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Sample records for subfamily polistinae evidence

  1. The phylogeny of the social wasp subfamily Polistinae: evidence from microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters

    Strassmann Joan E

    2004-03-01

    Full Text Available Abstract Background Social wasps in the subfamily Polistinae (Hymenoptera: Vespidae have been important in studies of the evolution of sociality, kin selection, and within colony conflicts of interest. These studies have generally been conducted within species, because a resolved phylogeny among species is lacking. We used nuclear DNA microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters to generate a phylogeny for the Polistinae (Hymenoptera using 69 species. Results Our phylogeny is largely concordant with previous phylogenies at higher levels, and is more resolved at the species level. Our results support the monophyly of the New World subgenera of Polistini, while the Old World subgenera are a paraphyletic group. All genera for which we had more than one exemplar were supported as monophyletic except Polybia which is not resolved, and may be paraphyletic. Conclusion The combination of DNA sequences from flanks of microsatellite repeats with mtCOI sequences and morphological characters proved to be useful characters establishing relationships among the different subgenera and species of the Polistini. This is the first detailed hypothesis for the species of this important group.

  2. Markiana nigripinnis (Perugia, 1891 as a putative member of the subfamily Stevardiinae (Characiformes: Characidae: spermatic evidence

    Clarianna Martins Baicere-Silva

    Full Text Available The genus Markiana was until recently recognized as incertae sedis in the family Characidae, even though alternative placements for this genus have been advanced since its original description. More recently, it was hypothesized that Markiana nigripinnis is part of a clade informally named the Astyanax clade, indicating the putative close relationship of Markiana with the genus Astyanax. Examination of sperm ultrastructure of representatives of Astyanax and M. nigripinnis shows no evidence for this hypothesized close relationship. Rather, the spermatozoa of M. nigripinnis share characters found in spermatozoa of the non-inseminating members of the subfamily Stevardiinae, such as an angle of nuclear rotation equal to 85º resulting in a lateral position of the double nuclear fossa and flagellum. As with the non-inseminating Stevardiinae, sperm nuclei are also slightly elongate toward the flagellum, the proximal centriole is partially inside the nuclear fossa and anterior and oblique to the distal centriole, and the midpiece is short and strongly asymmetric. Additionally, M. nigripinnis shares with the other members of the Stevardiinae the presence of only four teeth in the inner row of the premaxillary and a short triangular ectopterygoid, which is never more than twice the length of the palatine.

  3. An anocellar polistine wasp (Hymenoptera, Vespidae, Polistinae from Texas

    Volker Lohrmann

    2016-12-01

    Full Text Available A remarkable teratological female of Polistes (Fuscopolistes dorsalis neotropicus Bequaert, 1940 (Vespidae: Polistinae is described and illustrated. The specimen lacks all three external dorsal ocelli but is normally developed in almost every other aspect. Additionally, similar findings in other Hymenoptera are briefly discussed, as are the consequences and the reasons that might cause the random loss of ocelli.

  4. A checklist of Ropalidiini wasps (Hymenoptera: Vespidae: Polistinae in Indochina

    Pham Phong Huy

    2014-01-01

    Full Text Available As a basis for intensive study of the taxonomy and biogeography of Ropalidiini wasps in Indochina (Hymenoptera: Vespidae: Polistinae, a checklist of Ropalidiini wasps (Hymenoptera: Vespidae is presented. A total of 57 Ropalidiini species and subspecies belonging to three genera from Indochina are listed, together with information of the type material deposited in the Natural History Collection, Ibaraki University, Japan (IUNH and the Institute of Ecology and Biological Resources (IEBR. References of their distribution in Indochina are also provided.

  5. Diversity and aspects of the ecology of social wasps (Vespidae, Polistinae in Central Amazonian "terra firme" forest

    Alexandre Somavilla

    2014-12-01

    Full Text Available Diversity and aspects of the ecology of social wasps (Vespidae, Polistinae in Central Amazonian "terra firme" forest. The knowledge of social wasp richness and biology in the Amazonian region is considered insufficient. Although the Amazonas state is the largest in the region, until now only two brief surveys were conducted there. Considering that the systematic inventory of an area is the first step towards its conservation and wise use, this study presents faunal data on social wasp diversity in a 25 km² area of "terra firme" (upland forest at the Ducke Reserve, Manaus, Amazonas, Brazil. Wasps were collected in the understory, following a protocol of three collectors walking along 60 trails 1,000 m in extension for 16 days between August and October 2010. Methods used were active search of individuals with entomological nets and nest collecting. Fifty-eight species of social wasps, allocated in 13 genera, were recorded; 67% of the collected species belong to Polybia, Agelaia and Mischocyttarus; other genera were represented by only four species or less. The most frequent species in active searches were Agelaia fulvofasciata (DeGeer, 1773, Agelaia testacea (Fabricius, 1804 and Angiopolybia pallens (Lepeletier, 1836. Twelve species were collected in nests. Prior to this study, 65 Polistinae species were deposited at the INPA Collection. Collecting in the study grid, an area not previously sampled for wasps, resulted in an increase of 25% species, and species richness was 86. According to the results, there is evidence that the diversity of social wasps at the Ducke Reserve is even higher, making it one of the richest areas in the Brazilian Amazonia.

  6. Phylogeny of wasps of the genus Mischocyttarus de Saussure (Hymenoptera, Vespidae, Polistinae Filogenia das vespas do gênero Mischocyttarus de Saussure (Hymenoptera, Vespidae, Polistinae

    Orlando Tobias Silveira

    2008-01-01

    Full Text Available A phylogenetic analysis is presented of subgenera and species-groups of Mischocyttarus de Saussure, the largest genus of social wasps. The analysis is based on 62 morphological and nest architecture characters, coded for 71 terminals representing much of the taxonomic diversity within the genus, plus three outgroup terminals representing other polistine tribes. The main conclusions about phylogenetic relationships within the genus are based on parsimony analysis under implied weights. Monophyly of Mischocyttarus is confirmed as well as that of most of the previously recognized subgenera: Mischocyttarus s. str., Clypeopolybia, Monogynoecus, Scytokeraia, Phi, Kappa, Megacanthopus and Omega sensu Richards (1978. Haplometrobius as conceived by Richards (1978 is not a monophyletic taxon, but some of its species-groups are monophyletic. The groups of M.artifex and M.cerberus are raised to subgenus level, and a new concept of Haplometrobius restricts it to the group of M.iheringi (the type species of this subgenus in the sense of this work. The concept of subgenus Omega is widened to include the species-groups of M.surinamensis and M.prominulus. Besides the new subgeneric classification presented, limits and diagnoses of all species-groups of the subgenera Phi and Haplometrobius sensu Richards (1978 are discussed, and a new key for all subgenera and species-groups of Mischocyttarus is also presented.O artigo apresenta um estudo filogenético dos subgêneros e grupos de espécies de Mischocyttarus de Saussure, o maior dos gêneros de vespas sociais. A análise é baseada em 62 caracteres morfológicos e de arquitetura de ninhos, codificados para 71 terminais representantes da diversidade taxonômica do gênero e mais três terminais correspondentes às outras três tribos de Polistinae. As conclusões principais sobre relações filogenéticas são extraídas de análises usando pesagem implícita de caracteres. O monofiletismo de Mischocyttarus

  7. Tetrahymena metallothioneins fall into two discrete subfamilies.

    Silvia Díaz

    2007-03-01

    Full Text Available Metallothioneins are ubiquitous small, cysteine-rich, multifunctional proteins which can bind heavy metals.We report the results of phylogenetic and gene expression analyses that include two new Tetrahymena thermophila metallothionein genes (MTT3 and MTT5. Sequence alignments of all known Tetrahymena metallothioneins have allowed us to rationalize the structure of these proteins. We now formally subdivide the known metallothioneins from the ciliate genus Tetrahymena into two well defined subfamilies, 7a and 7b, based on phylogenetic analysis, on the pattern of clustering of Cys residues, and on the pattern of inducibility by the heavy metals Cd and Cu. Sequence alignment also reveals a remarkably regular, conserved and hierarchical modular structure of all five subfamily 7a MTs, which include MTT3 and MTT5. The former has three modules, while the latter has only two. Induction levels of the three T. thermophila genes were determined using quantitative real time RT-PCR. Various stressors (including heavy metals brought about dramatically different fold-inductions for each gene; MTT5 showed the highest fold-induction. Conserved DNA motifs with potential regulatory significance were identified, in an unbiased way, upstream of the start codons of subfamily 7a MTs. EST evidence for alternative splicing in the 3' UTR of the MTT5 mRNA with potential regulatory activity is reported.The small number and remarkably regular structure of Tetrahymena MTs, coupled with the experimental tractability of this model organism for studies of in vivo function, make it an attractive system for the experimental dissection of the roles, structure/function relationships, regulation of gene expression, and adaptive evolution of these proteins, as well as for the development of biotechnological applications for the environmental monitoring of toxic substances.

  8. Guia de identificação dos ninhos de vespas sociais (Hymenoptera, Vespidae, Polistinae na Reserva Ducke, Manaus, Amazonas, Brasil Identification guide for nests of social wasps (Hymenoptera: Vespidae: Polistinae in Reserva Ducke, Manaus, Amazonas, Brazil

    Alexandre Somavilla

    2012-12-01

    Full Text Available Vespidae sociais utilizam principalmente material vegetal para a elaboração de seus ninhos. Embora existam alguns estudos referentes à fauna de vespas na região Amazônica, nenhum trabalho trata exclusivamente dos ninhos. Além disso, nas coleções biológicas poucos são os ninhos tombados, devido principalmente à fragilidade e difícil conservação dos mesmos. O objetivo desse trabalho foi o conhecimento de alguns ninhos encontrados na Reserva Ducke, apresentando informações a respeito dos mesmos e uma chave de identificação dos gêneros. Os ninhos foram coletados através da busca direta, percorrendo os transectos da grade do Programa de Pesquisa em Biodiversidade; locais como margens de igarapés, bordas de acampamentos e construções na sede da reserva também foram explorados. Para todos os ninhos obteve-se o registro fotográfico e a localização exata por GPS. Foram registrados 39 ninhos de vespas sociais alocados em 17 espécies de Polistinae: Agelaia constructor, A. pallipes, Angiopolybia pallens, Apoica pallens, Metapolybia unilineata, Mischocyttarus lecointei, M. saturatus, Polybia bistriata, P. dimidiata, P. jurinei, P. liliacea, P. occidentalis, P. procellosa, P. rejecta, Protopolybia bituberculata, P. chartergoides e Synoeca virginea. Cinco ninhos desabitados de Mischocyttarus, Polybia e Polistes também foram coletados.Nests of social wasps are composed mainly out of plant material. Although there are some studies about the social wasp fauna in the Amazon region, there is no work exclusively about these wasps' nests. Also, there are few catalogued nests in biological collections, because of their fragility and difficult conservation. The purpose of this study was to evaluate the kinds of nests found at "Reserva Ducke", compiling information about them and developing a key to identify the nests of each genera. The nests were actively collected in tracks of the "Programa de Pesquisa em Biodiversidade" plot; areas such

  9. The flower-visiting social wasps (Hymenoptera, Vespidae, Polistinae in two areas of Rio Grande do Sul State, southern Brazil

    Marcel G. Hermes

    2006-06-01

    Full Text Available The flower-visiting social wasps (Hymenoptera, Vespidae, Polistinae in two areas of Rio Grande do Sul State, southern Brazil. The structure of flower-visiting social wasps' assemblages in the CPCN Pró-Mata of São Francisco de Paula and in the Green Belt of Santa Cruz do Sul, Rio Grande do Sul, are characterized. A total of 879 polistine wasps were collected, of which 475 (11 spp. in the CPCN and 404 (21 spp. in the Green Belt, from September 1997 to April 2001 and from September 2001 to April 2004, respectively. Foraging social wasps were observed on flowers of 36 species of angiosperms (20 families in the Green Belt, and on flowers of 54 species of angiosperms (21 families in the CPCN. Asteraceae was the most visited plant family on both studied localities. A list of pant species visited by the polistines is provided.Vespas sociais (Hymenoptera, Vespidae, Polistinae visitantes de flores em duas áreas no Rio Grande do Sul, Brasil. A estrutura da assembléia de vespas sociais que visitam flores no CPCN Pró-Mata de São Francisco de Paula e no Cinturão Verde de Santa Cruz do Sul, Rio Grande do Sul, são caracterizadas. Do total de 879 polistíneos, 475 (11 spp. foram coletados no CPCN, e 404 (21 spp. no Cinturão Verde entre Setembro de 1997 a Abril de 2000 e Setembro de 2001 a Abril de 2004, respectivamente. Vespas sociais foram observadas em flores de 36 espécies de angiospermas (20 famílias no Cinturão Verde, e em flores de 54 espécies de angiospermas (21 famílias no CPCN. Asteraceae foi a família de planta que mais recebeu visitas por parte das vespas nas duas localidades estudadas. Uma lista com as espécies de plantas visitadas pelos polistíneos é apresentada.

  10. The PANTHER database of protein families, subfamilies, functions and pathways

    Mi, Huaiyu; Lazareva-Ulitsky, Betty; Loo, Rozina; Kejariwal, Anish; Vandergriff, Jody; Rabkin, Steven; Guo, Nan; Muruganujan, Anushya; Doremieux, Olivier; Campbell, Michael J.; Kitano, Hiroaki; Thomas, Paul D.

    2004-01-01

    PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise. These subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function (ontology terms and pathways), as well as inference of amino acids important for functional specificity. Hidden Markov models (HMMs) are built for each family and subfamily for classifying additional protein sequences. The l...

  11. Guia de identificação dos ninhos de vespas sociais (Hymenoptera, Vespidae, Polistinae na Reserva Ducke, Manaus, Amazonas, Brasil

    Alexandre Somavilla

    2012-12-01

    Full Text Available Vespidae sociais utilizam principalmente material vegetal para a elaboração de seus ninhos. Embora existam alguns estudos referentes à fauna de vespas na região Amazônica, nenhum trabalho trata exclusivamente dos ninhos. Além disso, nas coleções biológicas poucos são os ninhos tombados, devido principalmente à fragilidade e difícil conservação dos mesmos. O objetivo desse trabalho foi o conhecimento de alguns ninhos encontrados na Reserva Ducke, apresentando informações a respeito dos mesmos e uma chave de identificação dos gêneros. Os ninhos foram coletados através da busca direta, percorrendo os transectos da grade do Programa de Pesquisa em Biodiversidade; locais como margens de igarapés, bordas de acampamentos e construções na sede da reserva também foram explorados. Para todos os ninhos obteve-se o registro fotográfico e a localização exata por GPS. Foram registrados 39 ninhos de vespas sociais alocados em 17 espécies de Polistinae: Agelaia constructor, A. pallipes, Angiopolybia pallens, Apoica pallens, Metapolybia unilineata, Mischocyttarus lecointei, M. saturatus, Polybia bistriata, P. dimidiata, P. jurinei, P. liliacea, P. occidentalis, P. procellosa, P. rejecta, Protopolybia bituberculata, P. chartergoides e Synoeca virginea. Cinco ninhos desabitados de Mischocyttarus, Polybia e Polistes também foram coletados.

  12. Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project.

    Konkel, Miriam K; Walker, Jerilyn A; Hotard, Ashley B; Ranck, Megan C; Fontenot, Catherine C; Storer, Jessica; Stewart, Chip; Marth, Gabor T; Batzer, Mark A

    2015-08-29

    The goal of the 1000 Genomes Consortium is to characterize human genome structural variation (SV), including forms of copy number variations such as deletions, duplications, and insertions. Mobile element insertions, particularly Alu elements, are major contributors to genomic SV among humans. During the pilot phase of the project we experimentally validated 645 (611 intergenic and 34 exon targeted) polymorphic "young" Alu insertion events, absent from the human reference genome. Here, we report high resolution sequencing of 343 (322 unique) recent Alu insertion events, along with their respective target site duplications, precise genomic breakpoint coordinates, subfamily assignment, percent divergence, and estimated A-rich tail lengths. All the sequenced Alu loci were derived from the AluY lineage with no evidence of retrotransposition activity involving older Alu families (e.g., AluJ and AluS). AluYa5 is currently the most active Alu subfamily in the human lineage, followed by AluYb8, and many others including three newly identified subfamilies we have termed AluYb7a3, AluYb8b1, and AluYa4a1. This report provides the structural details of 322 unique Alu variants from individual human genomes collectively adding about 100 kb of genomic variation. Many Alu subfamilies are currently active in human populations, including a surprising level of AluY retrotransposition. Human Alu subfamilies exhibit continuous evolution with potential drivers sprouting new Alu lineages. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  13. Taxonomic Study of the Subfamily Lycorininae (Hymenoptera: Ichneumonidae from Korea

    Jong-Wook Lee

    2014-01-01

    Full Text Available Korean species of the subfamily Lycorininae Cushman & Rohwer are reviewed. This subfamily along with three species, Lycorina triangulifera Holmgren, 1859, L. spilonotae Chao, 1980, and L. ruficornis Kasparyan, 2007, are reported for the first time from Korea. In this genus, five species have been reported from the Eastern Palaearctic region, six species from China and two species from Japan. Some species of this subfamily is known as parasitoids of Crambidae and Tortricidae. We report three newly recorded species from Korea, Lycorina triangulifera, L. spilonotae, and L. ruficornis, and provide diagnoses with photographs of lycorinine species and a key to the Korean species.

  14. Vespas Sociais (Vespidae: Polistinae em Fitofisionomias Urbanas: um Checklist do Município de Barra Mansa, Rio de Janeiro, Brasil

    Carlos Alberto Souza

    2016-12-01

    Checklist of Social Wasps (Vespidae: Polistinae in Two Green Urban Areas in the Municipality of Barra Mansa, Rio de Janeiro, Brazil Abstract. New concepts on city planning and urbanization have progressively encouraged the creation and maintenance of public or private green areas, which are important feeding and shelter zones for several species of social wasps. However, in spite of the sampling effort and representativeness of southeastern Brazil, knowledge of richness and abundance of social wasps in Rio de Janeiro is still poor. The present study aimed at inventorying the fauna of social wasps in urban phytophysiognomies in downtown Barra Mansa, state of Rio de Janeiro, within the campus of Barra Mansa University. We sampled two areas for 12 months - a human-modified grassland and a reforested area, through active search with insect nests, Möericke traps, and aromatic traps. We collected 148 wasps of three tribes, four genera, and 17 species. Through active search we recorded 70.7% of the species sampled. The tribe Epiponini showed the highest species richness, and Polybia chrysothorax Lichtenstein and Polybia erythrothoraxla Richards were recorded for the first time in the state of Rio de Janeiro. In the anthropic field it was observed greater diversity (H’ = 1,890, equitability (J = 0,7605, and minor dominance (D(1/D = 0,2124, while in the reforested area was obtained H’ = 1,582, J = 0,6366 e D(1/D = 0,3465. The configuration and size of the reforested area in the campus Barra Mansa (UBM are insufficient elements to restrict the movement of species or segregate communities when considering the anthropic field, thereby still allowing that species could also be sampled between the areas.

  15. Social wasp species of Mischocyttarus (Phi related to M. alfkenii (Ducke and M. paraguayensis Zikán (Hymenoptera, Vespidae, Polistinae

    Orlando Tobias Silveira

    2013-06-01

    Full Text Available Social wasp species of Mischocyttarus (Phi related to M. alfkenii (Ducke and M. paraguayensis Zikán (Hymenoptera, Vespidae, Polistinae. A revision of the taxonomic status and an identification key are presented for species of the genus Mischocyttarus related to M. alfkenii (Ducke and M. paraguayensis Zikán. Seven new species are proposed in the alfkenii and basimacula groups (M. achagua sp. nov.; M. arawak sp. nov.; M. awa sp. nov.; M. embera sp. nov.; M. muisca sp. nov.; M. uniformis sp. nov.; M. waunan sp. nov., with five new synonymies [M. mamirauae Raw = M. alfkenii (Ducke; M. alfkenii excrucians Richards = M. flavicornis nigricornis Zikán = M. flavicornis Zikán; M. basimacula superpictus Richards = M. basimacula (Cameron]. Specific status is also newly recognized for M. trinitatis Richards. Two new species are described in the paraguayensis and bahiae group (M. suzannae sp. nov.; M. tayacaja sp. nov., while fifteen new synonymies are proposed (M. aracatubaensis Zikán = M. araujoi Zikán = M. costalimai Zikán = M. gilvus Zikán = M. infrastrigatoides Zikán = M. infrastrigatus Zikán = M. infrastrigatus Zikán = M. ornatulus Zikán = M. riograndensis Richards = M. rivulorum Richards = M. schrottkyi Zikán = M. scitulus Zikán = M. similaris Zikán = M. similatus Zikán = M. paraguayensis Zikán. These numbers change the picture of diversity in these species groups, as partly found in Richards's revision, published in 1978, reflecting higher diversity in northern Andean areas than in the Brazilian Atlantic region.

  16. Trichomes morphology as a taxonomic marker in the subfamily heliotropioideae (boraginaceae from Pakistan and Kashmir)

    Parveen, A.

    2009-01-01

    Trichomes morphology of the subfamily heliotropioideae (Boraginaceae representing by 18 spectes has been examined by light and scanning microscope. Within the subfamily Heliotropoideae trichomes are generally eglandular rarely glandular as in Heliotropium ohioglossum Boiss. Within the subfamily Heliotropoideae 1-celled unicellular and two celled uniseriate trichomes are observed. Shape of the trichomes usually comical with pointed tims and distinct trichomes base. However few species have indistinct trichome base. The data is significantly useful at specific and generic level within the subfamily Heliotropioideae. (author)

  17. Unequal subfamily proportions among honey bee queen and worker brood

    Tilley; Oldroyd

    1997-12-01

    Queens from three colonies of feral honey bees, Apis mellifera were removed and placed in separate nucleus colonies. For each colony, eggs and larvae were taken from the nucleus and placed in the main hive on each of 3-4 consecutive weeks. Workers in the queenless parts selected young larvae to rear as queens. Queen pupae, together with the surrounding worker pupae, were removed from each colony and analysed at two to three microsatellite loci to determine their paternity. In all three colonies, the paternity of larvae chosen by the bees to rear as queens was not a random sample of the paternities in the worker brood, with certain subfamilies being over-represented in queens. These results support an important prediction of kin selection theory: when colonies are queenless, unequal relatedness within colonies could lead to the evolution of reproductive competition, that is some subfamilies achieving greater reproductive success than others. The mechanism by which such dominance is achieved could be through a system of kin recognition and nepotism, but we conclude that genetically based differential attractiveness of larvae for rearing as queens is more likely.Copyright 1997 The Association for the Study of Animal BehaviourCopyright 1997The Association for the Study of Animal Behaviour.

  18. Subfamily logos: visualization of sequence deviations at alignment positions with high information content

    Beitz Eric

    2006-06-01

    Full Text Available Abstract Background Recognition of relevant sequence deviations can be valuable for elucidating functional differences between protein subfamilies. Interesting residues at highly conserved positions can then be mutated and experimentally analyzed. However, identification of such sites is tedious because automated approaches are scarce. Results Subfamily logos visualize subfamily-specific sequence deviations. The display is similar to classical sequence logos but extends into the negative range. Positive, upright characters correspond to residues which are characteristic for the subfamily, negative, upside-down characters to residues typical for the remaining sequences. The symbol height is adjusted to the information content of the alignment position. Residues which are conserved throughout do not appear. Conclusion Subfamily logos provide an intuitive display of relevant sequence deviations. The method has proven to be valid using a set of 135 aligned aquaporin sequences in which established subfamily-specific positions were readily identified by the algorithm.

  19. Local-scale spatial variation in diversity of social wasps in an Amazonian rain forest in Caxiuanã, Pará, Brazil (Hymenoptera, Vespidae, Polistinae Variação na diversidade de vespas sociais em escala local numa floresta pluvial amazônica em Caxiuanã, Pará, Brasil (Hymenoptera, Vespidae, Polistinae

    Orlando Tobias Silveira

    2012-09-01

    analisa em escala local padrões espaciais de registros de coleta, investigando também a variação espacial de descritores de diversidade numa área de 2.500 hectares de floresta amazônica no Brasil. Espécies raras constituíram a maior parte da fauna. Efeitos espaciais de curta distância foram detectados para a maioria das espécies mais comuns, com agregação de registros em distâncias até ca. 800 metros. Hiatos espaciais maiores foram identificados para algumas espécies, constituindo provavelmente autocorrelação exógena e candidatos a explicação por fatores ambientais. Nalguns casos, foram encontradas correlações significativas (ou quase entre cinco espécies (de Agelaia, Angiopolybia e Mischocyttarus e três variáveis ambientais estudadas: distância ao riacho mais próximo, altitude topográfica e tipo de copa da floresta. A associação desses fatores com variáveis de biodiversidade foi geralmente baixa. Quando utilizados como preditores de riqueza de Polistinae numa regressão linear múltipla, apenas o coeficiente para tipo de dossel florestal resultou significativo. Alguma predição mostra-se possível sobre variáveis de biodiversidade com base no conhecimento de condições ambientais, especialmente estrutura da vegetação. Estudos devem ser agendados para tratar do assunto em escalas espaciais mais amplas.

  20. The nuclear receptor gene family in the Pacific oyster, Crassostrea gigas, contains a novel subfamily group.

    Vogeler, Susanne; Galloway, Tamara S; Lyons, Brett P; Bean, Tim P

    2014-05-15

    Nuclear receptors are a superfamily of transcription factors important in key biological, developmental and reproductive processes. Several of these receptors are ligand- activated and through their ability to bind endogenous and exogenous ligands, are potentially vulnerable to xenobiotics. Molluscs are key ecological species in defining aquatic and terrestrial habitats and are sensitive to xenobiotic compounds in the environment. However, the understanding of nuclear receptor presence, function and xenobiotic disruption in the phylum Mollusca is limited. Here, forty-three nuclear receptor sequences were mined from the genome of the Pacific oyster, Crassostrea gigas. They include members of NR0-NR5 subfamilies, notably lacking any NR6 members. Phylogenetic analyses of the oyster nuclear receptors have been conducted showing the presence of a large novel subfamily group not previously reported, which is named NR1P. Homologues to all previous identified nuclear receptors in other mollusc species have also been determined including the putative heterodimer partner retinoid X receptor, estrogen receptor and estrogen related receptor. C. gigas contains a highly diverse set of nuclear receptors including a novel NR1 group, which provides important information on presence and evolution of this transcription factor superfamily in invertebrates. The Pacific oyster possesses two members of NR3, the sex steroid hormone receptor analogues, of which there are 9 in humans. This provides increasing evidence that steroid ligand specific expansion of this family is deuterostome specific. This new knowledge on divergence and emergence of nuclear receptors in C. gigas provides essential information for studying regulation of molluscan gene expression and the potential effects of xenobiotics.

  1. On the correct name for some subfamilies of Mustelidae (Mammalia, Carnivora

    Fabio Oliveira do Nascimento

    2014-01-01

    Full Text Available Mustelids (Mustelidae exhibit a wide morphological and ecological diversity, ranging from aquatic to semi arboreal and fossorial forms. It is the most diversity family in Carnivora, and this has promoted a great number of taxonomic arrangements for subfamilies, which can range from two to 15 depending on the author. The relatively recent use of molecular data has helped to elucidate the classification of mustelids, and eight subfamilies are currently recognized: Mustelinae, Galictinae, Helictidinae, Martinae, Melinae, Mellivorinae, Taxidiinae and Lutrinae. However, some of these subfamilies have nomenclatural problems, not receiving the oldest available name. The subfamily that includes martens (Martes, Charronia and Pekania, tayra (Eira and wolverine (Gulo has received the name of Martinae Wagner, 1841, but the oldest available name is Guloninae Gray, 1825. This problem also occurs for the subfamily that includes the grisons (Galictis, Patagonian weasel (Lyncodon, marbled polecat (Vormela and striped weasels (Ictonyx and Poecilogale, which are known as Grisoninae Pocock, 1921, but the correct name for this group is Ictonychinae, Pocock, 1921. The subfamily that includes ferret badgers (Melogale retains the name Helictidinae Gray, 1865, because its validity is not affected when the type-genus of the subfamily becomes a junior synonym of another genus. Furthermore, a list of the extant subfamilies of Mustelidae and their respective synonyms and included genera is provided.

  2. Phantoms of Gondwana?-phylogeny of the spider subfamily Mynogleninae (Araneae: Linyphiidae)

    Frick, Holger; Scharff, Nikolaj

    2014-01-01

    This is the first genus-level phylogeny of the subfamily Mynogleninae. It is based on 190 morphological characters scored for 44 taxa: 37 mynoglenine taxa (ingroup) representing 15 of the 17 known genera and seven outgroup taxa representing the subfamilies Stemonyphantinae, Linyphiinae (Linyphiin...

  3. Sea snakes in Australian waters (Serpentes: subfamilies Hydrophiinae and Laticaudinae)—a review with an updated identification key

    Redsted Rasmussen, Arne; Sanders, Kate Laura; Guinea, Michael L

    2014-01-01

    Sea snakes (Elapidae, subfamilies Hydrophiinae and Laticaudinae) reach high species richness in the South China Sea and in the Australian region; however, most countries in the two regions still lack up-to-date checklists and identification tools for these snakes. We present an updated reviewed...... checklist and a new complete identification key to sea snakes in Australian waters. The identification key includes 29 species documented and 4 possibly occurring taxa and is based mostly on easy-to-use external characters. We find no evidence for breeding populations of Laticauda in Australian waters...

  4. Molecular systematics of selected genera of subfamily mimosoidae-fabaceae

    Shinwari, Z.K.; Jamil, K.; Zahra, N.B.

    2014-01-01

    Family Mimosoidae-Fabaceae is of economic importance to local communities for its medicinal usage. It has commercial value, but the parts sold in the market are difficult to identify on the basis of morphological characters and therefore needs molecular systematics approaches. Hence, the utility of potential DNA barcodes for selected Acacia and Albizia species by using three cpDNA regions rbcL, matK and trnH-psbA was tested in this study. Our study suggests that the rbcL region can be used to identify these species and discriminate among them more effectively than matK and trnH-psbA. The latter regions proved to be less successful in sequencing particularly trnH-psbA. Therefore, rbcL is an improved and efficient tool for species identification of these medicinal plants and may be recommended for a broad series of subfamily Mimosoideae (Family: Fabaceae) plants, making it a potential DNA barcode for these taxa. Sequence data obtained from rbcL and matK also indicated that Acacia and Albizia are polyphyletic. The phylogenetic analysis on the basis of rbcL proved that Acacia nilotica and Acacia nilotica ssp. hemispherica are closely related as they form the sister groups. (author)

  5. Anatomy of 31 species from Mimosoideae (Leguminosae) subfamily on Venezuela

    Leon, H; Williams, J.

    2008-01-01

    This paper is about the wood anatomy of 31 species, belonging to 17 genera, of the Mimosoideae subfamily (Leguminosae), proceeding from different geographical regions of Venezuela. For each species, one to five individuals were studied. The descriptions were realized according to the IAWA Committee(1989). The studied species may be divided in two groups according to the presence or absence of septate fibers. All species of Inga showed septate fibers, whereas Albizia and Enterolobium included species with septate fibers and also species with non-septate fibers. The quantitative characteristics of the vessels and the width of rays showed sufficient variation as to be considered important characteristics from ataxonomic point of view. The most common parenchyma type was vasicetric, aliform and confluent. In Calliandra laxa, Prosopis juliflora and Zygia longifolia the main parenchyma type was in wide bands; whereas in Cedrelinga cateniformis, the main parenchyma type was thin vasicentric. All species studied, with the exception of Cedrelinga cateniformis, presented prismatic crystals in the parenchymatous axials cells. In spite of finding certain anatomical uniformity, it was possible to elaborate a key for the identification of the studied species.

  6. Mid-tertiary dispersal, not gondwanan vicariance explains distribution patterns in the wax palm subfamily (Ceroxyloideae: Arecaceae)

    Trénel, Philipp; Gustafsson, Mats H.G.; Baker, William J.

    2007-01-01

    The Ceroxyloideae is a small but heterogeneous subfamily of palms (Arecaceae, Palmae). It includes a Caribbean lineage (tribe Cyclospathae), a southern hemisphere disjunction (tribe Ceroxyleae), and an amphi-Andean element (tribe Phytelepheae), until recently considered a distinct subfamily (Phyt...

  7. Synopsis Of The subfamily Spiranthoideae (Orchidaceae) In Colombia, Part II

    Duenas Gomez, Hilda del Carmen; Fernandez Alonso, Jose Luis

    2009-01-01

    As second and last contribution to the synoptic treatment of the Spiranthoideae for Colombia, the synopsis of the tribes Spirantheae (subtribes Cyclopogoninae: 3 genera, 41 species and Stenorrhynchidinae: 9 genera, 15 species) and Cranichideae (5 genera, 53 species), is presented. The most diverse genera in these tribes are: Cranichis (20 species), Cyclopogon (17), Ponthieva (15) and Pelexia (14). As part of the results of this study: a)- The transfer of Cybebus from the subtribe Spiranthinae (where it was commonly placed) to the subtribe Stenorhinchidinae, is proposed, based on the floral morphology (the rostellum and viscidium structure). b)- two genera are reported for Colombia as new records, each one with one species: Lyroglossa (L. grisebachii) and Helonoma; for the latter the new combination Helonoma peruviana (Szlach.) Salazar, Duenas and Fern. Alonso is proposed. c) New records in the previously known list of Colombian orchids are presented: Coccineorchis (C. cristata, C. navarrensis), Cyclopogon (C. maldonadoanus, C. olivaceus, C. rimbachii), Pelexia (P. hirta, P. palmorchidis), Ponthieva (P. venusta), and Sarcoglottis (S. grandiflora, S. maasorum, S. neglecta, S. stergiosii). d)- And additional 19 new records of species belonging to Aspidogyne and Microchilus, not reported in Duenas and Fernandez-Alonso (2007), are also included. e)- Finally an analysis of the distribution and diversity of the genera of this subfamily, according to altitude ranges in Colombia is presented. This group has predominant Andean distribution, being found mainly between 1300 and 3600 m of altitude. Genera broadly distributed as Microchilus, Gomphichis, Cyclopogon, Pelexia, Sarcoglottis, Coccineorchis, Stenorrhynchos, Cranichis and Ponthieva, are found almost from the level up to 3000 m, in all the regions of the country. In contrast, Beloglottis, Brachystele, Cybebus, Eltroplectris, Hapalorchis, Helonoma, Lankesterella, Lyroglossa, Kreodanthus, Pteroglossa and Sauroglossum

  8. Species-specific evolution of class I MHC genes in iguanas (order: Squamata; subfamily: Iguaninae).

    Glaberman, Scott; Caccone, Adalgisa

    2008-07-01

    Over the last few decades, the major histocompatibility complex (MHC) has emerged as a model for understanding the influence of natural selection on genetic diversity in populations as well as for investigating the genetic basis of host resistance to pathogens. However, many vertebrate taxa remain underrepresented in the field of MHC research, preventing its application to studies of disease, evolution, and conservation genetics in these groups. This is particularly true for squamates, which are by far the most diversified order of non-avian reptiles but have not been the subject of any recent MHC studies. In this paper, we present MHC class I complementary DNA data from three squamate species in the subfamily Iguaninae (iguanas): the Galápagos marine iguana (Amblyrhynchus cristatus), the Galápagos land iguana (Conolophus subcristatus), and the green iguana (Iguana iguana). All sequences obtained are related to the few published class I genes from other squamates. There is evidence for multiple loci in each species, and the conserved alpha-3 domain appears to be evolving in a species-specific manner. Conversely, there is some indication of shared polymorphism between species in the peptide-binding alpha-1 and alpha-2 domains, suggesting that these two regions have different phylogenetic histories. The great similarity between alpha-3 sequences in marine iguanas in particular suggests that concerted evolution is acting to homogenize class I loci within species. However, while less likely, the data are also compatible with a birth and death model of evolution.

  9. Evident?

    Plant, Peter

    2012-01-01

    Quality assurance and evidence in career guidance in Europe are often seen as self-evident approaches, but particular interests lie behind......Quality assurance and evidence in career guidance in Europe are often seen as self-evident approaches, but particular interests lie behind...

  10. Homologous subfamilies of human alphoid repetitive DNA on different nucleolus organizing chromosomes

    Joergensen, A.L.; Bostock, C.J.; Bak, A.L.

    1987-01-01

    The organization of alphoid repeated sequences on human nucleolus-organizing (NOR) chromosomes 13, 21, and 22 has been investigated. Analysis of hybridization of alphoid DNA probes to Southern transfers of restriction enzyme-digested DNA fragments from hybrid cells containing single human chromosomes shows that chromosomes 13 and 21 share one subfamily of alphoid repeats, whereas a different subfamily may be held in common by chromosomes 13 and 22. The sequences of cloned 680-base-pair EcoRI fragments of the alphoid DNA from chromosomes 13 and 21 show that the basic unit of this subfamily is indistinguishable on each chromosome. The sequence of cloned 1020-base-pair Xba I fragments from chromosome 22 is related to, but distinguishable from, that of the 680-base-pair EcoRI alphoid subfamily of chromosomes 13 and 21. These results suggest that, at some point after they originated and were homogenized, different subfamilies of alphoid sequences must have exchanged between chromosomes 13 and 21 and separately between chromosomes 13 and 22

  11. Systematics of the subfamily Poeciliinae Bonaparte (Cyprinodontiformes: Poeciliidae, with an emphasis on the tribe Cnesterodontini Hubbs

    Paulo Henrique Franco Lucinda

    Full Text Available Osteological and soft anatomical features of representatives of poeciliine genera were studied to test the monophyly of the poeciliine tribes and to advance a hypothesis of relationships within the subfamily. The resultant hypothesis supports the proposal of a new classification for the subfamily Poeciliinae. Diagnoses are provided for suprageneric clades. The tribe Tomeurini is resurrected and the new tribes Brachyrhaphini and Priapichthyini as well as the supertribe Poeciliini are described. New usages of old tribe names are proposed based on the phylogenetic framework.

  12. Flora of subfamily Prunoideae of family Rosaceae in botanical garden of Dnipropetrovsk university

    V. F. Opanasenko

    2008-02-01

    Full Text Available The present state of genofond of the 24 taxa collection of subfamily Prunoideae Focke (family Rosaceae Juss in DNU botanical garden has been analysed. Valuable genotypes for practical use in the development of landscape, farm horticulture and further selection were marked out. The ways of further exploit was planned.

  13. Seed morphology and anatomy and its utility in recognizing subfamilies and tribes of Zingiberaceae

    Benedict, John C.; Smith, Selena Y.; Collinson, Margaret E.; Leong-Skornickova, Jana; Specht, Chelsea D.; Marone, Federica; Xiao, Xianghui; Parkinson, Dilworth Y.

    2015-11-01

    PREMISE OF THE STUDY: Recent phylogenetic analyses based on molecular data suggested that the monocot family Zingiberaceae be separated into four subfamilies and four tribes. Robust morphological characters to support these clades are lacking. Seeds were analyzed in a phylogenetic context to test independently the circumscription of clades and to better understand evolution of seed characters within Zingiberaceae. METHODS: Seventy-five species from three of the four subfamilies were analyzed using synchrotron based x-ray tomographic microscopy (SRXTM) and scored for 39 morphoanatomical characters. KEY RESULTS: Zingiberaceae seeds are some of the most structurally complex seeds in angiosperms. No single seed character was found to distinguish each subfamily, but combinations of characters were found to differentiate between the subfamilies. Recognition of the tribes based on seeds was possible for Globbeae, but not for Alpinieae, Riedelieae, or Zingibereae, due to considerable variation. CONCLUSIONS: SRXTM is an excellent, nondestructive tool to capture morphoanatomical variation of seeds and allows for the study of taxa with limited material available. Alpinioideae, Siphonochiloideae, Tamijioideae, and Zingiberoideae are well supported based on both molecular and morphological data, including multiple seed characters. Globbeae are well supported as a distinctive tribe within the Zingiberoideae, but no other tribe could be differentiated using seeds due to considerable homoplasy when compared with currently accepted relationships based on molecular data. Novel seed characters suggest tribal affinities for two currently unplaced Zingiberaceae taxa: Siliquamomum may be related to Riedelieae and Monolophus to Zingibereae, but further work is needed before formal revision of the family.

  14. First contact pheromone identified for a longhorned beetle (Coleoptera: Cerambycidae) in the subfamily Prioninae

    Annie E. Spikes; Matthew A. Paschen; Jocelyn G. Miller; Jardel A. Moreira; Paul B. Hamel; Nathan M. Schiff; Matthew D. Ginzel

    2010-01-01

    Little is known of the reproductive behavior of longhorned beetles (Coleoptera: Cerambycidae) in the subfamily Prioninae. Mallodon dasystomus (Say), the hardwood stump borer, is a widely distributed prionine that is native to the southern U.S. Here, we explored the chemically-mediated mating behavior of M dasystomus, and tested the hypothesis that males recognize...

  15. Generic revision of the subfamily Cenocoeliinae Szépligeti (Hymenoptera: Braconidae)

    Achterberg, van C.

    1994-01-01

    The genera of the subfamily Cenocoeliinae Szépligeti are revised, keyed and illustrated. The genera Capitonius Brullé, 1846, Aulacodes Cresson, 1865, Lestricus Reinhard, 1866, Promachus Cresson, 1887, and Evaniomorpha Szépligeti, 1901, are re-instated. One new genus is described and illustrated:

  16. Wood anatomy of the Euphorbiaceae, in particular of the subfamily Phyllanthoideae

    Mennega, Alberta M.W.

    1985-01-01

    The great variety in wood structure of the large family Euphorbiaceae makes it impossible to describe briefly a general wood pattern. Nevertheless, a more or less clear division into four anatomical groups can be made. A short overview is given of the wood structure of the uni-ovulate subfamilies

  17. Revision of the subfamily Euphorinae (excluding the tribe Meteorini Cresson) (Hymenoptera: Braconidae) from China

    Chen, X.; Achterberg, van C.

    1997-01-01

    The subfamily Euphorinae (excluding the tribe Meteorini Cresson) (Hymenoptera: Braconidae) from China is revised. In total 150 species, belonging to 24 genera, are treated and keyed. One genus (Heia gen. nov.; type species: Heia robustipes spec. nov.) and 69 species are described as new to science.

  18. Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid loci.

    Coughenour, Jennifer M; Simmons, Mark P; Lombardi, Julio A; Yakobson, Kendra; Archer, Robert H

    2011-05-01

    The phylogeny of Celastraceae subfamily Hippocrateoideae (∼ 100 species and 19 genera in the Old and New World tropics) was inferred using morphological characters together with plastid (matK, trnL-F) and nuclear (ITS and 26S rDNA) genes. The subfamily is easily recognized by the synapomorphies of transversely flattened, deeply lobed capsules and seeds with membranous basal wings or narrow stipes together with bisexual, 5-merous flowers that generally have an extrastaminal disk and three stamens. Hippocrateoideae, like Salacioideae, are inferred to have an Old World origin. The narrow stipes of Neotropical species that are water-dispersed are inferred to be derived within the subfamily from ancestral species with wind-dispersed winged seeds. Helictonema, a monotypic genus endemic to tropical Africa, has a small, white, spongy aril that is located at the base of the seed wing and appears to be unique within Hippocrateoideae. Our inference that Helictonema is sister to the remaining members of the subfamily, considered in the context of Sarawakodendron being sister to Salacioideae, suggests that small arils and capsular fruit were primitive within both subfamilies. The aril became dramatically enlarged within Salacioideae, in which the fruits are berries, and lost entirely within Hippocrateoideae, in which the fruits are transversely flattened capsules. All five Old World taxa of Prionostemma and all eight currently recognized species within Simirestis are transferred to Pristimera, one South African variety of Pristimera is raised to species level, and all three taxa in Pristimera subgenus Trochantha are transferred to the new genus Trochantha. Copyright © 2011 Elsevier Inc. All rights reserved.

  19. Revision of Drusinae subfamily (Trichoptera, Limnephilidae: divergence by paraproct and paramere: speciation in isolation by integration

    Oláh, János

    2017-08-01

    Full Text Available In the last few years we have described over 70 new incipient sibling limnephild species applying the discovered Trichoptera speciation traits of the paraproct and paramere for species recognition and delimitation. In this revision on Drusinae subfamily, comprising 177 species, we have applied these subtle, but rapid and stable speciation traits and described 49 new sibling species from the “well studied” European mountain ranges. Discussing the theoretical background we have elaborated and adapted a new character state ranking system of phenomics to revise the long-neglected taxonomy of the Drusinae subfamily and synonymised the Cryptothrix, Monocentra, Metanoea, Leptodrusus, Anomalopterygella, Hadimina genera with the Drusus genus. These old genera of artificial constructs were established exclusively by divergences of secondary sexual traits known already to have only species level ranking value. According to our new character ranking system in the Drusinae subfamily, beside the Drusus genus, only the Ecclisopteryx genus has been retained having robust generic level divegences of paraproct loss and ancestral duplication of spine organising centre on the paramere pattern. Speciation trait function of the peg-packed surface on the paraproct head in Drusus genus moved to the gonopod apices and integrated into variously shaped stimulatory organ in the Ecclisopteryx genus. In the Drusus genus the ancestral divergence of the single spine organising centre has integrated 11 species groups with remarkably stable paramere spine pattern. Based upon ancestral divergences in the paraproct architecture we have differenciated 28 species complexes inside the 11 species groups. The delineation of the 163 mostly incipient siblings species, inside the 28 species complexes with 44 new Drusus species, was based primarily on the divergences of speciation trait, that is in the stimulatory head shape of the apical arms on the dorsal branches of the paraproct

  20. Nine novel microsatellite markers for the army ant Simopelta pergandei (subfamily Ponerinae)

    Kronauer, D.J.C.; Boomsma, J.J.; Pierce, N.E.

    2011-01-01

    Simopelta (subfamily Ponerinae) army ants are specialized predators of other ants in New World tropical forests. Although they show a striking convergence in overall life-history with the well known army ants of the subfamilies Aenictinae, Dorylinae, and Ecitoninae, the genus has been little...... studied. We developed and characterized nine novel microsatellite loci for S. pergandei with 2-8 observed alleles (mean: 5.2) and expected heterozygosities between 0.16 and 0.87 (mean: 0.68). Three of these loci reliably cross-amplified in a second species, S. pentadentata, with 4-8 alleles (mean: 8.......0) and expected heterozygosities between 0.32 and 0.85 (mean: 0.65). These genetic markers will be useful in studying the sociobiology and molecular ecology of Simopelta army ants and in elucidating convergent evolutionary trajectories that have culminated in the army ant lifestyle...

  1. Variability of Pyrrolizidine Alkaloid Occurrence in Species of the Grass Subfamily Pooideae (Poaceae)

    Wesseling, Anne-Maria; Demetrowitsch, Tobias J.; Schwarz, Karin; Ober, Dietrich

    2017-01-01

    Pyrrolizidine alkaloids (PAs) are a class of secondary metabolites found in various unrelated angiosperm lineages including cool-season grasses (Poaceae, subfamily Pooideae). Thesinine conjugates, saturated forms of PA that are regarded as non-toxic, have been described to occur in the two grass species Lolium perenne and Festuca arundinacea (Poaceae, subfamily Pooideae). In a wider screen, we tested various species of the Pooideae lineage, grown under controlled conditions, for their ability to produce thesinine conjugates or related structures. Using an LC-MS based targeted metabolomics approach we were able to show that PA biosynthesis in grasses is limited to a group of very closely related Pooideae species that produce a limited diversity of PA structures. High variability in PA levels was observed even between individuals of the same species. These individual accumulation patterns are discussed with respect to a possible function and evolution of this type of alkaloid. PMID:29250094

  2. Variability of Pyrrolizidine Alkaloid Occurrence in Species of the Grass Subfamily Pooideae (Poaceae

    Anne-Maria Wesseling

    2017-11-01

    Full Text Available Pyrrolizidine alkaloids (PAs are a class of secondary metabolites found in various unrelated angiosperm lineages including cool-season grasses (Poaceae, subfamily Pooideae. Thesinine conjugates, saturated forms of PA that are regarded as non-toxic, have been described to occur in the two grass species Lolium perenne and Festuca arundinacea (Poaceae, subfamily Pooideae. In a wider screen, we tested various species of the Pooideae lineage, grown under controlled conditions, for their ability to produce thesinine conjugates or related structures. Using an LC-MS based targeted metabolomics approach we were able to show that PA biosynthesis in grasses is limited to a group of very closely related Pooideae species that produce a limited diversity of PA structures. High variability in PA levels was observed even between individuals of the same species. These individual accumulation patterns are discussed with respect to a possible function and evolution of this type of alkaloid.

  3. Molecular Phylogenetics of the Serranid Subfamily Epinephelinae: Speciation and Biogeography in a Nearshore Marine Fish Clade

    Craig, Matthew T,

    2005-01-01

    The processes that shape present day distributions of marine organisms have remained a central topic in evolutionary biology, conservation biology, and ecology. In this thesis, genetic data from mitochondrial and nuclear genes were used to create a phylogenetic hypothesis for the groupers of the subfamily Epinephelinae as a means of evaluating the current taxonomy of the group and the geography of speciation in marine organisms. The molecular phylogenetic hypothesis presented in Chap...

  4. Gene Structures, Classification, and Expression Models of the DREB Transcription Factor Subfamily in Populus trichocarpa

    Yunlin Chen

    2013-01-01

    Full Text Available We identified 75 dehydration-responsive element-binding (DREB protein genes in Populus trichocarpa. We analyzed gene structures, phylogenies, domain duplications, genome localizations, and expression profiles. The phylogenic construction suggests that the PtrDREB gene subfamily can be classified broadly into six subtypes (DREB A-1 to A-6 in Populus. The chromosomal localizations of the PtrDREB genes indicated 18 segmental duplication events involving 36 genes and six redundant PtrDREB genes were involved in tandem duplication events. There were fewer introns in the PtrDREB subfamily. The motif composition of PtrDREB was highly conserved in the same subtype. We investigated expression profiles of this gene subfamily from different tissues and/or developmental stages. Sixteen genes present in the digital expression analysis had high levels of transcript accumulation. The microarray results suggest that 18 genes were upregulated. We further examined the stress responsiveness of 15 genes by qRT-PCR. A digital northern analysis showed that the PtrDREB17, 18, and 32 genes were highly induced in leaves under cold stress, and the same expression trends were shown by qRT-PCR. Taken together, these observations may lay the foundation for future functional analyses to unravel the biological roles of Populus’ DREB genes.

  5. Plastid Genome Evolution in the Early-Diverging Legume Subfamily Cercidoideae (Fabaceae

    Yin-Huan Wang

    2018-02-01

    Full Text Available The subfamily Cercidoideae is an early-branching legume lineage, which consists of 13 genera distributed in the tropical and warm temperate Northern Hemisphere. A previous study detected two plastid genomic variations in this subfamily, but the limited taxon sampling left the overall plastid genome (plastome diversification across the subfamily unaddressed, and phylogenetic relationships within this clade remained unresolved. Here, we assembled eight plastomes from seven Cercidoideae genera and conducted phylogenomic-comparative analyses in a broad evolutionary framework across legumes. The plastomes of Cercidoideae all exhibited a typical quadripartite structure with a conserved gene content typical of most angiosperm plastomes. Plastome size ranged from 151,705 to 165,416 bp, mainly due to the expansion and contraction of inverted repeat (IR regions. The order of genes varied due to the occurrence of several inversions. In Tylosema species, a plastome with a 29-bp IR-mediated inversion was found to coexist with a canonical-type plastome, and the abundance of the two arrangements of isomeric molecules differed between individuals. Complete plastome data were much more efficient at resolving intergeneric relationships of Cercidoideae than the previously used selection of only a few plastid or nuclear loci. In sum, our study revealed novel insights into the structural diversification of plastomes in an early-branching legume lineage, and, thus, into the evolutionary trajectories of legume plastomes in general.

  6. Pollen morphology of the subfamily arecoideae griff. (family-arecaceae) from pakistan and kashmir

    Rasheed, A.A.; Perveen, A.; Abid, R.

    2016-01-01

    Pollen morphological characters are potentially informative in the systematic of monocotyledons including (Arecaceae), at supra and infra familial level. The pollen morphology of 8 species (subfamily Arecoideae) clearly shows that the qualitative pollen characters (such as aperture, exine pattern and shape) are found to be taxonomically important as compared to the quantitative characters (such as size of the grain and exine thickness).Considerable pollen variations have been found within the subfamily Arecoideae with regard to size, shape, aperture type and exine pattern. For instance, 7 out of 8 species have monosulcate pollen (i.e., 87.5%) and a remaining species (viz., Elaeis guineensis Jacq.) have trichotomosulcate pollen. The pollen are frequently elliptical, but in some cases rounded-triangular pollen were also found. Similarly, there is a great diversity in exine pattern such as punctate, reticulate, vermiculate, spinose, rugulate and perforate or combination of these types have also been found, but the most predominant pattern is the reticulate type. On the basis of pollen aperture, size and exine pattern, four pollen types have been recognized such as Areca-type, Dypsis-type, Cocos-type and Elaies-type. The data obtained from the palynological studies have been analyzed by Agglomerative cluster analysis choosing the Euclidean distance and Ward's method for a group linkage method. The objective of the present work is to classify studied taxa on the basis of pollen characters and to quantify the species relationships representing the subfamily Arecoideae based on numerical techniques. (author)

  7. The BBX subfamily IV: additional cogs and sprockets to fine-tune light-dependent development.

    Sarmiento, Felipe

    2013-04-01

    Plants depend on light during all phases of its life cycle, and have evolved a complex signaling network to constantly monitor its surroundings. Photomorphogenesis, a process during which the plant reprograms itself in order to dwell life in presence of light is one of the most studied phenomena in plants. Recent mutant analyses using model plant Arabidopsis thaliana and protein interaction assays have unraveled a new set of players, an 8-member subfamily of B-box proteins, known as BBX subfamily IV. For the members of this subfamily, positive (BBX21, BBX22) as well as negative (BBX24) functions have been described for its members, showing a strong association to two major players of the photomorphogenic cascade, HY5 and COP1. The roles of these new BBX regulators are not restricted to photomorphogenesis, but also have functions in other facets of light-dependent development. Therefore this newly identified set of regulators has opened up new insights into the understanding of the fine-tuning of this complex process.

  8. Molecular Evolutionary Characterization of a V1R Subfamily Unique to Strepsirrhine Primates

    Yoder, Anne D.; Chan, Lauren M.; dos Reis, Mario; Larsen, Peter A.; Campbell, C. Ryan; Rasoloarison, Rodin; Barrett, Meredith; Roos, Christian; Kappeler, Peter; Bielawski, Joseph; Yang, Ziheng

    2014-01-01

    Vomeronasal receptor genes have frequently been invoked as integral to the establishment and maintenance of species boundaries among mammals due to the elaborate one-to-one correspondence between semiochemical signals and neuronal sensory inputs. Here, we report the most extensive sample of vomeronasal receptor class 1 (V1R) sequences ever generated for a diverse yet phylogenetically coherent group of mammals, the tooth-combed primates (suborder Strepsirrhini). Phylogenetic analysis confirms our intensive sampling from a single V1R subfamily, apparently unique to the strepsirrhine primates. We designate this subfamily as V1Rstrep. The subfamily retains extensive repertoires of gene copies that descend from an ancestral gene duplication that appears to have occurred prior to the diversification of all lemuriform primates excluding the basal genus Daubentonia (the aye-aye). We refer to the descendent clades as V1Rstrep-α and V1Rstrep-β. Comparison of the two clades reveals different amino acid compositions corresponding to the predicted ligand-binding site and thus potentially to altered functional profiles between the two. In agreement with previous studies of the mouse lemur (genus, Microcebus), the majority of V1Rstrep gene copies appear to be intact and under strong positive selection, particularly within transmembrane regions. Finally, despite the surprisingly high number of gene copies identified in this study, it is nonetheless probable that V1R diversity remains underestimated in these nonmodel primates and that complete characterization will be limited until high-coverage assembled genomes are available. PMID:24398377

  9. Two ways of legumin-precursor processing in conifers. Characterization and evolutionary relationships of Metasequoia cDNAs representing two divergent legumin gene subfamilies.

    Häger, K P; Wind, C

    1997-06-15

    Subunit monomers and oligomers of crystalloid-type legumins are major components of SDS-soluble fractions from Metasequoia glyptostroboides (Dawn redwood, Taxodiaceae) seed proteins. The subunits are made up of disulfide linked alpha-polypeptides and beta-polypeptides with molecular masses of 33 kDa and 23-25 kDa, respectively. Unusually for legumins, those from Metasequoia are glycosylated and the carbohydrate moieties are residing in the C-terminal region of the respective beta-polypeptides. A Metasequoia endosperm cDNA library has been constructed and legumin-encoding transcripts representing two divergent gene subfamilies have been characterized. Intersubfamily comparisons reveal 75% identity at the amino acid level and the values range from 53-35% when the legumin precursors deduced were compared with those from angiosperms. The predicted sequences together with data from amino acid sequencing prove that post-translational processing of Metasequoia prolegumins is directed to two different processing sites, each of them specific for one of the legumin subfamilies. The sites involved differ in their relative position and in the junction to be cleaved: Metasequoia legumin precursors MgLeg18 and MgLeg26 contain the conventional post-translational Asn-Gly processing site, which is generally regarded as highly conserved. In contrast, the MgLeg4 precursor is lacking this site and post-translational cleavage is directed to an unusual Asn-Thr processing site located in its hypervariable region, causing N-terminal extension of the beta-polypeptide relative to those hitherto known. Evidence is given that the unusual variant of processing also occurs in other conifers. Phylogenetic analysis reveals the precursors concerned as representatives of a distinct legumin subfamily, originating from duplication of an ancestral gene prior to or at the beginning of Taxodiaceae diversification.

  10. Insect Resistance to Bacillus thuringiensis Toxin Cry2Ab Is Conferred by Mutations in an ABC Transporter Subfamily A Protein.

    Wee Tek Tay

    2015-11-01

    Full Text Available The use of conventional chemical insecticides and bacterial toxins to control lepidopteran pests of global agriculture has imposed significant selection pressure leading to the rapid evolution of insecticide resistance. Transgenic crops (e.g., cotton expressing the Bt Cry toxins are now used world wide to control these pests, including the highly polyphagous and invasive cotton bollworm Helicoverpa armigera. Since 2004, the Cry2Ab toxin has become widely used for controlling H. armigera, often used in combination with Cry1Ac to delay resistance evolution. Isolation of H. armigera and H. punctigera individuals heterozygous for Cry2Ab resistance in 2002 and 2004, respectively, allowed aspects of Cry2Ab resistance (level, fitness costs, genetic dominance, complementation tests to be characterised in both species. However, the gene identity and genetic changes conferring this resistance were unknown, as was the detailed Cry2Ab mode of action. No cross-resistance to Cry1Ac was observed in mutant lines. Biphasic linkage analysis of a Cry2Ab-resistant H. armigera family followed by exon-primed intron-crossing (EPIC marker mapping and candidate gene sequencing identified three independent resistance-associated INDEL mutations in an ATP-Binding Cassette (ABC transporter gene we named HaABCA2. A deletion mutation was also identified in the H. punctigera homolog from the resistant line. All mutations truncate the ABCA2 protein. Isolation of further Cry2Ab resistance alleles in the same gene from field H. armigera populations indicates unequal resistance allele frequencies and the potential for Bt resistance evolution. Identification of the gene involved in resistance as an ABC transporter of the A subfamily adds to the body of evidence on the crucial role this gene family plays in the mode of action of the Bt Cry toxins. The structural differences between the ABCA2, and that of the C subfamily required for Cry1Ac toxicity, indicate differences in the

  11. Reassessment of Species Diversity of the Subfamily Denticollinae (Coleoptera: Elateridae through DNA Barcoding.

    Taeman Han

    Full Text Available The subfamily Denticollinae is a taxonomically diverse group in the family Elateridae. Denticollinae includes many morphologically similar species and crop pests, as well as many undescribed species at each local fauna. To construct a rapid and reliable identification system for this subfamily, the effectiveness of molecular species identification was assessed based on 421 cytochrome c oxidase subunit I (COI sequences of 84 morphologically identified species. Among the 84 morphospecies, molecular species identification of 60 species (71.4% was consistent with their morphological identifications. Six cryptic and/or pseudocryptic species with large genetic divergence (>5% were confirmed by their sympatric or allopatric distributions. However, 18 species, including a subspecies, had ambiguous genetic distances and shared overlapping intra- and interspecific genetic distances (range: 2.12%-3.67% suggesting incomplete lineage sorting, introgression of mitochondrial genome, or affection by endosymbionts, such as Wolbachia infection, between species and simple genetic variation within species. In this study, we propose a conservative threshold of 3.6% for convenient molecular operational taxonomic unit (MOTU identification in the subfamily Denticollinae based on the results of pairwise genetic distances analyses using neighbor-joining, mothur, Automatic Barcode Gap Discovery analysis, and tree-based species delimitation by Poisson Tree Processes analysis. Using the 3.6% threshold, we identified 87 MOTUs and found 8 MOTUs in the interval between 2.5% to 3.5%. Evaluation of MOTUs identified in this range requires integrative species delimitation, including review of morphological and ecological differences as well as sensitive genetic markers. From this study, we confirmed that COI sequence is useful for reassessing species diversity for polymorphic and polytypic species occurring in sympatric and allopatric distributions, and for a single species having

  12. Identification and characterization of a novel gene differentially expressed in zebrafish cross-subfamily cloned embryos

    Wang Ya-Ping

    2008-03-01

    Full Text Available Abstract Background Cross-species nuclear transfer has been shown to be a potent approach to retain the genetic viability of a certain species near extinction. However, most embryos produced by cross-species nuclear transfer were compromised because that they were unable to develop to later stages. Gene expression analysis of cross-species cloned embryos will yield new insights into the regulatory mechanisms involved in cross-species nuclear transfer and embryonic development. Results A novel gene, K31, was identified as an up-regulated gene in fish cross-subfamily cloned embryos using SSH approach and RACE method. K31 complete cDNA sequence is 1106 base pairs (bp in length, with a 342 bp open reading frame (ORF encoding a putative protein of 113 amino acids (aa. Comparative analysis revealed no homologous known gene in zebrafish and other species database. K31 protein contains a putative transmembrane helix and five putative phosphorylation sites but without a signal peptide. Expression pattern analysis by real time RT-PCR and whole-mount in situ hybridization (WISH shows that it has the characteristics of constitutively expressed gene. Sub-cellular localization assay shows that K31 protein can not penetrate the nuclei. Interestingly, over-expression of K31 gene can cause lethality in the epithelioma papulosum cyprinid (EPC cells in cell culture, which gave hint to the inefficient reprogramming events occurred in cloned embryos. Conclusion Taken together, our findings indicated that K31 gene is a novel gene differentially expressed in fish cross-subfamily cloned embryos and over-expression of K31 gene can cause lethality of cultured fish cells. To our knowledge, this is the first report on the determination of novel genes involved in nucleo-cytoplasmic interaction of fish cross-subfamily cloned embryos.

  13. Phylogeny and evolutionary patterns in the Dwarf crayfish subfamily (Decapoda: Cambarellinae.

    Carlos Pedraza-Lara

    Full Text Available The Dwarf crayfish or Cambarellinae, is a morphologically singular subfamily of decapod crustaceans that contains only one genus, Cambarellus. Its intriguing distribution, along the river basins of the Gulf Coast of United States (Gulf Group and into Central México (Mexican Group, has until now lacked of satisfactory explanation. This study provides a comprehensive sampling of most of the extant species of Cambarellus and sheds light on its evolutionary history, systematics and biogeography. We tested the impact of Gulf Group versus Mexican Group geography on rates of cladogenesis using a maximum likelihood framework, testing different models of birth/extinction of lineages. We propose a comprehensive phylogenetic hypothesis for the subfamily based on mitochondrial and nuclear loci (3,833 bp using Bayesian and Maximum Likelihood methods. The phylogenetic structure found two phylogenetic groups associated to the two main geographic components (Gulf Group and Mexican Group and is partially consistent with the historical structure of river basins. The previous hypothesis, which divided the genus into three subgenera based on genitalia morphology was only partially supported (P = 0.047, resulting in a paraphyletic subgenus Pandicambarus. We found at least two cases in which phylogenetic structure failed to recover monophyly of recognized species while detecting several cases of cryptic diversity, corresponding to lineages not assigned to any described species. Cladogenetic patterns in the entire subfamily are better explained by an allopatric model of speciation. Diversification analyses showed similar cladogenesis patterns between both groups and did not significantly differ from the constant rate models. While cladogenesis in the Gulf Group is coincident in time with changes in the sea levels, in the Mexican Group, cladogenesis is congruent with the formation of the Trans-Mexican Volcanic Belt. Our results show how similar allopatric

  14. Current status of subfamily Ichneumoninae (Hymenoptera: Ichneumonidae) from Malaysia and Singapore

    Norhafiza, A. F.; Idris, A. B.

    2013-11-01

    In this paper, 25 genera and 38 species under 10 tribes (Alomyini, Compsophorini, Goedartiini, Heresiarchini, Ichneumonini, Ischnojoppini, Joppocryptini, Listrodromini, Oedicephalini and Platylabini) of the subfamily Ichneumoninae housed in the Centre for Insect Systematics, UKM and Raffles Museum of Biodiversity Research (National University of Singapore) are reported from Malaysia and Singapore. The tribe Heresiarchini has the greatest number of species (13) followed by Ichneumonini with six species. Imeria is the largest genus which contains five species recorded. Six species in this study are new records for Malaysia.

  15. Rediscovered and new perisphaerine cockroaches from SW China with a review of subfamilial diagnosis (Blattodea: Blaberidae).

    Li, Xin-Ran; Wang, Li-Li; Wang, Zong-Qing

    2018-04-17

    The taxonomic records of Chinese perisphaerine cockroaches were scattered in literature, and therefore a dedicated study is desired to update our knowledge. This paper reviews the subfamilial diagnosis and Chinese species, mostly from southwestern China. We provide high-definition habitus photos and drawings, the latter emphasizes the genitalia of both sexes, which are generalized with diagrams, abstracted from specimens examined. A total of 18 species are recorded in four genera, including Perisphaerus, or pill cockroach, the type genus of the subfamily. Two new genera and three new species are proposed: Achatiblatta achates gen. sp. nov., Frumentiforma frumentiformis gen. sp. nov., and Pseudoglomeris montana sp. nov.. Pseudoglomeris has five new junior synonyms: Corydidarum, Trichoblatta, Kurokia, Glomerexis, and Glomeriblatta; the following combinations are thus revived or new: Ps. aerea comb. nov., Ps. angustifolia comb. nov., Ps. beybienkoi comb. nov., Ps. fallax comb. nov., Ps. magnifica comb. rev., Ps. montshadskii comb. nov., Ps. nigra comb. nov., Ps. sculpta comb. nov., Ps. semisulcata comb. rev., Ps. tibetana comb. nov., and Ps. valida moderata comb. nov.. The following species are revalidated and combinations revived: Pe. pygmaeus comb. rev., Ps. dubia comb. sp. rev., and Ps. planiuscla comb. sp. rev.

  16. Identification of multiple distinct Snf2 subfamilies with conserved structural motifs.

    Flaus, Andrew; Martin, David M A; Barton, Geoffrey J; Owen-Hughes, Tom

    2006-01-01

    The Snf2 family of helicase-related proteins includes the catalytic subunits of ATP-dependent chromatin remodelling complexes found in all eukaryotes. These act to regulate the structure and dynamic properties of chromatin and so influence a broad range of nuclear processes. We have exploited progress in genome sequencing to assemble a comprehensive catalogue of over 1300 Snf2 family members. Multiple sequence alignment of the helicase-related regions enables 24 distinct subfamilies to be identified, a considerable expansion over earlier surveys. Where information is known, there is a good correlation between biological or biochemical function and these assignments, suggesting Snf2 family motor domains are tuned for specific tasks. Scanning of complete genomes reveals all eukaryotes contain members of multiple subfamilies, whereas they are less common and not ubiquitous in eubacteria or archaea. The large sample of Snf2 proteins enables additional distinguishing conserved sequence blocks within the helicase-like motor to be identified. The establishment of a phylogeny for Snf2 proteins provides an opportunity to make informed assignments of function, and the identification of conserved motifs provides a framework for understanding the mechanisms by which these proteins function.

  17. A consistent nomenclature of antimicrobial peptides isolated from frogs of the subfamily Phyllomedusinae.

    Amiche, Mohamed; Ladram, Ali; Nicolas, Pierre

    2008-11-01

    A growing number of cationic antimicrobial peptides have been isolated from the skin of hylid frogs belonging to the Phyllomedusinae subfamily. The amino acid sequences of these peptides are currently located in several databases under identifiers with no consistent system of nomenclature to describe them. In order to provide a workable terminology for antimicrobial peptides from Phyllomedusid frogs, we have made a systematic effort to collect, analyze, and classify all the Phyllomedusid peptide sequences available in databases. We propose that frogs belonging to the Phyllomedusinae subfamily should be described by the species names set out in Amphibian Species of the World: http://research.amnh.org/herpetology/amphibia/index.php, American Museum of Natural History, New York, USA. Multiple alignments analysis of at least 80 antimicrobial peptides isolated from 12 Phyllomedusinae species were distributed in seven distinct peptide families including dermaseptin, phylloseptin, plasticin, dermatoxin, phylloxin, hyposin and orphan peptides, and will be considered as the name of the headgroup of each family. The parent peptide's name should be followed by the first upper letter of the species for orthologous peptides and publication date determines priority. For example, the abbreviation B for bicolor and H for hypochondrialis. When two species begin with the same letter, two letters in upper case should be used (the first letter followed by the second or the third letter and so on). For example, the abbreviation DI for distincta, DU for duellmani, VA for vaillanti and VN for vanzolinii. Paralogous peptides should bear letter(s) in upper case followed by numbers.

  18. Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts.

    Asakura, Yukari; Bayraktar, Omer Ali; Barkan, Alice

    2008-11-01

    Chloroplast genomes in angiosperms encode approximately 20 group II introns, approximately half of which are classified as subgroup IIB. The splicing of all but one of the subgroup IIB introns requires a heterodimer containing the peptidyl-tRNA hydrolase homolog CRS2 and one of two closely related proteins, CAF1 or CAF2, that harbor a recently recognized RNA binding domain called the CRM domain. Two CRS2/CAF-dependent introns require, in addition, a CRM domain protein called CFM2 that is only distantly related to CAF1 and CAF2. Here, we show that CFM3, a close relative of CFM2, associates in vivo with those CRS2/CAF-dependent introns that are not CFM2 ligands. Mutant phenotypes in rice and Arabidopsis support a role for CFM3 in the splicing of most of the introns with which it associates. These results show that either CAF1 or CAF2 and either CFM2 or CFM3 simultaneously bind most chloroplast subgroup IIB introns in vivo, and that the CAF and CFM subunits play nonredundant roles in splicing. These results suggest that the expansion of the CRM protein family in plants resulted in two subfamilies that play different roles in group II intron splicing, with further diversification within a subfamily to accommodate multiple intron ligands.

  19. Functional interactome of Aquaporin 1 sub-family reveals new physiological functions in Arabidopsis Thaliana

    Mohamed Ragab Abdel Gawwad

    2013-09-01

    Full Text Available Aquaporins are channel proteins found in plasma membranes and intercellular membranes of different cellular compartments, facilitate the water flux, solutes and gases across the cellular plasma membranes. The present study highlights the sub-family plasma membrane intrinsic protein (PIP predicting the 3-D structure and analyzing the functional interactome of it homologs. PIP1 homologs integrate with many proteins with different plant physiological roles in Arabidopsis thaliana including; PIP1A and PIP1B: facilitate the transport of water, diffusion of amino acids and/or peptides from the vacuolar compartment to the cytoplasm, play a role in the control of cell turgor and cell expansion and involved in root water uptake respectively. In addition we found that PIP1B plays a defensive role against Pseudomonas syringae infection through the interaction with the plasma membrane Rps2 protein. Another substantial function of PIP1C via the interaction with PIP2E is the response to nematode infection. Generally, PIP1 sub-family interactome controlling many physiological processes in plant cell like; osmoregulation in plants under high osmotic stress such as under a high salt, response to nematode, facilitate the transport of water across cell membrane and regulation of floral initiation in Arabidopsis thaliana.

  20. Flight patterns and sex ratio of beetles of the subfamily Dynastinae (Coleoptera, Melolonthidae

    Larissa Simões Corrêa de Albuquerque

    2016-09-01

    Full Text Available ABSTRACT Dynastinae is one of the most representative subfamilies of Melolonthidae (Scarabaeoidea and has considerable ecological importance due mainly to interactions with plants of the families Araceae and Annonaceae. This relationship has led to the evolution of nocturnal activity patterns, which are influenced by environmental conditions. In the present study, abiotic factors were investigated to comprehend the influence on the flight patterns and identify the sex ratio of beetles from this subfamily. A study was conducted at Campo de Instrução Marechal Newton Cavalcanti in northeastern Brazil between December 2010 and November 2011. Thirteen species of Dynastinae were identified, most of which were from the genus Cyclocephala. Abundance and richness were greater in the dry season. Six species exhibited peak flight activity at specific periods of the night. More females than males were recorded for Cyclocephala distincta and C. paraguayensis. The present findings suggest that rainfall reduces the flight activity of these beetles and different time schedules may be related to mating behavior, foraging behavior and the avoidance of interspecific resource competition.

  1. A Rationally Designed Agonist Defines Subfamily IIIA Abscisic Acid Receptors As Critical Targets for Manipulating Transpiration.

    Vaidya, Aditya S; Peterson, Francis C; Yarmolinsky, Dmitry; Merilo, Ebe; Verstraeten, Inge; Park, Sang-Youl; Elzinga, Dezi; Kaundal, Amita; Helander, Jonathan; Lozano-Juste, Jorge; Otani, Masato; Wu, Kevin; Jensen, Davin R; Kollist, Hannes; Volkman, Brian F; Cutler, Sean R

    2017-11-17

    Increasing drought and diminishing freshwater supplies have stimulated interest in developing small molecules that can be used to control transpiration. Receptors for the plant hormone abscisic acid (ABA) have emerged as key targets for this application, because ABA controls the apertures of stomata, which in turn regulate transpiration. Here, we describe the rational design of cyanabactin, an ABA receptor agonist that preferentially activates Pyrabactin Resistance 1 (PYR1) with low nanomolar potency. A 1.63 Å X-ray crystallographic structure of cyanabactin in complex with PYR1 illustrates that cyanabactin's arylnitrile mimics ABA's cyclohexenone oxygen and engages the tryptophan lock, a key component required to stabilize activated receptors. Further, its sulfonamide and 4-methylbenzyl substructures mimic ABA's carboxylate and C6 methyl groups, respectively. Isothermal titration calorimetry measurements show that cyanabactin's compact structure provides ready access to high ligand efficiency on a relatively simple scaffold. Cyanabactin treatments reduce Arabidopsis whole-plant stomatal conductance and activate multiple ABA responses, demonstrating that its in vitro potency translates to ABA-like activity in vivo. Genetic analyses show that the effects of cyanabactin, and the previously identified agonist quinabactin, can be abolished by the genetic removal of PYR1 and PYL1, which form subclade A within the dimeric subfamily III receptors. Thus, cyanabactin is a potent and selective agonist with a wide spectrum of ABA-like activities that defines subfamily IIIA receptors as key target sites for manipulating transpiration.

  2. A new species of Glaphyropoma: the first subterranean copionodontine catfish and the first occurrence of opercular odontodes in the subfamily (Siluriformes: Trichomycteridae

    Maria Elina Bichuette

    Full Text Available A new species of the rare copionodontine genus Glaphyropoma is described from subterranean waters in the Diamantina Plateau, Bahia State, central northeastern Brazil. This is the first troglomorphic species in the subfamily Copionodontinae. It is distinguished from all other copionodontines by the presence of opercular odontodes, and further distinguished from its only congener, G. rodriguesi, by the reduction of dark integumentary pigmentation. The new species shares the single synapomorphy previously proposed for Glaphyropoma, the marked narrowing of the first hypobranchial and indirect character evidence also supports its inclusion in the genus. The presence of opercular odontodes in the new species, in combination with a reviewed hypothesis of sister group relationship between Copionodontinae and Trichogeninae, indicate that the absence of opercular odontodes in previously-known copionodontines is secondary, rather than primitive.

  3. Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies.

    Fetterman, Christina D; Rannala, Bruce; Walter, Michael A

    2008-09-24

    Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP. Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters. Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and

  4. Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies

    Rannala Bruce

    2008-09-01

    Full Text Available Abstract Background Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP. Results Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters. Conclusion Consideration of selection pressures observed in conjunction with known

  5. Identification and expression analysis of zebrafish polypeptide α-N-acetylgalactosaminyltransferase Y-subfamily genes during embryonic development.

    Nakayama, Yoshiaki; Nakamura, Naosuke; Kawai, Tamiko; Kaneda, Eiichi; Takahashi, Yui; Miyake, Ayumi; Itoh, Nobuyuki; Kurosaka, Akira

    2014-09-01

    Mucin-type glycosylation is one of the most common posttranslational modifications of secretory and membrane proteins and has diverse physiological functions. The initial biosynthesis of mucin-type carbohydrates is catalyzed by UDP-GalNAc: polypeptide α-N-acetylgalactosaminyltransferases (GalNAc-Ts) encoded by GALNT genes. Among these, GalNAc-T8, -T9, -T17, and -T18 form a characteristic subfamily called "Y-subfamily" and have no or very low in vitro transferase activities when assayed with typical mucin peptides as acceptor substrates. Although the Y-subfamily isozymes have been reported to be possibly involved in various diseases, their in vivo functions have not been reported. Here, we isolated zebrafish Y-subfamily galnt genes, and determined their spatial and temporal expressions during the early development of zebrafish. Our study demonstrated that all the Y-subfamily isozymes were well conserved in zebrafish with GalNAc-T18 having two orthologs, galnt18a and galnt18b, and with the other three isozymes each having a corresponding ortholog, galnt8, galnt9, and galnt17. The galnt8 was expressed in the cephalic mesoderm and hatching gland during early developmental stages, and differently expressed in the head, somatic muscles, and liver in the later stages. The other three orthologs also exhibited the characteristic expression patterns, although their expressions were generally strong in the nervous systems. In addition to the expression in the brain, galnt17 and galnt18a were expressed in the somitic muscles, and galnt18a and galnt18b in the notochord. These expression patterns may contribute to the functional analysis of the Y-subfamily, whose physiological roles still remain to be elucidated. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Relevance of the NR4A sub-family of nuclear orphan receptors in trophoblastic BeWo cell differentiation.

    Malhotra, Sudha Saryu; Gupta, Satish Kumar

    2017-01-01

    Nur-77, a member of the NR4A sub-family of nuclear orphan receptors, is downregulated in the placentae of pre-eclamptic women. Here, we investigate the relevance of Nor-1, Nurr-1 and Nur-77 in trophoblastic cell differentiation. Their transcript levels were found to be significantly upregulated in BeWo cells treated with forskolin. The maximum increase was observed after 2 h, with a second peak in the expression levels after 48 h. The expression of NR4A sub-family members was also found to be upregulated in BeWo cells after treatment with hCG and GnRH. A similar significant increase was observed at the respective protein levels after 2 and 48 h of treatment with forskolin, hCG or GnRH. Silencing Nor-1, Nurr-1 or Nur-77 individually did not show any effect on forskolin-, hCG- and/or GnRH-mediated BeWo cell fusion and/or hCG secretion. After silencing any one member of the NR4A sub-family, an increase in the transcript levels of the other sub-family members was observed, indicating a compensatory effect due to their functional redundancy. Simultaneously silencing all three NR4A sub-family members significantly downregulated forskolin- and hCG-mediated BeWo cell fusion and/or hCG secretion. However, a considerable amount of cell death occurred after forskolin or hCG treatment as compared to the control siRNA-transfected cells. These results suggest that the NR4A sub-family of nuclear orphan receptors has a role in trophoblastic cell differentiation.

  7. On the entomofauna of Mt. Durmitor (Northern Montenegro: Braconid wasps of the subfamily Opiinae (Braconidae, Hymenoptera

    Brajković M.M.

    2005-01-01

    Full Text Available Braconids are primary parasites of other insects and their eggs, larvae, and adults, and species have been recently discovered that lay their eggs in plant seeds. Classified into about 25 genera, more than 1,400 species of Opiinae are known at the present time in the world fauna. They have been registered in all zoogeographic regions. The Opiinae are solitary endoparasites of the larvae of cyclorhaphous Diptera, most often those of species belonging to the families Agromyzidae, Tephritidae, Anthomyiidae Ephydridae. In investigations conducted on Mt. Durmitor since 1982, we have up to now established 10 species of braconids of the subfamily Opiinae (Opius peterseni Fi., O. caudatus Wesm., O. parvungula Th., O. levisWesm., O. pallipesWesm., O. quasiquisti Fi., O. exilis Hal., O. filicornis Th., O. lugens Hal., and O. meracus Fi, eight of which are new for the fauna of Serbia and Montenegro.

  8. Molecular phylogeny of moth-specialized spider sub-family Cyrtarachninae, which includes bolas spiders.

    Tanikawa, Akio; Shinkai, Akira; Miyashita, Tadashi

    2014-11-01

    The evolutionary process of the unique web architectures of spiders of the sub-family Cyrtarachninae, which includes the triangular web weaver, bolas spider, and webless spider, is thought to be derived from reduction of orbicular 'spanning-thread webs' resembling ordinal orb webs. A molecular phylogenetic analysis was conducted to explore this hypothesis using orbicular web spiders Cyrtarachne, Paraplectana, Poecilopachys, triangular web spider Pasilobus, bolas spiders Ordgarius and Mastophora, and webless spider Celaenia. The phylogeny inferred from partial sequences of mt-COI, nuclear 18S-rRNA and 28S-rRNA showed that the common ancestor of these spiders diverged into two clades: a spanning-thread web clade and a bolas or webless clade. This finding suggests that the triangular web evolved by reduction of an orbicular spanning web, but that bolas spiders evolved in the early stage, which does not support the gradual web reduction hypothesis.

  9. A Taxonomic Review of the Sword-tailed Cricket Subfamily Trigonidiinae (Orthoptera: Ensifera: Gryllidae from Korea

    Tae-Woo Kim

    2013-01-01

    Full Text Available The Korean population of the sword-tailed cricket subfamily Trigonidiinae is reviewed for the first time. Four members of the crickets are confirmed based on the examined material, those are Metioche japonica (Ichikawa, 2001, Svistella bifasciata (Shiraki, 1911, Homoeoxipha obliterata (Caudell, 1927 and Natula matsuurai Sugimoto, 2001, each of them belonging to a different genera. Among them, the former two are reconfirmed since earlier records, and latter two are newly recognized genera and species from the far southern provinces Jeollanam-do and Jeju-do Island in Korea. The type locality of both crickets is Japan, and are also only previously referred to in Japan, but their distributional ranges include neighboring South Korea. A key to the species, descriptions, photographs, figures, and oscillograms of male’s calling sounds are provided to aid their identification.

  10. Comparative Mitogenomic Analysis of Species Representing Six Subfamilies in the Family Tenebrionidae

    Hong-Li Zhang

    2016-05-01

    Full Text Available To better understand the architecture and evolution of the mitochondrial genome (mitogenome, mitogenomes of ten specimens representing six subfamilies in Tenebrionidae were selected, and comparative analysis of these mitogenomes was carried out in this study. Ten mitogenomes in this family share a similar gene composition, gene order, nucleotide composition, and codon usage. In addition, our results show that nucleotide bias was strongly influenced by the preference of codon usage for A/T rich codons which significantly correlated with the G + C content of protein coding genes (PCGs. Evolutionary rate analyses reveal that all PCGs have been subjected to a purifying selection, whereas 13 PCGs displayed different evolution rates, among which ATPase subunit 8 (ATP8 showed the highest evolutionary rate. We inferred the secondary structure for all RNA genes of Tenebrio molitor (Te2 and used this as the basis for comparison with the same genes from other Tenebrionidae mitogenomes. Some conserved helices (stems and loops of RNA structures were found in different domains of ribosomal RNAs (rRNAs and the cloverleaf structure of transfer RNAs (tRNAs. With regard to the AT-rich region, we analyzed tandem repeat sequences located in this region and identified some essential elements including T stretches, the consensus motif at the flanking regions of T stretch, and the secondary structure formed by the motif at the 3′ end of T stretch in major strand, which are highly conserved in these species. Furthermore, phylogenetic analyses using mitogenomic data strongly support the relationships among six subfamilies: ((Tenebrionidae incertae sedis + (Diaperinae + Tenebrioninae + (Pimeliinae + Lagriinae, which is consistent with phylogenetic results based on morphological traits.

  11. Molecular characterization of two sub-family specific monoclonal antibodies to meningococcal Factor H binding protein

    C. Lo Passo

    2018-04-01

    Full Text Available Factor H binding protein (FHbp is a component of two licensed vaccines for prevention of sepsis and meningitis caused by serogroup B meningococci. FHbp binds human Factor H (FH, which contributes to evasion of host immunity and FHbp sequence variants can be classified into two sub-families. Antibodies against FHbp elicit complement-mediated killing and can inhibit recruitment of FH to the bacterial surface. We report epitope mapping studies of two murine IgG mAbs, designated JAR 31 and JAR 36, isolated from a mouse immunized with FHbp in sub-family A, which is present in ∼30–40% of invasive isolates. In the present study, we tested the reactivity of mAbs JAR 31 and JAR 36 with seven natural FHbp sequence variants from different phylogenic groups. We screened bacteriophage-displayed peptide libraries to identify amino acid residues contributing to the JAR 36 epitope. Based on the reactivities of mAbs JAR 31 and JAR 36 with the seven FHbp variants, and the frequent occurrences of aspartate (D and lysine (K residues in the JAR 36-bound phage peptides, we selected six residues in the carboxyl-terminal region of FHbp for replacement with alanine (A. The D201A and K203A substitutions respectively eliminated and decreased binding of mAbs JAR 31 and JAR 36 to FHbp. These substitutions did not affect binding of the control mAb JAR 33 or of human FH. JAR 31 or JAR 36 mediated cooperative complement-mediated bactericidal activity with other anti-FHbp mAbs. The identification of two amino acid residues involved in the epitopes recognized by these anti-FHbp mAbs may contribute to a more complete understanding of the spatial requirements for cooperative anti-FHbp mAb bactericidal activity. Keywords: Biochemistry, Immunology, Microbiology, Molecular biology

  12. Frames of exponentials:lower frame bounds for finite subfamilies, and approximation of the inverse frame operator

    Christensen, Ole; Lindner, Alexander M

    2001-01-01

    We give lower frame bounds for finite subfamilies of a frame of exponentials {e(i lambdak(.))}k is an element ofZ in L-2(-pi,pi). We also present a method for approximation of the inverse frame operator corresponding to {e(i lambdak(.))}k is an element ofZ, where knowledge of the frame bounds for...

  13. ROLE OF ATP BINDING CASSETTE SUB-FAMILY MEMBER 2 (ABCG2) IN MOUSE EMBRYONIC STEM CELL DEVELOPMENT.

    ATP binding cassette sub-family member 2 (ABCG2), is a member of the ABC transporter superfamily and a principal xenobiotic transporter. ABCG2 is also highly expressed in certain stem cell populations where it is thought to be related to stem cell plasticity, although the role o...

  14. Australian water mites of the subfamily Notoaturinae Besch (Acari: Hydrachnidia: Aturidae), with the description of 24 new species

    Smit, H.

    2010-01-01

    New data are presented on the subfamily Notoaturinae from Australia. Twenty-four new species are described: Austraturus aculeatus n. sp., A. canaliculatus n. sp., A. lamingtonensis n. sp., A. longigenitalis n. sp., A. montanus n. sp., A. otwayensis n. sp., A. tasmanicus n. sp., Azugaturus

  15. Checklist of the subfamilies Mirinae and Orthotylinae (Hemiptera: Heteroptera: Miridae in western parts of Kerman Province, Iran

    Mohsen Shamsi

    2014-03-01

    Full Text Available A faunal study was carried out on the subfamilies Mirinae and Orthotylinae (Heteroptera: Miridae from different parts of western Kerman Province on various host plants. In total 16 species belonging to 14 genera were collected and identified from different host plants and localities.

  16. Whole genome identification, phylogeny and evolution of the cytochrome P450 family 2 (CYP2) sub-families in birds

    Almeida, Daniela; Maldonado, Emanuel; Khan, Imran

    2016-01-01

    The cytochrome P450 (CYP) superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. However, beyond mammals the molecular evolution of CYP2 subfamilies is poorly understood. Here, we characterized the CYP2 family across 48 novel avian who...

  17. Functional characterization of AGAMOUS-subfamily members from cotton during reproductive development and in response to plant hormones.

    de Moura, Stéfanie Menezes; Artico, Sinara; Lima, Cássio; Nardeli, Sarah Muniz; Berbel, Ana; Oliveira-Neto, Osmundo Brilhante; Grossi-de-Sá, Maria Fátima; Ferrándiz, Cristina; Madueño, Francisco; Alves-Ferreira, Márcio

    2017-03-01

    Expression analysis of the AG -subfamily members from G. hirsutum during flower and fruit development. Reproductive development in cotton, including the fruit and fiber formation, is a complex process; it involves the coordinated action of gene expression regulators, and it is highly influenced by plant hormones. Several studies have reported the identification and expression of the transcription factor family MADS-box members in cotton ovules and fibers; however, their roles are still elusive during the reproductive development in cotton. In this study, we evaluated the expression profiles of five MADS-box genes (GhMADS3, GhMADS4, GhMADS5, GhMADS6 and GhMADS7) belonging to the AGAMOUS-subfamily in Gossypium hirsutum. Phylogenetic and protein sequence analyses were performed using diploid (G. arboreum, G. raimondii) and tetraploid (G. barbadense, G. hirsutum) cotton genomes, as well as the AG-subfamily members from Arabidopsis thaliana, Petunia hybrida and Antirrhinum majus. qPCR analysis showed that the AG-subfamily genes had high expression during flower and fruit development in G. hirsutum. In situ hybridization analysis also substantiates the involvement of AG-subfamily members on reproductive tissues of G. hirsutum, including ovule and ovary. The effect of plant hormones on AG-subfamily genes expression was verified in cotton fruits treated with gibberellin, auxin and brassinosteroid. All the genes were significantly regulated in response to auxin, whereas only GhMADS3, GhMADS4 and GhMADS7 genes were also regulated by brassinosteroid treatment. In addition, we have investigated the GhMADS3 and GhMADS4 overexpression effects in Arabidopsis plants. Interestingly, the transgenic plants from both cotton AG-like genes in Arabidopsis significantly altered the fruit size compared to the control plants. This alteration suggests that cotton AG-like genes might act regulating fruit formation. Our results demonstrate that members of the AG-subfamily in G. hirsutum

  18. Structure and dynamics of the human pleckstrin DEP domain: distinct molecular features of a novel DEP domain subfamily.

    Civera, Concepcion; Simon, Bernd; Stier, Gunter; Sattler, Michael; Macias, Maria J

    2005-02-01

    Pleckstrin1 is a major substrate for protein kinase C in platelets and leukocytes, and comprises a central DEP (disheveled, Egl-10, pleckstrin) domain, which is flanked by two PH (pleckstrin homology) domains. DEP domains display a unique alpha/beta fold and have been implicated in membrane binding utilizing different mechanisms. Using multiple sequence alignments and phylogenetic tree reconstructions, we find that 6 subfamilies of the DEP domain exist, of which pleckstrin represents a novel and distinct subfamily. To clarify structural determinants of the DEP fold and to gain further insight into the role of the DEP domain, we determined the three-dimensional structure of the pleckstrin DEP domain using heteronuclear NMR spectroscopy. Pleckstrin DEP shares main structural features with the DEP domains of disheveled and Epac, which belong to different DEP subfamilies. However, the pleckstrin DEP fold is distinct from these structures and contains an additional, short helix alpha4 inserted in the beta4-beta5 loop that exhibits increased backbone mobility as judged by NMR relaxation measurements. Based on sequence conservation, the helix alpha4 may also be present in the DEP domains of regulator of G-protein signaling (RGS) proteins, which are members of the same DEP subfamily. In pleckstrin, the DEP domain is surrounded by two PH domains. Structural analysis and charge complementarity suggest that the DEP domain may interact with the N-terminal PH domain in pleckstrin. Phosphorylation of the PH-DEP linker, which is required for pleckstrin function, could regulate such an intramolecular interaction. This suggests a role of the pleckstrin DEP domain in intramolecular domain interactions, which is distinct from the functions of other DEP domain subfamilies found so far.

  19. Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes.

    Saarela, Jeffery M; Wysocki, William P; Barrett, Craig F; Soreng, Robert J; Davis, Jerrold I; Clark, Lynn G; Kelchner, Scot A; Pires, J Chris; Edger, Patrick P; Mayfield, Dustin R; Duvall, Melvin R

    2015-05-04

    Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae

  20. Out of Africa:Miocene Dispersal, Vicariance, and Extinction within Hyacinthaceae Subfamily Urgineoideae

    Syed Shujait Ali; Martin Pfosser; Wolfgang Wetschnig; Mario MartnezAzorn; Manuel B. Crespo; Yan Yu

    2013-01-01

    Disjunct distribution patterns in plant lineages are usually explained according to three hypotheses:vicariance, geodispersal, and long-distance dispersal. The role of these hypotheses is tested in Urgineoideae (Hyacinthaceae), a subfamily disjunctly distributed in Africa, Madagascar, India, and the Mediterranean region. The potential ancestral range, dispersal routes, and factors responsible for the current distribution in Urgineoideae are investigated using divergence time estimations. Urgineoideae originated in Southern Africa approximately 48.9 Mya. Two independent dispersal events in the Western Mediterranean region possibly occurred during Early Oligocene and Miocene (29.9-8.5 Mya) via Eastern and Northwestern Africa. A dispersal from Northwestern Africa to India could have occurred between 16.3 and 7.6 Mya. Vicariance and extinction events occurred approximately 21.6 Mya. Colonization of Madagascar occurred between 30.6 and 16.6 Mya, after a single transoceanic dispersal event from Southern Africa. The current disjunct distributions of Urgineoideae are not satisfactorily explained by Gondwana fragmentation or dispersal via boreotropical forests, due to the younger divergence time estimates. The flattened winged seeds of Urgineoideae could have played an important role in long-distance dispersal by strong winds and big storms, whereas geodispersal could have also occurred from Southern Africa to Asia and the Mediterranean region via the so-called arid and high-altitude corridors.

  1. Low dose trichloroethylene alters cytochrome P450 - 2C subfamily expression in the developing chick heart

    Makwana, Om; Ahles, Lauren; Lencinas, Alejandro; Selmin, Ornella I.; Runyan, Raymond B.

    2013-01-01

    Trichloroethylene (TCE) is an organic solvent and common environmental contaminant. TCE exposure is associated with heart defects in humans and animal models. Primary metabolism of TCE in adult rodent models is by specific hepatic cytochrome P450 enzymes (Lash et al., 2000). As association of TCE exposure with cardiac defects is in exposed embryos prior to normal liver development, we investigated metabolism of TCE in the early embryo. Developing chick embryos were dosed in ovo with environmentally relevant doses of TCE (8 ppb and 800 ppb) and RNA was extracted from cardiac and extra-cardiac tissue (whole embryo without heart). Real time PCR showed upregulation of CYP2H1 transcripts in response to TCE exposure in the heart. No detectable cytochrome expression was found in extra-cardiac tissue. As seen previously, the dose response was non-monotonic and 8ppb elicited stronger upregulation than 800 ppb. Immunostaining for CYP2C subfamily expression confirmed protein expression and showed localization in both myocardium and endothelium. TCE exposure increased protein expression in both tissues. These data demonstrate that the earliest embryonic expression of phase I detoxification enzymes is in the developing heart. Expression of these CYPs is likely to be relevant to the susceptibility of the developing heart to environmental teratogens. PMID:22855351

  2. A novel MSCRAMM sub-family in Coagulase negative staphylococcal species

    Srishtee eArora

    2016-04-01

    Full Text Available Coagulase negative staphylococci are important opportunistic pathogens. Staphylococcus epidermidis, a coagulase negative staphylococcus, is the third leading cause of nosocomial infections in the US. Surface proteins like Microbial Surface Components Recognizing Adhesive Matrix Molecules (MSCRAMMs are major virulence factors of pathogenic gram positive bacteria. Here, we identified a new chimeric protein; SesJ in S. epidermidis, which represents a prototype of a new subfamily of MSCRAMMs. Structural predictions show that SesJ has structural features characteristic of a MSCRAMM along with a N-Terminal repeat region and an Aspartic acid containing repeat region, features that have not been previously observed in staphylococcal MSCRAMMs but have been found in other surface proteins from gram positive bacteria. We identified and analyzed structural homologs of SesJ in three other coagulase negative staphylococci. These homologs of SesJ have an identical structural organization but varying sequence identities within the domains. Using flow cytometry, we also show that SesJ is expressed constitutively on the surface of a representative S. epidermidis strain, from early exponential to stationary growth phase. Thus SesJ is positioned to interact with protein targets in the environment and play a role in S. epidermidis virulence.

  3. Crusticorallina gen. nov., a nongeniculate genus in the subfamily Corallinoideae (Corallinales, Rhodophyta).

    Hind, Katharine R; Gabrielson, Paul W; P Jensen, Cassandra; Martone, Patrick T

    2016-12-01

    Molecular phylogenetic analyses of 18S rDNA (SSU) gene sequences confirm the placement of Crusticorallina gen. nov. in Corallinoideae, the first nongeniculate genus in an otherwise geniculate subfamily. Crusticorallina is distinguished from all other coralline genera by the following suite of morpho-anatomical characters: (i) sunken, uniporate gametangial and bi/tetrasporangial conceptacles, (ii) cells linked by cell fusions, not secondary pit connections, (iii) an epithallus of 1 or 2 cell layers, (iv) a hypothallus that occupies 50% or more of the total thallus thickness, (v) elongate meristematic cells, and (vi) trichocytes absent. Four species are recognized based on rbcL, psbA and COI-5P sequences, C. painei sp. nov., the generitype, C. adhaerens sp. nov., C. nootkana sp. nov. and C. muricata comb. nov., previously known as Pseudolithophyllum muricatum. Type material of Lithophyllum muricatum, basionym of C. muricata, in TRH comprises at least two taxa, and therefore we accept the previously designated lectotype specimen in UC that we sequenced to confirm its identity. Crusticorallina species are very difficult to distinguish using morpho-anatomical and/or habitat characters, although at specific sites, some species may be distinguished by a combination of morpho-anatomy, habitat and biogeography. The Northeast Pacific now boasts six coralline endemic genera, far more than any other region of the world. © 2016 Phycological Society of America.

  4. Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification.

    Covain, Raphaël; Fisch-Muller, Sonia; Oliveira, Claudio; Mol, Jan H; Montoya-Burgos, Juan I; Dray, Stéphane

    2016-01-01

    The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily. To fill this gap, we present a molecular phylogeny of this group, including 350 representatives, based on the analysis of mitochondrial and nuclear genes (8426 positions). The resulting phylogeny indicates that Loricariinae are distributed into two sister tribes: Harttiini and Loricariini. The Harttiini tribe, as classically defined, constitutes a paraphyletic assemblage and is here restricted to the three genera Harttia, Cteniloricaria, and Harttiella. Two subtribes are distinguished within Loricariini: Farlowellina and Loricariina. Within Farlowellina, the nominal genus formed a paraphyletic group, as did Sturisoma and Sturisomatichthys. Within Loricariina, Loricaria, Crossoloricaria, and Apistoloricaria are also paraphyletic. To solve these issues, and given the lack of clear morphological diagnostic features, we propose here to synonymize several genera (Quiritixys with Harttia; East Andean members of Crossoloricaria, and Apistoloricaria with Rhadinoloricaria; Ixinandria, Hemiloricaria, Fonchiiichthys, and Leliella with Rineloricaria), to restrict others (Crossoloricaria, and Sturisomatichthys to the West Andean members, and Sturisoma to the East Andean species), and to revalidate the genus Proloricaria. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. The tomato RLK superfamily: phylogeny and functional predictions about the role of the LRRII-RLK subfamily in antiviral defense.

    Sakamoto, Tetsu; Deguchi, Michihito; Brustolini, Otávio J B; Santos, Anésia A; Silva, Fabyano F; Fontes, Elizabeth P B

    2012-12-02

    Receptor-like kinases (RLKs) play key roles during development and in responses to the environment. Despite the relevance of the RLK family and the completion of the tomato genome sequencing, the tomato RLK family has not yet been characterized, and a framework for functional predictions of the members of the family is lacking. To generate a complete list of all the members of the tomato RLK family, we performed a phylogenetic analysis using the Arabidopsis family as a template. A total of 647 RLKs were identified in the tomato genome, which were organized into the same subfamily clades as Arabidopsis RLKs. Only eight of 58 RLK subfamilies exhibited specific expansion/reduction compared to their Arabidopsis counterparts. We also characterized the LRRII-RLK family by phylogeny, genomic analysis, expression profile and interaction with the virulence factor from begomoviruses, the nuclear shuttle protein (NSP). The LRRII subfamily members from tomato and Arabidopsis were highly conserved in both sequence and structure. Nevertheless, the majority of the orthologous pairs did not display similar conservation in the gene expression profile, indicating that these orthologs may have diverged in function after speciation. Based on the fact that members of the Arabidopsis LRRII subfamily (AtNIK1, AtNIK2 and AtNIK3) interact with the begomovirus nuclear shuttle protein (NSP), we examined whether the tomato orthologs of NIK, BAK1 and NsAK genes interact with NSP of Tomato Yellow Spot Virus (ToYSV). The tomato orthologs of NSP interactors, SlNIKs and SlNsAK, interacted specifically with NSP in yeast and displayed an expression pattern consistent with the pattern of geminivirus infection. In addition to suggesting a functional analogy between these phylogenetically classified orthologs, these results expand our previous observation that NSP-NIK interactions are neither virus-specific nor host-specific. The tomato RLK superfamily is made-up of 647 proteins that form a

  6. The tomato RLK superfamily: phylogeny and functional predictions about the role of the LRRII-RLK subfamily in antiviral defense

    Sakamoto Tetsu

    2012-12-01

    Full Text Available Abstract Background Receptor-like kinases (RLKs play key roles during development and in responses to the environment. Despite the relevance of the RLK family and the completion of the tomato genome sequencing, the tomato RLK family has not yet been characterized, and a framework for functional predictions of the members of the family is lacking. Results To generate a complete list of all the members of the tomato RLK family, we performed a phylogenetic analysis using the Arabidopsis family as a template. A total of 647 RLKs were identified in the tomato genome, which were organized into the same subfamily clades as Arabidopsis RLKs. Only eight of 58 RLK subfamilies exhibited specific expansion/reduction compared to their Arabidopsis counterparts. We also characterized the LRRII-RLK family by phylogeny, genomic analysis, expression profile and interaction with the virulence factor from begomoviruses, the nuclear shuttle protein (NSP. The LRRII subfamily members from tomato and Arabidopsis were highly conserved in both sequence and structure. Nevertheless, the majority of the orthologous pairs did not display similar conservation in the gene expression profile, indicating that these orthologs may have diverged in function after speciation. Based on the fact that members of the Arabidopsis LRRII subfamily (AtNIK1, AtNIK2 and AtNIK3 interact with the begomovirus nuclear shuttle protein (NSP, we examined whether the tomato orthologs of NIK, BAK1 and NsAK genes interact with NSP of Tomato Yellow Spot Virus (ToYSV. The tomato orthologs of NSP interactors, SlNIKs and SlNsAK, interacted specifically with NSP in yeast and displayed an expression pattern consistent with the pattern of geminivirus infection. In addition to suggesting a functional analogy between these phylogenetically classified orthologs, these results expand our previous observation that NSP-NIK interactions are neither virus-specific nor host-specific. Conclusions The tomato RLK

  7. Taxonomy of the genus Brachyteles Spix, 1823 and its phylogenetic position within the subfamily Atelinae Gray, 1825

    José Eduardo Serrano Villavicencio

    2016-01-01

    Muriquis, genus Brachyteles Spix, 1823, are the largest of the extant New World primates, and they are one of the three extant genera of the subfamily Atelinae along with Ateles (spider monkeys) and Lagothrix (wooly monkeys). The taxonomy of Brachyteles has constantly changed since its first description in the 19th century. First treated as a monotypic genus, and after several modifications in the number of species, Brachyteles currently contains two species, B. arachnoides (Southern muriqui)...

  8. Crystal structure of Staphylococcus aureus Zn-glyoxalase I: new subfamily of glyoxalase I family

    Chirgadze, Yuri N. [Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia; Boshkova, Eugenia A. [Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia; Battaile, Kevin P. [Advanced Photon Source, Argonne National Laboratory, Hauptman–Woodward Medical Research Institute, IMCA-CAT, Argonne, IL 60439, USA; Mendes, Vitor G. [Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK; Lam, Robert [Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4, Canada; Chan, Tiffany S. Y. [Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4, Canada; Romanov, Vladimir [Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4, Canada; Pai, Emil F. [Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Chirgadze, Nickolay Y. [Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada; X-CHIP Technologies Inc., Toronto, Ontario, Canada

    2017-01-16

    The crystal structures of protein SA0856 from Staphylococcus aureus in its apo-form and in complex with a Zn2+-ion have been presented. The 152 amino acid protein consists of two similar domains with α + β topology. In both crystalline state and in solution, the protein forms a dimer with monomers related by a twofold pseudo-symmetry rotation axis. A sequence homology search identified the protein as a member of the structural family Glyoxalase I. We have shown that the enzyme possesses glyoxalase I activity in the presence of Zn2+, Mg2+, Ni2+, and Co2+, in this order of preference. Sequence and structure comparisons revealed that human glyoxalase I should be assigned to a subfamily A, while S. aureus glyoxalase I represents a new subfamily B, which includes also proteins from other bacteria. Both subfamilies have a similar protein chain fold but rather diverse sequences. The active sites of human and staphylococcus glyoxalases I are also different: the former contains one Zn-ion per chain; the latter incorporates two of these ions. In the active site of SA0856, the first Zn-ion is well coordinated by His58, Glu60 from basic molecule and Glu40*, His44* from adjacent symmetry-related molecule. The second Zn3-ion is coordinated only by residue His143 from protein molecule and one acetate ion. We suggest that only single Zn1-ion plays the role of catalytic center. The newly found differences between the two subfamilies could guide the design of new drugs against S. aureus, an important pathogenic micro-organism.

  9. Origin and evolution of GALA-LRR, a new member of the CC-LRR subfamily: from plants to bacteria?

    Andrey V Kajava

    Full Text Available The phytopathogenic bacterium Ralstonia solanacearum encodes type III effectors, called GALA proteins, which contain F-box and LRR domains. The GALA LRRs do not perfectly fit any of the previously described LRR subfamilies. By applying protein sequence analysis and structural prediction, we clarify this ambiguous case of LRR classification and assign GALA-LRRs to CC-LRR subfamily. We demonstrate that side-by-side packing of LRRs in the 3D structures may control the limits of repeat variability within the LRR subfamilies during evolution. The LRR packing can be used as a criterion, complementing the repeat sequences, to classify newly identified LRR domains. Our phylogenetic analysis of F-box domains proposes the lateral gene transfer of bacterial GALA proteins from host plants. We also present an evolutionary scenario which can explain the transformation of the original plant LRRs into slightly different bacterial LRRs. The examination of the selective evolutionary pressure acting on GALA proteins suggests that the convex side of their horse-shoe shaped LRR domains is more prone to positive selection than the concave side, and we therefore hypothesize that the convex surface might be the site of protein binding relevant to the adaptor function of the F-box GALA proteins. This conclusion provides a strong background for further functional studies aimed at determining the role of these type III effectors in the virulence of R. solanacearum.

  10. RINL, guanine nucleotide exchange factor Rab5-subfamily, is involved in the EphA8-degradation pathway with odin.

    Hiroaki Kajiho

    Full Text Available The Rab family of small guanosine triphosphatases (GTPases plays a vital role in membrane trafficking. Its active GTP-bound state is driven by guanine nucleotide-exchange factors (GEFs. Ras and Rab interactor (or Ras interaction/interference-like (RINL, which contains a conserved VPS9 domain critical for GEF action, was recently identified as a new Rab5 subfamily GEF in vitro. However, its detailed function and interacting molecules have not yet been fully elucidated. Here we found that RINL has GEF activity for the Rab5 subfamily proteins by measuring their GTP-bound forms in cultured cells. We also found that RINL interacts with odin, a member of the ankyrin-repeat and sterile-alpha motif (SAM domain-containing (Anks protein family. In addition, the Eph tyrosine kinase receptor EphA8 formed a ternary complex with both RINL and odin. Interestingly, RINL expression in cultured cells reduced EphA8 levels in a manner dependent on both its GEF activity and interaction with odin. In addition, knockdown of RINL increased EphA8 level in HeLa cells. Our findings suggest that RINL, as a GEF for Rab5 subfamily, is implicated in the EphA8-degradation pathway via its interaction with odin.

  11. Unusual evolutionary conservation and further species-specific adaptations of a large family of nonclassical MHC class Ib genes across different degrees of genome ploidy in the amphibian subfamily Xenopodinae.

    Edholm, Eva-Stina; Goyos, Ana; Taran, Joseph; De Jesús Andino, Francisco; Ohta, Yuko; Robert, Jacques

    2014-06-01

    Nonclassical MHC class Ib (class Ib) genes are a family of highly diverse and rapidly evolving genes wherein gene numbers, organization, and expression markedly differ even among closely related species rendering class Ib phylogeny difficult to establish. Whereas among mammals there are few unambiguous class Ib gene orthologs, different amphibian species belonging to the anuran subfamily Xenopodinae exhibit an unusually high degree of conservation among multiple class Ib gene lineages. Comparative genomic analysis of class Ib gene loci of two divergent (~65 million years) Xenopodinae subfamily members Xenopus laevis (allotetraploid) and Xenopus tropicalis (diploid) shows that both species possess a large cluster of class Ib genes denoted as Xenopus/Silurana nonclassical (XNC/SNC). Our study reveals two distinct phylogenetic patterns among these genes: some gene lineages display a high degree of flexibility, as demonstrated by species-specific expansion and contractions, whereas other class Ib gene lineages have been maintained as monogenic subfamilies with very few changes in their nucleotide sequence across divergent species. In this second category, we further investigated the XNC/SNC10 gene lineage that in X. laevis is required for the development of a distinct semi-invariant T cell population. We report compelling evidence of the remarkable high degree of conservation of this gene lineage that is present in all 12 species of the Xenopodinae examined, including species with different degrees of ploidy ranging from 2, 4, 8 to 12 N. This suggests that the critical role of XNC10 during early T cell development is conserved in amphibians.

  12. Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies.

    Jung, Sook; Cestaro, Alessandro; Troggio, Michela; Main, Dorrie; Zheng, Ping; Cho, Ilhyung; Folta, Kevin M; Sosinski, Bryon; Abbott, Albert; Celton, Jean-Marc; Arús, Pere; Shulaev, Vladimir; Verde, Ignazio; Morgante, Michele; Rokhsar, Daniel; Velasco, Riccardo; Sargent, Daniel James

    2012-04-04

    Rosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes. Our analysis using the whole genome sequences of peach, apple and strawberry identified 1399 orthologous regions between the three genomes, with a mean length of around 100 kb. Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera. However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA) algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor. Using the contiguous ancestral regions, we reconstructed a hypothetical ancestral genome for the Rosaceae 7 composed of nine chromosomes and propose the evolutionary steps from the ancestral genome to the extant Fragaria, Prunus and Malus genomes. Our analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae. The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae.

  13. The Crystal Structure of Streptococcus pyogenes Uridine Phosphorylase Reveals a Distinct Subfamily of Nucleoside Phosphorylases

    Tran, Timothy H.; Christoffersen, S.; Allan, Paula W.; Parker, William B.; Piskur, Jure; Serra, I.; Terreni, M.; Ealick, Steven E. (Cornell); (Pavia); (Lund); (Southern Research)

    2011-09-20

    Uridine phosphorylase (UP), a key enzyme in the pyrimidine salvage pathway, catalyzes the reversible phosphorolysis of uridine or 2'-deoxyuridine to uracil and ribose 1-phosphate or 2'-deoxyribose 1-phosphate. This enzyme belongs to the nucleoside phosphorylase I superfamily whose members show diverse specificity for nucleoside substrates. Phylogenetic analysis shows Streptococcus pyogenes uridine phosphorylase (SpUP) is found in a distinct branch of the pyrimidine subfamily of nucleoside phosphorylases. To further characterize SpUP, we determined the crystal structure in complex with the products, ribose 1-phosphate and uracil, at 1.8 {angstrom} resolution. Like Escherichia coli UP (EcUP), the biological unit of SpUP is a hexamer with an ?/? monomeric fold. A novel feature of the active site is the presence of His169, which structurally aligns with Arg168 of the EcUP structure. A second active site residue, Lys162, is not present in previously determined UP structures and interacts with O2 of uracil. Biochemical studies of wild-type SpUP showed that its substrate specificity is similar to that of EcUP, while EcUP is {approx}7-fold more efficient than SpUP. Biochemical studies of SpUP mutants showed that mutations of His169 reduced activity, while mutation of Lys162 abolished all activity, suggesting that the negative charge in the transition state resides mostly on uracil O2. This is in contrast to EcUP for which transition state stabilization occurs mostly at O4.

  14. Multilocus molecular phylogeny of the suckermouth armored catfishes (Siluriformes: Loricariidae) with a focus on subfamily Hypostominae.

    Lujan, Nathan K; Armbruster, Jonathan W; Lovejoy, Nathan R; López-Fernández, Hernán

    2015-01-01

    The Neotropical catfish family Loricariidae is the fifth most species-rich vertebrate family on Earth, with over 800 valid species. The Hypostominae is its most species-rich, geographically widespread, and ecomorphologically diverse subfamily. Here, we provide a comprehensive molecular phylogenetic reappraisal of genus-level relationships in the Hypostominae based on our sequencing and analysis of two mitochondrial and three nuclear loci (4293bp total). Our most striking large-scale systematic discovery was that the tribe Hypostomini, which has traditionally been recognized as sister to tribe Ancistrini based on morphological data, was nested within Ancistrini. This required recognition of seven additional tribe-level clades: the Chaetostoma Clade, the Pseudancistrus Clade, the Lithoxus Clade, the 'Pseudancistrus' Clade, the Acanthicus Clade, the Hemiancistrus Clade, and the Peckoltia Clade. Results of our analysis, which included type- and non-type species for every valid genus in Hypostominae, support the reevaluation and restriction of several historically problematic genera, including Baryancistrus, Cordylancistrus, Hemiancistrus, and Peckoltia. Much of the deep lineage diversity in Hypostominae is restricted to Guiana Shield and northern Andean drainages, with three tribe-level clades still largely restricted to the Guiana Shield. Of the six geographically widespread clades, a paraphyletic assemblage of three contain lineages restricted to drainages west of the Andes Mountains, suggesting that early diversification of the Hypostominae predated the late Miocene surge in Andean uplift. Our results also highlight examples of trophic ecological diversification and convergence in the Loricariidae, including support for three independent origins of highly similar and globally unique morphological specializations for eating wood. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies

    Jung Sook

    2012-04-01

    Full Text Available Abstract Background Rosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes. Results Our analysis using the whole genome sequences of peach, apple and strawberry identified 1399 orthologous regions between the three genomes, with a mean length of around 100 kb. Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera. However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor. Using the contiguous ancestral regions, we reconstructed a hypothetical ancestral genome for the Rosaceae 7 composed of nine chromosomes and propose the evolutionary steps from the ancestral genome to the extant Fragaria, Prunus and Malus genomes. Conclusion Our analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae. The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae.

  16. Identification and Structure-Function Analysis of Subfamily Selective G Protein-Coupled Receptor Kinase Inhibitors

    Homan, Kristoff T.; Larimore, Kelly M.; Elkins, Jonathan M.; Szklarz, Marta; Knapp, Stefan; Tesmer, John J.G. [Michigan; (Oxford)

    2015-02-13

    Selective inhibitors of individual subfamilies of G protein-coupled receptor kinases (GRKs) would serve as useful chemical probes as well as leads for therapeutic applications ranging from heart failure to Parkinson’s disease. To identify such inhibitors, differential scanning fluorimetry was used to screen a collection of known protein kinase inhibitors that could increase the melting points of the two most ubiquitously expressed GRKs: GRK2 and GRK5. Enzymatic assays on 14 of the most stabilizing hits revealed that three exhibit nanomolar potency of inhibition for individual GRKs, some of which exhibiting orders of magnitude selectivity. Most of the identified compounds can be clustered into two chemical classes: indazole/dihydropyrimidine-containing compounds that are selective for GRK2 and pyrrolopyrimidine-containing compounds that potently inhibit GRK1 and GRK5 but with more modest selectivity. The two most potent inhibitors representing each class, GSK180736A and GSK2163632A, were cocrystallized with GRK2 and GRK1, and their atomic structures were determined to 2.6 and 1.85 Å spacings, respectively. GSK180736A, developed as a Rho-associated, coiled-coil-containing protein kinase inhibitor, binds to GRK2 in a manner analogous to that of paroxetine, whereas GSK2163632A, developed as an insulin-like growth factor 1 receptor inhibitor, occupies a novel region of the GRK active site cleft that could likely be exploited to achieve more selectivity. However, neither compound inhibits GRKs more potently than their initial targets. This data provides the foundation for future efforts to rationally design even more potent and selective GRK inhibitors.

  17. Comparative anatomy of the cheek muscles within the Centromochlinae subfamily (Ostariophysi, Siluriformes, Auchenipteridae).

    Sarmento-Soares, Luisa Maria; Porto, Marcovan

    2006-02-01

    Glanidium melanopterum Miranda Ribeiro, a typical representative of the subfamily Centromochlinae (Siluriformes: Auchenipteridae), is herein described myologically and compared to other representative species within the group, Glanidium ribeiroi, G. leopardum, Tatia neivai, T. intermedia, T. creutzbergi, Centromochlus heckelii, and C. existimatus. The structure of seven pairs of striated cephalic muscles was compared anatomically: adductor mandibulae, levator arcus palatini, dilatator operculi, adductor arcus palatini, extensor tentaculi, retractor tentaculi, and levator operculi. We observed broad adductor mandibulae muscles in both Glanidium and Tatia, catfishes with depressed heads and smaller eyes. Similarities between muscles were observed: the presence of a large aponeurotic insertion for the levator arcus palatini muscle; an adductor arcus palatini muscle whose origin spread over the orbitosphenoid, pterosphenoid, and parasphenoid; and the extensor tentaculi muscle broadly attached to the autopalatine. There is no retractor tentaculi muscle in either the Glanidium or Tatia species. On the other hand, in Centromochlus, with forms having large eyes and the tallest head, the adductor mandibulae muscles are slim; there is a thin aponeurotic or muscular insertion for the levator arcus palatini muscle; the adductor arcus palatini muscle originates from a single osseous process, forming a keel on the parasphenoid; the extensor tentaculi muscle is loosely attached to the autopalatine, permitting exclusive rotating and sliding movements between this bone and the maxillary. The retractor tentaculi muscle is connected to the maxilla through a single tendon, so that both extensor and retractor tentaculi muscles contribute to a wide array of movements of the maxillary barbels. A discussion on the differences in autopalatine-maxillary movements among the analyzed groups is given. (c) 2005 Wiley-Liss, Inc.

  18. List of the primary types of social wasps (Hymenoptera: Vespidae) deposited in the Nationaal Natuurhistorisch Museum, Leiden, and the Zoölogisch Museum, Amsterdam

    Kojima, J.; Achterberg, van C.

    1997-01-01

    The primary types of social wasp subfamilies Vespinae, Polistinae and Stenogastrinae housed in the Nationaal Natuurhistorisch Museum in Leiden and the Zoölogisch Museum in Amsterdam are listed. Their complete label data are given unless they are available elsewhere. Lectotypes of Polistes snelleni

  19. Comparative studies of a new subfamily of human Ste20-like kinases: homodimerization, subcellular localization, and selective activation of MKK3 and p38.

    Yustein, Jason T; Xia, Liang; Kahlenburg, J Michelle; Robinson, Dan; Templeton, Dennis; Kung, Hsing-Jien

    2003-09-18

    The Sterile-20 or Ste20 family of serine/threonine kinases is a group of signaling molecules whose physiological roles within mammalian cells are just starting to be elucidated. Here, in this report we present the characterization of three human Ste20-like kinases with greater than 90% similarity within their catalytic domains that define a novel subfamily of Ste20s. Members of this kinase family include rat thousand and one (TAO1) and chicken KFC (kinase from chicken). For the lack of a consensus nomenclature in the literature, in this report, we shall call this family hKFC (for their homology to chicken KFC) and the three members hKFC-A, hKFC-B, and hKFC-C, respectively. These kinases have many similarities including an aminoterminal kinase domain, a serine-rich region, and a coiled-coil configuration within the C-terminus. All three kinases are able to activate the p38 MAP kinase pathway through the specific activation of the upstream MKK3 kinase. We also offer evidence, both theoretical and biochemical, showing that these kinases can undergo self-association. Despite these similarities, these kinases differ in tissue distribution, apparent subcellular localization, and feature structural differences largely within the carboxyl-terminal sequence.

  20. Freyinae, a major new subfamily of Neotropical jumping spiders (Araneae: Salticidae).

    Edwards, G B

    2015-11-02

    Freyinae, new subfamily, is described for a group of genera of Neotropical jumping spiders that can be distinguished from other non-ant mimic salticoid Neotropical salticids by having the following three morphological features: a slightly more elongate carapace, a distinctive prolateral tibial macrosetae arrangement (medially placed subdistal and subproximal macrosetae, with a subdorsal medial macroseta in some males), and an unusual dorsoventrally thick tegulum basal division (although one or two of these features are sometimes lost). It includes 20 genera previously considered valid, of which 19 are retained: Akela Peckham & Peckham, 1896, Aphirape C.L. Koch, 1850, Asaracus C.L. Koch, 1846, Capidava Simon, 1902, Chira Peckham & Peckham, 1896, Edilemma Ruiz & Brescovit, 2006, Eustiromastix Simon, 1902, Freya C.L. Koch, 1850, Frigga C.L. Koch, 1850, Kalcerrytus Galiano, 2000, Nycerella Galiano, 1982, Onofre Ruiz & Brescovit, 2007, Pachomius Peckham & Peckham, 1896, Phiale C.L. Koch, 1846, Rishaschia Makhan, 2006, Sumampattus Galiano, 1983, Trydarssus Galiano, 1995, Tullgrenella Mello‑Leitão, 1941, and Wedoquella Galiano, 1984. Romitia Caporiacco, 1947 (and its synonym Uspachus Galiano, 1995) is synonymized with Pachomius, new synonymy. New genera described in the subfamily are: Drizztius, Leptofreya, Megafreya, Philira, Tarkas, Triggella, and Xanthofreya. The following nomenclatorial changes are made: New synonyms: Freya demarcata Chamberlin & Ivie, 1936 = Freya (sub Cyrene) albosignata (F.O.P.-Cambridge, 1901); Freya (sub Cyrene) grisea (F.O.P.-Cambridge, 1901) = Freya (sub Cyrene) infuscata (F.O.P.-Cambridge, 1901); Freya (sub Cyrene) emarginata (F.O.P.-Cambridge, 1901) and Nycerella (sub Heraclea) sanguinea paradoxa (Peckham & Peckham, 1896) = Nycerella (sub Heraclea) sanguinea (Peckham & Peckham, 1896); Pachomius (sub Phiale) maculosus (Chickering, 1946) = Phiale (sub Cyrene) bilobata (F.O.P.-Cambridge, 1901); Phiale (sub Cyrene) mediocava (F

  1. Alu Sb2 subfamily is present in all higher primates but was most succesfully amplified in humans

    Richer, C.; Zietkiewicz, E.; Labuda, D. [Universite de Montreal, Que (Canada)

    1994-09-01

    Alu repeats can be classified into subfamilies which amplified in primate genomes at different evolutionary time periods. A young Alu subfamily, Sb2, with a characteristic 7-nucleotide duplication at position 256, has been described in seven human loci. An Sb2 insertion found near the HD gene was unique to two HD families, indicating that Sb2 was still retropositionally active. Here, we have shown that the Sb2 insertion in the CHOL locus was similarly rare, being absent in 120 individuals of Caucasian, Oriental and Black origin. In contrast, Sb2 inserts in five other loci were found fixed (non-polymorphic), based on measurements in the same population sample, but absent from orthologous positions in higher apes. This suggest that Sb2 repeats spread relatively early in the human lineage following divergence from other primates and that these elements may be human-specific. By quantitative PCR, we investigated the presence of Sb2 sequences in different primate DNA, using one PCR primer anchored at the 5{prime} Alu-end and the other complementary to the duplicated Sb2-specific segment. With an Sb2-containing plasmid as a standard, we estimated the number of Sb2 repeats at 1500-1800 copies per human haploid equivalent; corresponding numbers in chimpanzee and gorilla were almost two orders of magnitude lower, while the signal observed in orangutan and gibbon DNAs was consistent with the presence of a single copy. The analysis of 22 human, 11 chimpanzee and 10 gorilla sequences indicates that the Alu Sb2 dispersed independently in these three primate lineages; gorilla consensus differs from the human Sb2 sequence by one position, while all chimpanzee repeats have their linker expanded by up to eight A-residues. Should they be thus considered as separate subfamilies? It is possible that sequence modifications with respect to the human consensus are responsible for poor retroposition of Sb2 in apes.

  2. Cloning of MASK, a novel member of mammalian germinal center kinase-III subfamily, with apoptosis-inducing properties

    Dan, Ippeita; Ong, Shao-En; Watanabe, Norinobu M

    2002-01-01

    We have cloned a novel human GCK family kinase that has been designated as MASK (Mst3 and SOK1-related kinase). MASK is widely expressed and encodes a protein of 416 amino acid residues, with an N-terminal kinase domain and a unique C-terminal region. Like other GCK-III subfamily kinases, MASK do...... apoptosis upon overexpression in mammalian cells that is abrogated by CrmA, suggesting involvement of MASK in the apoptotic machinery in mammalian cells. Udgivelsesdato: 2002-Feb-22...

  3. The first mitochondrial genome for the fishfly subfamily Chauliodinae and implications for the higher phylogeny of Megaloptera.

    Yuyu Wang

    Full Text Available Megaloptera are a basal holometabolous insect order with larvae exclusively predacious and aquatic. The evolutionary history of Megaloptera attracts great interest because of its antiquity and important systematic status in Holometabola. However, due to the difficulties identifying morphological apomorphies for the group, controversial hypotheses on the monophyly and higher phylogeny of Megaloptera have been proposed. Herein, we describe the complete mitochondrial (mt genome of a fishfly species, Neochauliodes punctatolosus Liu & Yang, 2006, representing the first mt genome of the subfamily Chauliodinae. A phylogenomic analysis was carried out based on the mt genomic sequences of 13 mt protein-coding genes (PCGs and two rRNA genes of nine Neuropterida species, comprising all three orders of Neuropterida and all families and subfamilies of Megaloptera. Both maximum likelihood and Bayesian inference analyses highly support the monophyly of Megaloptera, which was recovered as the sister of Neuroptera. Within Megaloptera, the sister relationship between Corydalinae and Chauliodinae was corroborated. The divergence time estimation suggests that stem lineage of Neuropterida and Coleoptera separated in the Early Permian. The interordinal divergence within Neuropterida might have occurred in the Late Permian.

  4. Role for ribosome-associated complex and stress-seventy subfamily B (RAC-Ssb) in integral membrane protein translation.

    Acosta-Sampson, Ligia; Döring, Kristina; Lin, Yuping; Yu, Vivian Y; Bukau, Bernd; Kramer, Günter; Cate, Jamie H D

    2017-12-01

    Targeting of most integral membrane proteins to the endoplasmic reticulum is controlled by the signal recognition particle, which recognizes a hydrophobic signal sequence near the protein N terminus. Proper folding of these proteins is monitored by the unfolded protein response and involves protein degradation pathways to ensure quality control. Here, we identify a new pathway for quality control of major facilitator superfamily transporters that occurs before the first transmembrane helix, the signal sequence recognized by the signal recognition particle, is made by the ribosome. Increased rates of translation elongation of the N-terminal sequence of these integral membrane proteins can divert the nascent protein chains to the ribosome-associated complex and stress-seventy subfamily B chaperones. We also show that quality control of integral membrane proteins by ribosome-associated complex-stress-seventy subfamily B couples translation rate to the unfolded protein response, which has implications for understanding mechanisms underlying human disease and protein production in biotechnology. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Plastome-Wide Nucleotide Substitution Rates Reveal Accelerated Rates in Papilionoideae and Correlations with Genome Features Across Legume Subfamilies.

    Schwarz, Erika N; Ruhlman, Tracey A; Weng, Mao-Lun; Khiyami, Mohammad A; Sabir, Jamal S M; Hajarah, Nahid H; Alharbi, Njud S; Rabah, Samar O; Jansen, Robert K

    2017-04-01

    This study represents the most comprehensive plastome-wide comparison of nucleotide substitution rates across the three subfamilies of Fabaceae: Caesalpinioideae, Mimosoideae, and Papilionoideae. Caesalpinioid and mimosoid legumes have large, unrearranged plastomes compared with papilionoids, which exhibit varying levels of rearrangement including the loss of the inverted repeat (IR) in the IR-lacking clade (IRLC). Using 71 genes common to 39 legume taxa representing all the three subfamilies, we show that papilionoids consistently have higher nucleotide substitution rates than caesalpinioids and mimosoids, and rates in the IRLC papilionoids are generally higher than those in the IR-containing papilionoids. Unsurprisingly, this pattern was significantly correlated with growth habit as most papilionoids are herbaceous, whereas caesalpinioids and mimosoids are largely woody. Both nonsynonymous (dN) and synonymous (dS) substitution rates were also correlated with several biological features including plastome size and plastomic rearrangements such as the number of inversions and indels. In agreement with previous reports, we found that genes in the IR exhibit between three and fourfold reductions in the substitution rates relative to genes within the large single-copy or small single-copy regions. Furthermore, former IR genes in IR-lacking taxa exhibit accelerated rates compared with genes contained in the IR.

  6. Analysis of Comparative Sequence and Genomic Data to Verify Phylogenetic Relationship and Explore a New Subfamily of Bacterial Lipases.

    Malihe Masomian

    Full Text Available Thermostable and organic solvent-tolerant enzymes have significant potential in a wide range of synthetic reactions in industry due to their inherent stability at high temperatures and their ability to endure harsh organic solvents. In this study, a novel gene encoding a true lipase was isolated by construction of a genomic DNA library of thermophilic Aneurinibacillus thermoaerophilus strain HZ into Escherichia coli plasmid vector. Sequence analysis revealed that HZ lipase had 62% identity to putative lipase from Bacillus pseudomycoides. The closely characterized lipases to the HZ lipase gene are from thermostable Bacillus and Geobacillus lipases belonging to the subfamily I.5 with ≤ 57% identity. The amino acid sequence analysis of HZ lipase determined a conserved pentapeptide containing the active serine, GHSMG and a Ca(2+-binding motif, GCYGSD in the enzyme. Protein structure modeling showed that HZ lipase consisted of an α/β hydrolase fold and a lid domain. Protein sequence alignment, conserved regions analysis, clustal distance matrix and amino acid composition illustrated differences between HZ lipase and other thermostable lipases. Phylogenetic analysis revealed that this lipase represented a new subfamily of family I of bacterial true lipases, classified as family I.9. The HZ lipase was expressed under promoter Plac using IPTG and was characterized. The recombinant enzyme showed optimal activity at 65 °C and retained ≥ 97% activity after incubation at 50 °C for 1h. The HZ lipase was stable in various polar and non-polar organic solvents.

  7. HCV Proteins and Immunoglobulin Variable Gene (IgV Subfamilies in HCV-Induced Type II Mixed Cryoglobulinemia: A Concurrent Pathogenetic Role

    Giuseppe Sautto

    2012-01-01

    Full Text Available The association between hepatitis C virus (HCV infection and type II mixed cryoglobulinemia (MCII is well established, but the role played by distinct HCV proteins and by specific components of the anti-HCV humoral immune response remains to be clearly defined. It is widely accepted that HCV drives the expansion of few B-cell clones expressing a restricted pool of selected immunoglobulin variable (IgV gene subfamilies frequently endowed with rheumatoid factor (RF activity. Moreover, the same IgV subfamilies are frequently observed in HCV-transformed malignant B-cell clones occasionally complicating MCII. In this paper, we analyze both the humoral and viral counterparts at the basis of cryoglobulins production in HCV-induced MCII, with particular attention reserved to the single IgV subfamilies most frequently involved.

  8. HCV proteins and immunoglobulin variable gene (IgV) subfamilies in HCV-induced type II mixed cryoglobulinemia: a concurrent pathogenetic role.

    Sautto, Giuseppe; Mancini, Nicasio; Solforosi, Laura; Diotti, Roberta A; Clementi, Massimo; Burioni, Roberto

    2012-01-01

    The association between hepatitis C virus (HCV) infection and type II mixed cryoglobulinemia (MCII) is well established, but the role played by distinct HCV proteins and by specific components of the anti-HCV humoral immune response remains to be clearly defined. It is widely accepted that HCV drives the expansion of few B-cell clones expressing a restricted pool of selected immunoglobulin variable (IgV) gene subfamilies frequently endowed with rheumatoid factor (RF) activity. Moreover, the same IgV subfamilies are frequently observed in HCV-transformed malignant B-cell clones occasionally complicating MCII. In this paper, we analyze both the humoral and viral counterparts at the basis of cryoglobulins production in HCV-induced MCII, with particular attention reserved to the single IgV subfamilies most frequently involved.

  9. Current knowledge on bioacoustics of the subfamily Lophyohylinae (Hylidae, Anura and description of Ocellated treefrog Itapotihyla langsdorffii vocalizations

    Lucas Rodriguez Forti

    2018-05-01

    Full Text Available Background Anuran vocalizations, such as advertisement and release calls, are informative for taxonomy because species recognition can be based on those signals. Thus, a proper acoustic description of the calls may support taxonomic decisions and may contribute to knowledge about amphibian phylogeny. Methods Here we present a perspective on advertisement call descriptions of the frog subfamily Lophyohylinae, through a literature review and a spatial analysis presenting bioacoustic coldspots (sites with high diversity of species lacking advertisement call descriptions for this taxonomic group. Additionally, we describe the advertisement and release calls of the still poorly known treefrog, Itapotihyla langsdorffii. We analyzed recordings of six males using the software Raven Pro 1.4 and calculated the coefficient of variation for classifying static and dynamic acoustic properties. Results and Discussion We found that more than half of the species within the subfamily do not have their vocalizations described yet. Most of these species are distributed in the western and northern Amazon, where recording sampling effort should be strengthened in order to fill these gaps. The advertisement call of I. langsdorffii is composed of 3–18 short unpulsed notes (mean of 13 ms long, presents harmonic structure, and has a peak dominant frequency of about 1.4 kHz. This call usually presents amplitude modulation, with decreasing intensity along the sequence of notes. The release call is a simple unpulsed note with an average duration of 9 ms, and peak dominant frequency around 1.8 kHz. Temporal properties presented higher variations than spectral properties at both intra- and inter-individual levels. However, only peak dominant frequency was static at intra-individual level. High variability in temporal properties and lower variations related to spectral ones is usual for anurans; The first set of variables is determined by social environment or temperature

  10. Intragastric Dai-Kenchu-To, a Japanese herbal medicine, stimulates colonic motility via transient receptor potential cation channel subfamily V member 1 in dogs.

    Kikuchi, Daisuke; Shibata, Chikashi; Imoto, Hirofumi; Naitoh, Takeshi; Miura, Koh; Unno, Michiaki

    2013-08-01

    Japanese herbal medicine, also known as Kampo, is used for various diseases in Japan. One of those medicines, Dai-Kenchu-To (DKT), is considered clinically effective for adhesive bowel obstruction and chronic constipation. Although scientific evidence of DKT to improve adhesive bowel obstruction was shown in several previous reports, mechanism of DKT to improve constipation remains unknown. Our aim was to study the effect of intragastric DKT on colonic motility and defecation, and the involvement of various receptors in DKT-induced colonic contractions. Five beagle dogs were instructed with serosal strain-gauge force transducers to measure circular muscle activity at the proximal, middle, and distal colon. Dogs are suitable for a present study to administer the drugs repeatedly to the same individual and look at its effect on colonic motility. We studied the effects of DKT (2.5 or 5 g) administered into the stomach on colonic motility. Muscarinic receptor antagonist atropine, nicotinic receptor antagonist hexamthonium, or 5-hydroxytryptamine-3 receptor antagonist ondansetron was injected intravenously 10 min before DKT administration. Capsazepine, an antagonist to transient receptor potential cation channel subfamily V member 1 (TRPV1), was administered into the stomach 5 min before DKT administration. Intragastric DKT (2.5 or 5 g) induced colonic contractions within 10 min after administration but did not induce defecation. Pretreatment with atropine, hexamthonium, ondansetron, or capsazepine inhibited DKT-induced colonic contractions. These results indicate that orally administered DKT stimulates colonic motility via TRPV1, muscarinic, nicotinic, and 5-hydroxytryptamine-3 receptors, thereby providing scientific support for the efficacy of oral DKT in chronic constipation.

  11. 2D or Not 2D? Testing the Utility of 2D Vs. 3D Landmark Data in Geometric Morphometrics of the Sculpin Subfamily Oligocottinae (Pisces; Cottoidea).

    Buser, Thaddaeus J; Sidlauskas, Brian L; Summers, Adam P

    2018-05-01

    We contrast 2D vs. 3D landmark-based geometric morphometrics in the fish subfamily Oligocottinae by using 3D landmarks from CT-generated models and comparing the morphospace of the 3D landmarks to one based on 2D landmarks from images. The 2D and 3D shape variables capture common patterns across taxa, such that the pairwise Procrustes distances among taxa correspond and the trends captured by principal component analysis are similar in the xy plane. We use the two sets of landmarks to test several ecomorphological hypotheses from the literature. Both 2D and 3D data reject the hypothesis that head shape correlates significantly with the depth at which a species is commonly found. However, in taxa where shape variation in the z-axis is high, the 2D shape variables show sufficiently strong distortion to influence the outcome of the hypothesis tests regarding the relationship between mouth size and feeding ecology. Only the 3D data support previous studies which showed that large mouth sizes correlate positively with high percentages of elusive prey in the diet. When used to test for morphological divergence, 3D data show no evidence of divergence, while 2D data show that one clade of oligocottines has diverged from all others. This clade shows the greatest degree of z-axis body depth within Oligocottinae, and we conclude that the inability of the 2D approach to capture this lateral body depth causes the incongruence between 2D and 3D analyses. Anat Rec, 301:806-818, 2018. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  12. A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus.

    Figueroa, Alex; McKelvy, Alexander D; Grismer, L Lee; Bell, Charles D; Lailvaux, Simon P

    2016-01-01

    With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes.

  13. Sonorensin: an antimicrobial peptide, belonging to the heterocycloanthracin subfamily of bacteriocins, from a new marine isolate, Bacillus sonorensis MT93.

    Chopra, Lipsy; Singh, Gurdeep; Choudhary, Vikas; Sahoo, Debendra K

    2014-05-01

    Marine environments are the greatest fronts of biodiversity, representing a resource of unexploited or unknown microorganisms and new substances having potential applications. Among microbial products, antimicrobial peptides (AMPs) have received great attention recently due to their applications as food preservatives and therapeutic agents. A new marine soil isolate producing an AMP was identified as Bacillus sonorensis based on 16S rRNA gene sequence analysis. It produced an AMP that showed a broad spectrum of activity against both Gram-positive and Gram-negative bacteria. The peptide, named sonorensin, was purified to homogeneity using a combination of chromatographic techniques. The intact molecular mass of the purified peptide, 6,274 Da, as revealed by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF), was in agreement with Tricine-SDS-PAGE analysis. A PCR array of primers was used to identify AMP structural genes, which allowed the successful amplification of the related genes from strain MT93. The putative open reading frame of sonorensin was amplified, cloned into the pET-32a(+) vector, expressed as a thioredoxin (Trx) fusion protein in Escherichia coli, and then purified. Sequence alignment analysis revealed that the bacteriocin being reported could belong to new subfamily of bacteriocins, heterocycloanthracin. The peptide indicated its potential as a biocontrol agent or food antimicrobial agent, due to its antimicrobial activity against bacteria such as Listeria monocytogenes and Staphylococcus aureus. This is the first report of the production, purification, and characterization of wild-type and recombinant bacteriocin by B. sonorensis and the first bacteriocin of the heterocycloanthracin subfamily to be characterized.

  14. A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

    McKelvy, Alexander D.; Grismer, L. Lee; Bell, Charles D.; Lailvaux, Simon P.

    2016-01-01

    Background With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). Results Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. Conclusion Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes. PMID:27603205

  15. Caste differences in Pseudopolybia compressa (Hymenoptera: Vespidae: Polistinae

    Laura Chavarría Pizarro

    2009-12-01

    Full Text Available Studies of morphological caste syndromes in the tribe Epiponini help us to understand the evolution of social behavior in insects. Few studies have integrated morphological syndromes of various species from the same or distinct genera. We studied morphological differences between castes from three colonies of Pseudopolybia compressa de Saussure, 1854, in order to relate their caste syndrome with those of other species in the genus. We took eight morphometric measures and females were classified in relation to ovarian development and spermathecal contents. Females of Colony 1 (C1 present a higher distinction between castes than females of Colonies 2 and 3 (C2 and C3, and, in general, queens of the three colonies are larger than workers in some measures but smaller in others. In Pseudopolybia Dalla Torre, 1894, shape rather than size is a more important trait in caste divergence.

  16. First record of the subfamily Anoplophilinae (Orthoptera: Rhaphidophoridae) from Russia with description of a new species of the genus Alpinanoplophilus Ishikawa, 1993.

    Storozhenko, Sergey Yu

    2015-06-17

    The subfamily Anoplophilinae (Rhaphidophopridae) is recorded from Russia for the first time. Alpinanoplophilus kurilensis Storozhenko, sp. nov. is described from Kunashir Island. The holotype of the new species is deposited in the Zoological Institute of Russian Academy of Science (St. Petersburg, Russia). A revised key to the species of the genus Alpinanoplophilus Ishikawa, 1993 is provided.

  17. Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members

    Godoy, Andre S.; Pereira, Caroline S.; Ramia, Marina Paglione

    2018-01-01

    The glycoside hydrolase family 45 (GH45) of carbohydrate modifying enzymes is mostly comprised of ß-1,4-endoglucanases. Significant diversity between the GH45 members has prompted the division of this family into three subfamilies: A, B and C, which may differ in terms of the mechanism, general a...

  18. Phylogenetic and functional characterization of ten P450 genes from the CYP6AE subfamily of Helicoverpa armigera involved in xenobiotic metabolism

    Shi, Yu; Wang, Huidong; Liu, Zhi

    2018-01-01

    450s in this subfamily can metabolise imidacloprid, but with lower efficiency than Bemisia tabaci CYP6CM1vQ. CYP6AE20 had virtually no metabolic competence to these four compounds but could metabolise several model fluorogenic substrates. These results showed the broad substrate spectrum of H...

  19. Morphology of dental bones and teeth of selected representatives of the subfamily Anguinae (Squamata, Anguidae); Morfologia dentalnej kosti a zubov vybranych zastupcov podcelade Anguinae (Squamata, Anguinae)

    Dobiasova, K [Univerzita Komenskeho v Bratislave, Prirodovedecka fakulta, Katedra ekologie, 84215 Bratislava (Slovakia)

    2012-04-25

    The present study is focused on the comparative morphology of dental bones and teeth of all genuses of the subfamily Anguinae. The research did not show any relevant difference, which would serve as the basis for the return use of the original generic names. (authors)

  20. The phylogeny of the family Lacertidae (Reptilia) based on nuclear DNA sequences: convergent adaptations to arid habitats within the subfamily Eremiainae.

    Mayer, Werner; Pavlicev, Mihaela

    2007-09-01

    The family Lacertidae encompasses more than 250 species distributed in the Palearctis, Ethiopis and Orientalis. Lacertids have been subjected in the past to several morphological and molecular studies to establish their phylogeny. However, the problems of convergent adaptation in morphology and of excessively variable molecular markers have hampered the establishment of well supported deeper phylogenetic relationships. Particularly the adaptations to xeric environments have often been used to establish a scenario for the origin and radiation of major lineages within lacertids. Here we present a molecular phylogenetic study based on two nuclear marker genes and representatives of 37 lacertid genera and distinct species groups (as in the case of the collective genus Lacerta). Roughly 1600 bp of the nuclear rag1 and c-mos genes were sequenced and analyzed. While the results provide good support to the hitherto suggested main subfamilies of Gallotiinae (Gallotia and Psammodromus), Eremiainae and Lacertinae [Harris, D.J., Arnold, E.N., Thomas, R.H., 1998. Relationships of lacertid lizards (Reptilia: Lacertidae) estimated from mitochondrial DNA sequences and morphology. Proc. R. Soc. Lond. B 265, 1939-1948], they also suggest unexpected relationships. In particular, the oriental genus Takydromus, previously considered the sister-group to the three subfamilies, is nested within Lacertinae. Moreover, the genera within the Eremiainae are further divided into two groups, roughly corresponding to their respective geographical distributions in the Ethiopian and the Saharo-Eurasian ranges. The results support an independent origin of adaptations to xeric conditions in different subfamilies. The relationships within the subfamily Lacertinae could not be resolved with the markers used. The species groups of the collective genus Lacerta show a bush-like topology in the inferred Bayesian tree, suggesting rapid radiation. The composition of the subfamilies Eremiainae and Lacertinae

  1. Significant Microsynteny with New Evolutionary Highlights Is Detected through Comparative Genomic Sequence Analysis of Maize CCCH IX Gene Subfamily

    Wei-Jun Chen

    2015-01-01

    Full Text Available CCCH zinc finger proteins, which are characterized by the presence of three cysteine residues and one histidine residue, play important roles in RNA processing in plants. Subfamily IX CCCH proteins were recently shown to function in stress tolerances. In this study, we analyzed CCCH IX genes in Zea mays, Oryza sativa, and Sorghum bicolor. These genes, which are almost intronless, were divided into four groups based on phylogenetic analysis. Microsynteny analysis revealed microsynteny in regions of some gene pairs, indicating that segmental duplication has played an important role in the expansion of this gene family. In addition, we calculated the dates of duplication by Ks analysis, finding that all microsynteny blocks were formed after the monocot-eudicot divergence. We found that deletions, multiplications, and inversions were shown to have occurred over the course of evolution. Moreover, the Ka/Ks ratios indicated that the genes in these three grass species are under strong purifying selection. Finally, we investigated the evolutionary patterns of some gene pairs conferring tolerance to abiotic stress, laying the foundation for future functional studies of these transcription factors.

  2. Molecular Docking Analysis of Ginger Active Compound on Transient Receptor Potential Cation Channel Subfamily V Member 1 (TRPV1

    Fifteen Aprila Fajrin

    2018-02-01

    Full Text Available Ginger had been reported to ameliorate painful diabetic neuropathy (PDN in an animal model. Gingerol and shogaol were active compounds of ginger that potentially act on transient receptor potential cation channel subfamily V member 1 (TRPV1, a key receptor in PDN. This study aims to predict the binding of gingerol and shogaol to TRPV1 using an in silico model. The ligands of the docking study were 3 chemical compounds of each gingerol and shogaol, i.e. 6-shogaol, 8-shogaol, 10-shogaol, 6-gingerol, 8 gingerol and 10-gingerol. Capsaicin, a TRPV1 agonist, was used as a native ligand. The TRPV1 structure was taken from Protein Data Bank (ID 3J9J. The docking analysis was performed using Autodock Vina. The result showed that among the ginger active compounds, 6-shogaol had the strongest binding energy (-7.10 kcal/mol to TRPV1. The 6-shogaol lacked the potential hydrogen bond to Ile265 of TRPV1 protein, which capsacin had. However, it's binding energy towards TRPV1 was not significantly different compared to capsaicin. Therefore, 6-shogaol had potential to be developed as a treatment for PDN.

  3. Paralog-divergent Features May Help Reduce Off-target Effects of Drugs: Hints from Glucagon Subfamily Analysis

    Zhining Sa

    2017-08-01

    Full Text Available Side effects from targeted drugs remain a serious concern. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which are highly homologous in sequences and have similar structures and drug-binding pockets. To identify targetable differences between paralogs, we analyzed two types (type-I and type-II of functional divergence between two paralogs in the known target protein receptor family G-protein coupled receptors (GPCRs at the amino acid level. Paralogous protein receptors in glucagon-like subfamily, glucagon receptor (GCGR and glucagon-like peptide-1 receptor (GLP-1R, exhibit divergence in ligands and are clinically validated drug targets for type 2 diabetes. Our data showed that type-II amino acids were significantly enriched in the binding sites of antagonist MK-0893 to GCGR, which had a radical shift in physicochemical properties between GCGR and GLP-1R. We also examined the role of type-I amino acids between GCGR and GLP-1R. The divergent features between GCGR and GLP-1R paralogs may be helpful in their discrimination, thus enabling the identification of binding sites to reduce undesirable side effects and increase the target specificity of drugs.

  4. G Protein-coupled Receptor Kinases of the GRK4 Protein Subfamily Phosphorylate Inactive G Protein-coupled Receptors (GPCRs).

    Li, Lingyong; Homan, Kristoff T; Vishnivetskiy, Sergey A; Manglik, Aashish; Tesmer, John J G; Gurevich, Vsevolod V; Gurevich, Eugenia V

    2015-04-24

    G protein-coupled receptor (GPCR) kinases (GRKs) play a key role in homologous desensitization of GPCRs. It is widely assumed that most GRKs selectively phosphorylate only active GPCRs. Here, we show that although this seems to be the case for the GRK2/3 subfamily, GRK5/6 effectively phosphorylate inactive forms of several GPCRs, including β2-adrenergic and M2 muscarinic receptors, which are commonly used as representative models for GPCRs. Agonist-independent GPCR phosphorylation cannot be explained by constitutive activity of the receptor or membrane association of the GRK, suggesting that it is an inherent ability of GRK5/6. Importantly, phosphorylation of the inactive β2-adrenergic receptor enhanced its interactions with arrestins. Arrestin-3 was able to discriminate between phosphorylation of the same receptor by GRK2 and GRK5, demonstrating preference for the latter. Arrestin recruitment to inactive phosphorylated GPCRs suggests that not only agonist activation but also the complement of GRKs in the cell regulate formation of the arrestin-receptor complex and thereby G protein-independent signaling. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Evolution of the miR5200-FLOWERING LOCUS T flowering time regulon in the temperate grass subfamily Pooideae.

    McKeown, Meghan; Schubert, Marian; Preston, Jill C; Fjellheim, Siri

    2017-09-01

    Flowering time is a carefully regulated trait controlled primarily through the action of the central genetic regulator, FLOWERING LOCUS T (FT). Recently it was demonstrated that a microRNA, miR5200, targets the end of the second exon of FT under short-day photoperiods in the grass subfamily Pooideae, thus preventing FT transcripts from reaching threshold levels under non-inductive conditions. Pooideae are an interesting group in that they rapidly diversified from the tropics into the northern temperate region during a major global cooling event spanning the Eocene-Oligocene transition. We hypothesize that miR5200 photoperiod-sensitive regulation of Pooideae flowering time networks assisted their transition into northern seasonal environments. Here, we test predictions derived from this hypothesis that miR5200, originally found in bread wheat and later identified in Brachypodium distachyon, (1) was present in the genome of the Pooideae common ancestor, (2) is transcriptionally regulated by photoperiod, and (3) is negatively correlated with FT transcript abundance, indicative of miR5200 regulating FT. Our results demonstrate that miR5200 did evolve at or around the base of Pooideae, but only acquired photoperiod-regulated transcription within the Brachypodium lineage. Based on expression profiles and previous data, we posit that the progenitor of miR5200 was co-regulated with FT by an unknown mechanism. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  6. Genome wide identification and expression analysis of Homeodomain leucine zipper subfamily IV (HDZ IV gene family from Musa accuminata

    Ashutosh ePandey

    2016-02-01

    Full Text Available The homedodomain zipper family (HD-ZIP of transcription factors is present only in plants and plays important role in the regulation of plant-specific processes. The subfamily IV of HDZ transcription factors (HD-ZIP IV has primarily been implicated in the regulation of epidermal structure development. Though this gene family is present in all lineages of land plants, members of this gene family have not been identified in banana, which is one of the major staple fruit crops. In the present work, we identified 21 HDZIV genes in banana by the computational analysis of banana genome resource. Our analysis suggested that these genes putatively encode proteins having all the characteristic domains of HDZIV transcription factors. The phylogenetic analysis of the banana HDZIV family genes further confirmed that after separation from a common ancestor, the banana and poales lineages might have followed distinct evolutionary paths. Further, we conclude that segmental duplication played a major role in the evolution of banana HDZIV genes. All the identified banana HDZIV genes expresses in different banana tissue, however at varying levels. The transcript levels of some of the banana HDZIV genes were also detected in banana fruit pulp, suggesting their putative role in fruit attributes. A large number of genes of this family showed modulated expression under drought and salinity stress. Taken together, the present work lays a foundation for elucidation of functional aspects of the banana HDZIV genes and for their possible use in the banana improvement programs.

  7. Vaccinomics Approach for Designing Potential Peptide Vaccine by Targeting Shigella spp. Serine Protease Autotransporter Subfamily Protein SigA

    Arafat Rahman Oany

    2017-01-01

    Full Text Available Shigellosis, a bacillary dysentery, is closely associated with diarrhoea in human and causes infection of 165 million people worldwide per year. Casein-degrading serine protease autotransporter of enterobacteriaceae (SPATE subfamily protein SigA, an outer membrane protein, exerts both cytopathic and enterotoxic effects especially cytopathic to human epithelial cell type-2 (HEp-2 and is shown to be highly immunogenic. In the present study, we have tried to impose the vaccinomics approach for designing a common peptide vaccine candidate against the immunogenic SigA of Shigella spp. At first, 44 SigA proteins from different variants of S. flexneri, S. dysenteriae, S. boydii, and S. sonnei were assessed to find the most antigenic protein. We retrieved 12 peptides based on the highest score for human leukocyte antigen (HLA supertypes analysed by NetCTL. Initially, these peptides were assessed for the affinity with MHC class I and class II alleles, and four potential core epitopes VTARAGLGY, FHTVTVNTL, HTTWTLTGY, and IELAGTLTL were selected. From these, FHTVTVNTL and IELAGTLTL peptides were shown to have 100% conservancy. Finally, IELAGTLTL was shown to have the highest population coverage (83.86% among the whole world population. In vivo study of the proposed epitope might contribute to the development of functional and unique widespread vaccine, which might be an operative alleyway to thwart dysentery from the world.

  8. Cloning and characterization of PAK5, a novel member of mammalian p21-activated kinase-II subfamily that is predominantly expressed in brain

    Pandey, A.; Dan, I.; Kristiansen, T.Z.

    2002-01-01

    cloned a novel human PAK family kinase that has been designated as PAK5. PAK5 contains a CDC42/Rac1 interactive binding (CRIB) motif at the N-terminus and a Ste20-like kinase domain at the C-terminus. PAK5 is structurally most related to PAK4 and PAK6 to make up the PAK-II subfamily. We have shown...

  9. Molecular Evolution of the CYP2D Subfamily in Primates: Purifying Selection on Substrate Recognition Sites without the Frequent or Long-Tract Gene Conversion

    Yasukochi, Yoshiki; Satta, Yoko

    2015-01-01

    The human cytochrome P450 (CYP) 2D6 gene is a member of the CYP2D gene subfamily, along with the CYP2D7P and CYP2D8P pseudogenes. Although the CYP2D6 enzyme has been studied extensively because of its clinical importance, the evolution of the CYP2D subfamily has not yet been fully understood. Therefore, the goal of this study was to reveal the evolutionary process of the human drug metabolic system. Here, we investigate molecular evolution of the CYP2D subfamily in primates by comparing 14 CYP2D sequences from humans to New World monkey genomes. Window analysis and statistical tests revealed that entire genomic sequences of paralogous genes were extensively homogenized by gene conversion during molecular evolution of CYP2D genes in primates. A neighbor-joining tree based on genomic sequences at the nonsubstrate recognition sites showed that CYP2D6 and CYP2D8 genes were clustered together due to gene conversion. In contrast, a phylogenetic tree using amino acid sequences at substrate recognition sites did not cluster the CYP2D6 and CYP2D8 genes, suggesting that the functional constraint on substrate specificity is one of the causes for purifying selection at the substrate recognition sites. Our results suggest that the CYP2D gene subfamily in primates has evolved to maintain the regioselectivity for a substrate hydroxylation activity between individual enzymes, even though extensive gene conversion has occurred across CYP2D coding sequences. PMID:25808902

  10. Molecular cloning and 3D model of first cytochrome P450 from CYP3A subfamily in saltwater crocodile (Crocodylus porosus).

    Tabassum, Rabia

    2017-10-18

    Cytochrome P450s (CYPs) play critical role in oxidative metabolism of numerous xenobiotics and endogenous compounds. The first CYP3A subfamily member in saltwater crocodile has been cloned and modelled for three-dimensional (3D) structure. The full-length cDNA was obtained employing reverse transcription polymerase chain reaction (RT-PCR) strategy and rapid amplification of cDNA ends (RACE). The cDNA sequence of 1659 nucleotides includes 132 nucleotides from 5' untranslated region (UTR), an open reading frame of 1527 nucleotides encoding 509 amino acids designated as CYP3A163. The alignment of CYP3A163 sequence with CYP3A subfamily across the lineages exhibit the loss of 1 residue in birds and 7 residues in mammals in comparison to reptiles suggesting the adaptation processes during evolution. The amino acid identity of CYP3A163 with Alligator mississippiensis CYP3A77 and Homo sapiens CYP3A4 is 91% and 62% respectively. The 3D structure of CYP3A163 modelled using human CYP3A4 structure as a template with Phyre 2 software, represents high similarity with its functionally important motifs and catalytic domain. Both sequence and structure of CYP3A163 display the common and conserved features of CYP3A subfamily. Overall, this study provides primary molecular and structural data of CYP3A163 required to investigate the xenobiotic metabolism in saltwater crocodiles. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. The ZNF75 zinc finger gene subfamily: Isolation and mapping of the four members in humans and great apes

    Villa, A.; Strina, D.; Frattini, A. [Consiglio Nazionale delle Ricerche, Milan (Italy)] [and others

    1996-07-15

    We have previously reported the characterization of the human ZNF75 gene located on Xq26, which has only limited homology (less than 65%) to other ZF genes in the databases. Here, we describe three human zinc finger genes with 86 to 95% homology to ZNF75 at the nucleotide level, which represent all the members of the human ZNF75 subfamily. One of these, ZNF75B, is a pseudogene mapped to chromosome 12q13. The other two, ZNF75A and ZNF75C, maintain on ORF in the sequenced region, and at least the latter is expressed in the U937 cell line. They were mapped to chromosomes 16 and 11, respectively. All these genes are conserved in chimpanzees, gorillas, and orangutans. The ZNF75B homologue is a pseudogene in all three great apes, and in chimpanzee it is located on chromosome 10 (phylogenetic XII), at p13 (corresponding to the human 12q13). The chimpanzee homologue of ZNF75 is also located on the Xq26 chromosome, in the same region, as detected by in situ hybridization. As expected, nucleotide changes were clearly more abundant between human and organutan than between human and chimpanzee or gorilla homologues. Members of the same class were more similar to each other than to the other homologues within the same species. This suggests that the duplication and/or retrotranscription events occurred in a common ancestor long before great ape speciation. This, together with the existance of at least two genes in cows and horses, suggests a relatively high conservation of this gene family. 20 refs., 5 figs., 1 tab.

  12. Convergent, Parallel and Correlated Evolution of Trophic Morphologies in the Subfamily Schizothoracinae from the Qinghai-Tibetan Plateau

    Qi, Delin; Chao, Yan; Guo, Songchang; Zhao, Lanying; Li, Taiping; Wei, Fulei; Zhao, Xinquan

    2012-01-01

    Schizothoracine fishes distributed in the water system of the Qinghai-Tibetan plateau (QTP) and adjacent areas are characterized by being highly adaptive to the cold and hypoxic environment of the plateau, as well as by a high degree of diversity in trophic morphology due to resource polymorphisms. Although convergent and parallel evolution are prevalent in the organisms of the QTP, it remains unknown whether similar evolutionary patterns have occurred in the schizothoracine fishes. Here, we constructed for the first time a tentative molecular phylogeny of the schizothoracine fishes based on the complete sequences of the cytochrome b gene. We employed this molecular phylogenetic framework to examine the evolution of trophic morphologies. We used Pagel's maximum likelihood method to estimate the evolutionary associations of trophic morphologies and food resource use. Our results showed that the molecular and published morphological phylogenies of Schizothoracinae are partially incongruent with respect to some intergeneric relationships. The phylogenetic results revealed that four character states of five trophic morphologies and of food resource use evolved at least twice during the diversification of the subfamily. State transitions are the result of evolutionary patterns including either convergence or parallelism or both. Furthermore, our analyses indicate that some characters of trophic morphologies in the Schizothoracinae have undergone correlated evolution, which are somewhat correlated with different food resource uses. Collectively, our results reveal new examples of convergent and parallel evolution in the organisms of the QTP. The adaptation to different trophic niches through the modification of trophic morphologies and feeding behaviour as found in the schizothoracine fishes may account for the formation and maintenance of the high degree of diversity and radiations in fish communities endemic to QTP. PMID:22470515

  13. Transient receptor potential melastatin subfamily member 2 cation channel regulates detrimental immune cell invasion in ischemic stroke.

    Gelderblom, Mathias; Melzer, Nico; Schattling, Benjamin; Göb, Eva; Hicking, Gordon; Arunachalam, Priyadharshini; Bittner, Stefan; Ufer, Friederike; Herrmann, Alexander M; Bernreuther, Christian; Glatzel, Markus; Gerloff, Christian; Kleinschnitz, Christoph; Meuth, Sven G; Friese, Manuel A; Magnus, Tim

    2014-11-01

    Brain injury during stroke results in oxidative stress and the release of factors that include extracellular Ca(2+), hydrogen peroxide, adenosine diphosphate ribose, and nicotinic acid adenine dinucleotide phosphate. These alterations of the extracellular milieu change the activity of transient receptor potential melastatin subfamily member 2 (TRPM2), a nonselective cation channel expressed in the central nervous system and the immune system. Our goal was to evaluate the contribution of TRPM2 to the tissue damage after stroke. In accordance with current quality guidelines, we independently characterized Trpm2 in a murine ischemic stroke model in 2 different laboratories. Gene deficiency of Trpm2 resulted in significantly improved neurological outcome and decreased infarct size. Besides an already known moderate neuroprotective effect of Trpm2 deficiency in vitro, ischemic brain invasion by neutrophils and macrophages was particularly reduced in Trpm2-deficient mice. Bone marrow chimeric mice revealed that Trpm2 deficiency in the peripheral immune system is responsible for the protective phenotype. Furthermore, experiments with mixed bone marrow chimeras demonstrated that Trpm2 is essential for the migration of neutrophils and, to a lesser extent, also of macrophages into ischemic hemispheres. Notably, the pharmacological TRPM2 inhibitor, N-(p-amylcinnamoyl)anthranilic acid, was equally protective in the stroke model. Although a neuroprotective effect of TRPM2 in vitro is well known, we can show for the first time that the detrimental role of TRPM2 in stroke primarily depends on its role in activating peripheral immune cells. Targeting TRPM2 systemically represents a promising therapeutic approach for ischemic stroke. © 2014 American Heart Association, Inc.

  14. A novel fractal approach for predicting G-protein-coupled receptors and their subfamilies with support vector machines.

    Nie, Guoping; Li, Yong; Wang, Feichi; Wang, Siwen; Hu, Xuehai

    2015-01-01

    G-protein-coupled receptors (GPCRs) are seven membrane-spanning proteins and regulate many important physiological processes, such as vision, neurotransmission, immune response and so on. GPCRs-related pathways are the targets of a large number of marketed drugs. Therefore, the design of a reliable computational model for predicting GPCRs from amino acid sequence has long been a significant biomedical problem. Chaos game representation (CGR) reveals the fractal patterns hidden in protein sequences, and then fractal dimension (FD) is an important feature of these highly irregular geometries with concise mathematical expression. Here, in order to extract important features from GPCR protein sequences, CGR algorithm, fractal dimension and amino acid composition (AAC) are employed to formulate the numerical features of protein samples. Four groups of features are considered, and each group is evaluated by support vector machine (SVM) and 10-fold cross-validation test. To test the performance of the present method, a new non-redundant dataset was built based on latest GPCRDB database. Comparing the results of numerical experiments, the group of combined features with AAC and FD gets the best result, the accuracy is 99.22% and Matthew's correlation coefficient (MCC) is 0.9845 for identifying GPCRs from non-GPCRs. Moreover, if it is classified as a GPCR, it will be further put into the second level, which will classify a GPCR into one of the five main subfamilies. At this level, the group of combined features with AAC and FD also gets best accuracy 85.73%. Finally, the proposed predictor is also compared with existing methods and shows better performances.

  15. Morphological "primary homology" and expression of AG-subfamily MADS-box genes in pines, podocarps, and yews.

    Englund, Marie; Carlsbecker, Annelie; Engström, Peter; Vergara-Silva, Francisco

    2011-01-01

    The morphological variation among reproductive organs of extant gymnosperms is remarkable, especially among conifers. Several hypotheses concerning morphological homology between various conifer reproductive organs have been put forward, in particular in relation to the pine ovuliferous scale. Here, we use the expression patterns of orthologs of the ABC-model MADS-box gene AGAMOUS (AG) for testing morphological homology hypotheses related to organs of the conifer female cone. To this end, we first developed a tailored 3'RACE procedure that allows reliable amplification of partial sequences highly similar to gymnosperm-derived members of the AG-subfamily of MADS-box genes. Expression patterns of two novel conifer AG orthologs cloned with this procedure-namely PodAG and TgAG, obtained from the podocarp Podocarpus reichei and the yew Taxus globosa, respectively-are then further characterized in the morphologically divergent female cones of these species. The expression patterns of PodAG and TgAG are compared with those of DAL2, a previously discovered Picea abies (Pinaceae) AG ortholog. By treating the expression patterns of DAL2, PodAG, and TgAG as character states mapped onto currently accepted cladogram topologies, we suggest that the epimatium-that is, the podocarp female cone organ previously postulated as a "modified" ovuliferous scale-and the canonical Pinaceae ovuliferous scale can be legitimally conceptualized as "primary homologs." Character state mapping for TgAG suggests in turn that the aril of Taxaceae should be considered as a different type of organ. This work demonstrates how the interaction between developmental-genetic data and formal cladistic theory could fruitfully contribute to gymnosperm systematics. © 2011 Wiley Periodicals, Inc.

  16. Towards a molecular taxonomic key of the Aurantioideae subfamily using chloroplastic SNP diagnostic markers of the main clades genotyped by competitive allele-specific PCR.

    Oueslati, Amel; Ollitrault, Frederique; Baraket, Ghada; Salhi-Hannachi, Amel; Navarro, Luis; Ollitrault, Patrick

    2016-08-18

    Chloroplast DNA is a primary source of molecular variations for phylogenetic analysis of photosynthetic eukaryotes. However, the sequencing and analysis of multiple chloroplastic regions is difficult to apply to large collections or large samples of natural populations. The objective of our work was to demonstrate that a molecular taxonomic key based on easy, scalable and low-cost genotyping method should be developed from a set of Single Nucleotide Polymorphisms (SNPs) diagnostic of well-established clades. It was applied to the Aurantioideae subfamily, the largest group of the Rutaceae family that includes the cultivated citrus species. The publicly available nucleotide sequences of eight plastid genomic regions were compared for 79 accessions of the Aurantioideae subfamily to search for SNPs revealing taxonomic differentiation at the inter-tribe, inter-subtribe, inter-genus and interspecific levels. Diagnostic SNPs (DSNPs) were found for 46 of the 54 clade levels analysed. Forty DSNPs were selected to develop KASPar markers and their taxonomic value was tested by genotyping 108 accessions of the Aurantioideae subfamily. Twenty-seven markers diagnostic of 24 clades were validated and they displayed a very high rate of transferability in the Aurantioideae subfamily (only 1.2 % of missing data on average). The UPGMA from the validated markers produced a cladistic organisation that was highly coherent with the previous phylogenetic analysis based on the sequence data of the eight plasmid regions. In particular, the monophyletic origin of the "true citrus" genera plus Oxanthera was validated. However, some clarification remains necessary regarding the organisation of the other wild species of the Citreae tribe. We validated the concept that with well-established clades, DSNPs can be selected and efficiently transformed into competitive allele-specific PCR markers (KASPar method) allowing cost-effective highly efficient cladistic analysis in large collections at

  17. Crystal structures of two transcriptional regulators from Bacillus cereus define the conserved structural features of a PadR subfamily.

    Guntur Fibriansah

    Full Text Available PadR-like transcriptional regulators form a structurally-related family of proteins that control the expression of genes associated with detoxification, virulence and multi-drug resistance in bacteria. Only a few members of this family have been studied by genetic, biochemical and biophysical methods, and their structure/function relationships are still largely undefined. Here, we report the crystal structures of two PadR-like proteins from Bacillus cereus, which we named bcPadR1 and bcPadR2 (products of gene loci BC4206 and BCE3449 in strains ATCC 14579 and ATCC 10987, respectively. BC4206, together with its neighboring gene BC4207, was previously shown to become significantly upregulated in presence of the bacteriocin AS-48. DNA mobility shift assays reveal that bcPadR1 binds to a 250 bp intergenic region containing the putative BC4206-BC4207 promoter sequence, while in-situ expression of bcPadR1 decreases bacteriocin tolerance, together suggesting a role for bcPadR1 as repressor of BC4206-BC4207 transcription. The function of bcPadR2 (48% identical in sequence to bcPadR1 is unknown, but the location of its gene just upstream from genes encoding a putative antibiotic ABC efflux pump, suggests a role in regulating antibiotic resistance. The bcPadR proteins are structurally similar to LmrR, a PadR-like transcription regulator in Lactococcus lactis that controls expression of a multidrug ABC transporter via a mechanism of multidrug binding and induction. Together these proteins define a subfamily of conserved, relatively small PadR proteins characterized by a single C-terminal helix for dimerization. Unlike LmrR, bcPadR1 and bcPadR2 lack a central pore for ligand binding, making it unclear whether the transcriptional regulatory roles of bcPadR1 and bcPadR2 involve direct ligand recognition and induction.

  18. Oxidative metabolism of monensin in rat liver microsomes and interactions with tiamulin and other chemotherapeutic agents: evidence for the involvement of cytochrome P-450 3A subfamily.

    Nebbia, C; Ceppa, L; Dacasto, M; Carletti, M; Nachtmann, C

    1999-09-01

    Monensin (MON) is an ionophore antibiotic widely used in veterinary practice as a coccidiostatic or a growth promoter. The aims of this study were to characterize the P-450 isoenzyme(s) involved in the biotransformation of the ionophore and to investigate how this process may be affected by tiamulin and other chemotherapeutic agents known to produce toxic interactions with MON when administered concurrently in vivo. In liver microsomes from untreated rats (UT) or from rats pretreated, respectively, with ethanol (ETOH), beta-naphthoflavone (betaNAF), phenobarbital (PB), pregnenolone 16alpha-carbonitrile (PCN), or dexamethasone (DEX), the rate of MON O-demethylation was the following: DEX > PCN > PB > UT = ETOH > betaNAF; similar results were obtained by measuring total MON metabolism. In addition, the extent of triacetyloleandomycin-mediated P-450 complexes was greatly reduced by the prior addition of 100 microM MON. In DEX-treated microsomes, MON O-demethylation was found to fit monophasic Michaelis-Menten kinetics (K(M) = 67.6 +/- 0.01 microM; V(max) = 4.75 +/- 0.76 nmol/min/mg protein). Tiamulin markedly inhibited this activity in an apparent competitive manner, with a calculated K(i) (Dixon plot) of 8.2 microM and an IC(50) of about 25 microM. At the latter concentration, only ketoconazole or metyrapone, which can bind P-450 3A, inhibited MON O-demethylase to a greater extent than tiamulin, whereas alpha-naphthoflavone, chloramphenicol, or sulphametasine was less effective. These results suggest that P-450 3A plays an important role in the oxidative metabolism of MON and that compounds capable of binding or inhibiting this isoenzyme could be expected to give rise to toxic interactions with the ionophore.

  19. A putative autonomous 20.5 kb-CACTA transposon insertion in an F3'H allele identifies a new CACTA transposon subfamily in Glycine max

    Vodkin Lila

    2008-12-01

    in the gray trichome allele t*. Conclusion The molecular characterization of a 20.5 kb insertion in the flavonoid 3'-hydroxylase (F3'H gene of a soybean gray pubescence allele (t* identified the structure of a CACTA transposon designated Tgmt*. Besides the terminal inverted repeats and subterminal repeated motifs,Tgmt* encoded a large gene with two putative functions that are required for excision and transposition of a CACTA element, a transposase and the DNA binding protein known to associate to the subterminal repeated motifs. The degree of dissimilarity between Tgmt* transposase and subterminal repeated motifs with those of previously characterized defective CACTA elements (Tgm1-7 were evidence of the existence of two subfamilies of CACTA transposons in soybean, an observation not previously reported in other plants. In addition, our analyses of a genetically active and potentially autonomous element sheds light on the complete structure of a soybean element that is useful for annotation of the repetitive fraction of the soybean genome sequence and may prove useful for transposon tagging or transposon display experiments in different genetic lines.

  20. Subcellular location of Arabidopsis thaliana subfamily a1 β-galactosidases and developmental regulation of transcript levels of their coding genes.

    Moneo-Sánchez, María; Izquierdo, Lucía; Martín, Ignacio; Labrador, Emilia; Dopico, Berta

    2016-12-01

    The aim of this work is to gain insight into the six members of the a1 subfamily of the β-galactosidases (BGAL) from Arabidopsis thaliana. First, the subcellular location of all these six BGAL proteins from a1 subfamily has been established in the cell wall by the construction of transgenic plants producing the enhanced green fluorescent protein (eGFP) fused to the BGAL proteins. BGAL12 is also located in the endoplasmic reticulum. Our study of the AtBGAL transcript accumulation along plant development indicated that all AtBGAL transcript appeared in initial stages of development, both dark- and light-grown seedlings, being AtBGAL1, AtBGAL2 and AtBGAL3 transcripts the predominant ones in the latter condition, mainly in the aerial part and with levels decreasing with age. The high accumulation of transcript of AtBGAL4 in basal internodes and in leaves at the end of development, and their strong increase after treatment both with BL and H 3 BO 3 point to an involvement of BGAL4 in cell wall changes leading to the cease of elongation and increased rigidity. The changes of AtBGAL transcript accumulation in relation to different stages and conditions of plant development, suggest that each of the different gene products have a plant-specific function and provides support for the proposed function of the subfamily a1 BGAL in plant cell wall remodelling for cell expansion or for cell response to stress conditions. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  1. Expression analysis of two gene subfamilies encoding the plasma membrane H+-ATPase in Nicotiana plumbaginifolia reveals the major transport functions of this enzyme.

    Moriau, L; Michelet, B; Bogaerts, P; Lambert, L; Michel, A; Oufattole, M; Boutry, M

    1999-07-01

    The plasma membrane H+-ATPase couples ATP hydrolysis to proton transport, thereby establishing the driving force for solute transport across the plasma membrane. In Nicotiana plumbaginifolia, this enzyme is encoded by at least nine pma (plasma membrane H+-ATPase) genes. Four of these are classified into two gene subfamilies, pma1-2-3 and pma4, which are the most highly expressed in plant species. We have isolated genomic clones for pma2 and pma4. Mapping of their transcript 5' end revealed the presence of a long leader that contained small open reading frames, regulatory features typical of other pma genes. The gusA reporter gene was then used to determine the expression of pma2, pma3 and pma4 in N. tabacum. These data, together with those obtained previously for pma1, led to the following conclusions. (i) The four pma-gusA genes were all expressed in root, stem, leaf and flower organs, but each in a cell-type specific manner. Expression in these organs was confirmed at the protein level, using subfamily-specific antibodies. (ii) pma4-gusA was expressed in many cell types and notably in root hair and epidermis, in companion cells, and in guard cells, indicating that in N. plumbaginifolia the same H+-ATPase isoform might be involved in mineral nutrition, phloem loading and control of stomata aperture. (iii) The second gene subfamily is composed, in N. plumbaginifolia, of a single gene (pma4) with a wide expression pattern and, in Arabidopsis thaliana, of three genes (aha1, aha2, aha3), at least two of them having a more restrictive expression pattern. (iv) Some cell types expressed pma2 and pma4 at the same time, which encode H+-ATPases with different enzymatic properties.

  2. The subfamily-specific interaction between Kv2.1 and Kv6.4 subunits is determined by interactions between the N- and C-termini.

    Elke Bocksteins

    Full Text Available The "silent" voltage-gated potassium (KvS channel subunit Kv6.4 does not form electrically functional homotetramers at the plasma membrane but assembles with Kv2.1 subunits, generating functional Kv2.1/Kv6.4 heterotetramers. The N-terminal T1 domain determines the subfamily-specific assembly of Kv1-4 subunits by preventing interactions between subunits that belong to different subfamilies. For Kv6.4, yeast-two-hybrid experiments showed an interaction of the Kv6.4 N-terminus with the Kv2.1 N-terminus, but unexpectedly also with the Kv3.1 N-terminus. We confirmed this interaction by Fluorescence Resonance Energy Transfer (FRET and co-immunoprecipitation (co-IP using N-terminal Kv3.1 and Kv6.4 fragments. However, full-length Kv3.1 and Kv6.4 subunits do not form heterotetramers at the plasma membrane. Therefore, additional interactions between the Kv6.4 and Kv2.1 subunits should be important in the Kv2.1/Kv6.4 subfamily-specificity. Using FRET and co-IP approaches with N- and C-terminal fragments we observed that the Kv6.4 C-terminus physically interacts with the Kv2.1 N-terminus but not with the Kv3.1 N-terminus. The N-terminal amino acid sequence CDD which is conserved between Kv2 and KvS subunits appeared to be a key determinant since charge reversals with arginine substitutions abolished the interaction between the N-terminus of Kv2.1 and the C-terminus of both Kv2.1 and Kv6.4. In addition, the Kv6.4(CKv3.1 chimera in which the C-terminus of Kv6.4 was replaced by the corresponding domain of Kv3.1, disrupted the assembly with Kv2.1. These results indicate that the subfamily-specific Kv2.1/Kv6.4 heterotetramerization is determined by interactions between Kv2.1 and Kv6.4 that involve both the N- and C-termini in which the conserved N-terminal CDD sequence plays a key role.

  3. Revision of the subfamily Opiinae (Hymenoptera, Braconidae from Hunan (China, including thirty-six new species and two new genera

    Li Xi-Ying

    2013-02-01

    Full Text Available The species of the subfamily Opiinae (Hymenoptera: Braconidae from Hunan (Oriental China are revised and illustrated. Thirty-six new species are described: Apodesmia bruniclypealis Li & van Achterberg, sp. n., A. melliclypealis Li & van Achterberg, sp. n., Areotetes albiferus Li & van Achterberg, sp. n., Areotetes carinuliferus Li & van Achterberg, sp. n., A. striatiferus Li & van Achterberg, sp. n., Coleopioides diversinotum Li & van Achterberg, sp. n., C. postpectalis Li & van Achterberg, sp. n., Fopius dorsopiferus Li, van Achterberg & Tan, sp. n., Indiopius chenae Li & van Achterberg, sp. n., Opiognathus aulaciferus Li & van Achterberg, sp. n., O. brevibasalis Li & van Achterberg, sp. n., Opius crenuliferus Li & van Achterberg, sp. n., O. malarator Li, van Achterberg & Tan, sp. n., O. monilipalpis Li & van Achterberg, sp. n., O. pachymerus Li & van Achterberg, sp. n., O. songi Li & van Achterberg, sp. n., O. youi Li & van Achterberg, sp. n., O. zengi Li & van Achterberg, sp. n., Phaedrotoma acuticlypeata Li & van Achterberg, sp. n., P.angiclypeata Li & van Achterberg, sp. n., P. antenervalis Li & van Achterberg, sp. n., P. depressiclypealis Li & van Achterberg, sp. n., P. flavisoma Li & van Achterberg, sp. n., P. nigrisoma Li & van Achterberg, sp. n., P. protuberator Li & van Achterberg, sp. n., P. rugulifera Li & van Achterberg, sp. n., Li & van Achterberg, P. striatinota Li & van Achterberg, sp. n., P. vermiculifera Li & van Achterberg, sp. n., Rhogadopsis latipennis Li & van Achterberg, sp. n., R. longicaudifera Li & van Achterberg, sp. n., R. maculosa Li, van Achterberg & Tan, sp. n., R. obliqua Li & van Achterberg, sp. n., R. sculpturator Li & van Achterberg, sp. n., Utetes longicarinatus Li & van Achterberg, sp. n. and Xynobius notauliferus Li & van Achterberg, sp. n. Areotetes van Achterberg & Li, gen. n. (type species: Areotetes carinuliferus sp. n. and Coleopioides van Achterberg & Li, gen. n. (type species: Coleopioides

  4. Heterogeneous nuclear ribonucleoproteins H, H', and F are members of a ubiquitously expressed subfamily of related but distinct proteins encoded by genes mapping to different chromosomes

    Honoré, B; Rasmussen, H H; Vorum, H

    1995-01-01

    Molecular cDNA cloning, two-dimensional gel immunoblotting, and amino acid microsequencing identified three sequence-unique and distinct proteins that constitute a subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins corresponding to hnRNPs H, H', and F. These proteins share...... epitopes and sequence identity with two other proteins, isoelectric focusing sample spot numbers 2222 (37.6 kDa; pI 6.5) and 2326 (39.5 kDa; pI 6.6), indicating that the subfamily may contain additional members. The identity between hnRNPs H and H' is 96%, between H and F 78%, and between H' and F 75......%, respectively. The three proteins contain three repeats, which we denote quasi-RRMs (qRRMs) since they have a remote similarity to the RNA recognition motif (RRM). The three qRRMs of hnRNP H, with a few additional NH2-terminal amino acids, were constructed by polymerase chain reaction amplification and used...

  5. pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families.

    Suplatov, Dmitry; Kirilin, Eugeny; Arbatsky, Mikhail; Takhaveev, Vakil; Svedas, Vytas

    2014-07-01

    The new web-server pocketZebra implements the power of bioinformatics and geometry-based structural approaches to identify and rank subfamily-specific binding sites in proteins by functional significance, and select particular positions in the structure that determine selective accommodation of ligands. A new scoring function has been developed to annotate binding sites by the presence of the subfamily-specific positions in diverse protein families. pocketZebra web-server has multiple input modes to meet the needs of users with different experience in bioinformatics. The server provides on-site visualization of the results as well as off-line version of the output in annotated text format and as PyMol sessions ready for structural analysis. pocketZebra can be used to study structure-function relationship and regulation in large protein superfamilies, classify functionally important binding sites and annotate proteins with unknown function. The server can be used to engineer ligand-binding sites and allosteric regulation of enzymes, or implemented in a drug discovery process to search for potential molecular targets and novel selective inhibitors/effectors. The server, documentation and examples are freely available at http://biokinet.belozersky.msu.ru/pocketzebra and there are no login requirements. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Genome-wide identification of nuclear receptor (NR) genes and the evolutionary significance of the NR1O subfamily in the monogonont rotifer Brachionus spp.

    Kim, Duck-Hyun; Kim, Hui-Su; Hwang, Dae-Sik; Kim, Hee-Jin; Hagiwara, Atsushi; Lee, Jae-Seong; Jeong, Chang-Bum

    2017-10-01

    Nuclear receptors (NRs) are a large family of transcription factors that are involved in many fundamental biological processes. NRs are considered to have originated from a common ancestor, and are highly conserved throughout the whole animal taxa. Therefore, the genome-wide identification of NR genes in an animal taxon can provide insight into the evolutionary tendencies of NRs. Here, we identified all the NR genes in the monogonont rotifer Brachionus spp., which are considered an ecologically key species due to their abundance and world-wide distribution. The NR family was composed of 40, 32, 29, and 32 genes in the genomes of the rotifers B. calyciflorus, B. koreanus, B. plicatilis, and B. rotundiformis, respectively, which were classified into seven distinct subfamilies. The composition of each subfamily was highly conserved between species, except for NR1O genes, suggesting that they have undergone sporadic evolutionary processes for adaptation to their different environmental pressures. In addition, despite the dynamics of NR evolution, the significance of the conserved endocrine system, particularly for estrogen receptor (ER)-signaling, in rotifers was discussed on the basis of phylogenetic analyses. The results of this study may help provide a better understanding the evolution of NRs, and expand our knowledge of rotifer endocrine systems. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Revision of the subfamily Opiinae (Hymenoptera, Braconidae) from Hunan (China), including thirty-six new species and two new genera

    Li, Xi-Ying; van Achterberg, Cornelis; Tan, Ji-Cai

    2013-01-01

    Abstract The species of the subfamily Opiinae (Hymenoptera: Braconidae) from Hunan (Oriental China) are revised and illustrated. Thirty-six new species are described: Apodesmia bruniclypealis Li & van Achterberg, sp. n., Apodesmia melliclypealis Li & van Achterberg, sp. n., Areotetes albiferus Li & van Achterberg, sp. n., Areotetes carinuliferus Li & van Achterberg, sp. n., Areotetes striatiferus Li & van Achterberg, sp. n., Coleopioides diversinotum Li & van Achterberg, sp. n., Coleopioides postpectalis Li & van Achterberg, sp. n., Fopius dorsopiferus Li, van Achterberg & Tan, sp. n., Indiopius chenae Li & van Achterberg, sp. n., Opiognathus aulaciferus Li & van Achterberg, sp. n., Opiognathus brevibasalis Li & van Achterberg, sp. n., Opius crenuliferus Li & van Achterberg, sp. n., Opius malarator Li, van Achterberg & Tan, sp. n., Opius monilipalpis Li & van Achterberg, sp. n., Opius pachymerus Li & van Achterberg, sp. n., Opius songi Li & van Achterberg, sp. n., Opius youi Li & van Achterberg, sp. n., Opius zengi Li & van Achterberg, sp. n., Phaedrotoma acuticlypeata Li & van Achterberg, sp. n., Phaedrotoma angiclypeata Li & van Achterberg, sp. n., Phaedrotoma antenervalis Li & van Achterberg, sp. n., Phaedrotoma depressiclypealis Li & van Achterberg, sp. n., Phaedrotoma flavisoma Li & van Achterberg, sp. n., Phaedrotoma nigrisoma Li & van Achterberg, sp. n., Phaedrotoma protuberator Li & van Achterberg, sp. n., Phaedrotoma rugulifera Li & van Achterberg, sp. n., Li & van Achterberg,Phaedrotoma striatinota Li & van Achterberg, sp. n., Phaedrotoma vermiculifera Li & van Achterberg, sp. n., Rhogadopsis latipennis Li & van Achterberg, sp. n., Rhogadopsis longicaudifera Li & van Achterberg, sp. n., Rhogadopsis maculosa Li, van Achterberg & Tan, sp. n., Rhogadopsis obliqua Li & van Achterberg, sp. n., Rhogadopsis sculpturator Li & van Achterberg, sp. n., Utetes longicarinatus Li & van Achterberg, sp. n. and Xynobius notauliferus Li & van Achterberg, sp. n. Areotetes

  8. iNR-PhysChem: a sequence-based predictor for identifying nuclear receptors and their subfamilies via physical-chemical property matrix.

    Xuan Xiao

    Full Text Available Nuclear receptors (NRs form a family of ligand-activated transcription factors that regulate a wide variety of biological processes, such as homeostasis, reproduction, development, and metabolism. Human genome contains 48 genes encoding NRs. These receptors have become one of the most important targets for therapeutic drug development. According to their different action mechanisms or functions, NRs have been classified into seven subfamilies. With the avalanche of protein sequences generated in the postgenomic age, we are facing the following challenging problems. Given an uncharacterized protein sequence, how can we identify whether it is a nuclear receptor? If it is, what subfamily it belongs to? To address these problems, we developed a predictor called iNR-PhysChem in which the protein samples were expressed by a novel mode of pseudo amino acid composition (PseAAC whose components were derived from a physical-chemical matrix via a series of auto-covariance and cross-covariance transformations. It was observed that the overall success rate achieved by iNR-PhysChem was over 98% in identifying NRs or non-NRs, and over 92% in identifying NRs among the following seven subfamilies: NR1--thyroid hormone like, NR2--HNF4-like, NR3--estrogen like, NR4--nerve growth factor IB-like, NR5--fushi tarazu-F1 like, NR6--germ cell nuclear factor like, and NR0--knirps like. These rates were derived by the jackknife tests on a stringent benchmark dataset in which none of protein sequences included has ≥60% pairwise sequence identity to any other in a same subset. As a user-friendly web-server, iNR-PhysChem is freely accessible to the public at either http://www.jci-bioinfo.cn/iNR-PhysChem or http://icpr.jci.edu.cn/bioinfo/iNR-PhysChem. Also a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics involved in developing the predictor. It is anticipated that iNR-PhysChem may

  9. The Exiguobacterium sibiricum 255-15 GtfC Enzyme Represents a Novel Glycoside Hydrolase 70 Subfamily of 4,6-α-Glucanotransferase Enzymes.

    Gangoiti, Joana; Pijning, Tjaard; Dijkhuizen, Lubbert

    2016-01-15

    The glycoside hydrolase 70 (GH70) family originally was established for glucansucrase enzymes found solely in lactic acid bacteria synthesizing α-glucan polysaccharides from sucrose (e.g., GtfA). In recent years, we have characterized GtfB and related Lactobacillus enzymes as 4,6-α-glucanotransferase enzymes. These GtfB-type enzymes constitute the first GH70 subfamily of enzymes that are unable to act on sucrose as a substrate but are active with maltodextrins and starch, cleave α1→4 linkages, and synthesize linear α1→6-glucan chains. The GtfB disproportionating type of activity results in the conversion of malto-oligosaccharides into isomalto/malto-polysaccharides with a relatively high percentage of α1→6 linkages. This paper reports the identification of the members of a second GH70 subfamily (designated GtfC enzymes) and the characterization of the Exiguobacterium sibiricum 255-15 GtfC enzyme, which is also inactive with sucrose and displays 4,6-α-glucanotransferase activity with malto-oligosaccharides. GtfC differs from GtfB in synthesizing isomalto/malto-oligosaccharides. Biochemically, the GtfB- and GtfC-type enzymes are related, but phylogenetically, they clearly constitute different GH70 subfamilies, displaying only 30% sequence identity. Whereas the GtfB-type enzyme largely has the same domain order as glucansucrases (with α-amylase domains A, B, and C plus domains IV and V), this GtfC-type enzyme differs in the order of these domains and completely lacks domain V. In GtfC, the sequence of conserved regions I to IV of clan GH-H is identical to that in GH13 (I-II-III-IV) but different from that in GH70 (II-III-IV-I because of a circular permutation of the (β/α)8 barrel. The GtfC 4,6-α-glucanotransferase enzymes thus represent structurally and functionally very interesting evolutionary intermediates between α-amylase and glucansucrase enzymes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  10. Characterization of ppGalNAc-T18, a member of the vertebrate-specific Y subfamily of UDP-N-acetyl-α-D-galactosamine:polypeptide N-acetylgalactosaminyltransferases.

    Li, Xing; Wang, Jing; Li, Wei; Xu, Yingjiao; Shao, Dong; Xie, Yinyin; Xie, Wenxian; Kubota, Tomomi; Narimatsu, Hisashi; Zhang, Yan

    2012-05-01

    The first step of mucin-type O-glycosylation is catalyzed by members of the UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase (ppGalNAc-T; EC 2.4.1.41) family. Each member of this family has unique substrate specificity and expression profiles. In this report, we describe a new subfamily of ppGalNAc-Ts, designated the Y subfamily. The Y subfamily consists of four members, ppGalNAc-T8, -T9, -T17 and -T18, in which the conserved YDX(5)WGGENXE sequence in the Gal/GalNAc-T motif of ppGalNAc-Ts is mutated to LDX(5)YGGENXE. Phylogenetic analysis revealed that the Y subfamily members only exist in vertebrates. All four Y subfamily members lack in vitro GalNAc-transferase activity toward classical substrates possibly because of the UDP-GalNAc-binding pocket mutants. However, ppGalNAc-T18, the newly identified defining member, was localized in the endoplasmic reticulum rather than the Golgi apparatus in lung carcinoma cells. The knockdown of ppGalNAc-T18 altered cell morphology, proliferation potential and changed cell O-glycosylation. ppGalNAc-T18 can also modulate the in vitro GalNAc-transferase activity of ppGalNAc-T2 and -T10, suggesting that it may be a chaperone-like protein. These findings suggest that the new Y subfamily of ppGalNAc-Ts plays an important role in protein glycosylation; characterizing their functions will provide new insight into the role of ppGalNAc-Ts.

  11. Characterization of the Paenibacillus beijingensis DSM 24997 GtfD and its glucan polymer products representing a new glycoside hydrolase 70 subfamily of 4,6-α-glucanotransferase enzymes.

    Joana Gangoiti

    Full Text Available Previously we have reported that the Gram-negative bacterium Azotobacter chroococcum NCIMB 8003 uses the 4,6-α-glucanotransferase GtfD to convert maltodextrins and starch into a reuteran-like polymer consisting of (α1→4 glucan chains connected by alternating (α1→4/(α1→6 linkages and (α1→4,6 branching points. This enzyme constituted the single evidence for this reaction and product specificity in the GH70 family, mostly containing glucansucrases encoded by lactic acid bacteria (http://www.CAZy.org. In this work, 4 additional GtfD-like proteins were identified in taxonomically diverse plant-associated bacteria forming a new GH70 subfamily with intermediate characteristics between the evolutionary related GH13 and GH70 families. The GtfD enzyme encoded by Paenibacillus beijingensis DSM 24997 was characterized providing the first example of a reuteran-like polymer synthesizing 4,6-α-glucanotransferase in a Gram-positive bacterium. Whereas the A. chroococcum GtfD activity on amylose resulted in the synthesis of a high molecular polymer, in addition to maltose and other small oligosaccharides, two reuteran-like polymer distributions are produced by P. beijingensis GtfD: a high-molecular mass polymer and a low-molecular mass polymer with an average Mw of 27 MDa and 19 kDa, respectively. Compared to the A. chroooccum GtfD product, both P. beijingensis GtfD polymers contain longer linear (α1→4 sequences in their structure reflecting a preference for transfer of even longer glucan chains by this enzyme. Overall, this study provides new insights into the evolutionary history of GH70 enzymes, and enlarges the diversity of natural enzymes that can be applied for modification of the starch present in food into less and/or more slowly digestible carbohydrate structures.

  12. The reprogramming factor nuclear receptor subfamily 5, group A, member 2 cannot replace octamer-binding transcription factor 4 function in the self-renewal of embryonic stem cells.

    Choi, Kyeng-Won; Oh, Hye-Rim; Lee, Jaeyoung; Lim, Bobae; Han, Yong-Mahn; Oh, Junseo; Kim, Jungho

    2014-02-01

    Although octamer-binding transcription factor 4 (Oct-4) is one of the most intensively studied factors in mammalian development, no cellular genes capable of replacing Oct-4 function in embryonic stem (ES) cells have been found. Recent data show that nuclear receptor subfamily 5, group A, member 2 (Nr5a2) is able to replace Oct-4 function in the reprogramming process; however, it is unclear whether Nr5a2 can replace Oct-4 function in ES cells. In this study, the ability of Nr5a2 to maintain self-renewal and pluripotency in ES cells was investigated. Nr5a2 localized to the nucleus in ES cells, similarly to Oct-4. However, expression of Nr5a2 failed to rescue the stem cell phenotype or to maintain the self-renewal ability of ES cells. Furthermore, as compared with Oct-4-expressing ES cells, Nr5a2-expressing ES cells showed a reduced number of cells in S-phase, did not expand normally, and did not remain in an undifferentiated state. Ectopic expression of Nr5a2 in ES cells was not able to activate transcription of ES cell-specific genes, and gene expression profiling demonstrated differences between Nr5a2-expressing and Oct-4-expressing ES cells. In addition, Nr5a2-expressing ES cells were not able to form teratomas in nude mice. Taken together, these results strongly suggest that the gene regulation properties of Nr5a2 and Oct-4 and their abilities to confer self-renewal and pluripotency of ES cells differ. The present study provides strong evidence that Nr5a2 cannot replace Oct-4 function in ES cells. © 2013 FEBS.

  13. Getting from A to B-exploring the activation motifs of the class B adhesion G protein-coupled receptor subfamily G member 4/GPR112

    Cornelia Peeters, Miriam; Mos, Iris; Lenselink, Eelke B

    2016-01-01

    The adhesion G protein-coupled receptors (ADGRs/class B2 G protein-coupled receptors) constitute an ancient family of G protein-coupled receptors that have recently been demonstrated to play important roles in cellular and developmental processes. Here, we describe a first insight...... into the structure-function relationship of ADGRs using the family member ADGR subfamily G member 4 (ADGRG4)/GPR112 as a model receptor. In a bioinformatics approach, we compared conserved, functional elements of the well-characterized class A and class B1 secretin-like G protein-coupled receptors with the ADGRs. We...... identified several potential equivalent motifs and subjected those to mutational analysis. The importance of the mutated residues was evaluated by examining their effect on the high constitutive activity of the N-terminally truncated ADGRG4/GPR112 in a 1-receptor-1-G protein Saccharomyces cerevisiae...

  14. The effects of IL-20 subfamily cytokines on reconstituted human epidermis suggest potential roles in cutaneous innate defense and pathogenic adaptive immunity in psoriasis.

    Sa, Susan M; Valdez, Patricia A; Wu, Jianfeng; Jung, Kenneth; Zhong, Fiona; Hall, Linda; Kasman, Ian; Winer, Jane; Modrusan, Zora; Danilenko, Dimitry M; Ouyang, Wenjun

    2007-02-15

    IL-19, IL-20, IL-22, IL-24, and IL-26 are members of the IL-10 family of cytokines that have been shown to be up-regulated in psoriatic skin. Contrary to IL-10, these cytokines signal using receptor complex R1 subunits that are preferentially expressed on cells of epithelial origin; thus, we henceforth refer to them as the IL-20 subfamily cytokines. In this study, we show that primary human keratinocytes (KCs) express receptors for these cytokines and that IL-19, IL-20, IL-22, and IL-24 induce acanthosis in reconstituted human epidermis (RHE) in a dose-dependent manner. These cytokines also induce expression of the psoriasis-associated protein S100A7 and keratin 16 in RHE and cause persistent activation of Stat3 with nuclear localization. IL-22 had the most pronounced effects on KC proliferation and on the differentiation of KCs in RHE, inducing a decrease in the granular cell layer (hypogranulosis). Furthermore, gene expression analysis performed on cultured RHE treated with these cytokines showed that IL-19, IL-20, IL-22, and IL-24 regulate many of these same genes to variable degrees, inducing a gene expression profile consistent with inflammatory responses, wound healing re-epithelialization, and altered differentiation. Many of these genes have also been found to be up-regulated in psoriatic skin, including several chemokines, beta-defensins, S100 family proteins, and kallikreins. These results confirm that IL-20 subfamily cytokines are important regulators of epidermal KC biology with potentially pivotal roles in the immunopathology of psoriasis.

  15. Regulation of protease-activated receptor 1 signaling by the adaptor protein complex 2 and R4 subfamily of regulator of G protein signaling proteins.

    Chen, Buxin; Siderovski, David P; Neubig, Richard R; Lawson, Mark A; Trejo, Joann

    2014-01-17

    The G protein-coupled protease-activated receptor 1 (PAR1) is irreversibly proteolytically activated by thrombin. Hence, the precise regulation of PAR1 signaling is important for proper cellular responses. In addition to desensitization, internalization and lysosomal sorting of activated PAR1 are critical for the termination of signaling. Unlike most G protein-coupled receptors, PAR1 internalization is mediated by the clathrin adaptor protein complex 2 (AP-2) and epsin-1, rather than β-arrestins. However, the function of AP-2 and epsin-1 in the regulation of PAR1 signaling is not known. Here, we report that AP-2, and not epsin-1, regulates activated PAR1-stimulated phosphoinositide hydrolysis via two different mechanisms that involve, in part, a subset of R4 subfamily of "regulator of G protein signaling" (RGS) proteins. A significantly greater increase in activated PAR1 signaling was observed in cells depleted of AP-2 using siRNA or in cells expressing a PAR1 (420)AKKAA(424) mutant with defective AP-2 binding. This effect was attributed to AP-2 modulation of PAR1 surface expression and efficiency of G protein coupling. We further found that ectopic expression of R4 subfamily members RGS2, RGS3, RGS4, and RGS5 reduced activated PAR1 wild-type signaling, whereas signaling by the PAR1 AKKAA mutant was minimally affected. Intriguingly, siRNA-mediated depletion analysis revealed a function for RGS5 in the regulation of signaling by the PAR1 wild type but not the AKKAA mutant. Moreover, activation of the PAR1 wild type, and not the AKKAA mutant, induced Gαq association with RGS3 via an AP-2-dependent mechanism. Thus, AP-2 regulates activated PAR1 signaling by altering receptor surface expression and through recruitment of RGS proteins.

  16. Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

    Matus, José Tomás; Aquea, Felipe; Arce-Johnson, Patricio

    2008-01-01

    Background The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality. Results We describe and classify 108 members of the grape R2R3 MYB gene subfamily in terms of their genomic gene structures and similarity to their putative Arabidopsis thaliana orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across Arabidopsis and Vitis, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the Arabidopsis and rice MYB subfamilies. Two anthocyanin MYBA related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11. Conclusion This genome wide transcription factor analysis in Vitis suggests that clade-specific grape R2R3 MYB genes are expanded while other MYB genes could be well conserved compared to Arabidopsis. MYB gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions. PMID:18647406

  17. Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

    Arce-Johnson Patricio

    2008-07-01

    Full Text Available Abstract Background The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality. Results We describe and classify 108 members of the grape R2R3 MYB gene subfamily in terms of their genomic gene structures and similarity to their putative Arabidopsis thaliana orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across Arabidopsis and Vitis, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the Arabidopsis and rice MYB subfamilies. Two anthocyanin MYBA related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11. Conclusion This genome wide transcription factor analysis in Vitis suggests that clade-specific grape R2R3 MYB genes are expanded while other MYB genes could be well conserved compared to Arabidopsis. MYB gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions.

  18. Crystal Structure of Perakine Reductase, Founding Member of a Novel Aldo-Keto Reductase (AKR) Subfamily That Undergoes Unique Conformational Changes during NADPH Binding*

    Sun, Lianli; Chen, Yixin; Rajendran, Chitra; Mueller, Uwe; Panjikar, Santosh; Wang, Meitian; Mindnich, Rebekka; Rosenthal, Cindy; Penning, Trevor M.; Stöckigt, Joachim

    2012-01-01

    Perakine reductase (PR) catalyzes the NADPH-dependent reduction of the aldehyde perakine to yield the alcohol raucaffrinoline in the biosynthetic pathway of ajmaline in Rauvolfia, a key step in indole alkaloid biosynthesis. Sequence alignment shows that PR is the founder of the new AKR13D subfamily and is designated AKR13D1. The x-ray structure of methylated His6-PR was solved to 2.31 Å. However, the active site of PR was blocked by the connected parts of the neighbor symmetric molecule in the crystal. To break the interactions and obtain the enzyme-ligand complexes, the A213W mutant was generated. The atomic structure of His6-PR-A213W complex with NADPH was determined at 1.77 Å. Overall, PR folds in an unusual α8/β6 barrel that has not been observed in any other AKR protein to date. NADPH binds in an extended pocket, but the nicotinamide riboside moiety is disordered. Upon NADPH binding, dramatic conformational changes and movements were observed: two additional β-strands in the C terminus become ordered to form one α-helix, and a movement of up to 24 Å occurs. This conformational change creates a large space that allows the binding of substrates of variable size for PR and enhances the enzyme activity; as a result cooperative kinetics are observed as NADPH is varied. As the founding member of the new AKR13D subfamily, PR also provides a structural template and model of cofactor binding for the AKR13 family. PMID:22334702

  19. Functional diversity for biomass deconstruction in family 5 subfamily 5 (GH5_5) of fungal endo-β1,4-glucanases.

    Li, Bingyao; Walton, Jonathan D

    2017-05-01

    Endo-β1,4-glucanases in glycosyl hydrolase family 5 (GH5) are ubiquitous enzymes in the multicellular fungi and are common components of enzyme cocktails for biomass conversion. We recently showed that an endo-glucanase of subfamily 5 of GH5 (GH5_5) from Sporotrichum thermophile (StCel5A) was more effective at releasing glucose from pretreated corn stover, when part of an eight-component synthetic enzyme mixture, compared to its closely related counterpart from Trichoderma reesei, TrCel5A. StCel5A and TrCel5A belong to different clades of GH5_5 (GH5_5_1 and GH5_5_2, respectively). To test whether the superior activity of StCel5A was a general property of all enzymes in the GH5_5_2 clade, StCel5A, TrCel5A, and two additional members of each subfamily were expressed in a common host that had been engineered to suppress its native cellulases (T. reesei Δxyr1) and compared against each other alone on pure substrates, in synthetic mixtures on pure substrates, and against each other in synthetic mixtures on real biomass. The results indicated that superiority is a unique property of StCel5A and not of GH5_5_2 generally. The six Cel5A enzymes had significant differences in relative activities on different substrates, in specific activities, and in sensitivities to mannan inhibition. Importantly, the behavior of the six endo-glucanases on pure cellulose substrates did not predict their behavior in combination with other cellulolytic enzymes on a real lignocellulosic biomass substrate.

  20. Sobre um novo gênero neotrópico da subfamília Tanypodinae (Diptera, Chironomidae On a new neotropical genus of the subfamily Tanypodinae (Diptera, Chironomidae

    Sebastião José de Oliveira

    1992-01-01

    Full Text Available A new neotropical genus and a new species of a non-biting midge for the subfamily Tanypodinae from Brazil are described. The new genus is near Tanypus Meigen, 1803 and Procladius Skuse, 1889, but differs of both by wings and male terminalia.

  1. Leaf and stem CO/sub 2/ uptake in the three subfamilies of the Cactaceae. [Pereskia aculeata; Pereskia grandifolia; Maihuenia poeppigii; Carnegiea gigantea; Ferocactus acanthodes; Coryphantha vivipara; Mammillaria dioica; Opuntia ficus-inidica; Pereskiopsis porteri; Quiabentia chacoensis; Austrocylindropuntia subulata

    Nobel, P.S.; Hartsock, T.L.

    1986-04-01

    Net CO/sub 2/ uptake over 24-hour periods was examined for the leaves and for the stems of 11 species of cacti representing all three subfamilies. For Pereskia aculeata, Pereskia grandifolia, and Maihuenia poeppigii (subfamily Pereskioideae), all the net shoot CO/sub 2/ uptake was by the leaves and during the daytime. In contrast, for the leafless species Carnegiea gigantea, Ferocactus acanthodes, Coryphantha vivipara, and Mammillaria dioica (subfamily Cactoideae), all the shoot net CO/sub 2/ uptake was by the stems and at night. Similarly, for leafless Opuntia ficus-indica (subfamily Opuntioideae), all net CO/sub 2/ uptake occurred at night. For leafy members of the Opuntioideae (Pereskiopsis porteri, Quiabentia chacoensis, Austrocylindropuntia subulata), at least 88% of the shoot CO/sub 2/ uptake over 24 hours was by the leaves and some CO/sub 2/ uptake occurred at night. Leaves responded to the instantaneous level of photosynthetically active radiation (PAR) during the daytime, as occurs for C/sub 3/ plants, whereas nocturnal CO/sub 2/ uptake by stems of O. ficus-indica and F. acanthodes responded to the total daily PAR, as occurs for Crassulacean acid metabolism (CAM) plants. Thus, under the well-watered conditions employed, the Pereskioideae behaved as C/sub 3/ plants, the Cactoideae behaved as CAM plants, and the Opuntioideae exhibited characteristics of both pathways.

  2. Submission to GenBank of the Plasma membrane intrinsic protein (PIP) Subfamily in Cotton – GenBank Accession No. GU998827-GU998830 and GenBank Accession TPA;inferential No. BK007045-BK007052

    The plasma membrane intrinsic proteins (PIP) are one of the five aquaporin protein subfamilies. Aquaporin proteins are known to facilitate water transport through biological membranes. In order to identify NIP aquaporin gene candidates in cotton (Gossypium hirsutum L.), in silico and molecular clon...

  3. Glycosyltransferase family 43 is also found in early eukaryotes and has three subfamilies in Charophycean green algae.

    Rahil Taujale

    Full Text Available The glycosyltransferase family 43 (GT43 has been suggested to be involved in the synthesis of xylans in plant cell walls and proteoglycans in animals. Very recently GT43 family was also found in Charophycean green algae (CGA, the closest relatives of extant land plants. Here we present evidence that non-plant and non-animal early eukaryotes such as fungi, Haptophyceae, Choanoflagellida, Ichthyosporea and Haptophyceae also have GT43-like genes, which are phylogenetically close to animal GT43 genes. By mining RNA sequencing data (RNA-Seq of selected plants, we showed that CGA have evolved three major groups of GT43 genes, one orthologous to IRX14 (IRREGULAR XYLEM14, one orthologous to IRX9/IRX9L and the third one ancestral to all land plant GT43 genes. We confirmed that land plant GT43 has two major clades A and B, while in angiosperms, clade A further evolved into three subclades and the expression and motif pattern of A3 (containing IRX9 are fairly different from the other two clades likely due to rapid evolution. Our in-depth sequence analysis contributed to our overall understanding of the early evolution of GT43 family and could serve as an example for the study of other plant cell wall-related enzyme families.

  4. Cytochrome P450 CYP3A in marsupials: cloning and characterisation of the second identified CYP3A subfamily member, isoform 3A78 from koala (Phascolarctos cinereus).

    El-Merhibi, Adaweyah; Ngo, Suong N T; Crittenden, Tamara A; Marchant, Ceilidh L; Stupans, Ieva; McKinnon, Ross A

    2011-11-01

    Cytochromes P450 (CYPs) are critically important in the oxidative metabolism of a diverse array of xenobiotics and endogenous substrates. Previously, we cloned and characterised the CYP2C, CYP4A, and CYP4B gene subfamilies from marsupials and demonstrated important species-differences in both activity and tissue expression of these CYP enzymes. Recently, we isolated the Eastern grey kangaroo CYP3A70. Here we have cloned and characterised the second identified member of marsupial CYP3A gene subfamily, CYP3A78 from the koala (Phascolarctos cinereus). In addition, we have examined the gender-differences in microsomal erythromycin N-demethylation activity (a CYP3A marker) and CYP3A protein expression across test marsupial species. Significant differences in hepatic erythromycin N-demethylation activity were observed between male and female koalas, with the activity detected in female koalas being 2.5-fold higher compared to that in male koalas (p<0.01). No gender-differences were observed in tammar wallaby or Eastern grey kangaroo. Immunoblot analysis utilising anti-human CYP3A4 antibody detected immunoreactive proteins in liver microsomes from all test male and female marsupials including the koala, tammar wallaby, and Eastern grey kangaroo, with no gender-differences detected across test marsupials. A 1610 bp koala hepatic CYP3A complete cDNA, designated CYP3A78, was cloned by reverse transcription-polymerase chain reaction approaches. It displays 64% nucleotide and 57% amino acid sequence identity to the Eastern grey kangaroo CYP3A70. The CYP3A78 cDNA encodes a protein of 515 amino acids, shares approximately 68% nucleotide and 56% amino acid sequence identity to human CYP3A4, and displays high sequence similarity to other published mammalian CYP3As from human, monkey, cow, pig, dog, rat, rabbit, mouse, hamster, and guinea pig. Collectively, this study provides primary molecular data regarding koala hepatic CYP3A78 gene and enables further functional analyses of CYP

  5. Modelling and mutational analysis of Aspergillus nidulans UreA, a member of the subfamily of urea/H+ transporters in fungi and plants

    Sanguinetti, Manuel; Amillis, Sotiris; Pantano, Sergio; Scazzocchio, Claudio; Ramón, Ana

    2014-01-01

    We present the first account of the structure–function relationships of a protein of the subfamily of urea/H+ membrane transporters of fungi and plants, using Aspergillus nidulans UreA as a study model. Based on the crystal structures of the Vibrio parahaemolyticus sodium/galactose symporter (vSGLT) and of the Nucleobase-Cation-Symport-1 benzylhydantoin transporter from Microbacterium liquefaciens (Mhp1), we constructed a three-dimensional model of UreA which, combined with site-directed and classical random mutagenesis, led to the identification of amino acids important for UreA function. Our approach allowed us to suggest roles for these residues in the binding, recognition and translocation of urea, and in the sorting of UreA to the membrane. Residues W82, Y106, A110, T133, N275, D286, Y388, Y437 and S446, located in transmembrane helixes 2, 3, 7 and 11, were found to be involved in the binding, recognition and/or translocation of urea and the sorting of UreA to the membrane. Y106, A110, T133 and Y437 seem to play a role in substrate selectivity, while S446 is necessary for proper sorting of UreA to the membrane. Other amino acids identified by random classical mutagenesis (G99, R141, A163, G168 and P639) may be important for the basic transporter's structure, its proper folding or its correct traffic to the membrane. PMID:24966243

  6. Role of NH2-terminal hydrophobic motif in the subcellular localization of ATP-binding cassette protein subfamily D: Common features in eukaryotic organisms

    Lee, Asaka; Asahina, Kota; Okamoto, Takumi; Kawaguchi, Kosuke; Kostsin, Dzmitry G.; Kashiwayama, Yoshinori; Takanashi, Kojiro; Yazaki, Kazufumi; Imanaka, Tsuneo; Morita, Masashi

    2014-01-01

    Highlights: • ABCD proteins classifies based on with or without NH 2 -terminal hydrophobic segment. • The ABCD proteins with the segment are targeted peroxisomes. • The ABCD proteins without the segment are targeted to the endoplasmic reticulum. • The role of the segment in organelle targeting is conserved in eukaryotic organisms. - Abstract: In mammals, four ATP-binding cassette (ABC) proteins belonging to subfamily D have been identified. ABCD1–3 possesses the NH 2 -terminal hydrophobic region and are targeted to peroxisomes, while ABCD4 lacking the region is targeted to the endoplasmic reticulum (ER). Based on hydropathy plot analysis, we found that several eukaryotes have ABCD protein homologs lacking the NH 2 -terminal hydrophobic segment (H0 motif). To investigate whether the role of the NH 2 -terminal H0 motif in subcellular localization is conserved across species, we expressed ABCD proteins from several species (metazoan, plant and fungi) in fusion with GFP in CHO cells and examined their subcellular localization. ABCD proteins possessing the NH 2 -terminal H0 motif were localized to peroxisomes, while ABCD proteins lacking this region lost this capacity. In addition, the deletion of the NH 2 -terminal H0 motif of ABCD protein resulted in their localization to the ER. These results suggest that the role of the NH 2 -terminal H0 motif in organelle targeting is widely conserved in living organisms

  7. Giant panda (Ailuropoda melanoleuca) population dynamics and bamboo (subfamily Bambusoideae) life history: a structured population approach to examining carrying capacity when the prey are semelparous

    Carter, J.; Ackleh, A.S.; Leonard, B.P.; Wang, Hongfang

    1999-01-01

    The giant panda, Ailuropoda melanoleuca, is a highly specialized Ursid whose diet consists almost entirely of various species of bamboo. Bamboo (Bambusoideae) is a grass subfamily whose species often exhibit a synchronous semelparity. Synchronous semelparity can create local drops in carrying capacity for the panda. We modeled the interaction of pandas and their bamboo food resources with an age structured panda population model linked to a natural history model of bamboo biomass dynamics based on literature values of bamboo biomass, and giant panda life history dynamics. This paper reports the results of our examination of the interaction between pandas and their bamboo food resource and its implications for panda conservation. In the model all panda populations were well below the carrying capacity of the habitat. The giant panda populations growth was most sensitive to changes in birth rates and removal of reproductive aged individuals. Periodic starvation that has been documented in conjunction with bamboo die-offs is probably related to the inability to move to other areas within the region where bamboo is still available. Based on the results of this model, giant panda conservation should concentrate on keeping breeding individuals in the wild, keep corridors to different bamboo species open to pandas, and to concentrate research on bamboo life history.

  8. An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice.

    Chen, Guoxiong; Komatsuda, Takao; Ma, Jian Feng; Nawrath, Christiane; Pourkheirandish, Mohammad; Tagiri, Akemi; Hu, Yin-Gang; Sameri, Mohammad; Li, Xinrong; Zhao, Xin; Liu, Yubing; Li, Chao; Ma, Xiaoying; Wang, Aidong; Nair, Sudha; Wang, Ning; Miyao, Akio; Sakuma, Shun; Yamaji, Naoki; Zheng, Xiuting; Nevo, Eviatar

    2011-07-26

    Land plants have developed a cuticle preventing uncontrolled water loss. Here we report that an ATP-binding cassette (ABC) subfamily G (ABCG) full transporter is required for leaf water conservation in both wild barley and rice. A spontaneous mutation, eibi1.b, in wild barley has a low capacity to retain leaf water, a phenotype associated with reduced cutin deposition and a thin cuticle. Map-based cloning revealed that Eibi1 encodes an HvABCG31 full transporter. The gene was highly expressed in the elongation zone of a growing leaf (the site of cutin synthesis), and its gene product also was localized in developing, but not in mature tissue. A de novo wild barley mutant named "eibi1.c," along with two transposon insertion lines of rice mutated in the ortholog of HvABCG31 also were unable to restrict water loss from detached leaves. HvABCG31 is hypothesized to function as a transporter involved in cutin formation. Homologs of HvABCG31 were found in green algae, moss, and lycopods, indicating that this full transporter is highly conserved in the evolution of land plants.

  9. Transient receptor potential cation channel, subfamily C, member 5 (TRPC5) is a cold-transducer in the peripheral nervous system.

    Zimmermann, Katharina; Lennerz, Jochen K; Hein, Alexander; Link, Andrea S; Kaczmarek, J Stefan; Delling, Markus; Uysal, Serdar; Pfeifer, John D; Riccio, Antonio; Clapham, David E

    2011-11-01

    Detection and adaptation to cold temperature is crucial to survival. Cold sensing in the innocuous range of cold (>10-15 °C) in the mammalian peripheral nervous system is thought to rely primarily on transient receptor potential (TRP) ion channels, most notably the menthol receptor, TRPM8. Here we report that TRP cation channel, subfamily C member 5 (TRPC5), but not TRPC1/TRPC5 heteromeric channels, are highly cold sensitive in the temperature range 37-25 °C. We found that TRPC5 is present in mouse and human sensory neurons of dorsal root ganglia, a substantial number of peripheral nerves including intraepithelial endings, and in the dorsal lamina of the spinal cord that receives sensory input from the skin, consistent with a potential TRPC5 function as an innocuous cold transducer in nociceptive and thermosensory nerve endings. Although deletion of TRPC5 in 129S1/SvImJ mice resulted in no temperature-sensitive behavioral changes, TRPM8 and/or other menthol-sensitive channels appear to underpin a much larger component of noxious cold sensing after TRPC5 deletion and a shift in mechanosensitive C-fiber subtypes. These findings demonstrate that highly cold-sensitive TRPC5 channels are a molecular component for detection and regional adaptation to cold temperatures in the peripheral nervous system that is distinct from noxious cold sensing.

  10. A new member of the GM130 golgin subfamily is expressed in the optic lobe anlagen of the metamorphosing brain of Manduca sexta

    Chiou-Miin Wang

    2003-12-01

    Full Text Available During metamorphosis of the insect brain, the optic lobe anlagen generate the proliferation centers for the visual cortices. We show here that, in the moth Manduca sexta, an 80 kDa Golgi complex protein (Ms-golgin80 is abundantly expressed in the cytoplasm of neuroblasts and ganglion mother cells in the optic lobe anlagen and proliferation centers. The predicted amino acid sequence for Ms-golgin80 is similar to that of several members of the GM130 subfamily of Golgi-associated proteins, including rat GM130 and human golgin-95. Homologs of Ms-golgin80 from Drosophila melanogaster, Caenorhabditis elegans, and Brugia malayi were identified through homology sequence search. Sequence similarities are present in three regions: the N-terminus, an internal domain of 89 amino acids, and another domain of 89 amino acids near the C-terminus. Structural similarities further suggest that these molecules play the same cellular role as GM130. GM130 is involved in the docking and fusion of coatomer (COP I coated vesicles to the Golgi membranes; it also regulates the fragmentation and subsequent reassembly of the Golgi complex during mitosis. Abundant expression of Ms-golgin80 in neuroblasts and ganglion mother cells and its reduced expression in the neuronal progeny of these cells suggest that this protein may be involved in the maintenance of the proliferative state.

  11. AOX1-Subfamily Gene Members in Olea europaea cv. "Galega Vulgar"-Gene Characterization and Expression of Transcripts during IBA-Induced in Vitro Adventitious Rooting.

    Velada, Isabel; Grzebelus, Dariusz; Lousa, Diana; M Soares, Cláudio; Santos Macedo, Elisete; Peixe, Augusto; Arnholdt-Schmitt, Birgit; G Cardoso, Hélia

    2018-02-17

    Propagation of some Olea europaea L. cultivars is strongly limited due to recalcitrant behavior in adventitious root formation by semi-hardwood cuttings. One example is the cultivar "Galega vulgar". The formation of adventitious roots is considered a morphological response to stress. Alternative oxidase (AOX) is the terminal oxidase of the alternative pathway of the plant mitochondrial electron transport chain. This enzyme is well known to be induced in response to several biotic and abiotic stress situations. This work aimed to characterize the alternative oxidase 1 (AOX1)-subfamily in olive and to analyze the expression of transcripts during the indole-3-butyric acid (IBA)-induced in vitro adventitious rooting (AR) process. OeAOX1a (acc. no. MF410318) and OeAOX1d (acc. no. MF410319) were identified, as well as different transcript variants for both genes which resulted from alternative polyadenylation events. A correlation between transcript accumulation of both OeAOX1a and OeAOX1d transcripts and the three distinct phases (induction, initiation, and expression) of the AR process in olive was observed. Olive AOX1 genes seem to be associated with the induction and development of adventitious roots in IBA-treated explants. A better understanding of the molecular mechanisms underlying the stimulus needed for the induction of adventitious roots may help to develop more targeted and effective rooting induction protocols in order to improve the rooting ability of difficult-to-root cultivars.

  12. Phylogenetic analysis of the spider mite sub-family Tetranychinae (Acari: Tetranychidae based on the mitochondrial COI gene and the 18S and the 5' end of the 28S rRNA genes indicates that several genera are polyphyletic.

    Tomoko Matsuda

    Full Text Available The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS region of nuclear ribosomal RNA genes and the cytochrome c oxidase subunit I (COI gene of mitochondrial DNA have been used for species identification and phylogenetic reconstruction within the sub-family Tetranychinae, although they have not always been successful. The 18S and 28S rRNA genes should be more suitable for resolving higher levels of phylogeny, such as tribes or genera of Tetranychinae because these genes evolve more slowly and are made up of conserved regions and divergent domains. Therefore, we used both the 18S (1,825-1,901 bp and 28S (the 5' end of 646-743 bp rRNA genes to infer phylogenetic relationships within the sub-family Tetranychinae with a focus on the tribe Tetranychini. Then, we compared the phylogenetic tree of the 18S and 28S genes with that of the mitochondrial COI gene (618 bp. As observed in previous studies, our phylogeny based on the COI gene was not resolved because of the low bootstrap values for most nodes of the tree. On the other hand, our phylogenetic tree of the 18S and 28S genes revealed several well-supported clades within the sub-family Tetranychinae. The 18S and 28S phylogenetic trees suggest that the tribes Bryobiini, Petrobiini and Eurytetranychini are monophyletic and that the tribe Tetranychini is polyphyletic. At the genus level, six genera for which more than two species were sampled appear to be monophyletic, while four genera (Oligonychus, Tetranychus, Schizotetranychus and Eotetranychus appear to be polyphyletic. The topology presented here does not fully agree with the current morphology-based taxonomy, so that the diagnostic morphological characters of Tetranychinae need to be reconsidered.

  13. Sex difference in induction of hepatic CYP2B and CYP3A subfamily enzymes by nicardipine and nifedipine in rats

    Konno, Yoshihiro; Sekimoto, Masashi; Nemoto, Kiyomitsu; Degawa, Masakuni

    2004-01-01

    Male and female of F344 rats were treated per os with nicardipine (Nic) and nifedipine (Nif), and changes in the levels of mRNA and protein of hepatic cytochrome P450 (P450) enzymes, CYP2B1, CYP2B2, CYP3A1, CYP3A2, CYP3A9, and CYP3A18 were examined. Furthermore, hepatic microsomal activities for pentoxyresorufin O-dealkylation (PROD) and nifedipine oxidation, which are mainly mediated by CYP2B and CYP3A subfamily enzymes, respectively, were measured. Analyses of RT-PCR and Western blotting revealed that Nic and Nif induced predominantly CYP3A and CYP2B enzymes, respectively. As for the gene activation of CYP2B enzymes, especially CYP2B1, Nif showed high capacity in both sexes of rats, whereas Nic did a definite capacity in the males but little in the females. Gene activations of CYP3A1, CYP3A2, and CYP3A18 by Nic occurred in both sexes of rats, although that of CYP3A9 did only in the male rats. Although gene activations of CYP3A1 and CYP3A2 by Nif were observed in both sexes of rats, a slight activation of the CYP3A9 gene occurred only in female rats, and the CYP3A18 gene activation, in neither male nor female rats. Thus, changes in levels of the mRNA or protein of CYP2B and CYP3A enzymes, especially CYP2B1 and CYP3A2, were closely correlated with those in hepatic PROD and nifedipine oxidation activities, respectively. The present findings demonstrate for the first time the sex difference in the Nic- and Nif-mediated induction of hepatic P450 enzymes in rats and further indicate that Nic and Nif show different specificities and sex dependencies in the induction of hepatic P450 enzymes

  14. Over-expression in Escherichia coli, purification and reconstitution in liposomes of the third member of the OCTN sub-family: The mouse carnitine transporter OCTN3

    Scalise, Mariafrancesca; Galluccio, Michele; Pochini, Lorena [Department of Cell Biology, University of Calabria, Via P. Bucci 4c, 87036 Arcavacata di Rende (Italy); Indiveri, Cesare, E-mail: indiveri@unical.it [Department of Cell Biology, University of Calabria, Via P. Bucci 4c, 87036 Arcavacata di Rende (Italy)

    2012-05-25

    Highlights: Black-Right-Pointing-Pointer mOCTN3 transport protein has been cloned in pET-21a(+) and over-expressed in Escherichia coli. Black-Right-Pointing-Pointer The expressed mOCTN3 has been purified to homogeneity by Ni-chelating chromatography. Black-Right-Pointing-Pointer The protein solubilised in Triton X-100 has been reconstituted in liposomes. Black-Right-Pointing-Pointer Recombinant mOCTN3 catalyses transport of carnitine by a uniport mode. -- Abstract: pET-21a(+)-mOCTN3-6His was constructed and used for over-expression in Escherichia coli Rosetta(DE3)pLysS. After IPTG induction a protein with apparent molecular mass of 53 kDa was collected in the insoluble fraction of the cell lysate and purified by Ni{sup 2+}-chelating chromatography with a yield of 2 mg/l of cell culture. The over-expressed protein was identified with mOCTN3 by anti-His antibody and reconstitution in liposomes. mOCTN3 required peculiar conditions for optimal expression and reconstitution in liposomes. The protein catalyzed a time dependent [{sup 3}H]carnitine uptake which was stimulated by intraliposomal ATP and nearly independent of the pH. The K{sub m} for carnitine was 36 {mu}M. [{sup 3}H]carnitine transport was inhibited by carnitine analogues and some Cys and NH{sub 2} reagents. This paper represents the first outcome in over-expressing, in active form, the third member of the OCTN sub-family, mOCTN3, in E. coli.

  15. Over-expression in Escherichia coli, purification and reconstitution in liposomes of the third member of the OCTN sub-family: The mouse carnitine transporter OCTN3

    Scalise, Mariafrancesca; Galluccio, Michele; Pochini, Lorena; Indiveri, Cesare

    2012-01-01

    Highlights: ► mOCTN3 transport protein has been cloned in pET-21a(+) and over-expressed in Escherichia coli. ► The expressed mOCTN3 has been purified to homogeneity by Ni-chelating chromatography. ► The protein solubilised in Triton X-100 has been reconstituted in liposomes. ► Recombinant mOCTN3 catalyses transport of carnitine by a uniport mode. -- Abstract: pET-21a(+)-mOCTN3-6His was constructed and used for over-expression in Escherichia coli Rosetta(DE3)pLysS. After IPTG induction a protein with apparent molecular mass of 53 kDa was collected in the insoluble fraction of the cell lysate and purified by Ni 2+ -chelating chromatography with a yield of 2 mg/l of cell culture. The over-expressed protein was identified with mOCTN3 by anti-His antibody and reconstitution in liposomes. mOCTN3 required peculiar conditions for optimal expression and reconstitution in liposomes. The protein catalyzed a time dependent [ 3 H]carnitine uptake which was stimulated by intraliposomal ATP and nearly independent of the pH. The K m for carnitine was 36 μM. [ 3 H]carnitine transport was inhibited by carnitine analogues and some Cys and NH 2 reagents. This paper represents the first outcome in over-expressing, in active form, the third member of the OCTN sub-family, mOCTN3, in E. coli.

  16. Association with the Plasma Membrane Is Sufficient for Potentiating Catalytic Activity of Regulators of G Protein Signaling (RGS) Proteins of the R7 Subfamily.

    Muntean, Brian S; Martemyanov, Kirill A

    2016-03-25

    Regulators of G protein Signaling (RGS) promote deactivation of heterotrimeric G proteins thus controlling the magnitude and kinetics of responses mediated by G protein-coupled receptors (GPCR). In the nervous system, RGS7 and RGS9-2 play essential role in vision, reward processing, and movement control. Both RGS7 and RGS9-2 belong to the R7 subfamily of RGS proteins that form macromolecular complexes with R7-binding protein (R7BP). R7BP targets RGS proteins to the plasma membrane and augments their GTPase-accelerating protein (GAP) activity, ultimately accelerating deactivation of G protein signaling. However, it remains unclear if R7BP serves exclusively as a membrane anchoring subunit or further modulates RGS proteins to increase their GAP activity. To directly answer this question, we utilized a rapidly reversible chemically induced protein dimerization system that enabled us to control RGS localization independent from R7BP in living cells. To monitor kinetics of Gα deactivation, we coupled this strategy with measuring changes in the GAP activity by bioluminescence resonance energy transfer-based assay in a cellular system containing μ-opioid receptor. This approach was used to correlate changes in RGS localization and activity in the presence or absence of R7BP. Strikingly, we observed that RGS activity is augmented by membrane recruitment, in an orientation independent manner with no additional contributions provided by R7BP. These findings argue that the association of R7 RGS proteins with the membrane environment provides a major direct contribution to modulation of their GAP activity. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. A tandem array of UDP-glycosyltransferases from the UGT73C subfamily glycosylate sapogenins, forming a spectrum of mono- and bisdesmosidic saponins.

    Erthmann, Pernille Østerbye; Agerbirk, Niels; Bak, Søren

    2018-05-01

    This study identifies six UGT73Cs all able to glucosylate sapogenins at positions 3 and/or 28 which demonstrates that B. vulgaris has a much richer arsenal of UGTs involved in saponin biosynthesis than initially anticipated. The wild cruciferous plant Barbarea vulgaris is resistant to some insects due to accumulation of two monodesmosidic triterpenoid saponins, oleanolic acid 3-O-β-cellobioside and hederagenin 3-O-β-cellobioside. Insect resistance depends on the structure of the sapogenin aglycone and the glycosylation pattern. The B. vulgaris saponin profile is complex with at least 49 saponin-like metabolites, derived from eight sapogenins and including up to five monosaccharide units. Two B. vulgaris UDP-glycosyltransferases, UGT73C11 and UGT73C13, O-glucosylate sapogenins at positions 3 and 28, forming mainly 3-O-β-D-glucosides. The aim of this study was to identify UGTs responsible for the diverse saponin oligoglycoside moieties observed in B. vulgaris. Twenty UGT genes from the insect resistant genotype were selected and heterologously expressed in Nicotiana benthamiana and/or Escherichia coli. The extracts were screened for their ability to glycosylate sapogenins (oleanolic acid, hederagenin), the hormone 24-epibrassinolide and sapogenin monoglucosides (hederagenin and oleanolic acid 3-O-β-D-glucosides). Six UGTs from the UGT73C subfamily were able to glucosylate both sapogenins and both monoglucosides at positions 3 and/or 28. Some UGTs formed bisdesmosidic saponins efficiently. At least four UGT73C genes were localized in a tandem array with UGT73C11 and possibly UGT73C13. This organization most likely reflects duplication events followed by sub- and neofunctionalization. Indeed, signs of positive selection on several amino acid sites were identified and modelled to be localized on the UGT protein surface. This tandem array is proposed to initiate higher order bisdesmosidic glycosylation of B. vulgaris saponins, leading to the recently discovered

  18. A REVISION OF THE PLIOCENE NATICIDS OF NORTHERN AND CENTRAL ITALY. II. THE SUBFAMILY NATICINAE: ADDITIONS TO COCHLIS, TANEA AND TECTONATICA

    LUCA PEDRIALI

    2008-03-01

    Full Text Available The present paper is the second in a series devoted to the revision of the Pliocene naticids of Northern and Central Italy. It concludes the section covering the calcareous operculum-bearing Naticinae and expands to 18 the total number of species and subspecies of this subfamily recovered so far from the Pliocene deposits of Italy. Of the six taxa considered in this study, two (epigloafuniculata and fredianii fully match the characters of the genus Cochlis Röding, 1798, one (koeneni is assigned to the genus Tanea Marwick, 1931, the rest (astensis, prietoi and tectula belong to the genus Tectonatica Sacco, 1890. All the six taxa considered in this paper are described and commented in the systematic account. One, Cochlis fredianii, is proposed as new. In the chapter treating the generic assignment of the studied taxa, the range of Tanea, hitherto used to allocate several Indo-Pacific species, is extended to the Mediterranean Basin as well, and the relations between Tectonatica and Cryptonatica Dall, 1892 are discussed. This study further demonstrates that the morphological characters of the teleoconch are of low significance in species recognition. In fact, should the characters be ranked, the operculum comes first and is the primary element, sufficient to distinguish each species. The protoconch and the color pattern are the second and third relevant attributes that can be used diagnostically for several taxa, but not always. The other shell features appear to be useful tools in separating species only occasionally. Some species lack distinctive shell characters and do require operculate specimens in order to be confidently 

  19. Potential role of melastatin-related transient receptor potential cation channel subfamily M gene expression in the pathogenesis of urinary bladder cancer.

    Ceylan, Gülay Güleç; Önalan, Ebru Etem; Kuloğlu, Tuncay; Aydoğ, Gülten; Keleş, İbrahim; Tonyali, Şenol; Ceylan, Cavit

    2016-12-01

    Urinary bladder cancer is one of the most common malignancies of the urinary tract. Ion channels and calcium homeostasis are involved in almost all basic cellular mechanisms. The transient receptor potential cation channel subfamily M (TRPM) takes its name from the melastatin protein, which is classified as potential tumor suppressor. To the best of our knowledge, there have been no previous studies in the literature investigating the role of these ion channels in bladder cancer. The present study aimed to determine whether bladder cancer is associated with mRNA expression levels of TRPM ion channel genes, and whether there is the potential to conduct further studies to establish novel treatment modalities. The present study included a total of 47 subjects, of whom 40 were bladder cancer patients and 7 were controls. Following the histopathological evaluation for bladder carcinoma, the mRNA and protein expression of TRPM were examined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry in tumor and normal tissues, in order to determine whether there is a difference in the expression of these channels in tumor and normal tissues. Immunoreactivity for TRPM2, TRPM4, TRPM7 and TRPM8 was observed in epithelial bladder cells in the two groups. RT-qPCR revealed a significant increase in TRPM7 expression in bladder cancer tissue compared to the controls (healthy bladder tissue), whereas no differences in TRPM2 or TRPM4 expression levels were observed. There were significant reductions in the expression levels of TRPM5 and TRPM8 in bladder cancer tissues. In the present study, the effects of TRP ion channels on the formation of bladder cancer was investigated. This study is instructive for TRPM2, TRPM4, TRPM5, TRPM7 and TRPM8 and their therapeutic role in bladder cancer. The results support the fact that these gens can be novel targets and can also be tested for during the treatment of bladder cancer.

  20. Selective ATP-Binding Cassette Subfamily C Gene Expression and Proinflammatory Mediators Released by BEAS-2B after PM2.5, Budesonide, and Cotreated Exposures

    Jarline Encarnación-Medina

    2017-01-01

    Full Text Available ATP-binding cassette subfamily C (ABCC genes code for phase III metabolism proteins that translocate xenobiotic (e.g., particulate matter 2.5 (PM2.5 and drug metabolites outside the cells. IL-6 secretion is related with the activation of the ABCC transporters. This study assesses ABCC1–4 gene expression changes and proinflammatory cytokine (IL-6, IL-8 release in human bronchial epithelial cells (BEAS-2B exposed to PM2.5 organic extract, budesonide (BUD, used to control inflammation in asthmatic patients, and a cotreatment (Co-T: PM2.5 and BUD. A real-time PCR assay shows that ABCC1 was upregulated in BEAS-2B exposed after 6 and 7 hr to PM2.5 extract or BUD but downregulated after 6 hr of the Co-T. ABCC3 was downregulated after 6 hr of BUD and upregulated after 6 hr of the Co-T exposures. ABCC4 was upregulated after 5 hr of PM2.5 extract, BUD, and the Co-T exposures. The cytokine assay revealed an increase in IL-6 release by BEAS-2B exposed after 5 hr to PM2.5 extract, BUD, and the Co-T. At 7 hr, the Co-T decreases IL-6 release and IL-8 at 6 hr. In conclusion, the cotreatment showed an opposite effect on exposed BEAS-2B as compared with BUD. The results suggest an interference of the BUD therapeutic potential by PM2.5.

  1. Evidence logics with relational evidence

    Baltag, Alexandru; Occhipinti, Andrés

    2017-01-01

    We introduce a family of logics for reasoning about relational evidence: evidence that involves an ordering of states in terms of their relative plausibility. We provide sound and complete axiomatizations for the logics. We also present several evidential actions and prove soundness...

  2. Amphibious shelter-builder Oniscidea species from the New World with description of a new subfamily, a new genus and a new species from Brazilian cave (Isopoda, Synocheta, Styloniscidae.

    Leila A Souza

    Full Text Available The new subfamily Iuiuniscinae, Styloniscidae, is erected for the new genus Iuiuniscus and the new species I. iuiuensis, which is described from cave of the State of Bahia, Northeastern Brazil. A special ecological character is shown here for the first time for a New World Oniscidea: the construction of mud shelters. An introduction addressing the systematics of Synocheta with emphasis on Styloniscidae Vandel, 1952 is provided, as well as general comments about the dependence of water in some Oniscidea and ecological traits of amphibious Synocheta. The problems referring to nomenclature, taxonomy and the interrelationships in Styloniscidae are discussed.

  3. Amphibious shelter-builder Oniscidea species from the New World with description of a new subfamily, a new genus and a new species from Brazilian cave (Isopoda, Synocheta, Styloniscidae).

    Souza, Leila A; Ferreira, Rodrigo L; Senna, André R

    2015-01-01

    The new subfamily Iuiuniscinae, Styloniscidae, is erected for the new genus Iuiuniscus and the new species I. iuiuensis, which is described from cave of the State of Bahia, Northeastern Brazil. A special ecological character is shown here for the first time for a New World Oniscidea: the construction of mud shelters. An introduction addressing the systematics of Synocheta with emphasis on Styloniscidae Vandel, 1952 is provided, as well as general comments about the dependence of water in some Oniscidea and ecological traits of amphibious Synocheta. The problems referring to nomenclature, taxonomy and the interrelationships in Styloniscidae are discussed.

  4. New potent antimicrobial peptides from the venom of Polistinae wasps and their analogs

    Čeřovský, Václav; Slaninová, Jiřina; Fučík, Vladimír; Hulačová, Hana; Borovičková, Lenka; Ježek, Rudolf; Bednárová, Lucie

    2008-01-01

    Roč. 29, č. 6 (2008), s. 992-1003 ISSN 0196-9781 Institutional research plan: CEZ:AV0Z40550506 Keywords : antimicrobial peptides * wasp venom * circular dichroism * hemolytic activity Subject RIV: CC - Organic Chemistry Impact factor: 2.565, year: 2008

  5. Actinomycetes with antimicrobial activity isolated from paper wasp (Hymenoptera: Vespidae: Polistinae) nests.

    Madden, Anne A; Grassetti, Andrew; Soriano, Jonathan-Andrew N; Starks, Philip T

    2013-08-01

    Actinomycetes-a group of antimicrobial producing bacteria-have been successfully cultured and characterized from the nest material of diverse arthropods. Some are symbionts that produce antimicrobial chemicals found to protect nest brood and resources from pathogenic microbes. Others have no known fitness relationship with their associated insects, but have been found to produce antimicrobials in vitro. Consequently, insect nest material is being investigated as a new source of novel antimicrobial producing actinomycetes, which could be harnessed for therapeutic potential. To extend studies of actinomycete-insect associations beyond soil-substrate dwelling insects and wood boring excavators, we conducted a preliminary assessment of the actinomycetes within the nests of the paper wasp, Polistes dominulus (Christ). We found that actinomycetes were readily cultured from nest material across multiple invasive P. dominulus populations-including members of the genera Streptomyces, Micromonospora, and Actinoplanes. Thirty of these isolates were assayed for antimicrobial activity against the challenge bacteria Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, Serratia marcescens, and Bacillus subtilis. Sixty percent of isolates inhibited the growth of at least one challenge strain. This study provides the first assessment of bacteria associated with nests of P. dominulus, and the first record of antimicrobial producing actinomycetes isolated from social wasps. We provide a new system to explore nest associated actinomycetes from a ubiquitous and cosmopolitan group of insects.

  6. Social wasps (Polistinae from Pampa Biome: South Brazil, Northeastern Argentina and Uruguay

    Alexandre Somavilla

    2017-08-01

    Full Text Available Abstract. This study aimed to determine social wasps’ species from Pampa Biome. Were examined samples of social wasps from south-central of Rio Grande do Sul state (Brazil, parts of Buenos Aires, Entre Rios, Corrientes, Cordoba, Santa Fé and La Pampa provinces (Argentina and in Uruguay maintained in the Coleção Entomológica de Santa Cruz do Sul (Santa Cruz do Sul-Brazil, American Museum of Natural History (USA, Natural History Museum (London-United Kingdom and Muséum National d’Histoire Naturelle (Paris-France. Thirty species were recorded: Agelaia (01, Brachygastra (01, Mischocyttarus (04, Polistes (15, Polybia (08 and Protonectarina (01. Vespas sociais do Bioma Pampa: sul do Brasil, nordeste da Argentina e Uruguai. Resumo. Este estudo objetivou determinar as espécies de vespas sociais provenientes do Bioma Pampa. Foram examinadas vespas sociais provenientes de coletas da região centro-sul do Rio Grande do Sul (Brasil, parte das províncias de Buenos Aires, Entre Rios, Corrientes, Cordoba, Santa Fé e La Pampa (Argentina e Uruguai depositadas na Coleção Entomológica de Santa Cruz do Sul (Santa Cruz do Sul-Brasil, American Museum of Natural History (Nova Iorque-USA, Natural History Museum (Londres-Reino Unido e Muséum National d’Histoire Naturelle (Paris-França. Trinta espécies foram registradas: Agelaia (01, Brachygastra (01, Mischocyttarus (04, Polistes (15, Polybia (08 e Protonectarina (01.

  7. Digital evidence

    Lukić Tatjana

    2012-01-01

    Full Text Available Although computer makes human activities faster and easier, innovating and creating new forms of work and other kinds of activities, it also influenced the criminal activity. The development of information technology directly affects the development of computer forensics without which, it can not even imagine the discovering and proving the computer offences and apprehending the perpetrator. Information technology and computer forensic allows us to detect and prove the crimes committed by computer and capture the perpetrators. Computer forensics is a type of forensics which can be defined as a process of collecting, preserving, analyzing and presenting digital evidence in court proceedings. Bearing in mind, that combat against crime, in which computers appear as an asset or object of the offense, requires knowledge of digital evidence as well as specific rules and procedures, the author in this article specifically addresses the issues of digital evidence, forensic (computer investigation, specific rules and procedures for detecting, fixing and collecting digital evidence and use of this type of evidence in criminal proceedings. The author also delas with international standards regarding digital evidence and cyber-space investigation.

  8. A role for calcium in the regulation of ATP-binding cassette, sub-family C, member 3 (ABCC3) gene expression in a model of epidermal growth factor-mediated breast cancer epithelial-mesenchymal transition.

    Stewart, Teneale A; Azimi, Iman; Thompson, Erik W; Roberts-Thomson, Sarah J; Monteith, Gregory R

    2015-03-13

    Epithelial-mesenchymal transition (EMT), a process implicated in cancer metastasis, is associated with the transcriptional regulation of members of the ATP-binding cassette superfamily of efflux pumps, and drug resistance in breast cancer cells. Epidermal growth factor (EGF)-induced EMT in MDA-MB-468 breast cancer cells is calcium signal dependent. In this study induction of EMT was shown to result in the transcriptional up-regulation of ATP-binding cassette, subfamily C, member 3 (ABCC3), a member of the ABC transporter superfamily, which has a recognized role in multidrug resistance. Buffering of cytosolic free calcium inhibited EGF-mediated ABCC3 increases, indicating a calcium-dependent mode of regulation. Silencing of TRPM7 (an ion channel involved in EMT associated vimentin induction) did not inhibit ABCC3 up-regulation. Silencing of the store operated calcium entry (SOCE) pathway components ORAI1 and STIM1 also did not alter ABCC3 induction by EGF. However, the calcium permeable ion channel transient receptor potential cation channel, subfamily C, member 1 (TRPC1) appears to contribute to the regulation of both basal and EGF-induced ABCC3 mRNA. Improved understanding of the relationship between calcium signaling, EMT and the regulation of genes important in therapeutic resistance may help identify novel therapeutic targets for breast cancer. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Systematics and phylogeny of the Neotropical treehopper subfamily Nicomiinae (Hemiptera, Membracidae Sistemática e filogenia das cigarrinhas neotropicais da subfamília Nicomiinae (Hemiptera, Membracidae

    Jesse L. Albertson

    2005-03-01

    Full Text Available Morphological characters of adults of the treehopper subfamily Nicomiinae Haupt, 1929 (Hemiptera, Membracidae including seven genera (Eudonica gen. nov.; Euwalkeria Goding, 1926; Holdgatiella Evans, 1962; Nicomia Stål, 1858; Nodonica Dietrich, McKamey& Deitz, 2001; Stalomia gen. nov.; and Tolania Stål, 1858 and 22 species (16 new are described and illustrated. Keys are provided for genera and for species of Euwalkeria, Holdgatiella, and Nicomia. Nomenclatural changes, based on study of the primary type material of 15 species, include three new combinations, one new synonymy, and reinstatement of one junior synonym. Eudonica has one species, Eudonica nanella sp. nov.; Euwalkeria has five species, including four new species: E. colorata sp. nov., E. distincta sp. nov., E. perdita sp. nov., E. rubrica sp. nov.; Holdgatiella has two species, one of which is described as new: Holdgatiella chiloensis sp. nov.; Nicomia has twelve species, nine of which are described as new: N. buccina sp. nov., N. harenosa sp. nov., N. inscripta sp. nov., N. jucunda sp. nov., N. monticola sp. nov., N. nigrifasciata sp. nov., N. notidana sp. nov., N. pulchella sp. nov., N. serrata sp. nov.; Nodonica has one species, Nodonica bispinigera Dietrich, McKamey & Deitz; and Stalomia has one species, Stalomia veruta sp. nov. Tolania contains eleven previously described species and nearly 60 new species, which will be treated in a later publication. Three new combinations are proposed: one species described in Nicomia is placed in the tribe Abelini (Centrotinae as Abelus retrospinosus (Lethierry comb. nov.; one species previously placed in Nicomia is transferred to the genus Tolania as T. obliqua (Walker, 1858, comb. nov.; one species described in Holdgatiella is placed in the genus Tolania as T. stria (Cryan & Deitz, 2002, comb. nov. One new synonymy is proposed: Hoplophera [sic] cicadoides Walker, 1862, syn. nov., a junior synonym of Nicomia interrupta Stål, 1858. Nicomia

  10. Key to the subfamilies, tribes and genera of adult Dytiscidae of Argentina (Coleoptera: Adephaga Clave para los adultos de las subfamilias, tribus y géneros de Dytiscidae de la Argentina (Coleoptera: Adephaga

    María L. Libonatti

    2011-12-01

    Full Text Available Dytiscids constitute the world's most speciose family of water beetles, whose identifi cation in Argentina is problematic with current keys. In this work, a key (both in English and Spanish to the eight subfamilies, 16 tribes and 31 genera of adult Dytiscidae of Argentina is presented. The key was constructed using stable qualitative characters of the external morphology and chaetotaxy, easily visualizable and interpretable. Characters such as size and shape of the body, color pattern and geographic distribution were also used. Illustrations of a great number of morphological structures as well as SEM micrographs were included to aid in the interpretation of the text. One subfamily (Hydrodytinae and fi ve genera (Agaporomorphus Zimmermann, Bidessodes Régimbart, Hydrodytes Miller, Queda Sharp and an unpublished genus of the subfamily Laccophilinae are cited for the fi rst time for Argentina.Los ditíscidos constituyen la familia más numerosa de escarabajos acuáticos a nivel mundial, cuya identifi cación en la Argentina resulta problemática con las claves actuales. En este trabajo, se presenta una clave (en inglés y español para los adultos de las ocho subfamilias, 16 tribus y 31 géneros de Dytiscidae de la Argentina. La clave fue construida priorizando la inclusión de caracteres cualitativos estables de la morfología externa y quetotaxia, fácilmente visibles e interpretables. También, se utilizaron caracteres como el tamaño y la forma del cuerpo, el patrón de coloración y la distribución geográfi ca. Se incluyeron ilustraciones de un gran número de estructuras morfológicas y fotografías tomadas con el microscopio electrónico, para ayudar a la interpretación del texto. Se citan, por primera vez para la Argentina, una subfamilia (Hydrodytinae y cinco géneros (Agaporomorphus Zimmermann, Bidessodes Régimbart, Hydrodytes Miller, Queda Sharp y un género inédito de la subfamilia Laccophilinae.

  11. A new genus and species of entocytherid ostracod (Ostracoda: Entocytheridae) from the John Day River Basin of Oregon, U.S.A., with a key to genera of the subfamily Entocytherinae.

    Weaver, Patricia G; Williams, Bronwyn W

    2017-06-07

    Targeted sampling efforts by the authors for the signal crayfish, Pacifastacus leniusculus, from its native range in the John Day River Basin, Oregon, U.S.A. yielded entocytherid ostracods with a male copulatory complex so clearly different from other entocytherines that a new genus, Aurumcythere gen. nov. is proposed to receive them. This newly proposed, apparently nonsclerotized, genus with hook and spur-like prominences of the posteroventral end of the peniferum is the first new genus of the subfamily Entocytherinae named since Hobbs & Peters described Aphelocythere (= Waltoncythere) in 1977. Aurumcythere gen. nov. represents only the second genus of entocytherid known from the Pacific Northwest. Lack of sclerotization in Aurumcythere gen. nov. provides new insight into poorly understood mating behaviors of entocytherid ostracods.

  12. Population-Specific Resequencing Associates the ATP-Binding Cassette Subfamily C Member 4 Gene With Gout in New Zealand Māori and Pacific Men.

    Tanner, Callum; Boocock, James; Stahl, Eli A; Dobbyn, Amanda; Mandal, Asim K; Cadzow, Murray; Phipps-Green, Amanda J; Topless, Ruth K; Hindmarsh, Jennie Harré; Stamp, Lisa K; Dalbeth, Nicola; Choi, Hyon K; Mount, David B; Merriman, Tony R

    2017-07-01

    There is no evidence for a genetic association between organic anion transporters 1-3 (SLC22A6, SLC22A7, and SLC22A8) and multidrug resistance protein 4 (MRP4; encoded by ABCC4) with the levels of serum urate or gout. The Māori and Pacific (Polynesian) population of New Zealand has the highest prevalence of gout worldwide. The aim of this study was to determine whether any Polynesian population-specific genetic variants in SLC22A6-8 and ABCC4 are associated with gout. All participants had ≥3 self-reported Māori and/or Pacific grandparents. Among the total sample set of 1,808 participants, 191 hyperuricemic and 202 normouricemic individuals were resequenced over the 4 genes, and the remaining 1,415 individuals were used for replication. Regression analyses were performed, adjusting for age, sex, and Polynesian ancestry. To study the functional effect of nonsynonymous variants of ABCC4, transport assays were performed in Xenopus laevis oocytes. A total of 39 common variants were detected, with an ABCC4 variant (rs4148500) significantly associated with hyperuricemia and gout. This variant was monomorphic for the urate-lowering allele in Europeans. There was evidence for an association of rs4148500 with gout in the resequenced samples (odds ratio [OR] 1.62 [P = 0.012]) that was replicated (OR 1.25 [P = 0.033]) and restricted to men (OR 1.43 [P = 0.001] versus OR 0.98 [P = 0.89] in women). The gout risk allele was associated with fractional excretion of uric acid in male individuals (β = -0.570 [P = 0.01]). A rare population-specific allele (P1036L) with predicted strong functional consequence reduced the uric acid transport activity of ABCC4 by 30%. An association between ABCC4 and gout and fractional excretion of uric acid is consistent with the established role of MRP4 as a unidirectional renal uric acid efflux pump. © 2017, American College of Rheumatology.

  13. Elephant Endotheliotropic Herpesviruses EEHV1A, EEHV1B, and EEHV2 from Cases of Hemorrhagic Disease Are Highly Diverged from Other Mammalian Herpesviruses and May Form a New Subfamily

    Richman, Laura K.; Zong, Jian-Chao; Latimer, Erin M.; Lock, Justin; Fleischer, Robert C.; Heaggans, Sarah Y.

    2014-01-01

    ABSTRACT A family of novel endotheliotropic herpesviruses (EEHVs) assigned to the genus Proboscivirus have been identified as the cause of fatal hemorrhagic disease in 70 young Asian elephants worldwide. Although EEHV cannot be grown in cell culture, we have determined a total of 378 kb of viral genomic DNA sequence directly from clinical tissue samples from six lethal cases and two survivors. Overall, the data obtained encompass 57 genes, including orthologues of 32 core genes common to all herpesviruses, 14 genes found in some other herpesviruses, plus 10 novel genes, including a single large putative transcriptional regulatory protein (ORF-L). On the basis of differences in gene content and organization plus phylogenetic analyses of conserved core proteins that have just 20% to 50% or less identity to orthologues in other herpesviruses, we propose that EEHV1A, EEHV1B, and EEHV2 could be considered a new Deltaherpesvirinae subfamily of mammalian herpesviruses that evolved as an intermediate branch between the Betaherpesvirinae and Gammaherpesvirinae. Unlike cytomegaloviruses, EEHV genomes encode ribonucleotide kinase B subunit (RRB), thymidine kinase (TK), and UL9-like origin binding protein (OBP) proteins and have an alphaherpesvirus-like dyad symmetry Ori-Lyt domain. They also differ from all known betaherpesviruses by having a 40-kb large-scale inversion of core gene blocks I, II, and III. EEHV1 and EEHV2 DNA differ uniformly by more than 25%, but EEHV1 clusters into two major subgroups designated EEHV1A and EEHV1B with ancient partially chimeric features. Whereas large segments are nearly identical, three nonadjacent loci totaling 15 kb diverge by between 21 and 37%. One strain of EEHV1B analyzed is interpreted to be a modern partial recombinant with EEHV1A. IMPORTANCE Asian elephants are an endangered species whose survival is under extreme pressure in wild range countries and whose captive breeding populations in zoos are not self-sustaining. In 1999, a

  14. AOX1-Subfamily Gene Members in Olea europaea cv. “Galega Vulgar”—Gene Characterization and Expression of Transcripts during IBA-Induced in Vitro Adventitious Rooting

    Lousa, Diana; M. Soares, Cláudio; Santos Macedo, Elisete; Arnholdt-Schmitt, Birgit

    2018-01-01

    Propagation of some Olea europaea L. cultivars is strongly limited due to recalcitrant behavior in adventitious root formation by semi-hardwood cuttings. One example is the cultivar ”Galega vulgar”. The formation of adventitious roots is considered a morphological response to stress. Alternative oxidase (AOX) is the terminal oxidase of the alternative pathway of the plant mitochondrial electron transport chain. This enzyme is well known to be induced in response to several biotic and abiotic stress situations. This work aimed to characterize the alternative oxidase 1 (AOX1)-subfamily in olive and to analyze the expression of transcripts during the indole-3-butyric acid (IBA)-induced in vitro adventitious rooting (AR) process. OeAOX1a (acc. no. MF410318) and OeAOX1d (acc. no. MF410319) were identified, as well as different transcript variants for both genes which resulted from alternative polyadenylation events. A correlation between transcript accumulation of both OeAOX1a and OeAOX1d transcripts and the three distinct phases (induction, initiation, and expression) of the AR process in olive was observed. Olive AOX1 genes seem to be associated with the induction and development of adventitious roots in IBA-treated explants. A better understanding of the molecular mechanisms underlying the stimulus needed for the induction of adventitious roots may help to develop more targeted and effective rooting induction protocols in order to improve the rooting ability of difficult-to-root cultivars. PMID:29462998

  15. ATP-binding cassette subfamily A, member 4 intronic variants c.4773+3A>G and c.5461-10T>C cause Stargardt disease due to defective splicing.

    Jonsson, Frida; Westin, Ida Maria; Österman, Lennart; Sandgren, Ola; Burstedt, Marie; Holmberg, Monica; Golovleva, Irina

    2018-02-20

    Inherited retinal dystrophies (IRDs) represent a group of progressive conditions affecting the retina. There is a great genetic heterogeneity causing IRDs, and to date, more than 260 genes are associated with IRDs. Stargardt disease, type 1 (STGD1) or macular degeneration with flecks, STGD1 represents a disease with early onset, central visual impairment, frequent appearance of yellowish flecks and mutations in the ATP-binding cassette subfamily A, member 4 (ABCA4) gene. A large number of intronic sequence variants in ABCA4 have been considered pathogenic although their functional effect was seldom demonstrated. In this study, we aimed to reveal how intronic variants present in patients with Stargardt from the same Swedish family affect splicing. The splicing of the ABCA4 gene was studied in human embryonic kidney cells, HEK293T, and in human retinal pigment epithelium cells, ARPE-19, using a minigene system containing variants c.4773+3A>G and c.5461-10T>C. We showed that both ABCA4 variants, c.4773+3A>G and c.5461-10T>C, cause aberrant splicing of the ABCA4 minigene resulting in exon skipping. We also demonstrated that splicing of ABCA4 has different outcomes depending on transfected cell type. Two intronic variants c.4773+3A>G and c.5461-10T>C, both predicted to affect splicing, are indeed disease-causing mutations due to skipping of exons 33, 34, 39 and 40 of ABCA4 gene. The experimental proof that ABCA4 mutations in STGD patients affect protein function is crucial for their inclusion to future clinical trials; therefore, functional testing of all ABCA4 intronic variants associated with Stargardt disease by minigene technology is desirable. © 2018 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

  16. Survey of familial glaucoma shows a high incidence of cytochrome P450, family 1, subfamily B, polypeptide 1 (CYP1B1) mutations in non-consanguineous congenital forms in a Spanish population

    Millá, Elena; Mañé, Begoña; Duch, Susana; Hernan, Imma; Borràs, Emma; Planas, Ester; Dias, Miguel de Sousa; Carballo, Miguel

    2013-01-01

    Purpose To identify myocilin (MYOC) and cytochrome P450, family 1, subfamily B, polypeptide 1 (CYP1B1) mutations in a Spanish population with different clinical forms of familial glaucoma or ocular hypertension (OHT). Methods Index patients from 226 families participated in this study. Patients were diagnosed with familial glaucoma or OHT by complete ophthalmologic examination. Screening for MYOC mutations was performed in 207 index patients: 96 with adult-onset primary open-angle glaucoma (POAG), 21 with primary congenital glaucoma (PCG), 18 with juvenile-onset open-angle glaucoma (JOAG), five with Axenfeld-Rieger syndrome (ARS), and 67 with other types of glaucoma. One hundred two of the families (including all those in whom a MYOC mutation was detected) were also screened for CYP1B1 mutations: 45 POAG, 25 PCG, 21 JOAG, four ARS, and seven others. Results We examined 292 individuals (patients and relatives) with a positive family history of glaucoma or OHT. We identified two novel MYOC variants, p.Lys39Arg and p.Glu218Lys, in two families with POAG, and six previously reported MYOC mutations in seven families with POAG (four), JOAG (one), PCG (one), and normotensive glaucoma (one). CYP1B1 mutations were found in 16 index patients with PCG (nine), POAG (three), JOAG (two), and ARS (two). Conclusions The high percentage (9/25=36%) of mutations in CYP1B1 found in non-consanguineous patients with congenital glaucoma mandates genetic testing. However, the percentage of mutations (9/207=4.4%) in MYOC associated with glaucoma is relatively low in our population. The variable phenotype expression of glaucoma, even in families, cannot be explained with a digenic mechanism between MYOC and CYP1B1. PMID:23922489

  17. Comprehensive behavioral analysis of mice deficient in Rapgef2 and Rapgef6, a subfamily of guanine nucleotide exchange factors for Rap small GTPases possessing the Ras/Rap-associating domain.

    Maeta, Kazuhiro; Hattori, Satoko; Ikutomo, Junji; Edamatsu, Hironori; Bilasy, Shymaa E; Miyakawa, Tsuyoshi; Kataoka, Tohru

    2018-05-10

    Rapgef2 and Rapgef6 define a subfamily of guanine nucleotide exchange factors for Rap small GTPases, characterized by the possession of the Ras/Rap-associating domain. Previous genomic analyses suggested their possible involvement in the etiology of schizophrenia. We recently demonstrated the development of an ectopic cortical mass (ECM), which resembles the human subcortical band heterotopia, in the dorsal telencephalon-specific Rapgef2 conditional knockout (Rapgef2-cKO) brains. Additional knockout of Rapgef6 in Rapgef2-cKO mice resulted in gross enlargement of the ECM whereas knockout of Rapgef6 alone (Rapgef6-KO) had no discernible effect on the brain morphology. Here, we performed a battery of behavioral tests to examine the effects of Rapgef2 or Rapgef6 deficiency on higher brain functions. Rapgef2-cKO mice exhibited hyperlocomotion phenotypes. They showed decreased anxiety-like behavior in the elevated plus maze and the open-field tests as well as increased depression-like behavior in the Porsolt forced swim and tail suspension tests. They also exhibited increased sociability especially in novel environments. They showed defects in cognitive function as evidenced by reduced learning ability in the Barnes circular maze test and by impaired working memory in the T maze tests. In contrast, although Rapgef6 and Rapgef2 share similarities in biochemical roles, Rapgef6-KO mice exhibited mild behavioral abnormalities detected with a number of behavioral tests, such as hyperlocomotion phenotype in the open-field test and the social interaction test with a novel environment and working-memory defects in the T-maze test. In conclusion, although there were differences in their brain morphology and the magnitude of the behavioral abnormalities, Rapgef2-cKO mice and Rapgef6-KO mice exhibited hyperlocomotion phenotype and working-memory defect, both of which could be recognized as schizophrenia-like behavior.

  18. Upregulated Expression of Transient Receptor Potential Cation Channel Subfamily V Receptors in Mucosae of Patients with Oral Squamous Cell Carcinoma and Patients with a History of Alcohol Consumption or Smoking.

    Sakakibara, Akiko; Sakakibara, Shunsuke; Kusumoto, Junya; Takeda, Daisuke; Hasegawa, Takumi; Akashi, Masaya; Minamikawa, Tsutomu; Hashikawa, Kazunobu; Terashi, Hiroto; Komori, Takahide

    2017-01-01

    Transient receptor potential cation channel (subfamily V, members 1-4) (TRPV1-4) are expressed in skin and neurons and activated by external stimuli in normal mucosae of all oral cavity sites. The oral cavity is exposed to various stimuli, including temperature, mechanical stimuli, chemical substances, and changes in pH, and, notably, the risk factors for oncogenic transformation in oral squamous epithelium are the same as the external stimuli received by TRPV1-4 receptors. Hence, we examined the relationship between oral squamous cell carcinoma (SCC) and TRPV1-4 expression. Oral SCC patients (n = 37) who underwent surgical resection were included in this study. We investigated the expression of TRPV1-4 by immunohistochemical staining and quantification of TRPV1-4 mRNA in human oral mucosa. In addition, we compared the TRPV1-4 levels in mucosa from patients with SCC to those in normal oral mucosa. The receptors were expressed in oral mucosa at all sites (tongue, buccal mucosa, gingiva, and oral floor) and the expression was stronger in epithelia from patients with SCC than in normal epithelia. Furthermore, alcohol consumption and tobacco use were strongly associated with the occurrence of oral cancer and were found to have a remarkable influence on TRPV1-4 receptor expression in normal oral mucosa. In particular, patients with a history of alcohol consumption demonstrated significantly higher expression levels. Various external stimuli may influence the behavior of cancer cells. Overexpression of TRPV1-4 is likely to be a factor in enhanced sensitivity to external stimuli. These findings could contribute to the establishment of novel strategies for cancer therapy or prevention.

  19. Who are the Philippine negritos? Evidence from language.

    Reid, Lawrence A

    2013-01-01

    This article addresses the linguistic evidence from which details about Philippine "negritos" can be inferred. This evidence comes from the naming practices of both negrito and non-negrito peoples, from which it can be inferred that many negrito groups have maintained a unique identity distinct from other groups since the dispersal of Malayo-Polynesian languages. Other names, such as Dupaningan and Dumagat, reference locations, from which it is assumed the negritos left after contact with Malayo-Polynesian people. Evidence also comes from the relative positions of negrito groups vis-à-vis other groups within the subfamily with which their current language can be grouped. Many of these languages can be shown to be first order branches, suggesting early separation from the people whose languages they first acquired. The geospatial distribution of the northern languages of the Philippines closely matches the proposed dispersal routes of early Malayo-Polynesian peoples into the Cagayan River Valley and up the Chico and Magat tributaries from which negrito groups were displaced. One lexical item that is discussed is the word for the traditionally widespread practice of head-hunting, the term for which is reconstructible to Proto-Austronesian with reflexes throughout the Philippines and countries to the south. The practice was probably associated with agriculture and not only may have contributed to the early rapid spread south of Malayo-Polynesian languages through the Philippines and ultimately into the Pacific but also was later a major factor in the long periods of isolation of negrito peoples, during which the languages they had first acquired became very different from that of their former neighbors. Copyright © 2013 Wayne State University Press, Detroit, Michigan 48201-1309.

  20. Cytochrome P450 CYP3A in marsupials: cloning and identification of the first CYP3A subfamily member, isoform 3A70 from Eastern gray kangaroo (Macropus giganteus).

    El-Merhibi, Adaweyah; Ngo, Suong N T; Marchant, Ceilidh L; Height, Tamara A; Stupans, Ieva; McKinnon, Ross A

    2012-09-15

    Australian marsupials are unique fauna that have evolved and adapted to unique environments and thus it is likely that their detoxification systems differ considerably from those of well-studied eutherian mammals. Knowledge of these processes in marsupials is therefore vital to understanding the consequences of exposure to xenobiotics. Cytochromes P450 (CYPs) are critically important in the oxidative metabolism of a diverse array of both xenobiotics and endogenous substrates. In this study we have cloned and characterized CYP3A70, the first identified member of the CYP3A gene subfamily from Eastern gray kangaroo (Macropus giganteus). A 1665 base pair kangaroo hepatic CYP3A complete cDNA, designated CYP3A70, was cloned by reverse transcription-polymerase chain reaction approaches, which encodes a protein of 506 amino acids. The CYP3A70 cDNA shares approximately 71% nucleotide and 65% amino acid sequence homology to human CYP3A4 and displays high sequence similarity to other published mammalian CYP3As from human, monkey, cow, pig, dog, rat, rabbit, mouse, hamster, and guinea pig. Transfection of the CYP3A70 cDNAs into 293T cells resulted in stable cell lines expressing a CYP3A immuno-reactive protein that was recognized by a goat anti-human CYP3A4 polyclonal antibody. The anti-human CYP3A4 antibody also detected immunoreactive proteins in liver microsomes from all test marsupials, including the kangaroo, koala, wallaby, and wombat, with multiple CYP3A immunoreactive bands observed in kangaroo and wallaby tissues. Relatively, very low CYP catalytic activity was detected for the kangaroo CYP3A70 cDNA-expressed proteins (19.6 relative luminescent units/μg protein), which may be due to low protein expression levels. Collectively, this study provides primary molecular data regarding the Eastern kangaroo hepatic CYP3A70 gene and enables further functional analyses of CYP3A enzymes in marsupials. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Evidence and evidence gaps in tinnitus therapy

    Hesse, Gerhard

    2016-01-01

    A nearly endless number of procedures has been tried and in particular sold for the treatment of tinnitus, unfortunately they have not been evaluated appropriately in an evidence-based way. A causal therapy, omitting the tinnitus still does not exist, actually it cannot exist because of the various mechanisms of its origin. However or perhaps because of that, medical interventions appear and reappear like fashion trends that can never be proven by stable and reliable treatment success. This contribution will discuss and acknowledge all current therapeutic procedures and the existing or non-existing evidence will be assessed. Beside external evidence, the term of evidence also encompasses the internal evidence, i.e. the experience of the treating physician and the patient’s needs shall be included. While there is no evidence for nearly all direct procedures that intend modulating or stimulating either the cochlea or specific cervical regions such as the auditory cortex, there are therapeutic procedures that are acknowledged in clinical practice and have achieved at least a certain degree of evidence and generate measurable effect sizes. Those are in particular habituation therapy and psychotherapeutic measures, especially if they are combined with concrete measures for improved audio perception (hearing aids, CI, hearing therapies). PMID:28025604

  2. Fossil evidence for open, Proteaceae-dominated heathlands and fire in the Late Cretaceous of Australia.

    Carpenter, Raymond J; Macphail, Michael K; Jordan, Gregory J; Hill, Robert S

    2015-12-01

    The origin of biomes is of great interest globally. Molecular phylogenetic and pollen evidence suggest that several plant lineages that now characterize open, burnt habitats of the sclerophyll biome, became established during the Late Cretaceous of Australia. However, whether this biome itself dates to that time is problematic, fundamentally because of the near-absence of relevant, appropriately aged, terrestrial plant macro- or mesofossils. We recovered, identified, and interpreted the ecological significance of fossil pollen, foliar and other remains from a section of core drilled in central Australia, which we dated as Late Campanian-Maastrichtian. The sediments contain plant fossils that indicate nutrient-limited, open, sclerophyllous vegetation and abundant charcoal as evidence of fire. Most interestingly, >30 pollen taxa and at least 12 foliage taxa are attributable to the important Gondwanan family Proteaceae, including several minute, amphistomatic, and sclerophyllous foliage forms consistent with subfamily Proteoideae. Microfossils, including an abundance of Sphagnales and other wetland taxa, provided strong evidence of a fenland setting. The local vegetation also included diverse Ericaceae and Liliales, as well as a range of ferns and gymnosperms. The fossils provide strong evidence in support of hypotheses of great antiquity for fire and open vegetation in Australia, point to extraordinary persistence of Proteaceae that are now emblematic of the Mediterranean-type climate southwestern Australian biodiversity hotspot and raise the profile of open habitats as centers of ancient lineages. © 2015 Botanical Society of America.

  3. Taxonomia da subfamília Corinninae (Araneae, Corinnidae nas regiões neotropical e neártica Taxonomy of the subfamily Corinninae (Araneae, Corinnidae in neotropical and neartic regions

    Alexandre Bragio Bonaldo

    2000-11-01

    Full Text Available The subfamily Corinninae is characterized and diagnosed. Two synapomorphies are hypothesized for the subfamily, both regarding the male palpal reservoir, which is primarily coiled and presents a sclerotized distal sector. Seventeen genera are recognized, six of which are new: Abapeba (type species Corinna lacertosa Simon, Erendira (type species Corinna pallidoguttata Simon, Septentrinna (type species Corinna bicalcarata Simon, Simonestus (type species Diestus validus Simon, Tapixaua (type species T. callida sp. nov. and Tupirinna (type species T. rosae sp. nov.. The genera Creugas Thorell, Falconina Brignoli and Paradiestus Mello-Leitão are revalidated. Diestus Simon and Lausus Simon are newly synonymized with Corinna C. L. Koch. Chemmis Simon is included in the synonymy of Megalostrata Karsch. Hypsinotus L. Koch is removed from the synonymy of Corinna and included in the synonymy of Creugas. Thirteen new species are described: Septentrinna yucatan and S. potosi from Mexico; Tupirinna rosae from Venezuela and Brazil; Tapixaua callida from Brazil and Peru; Abapeba hoeferi, A. rioclaro, A. taruma, Corinna ducke, C. colombo, C. mourai, C. recurva and Parachemmis manauara from Brazil; Creugas lisei from Brazil, Argentina and Uruguay. Twenty seven species are redescribed. Fifty eight new combinations are presented: from Chemmis, Septentrinna steckleri (Gertsch; from Corinna, Abapeba abalosi (Mello-Leitão, A. cleonei (Petrunkevitch, A. echinus (Simon, A. grassima (Chickering, A. guanicae (Petrunkevitch, A. lacertosa (Simon, A. luctuosa (F. O. Pickard-Cambridge, A. lugubris (Schenkel, A. pennata (Caporiacco, A. kochi (Petrunkevitch, A. saga (F. O. Pickard-Cambridge, A. wheeleri (Petrunkevitch, Creugas annamae (Gertsch & Davis, C. apophysarius (Caporiacco, C. bajulus (Gertsch, C. bellator (L. Koch, C. bicuspis (F.O. Pickard-Cambridge, C. epicureanus (Chamberlin, C. falculus (F. O. Pickard-Cambridge, C. mucronatus (F. O. Pickard-Cambridge, C. navus (F

  4. Evidence and evidence gaps - an introduction.

    Dreier, Gabriele; Löhler, Jan

    2016-01-01

    Background: Medical treatment requires the implementation of existing evidence in the decision making process in order to be able to find the best possible diagnostic, therapeutic or prognostic measure for the individual patient based on the physician's own expertise. Clinical trials form the evidence base and ideally, their results are assembled, analyzed, summarized, and made available in systematic review articles. Beside planning, conducting, and evaluating clinical trials in conformity with GCP (good clinical practice), it is essential that all results of conducted studies are publicly available in order to avoid publication bias. This includes also the public registration of planned and cancelled trials. History: During the last 25 years, evidence-based medicine became increasingly important in medical care and research. It is closely associated with the names of Archibald Cochrane and David Sackett. About 15 years ago, the Deutsche Cochrane Zentrum (Cochrane Germany) and the Deutsche Netzwerk Evidenzbasierte Medizin e.V. (German Network for Evidence-based Medicine, DNEbM) were founded in Germany. In the International Cochrane Collaboration, clinicians and methodologists come together on an interdisciplinary level to further develop methods of evidence-based medicine and to discuss the topics of evidence generation and processing as well as knowledge transfer. Problem: Evidence is particularly important for physicians in the process of decision making, however, at the same time it is the base of a scientific proof of benefit for the patient and finally for the payers in health care. The closure of evidence gaps requires enormously high staff and financial resources, significant organizational efforts, and it is only successful when clinical and methodical expertise as well as specific knowledge in the field of clinical research are included. On the other hand, the knowledge has to be transferred into practice. For this purpose, practice guidelines, meetings

  5. [Evidence and Evidence Gaps - an Introduction].

    Dreier, G; Löhler, J

    2016-04-01

    Treating patients requires the inclusion of existing evidence in any health care decision, to be able to choose the best diagnosis or treatment measure or to make valid prognosis statements for a particular patient in consideration of the physician's own expertise.The basis are clinical trials, the results of which are ideally gathered in systematic reviews, rated, summarized and published. In addition to the GCP (Good Clinical Practice)-compliant planning, conducting and analysis of clinical studies it is essential, that all study results are made publicly available, in order to avoid publication bias. This includes the public registration of planned and discontinued trials. In the last 25 years, the evidence-based medicine (EbM) has increasingly found its way into clinical practice and research. Here EbM is closely associated with the names Archibald Cochrane and David Sackett. In Germany, both the German Cochrane Centre (DCZ) and the network of evidence-based medicine (DNEbM) were established approximately 15 years ago. In the international Cochrane Collaboration clinicians and other scientists like statisticians interdisciplinary work side by side to develop the methods of evidence-based medicine and to address the topics of evidence generation and processing as well as the transfer of knowledge. Challenge: Existing evidence primarily serves doctors to support their decision-making, but is also the basis for providing scientific proof for a health care intervention's benefit to patients and ultimately payers/health insurances. The closure of existing evidence gaps requires substantial human and financial resources, a complex organizational structure and can only succeed with the involvement of clinical and methodological expertise and specific knowledge in the field of clinical research. In addition, the knowledge must be transferred into practice, using journals, guidelines, conferences, databases, information portals with processed evidence and not least the

  6. LTDNA evidence on trial

    Roberts, Paul

    2016-01-01

    Adopting the interpretative/hermeneutical method typical of much legal scholarship, this article considers two sets of issues pertaining to LTDNA profiles as evidence in criminal proceedings. The section titled Expert Evidence as Forensic Epistemic Warrant addresses some rather large questions about the epistemic status and probative value of expert testimony in general. It sketches a theoretical model of expert evidence, highlighting five essential criteria: (1) expert competence; (2) discip...

  7. What is Evidence? (editorial

    Denise Koufogiannakis

    2011-06-01

    Full Text Available Lately, I have been pondering what we really mean when we say “evidence based practice”? In LIS, we all know the definitions that have been proposed (Booth 2000, Eldredge 2000, Crumley and Koufogiannakis 2002, and which have not ever really been challenged. But have we ever said explicitly what qualifies as evidence in this model? The underlying assumption seems to be that evidence is research, hence, we are really talking about research-based practice, but we don’t actually use that term.Higgs and Jones (2000 note that evidence is “knowledge derived from a variety of sources that has been subjected to testing and has found to be credible.” The Oxford English Dictionary states that evidence is “something serving as a proof” (OED, 2011. Neither of these definitions of evidence notes that evidence equals research; research is only one form of evidence. It certainly isn’t the only form of evidence – so what, then, constitutes evidence?Rycroff-Malone et al. (2004 state that that in order for evidence based practice to create a broader evidence base in nursing, “the external, scientific and the internal, intuitive” need to be brought together. The external, scientific is what evidence based practice has been focused on, in the form of scientific research, but Rycroff-Malone et al. note that other elements such as clinical experience, patient experience, and information from the local context also need to be considered.In library and information practice, what are the other forms of evidence we need to consider? I propose that while research evidence is of high importance to our profession and knowledge, LIS practitioners need to first of all consider local evidence. Local evidence is found in our working environment and specific to the context in which we carry out our work. It includes such things as our experiences with patrons in particular contexts, and what we observe to work in such situations, assessment of programs

  8. Hermeneutics, evidence ad judgment

    Michele Taruffo

    2018-03-01

    Full Text Available The text analyzes several topics of the judicial process from the point of view of the important contributions offered by the hermeneutical philosophy. It deals mainly with the construction of factual narratives, the presentation of evidence and the discovery of truth made by the judge in his final judgment based upon the evidence.

  9. The Evidence Movement

    Hansen, Hanne Foss; Rieper, Olaf

    2009-01-01

    The evidence movement and the idea of systematic reviews, defined as summaries of the results of already existing evaluation and research projects, have gained considerable support in recent years as many international as well as national evidence-producing organizations have been established...

  10. Teaching with Evidence

    Crocco, Margaret; Halvorsen, Anne-Lise; Jacobsen, Rebecca; Segall, Avner

    2017-01-01

    In this age of real and fake news, students need to be able to assess the trustworthiness of evidence. The authors' current research examines students' use of evidence in secondary social studies classrooms as students deliberate contemporary public policy issues. The authors found that students shifted their evaluations of the trustworthiness of…

  11. Observational Evidence for Atoms.

    Jones, Edwin R., Jr.; Childers, Richard L.

    1984-01-01

    Discusses the development of the concept of atomicity and some of the many which can be used to establish its validity. Chemical evidence, evidence from crystals, Faraday's law of electrolysis, and Avogadro's number are among the areas which show how the concept originally developed from a purely philosophical idea. (JN)

  12. Evidence-based radiography

    Hafslund, Bjorg; Clare, Judith; Graverholt, Birgitte; Wammen Nortvedt, Monica

    2008-01-01

    Evidence-based practice (EBP) offers the integration of the best research evidence with clinical knowledge and expertise and patient values. EBP is a well known term in health care. This paper discusses the implementation of EBP into radiography and introduces the term evidence-based radiography. Evidence-based radiography is radiography informed and based on the combination of clinical expertise and the best available research-based evidence, patient preferences and resources available. In Norway, EBP in radiography is being debated and radiographers are discussing the challenges of implementing EBP in both academic and clinical practice. This discussion paper explains why EBP needs to be a basis for a radiography curriculum and a part of radiographers' practice. We argue that Norwegian radiographers must increase participation in research and developing practice within their specific radiographic domain

  13. Reproductive Status of Females in the Eusocial Wasp Polistes ferreri Saussure (Hymenoptera: Vespidae).

    Soares, E R P; Torres, V O; Antonialli-Junior, W F

    2014-12-01

    In the subfamily Polistinae, caste dimorphism is not pronounced and differences among females are primarily physiological and behavioral. We investigated factors that indicate the reproductive status in females of Polistes ferreri Saussure. We analyzed females from nine colonies and evaluated morphometric parameters, ovarian development, occurrence of insemination, relative age, and cuticular chemical profile. The colony females showed three kinds of ovarian development: type A, filamentous ovarioles; type B, ovarioles containing partially developed oocytes; and type C, long and well-developed ovarioles containing two or more mature oocytes. The stepwise discriminant analysis of the cuticular chemical profile showed that it was possible to distinguish the three groups of females: workers 1, workers 2, and queens. However, the stepwise discriminant analysis of the morphological differences did not show significant differences among these groups. The queens were among the older females in the colony and were always inseminated, while the age of the workers varied according to the stage of colony development.

  14. The vespid fauna of Pakistan.

    Rafi, Muhammad Ather; Carpenter, James M; Qasim, Muhammad; Shehzad, Anjum; Zia, Ahmed; Khan, Muhammad Rafique; Mastoi, Muhammad Ishaque; Naz, Falak; Ilyas, Muhammad; Shah, Mazafar; Bhatti, Abdul Rauf

    2017-12-04

    This study provides the first annotated check list of the Vespidae of Pakistan. It is based on the National Insect Museum collection and various studies in Pakistan. Among 105 identified taxa, 77 species and 28 subspecies are recorded in the four subfamilies Eumeninae, Masarinae, Polistinae and Vespinae. Three new records for the fauna of Pakistan are added, namely Anterhynchium mellyi, Antepipona ovalis and Eumenes coronatus coronatus. Among the total, 12 species/subspecies are endemic to Pakistan, namely Ancistrocerus pakistanus, Antepipona luteipes, Antodynerus flavescens karachiensis, Celonites nursei, Cyrtolabulus karachiensis, Eustenancistrocerus (Parastenancistrocerus) baluchistanensis, Katamenes dimidiatus watsoni, Knemodynerus lahorensis, Leptochilus (Neoleptochilus) hina, Leptochilus (Neoleptochilus) mirificus, Leptochilus (Neoleptochilus) umerolatus and Tachyancistrocerus pakistanus. Antepipona varentzowi (Morawitz, 1896) and Polistes rothneyi quatei van der Vecht, 1968 were incorrectly reported from Pakistan.

  15. Evidence: Study Guide. Revision

    1997-01-01

    ...) correct application of principles of military rules of evidence. This study guide is also intended to be a convenient reference for use by Navy and Marine Corps judge advocates and Coast Guard law...

  16. LTDNA Evidence on Trial

    Paul Roberts; Paul Roberts; Paul Roberts

    2016-01-01

    Adopting the interpretative/hermeneutical method typical of much legal scholarship, this article considers two sets of issues pertaining to LTDNA profiles as evidence in criminal proceedings. Section 1 addresses some rather large questions about the epistemic status and probative value of expert testimony in general. It sketches a theoretical model of expert evidence, highlighting five essential criteria: (1) expert competence; (2) disciplinary domain; (3) methodological validity; (4) materia...

  17. Genetic evidence that two independent S-loci control RNase-based self-incompatibility in diploid strawberry.

    Bosković, Radovan I; Sargent, Daniel J; Tobutt, Kenneth R

    2010-03-01

    The self-incompatibility mechanism that reduces inbreeding in many plants of the Rosaceae is attributed to a multi-allelic S locus which, in the Prunoideae and Maloideae subfamilies, comprises two complementary genes, a stylar-expressed S-RNase and a pollen-expressed SFB. To elucidate incompatibility in the subfamily Rosoideae, stylar-specific RNases and self-(in)compatibility status were analysed in various diploid strawberries, especially Fragaria nubicola and F. viridis, both self-incompatible, and F. vesca, self-compatible, and in various progenies derived from them. Unexpectedly, two unlinked RNase loci, S and T, were found, encoding peptides distinct from Prunoideae and Maloideae S-RNases; the presence of a single active allele at either is sufficient to confer self-incompatibility. By contrast, in diploid Maloideae and Prunoideae a single locus encodes S-RNases that share several conserved regions and two active alleles are required for self-incompatibility. Our evidence implicates the S locus in unilateral inter-specific incompatibility and shows that S and T RNases can, remarkably, confer not only allele-specific rejection of cognate pollen but also unspecific rejection of Sn Tn pollen, where n indicates a null allele, consistent with the the presence of the pollen component, SFB, activating the cognitive function of these RNases. Comparison of relevant linkage groups between Fragaria and Prunus suggests that Prunus S-RNases, unique in having two introns, may have resulted from gene conversion in an ancestor of Prunus. In addition, it is shown that there is a non-S locus that is essential for self-incompatibility in diploid Fragaria.

  18. LTDNA Evidence on Trial

    Roberts, Paul

    2016-01-01

    Adopting the interpretative/hermeneutical method typical of much legal scholarship, this article considers two sets of issues pertaining to LTDNA profiles as evidence in criminal proceedings. The section titled Expert Evidence as Forensic Epistemic Warrant addresses some rather large questions about the epistemic status and probative value of expert testimony in general. It sketches a theoretical model of expert evidence, highlighting five essential criteria: (1) expert competence; (2) disciplinary domain; (3) methodological validity; (4) materiality; and (5) legal admissibility. This generic model of expert authority, highlighting law's fundamentally normative character, applies to all modern forms of criminal adjudication, across Europe and farther afield. The section titled LTDNA Evidence in UK Criminal Trials then examines English and Northern Irish courts' attempts to get to grips with LTDNA evidence in recent cases. Better appreciating the ways in which UK courts have addressed the challenges of LTDNA evidence may offer some insights into parallel developments in other legal systems. Appellate court rulings follow a predictable judicial logic, which might usefully be studied and reflected upon by any forensic scientist or statistician seeking to operate effectively in criminal proceedings. Whilst each legal jurisdiction has its own unique blend of jurisprudence, institutions, cultures and historical traditions, there is considerable scope for comparative analysis and cross-jurisdictional borrowing and instruction. In the spirit of promoting more nuanced and sophisticated international interdisciplinary dialogue, this article examines UK judicial approaches to LTDNA evidence and begins to elucidate their underlying institutional logic. Legal argument and broader policy debates are not confined to considerations of scientific validity, contamination risks and evidential integrity, or associated judgments of legal admissibility or exclusion. They also crucially

  19. LTDNA Evidence on Trial.

    Roberts, Paul

    2016-01-01

    Adopting the interpretative/hermeneutical method typical of much legal scholarship, this article considers two sets of issues pertaining to LTDNA profiles as evidence in criminal proceedings. The section titled Expert Evidence as Forensic Epistemic Warrant addresses some rather large questions about the epistemic status and probative value of expert testimony in general. It sketches a theoretical model of expert evidence, highlighting five essential criteria: (1) expert competence; (2) disciplinary domain; (3) methodological validity; (4) materiality; and (5) legal admissibility. This generic model of expert authority, highlighting law's fundamentally normative character, applies to all modern forms of criminal adjudication, across Europe and farther afield. The section titled LTDNA Evidence in UK Criminal Trials then examines English and Northern Irish courts' attempts to get to grips with LTDNA evidence in recent cases. Better appreciating the ways in which UK courts have addressed the challenges of LTDNA evidence may offer some insights into parallel developments in other legal systems. Appellate court rulings follow a predictable judicial logic, which might usefully be studied and reflected upon by any forensic scientist or statistician seeking to operate effectively in criminal proceedings. Whilst each legal jurisdiction has its own unique blend of jurisprudence, institutions, cultures and historical traditions, there is considerable scope for comparative analysis and cross-jurisdictional borrowing and instruction. In the spirit of promoting more nuanced and sophisticated international interdisciplinary dialogue, this article examines UK judicial approaches to LTDNA evidence and begins to elucidate their underlying institutional logic. Legal argument and broader policy debates are not confined to considerations of scientific validity, contamination risks and evidential integrity, or associated judgments of legal admissibility or exclusion. They also crucially

  20. Evidence-based dentistry.

    Chambers, David W

    2010-01-01

    Both panegyric and criticism of evidence-based dentistry tend to be clumsy because the concept is poorly defined. This analysis identifies several contributions to the profession that have been made under the EBD banner. Although the concept of clinicians integrating clinical epidemiology, the wisdom of their practices, and patients' values is powerful, its implementation has been distorted by a too heavy emphasis of computerized searches for research findings that meet the standards of academics. Although EBD advocates enjoy sharing anecdotal accounts of mistakes others have made, faulting others is not proof that one's own position is correct. There is no systematic, high-quality evidence that EBD is effective. The metaphor of a three-legged stool (evidence, experience, values, and integration) is used as an organizing principle. "Best evidence" has become a preoccupation among EBD enthusiasts. That overlong but thinly developed leg of the stool is critiqued from the perspectives of the criteria for evidence, the difference between internal and external validity, the relationship between evidence and decision making, the ambiguous meaning of "best," and the role of reasonable doubt. The strongest leg of the stool is clinical experience. Although bias exists in all observations (including searches for evidence), there are simple procedures that can be employed in practice to increase useful and objective evidence there, and there are dangers in delegating policy regarding allowable treatments to external groups. Patient and practitioner values are the shortest leg of the stool. As they are so little recognized, their integration in EBD is problematic and ethical tensions exist where paternalism privileges science over patient's self-determined best interests. Four potential approaches to integration are suggested, recognizing that there is virtually no literature on how the "seat" of the three-legged stool works or should work. It is likely that most dentists

  1. Evidence-Based Toxicology.

    Hoffmann, Sebastian; Hartung, Thomas; Stephens, Martin

    Evidence-based toxicology (EBT) was introduced independently by two groups in 2005, in the context of toxicological risk assessment and causation as well as based on parallels between the evaluation of test methods in toxicology and evidence-based assessment of diagnostics tests in medicine. The role model of evidence-based medicine (EBM) motivated both proposals and guided the evolution of EBT, whereas especially systematic reviews and evidence quality assessment attract considerable attention in toxicology.Regarding test assessment, in the search of solutions for various problems related to validation, such as the imperfectness of the reference standard or the challenge to comprehensively evaluate tests, the field of Diagnostic Test Assessment (DTA) was identified as a potential resource. DTA being an EBM discipline, test method assessment/validation therefore became one of the main drivers spurring the development of EBT.In the context of pathway-based toxicology, EBT approaches, given their objectivity, transparency and consistency, have been proposed to be used for carrying out a (retrospective) mechanistic validation.In summary, implementation of more evidence-based approaches may provide the tools necessary to adapt the assessment/validation of toxicological test methods and testing strategies to face the challenges of toxicology in the twenty first century.

  2. A família Rubiaceae na Reserva Biológica Guaribas, Paraíba, Brasil: subfamílias Antirheoideae, Cinchonoideae e Ixoroideae The family Rubiaceae in the Guaribas Biological Reserve, Paraíba State, Brazil: subfamilies Antirheoideae, Cinchonoideae and Ixoroideae

    Maria do Socorro Pereira

    2004-06-01

    Full Text Available Este trabalho consiste no levantamento dos representantes das subfamílias Antirheoideae, Cinchonoideae e Ixoroideae na Reserva Biológica Guaribas, Paraíba, Brasil. Foram realizadas coletas intensivas no período de outubro/2000 a outubro/2001, as quais resultaram no reconhecimento de 12 espécies, 10 gêneros e cinco tribos, distribuídos nas três subfamílias. A subfamília melhor representada foi Antirheoideae, com cinco espécies, quatro gêneros e duas tribos. Os gêneros com maior número de espécies foram Guettarda L. (2 e Tocoyena Aubl. (2. Alibertia A. Rich. ex DC., Alseis Schott, Chiococca P. Browne, Chomelia Jacq., Coutarea Aubl., Posoqueria Aubl., Sabicea Aubl. e Salzmannia DC. apresentaram uma única espécie cada. São apresentadas chaves para identificação, descrições, comentários sobre morfologia e distribuição das espécies, e ilustrações dos táxons verificados.This paper is a survey of Rubiaceae subfamilies Antirheoideae, Cinchonoideae and Ixoroideae in the Guaribas Biological Reserve, Paraíba, Brazil. Intensive collections were made from October/2000 to October/2001. Twelve species, 10 genera and five tribes were recognized. The most diverse subfamily was Antirheoideae, with five species, four genera and two tribes. The genera with the most species were Guettarda L. (2 and Tocoyena Aubl. (2. Alibertia A. Rich. ex DC., Alseis Schott, Chiococca P. Browne, Chomelia Jacq., Coutarea Aubl., Posoqueria Aubl., Sabicea Aubl., and Salzmannia DC. were represented by only one species each. Keys, descriptions, comments on morphology and species distributions, as well as illustrations of the taxa are provided.

  3. Evidence-Based Development

    Hertzum, Morten; Simonsen, Jesper

    2004-01-01

    Systems development is replete with projects that represent substantial resource investments but result in systems that fail to meet users’ needs. Evidence-based development is an emerging idea intended to provide means for managing customer-vendor relationships and working systematically toward...... meeting customer needs. We are suggesting that the effects of the use of a system should play a prominent role in the contractual definition of IT projects and that contract fulfilment should be determined on the basis of evidence of these effects. Based on two ongoing studies of home-care management...

  4. Gait as evidence

    Lynnerup, Niels; Larsen, Peter Kastmand

    2014-01-01

    This study examines what in Denmark may constitute evidence based on forensic anthropological gait analyses, in the sense of pointing to a match (or not) between a perpetrator and a suspect, based on video and photographic imagery. Gait and anthropometric measures can be used when direct facial...

  5. Evidence-based policy

    Vohnsen, Nina Holm

    2013-01-01

    -makers and the research community (e.g. Boden & Epstein 2006; House of Commons 2006; Cartwright et al 2009; Rod 2010; Vohnsen 2011). This article intends to draw out some general pitfalls in the curious meeting of science and politics by focusing on a particular attempt to make evidence-based legislation in Denmark (for...

  6. Turning Evidence into Practice

    CGH CRTA, Hillary Topazian, attended the National Cancer Institute’s 3rd Symposium on Global Cancer Research; a satellite meeting to the 6th Annual Consortium of Universities for Global Health (CUGH) Conference in Boston. The Symposium centered on the theme of implementation science, a field which studies the integration of research findings and evidence into healthcare policy and practice.

  7. Evidence of Absence software

    Dalthorp, Daniel; Huso, Manuela M. P.; Dail, David; Kenyon, Jessica

    2014-01-01

    Evidence of Absence software (EoA) is a user-friendly application used for estimating bird and bat fatalities at wind farms and designing search protocols. The software is particularly useful in addressing whether the number of fatalities has exceeded a given threshold and what search parameters are needed to give assurance that thresholds were not exceeded. The software is applicable even when zero carcasses have been found in searches. Depending on the effectiveness of the searches, such an absence of evidence of mortality may or may not be strong evidence that few fatalities occurred. Under a search protocol in which carcasses are detected with nearly 100 percent certainty, finding zero carcasses would be convincing evidence that overall mortality rate was near zero. By contrast, with a less effective search protocol with low probability of detecting a carcass, finding zero carcasses does not rule out the possibility that large numbers of animals were killed but not detected in the searches. EoA uses information about the search process and scavenging rates to estimate detection probabilities to determine a maximum credible number of fatalities, even when zero or few carcasses are observed.

  8. Fossil wood evidences

    Climate has played a crucial role in assigning a different kind of topography to Rajasthan and Gujarat since the Cenozoic time. Evidently, three genera, namely, Dipterocarpus Gaert. f., Hopea Roxb. And Shorea Roxb. of the Dipterocarpaceae are described from the Neogene sediments of western India (Rajasthan and ...

  9. LTDNA Evidence on Trial

    Paul Roberts

    2016-10-01

    Full Text Available Adopting the interpretative/hermeneutical method typical of much legal scholarship, this article considers two sets of issues pertaining to LTDNA profiles as evidence in criminal proceedings. Section 1 addresses some rather large questions about the epistemic status and probative value of expert testimony in general. It sketches a theoretical model of expert evidence, highlighting five essential criteria: (1 expert competence; (2 disciplinary domain; (3 methodological validity; (4 materiality; and (5 legal admissibility. This generic model of expert authority, highlighting law’s fundamentally normative character, applies to all modern forms of criminal adjudication, across Europe and farther afield. Section 2 then examines English and Northern Irish courts’ attempts to get to grips with LTDNA evidence in recent cases. Better appreciating the ways in which UK courts have addressed the challenges of LTDNA evidence may offer some insights into parallel developments in other legal systems. Appellate court rulings follow a predictable judicial logic, which might usefully be studied and reflected upon by any forensic scientist or statistician seeking to operate effectively in criminal proceedings. Whilst each legal jurisdiction has its own unique blend of jurisprudence, institutions, cultures and historical traditions, there is considerable scope for comparative analysis and cross-jurisdictional borrowing and instruction. In the spirit of promoting more nuanced and sophisticated international interdisciplinary dialogue, this article examines UK judicial approaches to LTDNA evidence and begins to elucidate their underlying institutional logic. Legal argument and broader policy debates are not confined to considerations of scientific validity, contamination risks and evidential integrity, or associated judgments of legal admissibility or exclusion. They also crucially concern the manner in which LTDNA profiling results are presented and explained to

  10. Multiple Lines of Evidence

    Amidan, Brett G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Venzin, Alexander M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bramer, Lisa M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-06-03

    This paper discusses the process of identifying factors that influence the contamination level of a given decision area and then determining the likelihood that the area remains unacceptable. This process is referred to as lines of evidence. These lines of evidence then serve as inputs for the stratified compliance sampling (SCS) method, which requires a decision area to be divided into strata based upon contamination expectations. This is done in order to focus sampling efforts more within stratum where contamination is more likely and to use the domain knowledge about these likelihoods of the stratum remaining unacceptable to buy down the number of samples necessary, if possible. Two different building scenarios were considered as an example (see Table 3.1). SME expertise was elicited concerning four lines of evidence factors (see Table 3.2): 1) amount of contamination that was seen before decontamination, 2) post-decontamination air sampling information, 3) the applied decontaminant information, and 4) the surface material. Statistical experimental design and logistic regression modelling were used to help determine the likelihood that example stratum remained unacceptable for a given example scenario. The number of samples necessary for clearance was calculated by applying the SCS method to the example scenario, using the estimated likelihood of each stratum remaining unacceptable as was determined using the lines of evidence approach. The commonly used simple random sampling (SRS) method was also used to calculate the number of samples necessary for clearance for comparison purposes. The lines of evidence with SCS approach resulted in a 19% to 43% reduction in total number of samples necessary for clearance (see Table 3.6). The reduction depended upon the building scenario, as well as the level of percent clean criteria. A sensitivity analysis was also performed showing how changing the estimated likelihoods of stratum remaining unacceptable affect the number

  11. Evidence on acne therapy

    Caroline Sousa Costa

    Full Text Available Among the current treatments available for acne vulgaris, many widely practiced options lack support from studies at the best level of scientific evidence. The aim of this narrative review was to present the very latest information on topical and systemic treatments for acne vulgaris. Information from systematic reviews and well-designed clinical trials, obtained through a systematic search of the major medical databases, is emphasized. There are important issues regarding the clinical management of acne that still lack consistent grounding in scientific evidence. Among these are the optimum dose and duration of treatment with oral antibiotics that can be given without inducing bacterial resistance, and the safety of oral isotretinoin.

  12. Observational evidence for mergers

    Schweizer, F.

    1983-01-01

    Theory has long suggested that dynamical friction between colliding galaxies must lead to mergers. The problem for observers has been to find which galaxies are mergers. The author first reviews the available evidence for mergers in various kinds of galaxies, then proposes a tentative classification scheme for mergers, and finally discusses mergers in giant ellipticals and their relation to the evolution and perhaps even the formation of ellipticals. (Auth.)

  13. Evidence informed decision making

    Sharma, Tarang; Choudhury, Moni; Kaur, Bindweep

    2015-01-01

    from the literature and a combined best practice checklist has been proposed. CONCLUSIONS: As decisions often need to be made in areas where there is a lack of published scientific evidence, CE is employed. Therefore to ensure its appropriateness the development of a validated CE data quality check......-list to assist decision makers is essential and further research in this area is a priority....

  14. Evidence-based management.

    Pfeffer, Jeffrey; Sutton, Robert I

    2006-01-01

    For the most part, managers looking to cure their organizational ills rely on obsolete knowledge they picked up in school, long-standing but never proven traditions, patterns gleaned from experience, methods they happen to be skilled in applying, and information from vendors. They could learn a thing or two from practitioners of evidence-based medicine, a movement that has taken the medical establishment by storm over the past decade. A growing number of physicians are eschewing the usual, flawed resources and are instead identifying, disseminating, and applying research that is soundly conducted and clinically relevant. It's time for managers to do the same. The challenge is, quite simply, to ground decisions in the latest and best knowledge of what actually works. In some ways, that's more difficult to do in business than in medicine. The evidence is weaker in business; almost anyone can (and many people do) claim to be a management expert; and a motley crew of sources--Shakespeare, Billy Graham,Jack Welch, Attila the Hunare used to generate management advice. Still, it makes sense that when managers act on better logic and strong evidence, their companies will beat the competition. Like medicine, management is learned through practice and experience. Yet managers (like doctors) can practice their craft more effectively if they relentlessly seek new knowledge and insight, from both inside and outside their companies, so they can keep updating their assumptions, skills, and knowledge.

  15. EPR: Evidence and fallacy.

    Nichols, Joseph W; Bae, You Han

    2014-09-28

    The enhanced permeability and retention (EPR) of nanoparticles in tumors has long stood as one of the fundamental principles of cancer drug delivery, holding the promise of safe, simple and effective therapy. By allowing particles preferential access to tumors by virtue of size and longevity in circulation, EPR provided a neat rationale for the trend toward nano-sized drug carriers. Following the discovery of the phenomenon by Maeda in the mid-1980s, this rationale appeared to be well justified by the flood of evidence from preclinical studies and by the clinical success of Doxil. Clinical outcomes from nano-sized drug delivery systems, however, have indicated that EPR is not as reliable as previously thought. Drug carriers generally fail to provide superior efficacy to free drug systems when tested in clinical trials. A closer look reveals that EPR-dependent drug delivery is complicated by high tumor interstitial fluid pressure (IFP), irregular vascular distribution, and poor blood flow inside tumors. Furthermore, the animal tumor models used to study EPR differ from clinical tumors in several key aspects that seem to make EPR more pronounced than in human patients. On the basis of this evidence, we believe that EPR should only be invoked on a case-by-case basis, when clinical evidence suggests the tumor type is susceptible. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Case histories as evidence.

    Herxheimer, Andrew; Healy, David; Menkes, David B

    2012-01-01

    In courts case histories play a central part when a crime may have resulted from an effect of a prescribed drug; in civil cases where a person may have suffered damage from a drug; and in coroners' enquiries into the cause of unexplained deaths. The court must decide two important questions: 1. Can the suspected medication(s) cause this kind of effect? 2. Did it (or they) do so in this particular case? Many judges and coroners have not addressed these questions clearly and have not used expert witnesses consistently, on occasion disregarding scientific evidence. Courts need to appoint experts to explain and interpret the scientific evidence. Few judges are equipped to resolve contradictions between different experts. Brief accounts of five cases from four countries illustrate these points. The reluctance of legal processes to implicate drugs as a possible cause of violent behaviour leads to injustice. Courts must be required to obtain appropriate expert evidence, and be given independent data on which drugs can cause such behaviour.

  17. Evidence-based surgery

    Miran Rems

    2007-04-01

    Full Text Available Background: Surgery is setting a new ground by the reign of evidence that was brought up by the Evidence Based Medicine (EBM. While experiences and opinion of an expert count the least by the principles of EBM, randomized controlled trials (RCT and other comparative studies have gained their importance. Recommendations that were included in guidelines represent a demanding shift in surgeon’s professional thinking. Their thinking and classical education have not yet been completely based on the results of such studies and are still very very much master-pupil centred. Assessment of someone’s own experiences is threatened by objectivity as negative experiences get recorded in deeper memory. Randomized studies and meta-analyses do appear also in surgery. However, they demand an extra knowledge about critical assessment.Conclusions: Setting a patient to the foreground brings a surgeon’s decision to the field of EBM. The process has already begun and cannot be avoided. Decision hierarchy moves from the experience field to the evidence territory but to a lesser extent when compared to the rest of medicine. There exist objective restrictions with approving a new paradigm. However, these should not stop the process of EBM implementation. Finally, there is an ethic issue to be considered. Too slow activities in research, education and critical assessment can bring the surgeon to the position when a well-informed patient loses his/her trust.

  18. Gene Expression by PBMC in Primary Sclerosing Cholangitis: Evidence for Dysregulation of Immune Mediated Genes

    Christopher A. Aoki

    2006-01-01

    Full Text Available Primary sclerosing cholangitis (PSC is a chronic disease of the bile ducts characterized by an inflammatory infiltrate and obliterative fibrosis. The precise role of the immune system in the pathogenesis of PSC remains unknown. We used RNA microarray analysis to identify immune-related genes and pathways that are differentially expressed in PSC. Messenger RNA (mRNA from peripheral blood mononuclear cells (PBMC was isolated from both patients with PSC and age and sex matched healthy controls. Samples from 5 PSC patients and 5 controls were analyzed by microarray and based upon rigorous statistical analysis of the data, relevant genes were chosen for confirmation by RT-PCR in 10 PSC patients and 10 controls. Using unsupervised hierarchical clustering, gene expression in PSC was statistically different from our control population. Interestingly, genes within the IL-2 receptor beta, IL-6 and MAP Kinase pathways were found to be differently expressed in patients with PSC compared to controls. Further, individual genes, TNF-α induced protein 6 (TNFaip6 and membrane-spanning 4-domains, subfamily A (ms4a were found to be upregulated in PSC while similar to Mothers against decapentaplegic homolog 5 (SMAD 5 was downregulated. In conclusion, several immune-related pathways and genes were differentially expressed in PSC compared to control patients, giving further evidence that this disease is systemic and immune-mediated.

  19. Molecular evidence for ongoing complementarity and horizontal gene transfer in endosymbiotic systems of mealybugs

    Sergio eLópez-Madrigal

    2014-08-01

    Full Text Available Intracellular bacterial supply of essential amino acids is common among sap-feeding insects, thus complementing the scarcity of nitrogenous compounds in plant phloem. This is also the role of the two mealybug endosymbiotic systems whose genomes have been sequenced. In the nested endosymbiotic system from Planococcus citri (Pseudococcinae, Candidatus Tremblaya princeps and Candidatus Moranella endobia cooperate to synthesize essential amino acids, while in Phenacoccus avenae (Phenacoccinae this function is performed by its single endosymbiont Candidatus Tremblaya phenacola. However, little is known regarding the evolution of essential amino acid supplementation strategies in other mealybug systems. To address this knowledge gap, we screened for the presence of six selected loci involved in essential amino acid biosynthesis in five additional mealybug species. We found evidence of ongoing complementarity among endosymbionts from insects of subfamily Pseudococcinae, as well as horizontal gene transfer affecting endosymbionts from insects of family Phenacoccinae, providing a more comprehensive picture of the evolutionary history of these endosymbiotic systems. Additionally, we report two diagnostic motifs to help identify invasive mealybug species.

  20. Total evidence phylogeny and the evolution of adult bioluminescence in fireflies (Coleoptera: Lampyridae).

    Martin, Gavin J; Branham, Marc A; Whiting, Michael F; Bybee, Seth M

    2017-02-01

    Fireflies are some of the most captivating organisms on the planet. They have a rich history as subjects of scientific study, especially in relation to their bioluminescent behavior. Yet, the phylogenetic relationships of fireflies are still poorly understood. Here, we present the first total evidence approach to reconstruct lampyrid phylogeny using both a molecular matrix from six loci and an extensive morphological matrix. Using this phylogeny we test the hypothesis that adult bioluminescence evolved after the origin of the firefly clade. The ancestral state of adult bioluminescence is recovered as non-bioluminescent with one to six gains and five to ten subsequent losses. The monophyly of the family, as well as the subfamilies is also tested. Ototretinae, Cyphonocerinae, Luciolinae (incl. Pristolycus), Amydetinae, "cheguevarinae" sensu Jeng 2008, and Photurinae are highly supported as monophyletic. With the exception of four taxa, Lampyrinae is also recovered as monophyletic with high support. Based on phylogenetic and morphological data Lamprohiza, Phausis, and Lamprigera are transferred to Lampyridae incertae sedis. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. INADMISSIBLE EVIDENCE IN CIVIL PROCEDURE

    Mihajlo Dika

    2016-01-01

    Full Text Available This paper examines the exclusion of specific means of evidence as instruments for determining the object of evidence, as well as the taking of evidence in the framework of the Croatian civil procedure law. The introduction lays the grounds for classifying and qualifying exclusion of evidence (general, special; absolute, relative; removable, irremovable; direct, indirect, after which greater attention is paid to the so called absolute and relative type; exclusionary evidence of the direct relative type pertaining to the establishing of facts, and evidence dismissals. With regard to the indirect relative type, the paper examines exclusionary evidence concerning the object of evidence. The remainder of the paper focuses on illegally obtained evidence, while outlining the constitutional, statutory, judicature and doctrinaire premises of bearing for such evidence. Subsequently, the question of evidence obtained in violation of the Constitutional guarantee of respect and legal protection of private and family life, dignity, reputation and honour, as well as evidence obtained by breach of the Constitutional guarantee of freedom and secrecy of correspondence and all other forms of communication, and in violation of the right to safety and privacy of personal data, are discussed too. In addition, the paper analyses the institutions of preclusion of evidence and the so called informative evidence. Concluding, the author points to a lacking regulation of inadmissible evidence within the Croatian civil procedure law, underlining the need to determine de lege ferenda legal requirements with a view to operationalizing inadmissible evidence within the Croatian civil procedure law.

  2. Evidence-based librarianship: searching for the needed EBL evidence.

    Eldredge, J D

    2000-01-01

    This paper discusses the challenges of finding evidence needed to implement Evidence-Based Librarianship (EBL). Focusing first on database coverage for three health sciences librarianship journals, the article examines the information contents of different databases. Strategies are needed to search for relevant evidence in the library literature via these databases, and the problems associated with searching the grey literature of librarianship. Database coverage, plausible search strategies, and the grey literature of library science all pose challenges to finding the needed research evidence for practicing EBL. Health sciences librarians need to ensure that systems are designed that can track and provide access to needed research evidence to support Evidence-Based Librarianship (EBL).

  3. Evidence for homosexuality gene

    Pool, R.

    1993-07-16

    A genetic analysis of 40 pairs of homosexual brothers has uncovered a region on the X chromosome that appears to contain a gene or genes for homosexuality. When analyzing the pedigrees of homosexual males, the researcheres found evidence that the trait has a higher likelihood of being passed through maternal genes. This led them to search the X chromosome for genes predisposing to homosexuality. The researchers examined the X chromosomes of pairs of homosexual brothers for regions of DNA that most or all had in common. Of the 40 sets of brothers, 33 shared a set of five markers in the q28 region of the long arm of the X chromosome. The linkage has a LOD score of 4.0, which translates into a 99.5% certainty that there is a gene or genes in this area that predispose males to homosexuality. The chief researcher warns, however, that this one site cannot explain all instances of homosexuality, since there were some cases where the trait seemed to be passed paternally. And even among those brothers where there was no evidence that the trait was passed paternally, seven sets of brothers did not share the Xq28 markers. It seems likely that homosexuality arises from a variety of causes.

  4. Phylogeny and systematics of the brake fern genus Pteris (Pteridaceae) based on molecular (plastid and nuclear) and morphological evidence.

    Zhang, Liang; Zhang, Li-Bing

    2018-01-01

    The brake fern genus Pteris belongs to Pteridaceae subfamily Pteridoideae. It is one of the largest fern genera and has been estimated to contain 200-250 species distributed on all continents except Antarctica. Previous studies were either based on plastid data only or based on both plastid and nuclear data but the sampling was small. In addition, an infrageneric classification of Pteris based on morphological and molecular evidence has not been available yet. In the present study, based on molecular data of eight plastid markers and one nuclear marker (gapCp) of 256 accessions representing ca. 178 species of Pteris, we reconstruct a global phylogeny of Pteris. The 15 major clades identified earlier are recovered here and we further identified a new major clade. Our nuclear phylogeny recovered 11 of these 16 major clades, seven of which are strongly supported. The inclusion of Schizostege in Pteris is confirmed for the first time. Based on the newly reconstructed phylogeny and evidence from morphology, distribution and/or ecology, we classify Pteris into three subgenera: P. subg. Pteris, P. subg. Campteria, and P. subg. Platyzoma. The former two are further divided into three and 12 sections, respectively. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Evidence on Inclusion

    Dyssegaard, Camilla Brørup; Larsen, Michael Søgaard

    The purpose of this publication is to examine existing research on inclusion to identify strategies of inclusion that have generated positive effects. To do so it is necessary to understand the effect of the applied strategies. One approach, which is being discussed, is to use evidence to determine...... which methods have proven more effective than others. The desire to gain insight into research on inclusion forms the basis of the current systematic review. The task was to determine which strategies primary research has found to be most effective for inclusion purposes. We have solved this task...... by addressing the existing research with the following question: What is the effect of including children with special needs in mainstream teaching in basic school, and which of the applied educational methods have proved to have a positive effect?...

  6. Evidence for robots.

    Shenoy, Ravikiran; Nathwani, Dinesh

    2017-01-01

    Robots have been successfully used in commercial industry and have enabled humans to perform tasks which are repetitive, dangerous and requiring extreme force. Their role has evolved and now includes many aspects of surgery to improve safety and precision. Orthopaedic surgery is largely performed on bones which are rigid immobile structures which can easily be performed by robots with great precision. Robots have been designed for use in orthopaedic surgery including joint arthroplasty and spine surgery. Experimental studies have been published evaluating the role of robots in arthroscopy and trauma surgery. In this article, we will review the incorporation of robots in orthopaedic surgery looking into the evidence in their use. © The Authors, published by EDP Sciences, 2017.

  7. Hazardous factories: Nigerian evidence.

    Oloyede, Olajide

    2005-06-01

    The past 15 years have seen an increasing governmental and corporate concern for the environment worldwide. For governments, information about the environmental performance of the industrial sector is required to inform macro-level decisions about environmental targets such as those required to meet UN directives. However, in many African, Asian, and Latin American countries, researching and reporting company environmental performance is limited. This article serves as a contribution to filling the gap by presenting evidence of physical and chemical risk in Nigerian factories. One hundred and three factories with a total of 5,021 workers were studied. One hundred and twenty physical and chemical hazards were identified and the result shows a high number of workers exposed to such hazards. The study also reveals that workers' awareness level of chemical hazards was high. Yet the danger was perceived in behavioral terms, especially by manufacturing firms, which tend to see environmental investment in an increasingly global economy as detrimental to profitability.

  8. Expert opinion vs. empirical evidence

    Herman, Rod A; Raybould, Alan

    2014-01-01

    Expert opinion is often sought by government regulatory agencies when there is insufficient empirical evidence to judge the safety implications of a course of action. However, it can be reckless to continue following expert opinion when a preponderance of evidence is amassed that conflicts with this opinion. Factual evidence should always trump opinion in prioritizing the information that is used to guide regulatory policy. Evidence-based medicine has seen a dramatic upturn in recent years spurred by examples where evidence indicated that certain treatments recommended by expert opinions increased death rates. We suggest that scientific evidence should also take priority over expert opinion in the regulation of genetically modified crops (GM). Examples of regulatory data requirements that are not justified based on the mass of evidence are described, and it is suggested that expertise in risk assessment should guide evidence-based regulation of GM crops. PMID:24637724

  9. Expert opinion vs. empirical evidence

    Herman, Rod A; Raybould, Alan

    2014-01-01

    Expert opinion is often sought by government regulatory agencies when there is insufficient empirical evidence to judge the safety implications of a course of action. However, it can be reckless to continue following expert opinion when a preponderance of evidence is amassed that conflicts with this opinion. Factual evidence should always trump opinion in prioritizing the information that is used to guide regulatory policy. Evidence-based medicine has seen a dramatic upturn in recent years sp...

  10. An N-terminal Retention Module Anchors the Giant Adhesin LapA of Pseudomonas fluorescens at the Cell Surface: A Novel Sub-family of Type I Secretion Systems.

    Smith, T Jarrod; Font, Maria E; Kelly, Carolyn M; Sondermann, Holger; O'Toole, George A

    2018-02-05

    LapA of Pseudomonas fluorescens Pf0-1 belongs to a diverse family of cell surface associated bacterial adhesins that are secreted via the type-1 secretion system (T1SS). We previously reported that the periplasmic protease LapG cleaves the N-terminus of LapA at a canonical dialanine motif to release the adhesin from the cell surface under conditions unfavorable to biofilm formation, thus decreasing biofilm formation. Here, we characterize LapA as the first type 1 secreted substrate that does not follow the "one-step" rule of T1SS. Rather, a novel N-terminal element, called the retention module (RM), localizes LapA at the cell surface as a secretion intermediate. Our genetic, biochemical, and molecular modeling analysis support a model wherein LapA is tethered to the cell surface through its T1SS outer membrane TolC-like pore, LapE, until LapG cleaves LapA in the periplasm. We further demonstrate this unusual retention strategy is likely conserved among LapA-like proteins, and reveals a new subclass of T1SS ABC transporters involved in transporting this group of surface-associated, LapA-like adhesins. These studies demonstrate a novel cell surface retention strategy used throughout the Proteobacteria and highlight a previously unappreciated flexibility of function for T1SS. Importance. Bacteria have evolved multiple secretion strategies to interact with their environment. For many bacteria, the secretion of cell surface associated adhesins is key for initiating contact with a preferred substratum to facilitate biofilm formation. Our work demonstrates that P. fluorescens uses a previously unrecognized secretion strategy to retain the giant adhesin LapA at its cell surface. Further, we identify likely LapA-like adhesins in various pathogenic and commensal Proteobacteria and provide phylogenetic evidence that these adhesins are secreted by a new subclass of T1SS ABC transporters. Copyright © 2018 American Society for Microbiology.

  11. Comparative ribotyping of Staphylococcus intermedius isolated from members of the Canoidea gives possible evidence for host-specificity and co-evolution of bacteria and hosts

    Aarestrup, Frank Møller

    2001-01-01

    A total of 41 Staphylococcus intermedius isolates were isolated from skin of healthy members of six phylogenetic groups within the Canoidea (the dog family, skunk subfamily, weasel subfamily, racoon family, red panda and bear family) of different geographical origin and compared by EcoRI ribotyping...

  12. Weighing evidence: quantitative measures of the importance of bitemark evidence.

    Kittelson, J M; Kieser, J A; Buckingham, D M; Herbison, G P

    2002-12-01

    Quantitative measures of the importance of evidence such as the "likelihood ratio" have become increasingly popular in the courtroom. These measures have been used by expert witnesses formally to describe their certainty about a piece of evidence. These measures are commonly interpreted as the amount by which the evidence should revise the opinion of guilt, and thereby summarize the importance of a particular piece of evidence. Unlike DNA evidence, quantitative measures have not been widely used by forensic dentists to describe their certainty when testifying about bitemark evidence. There is, however, no inherent reason why they should not be used to evaluate bitemarks. The purpose of this paper is to describe the likelihood ratio as it might be applied to bitemark evidence. We use a simple bitemark example to define the likelihood ratio, its application, and interpretation. In particular we describe how the jury interprets the likelihood ratio from a Bayesian perspective when evaluating the impact of the evidence on the odds that the accused is guilty. We describe how the dentist would calculate the likelihood ratio based on frequentist interpretations. We also illustrate some of the limitations of the likelihood ratio, and show how those limitations apply to bitemark evidence. We conclude that the quality of bitemark evidence cannot be adequately summarized by the likelihood ratio, and argue that its application in this setting may be more misleading than helpful.

  13. Evidence synthesis software.

    Park, Sophie Elizabeth; Thomas, James

    2018-06-07

    It can be challenging to decide which evidence synthesis software to choose when doing a systematic review. This article discusses some of the important questions to consider in relation to the chosen method and synthesis approach. Software can support researchers in a range of ways. Here, a range of review conditions and software solutions. For example, facilitating contemporaneous collaboration across time and geographical space; in-built bias assessment tools; and line-by-line coding for qualitative textual analysis. EPPI-Reviewer is a review software for research synthesis managed by the EPPI-centre, UCL Institute of Education. EPPI-Reviewer has text mining automation technologies. Version 5 supports data sharing and re-use across the systematic review community. Open source software will soon be released. EPPI-Centre will continue to offer the software as a cloud-based service. The software is offered via a subscription with a one-month (extendible) trial available and volume discounts for 'site licences'. It is free to use for Cochrane and Campbell reviews. The next EPPI-Reviewer version is being built in collaboration with National Institute for Health and Care Excellence using 'surveillance' of newly published research to support 'living' iterative reviews. This is achieved using a combination of machine learning and traditional information retrieval technologies to identify the type of research each new publication describes and determine its relevance for a particular review, domain or guideline. While the amount of available knowledge and research is constantly increasing, the ways in which software can support the focus and relevance of data identification are also developing fast. Software advances are maximising the opportunities for the production of relevant and timely reviews. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise

  14. Synthesizing Quantitative Evidence for Evidence-based Nursing: Systematic Review.

    Oh, Eui Geum

    2016-06-01

    As evidence-based practice has become an important issue in healthcare settings, the educational needs for knowledge and skills for the generation and utilization of healthcare evidence are increasing. Systematic review (SR), a way of evidence generation, is a synthesis of primary scientific evidence, which summarizes the best evidence on a specific clinical question using a transparent, a priori protocol driven approach. SR methodology requires a critical appraisal of primary studies, data extraction in a reliable and repeatable way, and examination for validity of the results. SRs are considered hierarchically as the highest form of evidence as they are a systematic search, identification, and summarization of the available evidence to answer a focused clinical question with particular attention to the methodological quality of studies or the credibility of opinion and text. The purpose of this paper is to introduce an overview of the fundamental knowledge, principals and processes in SR. The focus of this paper is on SR especially for the synthesis of quantitative data from primary research studies that examines the effectiveness of healthcare interventions. To activate evidence-based nursing care in various healthcare settings, the best and available scientific evidence are essential components. This paper will include some examples to promote understandings. Copyright © 2016. Published by Elsevier B.V.

  15. Synthesizing Quantitative Evidence for Evidence-based Nursing: Systematic Review

    Eui Geum Oh, PhD, RN

    2016-06-01

    Full Text Available As evidence-based practice has become an important issue in healthcare settings, the educational needs for knowledge and skills for the generation and utilization of healthcare evidence are increasing. Systematic review (SR, a way of evidence generation, is a synthesis of primary scientific evidence, which summarizes the best evidence on a specific clinical question using a transparent, a priori protocol driven approach. SR methodology requires a critical appraisal of primary studies, data extraction in a reliable and repeatable way, and examination for validity of the results. SRs are considered hierarchically as the highest form of evidence as they are a systematic search, identification, and summarization of the available evidence to answer a focused clinical question with particular attention to the methodological quality of studies or the credibility of opinion and text. The purpose of this paper is to introduce an overview of the fundamental knowledge, principals and processes in SR. The focus of this paper is on SR especially for the synthesis of quantitative data from primary research studies that examines the effectiveness of healthcare interventions. To activate evidence-based nursing care in various healthcare settings, the best and available scientific evidence are essential components. This paper will include some examples to promote understandings.

  16. Finding and applying evidence during clinical rounds: the "evidence cart".

    Sackett, D L; Straus, S E

    1998-10-21

    Physicians need easy access to evidence for clinical decisions while they care for patients but, to our knowledge, no investigators have assessed use of evidence during rounds with house staff. To determine if it was feasible to find and apply evidence during clinical rounds, using an "evidence cart" that contains multiple sources of evidence and the means for projecting and printing them. Descriptive feasibility study of use of evidence during 1 month (April 1997) and anonymous questionnaire (May 1997). General medicine inpatient service. Medical students, house staff, fellows, and attending consultant. Evidence cart that included 2 secondary sources developed by the department (critically appraised topics [CATs] and Redbook), Best Evidence, JAMA Rational Clinical Examination series, the Cochrane Library, MEDLINE, a physical examination textbook, a radiology anatomy textbook, and a Simulscope, which allows several people to listen simultaneously to the same signs on physical examination. Number of times sources were used, type of sources searched and success of searches, time needed to search, and whether the search affected patient care. The evidence cart was used 98 times, but could not be taken on bedside rounds because of its bulk; hard copies of several sources were taken instead. When the evidence cart was used during team rounds and student rounds, some sources could be accessed quickly enough (10.2-25.4 seconds) to be practical on our service. Of 98 searches, 79 (81%) sought evidence that could affect diagnostic and/or treatment decisions. Seventy-one (90%) of 79 searches regarding patient management were successful, and when assessed from the perspective of the most junior team members responsible for each patient's evaluation and management, 37 (52%) of the 71 successful searches confirmed their current or tentative diagnostic or treatment plans, 18 (25%) led to a new diagnostic skill, an additional test, or a new management decision, and 16 (23

  17. Evidence based medical imaging (EBMI)

    Smith, Tony

    2008-01-01

    Background: The evidence based paradigm was first described about a decade ago. Previous authors have described a framework for the application of evidence based medicine which can be readily adapted to medical imaging practice. Purpose: This paper promotes the application of the evidence based framework in both the justification of the choice of examination type and the optimisation of the imaging technique used. Methods: The framework includes five integrated steps: framing a concise clinical question; searching for evidence to answer that question; critically appraising the evidence; applying the evidence in clinical practice; and, evaluating the use of revised practices. Results: This paper illustrates the use of the evidence based framework in medical imaging (that is, evidence based medical imaging) using the examples of two clinically relevant case studies. In doing so, a range of information technology and other resources available to medical imaging practitioners are identified with the intention of encouraging the application of the evidence based paradigm in radiography and radiology. Conclusion: There is a perceived need for radiographers and radiologists to make greater use of valid research evidence from the literature to inform their clinical practice and thus provide better quality services

  18. Evidence and Ethics (Editorial

    Alison Brettle

    2012-12-01

    Full Text Available Welcome to the December issue of EBLIP, the final issue of my first year as Editor-in-Chief. A year which I have thoroughly enjoyed and one where the fears over what to write in my editorials haven’t materialised. This quarter, ethics has featured quite heavily in my working life so I decided to make this the topic of the editorial, sharing some of my thoughts regarding evidence, ethics and how ethical principles are implemented within the EBLIP journal.Ethics are “principles of conduct or standards of behaviour governing an individual or profession” (Library and Information Science Editorial Committee, 2010, and as individuals or professionals we may be governed by various ethical codes. As I'm sure you know, EBLIP originated in the health domain, where ethical values and ethical research feature strongly. Indeed, by its formal definition, research cannot take place unless “ethical approval” from an appropriate committee has been granted. The practicalities of taking research through the ethical approval process can often be time consuming, and those involved in research need to bear this in mind when planning a project. Each committee will have a slightly different form and process (which can add to the frustration of the researcher, but basically will make their decision to approve on the basis that the research includes obtaining informed consent from participants (i.e., participants know what the research is about and what their involvement will mean; that the research will not cause harm to participants; that confidentiality will be maintained; and that the research undertaken is methodologically rigorous and worthwhile. Preparing a proposal for ethical approval, whilst time consuming, makes the researcher think about all aspects of the research and how it is going to be operationalized, which can save lots of time and effort in the long run and may well also improve the research design. These principles are the same whatever

  19. Space-time variation in the composition, richness and abundance of social wasps (Hymenoptera: Vespidae: Polistinae in a forest-agriculture mosaic in Rio Grande do Sul, Brazil

    Ricardo Pablo Klein

    2015-07-01

    Full Text Available Wasps, important agents for the control of insect population, have been scantily studied in the Brazilian State of Rio Grande do Sul. Current study investigates monthly variations of social wasps in microhabitats within a forest-agriculture mosaic. Samples were collected between February 2013 and February 2014, through active search and baited traps made from 2 L transparent PET bottles, in five microhabitats, namely, forest, monoculture, polyculture and the edges between the forest fragment and monoculture and polyculture, in the municipality of Doutor Maurício Cardoso. Statistical tests, similarity indices, dominance and constancy as well as PCoA were used for data analysis to group the collection. A total of 953 specimens were collected, distributed across 15 species and seven genera. Abundance differed between microhabitats and the monoculture cultivation was least similar to the other microhabitats. PCoA identified three different groups. Abundance was positively correlated with temperature, negatively correlated with air humidity and was not correlated with wind velocity. Social wasps are able to utilize resources outside the forest fragments, but monocultures may create barriers for their dispersal.

  20. Distribution and nests of paper wasps of Polistes (Polistella) in northeastern Vietnam, with description of a new species (Hymenoptera, Vespidae, Polistinae)

    Nguyen, Lien Thi Phuong; Kojima, Jun-ichi

    2014-01-01

    Abstract Seven species of the subgenus Polistella Ashmead of the genus Polistes Latreille including a new species, P. brunetus Nguyen & Kojima, sp. n. described here, are recognized to occur in northeastern Vietnam, the easternmost part of the eastern slope of the Himalayas. A key to these species is provided. Their distributional records are remarked. Nests of P. delhiensis Das & Gupta, P. mandarinus de Saussure and P. brunetus are also described. PMID:24478582

  1. Local-scale spatial variation in diversity of social wasps in an Amazonian rain forest in Caxiuanã, Pará, Brazil (Hymenoptera, Vespidae, Polistinae

    Orlando Tobias Silveira

    2012-09-01

    Full Text Available Polistine wasps are important in Neotropical ecosystems due to their ubiquity and diversity. Inventories have not adequately considered spatial attributes of collected specimens. Spatial data on biodiversity are important for study and mitigation of anthropogenic impacts over natural ecosystems and for protecting species. We described and analyzed local-scale spatial patterns of collecting records of wasp species, as well as spatial variation of diversity descriptors in a 2500-hectare area of an Amazon forest in Brazil. Rare species comprised the largest fraction of the fauna. Close range spatial effects were detected for most of the more common species, with clustering of presence-data at short distances. Larger spatial lag effects could also be identified in some species, constituting probably cases of exogenous autocorrelation and candidates for explanations based on environmental factors. In a few cases, significant or near significant correlations were found between five species (of Agelaia, Angiopolybia, and Mischocyttarus and three studied environmental variables: distance to nearest stream, terrain altitude, and the type of forest canopy. However, association between these factors and biodiversity variables were generally low. When used as predictors of polistine richness in a linear multiple regression, only the coefficient for the forest canopy variable resulted significant. Some level of prediction of wasp diversity variables can be attained based on environmental variables, especially vegetation structure. Large-scale landscape and regional studies should be scheduled to address this issue.

  2. Notes on social wasps of the group of Mischocyttarus(Omega punctatus (Ducke, with description of six new species (Hymenoptera, Vespidae, Polistinae

    Orlando Tobias Silveira

    2015-09-01

    Full Text Available ABSTRACTA revision of the taxonomic status and an identification key for wasp species of the genus Mischocyttarus related to M. punctatus (Ducke, 1904 are presented here. Six new species are proposed (M. tayrona Silveira sp. nov.; M. anchicaya Silveira sp. nov.; M. caxiuana Silveira sp. nov.; M. verissimoi Silveira sp. nov.; M. rodriguesi Silveira sp. nov.; M. ryani Silveira sp. nov., raising to nine the number of species in the M. punctatus group. The highest diversity of the group concentrates in northern South America, in Andean areas and Amazonia. New information concerning the very peculiar nests of these wasps is also given.

  3. Evidence-based clinical practice

    Gluud, Christian

    2002-01-01

    , and single clinics. Accordingly, there is an urgent need to improve this situation. Guidelines for Good Clinical (Research) Practice, conduct of more trials as multicentre trials, The Consort Statement, and The Cochrane Collaboration may all help in the application of the best research evidence in clinical......Evidence-based medicine combines the patient's preferences with clinical experience and the best research evidence. Randomized clinical trials are considered the most valid research design for evaluating health-care interventions. However, empirical research shows that intervention effects may...... practice. By investments in education, applied research, and The Cochrane Collaboration, evidence-based medicine may form a stronger basis for clinical practice....

  4. Psiquiatria baseada em evidências Evidence-based psychiatry

    Maurício S de Lima

    2000-09-01

    Full Text Available Em psiquiatria, observa-se grande variabilidade de práticas clínicas, muitas vezes desnecessária. Essas variações podem estar relacionadas à ausência de evidência científica confiável ou ao desconhecimento das evidências de boa qualidade disponíveis. A medicina baseada em evidências (MBE é uma combinação de estratégias que busca assegurar que o cuidado individual do paciente seja baseado na melhor informação disponível, a qual deve ser incorporada à prática clínica. Neste artigo, conceitos de MBE são discutidos com relação a aspectos e desafios no tratamento de pacientes com distimia, bulimia nervosa e esquizofrenia. A partir de resultados de três revisões sistemáticas recentemente publicadas, conclui-se que a prática de psiquiatria baseada em evidências acrescenta qualidade à prática psiquiátrica tradicional.The unnecessary variability often seen in the clinical practice can be related to both the absence of reliable evidence and unawareness of the existence of good quality evidence. Evidence-Based Medicine (EBM is a set of linked strategies designed to assist clinicians in keeping themselves up-to-date with the best available evidence. Such evidence must be incorporated into the clinical practice. EBM concepts are discussed here through common aspects and challenges doctors face when treating patients with dysthymia, bulimia nervosa, and schizophrenia. In the light of some results from three systematic reviews it is concluded that Evidence-Based Psychiatry strategies, rather than replacing the traditional ones, may be a valuable tool to improving quality in a good clinical practice.

  5. Expression and regulation of prostaglandin transporters, ATP-binding cassette, subfamily C, member 1 and 9, and solute carrier organic anion transporter family, member 2A1 and 5A1 in the uterine endometrium during the estrous cycle and pregnancy in pigs

    Hwanhee Jang

    2017-05-01

    Full Text Available Objective Prostaglandins (PGs function in various reproductive processes, including luteolysis, maternal pregnancy recognition, conceptus development, and parturition. Our earlier study has shown that PG transporters ATP-binding cassette, subfamily C, member 4 (ABCC4 and solute carrier organic anion transporter family, member 2A1 (SLCO2A1 are expressed in the uterine endometrium in pigs. Since several other PG transporters such as ABCC1, ABCC9, SLCO4C1, and SLCO5A1 are known to be present in the uterine endometrium, this study investigated the expression of these PG transporters in the porcine uterine endometrium and placenta. Methods Uterine endometrial tissues were obtained from gilts on day (D 12 and D15 of the estrous cycle and days 12, 15, 30, 60, 90, and 114 of pregnancy. Results ABCC1, ABCC9, SLCO4C1, and SLCO5A1 mRNAs were expressed in the uterine endometrium, and levels of expression changed during the estrous cycle and pregnancy. Expression of ABCC1 and ABCC9 mRNAs was localized mainly to luminal and glandular epithelial cells in the uterine endometrium, and chorionic epithelial cells during pregnancy. Conceptuses during early pregnancy and chorioallantoic tissues from mid to late pregnancy also expressed these PG transporters. Estradiol-17β increased the expression of ABCC1 and SLCO5A1, but not ABCC9 and SLCO4C1 mRNAs and increasing doses of interleukin-1β induced the expression of ABCC9, SLCO4C1, and SLCO5A1 mRNAs in endometrial explant tissues. Conclusion These data showed that several PG transporters such as ABCC1, ABCC9, SLCO4C1, and SLCO5A1 were expressed at the maternal-conceptus interface, suggesting that these PG transporters may play an important role in the establishment and maintenance of pregnancy by regulating PG transport in the uterine endometrium and placenta in pigs.

  6. Systematic gene deletions evidences that laccases are involved in several stages of wood degradation in the filamentous fungus Podospora anserina.

    Xie, Ning; Chapeland-Leclerc, Florence; Silar, Philippe; Ruprich-Robert, Gwenaël

    2014-01-01

    Transformation of plant biomass into biofuels may supply environmentally friendly alternative biological sources of energy. Laccases are supposed to be involved in the lysis of lignin, a prerequisite step for efficient breakdown of cellulose into fermentable sugars. The role in development and plant biomass degradation of the nine canonical laccases belonging to three different subfamilies and one related multicopper oxidase of the Ascomycota fungus Podospora anserina was investigated by targeted gene deletion. The 10 genes were inactivated singly, and multiple mutants were constructed by genetic crosses. lac6(Δ), lac8(Δ) and mco(Δ) mutants were significantly reduced in their ability to grow on lignin-containing materials, but also on cellulose and plastic. Furthermore, lac8(Δ), lac7(Δ), mco(Δ) and lac6(Δ) mutants were defective towards resistance to phenolic substrates and H2 O2 , which may also impact lignocellulose breakdown. Double and multiple mutants were generally more affected than single mutants, evidencing redundancy of function among laccases. Our study provides the first genetic evidences that laccases are major actors of wood utilization in a fungus and that they have multiple roles during this process apart from participation in lignin lysis. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  7. How to map the evidence

    Møller, Ann

    2012-01-01

    and sponsored many projects in order to get new products onto the market. The lack of an overview and control has led to an abundance of evidence within certain areas of our specialty, whereas other areas are scarcely, or not at all, researched. One way of 'mapping' the evidence in order to find out what we...

  8. Conversational evidence in therapeutic dialogue.

    Strong, Tom; Busch, Robbie; Couture, Shari

    2008-07-01

    Family therapists' participation in therapeutic dialogue with clients is typically informed by evidence of how such dialogue is developing. In this article, we propose that conversational evidence, the kind that can be empirically analyzed using discourse analyses, be considered a contribution to widening psychotherapy's evidence base. After some preliminaries about what we mean by conversational evidence, we provide a genealogy of evaluative practice in psychotherapy, and examine qualitative evaluation methods for their theoretical compatibilities with social constructionist approaches to family therapy. We then move on to examine the notion of accomplishment in therapeutic dialogue given how such accomplishments can be evaluated using conversation analysis. We conclude by considering a number of research and pedagogical implications we associate with conversational evidence.

  9. Molecular phylogeny of tribe Stachydeae (Lamiaceae subfamily Lamioideae)

    Salmaki, Yasaman; Zarre, Shahin; Ryding, Olof

    2013-01-01

    this largest of all lamioid tribes. We included 143 accessions corresponding to 121 species, representing both Old and New World species, and all 12 recognized genera of tribe Stachydeae. Both nuclear and plastid data corroborate monophyly of the tribe, with Melittis as sister to all remaining Stachydeae...... subclades are congruent between the plastid and nuclear tree topologies, whereas their relative phylogenetic placements are often not. This level of plastid-nuclear incongruence suggests considerable impact of hybridization in the evolution of Stachydeae. (C) 2013 Elsevier Inc. All rights reserved....

  10. Children under 5 in Families and Subfamilies in 1990

    U.S. Environmental Protection Agency — Variable was created as part of a set of indicators that demonstrate links between the condition of natural areas and human concerns and that quantify dependencies...

  11. Integrating Evidence Within and Across Evidence Streams Using Qualitative Methods

    There is high demand in environmental health for adoption of a structured process that evaluates and integrates evidence while making decisions transparent. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) framework holds promise to address this deman...

  12. Using evidence to make decisions

    Jenkins, Charles

    2014-12-01

    Bayesian evidence ratios give a very attractive way of comparing models, and being able to quote the odds on a particular model seems a very clear motivation for making a choice. Jeffreys' scale of evidence is often used in the interpretation of evidence ratios. A natural question is, how often will you get it right when you choose on the basis of some threshold value of the evidence ratio? The evidence ratio will be different in different realizations of the data, and its utility can be examined in a Neyman-Pearson like way to see what the trade-offs are between statistical power (the chance of "getting it right") versus the false alarm rate, picking the alternative hypothesis when the null is actually true. I will show some simple examples which show that there can be a surprisingly large range for an evidence ratio under different realizations of the data. It seems best not to simply rely on Jeffrey's scale when decisions have to be taken, but also to examine the probability of taking the "wrong" decision if some evidence ratio is taken to be decisive. Interestingly, Turing knew this and applied it during WWII, although (like much else) he did not publish it.

  13. Gravitational Waves: The Evidence Mounts

    Wick, Gerald L.

    1970-01-01

    Reviews the work of Weber and his colleagues in their attempts at detecting extraterrestial gravitational waves. Coincidence events recorded by special detectors provide the evidence for the existence of gravitational waves. Bibliography. (LC)

  14. Values, Evidence, and Mastery Learning.

    Anderson, Lorin W.; Burns, Robert B.

    1987-01-01

    Responds to R. Slavin's best-evidence synthesis of research on mastery learning. Contends that at the heart of decisions about education are value judgments about how the mind should be cultivated and for what goal. (RB)

  15. Evidence-based cancer imaging

    Shinagare, Atul B.; Khorasani, Ramin [Dept. of Radiology, Brigham and Women' s Hospital, Boston (Korea, Republic of)

    2017-01-15

    With the advances in the field of oncology, imaging is increasingly used in the follow-up of cancer patients, leading to concerns about over-utilization. Therefore, it has become imperative to make imaging more evidence-based, efficient, cost-effective and equitable. This review explores the strategies and tools to make diagnostic imaging more evidence-based, mainly in the context of follow-up of cancer patients.

  16. Phylogenetic reconstruction by cross-species chromosome painting and G-banding in four species of Phyllostomini tribe (Chiroptera, Phyllostomidae) in the Brazilian Amazon: an independent evidence for monophyly.

    Ribas, Talita Fernanda Augusto; Rodrigues, Luis Reginaldo Ribeiro; Nagamachi, Cleusa Yoshiko; Gomes, Anderson José Baia; Rissino, Jorge das Dores; O'Brien, Patricia Caroline Mary; Yang, Fengtang; Ferguson-Smith, Malcolm Andrew; Pieczarka, Julio Cesar

    2015-01-01

    The subfamily Phyllostominae comprises taxa with a variety of feeding strategies. From the cytogenetic point of view, Phyllostominae shows different rates of chromosomal evolution between genera, with Phyllostomus hastatus probably retaining the ancestral karyotype for the subfamily. Since chromosomal rearrangements occur rarely in the genome and have great value as phylogenetic markers and in taxonomic characterization, we analyzed three species: Lophostoma silvicola (LSI), Phyllostomus discolor (PDI) and Tonatia saurophila (TSA), representing the tribe Phyllostomini, collected in the Amazon region, by classic and molecular cytogenetic techniques in order to reconstruct the phylogenetic relationships within this tribe. LSA has a karyotype of 2n=34 and FN=60, PDI has 2n=32 and FN=60 and TSA has 2n=16 and FN=20. Comparative analysis using G-banding and chromosome painting show that the karyotypic complement of TSA is highly rearranged relative to LSI and PHA, while LSI, PHA and PDI have similar karyotypes, differing by only three chromosome pairs. Nearly all chromosomes of PDI and PHA were conserved in toto, except for chromosome 15 that was changed by a pericentric inversion. A strongly supported phylogeny (bootstrap=100 and Bremer=10 steps), confirms the monophyly of Phyllostomini. In agreement with molecular topologies, TSA was in the basal position, while PHA and LSI formed sister taxa. A few ancestral syntenies are conserved without rearrangements and most associations are autapomorphic traits for Tonatia or plesiomorphic for the three genera analyzed here. The karyotype of TSA is highly derived in relation to that of other phyllostomid bats, differing from the supposed ancestral karyotype of Phyllostomidae by multiple rearrangements. Phylogenies based on chromosomal data are independent evidence for the monophyly of tribe Phyllostomini as determined by molecular topologies and provide additional support for the paraphyly of the genus Tonatia by the exclusion

  17. Phylogenetic reconstruction by cross-species chromosome painting and G-banding in four species of Phyllostomini tribe (Chiroptera, Phyllostomidae in the Brazilian Amazon: an independent evidence for monophyly.

    Talita Fernanda Augusto Ribas

    Full Text Available The subfamily Phyllostominae comprises taxa with a variety of feeding strategies. From the cytogenetic point of view, Phyllostominae shows different rates of chromosomal evolution between genera, with Phyllostomus hastatus probably retaining the ancestral karyotype for the subfamily. Since chromosomal rearrangements occur rarely in the genome and have great value as phylogenetic markers and in taxonomic characterization, we analyzed three species: Lophostoma silvicola (LSI, Phyllostomus discolor (PDI and Tonatia saurophila (TSA, representing the tribe Phyllostomini, collected in the Amazon region, by classic and molecular cytogenetic techniques in order to reconstruct the phylogenetic relationships within this tribe. LSA has a karyotype of 2n=34 and FN=60, PDI has 2n=32 and FN=60 and TSA has 2n=16 and FN=20. Comparative analysis using G-banding and chromosome painting show that the karyotypic complement of TSA is highly rearranged relative to LSI and PHA, while LSI, PHA and PDI have similar karyotypes, differing by only three chromosome pairs. Nearly all chromosomes of PDI and PHA were conserved in toto, except for chromosome 15 that was changed by a pericentric inversion. A strongly supported phylogeny (bootstrap=100 and Bremer=10 steps, confirms the monophyly of Phyllostomini. In agreement with molecular topologies, TSA was in the basal position, while PHA and LSI formed sister taxa. A few ancestral syntenies are conserved without rearrangements and most associations are autapomorphic traits for Tonatia or plesiomorphic for the three genera analyzed here. The karyotype of TSA is highly derived in relation to that of other phyllostomid bats, differing from the supposed ancestral karyotype of Phyllostomidae by multiple rearrangements. Phylogenies based on chromosomal data are independent evidence for the monophyly of tribe Phyllostomini as determined by molecular topologies and provide additional support for the paraphyly of the genus Tonatia by

  18. Persuasive Evidence: Improving Customer Service through Evidence Based Librarianship

    Wendy A. Abbott

    2006-03-01

    Full Text Available Objective - To demonstrate how evidence based practice has contributed to informaing decisions and resolving issues if concern in service delivery at Bond University Librray. Methods - This paper critically analyses three evidence based research projects conducted at Bond University Library. Each project combined a range of research methods including surveys, literature reviews and the analysis of internal performance data to find solutions to problems in library service delivery. The first research project investigated library opening hours and the feasability of twenty-four hour opening. Another project reseached questions about the management of a collection of feature films on DVD and video. The thrd project investigated issues surrounding the teaching of EndNote to undergarduate students. Results - Despite some deficiencies in the methodologies used, each evidence based research project had positive outcomes. One of the highlights asn an essential feature of the process at Bond University Library was the involvement of stakeholders. The ability to build consensus and agree action plans with stakeholders was an important outcome of that process. Conclusion - Drawing on the experience of these research projects, the paper illustrates the benefits of evidence based information practice to stimulate innovation and improve library services. Librarians, like most professionals, need to continue to develop the skills and a culture to effectively carry out evidence based practice.

  19. Evidence in the learning organization

    Umscheid Craig A

    2009-03-01

    Full Text Available Abstract Background Organizational leaders in business and medicine have been experiencing a similar dilemma: how to ensure that their organizational members are adopting work innovations in a timely fashion. Organizational leaders in healthcare have attempted to resolve this dilemma by offering specific solutions, such as evidence-based medicine (EBM, but organizations are still not systematically adopting evidence-based practice innovations as rapidly as expected by policy-makers (the knowing-doing gap problem. Some business leaders have adopted a systems-based perspective, called the learning organization (LO, to address a similar dilemma. Three years ago, the Society of General Internal Medicine's Evidence-based Medicine Task Force began an inquiry to integrate the EBM and LO concepts into one model to address the knowing-doing gap problem. Methods During the model development process, the authors searched several databases for relevant LO frameworks and their related concepts by using a broad search strategy. To identify the key LO frameworks and consolidate them into one model, the authors used consensus-based decision-making and a narrative thematic synthesis guided by several qualitative criteria. The authors subjected the model to external, independent review and improved upon its design with this feedback. Results The authors found seven LO frameworks particularly relevant to evidence-based practice innovations in organizations. The authors describe their interpretations of these frameworks for healthcare organizations, the process they used to integrate the LO frameworks with EBM principles, and the resulting Evidence in the Learning Organization (ELO model. They also provide a health organization scenario to illustrate ELO concepts in application. Conclusion The authors intend, by sharing the LO frameworks and the ELO model, to help organizations identify their capacities to learn and share knowledge about evidence-based practice

  20. Electrophysiological evidence for phenomenal consciousness.

    Revonsuo, Antti; Koivisto, Mika

    2010-09-01

    Abstract Recent evidence from event-related brain potentials (ERPs) lends support to two central theses in Lamme's theory. The earliest ERP correlate of visual consciousness appears over posterior visual cortex around 100-200 ms after stimulus onset. Its scalp topography and time window are consistent with recurrent processing in the visual cortex. This electrophysiological correlate of visual consciousness is mostly independent of later ERPs reflecting selective attention and working memory functions. Overall, the ERP evidence supports the view that phenomenal consciousness of a visual stimulus emerges earlier than access consciousness, and that attention and awareness are served by distinct neural processes.

  1. Evidence-based playground design

    Refshauge, Anne Dahl; Stigsdotter, Ulrika K.; Lamm, Bettina

    2015-01-01

    , best practice, and the theories of Affordances and Behaviour Settings. A post-occupancy evaluation was carried out through a questionnaire survey and observation studies, which revealed that a majority of the potential evidence-based affordances were actualised, and that the application of the theories...

  2. Evidence-Based IT Development

    Simonsen, Jesper; Hertzum, Morten

    2005-01-01

    Evidence-based IT development aims at developing a new commercial contract model for IT projects where the cus-tomers payment is dependent on measurable effects of using the vendors system. The idea is to establish a strategic part-nership in which customer and IT vendor share the responsi-bility...

  3. Anatomy of an Evidence Base

    Malouf, David B.; Taymans, Juliana M.

    2016-01-01

    An analysis was conducted of the What Works Clearinghouse (WWC) research evidence base on the effectiveness of replicable education interventions. Most interventions were found to have little or no support from technically adequate research studies, and intervention effect sizes were of questionable magnitude to meet education policy goals. These…

  4. Killing fields; The epidemiological evidence

    Best, Simon

    1990-02-01

    The threat posed by low frequency fields emerged initially because a researcher, looking for environmental factors in childhood leukaemia, observed a link between low voltage, high current power lines and disease occurrence. Cellular evidence now supports the findings but epidemiology still leads the argument. (43 references). (author).

  5. Learned Helplessness: Theory and Evidence

    Maier, Steven F.; Seligman, Martin E. P.

    1976-01-01

    Authors believes that three phenomena are all instances of "learned helplessness," instances in which an organism has learned that outcomes are uncontrollable by his responses and is seriously debilitated by this knowledge. This article explores the evidence for the phenomena of learned helplessness, and discussed a variety of theoretical…

  6. Evidence-Based Psychological Assessment.

    Bornstein, Robert F

    2017-01-01

    In recent years there has been increasing emphasis on evidence-based practice in psychology (EBPP), and as is true in most health care professions, the primary focus of EBPP has been on treatment. Comparatively little attention has been devoted to applying the principles of EBPP to psychological assessment, despite the fact that assessment plays a central role in myriad domains of empirical and applied psychology (e.g., research, forensics, behavioral health, risk management, diagnosis and classification in mental health settings, documentation of neuropsychological impairment and recovery, personnel selection and placement in organizational contexts). This article outlines the central elements of evidence-based psychological assessment (EBPA), using the American Psychological Association's tripartite definition of EBPP as integration of the best available research with clinical expertise in the context of patient characteristics, culture, and preferences. After discussing strategies for conceptualizing and operationalizing evidence-based testing and evidence-based assessment, 6 core skills and 3 meta-skills that underlie proficiency in psychological assessment are described. The integration of patient characteristics, culture, and preferences is discussed in terms of the complex interaction of patient and assessor identities and values throughout the assessment process. A preliminary framework for implementing EBPA is offered, and avenues for continued refinement and growth are described.

  7. The evidence for Allee effects

    Andrew M. Kramer; Brian Dennis; Andrew M. Liebhold; John M. Drake

    2009-01-01

    Allee effects are an important dynamic phenomenon believed to be manifested in several population processes, notably extinction and invasion. Though widely cited in these contexts, the evidence for their strength and prevalence has not been critically evaluated. We review results from 91 studies on Allee effects in natural animal populations. We focus on empirical...

  8. Evidence-based clinical practice

    Garattini, Silvio; Jakobsen, Janus C; Wetterslev, Jørn

    2016-01-01

    was considered through literature searches combined with personal files. Treatments should generally not be chosen based only on evidence from observational studies or single randomised clinical trials. Systematic reviews with meta-analysis of all identifiable randomised clinical trials with Grading...

  9. Utilização de frutos de cactos (Cactaceae como recurso alimentar por vespas sociais (Hymenoptera, Vespidae, Polistinae em uma área de caatinga (Ipirá, Bahia, Brasil The use of cactus fruit food resources by social wasp (Hymenoptera, Vespidae, Polistinae in an area of Caatinga (lpirá, Bahia, Brazil

    Gilberto M. M. Santos

    2007-12-01

    Full Text Available Este estudo teve por objetivo identificar as espécies utilizadas como recurso alimentar e descrever os padrões locais de utilização de frutos de cactos como recurso alimentar por vespas sociais em uma área de Caatinga. Novecentos e oito indivíduos de nove espécies de vespas foram capturados visitando seis espécies de cactáceas. Cereus jamacaru DC. e Pilosocereus catingicola (Gurke Byles & G.D foram as cactáceas mais utilizadas por vespas sociais, tanto em número de espécies quanto de indivíduos. Polybia paulista von Ihering, 1896, Polybia ignobilis (Haliday, 1836, Polistes versicolor (Olivier, 1791, Polistes simillimus Zikán, 1951, Polistes billardieri Fabricius, 1804, Polistes canadensis (Linnaeus, 1758, Polybia occidentalis (Olivier, 1791 e Polybia sericea (Olivier, 1705 apresentaram as maiores amplitudes de nicho trófico. As maiores sobreposições no nicho trófico foram observadas entre Mischocyttarus lanei Zikán, 1949 e Polistes simillimus Zikán, 1951 (0,83. Os altos níveis de sobreposição de nichos observados são explicados em função do comportamento generalista das vespas sociais, bem como da exploração intensiva de poucas espécies de cactáceas.This study aims to identify food resource plants used by social wasp species in a Caatinga area, as well as describe the local patterns of cactus fruit resources used by wasps. Nine hundreds and eight foraging wasps, belonging to nine species, were captured while visiting six cactus species. Cereus jamacaru DC. and Pilosocereus catingicola (Gurke Byles & G.D. were the most frequently visited plants. Several wasp species and a great number of individuals visited them. Polybia paulista von Ihering, 1896, Polybia ignobilis (Haliday, 1836, Polistes versicolor (Olivier, 1791, Polistes simillimus Zikán, 1951, Polistes billardieri Fabricius, 1804, Polistes canadensis (Linnaeus, 1758, Polybia occidentalis (Olivier, 1791 and Polybia sericea (Olivier, 1705 had the larger trophic niche breadth. The highest trophic niche overlap was between Mischocyttarus lanei Zikán, 1949 and Polistes simillimus Zikán, 1951 (0.83. The high niche overlap among social wasps seems to be resulting of the generalist behavior of the social wasp, as well as of the intensive exploration of few cactus species.

  10. From evidence-based to evidence-reflected practice

    Lystbæk, Christian Tang

    “Knowledge” is of the utmost significance for professional practice and learning. Today, though, the established knowledge base is changing in all areas of the labour market (Alvesson, 2004). Work and society are dominated by commitment to demands for high levels of demonstrable accountability......, cost-efficiency and measurable quality. Thus, today, evidence-based practice has become an expectation and fashion, often used to emphasize the grounding of practice in research based knowledge that provides measurable evidence for best practice. But at the same time, there is a growing distrust...... of the supremacy of this kind of knowledge, and traditional monopolies of knowledge are challenged (Gabbay & May, 2010). In the literature, there is an on-going debate about professional knowledge enacted in diverse settings. This debate presents a wide range of epistemological terminologies and typologies, which...

  11. Evidence, Ethics & Social Policy Dilemmas

    Steven I. Miller

    1993-07-01

    Full Text Available Within the philosophy of the social sciences, the relationship between evidence, ethics, and social policy is in need of further analysis. The present paper is an attempt to argue that while important social policies can, and perhaps ought to be, grounded in ethical theory, they are seldom articulated in this fashion due to the ambiguity surrounding the "evidence condition." Using a consequentialist-utilitarian framework, and a case study of a policy dilemma, the authors analyze the difficulties associated with resolving policy-based dilemmas which must appeal to evidential support as a justification for an ethical stand. Implication for the relevance of ethics to social policy formulation are discussed in detail.

  12. Experimental Evidence on Transfer Pricing

    Tran Quoc H.

    2016-06-01

    Full Text Available We use incentivized economics experiments to test both the point predictions and comparative static predictions of optimal transfer pricing models, comparing behavior under varying conditions, including wholly versus partially-owned subsidiaries and different tariff and tax rates. As predicted, we find that transfer prices are responsive to relative tax and tariff rates as well as ownership proportions. Additionally, we examine convergence and learning in this setting. While individuals do not choose optimal transfer prices, their choices converge to optimal levels with experience. This paper thus makes two important contributions. First, by comparing behavior with theoretical predictions it provides evidence of whether (and when individuals set transfer prices optimally. Second, by comparing behavior under conditions of full and partial ownership it provides evidence on the impact of policy interventions (like regulating ownership proportions by MNEs on tax revenues.

  13. Mass spectrometric and enzymatic evidence confirm the existence of anthocyanidin 3,5-O-diglucosides in cabernet sauvignon (Vitis vinifera L.) grape berries.

    Xing, Ran-Ran; Li, Si-Yu; He, Fei; Yang, Zhe; Duan, Chang-Qing; Li, Zheng; Wang, Jun; Pan, Qiu-Hong

    2015-04-01

    It has been widely accepted that anthocyanidin 3,5-O-diglucosides do not exist in Vitis vinifera L. Cabernet Sauvignon (CS) berries. However, our anthocyanin analyses using HPLC-ESI-MS/MS detected the existence of a low level of anthocyanidin 3,5-O-diglucosides in the Cabernet Sauvignon grape berries grown in China. The authenticity of these samples was confirmed with microsatellite markers. The existence of anthocyanidin 3,5-O-diglucoside was further verified by the enzymatic evidence for the first time. Four putative 5-O-glucosyltransferase (5GT) genes were isolated from the Cabernet Sauvignon berries. The enzymatic analysis showed that a recombinant protein (designated as Vv5GT3) glucosylated the 3-O- and 5-O-positions of anthocyanidins and flavonols. A phylogenetic analysis revealed that this bifunctional enzyme belongs to the 5GT subfamily of UDP-glycosyltransferases. This finding brought a new understanding of the anthocyanins' profile and their biosynthesis in V. vinifera and would be helpful for further investigations of the mechanism of accumulation of anthocyanidin diglucosides in Cabernet Sauvignon berries in China's wine-producing regions.

  14. The evidence base for diabetes care

    Williams, D. R. R. (David Robert Rhys)

    2002-01-01

    ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix 1. The Evidence Base for Diabetes Care . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Rhys Williams, William Herman, Ann-Louise Kinmonth...

  15. 20 CFR 422.107 - Evidence requirements.

    2010-04-01

    .... (2) Additional evidence rules for F-1 students—(i) Evidence from your designated school official. If... may consist of a driver's license, identity card, school record, medical record, marriage record... satisfactory evidence of U.S. citizenship is furnished. Any of the following is generally acceptable evidence...

  16. Hearsay Evidence | Abebe | Mizan Law Review

    Hearsay evidence is the submission of evidence by a person based on what s/he has heard from another person who has not appeared in court. This article examines the extent to which hearsay evidence is admissible in common law and civil law. The core theme addressed in this article is whether hearsay evidence ...

  17. Leading teaming: Evidence from Jazz

    Araújo, Francisco Maria Trigo da Roza Carvalho

    2013-01-01

    A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics In this research we conducted qualitative analysis to study the team dynamics of jazz combos in order to explore deeper the leadership behaviors in a creative environment where teaming occurs. We found evidence of a dual leader, one that shifts his/her role between ‘leader as leader’ and ‘leader as member’, embracing both leaderfulness an...

  18. Proof of evidence [BNFL 2

    Avery, D.G.

    1982-01-01

    It is shown that the fuel cycle requirements of the proposed Sizewell B nuclear power station could be supplied by British Nuclear Fuels Limited. It is demonstrated that any facilities which may be required in the future could be provided from established technology. Evidence is presented in support of the responses which the Company has made to requests from the CEGB for guidance on the charges it should assume for some fuel cycle services in a variety of circumstances. Reference is made throughout to the fuel cycle needs of other possible future nuclear power stations as postulated by CEGB in its Statement of Case. (U.K.)

  19. Evidence for the MSW effect

    Fogli, Gianluigi; Lisi, Eligio

    2004-01-01

    Recent solar and reactor neutrino data have convincingly established that electron neutrinos and antineutrinos are subject to flavour transitions driven by neutrino masses and mixing. In addition, such data can be used to prove that the interaction of neutrinos in matter modifies the flavour transition pattern with respect to the case of propagation in vacuum, as predicted long ago by Mikheyev, Smirnov and Wolfenstein (MSW). We present a brief review of how the current evidence for MSW solar neutrino transitions has developed in recent years, and how it has been strengthened by the latest reactor neutrino data presented at the Neutrino 2004 Conference

  20. Evidence for the MSW effect

    Fogli, Gianluigi; Lisi, Eligio

    2004-10-01

    Recent solar and reactor neutrino data have convincingly established that electron neutrinos and antineutrinos are subject to flavour transitions driven by neutrino masses and mixing. In addition, such data can be used to prove that the interaction of neutrinos in matter modifies the flavour transition pattern with respect to the case of propagation in vacuum, as predicted long ago by Mikheyev, Smirnov and Wolfenstein (MSW). We present a brief review of how the current evidence for MSW solar neutrino transitions has developed in recent years, and how it has been strengthened by the latest reactor neutrino data presented at the Neutrino 2004 Conference.

  1. Hard evidence on soft skills.

    Heckman, James J; Kautz, Tim

    2012-08-01

    This paper summarizes recent evidence on what achievement tests measure; how achievement tests relate to other measures of "cognitive ability" like IQ and grades; the important skills that achievement tests miss or mismeasure, and how much these skills matter in life. Achievement tests miss, or perhaps more accurately, do not adequately capture, soft skills -personality traits, goals, motivations, and preferences that are valued in the labor market, in school, and in many other domains. The larger message of this paper is that soft skills predict success in life, that they causally produce that success, and that programs that enhance soft skills have an important place in an effective portfolio of public policies.

  2. Direct enzyme assay evidence confirms aldehyde reductase function of Ydr541cp and Ygl039wp from Saccharomyces cerevisiae.

    Moon, Jaewoong; Liu, Z Lewis

    2015-04-01

    The aldehyde reductase gene ARI1 is a recently characterized member of an intermediate subfamily within the short-chain dehydrogenase/reductase (SDR) superfamily that clarified mechanisms of in situ detoxification of 2-furaldehyde and 5-hydroxymethyl-2-furaldehyde by Saccharomyces cerevisiae. Uncharacterized open reading frames (ORFs) are common among tolerant candidate genes identified for lignocellulose-to-advanced biofuels conversion. This study presents partially purified proteins of two ORFs, YDR541C and YGL039W, and direct enzyme assay evidence against aldehyde-inhibitory compounds commonly encountered during lignocellulosic biomass fermentation processes. Each of the partially purified proteins encoded by these ORFs showed a molecular mass of approximately 38 kDa, similar to Ari1p, a protein encoded by aldehyde reductase gene. Both proteins demonstrated strong aldehyde reduction activities toward 14 aldehyde substrates, with high levels of reduction activity for Ydr541cp toward both aromatic and aliphatic aldehydes. While Ydr541cp was observed to have a significantly higher specific enzyme activity at 20 U/mg using co-factor NADPH, Ygl039wp displayed a NADH preference at 25 U/mg in reduction of butylaldehyde. Amino acid sequence analysis identified a characteristic catalytic triad, Ser, Tyr and Lys; a conserved catalytic motif of Tyr-X-X-X-Lys; and a cofactor-binding sequence motif, Gly-X-X-Gly-X-X-Ala, near the N-terminus that are shared by Ydr541cp, Ygl039wp, Yol151wp/GRE2 and Ari1p. Findings of aldehyde reductase genes contribute to the yeast gene annotation and aids development of the next-generation biocatalyst for advanced biofuels production. Copyright © 2015 John Wiley & Sons, Ltd.

  3. Digital forensics digital evidence in criminal investigations

    Marshall, Angus McKenzie

    2009-01-01

    The vast majority of modern criminal investigations involve some element of digital evidence, from mobile phones, computers, CCTV and other devices. Digital Forensics: Digital Evidence in Criminal Investigations provides the reader with a better understanding of how digital evidence complements "traditional" scientific evidence and examines how it can be used more effectively and efficiently in a range of investigations. Taking a new approach to the topic, this book presents digital evidence as an adjunct to other types of evidence and discusses how it can be deployed effectively in s

  4. Studies on Neotropical Phasmatodea XVI: Revision of Haplopodini Günther, 1953 (rev. stat.), with notes on the subfamily Cladomorphinae Bradley & Galil, 1977 and the descriptions of a new tribe, four new genera and nine new species (Phasmatodea: "Anareolatae": Phasmatidae: Cladomorphinae).

    Hennemann, Frank H; Conle, Oskar V; Perez-Gelabert, Daniel E

    2016-06-27

    The anareolate New World subfamily Cladomorphinae Bradley & Galil, 1977 is reviewed and keys to the six tribes currently included are presented; these are: Cladomorphini Bradley & Galil, 1977, Cladoxerini Karny, 1923, Cranidiini Günther, 1953, Pterinoxylini n. trib., Hesperophasmatini Bradley & Galil, 1977 and Haplopodini Günther, 1953 rev. stat.. New diagnoses are presented for all these tribes and possible relationships within Cladomorphinae are discusssed. Morphology of the genitalia and egg-structures indicate Cladomorphinae as presently treated to be polyphyletic. Two subordinate groups are recognized within present Cladomorphinae, which differ considerably in numerous morphological characters of the insects and eggs. The first group and here regarded as Cladomorphinae sensu stricto is formed by the mostly South American Cladomorphini + Cranidiini + Cladoxerini, while the second group is formed by the predominantly Caribbean Hesperophasmatini + Pterinoxylini n. trib. + Haplopodini.        Members of the first group (= Cladomorphini sensu stricto) share the dorsally carinate basitarsus in which the two dorsal carinae are melted with another, increasingly elongated gonapophyses VIII of females which are noticeably longer than gonapophyses IX and lamellate as well as strongly displaced medioventral carina of the profemora. Cranidiini + Cladomorphini share the strongly elongated and filiform gonapophyses VIII and presence of gonoplacs in the females, specialized poculum of males and presence of a median line in the eggs. Cranidiini differs from all other tribes of Cladomorphinae by the entirely unarmed legs of both sexes, distinctly broadened and leaf-like body and prominent longitudinal keel of the mesosternum of females, prominently enlarged poculum and spinulose phallus of males as well as the conspicuous narrowing of the posteromedian gap of the internal micropylar plate of the eggs and noticeably separated median line. Cladomorphini is characteristic

  5. Evidence for Ancient Mesoamerican Earthquakes

    Kovach, R. L.; Garcia, B.

    2001-12-01

    Evidence for past earthquake damage at Mesoamerican ruins is often overlooked because of the invasive effects of tropical vegetation and is usually not considered as a casual factor when restoration and reconstruction of many archaeological sites are undertaken. Yet the proximity of many ruins to zones of seismic activity would argue otherwise. Clues as to the types of damage which should be soughtwere offered in September 1999 when the M = 7.5 Oaxaca earthquake struck the ruins of Monte Alban, Mexico, where archaeological renovations were underway. More than 20 structures were damaged, 5 of them seriously. Damage features noted were walls out of plumb, fractures in walls, floors, basal platforms and tableros, toppling of columns, and deformation, settling and tumbling of walls. A Modified Mercalli Intensity of VII (ground accelerations 18-34 %b) occurred at the site. Within the diffuse landward extension of the Caribbean plate boundary zone M = 7+ earthquakes occur with repeat times of hundreds of years arguing that many Maya sites were subjected to earthquakes. Damage to re-erected and reinforced stelae, walls, and buildings were witnessed at Quirigua, Guatemala, during an expedition underway when then 1976 M = 7.5 Guatemala earthquake on the Motagua fault struck. Excavations also revealed evidence (domestic pttery vessels and skeleton of a child crushed under fallen walls) of an ancient earthquake occurring about the teim of the demise and abandonment of Quirigua in the late 9th century. Striking evidence for sudden earthquake building collapse at the end of the Mayan Classic Period ~A.D. 889 was found at Benque Viejo (Xunantunich), Belize, located 210 north of Quirigua. It is argued that a M = 7.5 to 7.9 earthquake at the end of the Maya Classic period centered in the vicinity of the Chixoy-Polochic and Motagua fault zones cound have produced the contemporaneous earthquake damage to the above sites. As a consequences this earthquake may have accelerated the

  6. Radioactive waste management - with evidence

    1988-01-01

    The select committee was appointed to report on the present (1988) situation and future prospects in the field of radioactive waste management in the European Community. The report covers all aspects of the subject. After an introduction the parts of the report are concerned with the control of radiation hazards, the nuclear fuel cycle and radioactive waste, the control of radioactive effluents, storage and disposal of solid radioactive wastes, research programmes, surface storage versus deep geological disposal of long-term wastes, the future of reprocessing and the public debate. Part 10 is a resume of the main conclusions and recommendations. It is recommended that the House of Lords debate the issue. The oral and written evidence presented to the committee is included in the report. (U.K.)

  7. Reconsidering Subextraction: Evidence from Spanish

    Ignacio Bosque

    2014-11-01

    Full Text Available This paper argues that so-called subextraction (e.g., Whoi has John seen a picture of ti ?; cf. Corver 2006 for recent discussion does not involve movement of a wh-phrase to a DP internal escape hatch position before reaching the CP layer. Instead, we claim that apparently subextracted wh-phrases are actually direct dependents of the verb after a process of reanalysis (or readjustment; cf. Chomsky 1977, Kayne 2002 applies. Our proposal rethinks an old (Bach & Horn 1976 idea, reframes it in modern terms and argues against the cyclic status of DPs (cf. Bruening 2009, Leu 2008, Ott 2008, and references therein, by leaning on new evidence from Spanish. The non-cyclic status of DPs is a fairly standard idea ever since clausal properties were assumed to hold for nominal domains (cf. Chomsky 1970, Brame 1982, Abney 1987, and much subsequent literature.

  8. Detecting New Evidences for Evidence-Based Medical Guidelines with Journal Filtering

    Hu, Qing; Huang, Zisheng; ten Teije, Annette; van Harmelen, Frank; Riaño, David; Lenz, Richard; Reichert, Manfred

    2017-01-01

    Evidence-based medical guidelines are systematically developed recommendations with the aim to assist practitioner and patients decisions regarding appropriate health care for specific clinical circumstances, and are based on evidence described in medical research papers. Evidence-based medical

  9. 32 CFR 644.62 - Title evidence.

    2010-07-01

    ... HANDBOOK Acquisition Procurement of Title Evidence, Title Clearance, and Closings § 644.62 Title evidence... and their charter to issue the same. They must also be financially sound and be willing and able to...

  10. Improving GRADE evidence tables part 2

    Langendam, Miranda; Carrasco-Labra, Alonso; Santesso, Nancy

    2016-01-01

    OBJECTIVES: The Grading of Recommendations Assessment, Development, and Evaluation (GRADE) working group has developed GRADE evidence profiles (EP) and summary of findings (SoF) tables to present evidence summaries in systematic reviews, clinical guidelines, and health technology assessments. Exp...

  11. Science and evidence: separating fact from fiction.

    Hess, Dean R

    2013-10-01

    Evidence-based medicine (EBM) is the integration of individual clinical expertise with the best available research evidence from systematic research and the patient's values and expectations. A hierarchy of evidence can be used to assess the strength upon which clinical decisions are made. The efficient approach to finding the best evidence is to identify systematic reviews or evidence-based clinical practice guidelines. Respiratory therapies that evidence supports include noninvasive ventilation for appropriately selected patients, lung-protective ventilation, and ventilator discontinuation protocols. Evidence does not support use of weaning parameters, albuterol for ARDS, and high frequency oscillatory ventilation for adults. Therapy with equivocal evidence includes airway clearance, selection of an aerosol delivery device, and PEEP for ARDS. Although all tenets of EBM are not universally accepted, the principles of EBM nonetheless provide a valuable approach to respiratory care practice.

  12. The Ethical Use of Evidence in Biomedicine.

    Pellegrino, Edmund D.

    1999-01-01

    Examines the ethics of data collection and dissemination, suggesting criteria for the morally responsible treatment of evidence collection, dissemination, and use. Comments on the importance of V. Mike's proposal of an "ethics of evidence." (SLD)

  13. Anatomy of Brazilian Cereeae (subfamily Cactoideae, Cactaceae: Arrojadoa Britton & Rose, Stephanocereus A. Berger and Brasilicereus Backeberg Anatomia de espécies brasileiras pertencentes à tribo Cereeae (subfamília Cactoideae, Cactaceae: Arrojadoa Britton & Rose, Stephanocereus A. Berger and Brasilicereus Backeberg

    Patricia Soffiatti

    2007-12-01

    Full Text Available (Anatomy of Brazilian Cereeae (subfamily Cactoideae, Cactaceae: Arrojadoa Britton & Rose, Stephanocereus A. Berger wâBrasilicereus Backeberg. Arrojadoa, Stephanocereus and Brasilicereus are endemic Brazilian Cereeae, occurring along the Espinhaço Range, in the campos rupestres, cerrados and caatingas, from northern Minas Gerais to southern Bahia. The genera are columnar, erect to semi-erect cacti, except for one species, A bahiensis, which is globose. This study describes the anatomy of dermal, fundamental and vascular systems, aiming to find diagnostic characters for the genera and species. Basal portions of stems were sectioned transversely and longitudinally, and stained with Astrablue and Safranin. The species share a uniseriate epidermis, with thick cuticle; well developed collenchymatic hypodermis, containing prismatic crystals; cortex with numerous mucilage cells, druses and vascular bundles; outside cortex as a palisade parenchyma; periderm composed of lignified cork cells alternating with suberized cells; pheloderm consisting of a few layers of thin-walled cells; phloem composed of solitary or multiple of two to three sieve tube elements, companion cells, axial and radial parenchyma; secondary xylem with solitary to multiple vessels, with simple perforation plates and alternate bordered to semi-bordered pits; axial parenchyma scanty vasicentric to incomplete; libriform septate fibres; large rays. Unlignified parenchyma is seen in the secondary xylem, varying from a few cells to bands among axial and radial elements. The following are considered diagnostic characters: the shape of lignified phellem cells, cubic to radially elongate, which individualizes S. leucostele; an underdeveloped hypodermis and the occurrence of sclereids in the cortex are exclusive to Brasilicereus markgrqfii.(Anatomia de espécies brasileiras pertencentes à tribo Cereeae (subfamília Cactoideae, Cactaceae: Arrojadoa Britton & Rose, Stephanocereus A. Berger and

  14. Historical perspectives on evidence-based nursing.

    Beyea, Suzanne C; Slattery, Mary Jo

    2013-04-01

    The authors of this article offer a review and historical perspective on research utilization and evidence-based practice in nursing. They present the evolution of research utilization to the more contemporary framework of evidence-based nursing practice. The authors address the role of qualitative research in the context of evidence-based practice. Finally, some approaches and resources for learning more about the fundamentals of evidence-based healthcare are provided.

  15. Evidence-based practice of periodontics.

    Cobb, Charles M; MacNeill, Simon R; Satheesh, Keerthana

    2010-01-01

    Evidence-based practice involves complex and conscientious decision making based not only on the available evidence but also on patient characteristics, situations, and preferences. It recognizes that care is individualized and ever-changing and involves uncertainties and probabilities. The specialty of periodontics has abundant high-level evidence upon which treatment decisions can be determined. This paper offers a brief commentary and overview of the available evidence commonly used in the private practice of periodontics.

  16. Is Probabilistic Evidence a Source of Knowledge?

    Friedman, Ori; Turri, John

    2015-01-01

    We report a series of experiments examining whether people ascribe knowledge for true beliefs based on probabilistic evidence. Participants were less likely to ascribe knowledge for beliefs based on probabilistic evidence than for beliefs based on perceptual evidence (Experiments 1 and 2A) or testimony providing causal information (Experiment 2B).…

  17. 6 CFR 13.34 - Evidence.

    2010-01-01

    ... 6 Domestic Security 1 2010-01-01 2010-01-01 false Evidence. 13.34 Section 13.34 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY PROGRAM FRAUD CIVIL REMEDIES § 13.34 Evidence. (a) The ALJ will determine the admissibility of evidence. (b) Except as provided in this part, the ALJ...

  18. Polyphyly of the spring-parsleys (Cymopterus): molecular and morphological evidence suggests complex relationships among the perennial endemic genera of western North American Apiaceae

    Downie, S.R.; Hartman, R.L.; Sun, F.-J.; Katz-Downie, D.S.

    2002-01-01

    Cladistic analyses of DNA sequences from the nuclear rDNA internal transcribed spacer region and cpDNA rps16 intron and, for a subset of taxa, the cpDNA trnF-trnL-trnT locus were carried out to evaluate the monophyly of Cymopterus and to ascertain its phylogenetic placement among the other perennial genera of Apiaceae (Umbelliferae) subfamily Apioideae endemic to western North America. To elucidate patterns in the evolution of specific fruit characters and to evaluate their utility in circumscribing genera unambiguously, additional evidence was procured from cross-sections of mature fruits and the results of cladistic analysis of 25 morphological characters. Analyses of the partitioned data sets resulted in weakly supported and largely unresolved phylogenetic hypotheses, possibly due to the rapid radiation of the group, whereas the combined analysis of all molecular evidence resulted in a well-resolved phylogeny with higher bootstrap support. The traditionally used fruit characters of wing shape and composition and orientation of mericarp compression are highly variable. The results of these analyses reveal that Cymopterus and Lomatium, the two largest genera of western North American Apiaceae, are polyphyletic, and that their species are inextricably linked with those of other endemic perennial genera of the region (such as, Aletes, Musineon, Oreoxis, Pseudocymopterus, Pteryxia, and Tauschia), many of which are also not monophyletic. Prior emphasis on characters of the fruit in all systems of classification of the group has led to highly artificial assemblages of species. A complete reassessment of generic limits of all western endemic Apiaceae is required, as is further systematic study of this intractable group. (author)

  19. The Electronic Evidence in Trial Proceedings

    Monica Pocora

    2015-05-01

    Full Text Available This paper will consider theoretical and practical issues which arise in trial proceedings, throughout the virtual presence of persons involved. The EU Convention of 2000 provide the legal base for the use of video conference. In most jurisdictions, all forms of evidence is admissible, subject to rules relating to the exclusion of evidence because of improper actions or because the inclusion of the evidence would be unfair to the defendant. There is a difference between the admissibility of the evidence and laying the correct foundations before the evidence can be admitted.

  20. Evidence based practice readiness: A concept analysis.

    Schaefer, Jessica D; Welton, John M

    2018-01-15

    To analyse and define the concept "evidence based practice readiness" in nurses. Evidence based practice readiness is a term commonly used in health literature, but without a clear understanding of what readiness means. Concept analysis is needed to define the meaning of evidence based practice readiness. A concept analysis was conducted using Walker and Avant's method to clarify the defining attributes of evidence based practice readiness as well as antecedents and consequences. A Boolean search of PubMed and Cumulative Index for Nursing and Allied Health Literature was conducted and limited to those published after the year 2000. Eleven articles met the inclusion criteria for this analysis. Evidence based practice readiness incorporates personal and organisational readiness. Antecedents include the ability to recognize the need for evidence based practice, ability to access and interpret evidence based practice, and a supportive environment. The concept analysis demonstrates the complexity of the concept and its implications for nursing practice. The four pillars of evidence based practice readiness: nursing, training, equipping and leadership support are necessary to achieve evidence based practice readiness. Nurse managers are in the position to address all elements of evidence based practice readiness. Creating an environment that fosters evidence based practice can improve patient outcomes, decreased health care cost, increase nurses' job satisfaction and decrease nursing turnover. © 2018 John Wiley & Sons Ltd.

  1. Active oxygen doctors the evidence

    Castelló, Ana; Francès, Francesc; Corella, Dolores; Verdú, Fernando

    2009-02-01

    Investigation at the scene of a crime begins with the search for clues. In the case of bloodstains, the most frequently used reagents are luminol and reduced phenolphthalein (or phenolphthalin that is also known as the Kastle-Meyer colour test). The limitations of these reagents have been studied and are well known. Household cleaning products have evolved with the times, and new products with active oxygen are currently widely used, as they are considered to be highly efficient at removing all kinds of stains on a wide range of surfaces. In this study, we investigated the possible effects of these new cleaning products on latent bloodstains that may be left at a scene of a crime. To do so, various fabrics were stained with blood and then washed using cleaning agents containing active oxygen. The results of reduced phenolphthalein, luminol and human haemoglobin tests on the washed fabrics were negative. The conclusion is that these new products alter blood to such an extent that it can no longer be detected by currently accepted methods employed in criminal investigations. This inability to locate bloodstains means that highly important evidence (e.g. a DNA profile) may be lost. Consequently, it is important that investigators are aware of this problem so as to compensate for it.

  2. Museums? Evidence from two Countries

    Azilah Kasim

    2014-12-01

    Full Text Available This paper provides evidence on Young Adults’ motivations for visiting and not visiting museums. Using purposive sampling, self-administered questionnaires were distributed to respondents in Kedah, Malaysia and Eskisehir, Turkey. Both Kedah and Eskisehir share one similarity – they both have many museums. The findings revealed that in both study contexts, young people tended to visit museums for practical reasons such as to help them prepare homework or a project. They also visit for intrinsic reasons such as to satisfy their curiosity. Both samples also illustrate Davies (2001 contention that awareness is an important precursor to potential visits. On the other hand, both samples are different in reasons for not visiting. While young people in Eskisehir cite emotional reasons for deciding not to visit, young people in Kedah offered more practical ones such as lack of time and interest, or more interested in other activities. The study findings are useful for understanding reasons behind the generally low museum visits among youth. Several managerial implications of the study were also proposed.

  3. Evidence gap maps -- a tool for promoting evidence-informed policy and prioritizing future research

    Snilstveit, Birte; Vojtkova, Martina; Bhavsar, Ami; Gaarder, Marie

    2013-01-01

    Evidence-gap maps present a new addition to the tools available to support evidence-informed policy making. Evidence-gap maps are thematic evidence collections covering a range of issues such as maternal health, HIV/AIDS, and agriculture. They present a visual overview of existing systematic reviews or impact evaluations in a sector or subsector, schematically representing the types of int...

  4. No evidence-based restoration without a sound evidence base: a reply to Guldemond et al.

    Ntshotsho, P

    2012-03-01

    Full Text Available Evidence-based practice is not possible without an evidence base. Guldemond et al. confuse our attempt at assessing the status of the evidence base of restoration programs in South Africa with attempting to assess whether restoration is evidence...

  5. Geological evidence of smectite longevity

    Pusch, R.; Karnland, O.

    1988-12-01

    Search is going on for geological evidence of natural smectite clay materials that have been exposed to conditions that are similar to those radioactive in repositories. Cases in which heating to 90 degree C or more for long periods has taken place, are of particular interest. The report describes two bentonite layers, one of Miocenic age located at central Sardinia (Busachi), and the other of Ordovician age, forming a basal stratum of southern Gotland, (Hamra), Sweden. They both serve as excellent examples of the survival potential of montmorillonite-rich clays. The more than 10 m thick Sardinian bentonite bed was very significantly heated when the magma moved in and covered it. The upper meter was heated to more than 200 degree C for several days, while at more than 4 m depth, the temperature did note exceed 80 degree C. The test show that the smectite content was not reduced to less than 60 percent in any part of the layer sequence, while slight cementation was caused by precipitation of heat-released silica in the uppermost layer. The 0.3 m thick bed on Gotland is presently located at 515 m depth. Various investigations indicate that it has been exposed to an effective pressure of 300 MPa and a temperature of 110 degree C for several million years due to burial under almost 3 km of Devonian sediments. The content of smectite is around 25 percent of the bulk material, and 30-40 percent of the clay fraction. Illite appears to have been neoformed in small voids of the smectite matrix and the identified apparent I/S material is suggested to consist of mixed-layer minerals with hydrous mica and Ca or Na locked in instead of K, which would be the conventional interpretation. The earlier developed alteration model appears to be valid and it is extended in the present report on the basis of the findings. (28 illustrations, 9 tables)

  6. Evidence-Based ACL Reconstruction

    E. Carlos RODRIGUEZ-MERCHAN

    2015-01-01

    Full Text Available There is controversy in the literature regarding a number of topics related to anterior cruciate ligament (ACLreconstruction. The purpose of this article is to answer the following questions: 1 Bone patellar tendon bone (BPTB reconstruction or hamstring reconstruction (HR; 2 Double bundle or single bundle; 3 Allograft or authograft; 4 Early or late reconstruction; 5 Rate of return to sports after ACL reconstruction; 6 Rate of osteoarthritis after ACL reconstruction. A Cochrane Library and PubMed (MEDLINE search of systematic reviews and meta-analysis related to ACL reconstruction was performed. The key words were: ACL reconstruction, systematic reviews and meta-analysis. The main criteria for selection were that the articles were systematic reviews and meta-analysesfocused on the aforementioned questions. Sixty-nine articles were found, but only 26 were selected and reviewed because they had a high grade (I-II of evidence. BPTB-R was associated with better postoperative knee stability but with a higher rate of morbidity. However, the results of both procedures in terms of functional outcome in the long-term were similar. The double-bundle ACL reconstruction technique showed better outcomes in rotational laxity, although functional recovery was similar between single-bundle and double-bundle. Autograft yielded better results than allograft. There was no difference between early and delayed reconstruction. 82% of patients were able to return to some kind of sport participation. 28% of patients presented radiological signs of osteoarthritis with a follow-up of minimum 10 years.

  7. Direct enzyme assay evidence confirms aldehyde reductase function of Ydr541cp and Ygl039wp from Saccharomyces cerevisiae

    Aldehyde reductase gene ARI1 is a recently characterized member of intermediate subfamily under SDR (short-chain dehydrogenase/reductase) superfamily that revealed mechanisms of in situ detoxification of furfural and HMF for tolerance of Saccharomyces cerevisiae. Uncharacterized open reading frames ...

  8. Level of evidence gap in orthopedic research.

    Baldwin, Keith D; Bernstein, Joseph; Ahn, Jaimo; McKay, Scott D; Sankar, Wudbhav N

    2012-09-01

    Level of evidence is the most widely used metric for the quality of a publication, but instances exist in which a Level I study is neither feasible nor desirable. The goal of this study was to evaluate the level of evidence gap in current orthopedic research, which the authors defined as the disparity between the level of evidence that would be required to optimally answer the primary research question and the level of evidence that was actually used. Five orthopedic surgeons (K.D.B., J.B., J.A., S.D.M., W.N.S.) evaluated blinded articles from the first 6 months of 2010 in the Journal of Bone and Joint Surgery (American Volume) (JBJS-Am), classifying the study type and design and extracting a primary research question from each article. Each evaluator then defined the study type and method, along with the level of evidence that would ideally be used to address the primary research question. The level of evidence gap was then calculated by subtracting the actual level of evidence of the manuscript from the level of evidence of the idealized study. Of the 64 JBJS-Am manuscripts eligible for analysis, the average level of evidence was between Level II and III (mean, 2.73). The average level of evidence gap was 1.06 compared with the JBJS-Am-designated level of evidence and 1.28 compared with the evaluators' assessment. Because not all questions require Level I studies, level of evidence alone may not be the best metric for the quality of orthopedic surgery literature. Instead, the authors' concept of a level of evidence gap may be a better tool for assessing the state of orthopedic research publications. Copyright 2012, SLACK Incorporated.

  9. Evidence-based management - healthcare manager viewpoints.

    Janati, Ali; Hasanpoor, Edris; Hajebrahimi, Sakineh; Sadeghi-Bazargani, Homayoun

    2018-06-11

    Purpose Hospital manager decisions can have a significant impact on service effectiveness and hospital success, so using an evidence-based approach can improve hospital management. The purpose of this paper is to identify evidence-based management (EBMgt) components and challenges. Consequently, the authors provide an improving evidence-based decision-making framework. Design/methodology/approach A total of 45 semi-structured interviews were conducted in 2016. The authors also established three focus group discussions with health service managers. Data analysis followed deductive qualitative analysis guidelines. Findings Four basic themes emerged from the interviews, including EBMgt evidence sources (including sub-themes: scientific and research evidence, facts and information, political-social development plans, managers' professional expertise and ethical-moral evidence); predictors (sub-themes: stakeholder values and expectations, functional behavior, knowledge, key competencies and skill, evidence sources, evidence levels, uses and benefits and government programs); EBMgt barriers (sub-themes: managers' personal characteristics, decision-making environment, training and research system and organizational issues); and evidence-based hospital management processes (sub-themes: asking, acquiring, appraising, aggregating, applying and assessing). Originality/value Findings suggest that most participants have positive EBMgt attitudes. A full evidence-based hospital manager is a person who uses all evidence sources in a six-step decision-making process. EBMgt frameworks are a good tool to manage healthcare organizations. The authors found factors affecting hospital EBMgt and identified six evidence sources that healthcare managers can use in evidence-based decision-making processes.

  10. Expert Evidence and International Criminal Justice

    Appazov, Artur

    The book is a comprehensive narration of the use of expertise in international criminal trials offering reflection on standards concerning the quality and presentation of expert evidence. It analyzes and critiques the rules governing expert evidence in international criminal trials...... and the strategies employed by counsel and courts relying upon expert evidence and challenges that courts face determining its reliability. In particular, the author considers how the procedural and evidentiary architecture of international criminal courts and tribunals influences the courts' ability to meaningfully...... incorporate expert evidence into the rational fact-finding process. The book provides analysis of the unique properties of expert evidence as compared with other forms of evidence and the challenges that these properties present for fact-finding in international criminal trials. It draws conclusions about...

  11. Evidence-Based Psychotherapy: Advantages and Challenges.

    Cook, Sarah C; Schwartz, Ann C; Kaslow, Nadine J

    2017-07-01

    Evidence-based psychotherapies have been shown to be efficacious and cost-effective for a wide range of psychiatric conditions. Psychiatric disorders are prevalent worldwide and associated with high rates of disease burden, as well as elevated rates of co-occurrence with medical disorders, which has led to an increased focus on the need for evidence-based psychotherapies. This chapter focuses on the current state of evidence-based psychotherapy. The strengths and challenges of evidence-based psychotherapy are discussed, as well as misperceptions regarding the approach that may discourage and limit its use. In addition, we review various factors associated with the optimal implementation and application of evidence-based psychotherapies. Lastly, suggestions are provided on ways to advance the evidence-based psychotherapy movement to become truly integrated into practice.

  12. Evidence-Based Dentistry in Everyday Practice.

    Gudray, Kiran; Walmsley, Anthony Damien

    2016-12-01

    This article informs readers of a method of implementing evidence-based dentistry in practice. Following these steps, practitioners should be able to use this skill in an efficient manner. The importance of evidence-based dentistry and its relevance to situations encountered in everyday practice is also highlighted. Clinical relevance: This article highlights a series of steps to be followed by practitioners to ensure that treatment provided is supported by the most recent, good quality evidence.

  13. Evidence-Based Practice: Management of Vertigo

    Nguyen-Huynh, Anh T.

    2012-01-01

    Synopsis The article focuses on the evidence basis for the management of benign paroxysmal positional vertigo (BPPV), the most common diagnosis of vertigo in both primary care and subspecialty settings. Like all articles in this compilation of evidence-based practice, an overview is presented along with evidence based clinical assessment, diagnosis, and management. Summaries of differential diagnosis of vertigo and outcomes are presented. PMID:22980676

  14. Evidence and First-Person Authority

    Corbí, Josep E.

    2011-01-01

    In this paper, I challlenge David Finkelstein's claim that evidence does not contribute to first-person authority. To this end, I first argue that the phenomenon of first-person authority involves a certain combination of two kinds of authority, namely: an epistemic (insofar as evidence is at issue here) and a practical (insofar as the capacity to shape one's own psychological and dispositions is the central concern) kind of authority. Secondly, I defend the view that gathering evidence plays...

  15. What is the Best Evidence Medical Education?

    Rasoul Masoomi

    2012-07-01

    Full Text Available Best Evidence Medical Education (BEME is defined as: “The implementation by teachers and educational bodies in their practice, of methods and approaches to education based on the best evidence available.” Five steps have been recognized in the practice of BEME. These are: framing the question, developing a search strategy, evaluating the evidence, implementing change and evaluating that change. In this paper, I described the concept of BEME, its steps, and challenges.

  16. The Economics of Discrimination: Evidence from Basketball

    Kahn, Lawrence M.

    2009-01-01

    This Chapter reviews evidence on discrimination in basketball, primarily examining studies on race but with some discussion of gender as well. I focus on discrimination in pay, hiring, and retention against black NBA players and coaches and pay disparities by gender among college coaches. There was much evidence for each of these forms of discrimination against black NBA players in the 1980s. However, there appears to be less evidence of racial compensation, hiring and retention discriminatio...

  17. Design of smartphone evidence awareness (SEAWARE) training

    Dlamini, Zama I

    2016-01-01

    Full Text Available be good sources of digital evidence, which might be inadmissible in a court of law if it is not handled properly. This paper presents the design of the smartphone evidence awareness (SEAware) training program for smartphone users. This training program... aware that their devices could be good sources of digital evidence, which might be inadmissible in a court of law if it is not handled properly Objective - To test smartphone evidence awareness skills before and after the training - To train a...

  18. Sicily statement on evidence-based practice

    Hopayian Kevork

    2005-01-01

    Full Text Available Abstract Background A variety of definitions of evidence-based practice (EBP exist. However, definitions are in themselves insufficient to explain the underlying processes of EBP and to differentiate between an evidence-based process and evidence-based outcome. There is a need for a clear statement of what Evidence-Based Practice (EBP means, a description of the skills required to practise in an evidence-based manner and a curriculum that outlines the minimum requirements for training health professionals in EBP. This consensus statement is based on current literature and incorporating the experience of delegates attending the 2003 Conference of Evidence-Based Health Care Teachers and Developers ("Signposting the future of EBHC". Discussion Evidence-Based Practice has evolved in both scope and definition. Evidence-Based Practice (EBP requires that decisions about health care are based on the best available, current, valid and relevant evidence. These decisions should be made by those receiving care, informed by the tacit and explicit knowledge of those providing care, within the context of available resources. Health care professionals must be able to gain, assess, apply and integrate new knowledge and have the ability to adapt to changing circumstances throughout their professional life. Curricula to deliver these aptitudes need to be grounded in the five-step model of EBP, and informed by ongoing research. Core assessment tools for each of the steps should continue to be developed, validated, and made freely available. Summary All health care professionals need to understand the principles of EBP, recognise EBP in action, implement evidence-based policies, and have a critical attitude to their own practice and to evidence. Without these skills, professionals and organisations will find it difficult to provide 'best practice'.

  19. Towards Evidence Based Usability in Health Informatics?

    Marcilly, Romaric; Peute, Linda W.; Beuscart-Zephir, Marie-Catherine; Jaspers, Monique W.

    2015-01-01

    In a Health Information Technology (HIT) regulatory context in which the usability of this technology is more and more a critical issue, there is an increasing need for evidence based usability practice. However, a clear definition of evidence based usability practice and how to achieve it is still

  20. 15 CFR 904.251 - Evidence.

    2010-01-01

    ... taken to establish matters of aggravation or mitigation. (b) Objections and offers of proof. (1) A party...) Whenever evidence is excluded from the record, the party offering such evidence may make an offer of proof... the agency as an expert body. Where a decision or part thereof rests on official notice of a material...

  1. 45 CFR 99.25 - Evidence.

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Evidence. 99.25 Section 99.25 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION PROCEDURE FOR HEARINGS FOR THE CHILD CARE AND DEVELOPMENT FUND Hearing Procedures § 99.25 Evidence. (a) Testimony. Testimony shall be given orally under...

  2. 44 CFR 68.9 - Admissible evidence.

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Admissible evidence. 68.9 Section 68.9 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF... admissible. (b) Documentary and oral evidence shall be admissible. (c) Admissibility of non-expert testimony...

  3. Intelligence as evidence in criminal proceedings

    Lukić Tatjana

    2011-01-01

    Full Text Available The fight against modern forms of crime such as organized crime, terrorism and other very serious crimes caused not only modification of procedural principles and procedural rules, but also the necessity of re-examination of evidence in terms of introducing new evidence in criminal proceedings. Given that the prevention, detection and proving in cases of mentioned offenses represent the systemic issue and that the efficiency is caused by cohesion of preventive and repressive mechanisms in each strategy of preventing and combating serious crimes, the more often raised question, aroused from the practice, is the issue of the use of information gathered by the police or security services as evidence in criminal proceedings. In addition, there is the issue of use of illegal evidence, the ways in which these evidence are defined in some jurisdictions and which are the legal consequences of their use in judicial decision, whether it is based only on them, or on some other evidence beside them. The author addresses the issues of necessity and justification for use of information of security services as evidence in criminal proceedings, their definition and difference with respect to data, experiences and practices in other countries and of course their use as evidence in criminal proceedings of Serbia. Also, the paper addresses the Criminal Intelligence Analytics, exchange of information between the competent authorities at national and international level.

  4. 19 CFR 210.37 - Evidence.

    2010-04-01

    ... 19 Customs Duties 3 2010-04-01 2010-04-01 false Evidence. 210.37 Section 210.37 Customs Duties UNITED STATES INTERNATIONAL TRADE COMMISSION INVESTIGATIONS OF UNFAIR PRACTICES IN IMPORT TRADE ADJUDICATION AND ENFORCEMENT Prehearing Conferences and Hearings § 210.37 Evidence. (a) Burden of proof. The...

  5. Quality of evidence-based pediatric guidelines

    Boluyt, Nicole; Lincke, Carsten R.; Offringa, Martin

    2005-01-01

    Objective. To identify evidence-based pediatric guidelines and to assess their quality. Methods. We searched Medline, Embase, and relevant Web sites of guideline development programs and national pediatric societies to identify evidence-based pediatric guidelines. A list with titles of identified

  6. 20 CFR 410.240 - Evidence.

    2010-04-01

    ... evidence may be submitted as part of a prescribed application form if the form provides for its inclusion... disability or death due to pneumoconiosis. For evidence requirements to support allegations of total disability or death due to pneumoconiosis; for the effect of the failure or refusal of an individual to...

  7. Total Evidence, Uncertainty and A Priori Beliefs

    Bewersdorf, Benjamin; Felline, Laura; Ledda, Antonio; Paoli, Francesco; Rossanese, Emanuele

    2016-01-01

    Defining the rational belief state of an agent in terms of her initial or a priori belief state as well as her total evidence can help to address a number of important philosophical problems. In this paper, I discuss how this strategy can be applied to cases in which evidence is uncertain. I argue

  8. Evidence-based librarianship: an overview.

    Eldredge, J D

    2000-10-01

    To demonstrate how the core characteristics of both evidence-based medicine (EBM) and evidence-based health care (EBHC) can be adapted to health sciences librarianship. Narrative review essay involving development of a conceptual framework. The author describes the central features of EBM and EBHC. Following each description of a central feature, the author then suggests ways that this feature applies to health sciences librarianship. First, the decision-making processes of EBM and EBHC are compatible with health sciences librarianship. Second, the EBM and EBHC values of favoring rigorously produced scientific evidence in decision making are congruent with the core values of librarianship. Third, the hierarchical levels of evidence can be applied to librarianship with some modifications. Library researchers currently favor descriptive-survey and case-study methods over systematic reviews, randomized controlled trials, or other higher levels of evidence. The library literature nevertheless contains diverse examples of randomized controlled trials, controlled-comparison studies, and cohort studies conducted by health sciences librarians. Health sciences librarians are confronted with making many practical decisions. Evidence-based librarianship offers a decision-making framework, which integrates the best available research evidence. By employing this framework and the higher levels of research evidence it promotes, health sciences librarians can lay the foundation for more collaborative and scientific endeavors.

  9. 31 CFR 10.73 - Evidence.

    2010-07-01

    ... 31 Money and Finance: Treasury 1 2010-07-01 2010-07-01 false Evidence. 10.73 Section 10.73 Money and Finance: Treasury Office of the Secretary of the Treasury PRACTICE BEFORE THE INTERNAL REVENUE SERVICE Rules Applicable to Disciplinary Proceedings § 10.73 Evidence. (a) In general. The rules of...

  10. Utility-driven evidence for healthy cities

    de Leeuw, Evelyne; Skovgaard, Thomas

    2005-01-01

    The question whether the WHO Healthy Cities project 'works' has been asked ever since a number of novel ideas and actions related to community health, health promotion and healthy public policy in the mid 1980s came together in the Healthy Cities Movement initiated by the World Health Organization....... The question, however, has become more urgent since we have entered an era in which the drive for 'evidence' seems all-pervasive. The article explores the nature of evidence, review available evidence on Healthy Cities accomplishments, and discusses whether enough evidence has been accumulated on different...... performances within the realm of Healthy Cities. A main point of reference is the European Healthy Cities Project (E-HCP). Building on the information gathered through documentary research on the topic, it is concluded that there is fair evidence that Healthy Cities works. However, the future holds great...

  11. Evidence for Mental Health Occupational Therapy

    Danielle Hitch

    2015-09-01

    Full Text Available This article reports on the evidence for mental health occupational therapy in peer-reviewed journals from 2000 to 2013. Descriptive and inductive methods were used to address this question, with evidence from CINAHL, OTDBase, PSYCInfo, SCOPUS, and Google Scholar® included. Many articles (n = 1,747 were found that met the inclusion and exclusion criteria. A total of 47 different methods were used to develop evidence for mental health occupational therapy, and evidence appeared in 300 separate peer-reviewed journals. It takes on average 7 months for an article to progress from submission to acceptance, and a further 7 months to progress from acceptance to publication. More than 95% of articles published between 2000 and 2002 were cited at least once in the following decade, and around 70% of these citations were recorded in non-occupational therapy journals. The current evidence base for mental health occupational therapy is both substantial and diverse.

  12. Evidence development and publication planning: strategic process.

    Wittek, Michael R; Jo Williams, Mary; Carlson, Angeline M

    2009-11-01

    A number of decisions in the health care field rely heavily on published clinical evidence. A systematic approach to evidence development and publication planning is required to develop a portfolio of evidence that includes at minimum information on efficacy, safety, durability of effect, quality of life, and economic outcomes. The approach requires a critical assessment of available literature, identification of gaps in the literature, and a strategic plan to fill the gaps to ensure the availability of evidence demanded for clinical decisions, coverage/payment decisions and health technology assessments. The purpose of this manuscript is to offer a six-step strategic process leading to a portfolio of evidence that meets the informational needs of providers, payers, and governmental agencies concerning patient access to a therapy.

  13. Association Between Cannabis and Psychosis: Epidemiologic Evidence.

    Gage, Suzanne H; Hickman, Matthew; Zammit, Stanley

    2016-04-01

    Associations between cannabis use and psychotic outcomes are consistently reported, but establishing causality from observational designs can be problematic. We review the evidence from longitudinal studies that have examined this relationship and discuss the epidemiologic evidence for and against interpreting the findings as causal. We also review the evidence identifying groups at particularly high risk of developing psychosis from using cannabis. Overall, evidence from epidemiologic studies provides strong enough evidence to warrant a public health message that cannabis use can increase the risk of psychotic disorders. However, further studies are required to determine the magnitude of this effect, to determine the effect of different strains of cannabis on risk, and to identify high-risk groups particularly susceptible to the effects of cannabis on psychosis. We also discuss complementary epidemiologic methods that can help address these questions. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  14. [Looking for evidence-based medical informatics].

    Coiera, Enrico

    2016-03-01

    e-Health is experiencing a difficult time. On the one side, the forecast is for a bright digital health future created by precision medicine and smart devices. On the other hand, most large scale e-health projects struggle to make a difference and are often controversial. Both futures fail because they are not evidence-based. Medical informatics should follow the example of evidence-based medicine, i.e. conduct rigorous research that gives us evidence to solve real world problems, synthesise that evidence and then apply it strictly. We already have the tools for creating a different universe. What we need is evidence, will, a culture of learning, and hard work.

  15. Semantic Modelling of Digital Forensic Evidence

    Kahvedžić, Damir; Kechadi, Tahar

    The reporting of digital investigation results are traditionally carried out in prose and in a large investigation may require successive communication of findings between different parties. Popular forensic suites aid in the reporting process by storing provenance and positional data but do not automatically encode why the evidence is considered important. In this paper we introduce an evidence management methodology to encode the semantic information of evidence. A structured vocabulary of terms, ontology, is used to model the results in a logical and predefined manner. The descriptions are application independent and automatically organised. The encoded descriptions aim to help the investigation in the task of report writing and evidence communication and can be used in addition to existing evidence management techniques.

  16. Evidence at a glance: error matrix approach for overviewing available evidence

    Keus, Frederik; Wetterslev, Jørn; Gluud, Christian

    2010-01-01

    Clinical evidence continues to expand and is increasingly difficult to overview. We aimed at conceptualizing a visual assessment tool, i.e., a matrix for overviewing studies and their data in order to assess the clinical evidence at a glance....

  17. The Heart of the Matter of Opinion and Evidence: The Value of Evidence-Based Medicine

    Masvidal, Daniel; Lavie, Carl J.

    2012-01-01

    Evidence-based medicine is an important aspect of continuing medical education. This article reviews previous and current examples of conflicting topics that evidence-based medicine has clarified to allow us to provide the best possible patient care.

  18. Evidence and Obesity Prevention: Developing Evidence Summaries to Support Decision Making

    Clark, Rachel; Waters, Elizabeth; Armstrong, Rebecca; Conning, Rebecca; Allender, Steven; Swinburn, Boyd

    2013-01-01

    Public health practitioners make decisions based on research evidence in combination with a variety of other influences. Evidence summaries are one of a range of knowledge translation options used to support evidence-informed decision making. The literature relevant to obesity prevention requires synthesis for it to be accessible and relevant to…

  19. The importance of associations with saprotrophic non-Rhizoctonia fungi among fully mycoheterotrophic orchids is currently under-estimated: novel evidence from sub-tropical Asia.

    Lee, Yung-I; Yang, Chih-Kai; Gebauer, Gerhard

    2015-09-01

    Most fully mycoheterotrophic (MH) orchids investigated to date are mycorrhizal with fungi that simultaneously form ectomycorrhizas with forest trees. Only a few MH orchids are currently known to be mycorrhizal with saprotrophic, mostly wood-decomposing, fungi instead of ectomycorrhizal fungi. This study provides evidence that the importance of associations between MH orchids and saprotrophic non-Rhizoctonia fungi is currently under-estimated. Using microscopic techniques and molecular approaches, mycorrhizal fungi were localized and identified for seven MH orchid species from four genera and two subfamilies, Vanilloideae and Epidendroideae, growing in four humid and warm sub-tropical forests in Taiwan. Carbon and nitrogen stable isotope natural abundances of MH orchids and autotrophic reference plants were used in order to elucidate the nutritional resources utilized by the orchids. Six out of the seven MH orchid species were mycorrhizal with either wood- or litter-decaying saprotrophic fungi. Only one orchid species was associated with ectomycorrhizal fungi. Stable isotope abundance patterns showed significant distinctions between orchids mycorrhizal with the three groups of fungal hosts. Mycoheterotrophic orchids utilizing saprotrophic non-Rhizoctonia fungi as a carbon and nutrient source are clearly more frequent than hitherto assumed. On the basis of this kind of nutrition, orchids can thrive in deeply shaded, light-limiting forest understoreys even without support from ectomycorrhizal fungi. Sub-tropical East Asia appears to be a hotspot for orchids mycorrhizal with saprotrophic non-Rhizoctonia fungi. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  20. Evidence-based management: a literature review.

    Young, Sam K

    2002-05-01

    This paper presents a review of evidence-based management (EBM), exploring whether management activities within healthcare have been, or can be, subject to the same scientific framework as clinical practice. The evidence-based approach was initially examined, noting the hierarchy of evidence ranging from randomized control trials to clinical anecdote. The literature varied in its degree of criticism of this approach; the most common concern referring to the assumed superiority of positivism. However, evidence-based practice was generally accepted as the best way forward. Stewart (1998) offered the only detailed exposition of EBM, outlining a necessary 'attitude of mind' both for EBM and for the creation of a research culture. However, the term 'clinical effectiveness' emerged as a possible replacement buzz-word for EBM (McClarey 1998). The term appears to encompass the sentiments of the evidence-based approach, but with a concomitant concern for economic factors. In this paper the author has examined the divide between those who viewed EBM as an activity for managers to make their own practice accountable and those who believed it to be a facilitative practice to help clinicians with evidence-based practice. Most papers acknowledged the limited research base for management activities within the health service and offered some explanation such as government policy constraints and lack of time. Nevertheless, the overall emphasis is that ideally there should be a management culture firmly based in evidence.

  1. Epistemologic inquiries in evidence-based medicine.

    Djulbegovic, Benjamin; Guyatt, Gordon H; Ashcroft, Richard E

    2009-04-01

    Since the term "evidence-based medicine" (EBM) first appeared in the scientific literature in 1991, the concept has had considerable influence in many parts of the world. Most professional societies, the public,and funding agencies have accepted EBM with remarkable enthusiasm. The concept of evidence-based practice is now applied in management, education, criminology, and social work. Yet, EBM has attracted controversy: its critics allege that EBM uses a narrow concept of evidence and a naive conception of the relationships between evidence, theory, and practice. They also contend that EBM presents itself as a radical restructuring of medical knowledge that discredits more traditional ways of knowing in medicine, largely in the interests of people with a particular investment in the enterprise of large-scale clinical trials. Because EBM proposes aspecific relationship between theory, evidence, and knowledge, its theoretical basis can be understood as an epistemological system. Undertaking epistemological inquiry is important because the adoption of a particular epistemological view defines how science is conducted. In this paper, we challenge this critical view of EBM by examining how EBM fits into broad epistemological debates within the philosophy of science. We consider how EBM relates to some classical debates regarding the nature of science and knowledge. We investigate EBM from the perspective of major epistemological theories (logical-positivism/inductivism, deductivism/falsificationism/theory-ladeness of observations, explanationism/holism, instrumentalism, underdetermination theory by evidence). We first explore the relationship between evidence and knowledge and discuss philosophical support for the main way that evidence is used in medicine: (1) in the philosophical tradition that "rational thinkers respect their evidence," we show that EBM refers to making medical decisions that are consistent with evidence, (2) as a reliable sign, symptom, or mark to

  2. The religion of evidence-based practice

    Wigram, Tony; Gold, Christian

    2012-01-01

    This chapter begins by outlining the challenges of preparing a chapter on evidence-based practice (EBP) to underpin the use of music as a therapeutic tool in treatment, in the overall frame of music, health, and wellbeing. It then reviews the terminology of EBP and evidence-based medicine...... practice as health, education, and social services tighten their belts and the demand on their resources grows, there is increasing interest in the value of music for health and wellbeing, despite even less ‘hard’ evidence that it is effective against illness and disability....

  3. History of evidence-based medicine

    Roger L Sur

    2011-01-01

    Full Text Available This essay reviews the historical circumstances surrounding the introduction and evolution of evidence-based medicine. Criticisms of the approach are also considered. Weaknesses of existing standards of clinical practice and efforts to bring more certainty to clinical decision making were the foundation for evidence-based medicine, which integrates epidemiology and medical research. Because of its utility in designing randomized clinical trials, assessing the quality of the literature, and applying medical research at the bedside, evidence-based medicine will continue to have a strong influence on everyday clinical practice.

  4. Strengthening Chronic Disease Prevention Programming: The Toward Evidence-Informed Practice (TEIP) Program Evidence Tool

    Albert, Dayna; Fortin, Rebecca; Herrera, Christine; Hanning, Rhona; Lessio, Anne; Rush, Brian

    2013-01-01

    In public health and chronic disease prevention there is increasing priority for effective use of evidence in practice. In Ontario, Canada, despite various models being advanced, public health practitioners are seeking ways to identify and apply evidence in their work in practical and meaningful ways. In a companion article, “Strengthening Chronic Disease Prevention Programming: The Toward Evidence-Informed Practice (TEIP) Program Assessment Tool,” we describe use of a tool to assess and strengthen program planning and implementation processes using 19 criteria derived from best and promising practices literature. In this article, we describe use of a complementary Program Evidence Tool to identify, synthesize, and apply a range of evidence sources to strengthen the content of chronic disease prevention programming. The Program Evidence Tool adapts tools of evidence-based medicine to the unique contexts of community-based health promotion and chronic disease prevention. Knowledge management tools and a guided dialogue process known as an Evidence Forum enable community stakeholders to make appropriate use of evidence in diverse social, political, and structural contexts. Practical guidelines and worksheets direct users through 5 steps: 1) define an evidence question, 2) develop a search strategy, 3) collect and synthesize evidence, 4) interpret and adapt evidence, and 5) implement and evaluate. We describe the Program Evidence Tool’s benefits, strengths, challenges, and what was learned from its application in 4 Ontario public health departments. The Program Evidence Tool contributes to the development and understanding of the complex use of evidence in community-based chronic disease prevention. PMID:23721788

  5. The Evidence-Based Manifesto for School Librarians

    Todd, Ross

    2008-01-01

    School Library Journal's 2007 Leadership Summit, "Where's the Evidence? Understanding the Impact of School Libraries," focused on the topic of evidence-based practice. Evidence-based school librarianship is a systematic approach that engages research-derived evidence, school librarian-observed evidence, and user-reported evidence in the processes…

  6. 20 CFR 219.23 - Evidence to prove death.

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Evidence to prove death. 219.23 Section 219... EVIDENCE REQUIRED FOR PAYMENT Evidence of Age and Death § 219.23 Evidence to prove death. (a) Preferred evidence of death. The best evidence of a person's death is— (1) A certified copy of or extract from the...

  7. Evidence-based recommendations to facilitate professional ...

    Rachel Magdalena (Dalena) van Rooyen

    Purpose of the research: To develop evidence-based recommendations ... attitudes by not referring patients to traditional practitioners based on lack of knowledge ...... Longman Dictionary of Contemporary English. ... A case study from Chile.

  8. [What else is Evidence-based Medicine?].

    Hauswaldt, Johannes

    2010-01-01

    The practice of evidence-based medicine means integrating individual clinical expertise with the best available external clinical evidence. Strange enough, scientific discussion focuses on external evidence from systematic research, but neglects its counterpart, i.e., individual clinical expertise. Apart from a lack of appropriate intellectual tools for approaching the latter, this might be due to the mutual concealment of thought and action, of sensor and motor activity (Viktor von Weizsaecker's principle of the revolving door). Behind this, and incommensurably different from each other, lie the world of physics and the world of biology with an ego animal, that is, the dilemma of the self-conscious subject in a world of objects. When practicing medicine, this dilemma of self-reference is being resolved but only through a holistic approach combining rational and external evidence with biographical, spiritual, emotional and pre-rational elements represented in the physician's individual clinical expertise. Copyright © 2010. Published by Elsevier GmbH.

  9. 16 CFR 3.43 - Evidence.

    2010-01-01

    .... Evidence, even if relevant, may be excluded if its probative value is substantially outweighed by the... constitutes hearsay may be admitted if it is relevant, material, and bears satisfactory indicia of reliability...

  10. Ethics, equality and evidence in health promotion

    Vallgårda, Signild

    2014-01-01

    Abstract Aim: The Danish National Board of Health has expressed its commitment to social equality in health, evidence-informed health promotion and public health ethics, and has issued guidelines for municipalities on health promotion, in Danish named prevention packages.The aim of this article...... is to analyse whether the Board of Health adheres to ideals of equality, evidence and ethics in these guidelines. Methods: An analysis to detect statements about equity, evidence and ethics in 10 health promotion packages directed at municipalities with the aim of guiding the municipalities towards evidence......-informed disease prevention and health promotion. Results: Despite declared intentions of prioritizing social equality in health, these intentions are largely absent from most of the packages.When health inequalities are mentioned, focus is on the disadvantaged or the marginalized. Several interventions...

  11. Evidence for subwavelength imaging with positive refraction

    Ma, Yun Gui [Temasek Laboratories, National University of Singapore, Singapore 119260 (Singapore); Sahebdivan, Sahar; Tyc, Tomas; Leonhardt, Ulf [School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS (United Kingdom); Ong, C K, E-mail: ulf@st-andrews.ac.uk [Centre for Superconducting and Magnetic Materials, Department of Physics, National University of Singapore, Singapore 117542 (Singapore)

    2011-03-15

    The resolution of lenses is normally limited by the wave nature of light. Imaging with perfect resolution was believed to rely on negative refraction, but here we present experimental evidence for subwavelength imaging with positive refraction.

  12. Evidence for subwavelength imaging with positive refraction

    Ma, Yun Gui; Sahebdivan, Sahar; Tyc, Tomas; Leonhardt, Ulf; Ong, C K

    2011-01-01

    The resolution of lenses is normally limited by the wave nature of light. Imaging with perfect resolution was believed to rely on negative refraction, but here we present experimental evidence for subwavelength imaging with positive refraction.

  13. The evidence base for diabetes care

    Williams, D. R. R. (David Robert Rhys)

    2002-01-01

    ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 3. Evidence-Based Definition and Classification: A Commentary . . . . . . Steve O'Rahilly 37 PART II: PREVENTION OF DIABETES 4. Prevention of Type 1 Diabetes...

  14. Evidence based policy-making: A review

    Strydom, FW

    2010-04-01

    Full Text Available The process of facilitating the uptake of evidence, for example, scientific research findings, into the policymaking process is multifaceted and thus complex. It is therefore important for scientists to understand this process in order to influence...

  15. Validity evidence based on test content.

    Sireci, Stephen; Faulkner-Bond, Molly

    2014-01-01

    Validity evidence based on test content is one of the five forms of validity evidence stipulated in the Standards for Educational and Psychological Testing developed by the American Educational Research Association, American Psychological Association, and National Council on Measurement in Education. In this paper, we describe the logic and theory underlying such evidence and describe traditional and modern methods for gathering and analyzing content validity data. A comprehensive review of the literature and of the aforementioned Standards is presented. For educational tests and other assessments targeting knowledge and skill possessed by examinees, validity evidence based on test content is necessary for building a validity argument to support the use of a test for a particular purpose. By following the methods described in this article, practitioners have a wide arsenal of tools available for determining how well the content of an assessment is congruent with and appropriate for the specific testing purposes.

  16. Shaping accountabilities for erroneously enacted environmental evidence

    Lippert, Ingmar

    of accountability: first, the company was performing itself as a socially and environmentally accountable and responsible "corporate citizen"; second, the company was inhabiting a discourse of evidence-based decision-making, requiring the evidence to be produced accountably. I analyse a limited set of ethnographic......Drawing on fieldwork in and around a transnational Fortune 50 company's "corporate social responsibility" unit, this paper opens up a range of situations that took part in enacting the company's evidence of its impact on global warming. This evidence was implicated in at least two significant modes...... vignettes of situated work practice that (con)figured the company's accounting for their carbon emissions. Common to all these situations was that the environmental realities enacted have been categorised by some members as erroneous or as not good enough. In this paper I am interested, thence...

  17. Evidence for subwavelength imaging with positive refraction

    Ma, Yun Gui; Sahebdivan, Sahar; Ong, C. K.; Tyc, Tomas; Leonhardt, Ulf

    2011-01-01

    The resolution of lenses is normally limited by the wave nature of light. Imaging with perfect resolution was believed to rely on negative refraction, but here we present experimental evidence for subwavelength imaging with positive refraction. Publisher PDF Peer reviewed

  18. Drug companies' evidence to justify advertising.

    Wade, V A; Mansfield, P R; McDonald, P J

    1989-11-25

    Ten international pharmaceutical companies were asked by letter to supply their best evidence in support of marketing claims for seventeen products. Fifteen replies were received. Seven replies cited a total of 67 references: 31 contained relevant original data and only 13 were controlled trials, all of which had serious methodological flaws. There were four reports of changes in advertising claims and one company ceased marketing nikethamide in the third world. Standards of evidence used to justify advertising claims are inadequate.

  19. Queer challenges to evidence-based practice.

    Zeeman, Laetitia; Aranda, Kay; Grant, Alec

    2014-06-01

    This paper aims to queer evidence-based practice by troubling the concepts of evidence, knowledge and mental illness. The evidence-based narrative that emerged within biomedicine has dominated health care. The biomedical notion of 'evidence' has been critiqued extensively and is seen as exclusive and limiting, and even though the social constructionist paradigm attempts to challenge the authority of biomedicine to legitimate what constitutes acceptable evidence or knowledge for those experiencing mental illness, biomedical notions of evidence appear to remain relatively intact. Queer theory offers theoretical tools to disrupt biomedical norms and challenges biomedical normativity to indicate how marginalisation occurs when normative truths about mental health classify those who differ from the norm as 'ill' or 'disordered'. Queer theory's emphasis on normativity serves the political aim to subvert marginalisation and bring about radical social and material change. Reference will be made to mental health subjects within each discourse by indicating how the body acts as a vehicle for knowing. Deleuzian notions of the rhizome are used as metaphor to suggest a relational approach to knowledge that does away with either/or positions in either biomedical, or queer knowledge to arrive at a both/and position where the biomedical, constructionist and queer are interrelated and entangled in needing the other for their own evolution. However, queer does not ask for assimilation but celebrates difference by remaining outside to disrupt that which is easily overlooked, assumed to be natural or represented as the norm. The task of queer knowledge is to do justice to the lives lived in the name of evidence-based practice and demands that we consider the relations of power where knowledge is produced. This pursuit creates different knowledge spaces where we identify new intersections that allow for socially just understandings of knowing or evidence to emerge. © 2013 John Wiley

  20. Can Scholarly Communication be Evidence Based? (Editorial)

    Denise Koufogiannakis

    2010-01-01

    This issue of Evidence Based Library and Information Practice includes three papers from the Evidence Based Scholarly Communication Conference (EBSCC) that took place in March 2010i. Kroth, Philips and Eldredge have written a commentary that gives an overview of the conference, and introduces us to the research papers that were presented. As well, two research presentations from the conference appear in this issue, an article by Donahue about a potential new method of communicating between sc...

  1. Plausibility and evidence: the case of homeopathy.

    Rutten, Lex; Mathie, Robert T; Fisher, Peter; Goossens, Maria; van Wassenhoven, Michel

    2013-08-01

    Homeopathy is controversial and hotly debated. The conclusions of systematic reviews of randomised controlled trials of homeopathy vary from 'comparable to conventional medicine' to 'no evidence of effects beyond placebo'. It is claimed that homeopathy conflicts with scientific laws and that homoeopaths reject the naturalistic outlook, but no evidence has been cited. We are homeopathic physicians and researchers who do not reject the scientific outlook; we believe that examination of the prior beliefs underlying this enduring stand-off can advance the debate. We show that interpretations of the same set of evidence--for homeopathy and for conventional medicine--can diverge. Prior disbelief in homeopathy is rooted in the perceived implausibility of any conceivable mechanism of action. Using the 'crossword analogy', we demonstrate that plausibility bias impedes assessment of the clinical evidence. Sweeping statements about the scientific impossibility of homeopathy are themselves unscientific: scientific statements must be precise and testable. There is growing evidence that homeopathic preparations can exert biological effects; due consideration of such research would reduce the influence of prior beliefs on the assessment of systematic review evidence.

  2. Teaching evidence based medicine in family medicine

    Davorka Vrdoljak

    2012-05-01

    Full Text Available The concept of evidence based medicine (EBM as the integrationof clinical expertise, patient values and the best evidence was introduced by David Sackett in the 1980’s. Scientific literature in medicine is often marked by expansion, acummulation and quick expiration. Reading all important articles to keep in touch with relevant information is impossible. Finding the best evidence that answers a clinical question in general practice (GP in a short time is not easy. Five useful steps are described –represented by the acronym “5A+E”: assess, ask, acquire, appraise, apply and evaluate.The habit of conducting an evidence search “on the spot’’ is proposed. Although students of medicine at University of Split School of Medicine are taught EBM from the first day of their study and in all courses, their experience of evidence-searching and critical appraisal of the evidence, in real time with real patient is inadequate. Teaching the final-year students the practical use of EBM in a GP’s office is different and can have an important role in their professional development. It can positively impact on quality of their future work in family practice (or some other medical specialty by acquiring this habit of constant evidence-checking to ensure that best practice becomes a mechanism for life-long learning. Conclusion. EBM is a foundation stone of every branch of medicine and important part of Family Medicine as scientific and professional discipline. To have an EB answer resulting from GP’s everyday work is becoming a part of everyday practice.

  3. Evidence Aid: Using Systematic Reviews to Improve Access to Evidence for Humanitarian Emergencies

    Mike Clarke

    2017-10-01

    Full Text Available Evidence Aid is an international initiative to improve access to reliable evidence that will help people and organisations make well-informed decisions about interventions, actions and strategies in the disaster setting. It focuses on systematic reviews as the most reliable source of research evidence, maximising the power of existing research, avoiding undue emphasis on single studies and reducing the waste associated with research that is ignored or not accessible to decision makers. Evidence Aid is knowledge champion for influencers of the humanitarian sector, including funders, policy makers, NGOs, and humanitarian professionals. Evidence Aid was established by members of the Cochrane Collaboration after the Indian Ocean tsunami of December 2004. It provides access to information relevant to disaster risk reduction, planning, response, recovery, resilience and rehabilitation. This presentation will discuss the need for Evidence Aid, and describes its activities.Find out more about Mike.

  4. Court presentation of bite mark evidence.

    Drinnan, A J; Melton, M J

    1985-12-01

    The uniqueness of an individual's bite mark is generally accepted. The use of bite mark analysis to identify or exclude those suspected of crimes is now a well established activity in forensic dentistry. Although the techniques for evaluating bite mark evidence are extremely sophisticated, it is important that the courtroom presentation of such evidence should be as simple as possible and be directed towards those who must judge it. Dentists likely to be involved in the courtroom presentation of bite mark evidence should: be certain that their local law enforcement personnel are frequently updated on the techniques to be used for producing the optimum evidence needed to evaluate bite marks; become acquainted with the current techniques of evaluating bite mark evidence and understand their difficulties and pitfalls; meet with the lawyers (prosecution or defence) before a courtroom appearance, briefing them on the significance of the particular findings; prepare clear and easily understandable visual aids to present to the court the techniques used in the analysis and the bases for the conclusion reached; and offer conclusions derived from the bite mark investigation.

  5. Evidence-based radiology: why and how?

    Sardanelli, Francesco; Di Leo, Giovanni; Hunink, Myriam G.; Gilbert, Fiona J.; Krestin, Gabriel P.

    2010-01-01

    To provide an overview of evidence-based medicine (EBM) in relation to radiology and to define a policy for adoption of this principle in the European radiological community. Starting from Sackett's definition of EBM we illustrate the top-down and bottom-up approaches to EBM as well as EBM's limitations. Delayed diffusion and peculiar features of evidence-based radiology (EBR) are defined with emphasis on the need to shift from the demonstration of the increasing ability to see more and better, to the demonstration of a significant change in treatment planning or, at best, of a significant gain in patient outcome. The ''as low as reasonably achievable'' (ALARA) principle is thought as a dimension of EBR while EBR is proposed as part of the core curriculum of radiology residency. Moreover, we describe the process of health technology assessment in radiology with reference to the six-level scale of hierarchy of studies on diagnostic tests, the main sources of bias in studies on diagnostic performance, and levels of evidence and degrees of recommendations according to the Centre for Evidence-Based Medicine (Oxford, UK) as well as the approach proposed by the GRADE working group. Problems and opportunities offered by evidence-based guidelines in radiology are considered. Finally, we suggest nine points to be actioned by the ESR in order to promote EBR. Radiology will benefit greatly from the improvement in practice that will result from adopting this more rigorous approach to all aspects of our work. (orig.)

  6. Promoting evidence-based practice in pharmacies.

    Toklu, Hale Zerrin

    2015-01-01

    Evidence-based medicine aims to optimize decision-making by using evidence from well-designed and conducted research. The concept of reliable evidence is essential, since the number of electronic information resources is increasing in parallel to the increasing number and type of drugs on the market. The decision-making process is a complex and requires an extensive evaluation as well as the interpretation of the data obtained. Different sources provide different levels of evidence for decision-making. Not all the data have the same value as the evidence. Rational use of medicine requires that the patients receive "medicines appropriate to their clinical needs, in doses that meet their own individual requirements, for an adequate period of time, and at the lowest cost to them and their community." Pharmacists have a crucial role in the health system to maintain the rational use of medicine and provide pharmaceutical care to patients, because they are the drug experts who are academically trained for this purpose. The rational use of the pharmacist's workforce will improve the outcome of pharmacotherapy as well as decreasing the global health costs.

  7. Promoting evidence-based practice in pharmacies

    Toklu HZ

    2015-09-01

    Full Text Available Hale Zerrin Toklu Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, FL, USA Abstract: Evidence-based medicine aims to optimize decision-making by using evidence from well-designed and conducted research. The concept of reliable evidence is essential, since the number of electronic information resources is increasing in parallel to the increasing number and type of drugs on the market. The decision-making process is a complex and requires an extensive evaluation as well as the interpretation of the data obtained. Different sources provide different levels of evidence for decision-making. Not all the data have the same value as the evidence. Rational use of medicine requires that the patients receive “medicines appropriate to their clinical needs, in doses that meet their own individual requirements, for an adequate period of time, and at the lowest cost to them and their community.” Pharmacists have a crucial role in the health system to maintain the rational use of medicine and provide pharmaceutical care to patients, because they are the drug experts who are academically trained for this purpose. The rational use of the pharmacist's workforce will improve the outcome of pharmacotherapy as well as decreasing the global health costs. Keywords: pharmacist, rational use of medicine, pharmacotherapy, pharmaceutical, outcome

  8. Evidence, temperature, and the laws of thermodynamics.

    Vieland, Veronica J

    2014-01-01

    A primary purpose of statistical analysis in genetics is the measurement of the strength of evidence for or against hypotheses. As with any type of measurement, a properly calibrated measurement scale is necessary if we want to be able to meaningfully compare degrees of evidence across genetic data sets, across different types of genetic studies and/or across distinct experimental modalities. In previous papers in this journal and elsewhere, my colleagues and I have argued that geneticists ought to care about the scale on which statistical evidence is measured, and we have proposed the Kelvin temperature scale as a template for a context-independent measurement scale for statistical evidence. Moreover, we have claimed that, mathematically speaking, evidence and temperature may be one and the same thing. On first blush, this might seem absurd. Temperature is a property of systems following certain laws of nature (in particular, the 1st and 2nd Law of Thermodynamics) involving very physical quantities (e.g., energy) and processes (e.g., mechanical work). But what do the laws of thermodynamics have to do with statistical systems? Here I address that question. © 2014 S. Karger AG, Basel.

  9. In the teeth of the evidence: the curious case of evidence-based medicine.

    Davidoff, F

    1999-03-01

    For a very long time, evidence from research has contributed to clinical decision making. Over the past 50 years, however, the nature of clinical research evidence has drastically changed compared with previous eras: its standards are higher, the tools for assembling and analyzing it are more powerful, and the context in which it is used is less authoritarian. The consequence has been a shift in both the concept and the practice of clinical decision making known as evidence-based medicine. Evidence-based decisions, by definition, use the strongest available evidence, are often more quantitatively informed than decisions made in the traditional fashion; and sometimes run counter to expert opinion. The techniques of evidence-based medicine are also helpful in resolving conflicting opinions. Evidence-based medicine did not simply appear in vacuo; its roots extend back at least as far as the great French Encyclopedia of the 18th century, and the subsequent work of Pierre Louis in Paris in the early 19th century. The power of the evidence-based approach has been enhanced in recent years by the development of the techniques of systematic review and meta-analysis. While this approach has its critics, we would all want the best available evidence used in making decisions about our care if we got sick. It is only fair that the patients under our care receive nothing less.

  10. Weighted Evidence Combination Rule Based on Evidence Distance and Uncertainty Measure: An Application in Fault Diagnosis

    Lei Chen

    2018-01-01

    Full Text Available Conflict management in Dempster-Shafer theory (D-S theory is a hot topic in information fusion. In this paper, a novel weighted evidence combination rule based on evidence distance and uncertainty measure is proposed. The proposed approach consists of two steps. First, the weight is determined based on the evidence distance. Then, the weight value obtained in first step is modified by taking advantage of uncertainty. Our proposed method can efficiently handle high conflicting evidences with better performance of convergence. A numerical example and an application based on sensor fusion in fault diagnosis are given to demonstrate the efficiency of our proposed method.

  11. 20 CFR 219.24 - Evidence of presumed death.

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Evidence of presumed death. 219.24 Section... EVIDENCE REQUIRED FOR PAYMENT Evidence of Age and Death § 219.24 Evidence of presumed death. When a person cannot be proven dead but evidence of death is needed, the Board may presume he or she died at a certain...

  12. 20 CFR 404.720 - Evidence of a person's death.

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Evidence of a person's death. 404.720 Section... INSURANCE (1950- ) Evidence Evidence of Age, Marriage, and Death § 404.720 Evidence of a person's death. (a) When evidence of death is required. If you apply for benefits on the record of a deceased person, we...

  13. 20 CFR 404.728 - Evidence a marriage has ended.

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Evidence a marriage has ended. 404.728... DISABILITY INSURANCE (1950- ) Evidence Evidence of Age, Marriage, and Death § 404.728 Evidence a marriage has ended. (a) When evidence is needed that a marriage has ended. If you apply for benefits as the insured...

  14. How jurors use and misuse character evidence.

    Hunt, Jennifer S; Budesheim, Thomas Lee

    2004-04-01

    The Federal Rules of Evidence allow defendants to offer testimony about their good character, but that testimony can be impeached with cross-examination or a rebuttal witness. It is assumed that jurors use the defense's character evidence (CE) to form guilt and conviction judgments but use impeachment evidence only to assess the character witness's credibility. Two experiments tested these assumptions by presenting mock jurors with various forms of CE and impeachment. Participants made trait ratings for the character witness and defendant and guilt and conviction judgments. Positive CE did not affect guilt or conviction judgments, but cross-examination caused a backlash in which judgments were harsher than when no CE was given. Using path analysis, the authors tested a model of the process by which CE and impeachment affect defendant and witness impressions and guilt and conviction judgments. Implications for juror decision making are discussed.

  15. A consumer guide to phonological evidence

    Marc van Oostendorp

    2013-02-01

    Full Text Available Modern phonological theory is confronted with a wealth of new data from many different sources. This paper gives a summary and taxonomy of the kinds of evidence we currently have at our disposal. For each type it briefly discusses how it has been used, and gives some of the advantages and disadvantages. The main distinction made is between ‘existing’ data and ‘invented’ data, even though it is shown that such distinctions should be considered very carefully. I argue that each type of data can have a function in phonological argumentation, but also that each type of data has some very specific problems. The best evidence is converging evidence from different sources.

  16. Measuring uncertainty within the theory of evidence

    Salicone, Simona

    2018-01-01

    This monograph considers the evaluation and expression of measurement uncertainty within the mathematical framework of the Theory of Evidence. With a new perspective on the metrology science, the text paves the way for innovative applications in a wide range of areas. Building on Simona Salicone’s Measurement Uncertainty: An Approach via the Mathematical Theory of Evidence, the material covers further developments of the Random Fuzzy Variable (RFV) approach to uncertainty and provides a more robust mathematical and metrological background to the combination of measurement results that leads to a more effective RFV combination method. While the first part of the book introduces measurement uncertainty, the Theory of Evidence, and fuzzy sets, the following parts bring together these concepts and derive an effective methodology for the evaluation and expression of measurement uncertainty. A supplementary downloadable program allows the readers to interact with the proposed approach by generating and combining ...

  17. Professionalism and evidence-based practice

    Rasmussen, Palle

    2015-01-01

    of evidence- based methods in Danish pre-school education and care. The management sees the use of these methods as strengthening pre- school teacher professionalism, but the actual practices in the day-careinstitutions are ambiguous. In some cases, using the methods becomes an end in itself and tends......The idea of evidence- based practice is influential in public welfare services, including education. The idea is controversial, however, not least because it involves a poten tial redefinition of the relation ship between knowledge, authority and professionalism. This is discussed based on a study...... to displace important educational objectives. In other cases, the methods are reflectively adjusted to a given context. Used in this way only, evid ence-based practice and methodology is a valuable resource for professional practice in education. From such a perspective, at least some types of research based...

  18. Ancient bacteria show evidence of DNA repair

    Johnson, Sarah Stewart; Hebsgaard, Martin B; Christensen, Torben R

    2007-01-01

    -term survival of bacteria sealed in frozen conditions for up to one million years. Our results show evidence of bacterial survival in samples up to half a million years in age, making this the oldest independently authenticated DNA to date obtained from viable cells. Additionally, we find strong evidence...... geological timescales. There has been no direct evidence in ancient microbes for the most likely mechanism, active DNA repair, or for the metabolic activity necessary to sustain it. In this paper, we couple PCR and enzymatic treatment of DNA with direct respiration measurements to investigate long...... that this long-term survival is closely tied to cellular metabolic activity and DNA repair that over time proves to be superior to dormancy as a mechanism in sustaining bacteria viability....

  19. When general practitioners meet new evidence

    Olsen, Ole

    2017-01-01

    out the local information leaflet about home birth were prepared to do so. The time lag between presentation of the evidence and the GPs’ decision to hand out the leaflets was up to one and a half year. Conclusions: A significant number of GPs were prepared to change their information practices......Objective: To explore how general practitioners (GPs) think and act when presented with new evidence in relation to planned home birth and a proposal to change information practices. Design: Exploratory ethnographic study of GPs. The GPs were encountered one or more times during a two-year period......, 2011–2013, while the author tried to set up formal focus group interviews. Dialogues about the evidence, personal experiences, values and other issues unavoidably occurred. Field notes were written concomitantly. Setting: Danish GPs, primarily in Copenhagen. Subjects: Fifty Danish GPs. Results: The GPs...

  20. Learning from Evidence in a Complex World

    Sterman, John D.

    2006-01-01

    Policies to promote public health and welfare often fail or worsen the problems they are intended to solve. Evidence-based learning should prevent such policy resistance, but learning in complex systems is often weak and slow. Complexity hinders our ability to discover the delayed and distal impacts of interventions, generating unintended “side effects.” Yet learning often fails even when strong evidence is available: common mental models lead to erroneous but self-confirming inferences, allowing harmful beliefs and behaviors to persist and undermining implementation of beneficial policies. Here I show how systems thinking and simulation modeling can help expand the boundaries of our mental models, enhance our ability to generate and learn from evidence, and catalyze effective change in public health and beyond. PMID:16449579

  1. Evidence-based policymaking: A review

    Karen Nortje

    2010-05-01

    Full Text Available The process of facilitating the uptake of evidence, for example, scientific research findings, into the policymaking process is multifaceted and thus complex. It is therefore important for scientists to understand this process in order to influence it more effectively. Similarly, policymakers need to understand the complexities of the scientific process to improve their interaction with the scientific sphere. This literature review addresses those factors that influence the uptake of scientific evidence into policymaking, the barriers to using science in policymaking, as well as recommendations for improved science–policymaking interaction. A visual diagram of the gears of a car is used to convey the message of the complexities around the engagement between science and policymaking. It is concluded that the issue of evidence-based policymaking remains unresolved and questions for future research on the science–policy interface are raised.

  2. Limited Evidence for Robot-assisted Surgery

    Broholm, Malene; Onsberg Hansen, Iben; Rosenberg, Jacob

    2016-01-01

    -assisted surgery. Open versus robot-assisted surgery was investigated in 3 studies. A lower blood loss and a longer operative time were found after robot-assisted surgery. No other difference was detected. CONCLUSIONS: At this point there is not enough evidence to support the significantly higher costs......PURPOSE: To evaluate available evidence on robot-assisted surgery compared with open and laparoscopic surgery. METHOD: The databases Medline, Embase, and Cochrane Library were systematically searched for randomized controlled trials comparing robot-assisted surgery with open and laparoscopic...... surgery regardless of surgical procedure. Meta-analyses were performed on each outcome with appropriate data material available. Cochrane Collaboration's tool for assessing risk of bias was used to evaluate risk of bias on a study level. The GRADE approach was used to evaluate the quality of evidence...

  3. Spinosaur taxonomy and evolution of craniodental features: Evidence from Brazil.

    Marcos A F Sales

    Full Text Available Fossil sites from Brazil have yielded specimens of spinosaurid theropods, among which the most informative include the cranial remains of Irritator, Angaturama, and Oxalaia. In this work some of their craniodental features are reinterpreted, providing new data for taxonomic and evolutionary issues concerning this particular clade of dinosaurs. The mesial-most tooth of the left maxilla of the holotype of Irritator is regarded as representing the third tooth position, which is also preserved in the holotype of Angaturama. Thus, both specimens cannot belong to the same individual, contrary to previous assumptions, although they could have been the same taxon. In addition, the position of the external nares of Irritator is more comparable to those of Baryonyx and Suchomimus instead of other spinosaurine spinosaurids. In fact, with regards to some craniodental features, Brazilian taxa represent intermediate conditions between Baryonychinae and Spinosaurinae. Such a scenario is corroborated by our cladistic results, which also leave open the possibility of the former subfamily being non-monophyletic. Furthermore, the differences between spinosaurids regarding the position and size of the external nares might be related to distinct feeding habits and degrees of reliance on olfaction. Other issues concerning the evolution and taxonomy of Spinosauridae require descriptions of additional material for their clarification.

  4. Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics

    Sicheritz-Pontén, Thomas; Noel, CJ; Diaz, N

    2010-01-01

    Trichomonas vaginalis is the most common non-viral human sexually transmitted pathogen and importantly, contributes to facilitating the spread of HIV. Yet very little is known about its surface and secreted proteins mediating interactions with, and permitting the invasion and colonisation of...... potential extracellular proteins for the pathogen. A broad range of microorganisms encoding BspA-like proteins was identified and these are mainly known to live on mucosal surfaces, among these T. vaginalis is endowed with the largest gene family. Over 180 TvBspA proteins with inferred transmembrane domains...... were characterized by a considerable structural diversity between their TpLRR and other types of repetitive sequences and two subfamilies possessed distinct classic sorting signal motifs for endocytosis. One TvBspA subfamily also shared a glycine-rich protein domain with proteins from Clostridium...

  5. An evidence-based update on vitamins.

    Orr, K Kelly; Hume, Anne L

    2010-04-01

    American adults take many types of vitamin supplements, despite limited evidence of their efficacy, especially in preventing chronic diseases such as cardiovascular disease and cancer. Supplements contain significant amounts of vitamins when consumed from multiple sources. Excess consumption of some vitamins may have detrimental health effects. Use of MMVM products appears to be safe; however, clinical outcomes have not been established. Although vitamin D and preconception folic acid may be appropriate for self care, a health care provider should monitor other vitamin supplements for disease prevention, such as niacin. Beyond supplementation as treatment for vitamin deficiencies, evidence is lacking.

  6. Evidence-Based Advances in Ferret Medicine.

    Huynh, Minh; Chassang, Lucile; Zoller, Graham

    2017-09-01

    This literature review covers approximately 35 years of veterinary medicine. This article develops the current state of knowledge in pet ferret medicine regarding the most common diseases according to evidence-based data and gives insight into further axis of research. Literature review was conducted through identification of keywords (title + ferret) with Web-based database searching. To appreciate the methodological quality and the level of evidence of each article included in the review, full-text versions were reviewed and questions addressed in the articles were formulated. Analysis of the articles' content was performed by the authors, and relevant clinical information was extracted. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Observation, Sherlock Holmes, and Evidence Based Medicine.

    Osborn, John

    2002-01-01

    Sir Arthur Conan Doyle, the creator of the fictional detective Sherlock Holmes, studied medicine at the University of Edinburgh between 1876 and 1881 under Doctor Joseph Bell who emphasised in his teaching the importance of observation, deduction and evidence. Sherlock Holmes was modelled on Joseph Bell. The modern notions of Evidence Based Medicine (EBM) are not new. A very brief indication of some of the history of EBM is presented including a discussion of the important and usually overlooked contribution of statisticians to the Popperian philosophy of EBM.

  8. Evidence Study Guide. Revision (Naval Justice School)

    1992-07-01

    404(b). See United States v. Thomas, 11 M.J. 388 (C.M.A. 1981) and United States v. Dawkins 2 M.J. 898 (A.C.M.R. 1976) (pre-Mil.R.Evid. cases applying...criminal activity). 1313 BODY INTRUSiONS (Key N-;i-,crs 1049 et seq) A. Genes - 1. Mil.R.Evid. 312. Certain searches, such as searches of body cavities...inflammatory. For example, the trial counsel may not assert that the members are " selfish , self-centered and are not fulfilling [their] responsibility to

  9. Stock Returns and Risk: Evidence from Quantile

    Thomas C. Chiang

    2012-12-01

    Full Text Available This paper employs weighted least squares to examine the risk-return relation by applying high-frequency data from four major stock indexes in the US market and finds some evidence in favor of a positive relation between the mean of the excess returns and expected risk. However, by using quantile regressions, we find that the risk-return relation moves from negative to positive as the returns’ quantile increases. A positive risk-return relation is valid only in the upper quantiles. The evidence also suggests that intraday skewness plays a dominant role in explaining the variations of excess returns.

  10. Evidence & Gap Maps: A tool for promoting evidence informed policy and strategic research agendas.

    Snilstveit, Birte; Vojtkova, Martina; Bhavsar, Ami; Stevenson, Jennifer; Gaarder, Marie

    2016-11-01

    A range of organizations are engaged in the production of evidence on the effects of health, social, and economic development programs on human welfare outcomes. However, evidence is often scattered around different databases, web sites, and the gray literature and is often presented in inaccessible formats. Lack of overview of the evidence in a specific field can be a barrier to the use of existing research and prevent efficient use of limited resources for new research. Evidence & Gap Maps (EGMs) aim to address these issues and complement existing synthesis and mapping approaches. EGMs are a new addition to the tools available to support evidence-informed policymaking. To provide an accessible resource for researchers, commissioners, and decision makers, EGMs provide thematic collections of evidence structured around a framework which schematically represents the types of interventions and outcomes of relevance to a particular sector. By mapping the existing evidence using this framework, EGMs provide a visual overview of what we know and do not know about the effects of different programs. They make existing evidence available, and by providing links to user-friendly summaries of relevant studies, EGMs can facilitate the use of existing evidence for decision making. They identify key "gaps" where little or no evidence from impact evaluations and systematic reviews is available and can be a valuable resource to inform a strategic approach to building the evidence base in a particular sector. The article will introduce readers to the concept and methods of EGMs and present a demonstration of the EGM tool using existing examples. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Geographical distribution of present day Poaceae as evidence for the origin of African floras

    W. D. Clayton

    1983-11-01

    Full Text Available The major tribes and sub-families of grasses occupy worldwide latitudinal belts, which can be related to an evolutionary sequence of climatic adaptations. However, genera tend to be confined to individual continents, suggesting that grasses do not easily cross the oceans, and that the worldwide distribution of the family may have been achieved when the continents were closer together. Species distributions are likewise strongly influenced by the effect of climatic adaptation and continental isolation, but they show a number of aberrations. These are probably a legacy of climatic disturbance during the Pleistocene.

  12. Evidence-based medicine Training: Kazakhstan experience.

    Kamalbekova, G; Kalieva, M

    2015-01-01

    Understanding principles of evidence-based medicine is of vital importance for improving quality of care, promoting public health and health system development. Understanding principles of evidence-based medicine allows using the most powerful information source, which have ever existed in medicine. To evaluate the effectiveness of teaching Evidence-Based Medicine, including long-term outcomes of training. The study was conducted at the Medical University of Astana, where the Scientific and Educational Center of Evidence-Based Medicine was established in 2010 with the help of the corresponding project of the World Bank. The participants of the study were the faculty trained in Evidence-Based Medicine at the workshop "Introduction to Evidence-Based Medicine" for the period of 2010-2015 years. There were a total of 16 workshops during the period, and 323 employees were trained. All participants were asked to complete our questionnaire two times: before the training - pre-training (to determine the initial level of a listener) and after the training - post-training (to determine the acquired level and get the feedback). Questionnaires were prepared in such a way, that the majority of questions before and after training were identical. Thus, it provided a clear picture of the effectiveness of training. Questions in the survey were open-ended so that the respondents had the opportunity to freely and fully express their views. The main part of the questionnaires included the following questions: "Do you understand what evidence-based medicine is", "how do you understand what the study design means", "what is randomization", "how research is classified", "do you know the steps of decision-making according to Evidence-Based Medicine, list them", "what literature do you prefer to use when searching for information (print, electronic, etc.)", "what resources on the Internet do you prefer to use". Only 30-35% of respondents gave correct answers to the questions on

  13. Towards Trustable Digital Evidence with PKIDEV: PKI Based Digital Evidence Verification Model

    Uzunay, Yusuf; Incebacak, Davut; Bicakci, Kemal

    How to Capture and Preserve Digital Evidence Securely? For the investigation and prosecution of criminal activities that involve computers, digital evidence collected in the crime scene has a vital importance. On one side, it is a very challenging task for forensics professionals to collect them without any loss or damage. On the other, there is the second problem of providing the integrity and authenticity in order to achieve legal acceptance in a court of law. By conceiving digital evidence simply as one instance of digital data, it is evident that modern cryptography offers elegant solutions for this second problem. However, to our knowledge, there is not any previous work proposing a systematic model having a holistic view to address all the related security problems in this particular case of digital evidence verification. In this paper, we present PKIDEV (Public Key Infrastructure based Digital Evidence Verification model) as an integrated solution to provide security for the process of capturing and preserving digital evidence. PKIDEV employs, inter alia, cryptographic techniques like digital signatures and secure time-stamping as well as latest technologies such as GPS and EDGE. In our study, we also identify the problems public-key cryptography brings when it is applied to the verification of digital evidence.

  14. Military Rule of Evidence 404(b): Toothless Giant of the Evidence World

    1996-04-01

    be confident that the evidence will do more harm than good before excluding it and removing it entirely from the case."). 503 See FED. R. EvID. 403...including genital-genital, oral-genital, or oral-anal, whether between persons of the same or opposite sex; (2) Bestiality; (3) Masturbation ; (4) Sadistic

  15. Evidence and evidence gaps in the treatment of Eustachian tube dysfunction and otitis media

    Teschner, Magnus

    2016-01-01

    Evidence-based medicine is an approach to medical treatment intended to optimize patient-oriented decision-making on the basis of empirically proven effectiveness. For this purpose, a classification system has been established to categorize studies – and hence therapy options – in respect of associated evidence according to defined criteria. The Eustachian tube connects the nasopharynx with the middle ear cavity. Its key function is to ensure middle ear ventilation. Compromised ventilation results in inflammatory middle ear disorders. Numerous evidence-based therapy options are available for the treatment of impaired middle ear ventilation and otitis media, the main therapeutic approach being antibiotic treatment. More recent procedures such as balloon dilation of the Eustachian tube have also shown initial success but must undergo further evaluation with regard to evidence. There is, as yet, no evidence for some of the other long-established procedures. Owing to the multitude of variables, the classification of evidence levels for various treatment approaches calls for highly diversified assessment. Numerous evidence-based studies are therefore necessary in order to evaluate the evidence pertaining to existing and future therapy solutions for impaired middle ear ventilation and otitis media. If this need is addressed, a wealth of implications can be expected for therapeutic approaches in the years to come. PMID:28025605

  16. The Heart of the Matter of Opinion and Evidence: The Value of Evidence-Based Medicine

    Masvidal, Daniel; Lavie, Carl J.

    2012-01-01

    Evidence-based medicine is an important aspect of continuing medical education. This article reviews previous and current examples of conflicting topics that evidence-based medicine has clarified to allow us to provide the best possible patient care. PMID:22438783

  17. How evidence-based are the recommendations in evidence-based guidelines?

    Finlay A McAlister

    2007-08-01

    Full Text Available BACKGROUND: Treatment recommendations for the same condition from different guideline bodies often disagree, even when the same randomized controlled trial (RCT evidence is cited. Guideline appraisal tools focus on methodology and quality of reporting, but not on the nature of the supporting evidence. This study was done to evaluate the quality of the evidence (based on consideration of its internal validity, clinical relevance, and applicability underlying therapy recommendations in evidence-based clinical practice guidelines. METHODS AND FINDINGS: A cross-sectional analysis of cardiovascular risk management recommendations was performed for three different conditions (diabetes mellitus, dyslipidemia, and hypertension from three pan-national guideline panels (from the United States, Canada, and Europe. Of the 338 treatment recommendations in these nine guidelines, 231 (68% cited RCT evidence but only 105 (45% of these RCT-based recommendations were based on high-quality evidence. RCT-based evidence was downgraded most often because of reservations about the applicability of the RCT to the populations specified in the guideline recommendation (64/126 cases, 51% or because the RCT reported surrogate outcomes (59/126 cases, 47%. CONCLUSIONS: The results of internally valid RCTs may not be applicable to the populations, interventions, or outcomes specified in a guideline recommendation and therefore should not always be assumed to provide high-quality evidence for therapy recommendations.

  18. How to proceed when evidence-based practice is required but very little evidence available?

    Leboeuf-Yde, Charlotte; Lanlo, Olivier; Walker, Bruce F

    2013-01-01

    All clinicians of today know that scientific evidence is the base on which clinical practice should rest. However, this is not always easy, in particular in those disciplines, where the evidence is scarce. Although the last decades have brought an impressive production of research that is of inte...

  19. Current Evidence Supporting Obstetric Fistula Prevention Strategies ...

    Evidences from the articles were linked to prevention strategies retrieved from grey literature. The strategies were classified using an innovative target-focused method. Gaps in the literature show the need for fistula prevention research to aim at systematically measuring incidence and prevalence of the disease, identify the ...

  20. 20 CFR 726.311 - Evidence.

    2010-04-01

    ... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Evidence. 726.311 Section 726.311 Employees' Benefits EMPLOYMENT STANDARDS ADMINISTRATION, DEPARTMENT OF LABOR FEDERAL COAL MINE HEALTH AND SAFETY ACT OF 1969, AS AMENDED BLACK LUNG BENEFITS; REQUIREMENTS FOR COAL MINE OPERATOR'S INSURANCE Civil Money...

  1. Evidence for Future Cognition in Animals

    Roberts, William A.

    2012-01-01

    Evidence concerning the possibility of mental time travel into the future by animals was reviewed. Both experimental laboratory studies and field observations were considered. Paradigms for the study of future anticipation and planning included inhibition of consumption of current food contingent on future receipt of either a larger quantity or…

  2. 32 CFR 637.16 - Evidence.

    2010-07-01

    ... INVESTIGATIONS MILITARY POLICE INVESTIGATION Investigations § 637.16 Evidence. Military police are authorized to... accordance with AR 195-5. If no suitable facility is available for the establishment of a military police... appropriate USACIDC element may be requested to receipt for and assume responsibility for military police...

  3. is planning in Nigeria becoming evidence based?

    related Millennium Development Goals high on the policy agendas of many developing nations, the costs and as well as benefits of these health interventions are extremely vital in resource poor settings such as Nigeria. Despite the body of evidence ...

  4. 5 CFR 831.1109 - Evidence.

    2010-01-01

    ... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Evidence. 831.1109 Section 831.1109 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED... exhibit of a documentary character shall be submitted to the presiding officer, duly marked, and made a...

  5. 21 CFR 514.4 - Substantial evidence.

    2010-04-01

    ... adequate and well-controlled studies, such as a study in a target species, study in laboratory animals... and conditions of use. Substantial evidence of effectiveness of a new animal drug shall demonstrate that the new animal drug is effective for each intended use and associated conditions of use for and...

  6. Learning From Others About Research Evidence (editorial

    Alison Brettle

    2012-06-01

    Full Text Available Welcome to the June issue of EBLIP, our firstto be published with an HTML version as wellas PDFs for each article. I hope you enjoy andfind the alternative formats useful. As usualthe issue comprises an interesting range ofevidence summaries and articles that I hopeyou will find useful in applying evidence toyour practice.When considering evidence, two recent trips toEdinburgh got me thinking about the widerange of study designs or methods that areuseful for generating evidence, and also howwe can learn about their use from otherprofessions.The first trip was as part of the cadre of the LISDREaM project (http://lisresearch.org/dreamproject/.DREaM has been set up by the LISResearch Coalition to develop a sustainableLIS research network in the UK. As part ofthis, a series of workshops aims to introduceLIS practitioners to a wider range of researchmethods, thus expanding the methods used inLIS research. Indeed, a quick scan of thecontents of this issue show a preponderance ofsurveys, interviews, and citation analysis,suggesting that broadening our knowledge ofmethods may well be a useful idea. Theworkshops are highly interactive and, at eachsession experts from outside the LIS disciplineintroduce particular research methods andoutline how they could be used in LISapplications. As a result, I can see the valueand understand when to use research methodssuch as social network analysis, horizonscanning, ethnography, discourse analysis, andrepertory grids – as well as knowing that datamining is something I’m likely to avoid! So farI’ve shared my new knowledge with a PhDstudent who was considering her methodologyand incorporated my new knowledge ofhorizon scanning into a bid for researchfunding. The next (and more exciting step isto think of a situation where I can apply one ofthese methods to examining an aspect of LIS practice.The second trip was the British Association ofCounselling and Psychotherapy ResearchConference, an event which I

  7. Getting to Scale: Evidence, Professionalism, and Community

    Slavin, Robert E.

    2016-01-01

    Evidence-based reform, in which proven programs are scaled up to reach many students, is playing an increasing role in American education. This article summarizes articles in this issue to explain how Reading Recovery has managed to sustain itself and go to scale over more than 30 years. It argues that Reading Recovery has succeeded due to a focus…

  8. Justifying Physical Education Based on Neuroscience Evidence

    Berg, Kris

    2010-01-01

    Research has shown that exercise improves cognitive function and psychological traits that influence behavior (e.g., mood, level of motivation). The evidence in the literature also shows that physical education may enhance learning or that academic performance is at least maintained despite a reduction in classroom time in order to increase time…

  9. IPJP 12(2) - Evidence.indb

    denise

    ... be found at www.ipjp.org. This work is licensed to the publisher under the Creative Commons Attributions License 3.0 ... Exploring the evidence-based nature of phenomeno- .... Smith is its balanced composition of logos, ethos, and pathos. ..... Life-world experience: Existential phenomenological research approaches in.

  10. Environment and Happiness: New Evidence for Spain

    Cunado, Juncal; Perez de Gracia, Fernando

    2013-01-01

    This paper explores the relationship between air pollution, climate and reported subjective well-being (or happiness) in Spanish regions. The results show that, after controlling for most of the socio-economic variables affecting happiness, there are still significant regional differences in subjective well-being. Evidence also suggests that…

  11. Radiographers' preconditions for evidence-based radiography

    Ahonen, Sanna-Mari; Liikanen, Eeva

    2010-01-01

    Evidence-based practice (EBP) is essential in today's health care, but its establishment requires several preconditions from individuals and organizations (e.g. knowledge, understanding, attitudes, abilities, self-confidence, support, and resources). Previous studies suggest that radiographers do generate and use evidence in their work, but evidence-based radiography (EBR) is not yet used routinely as established practice, especially in terms of research utilization. This paper aims to describe radiographers' preconditions for EBR, and their participation in research activities. Main focus is on research utilization. Using an electronic questionnaire developed for this study, a survey was conducted: data collected from Finnish radiographers and radiotherapists (N = 438) were analysed both statistically and qualitatively. The final response rate was 39%. The results suggest radiographers' preconditions for EBR to consist of knowledge of research, significance of research activities, research-orientated way of working, and support. In addition, adequate resourcing is essential. Reading scientific journals, participation in research activities, a higher degree of education, and senior post seem to be significant promoters of EBR and research utilization. The results support the notion that EBR, and especially research utilization, are not yet well-established in Finland, and radiographers' viewpoints concerning the role and significance of research evidence and research activities still seem to vary.

  12. Angiographic Evidence of Coronary Embolism and Resolution*

    1971-04-27

    Apr 27, 1971 ... on exertion, orthopnoea and haemoptysis. She had atrial fibrillation, there was no evidence of heart failure and a right ventricular lift was palpable; auscultation revealed the classical findings of pure mitral stenosis with mobile valve cusps. The electrocardiogram (Fig. 1) showed atrial fibrillation, a mean ...

  13. Comment on "Evidence for mesothermy in dinosaurs".

    Myhrvold, Nathan P

    2015-05-29

    Grady et al. (Reports, 13 June 2014, p. 1268) studied dinosaur metabolism by comparison of maximum somatic growth rate allometry with groups of known metabolism. They concluded that dinosaurs exhibited mesothermy, a metabolic rate intermediate between endothermy and ectothermy. Multiple statistical and methodological issues call into question the evidence for dinosaur mesothermy. Copyright © 2015, American Association for the Advancement of Science.

  14. Evidence-based Practice of Radiology.

    Lavelle, Lisa P; Dunne, Ruth M; Carroll, Anne G; Malone, Dermot E

    2015-10-01

    Current health care reform in the United States is producing a shift in radiology practice from the traditional volume-based role of performing and interpreting a large number of examinations to providing a more affordable and higher-quality service centered on patient outcomes, which is described as a value-based approach to the provision of health care services. In the 1990 s, evidence-based medicine was defined as the integration of current best evidence with clinical expertise and patient values. When these methods are applied outside internal medicine, the process is called evidence-based practice (EBP). EBP facilitates understanding, interpretation, and application of the best current evidence into radiology practice, which optimizes patient care. It has been incorporated into "Practice-based Learning and Improvement" and "Systems-based Practice," which are two of the six core resident competencies of the Accreditation Council for Graduate Medical Education and two of the 12 American Board of Radiology milestones for diagnostic radiology. Noninterpretive skills, such as systems-based practice, are also formally assessed in the "Quality and Safety" section of the American Board of Radiology Core and Certifying examinations. This article describes (a) the EBP framework, with particular focus on its relevance to the American Board of Radiology certification and maintenance of certification curricula; (b) how EBP can be integrated into a residency program; and (c) the current value and likely place of EBP in the radiology information technology infrastructure. Online supplemental material is available for this article. © RSNA, 2015.

  15. Evidence of Construct Validity for Work Values

    Leuty, Melanie E.; Hansen, Jo-Ida C.

    2011-01-01

    Despite the importance of work values in the process of career adjustment (Dawis, 2002), little empirical research has focused on articulating the domains represented within the construct of work values and the examination of evidence of validity for the construct has been limited. Furthermore, the larger number of work values measures has made it…

  16. An evidence-based view on hyperbilirubinaemia

    Dijk, Peter H.; Hulzebos, Christian V.

    Introduction: We conducted a review of the evidence which contributes to the current care of jaundiced newborn infants. Methods: Literature was searched for reviews and randomized controlled trials (RCTs). Results: Six Cochrane reviews and eight other reviews and eighteen recent RCTs are discussed.

  17. Quantitative Evidence Synthesis with Power Priors

    Rietbergen, C.|info:eu-repo/dai/nl/322847796

    2016-01-01

    The aim of this thesis is to provide the applied researcher with a practical approach for quantitative evidence synthesis using the conditional power prior that allows for subjective input and thereby provides an alternative tgbgo deal with the difficulties as- sociated with the joint power prior

  18. Fossil evidence of the zygomycetous fungi

    Krings, M.; Taylor, T.N.; Dotzler, N.

    2013-01-01

    Molecular clock data indicate that the first zygomycetous fungi occurred on Earth during the Precambrian, however, fossil evidence of these organisms has been slow to accumulate. In this paper, the fossil record of the zygomycetous fungi is compiled, with a focus on structurally preserved

  19. 7 CFR 1421.12 - Production evidence.

    2010-01-01

    ... OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS GRAINS AND SIMILARLY HANDLED COMMODITIES-MARKETING ASSISTANCE LOANS AND LOAN DEFICIENCY PAYMENTS FOR 2008 THROUGH 2012 General § 1421.12 Production evidence. (a) Producers who redeem marketing assistance loan collateral at the prevailing world market...

  20. On data transformations and evidence of nonlinearity

    P. de Bruin (Paul); Ph.H.B.F. Franses (Philip Hans)

    1998-01-01

    textabstractIn this paper we examine the interaction between data transformation and the empirical evidence obtained when testing for (non-)linearity. For this purpose we examine nonlinear features in 64 monthly and 53 quarterly US macroeconomic variables for a range of Box-Cox data

  1. Digital Natives: Where Is the Evidence?

    Helsper, Ellen Johanna; Eynon, Rebecca

    2010-01-01

    Generational differences are seen as the cause of wide shifts in our ability to engage with technologies and the concept of the digital native has gained popularity in certain areas of policy and practice. This paper provides evidence, through the analysis of a nationally representative survey in the UK, that generation is only one of the…

  2. 31 CFR 353.23 - Evidence.

    2010-07-01

    ... not more than six months prior to the presentation of the bond. (c) Receiver in equity or similar... BONDS, SERIES EE AND HH Judicial Proceedings § 353.23 Evidence. (a) General. To establish the validity... more than six months prior to the presentation of the bond, there must also be submitted a...

  3. 31 CFR 360.23 - Evidence.

    2010-07-01

    ... than six months prior to the presentation of the bond. (c) Receiver in equity or similar court officer... BONDS, SERIES I Judicial Proceedings § 360.23 Evidence. (a) General. To establish the validity of... months prior to the presentation of the bond, there must also be submitted a certification from the clerk...

  4. Income Aspirations and Cooperation : Experimental Evidence

    Dalton, P.S.

    2010-01-01

    This article is the first attempt to study the empirical link between income aspirations and cooperation in a one shot public good game. By combining experimental with survey data, we find evidence that the more frustrated people are with their income, the lower is their propensity to cooperate with

  5. Evidence-based practice within nutrition

    Laville, Martine; Segrestin, Berenice; Alligier, Maud

    2017-01-01

    BACKGROUND: Evidence-based clinical research poses special barriers in the field of nutrition. The present review summarises the main barriers to research in the field of nutrition that are not common to all randomised clinical trials or trials on rare diseases and highlights opportunities for im...

  6. Hydrocarbons biodegradation and evidence of mixed petroleum ...

    Chromatographic analysis of extracts from the Cross River system show evidence of variable composition of biogenic n-alkane profile with dominance of terrigenous over aquatic organic matter present (LHC/SHC-0.36-10.57) at upstream location reflecting the natural background levels and marked levels of petroleum ...

  7. 41 CFR 50-203.18 - Evidence.

    2010-07-01

    ... 41 Public Contracts and Property Management 1 2010-07-01 2010-07-01 true Evidence. 50-203.18 Section 50-203.18 Public Contracts and Property Management Other Provisions Relating to Public Contracts PUBLIC CONTRACTS, DEPARTMENT OF LABOR 203-RULES OF PRACTICE Minimum Wage Determinations Under the Walsh...

  8. Evidence for an isomer in 76Ni

    Sawicka, M.; Pfuetzner, M.; Grzywacz, R.; Daugas, J.M.; Belier, G.; Sauvestre, J.E.; Matea, I.; Lewitowicz, M.; Georgiev, G.; Grawe, H.; Mayet, P.; Becker, F.; Bingham, C.; Borcea, R.; Hammache, F.; Ibrahim, F.; Bouchez, E.; Buta, A.; Dragulescu, E.; Giovinazzo, J.; Meot, V.; Negoita, F.; De Oliveira Santos, F.; Perru, O.; Roig, O.; Rykaczewski, K.P.; Saint-Laurent, M.G.; Sorlin, O.; Stanoiu, M.; Stefan, I.; Stodel, C.; Theisen, C.; Verney, D.

    2004-01-01

    In the experiment performed at the LISE2000 spectrometer at GANIL neutron-rich nickel isotopes were studied by microsecond isomer spectroscopy. Evidence for an isomer in 76 Ni is found, consistently with the shell model prediction of an 8 + state of ν(g 9/2 ) 2 structure. (orig.)

  9. 8 CFR 1244.9 - Evidence.

    2010-01-01

    ... unavailable, and affirming that he or she is a national of the designated foreign state. A personal interview... of identity or nationality. During this interview, the applicant may present any secondary evidence..., or to appear for a scheduled interview, without good cause, will be deemed an abandonment of the...

  10. 8 CFR 244.9 - Evidence.

    2010-01-01

    ... affirming that he or she is a national of the designated foreign state. A personal interview before an... nationality. During this interview, the applicant may present any secondary evidence that he or she feels... appear for a scheduled interview, without good cause, will be deemed an abandonment of the application...

  11. 42 CFR 93.208 - Evidence.

    2010-10-01

    ... 42 Public Health 1 2010-10-01 2010-10-01 false Evidence. 93.208 Section 93.208 Public Health PUBLIC HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES HEALTH ASSESSMENTS AND HEALTH EFFECTS STUDIES OF HAZARDOUS SUBSTANCES RELEASES AND FACILITIES PUBLIC HEALTH SERVICE POLICIES ON RESEARCH...

  12. Fungal genomics: forensic evidence of sexual activity.

    Gow, Neil A R

    2005-07-12

    The genome sequence of the 'asexual' human pathogenic fungus Aspergillus fumigatus suggests it has the capability to undergo mating and meiosis. That this organism engages in clandestine sexual activity is also suggested by observations of two equally distributed complementary mating types in nature, the expression of mating type genes and evidence of recent genome recombination events.

  13. 21 CFR 17.39 - Evidence.

    2010-04-01

    ... AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL CIVIL MONEY PENALTIES... offering or promising to accept, a valuable consideration in settling or attempting to settle a civil money... liability for or invalidity of the civil money penalty or its amount. Evidence of conduct or statements made...

  14. Evidence-Based Laboratory Medicine: Is It Working in Practice?

    Price, Christopher P

    2012-01-01

    The principles of Evidence-Based Medicine have been established for about two decades, with the need for evidence-based clinical practice now being accepted in most health systems around the world. These principles can be employed in laboratory medicine. The key steps in evidence-based practice, namely (i) formulating the question; (ii) searching for evidence; (iii) appraising evidence; (iv) applying evidence; and (v) assessing the experience are all accepted but, as yet, translation into dai...

  15. Can Scholarly Communication be Evidence Based? (Editorial

    Denise Koufogiannakis

    2010-12-01

    Full Text Available This issue of Evidence Based Library and Information Practice includes three papers from the Evidence Based Scholarly Communication Conference (EBSCC that took place in March 2010i. Kroth, Philips and Eldredge have written a commentary that gives an overview of the conference, and introduces us to the research papers that were presented. As well, two research presentations from the conference appear in this issue, an article by Donahue about a potential new method of communicating between scholars, and a paper by Gilliland in our Using Evidence in Practice section, detailing a library’s Open Access Day preparations.Kroth, Philips and Eldredge note that “The EBSCC brought together librarians and information specialists to share evidence-based strategies for developing effective local scholarly communication support and training and, hopefully, form new coalitions to address this topic at a local and national level.” (p 108. This conference focused on translational medicine, and looked at how to promote new methods of scholarly communication, partially through the inclusion of research papers at the conference.The inclusion of these articles and the evidence based focus of the EBSCC conference, made me ask myself, can scholarly communication be evidence based? At its core, scholarly communication is anything but a scientific issue. It is charged with emotion; from authors, publishers, librarians and others involved in the business of publishing. The recent shift to look at new models of scholarly communication has been a threat to many of the established models and sparked much debate in the academic world, especially in relation to open access. In her 2006 EBLIP commentary on evidence based practice and open access, Morrison notes, “Open Access and evidence based librarianship are a natural combination” (p. 49, and outlines her perspective on many of the reasons why. Debate continues to rage, however, regarding how authors should

  16. On evidence and evidence-based medicine: lessons from the philosophy of science.

    Goldenberg, Maya J

    2006-06-01

    The evidence-based medicine (EBM) movement is touted as a new paradigm in medical education and practice, a description that carries with it an enthusiasm for science that has not been seen since logical positivism flourished (circa 1920-1950). At the same time, the term "evidence-based medicine" has a ring of obviousness to it, as few physicians, one suspects, would claim that they do not attempt to base their clinical decision-making on available evidence. However, the apparent obviousness of EBM can and should be challenged on the grounds of how 'evidence' has been problematised in the philosophy of science. EBM enthusiasm, it follows, ought to be tempered. The post-positivist, feminist, and phenomenological philosophies of science that are examined in this paper contest the seemingly unproblematic nature of evidence that underlies EBM by emphasizing different features of the social nature of science. The appeal to the authority of evidence that characterizes evidence-based practices does not increase objectivity but rather obscures the subjective elements that inescapably enter all forms of human inquiry. The seeming common sense of EBM only occurs because of its assumed removal from the social context of medical practice. In the current age where the institutional power of medicine is suspect, a model that represents biomedicine as politically disinterested or merely scientific should give pause.

  17. Evidence-based medicine and epistemological imperialism: narrowing the divide between evidence and illness.

    Crowther, Helen; Lipworth, Wendy; Kerridge, Ian

    2011-10-01

    Evidence-based medicine (EBM) has been rapidly and widely adopted because it claims to provide a method for determining the safety and efficacy of medical therapies and public health interventions more generally. However, as others have noted, EBM may be riven through with cultural bias, both in the generation of evidence and in its translation. We suggest that technological and scientific advances in medicine accentuate and entrench these cultural biases, to the extent that they may invalidate the evidence we have about disease and its treatment. This creates a significant ethical, epistemological and ontological challenge for medicine. © 2011 Blackwell Publishing Ltd.

  18. Fracture flow modelling. Proof of evidence

    Hencher, S.R.

    1996-01-01

    Proof of Evidence by an expert witness is presented in support of the case by Friends of the Earth (FOE) against the proposed construction by UK Nirex Ltd of an underground Rock Characterisation Facility (RCF) at a site in the Sellafield area. The RCF is part of an investigation by Nirex into a suitable site for an underground repository for the disposal of radioactive waste. The objections were raised at a Planning Inquiry in 1995. The evidence points out that current understanding of the factors which control flow through a network of interconnecting fractures, such as that at the Sellafield site, is at a very early stage of development. Neither are the methods of investigation and analysis required for a post-closure performance assessment (PCPA) for a repository well developed. These issues are being investigated in international underground research laboratories but the proposed RCF is intended to be confirmatory rather than experimental. (23 references). (UK)

  19. Evidence-Based Advances in Reptile Medicine.

    Mitchell, Mark A; Perry, Sean M

    2017-09-01

    Evidence-based medicine allows veterinarians to practice high-quality medicine, because the basis for all decision making is quantitative, objective, and reproducible. Case reports and case series are limited in their scope and application. Cross-sectional studies, likewise, cannot provide answers to specific variable testing with a temporal application. It is essential for the reptile specialty to expand into case-control studies, cohort studies, and experimental/intervention studies. Unfortunately, much of the reptile literature remains limited to descriptive studies. This article reviews current evidence-based topics in reptile medicine and shares how everyone practicing in the field can contribute to improving this specialty. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Evidence and research in rectal cancer

    Valentini, Vincenzo; Beets-Tan, Regina; Borras, Josep M.; Krivokapic, Zoran; Leer, Jan Willem; Pahlman, Lars; Roedel, Claus; Schmoll, Hans Joachim; Scott, Nigel; Velde, Cornelius Van de; Verfaillie, Christine

    2008-01-01

    The main evidences of epidemiology, diagnostic imaging, pathology, surgery, radiotherapy, chemotherapy and follow-up are reviewed to optimize the routine treatment of rectal cancer according to a multidisciplinary approach. This paper reports on the knowledge shared between different specialists involved in the design and management of the multidisciplinary ESTRO Teaching Course on Rectal Cancer. The scenario of ongoing research is also addressed. In this time of changing treatments, it clearly appears that a common standard for large heterogeneous patient groups have to be substituted by more individualised therapies based on clinical-pathological features and very soon on molecular and genetic markers. Only trained multidisciplinary teams can face this new challenge and tailor the treatments according to the best scientific evidence for each patient

  1. Motives for intergenerational transfers: evidence from Malaysia.

    Lillard, L A; Willis, R J

    1997-02-01

    In this paper we discuss a number of hypotheses about motives for intergenerational transfers within the family. We use data on time and money transfers between generations in Malaysia, where there is neither Social Security nor Medicare, to explore these hypotheses empirically. We find evidence supporting the hypotheses that children are an important source of old age security and that old age security is, in part, children's repayment for parental investments in their education. This repayment is partly a function of the children's income and, in the case of females, a function of their spouse's income. We also find evidence supporting the hypotheses that parents and children engage in the exchange of time help for money.

  2. Digital Evidence Education in Schools of Law

    Aaron Alva

    2012-06-01

    Full Text Available An examination of State of Connecticut v. Julie Amero provides insight into how a general lack of understanding of digital evidence can cause an innocent defendant to be wrongfully convicted. By contrast, the 101-page opinion in Lorraine v. Markel American Insurance Co. provides legal precedence and a detailed consideration for the admission of digital evidence. An analysis of both cases leads the authors to recommend additions to Law School curricula designed to raise the awareness of the legal community to ensure such travesties of justice, as in the Amero case, don’t occur in the future. Work underway at the University of Washington designed to address this deficiency is discussed.

  3. Evidence for criticality in financial data

    Ruiz, G.; de Marcos, A. F.

    2018-01-01

    We provide evidence that cumulative distributions of absolute normalized returns for the 100 American companies with the highest market capitalization, uncover a critical behavior for different time scales Δt. Such cumulative distributions, in accordance with a variety of complex - and financial - systems, can be modeled by the cumulative distribution functions of q-Gaussians, the distribution function that, in the context of nonextensive statistical mechanics, maximizes a non-Boltzmannian entropy. These q-Gaussians are characterized by two parameters, namely ( q, β), that are uniquely defined by Δt. From these dependencies, we find a monotonic relationship between q and β, which can be seen as evidence of criticality. We numerically determine the various exponents which characterize this criticality.

  4. Creative teaching an evidence-based approach

    Sale, Dennis

    2015-01-01

    This book contains an evidence-based pedagogic guide to enable any motivated teaching/training professional to be able to teach effectively and creatively. It firstly summarises the extensive research field on human psychological functioning relating to learning and how this can be fully utilised in the design and facilitation of quality learning experiences. It then demonstrates what creativity actually 'looks like' in terms of teaching practices, modelling the underpinning processes of creative learning design and how to apply these in lesson planning. The book, having established an evidence-based and pedagogically driven approach to creative learning design, extensively focuses on key challenges facing teaching professionals today. These include utilising information technologies in blended learning formats, differentiating instruction, and developing self-directed learners who can think well. The main purpose of the book is to demystify what it means to teach creatively, explicitly demonstrating the pr...

  5. BARNARD 59: NO EVIDENCE FOR FURTHER FRAGMENTATION

    Roman-Zuniga, C. G. [Instituto de Astronomia, Universidad Nacional Autonoma de Mexico, Km 103 Carr. Tijuana-Ensenada, Ensenada BC 22860 (Mexico); Frau, P.; Girart, J. M. [Institut de Ciencies de l' Espai (CSIC-IEEC), Campus UAB, Facultat de Ciencies, Torre C-5p, 08193 Bellaterra, Catalunya (Spain); Alves, Joao F., E-mail: croman@astrosen.unam.mx [Institute of Astronomy, University of Vienna, Tuerkenschanzstr. 17, 1180 Vienna (Austria)

    2012-03-10

    The dense molecular clump at the center of the Barnard 59 (B59) complex is the only region in the Pipe Nebula that has formed a small, stellar cluster. The previous analysis of a high-resolution near-IR dust extinction map revealed that the nuclear region in B59 is a massive, mostly quiescent clump of 18.9 M{sub Sun }. The clump shows a monolithic profile, possibly indicating that the clump is on the way to collapse, with no evident fragmentation that could lead to another group of star systems. In this paper, we present new analysis that compares the dust extinction map with a new dust emission radio-continuum map of higher spatial resolution. We confirm that the clump does not show any significant evidence for prestellar fragmentation at scales smaller than those probed previously.

  6. BARNARD 59: NO EVIDENCE FOR FURTHER FRAGMENTATION

    Román-Zúñiga, C. G.; Frau, P.; Girart, J. M.; Alves, João F.

    2012-01-01

    The dense molecular clump at the center of the Barnard 59 (B59) complex is the only region in the Pipe Nebula that has formed a small, stellar cluster. The previous analysis of a high-resolution near-IR dust extinction map revealed that the nuclear region in B59 is a massive, mostly quiescent clump of 18.9 M ☉ . The clump shows a monolithic profile, possibly indicating that the clump is on the way to collapse, with no evident fragmentation that could lead to another group of star systems. In this paper, we present new analysis that compares the dust extinction map with a new dust emission radio-continuum map of higher spatial resolution. We confirm that the clump does not show any significant evidence for prestellar fragmentation at scales smaller than those probed previously.

  7. Comparing Categorical and Probabilistic Fingerprint Evidence.

    Garrett, Brandon; Mitchell, Gregory; Scurich, Nicholas

    2018-04-23

    Fingerprint examiners traditionally express conclusions in categorical terms, opining that impressions do or do not originate from the same source. Recently, probabilistic conclusions have been proposed, with examiners estimating the probability of a match between recovered and known prints. This study presented a nationally representative sample of jury-eligible adults with a hypothetical robbery case in which an examiner opined on the likelihood that a defendant's fingerprints matched latent fingerprints in categorical or probabilistic terms. We studied model language developed by the U.S. Defense Forensic Science Center to summarize results of statistical analysis of the similarity between prints. Participant ratings of the likelihood the defendant left prints at the crime scene and committed the crime were similar when exposed to categorical and strong probabilistic match evidence. Participants reduced these likelihoods when exposed to the weaker probabilistic evidence, but did not otherwise discriminate among the prints assigned different match probabilities. © 2018 American Academy of Forensic Sciences.

  8. Evidence-based hypnotherapy for depression.

    Alladin, Assen

    2010-04-01

    Cognitive hypnotherapy (CH) is a comprehensive evidence-based hypnotherapy for clinical depression. This article describes the major components of CH, which integrate hypnosis with cognitive-behavior therapy as the latter provides an effective host theory for the assimilation of empirically supported treatment techniques derived from various theoretical models of psychotherapy and psychopathology. CH meets criteria for an assimilative model of psychotherapy, which is considered to be an efficacious model of psychotherapy integration. The major components of CH for depression are described in sufficient detail to allow replication, verification, and validation of the techniques delineated. CH for depression provides a template that clinicians and investigators can utilize to study the additive effects of hypnosis in the management of other psychological or medical disorders. Evidence-based hypnotherapy and research are encouraged; such a movement is necessary if clinical hypnosis is to integrate into mainstream psychotherapy.

  9. Evidence Based Education: un quadro storico

    Giuliano Vivanet

    2013-08-01

    Full Text Available Nel corso dell’ultimo decennio, nel pensiero pedagogico anglosassone, si è affermata una cultura dell’evidenza cui ci si riferisce con l’espressione “evidence based education” (EBE. Secondo tale prospettiva, le decisioni in ambito educativo dovrebbero essere assunte sulla base delle conoscenze che la ricerca empirica offre in merito alla minore o maggiore efficacia delle differenti opzioni didattiche. Si tratta di un approccio (denominato “evidence based practice” che ha origine in ambito medico e che in seguito ha trovato applicazione in differenti domini delle scienze sociali. L’autore presenta un quadro introduttivo all’EBE, dando conto delle sue origini e dei differenti significati di cui è portatrice.

  10. The China price: Evidence and some implications

    Álvarez, Roberto; Claro, Sebastián

    2006-01-01

    China´s import penetration in Chilean markets is higher in unskilled-labor intensive sectors as predicted by traditional endowment-based theories of comparative advantage. However, there is also evidence of within-industry specialization. In particular, high-income countries receive higher prices for its products, and Chinese products are not only cheaper in comparison to the world average but also relative to countries with similar income per capita. These price differences cannot account fo...

  11. Do Momentum Strategies Work?: - Australian Evidence

    Michael E. Drew; Madhu Veeraraghavan; Min Ye

    2004-01-01

    This paper investigates the profitability of momentum investment strategy and the predictive power of trading volume for equities listed in the Australian Stock Exchange. Recent research finds that momentum and trading volume appear to predict subsequent returns in U.S. market and past volume helps to reconcile intermediate-horizon “under reaction” and long-horizon “overreaction” effects. However, bulk of the evidence on this important relationship between past returns and future returns is l...

  12. Computational mate choice: theory and empirical evidence.

    Castellano, Sergio; Cadeddu, Giorgia; Cermelli, Paolo

    2012-06-01

    The present review is based on the thesis that mate choice results from information-processing mechanisms governed by computational rules and that, to understand how females choose their mates, we should identify which are the sources of information and how they are used to make decisions. We describe mate choice as a three-step computational process and for each step we present theories and review empirical evidence. The first step is a perceptual process. It describes the acquisition of evidence, that is, how females use multiple cues and signals to assign an attractiveness value to prospective mates (the preference function hypothesis). The second step is a decisional process. It describes the construction of the decision variable (DV), which integrates evidence (private information by direct assessment), priors (public information), and value (perceived utility) of prospective mates into a quantity that is used by a decision rule (DR) to produce a choice. We make the assumption that females are optimal Bayesian decision makers and we derive a formal model of DV that can explain the effects of preference functions, mate copying, social context, and females' state and condition on the patterns of mate choice. The third step of mating decision is a deliberative process that depends on the DRs. We identify two main categories of DRs (absolute and comparative rules), and review the normative models of mate sampling tactics associated to them. We highlight the limits of the normative approach and present a class of computational models (sequential-sampling models) that are based on the assumption that DVs accumulate noisy evidence over time until a decision threshold is reached. These models force us to rethink the dichotomy between comparative and absolute decision rules, between discrimination and recognition, and even between rational and irrational choice. Since they have a robust biological basis, we think they may represent a useful theoretical tool for

  13. Corruption and Firm Growth: Evidence from China

    Wang, Y.; You, J.

    2012-01-01

    Corruption is one of the most pervasive obstacles to economic and social development. However, in the existing literature it appears that corruption seems to be less harmful in some countries than in others. The most striking examples are well known as the "East Asian paradox": countries displaying exceptional growth records despite having thriving corruption cultures. The aim of this paper is to explain the high corruption but fast economic growth puzzle in China by providing firm-level evid...

  14. Poppers: more evidence of suppressed immunity.

    James, J S

    1999-08-20

    Evidence from studies in mice shows that exposure to isobutyl nitrite suppresses the immune system. This immune suppression allows for bacterial growth in the lungs and livers of infected mice and can inhibit the ability of mediastinal lymph nodes to respond to antigen-specific stimulation. The mechanism for immune suppression may be a reduction in CD4+ and CD8+ T cell populations in the mediastinal lymph nodes following pulmonary infection with Listeria monocytogenes.

  15. Evidence of chromaffin oxygen sensing in neuroblastoma.

    Hedborg, F; Franklin, G; Norrman, J; Grimelius, L; Wassberg, E; Hero, B; Schilling, F; Berthold, F; Harms, D; Sandstedt, B

    2001-01-01

    With the aid of IGF2 and VEGF in situ hybridization; tyrosine hydroxylase, chromogranin A, and Ki67 immunohistochemistry; and TUNEL staining applied to a large series of clinical neuroblastomas and to an animal model, we show here that stroma-poor neuroblastomas show evidence of chromaffin differentiation similar to that of type 1 small intensely fluorescent (SIF) cells and that this occurs in a vascular-dependent fashion, indicating a role for local tumor hypoxia in the differentiation process.

  16. Cocoa Polyphenols: Evidence from Epidemiological Studies.

    Matsumoto, Chisa

    2018-01-01

    Accumulating evidence suggests potential preventive effects of chocolate/cocoa on the risk of cardio vascular disease (CVD). However, cocoa products also contain high levels of sugar and fat, which increase CVD risk factors. Even, the identity of the substance in chocolate/cocoa that has a favorable effect on CVD and CVD risk factors remains unclear, growing evidence from experimental studies suggests that cocoa polyphenols might be a major contributor to cardiovascular-protective effects. However, epidemiological studies, which are necessary to evaluate an association between the risk of CVD and cocoa polyphenol, remain sparse. We will discuss recent evidence regarding the association between cocoa polyphenol consumption and the risks of CVD and its risk factors by reviewing recent epidemiological studies. We shall also provide some guidance for patient counseling and will discuss the public health implications for recommending cocoa polyphenol consumption to prevent CVD. Epidemiological studies evaluating the association between cocoa polyphenol itself and the risk of CVD are sparse. However, evidence from limited epidemiological studies suggests that cocoa polyphenol consumption may lower the risk of CVD. Given the potential adverse effects of the consumption of cocoa products with high fat and sugar and the fact that the most appropriate dose of cocoa polyphenol for cardio-protective effects has not yet been established, health care providers should remain cautious about recommending cocoa/cocoa polyphenol consumption to their patients to reduce the risk of CVD, taking the characteristics of individual patients into careful consideration. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. Geomorphic evidence for ancient seas on Mars

    Parker, Timothy J.; Schneeberger, Dale M.; Pieri, David C.; Saunders, R. Stephen

    1987-01-01

    Geomorphic evidence is presented for ancient seas on Mars. Several features, similar to terrestrial lacustrine and coastal features, were identified along the northern plains periphery from Viking images. The nature of these features argues for formation in a predominantly liquid, shallow body of standing water. Such a shallow sea would require either relatively rapid development of shoreline morphologies or a warmer than present climate at the time of outflow channel formation.

  18. Evidence-based dentistry: Future aspects

    Kanika Mohindra

    2017-01-01

    Full Text Available Traditionally, clinical decisions in dentistry have been based on the experience of the dentist. If the given treatment works, it was utilized again, but if the results were disappointing, the procedure was deserted. Evaluating clinical treatment in this fashion is difficult because it is hard to know which factors are important for success and which contribute to failure. This came with the concept of evidence-based approach which facilitates conclusions for clinical practice based on sound research studies.

  19. Barefoot running survey: Evidence from the field

    David Hryvniak; Jay Dicharry; Robert Wilder

    2014-01-01

    Background: Running is becoming an increasingly popular activity among Americans with over 50 million participants. Running shoe research and technology has continued to advance with no decrease in overall running injury rates. A growing group of runners are making the choice to try the minimal or barefoot running styles of the pre-modern running shoe era. There is some evidence of decreased forces and torques on the lower extremities with barefoot running, but no clear data regarding how thi...

  20. Health benefits of physical activity: the evidence

    Warburton, Darren E.R.; Nicol, Crystal Whitney; Bredin, Shannon S.D.

    2006-01-01

    The primary purpose of this narrative review was to evaluate the current literature and to provide further insight into the role physical inactivity plays in the development of chronic disease and premature death. We confirm that there is irrefutable evidence of the effectiveness of regular physical activity in the primary and secondary prevention of several chronic diseases (e.g., cardiovascular disease, diabetes, cancer, hypertension, obesity, depression and osteoporosis) and premature deat...

  1. Morphea: Evidence-based recommendations for treatment

    Nicole M Fett

    2012-01-01

    Morphea is a rare fibrosing disorder of the skin. Evidence-based treatment strategies in morphea are lacking. This review summarizes the available data on morphea treatment and provides therapeutic strategies based on morphea subtypes. The Cochrane Library, Medline and Embase from inception until May of 2011 were searched using the key words "morphea" and "morphea treatment." Reference lists of the resultant articles, as well as relevant reviews, were also searched. This review focuses on ran...

  2. Prostate cancer and inflammation: the evidence

    Sfanos, Karen S; De Marzo, Angelo M

    2012-01-01

    Chronic inflammation is now known to contribute to several forms of human cancer, with an estimated 20% of adult cancers attributable to chronic inflammatory conditions caused by infectious agents, chronic noninfectious inflammatory diseases and / or other environmental factors. Indeed, chronic inflammation is now regarded as an ‘enabling characteristic’ of human cancer. The aim of this review is to summarize the current literature on the evidence for a role for chronic inflammation in prosta...

  3. An evidence-based review: distracted driver.

    Llerena, Luis E; Aronow, Kathy V; Macleod, Jana; Bard, Michael; Salzman, Steven; Greene, Wendy; Haider, Adil; Schupper, Alex

    2015-01-01

    Cell phone use and texting are prevalent within society and have thus pervaded the driving population. This technology is a growing concern within the confines of distracted driving, as all diversions from attention to the road have been shown to increase the risk of crashes. Adolescent, inexperienced drivers, who have the greatest prevalence of texting while driving, are at a particularly higher risk of crashes because of distraction. Members of the Injury Control Violence Prevention Committee of the Eastern Association for the Surgery of Trauma performed a PubMed search of articles related to distracted driving and cell phone use as a distractor of driving between 2000 and 2013. A total of 19 articles were found to merit inclusion as evidence in the evidence-based review. These articles provided evidence regarding the relationship between distracted driving and crashes, cell phone use contributing to automobile accidents, and/or the relationship between driver experience and automobile accidents. (Adjust methods/results sections to the number of articles that correctly corresponds to the number of references, as well as the methodology for reference inclusion.) Based on the evidence reviewed, we can recommend the following. All drivers should minimize all in-vehicle distractions while on the road. All drivers should not text or use any touch messaging system (including the use of social media sites such as Facebook and Twitter) while driving. Younger, inexperienced drivers should especially not use cell phones, texting, or any touch messaging system while driving because they pose an increased risk for death and injury caused by distractions while driving.

  4. Evidence for supplemental treatments in androgenetic alopecia.

    Famenini, Shannon; Goh, Carolyn

    2014-07-01

    Currently, topical minoxidil and finasteride are the only treatments that have been FDA approved for the treatment of female pattern hair loss and androgenetic alopecia. Given the incomplete efficacy and sife effect profile of these medications, some patients utilize alternative treatments to help improve this condition. In this review, we illustrate the scientific evidence underlying the efficacy of these alternative approaches, including biotin, caffeine, melatonin, a marine extract, and zinc.

  5. Human mutagens: evidence from paternal exposure

    Narod, S.A.; Douglas, G.R.; Nestmann, E.R.; Blakey, D.H.

    1988-01-01

    The importance of inherited mutations as a cause of human disease has been established clearly through examples of well-defined genetic anomalies, such as Down syndrome and retinoblastoma. Furthermore, it is suspected that environmental contaminants induce mutations resulting in increased risk for such defects in subsequent generations of persons exposed. The present lack of direct evidence for induced inherited genetic disorders in human beings hampers the development of risk estimation techniques for extrapolation from animal models. The most extensive prospective epidemiologic studies of inherited genetic effects have involved survivors of atomic bomb detonations and patients treated with cancer chemotherapy. In neither case has a significant elevation in inherited genetic effects or cancer been detected in the offspring of exposed individuals. Epidemiologic studies of subjects receiving chronic exposure may be confounded by the effect of maternal exposure during pregnancy. Consideration of only paternal exposure can minimize the confounding influence of teratogenicity, enhancing the resolving power of studies for inherited effects. Using this approach, retrospective (case-control) studies of childhood cancer patients have provided limited but suggestive evidence for inheritance of induced effects. Endpoints, such as congenital malformations and spontaneous abortion following paternal exposure, can also be considered as indicators of heritable mutagenic effects. For example, there is limited evidence suggesting that paternal exposure to anaesthetic gases may cause miscarriage and congenital abnormalities as a result of induced male germ cell mutations. 104 references

  6. Epidemiology of osteoarthritis: state of the evidence

    Allen, Kelli D.; Golightly, Yvonne M.

    2015-01-01

    Purpose of review This review focuses on recent studies of osteoarthritis epidemiology, including research on prevalence, incidence, and a broad array of potential risk factors at the person level and joint level. Recent findings Studies continue to illustrate the high impact of osteoarthritis worldwide, with increasing incidence. Person-level risk factors with strong evidence regarding osteoarthritis incidence and/or progression include age, sex, socioeconomic status, family history, and obesity. Joint-level risk factors with strong evidence for incident osteoarthritis risk include injury and occupational joint loading; the associations of injury and joint alignment with osteoarthritis progression are compelling. Moderate levels of physical activity have not been linked to increased osteoarthritis risk. Some topics of high recent interest or emerging evidence for association with osteoarthritis include metabolic pathways, vitamins, joint shape, bone density, limb length inequality, muscle strength and mass, and early structural damage. Summary Osteoarthritis is a complex, multifactorial disease, and there is still much to learn regarding mechanisms underlying incidence and progression. However, there are several known modifiable and preventable risk factors, including obesity and joint injury; efforts to mitigate these risks can help to lessen the impact of osteoarthritis. PMID:25775186

  7. Evidence-based prevention of childhood malnutrition.

    Imdad, Aamer; Sadiq, Kamran; Bhutta, Zulfiqar A

    2011-05-01

    Childhood malnutrition is prevalent in developing countries and contributes to one-third of all deaths in these countries. There have been advances in prevention of childhood malnutrition and the purpose of this article was to review the current evidence in the field. Multiple micronutrient (MMN) supplements during pregnancy reduce the incidence of maternal anemia and small for gestational-age babies. Recent evidence suggest that combined supplementation of MMNs with protein energy supplement is more effective than MMN supplementation alone. It is now recommended that HIV-infected mothers can exclusively breast-feed their infants for 6 months when the mother or infant is on effective antiretroviral therapy. Home fortification of complementary foods reduces the prevalence of anemia in infancy and combined supplementation of MMNs with lipid-based supplements improves growth in young children. Ready-to-use therapeutic foods have been successfully used to manage severe acute malnutrition in the community. Zinc supplementation is associated with a reduction in diarrhea and respiratory disease morbidity and improves linear growth. Vitamin A supplementation decreases the incidence of diarrhea and measles. Water supply, sanitation, and hygiene are important for the prevention of malnutrition because of their direct impact on infectious disease. There is clear evidence on the causes and consequences of malnutrition as well as effective interventions to prevent undernutrition. The next step is to implement these packages of interventions at large scale. A global effort is required that should entail unified and compelling advocacy among governments, lead organizations, and institutions.

  8. Evidence-Based Management of Anticoagulant Therapy

    Schulman, Sam; Witt, Daniel M.; Vandvik, Per Olav; Fish, Jason; Kovacs, Michael J.; Svensson, Peter J.; Veenstra, David L.; Crowther, Mark; Guyatt, Gordon H.

    2012-01-01

    Background: High-quality anticoagulation management is required to keep these narrow therapeutic index medications as effective and safe as possible. This article focuses on the common important management questions for which, at a minimum, low-quality published evidence is available to guide best practices. Methods: The methods of this guideline follow those described in Methodology for the Development of Antithrombotic Therapy and Prevention of Thrombosis Guidelines: Antithrombotic Therapy and Prevention of Thrombosis, 9th ed: American College of Chest Physicians Evidence-Based Clinical Practice Guidelines in this supplement. Results: Most practical clinical questions regarding the management of anticoagulation, both oral and parenteral, have not been adequately addressed by randomized trials. We found sufficient evidence for summaries of recommendations for 23 questions, of which only two are strong rather than weak recommendations. Strong recommendations include targeting an international normalized ratio of 2.0 to 3.0 for patients on vitamin K antagonist therapy (Grade 1B) and not routinely using pharmacogenetic testing for guiding doses of vitamin K antagonist (Grade 1B). Weak recommendations deal with such issues as loading doses, initiation overlap, monitoring frequency, vitamin K supplementation, patient self-management, weight and renal function adjustment of doses, dosing decision support, drug interactions to avoid, and prevention and management of bleeding complications. We also address anticoagulation management services and intensive patient education. Conclusions: We offer guidance for many common anticoagulation-related management problems. Most anticoagulation management questions have not been adequately studied. PMID:22315259

  9. Practice management: observations, issues, and empirical evidence.

    Wong, H M; Braithwaite, J

    2001-02-01

    The primary objective of this study is to provide objective, empirical, evidence-based practice management information. This is a hitherto under-researched area of considerable interest for both the practitioner and educator. A questionnaire eliciting a mix of structured and free text responses was administered to a random sample of 480 practitioners who are members of the American Academy of Periodontology. Potential respondents not in private practice were excluded and the next listed person substituted. The results provide demographic and descriptive information about some of the main issues and problems facing practice managers, central to which are information technology (IT), financial, people management, and marketing. Human resource and marketing management appear to represent the biggest challenges. Periodontists running practices would prefer more information, development, and support in dealing with IT, finance, marketing, and people management. The empirical evidence reported here suggests that although tailored educational programs on key management issues at both undergraduate and postgraduate levels have become ubiquitous, nevertheless some respondents seek further training opportunities. Evidence-based practice management information will be invaluable to the clinician considering strategic and marketing planning, and also for those responsible for the design and conduct of predoctoral and postdoctoral programs.

  10. Evidence-based pathology: umbilical cord coiling.

    Khong, T Y

    2010-12-01

    The generation of a pathology test result must be based on criteria that are proven to be acceptably reproducible and clinically relevant to be evidence-based. This review de-constructs the umbilical cord coiling index to illustrate how it can stray from being evidence-based. Publications related to umbilical cord coiling were retrieved and analysed with regard to how the umbilical coiling index was calculated, abnormal coiling was defined and reference ranges were constructed. Errors and other influences that can occur with the measurement of the length of the umbilical cord or of the number of coils can compromise the generation of the coiling index. Definitions of abnormal coiling are not consistent in the literature. Reference ranges defining hypocoiling or hypercoiling have not taken those potential errors or the possible effect of gestational age into account. Even the way numerical test results in anatomical pathology are generated, as illustrated by the umbilical coiling index, warrants a critical analysis into its evidence base to ensure that they are reproducible or free from errors.

  11. 2013 Nutrition Risk Evidence Review Panel. Evidence Review for: The Risk Factor of Inadequate Nutrition

    2014-01-01

    The 2013 Nutrition Risk Standing Review Panel (from here on referred to as the SRP) met for a site visit in Houston, TX on November 20 - 21, 2013. The SRP reviewed the new Evidence Report for the Risk Factor of Inadequate Nutrition (from here on referred to as the 2013 Nutrition Evidence Report), as well as the Research Plan for this Risk. Overall, the SRP thinks the well-qualified research team has compiled an excellent summary of background information in the 2013 Nutrition Evidence Report. The SRP would like to commend the authors in general and particularly note that while the 2013 Nutrition Evidence Report has been written using a single nutrient approach, the research plan takes a much more integrated and physiologically based approach.

  12. An Evidence-Based Framework for Evidence-Based Management in ...

    2018-05-01

    May 1, 2018 ... BACKGROUND: Evidence-based management (EBMgt) is a growing literature ... organization and management, especially in the last decade (1-6). One of these models is ..... Organizational Behavior. 2017;4(1):235-61.

  13. An Evidence-Based Framework for Evidence-Based Management in ...

    2018-05-01

    May 1, 2018 ... BACKGROUND: Evidence-based management (EBMgt) is a growing literature concept in ... principles are developing across disciplines such as education, criminology ..... Australian Health Review. 2012;36(3):284-90. 17.

  14. Empirical methods for systematic reviews and evidence-based medicine

    van Enst, W.A.

    2014-01-01

    Evidence-Based Medicine is the integration of best research evidence with clinical expertise and patient values. Systematic reviews have become the cornerstone of evidence-based medicine, which is reflected in the position systematic reviews have in the pyramid of evidence-based medicine. Systematic

  15. Information provision in medical libraries: An evidence based ...

    The paper examined information provision in special libraries such as medical libraries. It provides an overview of evidence based practice as a concept for information provision by librarians. It specifically proffers meaning to the term evidence as used in evidence based practice and to evidence based medicine from where ...

  16. 20 CFR 219.43 - Evidence of child's dependency.

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Evidence of child's dependency. 219.43... EVIDENCE REQUIRED FOR PAYMENT Evidence of Relationship § 219.43 Evidence of child's dependency. (a) When the dependency requirement must be met. Usually the dependency requirement must be met at one of the...

  17. When Evidence Doesn’t Work (Editorial

    Lindsay Glynn

    2007-12-01

    Full Text Available I was listening intently to a discussion on the radio recently between Newfoundland and Labrador’s Minister of Education and aprofessor from Memorial University’s Math Department. They were debating the efficacy of the math curriculum in the province’s school system. As a parent of a grade 3 student, I have my own thoughts on how the curriculum is affecting kids’ math skills (and their anxiety levels, but let’s not go there. The professor echoed the concern that parents, teachers and students have been expressing: quite simply, it’s not working. Far too many children are failing math and are struggling with the both the content and pace of the required modules. Why am I telling you this? One particular comment made by the Minister of Education struck me. She said that there was evidence to suggest that this curriculum should work. While I’m always delighted to see the evidence based practice model being used, particularly for the betterment of my kids’education, it is dismaying to see that it is not always applied well. In this particular case, evidence was collected from somewhere and a decision was made to implement a new math curriculum based on the gathered evidence. Assuming that this truly was good evidence upon which to base such a decision, then I would have to concede that the appropriate steps were taken up until that point. Unfortunately, it appears that the entire process stopped there. As we know, one of the most important components of a thorough ebp‐based implementation is an internal evaluation. What might work somewhere else is not guaranteed to work in another environment, and it is essential to determine why an implementation or intervention worked or didn’t work. It would seem, in this case, that formal evaluations of the effectiveness of the new math curriculum have not been performed and therefore, the powers that be rely solely on the fact that it worked somewhere else. This is not evidence based

  18. Common pitfalls in statistical analysis: "No evidence of effect" versus "evidence of no effect"

    Priya Ranganathan

    2015-01-01

    Full Text Available This article is the first in a series exploring common pitfalls in statistical analysis in biomedical research. The power of a clinical trial is the ability to find a difference between treatments, where such a difference exists. At the end of the study, the lack of difference between treatments does not mean that the treatments can be considered equivalent. The distinction between "no evidence of effect" and "evidence of no effect" needs to be understood.

  19. Primary expatiation on micro material evidence and authentication

    Yang Mingtai; Wang Wen; Wu Lunqiang; Dai Changsong

    2012-01-01

    The micro material evidence is the impersonal and concrete material evidences, and the quantity and volume is small, but it plays an important role in judicature litigation. In the paper, the basic character, type and form mechanism of the micro material evidence have been analyzed and discussed, and the gist of the micro material evidence has been summarized. It must play a helpful role in the micro material evidence to correlative workers for cognizance and application. (authors)

  20. Judges Awareness, Understanding, and Application of Digital Evidence

    Gary C Kessler

    2011-01-01

    As digital evidence grows in both volume and importance in criminal and civil courts, judges need to fairly and justly evaluate the merits of the offered evidence. To do so, judges need a general understanding of the underlying technologies and applications from which digital evidence is derived. Due to the relative newness of the computer forensics field, there have been few studies on the use of digital forensic evidence and none about judges’ relationship with digital evidence.This paper d...