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Sample records for polyphasic taxonomic approach

  1. Polyphasic taxonomy, a consensus approach to bacterial systematics.

    PubMed Central

    Vandamme, P; Pot, B; Gillis, M; de Vos, P; Kersters, K; Swings, J

    1996-01-01

    Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on bacterial taxonomy. This problem is faced in polyphasic taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of taxonomy, integrating all available data maximally. In the future, polyphasic taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question. PMID

  2. A polyphasic taxonomic evaluation of Streptomyces strains isolated from equine placentas

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Actinomycete strains isolated from lesions on equine placentas were subjected to polyphasic taxonomic identification. All of the strains were isolated from placentas from horses in Kentucky. On the basis of phylogenetic analysis of 16S rDNA sequences, morphological observations, and the presence o...

  3. Prokaryotic taxonomy in the sequencing era--the polyphasic approach revisited.

    PubMed

    Kämpfer, Peter; Glaeser, Stefanie P

    2012-02-01

    The ultimate goal of taxonomy is to establish a system that mirrors the 'order in nature'. In prokaryote microbiology, almost all taxonomic concepts try to mirror the whole evolutionary order back to the origin of life with the cell as basic unit. The introduction of the 16S rRNA gene as molecular marker allowed for the first time the creation of a hierarchical taxonomic system based on one practical molecular marker. With the development of new and rapid sequencing technologies a wealth of new data can and will be used for critical evaluation of the taxonomic system. Comprehensive analyses of other molecular markers as well as total or partial genome comparisons confirmed the 16S rRNA based hierarchical system as 'backbone of prokaryote taxonomy' at least at the genus level and above. A tendency is visible to classify novel taxa more and more based on the genotype, i.e. comparative analyses of 16S rRNA and/or other gene sequence data (in multilocus sequence analysis, MLSA) at the genus and the species level, sometimes contrary to the indications of other (often phenotypic) data. The understanding of all the information behind these data is lagging far behind their accumulation. Genes and genomes do not function on its own and can only display their potential within the cell as the basic unit of evolution (and hence taxonomy). It is the phenotype and the natural selection that 'drive' evolution in a given environment. In this context, the 'polyphasic taxonomic approach' should be revisited again, taking into account the novel insights into genomes and other 'omic' sciences in a more strict and detailed context with the phenotype. This approach allows a more holistic view and provides a sound basis for describing the diversity of prokaryotes and has the potential to become the foundation of a more stable, in-depth taxonomy of the prokaryotes. PMID:22040009

  4. Taxonomic re-evaluation of species in Talaromyces section Islandici, using a polyphasic approach.

    PubMed

    Yilmaz, N; Visagie, C M; Frisvad, J C; Houbraken, J; Jacobs, K; Samson, R A

    2016-06-01

    The taxonomy of Talaromyces rugulosus, T. wortmannii and closely related species, classified in Talaromyces sect. Islandici, is reviewed in this paper. The species of Talaromyces sect. Islandici have restricted growth on MEA and CYA, generally have yellow mycelia and produce rugulosin and/or skyrin. They are important in biotechnology (e.g. T. rugulosus, T. wortmannii) and in medicine (e.g. T. piceus, T. radicus). The taxonomy of sect. Islandici was resolved using a combination of morphological, extrolite and phylogenetic data, using the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) concept, with special focus on the T. rugulosus and T. wortmannii species complexes. In this paper, we synonymise T. variabilis, Penicillium concavorugulosum and T. sublevisporus with T. wortmannii, and introduce four new species as T. acaricola, T. crassus, T. infraolivaceus and T. subaurantiacus. Finally, we provide a synoptic table for the identification of the 19 species classified in the section. PMID:27616787

  5. Characterization of Aspergillus section Flavi isolated from organic Brazil nuts using a polyphasic approach.

    PubMed

    Reis, T A; Baquião, A C; Atayde, D D; Grabarz, F; Corrêa, B

    2014-09-01

    Brazil nut (Bertholletia excelsa), an important non-timber forest product from Amazonia, is commercialized in worldwide markets. The main importers of this nut are North America and European countries, where the demand for organic products has grown to meet consumers concerned about food safety. Thus, the precise identification of toxigenic fungi is important because the Brazil nut is susceptible to colonization by these microorganisms. The present study aimed to characterize by polyphasic approach strains of Aspergillus section Flavi from organic Brazil nuts. The results showed Aspergillus flavus as the main species found (74.4%), followed by Aspergillus nomius (12.7%). The potential mycotoxigenic revealed that 80.0% of A. flavus were toxin producers, 14.3% of which produced only aflatoxin B (AFB), 22.85% of which produced only cyclopiazonic acid (CPA), and 42.85% produced both them. All strains of A. nomius were AFB and AFG producers and did not produce CPA. There is no consensus about what Aspergillus species predominates on Brazil nuts. Apparently, the origin, processing, transport and storage conditions of this commodity influence the species that are found. The understanding about population of fungi is essential for the development of viable strategies to control aflatoxins in organic Brazil nuts. PMID:24929714

  6. Phylogenetic comparison among the heterocystous cyanobacteria based on a polyphasic approach.

    PubMed

    Mishra, Arun Kumar; Shukla, Ekta; Singh, Satya Shila

    2013-02-01

    Phylogenetic comparison has been done among the selected heterocystous cyanobacteria belonging to the sections IV and V. The hierarchical cluster analysis based on antibiotics sensitivity showed a distant relationship between the members of Nostocales and Stigonematales. Thus, multiple antibiotic resistance pattern used as marker provide easy, fast, and reliable method for strain discrimination and genetic variability. However, morphological, physiological (both based on principal component analysis) and biochemical analysis grouped true branching cyanobacteria along with the members of section IV. Molecular analysis based on 16S rRNA gene sequences revealed that Hapalosiphon welwitschii and Westiellopsis sp. were grouped in cluster I whereas Scytonema bohnerii, a false branching genera showed a close proximity with Calothrix brevissima in cluster II. Cluster III of clade 2 included Nostoc calcicola and Anabaena oryzae which proved the heterogeneity at the generic level. Cluster IV the largest group of clade 2 based on 16S rRNA gene sequences includes six strains of the genera Nostoc, Anabaena, and Cylindrospermum showing ambiguous evolutionary relationship. In cluster IV, Anabaena sp. and Anabaena doliolum were phylogenetically linked by sharing 99% sequence similarity. Probably, they were of the same genetic makeup but appear differently under the diverse physiological conditions. Section IV showed polyphyletic origin whereas section V showed monophyletic origin. Results suggested that either morphological or physiological or biochemical or molecular attribute is not sufficient to provide true diversity and phylogeny of the cyanobacteria at the generic level and thus, a polyphasic approach would be more appropriate and reliable. PMID:22307204

  7. A polyphasic approach for the characterization of endophytic Alternaria strains isolated from grapevines.

    PubMed

    Polizzotto, Rachele; Andersen, Birgitte; Martini, Marta; Grisan, Simone; Assante, Gemma; Musetti, Rita

    2012-01-01

    A polyphasic approach was set up and applied to characterize 20 fungal endophytes belonging to the genus Alternaria, recovered from grapevine in different Italian regions. Morphological, microscopical, molecular and chemical investigations were performed and the obtained results were combined in a pooled cluster analysis. Following morphological analyses, all strains were grouped according to their three-dimensional sporulation pattern on PCA and to the colony characteristics on different substrates. After DNA extraction, all strains were analyzed by RAPD-PCR and the resulting profiles were subjected to cluster analysis. The metabolites extracted from the 20 Alternaria endophytes were analyzed by a HPLC and the resulting metabolite profiles were subjected to multivariate statistic analyses. In comparison with reference 'small-spored' Alternaria species, the 20 strains were segregated into two morphological groups: one belonging to the A. arborescens species-group and a second to the A. tenuissima species-group. RAPD analysis also showed that grapevine endophytes belonged to either the A. arborescens or the A. tenuissima species-group and that they were molecularly distinct from strains belonging to A. alternata. Chemotaxonomy gave the same grouping: the grapevine endophytic strains belong to A. arborescens or A. tenuissima species-groups producing known metabolites typical of these species-groups. Interestingly, the 20 grapevine endophytes were able to produce also a number of unknown metabolites, whose characterization could be useful for a more precise segregation of the two species-groups. The results show how complementary morphological, molecular and chemical data can clarify relationships among endophyte species-groups of low morphological divergence. PMID:22123507

  8. Examination of Taxonomic Uncertainties Surrounding Brucella abortus bv. 7 by Phenotypic and Molecular Approaches

    PubMed Central

    Garin-Bastuji, Bruno; Le Carrou, Gilles; Allix, Sebastien; Perrett, Lorraine L.; Dawson, Claire E.; Groussaud, Pauline; Stubberfield, Emma J.; Koylass, Mark; Whatmore, Adrian M.

    2014-01-01

    Brucella taxonomy is perpetually being reshuffled, at both the species and intraspecies levels. Biovar 7 of Brucella abortus was suspended from the Approved Lists of Bacterial Names Brucella classification in 1988, because of unpublished evidence that the reference strain 63/75 was a mixture of B. abortus biovars 3 and 5. To formally clarify the situation, all isolates previously identified as B. abortus bv. 7 in the AHVLA and ANSES strain collections were characterized by classical microbiological and multiple molecular approaches. Among the 14 investigated strains, including strain 63/75, only four strains, isolated in Kenya, Turkey, and Mongolia, were pure and showed a phenotypic profile in agreement with the former biovar 7, particularly agglutination with both anti-A/anti-M monospecific sera. These results were strengthened by molecular strategies. Indeed, genus- and species-specific methods allowed confirmation that the four pure strains belonged to the B. abortus species. The combination of most approaches excluded their affiliation with the recognized biovars (biovars 1 to 6 and 9), while some suggested that they were close to biovar 3.These assays were complemented by phylogenetic and/or epidemiological methods, such as multilocus sequence analysis (MLSA) and variable-number tandem repeat (VNTR) analysis. The results of this polyphasic investigation allow us to propose the reintroduction of biovar 7 into the Brucella classification, with at least three representative strains. Interestingly, the Kenyan strain, sharing the same biovar 7 phenotype, was genetically divergent from other three isolates. These discrepancies illustrate the complexity of Brucella taxonomy. This study suggests that worldwide collections could include strains misidentified as B. abortus bv. 7, and it highlights the need to verify their real taxonomic position. PMID:24362435

  9. A polyphasic approach for characterization of a collection of cereal isolates of the Fusarium incarnatum-equiseti species complex.

    PubMed

    Villani, Alessandra; Moretti, Antonio; De Saeger, Sarah; Han, Zheng; Di Mavungu, Jose Diana; Soares, Célia M G; Proctor, Robert H; Venâncio, Armando; Lima, Nelson; Stea, Gaetano; Paciolla, Costantino; Logrieco, Antonio F; Susca, Antonia

    2016-10-01

    DNA-based phylogenetic analyses have resolved the fungal genus Fusarium into multiple species complexes. The F. incarnatum-equiseti species complex (FIESC) includes fusaria associated with several diseases of agriculturally important crops, including cereals. Although members of FIESC are considered to be only moderately aggressive, they are able to produce a diversity of mycotoxins, including trichothecenes, which can accumulate to harmful levels in cereals. High levels of cryptic speciation have been detected within the FIESC. As a result, it is often necessary to use approaches other than morphological characterization to distinguish species. In the current study, we used a polyphasic approach to characterize a collection of 69 FIESC isolates recovered from cereals in Europe, Turkey, and North America. In a species phylogeny inferred from nucleotide sequences from four housekeeping genes, 65 of the isolates were resolved within the Equiseti clade of the FIESC, and four isolates were resolved within the Incarnatum clade. Seven isolates were resolved as a genealogically exclusive lineage, designated here as FIESC 31. Phylogenies based on nucleotide sequences of trichothecene biosynthetic genes and MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry) were largely concordant with phylogeny inferred from the housekeeping gene. Finally, Liquid Chromatography (Time-Of-Flight) Mass Spectrometry [LC-(TOF-)MS(/MS)] revealed variability in mycotoxin production profiles among the different phylogenetic species investigated in this study. PMID:27376677

  10. A polyphasic approach for studying the interaction between Ralstonia solanacearum and potential control agents in the tomato phytosphere.

    PubMed

    van Overbeek, Leo S; Cassidy, Mike; Kozdroj, Jacek; Trevors, Jack T; van Elsas, Jan D

    2002-01-01

    Ralstonia solanacearum biovar 2, the causative agent of brown rot in potato, has been responsible for large crop losses in Northwest Europe during the last decade. Knowledge on the ecological behaviour of R. solanacearum and its antagonists is required to develop sound procedures for its control and eradication in infested fields.A polyphasic approach was used to study the invasion of plants by a selected R. solanacearum biovar 2 strain, denoted 1609, either or not in combination with the antagonistic strains Pseudomonas corrugata IDV1 and P. fluorescens UA5-40. Thus, this study combined plating (spread and drop plate methods), reporter gene technology (gfp mutants) and serological (imunofluorescence colony staining [IFC]) and molecular techniques (fluorescent in situ hybridization [FISH], PCR with R. solanacearum specific primers and PCR-DGGE on plant DNA extracts). The behaviour of R. solanacearum 1609 and the two control strains was studied in bulk and (tomato) rhizosphere soil and the rhizoplane and stems of tomato plants. The results showed that an interaction between the pathogen and the control strains at the root surface was likely. In particular, R. solanacearum 1609 CFU numbers were significantly reduced on tomato roots treated with P. corrugata IDV1(chr:gfp1) cells as compared to those on untreated roots. Concomitant with the presence of P. corrugata IDV1(chr:gfp1), plant invasion by the pathogen was hampered, but not abolished.PCR-DGGE analyses of the tomato rhizoplane supported the evidence for antagonistic activity against the pathogen; as only weak R. solanacearum 1609 specific bands were detected in profiles derived from mixed systems versus strong bands in profiles from systems containing only the pathogen. Using FISH, a difference in root colonization was demonstrated between the pathogen and one of the two antagonists, i.e. P. corrugata IDV1(chr:gfp1); R. solanacearum strain 1609 was clearly detected in the vascular cylinder of tomato plants

  11. Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera

    PubMed Central

    Aveskamp, M.M.; de Gruyter, J.; Woudenberg, J.H.C.; Verkley, G.J.M.; Crous, P.W.

    2010-01-01

    Leptosphaerulina and Macroventuria in this clade. Based on the sequence data obtained, the Didymellaceae segregate into at least 18 distinct clusters, of which many can be associated with several specific taxonomic characters. Four of these clusters were defined well enough by means of phylogeny and morphology, so that the associated taxa could be transferred to separate genera. Aditionally, this study addresses the taxonomic description of eight species and two varieties that are novel to science, and the recombination of 61 additional taxa. PMID:20502538

  12. A Taxonomic Approach to the Gestalt Theory of Perls

    ERIC Educational Resources Information Center

    Raming, Henry E.; Frey, David H.

    1974-01-01

    This study applied content analysis and cluster analysis to the ideas of Fritz Perls to develop a taxonomy of Gestalt processes and goals. Summaries of the typal groups or clusters were written and the implications of taxonomic research in counseling discussed. (Author)

  13. Selection of autochthonous Saccharomyces cerevisiae strains as wine starters using a polyphasic approach and ochratoxin A removal.

    PubMed

    Petruzzi, Leonardo; Bevilacqua, Antonio; Corbo, Maria Rosaria; Garofalo, Carmela; Baiano, Antonietta; Sinigaglia, Milena

    2014-07-01

    Over the last few years, the selection of autochthonous strains of Saccharomyces cerevisiae as wine starters has been studied; however, researchers have not focused on the ability to remove ochratoxin A (OTA) as a possible trait to use in oenological characterization. In this article, a polyphasic approach, including yeast genotyping, evaluation of phenotypic traits, and fermentative performance in a model system (temperature, 25 and 30°C; sugar level, 200 and 250 g liter(-1)), was proposed as a suitable approach to select wine starters of S. cerevisiae from 30 autochthonous isolates from Uva di Troia cv., a red wine grape variety grown in the Apulian region (Southern Italy). The ability to remove OTA, a desirable trait to improve the safety of wine, was also assessed using enzyme-linked immunosorbent assay. The isolates, identified by PCR-restriction fragment length polymorphism analysis of the internal transcribed spacer region and DNA sequencing, were differentiated at strain level through the amplification of the interdelta region; 11 biotypes (I to XI) were identified and further studied. Four biotypes (II, III, V, VIII) were able to reduce OTA, with the rate of toxin removal from the medium (0.6 to 42.8%, wt/vol) dependent upon the strain and the temperature, and biotypes II and VIII were promising in terms of ethanol, glycerol, and volatile acidity production, as well as for their enzymatic and stress resistance characteristics. For the first time, the ability of S. cerevisiae to remove OTA during alcoholic fermentation was used as an additional trait in the yeast-selection program; the results could have application for evaluating the potential of autochthonous S. cerevisiae strains as starter cultures for the production of typical wines with improved quality and safety. PMID:24988024

  14. Taxonomic information exchange and copyright: the Plazi approach

    PubMed Central

    Agosti, Donat; Egloff, Willi

    2009-01-01

    Background A large part of our knowledge on the world's species is recorded in the corpus of biodiversity literature with well over hundred million pages, and is represented in natural history collections estimated at 2 – 3 billion specimens. But this body of knowledge is almost entirely in paper-print form and is not directly accessible through the Internet. For the digitization of this literature, new territories have to be chartered in the fields of technical, legal and social issues that presently impede its advance. The taxonomic literature seems especially destined for such a transformation. Discussion Plazi was founded as an association with the primary goal of transforming both the printed and, more recently, "born-digital" taxonomic literature into semantically enabled, enhanced documents. This includes the creation of a test body of literature, an XML schema modeling its logic content (TaxonX), the development of a mark-up editor (GoldenGATE) allowing also the enhancement of documents with links to external resources via Life Science Identifiers (LSID), a repository for publications and issuance of bibliographic identifiers, a dedicated server to serve the marked up content (the Plazi Search and Retrieval Server, SRS) and semantic tools to mine information. Plazi's workflow is designed to respect copyright protection and achieves extraction by observing exceptions and limitations existent in international copyright law. Conclusion The information found in Plazi's databases – taxonomic treatments as well as the metadata of the publications – are in the public domain and can therefore be used for further scientific research without any restriction, whether or not contained in copyrighted publications. PMID:19331688

  15. Analysis of bacterial community during the fermentation of pulque, a traditional Mexican alcoholic beverage, using a polyphasic approach.

    PubMed

    Escalante, Adelfo; Giles-Gómez, Martha; Hernández, Georgina; Córdova-Aguilar, María Soledad; López-Munguía, Agustín; Gosset, Guillermo; Bolívar, Francisco

    2008-05-31

    In this study, the characterization of the bacterial community present during the fermentation of pulque, a traditional Mexican alcoholic beverage from maguey (Agave), was determined for the first time by a polyphasic approach in which both culture and non-culture dependent methods were utilized. The work included the isolation of lactic acid bacteria (LAB), aerobic mesophiles, and 16S rDNA clone libraries from total DNA extracted from the maguey sap (aguamiel) used as substrate, after inoculation with a sample of previously produced pulque and followed by 6-h fermentation. Microbiological diversity results were correlated with fermentation process parameters such as sucrose, glucose, fructose and fermentation product concentrations. In addition, medium rheological behavior analysis and scanning electron microscopy in aguamiel and during pulque fermentation were also performed. Our results showed that both culture and non-culture dependent approaches allowed the detection of several new and previously reported species within the alpha-, gamma-Proteobacteria and Firmicutes. Bacteria diversity in aguamiel was composed by the heterofermentative Leuconostoc citreum, L. mesenteroides, L. kimchi, the gamma-Proteobacteria Erwinia rhapontici, Enterobacter spp. and Acinetobacter radioresistens. Inoculation with previously fermented pulque incorporated to the system microbiota, homofermentative lactobacilli related to Lactobacillus acidophilus, several alpha-Proteobacteria such as Zymomonas mobilis and Acetobacter malorum, other gamma-Proteobacteria and an important amount of yeasts, creating a starting metabolic diversity composed by homofermentative and heterofermentative LAB, acetic and ethanol producing microorganisms. At the end of the fermentation process, the bacterial diversity was mainly composed by the homofermentative Lactobacillus acidophilus, the heterofermentative L. mesenteroides, Lactococcus lactis subsp. lactis and the alpha-Proteobacteria A. malorum. After

  16. Molecular, proteomic and morphological characterization of the ascomycete Guignardia bidwellii, agent of grape black rot: a polyphasic approach to fungal identification.

    PubMed

    Wicht, Barbara; Petrini, Orlando; Jermini, Mauro; Gessler, Cesare; Broggini, Giovanni Antonio Lodovico

    2012-01-01

    Guignardia bidwellii is the etiological agent of grape black rot, a disease affecting Vitis and other Vitaceae that can cause heavy crop losses in vineyards. Its identification is based mainly on morphological characters and the symptoms on plants but, due to their variability, they may be difficult to interpret to reliably distinguish the pathogen to species. To date, despite the economic importance of G. bidwellii, no molecular investigations have been carried out on Vitis isolates and few sequence data are available for cultures derived from ornamental host plants. We analyzed samples of G. bidwellii collected from grapevine cultivars and ornamental plants of various geographic origins by morphological, molecular and proteomic techniques, including ITS1-ITS2 regions and calmodulin gene sequencing, as well as matrix-assisted laser desorption/ionization analysis by time-of-flight mass spectrometry (MALDI-TOF MS). This polyphasic approach allowed assessing the phylogenetic relationships among the different isolates and suggested the existence of two distinct species. The advantages of a polyphasic approach for the identification of G. bidwellii are highlighted. PMID:22492405

  17. Combining Taxonomic and Functional Approaches to Unravel the Spatial Distribution of an Amazonian Butterfly Community.

    PubMed

    Graça, Márlon B; Morais, José W; Franklin, Elizabeth; Pequeno, Pedro A C L; Souza, Jorge L P; Bueno, Anderson Saldanha

    2016-04-01

    This study investigated the spatial distribution of an Amazonian fruit-feeding butterfly assemblage by linking species taxonomic and functional approaches. We hypothesized that: 1) vegetation richness (i.e., resources) and abundance of insectivorous birds (i.e., predators) should drive changes in butterfly taxonomic composition, 2) larval diet breadth should decrease with increase of plant species richness, 3) small-sized adults should be favored by higher abundance of birds, and 4) communities with eyespot markings should be able to exploit areas with higher predation pressure. Fruit-feeding butterflies were sampled with bait traps and insect nets across 25 km(2) of an Amazonian ombrophilous forest in Brazil. We measured larval diet breadth, adult body size, and wing marking of all butterflies. Our results showed that plant species richness explained most of the variation in butterfly taxonomic turnover. Also, community average diet breadth decreased with increase of plant species richness, which supports our expectations. In contrast, community average body size increased with the abundance of birds, refuting our hypothesis. We detected no influence of environmental gradients on the occurrence of species with eyespot markings. The association between butterfly taxonomic and functional composition points to a mediator role of the functional traits in the environmental filtering of butterflies. The incorporation of the functional approach into the analyses allowed for the detection of relationships that were not observed using a strictly taxonomic perspective and provided an extra insight into comprehending the potential adaptive strategies of butterflies. PMID:26643123

  18. Taxonomic resolution and Biological Traits Analysis (BTA) approaches in estuarine free-living nematodes

    NASA Astrophysics Data System (ADS)

    Alves, A. S.; Veríssimo, H.; Costa, M. J.; Marques, J. C.

    2014-02-01

    The taxonomic and functional structure of the subtidal nematode assemblages from a temperate estuary (Mondego estuary, Portugal) was studied, focussing on different taxonomic levels (genus, family and order), on single functional groups and on multiple biological traits. Based on taxonomic levels and on four biological traits (feeding type, life strategy, tail and body shape), the analysis of the nematode assemblage distribution patterns revealed spatial differences but no clear temporal pattern. At the family and genus level, a separation of the upstream sections was observed, while a distinction of polyhaline and euhaline areas was less evident. The use of biological traits added new information regarding the relationships between diversity patterns and the environmental variables. Most nematodes encountered along the estuary were non-selective deposit feeders (1B) and omnivores/predators (2B), colonizer-persisters (score of 2 or 3), with clavate-conicocylindrical tails and slender bodies and with a distribution related essentially to salinity, oxygen and chlorophyll a. Applying a Biological Traits Analysis (BTA) showed the role of oxygen concentration in the distribution of the nematode communities. Although the BTA was no more powerful than the traditional taxonomic approach in detecting spatial differences along the Mondego estuary, it has increased our knowledge of the functional structure and characterization of nematode communities in the estuary.

  19. Polyphasic identification of cyanobacterial isolates from Australia.

    PubMed

    Lee, Elvina; Ryan, Una M; Monis, Paul; McGregor, Glenn B; Bath, Andrew; Gordon, Cameron; Paparini, Andrea

    2014-08-01

    Reliable identification of cyanobacterial isolates has significant socio-economic implications as many bloom-forming species affect the aesthetics and safety of drinking water, through the production of taste and odour compounds or toxic metabolites. The limitations of morphological identification have promoted the application of molecular tools, and encouraged the adoption of combined (polyphasic) approaches that include both microscopy- and DNA-based analyses. In this context, the rapid expansion of available sequence data is expected to allow increasingly reliable identification of cyanobacteria, and ultimately resolve current discrepancies between the two approaches. In the present study morphological and molecular characterisations of cyanobacterial isolates (n = 39), collected from various freshwater sites in Australia, were compared. Sequences were obtained for the small ribosomal subunit RNA gene (16S rDNA) (n = 36), the DNA-dependent RNA polymerase gene (rpoC1) (n = 22), and the phycocyanin operon, with its intergenic spacer region (cpcBA-IGS) (n = 19). Phylogenetic analyses identified three cyanobacterial orders: the Chroococcales (n = 8), Oscillatoriales (n = 6), and Nostocales (n = 25). Interestingly, multiple novel genotypes were identified, with 22% of the strains (17/77) having <95% similarity to available sequences in GenBank. Morphological and molecular data were in agreement at the species level for only 26% of the isolates obtained (10/39), while agreement at the genus level was obtained for 31% (12/39). Confident identification of the remaining 44% of the strains (17/39) beyond the order level was not possible. The present study demonstrates that, despite the taxonomic revisions, and advances in molecular-, and bioinformatics-tools, the lack of reliable morphological features, culture-induced pleomorphism, and proportion of misidentified or poorly described sequences in GenBank, still represent significant factors, impeding the

  20. Polyphasic Approach Including MALDI-TOF MS/MS Analysis for Identification and Characterisation of Fusarium verticillioides in Brazilian Corn Kernels.

    PubMed

    Chang, Susane; Porto Carneiro-Leão, Mariele; Ferreira de Oliveira, Benny; Souza-Motta, Cristina; Lima, Nelson; Santos, Cledir; Tinti de Oliveira, Neiva

    2016-01-01

    Fusarium verticillioides is considered one of the most important global sources of fumonisins contamination in food and feed. Corn is one of the main commodities produced in the Northeastern Region of Brazil. The present study investigated potential mycotoxigenic fungal strains belonging to the F. verticillioides species isolated from corn kernels in 3 different Regions of the Brazilian State of Pernambuco. A polyphasic approach including classical taxonomy, molecular biology, MALDI-TOF MS and MALDI-TOF MS/MS for the identification and characterisation of the F. verticillioides strains was used. Sixty F. verticillioides strains were isolated and successfully identified by classical morphology, proteomic profiles of MALDI-TOF MS, and by molecular biology using the species-specific primers VERT-1 and VERT-2. FUM1 gene was further detected for all the 60 F. verticillioides by using the primers VERTF-1 and VERTF-2 and through the amplification profiles of the ISSR regions using the primers (GTG)₅ and (GACA)₄. Results obtained from molecular analysis shown a low genetic variability among these isolates from the different geographical regions. All of the 60 F. verticillioides isolates assessed by MALDI-TOF MS/MS presented ion peaks with the molecular mass of the fumonisin B1 (721.83 g/mol) and B2 (705.83 g/mol). PMID:26927172

  1. Polyphasic Approach Including MALDI-TOF MS/MS Analysis for Identification and Characterisation of Fusarium verticillioides in Brazilian Corn Kernels

    PubMed Central

    Chang, Susane; Porto Carneiro-Leão, Mariele; Ferreira de Oliveira, Benny; Souza-Motta, Cristina; Lima, Nelson; Santos, Cledir; Tinti de Oliveira, Neiva

    2016-01-01

    Fusarium verticillioides is considered one of the most important global sources of fumonisins contamination in food and feed. Corn is one of the main commodities produced in the Northeastern Region of Brazil. The present study investigated potential mycotoxigenic fungal strains belonging to the F. verticillioides species isolated from corn kernels in 3 different Regions of the Brazilian State of Pernambuco. A polyphasic approach including classical taxonomy, molecular biology, MALDI-TOF MS and MALDI-TOF MS/MS for the identification and characterisation of the F. verticillioides strains was used. Sixty F. verticillioides strains were isolated and successfully identified by classical morphology, proteomic profiles of MALDI-TOF MS, and by molecular biology using the species-specific primers VERT-1 and VERT-2. FUM1 gene was further detected for all the 60 F. verticillioides by using the primers VERTF-1 and VERTF-2 and through the amplification profiles of the ISSR regions using the primers (GTG)5 and (GACA)4. Results obtained from molecular analysis shown a low genetic variability among these isolates from the different geographical regions. All of the 60 F. verticillioides isolates assessed by MALDI-TOF MS/MS presented ion peaks with the molecular mass of the fumonisin B1 (721.83 g/mol) and B2 (705.83 g/mol). PMID:26927172

  2. Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches.

    PubMed

    Li, Fuyong; Henderson, Gemma; Sun, Xu; Cox, Faith; Janssen, Peter H; Guan, Le Luo

    2016-01-01

    Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of this approach with the widely used targeted RNA/DNA amplicon sequencing technique. Total RNA isolated from rumen digesta samples from five beef steers was subjected to Illumina paired-end sequencing (RNA-seq), and bacterial and archaeal amplicons of partial 16S rRNA/rDNA were subjected to 454 pyrosequencing (RNA/DNA Amplicon-seq). Taxonomic assessments of the RNA-seq, RNA Amplicon-seq, and DNA Amplicon-seq datasets were performed using a pipeline developed in house. The detected major microbial phylotypes were common among the three datasets, with seven bacterial phyla, fifteen bacterial families, and five archaeal taxa commonly identified across all datasets. There were also unique microbial taxa detected in each dataset. Elusimicrobia and Verrucomicrobia phyla; Desulfovibrionaceae, Elusimicrobiaceae, and Sphaerochaetaceae families; and Methanobrevibacter woesei were only detected in the RNA-Seq and RNA Amplicon-seq datasets, whereas Streptococcaceae was only detected in the DNA Amplicon-seq dataset. In addition, the relative abundances of four bacterial phyla, eight bacterial families and one archaeal taxon were different among the three datasets. This is the first study to compare the outcomes of rumen microbiota profiling between RNA-seq and RNA/DNA Amplicon-seq datasets. Our results illustrate the differences between these methods in characterizing microbiota both qualitatively and quantitatively for the same sample, and so caution must be exercised when comparing data. PMID:27446027

  3. Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches

    PubMed Central

    Li, Fuyong; Henderson, Gemma; Sun, Xu; Cox, Faith; Janssen, Peter H.; Guan, Le Luo

    2016-01-01

    Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of this approach with the widely used targeted RNA/DNA amplicon sequencing technique. Total RNA isolated from rumen digesta samples from five beef steers was subjected to Illumina paired-end sequencing (RNA-seq), and bacterial and archaeal amplicons of partial 16S rRNA/rDNA were subjected to 454 pyrosequencing (RNA/DNA Amplicon-seq). Taxonomic assessments of the RNA-seq, RNA Amplicon-seq, and DNA Amplicon-seq datasets were performed using a pipeline developed in house. The detected major microbial phylotypes were common among the three datasets, with seven bacterial phyla, fifteen bacterial families, and five archaeal taxa commonly identified across all datasets. There were also unique microbial taxa detected in each dataset. Elusimicrobia and Verrucomicrobia phyla; Desulfovibrionaceae, Elusimicrobiaceae, and Sphaerochaetaceae families; and Methanobrevibacter woesei were only detected in the RNA-Seq and RNA Amplicon-seq datasets, whereas Streptococcaceae was only detected in the DNA Amplicon-seq dataset. In addition, the relative abundances of four bacterial phyla, eight bacterial families and one archaeal taxon were different among the three datasets. This is the first study to compare the outcomes of rumen microbiota profiling between RNA-seq and RNA/DNA Amplicon-seq datasets. Our results illustrate the differences between these methods in characterizing microbiota both qualitatively and quantitatively for the same sample, and so caution must be exercised when comparing data. PMID:27446027

  4. A polyphasic approach leading to the revision of the genus Planktothrix (Cyanobacteria) and its type species, P. agardhii, and proposal for integrating the emended valid botanical taxa, as well as three new species, Planktothrix paucivesiculata sp. nov.ICNP, Planktothrix tepida sp. nov.ICNP, and Planktothrix serta sp. nov.ICNP, as genus and species names with nomenclatural standing under the ICNP.

    PubMed

    Gaget, Virginie; Welker, Martin; Rippka, Rosmarie; de Marsac, Nicole Tandeau

    2015-05-01

    Twenty strains of Planktothrix and five of 'Oscillatoria' were characterized by a polyphasic approach, for clarification of their taxonomic relationships. Emphasis was given to the strains (17) of the Pasteur Culture Collection of Cyanobacteria (PCC). Phenotypic characters analyzed comprised morphology, phycobiliprotein composition, temperature and salinity tolerance. The gvpA gas vesicle gene was detected by PCR in all strains, and transmission electron microscopy confirmed gas vesicle formation in the strains of 'Oscillatoria'. MALDI-TOF mass spectrometry revealed 13 chemotypes, nine of which produce microcystins. A multi-locus sequence typing (MLST) analysis was conducted using individual and concatenated nucleotide sequences of the 16S rDNA, internal transcribed spacer (ITS), gyrB, rpoC1 and rpoB. The results highlighted an unexpected diversity within the genus Planktothrix, showing that the five strains of 'Oscillatoria' need to be included in this taxon. Consequently, the genus consists of seven phylogenetic clusters, three of which represent new species, named Planktothrix paucivesiculata sp. nov.ICNP (type strain: PCC 8926T), Planktothrix tepida sp. nov.ICNP (type strain: PCC 9214T) and Planktothrix serta sp. nov.ICNP (type strain: PCC 8927T). These, together with the emended genus Planktothrix and its type species P. agardhii, valid taxa under the ICN, are described/re-described for gaining nomenclatural standing under the ICNP. PMID:25757799

  5. A revision of Apteromantis (Mantodea: Mantidae, Amelinae): a comprehensive approach to manage old taxonomic and conservation problems .

    PubMed

    Battiston, Roberto; Ortego, Joaquín; Correas, José R; Cordero, Pedro J

    2014-01-01

    The genus Apteromantis Werner, 1931 comprises two species of wingless mantids, the Iberian A. aptera (Fuente, 1894) and the North African A. bolivari (Werner, 1929). Although A. aptera and A. bolivari have been traditionally considered as separate and valid species, their external appearance is quite similar and no comprehensive taxonomic study has analyzed their morphological and genetic characteristics. This taxonomic uncertainty has important implications for conservation because A. aptera is considered an Iberian endemic and the only praying mantis protected by international laws. In this study, we apply a comprehensive approach, including quantitative morphological and molecular analyses, to shed new light on the taxonomic and conservation status of the genus Apteromantis and the putative species. We have found that the Iberian and North African specimens analyzed herein significantly differ in female head shape, male genitalia morphology and several other traits related to body size. Molecular data suggest the presence of two main lineages, with sequence divergence rates of approximately 4 %, which are within the range reported for other well defined insect species. Overall, this study supports that A. aptera and A. bolivari are valid species despite their ecological and morphological similarity and highlights the importance of comprehensive approaches to resolve old taxonomic and conservation problems. PMID:24870858

  6. The Integrative Taxonomic Approach Reveals Host Specific Species in an Encyrtid Parasitoid Species Complex

    PubMed Central

    Chesters, Douglas; Wang, Ying; Yu, Fang; Bai, Ming; Zhang, Tong-Xin; Hu, Hao-Yuan; Zhu, Chao-Dong; Li, Cheng-De; Zhang, Yan-Zhou

    2012-01-01

    Integrated taxonomy uses evidence from a number of different character types to delimit species and other natural groupings. While this approach has been advocated recently, and should be of particular utility in the case of diminutive insect parasitoids, there are relatively few examples of its application in these taxa. Here, we use an integrated framework to delimit independent lineages in Encyrtus sasakii (Hymenoptera: Chalcidoidea: Encyrtidae), a parasitoid morphospecies previously considered a host generalist. Sequence variation at the DNA barcode (cytochrome c oxidase I, COI) and nuclear 28S rDNA loci were compared to morphometric recordings and mating compatibility tests, among samples of this species complex collected from its four scale insect hosts, covering a broad geographic range of northern and central China. Our results reveal that Encyrtus sasakii comprises three lineages that, while sharing a similar morphology, are highly divergent at the molecular level. At the barcode locus, the median K2P molecular distance between individuals from three primary populations was found to be 11.3%, well outside the divergence usually observed between Chalcidoidea conspecifics (0.5%). Corroborative evidence that the genetic lineages represent independent species was found from mating tests, where compatibility was observed only within populations, and morphometric analysis, which found that despite apparent morphological homogeneity, populations clustered according to forewing shape. The independent lineages defined by the integrated analysis correspond to the three scale insect hosts, suggesting the presence of host specific cryptic species. The finding of hidden host specificity in this species complex demonstrates the critical role that DNA barcoding will increasingly play in revealing hidden biodiversity in taxa that present difficulties for traditional taxonomic approaches. PMID:22666375

  7. A Reverse Taxonomic Approach to Assess Macrofaunal Distribution Patterns in Abyssal Pacific Polymetallic Nodule Fields

    PubMed Central

    Janssen, Annika; Kaiser, Stefanie; Meißner, Karin; Brenke, Nils; Menot, Lenaick; Martínez Arbizu, Pedro

    2015-01-01

    Heightened interest in the exploitation of deep seafloor minerals is raising questions on the consequences for the resident fauna. Assessing species ranges and determination of processes underlying current species distributions are prerequisites to conservation planning and predicting faunal responses to changing environmental conditions. The abyssal central Pacific nodule belt, located between the Clarion and Clipperton Fracture Zones (CCZ), is an area prospected for mining of polymetallic nodules. We examined variations in genetic diversity and broad-scale connectivity of isopods and polychaetes across the CCZ. Faunal assemblages were studied from two mining claims (the eastern German and French license areas) located 1300 km apart and influenced by different productivity regimes. Using a reverse taxonomy approach based on DNA barcoding, we tested to what extent distance and large-scale changes in environmental parameters lead to differentiation in two macrofaunal taxa exhibiting different functions and life-history patterns. A fragment of the mitochondrial gene Cytochrome Oxidase Subunit 1 (COI) was analyzed. At a 97% threshold the molecular operational taxonomic units (MOTUs) corresponded well to morphological species. Molecular analyses indicated high local and regional diversity mostly because of large numbers of singletons in the samples. Consequently, variation in composition of genotypic clusters between sites was exceedingly large partly due to paucity of deep-sea sampling and faunal patchiness. A higher proportion of wide-ranging species in polychaetes was contrasted with mostly restricted distributions in isopods. Remarkably, several cryptic lineages appeared to be sympatric and occurred in taxa with putatively good dispersal abilities, whereas some brooding lineages revealed broad distributions across the CCZ. Geographic distance could explain variation in faunal connectivity between regions and sites to some extent, while assumed dispersal

  8. A reverse taxonomic approach to assess macrofaunal distribution patterns in abyssal Pacific polymetallic nodule fields.

    PubMed

    Janssen, Annika; Kaiser, Stefanie; Meißner, Karin; Brenke, Nils; Menot, Lenaick; Martínez Arbizu, Pedro

    2015-01-01

    Heightened interest in the exploitation of deep seafloor minerals is raising questions on the consequences for the resident fauna. Assessing species ranges and determination of processes underlying current species distributions are prerequisites to conservation planning and predicting faunal responses to changing environmental conditions. The abyssal central Pacific nodule belt, located between the Clarion and Clipperton Fracture Zones (CCZ), is an area prospected for mining of polymetallic nodules. We examined variations in genetic diversity and broad-scale connectivity of isopods and polychaetes across the CCZ. Faunal assemblages were studied from two mining claims (the eastern German and French license areas) located 1300 km apart and influenced by different productivity regimes. Using a reverse taxonomy approach based on DNA barcoding, we tested to what extent distance and large-scale changes in environmental parameters lead to differentiation in two macrofaunal taxa exhibiting different functions and life-history patterns. A fragment of the mitochondrial gene Cytochrome Oxidase Subunit 1 (COI) was analyzed. At a 97% threshold the molecular operational taxonomic units (MOTUs) corresponded well to morphological species. Molecular analyses indicated high local and regional diversity mostly because of large numbers of singletons in the samples. Consequently, variation in composition of genotypic clusters between sites was exceedingly large partly due to paucity of deep-sea sampling and faunal patchiness. A higher proportion of wide-ranging species in polychaetes was contrasted with mostly restricted distributions in isopods. Remarkably, several cryptic lineages appeared to be sympatric and occurred in taxa with putatively good dispersal abilities, whereas some brooding lineages revealed broad distributions across the CCZ. Geographic distance could explain variation in faunal connectivity between regions and sites to some extent, while assumed dispersal

  9. Vectorial formalism for analysis and design of polyphase synchronous machines

    NASA Astrophysics Data System (ADS)

    Semail, E.; Bouscayrol, A.; Hautier, J.-P.

    2003-06-01

    A vectorial formalism for analysis and design of polyphase synchronous machines without reluctance and saturation effects is described. We prove the equivalence of such a machine with a set of magnetically independent machines, which are electrically and mechanically coupled. Specific problems of polyphase machines can thus be favorably analyzed with this concept. Rules of conception and constraints on electric supply can be deduced. Moreover the vectorial approach, which generalizes the complex phasor method, can also be used to control n-leg voltage source inverters. This methodology is applied to 3-phase and 6-phase synchronous machines.

  10. Polyphase-discrete Fourier transform spectrum analysis for the Search for Extraterrestrial Intelligence sky survey

    NASA Technical Reports Server (NTRS)

    Zimmerman, G. A.; Gulkis, S.

    1991-01-01

    The sensitivity of a matched filter-detection system to a finite-duration continuous wave (CW) tone is compared with the sensitivities of a windowed discrete Fourier transform (DFT) system and an ideal bandpass filter-bank system. These comparisons are made in the context of the NASA Search for Extraterrestrial Intelligence (SETI) microwave observing project (MOP) sky survey. A review of the theory of polyphase-DFT filter banks and its relationship to the well-known windowed-DFT process is presented. The polyphase-DFT system approximates the ideal bandpass filter bank by using as few as eight filter taps per polyphase branch. An improvement in sensitivity of approx. 3 dB over a windowed-DFT system can be obtained by using the polyphase-DFT approach. Sidelobe rejection of the polyphase-DFT system is vastly superior to the windowed-DFT system, thereby improving its performance in the presence of radio frequency interference (RFI).

  11. Low-voltage polyphasic circuits

    NASA Astrophysics Data System (ADS)

    Baird, William H.; Jaynes, Michael L.

    2010-05-01

    Experimentation with polyphasic voltages is greatly simplified when microcontrollers are used to generate multiple square waves with fixed phase offsets. Each square wave is sent through a simple second-order Sallen-Key filter to produce an approximately sinusoidal voltage signal. The microcontroller allows the reproduction of split-phase and three-phase voltage relationships, mirroring those commonly distributed on the North American power grid, at safe voltage levels.

  12. Taxonomic minimalism.

    PubMed

    Beattle, A J; Oliver, I

    1994-12-01

    Biological surveys are in increasing demand while taxonomic resources continue to decline. How much formal taxonomy is required to get the job done? The answer depends on the kind of job but it is possible that taxonomic minimalism, especially (1) the use of higher taxonomic ranks, (2) the use of morphospecies rather than species (as identified by Latin binomials), and (3) the involvement of taxonomic specialists only for training and verification, may offer advantages for biodiversity assessment, environmental monitoring and ecological research. As such, formal taxonomy remains central to the process of biological inventory and survey but resources may be allocated more efficiently. For example, if formal Identification is not required, resources may be concentrated on replication and increasing sample sizes. Taxonomic minimalism may also facilitate the inclusion in these activities of important but neglected groups, especially among the invertebrates, and perhaps even microorganisms. PMID:21236933

  13. Frequency-Offset Cartesian Feedback Based on Polyphase Difference Amplifiers

    PubMed Central

    Zanchi, Marta G.; Pauly, John M.; Scott, Greig C.

    2010-01-01

    A modified Cartesian feedback method called “frequency-offset Cartesian feedback” and based on polyphase difference amplifiers is described that significantly reduces the problems associated with quadrature errors and DC-offsets in classic Cartesian feedback power amplifier control systems. In this method, the reference input and feedback signals are down-converted and compared at a low intermediate frequency (IF) instead of at DC. The polyphase difference amplifiers create a complex control bandwidth centered at this low IF, which is typically offset from DC by 200–1500 kHz. Consequently, the loop gain peak does not overlap DC where voltage offsets, drift, and local oscillator leakage create errors. Moreover, quadrature mismatch errors are significantly attenuated in the control bandwidth. Since the polyphase amplifiers selectively amplify the complex signals characterized by a +90° phase relationship representing positive frequency signals, the control system operates somewhat like single sideband (SSB) modulation. However, the approach still allows the same modulation bandwidth control as classic Cartesian feedback. In this paper, the behavior of the polyphase difference amplifier is described through both the results of simulations, based on a theoretical analysis of their architecture, and experiments. We then describe our first printed circuit board prototype of a frequency-offset Cartesian feedback transmitter and its performance in open and closed loop configuration. This approach should be especially useful in magnetic resonance imaging transmit array systems. PMID:20814450

  14. Frequency-Offset Cartesian Feedback Based on Polyphase Difference Amplifiers.

    PubMed

    Zanchi, Marta G; Pauly, John M; Scott, Greig C

    2010-05-01

    A modified Cartesian feedback method called "frequency-offset Cartesian feedback" and based on polyphase difference amplifiers is described that significantly reduces the problems associated with quadrature errors and DC-offsets in classic Cartesian feedback power amplifier control systems.In this method, the reference input and feedback signals are down-converted and compared at a low intermediate frequency (IF) instead of at DC. The polyphase difference amplifiers create a complex control bandwidth centered at this low IF, which is typically offset from DC by 200-1500 kHz. Consequently, the loop gain peak does not overlap DC where voltage offsets, drift, and local oscillator leakage create errors. Moreover, quadrature mismatch errors are significantly attenuated in the control bandwidth. Since the polyphase amplifiers selectively amplify the complex signals characterized by a +90° phase relationship representing positive frequency signals, the control system operates somewhat like single sideband (SSB) modulation. However, the approach still allows the same modulation bandwidth control as classic Cartesian feedback.In this paper, the behavior of the polyphase difference amplifier is described through both the results of simulations, based on a theoretical analysis of their architecture, and experiments. We then describe our first printed circuit board prototype of a frequency-offset Cartesian feedback transmitter and its performance in open and closed loop configuration. This approach should be especially useful in magnetic resonance imaging transmit array systems. PMID:20814450

  15. An integrated approach to the taxonomic identification of prehistoric shell ornaments.

    PubMed

    Demarchi, Beatrice; O'Connor, Sonia; de Lima Ponzoni, Andre; de Almeida Rocha Ponzoni, Raquel; Sheridan, Alison; Penkman, Kirsty; Hancock, Y; Wilson, Julie

    2014-01-01

    Shell beads appear to have been one of the earliest examples of personal adornments. Marine shells identified far from the shore evidence long-distance transport and imply networks of exchange and negotiation. However, worked beads lose taxonomic clues to identification, and this may be compounded by taphonomic alteration. Consequently, the significance of this key early artefact may be underestimated. We report the use of bulk amino acid composition of the stable intra-crystalline proteins preserved in shell biominerals and the application of pattern recognition methods to a large dataset (777 samples) to demonstrate that taxonomic identification can be achieved at genus level. Amino acid analyses are fast (<2 hours per sample) and micro-destructive (sample size <2 mg). Their integration with non-destructive techniques provides a valuable and affordable tool, which can be used by archaeologists and museum curators to gain insight into early exploitation of natural resources by humans. Here we combine amino acid analyses, macro- and microstructural observations (by light microscopy and scanning electron microscopy) and Raman spectroscopy to try to identify the raw material used for beads discovered at the Early Bronze Age site of Great Cornard (UK). Our results show that at least two shell taxa were used and we hypothesise that these were sourced locally. PMID:24936797

  16. An Integrated Approach to the Taxonomic Identification of Prehistoric Shell Ornaments

    PubMed Central

    Demarchi, Beatrice; O'Connor, Sonia; de Lima Ponzoni, Andre; de Almeida Rocha Ponzoni, Raquel; Sheridan, Alison; Penkman, Kirsty; Hancock, Y.; Wilson, Julie

    2014-01-01

    Shell beads appear to have been one of the earliest examples of personal adornments. Marine shells identified far from the shore evidence long-distance transport and imply networks of exchange and negotiation. However, worked beads lose taxonomic clues to identification, and this may be compounded by taphonomic alteration. Consequently, the significance of this key early artefact may be underestimated. We report the use of bulk amino acid composition of the stable intra-crystalline proteins preserved in shell biominerals and the application of pattern recognition methods to a large dataset (777 samples) to demonstrate that taxonomic identification can be achieved at genus level. Amino acid analyses are fast (<2 hours per sample) and micro-destructive (sample size <2 mg). Their integration with non-destructive techniques provides a valuable and affordable tool, which can be used by archaeologists and museum curators to gain insight into early exploitation of natural resources by humans. Here we combine amino acid analyses, macro- and microstructural observations (by light microscopy and scanning electron microscopy) and Raman spectroscopy to try to identify the raw material used for beads discovered at the Early Bronze Age site of Great Cornard (UK). Our results show that at least two shell taxa were used and we hypothesise that these were sourced locally. PMID:24936797

  17. An integrated approach to the Taxonomic identification of prehistoric shell ornaments

    USGS Publications Warehouse

    Demarchi, Beatrice; O'Connor, Sonia; Ponzoni, Andre de Lima; Ponzoni, Raquel de Almeida Roch; Sheridan, Alison; Penkman, Kirsty; Hancock, Y.; Wilson, Julie

    2014-01-01

    Shell beads appear to have been one of the earliest examples of personal adornments. Marine shells identified far from the shore evidence long-distance transport and imply networks of exchange and negotiation. However, worked beads lose taxonomic clues to identification, and this may be compounded by taphonomic alteration. Consequently, the significance of this key early artefact may be underestimated. We report the use of bulk amino acid composition of the stable intra-crystalline proteins preserved in shell biominerals and the application of pattern recognition methods to a large dataset (777 samples) to demonstrate that taxonomic identification can be achieved at genus level. Amino acid analyses are fast (<2 hours per sample) and micro-destructive (sample size <2 mg). Their integration with non-destructive techniques provides a valuable and affordable tool, which can be used by archaeologists and museum curators to gain insight into early exploitation of natural resources by humans. Here we combine amino acid analyses, macro- and microstructural observations (by light microscopy and scanning electron microscopy) and Raman spectroscopy to try to identify the raw material used for beads discovered at the Early Bronze Age site of Great Cornard (UK). Our results show that at least two shell taxa were used and we hypothesise that these were sourced locally.

  18. Molecular (PCR-DGGE) versus morphological approach: analysis of taxonomic composition of potentially toxic cyanobacteria in freshwater lakes

    PubMed Central

    2014-01-01

    Background The microscopic Utermöhl method is commonly used for the recognition of the presence and taxonomic composition of potentially toxic cyanobacteria and is especially useful for monitoring reservoirs used as drinking water, recreation and fishery resources. However, this method is time-consuming and does not allow potentially toxic and nontoxic cyanobacterial strains to be distinguished. We have developed a method based on denaturing gradient gel electrophoresis (DGGE) of the marker gene ITS and the mcy-gene cluster, and DNA sequencing. We have attempted to calibrate the DGGE-method with a microscopic procedure, using water samples taken in 2011 from four lakes of the Great Mazurian Lakes system. Results Results showed that the classic microscopic method was much more precise and allowed the classification of the majority of cyanobacterial taxa to the species or genus. Using the molecular approach, most of the sequences could only be assigned to a genus or family. The results of DGGE and microscopic analyses overlapped in the detection of the filamentous cyanobacteria. For coccoid cyanobacteria, we only found two taxa using the molecular method, which represented 17% of the total taxa identified using microscopic observations. The DGGE method allowed the identification of two genera of cyanobacteria (Planktothrix and Microcystis) in the studied samples, which have the potential ability to produce toxins from the microcystins group. Conclusions The results confirmed that the molecular approach is useful for the rapid detection and taxonomic distinction of potentially toxic cyanobacteria in lake-water samples, also in very diverse cyanobacterial communities. Such rapid detection is unattainable by other methods. However, with still limited nucleotide sequences deposited in the public databases, this method is currently not sufficient to evaluate the entire taxonomic composition of cyanobacteria in lakes. PMID:24517495

  19. Heteropterys cotinifolia: a neuropharmacological and phytochemical approach with possible taxonomic implications.

    PubMed

    Huerta-Reyes, Maira; Zamilpa, Alejandro; Álvarez-Chimal, Rafael; Luna-Manzanares, José Ángel; León-Velasco, María Esther; Aguilar-Rojas, Arturo; Jiménez-Estrada, Manuel; Campos-Lara, María Guadalupe

    2013-01-01

    Heteropterys cotinifolia (Malpighiaceae) has been used in traditional Mexican medicine mainly for the treatment of nervous disorders. However, the specific neuropharmacological activities responsible for this use remain to be defined. The present study evaluates the antidepressant and anxiolytic effects produced by the methanolic extract of Heteropterys cotinifolia and the influence of such effects on motor activity in ICR mice. Our results show that the methanolic extract of Heteropterys cotinifolia produces a dose-dependent antidepressant effect in the forced swimming test in mice at doses from 31 to 310 mg/kg, with no reduction of mice locomotion. However, no anxiolytic properties were observed. Our findings suggest that the main extract compounds identified as chlorogenic acid and rutin may be involved in the antidepressant effects. To our knowledge, the present study constitutes the first report of pharmacological and phytochemical data of Heteropterys cotinifolia. The presence of flavonoids in the methanolic extract of Heteropterys cotinifolia may also provide further data to characterize taxonomically this species in order to be distinguished from others species closely related and belonging to the same genus. PMID:24453918

  20. A singular value decomposition approach for improved taxonomic classification of biological sequences

    PubMed Central

    2011-01-01

    Background Singular value decomposition (SVD) is a powerful technique for information retrieval; it helps uncover relationships between elements that are not prima facie related. SVD was initially developed to reduce the time needed for information retrieval and analysis of very large data sets in the complex internet environment. Since information retrieval from large-scale genome and proteome data sets has a similar level of complexity, SVD-based methods could also facilitate data analysis in this research area. Results We found that SVD applied to amino acid sequences demonstrates relationships and provides a basis for producing clusters and cladograms, demonstrating evolutionary relatedness of species that correlates well with Linnaean taxonomy. The choice of a reasonable number of singular values is crucial for SVD-based studies. We found that fewer singular values are needed to produce biologically significant clusters when SVD is employed. Subsequently, we developed a method to determine the lowest number of singular values and fewest clusters needed to guarantee biological significance; this system was developed and validated by comparison with Linnaean taxonomic classification. Conclusions By using SVD, we can reduce uncertainty concerning the appropriate rank value necessary to perform accurate information retrieval analyses. In tests, clusters that we developed with SVD perfectly matched what was expected based on Linnaean taxonomy. PMID:22369633

  1. Heteropterys cotinifolia: A Neuropharmacological and Phytochemical Approach with Possible Taxonomic Implications

    PubMed Central

    Huerta-Reyes, Maira; Zamilpa, Alejandro; Álvarez-Chimal, Rafael; Luna-Manzanares, José Ángel; León-Velasco, María Esther; Aguilar-Rojas, Arturo; Jiménez-Estrada, Manuel; Campos-Lara, María Guadalupe

    2013-01-01

    Heteropterys cotinifolia (Malpighiaceae) has been used in traditional Mexican medicine mainly for the treatment of nervous disorders. However, the specific neuropharmacological activities responsible for this use remain to be defined. The present study evaluates the antidepressant and anxiolytic effects produced by the methanolic extract of Heteropterys cotinifolia and the influence of such effects on motor activity in ICR mice. Our results show that the methanolic extract of Heteropterys cotinifolia produces a dose-dependent antidepressant effect in the forced swimming test in mice at doses from 31 to 310 mg/kg, with no reduction of mice locomotion. However, no anxiolytic properties were observed. Our findings suggest that the main extract compounds identified as chlorogenic acid and rutin may be involved in the antidepressant effects. To our knowledge, the present study constitutes the first report of pharmacological and phytochemical data of Heteropterys cotinifolia. The presence of flavonoids in the methanolic extract of Heteropterys cotinifolia may also provide further data to characterize taxonomically this species in order to be distinguished from others species closely related and belonging to the same genus. PMID:24453918

  2. Integrative Taxonomic Approach for Describing a New Cryptic Species of Bush Frog (Raorchestes: Anura: Rhacophoridae) from the Western Ghats, India.

    PubMed

    Priti, H; Roshmi, Rekha Sarma; Ramya, Badrinath; Sudhira, H S; Ravikanth, G; Aravind, Neelavara Anantharam; Gururaja, Kotambylu Vasudeva

    2016-01-01

    A new cryptic species of bush frog Raorchestes honnametti sp. nov. is described from the south-eastern part of the Western Ghats, India. This newly described species belongs to the Charius clade and is morphologically similar to other clade members--R. charius and R. griet. Therefore, an integrative taxonomic approach based on molecular and bioacoustic analysis along with morphology was used to delimit the new species. Raorchestes honnametti sp. nov., is currently known only from Biligiri Rangaswamy Temple Tiger Reserve, a part of Biligiri Rangaswamy horst mountain range (a mountain formed due movement of two faults) formed during the Late Quaternary period (1.8-2.58 Ma). Discovery of cryptic species from a highly speciose and well-studied genus Raorchestes hints at the possible existence of several more cryptic species in this genus. We discuss the possible reasons for crypsis and emphasize the need for continued systematic surveys of amphibians across the Western Ghats. PMID:26934213

  3. Integrative Taxonomic Approach for Describing a New Cryptic Species of Bush Frog (Raorchestes: Anura: Rhacophoridae) from the Western Ghats, India

    PubMed Central

    Roshmi, Rekha Sarma; Ramya, Badrinath; Sudhira, H. S.; Ravikanth, G.; Aravind, Neelavara Anantharam

    2016-01-01

    A new cryptic species of bush frog Raorchestes honnametti sp. nov. is described from the south-eastern part of the Western Ghats, India. This newly described species belongs to the Charius clade and is morphologically similar to other clade members—R. charius and R. griet. Therefore, an integrative taxonomic approach based on molecular and bioacoustic analysis along with morphology was used to delimit the new species. Raorchestes honnametti sp. nov., is currently known only from Biligiri Rangaswamy Temple Tiger Reserve, a part of Biligiri Rangaswamy horst mountain range (a mountain formed due movement of two faults) formed during the Late Quaternary period (1.8–2.58 Ma). Discovery of cryptic species from a highly speciose and well-studied genus Raorchestes hints at the possible existence of several more cryptic species in this genus. We discuss the possible reasons for crypsis and emphasize the need for continued systematic surveys of amphibians across the Western Ghats. PMID:26934213

  4. Phylogeny and Classification of the Trapdoor Spider Genus Myrmekiaphila: An Integrative Approach to Evaluating Taxonomic Hypotheses

    PubMed Central

    Bailey, Ashley L.; Brewer, Michael S.; Hendrixson, Brent E.; Bond, Jason E.

    2010-01-01

    Background Revised by Bond and Platnick in 2007, the trapdoor spider genus Myrmekiaphila comprises 11 species. Species delimitation and placement within one of three species groups was based on modifications of the male copulatory device. Because a phylogeny of the group was not available these species groups might not represent monophyletic lineages; species definitions likewise were untested hypotheses. The purpose of this study is to reconstruct the phylogeny of Myrmekiaphila species using molecular data to formally test the delimitation of species and species-groups. We seek to refine a set of established systematic hypotheses by integrating across molecular and morphological data sets. Methods and Findings Phylogenetic analyses comprising Bayesian searches were conducted for a mtDNA matrix composed of contiguous 12S rRNA, tRNA-val, and 16S rRNA genes and a nuclear DNA matrix comprising the glutamyl and prolyl tRNA synthetase gene each consisting of 1348 and 481 bp, respectively. Separate analyses of the mitochondrial and nuclear genome data and a concatenated data set yield M. torreya and M. millerae paraphyletic with respect to M. coreyi and M. howelli and polyphyletic fluviatilis and foliata species groups. Conclusions Despite the perception that molecular data present a solution to a crisis in taxonomy, studies like this demonstrate the efficacy of an approach that considers data from multiple sources. A DNA barcoding approach during the species discovery process would fail to recognize at least two species (M. coreyi and M. howelli) whereas a combined approach more accurately assesses species diversity and illuminates speciation pattern and process. Concomitantly these data also demonstrate that morphological characters likewise fail in their ability to recover monophyletic species groups and result in an unnatural classification. Optimizations of these characters demonstrate a pattern of “Dollo evolution” wherein a complex character evolves only once

  5. The integrative taxonomic approach applied to porifera: a case study of the homoscleromorpha.

    PubMed

    Boury-Esnault, Nicole; Lavrov, Dennis V; Ruiz, César A; Pérez, Thierry

    2013-09-01

    The two main scientific tasks of taxonomy are species' delineation and classification. These two tasks are often treated differently, with classification accomplished by newly-developed phylogenetic methods, often based on molecular sequences, while delimitation of species is conducted by what is often considered to be an "old-fashioned" typological approach based on morphological description. A new "integrative taxonomy" has been proposed which maintains that species delimitation should be a multidisciplinary undertaking combining several independent datasets. Here we argue that the same principle is relevant to the classification of species. In the past 20 years, we assembled various datasets based on the external morphology, anatomy, cytology, spicule shapes, geography, reproduction, genetic sequences, and metabolomics of homoscleromorph sponges. We show how we used these datasets to describe new species of homoscleromorph sponges and to elucidate their phylogenetic relationships and their phylogenetic position within the phylum Porifera. PMID:23670632

  6. Morphometric analysis and taxonomic revision of Anisopteromalus Ruschka (Hymenoptera: Chalcidoidea: Pteromalidae) – an integrative approach

    PubMed Central

    Baur, Hannes; Kranz-Baltensperger, Yvonne; Cruaud, Astrid; Rasplus, Jean-Yves; Timokhov, Alexander V; Gokhman, Vladimir E

    2014-01-01

    We use an integrative taxonomic approach to revise the genus Anisopteromalus. In particular, we apply multivariate ratio analysis (MRA), a rather new statistical method based on principal component analysis (PCA) and linear discriminant analysis (LDA), to numerous body measurements and combine the data with those from our molecular analysis of Cytb and ITS2 genetic markers (on a subset of species) and all available published data on morphology, karyology, behaviour, host associations and geographic distribution. We demonstrate that the analysis of quantitative characters using MRA plays a major role for the integration of name-bearing types and thus for the association of taxa with names. Six species are recognized, of which two are new: A. cornis Baur sp.n. and A. quinarius Gokhman & Baur sp.n. For Anisopteromalus calandrae (Howard), a well-known, cosmopolitan parasitoid of stored-product pests, we have selected a neotype to foster continuity and stability in the application of this important name. The species was sometimes confused with the related A. quinarius sp.n., another cosmopolitan species that is frequently encountered in similar environments. We also show that several species originally described or later put under Anisopteromalus actually belong to different genera: Cyrtoptyx camerunus (Risbec) comb.n.; Meraporus glaber (Szelényi) comb.n.; Dinarmus schwenkei (Roomi, Khan & Khan) comb.n. Neocatolaccus indicus Ayyar & Mani is confirmed as a junior synonym of Oxysychus sphenopterae (Ferrière) syn.n. and Anisopteromalus calandrae brasiliensis (Domenichini) stat.rev. must be considered as a valid but doubtful taxon. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:BDFE96D3-D0F4-4012-90F5-9A087F7F5864. PMID:26074661

  7. Polyphasic approach to characterize heterotrophic bacteria of biofilms and patina on walls of the Suburban Bath of the Herculaneum's archaeological excavations in Italy

    NASA Astrophysics Data System (ADS)

    Ventorino, V.; Pepe, O.; Sannino, L.; Blaiotta, G.; Palomba, S.

    2012-04-01

    plates were purified in the same growth medium by streaking and differentiated by assessing their morphological (phase-contrast microscopy) and biochemical characteristics (Gram-stains KOH-lysis and catalase activity). Cultural-based method allow us to identify by 16S and 26S rRNA partial sequence analysis, heterotrophic bacteria belonging to different genera as Bacillus, Pseudomonas, Aeromonas and Microbacterium. By using this approach, Bacillus-related species (B. benzoevorans, B. megaterium and B. pumilis and B. megaterium/B. simplex group) as well as Aeromonas sobria/Aeromonas salmonicida/Aeromonas hydrophila group, Pseudomonas plecoglossicida and Microbacterium esteraromaticum were isolated in different sample points analysed. DGGE analysis of PCR amplified V3 region of rDNA from DNA directly recovered from samples of biofilms and patina, enabled identification of bacterial species not found using culturable technology, as those closest related to Aeromonas, Paenibacillus, Brevibacterium, Exiguobacterium, Microbacterium, Brevibacterium, Stenothophomonas and Streptomyces. Combination of culture-dependent and independent methods provide a better characterization of heterotrophic microbiota that colonize the surface of ancient decorated walls and can contribute to understand the potential of biodeterioration activity by heterotrophic microorganisms.

  8. Polyphasic taxonomy of Aspergillus section Fumigati and its teleomorph Neosartorya

    PubMed Central

    Samson, R.A.; Hong, S.; Peterson, S.W.; Frisvad, J.C.; Varga, J.

    2007-01-01

    The taxonomy of Aspergillus section Fumigati with its teleomorph genus Neosartorya is revised. The species concept is based on phenotypic (morphology and extrolite profiles) and molecular (β-tubulin and calmodulin gene sequences) characters in a polyphasic approach. Four new taxa are proposed: N. australensis N. ferenczii, N. papuaensis and N. warcupii. All newly described and accepted species are illustrated. The section consists of 33 taxa: 10 strictly anamorphic Aspergillus species and 23 Neosartorya species. Four other Neosartorya species described previously were not available for this monograph, and consequently are relegated to the category of doubtful species. PMID:18490953

  9. Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi

    PubMed Central

    Nilsson, R Henrik; Kristiansson, Erik; Ryberg, Martin; Larsson, Karl-Henrik

    2005-01-01

    Background During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public databases such as GenBank increases exponentially, only a minuscule fraction of all organisms have been sequenced, leaving taxon sampling a momentous problem for sequence-based taxonomic identification. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. To alleviate these concerns, a project to automatically monitor select unidentified sequences in GenBank for taxonomic progress through repeated local BLAST searches was initiated. Mycorrhizal fungi – a field where species identification often is prohibitively complex – and the much used ITS locus were chosen as test bed. Results A Perl script package called emerencia is presented. On a regular basis, it downloads select sequences from GenBank, separates the identified sequences from those insufficiently identified, and performs BLAST searches between these two datasets, storing all results in an SQL database. On the accompanying web-service , users can monitor the taxonomic progress of insufficiently identified sequences over time, either through active searches or by signing up for e-mail notification upon disclosure of better matches. Other search categories, such as listing all insufficiently identified sequences (and their present best fully identified matches) publication-wise, are also available. Discussion The ever-increasing use of DNA sequences for identification purposes largely falls back on the assumption that public sequence databases

  10. Carrier synchronization and detection of polyphase signals.

    NASA Technical Reports Server (NTRS)

    Lindsey, W. C.; Simon, M. K.

    1972-01-01

    Digital communication networks used for the distribution of high-speed digital information are currently the subject of design studies for many civil and military applications. This paper presents results that are useful in such studies as well as in network planning. In particular, the paper is concerned with the problems of carrier synchronization and noisy reference detection of polyphase signals. Reconstruction of coherent references for the detection of polyphase signals is considered and analyzed for three carrier reconstruction loops, namely, Nth power (multiply-and-divide) loops, generalized Costas (I-Q) loops, and extensions of data-aided (modulation wipeoff) loops. General expressions for the error probability are developed when the reconstructed reference signals are noisy.

  11. Compression of polyphase codes with Doppler shift

    NASA Astrophysics Data System (ADS)

    Wirth, W. D.

    It is shown that pulse compression with sufficient Doppler tolerance may be achieved with polyphase codes derived from linear frequency modulation (LFM) and nonlinear frequency modulation (NLFM). Low sidelobes in range and Doppler are required especially for the radar search function. These may be achieved by an LFM derived phase coder together with Hamming weighting or by applying a PNL polyphase code derived from NLFM. For a discrete and known Doppler frequency with an expanded and mismatched reference vector a sidelobe reduction is possible. The compression is then achieved without a loss in resolution. A set up for the expanded reference gives zero sidelobes only in an interval around the signal peak or a least square minimization for all range elements. This version may be useful for target tracking.

  12. A Taxonomic Search Engine: Federating taxonomic databases using web services

    PubMed Central

    Page, Roderic DM

    2005-01-01

    Background The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism. Results The Taxonomic Search Engine (TSE) is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO) and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier (LSID) authority for the source taxonomic databases, providing globally unique identifiers (and associated metadata) for each name. Conclusion The Taxonomic Search Engine is available at and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names. PMID:15757517

  13. Real-Time, Polyphase-FFT, 640-MHz Spectrum Analyzer

    NASA Technical Reports Server (NTRS)

    Zimmerman, George A.; Garyantes, Michael F.; Grimm, Michael J.; Charny, Bentsian; Brown, Randy D.; Wilck, Helmut C.

    1994-01-01

    Real-time polyphase-fast-Fourier-transform, polyphase-FFT, spectrum analyzer designed to aid in detection of multigigahertz radio signals in two 320-MHz-wide polarization channels. Spectrum analyzer divides total spectrum of 640 MHz into 33,554,432 frequency channels of about 20 Hz each. Size and cost of polyphase-coefficient memory substantially reduced and much of processing loss of windowed FFTs eliminated.

  14. Polyphase antialiasing in resampling of images.

    PubMed

    Seidner, Daniel

    2005-11-01

    Changing resolution of images is a common operation. It is also common to use simple, i.e., small, interpolation kernels satisfying some "smoothness" qualities that are determined in the spatial domain. Typical applications use linear interpolation or piecewise cubic interpolation. These are popular since the interpolation kernels are small and the results are acceptable. However, since the interpolation kernel, i.e., impulse response, has a finite and small length, the frequency domain characteristics are not good. Therefore, when we enlarge the image by a rational factor of (L/M), two effects usually appear and cause a noticeable degradation in the quality of the image. The first is jagged edges and the second is low-frequency modulation of high-frequency components, such as sampling noise. Both effects result from aliasing. Enlarging an image by a factor of (L/M) is represented by first interpolating the image on a grid L times finer than the original sampling grid, and then resampling it every M grid points. While the usual treatment of the aliasing created by the resampling operation is aimed toward improving the interpolation filter in the frequency domain, this paper suggests reducing the aliasing effects using a polyphase representation of the interpolation process and treating the polyphase filters separately. The suggested procedure is simple. A considerable reduction in the aliasing effects is obtained for a small interpolation kernel size. We discuss separable interpolation and so the analysis is conducted for the one-dimensional case. PMID:16279186

  15. Radix dolgini: The integrative taxonomic approach supports the species status of a Siberian endemic snail (Mollusca, Gastropoda, Lymnaeidae).

    PubMed

    Vinarski, Maxim V; Aksenova, Olga V; Bespalaya, Yulia V; Bolotov, Ivan N; Schniebs, Katrin; Gofarov, Mikhail Yu; Kondakov, Alexander V

    2016-01-01

    The molecular techniques are the standard tool for the study of the taxonomic position and phylogenetic affinities of the lymnaeid genus Radix Montfort, 1810, and the majority of the European representatives of this taxon have been studied in this respect. However, a plethora of nominal species of Radix described from Northern Asia (Siberia and the Russian Far East) are still characterized only morphologically, raising some doubts concerning their validity. In this paper, we present the triple (morphological, molecular, and zoogeographical) evidence that there is at least one endemic species of Radix, Radix dolgini (Gundrizer and Starobogatov, 1979), widely distributed in Siberia and Western Mongolia. Phylogenetically, it is a sister species to the European R. labiata (Rossmaessler, 1835) [=R. peregra auct.], and their common ancestor most probably lived in the Pliocene, nearly 3.25Myr ago. Our results assume the existence of an extended dispersal barrier for freshwater hydrobionts between Europe and Siberia in the Late Pliocene that may be important for biogeographical explanations. Three other nominal Siberian species of Radix: R. kurejkae (Gundrizer and Starobogatov, 1979), R. gundrizeri (Kruglov and Starobogatov, 1983), and R. ulaganica (Kruglov and Starobogatov, 1983) proved to be the junior synonyms of R. dolgini. PMID:26705968

  16. Negative coupled inductors for polyphase choppers

    NASA Technical Reports Server (NTRS)

    Jamieson, Robert S. (Inventor)

    1984-01-01

    A technique for negatively coupling the outputs of polyphase choppers is disclosed, wherein the output inductance of each phase is divided into two windings, and each winding is negatively coupled to a corresponding winding of a neighboring phase. In a preferred embodiment for a three-phase chopper circuit, the output inductance of phase A is divided into windings 100 and 102, the output inductance of phase B is divided into windings 110 and 112, and the output inductance of phase C is divided into windings 120 and 122. Pairs of windings 100 and 110, 112 and 120, and 102 and 122 are respectively disposed in transformers arranged for negatively coupling the windings of each pair.

  17. Polyphase-coded incoherent scatter measurements at Millstone Hill

    NASA Astrophysics Data System (ADS)

    Virtanen, Ilkka I.; Lind, Frank D.; Roininen, Lassi; Erickson, Philip J.; Rideout, William C.; Orispää, Mikko; Vierinen, Juha; Lehtinen, Markku S.

    2013-09-01

    We report first results of polyphase-coded incoherent scatter measurements at Millstone Hill. To our knowledge, these are the first incoherent scatter measurements with polyphase alternating codes of Markkanen et al. (2008) and optimal quadriphase sequences of Damtie et al. (2008). The results demonstrate that an arbitrary waveform generator recently installed at the Millstone Hill incoherent scatter radar, part of the National Science Foundation Geospace Facility operated by the Massachusetts Institute of Technology Haystack Observatory, is capable of reproducing the polyphase waveforms with an accuracy sufficient for incoherent scatter measurements. Polyphase codes will allow incoherent scatter radar experiments to be better optimized, because they provide a larger variety of code and code cycle lengths than the traditional binary codes.

  18. mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences

    PubMed Central

    2013-01-01

    Background Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database. Results Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure. Conclusions mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly. PMID:24451012

  19. Polyphasic taxonomy of the genus Talaromyces

    PubMed Central

    Yilmaz, N.; Visagie, C.M.; Houbraken, J.; Frisvad, J.C.; Samson, R.A.

    2014-01-01

    The genus Talaromyces was described by Benjamin in 1955 as a sexual state of Penicillium that produces soft walled ascomata covered with interwoven hyphae. Phylogenetic information revealed that Penicillium subgenus Biverticillium and Talaromyces form a monophyletic clade distinct from the other Penicillium subgenera. Subsequently, in combination with the recent adoption of the one fungus one name concept, Penicillium subgenus Biverticillium was transferred to Talaromyces. At the time, the new combinations were made based only on phylogenetic information. As such, the aim of this study was to provide a monograph on Talaromyces applying a polyphasic species concept, including morphological, molecular and physiological characters. Based on an ITS, BenA and RPB2 multigene phylogeny, we propose a new sectional classification for the genus, placing the 88 accepted species into seven sections, named sections Bacillispori, Helici, Islandici, Purpurei, Subinflati, Talaromyces and Trachyspermi. We provide morphological descriptions for each of these species, as well as notes on their identification using morphology and DNA sequences. For molecular identification, BenA is proposed as a secondary molecular marker to the accepted ITS barcode for fungi. PMID:25492983

  20. 40 GSPS opto-electronic polyphase analog-to-digital converter

    NASA Astrophysics Data System (ADS)

    Villa, Carlos; Donkor, Eric; Hayduk, Michael; Bussjager, Rebecca

    2007-04-01

    A novel opto-electronic polyphase analog-to-digital converter scheme that entails parallel optical sampling of different phases of an input analog signal is presented. With this scheme higher sampling rate can be attained by scaling. We demonstrate the basic tenets of this approach by upscaling a 160MSPS optoelectronic analog-to-digital ADC system to design and implement a 40.96GSPS four-channel polyphase optoelectronic analog-to-digital system. An optoelectronic divide-by-two decimation technique is implemented for demultiplexing digital samples having a repetition rate f into its even and odd subsamples with each subsample having a repetition rate of f/2. A two stage concatenation of the basic divide-by-two decimation scheme is employed to demultiplex the 40.96GSPS sampled RF signals into 8 channels of demultiplexed data, each channel having a data-rate of 5.12GSPS. Detailed design parameters and experimental results are presented for both the 160MSPS and the 40GSPS, including the design and implementation of optical clock networks, polyphase RF sampling networks, and decimation or demultiplexing networks. In addition, the electronic quantization network for the 160MSPS ADC system is presented. The 160MSPS system was found to have effective bit-resolution of 6.97, third-harmonic distortion of 43.73dB, signal-to-noise-distortion of 43.73dB, and spurious free dynamic range of 41dB.

  1. Taxonomic identification of mediterranean pines and their hybrids based on the high resolution melting (HRM) and trnL approaches: from cytoplasmic inheritance to timber tracing.

    PubMed

    Ganopoulos, Ioannis; Aravanopoulos, Filippos; Madesis, Panagiotis; Pasentsis, Konstantinos; Bosmali, Irene; Ouzounis, Christos; Tsaftaris, Athanasios

    2013-01-01

    Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples. PMID:23577179

  2. Taxonomic Identification of Mediterranean Pines and Their Hybrids Based on the High Resolution Melting (HRM) and trnL Approaches: From Cytoplasmic Inheritance to Timber Tracing

    PubMed Central

    Ganopoulos, Ioannis; Aravanopoulos, Filippos; Madesis, Panagiotis; Pasentsis, Konstantinos; Bosmali, Irene; Ouzounis, Christos; Tsaftaris, Athanasios

    2013-01-01

    Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples. PMID:23577179

  3. [A pharmacokinetic study of subconjunctival polyphase liposome 5-fluorouracil].

    PubMed

    Ke, X F; Wei, H R; Yang, J X

    1994-03-01

    5-Fu polyphase liposome was prepared by fusing the drug with lecithin and cholesterol, the rate of encapsulation being 52%, and 97% of the particles were less than 2 microns in diameter and stable against heat and cold. 5 mg of tritiated 5-Fu in 0.5 ml of the polyphase liposome preparation was injected subconjunctivally in rabbits. The concentrations of 5-Fu in the conjunctiva, the sclera, and the conjunctiva-Tenen's capsule-sclera en bloc 180 degrees from the site of injection were measured by the scintillation method 12, 24, 48, 72 and 96 hours after injection to be no less than 0.2 microgram, the ID50 of fibroblast proliferation. These findings suggested that 5-Fu polyphase liposome preparation might be substituted for 5-Fu solution in the filtering operation to reduce the frequency of injections and to attenuate the side effects. PMID:8001446

  4. A polyphasic taxonomy of Daldinia (Xylariaceae)1

    PubMed Central

    Stadler, Marc; Læssøe, Thomas; Fournier, Jacques; Decock, Cony; Schmieschek, Beata; Tichy, Hans-Volker; Peršoh, Derek

    2014-01-01

    For a monograph based on a polythetic concept, several thousands of herbarium specimens, and several hundreds of freshly collected and cultured specimens of Daldinia and allied Xylariaceae, originating from around the world, were studied for morphological traits, including by SEM, and chemically by HPLC profiles using UV-visible and mass spectrometric detection. Emphasis was given to tropical material, and importantly, ancient specimens, including as many types as possible, were tracked and studied to review earlier taxonomic concepts. An epitype of D. eschscholtzii was selected as representative of the morphochemotype that is most widely distributed in the tropics. Six new species of Daldinia from the tropics and the southern Hemisphere are described. Daldinia asphalatum is resurrected, and D. cudonia is regarded as its synonym. In addition, the following binomials are epi-, iso-, neo- and/or lectotypified: Daldinia asphalatum, D. caldariorum, D. clavata, D. cuprea, D. durissima, D. eschscholtzii, D. grandis, D. loculata, and D. vernicosa. Annellosporium and Versiomyces are regarded as synonyms of Daldinia. Many new synonymies in Daldinia are proposed, and some previously published names are rejected. In total, 47 taxa in Daldinia are recognised and a key is provided. Their biogeography, chorology, and ecology, as well as the importance of their secondary metabolites, are also discussed. The previous definition of the genus is emended. The species concept is based mainly on morphological and other phenotype-derived characters because, despite diligent search, no molecular data or cultures of several of the accepted species could be obtained. Daldinia is segregated into five major groups, based on phenotypic characteristics. Some unnamed but aberrant specimens were not found in good condition and are therefore not formally described as new species. However, they are illustrated in detail in a hope that this will facilitate the discovery of fresh material in future

  5. Patterns of taxonomic diversity among terrestrial isopods

    PubMed Central

    Sfenthourakis, Spyros; Taiti, Stefano

    2015-01-01

    Abstract The publication of the world catalog of terrestrial isopods some ten years ago by Schmalfuss has facilitated research on isopod diversity patterns at a global scale. Furthermore, even though we still lack a comprehensive and robust phylogeny of Oniscidea, we do have some useful approaches to phylogenetic relationships among major clades which can offer additional insights into isopod evolutionary dynamics. Taxonomic diversity is one of many approaches to biodiversity and, despite its sensitiveness to biases in taxonomic practice, has proved useful in exploring diversification dynamics of various taxa. In the present work, we attempt an analysis of taxonomic diversity patterns among Oniscidea based on an updated world list of species containing 3,710 species belonging to 527 genera and 37 families (data till April 2014). The analysis explores species diversity at the genus and family level, as well as the relationships between species per genera, species per families, and genera per families. In addition, we consider the structure of isopod taxonomic system under the fractal perspective that has been proposed as a measure of a taxon’s diversification. Finally, we check whether there is any phylogenetic signal behind taxonomic diversity patterns. The results can be useful in a more detailed elaboration of Oniscidea systematics. PMID:26261437

  6. Computational analysis of nonlinear creep of polyphase aggregates: Influence of phase morphology

    NASA Astrophysics Data System (ADS)

    Cook, A. C.; Vel, S. S.; Gerbi, C.; Johnson, S. E.

    2014-09-01

    The constitutive laws of polyphase aggregates dominantly depend on the operative deformation mechanisms, phase morphology and modes, and environmental conditions. Each of these factors has the potential to dramatically affect bulk mechanical properties as well as the local stress and strain rate distributions. To focus on the effects of phase morphology, we have developed a rigorous multiscale approach based on asymptotic expansion homogenization. The proposed methodology has two fundamental goals: (1) accurately predict bulk behavior in aggregates by explicitly taking into account phase morphology and (2) calculate detailed distributions of strain rates, stresses, and viscosities in heterogeneous materials. The methodology is able to consider general nonlinear phase constitutive laws that relate strain rates to stresses, temperature, and other factors such as water fugacity and grain size. We demonstrate the approach by analyzing power law creep of computer-generated and natural polyphase systems and benchmarking the results against analytical solutions. As an outcome of this analysis, we find that the approximation of an aggregate as a power law material is reasonable for isotropic, homogeneous phase distributions but breaks down significantly with high degrees of phase organization. We also present distributions in strain rate, stress, and viscosity for different applied loading conditions. Results exhibit areas of high internal stresses and substantial localization. We describe and provide a freely available software package supporting these calculations.

  7. Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov

    NASA Technical Reports Server (NTRS)

    Venkateswaran, K.; Moser, D. P.; Dollhopf, M. E.; Lies, D. P.; Saffarini, D. A.; MacGregor, B. J.; Ringelberg, D. B.; White, D. C.; Nishijima, M.; Sano, H.; Burghardt, J.; Stackebrandt, E.; Nealson, K. H.

    1999-01-01

    The genus Shewanella has been studied since 1931 with regard to a variety of topics of relevance to both applied and environmental microbiology. Recent years have seen the introduction of a large number of new Shewanella-like isolates, necessitating a coordinated review of the genus. In this work, the phylogenetic relationships among known shewanellae were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them into a consensus classification. Based on information generated from this study and obtained from the literature, a scheme for the identification of Shewanella species has been compiled. Key phenotypic characteristics were sulfur reduction and halophilicity. Fatty acid and quinone profiling were used to impart an additional layer of information. Molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in some cases. As a result, DNA-DNA hybridization and sequence analyses of a more rapidly evolving molecule (gyrB gene) were performed. Species-specific PCR probes were designed for the gyrB gene and used for the rapid screening of closely related strains. With this polyphasic approach, in addition to the ten described Shewanella species, two new species, Shewanella oneidensis and 'Shewanella pealeana', were recognized; Shewanella oneidensis sp. nov. is described here for the first time.

  8. Taxonomic abstraction in psychobiology.

    PubMed

    Evans, S H; Chafetz, M D; Gage, F H

    1984-10-01

    If a body of knowledge in a scientific discipline is to be extended beyond empirical observation and into the realm of laws and principles, one of the fundamental requirements is a taxonomy which supports the systematic integration of observations. Psychobiology benefits from taxonomies provided by biology and chemistry, which include not only object oriented taxonomies such as species or chemical elements, but also process oriented taxonomies, such as oxidation, metabolism, phototaxis, or predation. Psychobiology has yet to provide equivalent taxonomies for its behavioral observations, although the common use of terms such as fear, anger, arousal, stress, and memory might lead one to suppose that these are based on a well established taxonomy of behavioral measures. In this report the logical and quantitative requirements for treating behavioral measures in terms of taxonomic classes are reviewed. A sample of studies representing recent research in psychobiology was examined to assess interest in such a taxonomy and to identify elements of current practice which might contribute to its development. Recent practice displays some evidence of interest in behavioral classes, in choice of language, and in frequent use of multiple dependent measures. Multivariate methods, which might elicit from such data evidence contributing to the development of a taxonomy, are rarely used. Recommendations are given on some appropriate analytic methods for data resulting from current practice and for new exploratory paradigms which could aim directly at the establishment of taxonomic classes for behaviors. PMID:6512516

  9. A polyphase filter for many-core architectures

    NASA Astrophysics Data System (ADS)

    Adámek, K.; Novotný, J.; Armour, W.

    2016-07-01

    In this article we discuss our implementation of a polyphase filter for real-time data processing in radio astronomy. The polyphase filter is a standard tool in digital signal processing and as such a well established algorithm. We describe in detail our implementation of the polyphase filter algorithm and its behaviour on three generations of NVIDIA GPU cards (Fermi, Kepler, Maxwell), on the Intel Xeon CPU and Xeon Phi (Knights Corner) platforms. All of our implementations aim to exploit the potential for data reuse that the algorithm offers. Our GPU implementations explore two different methods for achieving this, the first makes use of L1/Texture cache, the second uses shared memory. We discuss the usability of each of our implementations along with their behaviours. We measure performance in execution time, which is a critical factor for real-time systems, we also present results in terms of bandwidth (GB/s), compute (GFLOP/s/s) and type conversions (GTc/s). We include a presentation of our results in terms of the sample rate which can be processed in real-time by a chosen platform, which more intuitively describes the expected performance in a signal processing setting. Our findings show that, for the GPUs considered, the performance of our polyphase filter when using lower precision input data is limited by type conversions rather than device bandwidth. We compare these results to an implementation on the Xeon Phi. We show that our Xeon Phi implementation has a performance that is 1.5 × to 1.92 × greater than our CPU implementation, however is not insufficient to compete with the performance of GPUs. We conclude with a comparison of our best performing code to two other implementations of the polyphase filter, showing that our implementation is faster in nearly all cases. This work forms part of the Astro-Accelerate project, a many-core accelerated real-time data processing library for digital signal processing of time-domain radio astronomy data.

  10. Taxonomic description and genome sequence of Bacillus campisalis sp. nov., a member of the genus Bacillus isolated from a solar saltern.

    PubMed

    Kumar, Rajendran Mathan; Kaur, Gurwinder; Kumar, Anand; Bala, Monu; Singh, Nitin Kumar; Kaur, Navjot; Kumar, Narender; Mayilraj, Shanmugam

    2015-10-01

    The taxonomic position of a Gram-stain positive bacterium isolated from a solar saltern sample collected from Kanyakumari, coastal region of the Bay of Bengal, India, was analysed by using a polyphasic approach. The isolated strain, designated SA2-6T, had phenotypic characteristics that matched those of the genus Bacillus. The 16S rRNA gene sequence (1493 bases) of the novel strain was compared with those of previously studied Bacillus type strains and confirmed that the strain belongs to the genus Bacillus and was moderately closely related to the type strain of Bacillus foraminis at 97.5 % 16S rRNA gene sequence similarity, followed by those of Bacillus thioparans (96.9 %), Bacillus subterraneus (96.8 %), Bacillus jeotgali (96.6 %), Bacillus selenatarsenatis (96.6 %) and Bacillus boroniphilus (96.6 %). 16S rRNA gene sequence analysis indicated that strain SA2-6T differs from all other species of the genus Bacillus by at least 2.5 %. It contained MK-7 as the predominant menaquinone, meso-diaminopimelic acid as the diagnostic cell-wall diamino acid, and iso-C15 : 0 and anteiso-C15 : 0 as major fatty acids. Major lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). Based on data from this polyphasic study, strain SA2-6T is considered to represent a novel species of the genus Bacillus, for which the name Bacillus campisalis sp. nov. is proposed. The type strain is SA2-6T ( = MTCC 11848T = DSM 28801T). The draft genome of strain SA2-6T consisted of 5 183 363 bp with G+C content of 45.44 mol%, 5352 predicted coding sequences, 191 RNAs and 479 subsystems. PMID:26296567

  11. Incongruence between cladistic and taxonomic systems.

    PubMed

    Grant, Verne

    2003-09-01

    Cladistic and taxonomic treatments of the same plant group usually exhibit a mixture of congruences and incongruences. The question arises in the case of the incongruences as to which version is right and which is wrong. Many cladists believe that cladistics is a superior approach and gives the best results. There are several conceptual and methodological differences between cladistics and taxonomy that cause incongruence. One important conceptual difference is the use of different criteria for grouping: order of branching vs. similarity and difference (clades vs. taxa). Another is the policy regarding paraphyletic groups: to ban them in cladistics but ignore the ban in taxonomy. These two differences automatically lead to some incongruences. One approach is not right and the other wrong; each is operating by its own standards. However, when cladists apply the paraphyly rule to a taxonomic system and conclude that it needs revision to eliminate paraphyly, as cladists often do, they are judging the taxonomic system by a wrong standard. Several differences between the two schools in the use and handling of characters can also cause incongruence. First consider phenetic characters. Taxonomy uses a very wide range of these, whereas phenetic cladistics sets restrictions on the selection of characters, which deprive it of potentially useful evidence. Taxonomic systems generally rest on a broader empirical foundation than phenetic cladistic systems. Next, consider molecular cladistics, which is the leader in the use of DNA evidence. Two sources of incongruence between molecular cladistics and taxonomic systems can come into play here. First, the molecular evidence used in cladistics comes mainly from cytoplasmic organelles, whereas taxonomic systems are based on characters that are determined mainly by the chromosomal genome. More generally, the database in a molecular cladogram is, in itself, too narrow to serve as a foundation for an organismic classification. In cases

  12. On the detection of differentially encoded polyphase signals.

    NASA Technical Reports Server (NTRS)

    Lindsey, W. C.

    1972-01-01

    Discussion of the transmission and detection of differentially encoded polyphase signals and of the ambiguity resolution problem which results from suppression of the transmitted carrier. In particular, an analysis is made of the performance of differentially encoded coherent multiple phase-shift keyed (MPSK) systems which reconstruct coherent reference signals by means of generalized Costas or nth-power loops. The performance of such systems is then compared with that of ideal reception of MPSK signals and differentially coherent detection of differentially encoded MPSK signals. Emphasis is placed upon the special cases of quadriphase and octaphase signaling.

  13. On the detection of differentially encoded polyphase signals.

    NASA Technical Reports Server (NTRS)

    Lindsey, W. C.; Simon, M. K.

    1972-01-01

    Consideration of the transmission and detection of differentially encoded multiple phase-shift-keyed (MPSK) signals, paying particular attention to the ambiguity resolution problem resulting from suppression of the transmitted carrier. A study is made of the coherent detection of differentially encoded MPSK signals, and the performance of a differentially encoded MPSK system is compared with that of a system which transmits absolutely encoded polyphase signals and performs perfect ambiguity resolution. Both the perfect and noisy reference signal cases are treated. Also, the performance of coherent detection of differentially encoded MPSK signals is compared with that of differentially coherent reception of the same signal set.

  14. Taxonomic Approach to the Tachinid Flies Dinera carinifrons (Fallén) (Diptera: Tachinidae) and Dinera fuscata Zhang and Shima using Molecular and Morphometric Data

    PubMed Central

    Lutovinovas, Erikas; Malenovský, Igor; Tóthová, Andrea; Ziegler, Joachim; Vaňhara, Jaromír

    2013-01-01

    Molecular phylogenetic and traditional morphometric methods were applied to examine six Palaearctic taxa of the taxonomically difficult tachinid fly genus Dinera Robineau-Desvoidy (Diptera: Tachinidae), with particular reference to D. carinifrons (Fallén) and D. fuscata Zhang and Shima. Results of a phylogenetic analysis based on the mitochondrial markers 12S and 16S rDNA and multivariate statistical analyses of 19 morphometric characters were used to delimit both species. A lectotype was designated for D. carinifrons to stabilize the nomenclature in the group. Dinera carinifrons has a transpalaearctic distribution and is present in Central Europe, especially in high altitudes of the Alps. It differs from the similar and closely related D. fuscata in that it has a slightly larger body size, a dense greyish microtrichosity on the body, and different head proportions. Dinera fuscata, as delimited here, is widespread in the Palaearctic region, including Europe. Slight differences in both molecular and morphometric characters were found between western (Europe and Iran) and eastern (China and Japan) populations of D. fuscata, which are interpreted as an intraspecific variation. Differential diagnosis between D. carinifrons and D. fuscata is provided in the form of a revised portion of the determination key to the Palaearctic Dinera by Zhang and Shima (2006). PMID:24787238

  15. Designing and conducting in silico analysis for identifying of Echinococcus spp. with discrimination of novel haplotypes: an approach to better understanding of parasite taxonomic.

    PubMed

    Spotin, Adel; Gholami, Shirzad; Nasab, Abbas Najafi; Fallah, Esmaeil; Oskouei, Mahmoud Mahami; Semnani, Vahid; Shariatzadeh, Seyyed Ali; Shahbazi, Abbas

    2015-04-01

    The definitive identification of Echinococcus species is currently carried out by sequencing and phylogenetic strategies. However, the application of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) patterns is not broadly used as a result of heterogeneity traits of Echinococcus genome in different regions of the world. Therefore, designing and conducting a standardized pattern should indigenously be considered in under-studied areas. In this investigation, an in silico mapping was designed and developed for eight Echinococcus spp. on the basis of regional sequences in Iran and the world. The numbers of 60 Echinococcus isolates were collected from the liver and lungs of 15 human, 15 sheep, 15 cattle, and 15 camel cases in Semnan province, Central Iran. DNA samples were extracted and examined by polymerase chain reaction of ribosomal DNA (rDNA) internal transcribed spacer 1 (ITS1) and PCR-RFLP via Rsa1 endonuclease enzyme. Moreover, 15 amplicons of cytochrome oxidase 1 (Cox1) were directly sequenced in order to identify the strains/haplotypes. PCR-RFLP and phylogenetic analyses revealed firmly the presence of the G1 and G6 genotypes with heterogeneity (three novel haplotypes) of Cox1 gene although no other expected genotypes were found in the region. Finding shows that the identification of novel haplotypes along with discrimination of Echinococcus spp. through regional patterns can unambiguously illustrate the real taxonomic status of parasite in Central Iran. PMID:25645007

  16. Development of polyphase ceramics for the immobilization of high-level Defense nuclear waste

    SciTech Connect

    Morgan, P.E.D.; Harker, A.B.; Clarke, D.R.; Flintoff, J.J.; Shaw, T.M.

    1983-02-25

    The report contains two major sections: Section I - An Improved Polyphase Ceramic for High-Level Defense Nucleation Waste reports the work conducted on titanium-silica based ceramics for immobilizing Savannah River Plant waste. Section II - Formulation and Processing of Alumina Based Ceramic Nuclear Waste Forms describes the work conducted on developing a generic alumina and alumina-silica based ceramic waste form capable of immobilizing any nuclear waste with a high aluminum content. Such wastes include the Savannah River Plant wastes, Hanford neutralized purex wastes, and Hanford N-Reactor acid wastes. The design approach and process technology in the two reports demonstrate how the generic high waste loaded ceramic form can be applied to a broad range of nuclear waste compositions. The individual sections are abstracted and indexed separately.

  17. Polyphasic characterization of Gluconacetobacter diazotrophicus isolates obtained from different sugarcane varieties

    PubMed Central

    Guedes, Helma V.; dos Santos, Samuel T.; Perin, Liamara; Teixeira, Kátia R. dos S.; Reis, Veronica M.; Baldani, José I.

    2008-01-01

    A polyphasic approach was applied to characterize 35 G. diazotrophicus isolates obtained from sugarcane varieties cultivated in Brazil. The isolates were analyzed by phenotypic (use of different carbon sources) and genotypic tests (ARDRA and RISA–RFLP techniques). Variability among the isolates was observed in relation to the carbon source use preference. Glucose and sucrose were used by all isolates in contrast to myo-inositol, galactose and ribose that were not metabolized. The results of the analysis showed the presence of two groups clustered at 68% of similarity. The genetic distance was higher when RISA-RFLP analysis was used. Analysis of 16S rDNA sequences from isolates showed that all of them belonged to the G. diazotrophicus species. Neither effect of the plant part nor sugarcane variety was observed during the cluster analysis. The observed metabolic and genetic variability will be helpful during the strain selection studies for sugarcane inoculation in association with sugarcane breeding programs. PMID:24031296

  18. Polyphasic Analysis of a Middle Ages Coprolite Microbiota, Belgium

    PubMed Central

    Appelt, Sandra; Armougom, Fabrice; Le Bailly, Matthieu; Robert, Catherine; Drancourt, Michel

    2014-01-01

    Paleomicrobiological investigations of a 14th-century coprolite found inside a barrel in Namur, Belgium were done using microscopy, a culture-dependent approach and metagenomics. Results were confirmed by ad hoc PCR – sequencing. Investigations yielded evidence for flora from ancient environment preserved inside the coprolite, indicated by microscopic observation of amoebal cysts, plant fibers, seeds, pollens and mold remains. Seventeen different bacterial species were cultured from the coprolite, mixing organisms known to originate from the environment and organisms known to be gut inhabitants. Metagenomic analyses yielded 107,470 reads, of which known sequences (31.9%) comprised 98.98% bacterial, 0.52% eukaryotic, 0.44% archaeal and 0.06% viral assigned reads. Most abundant bacterial phyla were Proteobacteria, Gemmatimonadetes, Actinobacteria and Bacteroidetes. The 16 S rRNA gene dataset yielded 132,000 trimmed reads and 673 Operational Taxonomic Units. Most abundant bacterial phyla observed in the 16 S rRNA gene dataset belonged to Proteobacteria, Firmicutes, Actinobacteria and Chlamydia. The Namur coprolite yielded typical gut microbiota inhabitants, intestinal parasites Trichuris and Ascaris and systemic pathogens Bartonella and Bordetella. This study adds knowledge to gut microbiota in medieval times. PMID:24586319

  19. A holistic approach to taxonomic evaluation of two closely related endangered freshwater mussel species, the oyster mussel Epioblasma capsaeformis and tan riffleshell Epioblasma florentina walkeri (Bivalvia: Unionidae)

    USGS Publications Warehouse

    Jones, J.W.; Neves, R.J.; Ahlstedt, S.A.; Hallerman, E.M.

    2006-01-01

    Species in the genus Epioblasma have specialized life history requirements and represent the most endangered genus of freshwater mussels (Unionidae) in the world. A genetic characterization of extant populations of the oyster mussel E. capsaeformis and tan riffleshell E. florentina walkeri sensu late was conducted to assess taxonomic validity and to resolve conservation issues for recovery planning. These mussel species exhibit pronounced phenotypic variation, but were difficult to characterize phylogenetically using DNA sequences. Monophyletic lineages, congruent with phenotypic variation among species, were obtained only after extensive analysis of combined mitochondrial (1396 bp of 16S, cytochrome-b, and ND1) and nuclear (515 bp of ITS-1) DNA sequences. In contrast, analysis of variation at 10 hypervariable DNA microsatellite loci showed moderately to highly diverged populations based on FST and R ST values, which ranged from 0.12 to 0.39 and 0.15 to 0.71, respectively. Quantitative variation between species was observed in fish-host specificity, with transformation success of glochidia of E. capsaeformis significantly greater (P<0.05) on greenside darter Etheostoma blennioides, and that of E. f. walkeri significantly greater (P<0.05) on fantail darter Etheostoma flabellare. Lengths of glochidia differed significantly (P<0.001) among species and populations, with mean sizes ranging from 241 to 272 ??m. The texture and colour of the mantle-pad of E. capsaeformis sensu stricto is smooth and bluish-white, whereas that of E. f. walkeri is pustuled and brown, with tan mottling. Based on extensive molecular, morphological and life history data, the population of E. capsaeformis from the Duck River, Tennessee, USA is proposed as a separate species, and the population of E. f. walkeri from Indian Creek, upper Clinch River, Virginia, USA is proposed as a distinct subspecies.

  20. Instrumentality and Integration: A Taxonomic Approach to Analyzing Motivational Factors in Syllabus and Materials Design for English for Nursing Purposes in Japan.

    ERIC Educational Resources Information Center

    Bay, Dale

    1994-01-01

    A study investigated the content of commonly-used English-as-a-Second-Language textbooks used in Japanese nursing education and compared this information with the expressed language needs of nursing students. Seven English textbooks analyzed, all aimed at nursing students, presented instrumental language based on a situational approach to English…

  1. A 640-MHz 32-megachannel real-time polyphase-FFT spectrum analyzer

    NASA Technical Reports Server (NTRS)

    Zimmerman, G. A.; Garyantes, M. F.; Grimm, M. J.; Charny, B.

    1991-01-01

    A polyphase fast Fourier transform (FFT) spectrum analyzer being designed for NASA's Search for Extraterrestrial Intelligence (SETI) Sky Survey at the Jet Propulsion Laboratory is described. By replacing the time domain multiplicative window preprocessing with polyphase filter processing, much of the processing loss of windowed FFTs can be eliminated. Polyphase coefficient memory costs are minimized by effective use of run length compression. Finite word length effects are analyzed, producing a balanced system with 8 bit inputs, 16 bit fixed point polyphase arithmetic, and 24 bit fixed point FFT arithmetic. Fixed point renormalization midway through the computation is seen to be naturally accommodated by the matrix FFT algorithm proposed. Simulation results validate the finite word length arithmetic analysis and the renormalization technique.

  2. Properties of even length Barker codes and specific polyphase codes with Barker type autocorrelation functions

    NASA Astrophysics Data System (ADS)

    Gabbay, S.

    1982-07-01

    Properties of even-length Barker codes, if they exist, are derived. The analysis leads to the analysis of polyphase codes. Similar properties are derived for specific types of polyphase codes, with Barker type autocorrelation functions. The analysis is done in the time and frequency domains (including linear algebra and Z transform treatments), and suggests a procedure to search for codes with Barker type autocorrelation functions. The search problem is reduced by using the properties of such codes.

  3. Polyphasic Taxonomy of the GenusShewanellaand Description ofShewanellaoneidensis sp. nov.

    SciTech Connect

    Venkateswaran, K.

    1999-01-01

    The genus Shewanella has been studied since 1931 with regard to a variety of topics of relevance to both applied and environmental microbiology. Recent years have seen the introduction of a large number of new Shewanella-like isolates, necessitating a coordinated review of the genus. In this work, the phylogenetic relationships among known shewanellae were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them into a consensus classification. Based on information generated from this study and obtained from the literature, a scheme for the identification of Shewanella species has been compiled. Key phenotypic characteristics were sulfur reduction and halophilicity. Fatty acid and quinone profiling were used to impart an additional layer of information. Molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in some cases. As a result, DNA--DNA hybridization and sequence analyses of a more rapidly evolving molecule (gyrB gene) were performed. Species-specific PCR probes were designed for the gyrB gene and used for the rapid screening of closely related strains. With this polyphasic approach, in addition to the ten described Shewanella species, two new species, Shewanella oneidensis and 'Shewanella pealeana', were recognized; Shewanella oneidensis sp. nov. is described here for the first time.

  4. An OFDM System Using Polyphase Filter and DFT Architecture for Very High Data Rate Applications

    NASA Technical Reports Server (NTRS)

    Kifle, Muli; Andro, Monty; Vanderaar, Mark J.

    2001-01-01

    This paper presents a conceptual architectural design of a four-channel Orthogonal Frequency Division Multiplexing (OFDM) system with an aggregate information throughput of 622 megabits per second (Mbps). Primary emphasis is placed on the generation and detection of the composite waveform using polyphase filter and Discrete Fourier Transform (DFT) approaches to digitally stack and bandlimit the individual carriers. The four-channel approach enables the implementation of a system that can be both power and bandwidth efficient, yet enough parallelism exists to meet higher data rate goals. It also enables a DC power efficient transmitter that is suitable for on-board satellite systems, and a moderately complex receiver that is suitable for low-cost ground terminals. The major advantage of the system as compared to a single channel system is lower complexity and DC power consumption. This is because the highest sample rate is half that of the single channel system and synchronization can occur at most, depending on the synchronization technique, a quarter of the rate of a single channel system. The major disadvantage is the increased peak-to-average power ratio over the single channel system. Simulation results in a form of bit-error-rate (BER) curves are presented in this paper.

  5. Polyphasic study of Chryseobacterium strains isolated from diseased aquatic animals.

    PubMed

    Bernardet, J F; Vancanneyt, M; Matte-Tailliez, O; Grisez, L; Tailliez, P; Bizet, C; Nowakowski, M; Kerouault, B; Swings, J

    2005-09-01

    Members of most Chryseobacterium species occur in aquatic environments or food products, while strains of some other species are pathogenic to humans and animals. A collection of 52 Chryseobacterium sp. strains isolated from diseased fish, one frog isolate and 22 reference strains were included in a polyphasic taxonomy study. Fourteen clusters of strains were delineated following the comparison of whole-cell protein profiles. Most of these clusters were confirmed when the phenotypic and RAPD profiles and the 16S rRNA gene sequences were compared. Fatty acid composition helped differentiate the Chryseobacterium strains from members of related genera. None of the fish isolates could be allocated to the two species previously reported from fish but two isolates belonged to C. joostei, while the frog isolate was identified as Elizabethkingia meningoseptica, a human pathogen previously included in the genus Chryseobacterium. Three clusters grouping from 3 to 13 isolates will probably constitute the core of new Chryseobacterium species but all other isolates occupied separate or uncertain positions in the genus. This study further demonstrated the overall high similarity displayed by most Chryseobacterium strains whatever the technique used and the resulting difficulty in delineating new species in the genus. Members of this bacterial group should be considered potential emergent pathogens in various fish and frog species, farming conditions and geographical areas. PMID:16156122

  6. UHT granulite-facies metamorphism in Rogaland, S Norway, is polyphase in nature

    NASA Astrophysics Data System (ADS)

    Laurent, Antonin; Duchene, Stéphanie; Bingen, Bernard; Seydoux-Guillaume, Anne-Magali; Bosse, Valérie

    2016-04-01

    Propensity of metamorphic assemblages to remain metastable after melt extraction complicates singularly the petrologist's task to discriminate between a single granulite-facies P-T path and a polyphase one. Using an integrated petrological and in-situ geochronological approach in key rock-samples, we reconstruct the pressure-temperature-time path of Sveconorwegian metamorphism across a 30 km-wide metamorphic gradient ranging from upper amphibolite facies to ultra-high temperature (UHT) granulite-facies in Rogaland, S. Norway. Thermodynamic modelling of phase equilibria in the Na2O-CaO-K2O-FeO-MgO-Al2O3-SiO2-H2O-Ti2O-O2 chemical system (PerpleX code) are carried out with an emphasis on moderately oxidized, spinel-bearing assemblages resulting from either garnet or sapphirine breakdown. Geochronological U-(Th)-Pb data acquired on both monazite (LA-ICP-MS) and zircon (SIMS) are complemented by minor- and trace-elements signatures of both minerals, to monitor REE distribution through time and to evaluate garnet apparition or demise. Coupling field, petrological and geochronological data lead to a polyphase metamorphic history, lasting about 100 My. The onset of regional granulite facies metamorphism at 1035 Ma is associated with the emplacement of large volumes of granitic magmas in the amphibolite to granulite facies transition zone. In the deeper part of the crustal section, localized sapphirine-bearing restitic lithologies testify to UHT temperatures (900‑920 °C). These conditions were reached at ca. 1010 Ma following a tight clockwise P-T path associated with minor exhumation (7 to 5.5 kbar) and subsequent cooling to 700 °C. A distinct thermal episode, initiated at ca. 950 Ma, reached UHT granulite-facies conditions with the intrusion of massif-type anorthosite plutons at ca. 930 Ma producing a 5-km wide aureole. The aureole is delimited by the presence of osumilite in high Fe-Al rocks yielding quantitative estimates of 900-950 °C at a maximum pressure of 5

  7. PESI - a taxonomic backbone for Europe

    PubMed Central

    Kouwenberg, Juliana; Boumans, Louis; Hussey, Charles; Hyam, Roger; Nicolson, Nicola; Kirk, Paul; Paton, Alan; Michel, Ellinor; Guiry, Michael D.; Boegh, Phillip S.; Pedersen, Henrik Ærenlund; Enghoff, Henrik; von Raab-Straube, Eckhard; Güntsch, Anton; Geoffroy, Marc; Müller, Andreas; Kohlbecker, Andreas; Berendsohn, Walter; Appeltans, Ward; Arvanitidis, Christos; Vanhoorne, Bart; Declerck, Joram; Vandepitte, Leen; Hernandez, Francisco; Nash, Róisín; Costello, Mark John; Ouvrard, David; Bezard-Falgas, Pascale; Bourgoin, Thierry; Wetzel, Florian Tobias; Glöckler, Falko; Korb, Günther; Ring, Caroline; Hagedorn, Gregor; Häuser, Christoph; Aktaç, Nihat; Asan, Ahmet; Ardelean, Adorian; Borges, Paulo Alexandre Vieira; Dhora, Dhimiter; Khachatryan, Hasmik; Malicky, Michael; Ibrahimov, Shaig; Tuzikov, Alexander; De Wever, Aaike; Moncheva, Snejana; Spassov, Nikolai; Chobot, Karel; Popov, Alexi; Boršić, Igor; Sfenthourakis, Spyros; Kõljalg, Urmas; Uotila, Pertti; Olivier, Gargominy; Dauvin, Jean-Claude; Tarkhnishvili, David; Chaladze, Giorgi; Tuerkay, Michael; Legakis, Anastasios; Peregovits, László; Gudmundsson, Gudmundur; Ólafsson, Erling; Lysaght, Liam; Galil, Bella Sarah; Raimondo, Francesco M.; Domina, Gianniantonio; Stoch, Fabio; Minelli, Alessandro; Spungis, Voldermars; Budrys, Eduardas; Olenin, Sergej; Turpel, Armand; Walisch, Tania; Krpach, Vladimir; Gambin, Marie Therese; Ungureanu, Laurentia; Karaman, Gordan; Kleukers, Roy M.J.C.; Stur, Elisabeth; Aagaard, Kaare; Valland, Nils; Moen, Toril Loennechen; Bogdanowicz, Wieslaw; Tykarski, Piotr; Węsławski, Jan Marcin; Kędra, Monika; M. de Frias Martins, Antonio; Abreu, António Domingos; Silva, Ricardo; Medvedev, Sergei; Ryss, Alexander; Šimić, Smiljka; Marhold, Karol; Stloukal, Eduard; Tome, Davorin; Ramos, Marian A.; Valdés, Benito; Pina, Francisco; Kullander, Sven; Telenius, Anders; Gonseth, Yves; Tschudin, Pascal; Sergeyeva, Oleksandra; Vladymyrov, Volodymyr; Rizun, Volodymyr Bohdanovych; Raper, Chris; Lear, Dan; Stoev, Pavel; Penev, Lyubomir; Rubio, Ana Casino; Backeljau, Thierry; Saarenmaa, Hannu; Ulenberg, Sandrine

    2015-01-01

    Abstract Background Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. New information This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs. PMID:26491393

  8. TIPP: taxonomic identification and phylogenetic profiling

    PubMed Central

    Nguyen, Nam-phuong; Mirarab, Siavash; Liu, Bo; Pop, Mihai; Warnow, Tandy

    2014-01-01

    Motivation: Abundance profiling (also called ‘phylogenetic profiling’) is a crucial step in understanding the diversity of a metagenomic sample, and one of the basic techniques used for this is taxonomic identification of the metagenomic reads. Results: We present taxon identification and phylogenetic profiling (TIPP), a new marker-based taxon identification and abundance profiling method. TIPP combines SAT\\'e-enabled phylogenetic placement a phylogenetic placement method, with statistical techniques to control the classification precision and recall, and results in improved abundance profiles. TIPP is highly accurate even in the presence of high indel errors and novel genomes, and matches or improves on previous approaches, including NBC, mOTU, PhymmBL, MetaPhyler and MetaPhlAn. Availability and implementation: Software and supplementary materials are available at http://www.cs.utexas.edu/users/phylo/software/sepp/tipp-submission/. Contact: warnow@illinois.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25359891

  9. Lifted linear phase filter banks and the polyphase-with-advance representation

    SciTech Connect

    Brislawn, C. M.; Wohlberg, B. E.

    2004-01-01

    A matrix theory is developed for the noncausal polyphase-with-advance representation that underlies the theory of lifted perfect reconstruction filter banks and wavelet transforms as developed by Sweldens and Daubechies. This theory provides the fundamental lifting methodology employed in the ISO/IEC JPEG-2000 still image coding standard, which the authors helped to develop. Lifting structures for polyphase-with-advance filter banks are depicted in Figure 1. In the analysis bank of Figure 1(a), the first lifting step updates x{sub 0} with a filtered version of x{sub 1} and the second step updates x{sub 1} with a filtered version of x{sub 0}; gain factors 1/K and K normalize the lowpass- and highpass-filtered output subbands. Each of these steps is inverted by the corresponding operations in the synthesis bank shown in Figure 1(b). Lifting steps correspond to upper- or lower-triangular matrices, S{sub i}(z), in a cascade-form decomposition of the polyphase analysis matrix, H{sub a}(z). Lifting structures can also be implemented reversibly (i.e., losslessly in fixed-precision arithmetic) by rounding the lifting updates to integer values. Our treatment of the polyphase-with-advance representation develops an extensive matrix algebra framework that goes far beyond the results of. Specifically, we focus on analyzing and implementing linear phase two-channel filter banks via linear phase lifting cascade schemes. Whole-sample symmetric (WS) and half-sample symmetric (HS) linear phase filter banks are characterized completely in terms of the polyphase-with-advance representation. The theory benefits significantly from a number of new group-theoretic structures arising in the polyphase-with-advance matrix algebra from the lifting factorization of linear phase filter banks.

  10. Chronology of polyphase extension in the Windermere Hills, northeast Nevada

    USGS Publications Warehouse

    Mueller, K.J.; Cerveny, P.K.; Perkins, M.E.; Snee, L.W.

    1999-01-01

    Fission-track and 40Ar/39Ar dating and chemical correlation of volcanic strata exposed in the Windermere Hills and northern Pequop Mountains, northeast Nevada, indicate a protracted, polyphase history of Tertiary (late Eocene-late Miocene) extension along the northern margin of a major Cordilleran metamorphic core complex. Early extension is recorded by a west-tilted half graben filled with early Oligocene (34.79 ?? 0.18-39.18 ?? 0.12 Ma) sedimentary rocks in the eastern Windermere Hills above the low-angle Black Mountain detachment fault. The early Oligocene half graben conformably overlies a widespread suite of late Eocene (39.18 ?? 0.12-40.38 ?? 0.06 Ma) calc-alkaline volcanic rocks, reflecting a temporal link between early extension at a high structural level and the end of the ignimbrite flare-up. These strata are cut by east-west-striking normal faults, which are exposed along, and parallel to, the northern margin of the metamorphic complex. Available age data (e.g., between 14.93 ?? 0.08 and 34.79 ?? 0.18 Ma) permit the interpretation that the east-west-striking faults formed at the same time as, or after, large-magnitude unroofing of high-grade rocks. We interpret the east-west-striking faults to accommodate differential uplift of greenschist-grade metamorphic rocks in the upper crust, above a lateral ramp in a west-northwest-directed mylonitic shear zone. Subsequent extension in the Windermere Hills is defined by deep, rapidly filled half grabens of middle Miocene (<7.42 ?? 2.0 to 14.93 ?? 0.08 Ma) age that unconformably overlie older faults and synextensional deposits. These are the youngest half grabens in the region and are inferred to be initiated by extensional stresses imparted to the base of the lithosphere by a laterally spreading mantle plume (e.g., the Yellowstone hotspot) located in southeastern Oregon at this time.

  11. Dynamics and polyphasic characterization of odor-producing cyanobacterium Tychonema bourrellyi from Lake Erhai, China.

    PubMed

    Zhang, Hang; Song, Gaofei; Shao, Jihai; Xiang, Xianfen; Li, Qi; Chen, Youxin; Yang, Ping; Yu, Gongliang

    2016-03-01

    The previous studies indicated that Tychonema-like strains from Lake Erhai could release geosmin so that the species was listed as the potential harmful cyanobacteria influencing the drinking water safety around Lake Erhai. But, the dynamics and biological information of this species were too limited. In this study, the polyphasic approach was used to reveal its biological characterization and the dynamics in Lake Erhai. The characters of trichomes, including filaments with solitary or bundle state, reddish-brown or blue-green color, planktonic habitat, and presence of keritomized content, were examined by the microscopic method. The 16S rDNA sequences of these strains were used for phylogenetic analysis and molecular identification. The strains were morphologically classified as Tychonema bourrellyi, and geosmin and β-ionone were identified as the major volatile substances using gas chromatography-mass spectrometry (GC-MS) analysis. No strains of T. bourrellyi were found to produce microcystin by the HPLC and mcy gene approaches. Cell numbers at 12 sampling sites in Lake Erhai were shown as an average of 3 × 10(4) cells L(-1) in 2009 and 2010. The obvious peaks occurred in July and August each year. This was the first report on occurrence of T. bourrellyi from outside of Europe, and T. bourrellyi was also a newly recorded species in China. Such a result demonstrated that T. bourrellyi could distribute extending from cold waters in North Europe to the warm waters in subtropical regions. It was interesting to observe the coincidence of the occurrence of T. bourrellyi with slightly eutrophicated waters since Lake Erhai had been regarded as an early phase of eutrophicated lake. PMID:26564199

  12. Taxonomic status of Myotis occultus

    USGS Publications Warehouse

    Valdez, E.W.; Choate, Jerry R.; Bogan, M.A.; Yates, T.L.

    1999-01-01

    The taxonomic status of the Arizona myotis (Myotis occultus) is uncertain. Although the taxon was described as a distinct species and currently is regarded as such by some authors, others have noted what they interpreted as intergradation with the little brown bat (M. lucifugus carissima) near the Colorado-New Mexico state line. In this study, we used protein electrophoresis to compare bats of these nominal taxa. We examined 20 loci from 142 specimens referable to M. occultus and M. lucifugus from New Mexico, Colorado, and Wyoming. Nine of the 20 loci were polymorphic. Results show that there were high similarities among samples, no fixed alleles, and minor divergence from Hardy-Weinberg equilibrium. Our results suggest that the two nominal taxa represent only one species and that M. occultus should be regarded as a subspecies of M. lucifugus.

  13. Polyphasic taxonomy of Aspergillus section Candidi based on molecular, morphological and physiological data

    PubMed Central

    Varga, J.; Frisvad, J.C.; Samson, R.A.

    2007-01-01

    Aspergillus section Candidi historically included a single white-spored species, A. candidus. Later studies clarified that other species may also belong to this section. In this study, we examined isolates of species tentatively assigned to section Candidi using a polyphasic approach. The characters examined include sequence analysis of partial β-tubulin, calmodulin and ITS sequences of the isolates, morphological and physiological tests, and examination of the extrolite profiles. Our data indicate that the revised section Candidi includes 4 species: A. candidus, A. campestris, A. taichungensis and A. tritici. This is strongly supported by all the morphological characteristics that are characteristic of section Candidi: slow growing colonies with globose conidial heads having white to yellowish conidia, conidiophores smooth, small conidiophores common, metulae present and covering the entire vesicle, some large Aspergillus heads with large metulae, presence of diminutive heads in all species, conidia smooth or nearly so with a subglobose to ovoid shape, and the presence of sclerotia in three species (A. candidus, A. taichungensis and A. tritici). Aspergillus tritici has been suggested to be the synonym of A. candidus previously, however, sequence data indicate that this is a valid species and includes isolates came from soil, wheat grain, flour and drums from India, Ghana, Sweden, The Netherlands and Hungary, making it a relatively widespread species. All species produce terphenyllins and candidusins and three species (A. candidus, A. campestris and A. tritici) produce chlorflavonins. Xanthoascins have only been found in A. candidus. Each of the species in section Candidi produce several other species specific extrolites, and none of these have been found in any other Aspergillus species. A. candidus has often been listed as a human pathogenic species, but this is unlikely as this species cannot grow at 37 °C. The pathogenic species may be A. tritici or white

  14. Taxonomic, phylogenetic, and trait Beta diversity in South American hummingbirds.

    PubMed

    Weinstein, Ben G; Tinoco, Boris; Parra, Juan Luis; Brown, Leone M; McGuire, Jimmy A; Stiles, F Gary; Graham, Catherine H

    2014-08-01

    Comparison of the taxonomic, phylogenetic, and trait dimensions of beta diversity may uncover the mechanisms that generate and maintain biodiversity, such as geographic isolation, environmental filtering, and convergent adaptation. We developed an approach to predict the relationship between environmental and geographic distance and the dimensions of beta diversity. We tested these predictions using hummingbird assemblages in the northern Andes. We expected taxonomic beta diversity to result from recent geographic barriers limiting dispersal, and we found that cost distance, which includes barriers, was a better predictor than Euclidean distance. We expected phylogenetic beta diversity to result from historical connectivity and found that differences in elevation were the best predictors of phylogenetic beta diversity. We expected high trait beta diversity to result from local adaptation to differing environments and found that differences in elevation were correlated with trait beta diversity. When combining beta diversity dimensions, we observe that high beta diversity in all dimensions results from adaption to different environments between isolated assemblages. Comparisons with high taxonomic, low phylogenetic, and low trait beta diversity occurred among lowland assemblages separated by the Andes, suggesting that geographic barriers have recently isolated lineages in similar environments. We provide insight into mechanisms governing hummingbird biodiversity patterns and provide a framework that is broadly applicable to other taxonomic groups. PMID:25058281

  15. Evolutionary dynamics of taxonomic structure

    PubMed Central

    Foote, Michael

    2012-01-01

    The distribution of species among genera and higher taxa has largely untapped potential to reveal among-clade variation in rates of origination and extinction. The probability distribution of the number of species within a genus is modelled with a stochastic, time-homogeneous birth–death model having two parameters: the rate of species extinction, μ, and the rate of genus origination, γ, each scaled as a multiple of the rate of within-genus speciation, λ. The distribution is more sensitive to γ than to μ, although μ affects the size of the largest genera. The species : genus ratio depends strongly on both γ and μ, and so is not a good diagnostic of evolutionary dynamics. The proportion of monotypic genera, however, depends mainly on γ, and so may provide an index of the genus origination rate. Application to living marine molluscs of New Zealand shows that bivalves have a higher relative rate of genus origination than gastropods. This is supported by the analysis of palaeontological data. This concordance suggests that analysis of living taxonomic distributions may allow inference of macroevolutionary dynamics even without a fossil record. PMID:21865239

  16. Hitting the right target: taxonomic challenges for, and of, plant invasions

    PubMed Central

    Pyšek, Petr; Hulme, Philip E.; Meyerson, Laura A.; Smith, Gideon F.; Boatwright, James S.; Crouch, Neil R.; Figueiredo, Estrela; Foxcroft, Llewellyn C.; Jarošík, Vojtěch; Richardson, David M.; Suda, Jan; Wilson, John R. U.

    2013-01-01

    This paper explores how a lack of taxonomic expertise, and by implication a dearth of taxonomic products such as identification tools, has hindered progress in understanding and managing biological invasions. It also explores how the taxonomic endeavour could benefit from studies of invasive species. We review the literature on the current situation in taxonomy with a focus on the challenges of identifying alien plant species and explore how this has affected the study of biological invasions. Biosecurity strategies, legislation dealing with invasive species, quarantine, weed surveillance and monitoring all depend on accurate and rapid identification of non-native taxa. However, such identification can be challenging because the taxonomic skill base in most countries is diffuse and lacks critical mass. Taxonomic resources are essential for the effective management of invasive plants and incorrect identifications can impede ecological studies. On the other hand, biological invasions have provided important tests of basic theories about species concepts. Better integration of classical alpha taxonomy and modern genetic taxonomic approaches will improve the accuracy of species identification and further refine taxonomic classification at the level of populations and genotypes in the field and laboratory. Modern taxonomy therefore needs to integrate both classical and new concepts and approaches. In particular, differing points of view between the proponents of morphological and molecular approaches should be negotiated because a narrow taxonomic perspective is harmful; the rigour of taxonomic decision-making clearly increases if insights from a variety of different complementary disciplines are combined and confronted. Taxonomy plays a critical role in the study of plant invasions and in turn benefits from the insights gained from these studies.

  17. DNA from soil mirrors plant taxonomic and growth form diversity.

    PubMed

    Yoccoz, N G; Bråthen, K A; Gielly, L; Haile, J; Edwards, M E; Goslar, T; Von Stedingk, H; Brysting, A K; Coissac, E; Pompanon, F; Sønstebø, J H; Miquel, C; Valentini, A; De Bello, F; Chave, J; Thuiller, W; Wincker, P; Cruaud, C; Gavory, F; Rasmussen, M; Gilbert, M T P; Orlando, L; Brochmann, C; Willerslev, E; Taberlet, P

    2012-08-01

    Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually <100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versatile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with plant taxonomic and growth form diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that the number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site were efficiently recovered. The results open unprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches. PMID:22507540

  18. Physically consistent viscosity of polyphase rocks: a new method and its validation

    NASA Astrophysics Data System (ADS)

    Huet, B.; Yamato, P.; Grasemann, B.

    2012-04-01

    Metamorphic reactions constitute one of the major processes inducing strain localisation and influencing the strength of the lithosphere. However, this process has seldom been explicitly taken into account in large-scale thermomechanical models so far. Such a development requires the calculation of the strength of any rock knowing its mineralogical composition and the strength of its components. Most of the existing polyphase rocks strength models are empirical. Those that are physically consistent provide strength bounds and/or lead to long and complex calculations, which is not suitable for large scale modelling. Here, we present a new method to calculate the bulk viscosity of a polyphase rock knowing the fraction and the creep parameters of each phase constituting the rock. This analytical method uses a minimization procedure of the power dissipated in the polyphase rock with the Lagrange multiplier technique. This method is simple and quickly leads to values of the bulk viscosity as well as partitioning of stress and strain rate between phases. It allows us to revaluate the classical bounds and to compute a close approximate of bulk viscosity and bulk creep parameters, that are physically consistent. Then, this method is tested and validated against experimental data and numerical models under simple shear condition. Finally, we present an application of this method to the evolution of strength in a subducting slab.

  19. Taxonomical and functional microbial community selection in soybean rhizosphere

    PubMed Central

    Mendes, Lucas W; Kuramae, Eiko E; Navarrete, Acácio A; van Veen, Johannes A; Tsai, Siu M

    2014-01-01

    This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors. PMID:24553468

  20. Taxonomical and functional microbial community selection in soybean rhizosphere.

    PubMed

    Mendes, Lucas W; Kuramae, Eiko E; Navarrete, Acácio A; van Veen, Johannes A; Tsai, Siu M

    2014-08-01

    This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors. PMID:24553468

  1. Regional polyphase deformation of the Eastern Sierras Pampeanas (Argentina Andean foreland): strengths and weaknesses of paleostress inversion

    NASA Astrophysics Data System (ADS)

    Traforti, Anna; Zampieri, Dario; Massironi, Matteo; Viola, Giulio; Alvarado, Patricia; Di Toro, Giulio

    2016-04-01

    oriented WSW-ENE). Although remarkable differences in reactivation mechanisms have been observed for the various studied lithological domains (schist, gneiss and granitic rocks), the brittle regional polyphase deformation of the Eastern Sierras Pampeanas appears to be dominated by two extensional episodes (σ3 oriented NE/ENE and WNW, respectively), which can be associated with Middle-Late Permian to Early Cretaceous tectonism, followed by a compressional paleostress (σ1 oriented ENE), which is compatible with the present day Andean convergence. Paleostress inversion techniques, despite all uncertainties involved, represent a robust approach to disentangle complex polyphase deformation histories both in term of reactivation mechanisms and strain partitioning. References: Bense, F. A., Wemmer, K., Löbens, S., & Siegesmund, S. (2013). Fault gouge analyses: K-Ar illite dating, clay mineralogy and tectonic significance-a study from the Sierras Pampeanas, Argentina. International Journal of Earth Sciences, 103, 189-218. Martino, R. D. (2003). Las fajas de deformación dúctil de las Sierras Pampeanas de Córdoba : Una reseña general. Revista de La Asociación Geológica Argentina, 58(4), 549-571. Ramos, V. A., Cristallini, E. O., & Perez, D. J. (2002). The Pampean flat-slab of the Central Andes. Journal of South American Earth Sciences, 15, 59-78.

  2. Contrasting spatial patterns of taxonomic and functional richness offer insights into potential loss of ecosystem services

    PubMed Central

    Cumming, Graeme S.; Child, Matthew F.

    2009-01-01

    Functional and trophic perspectives on patterns of species occurrences have the potential to offer new and interesting insights into a range of spatially explicit problems in ecology and conservation. We present the function–area relationship (FAR) and explore linkages between functional and taxonomic species richness for South African birds. We first used beak morphology to classify a subset of 151 South African bird species into 18 functional groups and calculated both the species–area relationship and the FAR at quarter-degree resolution for South Africa. The relationship between functional and taxonomic richness by cell was quadratic rather than linear, with considerable scatter around the curve. We next looked at the spatial relationships between taxonomic diversity and response diversity (i.e. diversity within functional groups) using an a priori categorization of nearly all South African birds into nine functional groups. The spatial distribution of response richness also showed considerable variation in relation to taxonomic richness. Our results demonstrate a novel approach to linking taxonomic, functional and trophic patterns in space and suggest a way in which conservation planning, which has traditionally had a taxonomic focus, could formally incorporate a more functional and food-web-based approach. PMID:19451119

  3. Adaptive polyphase subband decomposition structures for image compression.

    PubMed

    Gerek, O N; Cetin, A E

    2000-01-01

    Subband decomposition techniques have been extensively used for data coding and analysis. In most filter banks, the goal is to obtain subsampled signals corresponding to different spectral regions of the original data. However, this approach leads to various artifacts in images having spatially varying characteristics, such as images containing text, subtitles, or sharp edges. In this paper, adaptive filter banks with perfect reconstruction property are presented for such images. The filters of the decomposition structure which can be either linear or nonlinear vary according to the nature of the signal. This leads to improved image compression ratios. Simulation examples are presented. PMID:18262904

  4. Current Taxonomical Situation of Streptococcus suis.

    PubMed

    Okura, Masatoshi; Osaki, Makoto; Nomoto, Ryohei; Arai, Sakura; Osawa, Ro; Sekizaki, Tsutomu; Takamatsu, Daisuke

    2016-01-01

    Streptococcus suis, a major porcine pathogen and an important zoonotic agent, is considered to be composed of phenotypically and genetically diverse strains. However, recent studies reported several "S. suis-like strains" that were identified as S. suis by commonly used methods for the identification of this bacterium, but were regarded as distinct species from S. suis according to the standards of several taxonomic analyses. Furthermore, it has been suggested that some S. suis-like strains can be assigned to several novel species. In this review, we discuss the current taxonomical situation of S. suis with a focus on (1) the classification history of the taxon of S. suis; (2) S. suis-like strains revealed by taxonomic analyses; (3) methods for detecting and identifying this species, including a novel method that can distinguish S. suis isolates from S. suis-like strains; and (4) current topics on the reclassification of S. suis-like strains. PMID:27348006

  5. Integrating macroecological metrics and community taxonomic structure.

    PubMed

    Harte, John; Rominger, Andrew; Zhang, Wenyu

    2015-10-01

    We extend macroecological theory based on the maximum entropy principle from species level to higher taxonomic categories, thereby predicting distributions of species richness across genera or families and the dependence of abundance and metabolic rate distributions on taxonomic tree structure. Predictions agree with qualitative trends reported in studies on hyper-dominance in tropical tree species, mammalian body size distributions and patterns of rarity in worldwide plant communities. Predicted distributions of species richness over genera or families for birds, arthropods, plants and microorganisms are in excellent agreement with data. Data from an intertidal invertebrate community, but not from a dispersal-limited forest, are in excellent agreement with a predicted new relationship between body size and abundance. Successful predictions of the original species level theory are unmodified in the extended theory. By integrating macroecology and taxonomic tree structure, maximum entropy may point the way towards a unified framework for understanding phylogenetic community structure. PMID:26248954

  6. Polyphasic characterization of 10 selected ecologically relevant filamentous cyanobacterial strains from the South Shetland Islands, Maritime Antarctica.

    PubMed

    Jancusova, Miroslava; Kovacik, Lubomir; Pereira, Antonio Batista; Dusinsky, Roman; Wilmotte, Annick

    2016-07-01

    The evolutionary relationships of 10 Antarctic cyanobacterial strains of the order Oscillatoriales isolated from King George and Deception Islands, South Shetland Islands were studied by a polyphasic approach (morphology, 16S rRNA and internal transcribed spacer sequences). The studied taxa are characteristic of coastal Antarctic biotopes, where they form distinct populations and ecologically delimited communities. They were isolated from terrestrial habitats: microbial mats in seepages; crusts on soil, rocks, bones and mosses; mud, sometimes close to bird colonies; and from guano. Based on major phenotypic features, the strains were divided into four distinct morphotypes: Leptolyngbya borchgrevinkii (A), Leptolyngbya frigida (B), Microcoleus sp. (C) and Wilmottia murrayi (D). This morphological identification was in agreement with the phylogenetic relationships. For the first time, the 16S rRNA gene sequence of a strain corresponding to the L. borchgrevinkii morphotype was determined. Morphotype B is most related to sequences assigned to L. frigida isolated from microbial mats of coastal lakes in East Antarctica. Morphotype C belongs to a cluster including strains with morphotypes corresponding to Microcoleus attenuatus, Microcoleus favosus and Microcoleus sp., which are from Antarctica and other continents. Morphotype D is grouped with sequences assigned to W. murrayi mostly isolated from Antarctica. PMID:27162184

  7. Avibase – a database system for managing and organizing taxonomic concepts

    PubMed Central

    Lepage, Denis; Vaidya, Gaurav; Guralnick, Robert

    2014-01-01

    Abstract Scientific names of biological entities offer an imperfect resolution of the concepts that they are intended to represent. Often they are labels applied to entities ranging from entire populations to individual specimens representing those populations, even though such names only unambiguously identify the type specimen to which they were originally attached. Thus the real-life referents of names are constantly changing as biological circumscriptions are redefined and thereby alter the sets of individuals bearing those names. This problem is compounded by other characteristics of names that make them ambiguous identifiers of biological concepts, including emendations, homonymy and synonymy. Taxonomic concepts have been proposed as a way to address issues related to scientific names, but they have yet to receive broad recognition or implementation. Some efforts have been made towards building systems that address these issues by cataloguing and organizing taxonomic concepts, but most are still in conceptual or proof-of-concept stage. We present the on-line database Avibase as one possible approach to organizing taxonomic concepts. Avibase has been successfully used to describe and organize 844,000 species-level and 705,000 subspecies-level taxonomic concepts across every major bird taxonomic checklist of the last 125 years. The use of taxonomic concepts in place of scientific names, coupled with efficient resolution services, is a major step toward addressing some of the main deficiencies in the current practices of scientific name dissemination and use. PMID:25061375

  8. Use of polyphase continuous excitation based on the Frank sequence in EPR.

    PubMed Central

    Tseitlin, Mark; Quine, Richard W.; Eaton, Sandra S.; Eaton, Gareth R.

    2011-01-01

    Polyphase continuous excitation based on the Frank sequence is suggested as an alternative to single pulse excitation in EPR. The method allows reduction of the source power, while preserving the excitation bandwidth of a single pulse. For practical EPR implementation the use of a cross-loop resonator is essential to provide isolation between the spin system and the resonator responses to the excitation. Provided that a line broadening of about 5% is acceptable, the cumulative turning angle of the magnetization vector generated by the excitation sequence can be quite large and can produce signal amplitudes that are comparable to that achieved with a higher power 90° pulse. PMID:21737326

  9. Use of polyphase continuous excitation based on the Frank sequence in EPR.

    PubMed

    Tseitlin, Mark; Quine, Richard W; Eaton, Sandra S; Eaton, Gareth R

    2011-08-01

    Polyphase continuous excitation based on the Frank sequence is suggested as an alternative to single pulse excitation in EPR. The method allows reduction of the source power, while preserving the excitation bandwidth of a single pulse. For practical EPR implementation the use of a cross-loop resonator is essential to provide isolation between the spin system and the resonator responses to the excitation. Provided that a line broadening of about 5% is acceptable, the cumulative turning angle of the magnetization vector generated by the excitation sequence can be quite large and can produce signal amplitudes that are comparable to that achieved with a higher power 90° pulse. PMID:21737326

  10. Apparatus for controlling the firing of rectifiers in polyphase rectifying circuits

    DOEpatents

    Yarema, R.J.

    1979-09-18

    A polyphase rectifier is controlled with precision by a circuit that filters and shifts a reference signal associated with each phase and that starts a ramp signal at a zero crossing of the shifted reference signal. The difference between the ramp signal and an external trigger signal is used to generate a pulse that switches power rectifiers into conduction. The circuit reduces effects of variations that introduce subharmonics into a rectified signal and it can be used for constant or time-varying external trigger signals.

  11. Taxonomic changes in Solanum section Petota

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 1990, the latest comprehensive taxonomic monograph of Solanum section Petota Dumort. recognized 236 species partitioned into 21 series. Of these, 227 were tuber-bearing and nine non-tuber-bearing. NSF-sponsored research has drastically altered knowledge of their species boundaries and interrelati...

  12. Taxonomic revision of Ustilago, Sporisorium and Macalpinomyces.

    PubMed

    McTaggart, A R; Shivas, R G; Geering, A D W; Vánky, K; Scharaschkin, T

    2012-12-01

    Morphological characters within the Ustilago-Sporisorium-Macalpinomyces complex are defined explicitly. The genera Sporisorium and Anthracocystis are emended to reflect morphological synapomorphies. Three new genera, Langdonia, Stollia and Triodiomyces are described based on soral synapomorphies and host classification. The new classification of the Ustilago-Sporisorium-Macalpinomyces complex incorporates 142 new taxonomic combinations. PMID:23606769

  13. Dating the polyphase evolution of the Western Alps

    NASA Astrophysics Data System (ADS)

    Villa, Igor M.

    2016-04-01

    Ma ages are best explained as complete Ar retention. The Ar record of an unrecrystallized Monte Rosa white mica was partly preserved during eclogitization at T > 600 °C, while the neighboring mylonitized phengite was reset completely at 47 Ma. In none of the studied areas do micas record "cooling ages". Cretaceous apparent mica ages, which were proposed to date eclogitization by earlier studies based on conventional "thermochronology", are due to Ar inheritance in incompletely recrystallized detrital mica grains. In summary, the "closure temperature" approach is unable to predict the three features that charac-terize the Western Alps traverse: Ar loss at T < 300 °C, contrasting Ar retention at T > 500 °C, and the tight correlation between age and phengitic substitution. A process-oriented petrological analysis demonstrates the predominance of retrogression reactions. Ar is lost mainly when deformation and/or fluids promote recrystallization. In the absence of major recrystallization, Ar retentivity by white mica is known to be very high (Di Vincenzo et al, CMP 141 (2001) 14 and JPetrol 45 (2004) 1013; Beltrando et al, GCA 119 (2013) 359).

  14. Asteroidal processes recorded by polyphase deformation in a harzburgitic diogenite NWA 5480

    NASA Astrophysics Data System (ADS)

    Tkalcec, Beverley J.; Brenker, Frank E.

    2015-08-01

    Expectations regarding structural deformation of asteroidal meteorites have typically revolved around impact-induced shock metamorphism or the gravity-driven axial compression of cumulates at the base of magma chambers. Recent structural analyses, however, of several olivine-rich diogenites (harzburgites) reveal solid-state plastic deformation not attributable to either scenario and propose dynamic mantle movements in the parent body, assumed to be Vesta. In this study we examine the microstructures of pyroxene and olivine in the olivine-rich diogenite NWA 5480. Coarse-grained, poikilitic texture, exsolution lamellae and plastic deformation attest to polyphase deformation and a re-heating event, followed by relatively slow cooling. Observations suggest that impact events alone are insufficient to generate and sustain the thermal and deformation conditions required to achieve all of the observed features. The proposed dynamic mantle movements in the Vestan interior may offer a means of heat transport to the system to provide a thermal environment inducive to slow cooling as well as generate the incremental stress fields required for the polyphase plastic deformation observed in the olivine.

  15. A 1 MEGAWATT POLYPHASE BOOST CONVERTER-MODULATOR FOR KLYSTRON PULSE APPLICATION

    SciTech Connect

    W.A. REASS; J.D. DOSS; R.F. GRIBBLE

    2001-06-01

    This paper describes electrical design criteria and first operational results a 140 kV, 1 MW average, 11 MW peak, zero-voltage-switching 20 kHz polyphase bridge, boost converter/modulator for klystron pulse application. The DC-DC converter derives the buss voltages from a standard 13.8 kV to 2300 Y substation cast-core transformer. Energy storage and filtering is provided by self-clearing metallized hazy polypropylene traction capacitors. Three ''H-Bridge'' Insulated Gate Bipolar Transistor (IGBT) switching networks are used to generate the polyphase 20 kHz transformer primary drive waveforms. The 20 kHz drive waveforms are chirped the appropriate duration to generate the desired klystron pulse width. PWM (pulse width modulation) of the individual 20 kHz pulses is utilized to provide regulated output waveforms with adaptive feedforward and feedback techniques. The boost transformer design utilizes amorphous nanocrystalline material that provides the required low core loss at design flux levels and switching frequencies. Resonant shunt-peaking is used on the transformer secondary to boost output voltage and resonate transformer leakage inductance. With the appropriate transformer leakage inductance and peaking capacitance, zero-voltage-switching of the IGBT's is attained, minimizing switching losses. A review of these design parameters and the first results of the performance characteristics will be presented.

  16. Asynchrony of taxonomic, functional and phylogenetic diversity in birds

    PubMed Central

    Monnet, Anne-Christine; Jiguet, Frédéric; Meynard, Christine N.; Mouillot, David; Mouquet, Nicolas; Thuiller, Wilfried; Devictor, Vincent

    2014-01-01

    Aim We assessed the temporal trends of taxonomic, functional and phylogenetic diversities in the French avifauna over the last two decades. Additionally, we investigated whether and how this multifaceted approach to biodiversity dynamics can reveal an increasing similarity of local assemblages in terms of species, traits and/or lineages. Location France. Methods We analysed a large-scale dataset that recorded annual changes in the abundance of 116 breeding birds in France between 1989 and 2012. We decomposed and analysed the spatio-temporal dynamics of taxonomic, phylogenetic and functional diversities and each of their α-, β- and γ-components. We also calculated the trend in the mean specialization of bird communities to track the relative success of specialist versus generalist species within communities during the same period. Results We found large variation within and among the temporal trends of each biodiversity facet. On average, we found a marked increase in species and phylogenetic diversity over the period considered, but no particular trend was found for functional diversity. Conversely, changes in β-diversities for the three facets were characterized by independent and nonlinear trends. We also found a general increase in the local occurrence and abundance of generalist species within local communities. Main conclusions These results highlight a relative asynchrony of the different biodiversity facets occurring at large spatial scales. We show why a multifaceted approach to biodiversity dynamics is needed to better describe and understand changes in community composition in macroecology and conservation biogeography. PMID:25067904

  17. Taxonomic distribution of large DNA viruses in the sea

    PubMed Central

    Monier, Adam; Claverie, Jean-Michel; Ogata, Hiroyuki

    2008-01-01

    Background Viruses are ubiquitous and the most abundant biological entities in marine environments. Metagenomics studies are increasingly revealing the huge genetic diversity of marine viruses. In this study, we used a new approach - 'phylogenetic mapping' - to obtain a comprehensive picture of the taxonomic distribution of large DNA viruses represented in the Sorcerer II Global Ocean Sampling Expedition metagenomic data set. Results Using DNA polymerase genes as a taxonomic marker, we identified 811 homologous sequences of likely viral origin. As expected, most of these sequences corresponded to phages. Interestingly, the second largest viral group corresponded to that containing mimivirus and three related algal viruses. We also identified several DNA polymerase homologs closely related to Asfarviridae, a viral family poorly represented among isolated viruses and, until now, limited to terrestrial animal hosts. Finally, our approach allowed the identification of a new combination of genes in 'viral-like' sequences. Conclusion Albeit only recently discovered, giant viruses of the Mimiviridae family appear to constitute a diverse, quantitatively important and ubiquitous component of the population of large eukaryotic DNA viruses in the sea. PMID:18598358

  18. Partial Knowledge of Word Meanings: Thematic and Taxonomic Representations

    ERIC Educational Resources Information Center

    Whitmore, Jeannette M.; Shore, Wendelyn J.; Smith, Peg Hull

    2004-01-01

    The type of information (taxonomic or thematic) available at different levels of knowledge was investigated. Following extensive norming to identify taxonomic and thematic associates of low-frequency nouns, participants determined if taxonomic or thematic associates were meaningfully related to target words at three levels of knowledge: target…

  19. Taxonomic triage and the poverty of phylogeny.

    PubMed Central

    Wheeler, Quentin D

    2004-01-01

    Revisionary taxonomy is frequently dismissed as merely descriptive, which belies its strong intellectual content and hypothesis-driven nature. Funding for taxonomy is inadequate and largely diverted to studies of phylogeny that neither improve classifications nor nomenclature. Phylogenetic classifications are optimal for storing and predicting information, but phylogeny divorced from taxonomy is ephemeral and erodes the accuracy and information content of the language of biology. Taxonomic revisions and monographs are efficient, high-throughput species hypothesis-testing devices that are ideal for the World Wide Web. Taxonomic knowledge remains essential to credible biological research and is made urgent by the biodiversity crisis. Theoretical and technological advances and threats of mass species extinctions indicate that this is the time for a renaissance in taxonomy. Clarity of vision and courage of purpose are needed from individual taxonomists and natural history museums to bring about this evolution of taxonomy into the information age. PMID:15253345

  20. Lactobacillus species: taxonomic complexity and controversial susceptibilities.

    PubMed

    Goldstein, Ellie J C; Tyrrell, Kerin L; Citron, Diane M

    2015-05-15

    The genus Lactobacillus is a taxonomically complex and is composed of over 170 species that cannot be easily differentiated phenotypically and often require molecular identification. Although they are part of the normal human gastrointestinal and vaginal flora, they can also be occasional human pathogens. They are extensively used in a variety of commercial products including probiotics. Their antimicrobial susceptibilities are poorly defined in part because of their taxonomic complexity and are compounded by the different methods recommended by Clinical Laboratory Standards Institute and International Dairy Foundation. Their use as probiotics for prevention of Clostridium difficile infection is prevalent among consumers worldwide but raises the question of will the use of any concurrent antibiotic effect their ability to survive. Lactobacillus species are generally acid resistant and are able to survive ingestion. They are generally resistant to metronidazole, aminoglycosides and ciprofloxacin with L. acidophilus being susceptible to penicillin and vancomycin, whereas L. rhamnosus and L. casei are resistant to metronidazole and vancomycin. PMID:25922408

  1. A Falsification of the Citation Impediment in the Taxonomic Literature

    PubMed Central

    Steiner, Florian M.; Pautasso, Marco; Zettel, Herbert; Moder, Karl; Arthofer, Wolfgang; Schlick-Steiner, Birgit C.

    2015-01-01

    Current science evaluation still relies on citation performance, despite criticisms of purely bibliometric research assessments. Biological taxonomy suffers from a drain of knowledge and manpower, with poor citation performance commonly held as one reason for this impediment. But is there really such a citation impediment in taxonomy? We compared the citation numbers of 306 taxonomic and 2291 non-taxonomic research articles (2009–2012) on mosses, orchids, ciliates, ants, and snakes, using Web of Science (WoS) and correcting for journal visibility. For three of the five taxa, significant differences were absent in citation numbers between taxonomic and non-taxonomic papers. This was also true for all taxa combined, although taxonomic papers received more citations than non-taxonomic ones. Our results show that, contrary to common belief, taxonomic contributions do not generally reduce a journal's citation performance and might even increase it. The scope of many journals rarely featuring taxonomy would allow editors to encourage a larger number of taxonomic submissions. Moreover, between 1993 and 2012, taxonomic publications accumulated faster than those from all biological fields. However, less than half of the taxonomic studies were published in journals in WoS. Thus, editors of highly visible journals inviting taxonomic contributions could benefit from taxonomy's strong momentum. The taxonomic output could increase even more than at its current growth rate if: (i) taxonomists currently publishing on other topics returned to taxonomy and (ii) non-taxonomists identifying the need for taxonomic acts started publishing these, possibly in collaboration with taxonomists. Finally, considering the high number of taxonomic papers attracted by the journal Zootaxa, we expect that the taxonomic community would indeed use increased chances of publishing in WoS indexed journals. We conclude that taxonomy's standing in the present citation-focused scientific landscape could

  2. [Studies on the stability and some other important physical properties of polysaccharides polyphase liposome (PPL)].

    PubMed

    Zou, Y Y; Su, D S; Han, G C; Gu, X Q

    1989-01-01

    The stability and some other important physical properties of PPL were investigated by means of electron microscopy and MPV-TAS experiments. The results are rated as follows: Good integrity of liposome homogeneity of its particle size were reached, and at 100 degrees C PPL was found to undergo sterilization without causing changes of its shape and encapsulation efficiency for 1 h. Also, the distribution of PPL particle size and the regularity of the change of PPL particle in size were determined by Coulter counter. Using this method, the kinetic equation of coalescence of polyphase liposome and the activation energy for coalescence were obtained, and through these results the stability of PPL is elucidated. PMID:2508432

  3. Possible Gems and Ultra-Fine Grained Polyphase Units in Comet Wild 2.

    NASA Technical Reports Server (NTRS)

    Gainsforth, Z.; Butterworth, A. L.; Jilly-Rehak, C. E.; Westphal, A. J.; Brownlee, D. E.; Joswiak, D.; Ogliore, R. C.; Zolensky, M. E.; Bechtel, H. A.; Ebel, D. S.; Huss, G. R.; Sandford, S. A.; White, A. J.

    2016-01-01

    GEMS and ultrafine grained polyphase units (UFG-PU) in anhydrous IDPs are probably some of the most primitive materials in the solar system. UFG-PUs contain nanocrystalline silicates, oxides, metals and sulfides. GEMS are rounded approximately 100 nm across amorphous silicates containing embedded iron-nickel metal grains and sulfides. GEMS are one of the most abundant constituents in some anhydrous CPIDPs, often accounting for half the material or more. When NASA's Stardust mission returned with samples from comet Wild 2 in 2006, it was thought that UFG-PUs and GEMS would be among the most abundant materials found. However, possibly because of heating during the capture process in aerogel, neither GEMS nor UFG-PUs have been clearly found.

  4. The polyphase resonant converter modulator for pulse power and plasma applications

    SciTech Connect

    Reass, W. A.; Baca, D. M.; Doss, James D.; Gribble, R.; North, W. R.

    2002-01-01

    This paper describes a new technique to generate high voltage pulses (100 kV and up) with high peak power (10 MW and up) and high average power (1 MW and up) from a low voltage input source (e.g. +/- 1.2 kV). This technology is presently being used to provide cathode pulse modulation for the Spallation Neutron Source (SNS) accelerator klystron RF amplifiers, which operate to 140 kV 11 MW peak power and 1.1 MW average power. The design of the modulator, referred to as the Polyphase Resonant Converter-Modulator takes advantage of high-power component advances, in response to the needs of the traction motor industry (in particular, railroad locomotives), such as Insulated Gate Bipolar Transistors (IGBT's) and self-clearing metallized hazy polypropylene capacitors. In addition, the use of amorphous nanocrystalline transformer core alloy permits high frequency voltage and current transformation with low loss and small size. Other unique concepts embodied in the converter-modulator topology are polyphase resonant voltage multiplication and resonant rectification. These techniques further reduce size and improve electrical efficiency. Because of the resonant conversion techniques, electronic 'crowbars' and other load protective networks are not required. A shorted load detunes the circuit resonance and little power transfer can occur. This yields a high-power, high-voltage system that is inherently self-protective. To provide regulated output voltages, Pulse Width Modulation (PWM) of the individual IGBT pulses is used. A Digital signal Processor (DSP) is used to control the IGBT's, with adaptive feed forward and feedback control algorithms that improve pulse fidelity. The converter-modulator has many attributes that make it attractive to various pulse power and plasma applications such as high power RF sources, neutral beam modulators, and various plasma applications. This paper will review the design as used for the SNS accelerator and speculate on related plasma

  5. Design, status and first operations of the spallation neutron source polyphase resonant converter modulator system

    SciTech Connect

    Reass, W. A.; Apgar, S. E.; Baca, D. M.; Doss, James D.; Gonzales, J.; Gribble, R. F.; Hardek, T. W.; Lynch, M. T.; Rees, D. E.; Tallerico, P. J.; Trujillo, P. B.; Anderson, D. E.; Heidenreich, D. A.; Hicks, J. D.; Leontiev, V. N.

    2003-01-01

    The Spallation Neutron Source (SNS) is a new 1.4 MW average power beam, 1 GeV accelerator being built at Oak Ridge National Laboratory. The accelerator requires 15 converter-modulator stations each providing between 9 and 11 MW pulses with up to a 1 .I MW average power. The converter-modulator can be described as a resonant 20 kHz polyphase boost inverter. Each converter modulator derives its buss voltage from a standard substation cast-core transformer. Each substation is followed by an SCR pre-regulator to accommodate voltage changes from no load to full load, in addition to providing a soft-start function. Energy storage is provided by self-clearing metallized hazy polypropylene traction capacitors. These capacitors do not fail short, but clear any internal anomaly. Three 'H-Bridge' IGBT transistor networks are used to generate the polyphase 20 kHz transformer primary drive waveforms. The 20 kHz drive waveforms are time-gated to generate the desired klystron pulse width. Pulse width modulation of the individual 20 lcHz pulses is utilized to provide regulated output waveforms with DSP based adaptive feedforward and feedback techniques. The boost transformer design utilizes nanocrystalline alloy that provides low core loss at design flux levels and switching frequencies. Capacitors are used on the transformer secondary networks to resonate the leakage inductance. The transformers are wound for a specific leakage inductance, not turns ratio. This design technique generates multiple secondary volts per turn as compared to the primary. With the appropriate tuning conditions, switching losses are minimized. The resonant topology has the added benefit of being deQed in a klystron fault condition, with little energy deposited in the arc. This obviates the need of crowbars or other related networks. A review of these design parameters, operational performance, production status, and OWL installation and performance to date will be presented.

  6. Taxonomic updates in Dolichandra Cham. (Bignonieae, Bignoniaceae)

    PubMed Central

    Fonseca, Luiz Henrique M.; Cabral, Simone Miranda; Agra, Maria de Fátima; Lohmann, Lúcia G.

    2015-01-01

    Abstract Dolichandra is a genus of lianas found in dry and wet Neotropical forests. The genus currently includes eight species and is well characterized by molecular and morphological synapomorphies. Here, Macfadyena hispida (DC.) Seemann is removed from synonomy with Dolichandra uncata (Andrews) L.G. Lohmann based on the presence of the hispid indument, vinaceus ovary, long fruits, and winged seeds. The combination Dolichandra hispida (DC.) L.H. Fonseca & L.G. Lohmann, comb. nov. is proposed, increasing the number of accepted species of Dolichandra to nine. A taxonomic key for all species of Dolichandra is presented. PMID:25878548

  7. A taxonomic analysis of multihospital systems.

    PubMed Central

    Lewis, B L; Alexander, J

    1986-01-01

    Research to date on multihospital systems has proved largely uninformative, in part because similarities and differences among these organizations have not been addressed systematically. Through numeric classification, this article identifies populations of multihospital systems that share similar organizational attributes. Drawing on McKelvey's classification theory, 16 organizational characteristics of 160 multihospital systems are analyzed using a series of taxonomic techniques, including cluster analysis, multiple discriminant analysis, and analysis of coefficients of variation. Fifteen distinct subgroups of systems are identified and described, and their implications for organization research discussed. PMID:3710802

  8. Taxonomic revision of Richardiodes Hendel (Diptera, Richardiidae).

    PubMed

    Wendt, Lisiane Dilli; Ale-Rocha, Rosaly

    2016-01-01

    Richardiodes Hendel is a genus scarcely known taxonomically and two species are recognized: Richardiodes rectinervis Hendel from Brazilian Amazon and R. trimaculata Hennig from Peru. Herein, these two species are revised and illustrated. Examination of non-type specimens revealed considerable variation in the general body color, and the geographic distribution of each species has been expanded, especially of R. rectinervis. The limits of the genus are revised and better supported with the addition of new diagnostic characters. The male and female terminalia are described and illustrated for the first time. PMID:27394237

  9. On some recent taxonomic advancement and the resultant problems in the arboreal skink genus Dasia Gray, 1839 (Reptilia: Scincidae).

    PubMed

    Chandramouli, S R; Amarasinghe, A A Thasun

    2015-01-01

    South Asian members of the arboreal skink genus Dasia Gray, 1839 were recently reviewed using morphological and molecular approaches (Wickramasinghe et al. 2011; Harikrishnan et al. 2012). Harikrishnan et al. (2012) described a new species, Dasia johnsinghi, from South India. Both reviews add considerably to our taxonomic knowledge of the genus, but are unfortunately marred by several inaccuracies and lapses in taxonomic and nomenclatural practice. Taxonomic research is socially relevant because it contributes to the understanding of biodiversity (Bhat & Sarma, 2014) and it is responsible for laying the foundation for conservation (Dubois 2003; Evenhaus 2007); consequently, we believe taxonomists must take responsibility for maintaining publication quality, to promote conservation and science, and in this case, herpetology. While pernicious descriptions are harmful to the growth of herpetology in the region [i.e. the Western Ghats] (Vasudevan et al. 2007) in a time expecting quality science (Shanker, 2014) inaccuracies and errors in taxonomic literature should be carefully guarded against. PMID:25661958

  10. Taxonomic assessment and enzymes production by yeasts isolated from marine and terrestrial Antarctic samples.

    PubMed

    Duarte, A W F; Dayo-Owoyemi, I; Nobre, F S; Pagnocca, F C; Chaud, L C S; Pessoa, A; Felipe, M G A; Sette, L D

    2013-11-01

    The aim of the present study was to investigate the taxonomic identity of yeasts isolated from the Antarctic continent and to evaluate their ability to produce enzymes (lipase, protease and xylanase) at low and moderate temperatures. A total of 97 yeast strains were recovered from marine and terrestrial samples collected in the Antarctica. The highest amount of yeast strains was obtained from marine sediments, followed by lichens, ornithogenic soils, sea stars, Salpa sp., algae, sea urchin, sea squirt, stone with lichens, Nacella concinna, sea sponge, sea isopod and sea snail. Data from polyphasic taxonomy revealed the presence of 21 yeast species, distributed in the phylum Ascomycota (n = 8) and Basidiomycota (n = 13). Representatives of encapsulated yeasts, belonging to genera Rhodotorula and Cryptococcus were recovered from 7 different Antarctic samples. Moreover, Candida glaebosa, Cryptococcus victoriae, Meyerozyma (Pichia) guilliermondii, Rhodotorula mucilaginosa and R. laryngis were the most abundant yeast species recovered. This is the first report of the occurrence of some species of yeasts recovered from Antarctic marine invertebrates. Additionally, results from enzymes production at low/moderate temperatures revealed that the Antarctic environment contains metabolically diverse cultivable yeasts, which could be considered as a target for biotechnological applications. Among the evaluated yeasts in the present study 46.39, 37.11 and 14.43 % were able to produce lipase (at 15 °C), xylanase (at 15 °C) and protease (at 25 °C), respectively. The majority of lipolytic, proteolytic and xylanolytic strains were distributed in the phylum Basidiomycota and were mainly recovered from sea stars, lichens, sea urchin and marine sediments. PMID:24114281

  11. Charting taxonomic knowledge through ontologies and ranking algorithms

    NASA Astrophysics Data System (ADS)

    Huber, Robert; Klump, Jens

    2009-04-01

    Since the inception of geology as a modern science, paleontologists have described a large number of fossil species. This makes fossilized organisms an important tool in the study of stratigraphy and past environments. Since taxonomic classifications of organisms, and thereby their names, change frequently, the correct application of this tool requires taxonomic expertise in finding correct synonyms for a given species name. Much of this taxonomic information has already been published in journals and books where it is compiled in carefully prepared synonymy lists. Because this information is scattered throughout the paleontological literature, it is difficult to find and sometimes not accessible. Also, taxonomic information in the literature is often difficult to interpret for non-taxonomists looking for taxonomic synonymies as part of their research. The highly formalized structure makes Open Nomenclature synonymy lists ideally suited for computer aided identification of taxonomic synonyms. Because a synonymy list is a list of citations related to a taxon name, its bibliographic nature allows the application of bibliometric techniques to calculate the impact of synonymies and taxonomic concepts. TaxonRank is a ranking algorithm based on bibliometric analysis and Internet page ranking algorithms. TaxonRank uses published synonymy list data stored in TaxonConcept, a taxonomic information system. The basic ranking algorithm has been modified to include a measure of confidence on species identification based on the Open Nomenclature notation used in synonymy list, as well as other synonymy specific criteria. The results of our experiments show that the output of the proposed ranking algorithm gives a good estimate of the impact a published taxonomic concept has on the taxonomic opinions in the geological community. Also, our results show that treating taxonomic synonymies as part of on an ontology is a way to record and manage taxonomic knowledge, and thus contribute

  12. Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case

    PubMed Central

    Franz, Nico M.; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

    2015-01-01

    Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations. PMID:25700173

  13. [Taxonomical status of the psychrotolerant Antarctic microorganisms].

    PubMed

    Romanovskaia, V A; Gladka, G V; Tashireva, A A; Tashirev, A B

    2013-01-01

    The aerobic chemoorganotrophic bacteria, dominating in soils and phytocenosis of the Antarctic Region, on combination of morphological and biochemical properties belong to several taxons of Bacteria domain. Gram-negative strains 3189, 3415 (fam. Halomonadaceae, Halomonas sp.) and 3088, 3468, 3469 (fam. Moraxellaceae, Psychrobacter sp.) belong to phylum Proteobacteria, to class Gammaproteobacteria. Gram-negative strains 3294 3392 (Rhizobiales, fam. Methylobacteriaceae, Methylobacterium sp.) relate to class Alphaproteobacteria of this phylum. Gram-positive strains 3179, 3275, 3470, 3471 (fam. Microbacteriaceae, Cryobacterium sp.), 3054, 3058, 3411 (fam. Corynebacteriaceae, Corynebacterium sp.) and 3194, 3398 (fam. Micrococcaceae, Micrococcus sp.) relate to phylum Actinobacteria, class Actinobacteria. Thus, the psychrophilic and psychrotolerant Antarctic bacteria (aerobic chemoorganotrophic) isolated from phytocenosis and soils of polar region are characterized by wide taxonomic variety. PMID:24450178

  14. Taxonomic etymology - in search of inspiration.

    PubMed

    Jóźwiak, Piotr; Rewicz, Tomasz; Pabis, Krzysztof

    2015-01-01

    We present a review of the etymology of zoological taxonomic names with emphasis on the most unusual examples. The names were divided into several categories, starting from the most common - given after morphological features - through inspiration from mythology, legends, and classic literature but also from fictional and nonfictional pop-culture characters (e.g., music, movies or cartoons), science, and politics. A separate category includes zoological names created using word-play and figures of speech such as tautonyms, acronyms, anagrams, and palindromes. Our intention was to give an overview of possibilities of how and where taxonomists can find the inspirations that will be consistent with the ICZN rules and generate more detail afterthought about the naming process itself, the meaningful character of naming, as well as the recognition and understanding of names. PMID:26257573

  15. Taxonomic etymology – in search of inspiration

    PubMed Central

    Jóźwiak, Piotr; Rewicz, Tomasz; Pabis, Krzysztof

    2015-01-01

    Abstract We present a review of the etymology of zoological taxonomic names with emphasis on the most unusual examples. The names were divided into several categories, starting from the most common – given after morphological features – through inspiration from mythology, legends, and classic literature but also from fictional and nonfictional pop-culture characters (e.g., music, movies or cartoons), science, and politics. A separate category includes zoological names created using word-play and figures of speech such as tautonyms, acronyms, anagrams, and palindromes. Our intention was to give an overview of possibilities of how and where taxonomists can find the inspirations that will be consistent with the ICZN rules and generate more detail afterthought about the naming process itself, the meaningful character of naming, as well as the recognition and understanding of names. PMID:26257573

  16. Global Taxonomic Diversity of Living Reptiles

    PubMed Central

    Pincheira-Donoso, Daniel; Bauer, Aaron M.; Meiri, Shai; Uetz, Peter

    2013-01-01

    Reptiles are one of the most ecologically and evolutionarily remarkable groups of living organisms, having successfully colonized most of the planet, including the oceans and some of the harshest and more environmentally unstable ecosystems on earth. Here, based on a complete dataset of all the world’s diversity of living reptiles, we analyse lineage taxonomic richness both within and among clades, at different levels of the phylogenetic hierarchy. We also analyse the historical tendencies in the descriptions of new reptile species from Linnaeus to March 2012. Although (non-avian) reptiles are the second most species-rich group of amniotes after birds, most of their diversity (96.3%) is concentrated in squamates (59% lizards, 35% snakes, and 2% amphisbaenians). In strong contrast, turtles (3.4%), crocodilians (0.3%), and tuataras (0.01%) are far less diverse. In terms of species discoveries, most turtles and crocodilians were described early, while descriptions of lizards, snakes and amphisbaenians are multimodal with respect to time. Lizard descriptions, in particular, have reached unprecedented levels during the last decade. Finally, despite such remarkably asymmetric distributions of reptile taxonomic diversity among groups, we found that the distributions of lineage richness are consistently right-skewed, with most clades (monophyletic families and genera) containing few lineages (monophyletic genera and species, respectively), while only a few have radiated greatly (notably the families Colubridae and Scincidae, and the lizard genera Anolis and Liolaemus). Therefore, such consistency in the frequency distribution of richness among clades and among phylogenetic levels suggests that the nature of reptile biodiversity is fundamentally fractal (i.e., it is scale invariant). We then compared current reptile diversity with the global reptile diversity and taxonomy known in 1980. Despite substantial differences in the taxonomies (relative to 2012), the patterns of

  17. Flexible taxonomic assignment of ambiguous sequencing reads

    PubMed Central

    2011-01-01

    Background To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads) are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it. Results We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed. Conclusions The assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the q parameter. Validation of our results in an artificial dataset confirm that a combination of values of q produces the most accurate results. PMID:21211059

  18. Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

    PubMed

    Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

    2016-06-01

    Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural

  19. Preschool Children's Taxonomic Knowledge of Animal Species

    ERIC Educational Resources Information Center

    Allen, Michael

    2015-01-01

    Although taxonomic proficiency is a prerequisite for understanding ideas central to biology, previous research has established that learners frequently misclassify animals by not following the tenets of accepted taxonomic rubrics. This has immediate relevance with the recently revised English National Curriculum now requiring concepts of animal…

  20. Designing Multimedia Games for Young Children's Taxonomic Concept Development

    ERIC Educational Resources Information Center

    Sung, Yao-Ting; Chang, Kuo-En; Lee, Meng-Da

    2008-01-01

    This study aimed to design and evaluate multimedia games which were based on the theories of children's development of taxonomic concepts. Factors that might affect children's classification skills, such as use of single physical characteristics of objects, competition between thematic and taxonomic relationships, difficulty in forming…

  1. Nanostructured Polyphase Catalysts Based on the Solid Component of Welding Aerosol for Ozone Decomposition.

    PubMed

    Rakitskaya, Tatyana; Truba, Alla; Ennan, Alim; Volkova, Vitaliya

    2015-12-01

    Samples of the solid component of welding aerosols (SCWAs) were obtained as a result of steel welding by ANO-4, TsL‑11, and UONI13/55 electrodes of Ukrainian manufacture. The phase compositions of the samples, both freshly prepared (FP) and modified (M) by water treatment at 60 °C, were studied by X-ray phase analysis and IR spectroscopy. All samples contain magnetite demonstrating its reflex at 2θ ~ 35° characteristic of cubic spinel as well as manganochromite and iron oxides. FP SCWA-TsL and FP SCWA-UONI contain such phases as СaF2, water-soluble fluorides, chromates, and carbonates of alkali metals. After modification of the SCWA samples, water-soluble phases in their composition are undetectable. The size of magnetite nanoparticles varies from 15 to 68 nm depending on the chemical composition of electrodes under study. IR spectral investigations confirm the polyphase composition of the SCWAs. As to IR spectra, the biggest differences are apparent in the regions of deformation vibrations of M-O-H bonds and stretching vibrations of M-O bonds (M-Fe, Cr). The catalytic activity of the SCWAs in the reaction of ozone decomposition decreases in the order SCWA-ANO > SCWA-UONI > SCWA-TsL corresponding to the decrease in the content of catalytically active phases in their compositions. PMID:26646686

  2. First results of the Los Alamos polyphase boost converter-modulator

    SciTech Connect

    Doss, James D.; Gribble, R. F.; Lynch, M. T.; Rees, D. E.; Tallerico, P. J.; Reass, W. A.

    2001-01-01

    This paper describes the first full-scale electrical test results of the Los Alamos polyphase boost converter-modulator being developed for the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory. The convertrr-modulator provides 140 kV, 1.2 mS, 60 Hz pulses to a 5 MW, 805 MHz klystron. The system, which has 1 MW average power, derives its +/- 1250 Volt DC buss link voltages from a standard 3-phase utility 13.8 kV to 2100 volt transformer. An SCR pre-regulator provides a soft-start function in addition to correction of line and load variations, from no-load to full-load. Energy storage is provided by low inductance self-clearing metallized hazy polypropylene traction capacitors. Each of the 3-phase H-bridge Insulated Gate Bipolar Transistor (IGBT) Pulse-Width Modulation (PWM) drivers are resonated with the amorphous nanocrystalline boost transformer and associated peaking circuits to provide zero-voltage-switching characteristics for the IGBT's. This design feature minimizes IGBT switching losses. By PWM of individual IGBT conduction angles, output pulse regulation with adaptive feedforward and feedback techniques is used to improve the klystron voltage pulse shape. In addition to the first operational results, this paper will discuss the relevant design techniques associated with the boost converter-modulator topology.

  3. New generation polyphase resonant converter-modulators for the Korean atomic energy research institute

    SciTech Connect

    Reass, William A; Baca, David M; Gribble, Robert F

    2009-01-01

    This paper will present operational data and performance parameters of the newest generation polyphase resonant high voltage converter modulator (HVCM) as developed and delivered to the KAERI 100 MeV ''PEFP'' accelerator [1]. The KAERI design realizes improvements from the SNS and SLAC designs [2]. To improve the IGBT switching performance at 20 kHz for the KAERI system, the HVCM utilizes the typical zero-voltage-switching (ZVS) at turn on and as well as artificial zero-current-switching (ZCS) at turn-off. The new technique of artificial ZCS technique should result in a 6 fold reduction of IGBT switching losses (3). This improves the HCVM conversion efficiency to better than 95% at full average power, which is 500 kW for the KAERI two klystron 105 kV, 50 A application. The artificial ZCS is accomplished by placing a resonant RLC circuit across the input busswork to the resonant boost transformer. This secondary resonant circuit provides a damped ''kick-back'' to assist in IGBT commutation. As the transformer input busswork is extremely low inductance (< 10 nH), the single RLC network acts like it is across each of the four IGBT collector-emitter terminals of the H-bridge switching network. We will review these topological improvements and the overall system as delivered to the KAERI accelerator and provide details of the operational results.

  4. Silicon controlled rectifier polyphase bridge inverter commutated with gate-turn-off thyristor

    NASA Technical Reports Server (NTRS)

    Edwards, Dean B. (Inventor); Rippel, Wally E. (Inventor)

    1986-01-01

    A polyphase SCR inverter (10) having N switching poles, each comprised of two SCR switches (1A, 1B; 2A, 2B . . . NA, NB) and two diodes (D1B; D1B; D2A, D2B . . . DNA, DNB) in series opposition with saturable reactors (L1A, L1B; L2A, L2B . . . LNA, LNB) connecting the junctions between the SCR switches and diodes to an output terminal (1, 2 . . . 3) is commutated with only one GTO thyristor (16) connected between the common negative terminal of a dc source and a tap of a series inductor (14) connected to the positive terminal of the dc source. A clamp winding (22) and diode (24) are provided, as is a snubber (18) which may have its capacitance (c) sized for maximum load current divided into a plurality of capacitors (C.sub.1, C.sub.2 . . . C.sub.N), each in series with an SCR switch S.sub.1, S.sub.2 . . . S.sub.N). The total capacitance may be selected by activating selected switches as a function of load current. A resistor 28 and SCR switch 26 shunt reverse current when the load acts as a generator, such as a motor while braking.

  5. Deformation partitioning during polyphase oblique convergence in the Karawanken Mountains, southeastern Alps

    NASA Astrophysics Data System (ADS)

    Polinski, Ralf K.; Eisbacher, Gerhard H.

    1992-11-01

    The Karawanken Mountains of southeastern Austria straddle the Insubric Line, a major fault zone that corresponds to the Austroalpine-South Alpine border of the eastern Alps. They display polyphase structural patterns that resulted from deformation partitioning at shallow crustal levels. Following a poorly constrained late Cretaceous deformation history, Paleogene contraction produced NW—SE-trending fold—thrust structures and possibly related sinistral (?) cross faults. Miocene deformation produced both NW- and SE-directed thrust faults and NW-striking high-angle dextral cross faults which merged with or displaced the W-striking Insubric Line. Distributed dextral strike-slip displacements of the order of 30-40 km and thrust displacement of 4-5 km along the northern Karawanken front initiated subsidence of a small foreland basin north of the Karawanken Mountains. Recent regional deformation seems to be concentrated along cross-cutting NNW-striking dextral faults within a shifting system of seismogenic transfer faults that probably merge with the convergent South Alpine thrust front to the west. There are conspicuous parallels in the style of deformation along the Karawanken Mountains with that found along other seismogenic convergent strike-slip faults, such as those of southern California, New Zealand and Anatolia.

  6. Nanostructured Polyphase Catalysts Based on the Solid Component of Welding Aerosol for Ozone Decomposition

    NASA Astrophysics Data System (ADS)

    Rakitskaya, Tatyana; Truba, Alla; Ennan, Alim; Volkova, Vitaliya

    2015-12-01

    Samples of the solid component of welding aerosols (SCWAs) were obtained as a result of steel welding by ANO-4, TsL-11, and UONI13/55 electrodes of Ukrainian manufacture. The phase compositions of the samples, both freshly prepared (FP) and modified (M) by water treatment at 60 °C, were studied by X-ray phase analysis and IR spectroscopy. All samples contain magnetite demonstrating its reflex at 2 θ ~ 35° characteristic of cubic spinel as well as manganochromite and iron oxides. FP SCWA-TsL and FP SCWA-UONI contain such phases as CaF2, water-soluble fluorides, chromates, and carbonates of alkali metals. After modification of the SCWA samples, water-soluble phases in their composition are undetectable. The size of magnetite nanoparticles varies from 15 to 68 nm depending on the chemical composition of electrodes under study. IR spectral investigations confirm the polyphase composition of the SCWAs. As to IR spectra, the biggest differences are apparent in the regions of deformation vibrations of M-O-H bonds and stretching vibrations of M-O bonds (M-Fe, Cr). The catalytic activity of the SCWAs in the reaction of ozone decomposition decreases in the order SCWA-ANO > SCWA-UONI > SCWA-TsL corresponding to the decrease in the content of catalytically active phases in their compositions.

  7. Polyphase rifting within Rodinia as seen through multiple episodes of mafic volcanism within the Canadian Cordillera

    NASA Astrophysics Data System (ADS)

    Cox, G. M.; Halverson, G. P.; Roots, C. F.; MacDonald, F. A.; Plavsa, D.

    2010-12-01

    Neoproterozoic continental flood basalts (CFB) are known from the North American Cordillera and are thought to be associated with the breakup of Rodinia. However, unlike the short eruptive timeframe of Phanerozoic flood basalt provinces, instances of Neoproterozoic CFB within the North American Cordillera are separated by the unusually long time interval of ca 56 My (ca 780 Ma Gunbarrel Event and the ca 717 Ma Franklin Igneous Event), suggestive of poly-phase rifting and a long lived thermal anomaly and/or fertile mantle situated under ancient Laurentia. The Neoproterozoic Tatonduk Inlier, spanning the Alaskan-Yukon border, preserves both mafic volcanics (Pleasant Creek Volcanics) and a large arcuate dyke swarm (Tindir Dyke Swarm). Previous K/Ar dates on the dikes ranging from 532 ± 11 Ma to 644 ± 18 Ma appear to be inconsistent with geological constraints and correlations between the Tatonduk strata and the Neoproterozoic sequence of the well-dated Coal Creek Inlier to the east. We present geochemical data and discuss age and correlative constraints on these mafic rocks and relate these results in terms of the breakup history of Rodinia, timing of mafic magmatism within the possible conjugate margins to Neoproterozoic Laurentia (e.g. Australia and South China) and the role of a mantle plume in the rifting of Rodinia.

  8. A Position Paper on the Electronic Publication of Nematode Taxonomic Manuscripts

    PubMed Central

    Eyualem-Abebe; Baldwin, James G.; Adams, Byron; Hope, Duane; Gardner, Scott; Huettel, Robin; Mullin, Peter; Powers, Topper; Sharma, Jyotsna; Ye, Weimin; Thomas, William K.

    2006-01-01

    Several nematode species have now attained ‘model organism’ status, yet there remain many niches in basic biological inquiry for which nematodes would be ideal model systems of study. However, furthering the model system approach is hindered by lack of information on nematode biodiversity. The shortage of taxonomic resources to inventory and characterize biodiversity hinders research programs in invasion biology, ecosystem functioning, conservation biology, and many others. The disproportion between numbers of species to be described and numbers of available taxonomic specialists is greater for Nematoda than for any other metazoan phylum. A partial solution to the taxonomic impediment is the adoption of recent advances in electronic publishing. Electronic publishing has the potential to increase the rate at which taxonomic papers are published, the breadth of their distribution, and the type, quantity, quality, and accessibility of data. We propose that the Journal of Nematology implement the advantageous aspects of electronic publication as a means to help ameliorate the limitations of an underdeveloped taxonomy and empower the nematological disciplines currently hindered by it. PMID:19259533

  9. A taxonomic approach to communicating maxims in interstellar messages

    NASA Astrophysics Data System (ADS)

    Vakoch, Douglas A.

    2011-02-01

    Previous discussions of interstellar messages that could be sent to extraterrestrial intelligence have focused on descriptions of mathematics, science, and aspects of human culture and civilization. Although some of these depictions of humanity have implicitly referred to our aspirations, this has not clearly been separated from descriptions of our actions and attitudes as they are. In this paper, a methodology is developed for constructing interstellar messages that convey information about our aspirations by developing a taxonomy of maxims that provide guidance for living. Sixty-six maxims providing guidance for living were judged for degree of similarity to each of other. Quantitative measures of the degree of similarity between all pairs of maxims were derived by aggregating similarity judgments across individual participants. These composite similarity ratings were subjected to a cluster analysis, which yielded a taxonomy that highlights perceived interrelationships between individual maxims and that identifies major classes of maxims. Such maxims can be encoded in interstellar messages through three-dimensional animation sequences conveying narratives that highlight interactions between individuals. In addition, verbal descriptions of these interactions in Basic English can be combined with these pictorial sequences to increase intelligibility. Online projects to collect messages such as the SETI Institute's Earth Speaks and La Tierra Habla, can be used to solicit maxims from participants around the world.

  10. 100 gigasamples per second 12 bits optoelectronic analog-to-digital converter design and implementation based on cellular polyphase-sampling architecture

    NASA Astrophysics Data System (ADS)

    Villa-Angulo, Carlos

    The next generation digital information systems such as high performance computers, multigigabit/sec communication networks, distributed sensors, three dimensional digital imaging systems etc, will require analog-to-digital converters (ADCs) with high sampling rates exceeding 10 Gigasamples per second (GSPS) and high bit resolution of at least 10 bits. Such performance criteria are difficult to achieve with silicon electronics technology because the switching speeds peak at about 10-20GHz. Also, timing jitters, amplitude fluctuations, phase noise, thermal noise, and harmonic distortion, all contribute to reductions in ADC bit resolution as sampling rate increases. Photonics ADCs are rapidly emerging as the enabling technologies for high-performance digital signal processing systems. For this technology, high optical pulses repetition rate (in the order of GHz) with low time jitter and pulse width in the femtoseconds regime are the major attractive characteristics of optical sources. In this dissertation work, a novel 102.4 GSPS 12-bit optoelectronic analog-to-digital converter architecture that is based on a Cellular Polyphase-Sampling architecture is introduced. First, a 102.4 GHz all-optical clock was designed and implemented using a femtosecond laser source and passive optical components. Second, a novel optoelectronic architecture for optical sampling and parallel demultiplexing of different phases (polyphase) of an input analog signal is presented. The optoelectronic sampling and demultiplexing architecture is composed by 20 optoelectronic subcircuit referred as "OE-Cell"; these have been designed and implemented using optical passive components and InGaAs PIN photodiodes. A unique feature of this approach is that the optically sampled RF signal always remains in the electrical domain and thus eliminates the need for electrical-to-optical and optical-to-electrical conversions. The electrical-in to electrical-out transfer functions of the sampling and

  11. TreeParser-Aided Klee Diagrams Display Taxonomic Clusters in DNA Barcode and Nuclear Gene Datasets

    PubMed Central

    Stoeckle, Mark Y.; Coffran, Cameron

    2013-01-01

    Indicator vector analysis of a nucleotide sequence alignment generates a compact heat map, called a Klee diagram, with potential insight into clustering patterns in evolution. However, so far this approach has examined only mitochondrial cytochrome c oxidase I (COI) DNA barcode sequences. To further explore, we developed TreeParser, a freely-available web-based program that sorts a sequence alignment according to a phylogenetic tree generated from the dataset. We applied TreeParser to nuclear gene and COI barcode alignments from birds and butterflies. Distinct blocks in the resulting Klee diagrams corresponded to species and higher-level taxonomic divisions in both groups, and this enabled graphic comparison of phylogenetic information in nuclear and mitochondrial genes. Our results demonstrate TreeParser-aided Klee diagrams objectively display taxonomic clusters in nucleotide sequence alignments. This approach may help establish taxonomy in poorly studied groups and investigate higher-level clustering which appears widespread but not well understood. PMID:24022383

  12. A Taxonomic Integrative Review of Short Message Service (SMS) Methodology

    PubMed Central

    Holcomb, Linda S.

    2015-01-01

    Background: To acquire self-management skills that affect clinical outcomes, collaboration and communication with one’s health care team is essential, yet many health care systems are not designed adequately to be responsive to a patient’s efforts to self-manage. This review synthesizes the intervention methodology of current studies facilitating the efforts of health care providers who wish to design, develop, and implement evidence-based SMS programs for patients with diabetes, focusing on clinical outcomes of A1C values, medication adherence rates, and participant satisfaction. Methods: This integrative review was conducted using an integrative taxonomic analysis approach. This approach involves creating a classification system with domains or characteristics, defining the relationships between those domains, and creating a foundation for new theories or constructs. Results: Synthesis of the evidence included in this integrated review suggests the best design for a SMS diabetes management program aimed at improving A1C levels, medication adherence rates, and participant satisfaction is an intervention providing weekly SMS education, with 2-way message direction, that is 3 months in length. Conclusions: The studies in this review have demonstrated that SMS interventions can be an important part of a viable and effective program in the effort to better manage adults with type 2 diabetes. PMID:25934517

  13. A taxonomic study of crested caracaras (Falconidae)

    USGS Publications Warehouse

    Dove, C.J.; Banks, R.C.

    1999-01-01

    The taxonomic status of the crested caracaras (Caracara spp., Falconidae) has been unsettled for many years. Current sources such as the AOU Check-list recognize a single species that includes three taxa formerly considered distinct, citing observations by Hellmayr and Conover (1949) on two specimens considered to be intermediate. We studied plumage characters and measurements of over 392 museum specimens and found no evidence of clinal change between the northern and southern continental populations. Sixteen specimens from localities near the Amazon River where these two populations sporadically meet exhibit a mosaic of plumage elements from both forms. Measurements of wing chord, bill length, and bill depth indicate that size is positively correlated with latitude north and south of the equator and that females are larger than males in the northern population. These populations do not meet in western South America. We conclude that three biological species can be identified in the crested caracaras: the insular Guadalupe Caracara (Caracara lutosus); and two continental species, Northern (C. cheriway) and Southern caracara (C. plancus), neither of which shows subspecific variation.

  14. Taxonomic Resolution as a Conceptual Problem for Understanding Ecological Science.

    NASA Astrophysics Data System (ADS)

    Lafrancois, T.

    2005-05-01

    The results of ecological analyses can vary with the taxonomic resolution(s) used to sort and quantify the organisms studied. It seems intuitive that the finest unit of taxonomy results in the finest discrimination of ecological processes, and this is certainly true in many cases (e.g. Hawkins 2000, Attayde 2001). However, other important work suggests that some ecological processes (e.g. Bowman 1997) or concepts (e.g. Schoener 1986, Olsgard 1998) are only supported by analysis at supra-specific taxonomic resolution. In fact, taxonomic levels above species are often necessary for detecting certain ecological relationships, such as key measurements of food webs (Vanderklift 1998) or stability of ecological communities over time (Bowman 1997). If some levels of organization result in different ecological outcomes, two questions are immediately raised. First, why do these levels lead to different outcomes, and second, what is the basis of choosing one resolution over another? I will address the first question by outlining four aspects of the problematic relationship between taxonomy and ecology: taxonomic variance, taxonomic heterogeneity, and taxonomic ambiguity both within and between groups. I aim to show that these interactions suggest a dependence relationship of ecological outcomes on taxonomic concepts.

  15. Predicting taxonomic and thematic relational responding

    PubMed Central

    Osborne, J. Grayson; Heath, John

    2003-01-01

    Pairs of pictures were classified by the authors and others as related by identity (A—A), basic taxonomy (A—B), superordinate taxonomy (A—C), or by theme (A—D). Two-choice matching-to-sample trial types were composed of these same picture pairs in which the sample was common to the two stimulus pairs in each configuration and, together with the sample, each comparison exemplified one of the relations in the picture pair; that is: A(AB), A(AC), A(AD), A(BC), A(BD), and A(CD). In five experiments, for each picture pair, college students classified the relation (as taxonomic or thematic) and rated its strength (Exps 1, 3) or its similarity (Exp 4); others matched to sample the foregoing trial types only (Exps 2, 5), or they classified and rated, too (Exp 3). With exceptions, students classed most pairs as the authors did. They also collectively ordered relational strengths from (1) identity, (2) basic taxonomy, and (3) theme, to (4) superordinate taxonomy based, in part, on the similarity of sample and comparison. Subjects chose the comparisons of the more strongly related picture pairs in the matching-to-sample task on 90 percent or more of the configurations. Subjects' selections in two-choice, matching-to-sample configurations using natural stimuli may be based on existing stimulus control topographies such as those exhibited by ratings of the relations in a configuration. ImagesFigure 1Figure 2Figure 3Figure 4Figure 5 PMID:22477256

  16. A taxonomic wish-list for community ecology.

    PubMed Central

    Gotelli, Nicholas J

    2004-01-01

    Community ecology seeks to explain the number and relative abundance of coexisting species. Four research frontiers in community ecology are closely tied to research in systematics and taxonomy: the statistics of species richness estimators, global patterns of biodiversity, the influence of global climate change on community structure, and phylogenetic influences on community structure. The most pressing needs for taxonomic information in community ecology research are usable taxonomic keys, current nomenclature, species occurrence records and resolved phylogenies. These products can best be obtained from Internet-based phylogenetic and taxonomic resources, but the lack of trained professional systematists and taxonomists threatens this effort. Community ecologists will benefit most directly from research in systematics and taxonomy by making better use of resources in museums and herbaria, and by actively seeking training, information and collaborations with taxonomic specialists. PMID:15253346

  17. Lab Practicums: Are We Teaching Sound Taxonomic Principles?

    ERIC Educational Resources Information Center

    Vogt, Kenneth D.

    1993-01-01

    Presents a series of exercises to help students understand the importance of the limits of taxonomic keys and to identify the appropriate levels. Introductory activities include having students classify screws, "gummy bears," and beans. (PR)

  18. Lightcurve Analysis of Five Taxonomic A-class Asteroids

    NASA Astrophysics Data System (ADS)

    Lucas, Michael P.; Ryan, Jeffrey G.; Fauerbach, Michael; Grasso, Salvatore

    2011-10-01

    We report lightcurve rotational periods for five taxonomic A-class asteroids observed at the Evelyn L. Egan Observatory: 246 Asporina, 289 Nenetta, 446 Aeternitas, 1600 Vyssotsky, and the Mars-crosser 1951 Lick.

  19. Individual differences in the strength of taxonomic versus thematic relations

    PubMed Central

    Mirman, Daniel; Graziano, Kristen M.

    2011-01-01

    Knowledge about word and object meanings can be organized taxonomically (fruits, mammals, etc.) based on shared features, or thematically (eating breakfast, taking a dog for a walk, etc.) based on participation in events or scenarios. An eye-tracking study showed that both kinds of knowledge are activated during comprehension of a single spoken word, even when the listener is not required to perform any active task. The results further revealed that an individual’s relative activation of taxonomic relations compared to thematic relations predicts that individual’s tendency to favor taxonomic over thematic relations when asked to choose between them in a similarity judgment task. These results argue that individuals differ in the relative strengths of their taxonomic and thematic semantic knowledge and suggest that meaning information is organized in two parallel, complementary semantic systems. PMID:22201413

  20. Polyphasic Identification and Susceptibility to Seven Antifungals of 102 Aspergillus Isolates Recovered from Immunocompromised Hosts in Greece▿

    PubMed Central

    Arabatzis, Michael; Kambouris, Manousos; Kyprianou, Miltiades; Chrysaki, Aikaterini; Foustoukou, Maria; Kanellopoulou, Maria; Kondyli, Lydia; Kouppari, Georgia; Koutsia-Karouzou, Chrysa; Lebessi, Evangelia; Pangalis, Anastasia; Petinaki, Efthimia; Stathi, Ageliki; Trikka-Graphakos, Eleftheria; Vartzioti, Erriketi; Vogiatzi, Aliki; Vyzantiadis, Timoleon-Achilleas; Zerva, Loukia; Velegraki, Aristea

    2011-01-01

    In this study, the first such study in Greece, we used polyphasic identification combined with antifungal susceptibility study to analyze Aspergillus clinical isolates comprising 102 common and rare members of sections Fumigati, Flavi, Terrei, Nidulantes, Nigri, Circumdati, Versicolores, and Usti. High amphotericin B MICs (>2 μg/ml) were found for 17.6% of strains. Itraconazole, posaconazole, and voriconazole MICs of >4 μg/ml were shown in 1%, 5%, and 0% of the isolates, respectively. Anidulafungin, micafungin, and caspofungin minimum effective concentrations (MECs) of ≥2 μg/ml were correspondingly recorded for 4%, 9%, and 33%, respectively, of the strains. PMID:21444701

  1. Developmental variations among Panagrolaimid nematodes indicate developmental system drift within a small taxonomic unit.

    PubMed

    Schiffer, Philipp H; Nsah, Ndifon A; Grotehusmann, Henny; Kroiher, Michael; Loer, Curtis; Schierenberg, Einhard

    2014-06-01

    Comparative studies of nematode embryogenesis among different clades revealed considerable variations. However, to what extent developmental differences exist between closely related species has mostly remained nebulous. Here, we explore the correlation between phylogenetic neighborhood and developmental variation in a restricted and morphologically particularly uniform taxonomic group (Panagrolaimidae) to determine to what extent (1) morphological and developmental characters go along with molecular data and thus can serve as diagnostic tools for the definition of kinship and (2) developmental system drift (DSD; modifications of developmental patterns without corresponding morphological changes) can be found within a small taxonomic unit. Our molecular approaches firmly support subdivision of Panagrolaimid nematodes into two monophyletic groups. These can be discriminated by distinct peculiarities in early embryonic cell lineages and a mirror-image expression pattern of the gene skn-1. This suggests major changes in the logic of cell specification and the action of DSD in the studied representatives of the two neighboring nematode taxa. PMID:24849338

  2. Delineating taxonomic boundaries in the largest species complex of black flies (Simuliidae) in the Oriental Region.

    PubMed

    Low, Van Lun; Takaoka, Hiroyuki; Pramual, Pairot; Adler, Peter H; Ya'cob, Zubaidah; Huang, Yao-Te; Da Pham, Xuan; Ramli, Rosli; Chen, Chee Dhang; Wannaket, Anukhcha; Sofian-Azirun, Mohd

    2016-01-01

    Perspicuous assessments of taxonomic boundaries and discovery of cryptic taxa are of paramount importance in interpreting ecological and evolutionary phenomena among black flies (Simuliidae) and combating associated vector-borne diseases. Simulium tani Takaoka & Davies is the largest and perhaps the most taxonomically challenging species complex of black flies in the Oriental Region. We use a DNA sequence-based method to delineate currently recognized chromosomal and morphological taxa in the S. tani complex on the Southeast Asian mainland and Taiwan, while elucidating their phylogenetic relationships. A molecular approach using multiple genes, coupled with morphological and chromosomal data, supported recognition of cytoform K and morphoform 'b' as valid species; indicated that S. xuandei, cytoform L, and morphoform 'a' contain possible cryptic species; and suggested that cytoform B is in the early stages of reproductive isolation whereas lineage sorting is incomplete in cytoforms A, C, and G. PMID:26839292

  3. Delineating taxonomic boundaries in the largest species complex of black flies (Simuliidae) in the Oriental Region

    PubMed Central

    Low, Van Lun; Takaoka, Hiroyuki; Pramual, Pairot; Adler, Peter H.; Ya’cob, Zubaidah; Huang, Yao-Te; Da Pham, Xuan; Ramli, Rosli; Chen, Chee Dhang; Wannaket, Anukhcha; Sofian-Azirun, Mohd

    2016-01-01

    Perspicuous assessments of taxonomic boundaries and discovery of cryptic taxa are of paramount importance in interpreting ecological and evolutionary phenomena among black flies (Simuliidae) and combating associated vector-borne diseases. Simulium tani Takaoka & Davies is the largest and perhaps the most taxonomically challenging species complex of black flies in the Oriental Region. We use a DNA sequence-based method to delineate currently recognized chromosomal and morphological taxa in the S. tani complex on the Southeast Asian mainland and Taiwan, while elucidating their phylogenetic relationships. A molecular approach using multiple genes, coupled with morphological and chromosomal data, supported recognition of cytoform K and morphoform ‘b’ as valid species; indicated that S. xuandei, cytoform L, and morphoform ‘a’ contain possible cryptic species; and suggested that cytoform B is in the early stages of reproductive isolation whereas lineage sorting is incomplete in cytoforms A, C, and G. PMID:26839292

  4. Comparison of Sewage and Animal Fecal Microbiomes by using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

    EPA Science Inventory

    Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but human and other animal gut microbiota contain an array of other taxonomic groups that might serve as indicators for sources of fecal pollution. High thr...

  5. Phylogeny-aware identification and correction of taxonomically mislabeled sequences

    PubMed Central

    Kozlov, Alexey M.; Zhang, Jiajie; Yilmaz, Pelin; Glöckner, Frank Oliver; Stamatakis, Alexandros

    2016-01-01

    Molecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic mislabelings in reference sequence databases can bias metagenetic studies which rely on the taxonomy. Despite significant efforts to improve the quality of taxonomic annotations, the curation rate is low because of the labor-intensive manual curation process. Here, we present SATIVA, a phylogeny-aware method to automatically identify taxonomically mislabeled sequences (‘mislabels’) using statistical models of evolution. We use the Evolutionary Placement Algorithm (EPA) to detect and score sequences whose taxonomic annotation is not supported by the underlying phylogenetic signal, and automatically propose a corrected taxonomic classification for those. Using simulated data, we show that our method attains high accuracy for identification (96.9% sensitivity/91.7% precision) as well as correction (94.9% sensitivity/89.9% precision) of mislabels. Furthermore, an analysis of four widely used microbial 16S reference databases (Greengenes, LTP, RDP and SILVA) indicates that they currently contain between 0.2% and 2.5% mislabels. Finally, we use SATIVA to perform an in-depth evaluation of alternative taxonomies for Cyanobacteria. SATIVA is freely available at https://github.com/amkozlov/sativa. PMID:27166378

  6. Phylogeny-aware identification and correction of taxonomically mislabeled sequences.

    PubMed

    Kozlov, Alexey M; Zhang, Jiajie; Yilmaz, Pelin; Glöckner, Frank Oliver; Stamatakis, Alexandros

    2016-06-20

    Molecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic mislabelings in reference sequence databases can bias metagenetic studies which rely on the taxonomy. Despite significant efforts to improve the quality of taxonomic annotations, the curation rate is low because of the labor-intensive manual curation process. Here, we present SATIVA, a phylogeny-aware method to automatically identify taxonomically mislabeled sequences ('mislabels') using statistical models of evolution. We use the Evolutionary Placement Algorithm (EPA) to detect and score sequences whose taxonomic annotation is not supported by the underlying phylogenetic signal, and automatically propose a corrected taxonomic classification for those. Using simulated data, we show that our method attains high accuracy for identification (96.9% sensitivity/91.7% precision) as well as correction (94.9% sensitivity/89.9% precision) of mislabels. Furthermore, an analysis of four widely used microbial 16S reference databases (Greengenes, LTP, RDP and SILVA) indicates that they currently contain between 0.2% and 2.5% mislabels. Finally, we use SATIVA to perform an in-depth evaluation of alternative taxonomies for Cyanobacteria. SATIVA is freely available at https://github.com/amkozlov/sativa. PMID:27166378

  7. Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

    PubMed Central

    Liu, Kuan-Liang; Porras-Alfaro, Andrea; Eichorst, Stephanie A.

    2012-01-01

    Taxonomic and phylogenetic fingerprinting based on sequence analysis of gene fragments from the large-subunit rRNA (LSU) gene or the internal transcribed spacer (ITS) region is becoming an integral part of fungal classification. The lack of an accurate and robust classification tool trained by a validated sequence database for taxonomic placement of fungal LSU genes is a severe limitation in taxonomic analysis of fungal isolates or large data sets obtained from environmental surveys. Using a hand-curated set of 8,506 fungal LSU gene fragments, we determined the performance characteristics of a naïve Bayesian classifier across multiple taxonomic levels and compared the classifier performance to that of a sequence similarity-based (BLASTN) approach. The naïve Bayesian classifier was computationally more rapid (>460-fold with our system) than the BLASTN approach, and it provided equal or superior classification accuracy. Classifier accuracies were compared using sequence fragments of 100 bp and 400 bp and two different PCR primer anchor points to mimic sequence read lengths commonly obtained using current high-throughput sequencing technologies. Accuracy was higher with 400-bp sequence reads than with 100-bp reads. It was also significantly affected by sequence location across the 1,400-bp test region. The highest accuracy was obtained across either the D1 or D2 variable region. The naïve Bayesian classifier provides an effective and rapid means to classify fungal LSU sequences from large environmental surveys. The training set and tool are publicly available through the Ribosomal Database Project (http://rdp.cme.msu.edu/classifier/classifier.jsp). PMID:22194300

  8. A study of the lethal and sublethal toxicity of polyphase P-100, an antisapstain fungicide containing 3-iodo-2-propynyl butyl carbamate (IPBC), on fish and aquatic invertebrates.

    PubMed

    Farrell, A P; Stockner, E; Kennedy, C J

    1998-10-01

    The acute toxicity of Polyphase P-100, an antisapstain wood preservative that contains 97% 3-iodo-2-propynyl butyl carbamate (IPBC), was determined for three species of fish (coho salmon, rainbow trout, and starry flounder) and three species of aquatic invertebrates (Daphnia magna, Hyalella azteca, and Neomysis mercedis). The 96-h LC50 values for the various fish species exposed to Polyphase P-100 ranged from 95 ppb for coho smolts (Oncorhynchus kisutch) to 370 ppm for juvenile starry flounder (Platichthys stellatus). The sensitivity of coho to Polyphase P-100 was altered by their developmental stage. Coho embryos were six to nine times more tolerant of Polyphase P-100 than coho alevins, which were twice as tolerant as coho smolts. The 48-h LC50 values for the invertebrates D. magna, H. azteca, and N. mercedis were 40 ppb, 500 ppb, and 2,920 ppb, respectively. In addition to a wider range of sensitivity to Polyphase P-100 compared with the fish species, the invertebrate species were characterized by a shallower concentration-response. In acute, 24-h sublethal tests with juvenile starry flounder and rainbow trout, there was no primary or secondary stress response (changes in hematocrit, leucocrit, hemoglobin concentration, plasma lactate concentration, and plasma cortisol concentration) at concentrations up to 50% of the 96-h LC50 value. The acute toxicity of a 1:8 mixture of Polyphase P-100 and Bardac 2280 (another antisapstain compound that contains didecyldimethylammonium chloride [DDAC] as the active ingredient) was close to additive for fish, but not for invertebrate species. The acute toxicity of the mixture was seven to eight times more than additive for H. azteca, but two to three times less than additive for D. magna. Some sublethal stress responses were revealed with the mixture that were not observed with the test chemicals alone. PMID:9732479

  9. Polyphase deformation of a Paleozoic metamorphosed subduction-accretionary complex in Beishan Orogen, southern Altaids

    NASA Astrophysics Data System (ADS)

    Song, Dongfang; Xiao, Wenjiao

    2014-05-01

    The Lebaquan Complex in central Beishan plays a significant role in understanding the subduction-accretion-collision processes of the Beishan orogenic collage, southern Altaids. This complex is a polyphase deformed upper greenschist to lower amphibolite facies metamorphic rock assemblages composed of metasedimentary sequence, gneissic plutons, metacherts, amphibolites and marbles, with multiple generations of syn-tectonic leucogranite-pegmatite and post-tectonic mafic dykes. Lithologic and geochemical characteristics show the Lebaquan Complex is a forearc-arc complex. Four stages of deformation can be recognized for the Lebaquan Complex. The D1 deformation is defined by pervasively developed foliations (S1) defined by alternative metamorphic layering and intrafolia isoclinal folds of quartz veins (F1). The D2 deformation is indicated by crenulation cleavage (S2) mainly developed in the schists, extensively-developed tight to open folds and asymmetric folds (F2) and pinch and swell structures. The D3 deformation is characterized by high-strain ductile shearing, which modified earlier structures. Small-scale asymmetric folds, σ-type porphyroclasts and S-C fabrics indicate dextral sense of shearing in east-west direction. The D4 deformation is represented by ductile to brittle structures including open/gentle folds, kink folds and small scale thrust faults which overprint earlier deformations. The overall deformation of this complex indicates a geodynamic setting change from initial north-south directed strong compression to later east-west directed transpression and finally extension. LA-ICP-MS zircon U-Pb dating was performed on key lithologies. Youngest age peak of detrital zircons from a garnet-mica-quartz schist is ~424 Ma, constraining the depositional age for the protolith of the metasedimentary sequence. A syn-deformation leucogranitic dyke that underwent D2 but did not experience D1 and a post-deformation mafic dyke that intrudes all the lithologies were

  10. Experimental Deformation of Polyphase Aggregates at Pressures and Temperatures of the Upper Mantle

    NASA Astrophysics Data System (ADS)

    Bejina, F.; Bystricky, M.; Ingrin, J.

    2011-12-01

    with numerical models for two-phase flow. Results on stress and strain partitioning in polyphase aggregates and on the effect of the presence of a weak phase on the rheology of forsterite-rich aggregates will be discussed.

  11. Stress and strain partitioning during high PT deformation of polyphase aggregates

    NASA Astrophysics Data System (ADS)

    Bejina, F.; Bystricky, M.; Ingrin, J.

    2013-12-01

    Previous experimental studies on the rheology of the upper mantle have mostly focused on the deformation properties of olivine. Yet minerals other than olivine constitute up to 40 vol% of upper mantle rocks and may have a significant effect on the rheological behavior of these rocks. In this study, and as a first step before focusing on more realistic mantle-like compositions, we have performed deformation experiments on polymineralic model aggregates of forsterite and MgO, at upper mantle pressures and temperatures. Commercial powders of Mg2SiO4 and MgO were mixed and ground in WC grinders and dried in a one-atmosphere furnace at 1000°C. Powders with different volume proportions of the two phases (up to 50 vol% of MgO) were sintered by spark plasma sintering at temperatures of 1300-1400°C and 100 MPa for a few minutes, resulting in dense pellets 8 mm in diameter and 3-4 mm in length. Deformation experiments on samples 1.2 mm in diameter and 1.2 mm in length were performed at 3-8 GPa and 1000-1300°C in a D-DIA apparatus coupled with synchrotron X-ray radiation. The technique permits in situ measurement of macroscopic strain rates as well as stress levels sustained by different subpopulations of grains of each phase. Typically, two specimens were deformed concurrently in order to minimize the relative uncertainties in temperature and pressure and to facilitate the comparison of their rheological properties. The samples were deformed to total strains of 15-25%. The harder phase, forsterite, sustains significantly higher stress levels than MgO, as predicted by numerical models for two-phase flow. Microstructural analysis by SEM reveals equilibrated microstructures in the starting samples, with well-mixed forsterite and MgO layers alternating with forsterite-rich layers. In the deformed samples, this compositional banding is accentuated, with more intense deformation in the well-mixed layers. Results on stress and strain partitioning in polyphase aggregates in the

  12. Operational results of the spallation neutron source (SNS) polyphase converter-modulator for the 140 KV klystron RF system

    SciTech Connect

    Reass, W. A.; Doss, James D.; Gribble, R. F.; Lynch, M. T.; Rees, D. E.; Tallerico, P. J.; Borovina, D. L.

    2001-01-01

    This paper describes the first operational results of the 140 kV, 1 MW average, 11 MW peak, zero-voltageswitching, 20 kHz polyphase bridge, boost converter-modulator for klystron pulse application. The DC-DC converter derives the buss voltages from a standard 13.8 kV to 2100 Y substation cast-core transformer. Energy storage and filtering is provided by self-clearing metallized hazy polypropylene traction capacitors. Three 'H-Bridge' Insulated Gate Bipolar Transistor (IGBT) switching networks are used to generate the polyphase 20 kHz transformer primary drive waveforms. The 20 kHz drive waveforms are chirped the appropriate duration to generate the desired klystron pulse width. Pulse-Width Modulation (PWM) of the individual 20 kHz pulses is utilized to provide regulated output waveforms with adaptive feedforward and feedback techniques. The boost transformer design utilizes amorphous nanocrystalline material that provides the required low core loss at design flux levels and switching frequencies. Resonant shunt peaking is used on the transformer secondary to boost output voltage and resonate transformer leakage inductance. With the appropriate transformer leakage inductance and peaking capacitance, zero-voltage-switching of the IGBT's is attained, minimizing switching losses. Reviews of these design parameters and an examination of the first operational results will be performed.

  13. OPERATIONAL RESULTS OF THE SPALLATION NEUTRON SOURCE (SNS) POLYPHASE CONVERTER-MODULATOR FOR THE 140 KV KLYSTRON RF SYSTEMS

    SciTech Connect

    W.A. REASS; J.D. DOSS; ET AL

    2001-06-01

    This paper describes the first operational results of the 140 kV, 1 MW average, 11 MW peak, zero-voltage-switching, 20 kHz polyphase bridge, boost converter-modulator for klystron pulse application. The DC-DC converter derives the buss voltages from a standard 13.8 kV to 2100 Y substation cast-core transformer. Energy storage and filtering is provided by self-clearing metallized hazy polypropylene traction capacitors. Three ''H-Bridge'' Insulated Gate Bipolar Transistor (IGBT) switching networks are used to generate the polyphase 20 kHz transformer primary drive waveforms. The 20 kHz drive waveforms are chirped the appropriate duration to generate the desired klystron pulse width. Pulse-Width Modulation (PWM) of the individual 20 kHz pulses is utilized to provide regulated output waveforms with adaptive feedforward and feedback techniques. The boost transformer design utilizes amorphous nanocrystalline material that provides the required low core loss at design flux levels and switching frequencies. Resonant shunt peaking is used on the transformer secondary to boost output voltage and resonate transformer leakage inductance. With the appropriate transformer leakage inductance and peaking capacitance, zero-voltage-switching of the IGBT's is attained, minimizing switching losses. Reviews of these design parameters and an examination of the first operational results will be performed.

  14. Production Of Multi-magnetron Plasma By Using Polyphase Ac Glow Discharge In An Improved Multi-pole Magnetic Field

    NASA Astrophysics Data System (ADS)

    Matsumoto, Kazunori; Motoki, Kentaro; Miyamoto, Masahiro; Uetani, Yasuhiro

    1998-10-01

    Effects of an improved multi-pole magnetic field on a plasma production generated by a polyphase ac glow discharge with multiple electrodes have been investigated. Conventional configuration of the multi-pole magnetic filed has been modified to suppress plasma losses at both ends of the chamber due to ExB drift motion. The modified multi-pole magnetic field has enabled us to produce a multiple magnetron-plasma at a considerably low pressure less than mTorr. The low temperature plasma has been widely used as the fine processing technology of a dry etching and as the thin film formation technology of a sputtering coating. Large-scale plasmas which can be generated at a low gas-pressure have been desired for more wider dry etching and greater sputter coating. The purpose of this study is to develop a large-scale and low-cost plasma generator by using a polyphase ac power source with the low frequency. In this session, we will present the experimental result as to a multiple magnetron-plasma generated in the modified twenty-four poles magnetic field by using the twenty-four-phase ac power source with the commercial electric power frequency of 60Hz. The ac power is supplied to twenty-four electrodes which are fixed to the water-cooled chamber-wall through sheet insulators so that the electrodes can be cooled indirectly.

  15. Molecular ecology and polyphasic characterization of the microbiota associated with semi-dry processed coffee (Coffea arabica L.).

    PubMed

    Vilela, Danielle Marques; Pereira, Gilberto Vinícius de M; Silva, Cristina Ferreira; Batista, Luís Roberto; Schwan, Rosane Freitas

    2010-12-01

    This work was aimed at isolating and identifying the microbiota present during the semi-dry method of coffee processing using polyphasic methods and to evaluate microbial diversity with PCR-DGGE. Samples of Coffea arabica L. were collected during different processing stages in southern Minas Gerais, Brazil. The bacterial and fungal isolates were phenotypically characterised and grouped according to the ARDRA technique, in which the 16-23S and ITS1-5.8S regions of the rDNA were sequenced for species identification. The bacterial counts varied from 3.7 to 7 log CFU g(-1). The yeast counts ranged from 3.4 to 6.9 log CFU g(-1), and the filamentous fungal population varied from 2 to 3.7 log CFU g(-1). Bacillus subtilis, Escherichia coli, Enterobacter agglomerans, Bacillus cereus and Klebsiella pneumoniae were the predominant bacteria detected during the processing of the coffee, and Pichia anomala, Torulaspora delbrueckii and Rhodotorula mucilaginosa were the dominant yeasts. All of the yeast and bacterial species detected by PCR-DGGE were isolated using culture-dependent methods, with the exception of one uncultivable bacterial species. Aspergillus was the most common genus among the filamentous fungal isolates. The use of polyphasic methods allowed a better characterization of the microbiota that is naturally present in semi-dry processed coffee. PMID:20832694

  16. Integrating and visualizing primary data from prospective and legacy taxonomic literature.

    PubMed

    Miller, Jeremy A; Agosti, Donat; Penev, Lyubomir; Sautter, Guido; Georgiev, Teodor; Catapano, Terry; Patterson, David; King, David; Pereira, Serrano; Vos, Rutger Aldo; Sierra, Soraya

    2015-01-01

    Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions. PMID

  17. Integrating and visualizing primary data from prospective and legacy taxonomic literature

    PubMed Central

    Agosti, Donat; Penev, Lyubomir; Sautter, Guido; Georgiev, Teodor; Catapano, Terry; Patterson, David; King, David; Pereira, Serrano; Vos, Rutger Aldo; Sierra, Soraya

    2015-01-01

    Abstract Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions

  18. Taxonomic characterization and metabolic analysis of the Halomonas sp. KM-1, a highly bioplastic poly(3-hydroxybutyrate)-producing bacterium.

    PubMed

    Kawata, Yoshikazu; Shi, Lian-Hua; Kawasaki, Kazunori; Shigeri, Yasushi

    2012-04-01

    In a brief previous report, the gram-negative moderately halophilic bacterium, Halomonas sp. KM-1, that was isolated in our laboratory was shown to produce the bioplastic, poly(3-hydroxybutyrate) (PHB), using biodiesel waste glycerol (Kawata and Aiba, Biosci. Biotechnol. Biochem., 74, 175-177, 2010). Here, we further characterized this KM-1 strain and compared it to other Halomonas strains. Strain KM-1 was subjected to a polyphasic taxonomic study. Strain KM-1 was rod-shaped and formed colonies on a plate that were cream-beige in color, smooth, opaque, and circular with entire edges. KM-1 grew under environmental conditions of 0.1%-10% (w/v) NaCl, pH 6.5-10.5 and at temperatures between 10°C and 45°C. The G+C content of strain KM-1 was 63.9 mol%. Of the 16 Halomonas strains examined in this study, the strain KM-1 exhibited the highest production of PHB (63.6%, w/v) in SOT medium supplemented with 10% glycerol, 10.0 g/L sodium nitrate and 2.0 g/L dipotassium hydrogen phosphate. The intracellular structures within which PHB accumulated had the appearance of intracellular granules with a diameter of approximately 0.5 μm, as assessed by electron microscopy. The intra- and extra-cellular metabolites of strain KM-1 were analyzed by capillary electrophoresis mass spectrometry. In spite of the high amount of PHB stored intra-cellularly, as possible precursors for PHB only a small quantity of 3-hydroxybutyric acid and acetyl CoA, and no quantity of 3-hydroxybutyl CoA, acetoacetyl CoA and acetoacetate were detected either intra- or extra-cellularly, suggesting highly efficient conversion of these precursors to PHB. PMID:22172913

  19. Thermochronological evidence for polyphase post-rift reactivation in SE Brazil

    NASA Astrophysics Data System (ADS)

    Cogné, N.; Gallagher, K.; Cobbold, P. R.; Riccomini, C.

    2012-04-01

    area cooled and uplifted during the Neogene. The synchronicity of the cooling phases with tectonic pulses in the Andes and in NE Brazil, as well as the tectonic setting of the Tertiary basins (Cogné et al., submitted) lead us to attribute these phases to a plate-wide compressive stress, which reactivated inherited structures during the Late Cretaceous and Tertiary. The relief of the margin is therefore due, more to polyphase post-rift reactivation and uplift, than to rifting itself. - Cobbold, P.R., Meisling, K.E., Mount, V.S., 2001. Reactivation of an obliquely rifted margin, Campos and Santos Basins, Southeastern Brazil. AAPG Bulletin 85, 1925-1944. - Cogné, N., Gallagher, K., Cobbold, P.R., 2011. Post-rift reactivation of the onshore margin of southeast Brazil: Evidence from apatite (U-Th)/He and fission-track data. Earth and Planetary Science Letters 309, 118-130. - Cogné, N., Cobbold, P.R., Riccomini, C., Gallagher, K. Tectonic setting of the Taubaté basin (southeastern Brazil): insights from regional seismic profiles and outcrop data. Submitted to Journal of South American Earth Sciences.

  20. A Taxonomic Study of the Genus Myelochroa in South Korea

    PubMed Central

    Jayalal, Udeni; Joshi, Santosh; Oh, Soon-Ok; Koh, Young Jin

    2012-01-01

    Myelochroa (Asahina) Elix & Hale is a common foliose lichen genus found on the Korean Peninsula. Since it was first recorded nearly two decades ago, no detailed taxonomic or revisionary study of the genus has been conducted. Thus, the current study was conducted to carry out a detailed taxonomic and revisionary study of Myelochroa in South Korea. This study was based on specimens deposited in the Korean Lichen Research Institute (KoLRI). Detailed taxonomic studies and a literature review confirmed the presence of twelve species of Myelochroa from S. Korea, including one new record, Myelochroa xantholepis (Mont. & Bosch) Elix & Hale. Descriptions of each species with their morphological, anatomical and chemical characters together with a key to all known Myelochroa species are presented. PMID:23323045

  1. DNA barcode-based delineation of putative species: efficient start for taxonomic workflows

    PubMed Central

    Kekkonen, Mari; Hebert, Paul D N

    2014-01-01

    The analysis of DNA barcode sequences with varying techniques for cluster recognition provides an efficient approach for recognizing putative species (operational taxonomic units, OTUs). This approach accelerates and improves taxonomic workflows by exposing cryptic species and decreasing the risk of synonymy. This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths. OTUs supported by all three approaches were viewed as robust, but 20% of the OTUs were only recognized by one or two of the methods. These OTUs were examined for three criteria to clarify their status. Monophyly and diagnostic nucleotides were both uninformative, but information on ranges was useful as sympatric sister OTUs were viewed as distinct, while allopatric OTUs were merged. This approach revealed 124 OTUs of Hypertrophinae, a more than twofold increase from the currently recognized 51 species. Because this analytical protocol is both fast and repeatable, it provides a valuable tool for establishing a basic understanding of species boundaries that can be validated with subsequent studies. PMID:24479435

  2. Polyphasic Characterization of a Thermotolerant Siderophilic Filamentous Cyanobacterium That Produces Intracellular Iron Deposits ▿ †

    PubMed Central

    Brown, Igor I.; Bryant, Donald A.; Casamatta, Dale; Thomas-Keprta, Kathie L.; Sarkisova, Svetlana A.; Shen, Gaozhong; Graham, Joel E.; Boyd, Eric S.; Peters, John W.; Garrison, Daniel H.; McKay, David S.

    2010-01-01

    Despite the high potential for oxidative stress stimulated by reduced iron, contemporary iron-depositing hot springs with circum-neutral pH are intensively populated with cyanobacteria. Therefore, studies of the physiology, diversity, and phylogeny of cyanobacteria inhabiting iron-depositing hot springs may provide insights into the contribution of cyanobacteria to iron redox cycling in these environments and new mechanisms of oxidative stress mitigation. In this study the morphology, ultrastructure, physiology, and phylogeny of a novel cyanobacterial taxon, JSC-1, isolated from an iron-depositing hot spring, were determined. The JSC-1 strain has been deposited in ATCC under the name Marsacia ferruginose, accession number BAA-2121. Strain JSC-1 represents a new operational taxonomical unit (OTU) within Leptolyngbya sensu lato. Strain JSC-1 exhibited an unusually high ratio between photosystem (PS) I and PS II, was capable of complementary chromatic adaptation, and is apparently capable of nitrogen fixation. Furthermore, it synthesized a unique set of carotenoids, but only chlorophyll a. Strain JSC-1 not only required high levels of Fe for growth (≥40 μM), but it also accumulated large amounts of extracellular iron in the form of ferrihydrite and intracellular iron in the form of ferric phosphates. Collectively, these observations provide insights into the physiological strategies that might have allowed cyanobacteria to develop and proliferate in Fe-rich, circum-neutral environments. PMID:20709851

  3. [A new lymph node imaging agent--99mTc-polyphase liposome oleatis (99mTc-plo)].

    PubMed

    Yu, B F

    1988-07-01

    A new lymph node radio-imaging agent, technetium-99m polyphase liposome oleatis (99mTc-plo), has recently been developed. Polyphase liposome oleatis was labelled with radionuclide by stannous chloride method. The labelled rate was 90% or more as technically identified by thin layer chromatography, external gamma-camera imaging and radioautography. In animal experiment, 0.2-0.3 ml (0.2 mci) of the 99mTc-plo was injected subcutaneously into the toes web of rats. After half an hour, the regional lymph nodes of popliteal fossa were visualized very clearly. The imaging figures may keep their distinct shadow up to 24 hours. The tested rabbits were sacrificed 10 hours after 99mTc-plo injection for detecting various kinds of tissue and organ with a scintillation counter. The regional lymph nodes revealed the highest uptake rate of the new agent, 12,116; 1,303; 1,615 times higher than that of the adjacent muscles, liver and spleen, respectively. In clinical experiment, 0.2-0.3 ml (0.5-0.8 mci) of the 99mTc-plo was injected subcutaneously into the toes web of patients. Half an hour later, the lymph nodes of inguinal, external iliac and common iliac regions appeared in sequence. If the new agent is injected perianally, the internal iliac lymph nodes will be seen. No side effect was observed in both types of experiment. This new agent has been tried in rats, rabbits and dogs with similar positive results. The new lymph node imaging technique is simple, safe, reliable and reproducible. This agent, being directed toward the lymph nodes and possessing affinity to cancer cells, is expected to be supplementary method to CT and B-ultrasonography for detecting lymphoid malignancy and lymph node metastasis. PMID:3248482

  4. Guidelines for quality assurance and quality control of fish taxonomic data collected as part of the National Water-Quality Assessment Program

    USGS Publications Warehouse

    Walsh, Stephen Joseph; Meador, Michael R.

    1998-01-01

    Fish community structure is characterized by the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program as part of a perennial, multidisciplinary approach to evaluating the physical, chemical, and biological conditions of the Nation's water resources. The objective of quality assurance and quality control of fish taxonomic data that are collected as part of the NAWQA Program is to establish uniform guidelines and protocols for the identification, processing, and archiving of fish specimens to ensure that accurate and reliable data are collected. Study unit biologists, collaborating with regional biologists and fish taxonomic specialists, prepare a pre-sampling study plan that includes a preliminary faunal list and identification of an ichthyological curation center for receiving preserved fish specimens. Problematic taxonomic issues and protected taxa also are identified in the study plan, and collecting permits are obtained in advance of sampling activities. Taxonomic specialists are selected to identify fish specimens in the field and to assist in determining what fish specimens should be sacrificed, fixed, and preserved for laboratory identification, independent taxonomic verification, and long-term storage in reference or voucher collections. Quantitative and qualitative sampling of fishes follows standard methods previously established for the NAWQA Program. Common ichthyological techniques are used to process samples in the field and prepare fish specimens to be returned to the laboratory or sent to an institutional repository. Taxonomic identifications are reported by using a standardized list of scientific names that provides nomenclatural consistency and uniformity across study units.

  5. Taxonomic scheme for the identification of marine bacteria

    NASA Astrophysics Data System (ADS)

    Oliver, James D.

    1982-06-01

    A recently developed taxonomic scheme for the identification of marine bacteria is presented. The scheme is based on numerous reviews and monographs on marine bacteria, as well as Bergey's Manual of Determinative Bacteriology. While fairly extensive, the scheme is designed to identify marine bacteria using relatively few tests.

  6. Natural products discovery needs improved taxonomic and geographic information.

    PubMed

    Leal, Miguel C; Hilário, Ana; Munro, Murray H G; Blunt, John W; Calado, Ricardo

    2016-06-01

    Covering: up to 2016Marine and terrestrial organisms yield a remarkable chemical diversity and are important sources for discovery of new chemical products. In order to maximize the bioprospecting efficiency of natural products (NP), taxonomy, geography and biodiversity are starting to be used to draw conclusions on which taxonomic groups and/or regions may be of interest for future research. However, accurate taxonomic information and sampling location of source organisms have often been overlooked. Although these issues were already reported a few decades ago and improvements have been made, such outstanding problems are still recurrent in recent peer-reviewed literature. Here, we focus on the importance of taxonomic and geographic identification of source material and illustrate how taxonomic and geographic data of source organisms continues to be poorly handled. It is our opinion that this issue needs to be discussed within the NP community with the ultimate goal of improving publication standards and guaranteeing the scientific principle of research reproducibility. Moreover, by doing so, it will be possible to take advantage of information available in the literature to develop cross-disciplinary meta-analyses that may help to advance the state of the art of NP research and future bioprospecting endeavours. PMID:26892141

  7. The Development of Taxonomic Structure in Lexical Memory.

    ERIC Educational Resources Information Center

    Blewitt, Pamela; Toppino, Thomas C.

    1991-01-01

    Recall of "to-be-remembered items" benefited from schematically related, superordinate, and slot filler cues, but not coordinate cues. The relative strength of different relationships does not appear to change with age. Findings are consistent with the view that lexical memory is schematically and taxonomically organized from early childhood.…

  8. Individual Differences in the Strength of Taxonomic versus Thematic Relations

    ERIC Educational Resources Information Center

    Mirman, Daniel; Graziano, Kristen M.

    2012-01-01

    Knowledge about word and object meanings can be organized taxonomically (fruits, mammals, etc.) on the basis of shared features or thematically (eating breakfast, taking a dog for a walk, etc.) on the basis of participation in events or scenarios. An eye-tracking study showed that both kinds of knowledge are activated during comprehension of a…

  9. e-DNA meta-barcoding: from NGS raw data to taxonomic profiling.

    PubMed

    Bruno, Fosso; Marinella, Marzano; Santamaria, Monica

    2015-01-01

    In recent years, thanks to the essential support provided by the Next-Generation Sequencing (NGS) technologies, Metagenomics is enabling the direct access to the taxonomic and functional composition of mixed microbial communities living in any environmental niche, without the prerequisite to isolate or culture the single organisms. This approach has already been successfully applied for the analysis of many habitats, such as water or soil natural environments, also characterized by extreme physical and chemical conditions, food supply chains, and animal organisms, including humans. A shotgun sequencing approach can lead to investigate both organisms and genes diversity. Anyway, if the purpose is limited to explore the taxonomic complexity, an amplicon-based approach, based on PCR-targeted sequencing of selected genetic species markers, commonly named "meta-barcodes", is desirable. Among the genomic regions most widely used for the discrimination of bacterial organisms, in some cases up to the species level, some hypervariable domains of the gene coding for the 16S rRNA occupy a prominent place. The amplification of a certain meta-barcode from a microbial community through the use of PCR primers able to work in the entire considered taxonomic group is the first task after the extraction of the total DNA. Generally, this step is followed by the high-throughput sequencing of the resulting amplicons libraries by means of a selected NGS platform. Finally, the interpretation of the huge amount of produced data requires appropriate bioinformatics tools and know-how in addition to efficient computational resources. Here a computational methodology suitable for the taxonomic characterization of 454 meta-barcode sequences is described in detail. In particular, a dataset covering the V1-V3 region belonging to the bacterial 16S rRNA coding gene and produced in the Human Microbiome Project (HMP) from a palatine tonsils sample is analyzed. The proposed exercise includes the

  10. A polyphasic approach for characterization of a collection of cereal isolates of the Fusarium incarnatum-equiseti species complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA-based phylogenetic analyses have resolved the fungal genus Fusarium into multiple species complexes. The F. incarnatum-equiseti species complex (FIESC) includes fusaria associated with several diseases of agriculturally important crops, including cereals. Although members of FIESC are considered...

  11. Beta Diversity in a Highly Heterogeneous Area: Disentangling Species and Taxonomic Dissimilarity for Terrestrial Vertebrates.

    PubMed

    Calderón-Patrón, Jaime M; Goyenechea, Irene; Ortiz-Pulido, Raúl; Castillo-Cerón, Jesús; Manriquez, Norma; Ramírez-Bautista, Aurelio; Rojas-Martínez, Alberto E; Sánchez-Rojas, Gerardo; Zuria, Iriana; Moreno, Claudia E

    2016-01-01

    Quantifying differences in species composition among communities provides important information related to the distribution, conservation and management of biodiversity, especially when two components are recognized: dissimilarity due to turnover, and dissimilarity due to richness differences. The ecoregions in central Mexico, within the Mexican Transition Zone, have outstanding environmental heterogeneity and harbor huge biological richness, besides differences in the origin of the biota. Therefore, biodiversity studies in this area require the use of complementary measures to achieve appropriate information that may help in the design of conservation strategies. In this work we analyze the dissimilarity of terrestrial vertebrates, and the components of turnover and richness differences, among six ecoregions in the state of Hidalgo, central Mexico. We follow two approaches: one based on species level dissimilarity, and the second on taxonomic dissimilarity. We used databases from the project "Biodiversity in the state of Hidalgo". Our results indicate that species dissimilarity is higher than taxonomic dissimilarity, and that turnover contributes more than richness differences, both for species and taxonomic total dissimilarity. Moreover, total dissimilarity, turnover dissimilarity and the dissimilarity due to richness differences were positively related in the four vertebrate groups. Reptiles had the highest values of dissimilarity, followed by mammals, amphibians and birds. For reptiles, birds, and mammals, species turnover was the most important component, while richness differences had a higher contribution for amphibians. The highest values of dissimilarity occurred between environmentally contrasting ecoregions (i.e., tropical and temperate forests), which suggests that environmental heterogeneity and differences in the origin of biotas are key factors driving beta diversity of terrestrial vertebrates among ecoregions in this complex area. PMID:27500934

  12. Beta Diversity in a Highly Heterogeneous Area: Disentangling Species and Taxonomic Dissimilarity for Terrestrial Vertebrates

    PubMed Central

    Calderón-Patrón, Jaime M.; Goyenechea, Irene; Ortiz-Pulido, Raúl; Castillo-Cerón, Jesús; Manriquez, Norma; Ramírez-Bautista, Aurelio; Rojas-Martínez, Alberto E.; Sánchez-Rojas, Gerardo; Zuria, Iriana

    2016-01-01

    Quantifying differences in species composition among communities provides important information related to the distribution, conservation and management of biodiversity, especially when two components are recognized: dissimilarity due to turnover, and dissimilarity due to richness differences. The ecoregions in central Mexico, within the Mexican Transition Zone, have outstanding environmental heterogeneity and harbor huge biological richness, besides differences in the origin of the biota. Therefore, biodiversity studies in this area require the use of complementary measures to achieve appropriate information that may help in the design of conservation strategies. In this work we analyze the dissimilarity of terrestrial vertebrates, and the components of turnover and richness differences, among six ecoregions in the state of Hidalgo, central Mexico. We follow two approaches: one based on species level dissimilarity, and the second on taxonomic dissimilarity. We used databases from the project “Biodiversity in the state of Hidalgo”. Our results indicate that species dissimilarity is higher than taxonomic dissimilarity, and that turnover contributes more than richness differences, both for species and taxonomic total dissimilarity. Moreover, total dissimilarity, turnover dissimilarity and the dissimilarity due to richness differences were positively related in the four vertebrate groups. Reptiles had the highest values of dissimilarity, followed by mammals, amphibians and birds. For reptiles, birds, and mammals, species turnover was the most important component, while richness differences had a higher contribution for amphibians. The highest values of dissimilarity occurred between environmentally contrasting ecoregions (i.e., tropical and temperate forests), which suggests that environmental heterogeneity and differences in the origin of biotas are key factors driving beta diversity of terrestrial vertebrates among ecoregions in this complex area. PMID:27500934

  13. A taxonomic synopsis of Altingiaceae with nine new combinations

    PubMed Central

    Ickert-Bond, Stefanie M.; Wen, Jun

    2013-01-01

    Abstract A taxonomic synopsis of the Altingiaceae is presented, including the taxonomic enumeration and distribution of 15 recognized species based on studies of 1,500 specimens from 24 herbaria throughout the distributional range of the taxa. Previous phylogenetic analyses based on several molecular markers have shown that Altingia and Semiliquidambar are nested within Liquidambar. All Altingia and Semiliquidambar species are now formally transferred to Liquidambar, which has the nomenclatural priority. The following nine new combinations are herein made: Liquidambar cambodiana(Lecomte) Ickert-Bond & J. Wen, Liquidambar caudata (H. T. Chang) Ickert-Bond & J. Wen, Liquidambar chingii (Metcalf) Ickert-Bond & J. Wen, Liquidambar gracilipes (Hemsl.) Ickert-Bond & J. Wen, Liquidambar multinervis(Cheng) Ickert-Bond & J. Wen, Liquidambar obovata (Merrill & Chun) Ickert-Bond & J. Wen, Liquidambar poilanei (Tardieu) Ickert-Bond & J. Wen, Liquidambar siamensis (Craib) Ickert-Bond & J. Wen, and Liquidambar yunnanensis (Rehder & Wilson) Ickert-Bond & J. Wen. PMID:24399902

  14. Minimum taxonomic criteria for bacterial genome sequence depositions and announcements.

    PubMed

    Bull, Matthew J; Marchesi, Julian R; Vandamme, Peter; Plummer, Sue; Mahenthiralingam, Eshwar

    2012-04-01

    Multiple bioinformatic methods are available to analyse the information encoded within the complete genome sequence of a bacterium and accurately assign its species status or nearest phylogenetic neighbour. However, it is clear that even now in what is the third decade of bacterial genomics, taxonomically incorrect genome sequence depositions are still being made. We outline a simple scheme of bioinformatic analysis and a set of minimum criteria that should be applied to all bacterial genomic data to ensure that they are accurately assigned to the species or genus level prior to database deposition. To illustrate the utility of the bioinformatic workflow, we analysed the recently deposited genome sequence of Lactobacillus acidophilus 30SC and demonstrated that this DNA was in fact derived from a strain of Lactobacillus amylovorus. Using these methods researchers can ensure that the taxonomic accuracy of genome sequence depositions is maintained within the ever increasing nucleic acid datasets. PMID:22366464

  15. BOTUX: Bayesian-like operational taxonomic unit examiner

    PubMed Central

    Koparde, Vishal N.; Adkins, Ricky S.; Fettweis, Jennifer M.; Serrano, Myrna G.; Buck, Gregory A.

    2015-01-01

    Bayesian-like operational taxonomic unit examiner (BOTUX) is a new tool for the classification of 16S rRNA gene sequences into operational taxonomic units (OTUs) that addresses the problem of overestimation caused by errors introduced during PCR amplification and DNA sequencing steps. BOTUX utilises a grammar-based assignment strategy, where Bayesian models are built from each word of a given length (e.g., 8-mers). de novo analysis is possible with BOTUX as it does not require a training set, and updates probabilistic models as new sequences are recruited to an OTU. In benchmarking tests performed with real and simulated datasets of 16S rDNA sequences, BOTUX accurately identifies OTUs with comparable or better clustering efficiency and lower execution times than other OTU algorithms tested. BOTUX is the only OTU classifier, which allows incremental analysis of large datasets, and is also adept in clustering both 454 and Illumina datasets in a reasonable timeframe. PMID:24878725

  16. A taxonomic catalogue of Japanese nemerteans (phylum Nemertea).

    PubMed

    Kajihara, Hiroshi

    2007-04-01

    A literature-based taxonomic catalogue of the nemertean species (Phylum Nemertea) reported from Japanese waters is provided, listing 19 families, 45 genera, and 120 species as valid. Applications of the following species names to forms previously recorded from Japanese waters are regarded as uncertain: Amphiporus cervicalis, Amphiporus depressus, Amphiporus lactifloreus, Cephalothrix filiformis, Cephalothrix linearis, Cerebratulus fuscus, Lineus vegetus, Lineus bilineatus, Lineus gesserensis, Lineus grubei, Lineus longifissus, Lineus mcintoshii, Nipponnemertes pulchra, Oerstedia venusta, Prostoma graecense, and Prostoma grande. The identities of the taxa referred to by the following four nominal species require clarification through future investigations: Cosmocephala japonica, Dicelis rubra, Dichilus obscurus, and Nareda serpentina. The nominal species established from Japanese waters are tabulated. In addition, a brief history of taxonomic research on Japanese nemerteans is reviewed. PMID:17867829

  17. Biogeographical and taxonomic biases in tropical forest fragmentation research.

    PubMed

    Deikumah, Justus P; McAlpine, Clive A; Maron, Martine

    2014-12-01

    Despite several decades of research on the effects of fragmentation and habitat change on biodiversity, there remain strong biases in the geographical regions and taxonomic species studied. The knowledge gaps resulting from these biases are of particular concern if the forests most threatened with modification are also those for which the effects of such change are most poorly understood. To quantify the nature and magnitude of such biases, we conducted a systematic review of the published literature on forest fragmentation in the tropics for the period 1980-2012. Studies included focused on any type of response of single species, communities, or assemblages of any taxonomic group to tropical forest fragmentation and on fragmentation-related changes to forests. Of the 853 studies we found in the SCOPUS database, 64% were conducted in the Neotropics, 13% in Asia, 10% in the Afrotropics, and 5% in Australasia. Thus, although the Afrotropics is subject to the highest rates of deforestation globally, it was the most disproportionately poorly studied biome. Significant taxonomic biases were identified. Of the taxonomic groups considered, herpetofauna was the least studied in the tropics, particularly in Africa. Research examining patterns of species distribution was by far the most common type (72%), and work focused on ecological processes (28%) was rare in all biomes, but particularly in the Afrotropics and for fauna. We suggest research efforts be directed toward less-studied biogeographic regions, particularly where the threat of forest fragmentation continues to be high. Increased research investment in the Afrotropics will be important to build knowledge of threats and inform responses in a region where almost no efforts to restore its fragmented landscapes have yet begun and forest protection is arguably most tenuous. PMID:25065550

  18. Insights from Zootaxa on potential trends in zoological taxonomic activity

    PubMed Central

    2011-01-01

    Background An opinion currently shared by taxonomists and non taxonomists alike is that the work of inventorying biodiversity is unbalanced: firstly, in favour of countries in which taxonomy has been studied for a long time, and, secondly, in favour of vertebrates. In the current context of threats of species extinction, access for taxonomists to biological material and information becomes crucial if the scientific community really aims at a better knowledge of biological diversity before it is severely and irreversibly impoverished. We performed an analysis of 748 papers published in Zootaxa in 2006 and 2007, as well as 434 questionnaires sent to their authors to test these opinions. A generalization of these results to zoological taxonomy as a whole is discussed. Discussion We found that the disequilibrium is not exactly what it usually considered to be. The USA, China and Brazil are currently the three leading countries in zoological taxonomy. Each of them presents, however, a different pattern. Taxonomists from Asia and South America are younger and mainly work in universities, not museums. A bias in favour of vertebrates still exists if we refer to the effort invested in each group to produce taxonomic data, but not to the number of papers. Finally, we insist on the idea that "describing a species" is very different from "knowing a species". Summary The taxonomic involvement of a country, in terms of manpower and funding, appears to be a key factor in the development of fruitful taxonomic research. This message seems to have been understood by the countries that recently decided to increase considerably their taxonomic involvement. It still has to be received by those who did not. PMID:21418568

  19. Taxonomic revision of oil-producing green algae, Chlorococcum oleofaciens (Volvocales, Chlorophyceae), and its relatives.

    PubMed

    Kawasaki, Yuriko; Nakada, Takashi; Tomita, Masaru

    2015-10-01

    Historically, species in Volvocales were classified based primarily on morphology. Although the taxonomy of Chlamydomonas has been re-examined using a polyphasic approach including molecular phylogeny, that of Chlorococcum (Cc.), the largest coccoid genus in Volvocales, has yet to be reexamined. Six species thought to be synonymous with the oil-producing alga Cc. oleofaciens were previously not confirmed by molecular phylogeny. In this study, seven authentic strains of Cc. oleofaciens and its putative synonyms, along with 11 relatives, were examined based on the phylogeny of the 18S ribosomal RNA (rRNA) gene, comparisons of secondary structures of internal transcribed spacer 1 (ITS1) and ITS2 rDNA, and morphological observations by light microscopy. Seven 18S rRNA types were recognized among these strains and three were distantly related to Cc. oleofaciens. Comparisons of ITS rDNA structures suggested possible separation of the remaining four types into different species. Shapes of vegetative cells, thickness of the cell walls in old cultures, the size of cells in old cultures, and stigma morphology of zoospores also supported the 18S rRNA grouping. Based on these results, the 18 strains examined were reclassified into seven species. Among the putative synonyms, synonymy of Cc. oleofaciens, Cc. croceum, and Cc. granulosum was confirmed, and Cc. microstigmatum, Cc. rugosum, Cc. aquaticum, and Cc. nivale were distinguished from Cc. oleofaciens. Furthermore, another related strain is described as a new species, Macrochloris rubrioleum sp. nov. PMID:26986894

  20. Taxonomic description and genome sequence of Rheinheimera mesophila sp. nov., isolated from an industrial waste site.

    PubMed

    Kumar, Anand; Bajaj, Abhay; Mathan Kumar, Rajendran; Kaur, Gurwinder; Kaur, Navjot; Kumar Singh, Nitin; Manickam, Natesan; Mayilraj, Shanmugam

    2015-10-01

    A novel Gram-staining-negative gammaproteobacterium, designated IITR-13T, was isolated from a pesticide-contaminated soil and characterized using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, the strain showed the closest similarity (98.7 %) to Rheinheimera tangshanensis JA3-B52T followed by Rheinheimera texasensis A62-14BT (97.7 %) and Rheinheimera soli BD-d46T (97.3 %). The 16S rRNA gene sequence similarity of the novel strain to other members of the genus Rheinheimera was < 97.3 %. However, DNA-DNA hybridization between strain IITR-13T and the type strains of R. tangshanensis, R. texasensis and R. soli was 47.5 ± 0.6, 42.4 ± 0.4 and 39.8 ± 0.3 %, respectively; these values are less than 70 %, a threshold value for delineation of a novel species. The strain had C12 : 0 3-OH, C16 : 0, C17 : 1ω8c, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c) and C18 : 1ω6c as the major fatty acids. The major isoprenoid quinones detected for strain IITR-13T were ubiquinone Q-8 and menaquinone MK-7.The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and seven unknown phospholipids. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the novel strain should be assigned to a novel species, for which the name Rheinheimera mesophila sp. nov. is proposed, with the type strain IITR-13T ( = MTCC 12064T = DSM 29723T). Also, we report the draft genome sequence of Rheinheimera mesophila IITR-13T; the draft genome sequence includes 3 749 903 bases and comprises 3449 predicted coding sequences, with a G+C content of 47.8 %. It consists of 102 contigs (>1000 bp). PMID:26220076

  1. Deformation of polyphase aggregates, forsterite+MgO, at pressures and temperatures of the Earth's upper mantle

    NASA Astrophysics Data System (ADS)

    Bejina, F.; Bystricky, M.; Ingrin, J.

    2012-12-01

    Modelling the solid-state flow of the upper mantle requires a thorough understanding of its rheology and therefore necessitates to perform deformation experiments on mantle rocks (or analogues) at very high pressures and temperatures. Minerals other than olivine constitute up to 40 vol% of upper mantle rocks and may have a significant effect on the rheological behavior of these rocks. Nevertheless, most experimental studies to date have focused on the deformation properties of olivine single crystals or monomineralic olivine aggregates. In this study, and as a first step before focusing on more realistic mantle-like compositions, we have performed deformation experiments on polymineralic model aggregates of forsterite and MgO, at upper mantle pressures and temperatures. Commercial powders of Mg2SiO4 and MgO were mixed and ground in WC grinders and dried in a one-atmosphere furnace at 1000°C. Powders with different volume proportions of the two phases were sintered by spark plasma sintering (SPS) at temperatures of 1300-1400°C and 100 MPa for a few minutes, resulting in dense pellets 8 mm in diameter and 3-4 mm in length. Microstructural analysis by SEM reveals equilibrated microstructures with forsterite and MgO grain sizes of a few microns. Deformation experiments on samples 1.2 mm in diameter and 1.2 mm in length were performed at 3-8 GPa and 1000-1300°C in a D-DIA apparatus coupled with synchrotron X-ray radiation. The technique permits in situ measurement of macroscopic strain rates as well as stress levels sustained by different subpopulations of grains of each phase. Typically, two specimens, respectively a monomineralic and a polyphase aggregate, were deformed concurrently in order to minimize the relative uncertainties in temperature and pressure and to facilitate the comparison of their rheological properties. The samples were deformed to total strains of 15-25%. As expected, the harder phase, forsterite, sustains much higher stress levels than MgO, in

  2. On the relevance of molecular tools for taxonomic revision in Malvales, Malvaceae s.l., and Dombeyoideae.

    PubMed

    Le Péchon, Timothée; Gigord, Luc D B

    2014-01-01

    In this article, we present an overview of changes to the taxonomy of Malvales. In traditional classifications, this order was variously circumscribed as including four main families (i.e., Malvaceae, Bombacaceae, Sterculiaceae, and Tiliaceae, also known now as "Core Malvales"), but major disagreements existed between different taxonomic treatments. Contributions from molecular data, new morpho-anatomical data, and progress in methodological approaches have recently led to a new broader concept of this order (namely, "expanded Malvales"). Now, expanded Malvales includes ten families (Neuradaceae, Thymelaeaceae, Sphaerosepalaceae, Bixaceae, Cistaceae, Sarcolaenaceae, Dipterocarpaceae, Cytinaceae, Muntingiaceae, Malvaceae s.l.) distributed among seven monophyletic lineages. All these families were previously considered to have malvalean affinities in some traditional treatments, except the holoparasitic and highly modified Cytinaceae. Although molecular evidence has clarified the Malvales taxonomy, the phylogenetic positions of Sarcolaenaceae, Thymelaeaceae, and Sphaerosepalaceae are still controversial and need new analyses focusing specifically on these families to assess their phylogenetic placement and their morphological evolution.In a phylogenetic context, molecular data combined with recent examination of morphological characters supported the hypothesis of a common origin of "core Malvales." However, these analyses also showed that the former families but Malvaceae s.s. were paraphyletic or polyphyletic. As a consequence, recent taxonomic treatments grouped taxa formerly included in "Core Malvales" in a broader concept of Malvaceae s.l. Additionally, the intrafamilial taxonomy has been deeply modified, and in its present circumscription, Malvaceae includes nine subfamilies (Grewioideae, Byttnerioideae, Sterculioideae, Dombeyoideae, Brownlowioideae, Tilioideae, Bombacoideae, Malvoideae, Helicteroideae) in two main lineages. Phylogenetic studies on subfamilial

  3. A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda)

    PubMed Central

    Mateus, Octávio; Benson, Roger B.J.

    2015-01-01

    Diplodocidae are among the best known sauropod dinosaurs. Several species were described in the late 1800s or early 1900s from the Morrison Formation of North America. Since then, numerous additional specimens were recovered in the USA, Tanzania, Portugal, and Argentina, as well as possibly Spain, England, Georgia, Zimbabwe, and Asia. To date, the clade includes about 12 to 15 nominal species, some of them with questionable taxonomic status (e.g., ‘Diplodocus’ hayi or Dyslocosaurus polyonychius), and ranging in age from Late Jurassic to Early Cretaceous. However, intrageneric relationships of the iconic, multi-species genera Apatosaurus and Diplodocus are still poorly known. The way to resolve this issue is a specimen-based phylogenetic analysis, which has been previously implemented for Apatosaurus, but is here performed for the first time for the entire clade of Diplodocidae. The analysis includes 81 operational taxonomic units, 49 of which belong to Diplodocidae. The set of OTUs includes all name-bearing type specimens previously proposed to belong to Diplodocidae, alongside a set of relatively complete referred specimens, which increase the amount of anatomically overlapping material. Non-diplodocid outgroups were selected to test the affinities of potential diplodocid specimens that have subsequently been suggested to belong outside the clade. The specimens were scored for 477 morphological characters, representing one of the most extensive phylogenetic analyses of sauropod dinosaurs. Character states were figured and tables given in the case of numerical characters. The resulting cladogram recovers the classical arrangement of diplodocid relationships. Two numerical approaches were used to increase reproducibility in our taxonomic delimitation of species and genera. This resulted in the proposal that some species previously included in well-known genera like Apatosaurus and Diplodocus are generically distinct. Of particular note is that the famous genus

  4. Genomic insights into the taxonomic status of the Bacillus cereus group

    PubMed Central

    Liu, Yang; Lai, Qiliang; Göker, Markus; Meier-Kolthoff, Jan P.; Wang, Meng; Sun, Yamin; Wang, Lei; Shao, Zongze

    2015-01-01

    The identification and phylogenetic relationships of bacteria within the Bacillus cereus group are controversial. This study aimed at determining the taxonomic affiliations of these strains using the whole-genome sequence-based Genome BLAST Distance Phylogeny (GBDP) approach. The GBDP analysis clearly separated 224 strains into 30 clusters, representing eleven known, partially merged species and accordingly 19–20 putative novel species. Additionally, 16S rRNA gene analysis, a novel variant of multi-locus sequence analysis (nMLSA) and screening of virulence genes were performed. The 16S rRNA gene sequence was not sufficient to differentiate the bacteria within this group due to its high conservation. The nMLSA results were consistent with GBDP. Moreover, a fast typing method was proposed using the pycA gene, and where necessary, the ccpA gene. The pXO plasmids and cry genes were widely distributed, suggesting little correlation with the phylogenetic positions of the host bacteria. This might explain why classifications based on virulence characteristics proved unsatisfactory in the past. In summary, this is the first large-scale and systematic study of the taxonomic status of the bacteria within the B. cereus group using whole-genome sequences, and is likely to contribute to further insights into their pathogenicity, phylogeny and adaptation to diverse environments. PMID:26373441

  5. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

    PubMed Central

    O'Leary, Nuala A.; Wright, Mathew W.; Brister, J. Rodney; Ciufo, Stacy; Haddad, Diana; McVeigh, Rich; Rajput, Bhanu; Robbertse, Barbara; Smith-White, Brian; Ako-Adjei, Danso; Astashyn, Alexander; Badretdin, Azat; Bao, Yiming; Blinkova, Olga; Brover, Vyacheslav; Chetvernin, Vyacheslav; Choi, Jinna; Cox, Eric; Ermolaeva, Olga; Farrell, Catherine M.; Goldfarb, Tamara; Gupta, Tripti; Haft, Daniel; Hatcher, Eneida; Hlavina, Wratko; Joardar, Vinita S.; Kodali, Vamsi K.; Li, Wenjun; Maglott, Donna; Masterson, Patrick; McGarvey, Kelly M.; Murphy, Michael R.; O'Neill, Kathleen; Pujar, Shashikant; Rangwala, Sanjida H.; Rausch, Daniel; Riddick, Lillian D.; Schoch, Conrad; Shkeda, Andrei; Storz, Susan S.; Sun, Hanzhen; Thibaud-Nissen, Francoise; Tolstoy, Igor; Tully, Raymond E.; Vatsan, Anjana R.; Wallin, Craig; Webb, David; Wu, Wendy; Landrum, Melissa J.; Kimchi, Avi; Tatusova, Tatiana; DiCuccio, Michael; Kitts, Paul; Murphy, Terence D.; Pruitt, Kim D.

    2016-01-01

    The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55 000 organisms (>4800 viruses, >40 000 prokaryotes and >10 000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management. PMID:26553804

  6. [Preliminary clinical application of new bone marrow imaging agent 99mTc-polyphase liposome in malignant lymphoma].

    PubMed

    Yu, B F

    1990-07-01

    Bone marrow (BM) imaging with 99mTc-polyphase liposome in 30 malignant lymphoma patients demonstrated that central BM hypoplasia accounted for 90% (28/30) and peripheral BM hypoplasia 20% (6/30) with peripheral BM expansion of 80% (23/30). Focal BM lesion was shown in 7 patients which conformed with the results of bone imaging and X-ray film. The uptake index of BM in patients treated with chemotherapy was low as compared to that in patients treated with radiotherapy (P less than 0.05). Although BM suppression by chemotherapy was more severe than by radiotherapy, BM function essentially recovered 1 month after cessation of chemotherapy, on the other hand, while central BM suppression by radiotherapy was mild, it lasted for longer periods of time. Peripheral BM suppression by radiotherapy was both shorter in duration and milder in severity in comparison with central BM suppression. BM imaging is valuable for the understanding of BM function, ascertainment of the appropriate interval between treatments and early detection of local BM involvement. PMID:2272267

  7. Taxonomic and thematic organisation of proper name conceptual knowledge.

    PubMed

    Crutch, Sebastian J; Warrington, Elizabeth K

    2011-01-01

    We report the investigation of the organisation of proper names in two aphasic patients (NBC and FBI). The performance of both patients on spoken word to written word matching tasks was inconsistent, affected by presentation rate and semantic relatedness of the competing responses, all hallmarks of a refractory semantic access dysphasia. In a series of experiments we explored the semantic relatedness effects within their proper name vocabulary, including brand names and person names. First we demonstrated the interaction between very fine grain organisation and personal experience, with one patient with a special interest in the cinema demonstrating higher error rates when identifying the names of actors working in a similar film genre (e.g., action movies: Arnold Schwarzenegger, Bruce Willis, Sylvester Stallone, Mel Gibson) than those working in different genres (e.g., Arnold Schwarzenegger, Gregory Peck, Robin Williams, Gene Kelly). Second we compared directly two potential principles of semantic organisation - taxonomic and thematic. Furthermore we considered these principles of organisation in the context of the individuals' personal knowledge base. We selected topics matching the interests and experience of each patient, namely cinema and literature (NBC) and naval history (FBI). The stimulus items were arranged in taxonomic arrays (e.g., Jane Austen, Emily Bronte, Agatha Christie), thematic arrays (e.g., Jane Austen, Pride and Prejudice, Mr Darcy), and unrelated arrays (e.g., Jane Austen, Wuthering Heights, Hercule Poirot). We documented that different patterns of taxonomic and thematic organisation were constrained by whether the individual has limited knowledge, moderate knowledge or detailed knowledge of a particular vocabulary. It is suggested that moderate proper name knowledge is primarily organised by taxonomy whereas extensive experience results in a more detailed knowledge base in which theme is a powerful organising principle. PMID:22063815

  8. Species Delimitation in Taxonomically Difficult Fungi: The Case of Hymenogaster

    PubMed Central

    Stielow, Benjamin; Bratek, Zoltan; Orczán, Akos Kund I.; Rudnoy, Szabolcs; Hensel, Gunnar; Hoffmann, Peter; Klenk, Hans-Peter; Göker, Markus

    2011-01-01

    Background False truffles are ecologically important as mycorrhizal partners of trees and evolutionarily highly interesting as the result of a shift from epigeous mushroom-like to underground fruiting bodies. Since its first description by Vittadini in 1831, inappropriate species concepts in the highly diverse false truffle genus Hymenogaster has led to continued confusion, caused by a large variety of prevailing taxonomical opinions. Methodology In this study, we reconsidered the species delimitations in Hymenogaster based on a comprehensive collection of Central European taxa comprising more than 140 fruiting bodies from 20 years of field work. The ITS rDNA sequence dataset was subjected to phylogenetic analysis as well as clustering optimization using OPTSIL software. Conclusions Among distinct species concepts from the literature used to create reference partitions for clustering optimization, the broadest concept resulted in the highest agreement with the ITS data. Our results indicate a highly variable morphology of H. citrinus and H. griseus, most likely linked to environmental influences on the phenology (maturity, habitat, soil type and growing season). In particular, taxa described in the 19th century frequently appear as conspecific. Conversely, H. niveus appears as species complex comprising seven cryptic species with almost identical macro- and micromorphology. H. intermedius and H. huthii are described as novel species, each of which with a distinct morphology intermediate between two species complexes. A revised taxonomy for one of the most taxonomically difficult genera of Basidiomycetes is proposed, including an updated identification key. The (semi-)automated selection among species concepts used here is of importance for the revision of taxonomically problematic organism groups in general. PMID:21311589

  9. Taxonomic and trophic-level differences in the climate sensitivity of seasonal events

    NASA Astrophysics Data System (ADS)

    Høye, T. T.; Thackeray, S.; Henrys, P. A.; Hemming, D.; Bell, J. R.; Botham, M. S.; Burthe, S.; Helaouet, P.; Johns, D.; Jones, I. D.; Leech, D. I.; Mackay, E. B.; Massimino, D.; Atkinson, S.; Bacon, P. J.; Brereton, T. M.; Carvalho, L.; Clutton-Brock, T. H.; Duck, C.; Edwards, M.; Elliott, J. M.; Hall, S.; Harrington, R.; Pearce-Higgins, J. W.; Kruuk, L. E.; Pemberton, J. M.; Sparks, T. H.; Thompson, P. M.; White, I.; Winfield, I. J.; Wanless, S.

    2015-12-01

    Among-species differences in phenological responses to climate change are of sufficient magnitude to desynchronise key ecological interactions, threatening ecosystem function and services. To assess these threats, it is vital to quantify the relative impact of climate change on species at different trophic levels. Here we apply a novel Climate Sensitivity Profile approach to 10,003 terrestrial and aquatic phenological data sets, spatially matched to temperature and precipitation data, quantifying among-species variation in climate sensitivity. The direction, magnitude and timing of climate sensitivity varied markedly among organisms sharing taxonomic affinities or trophic position. Despite this, we detected a systematic difference in the direction and magnitude, but not seasonal timing, of phenological climate sensitivity among trophic levels. Secondary consumers showed consistently lower climate sensitivity than other groups and are projected to lag behind phenological changes at lower trophic levels, potentially making them at higher risk of disconnection with seasonal resources.

  10. Taxonomic study of amanita subgenus lepidella and three unrecorded amanita species in Korea.

    PubMed

    Kim, Chang Sun; Jo, Jong Won; Kwag, Young-Nam; Kim, Jae-Hyeun; Shrestha, Bhushan; Sung, Gi-Ho; Han, Sang-Kuk

    2013-12-01

    Amanita Pers. is a well-known monophyletic mushroom genus with a broad distribution. However, the diversity of Korean Amanita species has been underestimated, and most taxonomic studies conducted in Korea have only investigated their morphological characteristics. This approach is frequently insufficient for correct identification in fungal classification; therefore, we constructed a phylogeny of Amanita subgen. Lepidella in order to understand the phylogenetic placements of 16 Amanita specimens collected in Korea in 2012. The phylogeny constructed using the sequence data of the internal transcribed spacers and the partial large subunit of ribosomal RNA identified nine Amanita species (A. citrina, A. excelsa var. spissa, A. flavipes, A. fritillaria, A. oberwinklerana, A. pallidorosea, A. rubescens, A. subjunquillea, and A. volvata); of these, A. fritillaria, A. oberwinklerana, and A. pallidorosea are new to Korea. PMID:24493938

  11. New world monkey nightmares: science, art, use, and abuse (?) in platyrrhine taxonomic nomenclature.

    PubMed

    Rosenberger, Alfred L

    2012-08-01

    The taxonomy and nomenclature of New World monkeys is becoming precariously unstable and impractical, plagued by revisions aimed at conforming to approaches that reject the Biological Species Concept for narrowly construed reasons and resulting in a hyperinflated taxonomy at species (often) and genus (sometimes) levels. This undermines a major goal of classification at the most basic taxonomic levels to ease communication and facilitate research. Since it is difficult to justify extensive changes in terminology without a deeply justified theoretical purpose or without showing what scientific benefits these alterations can bring, working primatologists need not accept this doctrinaire trend. Knowing as little as we do about what a species actually is, does not justify contorting the value of a species nomenclature so that it reflects nothing more than coat color, a node, or endpoint of a dendrogram. PMID:22605529

  12. Polyphasic characterization reveals the presence of novel fish-associated Chryseobacterium spp. in the Great Lakes of North America.

    PubMed

    Loch, Thomas P; Faisal, Mohamed

    2015-03-01

    Recent reports suggest an emergence of novel Chryseobacterium spp. associated with aquaculture-reared fish worldwide. Herein, we report on multiple Chryseobacterium spp. infecting Great Lakes fishes that are highly similar to previously detected isolates from Europe, Africa, and Asia but have never before been reported in North America. Polyphasic characterization, which included extensive physiological, morphological, and biochemical analyses, fatty acid profiling, and phylogenetic analyses based upon partial 16S rRNA gene sequences, highlighted the diversity of Great Lakes' fish-associated chryseobacteria and also suggested that at least 2 taxa represent potentially novel Chryseobacterium spp. Screening for the ability of representative chryseobacteria to elicit lesions in experimentally challenged fish showed that they induced varying degrees of pathology, some of which were severe and resulted in host death. Median lethal dose (LD50) experiments for the isolate that elicited the most extensive pathology (Chryseobacterium sp. T28) demonstrated that the LD50 exceeded 4.5 × 108 cfu, thereby suggesting its role as a facultative fish-pathogenic bacterium. Histopathological changes in T28-infected fish included epithelial hyperplasia of the secondary lamellae and interlamellar space that resulted in secondary lamellar fusion, monocytic infiltrate, and mucus cell hyperplasia, all of which are consistent with branchitis, along with monocytic myositis, hemorrhage within the muscle, liver, adipose tissue, and ovaries, spongiosis of white matter of the brain, multifocal edema within the granular cell layer of the cerebellar cortex, and renal tubular degeneration and necrosis. The findings of this study underscore the widespread presence of chryseobacteria infecting Great Lakes fish. PMID:25751854

  13. Polyphasic taxonomy of the basidiomycetous yeast genus Rhodosporidium: R. azoricum sp. nov.

    PubMed

    Gadanho, M; Sampaio, J P; Spencer-Martins, I

    2001-03-01

    This report presents the description of a new heterothallic Rhodosporidium species, R. azoricum sp. nov. The new species is based on two strains previously identified as Rhodotorula glutinis, which were isolated from soil in São Miguel island, Azores, Portugal. Evidence that the two strains were conspecific and distinct from Rhodotorula glutinis was obtained in DNA fingerprinting experiments using the microsatellite-primed PCR approach (MSP-PCR) and the primers M13 and (GTG)5. In order to determine the phylogenetic position of the new species, the nucleotide sequence of the D1/D2 region of the 26S rDNA was analysed and Rhodosporidium azoricum was found to belong to a cluster including R. fluviale, R. lusitaniae, Sporidiobolus microsporus, and S. ruineniae. The life cycle of R. azoricum was investigated and comparisons integrating physiological, morphological, and molecular data were made with related species. PMID:11315112

  14. Predicted taxonomic patterns in pheromone production by longhorned beetles

    NASA Astrophysics Data System (ADS)

    Ray, Ann M.; Lacey, Emerson S.; Hanks, Lawrence M.

    2006-11-01

    Males of five species of three tribes in the longhorned beetle subfamily Cerambycinae produce volatile pheromones that share a structural motif (hydroxyl or carbonyl groups at carbons two and three in straight-chains of six, eight, or ten carbons). Pheromone gland pores are present on the prothoraces of males, but are absent in females, suggesting that male-specific gland pores could provide a convenient morphological indication that a species uses volatile pheromones. In this article, we assess the taxonomic distribution of gland pores within the Cerambycinae by examining males and females of 65 species in 24 tribes using scanning electron microscopy. Gland pores were present in males and absent in females of 49 species, but absent in both sexes of the remaining 16 species. Pores were confined to indentations in the cuticle. Among the species that had male-specific gland pores were four species already known to produce volatile compounds consistent with the structural motif. These findings support the initial assumption that gland pores are associated with the production of pheromones by males. There were apparently no taxonomic patterns in the presence of gland pores. These findings suggest that volatile pheromones play an important role in reproduction for many species of the Cerambycinae, and that the trait is evolutionarily labile.

  15. Taxonomic revision of the genus Carasobarbus Karaman, 1971 (Actinopterygii, Cyprinidae).

    PubMed

    Borkenhagen, Kai; Krupp, Friedhelm

    2013-01-01

    Representatives of the fish genus Carasobarbus Karaman, 1971 (Actinopterygii: Cyprinidae) from the Middle East and North Africa were previously placed in 14 different genus-group taxa (Barbellion, Barbus, Barynotus, Capoeta, Carasobarbus, Cyclocheilichthys, Kosswigobarbus, Labeobarbus, Luciobarbus, Pseudotor, Puntius, Systomus, Tor and Varicorhinus). The generic assignment of several species changed frequently, necessitating a re-evaluation of their taxonomic status. In this study, the genus Carasobarbus is revised based on comparative morphological examinations of about 1300 preserved specimens from collections of several museums and freshly collected material. The species Carasobarbus apoensis, Carasobarbus canis, Carasobarbus chantrei, Carasobarbus exulatus, Carasobarbus fritschii, Carasobarbus harterti, Carasobarbus kosswigi, Carasobarbus luteus and Carasobarbus sublimus form a monophyletic group that shares the following combination of characters: medium-sized barbels with a smooth last unbranched dorsal-fin ray, nine or 10 branched dorsal-fin rays and six branched anal fin-rays; scales large, shield-shaped, with many parallel radii; the lateral line containing 25 to 39 scales; the pharyngeal teeth hooked, 2.3.5-5.3.2 or 2.3.4-4.3.2; one or two pairs of barbels. The species are described in detail, their taxonomic status is re-evaluated and an identification key is provided. A lectotype of Systomus luteus Heckel, 1843 is designated. Carasobarbus Karaman, 1971, Kosswigobarbus Karaman, 1971, and Pseudotor Karaman, 1971 are subjective synonyms, and acting as First Reviser we gave precedence to the name Carasobarbus. PMID:24146585

  16. Taxonomic revision of the genus Carasobarbus Karaman, 1971 (Actinopterygii, Cyprinidae)

    PubMed Central

    Borkenhagen, Kai; Krupp, Friedhelm

    2013-01-01

    Abstract Representatives of the fish genus Carasobarbus Karaman, 1971 (Actinopterygii: Cyprinidae) from the Middle East and North Africa were previously placed in 14 different genus-group taxa (Barbellion, Barbus, Barynotus, Capoeta, Carasobarbus, Cyclocheilichthys, Kosswigobarbus, Labeobarbus, Luciobarbus, Pseudotor, Puntius, Systomus, Tor and Varicorhinus). The generic assignment of several species changed frequently, necessitating a re-evaluation of their taxonomic status. In this study, the genus Carasobarbus is revised based on comparative morphological examinations of about 1300 preserved specimens from collections of several museums and freshly collected material. The species Carasobarbus apoensis, Carasobarbus canis, Carasobarbus chantrei, Carasobarbus exulatus, Carasobarbus fritschii, Carasobarbus harterti, Carasobarbus kosswigi, Carasobarbus luteus and Carasobarbus sublimus form a monophyletic group that shares the following combination of characters: medium-sized barbels with a smooth last unbranched dorsal-fin ray, nine or 10 branched dorsal-fin rays and six branched anal fin-rays; scales large, shield-shaped, with many parallel radii; the lateral line containing 25 to 39 scales; the pharyngeal teeth hooked, 2.3.5-5.3.2 or 2.3.4-4.3.2; one or two pairs of barbels. The species are described in detail, their taxonomic status is re-evaluated and an identification key is provided. A lectotype of Systomus luteus Heckel, 1843 is designated. Carasobarbus Karaman, 1971, Kosswigobarbus Karaman, 1971, and Pseudotor Karaman, 1971 are subjective synonyms, and acting as First Reviser we gave precedence to the name Carasobarbus. PMID:24146585

  17. The taxonomic status of Rhipicephalus sanguineus (Latreille, 1806).

    PubMed

    Nava, Santiago; Estrada-Peña, Agustín; Petney, Trevor; Beati, Lorenza; Labruna, Marcelo B; Szabó, Matias P J; Venzal, José M; Mastropaolo, Mariano; Mangold, Atilio J; Guglielmone, Alberto A

    2015-02-28

    The brown dog tick, Rhipicephalus sanguineus sensu stricto, is a species with considerable public health and economic importance. However, the taxonomic status of this species is far from resolved. After more than 110 years of scientific work on R. sanguineus s.s., the situation is that there is no type, no solid description, nor is there a consensus about the range of morphological variability within the species. Recent findings based on laboratory crosses and molecular genetics strongly suggest that there are several entities grouped under the same name. Here we review the history of the taxon, and we point out the caveats behind any further work on this tick. The current taxonomic status of R. sanguineus s.s. thus lacks an informative original description, and is based on the existence of several morphological descriptions based on ticks originating from different populations, which show, in some cases, biological incompatibility and significant genetic divergence. We suggests that as a result it is not possible to assign the specific name R. sanguineus s.s. to any population. Further work is required based on the rules issued by the International Code of Zoological Nomenclature to clearly define the morphological range of the different populations. PMID:25560924

  18. Accessing the black box of microbial diversity and ecophysiology: recent advances through polyphasic experiments.

    PubMed

    Collins, Gavin; Kavanagh, Siobhán; McHugh, Sharon; Connaughton, Sean; Kearney, Aileen; Rice, Olivia; Carrigg, Cora; Scully, Colm; Bhreathnach, Niamh; Mahony, Thérèse; Madden, Pádhraig; Enright, Anne-Marie; O'flaherty, Vincent

    2006-01-01

    The microbial ecology of a range of anaerobic biological assemblages (granular sludge) from full- and laboratory-scale wastewater treatment bioreactors, and of crop-growing and peat soils, was determined using a variety of 16S rRNA gene-based techniques, including clone library, terminal restriction fragment length polymorphism (TRFLP) and denaturing gradient gel electrophoresis (DGGE) analyses. Fluorescent in situ hybridization (FISH) using 16S rRNA gene-targeted probes was employed to complete a "full-cycle rRNA approach" with selected biomass. Genetic fingerprinting (TRFLP and DGGE) was effectively used to elucidate community structure-crop relationships, and to detect and monitor trends in bioreactor sludge and specific enrichment cultures of peat soil. Greater diversity was resolved within bacterial than within archaeal communities, and unexpected reservoirs of uncultured Crenarchaeota were detected in sludge granules. Advanced radiotracer incubations and micro-beta imaging were employed in conjunction with FISH to elucidate the eco-functionalism of these organisms. Crenarchaeota clusters were identified in close associated with methanogenic Archaea and both were localised with acetate uptake in biofilm structure. PMID:16702066

  19. Glycosides from Marine Sponges (Porifera, Demospongiae): Structures, Taxonomical Distribution, Biological Activities and Biological Roles

    PubMed Central

    Kalinin, Vladimir I.; Ivanchina, Natalia V.; Krasokhin, Vladimir B.; Makarieva, Tatyana N.; Stonik, Valentin A.

    2012-01-01

    Literature data about glycosides from sponges (Porifera, Demospongiae) are reviewed. Structural diversity, biological activities, taxonomic distribution and biological functions of these natural products are discussed. PMID:23015769

  20. Glycosides from marine sponges (Porifera, Demospongiae): structures, taxonomical distribution, biological activities and biological roles.

    PubMed

    Kalinin, Vladimir I; Ivanchina, Natalia V; Krasokhin, Vladimir B; Makarieva, Tatyana N; Stonik, Valentin A

    2012-08-01

    Literature data about glycosides from sponges (Porifera, Demospongiae) are reviewed. Structural diversity, biological activities, taxonomic distribution and biological functions of these natural products are discussed. PMID:23015769

  1. Taxonomic and numerical resolutions of nepomorpha (insecta: heteroptera) in cerrado streams.

    PubMed

    Giehl, Nubia França da Silva; Dias-Silva, Karina; Juen, Leandro; Batista, Joana Darc; Cabette, Helena Soares Ramos

    2014-01-01

    Transformations of natural landscapes and their biodiversity have become increasingly dramatic and intense, creating a demand for rapid and inexpensive methods to assess and monitor ecosystems, especially the most vulnerable ones, such as aquatic systems. The speed with which surveys can collect, identify, and describe ecological patterns is much slower than that of the loss of biodiversity. Thus, there is a tendency for higher-level taxonomic identification to be used, a practice that is justified by factors such as the cost-benefit ratio, and the lack of taxonomists and reliable information on species distributions and diversity. However, most of these studies do not evaluate the degree of representativeness obtained by different taxonomic resolutions. Given this demand, the present study aims to investigate the congruence between species-level and genus-level data for the infraorder Nepomorpha, based on taxonomic and numerical resolutions. We collected specimens of aquatic Nepomorpha from five streams of first to fourth order of magnitude in the Pindaíba River Basin in the Cerrado of the state of Mato Grosso, Brazil, totaling 20 sites. A principal coordinates analysis (PCoA) applied to the data indicated that species-level and genus-level abundances were relatively similar (>80% similarity), although this similarity was reduced when compared with the presence/absence of genera (R = 0.77). The presence/absence ordinations of species and genera were similar to those recorded for their abundances (R = 0.95 and R = 0.74, respectively). The results indicate that analyses at the genus level may be used instead of species, given a loss of information of 11 to 19%, although congruence is higher when using abundance data instead of presence/absence. This analysis confirms that the use of the genus level data is a safe shortcut for environmental monitoring studies, although this approach must be treated with caution when the objectives include conservation

  2. Taxonomic and Numerical Resolutions of Nepomorpha (Insecta: Heteroptera) in Cerrado Streams

    PubMed Central

    Giehl, Nubia França da Silva; Dias-Silva, Karina; Juen, Leandro; Batista, Joana Darc; Cabette, Helena Soares Ramos

    2014-01-01

    Transformations of natural landscapes and their biodiversity have become increasingly dramatic and intense, creating a demand for rapid and inexpensive methods to assess and monitor ecosystems, especially the most vulnerable ones, such as aquatic systems. The speed with which surveys can collect, identify, and describe ecological patterns is much slower than that of the loss of biodiversity. Thus, there is a tendency for higher-level taxonomic identification to be used, a practice that is justified by factors such as the cost-benefit ratio, and the lack of taxonomists and reliable information on species distributions and diversity. However, most of these studies do not evaluate the degree of representativeness obtained by different taxonomic resolutions. Given this demand, the present study aims to investigate the congruence between species-level and genus-level data for the infraorder Nepomorpha, based on taxonomic and numerical resolutions. We collected specimens of aquatic Nepomorpha from five streams of first to fourth order of magnitude in the Pindaíba River Basin in the Cerrado of the state of Mato Grosso, Brazil, totaling 20 sites. A principal coordinates analysis (PCoA) applied to the data indicated that species-level and genus-level abundances were relatively similar (>80% similarity), although this similarity was reduced when compared with the presence/absence of genera (R = 0.77). The presence/absence ordinations of species and genera were similar to those recorded for their abundances (R = 0.95 and R = 0.74, respectively). The results indicate that analyses at the genus level may be used instead of species, given a loss of information of 11 to 19%, although congruence is higher when using abundance data instead of presence/absence. This analysis confirms that the use of the genus level data is a safe shortcut for environmental monitoring studies, although this approach must be treated with caution when the objectives include conservation

  3. Contrasting changes in taxonomic vs. functional diversity of tropical fish communities after habitat degradation.

    PubMed

    Villéger, Sébastien; Ramos Miranda, Julia; Flores Hernández, Domingo; Mouillot, David

    2010-09-01

    Human activities have strong impacts on ecosystem functioning through their effect on abiotic factors and on biodiversity. There is also growing evidence that species functional traits link changes in species composition and shifts in ecosystem processes. Hence, it appears to be of utmost importance to quantify modifications in the functional structure of species communities after human disturbance in addition to changes in taxonomic structure. Despite this fact, there is still little consensus on the actual impacts of human-mediated habitat alteration on the components of biodiversity, which include species functional traits. Therefore, we studied changes in taxonomic diversity (richness and evenness), in functional diversity, and in functional specialization of estuarine fish communities facing drastic environmental and habitat alterations. The Terminos Lagoon (Gulf of Mexico) is a tropical estuary of primary concern for its biodiversity, its habitats, and its resource supply, which have been severely impacted by human activities. Fish communities were sampled in four zones of the Terminos Lagoon 18 years apart (1980 and 1998). Two functions performed by fish (food acquisition and locomotion) were studied through the measurement of 16 functional traits. Functional diversity of fish communities was quantified using three independent components: richness, evenness, and divergence. Additionally, we measured the degree of functional specialization in fish communities. We used a null model to compare the functional and the taxonomic structure of fish communities between 1980 and 1998. Among the four largest zones studied, three did not show strong functional changes. In the northern part of the lagoon, we found an increase in fish richness but a significant decrease of functional divergence and functional specialization. We explain this result by a decline of specialized species (i.e., those with particular combinations of traits), while newly occurring species are

  4. Integrating a Numerical Taxonomic Method and Molecular Phylogeny for Species Delimitation of Melampsora Species (Melampsoraceae, Pucciniales) on Willows in China

    PubMed Central

    Zhao, Peng; Wang, Qing-Hong; Tian, Cheng-Ming; Kakishima, Makoto

    2015-01-01

    The species in genus Melampsora are the causal agents of leaf rust diseases on willows in natural habitats and plantations. However, the classification and recognition of species diversity are challenging because morphological characteristics are scant and morphological variation in Melampsora on willows has not been thoroughly evaluated. Thus, the taxonomy of Melampsora species on willows remains confused, especially in China where 31 species were reported based on either European or Japanese taxonomic systems. To clarify the species boundaries of Melampsora species on willows in China, we tested two approaches for species delimitation inferred from morphological and molecular variations. Morphological species boundaries were determined based on numerical taxonomic analyses of morphological characteristics in the uredinial and telial stages by cluster analysis and one-way analysis of variance. Phylogenetic species boundaries were delineated based on the generalized mixed Yule-coalescent (GMYC) model analysis of the sequences of the internal transcribed spacer (ITS1 and ITS2) regions including the 5.8S and D1/D2 regions of the large nuclear subunit of the ribosomal RNA gene. Numerical taxonomic analyses of 14 morphological characteristics recognized in the uredinial-telial stages revealed 22 morphological species, whereas the GMYC results recovered 29 phylogenetic species. In total, 17 morphological species were in concordance with the phylogenetic species and 5 morphological species were in concordance with 12 phylogenetic species. Both the morphological and molecular data supported 14 morphological characteristics, including 5 newly recognized characteristics and 9 traditionally emphasized characteristics, as effective for the differentiation of Melampsora species on willows in China. Based on the concordance and discordance of the two species delimitation approaches, we concluded that integrative taxonomy by using both morphological and molecular variations was

  5. Taxonomic Study of the Genus Abundisporus in Korea

    PubMed Central

    Jargalmaa, Suldbold; Park, Myung Soo; Park, Jae Young; Fong, Jonathan J.; Jang, Yeongseon

    2015-01-01

    The polypore genus Abundisporus Ryvarden is characterized by resupinate to pileate fruitbodies with a purplish brown hymenophore, slightly thick-walled, pale yellowish and non-dextrinoid basidiospores, and causing white rot. A purple color hymenophore, an easily observable and striking character, was considered the main distinctive feature at the generic level within polypores. However, due to highly similar basidiocarp features, species identification within these purple polypores is particularly difficult. Three species of purple colored polypores have been reported in Korea (Abundisporus fuscopurpureus, A. pubertatis, and Fomitopsis rosea). Based on morphological re-examination, ecological information, and sequence analysis of the internal transcribed spacer, we showed that previous classification was incorrect and there is only one species (A. pubertatis) in Korea. We provide a detailed description of A. pubertatis in Korea, as well as a taxonomic key to distinguish wood rot fungi with a purple hymenophore. PMID:26539038

  6. Taxonomic Study of the Genus Abundisporus in Korea.

    PubMed

    Jargalmaa, Suldbold; Park, Myung Soo; Park, Jae Young; Fong, Jonathan J; Jang, Yeongseon; Lim, Young Woon

    2015-09-01

    The polypore genus Abundisporus Ryvarden is characterized by resupinate to pileate fruitbodies with a purplish brown hymenophore, slightly thick-walled, pale yellowish and non-dextrinoid basidiospores, and causing white rot. A purple color hymenophore, an easily observable and striking character, was considered the main distinctive feature at the generic level within polypores. However, due to highly similar basidiocarp features, species identification within these purple polypores is particularly difficult. Three species of purple colored polypores have been reported in Korea (Abundisporus fuscopurpureus, A. pubertatis, and Fomitopsis rosea). Based on morphological re-examination, ecological information, and sequence analysis of the internal transcribed spacer, we showed that previous classification was incorrect and there is only one species (A. pubertatis) in Korea. We provide a detailed description of A. pubertatis in Korea, as well as a taxonomic key to distinguish wood rot fungi with a purple hymenophore. PMID:26539038

  7. Memory systems, processes, and tasks: taxonomic clarification via factor analysis.

    PubMed

    Bruss, Peter J; Mitchell, David B

    2009-01-01

    The nature of various memory systems was examined using factor analysis. We reanalyzed data from 11 memory tasks previously reported in Mitchell and Bruss (2003). Four well-defined factors emerged, closely resembling episodic and semantic memory and conceptual and perceptual implicit memory, in line with both memory systems and transfer-appropriate processing accounts. To explore taxonomic issues, we ran separate analyses on the implicit tasks. Using a cross-format manipulation (pictures vs. words), we identified 3 prototypical tasks. Word fragment completion and picture fragment identification tasks were "factor pure," tapping perceptual processes uniquely. Category exemplar generation revealed its conceptual nature, yielding both cross-format priming and a picture superiority effect. In contrast, word stem completion and picture naming were more complex, revealing attributes of both processes. PMID:19507425

  8. Fossil struthionid eggshells from Laetoli, Tanzania: Taxonomic and biostratigraphic significance

    NASA Astrophysics Data System (ADS)

    Harrison, Terry; Msuya, Charles P.

    2005-04-01

    Recent paleontological investigations at Laetoli and neighboring localities in northern Tanzania have produced a large collection of fossil ostrich eggshells from the Pliocene-aged Laetolil Beds (˜3.5-4.5 Ma) and Ndolanya Beds (˜2.6-2.7 Ma). A detailed analysis of the morphology of the eggshells and their taxonomic affinities indicates that two different species of Struthio are represented. In the Lower Laetolil Beds and in the Upper Laetolil Beds below Tuff 3 a new species is recognized— Struthio kakesiensis. This is replaced in the Upper Laetolil Beds by Struthio camelus, the modern species of ostrich. Since radiometric age determinations are available for the stratigraphic sequence at Laetoli, it is possible to precisely date the first appearance of S. camelus at ˜3.6-3.8 Ma. Comparisons of the Laetoli material with specimens from the well-dated sequences at Lothagam and Kanapoi in northern Kenya, allow the taxonomic and biochronological analysis to be extended back in time to the late Miocene. At about 6.5 Ma, Diamantornis and elephant birds were replaced in East Africa by ostriches belonging to the genus Struthio. Three time-successive species of ostriches are identified in the fossil record of East Africa, beginning with Struthio. cf. karingarabensis (˜6.5-4.2 Ma), followed by S. kakesiensis (˜4.5-3.6 Ma) and then S. camelus (˜3.8 Ma onwards). A similar sequence of taxa has previously been recorded from localities in Namibia, but at these sites there is no possibility to precisely calibrate the ages of the different species using radiometric dating. Nevertheless, the broadly similar evolutionary sequence and the close correspondence in inferred ages for the succession of species in East Africa and Namibia suggest that ostrich eggshells are a very useful tool for biochronological correlation of paleontological sites in sub-Saharan Africa.

  9. Marine benthic ecological functioning over decreasing taxonomic richness

    NASA Astrophysics Data System (ADS)

    Törnroos, Anna; Bonsdorff, Erik; Bremner, Julie; Blomqvist, Mats; Josefson, Alf B.; Garcia, Clement; Warzocha, Jan

    2015-04-01

    Alterations to ecosystem function due to reductions in species richness are predicted to increase as humans continue to affect the marine environment, especially in coastal areas, which serve as the interface between land and sea. The potential functional consequences due to reductions in species diversity have attracted considerable attention recently but little is known about the consequence of such loss in natural communities. We examined how the potential for function is affected by natural reductions in taxon richness using empirical (non-simulated) coastal marine benthic macrofaunal data from the Skagerrak-Baltic Sea region (N. Europe), where taxon richness decreases 25-fold, from 151 to 6 taxa. To estimate functional changes we defined multiple traits (10 traits and 51 categories) on which trait category richness, functional diversity (FD) and number of taxa per trait category were calculated. Our results show that decrease in taxon richness leads to an overall reduction in function but functional richness remains comparatively high even at the lowest level of taxon richness. Although the taxonomic reduction was sharp, up to 96% of total taxon richness, we identified both potential thresholds in functioning and subtler changes where function was maintained along the gradient. The functional changes were not only caused by reductions in taxa per trait category, some categories were maintained or even increased. Primarily, the reduction in species richness altered trait categories related to feeding, living and movement and thus potentially could have an effect on various ecosystem processes. This highlights the importance of recognising ecosystem multifunctionality, especially at low taxonomic richness. We also found that in this system rare species (singletons) did not stand for the functional complexities and changes. Our findings were consistent with theoretical and experimental predictions and suggest that a large proportion of the information about

  10. Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges.

    PubMed

    Shah, Varun; Zakrzewski, Martha; Wibberg, Daniel; Eikmeyer, Felix; Schlüter, Andreas; Madamwar, Datta

    2013-10-01

    Industrial units, manufacturing dyes, chemicals,solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canalbank (N 22°57.878′; E 072°38.478′), Ahmeda bad, Gujarat,India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be “Proteobacteria”and “Pseudomonas,” respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other“-omic” studies, will help in designing future bioremediation strategies in effluent treatment

  11. Taxonomic Profiling and Metagenome Analysis of a Microbial Community from a Habitat Contaminated with Industrial Discharges.

    PubMed

    Shah, Varun; Zakrzewski, Martha; Wibberg, Daniel; Eikmeyer, Felix; Schlüter, Andreas; Madamwar, Datta

    2013-06-25

    Industrial units, manufacturing dyes, chemicals, solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canal bank (N 22°57.878'; E 072°38.478'), Ahmedabad, Gujarat, India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be "Proteobacteria" and "Pseudomonas," respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other "-omic" studies, will help in designing future bioremediation strategies in effluent treatment plants and

  12. Polyphase basin evolution of the Vienna Basin inferred from 3D visualization of sedimentation setting and quantitative subsidence

    NASA Astrophysics Data System (ADS)

    Lee, Eun Young; Novotny, Johannes; Wagreich, Michael

    2016-04-01

    This study analyzed and visualized data from 210 wells using a MATLAB-based program (BasinVis 1.0) for 3D visualization of sediment distribution, thickness, and quantitative subsidence of the northern and central Vienna Basin. The sedimentation settings for selected horizons were visualized to 3D sediment distribution maps, isopach maps, and cross-sections. Subsidence of the study area resulted in 3D subsidence depth and rate maps of basement and tectonic subsidences. Due to the special position of the Vienna Basin, the basin evolution was influenced by the regional tectonics of surrounding units. The 2D/3D maps provided insights into the polyphase evolution of the Vienna Basin, which is closely related to changes in the changing regional stress field and the paleoenvironmental setting. In the Early Miocene, the sedimentation and subsidence were shallow and E-W/NE-SW trending, indicating the development of piggy-back basins. During the late Early Miocene, maps show wider sedimentation and abruptly increasing subsidence by sinistral strike-slip faults, which initiated the Vienna pull-apart basin system. The sediments of the Early Miocene were supplied through a small deltaic system entering from the south. After thin sedimentation and shallow subsidence of the early Middle Miocene, the development of the Vienna Basin was controlled and accelerated mainly by NE-SW trending synsedimentary normal faults, especially the Steinberg fault. From the Middle Miocene, the subsidence was decreasing overall, however the tectonic subsidence show regionally different patterns. This study suggests that a major tensional regime change, from transtension to E-W extension, caused laterally varying subsidence across the Vienna Basin. The Late Miocene was characterized by the slowing down of basement and tectonic subsidence. From the middle Middle to Late Miocene, enormous amount of sediments supplied by a broad paleo-Danube delta complex on the western flank of the basin. The latest

  13. Ultramafic clasts from the South Chamorro serpentine mud volcano reveal a polyphase serpentinization history of the Mariana forearc mantle

    NASA Astrophysics Data System (ADS)

    Kahl, Wolf-Achim; Jöns, Niels; Bach, Wolfgang; Klein, Frieder; Alt, Jeffrey C.

    2015-06-01

    Serpentine seamounts located on the outer half of the pervasively fractured Mariana forearc provide an excellent window into the forearc devolatilization processes, which can strongly influence the cycling of volatiles and trace elements in subduction zones. Serpentinized ultramafic clasts recovered from an active mud volcano in the Mariana forearc reveal microstructures, mineral assemblages and compositions that are indicative of a complex polyphase alteration history. Petrologic phase relations and oxygen isotopes suggest that ultramafic clasts were serpentinized at temperatures below 200 °C. Several successive serpentinization events represented by different vein generations with distinct trace element contents can be recognized. Measured in situ Rb/Cs ratios are fairly uniform ranging between 1 and 10, which is consistent with Cs mobilization from sediments at lower temperatures and lends further credence to the low-temperature conditions proposed in models of the thermal structure in forearc settings. Late veins show lower fluid mobile element (FME) concentrations than early veins, suggesting a decreasing influence of fluid discharge from the subducting slab on the composition of the serpentinizing fluids. The continuous microfabric and mineral chemical evolution observed in the ultramafic clasts may have implications as to the origin and nature of the serpentinizing fluids. We hypothesize that opal and smectite dehydration produce quartz-saturated fluids with high FME contents and Rb/Cs between 1 and 4 that cause the early pervasive serpentinization. The partially serpentinized material may then be eroded from the basal plane of the suprasubduction mantle wedge. Serpentinization continued but the interacting fluids did not carry a pronounced sedimentary signature, either because FMEs were no longer released from the slab, or due to an en route loss of FMEs. Late chrysotile veins that document the increased access of fluids in a now fluid-dominated regime are

  14. Paleostress states at the south-western margin of the Central European Basin System — Application of fault-slip analysis to unravel a polyphase deformation pattern

    NASA Astrophysics Data System (ADS)

    Sippel, Judith; Scheck-Wenderoth, Magdalena; Reicherter, Klaus; Mazur, Stanislaw

    2009-05-01

    We analyse the deformation pattern along the south-western margin of the Central European Basin System (CEBS) where Upper Carboniferous-Mesozoic rocks are uplifted due to the Late Cretaceous basin inversion. The geometry of mesoscale faults and associated striae are used to calculate the stress state(s) responsible for the observed deformation. Each reduced stress tensor obtained comprises (i) the directions of the principal stress axes σ1, σ2, and σ3 ( σ1 ≥ σ2 ≥ σ3) and (ii) the ratio of principal stress differences R = ( σ2 - σ3) / ( σ1 - σ3). We present a stress inversion technique that allows each stress state inherent in a heterogeneous fault population to be identified by integrating the results of the PBT-Method [Turner, F.J., 1953. Nature and dynamic interpretation of deformation lamellae in calcite of three marbles. American Journal of Sciences, 251(4): 276-298; Sperner, B., Ratschbacher, L. and Ott, R., 1993. Fault-striae analysis: a Turbo Pascal program package for graphical presentation and reduced stress tensor calculation. Computers & Geosciences, 19: 1361-1388] and the Multiple Inverse Method [Yamaji, A., 2000. The multiple inverse method; a new technique to separate stresses from heterogeneous fault-slip data. Journal of Structural Geology, 22(4): 441-452]. This comprehensive approach not only facilitates the separation of complex data sets into homogeneous subsets but also guarantees that each stress state derived fulfils both the criteria of low-misfit angles (Wallace-Bott hypothesis) and high shear-to-normal-stress ratios (Mohr-Coulomb criterion). The reliability of our technique is confirmed by the fact that irrespective of (i) the number of fault-slip data from an outcrop, (ii) the number of subsets they represent and (iii) the proportion of newly formed and reactivated faults, we obtain consistent results from outcrops of variously aged rocks. This consistency concerns both calculated stress states as well as locally observed

  15. Polysemy and the Taxonomic Constraint: Children's Representation of Words That Label Multiple Kinds

    ERIC Educational Resources Information Center

    Srinivasan, Mahesh; Snedeker, Jesse

    2014-01-01

    How do children resolve the problem of indeterminacy when learning a new word? By one account, children adopt a "taxonomic assumption" and expect the word to denote only members of a particular taxonomic category. According to one version of this constraint, young children should represent polysemous words that label multiple kinds--for…

  16. Facet Theory Used to Establish Taxonomic Subclasses for "Application" with an Example from Science Teaching.

    ERIC Educational Resources Information Center

    Blum, Abraham

    1989-01-01

    Establishes taxonomic subclasses of application test items in the special case of the application of biological principles to familiar and unfamiliar, and agro-biological problems, in the framework of applied science teaching. Reports on the complexity of an application situation as a major criterion in the taxonomic subclassification. (YP)

  17. Taxonomic Organization Scaffolds Young Children's Learning from Storybooks: A Design Experiment

    ERIC Educational Resources Information Center

    Kaefer, Tanya; Pinkham, Ashley M.; Neuman, Susan B.

    2010-01-01

    The purpose of this design experiment was to research, test and iteratively design a set of taxonomically-organized storybooks that served to scaffold young children's word learning and concept development. Specifically, Phase 1 of the design experiment asked: (1) What are the effects of taxonomic organization on children's ability to acquire…

  18. A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units

    PubMed Central

    Bell, Jordana T.; Spector, Tim D.; Steves, Claire J.

    2016-01-01

    A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods’ ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts’ properties will produce the highest heritability estimates. Using 1,750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions.

  19. A new approach to species delimitation in Septoria

    PubMed Central

    Verkley, G.J.M.; Quaedvlieg, W.; Shin, H.-D.; Crous, P.W.

    2013-01-01

    Septoria is a large genus of asexual morphs of Ascomycota causing leaf spot diseases of many cultivated and wild plants. Host specificity has long been a decisive criterium in species delimitation in Septoria, mainly because of the paucity of useful morphological characters and the high level of variation therein. This study aimed at improving the species delimitation of Septoria by adopting a polyphasic approach, including multilocus DNA sequencing and morphological analyses on the natural substrate and in culture. To this end 365 cultures preserved in CBS, Utrecht, The Netherlands, among which many new isolates obtained from fresh field specimens were sequenced. Herbarium material including many types was also studied. Full descriptions of the morphology in planta and in vitro are provided for 57 species. DNA sequences were generated for seven loci, viz. nuclear ITS and (partial) LSU ribosomal RNA genes, RPB2, actin, calmodulin, Btub, and EF. The robust phylogeny inferred showed that the septoria-like fungi are distributed over three main clades, establishing the genera Septoria s. str., Sphaerulina, and Caryophylloseptoria gen. nov. Nine new combinations and one species, Sphaerulina tirolensis sp. nov. were proposed. It is demonstrated that some species have wider host ranges than expected, including hosts from more than one family. Septoria protearum, previously only associated with Proteaceae was found to be also associated with host plants from six additional families of phanerogams and cryptogams. To our knowledge this is the first study to provide DNA-based evidence that multiple family-associations occur for a single species in Septoria. The distribution of host families over the phylogenetic tree showed a highly dispersed pattern for 10 host plant families, providing new insight into the evolution of these fungi. It is concluded that trans-family host jumping is a major force driving the evolution of Septoria and Sphaerulina. Taxonomic novelties: New

  20. Anseriform brain and its parts versus taxonomic and ecological categories.

    PubMed

    Kalisińska, Elzbieta

    2005-01-01

    The size of the brain and its macro-anatomical parts in 206 birds representing 19 anseriform species and 4 tribes (Anserini, Anatini, Aythyini and Mergini) was the subject of a comparative analysis. The comparisons involved two aspects: taxonomic (differences among species within tribes and differences among tribes) and ecological (diet composition: vegetation, invertebrates, or fish and the foraging mode: browsing, dabbling, shallow diving, and deep diving). The relative size of the encephalon (E) and its parts (optic tectum, OT; cerebellum, C; brain stem, BS; hemispheres, H) were described using appropriate indices. Five of them, called the cerebral-body indices (E/BW, OT/BW, C/BW, BS/BW, H/BW), involved a ratio between the weight of E or its parts and that of the body (BW). Four intracerebral indices (OT/E, C/E, BS/E, H/E) and allometric equations were used as well. Almost all the indices showed a high intraspecific variability within the Anserini and Mergini; on the other hand, the intracerebral indices did not differ between the species of the Anatini and Aythyini (except for OT/E in the Aythyini). Between-tribe differences were reflected in all 9 indices. The birds feeding on different diets were found to differ in their OT/E and H/E. The herbivorous anserifom OT/E was clearly lower than that of those birds feeding on invertebrates and fish. The highest OT/E was that of the piscivorous birds. In terms of foraging mode, significant differences were revealed in 7 out of the 9 indices used (differences in OT/BW and C/BW proved non-significant). OT/E of the browsing birds was clearly lower than that of the deep diving ducks; BS/E of the browsers was much lower than that of the dabbling and shallow diving ducks. Geese and swans (browsers) showed much higher H/E compared to the deep diving sea ducks. The latter revealed the highest C/E, but significant differences were detected only in comparison with C/E of the shallow diving ducks. The taxonomic (among tribes

  1. Taxonomic Synopsis of the Ponto-Mediterranean Ants of Temnothorax nylanderi Species-Group

    PubMed Central

    Csősz, Sándor; Heinze, Jürgen; Mikó, István

    2015-01-01

    In the current revisionary work, the Temnothorax nylanderi species-group of myrmicine ants is characterized. Eighteen species belonging to this group in the Ponto-Mediterranean region are described or redefined based on an integrative approach that combines exploratory analyses of morphometric data and of a 658bp fragment of the mitochondrial gene for the cytochrome c oxidase subunit I (CO I). The species group is subdivided into five species complexes: T. angustifrons complex, T. lichtensteini complex, T. nylanderi complex, T. parvulus complex, T. sordidulus complex, and two species, T. angulinodis sp. n. and T. flavicornis (Emery, 1870) form their own lineages. We describe seven new species (T. angulinodis sp. n., T. angustifrons sp. n., T. ariadnae sp. n., T. helenae sp. n., T. lucidus sp. n., T. similis sp. n., T. subtilis sp. n.), raise T. tergestinus (FINZI, 1928) stat.n. to species level, and propose a new junior synonymy for T. saxonicus (SEIFERT, 1995) syn.n. (junior synonym of T. tergestinus). We describe the worker caste and provide high quality images and distributional maps for all eighteen species. Furthermore, we provide a decision tree as an alternative identification key that visually gives an overview of this species-group. We make the first application to Formicidae of the Semantic Phenotype approach that has been used in previous taxonomic revisions. PMID:26536033

  2. Taxamatch, an algorithm for near ('fuzzy') matching of scientific names in taxonomic databases.

    PubMed

    Rees, Tony

    2014-01-01

    Misspellings of organism scientific names create barriers to optimal storage and organization of biological data, reconciliation of data stored under different spelling variants of the same name, and appropriate responses from user queries to taxonomic data systems. This study presents an analysis of the nature of the problem from first principles, reviews some available algorithmic approaches, and describes Taxamatch, an improved name matching solution for this information domain. Taxamatch employs a custom Modified Damerau-Levenshtein Distance algorithm in tandem with a phonetic algorithm, together with a rule-based approach incorporating a suite of heuristic filters, to produce improved levels of recall, precision and execution time over the existing dynamic programming algorithms n-grams (as bigrams and trigrams) and standard edit distance. Although entirely phonetic methods are faster than Taxamatch, they are inferior in the area of recall since many real-world errors are non-phonetic in nature. Excellent performance of Taxamatch (as recall, precision and execution time) is demonstrated against a reference database of over 465,000 genus names and 1.6 million species names, as well as against a range of error types as present at both genus and species levels in three sets of sample data for species and four for genera alone. An ancillary authority matching component is included which can be used both for misspelled names and for otherwise matching names where the associated cited authorities are not identical. PMID:25247892

  3. Taxamatch, an Algorithm for Near (‘Fuzzy’) Matching of Scientific Names in Taxonomic Databases

    PubMed Central

    Rees, Tony

    2014-01-01

    Misspellings of organism scientific names create barriers to optimal storage and organization of biological data, reconciliation of data stored under different spelling variants of the same name, and appropriate responses from user queries to taxonomic data systems. This study presents an analysis of the nature of the problem from first principles, reviews some available algorithmic approaches, and describes Taxamatch, an improved name matching solution for this information domain. Taxamatch employs a custom Modified Damerau-Levenshtein Distance algorithm in tandem with a phonetic algorithm, together with a rule-based approach incorporating a suite of heuristic filters, to produce improved levels of recall, precision and execution time over the existing dynamic programming algorithms n-grams (as bigrams and trigrams) and standard edit distance. Although entirely phonetic methods are faster than Taxamatch, they are inferior in the area of recall since many real-world errors are non-phonetic in nature. Excellent performance of Taxamatch (as recall, precision and execution time) is demonstrated against a reference database of over 465,000 genus names and 1.6 million species names, as well as against a range of error types as present at both genus and species levels in three sets of sample data for species and four for genera alone. An ancillary authority matching component is included which can be used both for misspelled names and for otherwise matching names where the associated cited authorities are not identical. PMID:25247892

  4. Modeling phytoplankton community in reservoirs. A comparison between taxonomic and functional groups-based models.

    PubMed

    Di Maggio, Jimena; Fernández, Carolina; Parodi, Elisa R; Diaz, M Soledad; Estrada, Vanina

    2016-01-01

    In this paper we address the formulation of two mechanistic water quality models that differ in the way the phytoplankton community is described. We carry out parameter estimation subject to differential-algebraic constraints and validation for each model and comparison between models performance. The first approach aggregates phytoplankton species based on their phylogenetic characteristics (Taxonomic group model) and the second one, on their morpho-functional properties following Reynolds' classification (Functional group model). The latter approach takes into account tolerance and sensitivity to environmental conditions. The constrained parameter estimation problems are formulated within an equation oriented framework, with a maximum likelihood objective function. The study site is Paso de las Piedras Reservoir (Argentina), which supplies water for consumption for 450,000 population. Numerical results show that phytoplankton morpho-functional groups more closely represent each species growth requirements within the group. Each model performance is quantitatively assessed by three diagnostic measures. Parameter estimation results for seasonal dynamics of the phytoplankton community and main biogeochemical variables for a one-year time horizon are presented and compared for both models, showing the functional group model enhanced performance. Finally, we explore increasing nutrient loading scenarios and predict their effect on phytoplankton dynamics throughout a one-year time horizon. PMID:26406877

  5. Fast and sensitive taxonomic classification for metagenomics with Kaiju.

    PubMed

    Menzel, Peter; Ng, Kim Lee; Krogh, Anders

    2016-01-01

    Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows-Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk. PMID:27071849

  6. Taxonomic revision of the American spider genus Arachosia (Araneae: Anyphaenidae).

    PubMed

    Rubio, Gonzalo D; Ramírez, Martín J

    2015-01-01

    We review the American spider genus Arachosia O.P.-Cambridge, and present a descriptive taxonomic study with a comparative dichotomous key including 21 species, of which seven are newly described (A. avalosi sp. nov., A. carancho sp. nov., A. kapiipeoi sp. nov., A. magna sp. nov., A. monserrate sp. nov., A. pinhalito sp. nov. and A. tungurahua sp. nov.). Four species names are considered nomina dubia: Oxysoma dubium Berland, Gayenna duplovittata Mello-Leitão, Oxysoma polytrichium Mello-Leitão, and Arachosia sulfurea Mello-Leitão. Arachosia bonneti (Mello-Leitão) is newly synonymized with A. albiventris Mello-Leitão, and A. mezenioides Mello-Leitão with A. freiburgensis Keyserling. Previous problems with the identification of species in a species complex including A. cubana (Banks) are resolved. A disjunct distributional pattern is reported for A. kapiipeoi sp. nov.; a preliminary phylogenetic analysis based on mitochondrial COI sequences shows that these may correspond with two cryptic species. In this contribution, grassland and forests are discussed as the two main habitats inhabited by species of Arachosia. Finally, we propose a hypothesis of matching sexes based on functionality of some genital structures, involving sclerites of the male copulatory organ with structures of the epigyne: the prolateral projection on the primary conductor of the male would have a direct interaction with the lateral projections of the anterior pouch on the median epigynal field of females. PMID:25781851

  7. Fast and sensitive taxonomic classification for metagenomics with Kaiju

    PubMed Central

    Menzel, Peter; Ng, Kim Lee; Krogh, Anders

    2016-01-01

    Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows–Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk. PMID:27071849

  8. Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

    SciTech Connect

    Dees, C.; Ringleberg, D.; Scott, T.C.; Phelps, T.

    1994-06-01

    The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

  9. Alternative oxidase in animals: unique characteristics and taxonomic distribution.

    PubMed

    McDonald, Allison E; Vanlerberghe, Greg C; Staples, James F

    2009-08-01

    Alternative oxidase (AOX), a ubiquinol oxidase, introduces a branch point into the respiratory electron transport chain, bypassing complexes III and IV and resulting in cyanide-resistant respiration. Previously, AOX was thought to be limited to plants and some fungi and protists but recent work has demonstrated the presence of AOX in most kingdoms of life, including animals. In the present study we identified AOX in 28 animal species representing nine phyla. This expands the known taxonomic distribution of AOX in animals by 10 species and two phyla. Using bioinformatics we found AOX gene sequences in members of the animal phyla Porifera, Placozoa, Cnidaria, Mollusca, Annelida, Nematoda, Echinodermata, Hemichordata and Chordata. Using reverse-transcriptase polymerase chain reaction (RT-PCR) with degenerate primers designed to recognize conserved regions of animal AOX, we demonstrated that AOX genes are transcribed in several animals from different phyla. An analysis of full-length AOX sequences revealed an amino acid motif in the C-terminal region of the protein that is unique to animal AOXs. Animal AOX also lacks an N-terminal cysteine residue that is known to be important for AOX enzyme regulation in plants. We conclude that the presence of AOX is the ancestral state in animals and hypothesize that its absence in some lineages, including vertebrates, is due to gene loss events. PMID:19648408

  10. On the taxonomic affinities of the Dmanisi mandible (Georgia).

    PubMed

    Rosas, A; Bermúdez de Castro, J M

    1998-10-01

    The recent discovery of unexpectedly ancient human remains has fuelled interest about the first dispersion of Homo outside Africa. The Dmanisi mandible is perhaps one of the most interesting findings, as it supposedly represents one of the oldest hominids outside of Africa. Recently, different interpretations have been published about this specimen. Our comparison of the Dmanisi mandible with a large sample of mandibles and teeth has led us to a new interpretation. In our view, the Dmanisi mandible exhibits a unique combination of traits. Some of its features, taken in isolation, may be attributed to morphological extremes within the genus Homo. The architecture of the mandible as well as the morphology and dimensions of incisors, canines, and P3s are clearly primitive. However, dental traits such as the reduction of the talonid in the P4s and a distally decreasing molar series seems to be derived. Some combinations of these traits are found in specimens of Homo ergaster and differ from those generally present in later hominids. Thus, we propose that the Dmanisi mandible might be taxonomically classified as Homo sp. indet. (aff. ergaster). Furthermore, some aspects of the dentition in Dmanisi display close similarities to Asian Homo erectus. If the 1.8-1.6 Myr dating for the Dmanisi mandible is correct, the differentiation of the Asian branch of the genus Homo could be regarded as a very ancient event. PMID:9786330