxonomic units, OTUs), 对16株代表菌株16S rDNA序列系统发育分析。【结果】16个菌株都找到了与其相似性最高的菌株, 相似性达到95%?100%。其中6株为芽孢杆菌Bacillus属, 为对叶榕果实内生细菌优势菌属; 3株为Staphylococcus属, 2株为Pseudomonas属, 1株为Serrata属, 1株为非培养细菌的同源菌, 1株为Kocuria属, 1株为Delftia属, 还有1株为Acinetobacter属。【结论】这16株内生菌在系统发育树中明显聚为两大支; 在参与抑菌试验的14株内生菌中, 有13株对受试菌有不同程度的拮抗作用。尤其是其中的芽孢菌属的Swx15和不动杆菌属的Swx25菌株, 抑菌作用较强, 且有较广的抑菌谱性。     

Species-specificity of DNA trimer densities in chromosomes and their use in the classification of closely related organisms

16S rDNA sequences are conventionally used for classification of organisms. However, the use of these sequences is sometimes not successful, especially for closely related species. For better classification of these organisms, several methods that are genome sequence-based have been developed. Sequence alignment-based methods are tedious and time-consuming, as they need conserved coding sequences to be identified and deduced prior to sequence alignment. Likewise, method that relies on gene function needs genes to be assessed for function similarity. Other alignment-free methods, which are based on particular genome sequence properties, so far have been complex and not species-specific enough for classification of organisms below genus level. The present study found that the ratios of DNA trimer frequencies to chromosomal length were species-specific. Density of a trimer in a chromosomal sequence was defined as the average frequency of the trimer per 1 kbp. The species-specificity of trimer densities in chromosomes of many closely related bacteria was compared in parallel with 16S rDNA sequences in these same bacteria. The results of these comparisons indicate that trimer densities in chromosomes can be used to simply and efficiently classify the organisms below genus level.     

羊肚菌研究进展

综述了羊肚菌(MorchellaDill exPers)的种类、成份及在食品和医药方面的开发应用情况。现在对该属有两种分类方法,一种将其分为2 8个种,另一种分为3或4个种,并且在分子生物学和生化上应用一些方法证明了羊肚菌属内只含少数几个种。在成分方面主要研究的是羊肚菌的多糖、氨基酸和脂肪类化合物,另外关于酶、吡喃酮抗生素、无机元素及其他成分也有报道。羊肚菌的开发利用主要侧重在食用方面,尤其是在羊肚菌的液体培养上;药理学研究上证明羊肚菌具有多种活性,主要是增强免疫力。     

钝头蛇属Pareas（蛇亚目：钝头蛇科）系统分类研究进展

钝头蛇属（Pareas）蛇类形态高度保守,种间形态差异微弱。以分子系统学方法为中心的整合分类方法的应用,为本类群分类难题的解决作出了重要贡献,近8年有9个新种得以描述,其中,仅在近3年就增加了7个新种,并有6个同物异名被恢复。本文依据最新研究成果,对近期钝头蛇属蛇类系统分类研究成果进行了综述,并斟酌中文种名,整理了物种名录,并编制了分类检索表。截止目前,钝头蛇属共有26种,其中在我国有分布的18种,中国特有种9种。同时,对研究中存在的问题进行了探讨,并对下一步工作提出了建议：本属物种多样性估计过低、标本采集覆盖范围不足、证据使用不甚全面,大范围密集采样以及系统发育基因组学方法的应用有助于本类群系统关系的最终解决。     

Evaluation of methods for molecular typing and identification of members of the genus Brevibacterium and other related species

The genus Brevibacterium includes pleomorphic Gram-positive bacteria with a high mol% G+C content. Species in the genus are difficult to identify by classical methods. The discriminatory power of DNA-based methods is assessed. Strains representing the four well established Brevibacterium species, and other related bacteria, were compared by amplified ribosomal DNA restriction analysis (ARDRA), repetitive-sequence-based PCR (rep-PCR) and ribotyping. Fingerprinting by rep-PCR and ribotyping provided complex genomic profiles with the highest discriminatory potential for molecular typing at the strain level, whereas ARDRA showed differentiation from the genus to the species levels. A high degree of heterogeneity within the genus Brevibacterium is apparent, thus indicating that the taxonomy of the genus should be further studied.     

The genus Dietzia: a new home for some known and emerging opportunist pathogens

The genus Dietzia has only been established fairly recently. The Gram morphology and colony appearance of the species of this genus is remarkably similar to Rhodococcus equi . In the absence of simple, accurate methods for their identification, Dietzia spp. might have been misidentified as a Rhodococcus spp. and/or considered to be contaminants only. This MiniReview is designed to summarize current evidence on the clinical significance of Dietzia species, to consider their potential role as human pathogens, and to outline approaches that can be used to accurately classify and identify members of the genus, with the overall aim of alerting the medical microbiological community to a little known genus that contains clinically significant organisms.     

Comparative Studies of the Seed Proteins of Brassica campestris, Brassica oleracea, and Brassica nigra

The albumin and globulin fractions of the seeds of Brassicacampestris, B. oleracea, and B. nigra have been investigatedusing serological methods and separation by acrylamide gel electrophoresisin order to determine the usefulness of these techniques fortaxonomic studies of the genus Brassica. The results of theprotein analysis given in this paper agree with establishedtaxonomy and suggest that both methods may prove useful in varioustaxonomic problems in the genus Brassica.     

中国沟胸步甲属分类研究及一新种描述(鞘翅目： 步甲科： 壶步甲族)

【目的】沟胸步甲属Holcoderus属于鞘翅目(Coleoptera)步甲科(Carabidae)壶步甲族(Lebiini)。本研究旨在对该属在中国分布的各个种进行分类厘定。【方法】基于中国科学院动物研究所的馆藏标本以及欧洲多家博物馆的模式标本,采用形态比较学方法开展研究。【结果】共发现中国沟胸步甲属5种,其中包括新种1种(双毛沟胸步甲H. bisetus sp. n.,模式产地：云南西双版纳),中国新纪录种3种(雅沟胸步甲H. gracilis、绿沟胸步甲H. smaragdinus和红腿沟胸步甲H. aeripennis)。提供了中国所有种类的形态描述及特征图,并编制了分种检索表。【结论】至此,我国所分布的沟胸步甲属物种从此前记录的1种增加至5种。     

Monophyly and phylogenetic relationships of the catfish genus Glyptothorax (Teleostei: Sisoridae) inferred from nuclear and mitochondrial gene sequences

GlyptothoraxBlyth (1860) is the most species-diverse and widely-distributed genus in the Sisoridae, but few studies have examined monophyly of the genus and phylogenetic relations within it. We used the nuclear RAG2 gene and mitochondrial COI and Cyt b genes from 50 of the approximately 70 species to examine monophyly of Glyptothorax and phylogenetic relationships within the genus. Molecular phylogenetic trees were constructed using maximum parsimony, maximum likelihood and Bayesian inference methods. All methods strongly supported monophyly of Glyptothorax, with Bagarius as its sister group. Both analyses of two- and three-gene datasets recovered nine major subclades of Glyptothorax, but some internal nodes remained poorly resolved. The phylogenetic relationships within the genus and existing taxonomic problems are discussed.     

An overview of diversity,occurrence, genetics and toxin production of bloom-forming Dolichospermum (Anabaena) species

The new genus name Dolichospermum, for most of the planktonic former members of the genus Anabaena, is one of the most ubiquitous bloom-forming cyanobacterial genera. Its dominance and persistence have increased in recent years, due to eutrophication from anthropogenic activities and global climate change. Blooms of Dolichospermum species, with their production of secondary metabolites that commonly include toxins, present a worldwide threat to environmental and public health. In this review, recent advances of the genus Dolichospermum are summarized, including taxonomy, genetics, bloom occurrence, and production of toxin and taste-and-odor compounds. The recent and continuing acquisition of genome sequences is ushering in new methods for monitoring and understanding the factors regulating bloom dynamics.     

Transfer of Nocardia amarae Lechevalier and Lechevalier 1974 to the genus Gordona as Gordona amarae comb. nov.

The taxonomic status of Nocardia amarae strains was examined using chemical, microbiological and nucleic acid sequencing methods. It was evident from the results of this and previous studies that Nocardia amarae has properties that are at variance with its classification in the genus Nocardia but consistent with its transfer to the genus Gordona . It is proposed that Nocardia amarae Lechevalier and Lechevalier 1974 be transferred to the genus Gordona as Gordona amarae comb. nov.     

The shifting roles of dispersal and vicariance in biogeography

Dispersal and vicariance are often contrasted as competing processes primarily responsible for spatial and temporal patterns of biotic diversity. Recent methods of biogeographical reconstruction recognize the potential of both processes, and the emerging question is about discovering their relative frequencies. Relatively few empirical studies, especially those employing molecular phylogenies that allow a temporal perspective, have attempted to estimate the relative roles of dispersal and vicariance. In this study, the frequencies of vicariance and dispersal were estimated in six lineages of birds that occur mostly in the aridlands of North America. Phylogenetic trees derived from mitochondrial DNA sequence data were compared for towhees (genus Pipilo), gnatcatchers (genus Polioptila), quail (genus Callipepla), warblers (genus Vermivora) and two groups of thrashers (genus Toxostoma). Different area cladograms were obtained depending on how widespread and missing taxa were coded. Nonetheless, no cladogram was obtained for which all lineages were congruent. Although vicariance was the dominant mode of evolution in these birds, approximately 25% of speciation events could have been derived from dispersal across a preexisting barrier. An expanded database is now needed to estimate the relative roles of each process. Applying a molecular clock calibration, nearly all speciation events are of the order of a million or more years old, much older than typically presumed.     

Sesquiterpene and diterpene derivatives from Solidago species

The investigation of four Solidago species afforded, in addition to known compounds, four new caryophyllene derivatives, two eudesmanes, two abietanes, a clerodane, two labdanes, three kauranes and an anol angelate. The structures were elucidated by spectroscopic methods and by some chemical transformations. While the diterpenes isolated are widespread in the genus Solidago, the sesquiterpenes have not been obtained before from any species. The overall picture of the large genus, however, is relatively uniform.     

Cryptosporidium and cryptosporidiosis in Denmark--current status

The genus Cryptosporidium comprises a group of protozoan parasites that infect a broad variety of vertebrates causing severe diarrhoeal illness in immunocompromised as well as immunocompetent hosts. Although molecular heterogeneity of the genus is being increasingly recognised, traditional diagnostic methods do not discriminate all species/subtypes, and population genetic studies of these parasites, using discriminatory molecular markers, have only been published recently. In Denmark, Cryptosporidium research has focussed mainly on detection methods, pathogenicity and veterinary aspects. The present paper gives an overview of recent and ongoing Cryptosporidium research in Denmark with an emphasis on molecular approaches to study epidemiology and transmission.     

The genus Amycolatopsis: Indigenous plasmids, cloning vectors and gene transfer systems

The genus Amycolatopsis is a member of the phylogenetic group nocardioform actinomycetes. Most of the members of the genus Amycolatopsis are known to produce antibiotics. Additionally, members of this genus have been reported to metabolize aromatic compounds as the sole sources of carbon and energy. Development of genetic manipulation in Amycolatopsis has progressed slowly due to paucity of genetic tools and methods. The occurrence of indigenous plasmids in different species of Amycolatopsis is not very common. Till date, only three indigenous plasmids viz., pMEA100, pMEA300 and pA387 have been reported in Amycolatopsis species. Various vectors based on the indigenous plasmids, pMEA100, pMEA300 and pA387, have been constructed. These vectors have proved useful for molecular genetics studies of actinomycetes. Molecular genetic work with Amycolatopsis strains is not easy, since transformation methods have to be developed, or at least optimized, for each particular strain. Nonetheless, methods for efficient transformation (polyethyleneglycol (PEG) induced protoplast transformation, transformation by electroporation and direct transformation) have been developed and used successfully for the introduction of DNA into several Amycolatopsis species. The construction of plasmid cloning vectors and the development of gene transfer systems has opened up possibilities for studying the molecular genetics of these bacteria.     

Heads up: evolution of exaggerated head length in the minute litter bug genus <Emphasis Type="Italic">Nannocoris</Emphasis> Reuter (Hemiptera: Schizopteridae)

Evolutionary biologists have long been intrigued by exaggerated morphologies tied to sexual or natural selection. In insects, relatively few studies have investigated the evolution of such traits at the genus level and above and have used comparative phylogenetic methods to do so. We here investigate the interspecific evolution of head length in the minute litter bug genus Nannocoris Reuter based on the first phylogenetic hypothesis of the group (25 ingroup species, five gene regions, 3409 bp) and ancestral state reconstruction. Head lengths in this speciose genus range from approximately one sixth of the total body length to more than a quarter of the body length, while the head and mouthpart (rostrum) lengths are correlated. Different species therefore possess a markedly different reach of the rostrum when extended. The analyses show that head length evolution in Nannocoris is plastic, with head length elongations and reductions occurring in several clades, derived from ancestors with moderately elongated heads. Evidence is provided that exaggerated head lengths evolved through elongation of either the genal (pricei group) or the tip (arimensis group) region of the head. The biology of species in the genus Nannocoris is unknown, but given the lack of sexual dimorphism of head lengths, we speculate that head evolution in this genus may be driven by natural selection, potentially in the context of prey capture.