A contribution to the nomenclature and classification of chlamydiae

The results of molecular-genetic study of typical specimens of the genus Chlamydophila of the family Chlamydiaceae from the FSE FCTRSA collection of microorganisms are considered for the purpose of their taxonomy based on comparative analysis by the omp1-, omp2-, 16S rRNA-, and 23S rRNA-genes and by the presence of extrachromosomal plasmid with corresponding fragments of the genomes officially registered species of chlamydiae. According to the omp1-RFLP-AluI-profile, the Rostinovo-70, 250, PP-87, and KC-93 strains were characterized by new genotype of chlamydiae (genotype G). The new omp2-RFLP-AluI-profile of chlamydiae on carrying out the comparative analysis of Rostinovo-70, 250, PP-87 and KC-93 strains by omp2-gene was characterized. On the basis of the species identification of chlamydiae by genetical and ecological criteria, the chlamydia strains Rostinovo-70, 250, PP-87, and KC-93 can be included in the new chlamydia species Chlamydophila parapsittaci sp. nov. It was suggested to combine into a new species the following strains of Chlamydophila psittaci: WC, NJ1, 92-1293, TT3, 7344/2, GD, CT1, Par1, 84/2334, R54, VS225, 777B15, and Prk/Daruma.     

Semisystematic nomenclature of brassinosteroids

The assignment of the trivial name to new isolated or detected brassinosteroid is based on the trivial names of seven different brassinosteroids, with names assigned according to the plant source from which they were first isolated. To avoid some observed mistakes in assigning trivial names to these compounds and the impractical constant usage of their systematic names, we propose a semisystematic nomenclature of brassinosteroids, in which (22R,23R)-2,3,22,23-tetrahydroxy-5-campestane, the trivial name of which is 6-deoxocastasterone, is considered the functional parent compound and is named brassinostane or brassinane. A set of rules for naming the remaining natural brassinosteroids is presented.     

The cyclization of peptides and depsipeptides.

Constricting the peptide backbone into a more defined conformational form through cyclization is an activity evolved in nature and in synthetic work, the latter straddling only the most recent decades. The resulting conformational constraints increase the probability of an optimum response with bio-receptors. The purpose of this review is to highlight developments that have proved to be reasonably efficient in the macrocyclization of linear precursors into cyclic peptides and depsipeptides.     

Controlling production of brominated cyclic depsipeptides by Pseudoalteromonas maricaloris KMM 636T

AIMS: This study aims at evaluating the impact of the nutrient medium components on the in vitro production of the cytotoxic alterochromides. METHODS AND RESULTS: The employment matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) facilitated the identification of a range of brominated cyclic depsipeptides with molecular masses of 843/845, 857/859 and 922/924/926 Da, and 936/938/940 Da produced by the marine bacterium Pseudoalteromonas maricaloris KMM 636T. The fractions of cytotoxic yellow pigments yielded after methanol extraction of P. maricaloris KMM 636T cells grown on five nutrient media were solely composed of brominated cyclic depsipeptides. Bromo-alterochromides A and B were obtained after cultivation on low nutrient media, while dibrominated derivatives were the principal components of the biosynthesis during cultivation on nutrient rich media. CONCLUSIONS: The quantity of bromo-alterochromides and their dibromo- derivates varied depending on the media composition. SIGNIFICANCE AND IMPACT OF THE STUDY: MALDI-TOF mass spectrometry enables to generate accurate mass analysis for the identification of peptide and its derivates which is important in controlling the production of biologically active compounds in vitro.     

Phylogeny,classification and nomenclature: a reply to F. Pleijel and G. W. Rouse

In systematics, the uncovering of monophyletic units, of sister group relationships and also of paraphyla is an important part of primary research. The hypotheses derived are thus subject to falsification and are subject to change. In contrast, classifications are a secondary step, as they are derived from such hypotheses. Classifications are based on different philosophies, which permit different solutions as to how results in the fields of taxonomy and phylogenetics can be transposed into a ‘system’. The function of classifications is at least partly utilitarian, and this is even more true for the names and principles of nomenclature. Nomenclature is simply a tool for information retrieval and for safeguarding understanding. Directly linking names and cladograms or nodes, respectively – making them subject to changes by falsification – would deliberately ignore the primary, strictly utilitarian function of long‐established principles of nomenclature and would endanger an instrument that functions almost perfectly. Approaches to introduce a so‐called PhyloCode should therefore not be pursued, as there is no chance at all that this kind of code could be generally accepted.     

Proposals for the naming of chloroplast genes. II. Update to the nomenclature of genes for thylakoid membrane polypeptides

The nomenclature for genes for components of the photosynthetic membranes has been reviewed and updated. Newly discovered genes have been added to the existing convention for gene nomenclature. Genes designatedpetA throughpetI are described for components of the photosynthetic electron transport systems,psaA throughpsaK for photosystem I components, andpsbA throughpsbR for photosystem II, including the extrinsic polypeptides of the oxygen-evolving complex. References for representative examples of each gene are given.     

A nomenclature and data model to describe NMR experiments

Despite ongoing efforts in organising NMR information, there is no consistent and well-described generic standard for naming NMR experiments. The main reason for the absence of a universal naming system is that the information content of the coherence pathways is difficult to describe in full detail. We propose a system that describes the common and generic elements of the coherence pathways produced by pulse sequences. The system itself is formalised by an ‘NMR experiment protocol’ model, which is described in the Universal Modelling Language (UML) as part of the CCPN data model. Furthermore, normalized experiment names can be derived from this proposed model. We hope this article will stimulate discussion to organise the wealth of NMR experiments, and that by bringing this discussion into the public domain we can improve and expand our proposed system to include as much information and as many NMR experiments as possible. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.Joint first authors     

中国书带蕨科植物的分类和名称变化

对书带蕨科的分类进行了评论。承认中国该科植物24种,隶属于3属,即车前蕨属,书带蕨属和一条线蕨属。     

黑木耳复合群中种类学名说明

黑木耳在我国已经有1 000多年栽培历史,是我国最重要的栽培真菌之一,多年来我国黑木耳的学名一直使用模式产地为欧洲的Auricularia auricula-judae。最近的研究表明A. auricula-judae实际为一复合种,该复合种在全球范围内有5个种。其中A. auricula-judae仅分布于欧洲;美洲有2个种,生长在针叶树上的美洲木耳A. americana和生长在阔叶树上的尚未命名的木耳。中国该类群有3个种：自然分布和栽培最广泛的黑木耳的学名应为A. heimuer,此外,短毛木耳A. villosula在我国东北也广泛分布,并有少量栽培,生长针叶树上的木耳为美洲木耳A. americana,主要分布于中国东北和华北。     

Standard nomenclature for primate breeding and husbandry

Managers of primate colonies seek to record colony data in a systematic way which will be helpful in daily management. Each colony develops individual record systems, tailored to its specific operations and budget. These diversified systems provide the base for a set of uniform record items, which enables information to be shared among institutions, and used for the overall management of a self-sustaining captive primate population, as well as for national planning of primate resources. The present report identifies basic information needed for local colony management and data items that require standard nomenclature. Such data will provide the basic demographic profiles unavailable at most primate colonies today.     

An unambiguous nomenclature for xyloglucan-derived oligosaccharides

A revised system of abbreviated names is proposed for xyloglucan-derived oligosaccharides. Each (1→4)-linked β- d -glucosyl residue (and the reducing terminal d -glucose moiety) of the backbone is given a one-letter code according to its substituents. The name of the oligosaccharide consists of these code letters listed in sequence from non-reducing to reducing terminus of the backbone.     

Quirks of dye nomenclature. 6. Malachite green

Malachite green was discovered independently by two researchers in Germany in the 19^th century and found immediate employment as a dye and a pigment. Subsequently, other uses, such as staining biological specimens, emerged. A much later application was the control of fungal and protozoan infections in fish, for which the dye remains popular, although illegal in many countries owing to a variety of toxicity problems. In solution, malachite green can exist as five different species depending on the pH. The location of the positive charge of the colored cation on a carbon atom or a nitrogen atom is still debated. The original names of this dye, and their origins, are briefly surveyed.     

中国灵芝学名之管见

灵芝是最重要的药用真菌之一,在我国已有2,000多年的记载和利用历史。虽然早在一百多年前法国真菌学家Patouillard就有给中国的灵芝冠上Ganoderma lucidum这一学名,并沿用至今,但随着分子生物学技术的不断发展,人们认识到过去外国人的定名并不正确。实际上,G.lucidum是1871年由William Curtis根据采自英国的标本描述的新物种。最近的研究表明,我国广泛分布和栽培的灵芝与产于欧洲的G.lucidum不同,是一个独立的种,其合法的拉丁学名应为G.lingzhi。鉴于"灵芝"这一名称在中国已使用2,000余年,故建议"G.lingzhi"的汉语学名为"灵芝"(俗称赤芝),而灵芝属的模式种G.lucidum的汉语学名改为"亮盖灵芝"(俗称白肉灵芝或白灵芝)。灵芝Ganoderma lingzhi广泛分布于东亚暖温带和亚热带,其主要形态特征是孔口表面新鲜时浅黄色至硫磺色、成熟时菌肉中有黑褐色区带、管口壁厚度为80–120μm。亮盖灵芝G.lucidum主要分布于欧洲和亚洲,在我国分布于东北、华北、华中和西南海拔较高地区,其孔口表面新鲜时白色至奶油色、成熟时菌肉中无黑褐色区带、管口壁厚度为40–80μm。四川灵芝G.sichuanense尽管其担孢子与灵芝G.lingzhi相似,但基于其模式标本ITS序列的系统发育研究表明,该种与灵芝不同,是个独立的种,且在广东也有发现。     

International code for phytolith nomenclature 1.0

BACKGROUND: Phytoliths (microscopic opal silica particles produced in and between the cells of many plants) are a very resilient, often-preserved type of microfossil and today, phytolith analysis is widely used in palaeoenvironmental studies, botany, geology and archaeology. To date there has been little standardization in the way phytoliths are described and classified. SCOPE: This paper presents the first International Code for Phytolith Nomenclature (ICPN), proposing an easy to follow, internationally accepted protocol to describe and name phytoliths.     

New syntaxonomic contribution to the Vegetation Prodrome of Italy

New syntaxa of different hierarchical levels are here described in order to update the “Syntaxonomic checklist of the Italian classes, orders and alliances (Vegetation Prodrome of Italy)”, promoted in 2012 by the “Ministry of Environment, Land and Sea Protection” in collaboration with the “Italian Society of Botany”. The new alliances, suballiances and associations belong to the Salici purpureae-Populetea nigrae and Querco roboris-Fagetea sylvaticae classes.     

Ceci n'est pas une pipe: names, clades and phylogenetic nomenclature

An introduction is provided to the literature and to issues relating to phylogenetic nomenclature and the PhyloCode, together with a critique of the current Linnaean system of nomenclature. The Linnaean nomenclature fixes taxon names with types, and associates the names with ranks (genus, family, etc.). In phylogenetic nomenclature, names are instead defined with reference to cladistic relationships, and the names are not associated with ranks. We argue that taxon names under the Linnaean system are unclear in meaning and provide unstable group–name associations, notwithstanding whether or not there are agreements on relationships. Furthermore, the Linnaean rank assignments lack justification and invite unwarranted comparisons across taxa. On the contrary, the intention of taxon names in phylogenetic nomenclature is clear and stable, and the application of the names will be unambiguous under any given cladistic hypothesis. The extension of the names reflects current knowledge of relationships, and will shift as new hypotheses are forwarded. The extension of phylogenetic names is, therefore, clear but is associated to (and thus dependent upon) cladistic hypotheses. Stability in content can be maximized with carefully formulated name definitions. A phylogenetic nomenclature will shift the focus from discussions of taxon names towards the understanding of relationships. Also, we contend that species should not be recognized as taxonomic units. The term ‘species’ is ambiguous, it mixes several distinct classes of entities, and there is a large gap between most of the actual concepts and the evidence available to identify the entities. Instead, we argue that only clades should be recognized. Among these, it is useful to tag the smallest named clades, which all represent non-overlapping groups. Such taxa  – LITUs (Least Inclusive Taxonomic Units) – are distinguished from more inclusive clades by being spelled with lower-case initial letter. In contrast to species, LITUs are conceptually straightforward and are, like other clades, identified by apomorphies.     

A proposal for a coherent mammalian histone H1 nomenclature correlated with amino acid sequences.

Bio-Rex 70 chromatography was combined with reverse-phase (RP) HPLC to fractionate histone H1 zero and 4 histone H1 subtypes from human placental nuclei as previously described (Parseghian MH et al., 1993, Chromosome Res 1:127-139). After proteolytic digestion of the subtypes with Staphylococcus aureus V8 protease, peptides were fractionated by RP-HPLC and partially sequenced by Edman degradation in order to correlate them with human spleen subtypes (Ohe Y, Hayashi H, Iwai K, 1986, J Biochem (Tokyo) 100:359-368; 1989, J Biochem (Tokyo) 106:844-857). Based on comparisons with the sequence data available from other mammalian species, subtypes were grouped. These groupings were used to construct a coherent nomenclature for mammalian somatic H1s. Homologous subtypes possess characteristic patterns of growth-related and cAMP-dependent phosphorylation sites. The groupings defined by amino acid sequence also were used to correlate the elution profiles and electrophoretic mobilities of subtypes derived from different species. Previous attempts at establishing an H1 nomenclature by chromatographic or electrophoretic fractionations has resulted in several misidentifications. We present here, for the first time, a nomenclature for somatic H1s based on amino acid sequences that are analogous to those for H1 zero and H1t. The groupings defined should be useful in correlating the many observations regarding H1 subtypes in the literature.     

History and nomenclature of the theropod dinosaur tracks Bueckeburgichnus and Megalosauripus

The most recent account of Bueckeburgichnus maximus Kuhn 1958, a distinctive theropod dinosaur track from the Lower Cretaceous of Germany, is shown to be based on a referred specimen mistakenly identified as the holotype and the correct name of this taxon is deemed to be Megalosauripus maximus (Kuhn 1958). This minor revision has important consequences for nomenclature of the many European, Asian, North American and Australian dinosaur tracks attributed to megalosaurian theropods. Many of those tracks were named Megalosauripus, but that name has a confusing multiplicity of meanings and it should be restricted to the highly characteristic dinosaur track formerly identified as Bueckeburgichnus. Other tracks named "Megalosauripus”; (in its several other senses) will require new nomenclature, despite their extensive and repeated revision since 1996. It is recommended that future revision should adopt conventions of the International Code of Zoological Nomenclature. Although previous revisions expressed an intention to adhere to those conventions, these were not put into practice, with the unfortunate result of multiplying the problems that surround the nomenclature of megalosaur tracks. Introduction of the name Megalosauripus maximus (Kuhn 1958) eliminates those burgeoning problems and permits the introduction of new and objective nomenclature for presumed megalosaur tracks.     

A contribution to the nomenclature of peripheral sensory structures (sensory nerve endings)

The author has shown the variety in denominating peripheral sensory structures serving for mechanoreception, nociception, thermoreception and chemoreception. To term peripheral sensory structures as nerve endings is considered particularly unsuitable because this denomination is based only on morphogenesis of the ending. From the view of system approach, the peripheral sensory structures forms one unit formed by two or more structural subsystems. Even though the axon or its dendritic zone has the leading role in this unit, the function of the whole formation is influenced (modulated) by further non-nervous components. Although the causes of velocity of adaptation in some sensory structures have been already explained (e.g. in lamellar corpuscles with a thick capsule), different adaptation velocity of Merkel complexes in reptiles and birds on one side, and in mammals on the other, with the same structure has not been clear up to now. From the view of system approach as well as of the share of non-nervous components in the activity of the whole sensory structure, the author has suggested to introduce the term "sensory nerve formation" for peripheral sensory structures serving for mechanoreception, nociception, thermoreception and chemoreception. The term "complex sensory nerve formation" is suggested for more complex sensory structures in which either more sensory nerve formations of the same kind (Pinkus tactile dics) or different kinds of sensory formations (Eimer organ of a mole) are connected constantly or in which the connection of sensory nerve formations with other supporting structures (hairs, feathers) occurs.