关于规范涉及喜马拉雅山的物种中文命名的建议

虽然国际生物科学联合会已经明确了“学名”的法定地位,但在实际工作中仍然离不开中文名的使用。本文通过对以“himalaya”拉丁化命名的6个属、402个物种,以及涉及“喜马拉雅山”的1个属、37个种中文名的分析,发现有3个属和35个物种中文名命名不规范。这些命名中不恰当的简化违反了地名法定原则、史料记载和行业惯例,由此提出修订不规范命名的建议。     

Plants and geographical names in Croatia

The main purpose of this paper is to present some general observations, regularities and insights into a complex relationship between plants and people through symbolic systems like geographical names on the territory of Croatia. The basic sources of data for this research were maps from atlas of Croatia of the scale 1:100000. Five groups of maps or areas were selected in order to represent main Croatian phytogeographic regions. A selection of toponyms from each of the map was made in which the name for a plant in Croatian language was recognized (phytotoponyms). Results showed that of all plant names recognized in geographical names the most represented are trees, and among them birch and oak the most. Furthermore, an attempt was made to explain the presence of the most represented plant species in the phytotoponyms in the light of general phytogeographical and sociocultural differences and similarities of comparing areas. The findings confirm an expectation that the genera of climazonal vegetation of particular area are the most represented among the phytotoponyms. Nevertheless, there are ample examples where representation of a plant name in the names of human environment can only be ascribed to ethno-linguistic and socio-cultural motives. Despite the reductionist character of applied methodology, this research also points out some advantages of this approach for ethnobotanic and ethnolinguistic studies of greater areas of human environment.     

Forum – Taxonomic Stability is Ignorance

Absolute nomenclatural stability is undesirable in phylogenetic classifications because they reflect changing hypotheses of cladistic relationships. De Queiroz and Gauthier's (1990: Syst. Zool. 39, 307–322; 1992: A. Rev. Ecol. Syst. 23, 449–480; 1994: Trends Ecol. Evol. 9, 27–31) alternative to Linnaean nomenclature is concluded to provide stable names for unstable concepts. In terms of communicating either characters shared by species of a named taxon or elements (species) included in a taxon, de Queiroz and Gauthier's system is less stable than the Linnaean system. Linnaean ranks communicate limited information about inclusivity of taxa, but abandonment of ranks results in the loss of such information. As cladistic hypotheses advance, taxa named under de Queiroz and Gauthier's system can change their level of generality radically, from being part of a group to including it, without any indicative change in its spelling. The Linnaean system has been retained by taxonomists because its hierarchic ranks are logically compatible with nested sets of species, monophyletic groups, and characters. Other authors have offered conventions to increase the cladistic information content of Linnaean names or to replace them with names that convey cladistic knowledge in greater detail; de Queiroz and Gauthier sacrifice the meaning of taxon names and categorical ranks in favor of spelling stability.     

Cyclomaltodextrinase, neopullulanase, and maltogenic amylase are nearly indistinguishable from each other

Over 20 enzymes denoted as cyclomaltodextrinase, maltogenic amylase, or neopullulanase that share 40-86% sequence identity with each other are found in public data bases. These enzymes are distinguished from typical alpha-amylases by containing a novel N-terminal domain and exhibiting preferential substrate specificities for cyclomaltodextrins (CDs) over starch. In this research field, a great deal of confusion exists regarding the features distinguishing the three groups of enzymes from one another. Although a different enzyme code has been assigned to each of the three different enzyme names, even a single differentiating enzymatic property has not been documented in the literature. On the other hand, an outstanding question related to this issue concerns the structural basis for the preference of these enzymes for CDs. To clarify the confusion and to address this question, we have determined the structures of two enzymes, one from alkalophilic Bacillus sp. I-5 and named cyclomaltodextrinase and the other from a Thermus species and named maltogenic amylase. The structure of the Bacillus enzyme reveals a dodecameric assembly composed of six copies of the dimer, which is the structural and functional unit of the Thermus enzyme and an enzyme named neopullulanase. The structure of the Thermus enzyme in complex with beta-CD led to the conclusion that Trp47, a well conserved N-terminal domain residue, contributes greatly to the preference for beta-CD. The common dimer formation through the novel N-terminal domain, which contributes to the preference for CDs by lining the active-site cavity, convincingly indicates that the three groups of enzymes are not different enough to preserve the different names and enzyme codes.     

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.     

Generation of a large gene/protein lexicon by morphological pattern analysis

The identification of gene/protein names in natural language text is an important problem in named entity recognition. In previous work we have processed MEDLINE documents to obtain a collection of over two million names of which we estimate that perhaps two thirds are valid gene/protein names. Our problem has been how to purify this set to obtain a high quality subset of gene/protein names. Here we describe an approach which is based on the generation of certain classes of names that are characterized by common morphological features. Within each class inductive logic programming (ILP) is applied to learn the characteristics of those names that are gene/protein names. The criteria learned in this manner are then applied to our large set of names. We generated 193 classes of names and ILP led to criteria defining a select subset of 1,240,462 names. A simple false positive filter was applied to remove 8% of this set leaving 1,145,913 names. Examination of a random sample from this gene/protein name lexicon suggests it is composed of 82% (+/-3%) complete and accurate gene/protein names, 12% names related to genes/proteins (too generic, a valid name plus additional text, part of a valid name, etc.), and 6% names unrelated to genes/proteins. The lexicon is freely available at ftp.ncbi.nlm.nih.gov/pub/tanabe/Gene.Lexicon.     

Some Lithuanian ethnobotanical taxa: a linguistic view on Thorn Apple and related plants

Background

The perception and use of plants correspond with common plant names. The study of plant names may give insight into historical and recent use of plants.

Methods

Plant names in dictionaries and folklore have been evaluated. A etymological analysis of the names is provided. Onomasiological and semasiological aspects have been considered. Therefore, species named with names related to each other have been selected.

Results

Plant names containing the stem dag- or deg- may belong to either of two categories: incenses or thorny plants. Plants named in durn- have been in use as psychopharmaca. The name rymo points not to Rome but to the use of plants as anodyne or psychopharmaca.     

A Check-List of the Species of the Genus Leucocytozoon (Apicomplexa,Plasmodiidae)*

SYNOPSIS. A list is given of 67 named species of Leucocytozoon considered valid at present. Another list is given of 1 reptilian and 146 avian hosts of named species of Leucocytozoon. A 3rd list is given of 34 synonyms. Leucocytozoon has been named from about 0.7% of the approximately 8600 species of birds that exist. The following new taxonomic names are included: L. danilewskyi var. hirundinis Sergent & Sergent, 1905 is emended to L. hirundinis; Saurocytozoon tupinambi Lainson & Shaw, 1969 is changed to Leucocytozoon (Saurocytozoon) tupinambi (Lainson & Shaw, 1969).     

The role of glomeruli in the neural representation of odours: results from optical recording studies

Odours are received by olfactory receptors, which send their axons to the first sensory neuropils, the antennal lobes (in insects) or the olfactory bulb (in vertebrates). From here, processed olfactory information is relayed to higher-order brain centres. A striking similarity in olfactory systems across animal phyla is the presence of glomeruli in this first sensory neuropil. Various experiments have shown that odours elicit a mosaic of activated glomeruli, suggesting that odour quality is coded in an 'across-glomeruli' activity code. In recent years, studies using optical recording techniques have greatly improved our understanding of the resulting 'across-glomeruli pattern', making it possible to simultaneously measure responses in several, often identifiable, glomeruli. For the honeybee Apis mellifera, a functional atlas of odour representation is being created: in this atlas, the glomeruli that are activated by different odorants are named. However, several limitations remain to be investigated. In this paper, we review what optical recording of odour-evoked glomerular activity patterns has revealed so far, and discuss the necessary next steps, with emphasis on the honeybee.     

Immortality in a name

Have you ever wondered where flora and fauna found their names? Many are named for people--rich and poor, large and small. Even tabletop football is not immune.     

Chromodorid opisthobranch Mollusca from East Africa and the tropical West Pacific

Six species of Hypselodoris and three species of Chromodoris axe described from the coast of East Africa. Three species of Hypselodoris and one species of Chromodoris are new species. Two species of Chromodoris from the tropical West Pacific are also described. The eleven species fall into three groups of similarly coloured species.
Hypselodoris nigrostriata and a new species of Hypselodoris are compared with H. infucata, H. festiva, H. obscura and two unnamed species from the literature. It is concluded that all these are distinct species.
H. nigrolineata and two new species, are compared with H. lineata and H. hilaris and all are considered distinct.
H. regina, Chromodoris quadricolor, C. africana, C. elisabethina, C. magnified and a new species of Chromodoris, are compared with C. westraliensis and two unnamed species from the literature. All these species are considered distinct.
All other names for forms falling into these three colour groups are considered synonyms of one or other of the above named species. Full synonymies are given.     

A Statistical Parametric Mapping Toolbox Used for Voxel-Wise Analysis of FDG-PET Images of Rat Brain

Purpose

PET (positron emission tomography) imaging researches of functional metabolism using fluorodeoxyglucose (¹⁸F-FDG) of animal brain are important in neuroscience studies. FDG-PET imaging studies are often performed on groups of rats, so it is desirable to establish an objective voxel-based statistical methodology for group data analysis.

Material and Methods

This study establishes a statistical parametric mapping (SPM) toolbox (plug-ins) named spmratIHEP for voxel-wise analysis of FDG-PET images of rat brain, in which an FDG-PET template and an intracranial mask image of rat brain in Paxinos & Watson space were constructed, and the default settings were modified according to features of rat brain. Compared to previous studies, our constructed rat brain template comprises not only the cerebrum and cerebellum, but also the whole olfactory bulb which made the later cognitive studies much more exhaustive. And with an intracranial mask image in the template space, the brain tissues of individuals could be extracted automatically. Moreover, an atlas space is used for anatomically labeling the functional findings in the Paxinos & Watson space. In order to standardize the template image with the atlas accurately, a synthetic FDG-PET image with six main anatomy structures is constructed from the atlas, which performs as a target image in the co-registration.

Results

The spatial normalization procedure is evaluated, by which the individual rat brain images could be standardized into the Paxinos & Watson space successfully and the intracranial tissues could also be extracted accurately. The practical usability of this toolbox is evaluated using FDG-PET functional images from rats with left side middle cerebral artery occlusion (MCAO) in comparison to normal control rats. And the two-sample t-test statistical result is almost related to the left side MCA.

Conclusion

We established a toolbox of SPM8 named spmratIHEP for voxel-wise analysis of FDG-PET images of rat brain.     

Revision and checklist of the species (other than lecudina) of the aseptate gregarine family Lecudinidae.

A checklist is given of the 89 named species of the gregarine family Lecudininae, exclusive of the 42 named species of the genus Lecudina (phylum Apicomplexa, class Sporozoea, subclass Gregarinia, order Eugregarinida, suborder Aseptatina). The list includes also the synonyms, host names, locations in hosts, known geographic distributions of the species, as well as key references. Another list is given of synonyms, lapsi calami, nomina nuda, etc., associated with the genera. A new genus, Paraophioidina g.n., with type species, Paraophioidina haeckeli (Mingazzini, 1891) and a new species, Lankesteria ormieresi sp. n., are described. There are also new combinations in the genera Bhatiella, Ancora, Monocystella, Ascocystis, and Paraophioidina.     

A proposed nomenclature for bile acids.

A proposal is made for a system of nomenclature of the more common unconjugated and conjugated bile acids. Acceptable trivial names for bile acids are tabulated, and guidelines are proposed for using these existing trivial names as roots to create acceptable semi-systematic names for other bile acids, as well as for new natural bile acids that will be discovered in the future. The term alpha-hyocholic is recommended to replace hyocholic, and beta-hyocholic to replace omega-muricholic. The term murideoxycholic acid is recommended for 3 alpha,6 beta-dihydroxy-5 beta-cholan-24-oic acid. Proposals are also made for bile acids with epimeric hydroxy groups, for unsaturated bile acids, and for bile acids with oxo- and/or hydroxy-oxo- substituents on the nucleus and/or on the side chain. For conjugated bile acids, the term "aminoacyl amidates" is recommended to replace "amidates" for bile acids conjugated in N-acyl linkage with amino acids. Nomenclature for other types of conjugates (sulfates, glucuronides, glucosides) is included as well as abbreviations. It is recommended that the historic tradition of naming a newly discovered bile acid after the species from which it was isolated be abandoned, and that in the future such a bile acid should be named using the principles contained in this paper.     

A Mouthful of Diversity: Knowledge of Cider Apple Cultivars in the United Kingdom and Northwest United States

A Mouthful of Diversity: Knowledge of Cider Apple Cultivars in the United Kingdom and Northwest United States. There is a general assumption in the study of folk taxonomy that those people who have been interacting with a given crop the longest have the most knowledge about the crop’s names. We treated this as an hypothesis which can be tested with knowledge of cider apples. This use of apples extends back many generations in some places, while in other regions people are just learning to make cider. The experimental design is to assess quantitatively the cider apple diversity being used compared to the knowledge of this diversity by cider makers. The test involves two populations of cider makers: those who come from a long-standing tradition of cider making and those who recently learned to make cider. Research was conducted in parts of England, Wales, Northern Ireland, and Washington State, U.S.A. Semistructured interviews and questionnaires were used to elicit cider apple variety names. Traditional knowledge associated with cider production was also collected. Eighty-two cider apple variety names were obtained. In addition, it is estimated that between 111 and 328 varieties were recognized but could not be named. There was a significant difference between the cider apple cultivars that cider makers could name and those that they could discern. On average, cider makers could name eight varieties, but discern 16 varieties of cider apples largely on the basis of appearance, taste, and smell. There was no significant difference in the knowledge of cider apple variety names between long-standing cider makers and those that recently learned to make cider. As with cider apples, we would expect that farmers of other culturally-significant crops would not always know named diversity if there are other cues to let them track varietal difference, such as appearance, taste, or smell.     

A phylogenetic analysis of the mycoplasmas: basis for their classification

Small-subunit rRNA sequences were determined for almost 50 species of mycoplasmas and their walled relatives, providing the basis for a phylogenetic systematic analysis of these organisms. Five groups of mycoplasmas per se were recognized (provisional names are given): the hominis group (which included species such as Mycoplasma hominis, Mycoplasma lipophilum, Mycoplasma pulmonis, and Mycoplasma neurolyticum), the pneumoniae group (which included species such as Mycoplasma pneumoniae and Mycoplasma muris), the spiroplasma group (which included species such as Mycoplasma mycoides, Spiroplasma citri, and Spiroplasma apis), the anaeroplasma group (which encompassed the anaeroplasmas and acholeplasmas), and a group known to contain only the isolated species Asteroleplasma anaerobium. In addition to these five mycoplasma groups, a sixth group of variously named gram-positive, walled organisms (which included lactobacilli, clostridia, and other organisms) was also included in the overall phylogenetic unit. In each of these six primary groups, subgroups were readily recognized and defined. Although the phylogenetic units identified by rRNA comparisons are difficult to recognize on the basis of mutually exclusive phenotypic characters alone, phenotypic justification can be given a posteriori for a number of them.     

Mammalian septins nomenclature

There are 10 known mammalian septin genes, some of which produce multiple splice variants. The current nomenclature for the genes and gene products is very confusing, with several different names having been given to the same gene product and distinct names given to splice variants of the same gene. Moreover, some names are based on those of yeast or Drosophila septins that are not the closest homologues. Therefore, we suggest that the mammalian septin field adopt a common nomenclature system, based on that adopted by the Mouse Genomic Nomenclature Committee and accepted by the Human Genome Organization Gene Nomenclature Committee. The human and mouse septin genes will be named SEPT1-SEPT10 and Sept1-Sept10, respectively. Splice variants will be designated by an underscore followed by a lowercase "v" and a number, e.g., SEPT4_v1.