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Sample records for early transmitted clade

  1. Comparing the Effects of Symbiotic Algae (Symbiodinium) Clades C1 and D on Early Growth Stages of Acropora tenuis

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    Yuyama, Ikuko; Higuchi, Tomihiko

    2014-01-01

    Reef-building corals switch endosymbiotic algae of the genus Symbiodinium during their early growth stages and during bleaching events. Clade C Symbiodinium algae are dominant in corals, although other clades — including A and D — have also been commonly detected in juvenile Acroporid corals. Previous studies have been reported that only molecular data of Symbiodinium clade were identified within field corals. In this study, we inoculated aposymbiotic juvenile polyps with cultures of clades C1 and D Symbiodinium algae, and investigated the different effect of these two clades of Symbiodinium on juvenile polyps. Our results showed that clade C1 algae did not grow, while clade D algae grew rapidly during the first 2 months after inoculation. Polyps associated with clade C1 algae exhibited bright green fluorescence across the body and tentacles after inoculation. The growth rate of polyp skeletons was lower in polyps associated with clade C1 algae than those associated with clade D algae. On the other hand, antioxidant activity (catalase) of corals was not significantly different between corals with clade C1 and clade D algae. Our results suggested that clade D Symbiodinium algae easily form symbiotic relationships with corals and that these algae could contribute to coral growth in early symbiosis stages. PMID:24914677

  2. New clade of enigmatic early archosaurs yields insights into early pseudosuchian phylogeny and the biogeography of the archosaur radiation.

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    Butler, Richard J; Sullivan, Corwin; Ezcurra, Martín D; Liu, Jun; Lecuona, Agustina; Sookias, Roland B

    2014-06-10

    The origin and early radiation of archosaurs and closely related taxa (Archosauriformes) during the Triassic was a critical event in the evolutionary history of tetrapods. This radiation led to the dinosaur-dominated ecosystems of the Jurassic and Cretaceous, and the high present-day archosaur diversity that includes around 10,000 bird and crocodylian species. The timing and dynamics of this evolutionary radiation are currently obscured by the poorly constrained phylogenetic positions of several key early archosauriform taxa, including several species from the Middle Triassic of Argentina (Gracilisuchus stipanicicorum) and China (Turfanosuchus dabanensis, Yonghesuchus sangbiensis). These species act as unstable 'wildcards' in morphological phylogenetic analyses, reducing phylogenetic resolution. We present new anatomical data for the type specimens of G. stipanicicorum, T. dabanensis, and Y. sangbiensis, and carry out a new morphological phylogenetic analysis of early archosaur relationships. Our results indicate that these three previously enigmatic taxa form a well-supported clade of Middle Triassic archosaurs that we refer to as Gracilisuchidae. Gracilisuchidae is placed basally within Suchia, among the pseudosuchian (crocodile-line) archosaurs. The approximately contemporaneous and morphologically similar G. stipanicicorum and Y. sangbiensis may be sister taxa within Gracilisuchidae. Our results provide increased resolution of the previously poorly constrained relationships of early archosaurs, with increased levels of phylogenetic support for several key early pseudosuchian clades. Moreover, they falsify previous hypotheses suggesting that T. dabanensis and Y. sangbiensis are not members of the archosaur crown group. The recognition of Gracilisuchidae provides further support for a rapid phylogenetic diversification of crown archosaurs by the Middle Triassic. The disjunct distribution of the gracilisuchid clade in China and Argentina demonstrates that early

  3. Transmissibility of the monkeypox virus clades via respiratory transmission: investigation using the prairie dog-monkeypox virus challenge system.

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    Christina L Hutson

    Full Text Available Monkeypox virus (MPXV is endemic within Africa where it sporadically is reported to cause outbreaks of human disease. In 2003, an outbreak of human MPXV occurred in the US after the importation of infected African rodents. Since the eradication of smallpox (caused by an orthopoxvirus (OPXV related to MPXV and cessation of routine smallpox vaccination (with the live OPXV vaccinia, there is an increasing population of people susceptible to OPXV diseases. Previous studies have shown that the prairie dog MPXV model is a functional animal model for the study of systemic human OPXV illness. Studies with this model have demonstrated that infected animals are able to transmit the virus to naive animals through multiple routes of exposure causing subsequent infection, but were not able to prove that infected animals could transmit the virus exclusively via the respiratory route. Herein we used the model system to evaluate the hypothesis that the Congo Basin clade of MPXV is more easily transmitted, via respiratory route, than the West African clade. Using a small number of test animals, we show that transmission of viruses from each of the MPXV clade was minimal via respiratory transmission. However, transmissibility of the Congo Basin clade was slightly greater than West African MXPV clade (16.7% and 0% respectively. Based on these findings, respiratory transmission appears to be less efficient than those of previous studies assessing contact as a mechanism of transmission within the prairie dog MPXV animal model.

  4. Identification of full-length transmitted/founder viruses and their progeny in primary HIV-1 infection

    Energy Technology Data Exchange (ETDEWEB)

    Korber, Bette [Los Alamos National Laboratory; Hraber, Peter [Los Alamos National Laboratory; Giorgi, Elena [Los Alamos National Laboratory; Bhattacharya, T [Los Alamos National Laboratory

    2009-01-01

    Identification of transmitted/founder virus genomes and their progeny by is a novel strategy for probing the molecular basis of HIV-1 transmission and for evaluating the genetic imprint of viral and host factors that act to constrain or facilitate virus replication. Here, we show in a cohort of twelve acutely infected subjects (9 clade B; 3 clade C), that complete genomic sequences of transmitted/founder viruses could be inferred using single genome amplification of plasma viral RNA, direct amplicon sequencing, and a model of random virus evolution. This allowed for the precise identification, chemical synthesis, molecular cloning, and biological analysis of those viruses actually responsible for productive clinical infection and for a comprehensive mapping of sequential viral genomes and proteomes for mutations that are necessary or incidental to the establishment of HIV-1 persistence. Transmitted/founder viruses were CD4 and CCR5 tropic, replicated preferentially in activated primary T-Iymphocytes but not monocyte-derived macrophages, and were effectively shielded from most heterologous or broadly neutralizing antibodies. By 3 months of infection, the evolving viral quasispecies in three subjects showed mutational fixation at only 2-5 discreet genomic loci. By 6-12 months, mutational fixation was evident at 18-27 genomic loci. Some, but not all, of these mutations were attributable to virus escape from cytotoxic Tlymphocytes or neutralizing antibodies, suggesting that other viral or host factors may influence early HIV -1 fitness.

  5. Early evolution of the angiosperm clade Asteraceae in the Cretaceous of Antarctica.

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    Barreda, Viviana D; Palazzesi, Luis; Tellería, Maria C; Olivero, Eduardo B; Raine, J Ian; Forest, Félix

    2015-09-01

    The Asteraceae (sunflowers and daisies) are the most diverse family of flowering plants. Despite their prominent role in extant terrestrial ecosystems, the early evolutionary history of this family remains poorly understood. Here we report the discovery of a number of fossil pollen grains preserved in dinosaur-bearing deposits from the Late Cretaceous of Antarctica that drastically pushes back the timing of assumed origin of the family. Reliably dated to ∼76-66 Mya, these specimens are about 20 million years older than previously known records for the Asteraceae. Using a phylogenetic approach, we interpreted these fossil specimens as members of an extinct early diverging clade of the family, associated with subfamily Barnadesioideae. Based on a molecular phylogenetic tree calibrated using fossils, including the ones reported here, we estimated that the most recent common ancestor of the family lived at least 80 Mya in Gondwana, well before the thermal and biogeographical isolation of Antarctica. Most of the early diverging lineages of the family originated in a narrow time interval after the K/P boundary, 60-50 Mya, coinciding with a pronounced climatic warming during the Late Paleocene and Early Eocene, and the scene of a dramatic rise in flowering plant diversity. Our age estimates reduce earlier discrepancies between the age of the fossil record and previous molecular estimates for the origin of the family, bearing important implications in the evolution of flowering plants in general.

  6. Genetic recombination events between sympatric Clade A and Clade C lice in Africa.

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    Veracx, Aurélie; Boutellis, Amina; Raoult, Didier

    2013-09-01

    Human head and body lice have been classified into three phylogenetic clades (Clades A, B, and C) based on mitochondrial DNA. Based on nuclear markers (the 18S rRNA gene and the PM2 spacer), two genotypes of Clade A head and body lice, including one that is specifically African (Clade A2), have been described. In this study, we sequenced the PM2 spacer of Clade C head lice from Ethiopia and compared these sequences with sequences from previous works. Trees were drawn, and an analysis of genetic diversity based on the cytochrome b gene and the PM2 spacer was performed for African and non-African lice. In the tree drawn based on the PM2 spacer, the African and non-African lice formed separate clusters. However, Clade C lice from Ethiopia were placed within the African Clade A subcluster (Clade A2). This result suggests that recombination events have occurred between Clade A2 lice and Clade C lice, reflecting the sympatric nature of African lice. Finally, the PM2 spacer and cytochrome b gene sequences of human lice revealed a higher level of genetic diversity in Africa than in other regions.

  7. Transmission of a heterologous clade C Symbiodinium in a model anemone infection system via asexual reproduction

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    Wan-Nan U. Chen

    2016-08-01

    Full Text Available Anemones of genus Exaiptasia are used as model organisms for the study of cnidarian-dinoflagellate (genus Symbiodinium endosymbiosis. However, while most reef-building corals harbor Symbiodinium of clade C, Exaiptasia spp. anemones mainly harbor clade B Symbiodinium (ITS2 type B1 populations. In this study, we reveal for the first time that bleached Exaiptasia pallida anemones can establish a symbiotic relationship with a clade C Symbiodinium (ITS2 type C1. We further found that anemones can transmit the exogenously supplied clade C Symbiodinium cells to their offspring by asexual reproduction (pedal laceration. In order to corroborate the establishment of stable symbiosis, we used microscopic techniques and genetic analyses to examine several generations of anemones, and the results of these endeavors confirmed the sustainability of the system. These findings provide a framework for understanding the differences in infection dynamics between homologous and heterologous dinoflagellate types using a model anemone infection system.

  8. Why should we investigate the morphological disparity of plant clades?

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    Oyston, Jack W; Hughes, Martin; Gerber, Sylvain; Wills, Matthew A

    2016-04-01

    Disparity refers to the morphological variation in a sample of taxa, and is distinct from diversity or taxonomic richness. Diversity and disparity are fundamentally decoupled; many groups attain high levels of disparity early in their evolution, while diversity is still comparatively low. Diversity may subsequently increase even in the face of static or declining disparity by increasingly fine sub-division of morphological 'design' space (morphospace). Many animal clades reached high levels of disparity early in their evolution, but there have been few comparable studies of plant clades, despite their profound ecological and evolutionary importance. This study offers a prospective and some preliminary macroevolutionary analyses. Classical morphometric methods are most suitable when there is reasonable conservation of form, but lose traction where morphological differences become greater (e.g. in comparisons across higher taxa). Discrete character matrices offer one means to compare a greater diversity of forms. This study explores morphospaces derived from eight discrete data sets for major plant clades, and discusses their macroevolutionary implications. Most of the plant clades in this study show initial, high levels of disparity that approach or attain the maximum levels reached subsequently. These plant clades are characterized by an initial phase of evolution during which most regions of their empirical morphospaces are colonized. Angiosperms, palms, pines and ferns show remarkably little variation in disparity through time. Conifers furnish the most marked exception, appearing at relatively low disparity in the latest Carboniferous, before expanding incrementally with the radiation of successive, tightly clustered constituent sub-clades. Many cladistic data sets can be repurposed for investigating the morphological disparity of plant clades through time, and offer insights that are complementary to more focused morphometric studies. The unique structural and

  9. Anuran trypanosomes: phylogenetic evidence for new clades in Brazil.

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    da S Ferreira, Juliana I G; da Costa, Andrea P; Ramirez, Diego; Roldan, Jairo A M; Saraiva, Danilo; da S Founier, Gislene F R; Sue, Ana; Zambelli, Erick R; Minervino, Antonio H H; Verdade, Vanessa K; Gennari, Solange M; Marcili, Arlei

    2015-05-01

    Trypanosomes of anurans and fish are grouped into the Aquatic Clade which includes species isolated from fish, amphibians, turtles and platypus, usually transmitted by leeches and phlebotomine sand flies. Trypanosomes from Brazilian frogs are grouped within the Aquatic Clade with other anuran trypanosome species, where there seems to be coevolutionary patterns with vertebrate hosts and association to Brazilian biomes (Atlantic Forest, Pantanal and Amazonia Rainforest). We characterised the anuran trypanosomes from two different areas of the Cerrado biome and examined their phylogenetic relationships based on the SSU rRNA gene. A total of 112 anurans of six species was analysed and trypanosome prevalence evaluated through haemoculture was found to be 7% (8 positive frogs). However, only three isolates (2.7%) from two anuran species were recovered and cryopreserved. Analysis including SSU rDNA sequences from previous studies segregated the anuran trypanosomes into six groups, the previously reported An01 to An04, and An05 and An06 reported herein. Clade An05 comprises the isolates from Leptodactylus latrans (Steffen) and Pristimantis sp. captured in the Cerrado biome and Trypanosoma chattoni Mathis & Leger, 1911. The inclusion of new isolates in the phylogenetic analyses provided evidence for a new group (An06) of parasites from phlebotomine hosts. Our results indicate that the diversity of trypanosome species is underestimated since studies conducted in Brazil and other regions of the world are still few.

  10. A revision of the Solanum elaeagnifolium clade (Elaeagnifolium clade; subgenus Leptostemonum, Solanaceae

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    Sandra Knapp

    2017-08-01

    Full Text Available The Solanum elaeagnifolium clade (Elaeagnifolium clade contains five species of small, often rhizomatous, shrubs from deserts and dry forests in North and South America. Members of the clade were previously classified in sections Leprophora, Nycterium and Lathyrocarpum, and were not thought to be closely related. The group is sister to the species-rich monophyletic Old World clade of spiny solanums. The species of the group have an amphitropical distribution, with three species in Mexico and the southwestern United States and three species in Argentina. Solanum elaeagnifolium occurs in both North and South America, and is a noxious invasive weed in dry areas worldwide. Members of the group are highly variable morphologically, and this variability has led to much synonymy, particularly in the widespread S. elaeagnifolium. We here review the taxonomic history, morphology, relationships and ecology of these species and provide keys for their identification, descriptions, full synonymy (including designations of lectotypes and nomenclatural notes. Illustrations, distribution maps and preliminary conservation assessments are provided for all species.

  11. Overexpressed Proteins in Hypervirulent Clade 8 and Clade 6 Strains of Escherichia coli O157:H7 Compared to E. coli O157:H7 EDL933 Clade 3 Strain.

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    Natalia Amigo

    Full Text Available Escherichia coli O157:H7 is responsible for severe diarrhea and hemolytic uremic syndrome (HUS, and predominantly affects children under 5 years. The major virulence traits are Shiga toxins, necessary to develop HUS and the Type III Secretion System (T3SS through which bacteria translocate effector proteins directly into the host cell. By SNPs typing, E. coli O157:H7 was separated into nine different clades. Clade 8 and clade 6 strains were more frequently associated with severe disease and HUS. In this study, we aimed to identify differentially expressed proteins in two strains of E. coli O157:H7 (clade 8 and clade 6, obtained from cattle and compared them with the well characterized reference EDL933 strain (clade 3. Clade 8 and clade 6 strains show enhanced pathogenicity in a mouse model and virulence-related properties. Proteins were extracted and analyzed using the TMT-6plex labeling strategy associated with two dimensional liquid chromatography and mass spectrometry in tandem. We detected 2241 proteins in the cell extract and 1787 proteins in the culture supernatants. Attention was focused on the proteins related to virulence, overexpressed in clade 6 and 8 strains compared to EDL933 strain. The proteins relevant overexpressed in clade 8 strain were the curli protein CsgC, a transcriptional activator (PchE, phage proteins, Stx2, FlgM and FlgD, a dienelactone hydrolase, CheW and CheY, and the SPATE protease EspP. For clade 6 strain, a high overexpression of phage proteins was detected, mostly from Stx2 encoding phage, including Stx2, flagellin and the protease TagA, EDL933_p0016, dienelactone hydrolase, and Haemolysin A, amongst others with unknown function. Some of these proteins were analyzed by RT-qPCR to corroborate the proteomic data. Clade 6 and clade 8 strains showed enhanced transcription of 10 out of 12 genes compared to EDL933. These results may provide new insights in E. coli O157:H7 mechanisms of pathogenesis.

  12. Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections.

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    S Gnanakaran

    2011-09-01

    Full Text Available Here we have identified HIV-1 B clade Envelope (Env amino acid signatures from early in infection that may be favored at transmission, as well as patterns of recurrent mutation in chronic infection that may reflect common pathways of immune evasion. To accomplish this, we compared thousands of sequences derived by single genome amplification from several hundred individuals that were sampled either early in infection or were chronically infected. Samples were divided at the outset into hypothesis-forming and validation sets, and we used phylogenetically corrected statistical strategies to identify signatures, systematically scanning all of Env. Signatures included single amino acids, glycosylation motifs, and multi-site patterns based on functional or structural groupings of amino acids. We identified signatures near the CCR5 co-receptor-binding region, near the CD4 binding site, and in the signal peptide and cytoplasmic domain, which may influence Env expression and processing. Two signatures patterns associated with transmission were particularly interesting. The first was the most statistically robust signature, located in position 12 in the signal peptide. The second was the loss of an N-linked glycosylation site at positions 413-415; the presence of this site has been recently found to be associated with escape from potent and broad neutralizing antibodies, consistent with enabling a common pathway for immune escape during chronic infection. Its recurrent loss in early infection suggests it may impact fitness at the time of transmission or during early viral expansion. The signature patterns we identified implicate Env expression levels in selection at viral transmission or in early expansion, and suggest that immune evasion patterns that recur in many individuals during chronic infection when antibodies are present can be selected against when the infection is being established prior to the adaptive immune response.

  13. Signature proteins for the major clades of Cyanobacteria

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    Mathews Divya W

    2010-01-01

    Full Text Available Abstract Background The phylogeny and taxonomy of cyanobacteria is currently poorly understood due to paucity of reliable markers for identification and circumscription of its major clades. Results A combination of phylogenomic and protein signature based approaches was used to characterize the major clades of cyanobacteria. Phylogenetic trees were constructed for 44 cyanobacteria based on 44 conserved proteins. In parallel, Blastp searches were carried out on each ORF in the genomes of Synechococcus WH8102, Synechocystis PCC6803, Nostoc PCC7120, Synechococcus JA-3-3Ab, Prochlorococcus MIT9215 and Prochlor. marinus subsp. marinus CCMP1375 to identify proteins that are specific for various main clades of cyanobacteria. These studies have identified 39 proteins that are specific for all (or most cyanobacteria and large numbers of proteins for other cyanobacterial clades. The identified signature proteins include: (i 14 proteins for a deep branching clade (Clade A of Gloebacter violaceus and two diazotrophic Synechococcus strains (JA-3-3Ab and JA2-3-B'a; (ii 5 proteins that are present in all other cyanobacteria except those from Clade A; (iii 60 proteins that are specific for a clade (Clade C consisting of various marine unicellular cyanobacteria (viz. Synechococcus and Prochlorococcus; (iv 14 and 19 signature proteins that are specific for the Clade C Synechococcus and Prochlorococcus strains, respectively; (v 67 proteins that are specific for the Low B/A ecotype Prochlorococcus strains, containing lower ratio of chl b/a2 and adapted to growth at high light intensities; (vi 65 and 8 proteins that are specific for the Nostocales and Chroococcales orders, respectively; and (vii 22 and 9 proteins that are uniquely shared by various Nostocales and Oscillatoriales orders, or by these two orders and the Chroococcales, respectively. We also describe 3 conserved indels in flavoprotein, heme oxygenase and protochlorophyllide oxidoreductase proteins that

  14. Evidence of Sympatry of Clade A and Clade B Head Lice in a Pre-Columbian Chilean Mummy from Camarones

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    Boutellis, Amina; Drali, Rezak; Rivera, Mario A.; Mumcuoglu, Kosta Y.; Raoult, Didier

    2013-01-01

    Three different lineages of head lice are known to parasitize humans. Clade A, which is currently worldwide in distribution, was previously demonstrated to be present in the Americas before the time of Columbus. The two other types of head lice are geographically restricted to America and Australia for clade B and to Africa and Asia for clade C. In this study, we tested two operculated nits from a 4,000-year-old Chilean mummy of Camarones for the presence of the partial Cytb mitochondrial gene (270 bp). Our finding shows that clade B head lice were present in America before the arrival of the European colonists. PMID:24204678

  15. Genome-wide comparison of cowpox viruses reveals a new clade related to Variola virus.

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    Piotr Wojtek Dabrowski

    Full Text Available Zoonotic infections caused by several orthopoxviruses (OPV like monkeypox virus or vaccinia virus have a significant impact on human health. In Europe, the number of diagnosed infections with cowpox viruses (CPXV is increasing in animals as well as in humans. CPXV used to be enzootic in cattle; however, such infections were not being diagnosed over the last decades. Instead, individual cases of cowpox are being found in cats or exotic zoo animals that transmit the infection to humans. Both animals and humans reveal local exanthema on arms and legs or on the face. Although cowpox is generally regarded as a self-limiting disease, immunosuppressed patients can develop a lethal systemic disease resembling smallpox. To date, only limited information on the complex and, compared to other OPV, sparsely conserved CPXV genomes is available. Since CPXV displays the widest host range of all OPV known, it seems important to comprehend the genetic repertoire of CPXV which in turn may help elucidate specific mechanisms of CPXV pathogenesis and origin. Therefore, 22 genomes of independent CPXV strains from clinical cases, involving ten humans, four rats, two cats, two jaguarundis, one beaver, one elephant, one marah and one mongoose, were sequenced by using massive parallel pyrosequencing. The extensive phylogenetic analysis showed that the CPXV strains sequenced clearly cluster into several distinct clades, some of which are closely related to Vaccinia viruses while others represent different clades in a CPXV cluster. Particularly one CPXV clade is more closely related to Camelpox virus, Taterapox virus and Variola virus than to any other known OPV. These results support and extend recent data from other groups who postulate that CPXV does not form a monophyletic clade and should be divided into multiple lineages.

  16. Plastome phylogeny and early diversification of Brassicaceae.

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    Guo, Xinyi; Liu, Jianquan; Hao, Guoqian; Zhang, Lei; Mao, Kangshan; Wang, Xiaojuan; Zhang, Dan; Ma, Tao; Hu, Quanjun; Al-Shehbaz, Ihsan A; Koch, Marcus A

    2017-02-16

    The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family. Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.

  17. Evaluation of a fast single-photon avalanche photodiode for measurement of early transmitted photons through diffusive media.

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    Mu, Ying; Valim, Niksa; Niedre, Mark

    2013-06-15

    We tested the performance of a fast single-photon avalanche photodiode (SPAD) in measurement of early transmitted photons through diffusive media. In combination with a femtosecond titanium:sapphire laser, the overall instrument temporal response time was 59 ps. Using two experimental models, we showed that the SPAD allowed measurement of photon-density sensitivity functions that were approximately 65% narrower than the ungated continuous wave case at very early times. This exceeds the performance that we have previously achieved with photomultiplier-tube-based systems and approaches the theoretical maximum predicted by time-resolved Monte Carlo simulations.

  18. Identifikasi Secara Serologi Galur Virus Flu Burung Subtipe H5N1 Clade 2.1.3 dan Clade 2.3.2 pada Ayam Petelur (SEROLOGICAL IDENTIFICATION OF AVIAN INFLUENZA STRAIN VIRUS SUBTYPE H5N1 CLADE 2.1.3 AND CLADE 2.3.2 FROM LAYER

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    Aprilia Kusumastuti

    2015-10-01

    Full Text Available The aim of the study was to know avian influenza (AI infection in field by using serology test in threemarketing area of AI vaccines. Haemagglutination inhibition methode was used in this test. There werefour antigen strains of AI subtype H5N1 clade 2.1.3 (AIstrainA/Chicken/West Java/PWT-WIJ/2006, AIstrain A/Chicken/Garut/BBVW-223/2007, AI strain A/Chicken/West Java-Nagrak/30/2007, and AI strainA/Chicken/Pekalongan/BBVW-208/2007 and 2 antigen strains of AI subtype H5N1 clade 2.3.2 (AI strainA/duck/Sukoharjo/BBVW-1428-9/2012 and AI strain A/duck/Sleman/BBVW-1463-10/2012 was used inthis study for HI test. The result presents that 93,33% chicken farms in three marketing area of PT. SanbioLaboratories have positive antibody titre to AI subtype H5N1 clade 2.1.3. This titre may be obtained fromAI clade 2.1.3 vaccination. From 15 samples, 92,86% are positive to AI subtype H5N1 clade 2.3.2A/duck/Sukoharjo/BBVW-1428-9/2012 and 92,31% are positive to A/duck/Sleman/BBVW-1463-10/2012 evenwithout AI clade 2.3.2 vaccination. This antibody titre may be obtained from AI clade 2.1.3 vaccine crossprotection or field infection.

  19. Expansion of a urethritis-associated Neisseria meningitidis clade in the United States with concurrent acquisition of N. gonorrhoeae alleles.

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    Retchless, Adam C; Kretz, Cécilia B; Chang, How-Yi; Bazan, Jose A; Abrams, A Jeanine; Norris Turner, Abigail; Jenkins, Laurel T; Trees, David L; Tzeng, Yih-Ling; Stephens, David S; MacNeil, Jessica R; Wang, Xin

    2018-03-02

    Increased reports of Neisseria meningitidis urethritis in multiple U.S. cities during 2015 have been attributed to the emergence of a novel clade of nongroupable N. meningitidis within the ST-11 clonal complex, the "U.S. NmNG urethritis clade". Genetic recombination with N. gonorrhoeae has been proposed to enable efficient sexual transmission by this clade. To understand the evolutionary origin and diversification of the U.S. NmNG urethritis clade, whole-genome phylogenetic analysis was performed to identify its members among the N. meningitidis strain collection from the Centers for Disease Control and Prevention, including 209 urogenital and rectal N. meningitidis isolates submitted by U.S. public health departments in eleven states starting in 2015. The earliest representatives of the U.S. NmNG urethritis clade were identified from cases of invasive disease that occurred in 2013. Among 209 urogenital and rectal isolates submitted from January 2015 to September 2016, the clade accounted for 189/198 male urogenital isolates, 3/4 female urogenital isolates, and 1/7 rectal isolates. In total, members of the clade were isolated in thirteen states between 2013 and 2016, which evolved from a common ancestor that likely existed during 2011. The ancestor contained N. gonorrhoeae-like alleles in three regions of its genome, two of which may facilitate nitrite-dependent anaerobic growth during colonization of urogenital sites. Additional gonococcal-like alleles were acquired as the clade diversified. Notably, one isolate contained a sequence associated with azithromycin resistance in N. gonorrhoeae, but no other gonococcal antimicrobial resistance determinants were detected. Interspecies genetic recombination contributed to the early evolution and subsequent diversification of the U.S. NmNG urethritis clade. Ongoing acquisition of N. gonorrhoeae alleles by the U.S. NmNG urethritis clade may facilitate the expansion of its ecological niche while also increasing the

  20. increased specialisation causes the demise of animal clades

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    Raia, P.; Carotenuto, F.; Mondanaro, A.; Castiglione, S.; Passaro, F.; Saggese, F.; Melchionna, M.; Serio, C.; Alessio, L.; Silvestro, D.; Fortelius, M.

    2016-01-01

    Animal clades tend to follow a predictable path of waxing and waning during their existence, regardless of their total species richness or geographic coverage. Clades begin small and undifferentiated, then expand to a peak in diversity and range, only to shift into a rarely broken decline towards extinction. While this trajectory is now well documented and broadly recognised, the reasons underlying it remain obscure. In particular, it is unknown why clade extinction is universal and occurs wi...

  1. Evolution of the intercontinental disjunctions in six continents in the Ampelopsis clade of the grape family (Vitaceae)

    Science.gov (United States)

    2012-01-01

    Background The Ampelopsis clade (Ampelopsis and its close allies) of the grape family Vitaceae contains ca. 43 species disjunctly distributed in Asia, Europe, North America, South America, Africa, and Australia, and is a rare example to study both the Northern and the Southern Hemisphere intercontinental disjunctions. We reconstruct the temporal and spatial diversification of the Ampelopsis clade to explore the evolutionary processes that have resulted in their intercontinental disjunctions in six continents. Results The Bayesian molecular clock dating and the likelihood ancestral area analyses suggest that the Ampelopsis clade most likely originated in North America with its crown group dated at 41.2 Ma (95% HPD 23.4 - 61.0 Ma) in the middle Eocene. Two independent Laurasian migrations into Eurasia are inferred to have occurred in the early Miocene via the North Atlantic land bridges. The ancestor of the Southern Hemisphere lineage migrated from North America to South America in the early Oligocene. The Gondwanan-like pattern of intercontinental disjunction is best explained by two long-distance dispersals: once from South America to Africa estimated at 30.5 Ma (95% HPD 16.9 - 45.9 Ma), and the other from South America to Australia dated to 19.2 Ma (95% HPD 6.7 - 22.3 Ma). Conclusions The global disjunctions in the Ampelopsis clade are best explained by a diversification model of North American origin, two Laurasian migrations, one migration into South America, and two post-Gondwanan long-distance dispersals. These findings highlight the importance of both vicariance and long distance dispersal in shaping intercontinental disjunctions of flowering plants. PMID:22316163

  2. Origin and Population Dynamics of a Novel HIV-1 Subtype G Clade Circulating in Cape Verde and Portugal.

    Science.gov (United States)

    de Pina-Araujo, Isabel Inês M; Delatorre, Edson; Guimarães, Monick L; Morgado, Mariza G; Bello, Gonzalo

    2015-01-01

    The human immunodeficiency virus type 1 (HIV-1) subtype G is the most prevalent and second most prevalent HIV-1 clade in Cape Verde and Portugal, respectively; but there is no information about the origin and spatiotemporal dispersal pattern of this HIV-1 clade circulating in those countries. To this end, we used Maximum Likelihood and Bayesian coalescent-based methods to analyze a collection of 578 HIV-1 subtype G pol sequences sampled throughout Portugal, Cape Verde and 11 other countries from West and Central Africa over a period of 22 years (1992 to 2013). Our analyses indicate that most subtype G sequences from Cape Verde (80%) and Portugal (95%) branched together in a distinct monophyletic cluster (here called G(CV-PT)). The G(CV-PT) clade probably emerged after a single migration of the virus out of Central Africa into Cape Verde between the late 1970s and the middle 1980s, followed by a rapid dissemination to Portugal a couple of years later. Reconstruction of the demographic history of the G(CV-PT) clade circulating in Cape Verde and Portugal indicates that this viral clade displayed an initial phase of exponential growth during the 1980s and 1990s, followed by a decline in growth rate since the early 2000s. Our data also indicate that during the exponential growth phase the G(CV-PT) clade recombined with a preexisting subtype B viral strain circulating in Portugal, originating the CRF14_BG clade that was later disseminated to Spain and Cape Verde. Historical and recent human population movements between Angola, Cape Verde and Portugal probably played a key role in the origin and dispersal of the G(CV-PT )and CRF14_BG clades.

  3. Origin and diversification of major clades in parmelioid lichens (Parmeliaceae, Ascomycota during the Paleogene inferred by Bayesian analysis.

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    Guillermo Amo de Paz

    Full Text Available There is a long-standing debate on the extent of vicariance and long-distance dispersal events to explain the current distribution of organisms, especially in those with small diaspores potentially prone to long-distance dispersal. Age estimates of clades play a crucial role in evaluating the impact of these processes. The aim of this study is to understand the evolutionary history of the largest clade of macrolichens, the parmelioid lichens (Parmeliaceae, Lecanoromycetes, Ascomycota by dating the origin of the group and its major lineages. They have a worldwide distribution with centers of distribution in the Neo- and Paleotropics, and semi-arid subtropical regions of the Southern Hemisphere. Phylogenetic analyses were performed using DNA sequences of nuLSU and mtSSU rDNA, and the protein-coding RPB1 gene. The three DNA regions had different evolutionary rates: RPB1 gave a rate two to four times higher than nuLSU and mtSSU. Divergence times of the major clades were estimated with partitioned BEAST analyses allowing different rates for each DNA region and using a relaxed clock model. Three calibrations points were used to date the tree: an inferred age at the stem of Lecanoromycetes, and two dated fossils: Parmelia in the parmelioid group, and Alectoria. Palaeoclimatic conditions and the palaeogeological area cladogram were compared to the dated phylogeny of parmelioid. The parmelioid group diversified around the K/T boundary, and the major clades diverged during the Eocene and Oligocene. The radiation of the genera occurred through globally changing climatic condition of the early Oligocene, Miocene and early Pliocene. The estimated divergence times are consistent with long-distance dispersal events being the major factor to explain the biogeographical distribution patterns of Southern Hemisphere parmelioids, especially for Africa-Australia disjunctions, because the sequential break-up of Gondwana started much earlier than the origin of these

  4. Kretzoiarctos gen. nov., the oldest member of the giant panda clade.

    Science.gov (United States)

    Abella, Juan; Alba, David M; Robles, Josep M; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Raül; Montoya, Plinio; Morales, Jorge

    2012-01-01

    The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8-7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12-11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint.

  5. Kretzoiarctos gen. nov., the oldest member of the giant panda clade.

    Directory of Open Access Journals (Sweden)

    Juan Abella

    Full Text Available The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae, has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8-7 mya was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12-11 Ma Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos. The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint.

  6. Characterization of Prochlorococcus clades from iron-depleted oceanic regions.

    Science.gov (United States)

    Rusch, Douglas B; Martiny, Adam C; Dupont, Christopher L; Halpern, Aaron L; Venter, J Craig

    2010-09-14

    Prochlorococcus describes a diverse and abundant genus of marine photosynthetic microbes. It is primarily found in oligotrophic waters across the globe and plays a crucial role in energy and nutrient cycling in the ocean ecosystem. The abundance, global distribution, and availability of isolates make Prochlorococcus a model system for understanding marine microbial diversity and biogeochemical cycling. Analysis of 73 metagenomic samples from the Global Ocean Sampling expedition acquired in the Atlantic, Pacific, and Indian Oceans revealed the presence of two uncharacterized Prochlorococcus clades. A phylogenetic analysis using six different genetic markers places the clades close to known lineages adapted to high-light environments. The two uncharacterized clades consistently cooccur and dominate the surface waters of high-temperature, macronutrient-replete, and low-iron regions of the Eastern Equatorial Pacific upwelling and the tropical Indian Ocean. They are genetically distinct from each other and other high-light Prochlorococcus isolates and likely define a previously unrecognized ecotype. Our detailed genomic analysis indicates that these clades comprise organisms that are adapted to iron-depleted environments by reducing their iron quota through the loss of several iron-containing proteins that likely function as electron sinks in the photosynthetic pathway in other Prochlorococcus clades from high-light environments. The presence and inferred physiology of these clades may explain why Prochlorococcus populations from iron-depleted regions do not respond to iron fertilization experiments and further expand our understanding of how phytoplankton adapt to variations in nutrient availability in the ocean.

  7. Expanding the World of Marine Bacterial and Archaeal Clades

    Science.gov (United States)

    Yilmaz, Pelin; Yarza, Pablo; Rapp, Josephine Z.; Glöckner, Frank O.

    2016-01-01

    Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as

  8. A new hypothesis of dinosaur relationships and early dinosaur evolution.

    Science.gov (United States)

    Baron, Matthew G; Norman, David B; Barrett, Paul M

    2017-03-22

    For 130 years, dinosaurs have been divided into two distinct clades-Ornithischia and Saurischia. Here we present a hypothesis for the phylogenetic relationships of the major dinosaurian groups that challenges the current consensus concerning early dinosaur evolution and highlights problematic aspects of current cladistic definitions. Our study has found a sister-group relationship between Ornithischia and Theropoda (united in the new clade Ornithoscelida), with Sauropodomorpha and Herrerasauridae (as the redefined Saurischia) forming its monophyletic outgroup. This new tree topology requires redefinition and rediagnosis of Dinosauria and the subsidiary dinosaurian clades. In addition, it forces re-evaluations of early dinosaur cladogenesis and character evolution, suggests that hypercarnivory was acquired independently in herrerasaurids and theropods, and offers an explanation for many of the anatomical features previously regarded as notable convergences between theropods and early ornithischians.

  9. Progress to extinction: increased specialisation causes the demise of animal clades.

    Science.gov (United States)

    Raia, P; Carotenuto, F; Mondanaro, A; Castiglione, S; Passaro, F; Saggese, F; Melchionna, M; Serio, C; Alessio, L; Silvestro, D; Fortelius, M

    2016-08-10

    Animal clades tend to follow a predictable path of waxing and waning during their existence, regardless of their total species richness or geographic coverage. Clades begin small and undifferentiated, then expand to a peak in diversity and range, only to shift into a rarely broken decline towards extinction. While this trajectory is now well documented and broadly recognised, the reasons underlying it remain obscure. In particular, it is unknown why clade extinction is universal and occurs with such surprising regularity. Current explanations for paleontological extinctions call on the growing costs of biological interactions, geological accidents, evolutionary traps, and mass extinctions. While these are effective causes of extinction, they mainly apply to species, not clades. Although mass extinctions is the undeniable cause for the demise of a sizeable number of major taxa, we show here that clades escaping them go extinct because of the widespread tendency of evolution to produce increasingly specialised, sympatric, and geographically restricted species over time.

  10. Progress to extinction: increased specialisation causes the demise of animal clades

    Science.gov (United States)

    Raia, P.; Carotenuto, F.; Mondanaro, A.; Castiglione, S.; Passaro, F.; Saggese, F.; Melchionna, M.; Serio, C.; Alessio, L.; Silvestro, D.; Fortelius, M.

    2016-08-01

    Animal clades tend to follow a predictable path of waxing and waning during their existence, regardless of their total species richness or geographic coverage. Clades begin small and undifferentiated, then expand to a peak in diversity and range, only to shift into a rarely broken decline towards extinction. While this trajectory is now well documented and broadly recognised, the reasons underlying it remain obscure. In particular, it is unknown why clade extinction is universal and occurs with such surprising regularity. Current explanations for paleontological extinctions call on the growing costs of biological interactions, geological accidents, evolutionary traps, and mass extinctions. While these are effective causes of extinction, they mainly apply to species, not clades. Although mass extinctions is the undeniable cause for the demise of a sizeable number of major taxa, we show here that clades escaping them go extinct because of the widespread tendency of evolution to produce increasingly specialised, sympatric, and geographically restricted species over time.

  11. Rapid Differentiation between Livestock-Associated and Livestock-Independent Staphylococcus aureus CC398 Clades

    Science.gov (United States)

    Larsen, Jesper; Soldanova, Katerina; Aziz, Maliha; Contente-Cuomo, Tania; Petersen, Andreas; Vandendriessche, Stien; Jiménez, Judy N.; Mammina, Caterina; van Belkum, Alex; Salmenlinna, Saara; Laurent, Frederic; Skov, Robert L.; Larsen, Anders R.; Andersen, Paal S.; Price, Lance B.

    2013-01-01

    Staphylococcus aureus clonal complex 398 (CC398) isolates cluster into two distinct phylogenetic clades based on single-nucleotide polymorphisms (SNPs) revealing a basal human clade and a more derived livestock clade. The scn and tet(M) genes are strongly associated with the human and the livestock clade, respectively, due to loss and acquisition of mobile genetic elements. We present canonical single-nucleotide polymorphism (canSNP) assays that differentiate the two major host-associated S. aureus CC398 clades and a duplex PCR assay for detection of scn and tet(M). The canSNP assays correctly placed 88 S. aureus CC398 isolates from a reference collection into the human and livestock clades and the duplex PCR assay correctly identified scn and tet(M). The assays were successfully applied to a geographically diverse collection of 272 human S. aureus CC398 isolates. The simple assays described here generate signals comparable to a whole-genome phylogeny for major clade assignment and are easily integrated into S. aureus CC398 surveillance programs and epidemiological studies. PMID:24244535

  12. Protection level of AI H5N1 vaccine clade 2.1.3 commercial against AI H5N1 clade 2.3.2 virus from Ducks to SPF chicken in laboratory conditions

    Directory of Open Access Journals (Sweden)

    Indriani R

    2015-03-01

    Full Text Available Highly Pathogenic Avian Influenza (HPAI subtype H5N1 clade 2.3.2 has infected chickens in farms, causing mortality and a decrease in egg production. Vaccination is one of the strategies to control disease of AI subtype H5N1. AI H5N1 clade 2.1.3 vaccine is available commercially. The effectiveness of two vaccines of AI H5N1 clade 2.1.3 (product A and B, and AI H5N1 clade 2.3.2 (Sukoharjo against AI H5N1 clade 2.3.2 (Sukoharjo virus SPF chickens was tested in laboratory. Four groups of SPF chickens were used in this study, there were (1 vaccinated with H5N1 clade 2.1.3 (product A, (2 vaccinated with H5N1 clade 2.1.3 (product B, (3 vaccinated with AI H5N1 clade 2.3.2 and (4 unvaccinated (as a control. Each vaccinated group consisted of 10 chicken except 8 chicken for control group. SPF chicken were vaccinated with 1 dose of vaccine at 3 weeks olds, and then after 3 weeks post vaccination (at 6 weeks olds. All group of chicken were challenged with 106 EID50 per 0.1 ml via intranasal. The results showed, chicken vaccinated with H5N1 clade 2.1.3 product A and B gave 100 and 80% protection respectively, but showed challenged virus shedding, whereas vaccine of H5N1 clade 2.3.2 gave 100% protection from mortality and without virus shedding. Vaccines of AI H5N1 clade 2.1.3 product A was better than vaccine product B, and when chicken vaccinated against H5N1 clade 2.3.2, H5N1 clade 2.3.2 vaccine was the best to be used. In order to protect chicken from AI subtype H5N1 clade 2.1.3 and 2.3.2 in the field, a bivalent vaccine of H5N1 clade 2.1.3 and 2.3.2 subtypes should be developed.

  13. Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity.

    Science.gov (United States)

    Krishnan, Arunkumar; Iyer, Lakshminarayan M; Holland, Stephen J; Boehm, Thomas; Aravind, L

    2018-04-03

    AID/APOBEC deaminases (AADs) convert cytidine to uridine in single-stranded nucleic acids. They are involved in numerous mutagenic processes, including those underpinning vertebrate innate and adaptive immunity. Using a multipronged sequence analysis strategy, we uncover several AADs across metazoa, dictyosteliida, and algae, including multiple previously unreported vertebrate clades, and versions from urochordates, nematodes, echinoderms, arthropods, lophotrochozoans, cnidarians, and porifera. Evolutionary analysis suggests a fundamental division of AADs early in metazoan evolution into secreted deaminases (SNADs) and classical AADs, followed by diversification into several clades driven by rapid-sequence evolution, gene loss, lineage-specific expansions, and lateral transfer to various algae. Most vertebrate AADs, including AID and APOBECs1-3, diversified in the vertebrates, whereas the APOBEC4-like clade has a deeper origin in metazoa. Positional entropy analysis suggests that several AAD clades are diversifying rapidly, especially in the positions predicted to interact with the nucleic acid target motif, and with potential viral inhibitors. Further, several AADs have evolved neomorphic metal-binding inserts, especially within loops predicted to interact with the target nucleic acid. We also observe polymorphisms, driven by alternative splicing, gene loss, and possibly intergenic recombination between paralogs. We propose that biological conflicts of AADs with viruses and genomic retroelements are drivers of rapid AAD evolution, suggesting a widespread presence of mutagenesis-based immune-defense systems. Deaminases like AID represent versions "institutionalized" from the broader array of AADs pitted in such arms races for mutagenesis of self-DNA, and similar recruitment might have independently occurred elsewhere in metazoa. Copyright © 2018 the Author(s). Published by PNAS.

  14. The Longibrachiatum Clade of Trichoderma: a revision with new species

    Science.gov (United States)

    The Longibrachiatum Clade of Trichoderma is revised. Eight new species are described (T. aethiopicum, T. capillare, T. flagellatum, T. gillesii, T. gracile, T. pinnatum, T. saturnisporopsis, T. solani). The twenty-one species known to belong to the Longibrachiatum Clade are included in a synoptic ke...

  15. Rapid Identification of Different Escherichia coli Sequence Type 131 Clades.

    Science.gov (United States)

    Matsumura, Yasufumi; Pitout, Johann D D; Peirano, Gisele; DeVinney, Rebekah; Noguchi, Taro; Yamamoto, Masaki; Gomi, Ryota; Matsuda, Tomonari; Nakano, Satoshi; Nagao, Miki; Tanaka, Michio; Ichiyama, Satoshi

    2017-08-01

    Escherichia coli sequence type 131 (ST131) is a pandemic clonal lineage that is responsible for the global increase in fluoroquinolone resistance and extended-spectrum-β-lactamase (ESBL) producers. The members of ST131 clade C, especially subclades C2 and C1-M27, are associated with ESBLs. We developed a multiplex conventional PCR assay with the ability to detect all ST131 clades (A, B, and C), as well as C subclades (C1-M27, C1-nM27 [C1-non-M27], and C2). To validate the assay, we used 80 ST131 global isolates that had been fully sequenced. We then used the assay to define the prevalence of each clade in two Japanese collections consisting of 460 ESBL-producing E. coli ST131 (2001-12) and 329 E. coli isolates from extraintestinal sites (ExPEC) (2014). The assay correctly identified the different clades in all 80 global isolates: clades A ( n = 12), B ( n = 12), and C, including subclades C1-M27 ( n = 16), C1-nM27 ( n = 20), C2 ( n = 17), and other C ( n = 3). The assay also detected all 565 ST131 isolates in both collections without any false positives. Isolates from clades A ( n = 54), B ( n = 23), and C ( n = 483) corresponded to the O serotypes and the fimH types of O16-H41, O25b-H22, and O25b-H30, respectively. Of the 483 clade C isolates, C1-M27 was the most common subclade (36%), followed by C1-nM27 (32%) and C2 (15%). The C1-M27 subclade with bla CTX-M-27 became especially prominent after 2009. Our novel multiplex PCR assay revealed the predominance of the C1-M27 subclade in recent Japanese ESBL-producing E. coli isolates and is a promising tool for epidemiological studies of ST131. Copyright © 2017 American Society for Microbiology.

  16. Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets.

    Science.gov (United States)

    Herfst, Sander; Mok, Chris K P; van den Brand, Judith M A; van der Vliet, Stefan; Rosu, Miruna E; Spronken, Monique I; Yang, Zifeng; de Meulder, Dennis; Lexmond, Pascal; Bestebroer, Theo M; Peiris, J S Malik; Fouchier, Ron A M; Richard, Mathilde

    2018-01-01

    Since their emergence in 1997, A/H5N1 influenza viruses of the A/goose/Guangdong/1/96 lineage have diversified in multiple genetic and antigenic clades upon continued circulation in poultry in several countries in Eurasia and Africa. Since 2009, reassortant viruses carrying clade 2.3.4.4 hemagglutinin (HA) and internal and neuraminidase (NA) genes of influenza A viruses of different avian origin have been detected, yielding various HA-NA combinations, such as A/H5N1, A/H5N2, A/H5N3, A/H5N5, A/H5N6, and A/H5N8. Previous studies reported on the low pathogenicity and lack of airborne transmission of A/H5N2 and A/H5N8 viruses in the ferret model. However, although A/H5N6 viruses are the only clade 2.3.4.4 viruses that crossed the species barrier and infected humans, the risk they pose for human health remains poorly characterized. Here, the characterization of A/H5N6 A/Guangzhou/39715/2014 virus in vitro and in ferrets is described. This A/H5N6 virus possessed high polymerase activity, mediated by the E627K substitution in the PB2 protein, which corresponds to only one biological trait out of the three that were previously shown to confer airborne transmissibility to A/H5N1 viruses between ferrets. This might explain its lack of airborne transmission between ferrets. After intranasal inoculation, A/H5N6 virus replicated to high titers in the respiratory tracts of ferrets and was excreted for at least 6 days. Moreover, A/H5N6 virus caused severe pneumonia in ferrets upon intratracheal inoculation. Thus, A/H5N6 virus causes a more severe disease in ferrets than previously investigated clade 2.3.4.4 viruses, but our results demonstrate that the risk from airborne spread is currently low. IMPORTANCE Avian influenza A viruses are a threat to human health, as they cross the species barrier and infect humans occasionally, often with severe outcome. The antigenic and genetic diversity of A/H5 viruses from the A/goose/Guangdong/1/96 lineage is increasing, due to continued

  17. The Gondwana Breakup and the History of the Atlantic and Indian Oceans Unveils Two New Clades for Early Neobatrachian Diversification.

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    Annelise Frazão

    Full Text Available The largest anuran diversity belongs to the Neobatrachia, which harbor more than five thousand extant species. Here, we propose a new hypothesis for the historical aspects of the neobatrachian evolution with a formal biogeographical analysis. We selected 12 genes for 144 neobatrachian genera and four archaeobatrachian outgroups and performed a phylogenetic analysis using a maximum likelihood algorithm with the rapid bootstrap test. We also estimated divergence times for major lineages using a relaxed uncorrelated clock method. According to our time scale, the diversification of crown Neobatrachia began around the end of the Early Cretaceous. Our phylogenetic tree suggests that the first split of Neobatrachia is related to the geological events in the Atlantic and Indian Oceans. Hence, we propose names for these clades that indicate this connection, i.e., Atlanticanura and Indianura. The Atlanticanura is composed of three major neobatrachian lineages: Heleophrynidae, Australobatrachia and Nobleobatrachia. On the other hand, the Indianura consists of two major lineages: Sooglossoidea and Ranoides. The biogeographical analysis indicates that many neobatrachian splits occurred as a result of geological events such as the separation between South America and Africa, between India and the Seychelles, and between Australia and South America.

  18. The pathogenecity of H5N1 highly pathogenic Avian Influenza (HPAI virus clade 2.3.2. in Indonesian indigenous chicken by contact tranmission with infected duck

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    R. Damayanti

    2017-05-01

    Full Text Available An experimental transmission study was conducted using nine healthy Indonesian indigenous chickens placed together with two 30 days old ducks which were experimentally infected with H5N1 HPAI clade 2.3.2 virus in the Biosafety Laboratory Level 3 (BSL-3 facilities. The aim of the study was to find out the pathogenicity of H5N1 HPAI virus clade 2.3.2 in Indonesian indigenous chickens. The study showed that within twenty four hours rearing, the chickens were exhibited mild clinical signs and by 48 hours, all of the chickens died, whereas the ducks survived but with severe clinical signs. The H5N1 HPAI virus has been successfully isolated from chickens and ducks swabs, confirming that those animals were infected by the virus. Histologically, the infected chicken encountered with severe inflammation reaction namely non suppuratives encephalitis, tracheitis, myocarditis, interstitial pneumonia, hepatitis, proventriculitis, enteritis, pancreatitis, nephritis and bursitis. Necrotizing spleen and pancreas were also prominent. Viral antigen was detected by immunohistochemistry staining in various affected visceral organs. This suggests that Indonesian indigenous chickens were susceptible to H5N1 HPAI virus clade 2.3.2 and it can be transmitted easily to Indonesian indigenous chickens by contact transmission with infected ducks.

  19. Molecular characteristic and pathogenicity of Indonesian H5N1 clade 2.3.2 viruses

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    Dharmayanti NLPI

    2013-06-01

    Full Text Available The outbreak of disease in late 2012 in Indonesia caused high duck mortality. The agent of the disease was identified as H5N1 clade 2.3.2. The disease caused economic loss to the Indonesian duck farmer. The clade 2.3.2 of H5N1 virus has not previously been identified, so this study was conducted to characterize 4 of H5N1 clade 2.3.2 viruses by DNA sequencing in eight genes segment virus namely HA, NA, NS, M, PB1, PB2, PA and NP. The pathogenicity test of clade 2.3.2 viruses in ducks was compared to clade 2.1.3 viruses which predominat circulating in Indonesia. Results of phylogenetic tree analysis showed that the four of clade 2.3.2 viruses isolated in 2012 was the new introduced virus from abroad. Further analysis showed eight genes were in one group with the clade 2.3.2 viruses, especially those from VietNam and did not belong to Indonesia viruses group. The pathogenicity test in ducks showed that virus H5N1 clade 2.3.2 and clade 2.1.3 have similar clinical symptoms and pathogenicity and cause death in 75% of ducks on days 3-6 after infection.

  20. Influenza A H5N1 clade 2.3.4 virus with a different antiviral susceptibility profile replaced clade 1 virus in humans in northern Vietnam.

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    Mai T Q Le

    2008-10-01

    Full Text Available Prior to 2007, highly pathogenic avian influenza (HPAI H5N1 viruses isolated from poultry and humans in Vietnam were consistently reported to be clade 1 viruses, susceptible to oseltamivir but resistant to amantadine. Here we describe the re-emergence of human HPAI H5N1 virus infections in Vietnam in 2007 and the characteristics of the isolated viruses.Respiratory specimens from patients suspected to be infected with avian influenza in 2007 were screened by influenza and H5 subtype specific polymerase chain reaction. Isolated H5N1 strains were further characterized by genome sequencing and drug susceptibility testing. Eleven poultry outbreak isolates from 2007 were included in the sequence analysis. Eight patients, all of them from northern Vietnam, were diagnosed with H5N1 in 2007 and five of them died. Phylogenetic analysis of H5N1 viruses isolated from humans and poultry in 2007 showed that clade 2.3.4 H5N1 viruses replaced clade 1 viruses in northern Vietnam. Four human H5N1 strains had eight-fold reduced in-vitro susceptibility to oseltamivir as compared to clade 1 viruses. In two poultry isolates the I117V mutation was found in the neuraminidase gene, which is associated with reduced susceptibility to oseltamivir. No mutations in the M2 gene conferring amantadine resistance were found.In 2007, H5N1 clade 2.3.4 viruses replaced clade 1 viruses in northern Vietnam and were susceptible to amantadine but showed reduced susceptibility to oseltamivir. Combination antiviral therapy with oseltamivir and amantadine for human cases in Vietnam is recommended.

  1. Herbivory increases diversification across insect clades.

    Science.gov (United States)

    Wiens, John J; Lapoint, Richard T; Whiteman, Noah K

    2015-09-24

    Insects contain more than half of all living species, but the causes of their remarkable diversity remain poorly understood. Many authors have suggested that herbivory has accelerated diversification in many insect clades. However, others have questioned the role of herbivory in insect diversification. Here, we test the relationships between herbivory and insect diversification across multiple scales. We find a strong, positive relationship between herbivory and diversification among insect orders. However, herbivory explains less variation in diversification within some orders (Diptera, Hemiptera) or shows no significant relationship with diversification in others (Coleoptera, Hymenoptera, Orthoptera). Thus, we support the overall importance of herbivory for insect diversification, but also show that its impacts can vary across scales and clades. In summary, our results illuminate the causes of species richness patterns in a group containing most living species, and show the importance of ecological impacts on diversification in explaining the diversity of life.

  2. Photosynthetic pigments of oceanic Chlorophyta belonging to prasinophytes clade VII.

    Science.gov (United States)

    Lopes Dos Santos, Adriana; Gourvil, Priscillia; Rodríguez, Francisco; Garrido, José Luis; Vaulot, Daniel

    2016-02-01

    The ecological importance and diversity of pico/nanoplanktonic algae remains poorly studied in marine waters, in part because many are tiny and without distinctive morphological features. Amongst green algae, Mamiellophyceae such as Micromonas or Bathycoccus are dominant in coastal waters while prasinophytes clade VII, yet not formerly described, appear to be major players in open oceanic waters. The pigment composition of 14 strains representative of different subclades of clade VII was analyzed using a method that improves the separation of loroxanthin and neoxanthin. All the prasinophytes clade VII analyzed here showed a pigment composition similar to that previously reported for RCC287 corresponding to pigment group prasino-2A. However, we detected in addition astaxanthin for which it is the first report in prasinophytes. Among the strains analyzed, the pigment signature is qualitatively similar within subclades A and B. By contrast, RCC3402 from subclade C (Picocystis) lacks loroxanthin, astaxanthin, and antheraxanthin but contains alloxanthin, diatoxanthin, and monadoxanthin that are usually found in diatoms or cryptophytes. For subclades A and B, loroxanthin was lowest at highest light irradiance suggesting a light-harvesting role of this pigment in clade VII as in Tetraselmis. © 2015 Phycological Society of America.

  3. Are Clade Specific HIV Vaccines a Necessity? An Analysis Based on Mathematical Models

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    Dobromir Dimitrov

    2015-12-01

    Full Text Available As HIV-1 envelope immune responses are critical to vaccine related protection, most candidate HIV vaccines entering efficacy trials are based upon a clade specific design. This need for clade specific vaccine prototypes markedly reduces the implementation of potentially effective HIV vaccines. We utilized a mathematical model to determine the effectiveness of immediate roll-out of a non-clade matched vaccine with reduced efficacy compared to constructing clade specific vaccines, which would take considerable time to manufacture and test in safety and efficacy trials. We simulated the HIV epidemic in San Francisco (SF and South Africa (SA and projected effectiveness of three vaccination strategies: i immediate intervention with a 20–40% vaccine efficacy (VE non-matched vaccine, ii delayed intervention by developing a 50% VE clade-specific vaccine, and iii immediate intervention with a non-matched vaccine replaced by a clade-specific vaccine when developed. Immediate vaccination with a non-clade matched vaccine, even with reduced efficacy, would prevent thousands of new infections in SF and millions in SA over 30 years. Vaccination with 50% VE delayed for five years needs six and 12 years in SA to break-even with immediate 20 and 30% VE vaccination, respectively, while not able to surpass the impact of immediate 40% VE vaccination over 30 years. Replacing a 30% VE with a 50% VE vaccine after 5 years reduces the HIV acquisition by 5% compared to delayed vaccination. The immediate use of an HIV vaccine with reduced VE in high risk communities appears desirable over a short time line but higher VE should be the pursued to achieve strong long-term impact. Our analysis illustrates the importance of developing surrogate markers (correlates of protection to allow bridging types of immunogenicity studies to support more rapid assessment of clade specific vaccines.

  4. Phylogeny, evolutionary trends and classification of the Spathelia-Ptaeroxylon clade: morphological and molecular insights.

    Science.gov (United States)

    Appelhans, M S; Smets, E; Razafimandimbison, S G; Haevermans, T; van Marle, E J; Couloux, A; Rabarison, H; Randrianarivelojosia, M; Kessler, P J A

    2011-06-01

    The Spathelia-Ptaeroxylon clade is a group of morphologically diverse plants that have been classified together as a result of molecular phylogenetic studies. The clade is currently included in Rutaceae and recognized at a subfamilial level (Spathelioideae) despite the fact that most of its genera have traditionally been associated with other families and that there are no obvious morphological synapomorphies for the clade. The aim of the present study is to construct phylogenetic trees for the Spathelia-Ptaeroxylon clade and to investigate anatomical characters in order to decide whether it should be kept in Rutaceae or recognized at the familial level. Anatomical characters were plotted on a cladogram to help explain character evolution within the group. Moreover, phylogenetic relationships and generic limits within the clade are also addressed. A species-level phylogenetic analysis of the Spathelia-Ptaeroxylon clade based on five plastid DNA regions (rbcL, atpB, trnL-trnF, rps16 and psbA-trnH) was conducted using Bayesian, maximum parsimony and maximum likelihood methods. Leaf and seed anatomical characters of all genera were (re)investigated by light and scanning electron microscopy. With the exception of Spathelia, all genera of the Spathelila-Ptaeroxylon clade are monophyletic. The typical leaf and seed anatomical characters of Rutaceae were found. Further, the presence of oil cells in the leaves provides a possible synapomorphy for the clade. The Spathelia-Ptaeroxylon clade is well placed in Rutaceae and it is reasonable to unite the genera into one subfamily (Spathelioideae). We propose a new tribal classification of Spathelioideae. A narrow circumscription of Spathelia is established to make the genus monophyletic, and Sohnreyia is resurrected to accommodate the South American species of Spathelia. The most recent common ancestor of Spathelioideae probably had leaves with secretory cavities and oil cells, haplostemonous flowers with appendaged staminal

  5. Rates of morphological evolution are heterogeneous in Early Cretaceous birds

    Science.gov (United States)

    Lloyd, Graeme T.

    2016-01-01

    The Early Cretaceous is a critical interval in the early history of birds. Exceptional fossils indicate that important evolutionary novelties such as a pygostyle and a keeled sternum had already arisen in Early Cretaceous taxa, bridging much of the morphological gap between Archaeopteryx and crown birds. However, detailed features of basal bird evolution remain obscure because of both the small sample of fossil taxa previously considered and a lack of quantitative studies assessing rates of morphological evolution. Here we apply a recently available phylogenetic method and associated sensitivity tests to a large data matrix of morphological characters to quantify rates of morphological evolution in Early Cretaceous birds. Our results reveal that although rates were highly heterogeneous between different Early Cretaceous avian lineages, consistent patterns of significantly high or low rates were harder to pinpoint. Nevertheless, evidence for accelerated evolutionary rates is strongest at the point when Ornithuromorpha (the clade comprises all extant birds and descendants from their most recent common ancestors) split from Enantiornithes (a diverse clade that went extinct at the end-Cretaceous), consistent with the hypothesis that this key split opened up new niches and ultimately led to greater diversity for these two dominant clades of Mesozoic birds. PMID:27053742

  6. Trees of unusual size: biased inference of early bursts from large molecular phylogenies.

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    Matthew W Pennell

    Full Text Available An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive radiations. One often-overlooked source of bias in these studies is that of sampling at the level of whole clades, as researchers tend to choose large, speciose clades to study. In this paper, we investigate the performance of common methods across the distribution of clade sizes that can be generated by a constant-rate birth-death process. Clades which are larger than expected for a given constant-rate branching process tend to show a pattern of an early burst even when both speciation and extinction rates are constant through time. All methods evaluated were susceptible to detecting this false signature when extinction was low. Under moderate extinction, both the [Formula: see text]-statistic and diversity-dependent models did not detect such a slowdown but only because the signature of a slowdown was masked by subsequent extinction. Some models which estimate time-varying speciation rates are able to detect early bursts under higher extinction rates, but are extremely prone to sampling bias. We suggest that examining clades in isolation may result in spurious inferences that rates of diversification have changed through time.

  7. Phylogeny, evolutionary trends and classification of the Spathelia–Ptaeroxylon clade: morphological and molecular insights

    Science.gov (United States)

    Appelhans, M. S.; Smets, E.; Razafimandimbison, S. G.; Haevermans, T.; van Marle, E. J.; Couloux, A.; Rabarison, H.; Randrianarivelojosia, M.; Keßler, P. J. A.

    2011-01-01

    Background and Aims The Spathelia–Ptaeroxylon clade is a group of morphologically diverse plants that have been classified together as a result of molecular phylogenetic studies. The clade is currently included in Rutaceae and recognized at a subfamilial level (Spathelioideae) despite the fact that most of its genera have traditionally been associated with other families and that there are no obvious morphological synapomorphies for the clade. The aim of the present study is to construct phylogenetic trees for the Spathelia–Ptaeroxylon clade and to investigate anatomical characters in order to decide whether it should be kept in Rutaceae or recognized at the familial level. Anatomical characters were plotted on a cladogram to help explain character evolution within the group. Moreover, phylogenetic relationships and generic limits within the clade are also addressed. Methods A species-level phylogenetic analysis of the Spathelia–Ptaeroxylon clade based on five plastid DNA regions (rbcL, atpB, trnL–trnF, rps16 and psbA–trnH) was conducted using Bayesian, maximum parsimony and maximum likelihood methods. Leaf and seed anatomical characters of all genera were (re)investigated by light and scanning electron microscopy. Key Results With the exception of Spathelia, all genera of the Spathelila–Ptaeroxylon clade are monophyletic. The typical leaf and seed anatomical characters of Rutaceae were found. Further, the presence of oil cells in the leaves provides a possible synapomorphy for the clade. Conclusions The Spathelia–Ptaeroxylon clade is well placed in Rutaceae and it is reasonable to unite the genera into one subfamily (Spathelioideae). We propose a new tribal classification of Spathelioideae. A narrow circumscription of Spathelia is established to make the genus monophyletic, and Sohnreyia is resurrected to accommodate the South American species of Spathelia. The most recent common ancestor of Spathelioideae probably had leaves with secretory cavities

  8. Phylogenetic Signal of Threatening Processes among Hylids: The Need for Clade-Level Conservation Planning

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    Sarah J. Corey

    2010-01-01

    Full Text Available Rapid, global declines among amphibians are partly alarming because many occur for apparently unknown or enigmatic reasons. Moreover, the relationship between phylogeny and enigmatic declines in higher clades of the amphibian phylogeny appears at first to be an intractable problem. I present a working solution by assessing threatening processes potentially underlying enigmatic declines in the family, Hylidae. Applying comparative methods that account for various evolutionary scenarios, I find extreme concentrations of threatening processes, including pollution and habitat loss, in the clade Hylini, potentially influenced by traits under selection. The analysis highlights hotspots of declines under phylogenetic influence in the genera Isthmohyla, Plectrohyla and Ptychohyla, and geographically in Mexico and Guatemala. The conservation implications of concentrated phylogenetic influence across multiple threatening processes are twofold: Data Deficient species of threatened clades should be prioritized in future surveys and, perhaps, a greater vulnerability should be assigned to such clades for further consideration of clade-level conservation priorities.

  9. Genetic tools for the investigation of Roseobacter clade bacteria

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    Tielen Petra

    2009-12-01

    Full Text Available Abstract Background The Roseobacter clade represents one of the most abundant, metabolically versatile and ecologically important bacterial groups found in marine habitats. A detailed molecular investigation of the regulatory and metabolic networks of these organisms is currently limited for many strains by missing suitable genetic tools. Results Conjugation and electroporation methods for the efficient and stable genetic transformation of selected Roseobacter clade bacteria including Dinoroseobacter shibae, Oceanibulbus indolifex, Phaeobacter gallaeciensis, Phaeobacter inhibens, Roseobacter denitrificans and Roseobacter litoralis were tested. For this purpose an antibiotic resistance screening was performed and suitable genetic markers were selected. Based on these transformation protocols stably maintained plasmids were identified. A plasmid encoded oxygen-independent fluorescent system was established using the flavin mononucleotide-based fluorescent protein FbFP. Finally, a chromosomal gene knockout strategy was successfully employed for the inactivation of the anaerobic metabolism regulatory gene dnr from D. shibae DFL12T. Conclusion A genetic toolbox for members of the Roseobacter clade was established. This provides a solid methodical basis for the detailed elucidation of gene regulatory and metabolic networks underlying the ecological success of this group of marine bacteria.

  10. Integrative Taxonomy of Amazon Reefs' Arenosclera spp.: A New Clade in the Haplosclerida (Demospongiae

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    Camille V. Leal

    2017-10-01

    Full Text Available Two new Arenosclera are described here on the basis of materials obtained from Amazon reefs in 2014, A. amazonensis sp. nov. and A. klausi sp. nov. Both are clearly distinct from all other Arenosclera by their erect, solid funnel to lamellate habit, larger oxeas, and ectosomal architecture bearing occasional multispicular tracts. An integrative approach to find the best classification for both new species failed to group them and A. heroni, the genus' type species. Nearly complete 28S rRNA sequences obtained from these species' metagenomes suggested instead a better placement for the new species and A. brasiliensis in clade C (sensu Redmond et al., 2013, while A. heroni fits best in clade A. We propose to name three clades according to the rules of the PhyloCode: Arenospiculap, Dactyclonap, and Dactyspiculap, respectively for the clade originating with the most recent common ancestor of the three Brazilian Arenosclera spp.; the most inclusive clade containing Dactylia varia (Gray, 1843 and Haliclona curacaoensis (van Soest, 1980; and the least inclusive clade containing Arenospiculap and Dactyclonap. A Karlin dinucleotide dissimilarity analysis of metagenomes carried out on cryopreserved samples recognized A. amazonensis sp. nov. as the most dissimilar species, thus suggesting a more particular microbiota is present in this Amazon species, an open avenue for extended applied study of this holobiont.

  11. Predicting Mycobacterium tuberculosis Complex Clades Using Knowledge-Based Bayesian Networks

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    Minoo Aminian

    2014-01-01

    Full Text Available We develop a novel approach for incorporating expert rules into Bayesian networks for classification of Mycobacterium tuberculosis complex (MTBC clades. The proposed knowledge-based Bayesian network (KBBN treats sets of expert rules as prior distributions on the classes. Unlike prior knowledge-based support vector machine approaches which require rules expressed as polyhedral sets, KBBN directly incorporates the rules without any modification. KBBN uses data to refine rule-based classifiers when the rule set is incomplete or ambiguous. We develop a predictive KBBN model for 69 MTBC clades found in the SITVIT international collection. We validate the approach using two testbeds that model knowledge of the MTBC obtained from two different experts and large DNA fingerprint databases to predict MTBC genetic clades and sublineages. These models represent strains of MTBC using high-throughput biomarkers called spacer oligonucleotide types (spoligotypes, since these are routinely gathered from MTBC isolates of tuberculosis (TB patients. Results show that incorporating rules into problems can drastically increase classification accuracy if data alone are insufficient. The SITVIT KBBN is publicly available for use on the World Wide Web.

  12. Virulence differences among Francisella tularensis subsp. tularensis clades in mice.

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    Claudia R Molins

    Full Text Available Francisella tularensis subspecies tularensis (type A and holarctica (type B are of clinical importance in causing tularemia. Molecular typing methods have further separated type A strains into three genetically distinct clades, A1a, A1b and A2. Epidemiological analyses of human infections in the United States suggest that A1b infections are associated with a significantly higher mortality rate as compared to infections caused by A1a, A2 and type B. To determine if genetic differences as defined by molecular typing directly correlate with differences in virulence, A1a, A1b, A2 and type B strains were compared in C57BL/6 mice. Here we demonstrate significant differences between survival curves for infections caused by A1b versus A1a, A2 and type B, with A1b infected mice dying earlier than mice infected with A1a, A2 or type B; these results were conserved among multiple strains. Differences were also detected among type A clades as well as between type A clades and type B with respect to bacterial burdens, and gross anatomy in infected mice. Our results indicate that clades defined within F. tularensis subsp. tularensis by molecular typing methods correlate with virulence differences, with A1b strains more virulent than A1a, A2 and type B strains. These findings indicate type A strains are not equivalent with respect to virulence and have important implications for public health as well as basic research programs.

  13. Clade identification of symbiotic zooxanthellae of dominant ...

    African Journals Online (AJOL)

    Partial 28S nuclear ribosomal (nr) DNA of Symbiodinium were amplified by polymerase chain reaction (PCR) and then PCR products were analyzed by the phylogenetic analyses of the LSU DNA sequences based on PAUP and Clustal X software. The results showed that there are at least two clades of Symbiodinium from ...

  14. 1993 ABC of Sexually Transmitted Diseases· Introduction to Minimal ...

    African Journals Online (AJOL)

    covering the major sexually transmitted disease syndromes such as urethral and vaginal discharges and genital ... will certainly be a worthwhile investment. J. Terblanche. ABC of Brainstem Death· ... In the early 1980's the cultural implications of brainstem death were largely unexplored. Today the criteria must be.

  15. Phylogeny and taxonomy of the North American clade of the Ceratocystis fimbriata complex.

    Science.gov (United States)

    Johnson, Jason A; Harrington, Thomas C; Engelbrecht, C J B

    2005-01-01

    Ceratocystis fimbriata is a widely distributed, plant pathogenic fungus that causes wilts and cankers on many woody hosts. Earlier phylogenetic analyses of DNA sequences revealed three geographic clades within the C. fimbriata complex that are centered respectively in North America, Latin America and Asia. This study looked for cryptic species within the North American clade. The internal transcribed spacer regions (ITS) of the rDNA were sequenced, and phylogenetic analysis indicated that most isolates from the North American clade group into four host-associated lineages, referred to as the aspen, hickory, oak and cherry lineages, which were isolated primarily from wounds or diseased trees of Populus, Carya, Quercus and Prunus, respectively. A single isolate collected from P. serotina in Wisconsin had a unique ITS sequence. Allozyme electromorphs also were highly polymorphic within the North American clade, and the inferred phylogenies from these data were congruent with the ITS-rDNA analyses. In pairing experiments isolates from the aspen, hickory, oak and cherry lineages were interfertile only with other isolates from their respective lineages. Inoculation experiments with isolates of the four host-associated groupings showed strong host specialization by isolates from the aspen and hickory lineages on Populus tremuloides and Carya illinoensis, respectively, but isolates from the oak and cherry lineages did not consistently reveal host specialization. Morphological features distinguish isolates in the North American clade from those of the Latin American clade (including C. fimbriata sensu stricto). Based on the phylogenetic evidence, interfertility, host specialization and morphology, the oak and cherry lineages are recognized as the earlier described C. variospora, the poplar lineage as C. populicola sp. nov., and the hickory lineage as C. caryae sp. nov. A new species associated with the bark beetle Scolytus quadrispinosus on Carya is closely related to C

  16. Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis.

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    Jessica L Prince

    Full Text Available Initial studies of 88 transmission pairs in the Zambia Emory HIV Research Project cohort demonstrated that the number of transmitted HLA-B associated polymorphisms in Gag, but not Nef, was negatively correlated to set point viral load (VL in the newly infected partners. These results suggested that accumulation of CTL escape mutations in Gag might attenuate viral replication and provide a clinical benefit during early stages of infection. Using a novel approach, we have cloned gag sequences isolated from the earliest seroconversion plasma sample from the acutely infected recipient of 149 epidemiologically linked Zambian transmission pairs into a primary isolate, subtype C proviral vector, MJ4. We determined the replicative capacity (RC of these Gag-MJ4 chimeras by infecting the GXR25 cell line and quantifying virion production in supernatants via a radiolabeled reverse transcriptase assay. We observed a statistically significant positive correlation between RC conferred by the transmitted Gag sequence and set point VL in newly infected individuals (p = 0.02. Furthermore, the RC of Gag-MJ4 chimeras also correlated with the VL of chronically infected donors near the estimated date of infection (p = 0.01, demonstrating that virus replication contributes to VL in both acute and chronic infection. These studies also allowed for the elucidation of novel sites in Gag associated with changes in RC, where rare mutations had the greatest effect on fitness. Although we observed both advantageous and deleterious rare mutations, the latter could point to vulnerable targets in the HIV-1 genome. Importantly, RC correlated significantly (p = 0.029 with the rate of CD4+ T cell decline over the first 3 years of infection in a manner that is partially independent of VL, suggesting that the replication capacity of HIV-1 during the earliest stages of infection is a determinant of pathogenesis beyond what might be expected based on set point VL alone.

  17. Greatly reduced phylogenetic structure in the cultivated potato clade of potatoes, Solanum section Petota

    Science.gov (United States)

    The species boundaries of wild and cultivated potatoes, Solanum section Petota, are controversial with most of the taxonomic problems in a clade containing cultivated potatoes. We here provide the first in-depth phylogenetic study of the cultivated potato clade to explore possible causes of these pr...

  18. Draft genome and sequence variant data of the oomycete Pythium insidiosum strain Pi45 from the phylogenetically-distinct Clade-III

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    Weerayuth Kittichotirat

    2017-12-01

    Full Text Available Pythium insidiosum is a unique oomycete microorganism, capable of infecting humans and animals. The organism can be phylogenetically categorized into three distinct clades: Clade-I (strains from the Americas; Clade-II (strains from Asia and Australia, and Clade–III (strains from Thailand and the United States. Two draft genomes of the P. insidiosum Clade-I strain CDC-B5653 and Clade-II strain Pi-S are available in the public domain. The genome of P. insidiosum from the distinct Clade-III, which is distantly-related to the other two clades, is lacking. Here, we report the draft genome sequence of the P. insidiosum strain Pi45 (also known as MCC13; isolated from a Thai patient with pythiosis; accession numbers BCFM01000001-BCFM01017277 as a representative strain of the phylogenetically-distinct Clade-III. We also report a genome-scale data set of sequence variants (i.e., SNPs and INDELs found in P. insidiosum (accessible online at the Mendeley database: http://dx.doi.org/10.17632/r75799jy6c.1. Keywords: Pythium insidiosum, Pythiosis, Draft genome, Sequence variant

  19. A diminutive perinate European Enantiornithes reveals an asynchronous ossification pattern in early birds.

    Science.gov (United States)

    Knoll, Fabien; Chiappe, Luis M; Sanchez, Sophie; Garwood, Russell J; Edwards, Nicholas P; Wogelius, Roy A; Sellers, William I; Manning, Phillip L; Ortega, Francisco; Serrano, Francisco J; Marugán-Lobón, Jesús; Cuesta, Elena; Escaso, Fernando; Sanz, Jose Luis

    2018-03-05

    Fossils of juvenile Mesozoic birds provide insight into the early evolution of avian development, however such fossils are rare. The analysis of the ossification sequence in these early-branching birds has the potential to address important questions about their comparative developmental biology and to help understand their morphological evolution and ecological differentiation. Here we report on an early juvenile enantiornithine specimen from the Early Cretaceous of Europe, which sheds new light on the osteogenesis in this most species-rich clade of Mesozoic birds. Consisting of a nearly complete skeleton, it is amongst the smallest known Mesozoic avian fossils representing post-hatching stages of development. Comparisons between this new specimen and other known early juvenile enantiornithines support a clade-wide asynchronous pattern of osteogenesis in the sternum and the vertebral column, and strongly indicate that the hatchlings of these phylogenetically basal birds varied greatly in size and tempo of skeletal maturation.

  20. Sequential and Simultaneous Immunization of Rabbits with HIV-1 Envelope Glycoprotein SOSIP.664 Trimers from Clades A, B and C

    NARCIS (Netherlands)

    Klasse, P. J.; LaBranche, Celia C.; Ketas, Thomas J.; Ozorowski, Gabriel; Cupo, Albert; Pugach, Pavel; Ringe, Rajesh P.; Golabek, Michael; van Gils, Marit J.; Guttman, Miklos; Lee, Kelly K.; Wilson, Ian A.; Butera, Salvatore T.; Ward, Andrew B.; Montefiori, David C.; Sanders, Rogier W.; Moore, John P.

    2016-01-01

    We have investigated the immunogenicity in rabbits of native-like, soluble, recombinant SOSIP.664 trimers based on the env genes of four isolates of human immunodeficiency virus type 1 (HIV-1); specifically BG505 (clade A), B41 (clade B), CZA97 (clade C) and DU422 (clade C). The various trimers were

  1. Genotyping of Brucella species using clade specific SNPs

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    Foster Jeffrey T

    2012-06-01

    Full Text Available Abstract Background Brucellosis is a worldwide disease of mammals caused by Alphaproteobacteria in the genus Brucella. The genus is genetically monomorphic, requiring extensive genotyping to differentiate isolates. We utilized two different genotyping strategies to characterize isolates. First, we developed a microarray-based assay based on 1000 single nucleotide polymorphisms (SNPs that were identified from whole genome comparisons of two B. abortus isolates , one B. melitensis, and one B. suis. We then genotyped a diverse collection of 85 Brucella strains at these SNP loci and generated a phylogenetic tree of relationships. Second, we developed a selective primer-extension assay system using capillary electrophoresis that targeted 17 high value SNPs across 8 major branches of the phylogeny and determined their genotypes in a large collection ( n = 340 of diverse isolates. Results Our 1000 SNP microarray readily distinguished B. abortus, B. melitensis, and B. suis, differentiating B. melitensis and B. suis into two clades each. Brucella abortus was divided into four major clades. Our capillary-based SNP genotyping confirmed all major branches from the microarray assay and assigned all samples to defined lineages. Isolates from these lineages and closely related isolates, among the most commonly encountered lineages worldwide, can now be quickly and easily identified and genetically characterized. Conclusions We have identified clade-specific SNPs in Brucella that can be used for rapid assignment into major groups below the species level in the three main Brucella species. Our assays represent SNP genotyping approaches that can reliably determine the evolutionary relationships of bacterial isolates without the need for whole genome sequencing of all isolates.

  2. Cytogenetics of Legumes in the Phaseoloid Clade

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    Aiko Iwata

    2013-11-01

    Full Text Available Cytogenetics played an essential role in studies of chromosome structure, behavior, and evolution in numerous plant species. The advent of molecular cytogenetics combined with recent development of genomic resources has ushered in a new era of chromosome studies that have greatly advanced our knowledge of karyotypic diversity, genome and chromosome organization, and chromosomal evolution in legumes. This review summarizes some of the achievements of cytogenetic studies in legumes in the Phaseoloid clade, which includes several important legume crops such as common bean ( L., cowpea [ (L. Walp.], soybean [ (L. Merr.], and pigeonpea [ (L. Huth]. In the Phaseoloid clade, karyotypes are mostly stable. There are, however, several species with extensive chromosomal changes. Fluorescence in situ hybridization has been useful to reveal chromosomal structure by physically mapping transposons, satellite repeats, ribosomal DNA genes, and bacterial artificial chromosome clones onto chromosomes. Polytene chromosomes, which are much longer than the mitotic chromosomes, have been successfully found and used in cytogenetic studies in some and species. Molecular cytogenetics will continue to be an important tool in legume genetics and genomics, and we discuss future applications of molecular cytogenetics to better understand chromosome and genome structure and evolution in legumes.

  3. Characterization of humoral responses to soluble trimeric HIV gp140 from a clade A Ugandan field isolate.

    Science.gov (United States)

    Visciano, Maria Luisa; Tagliamonte, Maria; Stewart-Jones, Guillaume; Heyndrickx, Leo; Vanham, Guido; Jansson, Marianne; Fomsgaard, Anders; Grevstad, Berit; Ramaswamy, Meghna; Buonaguro, Franco M; Tornesello, Maria Lina; Biswas, Priscilla; Scarlatti, Gabriella; Buonaguro, Luigi

    2013-07-08

    Trimeric soluble forms of HIV gp140 envelope glycoproteins represent one of the closest molecular structures compared to native spikes present on intact virus particles. Trimeric soluble gp140 have been generated by several groups and such molecules have been shown to induce antibodies with neutralizing activity against homologous and heterologous viruses. In the present study, we generated a recombinant trimeric soluble gp140, derived from a previously identified Ugandan A-clade HIV field isolate (gp14094UG018). Antibodies elicited in immunized rabbits show a broad binding pattern to HIV envelopes of different clades. An epitope mapping analysis reveals that, on average, the binding is mostly focused on the C1, C2, V3, V5 and C5 regions. Immune sera show neutralization activity to Tier 1 isolates of different clades, demonstrating cross clade neutralizing activity which needs to be further broadened by possible structural modifications of the clade A gp14094UG018. Our results provide a rationale for the design and evaluation of immunogens and the clade A gp14094UG018 shows promising characteristics for potential involvement in an effective HIV vaccine with broad activity.

  4. Unique Phylogenetic Lineage Found in the Fusarium-like Clade after Re-examining BCCM/IHEM Fungal Culture Collection Material.

    Science.gov (United States)

    Triest, David; De Cremer, Koen; Piérard, Denis; Hendrickx, Marijke

    2016-09-01

    Recently, the Fusarium genus has been narrowed based upon phylogenetic analyses and a Fusarium -like clade was adopted. The few species of the Fusarium -like clade were moved to new, re-installed or existing genera or provisionally retained as " Fusarium ." Only a limited number of reference strains and DNA marker sequences are available for this clade and not much is known about its actual species diversity. Here, we report six strains, preserved by the Belgian fungal culture collection BCCM/IHEM as a Fusarium species, that belong to the Fusarium -like clade. They showed a slow growth and produced pionnotes, typical morphological characteristics of many Fusarium -like species. Multilocus sequencing with comparative sequence analyses in GenBank and phylogenetic analyses, using reference sequences of type material, confirmed that they were indeed member of the Fusarium -like clade. One strain was identified as "Fusarium" ciliatum whereas another strain was identified as Fusicolla merismoides . The four remaining strains were shown to represent a unique phylogenetic lineage in the Fusarium -like clade and were also found morphologically distinct from other members of the Fusarium -like clade. Based upon phylogenetic considerations, a new genus, Pseudofusicolla gen. nov., and a new species, Pseudofusicolla belgica sp. nov., were installed for this lineage. A formal description is provided in this study. Additional sampling will be required to gather isolates other than the historical strains presented in the present study as well as to further reveal the actual species diversity in the Fusarium -like clade.

  5. A new elasmosaurid from the early Maastrichtian of Angola and the implications of girdle morphology on swimming style in plesiosaurs

    NARCIS (Netherlands)

    Araújo, R.; Polcyn, Michael J.; Schulp, A. S.; Mateus, O.; Jacobs, L.; Gonçalves, António Olímpio; Morais, M.L.

    2014-01-01

    We report here a new elasmosaurid from the early Maastrichtian at Bentiaba, southern Angola. Phylogenetic analysis places the new taxon as the sister taxon to Styxosaurus snowii, and that clade as the sister of a clade composed of (Hydrotherosaurus alexandrae (Libonectes morgani + Elasmosaurus

  6. Plastid genome evolution across the genus Cuscuta (Convolvulaceae): two clades within subgenus Grammica exhibit extensive gene loss.

    Science.gov (United States)

    Braukmann, Thomas; Kuzmina, Maria; Stefanovic, Sasa

    2013-02-01

    The genus Cuscuta (Convolvulaceae, the morning glory family) is one of the most intensely studied lineages of parasitic plants. Whole plastome sequencing of four Cuscuta species has demonstrated changes to both plastid gene content and structure. The presence of photosynthetic genes under purifying selection indicates that Cuscuta is cryptically photosynthetic. However, the tempo and mode of plastid genome evolution across the diversity of this group (~200 species) remain largely unknown. A comparative investigation of plastid genome content, grounded within a phylogenetic framework, was conducted using a slot-blot Southern hybridization approach. Cuscuta was extensively sampled (~56% of species), including groups previously suggested to possess more altered plastomes compared with other members of this genus. A total of 56 probes derived from all categories of protein-coding genes, typically found within the plastomes of flowering plants, were used. The results indicate that two clades within subgenus Grammica (clades 'O' and 'K') exhibit substantially more plastid gene loss relative to other members of Cuscuta. All surveyed members of the 'O' clade show extensive losses of plastid genes from every category of genes typically found in the plastome, including otherwise highly conserved small and large ribosomal subunits. The extent of plastid gene losses within this clade is similar in magnitude to that observed previously in some non-asterid holoparasites, in which the very presence of a plastome has been questioned. The 'K' clade also exhibits considerable loss of plastid genes. Unlike in the 'O' clade, in which all species seem to be affected, the losses in clade 'K' progress phylogenetically, following a pattern consistent with the Evolutionary Transition Series hypothesis. This clade presents an ideal opportunity to study the reduction of the plastome of parasites 'in action'. The widespread plastid gene loss in these two clades is hypothesized to be a

  7. Phylogeny of the Ampelocissus-Vitis clade in Vitaceae supports the New World origin of the grape genus.

    Science.gov (United States)

    Liu, Xiu-Qun; Ickert-Bond, Stefanie M; Nie, Ze-Long; Zhou, Zhuo; Chen, Long-Qing; Wen, Jun

    2016-02-01

    The grapes and the close allies in Vitaceae are of great agronomic and economic importance. Our previous studies showed that the grape genus Vitis was closely related to three tropical genera, which formed the Ampelocissus-Vitis clade (including Vitis, Ampelocissus, Nothocissus and Pterisanthes). Yet the phylogenetic relationships of the four genera within this clade remain poorly resolved. Furthermore, the geographic origin of Vitis is still controversial, because the sampling of the close relatives of Vitis was too limited in the previous studies. This study reconstructs the phylogenetic relationships within the clade, and hypothesizes the origin of Vitis in a broader phylogenetic framework, using five plastid and two nuclear markers. The Ampelocissus-Vitis clade is supported to be composed of five main lineages. Vitis includes two described subgenera each as a monophyletic group. Ampelocissus is paraphyletic. The New World Ampelocissus does not form a clade and shows a complex phylogenetic relationship, with A. acapulcensis and A. javalensis forming a clade, and A. erdvendbergiana sister to Vitis. The majority of the Asian Ampelocissus species form a clade, within which Pterisanthes is nested. Pterisanthes is polyphyletic, suggesting that the lamellate inflorescence characteristic of the genus represents convergence. Nothocissus is sister to the clade of Asian Ampelocissus and Pterisanthes. The African Ampelocissus forms a clade with several Asian species. Based on the Bayesian dating and both the RASP and Lagrange analyses, Vitis is inferred to have originated in the New World during the late Eocene (39.4Ma, 95% HPD: 32.6-48.6Ma), then migrated to Eurasia in the late Eocene (37.3Ma, 95% HPD: 30.9-45.1Ma). The North Atlantic land bridges (NALB) are hypothesized to be the most plausible route for the Vitis migration from the New World to Eurasia, while intercontinental long distance dispersal (LDD) cannot be eliminated as a likely mechanism. Copyright © 2015

  8. Synergistic activity profile of griffithsin in combination with tenofovir, maraviroc and enfuvirtide against HIV-1 clade C

    International Nuclear Information System (INIS)

    Ferir, Geoffrey; Palmer, Kenneth E.; Schols, Dominique

    2011-01-01

    Griffithsin (GRFT) is possibly the most potent anti-HIV peptide found in natural sources. Due to its potent and broad-spectrum antiviral activity and unique safety profile it has great potential as topical microbicide component. Here, we evaluated various combinations of GRFT against HIV-1 clade B and clade C isolates in primary peripheral blood mononuclear cells (PBMCs) and in CD4 + MT-4 cells. In all combinations tested, GRFT showed synergistic activity profile with tenofovir, maraviroc and enfuvirtide based on the median effect principle with combination indices (CI) varying between 0.34 and 0.79 at the calculated EC 95 level. Furthermore, the different glycosylation patterns on the viral envelope of clade B and clade C gp120 had no observable effect on the synergistic interactions. Overall, we can conclude that the evaluated two-drug combination increases their antiviral potency and supports further clinical investigations in pre-exposure prophylaxis for GRFT combinations in the context of HIV-1 clade C infection.

  9. Sexually transmitted diphtheria.

    Science.gov (United States)

    Berger, Anja; Lensing, Carmen; Konrad, Regina; Huber, Ingrid; Hogardt, Michael; Sing, Andreas

    2013-03-01

    Diphtheria is caused by diphtheria toxin-producing Corynebacterium species. While classical respiratory diphtheria is transmitted by droplets, cutaneous diphtheria often results from minor trauma. This report concerns the first case of sexually transmitted diphtheria in a patient with non-gonococcal urethritis after orogenital contact.

  10. Unique Phylogenetic Lineage Found in the Fusarium-like Clade after Re-examining BCCM/IHEM Fungal Culture Collection Material

    Science.gov (United States)

    De Cremer, Koen; Piérard, Denis; Hendrickx, Marijke

    2016-01-01

    Recently, the Fusarium genus has been narrowed based upon phylogenetic analyses and a Fusarium-like clade was adopted. The few species of the Fusarium-like clade were moved to new, re-installed or existing genera or provisionally retained as "Fusarium." Only a limited number of reference strains and DNA marker sequences are available for this clade and not much is known about its actual species diversity. Here, we report six strains, preserved by the Belgian fungal culture collection BCCM/IHEM as a Fusarium species, that belong to the Fusarium-like clade. They showed a slow growth and produced pionnotes, typical morphological characteristics of many Fusarium-like species. Multilocus sequencing with comparative sequence analyses in GenBank and phylogenetic analyses, using reference sequences of type material, confirmed that they were indeed member of the Fusarium-like clade. One strain was identified as "Fusarium" ciliatum whereas another strain was identified as Fusicolla merismoides. The four remaining strains were shown to represent a unique phylogenetic lineage in the Fusarium-like clade and were also found morphologically distinct from other members of the Fusarium-like clade. Based upon phylogenetic considerations, a new genus, Pseudofusicolla gen. nov., and a new species, Pseudofusicolla belgica sp. nov., were installed for this lineage. A formal description is provided in this study. Additional sampling will be required to gather isolates other than the historical strains presented in the present study as well as to further reveal the actual species diversity in the Fusarium-like clade. PMID:27790062

  11. Meiotic Clade AAA ATPases: Protein Polymer Disassembly Machines.

    Science.gov (United States)

    Monroe, Nicole; Hill, Christopher P

    2016-05-08

    Meiotic clade AAA ATPases (ATPases associated with diverse cellular activities), which were initially grouped on the basis of phylogenetic classification of their AAA ATPase cassette, include four relatively well characterized family members, Vps4, spastin, katanin and fidgetin. These enzymes all function to disassemble specific polymeric protein structures, with Vps4 disassembling the ESCRT-III polymers that are central to the many membrane-remodeling activities of the ESCRT (endosomal sorting complexes required for transport) pathway and spastin, katanin p60 and fidgetin affecting multiple aspects of cellular dynamics by severing microtubules. They share a common domain architecture that features an N-terminal MIT (microtubule interacting and trafficking) domain followed by a single AAA ATPase cassette. Meiotic clade AAA ATPases function as hexamers that can cycle between the active assembly and inactive monomers/dimers in a regulated process, and they appear to disassemble their polymeric substrates by translocating subunits through the central pore of their hexameric ring. Recent studies with Vps4 have shown that nucleotide-induced asymmetry is a requirement for substrate binding to the pore loops and that recruitment to the protein lattice via MIT domains also relieves autoinhibition and primes the AAA ATPase cassettes for substrate binding. The most striking, unifying feature of meiotic clade AAA ATPases may be their MIT domain, which is a module that is found in a wide variety of proteins that localize to ESCRT-III polymers. Spastin also displays an adjacent microtubule binding sequence, and the presence of both ESCRT-III and microtubule binding elements may underlie the recent findings that the ESCRT-III disassembly function of Vps4 and the microtubule-severing function of spastin, as well as potentially katanin and fidgetin, are highly coordinated. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. High throughput generation and characterization of replication-competent clade C transmitter-founder simian human immunodeficiency viruses.

    Directory of Open Access Journals (Sweden)

    Debashis Dutta

    Full Text Available Traditional restriction endonuclease-based cloning has been routinely used to generate replication-competent simian-human immunodeficiency viruses (SHIV and simian tropic HIV (stHIV. This approach requires the existence of suitable restriction sites or the introduction of nucleotide changes to create them. Here, using an In-Fusion cloning technique that involves homologous recombination, we generated SHIVs and stHIVs based on epidemiologically linked clade C transmitted/founder HIV molecular clones from Zambia. Replacing vif from these HIV molecular clones with vif of SIVmac239 resulted in chimeric genomes used to generate infectious stHIV viruses. Likewise, exchanging HIV env genes and introducing N375 mutations to enhance macaque CD4 binding site and cloned into a SHIVAD8-EO backbone. The generated SHIVs and stHIV were infectious in TZMbl and ZB5 cells, as well as macaque PBMCs. Therefore, this method can replace traditional methods and be a valuable tool for the rapid generation and testing of molecular clones of stHIV and SHIV based on primary clinical isolates will be valuable to generate rapid novel challenge viruses for HIV vaccine/cure studies.

  13. Taxonomic evaluation of species in the Streptomyces hirsutus clade using multi-locus sequence analysis and proposals to reclassify several species in this clade

    Science.gov (United States)

    Previous phylogenetic analyses of species of Streptomyces based on 16S rRNA gene sequences resulted in a statistically well-supported clade (100% bootstrap value) containing 8 species that exhibited very similar gross morphology in producing open looped (Retinaculum-Apertum) to spiral (Spira) chains...

  14. Bird evolution: testing the Metaves clade with six new mitochondrial genomes

    Directory of Open Access Journals (Sweden)

    Phillips Matthew J

    2008-01-01

    Full Text Available Abstract Background Evolutionary biologists are often misled by convergence of morphology and this has been common in the study of bird evolution. However, the use of molecular data sets have their own problems and phylogenies based on short DNA sequences have the potential to mislead us too. The relationships among clades and timing of the evolution of modern birds (Neoaves has not yet been well resolved. Evidence of convergence of morphology remain controversial. With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade. Results Our mitochondrial trees did not return the Metaves clade that had been proposed based on one nuclear intron sequence. We suggest that the high number of indels within the seventh intron of the β-fibrinogen gene at this phylogenetic level, which left a dataset with not a single site across the alignment shared by all taxa, resulted in artifacts during analysis. With respect to the overall avian tree, we find the flamingo and grebe are sister taxa and basal to the shorebirds (Charadriiformes. Using a novel site-stripping technique for noise-reduction we found this relationship to be stable. The hummingbird/swift clade is outside the large and very diverse group of raptors, shore and sea birds. Unexpectedly the kagu is not closely related to the rail in our analysis, but because neither the kagu nor the rail have close affinity to any taxa within this dataset of 41 birds, their placement is not yet resolved. Conclusion Our phylogenetic hypothesis based on 41 avian mitochondrial genomes (13,229 bp rejects monophyly of seven Metaves species and we therefore conclude that the members of Metaves do not share a common evolutionary history within the Neoaves.

  15. Decoupled form and function in disparate herbivorous dinosaur clades

    Science.gov (United States)

    Lautenschlager, Stephan; Brassey, Charlotte A.; Button, David J.; Barrett, Paul M.

    2016-05-01

    Convergent evolution, the acquisition of morphologically similar traits in unrelated taxa due to similar functional demands or environmental factors, is a common phenomenon in the animal kingdom. Consequently, the occurrence of similar form is used routinely to address fundamental questions in morphofunctional research and to infer function in fossils. However, such qualitative assessments can be misleading and it is essential to test form/function relationships quantitatively. The parallel occurrence of a suite of morphologically convergent craniodental characteristics in three herbivorous, phylogenetically disparate dinosaur clades (Sauropodomorpha, Ornithischia, Theropoda) provides an ideal test case. A combination of computational biomechanical models (Finite Element Analysis, Multibody Dynamics Analysis) demonstrate that despite a high degree of morphological similarity between representative taxa (Plateosaurus engelhardti, Stegosaurus stenops, Erlikosaurus andrewsi) from these clades, their biomechanical behaviours are notably different and difficult to predict on the basis of form alone. These functional differences likely reflect dietary specialisations, demonstrating the value of quantitative biomechanical approaches when evaluating form/function relationships in extinct taxa.

  16. Decoupled form and function in disparate herbivorous dinosaur clades.

    Science.gov (United States)

    Lautenschlager, Stephan; Brassey, Charlotte A; Button, David J; Barrett, Paul M

    2016-05-20

    Convergent evolution, the acquisition of morphologically similar traits in unrelated taxa due to similar functional demands or environmental factors, is a common phenomenon in the animal kingdom. Consequently, the occurrence of similar form is used routinely to address fundamental questions in morphofunctional research and to infer function in fossils. However, such qualitative assessments can be misleading and it is essential to test form/function relationships quantitatively. The parallel occurrence of a suite of morphologically convergent craniodental characteristics in three herbivorous, phylogenetically disparate dinosaur clades (Sauropodomorpha, Ornithischia, Theropoda) provides an ideal test case. A combination of computational biomechanical models (Finite Element Analysis, Multibody Dynamics Analysis) demonstrate that despite a high degree of morphological similarity between representative taxa (Plateosaurus engelhardti, Stegosaurus stenops, Erlikosaurus andrewsi) from these clades, their biomechanical behaviours are notably different and difficult to predict on the basis of form alone. These functional differences likely reflect dietary specialisations, demonstrating the value of quantitative biomechanical approaches when evaluating form/function relationships in extinct taxa.

  17. Culture and hybridization experiments on an ulva clade including the Qingdao strain blooming in the yellow sea.

    Directory of Open Access Journals (Sweden)

    Masanori Hiraoka

    2011-05-01

    Full Text Available In the summer of 2008, immediately prior to the Beijing Olympics, a massive green tide of the genus Ulva covered the Qingdao coast of the Yellow Sea in China. Based on molecular analyses using the nuclear encoded rDNA internal transcribed spacer (ITS region, the Qingdao strains dominating the green tide were reported to be included in a single phylogenetic clade, currently regarded as a single species. On the other hand, our detailed phylogenetic analyses of the clade, using a higher resolution DNA marker, suggested that two genetically separate entities could be included within the clade. However, speciation within the Ulva clade has not yet been examined. We examined the occurrence of an intricate speciation within the clade, including the Qingdao strains, via combined studies of culture, hybridization and phylogenetic analysis. The two entities separated by our phylogenetic analyses of the clade were simply distinguished as U. linza and U. prolifera morphologically by the absence or presence of branches in cultured thalli. The inclusion of sexual strains and several asexual strains were found in each taxon. Hybridizations among the sexual strains also supported the separation by a partial gamete incompatibility. The sexually reproducing Qingdao strains crossed with U. prolifera without any reproductive boundary, but a complete reproductive isolation to U. linza occurred by gamete incompatibility. The results demonstrate that the U. prolifera group includes two types of sexual strains distinguishable by crossing affinity to U. linza. Species identification within the Ulva clade requires high resolution DNA markers and/or hybridization experiments and is not possible by reliance on the ITS markers alone.

  18. Culture and Hybridization Experiments on an Ulva Clade Including the Qingdao Strain Blooming in the Yellow Sea

    Science.gov (United States)

    Hiraoka, Masanori; Ichihara, Kensuke; Zhu, Wenrong; Ma, Jiahai; Shimada, Satoshi

    2011-01-01

    In the summer of 2008, immediately prior to the Beijing Olympics, a massive green tide of the genus Ulva covered the Qingdao coast of the Yellow Sea in China. Based on molecular analyses using the nuclear encoded rDNA internal transcribed spacer (ITS) region, the Qingdao strains dominating the green tide were reported to be included in a single phylogenetic clade, currently regarded as a single species. On the other hand, our detailed phylogenetic analyses of the clade, using a higher resolution DNA marker, suggested that two genetically separate entities could be included within the clade. However, speciation within the Ulva clade has not yet been examined. We examined the occurrence of an intricate speciation within the clade, including the Qingdao strains, via combined studies of culture, hybridization and phylogenetic analysis. The two entities separated by our phylogenetic analyses of the clade were simply distinguished as U. linza and U. prolifera morphologically by the absence or presence of branches in cultured thalli. The inclusion of sexual strains and several asexual strains were found in each taxon. Hybridizations among the sexual strains also supported the separation by a partial gamete incompatibility. The sexually reproducing Qingdao strains crossed with U. prolifera without any reproductive boundary, but a complete reproductive isolation to U. linza occurred by gamete incompatibility. The results demonstrate that the U. prolifera group includes two types of sexual strains distinguishable by crossing affinity to U. linza. Species identification within the Ulva clade requires high resolution DNA markers and/or hybridization experiments and is not possible by reliance on the ITS markers alone. PMID:21573216

  19. Regressive Evolution of Photosynthesis in the Roseobacter Clade

    Czech Academy of Sciences Publication Activity Database

    Koblížek, Michal; Zeng, Yonghui; Horák, A.; Oborník, Miroslav

    2013-01-01

    Roč. 66, č. 2013 (2013), s. 385-405 ISSN 0065-2296 R&D Projects: GA ČR GAP501/10/0221; GA ČR GBP501/12/G055; GA MŠk ED2.1.00/03.0110 Institutional support: RVO:61388971 Keywords : roseobacter clade * photosynthesis * marine microbial communities Subject RIV: EE - Microbiology, Virology Impact factor: 1.740, year: 2013

  20. Major clades of Agaricales: a multilocus phylogenetic overview.

    Science.gov (United States)

    P. Brandon Matheny; Judd M. Curtis; Valerie Hofstetter; M. Catherine Aime; Jean-Marc Moncalvo; Zai-Wei Ge; Zhu-Liang Yang; Joseph F. Ammirati; Timothy J. Baroni; Neale L. Bougher; Karen W. Lodge Hughes; Richard W. Kerrigan; Michelle T. Seidl; Aanen; Matthew Duur K. DeNitis; Graciela M. Daniele; Dennis E. Desjardin; Bradley R. Kropp; Lorelei L. Norvell; Andrew Parker; Else C. Vellinga; Rytas Vilgalys; David S. Hibbett

    2006-01-01

    An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes recovered six major clades, which are recognized informally and labeled the Agaricoid, Tricholomatoid, Marasmioid, Pluteoid,...

  1. A new ornithurine from the Early Cretaceous of China sheds light on the evolution of early ecological and cranial diversity in birds

    Directory of Open Access Journals (Sweden)

    Jiandong Huang

    2016-03-01

    Full Text Available Despite the increasing number of exceptional feathered fossils discovered in the Late Jurassic and Cretaceous of northeastern China, representatives of Ornithurae, a clade that includes comparatively-close relatives of crown clade Aves (extant birds and that clade, are still comparatively rare. Here, we report a new ornithurine species Changzuiornis ahgmi from the Early Cretaceous Jiufotang Formation. The new species shows an extremely elongate rostrum so far unknown in basal ornithurines and changes our understanding of the evolution of aspects of extant avian ecology and cranial evolution. Most of this elongate rostrum in Changzuiornis ahgmi is made up of maxilla, a characteristic not present in the avian crown clade in which most of the rostrum and nearly the entire facial margin is made up by premaxilla. The only other avialans known to exhibit an elongate rostrum with the facial margin comprised primarily of maxilla are derived ornithurines previously placed phylogenetically as among the closest outgroups to the avian crown clade as well as one derived enantiornithine clade. We find that, consistent with a proposed developmental shift in cranial ontogeny late in avialan evolution, this elongate rostrum is achieved through elongation of the maxilla while the premaxilla remains only a small part of rostral length. Thus, only in Late Cretaceous ornithurine taxa does the premaxilla begin to play a larger role. The rostral and postcranial proportions of Changzuiornis suggest an ecology not previously reported in Ornithurae; the only other species with an elongate rostrum are two marine Late Cretacous taxa interpreted as showing a derived picivorous diet.

  2. Revision of the fossil batomorphs from the Cretaceous of Lebanon, and their impact on our understanding of the early step of the evolution of the clade

    DEFF Research Database (Denmark)

    Kachacha, Georges

    group to the remaining batomorphs. The remaining guitarfish from Lebanon present a crown paraphyletic assemblage sister to Rajidae, which, together, are included in the order Rajiformes. Eight Lebanese guitarfishes are distributed into four different clades which allowed me to reconsider the generic...

  3. Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Moreau Hervé

    2008-10-01

    Full Text Available Abstract Background The Wuschel related homeobox (WOX family proteins are key regulators implicated in the determination of cell fate in plants by preventing cell differentiation. A recent WOX phylogeny, based on WOX homeodomains, showed that all of the Physcomitrella patens and Selaginella moellendorffii WOX proteins clustered into a single orthologous group. We hypothesized that members of this group might preferentially share a significant part of their function in phylogenetically distant organisms. Hence, we first validated the limits of the WOX13 orthologous group (WOX13 OG using the occurrence of other clade specific signatures and conserved intron insertion sites. Secondly, a functional analysis using expression data and mutants was undertaken. Results The WOX13 OG contained the most conserved plant WOX proteins including the only WOX detected in the highly proliferating basal unicellular and photosynthetic organism Ostreococcus tauri. A large expansion of the WOX family was observed after the separation of mosses from other land plants and before monocots and dicots have arisen. In Arabidopsis thaliana, AtWOX13 was dynamically expressed during primary and lateral root initiation and development, in gynoecium and during embryo development. AtWOX13 appeared to affect the floral transition. An intriguing clade, represented by the functional AtWOX14 gene inside the WOX13 OG, was only found in the Brassicaceae. Compared to AtWOX13, the gene expression profile of AtWOX14 was restricted to the early stages of lateral root formation and specific to developing anthers. A mutational insertion upstream of the AtWOX14 homeodomain sequence led to abnormal root development, a delay in the floral transition and premature anther differentiation. Conclusion Our data provide evidence in favor of the WOX13 OG as the clade containing the most conserved WOX genes and established a functional link to organ initiation and development in Arabidopsis, most

  4. Genomic differentiation among two strains of the PS1 clade isolated from geographically separated marine habitats

    KAUST Repository

    Jimenez Infante, Francy M.

    2014-05-22

    Using dilution-to-extinction cultivation, we isolated a strain affiliated with the PS1 clade from surface waters of the Red Sea. Strain RS24 represents the second isolate of this group of marine Alphaproteobacteria after IMCC14465 that was isolated from the East (Japan) Sea. The PS1 clade is a sister group to the OCS116 clade, together forming a putatively novel order closely related to Rhizobiales. While most genomic features and most of the genetic content are conserved between RS24 and IMCC14465, their average nucleotide identity (ANI) is < 81%, suggesting two distinct species of the PS1 clade. Next to encoding two different variants of proteorhodopsin genes, they also harbor several unique genomic islands that contain genes related to degradation of aromatic compounds in IMCC14465 and in polymer degradation in RS24, possibly reflecting the physicochemical differences in the environment they were isolated from. No clear differences in abundance of the genomic content of either strain could be found in fragment recruitment analyses using different metagenomic datasets, in which both genomes were detectable albeit as minor part of the communities. The comparative genomic analysis of both isolates of the PS1 clade and the fragment recruitment analysis provide first insights into the ecology of this group. © 2014 Federation of European Microbiological Societies.

  5. Early tetrapod relationships revisited.

    Science.gov (United States)

    Ruta, Marcello; Coates, Michael I; Quicke, Donald L J

    2003-05-01

    In an attempt to investigate differences between the most widely discussed hypotheses of early tetrapod relationships, we assembled a new data matrix including 90 taxa coded for 319 cranial and postcranial characters. We have incorporated, where possible, original observations of numerous taxa spread throughout the major tetrapod clades. A stem-based (total-group) definition of Tetrapoda is preferred over apomorphy- and node-based (crown-group) definitions. This definition is operational, since it is based on a formal character analysis. A PAUP* search using a recently implemented version of the parsimony ratchet method yields 64 shortest trees. Differences between these trees concern: (1) the internal relationships of aïstopods, the three selected species of which form a trichotomy; (2) the internal relationships of embolomeres, with Archeria crassidisca and Pholiderpeton scut collapsed in a trichotomy with a clade formed by Anthracosaurus russelli and Pholiderpeton attheyi; (3) the internal relationships of derived dissorophoids, with four amphibamid species forming an unresolved node with a clade consisting of micromelerpetontids and branchiosaurids and a clade consisting of albanerpetontids plus basal crown-group lissamphibians; (4) the position of albenerpetontids and Eocaecilia micropoda, which form an unresolved node with a trichotomy subtending Karaurus sharovi, Valdotriton gracilis and Triadobatrachus massinoti; (5) the branching pattern of derived diplocaulid nectrideans, with Batrachiderpeton reticulatum and Diceratosaurus brevirostris collapsed in a trichotomy with a clade formed by Diplocaulus magnicornis and Diploceraspis burkei. The results of the original parsimony run--as well as those retrieved from several other treatments of the data set (e.g. exclusion of postcranial and lower jaw data; character reweighting; reverse weighting)--indicate a deep split of early tetrapods between lissamphibian- and amniote-related taxa. Colosteids, Crassigyrinus

  6. Phylogenetic analysis of New Zealand earthworms (Oligochaeta: Megascolecidae) reveals ancient clades and cryptic taxonomic diversity.

    Science.gov (United States)

    Buckley, Thomas R; James, Sam; Allwood, Julia; Bartlam, Scott; Howitt, Robyn; Prada, Diana

    2011-01-01

    We have constructed the first ever phylogeny for the New Zealand earthworm fauna (Megascolecinae and Acanthodrilinae) including representatives from other major continental regions. Bayesian and maximum likelihood phylogenetic trees were constructed from 427 base pairs from the mitochondrial large subunit (16S) rRNA gene and 661 base pairs from the nuclear large subunit (28S) rRNA gene. Within the Acanthodrilinae we were able to identify a number of well-supported clades that were restricted to continental landmasses. Estimates of nodal support for these major clades were generally high, but relationships among clades were poorly resolved. The phylogenetic analyses revealed several independent lineages in New Zealand, some of which had a comparable phylogenetic depth to monophyletic groups sampled from Madagascar, Africa, North America and Australia. These results are consistent with at least some of these clades having inhabited New Zealand since rifting from Gondwana in the Late Cretaceous. Within the New Zealand Acanthodrilinae, major clades tended to be restricted to specific regions of New Zealand, with the central North Island and Cook Strait representing major biogeographic boundaries. Our field surveys of New Zealand and subsequent identification has also revealed extensive cryptic taxonomic diversity with approximately 48 new species sampled in addition to the 199 species recognized by previous authors. Our results indicate that further survey and taxonomic work is required to establish a foundation for future biogeographic and ecological research on this vitally important component of the New Zealand biota. Copyright © 2010 Elsevier Inc. All rights reserved.

  7. High Ancient Genetic Diversity of Human Lice, Pediculus humanus, from Israel Reveals New Insights into the Origin of Clade B Lice.

    Science.gov (United States)

    Amanzougaghene, Nadia; Mumcuoglu, Kosta Y; Fenollar, Florence; Alfi, Shir; Yesilyurt, Gonca; Raoult, Didier; Mediannikov, Oleg

    2016-01-01

    The human head louse, Pediculus humanus capitis, is subdivided into several significantly divergent mitochondrial haplogroups, each with particular geographical distributions. Historically, they are among the oldest human parasites, representing an excellent marker for tracking older events in human evolutionary history. In this study, ancient DNA analysis using real-time polymerase chain reaction (qPCR), combined with conventional PCR, was applied to the remains of twenty-four ancient head lice and their eggs from the Roman period which were recovered from Israel. The lice and eggs were found in three combs, one of which was recovered from archaeological excavations in the Hatzeva area of the Judean desert, and two of which found in Moa, in the Arava region, close to the Dead Sea. Results show that the head lice remains dating approximately to 2,000 years old have a cytb haplogroup A, which is worldwide in distribution, and haplogroup B, which has thus far only been found in contemporary lice from America, Europe, Australia and, most recently, Africa. More specifically, this haplogroup B has a B36 haplotype, the most common among B haplogroups, and has been present in America for at least 4,000 years. The present findings confirm that clade B lice existed, at least in the Middle East, prior to contacts between Native Americans and Europeans. These results support a Middle Eastern origin for clade B followed by its introduction into the New World with the early peoples. Lastly, the presence of Acinetobacter baumannii DNA was demonstrated by qPCR and sequencing in four head lice remains belonging to clade A.

  8. Phylogenetic analysis of Melon chlorotic leaf curl virus from Guatemala: Another emergent species in the Squash leaf curl virus clade

    KAUST Repository

    Brown, J.K.

    2011-06-01

    The genome of a new bipartite begomovirus Melon chlorotic leaf curl virus from Guatemala (MCLCuV-GT) was cloned and the genome sequence was determined. The virus causes distinct symptoms on melons that were not previously observed in melon crops in Guatemala or elsewhere. Phylogenetic analysis of MCLCuV-GT and begomoviruses infecting cucurbits and other host plant species indicated that its closest relative was MCLCuV from Costa Rica (MCLCuV-CR). The DNA-A components of two isolates shared 88.8% nucleotide identity, making them strains of the same species. Further, both MCLCuV-GT and MCLCuV-CR grouped with other Western Hemisphere cucurbit-infecting species in the SLCV-clade making them the most southerly cucurbit-infecting members of the clade to date. Although the common region of the cognate components of MCLCuV-GT and MCLCuV-CR, shared similar to 96.3% nucleotide identity. While DNA-A and DNA-B components of MCLCuV-GT were less than 86% nucleotide identity with the respective DNAA and DNA-B common regions of MCLCuV-CR. The late viral genes of the two strains shared the least nt identity (<88%) while their early genes shared the highest nt identity (>90%). The collective evidence suggests that these two strains of MCLCuV are evolutionarily divergent owing in part to recombination, but also due to the accumulation of a substantial number of mutations. In addition they are differentially host-adapted, as has been documented for other cucurbit-infecting, bean-adapted, species in the SLCV clade. (C) 2011 Elsevier B.V. All rights reserved.

  9. SRP-2 is a cross-class inhibitor that participates in postembryonic development of the nematode Caenorhabditis elegans: initial characterization of the clade L serpins.

    Science.gov (United States)

    Pak, Stephen C; Kumar, Vasantha; Tsu, Christopher; Luke, Cliff J; Askew, Yuko S; Askew, David J; Mills, David R; Brömme, Dieter; Silverman, Gary A

    2004-04-09

    High molecular weight serpins are members of a large superfamily of structurally conserved proteins that inactivate target proteinases by a suicide substrate-like mechanism. In vertebrates, different clades of serpins distribute predominantly to either the intracellular or extracellular space. Although much is known about the function, structure, and inhibitory mechanism of circulating serpins such as alpha(1)-antitrypsin (SERPINA1) and antithrombin III (SERPINC1), relatively little is known about the function of the vertebrate intracellular (clade B) serpins. To gain a better understanding of the biology of the intracellular serpins, we initiated a comparative genomics study using Caenorhabditis elegans as a model system. A screen of the C. elegans genomic and cDNA databases revealed nine serpin genes, tandemly arrayed on chromosome V. Although the C. elegans serpins represent a unique clade (L), they share significant functional homology with members of the clade B group of intracellular serpins, since they lack typical N-terminal signal peptides and reside intracellularly. To determine whether nematode serpins function as proteinase inhibitors, one family member, srp-2, was chosen for further characterization. Biochemical analysis of recombinant SRP-2 protein revealed SRP-2 to be a dual cross-class inhibitor of the apoptosis-related serine proteinase, granzyme B, and the lysosomal cysteine proteinases, cathepsins K, L, S, and V. Analysis of temporal and spatial expression indicated that SRP-2 was present during early embryonic development and highly expressed in the intestine and hypoderm of larval and adult worms. Transgenic animals engineered to overexpress SRP-2 were slow growing and/or arrested at the first, second, or third larval stages. These data suggest that perturbations of serpin-proteinase balance are critical for correct postembryonic development in C. elegans.

  10. Quantifying variation in speciation and extinction rates with clade data.

    Science.gov (United States)

    Paradis, Emmanuel; Tedesco, Pablo A; Hugueny, Bernard

    2013-12-01

    High-level phylogenies are very common in evolutionary analyses, although they are often treated as incomplete data. Here, we provide statistical tools to analyze what we name "clade data," which are the ages of clades together with their numbers of species. We develop a general approach for the statistical modeling of variation in speciation and extinction rates, including temporal variation, unknown variation, and linear and nonlinear modeling. We show how this approach can be generalized to a wide range of situations, including testing the effects of life-history traits and environmental variables on diversification rates. We report the results of an extensive simulation study to assess the performance of some statistical tests presented here as well as of the estimators of speciation and extinction rates. These latter results suggest the possibility to estimate correctly extinction rate in the absence of fossils. An example with data on fish is presented. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  11. In situ morphometric survey elucidates the evolutionary systematics of the Eurasian Himantoglossum clade (Orchidaceae: Orchidinae

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    Richard M. Bateman

    2017-01-01

    Full Text Available Background and Aims The charismatic Himantoglossum s.l. clade of Eurasian orchids contains an unusually large proportion of taxa that are of controversial circumscriptions and considerable conservation concern. Whereas our previously published study addressed the molecular phylogenetics and phylogeography of every named taxon within the clade, here we use detailed morphometric data obtained from the same populations to compare genotypes with associated phenotypes, in order to better explore taxonomic circumscription and character evolution within the clade. Methods Between one and 12 plants found in 25 populations that encompassed the entire distribution of the Himantoglossum s.l. clade were measured in situ for 51 morphological characters. Results for 45 of those characters were subjected to detailed multivariate and univariate analyses. Key Results Multivariate analyses readily separate subgenus Barlia and subgenus Comperia from subgenus Himantoglossum, and also the early-divergent H. formosum from the less divergent remainder of subgenus Himantoglossum. The sequence of divergence of these four lineages is confidently resolved. Our experimental approach to morphometric character analysis demonstrates clearly that phenotypic evolution within Himantoglossum is unusually multi-dimensional. Conclusions Degrees of divergence between taxa shown by morphological analyses approximate those previously shown using molecular analyses. Himantoglossum s.l. is readily divisible into three subgenera. The three sections of subgenus Himantoglossum—hircinum, caprinum and formosum—are arrayed from west to east with only limited geographical overlap. At this taxonomic level, their juxtaposition combines with conflict between contrasting datasets to complicate attempts to distinguish between clinal variation and the discontinuities that by definition separate bona fide species. All taxa achieve allogamy via food deceit and have only weak pollinator specificity

  12. Sexually transmitted diseases among adults who had been abused and neglected as children: a 30-year prospective study.

    Science.gov (United States)

    Wilson, Helen W; Widom, Cathy S

    2009-04-01

    We examined associations between childhood abuse and neglect and the risk in adulthood for sexually transmitted diseases. In a prospective cohort design, we matched children aged 0 to 11 years with documented cases of abuse or neglect during 1967 to 1971 with a control group of children who had not been maltreated (754 participants in all) and followed them into adulthood. Information about lifetime history of sexually transmitted diseases was collected as part of a medical status examination when participants were approximately 41 years old. Childhood sexual abuse increased risk for any sexually transmitted disease (odds ratio [OR] = 1.94; 95% confidence interval [CI] = 1.00, 3.77; P = .05) and more than 1 type of sexually transmitted disease (OR = 3.33; 95% CI = 1.33, 8.22; P = .01). Physical abuse increased risk for more than 1 type of sexually transmitted disease (OR = 3.61; 95% CI = 1.39, 9.38; P = .009). Our results provided the first prospective evidence that child physical and sexual abuse increases risk for sexually transmitted diseases. Early screening and interventions are needed to identify and prevent sexually transmitted diseases among child abuse victims.

  13. An efficiently cleaved HIV-1 clade C Env selectively binds to neutralizing antibodies.

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    Saikat Boliar

    Full Text Available An ideal HIV-1 Env immunogen is expected to mimic the native trimeric conformation for inducing broadly neutralizing antibody responses. The native conformation is dependent on efficient cleavage of HIV-1 Env. The clade B isolate, JRFL Env is efficiently cleaved when expressed on the cell surface. Here, for the first time, we report the identification of a native clade C Env, 4-2.J41 that is naturally and efficiently cleaved on the cell surface as confirmed by its biochemical and antigenic characteristics. In addition to binding to several conformation-dependent neutralizing antibodies, 4-2.J41 Env binds efficiently to the cleavage-dependent antibody PGT151; thus validating its native cleaved conformation. In contrast, 4-2.J41 Env occludes non-neutralizing epitopes. The cytoplasmic-tail of 4-2.J41 Env plays an important role in maintaining its conformation. Furthermore, codon optimization of 4-2.J41 Env sequence significantly increases its expression while retaining its native conformation. Since clade C of HIV-1 is the prevalent subtype, identification and characterization of this efficiently cleaved Env would provide a platform for rational immunogen design.

  14. Dermal neutrophil, macrophage and dendritic cell responses to Yersinia pestis transmitted by fleas.

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    Jeffrey G Shannon

    2015-03-01

    Full Text Available Yersinia pestis, the causative agent of plague, is typically transmitted by the bite of an infected flea. Many aspects of mammalian innate immune response early after Y. pestis infection remain poorly understood. A previous study by our lab showed that neutrophils are the most prominent cell type recruited to the injection site after intradermal needle inoculation of Y. pestis, suggesting that neutrophil interactions with Y. pestis may be important in bubonic plague pathogenesis. In the present study, we developed new tools allowing for intravital microscopy of Y. pestis in the dermis of an infected mouse after transmission by its natural route of infection, the bite of an infected flea. We found that uninfected flea bites typically induced minimal neutrophil recruitment. The magnitude of neutrophil response to flea-transmitted Y. pestis varied considerably and appeared to correspond to the number of bacteria deposited at the bite site. Macrophages migrated towards flea bite sites and interacted with small numbers of flea-transmitted bacteria. Consistent with a previous study, we observed minimal interaction between Y. pestis and dendritic cells; however, dendritic cells did consistently migrate towards flea bite sites containing Y. pestis. Interestingly, we often recovered viable Y. pestis from the draining lymph node (dLN 1 h after flea feeding, indicating that the migration of bacteria from the dermis to the dLN may be more rapid than previously reported. Overall, the innate cellular host responses to flea-transmitted Y. pestis differed from and were more variable than responses to needle-inoculated bacteria. This work highlights the importance of studying the interactions between fleas, Y. pestis and the mammalian host to gain a better understanding of the early events in plague pathogenesis.

  15. Distinct Processes Drive Diversification in Different Clades of Gesneriaceae.

    Science.gov (United States)

    Roalson, Eric H; Roberts, Wade R

    2016-07-01

    Using a time-calibrated phylogenetic hypothesis including 768 Gesneriaceae species (out of [Formula: see text]3300 species) and more than 29,000 aligned bases from 26 gene regions, we test Gesneriaceae for diversification rate shifts and the possible proximal drivers of these shifts: geographic distributions, growth forms, and pollination syndromes. Bayesian Analysis of Macroevolutionary Mixtures analyses found five significant rate shifts in Beslerieae, core Nematanthus, core Columneinae, core Streptocarpus, and Pacific Cyrtandra These rate shifts correspond with shifts in diversification rates, as inferred by Binary State Speciation and Extinction Model and Geographic State Speciation and Extinction model, associated with hummingbird pollination, epiphytism, unifoliate growth, and geographic area. Our results suggest that diversification processes are extremely variable across Gesneriaceae clades with different combinations of characters influencing diversification rates in different clades. Diversification patterns between New and Old World lineages show dramatic differences, suggesting that the processes of diversification in Gesneriaceae are very different in these two geographic regions. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  16. Molecular relationships of fungi within the Fusarium redolens - F. hostae clade

    NARCIS (Netherlands)

    Baayen, R.P.; O'Donnell, K.; Breeuwsma, S.; Geiser, D.M.; Waalwijk, C.

    2001-01-01

    The evolutionary relationships of fungi in the Fusarium redolens - F. hostae clade were investigated by constructing nuclear and mitochondrial gene genealogies for 37 isolates representing the known genetic and pathogenic diversity of this lineage, together with 15 isolates from putative sister

  17. Protein evolution in two co-occurring types of Symbiodinium: an exploration into the genetic basis of thermal tolerance in Symbiodinium clade D

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    Ladner Jason T

    2012-11-01

    Full Text Available Abstract Background The symbiosis between reef-building corals and photosynthetic dinoflagellates (Symbiodinium is an integral part of the coral reef ecosystem, as corals are dependent on Symbiodinium for the majority of their energy needs. However, this partnership is increasingly at risk due to changing climatic conditions. It is thought that functional diversity within Symbiodinium may allow some corals to rapidly adapt to different environments by changing the type of Symbiodinium with which they partner; however, very little is known about the molecular basis of the functional differences among symbiont groups. One group of Symbiodinium that is hypothesized to be important for the future of reefs is clade D, which, in general, seems to provide the coral holobiont (i.e., coral host and associated symbiont community with elevated thermal tolerance. Using high-throughput sequencing data from field-collected corals we assembled, de novo, draft transcriptomes for Symbiodinium clades C and D. We then explore the functional basis of thermal tolerance in clade D by comparing rates of coding sequence evolution among the four clades of Symbiodinium most commonly found in reef-building corals (A-D. Results We are able to highlight a number of genes and functional categories as candidates for involvement in the increased thermal tolerance of clade D. These include a fatty acid desaturase, molecular chaperones and proteins involved in photosynthesis and the thylakoid membrane. We also demonstrate that clades C and D co-occur within most of the sampled colonies of Acropora hyacinthus, suggesting widespread potential for this coral species to acclimatize to changing thermal conditions via ‘shuffling’ the proportions of these two clades from within their current symbiont communities. Conclusions Transcriptome-wide analysis confirms that the four main Symbiodinium clades found within corals exhibit extensive evolutionary divergence (18.5-27.3% avg

  18. Novel H5N8 clade 2.3.4.4 highly pathogenic avian influenza virus in wild awuatic birds, Russia, 2016

    Science.gov (United States)

    H5N1 high pathogenicity avian influenza virus (HPAIV) emerged in 1996 in Guangdong China (Gs/GD) and has evolved into multiple genetic clades. Since 2008, HPAIV H5 clade 2.3.4 with N2, N5 and N8 neuraminidase subtypes have been identified in mainland China and outbreak of HPAIV H5N8 clade 2.3.4.4 ou...

  19. Phylogeny of the sea hares in the aplysia clade based on mitochondrial DNA sequence data

    Energy Technology Data Exchange (ETDEWEB)

    Medina, Monica; Collins, Timothy; Walsh, Patrick J.

    2004-02-20

    Sea hare species within the Aplysia clade are distributed worldwide. Their phylogenetic and biogeographic relationships are, however, still poorly known. New molecular evidence is presented from a portion of the mitochondrial cytochrome oxidase c subunit 1 gene (cox1) that improves our understanding of the phylogeny of the group. Based on these data a preliminary discussion of the present distribution of sea hares in a biogeographic context is put forward. Our findings are consistent with only some aspects of the current taxonomy and nomenclatural changes are proposed. The first, is the use of a rank free classification for the different Aplysia clades and subclades as opposed to previously used genus and subgenus affiliations. The second, is the suggestion that Aplysia brasiliana (Rang, 1828) is a junior synonym of Aplysia fasciata (Poiret, 1789). The third, is the elimination of Neaplysia since its only member is confirmed to be part of the large Varria clade.

  20. Perception of health care providers about sexually transmitted infections

    International Nuclear Information System (INIS)

    Khan, A.; Izhar, V.

    2015-01-01

    Sexually transmitted infections represent a global health problem leading to social stigma and early morbidity and mortality. Prior to this study, different health care providers were dealing with sexually transmitted infections with various parameters and were not following the standard regime given by the WHO. The aim of this study was to investigate the perception of health care providers about sexually transmitted infections and its treatment guidelines. Methods: Cross sectional questionnaire based study was conducted from health care providers(specialists, family physicians, homeopaths and others )of Lahore from Jan 2014 to December 2014. Data was collected with consent through convenience purposive sampling of randomly selected 100 specialists, 200 family physicians, 100 homeopaths and 100 others. Trained investigators pre-tested the validity and reliability of the questionnaire before use. Data of response was coded, entered and analyzed using SPSS. Results: Out of 500 practitioners 475 (95%) completed the questionnaire. Those excluded were due to insufficient data in questionnaire. Almost all respondents were aware of STIs and the guidelines and claimed to have decent knowledge. Apart from some disagreement on the user- friendliness and communication facilitating properties, the health care provider's attitude were positive. Conclusion: Overall, all the health care providers knew about sexually transmitted infections. It was the treatment according to the guidelines, in which they differed. Specialists and Family physician in Lahore, Pakistan knew and followed the STIs guidelines while managing the patients. Homeopaths and others were receiving patients and treating most of these infections but were not aware of the standard guidelines yet somehow their patients were treated and satisfied. Enhancing the familiarity of the guidelines among users can result in a positive outcome on the treatment of STIs. (author)

  1. Structural and antigenic variation among diverse clade 2 H5N1 viruses.

    Directory of Open Access Journals (Sweden)

    David A Shore

    Full Text Available Antigenic variation among circulating H5N1 highly pathogenic avian influenza A viruses mandates the continuous production of strain-specific pre-pandemic vaccine candidates and represents a significant challenge for pandemic preparedness. Here we assessed the structural, antigenic and receptor-binding properties of three H5N1 HPAI virus hemagglutinins, which were recently selected by the WHO as vaccine candidates [A/Egypt/N03072/2010 (Egypt10, clade 2.2.1, A/Hubei/1/2010 (Hubei10, clade 2.3.2.1 and A/Anhui/1/2005 (Anhui05, clade 2.3.4]. These analyses revealed that antigenic diversity among these three isolates was restricted to changes in the size and charge of amino acid side chains at a handful of positions, spatially equivalent to the antigenic sites identified in H1 subtype viruses circulating among humans. All three of the H5N1 viruses analyzed in this study were responsible for fatal human infections, with the most recently-isolated strains, Hubei10 and Egypt10, containing multiple residues in the receptor-binding site of the HA, which were suspected to enhance mammalian transmission. However, glycan-binding analyses demonstrated a lack of binding to human α2-6-linked sialic acid receptor analogs for all three HAs, reinforcing the notion that receptor-binding specificity contributes only partially to transmissibility and pathogenesis of HPAI viruses and suggesting that changes in host specificity must be interpreted in the context of the host and environmental factors, as well as the virus as a whole. Together, our data reveal structural linkages with phylogenetic and antigenic analyses of recently emerged H5N1 virus clades and should assist in interpreting the significance of future changes in antigenic and receptor-binding properties.

  2. Amphitremida (poche, 1913 is a new major, ubiquitous labyrinthulomycete clade.

    Directory of Open Access Journals (Sweden)

    Fatma Gomaa

    Full Text Available Micro-eukaryotic diversity is poorly documented at all taxonomic levels and the phylogenetic affiliation of many taxa - including many well-known and common organisms - remains unknown. Among these incertae sedis taxa are Archerella flavum (Loeblich and Tappan, 1961 and Amphitrema wrightianum (Archer, 1869 (Amphitremidae, two filose testate amoebae commonly found in Sphagnum peatlands. To clarify their phylogenetic position, we amplified and sequenced the SSU rRNA gene obtained from four independent DNA extractions of A. flavum and three independent DNA extractions of A. wrightianum. Our molecular data demonstrate that genera Archerella and Amphitrema form a fully supported deep-branching clade within the Labyrinthulomycetes (Stramenopiles, together with Diplophrys sp. (ATCC50360 and several environmental clones obtained from a wide range of environments. This newly described clade we named Amphitremida is diverse genetically, ecologically and physiologically. Our phylogenetic analysis suggests that osmotrophic species evolved most likely from phagotrophic ancestors and that the bothrosome, an organelle that produces cytoplasmic networks used for attachment to the substratum and to absorb nutrients from the environments, appeared lately in labyrithulomycete evolution.

  3. [Infectious pathology: vulvovaginitis, sexually transmitted diseases, pelvic inflammatory disease, tubo-ovarian abscesses].

    Science.gov (United States)

    Ibarrola Vidaurre, M; Benito, J; Azcona, B; Zubeldía, N

    2009-01-01

    Sexually transmitted diseases are those where the principal path of infection is through intimate contact. Numerous patients attend Accidents and emergencies for this reason, both because of the clinical features and because of social implications. The most frequent symptoms are lower abdominal pain, vaginal bleeding or excessive or troubling vaginal flow. Vulvovaginites are one of the principal problems in the everyday clinical practice of gynaecology. A genital ulcer whose principal aetiology is herpes, followed by syphilis and chancroid, increases the risk of contracting HIV infection and alters the course of other sexually transmitted diseases. Inflammatory pelvic disease encompasses infections of the upper female genital tract. The importance of early diagnosis and suitable treatment is both due to the complications in its acute phase and to its sequels, which include chronic pain and sterility.

  4. Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species.

    Science.gov (United States)

    Lassiter, Erica S; Russ, Carsten; Nusbaum, Chad; Zeng, Qiandong; Saville, Amanda C; Olarte, Rodrigo A; Carbone, Ignazio; Hu, Chia-Hui; Seguin-Orlando, Andaine; Samaniego, Jose A; Thorne, Jeffrey L; Ristaino, Jean B

    2015-11-01

    Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.

  5. The other epidemics. Sexually transmitted diseases.

    Science.gov (United States)

    Jacobson, J L

    1993-01-01

    Around 70% of female infertility in developing countries is caused by sexually transmitted diseases (STDs) that can be traced back to husbands or partners. STDs and reproductive tract infections cause 750,000 deaths and 75 million illnesses among women each year worldwide, and these deaths may more than double by the year 2000. Death rates are rising fastest in Africa, followed by Asia and Latin America. About 450,000 cases of potentially fatal reproductive tract cancers are diagnosed annually: an estimated 354,000 occur in Third World women, virtually all of whom die. Worldwide, roughly 250 million new infections of chlamydia, gonorrhea, and the human papillomavirus are sexually transmitted each year. Chlamydia and the human papillomavirus account for 50 million and 30 million new cases per year, respectively. The human immunodeficiency virus (HIV) infected 1 million people worldwide between April and December 1991, according to the World Health Organization. A study in the Indian state of Maharashtra revealed that 92% of the 650 rural women examined had an average of 3.6 infections of gynecological type or sexually transmitted type per women. Another study in 2 rural Egyptian villages found that half of 509 nonpregnant women aged 20 to 60 years had infections. Only 2 facilities for the diagnosis and treatment of STDs exist in all of Kenya. In Ibadan, Nigeria, with a population of 2 million, there is only 1 recognized STD clinic. The physical consequences of several STDs have been linked to increased risks of AIDS transmission. Early recognition and treatment of STDs in pregnant women would cut infant mortality. Maternal infections with chlamydia, gonorrhea, or herpes are transferred to infants at birth 25% to 50% of the time. In Africa, infant blindness caused by gonorrhea infection is 50 times more common than in industrial countries. The International Women's Health Coalition's March 1992 meeting of more than 50 Third World scientists, health advocates, and

  6. 2012 Sexually Transmitted Diseases Surveillance, Other Sexually Transmitted Diseases

    Science.gov (United States)

    ... 2012 Sexually Transmitted Diseases Surveillance Table of Contents Introductory Section Foreword Preface Acronyms Figures- National Profile Figures - ... GISP Profiles Related Links STD Home STD Data & Statistics NCHHSTP Atlas Interactive STD Data - 1996-2013 STD ...

  7. Influenza A H5N1 clade 2.3.4 virus with a different antiviral susceptibility profile replaced clade 1 virus in humans in northern Vietnam

    NARCIS (Netherlands)

    Le, Mai T. Q.; Wertheim, Heiman F. L.; Nguyen, Hien D.; Taylor, Walter; Hoang, Phuong V. M.; Vuong, Cuong D.; Nguyen, Hang L. K.; Nguyen, Ha H.; Nguyen, Thai Q.; Nguyen, Trung V.; van, Trang D.; Ngoc, Bich T.; Bui, Thinh N.; Nguyen, Binh G.; Nguyen, Liem T.; Luong, San T.; Phan, Phuc H.; Pham, Hung V.; Nguyen, Tung; Fox, Annette; Nguyen, Cam V.; Do, Ha Q.; Crusat, Martin; Farrar, Jeremy; Nguyen, Hien T.; de Jong, Menno D.; Horby, Peter

    2008-01-01

    BACKGROUND: Prior to 2007, highly pathogenic avian influenza (HPAI) H5N1 viruses isolated from poultry and humans in Vietnam were consistently reported to be clade 1 viruses, susceptible to oseltamivir but resistant to amantadine. Here we describe the re-emergence of human HPAI H5N1 virus infections

  8. Two novel species representing a new clade and cluster of Phytophthora.

    Science.gov (United States)

    Yang, Xiao; Copes, Warren E; Hong, Chuanxue

    2014-01-01

    Phytophthora stricta sp. nov. and Phytophthora macilentosa sp. nov. are described based on morphological, physiological and molecular characters in this study. Phytophthora stricta represents a previously unknown clade in the rRNA internal transcribed spacer (ITS)-based phylogeny. Phytophthora macilentosa, along with nine other species, consistently forms a high temperature-tolerant cluster within ITS clade 9. These observations are supported by the sequence analysis of the mitochondrial cytochrome c oxidase 1 gene. Both species are heterothallic and all examined isolates are A1 mating type. Phytophthora stricta produces nonpapillate and slightly caducous sporangia. This species is named after its characteristic constrictions on sporangiophores. Phytophthora macilentosa produces nonpapillate and noncaducous sporangia, which are mostly elongated obpyriform with a high length to breadth ratio. Both species were recovered from irrigation water of an ornamental plant nursery in Mississippi, USA and P. stricta was also recovered from stream water in Virginia, USA. Copyright © 2013 The British Mycological Society. All rights reserved.

  9. Insights on the evolutionary origin of Detarioideae, a clade of ecologically dominant tropical African trees.

    Science.gov (United States)

    de la Estrella, Manuel; Forest, Félix; Wieringa, Jan J; Fougère-Danezan, Marie; Bruneau, Anne

    2017-06-01

    African tropical forests are generally considered less diverse than their Neotropical and Asian counterparts. By contrast, the Detarioideae is much more diverse in Africa than in South America and Asia. To better understand the evolution of this contrasting diversity pattern, we investigated the biogeographical and ecological origin of this subfamily, testing whether they originated in dry biomes surrounding the Tethys Seaway as currently hypothesized for many groups of Leguminosae. We constructed the largest time-calibrated phylogeny for the subfamily to date, reconstructed ancestral states for geography and biome/habitat, estimated diversification and extinction rates, and evaluated biome/habitat and geographic shifts in Detarioideae. The ancestral habitat of Detarioideae is postulated to be a primary forest (terra firme) originated in Africa-South America, in the early Palaeocene, after which several biome/habitat and geographic shifts occurred. The origin of Detarioideae is older than previous estimates, which postulated a dry (succulent) biome origin according to the Tethys Seaway hypothesis, and instead we reveal a post Gondwana and terra firme origin for this early branching clade of legumes. Detarioideae include some of the most dominant trees in evergreen forests and have likely played a pivotal role in shaping continental African forest diversity. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  10. Morphological features of the species of the genus Chlamydomonas s.l. (Chlorophyta from various molecular clades

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    Maria N. Pavlovska

    2012-03-01

    Full Text Available The morphology of 78 authentic strains from 5 clades into culture condition was investigated. The complex of phenotype features was established. Such features as: type of mucilage and their origin, mucilage collapse under methylene blue, saving papilla and stigma in not motile stage, extracellular matrix formation inside cell wall, the way of sporangium break, pyrenoid and stigma habit before cell division, cell shape, chloroplast morphology. Diagnostic features for determination of taxa on clades level are discussed.

  11. Early initiation of sexual activity: a risk factor for sexually transmitted diseases, HIV infection, and unwanted pregnancy among university students in China

    Directory of Open Access Journals (Sweden)

    Ravari Shahrzad

    2009-04-01

    Full Text Available Abstract Background To explore any association between the timing of the initiation of sexual activity and sexual behaviors and risks among university students in China. Methods Data were derived from a cross-sectional study on sexual behavior among university students conducted in Ningbo municipality, China, at the end of 2003. Students completed a self-administered, structured questionnaire. Of 1981 sexually active male students, 1908 (96.3% completed the item for timing of the initiation of sexual activity and were included in bivariate trend analyses and multiple logistic regression analyses to compare the association between this timing and sexual behavior and risks. Results Male early sexual initiators had a significantly higher risk profile, including a significantly higher proportion reporting non-regular partners (i.e., casual or commercial partners, multiple partners, diagnosis with a sexually transmitted disease (STD, partner history of pregnancy, partner history of induced abortion, and less condom and oral contraceptive use, compared with late initiators. Multivariate analyses confirmed the increased likelihood of these risks in early initiators versus late initiators, other than partner type during the last year. Conclusion Our results showed that, compared to late initiators, people who initiated sexual activity early engaged in more risky behaviors that could lead to elevated risks of unwanted pregnancies and STDs or human immunodeficiency virus infection. Sex-education strategies should be focused on an earlier age, should include advice on delaying the age of first sexual activity, and should target young people who continue to take sexual risks.

  12. Complete genome sequence of Campylobacter jejuni strain 12567 a livestock-associated clade representative

    Science.gov (United States)

    We report the complete genome sequence of the Campylobacter jejuni strain 12567, a member of a C. jejuni livestock-associated clade that expresses glycoconjugates linked to improved gastrointestinal tract persistence....

  13. Dobrogeria aegyssensis, a new early Spathian (Early Triassic) coelacanth from North Dobrogea (Romania)

    Science.gov (United States)

    Cavin, Lionel; Grădinaru, Eugen

    2014-06-01

    The Early Triassic witnessed the highest taxic diversity of coelacanths (or Actinistia), a clade with a single living genus today. This peak of diversity is accentuated here with the description of a new coelacanth discovered in the lower Spathian (Upper Olenekian, Lower Triassic) cropping out in the Tulcea Veche (Old Tulcea) promontory, in the city of Tulcea, in North Dobrogea, Romania. The bone remains were preserved in a block of limestone, which was chemically dissolved. The resulting 3D and matrix-free ossifications correspond mostly to elements of the skull and branchial apparatus. Posterior parietals, postparietal with associated prootic and basisphenoid allow a precise description of the neurocranium. Ossifications of the lower jaw, together with branchial and pectoral elements, complete the description of this coelacanth and support the coining of a new generic and specific name, Dobrogeria aegyssensis. A phylogenetic analysis of actinistians with the new species recovers clades which were found in most recent analyses, i.e. the Sasseniidae, the Laugiidae, the Coelacanthiformes, the Latimerioidei, the Mawsoniidae and the Latimeriidae, and identifies the new taxon as a non-latimerioid coelacanthiform.

  14. Reconstructing the early evolution of the fungi using a six gene phylogeny

    NARCIS (Netherlands)

    James, T.Y.; Kauff, F.; Schoch, C.L.; Matheny, P.B.; Hofstetter, V.; Cox, C.J.; Celio, G.; Gueidan, C.; Fraker, E.; Miadlikowska, J.; Lumbsch, H.T.; Rauhut, A.; Reeb, V.; Arnold, A.E.; Amtoft, A.; Stajich, J.E.; Hosaka, K.; Sung, G.H.; Johnson, D.; O'Rourke, B.; Binder, M.; Curtis, J.M.; Slot, J.C.; Wang, Z.; Wilson, A.W.; Schüßler, A.; Longcore, J.E.; O'Donnell, K.; Mozley-Standridge, S.; Porter, D.; Letcher, P.M.; Powell, M.J.; Taylor, J.W.; White, M.M.; Griffith, G.W.; Davies, D.R.; Sugiyama, J.; Rossman, A.Y.; Rogers, J.D.; Pfister, D.H.; Hewitt, D.; Hansen, K.; Hambleton, S.; Shoemaker, R.A.; Kohlmeyer, J.; Volkmann-Kohlmeyer, B.; Spotts, R.A.; Serdani, M.; Crous, P.W.; Hughes, K.W.; Matsuura, K.; Langer, E.; Langer, G.; Untereiner, W.A.; Lücking, R.; Büdel, B.; Geiser, D.M.; Aptroot, A.; Diederich, P.; Schmitt, I.; Schultz, M.; Yahr, R.; Hibbett, D.S.; Lutzoni, F.; McLaughlin, D.J.; Spatafora, J.W.; Vilgalys, R.

    2006-01-01

    The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore

  15. Molecular Phylogeny of the Parasitic Dinoflagellate Chytriodinium within the Gymnodinium Clade (Gymnodiniales, Dinophyceae).

    Science.gov (United States)

    Gómez, Fernando; Skovgaard, Alf

    2015-01-01

    The dinoflagellate genus Chytriodinium, an ectoparasite of copepod eggs, is reported for the first time in the North and South Atlantic Oceans. We provide the first large subunit rDNA (LSU rDNA) and Internal Transcribed Spacer 1 (ITS1) sequences, which were identical in both hemispheres for the Atlantic Chytriodinium sp. The first complete small subunit ribosomal DNA (SSU rDNA) of the Atlantic Chytriodinium sp. suggests that the specimens belong to an undescribed species. This is the first evidence of the split of the Gymnodinium clade: one for the parasitic forms of Chytriodiniaceae (Chytriodinium, Dissodinium), and other clade for the free-living species. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.

  16. SEXUALLY TRANSMITTED DISEASES - HISTORY, TYPES, PREVALENCE, EPIDEMIOLOGY

    Directory of Open Access Journals (Sweden)

    Valentin Irmov

    2017-12-01

    Full Text Available Sexually transmitted infections affect persons of active sex and cause serious consequences for the human organism, society and the generation. They spread sporadically, epidemically, and in some of them there are pandemics. For example, humanity is currently in a third viral hepatitis pandemic and a first AIDS pandemic. Another group of diseases can also be transmitted through sexual contact, but this is not the main mode of transmission. Such are salmonellosis, amoebiasis, influenza, various causes of meningitis and pneumonia. Despite being sexually transmitted, this is not a major and almost irrelevant way of transmitting the infection. Therefore, the diseases themselves are not included in the group of sexually transmitted diseases.

  17. The origin and early evolution of metatherian mammals: the Cretaceous record

    Directory of Open Access Journals (Sweden)

    Thomas E. Williamson

    2014-12-01

    Full Text Available Metatherians, which comprise marsupials and their closest fossil relatives, were one of the most dominant clades of mammals during the Cretaceous and are the most diverse clade of living mammals after Placentalia. Our understanding of this group has increased greatly over the past 20 years, with the discovery of new specimens and the application of new analytical tools. Here we provide a review of the phylogenetic relationships of metatherians with respect to other mammals, discuss the taxonomic definition and diagnosis of Metatheria, outline the Cretaceous history of major metatherian clades, describe the paleobiology, biogeography, and macroevolution of Cretaceous metatherians, and provide a physical and climatic background of Cretaceous metatherian faunas. Metatherians are a clade of boreosphendian mammals that must have originated by the Late Jurassic, but the first unequivocal metatherian fossil is from the Early Cretaceous of Asia. Metatherians have the distinctive tightly interlocking occlusal molar pattern of tribosphenic mammals, but differ from Eutheria in their dental formula and tooth replacement pattern, which may be related to the metatherian reproductive process which includes an extended period of lactation followed by birth of extremely altricial young. Metatherians were widespread over Laurasia during the Cretaceous, with members present in Asia, Europe, and North America by the early Late Cretaceous. In particular, they were taxonomically and morphologically diverse and relatively abundant in the Late Cretaceous of western North America, where they have been used to examine patterns of biogeography, macroevolution, diversification, and extinction through the Late Cretaceous and across the Cretaceous-Paleogene (K-Pg boundary. Metatherian diversification patterns suggest that they were not strongly affected by a Cretaceous Terrestrial Revolution, but they clearly underwent a severe extinction across the K-Pg boundary.

  18. Comparative Ability of Oropsylla montana and Xenopsylla cheopis Fleas to Transmit Yersinia pestis by Two Different Mechanisms.

    Directory of Open Access Journals (Sweden)

    B Joseph Hinnebusch

    2017-01-01

    Full Text Available Transmission of Yersinia pestis by flea bite can occur by two mechanisms. After taking a blood meal from a bacteremic mammal, fleas have the potential to transmit the very next time they feed. This early-phase transmission resembles mechanical transmission in some respects, but the mechanism is unknown. Thereafter, transmission occurs after Yersinia pestis forms a biofilm in the proventricular valve in the flea foregut. The biofilm can impede and sometimes completely block the ingestion of blood, resulting in regurgitative transmission of bacteria into the bite site. In this study, we compared the relative efficiency of the two modes of transmission for Xenopsylla cheopis, a flea known to become completely blocked at a high rate, and Oropsylla montana, a flea that has been considered to rarely develop proventricular blockage.Fleas that took an infectious blood meal containing Y. pestis were maintained and monitored for four weeks for infection and proventricular blockage. The number of Y. pestis transmitted by groups of fleas by the two modes of transmission was also determined. O. montana readily developed complete proventricular blockage, and large numbers of Y. pestis were transmitted by that mechanism both by it and by X. cheopis, a flea known to block at a high rate. In contrast, few bacteria were transmitted in the early phase by either species.A model system incorporating standardized experimental conditions and viability controls was developed to more reliably compare the infection, proventricular blockage and transmission dynamics of different flea vectors, and was used to resolve a long-standing uncertainty concerning the vector competence of O. montana. Both X. cheopis and O. montana are fully capable of transmitting Y. pestis by the proventricular biofilm-dependent mechanism.

  19. A dinosaur missing-link? Chilesaurus and the early evolution of ornithischian dinosaurs.

    Science.gov (United States)

    Baron, Matthew G; Barrett, Paul M

    2017-08-01

    The enigmatic dinosaur taxon Chilesaurus diegosuarezi was originally described as a tetanuran theropod, but this species possesses a highly unusual combination of features that could provide evidence of alternative phylogenetic positions within the clade. In order to test the relationships of Chilesaurus , we added it to a new dataset of early dinosaurs and other dinosauromorphs. Our analyses recover Chilesaurus in a novel position, as the earliest diverging member of Ornithischia, rather than a tetanuran theropod. The basal position of Chilesaurus within the clade and its suite of anatomical characters suggest that it might represent a 'transitional' taxon, bridging the morphological gap between Theropoda and Ornithischia, thereby offering potential insights into the earliest stages of ornithischian evolution, which were previously obscure. For example, our results suggest that pubic retroversion occurred prior to some of the craniodental and postcranial modifications that previously diagnosed the clade (e.g. the presence of a predentary bone and ossified tendons). © 2017 The Author(s).

  20. Repeated evolution of vertebrate pollination syndromes in a recently diverged Andean plant clade.

    Science.gov (United States)

    Lagomarsino, Laura P; Forrestel, Elisabeth J; Muchhala, Nathan; Davis, Charles C

    2017-08-01

    Although specialized interactions, including those involving plants and their pollinators, are often invoked to explain high species diversity, they are rarely explored at macroevolutionary scales. We investigate the dynamic evolution of hummingbird and bat pollination syndromes in the centropogonid clade (Lobelioideae: Campanulaceae), an Andean-centered group of ∼550 angiosperm species. We demonstrate that flowers hypothesized to be adapted to different pollinators based on flower color fall into distinct regions of morphospace, and this is validated by morphology of species with known pollinators. This supports the existence of pollination syndromes in the centropogonids, an idea corroborated by ecological studies. We further demonstrate that hummingbird pollination is ancestral, and that bat pollination has evolved ∼13 times independently, with ∼11 reversals. This convergence is associated with correlated evolution of floral traits within selective regimes corresponding to pollination syndrome. Collectively, our results suggest that floral morphological diversity is extremely labile, likely resulting from selection imposed by pollinators. Finally, even though this clade's rapid diversification is partially attributed to their association with vertebrate pollinators, we detect no difference in diversification rates between hummingbird- and bat-pollinated lineages. Our study demonstrates the utility of pollination syndromes as a proxy for ecological relationships in macroevolutionary studies of certain species-rich clades. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  1. Comparison of Monkeypox Virus Clade Kinetics and Pathology within the Prairie Dog Animal Model Using a Serial Sacrifice Study Design

    Directory of Open Access Journals (Sweden)

    Christina L. Hutson

    2015-01-01

    Full Text Available Monkeypox virus (MPXV infection of the prairie dog is valuable to studying systemic orthopoxvirus disease. To further characterize differences in MPXV clade pathogenesis, groups of prairie dogs were intranasally infected (8×103 p.f.u. with Congo Basin (CB or West African (WA MPXV, and 28 tissues were harvested on days 2, 4, 6, 9, 12, 17, and 24 postinfection. Samples were evaluated for the presence of virus and gross and microscopic lesions. Virus was recovered from nasal mucosa, oropharyngeal lymph nodes, and spleen earlier in CB challenged animals (day 4 than WA challenged animals (day 6. For both groups, primary viremia (indicated by viral DNA was seen on days 6–9 through day 17. CB MPXV spread more rapidly, accumulated to greater levels, and caused greater morbidity in animals compared to WA MPXV. Histopathology and immunohistochemistry (IHC findings, however, were similar. Two animals that succumbed to disease demonstrated abundant viral antigen in all organs tested, except for brain. Dual-IHC staining of select liver and spleen sections showed that apoptotic cells (identified by TUNEL tended to colocalize with poxvirus antigen. Interestingly splenocytes were labelled positive for apoptosis more often than hepatocytes in both MPXV groups. These findings allow for further characterization of differences between MPXV clade pathogenesis, including identifying sites that are important during early viral replication and cellular response to viral infection.

  2. Global cooling as a driver of diversification in a major marine clade

    Science.gov (United States)

    Davis, Katie E.; Hill, Jon; Astrop, Tim I.; Wills, Matthew A.

    2016-10-01

    Climate is a strong driver of global diversity and will become increasingly important as human influences drive temperature changes at unprecedented rates. Here we investigate diversification and speciation trends within a diverse group of aquatic crustaceans, the Anomura. We use a phylogenetic framework to demonstrate that speciation rate is correlated with global cooling across the entire tree, in contrast to previous studies. Additionally, we find that marine clades continue to show evidence of increased speciation rates with cooler global temperatures, while the single freshwater clade shows the opposite trend with speciation rates positively correlated to global warming. Our findings suggest that both global cooling and warming lead to diversification and that habitat plays a role in the responses of species to climate change. These results have important implications for our understanding of how extant biota respond to ongoing climate change and are of particular importance for conservation planning of marine ecosystems.

  3. Prototype of A/Duck/Sukoharjo/Bbvw-1428-9/2012 subtipe H5N1 clade 2.3.2 as vaccine on local duck

    Directory of Open Access Journals (Sweden)

    Risa Indriani

    2014-06-01

    Full Text Available A/Duck/Sukoharjo/Bbvw-1428-9/2012 virus subtipe H5N1 clade 2.3.2 as seed vaccine on local duck. AI H5N1 clade 2.3.2 vaccine containing 256 HAU per dose was formulated using adjuvant ISA 71VG Montanide ™. Six groups of one day old local duck were used in this study. Three groups (10 ducks per group were vaccinated and 3 groups (9 duck per group were served control. Vaccination was conducted when the duck were three weeks old of age using single dose. Three weeks after vaccination when the duck were challenged either with HPAI H5N1 clade 2.3.2, or HPAI H5N1 clade 2.1.3 virus at dose 106 EID50/ 0.1 ml by drops intranasaly. Result showed that vaccination produced 100% protection compared to unvaccinated ducks againt HPAI subtipe H5N1 clade 2.3.2, and 100% protection againt HPAI H5N1 clade 2.1.3 (A/ck/wj/Subang-29/2007 and A/ck/wj/Smi-Part/2006, while unvaccinated ducks showed virus shedding on day 3 post infection.

  4. SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes

    Directory of Open Access Journals (Sweden)

    Telonis-Scott Marina

    2010-09-01

    Full Text Available Abstract Background Vibrio vulnificus is the leading cause of reported death from consumption of seafood in the United States. Despite several decades of research on molecular pathogenesis, much remains to be learned about the mechanisms of virulence of this opportunistic bacterial pathogen. The two complete and annotated genomic DNA sequences of V. vulnificus belong to strains of clade 2, which is the predominant clade among clinical strains. Clade 2 strains generally possess higher virulence potential in animal models of disease compared with clade 1, which predominates among environmental strains. SOLiD sequencing of four V. vulnificus strains representing different clades (1 and 2 and biotypes (1 and 2 was used for comparative genomic analysis. Results Greater than 4,100,000 bases were sequenced of each strain, yielding approximately 100-fold coverage for each of the four genomes. Although the read lengths of SOLiD genomic sequencing were only 35 nt, we were able to make significant conclusions about the unique and shared sequences among the genomes, including identification of single nucleotide polymorphisms. Comparative analysis of the newly sequenced genomes to the existing reference genomes enabled the identification of 3,459 core V. vulnificus genes shared among all six strains and 80 clade 2-specific genes. We identified 523,161 SNPs among the six genomes. Conclusions We were able to glean much information about the genomic content of each strain using next generation sequencing. Flp pili, GGDEF proteins, and genomic island XII were identified as possible virulence factors because of their presence in virulent sequenced strains. Genomic comparisons also point toward the involvement of sialic acid catabolism in pathogenesis.

  5. A Ser29Leu substitution in the cytosine deaminase Fca1p is responsible for clade-specific flucytosine resistance in Candida dubliniensis.

    LENUS (Irish Health Repository)

    McManus, Brenda A

    2009-11-01

    The population structure of the opportunistic yeast pathogen Candida dubliniensis is composed of three main multilocus sequence typing clades (clades C1 to C3), and clade C3 predominantly consists of isolates from the Middle East that exhibit high-level resistance (MIC(50) > or = 128 microg\\/ml) to the fungicidal agent flucytosine (5FC). The close relative of C. dubliniensis, C. albicans, also exhibits clade-specific resistance to 5FC, and resistance is most commonly mediated by an Arg101Cys substitution in the FUR1 gene encoding uracil phosphoribosyltransferase. Broth microdilution assays with fluorouracil (5FU), the toxic deaminated form of 5FC, showed that both 5FC-resistant and 5FC-susceptible C. dubliniensis isolates exhibited similar 5FU MICs, suggesting that the C. dubliniensis cytosine deaminase (Fca1p) encoded by C. dubliniensis FCA1 (CdFCA1) may play a role in mediating C. dubliniensis clade-specific 5FC resistance. Amino acid sequence analysis of the CdFCA1 open reading frame (ORF) identified a homozygous Ser29Leu substitution in all 12 5FC-resistant isolates investigated which was not present in any of the 9 5FC-susceptible isolates examined. The tetracycline-inducible expression of the CdFCA1 ORF from a 5FC-susceptible C. dubliniensis isolate in two separate 5FC-resistant clade C3 isolates restored susceptibility to 5FC, demonstrating that the Ser29Leu substitution was responsible for the clade-specific 5FC resistance and that the 5FC resistance encoded by FCA1 genes with the Ser29Leu transition is recessive. Quantitative real-time PCR analysis showed no significant difference in CdFCA1 expression between 5FC-susceptible and 5FC-resistant isolates in either the presence or the absence of subinhibitory concentrations of 5FC, suggesting that the Ser29Leu substitution in the CdFCA1 ORF is the sole cause of 5FC resistance in clade C3 C. dubliniensis isolates.

  6. Mitochondrial molecular clocks and the origin of the major Otocephalan clades (Pisces: Teleostei)

    DEFF Research Database (Denmark)

    Peng, Zuogang; He, Shunping; Wang, Jun

    2006-01-01

    The Otocephala, a clade including ostariophysan and clupeomorph teleosts, represents about a quarter of total fish species diversity, with about 1000 genera and more than 7000 species. A series of recent papers have defended that the origin of this clade and of its major groups may be significantly...... otophysans could have originated before the splitting of the Pangean supercontinent is of extreme importance, since otophysan fishes are among the most useful animal groups for the determination of historical continental relationships. In the present work we examined divergence times for each major...... otocephalan group by an analysis of complete mtDNA sequences, in order to investigate if these divergence times support the hypotheses advanced in recent studies. The complete mtDNA sequences of nine representative non-otocephalan fish species and of twenty-one representative otocephalan species was compared...

  7. Sexually transmitted infections

    African Journals Online (AJOL)

    AJRH Managing Editor

    Sexually transmitted infections constitute economic burden for developing countries, exposure to causative agents is an occupational hazard ... In Nigeria, the deteriorating economic situation has led to ..... female sex workers from Mexico City.

  8. Effect of salt on the metabolism of 'Candidatus Accumulibacter' clade I and II

    NARCIS (Netherlands)

    Wang, Zhongwei; Dunne, Aislinn; van Loosdrecht, Mark C.M.; Saikaly, Pascal E.

    2018-01-01

    Saline wastewater is known to affect the performance of phosphate-accumulating organisms (PAOs) in enhanced biological phosphorus removal (EBPR) process. However, studies comparing the effect of salinity on different PAO clades are lacking. In this study, 'Candidatus Accumulibacter phosphatis'

  9. Taxonomy of the ant genus Proceratium Roger (Hymenoptera, Formicidae in the Afrotropical region with a revision of the P. arnoldi clade and description of four new species

    Directory of Open Access Journals (Sweden)

    Francisco Hita Garcia

    2014-10-01

    Full Text Available The taxonomy of the genus Proceratium Roger is updated for the Afrotropical region. We give an overview of the genus in the region, provide an illustrated identification key to the three clades (P. arnoldi, P. stictum and P. toschii clades and revise the P. arnoldi clade. Four new species from the P. arnoldi clade are described as new: P. sokoke sp. n. from Kenya, P. carri sp. n. from Mozambique, and P. nilo sp. n. and P. sali sp. n. from Tanzania. In order to integrate the new species into the existing taxonomic system we present an illustrated identification key to distinguish the seven Afrotropical species of the P. arnoldi clade. In addition, we provide accounts for all members of the P. arnoldi clade including detailed descriptions, diagnoses, taxonomic discussions, distribution data and high quality montage images.

  10. Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family.

    Science.gov (United States)

    Alnajar, Seema; Gupta, Radhey S

    2017-10-01

    The family Enterobacteriaceae harbors many important pathogens, however it has proven difficult to reliably distinguish different members of this family or discern their interrelationships. To understand the interrelationships among the Enterobacteriaceae species, we have constructed two comprehensive phylogenetic trees for 78 genome-sequenced Enterobacteriaceae species based on 2487 core genome proteins, and another set of 118 conserved proteins. The genome sequences of Enterobacteriaceae species were also analyzed for genetic relatedness based on average amino acid identity and 16S rRNA sequence similarity. In parallel, comparative genomic studies on protein sequences from the Enterobacteriaceae have identified 88 molecular markers in the form of conserved signature indels (CSIs) that are uniquely shared by specific members of the family. All of these multiple lines of investigations provide consistent evidence that most of the species/genera within the family can be assigned to 6 different subfamily level clades which are designated as the "Escherichia clade", "Klebsiella clade", "Enterobacter clade", "Kosakonia clade", "Cronobacter clade" and "Cedecea clade". The members of the six described clades, in addition to their distinct branching in phylogenetic trees, can now be reliably demarcated in molecular terms on the basis of multiple identified CSIs that are exclusively shared by the group members. Several additional CSIs identified in this work that are either specific for individual genera (viz. Kosakonia, Kluyvera and Escherichia-Shigella), or are present at various taxonomic depths, offer information regarding the interrelationships among the different clades. The described molecular markers provide novel means for diagnostic as well as genetic and biochemical studies on the Enterobacteriaceae species and for resolving the polyphyly of its several genera viz. Escherichia, Enterobacter and Kluyvera. On the bases of our results, we are proposing the

  11. Phylogeography of ostreopsis along west Pacific coast, with special reference to a novel clade from Japan.

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    Shinya Sato

    Full Text Available BACKGROUND: A dinoflagellate genus Ostreopsis is known as a potential producer of Palytoxin derivatives. Palytoxin is the most potent non-proteinaceous compound reported so far. There has been a growing number of reports on palytoxin-like poisonings in southern areas of Japan; however, the distribution of Ostreopsis has not been investigated so far. Morphological plasticity of Ostreopsis makes reliable microscopic identification difficult so the employment of molecular tools was desirable. METHODS/PRINCIPAL FINDING: In total 223 clones were examined from samples mainly collected from southern areas of Japan. The D8-D10 region of the nuclear large subunit rDNA (D8-D10 was selected as a genetic marker and phylogenetic analyses were conducted. Although most of the clones were unable to be identified, there potentially 8 putative species established during this study. Among them, Ostreopsis sp. 1-5 did not belong to any known clade, and each of them formed its own clade. The dominant species was Ostreopsis sp. 1, which accounted for more than half of the clones and which was highly toxic and only distributed along the Japanese coast. Comparisons between the D8-D10 and the Internal Transcribed Spacer (ITS region of the nuclear rDNA, which has widely been used for phylogenetic/phylogeographic studies in Ostreopsis, revealed that the D8-D10 was less variable than the ITS, making consistent and reliable phylogenetic reconstruction possible. CONCLUSIONS/SIGNIFICANCE: This study unveiled a surprisingly diverse and widespread distribution of Japanese Ostreopsis. Further study will be required to better understand the phylogeography of the genus. Our results posed the urgent need for the development of the early detection/warning systems for Ostreopsis, particularly for the widely distributed and strongly toxic Ostreopsis sp. 1. The D8-D10 marker will be suitable for these purposes.

  12. Detection and Characterization of Clade 1 Reassortant H5N1 Viruses Isolated from Human Cases in Vietnam during 2013.

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    Sharmi W Thor

    Full Text Available Highly pathogenic avian influenza (HPAI H5N1 is endemic in Vietnamese poultry and has caused sporadic human infection in Vietnam since 2003. Human infections with HPAI H5N1 are of concern due to a high mortality rate and the potential for the emergence of pandemic viruses with sustained human-to-human transmission. Viruses isolated from humans in southern Vietnam have been classified as clade 1 with a single genome constellation (VN3 since their earliest detection in 2003. This is consistent with detection of this clade/genotype in poultry viruses endemic to the Mekong River Delta and surrounding regions. Comparison of H5N1 viruses detected in humans from southern Vietnamese provinces during 2012 and 2013 revealed the emergence of a 2013 reassortant virus with clade 1.1.2 hemagglutinin (HA and neuraminidase (NA surface protein genes but internal genes derived from clade 2.3.2.1a viruses (A/Hubei/1/2010-like; VN12. Closer analysis revealed mutations in multiple genes of this novel genotype (referred to as VN49 previously associated with increased virulence in animal models and other markers of adaptation to mammalian hosts. Despite the changes identified between the 2012 and 2013 genotypes analyzed, their virulence in a ferret model was similar. Antigenically, the 2013 viruses were less cross-reactive with ferret antiserum produced to the clade 1 progenitor virus, A/Vietnam/1203/2004, but reacted with antiserum produced against a new clade 1.1.2 WHO candidate vaccine virus (A/Cambodia/W0526301/2012 with comparable hemagglutination inhibition titers as the homologous antigen. Together, these results indicate changes to both surface and internal protein genes of H5N1 viruses circulating in southern Vietnam compared to 2012 and earlier viruses.

  13. Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae.

    Science.gov (United States)

    Straub, Shannon C K; Moore, Michael J; Soltis, Pamela S; Soltis, Douglas E; Liston, Aaron; Livshultz, Tatyana

    2014-11-01

    Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way polytomy, leaving ambiguous the homology of aggregated pollen in two major lineages, the Periplocoideae, which possess pollen tetrads, and the milkweeds (Secamonoideae plus Asclepiadoideae), which possess pollinia. To assess whether greatly increased character sampling would resolve these relationships, a plastome sequence data matrix was assembled for 13 taxa of Apocynaceae, including nine newly generated complete plastomes, one partial new plastome, and three previously reported plastomes, collectively representing all primary crown clade lineages and outgroups. The effects of phylogenetic noise, long-branch attraction, and model selection (linked versus unlinked branch lengths among data partitions) were evaluated in a hypothesis-testing framework based on Shimodaira-Hasegawa tests. Discrimination among alternative crown clade resolutions was affected by all three factors. Exclusion of the noisiest alignment positions and topologies influenced by long-branch attraction resulted in a trichotomy along the spine of the crown clade consisting of Rhabdadenia+the Asian clade, Baisseeae+milkweeds, and Periplocoideae+the New World clade. Parsimony reconstruction on all optimal topologies after noise exclusion unambiguously supports parallel evolution of aggregated pollen in Periplocoideae (tetrads) and milkweeds (pollinia). Our phylogenomic approach has greatly advanced the resolution of one of the most perplexing radiations in Apocynaceae, providing the

  14. Phylogeny of Elatinaceae and the Tropical Gondwanan Origin of the Centroplacaceae(Malpighiaceae, Elatinaceae Clade.

    Directory of Open Access Journals (Sweden)

    Liming Cai

    Full Text Available The flowering plant family Elatinaceae is a widespread aquatic lineage inhabiting temperate and tropical latitudes, including ∼35(-50 species. Its phylogeny remains largely unknown, compromising our understanding of its systematics. Moreover, this group is particularly in need of attention because the biogeography of most aquatic plant clades has yet to be investigated, resulting in uncertainty about whether aquatic plants show histories that deviate from terrestrial plants. We inferred the phylogeny of Elatinaceae from four DNA regions spanning 59 accessions across the family. An expanded sampling was used for molecular divergence time estimation and ancestral area reconstruction to infer the biogeography of Elatinaceae and their closest terrestrial relatives, Malpighiaceae and Centroplacaceae. The two genera of Elatinaceae, Bergia and Elatine, are monophyletic, but several traditionally recognized groups within the family are non-monophyletic. Our results suggest two ancient biogeographic events in the Centroplacaceae(Malpighiaceae, Elatinaceae clade involving western Gondwana, while Elatinaceae shows a more complicated biogeographic history with a high degree of continental endemicity. Our results indicate the need for further taxonomic investigation of Elatinaceae. Further, our study is one of few to implicate ancient Gondwanan biogeography in extant angiosperms, especially significant given the Centroplacaceae(Malpighiaceae, Elatinaceae clade's largely tropical distribution. Finally, Elatinaceae demonstrates long-term continental in situ diversification, which argues against recent dispersal as a universal explanation commonly invoked for aquatic plant distributions.

  15. Into the Himalayan Exile: The Phylogeography of the Ground Beetle Ethira clade Supports the Tibetan Origin of Forest-Dwelling Himalayan Species Groups

    Science.gov (United States)

    Schmidt, Joachim; Opgenoorth, Lars; Höll, Steffen; Bastrop, Ralf

    2012-01-01

    The Himalayan mountain arc is one of the hotspots of biodiversity on earth, and species diversity is expected to be especially high among insects in this region. Little is known about the origin of the Himalayan insect fauna. With respect to the fauna of high altitude cloud forests, it has generally been accepted that Himalayan lineages are derived from ancestors that immigrated from Western Asia and from adjacent mountainous regions of East and Southeast Asia (immigration hypothesis). In this study, we sought to test a Tibetan Origin as an alternative hypothesis for groups with a poor dispersal ability through a phylogeographic analysis of the Ethira clade of the genus Pterostichus. We sequenced COI mtDNA and the 18S and 28S rDNA genes in 168 Pterostichini specimens, including 46 species and subspecies of the Ethira clade. In our analysis, we were able to show that the Ethira clade is monophyletic and, thus, represents a Himalayan endemic clade, supporting endemism of two of the basal lineages to the Central Himalaya and documenting large distributional gaps within the phylogeographic structure of the Ethira clade. Furthermore, the molecular data strongly indicate very limited dispersal abilities of species and subspecies of these primary wingless ground beetles. These results are consistent with the hypothesis of a Tibetan Origin, which explains the evolution, diversity and distribution of the Himalayan ground beetle Ethira clade much more parsimoniously than the original immigration hypothesis. PMID:23049805

  16. EVOLUTION OF NUCLEAR RDNA ITS SEQUENCES IN THE CLADOPHORA ALBIDA/SERICEA CLADE (CHLOROPHYTA)

    NARCIS (Netherlands)

    BAKKER, FT; OLSEN, JL; STAM, WT

    Ribosomal DNA ITS sequences were compared among 13 different species and biogeographic isolates from the monophyletic ''abbida/sericea clade'' in the green algal genus Cladophora. Six distinct ITS sequence types were found, characterized by multiple insertions and deletions and high levels of

  17. Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

    Science.gov (United States)

    Gao, Beile

    2012-01-01

    Summary: The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria. PMID:22390973

  18. Revision of the Middle American clade of the ant genus Stenamma Westwood (Hymenoptera, Formicidae, Myrmicinae

    Directory of Open Access Journals (Sweden)

    Michael Branstetter

    2013-04-01

    Full Text Available Stenamma is a cryptic “leaf-litter” ant genus that occurs in mesic forest habitats throughout the Holarctic region, Central America, and part of northwestern South America (Colombia and Ecuador. The genus was thought to be restricted primarily to the temperate zone, but recent collecting efforts have uncovered a large radiation of Neotropical forms, which rival the Holarctic species in terms of morphological and behavioral diversity. By inferring a broad-scale molecular phylogeny of Stenamma, Branstetter (2012 showed that all Neotropical species belong to a diverse Middle American clade (MAC, and that this clade is sister to an almost completely geographically separated Holarctic clade (HOC. Here, the Middle American clade of Stenamma is revised to recognize 40 species, of which 33 are described as new. Included in the revision are a key to species based on the worker caste, and for each species where possible, descriptions and images of workers and queens, images of males, information on geographic distribution, descriptions of intraspecific variation, and notes on natural history. Several species groups are defined, but the majority of species remain unassigned due to a lack of diagnostic morphological character states for most molecular clades. The following species are redescribed: S. alas Longino, S. diversum Mann, S. expolitum Smith, S. felixi Mann, S. huachucanum Smith, S. manni Wheeler, and S. schmidti Menozzi. The following are described as new: S. andersoni sp. n., S. atribellum sp. n., S. brujita sp. n., S. callipygium sp. n., S. catracho sp. n., S. connectum sp. n., S. crypticum sp. n., S. cusuco sp. n., S. excisum sp. n., S. expolitico sp. n., S. hojarasca sp. n., S. ignotum sp. n., S. lagunum sp. n., S. llama sp. n., S. leptospinum sp. n., S. lobinodus sp. n., S. longinoi sp. n., S. maximon sp. n., S. megamanni sp. n., S. monstrosum sp. n., S. muralla sp. n., S. nanozoi sp. n., S. nonotch sp. n., S. ochrocnemis sp. n., S

  19. Macroevolutionary dynamics in the early diversification of Asteraceae.

    Science.gov (United States)

    Panero, Jose L; Crozier, Bonnie S

    2016-06-01

    Spatial and temporal differences in ecological opportunity can result in disparity of net species diversification rates and consequently uneven distribution of taxon richness across the tree of life. The largest eudicotyledonous plant family Asteraceae has a global distribution and at least 460 times more species than its South American endemic sister family Calyceraceae. In this study, diversification rate dynamics across Asteraceae are examined in light of the several hypothesized causes for the family's evolutionary success that could be responsible for rate change. The innovations of racemose capitulum and pappus, and a whole genome duplication event occurred near the origin of the family, yet we found the basal lineages of Asteraceae that evolved in South America share background diversification rates with Calyceraceae and their Australasian sister Goodeniaceae. Instead we found diversification rates increased gradually from the origin of Asteraceae approximately 69.5Ma in the late Cretaceous through the Early Eocene Climatic Optimum at least. In contrast to earlier studies, significant rate shifts were not strongly correlated with intercontinental dispersals or polyploidization. The difference is due primarily to sampling more backbone nodes, as well as calibrations placed internally in Asteraceae that resulted in earlier divergence times than those found in most previous relaxed clock studies. Two clades identified as having transformed rate processes are the Vernonioid Clade and a clade within the Heliantheae alliance characterized by phytomelanic fruit (PF Clade) that represents an American radiation. In Africa, subfamilies Carduoideae, Pertyoideae, Gymnarrhenoideae, Cichorioideae, Corymbioideae, and Asteroideae diverged in a relatively short span of only 6.5millionyears during the Middle Eocene. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. The effect of abortion legalization on sexual behavior: evidence from sexually transmitted diseases.

    Science.gov (United States)

    Klick, Jonathan; Stratmann, Thomas

    2003-06-01

    Unwanted pregnancy represents a major cost of sexual activity. When abortion was legalized in a number of states in 1969 and 1970 (and nationally in 1973), this cost was reduced. We predict that abortion legalization generated incentives leading to an increase in sexual activity, accompanied by an increase in sexually transmitted diseases (STDs). Using Centers for Disease Control data on the incidence of gonorrhea and syphilis by state, we test the hypothesis that abortion legalization led to an increase in sexually transmitted diseases. We find that gonorrhea and syphilis incidences are significantly and positively correlated with abortion legalization. Further, we find a divergence in STD rates among early legalizing states and late legalizing states starting in 1970 and a subsequent convergence after the Roe v. Wade decision, indicating that the relation between STDs and abortion is casual. Abortion legalization accounts for about one-fourth of the average disease incidence.

  1. Vaginal microbiota and viral sexually transmitted diseases.

    Science.gov (United States)

    Nardis, C; Mosca, L; Mastromarino, P

    2013-01-01

    Healthy vaginal microbiota is an important biological barrier to pathogenic microorganisms. When this predominantly Lactobacillus community is disrupted, decreased in abundance and replaced by different anaerobes, bacterial vaginosis (BV) may occur. BV is associated with prevalence and incidence of several sexually transmitted infections. This review provides background on BV, discusses the epidemiologic data to support a role of altered vaginal microbiota for acquisition of sexually transmitted diseases and analyzes mechanisms by which lactobacilli could counteract sexually transmitted viral infections.

  2. Dynamic facial expressions of emotion transmit an evolving hierarchy of signals over time.

    Science.gov (United States)

    Jack, Rachael E; Garrod, Oliver G B; Schyns, Philippe G

    2014-01-20

    Designed by biological and social evolutionary pressures, facial expressions of emotion comprise specific facial movements to support a near-optimal system of signaling and decoding. Although highly dynamical, little is known about the form and function of facial expression temporal dynamics. Do facial expressions transmit diagnostic signals simultaneously to optimize categorization of the six classic emotions, or sequentially to support a more complex communication system of successive categorizations over time? Our data support the latter. Using a combination of perceptual expectation modeling, information theory, and Bayesian classifiers, we show that dynamic facial expressions of emotion transmit an evolving hierarchy of "biologically basic to socially specific" information over time. Early in the signaling dynamics, facial expressions systematically transmit few, biologically rooted face signals supporting the categorization of fewer elementary categories (e.g., approach/avoidance). Later transmissions comprise more complex signals that support categorization of a larger number of socially specific categories (i.e., the six classic emotions). Here, we show that dynamic facial expressions of emotion provide a sophisticated signaling system, questioning the widely accepted notion that emotion communication is comprised of six basic (i.e., psychologically irreducible) categories, and instead suggesting four. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Antigenic Variation in H5N1 clade 2.1 Viruses in Indonesia from 2005 to 2011

    Directory of Open Access Journals (Sweden)

    Vivi Setiawaty

    2013-01-01

    Full Text Available Influenza A (H5N1 virus, has spread to several countries in the world and has a high mortality rate. Meanwhile, the virus has evolved into several clades. The human influenza A (H5N1 virus circulating in Indonesia is a member of clade 2.1, which is different in antigenicity from other clades of influenza A (H5N1. An analysis of the antigenic variation in the H5 hemagglutinin gene (HA of the influenza A (H5N1 virus strains circulating in Indonesia has been undertaken. Several position of amino acid mutations, including mutations at positions 35, 53, 141, 145, 163, 174, 183, 184, 189, and 231, have been identified. The mutation Val-174-Iso appears to play an important role in immunogenicity and cross-reactivity with rabbit antisera. This study shows that the evolution of the H5HA antigenic variation of the influenza A (H5N1 virus circulating in Indonesia from 2005 to 2011 may affect the immunogenicity of the virus.

  4. Sexually transmitted diseases among psychiatric patients in Brazil.

    Science.gov (United States)

    Dutra, Maria Rita Teixeira; Campos, Lorenza Nogueira; Guimarães, Mark Drew Crosland

    2014-01-01

    Sexually transmitted diseases are still highly prevalent worldwide and represent an important public health problem. Psychiatric patients are at increased risk of sexually transmitted diseases but there are scarce published studies with representative data of this population. We sought to estimate the prevalence and correlates of self-reported sexually transmitted diseases among patients with mental illnesses under care in a national representative sample in Brazil (n=2145). More than one quarter of the sample (25.8%) reported a lifetime history of sexually transmitted disease. Multivariate analyses showed that patients with a lifetime sexually transmitted disease history were older, had history of homelessness, used more alcohol and illicit drugs, suffered violence, perceived themselves to be at greater risk for HIV and had high risk sexual behavioral: practised unprotected sex, started sexual life earlier, had more than ten sexual partners, exchanged money and/or drugs for sex and had a partner that refused to use condom. Our findings indicate a high prevalence of self-reported sexually transmitted diseases among psychiatric patients in Brazil, and emphasize the need for implementing sexually transmitted diseases prevention programs in psychiatric settings, including screening, treatment, and behavioral modification interventions. Copyright © 2013 Elsevier Editora Ltda. All rights reserved.

  5. Evolutionary history of Otophysi (Teleostei, a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

    Directory of Open Access Journals (Sweden)

    Saitoh Kenji

    2011-06-01

    Full Text Available Abstract Background Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp. and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families. Results Partitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi. The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes, and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei was more closely related to Siluriformes than to its own suborder (Citharinoidei, rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans. Conclusions The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the

  6. Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation.

    Science.gov (United States)

    Nakatani, Masanori; Miya, Masaki; Mabuchi, Kohji; Saitoh, Kenji; Nishida, Mutsumi

    2011-06-22

    Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families. Partitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp) confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi). The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes), and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei) was more closely related to Siluriformes than to its own suborder (Citharinoidei), rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans. The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the early Cretaceous 100-112 Ma, creating an over 100

  7. Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade.

    Science.gov (United States)

    Lo, Pei-Chun; Liu, Shu-Hui; Nor, Siti Azizah Mohd; Chen, Wei-Jen

    2017-01-01

    The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species) from one nuclear gene (RAG1) and one mitochondrial gene (COI); the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species); and the dataset with only COI gene sequences (308 samples from 51 currently recognized species). The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC). The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology). Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and suggested a

  8. Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade.

    Directory of Open Access Journals (Sweden)

    Pei-Chun Lo

    Full Text Available The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species from one nuclear gene (RAG1 and one mitochondrial gene (COI; the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species; and the dataset with only COI gene sequences (308 samples from 51 currently recognized species. The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC. The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology. Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and

  9. Molecular phylogeny and ecological diversification in a clade of New World songbirds (genus Vireo).

    Science.gov (United States)

    Cicero, C; Johnson, N K

    1998-10-01

    We constructed a molecular phylogeny for a clade of eye-ringed vireos (Vireo flavifrons and the V. solitarius complex) to examine existing hypotheses of speciation and ecological diversification. Complete sequences of the mtDNA cytochrome b gene were obtained from 47 individuals of this group plus four vireonid outgroups. Mean levels of sequence divergence in the clade varied from 0.29% to 5.7%. Differences were greatest between V. flavifrons and four taxa of 'V. solitarius'. The latter separated into three taxonomic, geographical and ecological groups: V. plumbeus plumbeus, V. cassinii cassinii, and V. solitarius solitarius plus V. solitarius alticola. These differed by an average of 2.6-3.2%. Populations within each group revealed low levels of sequence variation (x = 0.20%) and little geographical structuring. The mtDNA data generally corroborate results from allozymes. V. plumbeus shows a loss of yellow-green carotenoid pigmentation from the ancestral condition. The occupancy of relatively dry habitats by this species and V. cassinii represents a derived ecological shift from more-humid environments occupied by other species of vireonids. Ecological divergence in this clade occurred in allopatry and is associated with generic-level stability in morphometrics and foraging styles. Migratory behaviour and seasonal habitat shifts apparently evolved multiple times in vireos breeding in temperate environments. Present geographical and ecological distributions, and low levels of intrataxon genetic divergence, are hypothesized to be the result of postglacial regionalization of climate-plant associations and rapid northward expansion of breeding ranges.

  10. Characterization of the denitrification-associated phosphorus uptake properties of "Candidatus Accumulibacter phosphatis" clades in sludge subjected to enhanced biological phosphorus removal.

    Science.gov (United States)

    Kim, Jeong Myeong; Lee, Hyo Jung; Lee, Dae Sung; Jeon, Che Ok

    2013-03-01

    To characterize the denitrifying phosphorus (P) uptake properties of "Candidatus Accumulibacter phosphatis," a sequencing batch reactor (SBR) was operated with acetate. The SBR operation was gradually acclimated from anaerobic-oxic (AO) to anaerobic-anoxic-oxic (A2O) conditions by stepwise increases of nitrate concentration and the anoxic time. The communities of "Ca. Accumulibacter" and associated bacteria at the initial (AO) and final (A2O) stages were compared using 16S rRNA and polyphosphate kinase genes and using fluorescence in situ hybridization (FISH). The acclimation process led to a clear shift in the relative abundances of recognized "Ca. Accumulibacter" subpopulations from clades IIA > IA > IIF to clades IIC > IA > IIF, as well as to increases in the abundance of other associated bacteria (Dechloromonas [from 1.2% to 19.2%] and "Candidatus Competibacter phosphatis" [from 16.4% to 20.0%]), while the overall "Ca. Accumulibacter" abundance decreased (from 55.1% to 29.2%). A series of batch experiments combined with FISH/microautoradiography (MAR) analyses was performed to characterize the denitrifying P uptake properties of the "Ca. Accumulibacter" clades. In FISH/MAR experiments using slightly diluted sludge (∼0.5 g/liter), all "Ca. Accumulibacter" clades successfully took up phosphorus in the presence of nitrate. However, the "Ca. Accumulibacter" clades showed no P uptake in the presence of nitrate when the sludge was highly diluted (∼0.005 g/liter); under these conditions, reduction of nitrate to nitrite did not occur, whereas P uptake by "Ca. Accumulibacter" clades occurred when nitrite was added. These results suggest that the "Ca. Accumulibacter" cells lack nitrate reduction capabilities and that P uptake by "Ca. Accumulibacter" is dependent upon nitrite generated by associated nitrate-reducing bacteria such as Dechloromonas and "Ca. Competibacter."

  11. Lower Cambrian biogeography and the prehistory of early animals

    Energy Technology Data Exchange (ETDEWEB)

    Signor, P.W. (Univ. of California, Davis (United States))

    1991-02-01

    Biogeographic distributions of animals reflect the complex interplay of biological and physical processes acting over geological time. In particular, plate tectonics and the evolution of lineages within clades play fundamental roles in determining faunal distributions. Ranges expand through vicariant events or dispersal and contract through local and regional extinctions. Vicariance promotes the evolutionary divergence of closely related lineages. Viewed as historical phenomena, biogeographic distributions can be employed to infer prior tectonic and evolutionary events. For example, the existence of modern marine faunal provinces reflects the interaction of evolution and plate tectonics. The Proterozoic history of skeletogenous organisms (and their ancestors) is a contentious subject, with many authors arguing that skeletogenous clades have no significant prehistory before their appearance in the fossil record. The existence of trilobite provinces dominated by different suborders, for example, suggests the trilobites evolved and dispersed, or were separated by plate movement, and then evolved independently for an extended period prior to their appearance in the fossil record. Similar arguments can be applied to other groups. The paleobiogeographic distribution of organisms also provides useful insights into late Proterozoic and Early Cambrian paleogeography. The provincial distribution of Early Cambrian taxa suggests that the putative Proterozoic supercontinent, if it existed, began to separate well before the Early Cambrian. Separate provinces would not have evolved had the various plates remained united. Therefore, the dawn of the Phanerozoic could not have coincided with the breakup of the Proterozoic supercontinent.

  12. Evolution of the apomixis transmitting chromosome in Pennisetum

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    Yamada-Akiyama Hitomi

    2011-10-01

    Full Text Available Abstract Background Apomixis is an intriguing trait in plants that results in maternal clones through seed reproduction. Apomixis is an elusive, but potentially revolutionary, trait for plant breeding and hybrid seed production. Recent studies arguing that apomicts are not evolutionary dead ends have generated further interest in the evolution of asexual flowering plants. Results In the present study, we investigate karyotypic variation in a single chromosome responsible for transmitting apomixis, the Apospory-Specific Genomic Region carrier chromosome, in relation to species phylogeny in the genera Pennisetum and Cenchrus. A 1 kb region from the 3' end of the ndhF gene and a 900 bp region from trnL-F were sequenced from 12 apomictic and eight sexual species in the genus Pennisetum and allied genus Cenchrus. An 800 bp region from the Apospory-Specific Genomic Region also was sequenced from the 12 apomicts. Molecular cytological analysis was conducted in sixteen Pennisetum and two Cenchrus species. Our results indicate that the Apospory-Specific Genomic Region is shared by all apomictic species while it is absent from all sexual species or cytotypes. Contrary to our previous observations in Pennisetum squamulatum and Cenchrus ciliaris, retrotransposon sequences of the Opie-2-like family were not closely associated with the Apospory-Specific Genomic Region in all apomictic species, suggesting that they may have been accumulated after the Apospory-Specific Genomic Region originated. Conclusions Given that phylogenetic analysis merged Cenchrus and newly investigated Pennisetum species into a single clade containing a terminal cluster of Cenchrus apomicts, the presumed monophyletic origin of Cenchrus is supported. The Apospory-Specific Genomic Region likely preceded speciation in Cenchrus and its lateral transfer through hybridization and subsequent chromosome repatterning may have contributed to further speciation in the two genera.

  13. Soil transmitted helminths and schistosoma mansoni infections among school children in Zarima town, northwest Ethiopia.

    Science.gov (United States)

    Alemu, Abebe; Atnafu, Asmamaw; Addis, Zelalem; Shiferaw, Yitayal; Teklu, Takele; Mathewos, Biniam; Birhan, Wubet; Gebretsadik, Simon; Gelaw, Baye

    2011-07-09

    In Ethiopia, because of low quality drinking water supply and latrine coverage, helminths infections are the second most predominant causes of outpatient morbidity. Indeed, there is a scarcity of information on the prevalence of soil transmitted helminths and Schistosomiasis in Ethiopia, special in study area. Therefore, the aim of this study was to determine the prevalence and associated risk factors of soil transmitted helminths and intestinal Schistosomiasis. Cross-sectional study was conducted among 319 school children of Zarima town from April 1 to May 25, 2009. A pre-tested structured questionnaire was used to collect socio-demographic data and possible risk factors exposure. Early morning stool samples were collected and a Kato Katz semi concentration technique was used to examine and count parasitic load by compound light microscope. Data entry and analysis was done using SPSS-15 version and p-value transmitted helminths, Ascaris lumbricoides was the predominant isolate (22%) followed by Hookworms (19%) and Trichuris trichiura (2.5%). Schistosoma mansoni was also isolated in 37.9% of the study participants. Hookworm and S. mansoni infections showed statistically significant associations with shoe wearing and swimming habit of school children, respectively. Prevalence of soil transmitted helminths (STH) and S.mansoni was high and the diseases were still major health problem in the study area which alerts public health intervention as soon as possible.

  14. Pelagic larval duration predicts extinction risk in a freshwater fish clade

    OpenAIRE

    Douglas, Morgan; Keck, Benjamin P.; Ruble, Crystal; Petty, Melissa; Shute, J. R.; Rakes, Patrick; Hulsey, C. Darrin

    2013-01-01

    Pelagic larval duration (PLD) can influence evolutionary processes ranging from dispersal to extinction in aquatic organisms. Using estimates of PLD obtained from species of North American darters (Percidae: Etheostomatinae), we demonstrate that this freshwater fish clade exhibits surprising variation in PLD. Comparative analyses provide some evidence that higher stream gradients favour the evolution of shorter PLD. Additionally, similar to patterns in the marine fossil record in which lower ...

  15. Detection and genomic characterization of motility in Lactobacillus curvatus: confirmation of motility in a species outside the Lactobacillus salivarius clade.

    Science.gov (United States)

    Cousin, Fabien J; Lynch, Shónagh M; Harris, Hugh M B; McCann, Angela; Lynch, Denise B; Neville, B Anne; Irisawa, Tomohiro; Okada, Sanae; Endo, Akihito; O'Toole, Paul W

    2015-02-01

    Lactobacillus is the largest genus within the lactic acid bacteria (LAB), with almost 180 species currently identified. Motility has been reported for at least 13 Lactobacillus species, all belonging to the Lactobacillus salivarius clade. Motility in lactobacilli is poorly characterized. It probably confers competitive advantages, such as superior nutrient acquisition and niche colonization, but it could also play an important role in innate immune system activation through flagellin–Toll-like receptor 5 (TLR5) interaction. We now report strong evidence of motility in a species outside the L. salivarius clade, Lactobacillus curvatus (strain NRIC0822). The motility of L. curvatus NRIC 0822 was revealed by phase-contrast microscopy and soft-agar motility assays. Strain NRIC 0822 was motile at temperatures between 15 °C and 37 °C, with a range of different carbohydrates, and under varying atmospheric conditions. We sequenced the L. curvatus NRIC 0822 genome, which revealed that the motility genes are organized in a single operon and that the products are very similar (>98.5% amino acid similarity over >11,000 amino acids) to those encoded by the motility operon of Lactobacillus acidipiscis KCTC 13900 (shown for the first time to be motile also). Moreover, the presence of a large number of mobile genetic elements within and flanking the motility operon of L. curvatus suggests recent horizontal transfer between members of two distinct Lactobacillus clades: L. acidipiscis in the L. salivarius clade and L. curvatus inthe L. sakei clade. This study provides novel phenotypic, genetic, and phylogenetic insights into flagellum-mediated motility in lactobacilli.

  16. Full-Genome Sequence of a Novel Varicella-Zoster Virus Clade Isolated in Mexico

    OpenAIRE

    Garc?s-Ayala, Fabiola; Rodr?guez-Castillo, Araceli; Ortiz-Alc?ntara, Joanna Mar?a; Gonzalez-Dur?n, Elizabeth; Segura-Candelas, Jos? Miguel; P?rez-Ag?eros, Sandra Ivette; Escobar-Escamilla, No?; M?ndez-Tenorio, Alfonso; Diaz-Qui?onez, Jos? Alberto; Ramirez-Gonz?lez, Jos? Ernesto

    2015-01-01

    Varicella-zoster virus (VZV) is a member of the Herpesviridae family, which causes varicella (chicken pox) and herpes zoster (shingles) in humans. Here, we report the complete genome sequence of varicella-zoster virus, isolated from a vesicular fluid sample, revealing the circulation of VZV clade VIII in Mexico.

  17. Molecular phylogeny of the parasitic dinoflagellate Chytriodinium within the Gymnodinium clade (Gymnodiniales, Dinophyceae)

    DEFF Research Database (Denmark)

    Gómez, Fernando; Skovgaard, Alf

    2015-01-01

    for the Atlantic Chytriodinium sp. The first complete small subunit ribosomal DNA (SSU rDNA) of the Atlantic Chytriodinium sp. suggests that the specimens belong to an undescribed species. This is the first evidence of the split of the Gymnodinium clade: one for the parasitic forms of Chytriodiniaceae...

  18. Impacts of Abstinence Education on Teen Sexual Activity, Risk of Pregnancy, and Risk of Sexually Transmitted Diseases

    Science.gov (United States)

    Trenholm, Christopher; Devaney, Barbara; Fortson, Kenneth; Clark, Melissa; Bridgespan, Lisa Quay; Wheeler, Justin

    2008-01-01

    This paper examines the impacts of four abstinence-only education programs on adolescent sexual activity and risks of pregnancy and sexually transmitted diseases (STDs). Based on an experimental design, the impact analysis uses survey data collected in 2005 and early 2006 from more than 2,000 teens who had been randomly assigned to either a…

  19. Production of sophorolipids biosurfactants by multiple species of the Starmerella (Candida) bombicola yeast clade

    Science.gov (United States)

    Sophorolipid production was tested for 26 strains representing 19 species of the Starmerella yeast clade, including S. bombicola and Candida apicola, which were previously reported to produce sophorolipids. Five of the 19 species tested showed significant production of sophorolipids: S. bombicola, ...

  20. Pollen morphology within the Monodora clade, a diverse group of five African Annonaceae genera

    NARCIS (Netherlands)

    Couvreur, T.L.P.; Botermans, M.; Heuven, Van B.J.; Ham, van der R.W.J.M.

    2008-01-01

    Pollen morphology has played a major role in elucidating infrafamiliar-level systematics and evolution within Annonaceae, especially within the African genera. The Monodora clade is composed of five genera, Asteranthe, Hexalobus, Isolona, Monodora and Uvariastrum, which are restricted to Africa and

  1. Full-Genome Sequence of a Novel Varicella-Zoster Virus Clade Isolated in Mexico

    Science.gov (United States)

    Rodríguez-Castillo, Araceli; Ortiz-Alcántara, Joanna María; Gonzalez-Durán, Elizabeth; Segura-Candelas, José Miguel; Pérez-Agüeros, Sandra Ivette; Escobar-Escamilla, Noé; Méndez-Tenorio, Alfonso; Diaz-Quiñonez, José Alberto

    2015-01-01

    Varicella-zoster virus (VZV) is a member of the Herpesviridae family, which causes varicella (chicken pox) and herpes zoster (shingles) in humans. Here, we report the complete genome sequence of varicella-zoster virus, isolated from a vesicular fluid sample, revealing the circulation of VZV clade VIII in Mexico. PMID:26159533

  2. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

    NARCIS (Netherlands)

    Aflitos, S.A.; Schijlen, E.G.W.M.; Jong, de J.H.S.G.M.; Ridder, de D.; Smit, S.; Finkers, H.J.; Bakker, F.T.; Geest, van de H.C.; Lintel Hekkert, te B.; Haarst, van J.C.; Smits, L.W.M.; Koops, A.J.; Sanchez-Perez, M.J.; Heusden, van A.W.; Visser, R.G.F.; Schranz, M.E.; Peters, S.A.

    2014-01-01

    We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon, and Neolycopersicon groups which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new

  3. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

    NARCIS (Netherlands)

    Aflitos, S.; Schijlen, E.; de Jong, H.; de Ridder, D.; Smit, S.; Finkers, R.; Wang, J.; Zhang, G.; Li, N.; Mao, L.; Bakker, F.; Dirks, R.; Breit, T.; Gravendeel, B.; Huits, H.; Struss, D.; Swanson-Wagner, R.; van Leeuwen, H.; van Ham, R.C.H.J.; Fito, L.; Guignier, L.; Sevilla, M.; Ellul, P.; Ganko, E.; Kapur, A.; Reclus, E.; de Geus, B.; van de Geest, H.; te Lintel Hekkert, B.; van Haarst, J.; Smits, L.; Koops, A.; Sanchez-Perez, G.; van Heusden, A.W.; Visser, R.; Quan, Z.; Min, J.; Liao, L.; Wang, X.; Wang, G.; Yue, Z.; Yang, X.; Xu, N.; Schranz, E.; Smets, E.; Vos, R.; Rauwerda, J.; Ursem, R.; Schuit, C.; Kerns, M.; van den Berg, J.; Vriezen, W.; Janssen, A.; Datema, E.; Jahrman, T.; Moquet, F.; Bonnet, J.; Peters, S.

    2014-01-01

    We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups, which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new

  4. Advertisement call of Scinax camposseabrai (Bokermann, 1968) (Anura: Hylidae), with comments on the call of three species of the Scinax ruber clade.

    Science.gov (United States)

    Novaes, Gabriel; Zina, Juliana

    2016-02-25

    Scinax camposseabrai was allocated into the Scinax ruber clade by Caramaschi & Cardoso (2006) by overall similarities as snout not pointed, breeding in open areas, and an advertisement calls with multipulsed notes. This assumption about the call was based solely on an onomatopoeia provided by Bokermann (1968). Herein we provide a formal description of the advertisement call of S. camposseabrai and compare it with described calls of other S. ruber clade species. Additionally, we provide descriptions of the advertisement calls of three sympatric species of the S. ruber clade: S. eurydice (Bokermann), S. pachycrus (Miranda-Ribeiro) and S. cf. x-signatus.

  5. Soil-Transmitted Helminth Infections

    Science.gov (United States)

    ... Schistosomiasis and soil-transmitted helminth infections More about neglected tropical diseases News WHO recommends large-scale deworming to improve children’s health and nutrition 29 September 2017 About us ...

  6. Sexually transmitted diseases during pregnancy: a synthesis of particularities.

    Science.gov (United States)

    Costa, Mariana Carvalho; Bornhausen Demarch, Eduardo; Azulay, David Rubem; Périssé, André Reynaldo Santos; Dias, Maria Fernanda Reis Gavazzoni; Nery, José Augusto da Costa

    2010-01-01

    Sexually transmitted diseases (STDs) have a significant prevalence in both the general population and pregnant women. Accordingly, we consider the physiological changes of the maternal organism that can alter the clinical course of these diseases. In addition, obstetric and neonatal complications may occur, resulting in increased maternal and infant morbidity and mortality. We explore features of the natural course and treatment during pregnancy of the major STDs: soft chancre, donovanosis, gonorrhea, chlamydia, viral hepatitis, genital herpes, human papillomavirus (HPV) infection, lymphogranuloma venereum, syphilis, and vulvovaginitis. We believe that health professionals should pay careful attention to STDs, particularly in relation to early diagnosis and precautions on the use of drugs during pregnancy. Prevention and partner treatment to achieve effective results are also extremely relevant.

  7. The influence of sexual activity on the vaginal microbiota and Gardnerella vaginalis clade diversity in young women.

    Science.gov (United States)

    Vodstrcil, Lenka A; Twin, Jimmy; Garland, Suzanne M; Fairley, Christopher K; Hocking, Jane S; Law, Matthew G; Plummer, Erica L; Fethers, Katherine A; Chow, Eric P F; Tabrizi, Sepehr N; Bradshaw, Catriona S

    2017-01-01

    To examine the influence of sexual activity on the composition and consistency of the vaginal microbiota over time, and distribution of Gardnerella vaginalis clades in young women. Fifty-two participants from a university cohort were selected. Vaginal swabs were self-collected every 3-months for up to 12 months with 184 specimens analysed. The vaginal microbiota was characterised using Roche 454 V3/4 region 16S rRNA sequencing, and G.vaginalis clade typing by qPCR. A Lactobacillus crispatus dominated vaginal microbiota was associated with Caucasian ethnicity (adjusted relative risk ratio[ARRR] = 7.28, 95%CI:1.37,38.57,p = 0.020). An L.iners (ARRR = 17.51, 95%CI:2.18,140.33,p = 0.007) or G.vaginalis (ARRR = 14.03, 95%CI:1.22,160.69, p = 0.034) dominated microbiota was associated with engaging in penile-vaginal sex. Microbiota dominated by L.crispatus, L.iners or other lactobacilli exhibited greater longitudinal consistency of the bacterial communities present compared to ones dominated by heterogeneous non-lactobacilli (pvaginal sex (RRR = 9.55, 95%CI:1.33,68.38,p = 0.025) or were diagnosed with BV (RRR = 31.5, 95%CI:1.69,586.87,p = 0.021). Sexual activity and ethnicity influenced the composition of the vaginal microbiota of these young, relatively sexually inexperienced women. Women had consistent vaginal microbiota over time if lactobacilli were the dominant spp. present. Penile-vaginal sex did not alter the consistency of microbial communities but increased G.vaginalis clade diversity in young women with and without BV, suggesting sexual transmission of commensal and potentially pathogenic clades.

  8. A unique species in Phytophthora clade 10, Phytophthora intercalaris sp. nov., recovered from stream and irrigation water in the eastern USA

    Science.gov (United States)

    Balci, Y.; Brazee, N. J.; Loyd, A. L.; Hong, C. X.

    2016-01-01

    A novel species of the genus Phytophthora was recovered during surveys of stream and nursery irrigation water in Maryland, Massachusetts, North Carolina, Virginia and West Virginia in the USA. The novel species is heterothallic, and all examined isolates were A1 mating type. It produced rare ornamented oogonia and amphigynous antheridia when paired with A2 mating type testers of Phytophthora cinnamomi and Phytophthora cryptogea. Sporangia of this novel species were non-papillate and non-caducous. Thin-walled intercalary chlamydospores were abundant in hemp seed agar and carrot agar, while they were produced only rarely in aged cultures grown in clarified V8 juice agar. Phylogenetic analyses based on sequences of the internal transcribed spacer region and the β-tubulin and mitochondrial cytochrome-c oxidase 1 (cox1) genes indicated that the novel species is phylogenetically close to Phytophthora gallica in Phytophthora clade 10. The novel species has morphological and molecular features that are distinct from those of other species in Phytophthora clade 10. It is formally described here as Phytophthora intercalaris sp. nov. Description of this unique clade-10 species is important for understanding the phylogeny and evolution of Phytophthora clade 10. PMID:26620125

  9. Ichthyophonus parasite phylogeny based on ITS rDNA structure prediction and alignment identifies six clades, with a single dominant marine type

    Science.gov (United States)

    Gregg, Jacob; Thompson, Rachel L.; Purcell, Maureen; Friedman, Carolyn S.; Hershberger, Paul

    2016-01-01

    Despite their widespread, global impact in both wild and cultured fishes, little is known of the diversity, transmission patterns, and phylogeography of parasites generally identified as Ichthyophonus. This study constructed a phylogeny based on the structural alignment of internal transcribed spacer (ITS) rDNA sequences to compare Ichthyophonus isolates from fish hosts in the Atlantic and Pacific oceans, and several rivers and aquaculture sites in North America, Europe, and Japan. Structure of the Ichthyophonus ITS1–5.8S–ITS2 transcript exhibited several homologies with other eukaryotes, and 6 distinct clades were identified within Ichthyophonus. A single clade contained a majority (71 of 98) of parasite isolations. This ubiquitous Ichthyophonus type occurred in 13 marine and anadromous hosts and was associated with epizootics in Atlantic herring, Chinook salmon, and American shad. A second clade contained all isolates from aquaculture, despite great geographic separation of the freshwater hosts. Each of the 4 remaining clades contained isolates from single host species. This study is the first to evaluate the genetic relationships among Ichthyophonus species across a significant portion of their host and geographic range. Additionally, parasite infection prevalence is reported in 16 fish species.

  10. Ichthyophonus parasite phylogeny based on ITS rDNA structure prediction and alignment identifies six clades, with a single dominant marine type.

    Science.gov (United States)

    Gregg, Jacob L; Powers, Rachel L; Purcell, Maureen K; Friedman, Carolyn S; Hershberger, Paul K

    2016-07-07

    Despite their widespread, global impact in both wild and cultured fishes, little is known of the diversity, transmission patterns, and phylogeography of parasites generally identified as Ichthyophonus. This study constructed a phylogeny based on the structural alignment of internal transcribed spacer (ITS) rDNA sequences to compare Ichthyophonus isolates from fish hosts in the Atlantic and Pacific oceans, and several rivers and aquaculture sites in North America, Europe, and Japan. Structure of the Ichthyophonus ITS1-5.8S-ITS2 transcript exhibited several homologies with other eukaryotes, and 6 distinct clades were identified within Ichthyophonus. A single clade contained a majority (71 of 98) of parasite isolations. This ubiquitous Ichthyophonus type occurred in 13 marine and anadromous hosts and was associated with epizootics in Atlantic herring, Chinook salmon, and American shad. A second clade contained all isolates from aquaculture, despite great geographic separation of the freshwater hosts. Each of the 4 remaining clades contained isolates from single host species. This study is the first to evaluate the genetic relationships among Ichthyophonus species across a significant portion of their host and geographic range. Additionally, parasite infection prevalence is reported in 16 fish species.

  11. Ocular Manifestations of Mosquito-Transmitted Diseases.

    Science.gov (United States)

    Karesh, James W; Mazzoli, Robert A; Heintz, Shannon K

    2018-03-01

    Of the 3,548 known mosquito species, about 100 transmit human diseases. Mosquitoes are distributed globally throughout tropical and temperate regions where standing water sources are available for egg laying and the maturation of larva. Female mosquitoes require blood meals for egg production. This is the main pathway for disease transmission. Mosquitoes carry several pathogenic organisms responsible for significant ocular pathology and vision loss including West Nile, Rift Valley, chikungunya, dengue viruses, various encephalitis viruses, malarial parasites, Francisella tularensis, microfilarial parasites, including Dirofilaria, Wuchereria, and Brugia spp., and human botfly larvae. Health care providers may not be familiar with many of these mosquito-transmitted diseases or their associated ocular findings delaying diagnosis, treatment, and recovery of visual function. This article aims to provide an overview of the ocular manifestations associated with mosquito-transmitted diseases.

  12. Oral manifestations of sexually transmitted diseases identified in three stomatology services in South America

    Directory of Open Access Journals (Sweden)

    Martha Carmona-Lorduy

    2018-01-01

    Full Text Available Introduction: Sexually transmitted diseases are defined as a group of infections caused by various agents which are acquired during sexual intercourse. They also tend to generate manifestations in the mouth. Objective: To determine the typical lesions in oral cavity of sexually transmitted diseases. Materials and methods: A descriptive transversal study was conducted with 37 patients who attended the stomatology services of the University of Buenos Aires, University of Cartagena and the Aleman Hospital in Buenos Aires during 2015 and 2016. A complete clinical history was carried out with Venereal Disease Research Laboratory (VDRL and Fluorescent Treponemal Antibody Absortion (FTA-ABS tests in patients with presumption of syphilis. In addition, histopathological analysis and Polymerase Chain Reaction (PCR was made in patients with presumption of Human papillomavirus (HPV. Results: The average age of the patients was 38, where male sex predominated. 54.1% were diagnosed with syphilis and the most found lesion in them was the papule. The remaining 45.9% were diagnosed with HPV, the predominant lesion in them was a wart. Conclusions: The dentist should contribute to the early detection of sexually transmitted diseases by identifying manifestations of these in the mouth in order to prevent their evolution and prevent their transmission.

  13. Internationalism in sexually transmitted infections.

    Science.gov (United States)

    Waugh, M A

    1997-12-01

    The International Union Against the Venereal Diseases and the Treponematoses (IUVDT) became the International Union Against Sexually Transmitted Infections (IUSTI) at the Union's 37th General Assembly, held in Melbourne, Australia. The name change reflects the increasing use by international donor organizations of the term sexually transmitted infections (STIs). STIs are a major problem in Africa, South East Asia, India, Russia, and the European countries which were formerly within the Communist bloc. The epidemic of syphilis together with HIV increases daily in Eastern Europe and Russia. There have, however, been some successes in developing countries with the syndromic method, the promotion of sexual health, and the prevention of STIs. While the UK has the largest body of fully trained sexually transmitted disease (STD) specialists in the world, comparatively few of them participate in large international commitments. These specialists should instead become more involved with STIs in areas of need. Furthermore, more aid should be provided by governmental, nongovernmental, and charitable sources. IUSTI is willing to cooperate with any efforts to fight STDs anywhere in the world.

  14. A novel Haemosporida clade at the rank of genus in North American cranes (Aves: Gruiformes).

    Science.gov (United States)

    Bertram, Miranda R; Hamer, Sarah A; Hartup, Barry K; Snowden, Karen F; Medeiros, Matthew C; Outlaw, Diana C; Hamer, Gabriel L

    2017-04-01

    The unicellular blood parasites in the order Haemosporida are highly diverse, infect many vertebrates, are responsible for a large disease burden among humans and animals, and have reemerged as an important model system to understand the evolutionary and ecological dynamics of host-parasite interactions. The phylogenetics and systematics of Haemosporida are limited by poor sampling of different vertebrate host taxa. We surveyed the Haemosporida of wild whooping cranes (Grus americana) and sandhill cranes (Grus canadensis) (Aves: Gruiformes) using a combination of morphological and molecular approaches. We identified Haemoproteus antigonis in blood smears based on published morphological descriptions. Phylogenetic analysis based on partial cytochrome b (cytb) and cytochrome oxidase (coI) sequences placed H. antigonis parasites in a novel clade, distinct from all avian Haemosporida genera for which cytb and/or coI sequences are available. Molecular clock and divergence estimates suggest this crane clade may represent a new genus. This is the first molecular description of H. antigonis and the first report of H. antigonis in wild whooping cranes, an endangered bird in North America. Further sampling of Haemosporida, especially from hosts of the Gruiformes and other poorly sampled orders, will help to resolve the relationship of the H. antigonis clade to other avian Haemosporida genera. Our study highlights the potential of sampling neglected host species to discover novel lineages of diverse parasite groups. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments

    Science.gov (United States)

    Holmes, Dawn E.; O'Neil, Regina A.; Vrionis, Helen A.; N'Guessan, Lucie A.; Ortiz-Bernad, Irene; Larrahondo, Maria J.; Adams, Lorrie A.; Ward, Joy A.; Nicoll , Julie S.; Nevin, Kelly P.; Chavan, Milind A.; Johnson, Jessica P.; Long, Philip E.; Lovely, Derek R.

    2007-01-01

    There are distinct differences in the physiology of Geobacter species available in pure culture. Therefore, to understand the ecology of Geobacter species in subsurface environments, it is important to know which species predominate. Clone libraries were assembled with 16S rRNA genes and transcripts amplified from three subsurface environments in which Geobacter species are known to be important members of the microbial community: (1) a uranium-contaminated aquifer located in Rifle, CO, USA undergoing in situ bioremediation; (2) an acetate-impacted aquifer that serves as an analog for the long-term acetate amendments proposed for in situ uranium bioremediation and (3) a petroleum-contaminated aquifer in which Geobacter species play a role in the oxidation of aromatic hydrocarbons coupled with the reduction of Fe(III). The majority of Geobacteraceae 16S rRNA sequences found in these environments clustered in a phylogenetically coherent subsurface clade, which also contains a number of Geobacter species isolated from subsurface environments. Concatamers constructed with 43 Geobacter genes amplified from these sites also clustered within this subsurface clade. 16S rRNA transcript and gene sequences in the sediments and groundwater at the Rifle site were highly similar, suggesting that sampling groundwater via monitoring wells can recover the most active Geobacter species. These results suggest that further study of Geobacter species in the subsurface clade is necessary to accurately model the behavior of Geobacter species during subsurface bioremediation of metal and organic contaminants.

  16. Root evolution at the base of the lycophyte clade: insights from an Early Devonian lycophyte

    Science.gov (United States)

    Matsunaga, Kelly K. S.; Tomescu, Alexandru M. F.

    2016-01-01

    Background and Aims The evolution of complex rooting systems during the Devonian had significant impacts on global terrestrial ecosystems and the evolution of plant body plans. However, detailed understanding of the pathways of root evolution and the architecture of early rooting systems is currently lacking. We describe the architecture and resolve the structural homology of the rooting system of an Early Devonian basal lycophyte. Insights gained from these fossils are used to address lycophyte root evolution and homology. Methods Plant fossils are preserved as carbonaceous compressions at Cottonwood Canyon (Wyoming), in the Lochkovian–Pragian (∼411 Ma; Early Devonian) Beartooth Butte Formation. We analysed 177 rock specimens and documented morphology, cuticular anatomy and structural relationships, as well as stratigraphic position and taphonomic conditions. Key Results The rooting system of the Cottonwood Canyon lycophyte is composed of modified stems that bear fine, dichotomously branching lateral roots. These modified stems, referred to as root-bearing axes, are produced at branching points of the above-ground shoot system. Root-bearing axes preserved in growth position exhibit evidence of positive gravitropism, whereas the lateral roots extend horizontally. Consistent recurrence of these features in successive populations of the plant preserved in situ demonstrates that they represent constitutive structural traits and not opportunistic responses of a flexible developmental programme. Conclusions This is the oldest direct evidence for a rooting system preserved in growth position. These rooting systems, which can be traced to a parent plant, include some of the earliest roots known to date and demonstrate that substantial plant–substrate interactions were under way by Early Devonian time. The morphological relationships between stems, root-bearing axes and roots corroborate evidence that positive gravitropism and root identity were evolutionarily

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

    Directory of Open Access Journals (Sweden)

    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.

  18. Full-Genome Sequence of a Novel Varicella-Zoster Virus Clade Isolated in Mexico.

    Science.gov (United States)

    Garcés-Ayala, Fabiola; Rodríguez-Castillo, Araceli; Ortiz-Alcántara, Joanna María; Gonzalez-Durán, Elizabeth; Segura-Candelas, José Miguel; Pérez-Agüeros, Sandra Ivette; Escobar-Escamilla, Noé; Méndez-Tenorio, Alfonso; Diaz-Quiñonez, José Alberto; Ramirez-González, José Ernesto

    2015-07-09

    Varicella-zoster virus (VZV) is a member of the Herpesviridae family, which causes varicella (chicken pox) and herpes zoster (shingles) in humans. Here, we report the complete genome sequence of varicella-zoster virus, isolated from a vesicular fluid sample, revealing the circulation of VZV clade VIII in Mexico. Copyright © 2015 Garcés-Ayala et al.

  19. Plastid phylogenomics and adaptive evolution of Gaultheria series Trichophyllae (Ericaceae), a clade from sky islands of the Himalaya-Hengduan Mountains.

    Science.gov (United States)

    Zhang, Ming-Ying; Fritsch, Peter W; Ma, Peng-Fei; Wang, Hong; Lu, Lu; Li, De-Zhu

    2017-05-01

    Gaultheria series Trichophyllae Airy Shaw is an angiosperm clade of high-alpine shrublets endemic to the Himalaya-Hengduan Mountains and characterized by recent species divergence and convergent character evolution that has until recently caused much confusion in species circumscription. Although multiple DNA sequence regions have been employed previously, phylogenetic relationships among species in the group have remained largely unresolved. Here we examined the effectiveness of the plastid genome for improving phylogenetic resolution within the G. series Trichophyllae clade. Plastid genomes of 31 samples representing all 19 recognized species of the series and three outgroup species were sequenced with Illumina Sequencing technology. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) phylogenetic analyses were performed with various datasets, i.e., that from the whole plastid genome, coding regions, noncoding regions, large single-copy region (LSC) and inverted-repeat region a (IRa). The partitioned whole plastid genome with inverted-repeat region b (IRb) excluded was also analyzed with ML and BI. Tree topologies based on the whole plastid genome, noncoding regions, and LSC region datasets across all analyses, and that based on the partitioned dataset with ML and BI analyses, are identical and generally strongly supported. Gaultheria series Trichophyllae form a clade with three species and one variety that is sister to a clade of the remaining 16 species; the latter comprises seven main subclades. Interspecific relationships within the series are strongly supported except for those based on the coding-region and IRa-region datasets. Eight divergence hotspot regions, each possessing >5% percent variable sites, were screened across the whole plastid genome of the 28 individuals sampled in the series. Results of morphological character evolution reconstruction diagnose several clades, and a hypothesis of adaptive evolution for plant habit is

  20. Comparative Analysis of WUSCHEL-Related Homeobox Genes Revealed Their Parent-of-Origin and Cell Type-Specific Expression Pattern During Early Embryogenesis in Tobacco

    Directory of Open Access Journals (Sweden)

    Xuemei Zhou

    2018-03-01

    Full Text Available WUSCHEL-related homeobox (WOX gene is a plant-specific clade of homeobox transcription factors. Increasing evidences reveal that WOXs play critical roles in early embryogenesis, which involves zygote development, initiation of zygote division, and apical or basal cell lineage establishment. However, how WOXs regulate these developmental events remains largely unknown, and even detailed expression pattern in gametes and early proembryos is not yet available. Here, 13 WOX family genes were identified in Nicotiana tabacum genome. Comparative analysis of 13 WOX family genes with their homologs in Arabidopsis thaliana reveals relatively conserved expression pattern of WUS and WOX5 in shoot/root apical meristem. Whereas variations were also found, e.g., lacking homolog of WOX8 (a marker for suspensor cell in tobacco genome and the expression of WOX2/WOX9 in both apical cell and basal cell. Transient transcriptional activity analysis revealed that WOXs in WUS clade have repressive activities for their target's transcription, whereas WOXs in ancient and intermediate clade have activation activities, giving a molecular basis for the phylogenetic classification of tobacco WOXs into three major clades. Expression pattern analysis revealed that some WOXs (e.g., WOX 13a expressed in both male and female gametes and some WOXs (e.g., WOX 11 and WOX 13b displayed the characteristics of parent-of-origin genes. Interestingly, some WOXs (e.g., WOX2 and WOX9, which are essential for early embryo patterning, were de novo transcribed in zygote, indicating relevant mechanism for embryo pattern formation is only established in zygote right after fertilization and not carried in by gametes. We also found that most WOXs displayed a stage-specific and cell type-specific expression pattern. Taken together, this work provides a detailed landscape of WOXs in tobacco during fertilization and early embryogenesis, which will facilitate the understanding of their specific roles

  1. Secret-Sharing over Multiple-Antenna Channels with Transmit Correlation

    KAUST Repository

    Zorgui, Marwen

    2015-01-07

    We consider secret-key agreement with public discussion over Rayleigh fastfading channels with transmit correlation. The legitimate receiver and the eavesdropper are assumed to have perfect channel knowledge while the transmitter has only knowledge of the transmit correlation matrix. First, We derive the expression of the key capacity under the considered setup. Then, we show that the optimal transmit strategy achieving the key capacity consists in transmitting Gaussian signals along the eingenvectors of the channel covariance matrix. The powers allocated to each channel mode are determined as the solution of a numerical optimization problem that we derive. We also provide a waterfilling interpretation of the optimal power allocation. Finally, we develop a necessary and sufficient condition for beamforming to be optimal, i.e., transmitting along the strongest channel mode only is key capacity-achieving.

  2. Secret-Sharing over Multiple-Antenna Channels with Transmit Correlation

    KAUST Repository

    Zorgui, Marwen; Rezki, Zouheir; Alomair, Basel; Alouini, Mohamed-Slim

    2015-01-01

    We consider secret-key agreement with public discussion over Rayleigh fastfading channels with transmit correlation. The legitimate receiver and the eavesdropper are assumed to have perfect channel knowledge while the transmitter has only knowledge of the transmit correlation matrix. First, We derive the expression of the key capacity under the considered setup. Then, we show that the optimal transmit strategy achieving the key capacity consists in transmitting Gaussian signals along the eingenvectors of the channel covariance matrix. The powers allocated to each channel mode are determined as the solution of a numerical optimization problem that we derive. We also provide a waterfilling interpretation of the optimal power allocation. Finally, we develop a necessary and sufficient condition for beamforming to be optimal, i.e., transmitting along the strongest channel mode only is key capacity-achieving.

  3. Evidence of a Native Northwest Atlantic COI Haplotype Clade in the Cryptogenic Colonial Ascidian Botryllus schlosseri.

    Science.gov (United States)

    Yund, Philip O; Collins, Catherine; Johnson, Sheri L

    2015-06-01

    The colonial ascidian Botryllus schlosseri should be considered cryptogenic (i.e., not definitively classified as either native or introduced) in the Northwest Atlantic. Although all the evidence is quite circumstantial, over the last 15 years most research groups have accepted the scenario of human-mediated dispersal and classified B. schlosseri as introduced; others have continued to consider it native or cryptogenic. We address the invasion status of this species by adding 174 sequences to the growing worldwide database for the mitochondrial gene cytochrome c oxidase subunit I (COI) and analyzing 1077 sequences to compare genetic diversity of one clade of haplotypes in the Northwest Atlantic with two hypothesized source regions (the Northeast Atlantic and Mediterranean). Our results lead us to reject the prevailing view of the directionality of transport across the Atlantic. We argue that the genetic diversity patterns at COI are far more consistent with the existence of at least one haplotype clade in the Northwest Atlantic (and possibly a second) that substantially pre-dates human colonization from Europe, with this native North American clade subsequently introduced to three sites in Northeast Atlantic and Mediterranean waters. However, we agree with past researchers that some sites in the Northwest Atlantic have more recently been invaded by alien haplotypes, so that some populations are currently composed of a mixture of native and invader haplotypes. © 2015 Marine Biological Laboratory.

  4. Biotechnological Applications of the Roseobacter Clade

    DEFF Research Database (Denmark)

    Bentzon-Tilia, Mikkel; Gram, Lone

    2017-01-01

    spectrum of Gram-positive and Gram-negative bacteria in which resistance towards the compound does not arise easily. Mining the genomes of roseobacters also reveal that they are likely capable of producing other compounds than hitherto discovered by classical bio-assay guided fractionation, since...... the genomes contain genes/gene clusters probably encoding unknown bioactive secondary metabolites. Therefore, bacteria of the Roseobacter clade may serve as potential sources of novel bioactive compounds, including novel antibiotics, which is of paramount importance in the battle against antibiotic resistant...... pathogenic bacteria. The discovery of new antibiotic compounds is not the only means by which we can counter the spread of antibiotic resistance. Development of sustainable alternatives to the application of antibiotics in agri- and aquaculture may be equally important. Attributable to their inherent...

  5. Early Homo and the role of the genus in paleoanthropology.

    Science.gov (United States)

    Villmoare, Brian

    2018-01-01

    The history of the discovery of early fossils attributed to the genus Homo has been contentious, with scholars disagreeing over the generic assignment of fossils proposed as members of our genus. In this manuscript I review the history of discovery and debate over early Homo and evaluate the various taxonomic hypotheses for the genus. To get a sense of how hominin taxonomy compares to taxonomic practice outside paleoanthropology, I compare the diversity of Homo to genera in other vertebrate clades. Finally, I propose a taxonomic model that hews closely to current models for hominin phylogeny and is consistent with taxonomic practice across evolutionary biology. © 2018 American Association of Physical Anthropologists.

  6. Podargiform affinities of the enigmatic Fluvioviridavis platyrhamphus and the early diversification of Strisores ("Caprimulgiformes" + Apodiformes).

    Science.gov (United States)

    Nesbitt, Sterling J; Ksepka, Daniel T; Clarke, Julia A

    2011-01-01

    The early Eocene Green River Formation avifauna preserves exceptional exemplars of the earliest unambiguous stem representatives of many extant avian clades. We identify the basal-most member of Podargiformes (extant and fossil stem lineage frogmouths) based on a new specimen of Fluvioviridavis platyrhamphus, a unique neoavian bird from the Fossil Butte Member of the Green River Formation of Wyoming. Extant frogmouths (Podargidae) comprise approximately 13 nocturnal species with an exclusively Australasian distribution. The new specimen was included in a combined phylogenetic analysis of morphological (osteology and soft tissue) and molecular sequence (cytochrome b, c-myc exon 3, and RAG) data sampling species-level taxa from both extant and extinct members of Steatornithidae, Podargidae, Caprimulgidae, Nyctibiidae, Aegothelidae, and Apodiformes ( = Strisores). New data from F. platyrhamphus help resolve phylogenetic relationships within Strisores, supporting placement of F. platyrhamphus and the European fossil form Masillapodargus longipes as basal parts of Podargiformes and also supporting a sister taxon relationship between Podargiformes and Steatornithiformes (oilbirds) within Strisores. This relationship is recovered only when fossil taxa are included, reaffirming the potential impact of stem fossil taxa on inferences of phylogenetic relationships. The well-preserved mandible and palate of the new specimen demonstrate that many of the unique characteristics of the skull that characterize the crown frogmouth clade Podargidae arose early in the evolutionary history of the clade, over 50 million years ago. Comparisons with the new specimen also indicate that Eurofluvioviridavis and Fluvioviridavis are not closely related. Together with the European fossil frogmouth Masillapodargus, Fluvioviridavis shows that Podargiformes had a much wider geographic distribution in the past, whereas extant species are restricted to Australasia. The Eocene record of Strisores

  7. Podargiform affinities of the enigmatic Fluvioviridavis platyrhamphus and the early diversification of Strisores ("Caprimulgiformes" + Apodiformes.

    Directory of Open Access Journals (Sweden)

    Sterling J Nesbitt

    Full Text Available The early Eocene Green River Formation avifauna preserves exceptional exemplars of the earliest unambiguous stem representatives of many extant avian clades. We identify the basal-most member of Podargiformes (extant and fossil stem lineage frogmouths based on a new specimen of Fluvioviridavis platyrhamphus, a unique neoavian bird from the Fossil Butte Member of the Green River Formation of Wyoming. Extant frogmouths (Podargidae comprise approximately 13 nocturnal species with an exclusively Australasian distribution.The new specimen was included in a combined phylogenetic analysis of morphological (osteology and soft tissue and molecular sequence (cytochrome b, c-myc exon 3, and RAG data sampling species-level taxa from both extant and extinct members of Steatornithidae, Podargidae, Caprimulgidae, Nyctibiidae, Aegothelidae, and Apodiformes ( = Strisores. New data from F. platyrhamphus help resolve phylogenetic relationships within Strisores, supporting placement of F. platyrhamphus and the European fossil form Masillapodargus longipes as basal parts of Podargiformes and also supporting a sister taxon relationship between Podargiformes and Steatornithiformes (oilbirds within Strisores. This relationship is recovered only when fossil taxa are included, reaffirming the potential impact of stem fossil taxa on inferences of phylogenetic relationships. The well-preserved mandible and palate of the new specimen demonstrate that many of the unique characteristics of the skull that characterize the crown frogmouth clade Podargidae arose early in the evolutionary history of the clade, over 50 million years ago. Comparisons with the new specimen also indicate that Eurofluvioviridavis and Fluvioviridavis are not closely related.Together with the European fossil frogmouth Masillapodargus, Fluvioviridavis shows that Podargiformes had a much wider geographic distribution in the past, whereas extant species are restricted to Australasia. The Eocene record

  8. Adaptive transmit selection with interference suppression

    KAUST Repository

    Radaydeh, Redha Mahmoud Mesleh

    2010-01-01

    This paper studies the performance of adaptive transmit channel selection in multipath fading channels. The adaptive selection algorithms are configured for single-antenna bandwidth-efficient or power-efficient transmission with as low transmit channel estimations as possible. Due to the fact that the number of active co-channel interfering signals and their corresponding powers experience random behavior, the adaptation to channels conditions, assuming uniform buffer and traffic loading, is proposed to be jointly based on the transmit channels instantaneous signal-to-noise ratios (SNRs) and signal-to- interference-plus- noise ratios (SINRs). Two interference cancelation algorithms, which are the dominant cancelation and the less complex arbitrary cancelation, are considered, for which the receive antenna array is assumed to have small angular spread. Analytical formulation for some performance measures in addition to several processing complexity and numerical comparisons between various adaptation schemes are presented. ©2010 IEEE.

  9. Nematode infections: soil-transmitted helminths and trichinella.

    Science.gov (United States)

    Knopp, Stefanie; Steinmann, Peter; Keiser, Jennifer; Utzinger, Jürg

    2012-06-01

    Infection with soil-transmitted helminths occurs via ingestion of nematode eggs with contaminated food and water, via hands, or inhalation of dust, or by penetration of larvae through the skin. Trichinella infections are caused by the ingestion of larvae contained in undercooked meat. In highly endemic areas, preventive chemotherapy (ie, regular administration of anthelmintic drugs to at-risk populations) is the key strategy against soil-transmitted helminthiasis. Integrated control approaches, including improved hygiene, sanitation, and water, are required for lasting effects. Because of growing tourism, travel, and migration, clinicians and specialized travel clinics must remain aware of the diagnosis, prevention, and treatment of soil-transmitted helminth and Trichinella infections. Copyright © 2012 Elsevier Inc. All rights reserved.

  10. Revision of the Middle American clade of the ant genus Stenamma Westwood (Hymenoptera, Formicidae, Myrmicinae)

    Science.gov (United States)

    Branstetter, Michael G.

    2013-01-01

    Abstract Stenamma is a cryptic “leaf-litter” ant genus that occurs in mesic forest habitats throughout the Holarctic region, Central America, and part of northwestern South America (Colombia and Ecuador). The genus was thought to be restricted primarily to the temperate zone, but recent collecting efforts have uncovered a large radiation of Neotropical forms, which rival the Holarctic species in terms of morphological and behavioral diversity. By inferring a broad-scale molecular phylogeny of Stenamma, Branstetter (2012) showed that all Neotropical species belong to a diverse Middle American clade (MAC), and that this clade is sister to an almost completely geographically separated Holarctic clade (HOC). Here, the Middle American clade of Stenamma is revised to recognize 40 species, of which 33 are described as new. Included in the revision are a key to species based on the worker caste, and for each species where possible, descriptions and images of workers and queens, images of males, information on geographic distribution, descriptions of intraspecific variation, and notes on natural history. Several species groups are defined, but the majority of species remain unassigned due to a lack of diagnostic morphological character states for most molecular clades. The following species are redescribed: Stenamma alas Longino, Stenamma diversum Mann, Stenamma expolitum Smith, Stenamma felixi Mann, Stenamma huachucanum Smith, Stenamma manni Wheeler, and Stenamma schmidti Menozzi. The following are described as new: Stenamma andersoni sp. n., Stenamma atribellum sp. n., Stenamma brujita sp. n., Stenamma callipygium sp. n., Stenamma catracho sp. n., Stenamma connectum sp. n., Stenamma crypticum sp. n., Stenamma cusuco sp. n., Stenamma excisum sp. n., Stenamma expolitico sp. n., Stenamma hojarasca sp. n., Stenamma ignotum sp. n., Stenamma lagunum sp. n., Stenamma llama sp. n., Stenamma leptospinum sp. n., Stenamma lobinodus sp. n., Stenamma longinoi sp. n., Stenamma

  11. GNSS satellite transmit power and its impact on orbit determination

    Science.gov (United States)

    Steigenberger, Peter; Thoelert, Steffen; Montenbruck, Oliver

    2018-06-01

    Antenna thrust is a small acceleration acting on Global Navigation Satellite System satellites caused by the transmission of radio navigation signals. Knowledge about the transmit power and the mass of the satellites is required for the computation of this effect. The actual transmit power can be obtained from measurements with a high-gain antenna and knowledge about the properties of the transmit and receive antennas as well as losses along the propagation path. Transmit power measurements for different types of GPS, GLONASS, Galileo, and BeiDou-2 satellites were taken with a 30-m dish antenna of the German Aerospace Center (DLR) located at its ground station in Weilheim. For GPS, total L-band transmit power levels of 50-240 W were obtained, 20-135 W for GLONASS, 95-265 W for Galileo, and 130-185 W for BeiDou-2. The transmit power differs usually only slightly for individual spacecraft within one satellite block. An exception are the GLONASS-M satellites where six subgroups with different transmit power levels could be identified. Considering the antenna thrust in precise orbit determination of GNSS satellites decreases the orbital radius by 1-27 mm depending on the transmit power, the satellite mass, and the orbital period.

  12. Integrated reconfigurable high-voltage transmitting circuit for CMUTs

    DEFF Research Database (Denmark)

    Llimos Muntal, Pere; Larsen, Dennis Øland; Jørgensen, Ivan Harald Holger

    2015-01-01

    In this paper a high-voltage transmitting circuit aimed for capacitive micromachined ultrasonic transducers (CMUTs) used in scanners for medical applications is designed and implemented in a 0.35 μm high-voltage CMOS process. The transmitting circuit is reconfigurable externally making it able...... to drive a wide variety of CMUTs. The transmitting circuit can generate several pulse shapes with voltages up to 100 V, maximum pulse range of 50 V, frequencies up to 5 MHz and different driving slew rates. Measurements are performed on the circuit in order to assess its functionality and power consumption...... performance. The design occupies an on-chip area of 0.938 mm2 and the power consumption of a 128-element transmitting circuit array that would be used in an portable ultrasound scanner is found to be a maximum of 181 mW....

  13. Soil transmitted helminths and schistosoma mansoni infections among school children in zarima town, northwest Ethiopia

    Directory of Open Access Journals (Sweden)

    Birhan Wubet

    2011-07-01

    Full Text Available Abstract Background In Ethiopia, because of low quality drinking water supply and latrine coverage, helminths infections are the second most predominant causes of outpatient morbidity. Indeed, there is a scarcity of information on the prevalence of soil transmitted helminths and Schistosomiasis in Ethiopia, special in study area. Therefore, the aim of this study was to determine the prevalence and associated risk factors of soil transmitted helminths and intestinal Schistosomiasis. Methods Cross-sectional study was conducted among 319 school children of Zarima town from April 1 to May 25, 2009. A pre-tested structured questionnaire was used to collect socio-demographic data and possible risk factors exposure. Early morning stool samples were collected and a Kato Katz semi concentration technique was used to examine and count parasitic load by compound light microscope. Data entry and analysis was done using SPSS-15 version and p-value Results Out of 319 study subjects, 263 (82.4% of the study participants infected with one or more parasites. From soil transmitted helminths, Ascaris lumbricoides was the predominant isolate (22% followed by Hookworms (19% and Trichuris trichiura (2.5%. Schistosoma mansoni was also isolated in 37.9% of the study participants. Hookworm and S. mansoni infections showed statistically significant associations with shoe wearing and swimming habit of school children, respectively. Conclusion Prevalence of soil transmitted helminths (STH and S.mansoni was high and the diseases were still major health problem in the study area which alerts public health intervention as soon as possible.

  14. Platelet concentrates: reducing the risk of transfusion-transmitted bacterial infections

    Directory of Open Access Journals (Sweden)

    de Korte D

    2014-06-01

    Full Text Available Dirk de Korte,1 Jan H Marcelis2 1Department of Product and Process Development, Sanquin Blood Bank, Amsterdam, 2Department of Microbiology, St Elisabeth Hospital, Tilburg, the Netherlands Abstract: The introduction of a combination of interventions during collection of whole-blood or platelet concentrates has been successful in lowering the degree of bacterial contamination in the final product, the platelet concentrate, by 50%–75%. These interventions were improved donor questionnaires, best-practice skin disinfection, and diversion of first blood volume. These interventions have reduced the number of bacteria present in the platelet concentrates. In combination with screening for bacterial contamination of platelet concentrates with a culture method, the degree of transfusion-transmitted bacterial infection has been reduced significantly. Due to the very low initial bacteria counts upon collection of the products, the need for improved sensitivity of early screenings tests or highly selective point-of-issue tests remains. The latter should be rapid and easy to perform. An alternative approach might be the implementation of pathogen-inactivation methods for cellular blood products to reduce the amount of pathogens. However, these methods are costly, and so far not proved to be cost-effective, especially in countries with an already-low incidence of transfusion-transmitted infections by viruses, parasites, or bacteria. Keywords: blood products, bacterial contamination, screening, point of issue, pathogen inactivation

  15. Skull ontogeny: developmental patterns of fishes conserved across major tetrapod clades.

    Science.gov (United States)

    Schoch, Rainer R

    2006-01-01

    In vertebrates, the ontogeny of the bony skull forms a particularly complex part of embryonic development. Although this area used to be restricted to neontology, recent discoveries of fossil ontogenies provide an additional source of data. One of the most detailed ossification sequences is known from Permo-Carboniferous amphibians, the branchiosaurids. These temnospondyls form a near-perfect link between the piscine osteichthyans and the various clades of extant tetrapods, retaining a full complement of dermal bones in the skull. For the first time, the broader evolutionary significance of these event sequences is analyzed, focusing on the identification of sequence heterochronies. A set of 120 event pairs was analyzed by event pair cracking, which helped identify active movers. A cladistic analysis of the event pair data was also carried out, highlighting some shared patterns between widely divergent clades of tetrapods. The analyses revealed an unexpected degree of similarity between the widely divergent taxa. Most interesting is the apparently modular composition of the cranial sequence: five clusters of bones were discovered in each of which the elements form in the same time window: (1) jaw bones, (2) marginal palatal elements, (3) circumorbital bones, (4) skull roof elements, and (5) neurocranial ossifications. In the studied taxa, these "modules" have in most cases been shifted fore and back on the trajectory relative to the Amia sequence, but did not disintegrate. Such "modules" might indicate a high degree of evolutionary limitation (constraint).

  16. Podargiform Affinities of the Enigmatic Fluvioviridavis platyrhamphus and the Early Diversification of Strisores (“Caprimulgiformes” + Apodiformes)

    Science.gov (United States)

    Nesbitt, Sterling J.; Ksepka, Daniel T.; Clarke, Julia A.

    2011-01-01

    Background The early Eocene Green River Formation avifauna preserves exceptional exemplars of the earliest unambiguous stem representatives of many extant avian clades. We identify the basal-most member of Podargiformes (extant and fossil stem lineage frogmouths) based on a new specimen of Fluvioviridavis platyrhamphus, a unique neoavian bird from the Fossil Butte Member of the Green River Formation of Wyoming. Extant frogmouths (Podargidae) comprise approximately 13 nocturnal species with an exclusively Australasian distribution. Methodology/Principal Findings The new specimen was included in a combined phylogenetic analysis of morphological (osteology and soft tissue) and molecular sequence (cytochrome b, c-myc exon 3, and RAG) data sampling species-level taxa from both extant and extinct members of Steatornithidae, Podargidae, Caprimulgidae, Nyctibiidae, Aegothelidae, and Apodiformes ( = Strisores). New data from F. platyrhamphus help resolve phylogenetic relationships within Strisores, supporting placement of F. platyrhamphus and the European fossil form Masillapodargus longipes as basal parts of Podargiformes and also supporting a sister taxon relationship between Podargiformes and Steatornithiformes (oilbirds) within Strisores. This relationship is recovered only when fossil taxa are included, reaffirming the potential impact of stem fossil taxa on inferences of phylogenetic relationships. The well-preserved mandible and palate of the new specimen demonstrate that many of the unique characteristics of the skull that characterize the crown frogmouth clade Podargidae arose early in the evolutionary history of the clade, over 50 million years ago. Comparisons with the new specimen also indicate that Eurofluvioviridavis and Fluvioviridavis are not closely related. Conclusions/Significance Together with the European fossil frogmouth Masillapodargus, Fluvioviridavis shows that Podargiformes had a much wider geographic distribution in the past, whereas extant

  17. 47 CFR 25.271 - Control of transmitting stations.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 2 2010-10-01 2010-10-01 false Control of transmitting stations. 25.271 Section 25.271 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Technical Operations § 25.271 Control of transmitting stations. (a) The licensee of...

  18. Conserved relative timing of cranial ossification patterns in early mammalian evolution.

    Science.gov (United States)

    Sánchez-Villagra, Marcelo R; Goswami, Anjali; Weisbecker, Vera; Mock, Orin; Kuratani, Shigeru

    2008-01-01

    We analyzed a comprehensive data set of ossification sequences including seven marsupial, 13 placental and seven sauropsid species. Data are provided for the first time for two major mammalian clades, Chiroptera and Soricidae, and for two rodent species; the published sequences of three species were improved with additional sampling. The relative timing of the onset of ossification in 17 cranial elements was recorded, resulting in 136 event pairs, which were treated as characters for each species. Half of these characters are constant across all taxa, 30% are variable but phylogenetically uninformative, and 19% potentially deliver diagnostic features for clades of two or more taxa. Using the conservative estimate of heterochronic changes provided by the program Parsimov, only a few heterochronies were found to diagnose mammals, marsupials, or placentals. A later onset of ossification of the pterygoid with respect to six other cranial bones characterizes therian mammals. This result may relate to the relatively small size of this bone in this clade. One change in relative onset of ossification is hypothesized as a potential human autapomorphy in the context of the sampling made: the earlier onset of the ossification of the periotic with respect to the lacrimal and to three basicranial bones. Using the standard error of scaled ranks across all species as a measure of each element's lability in developmental timing, we found that ossification of early, middle, and late events are similarly labile, with basicranial traits the most labile in timing of onset of ossification. Despite marsupials and placental mammals diverging at least 130 Ma, few heterochronic shifts in cranial ossification diagnose these clades.

  19. [Condom effectiveness to prevent sexually transmitted diseases].

    Science.gov (United States)

    Vera, Eduardo Gayón; Orozco, Hilda Hernández; Soto, Selene Sam; Aburto, Esther Lombardo

    2008-02-01

    Sexual transmitted diseases (included HIV/AIDS) are a common and preventable cause of perinatal morbidity and mortality. When used consistently and correctly, condoms are effective to prevent these diseases, however, its protection does not account for 100%. To know the effectiveness of male condom, through bibliographic evidence, to prevent sexual transmitted infections in heterosexual serodiscordant partners. A bibliographical review of Medline/Pubmed, LILACS and Cochrane databases, and publications of the National Health Institutes, Centers for Disease Control and Prevention, World Health Organization, and WHO AIDS Global Program was done to analyze male condom effectiveness to prevent sexual transmitted diseases. Reports demonstrated that male condom protection against HIV/AIDS in heterosexual serodiscordant partners goes from 60 to 95%. Most recent information (2006) showed 80%. Two studies demonstrated no HPV protection with male condom, and another one 70% of protection. Male condom demonstrated no HPV-1 protection, but decrease of risk in HVS-2 transmission in women (0.85 of protection). Male condom protection against sexual transmitted diseases is not 100%. There must be used additional measures that have demonstrated its utility to decrease transmission risk.

  20. Transmit beamforming for optimal second-harmonic generation.

    Science.gov (United States)

    Hoilund-Kaupang, Halvard; Masoy, Svein-Erik

    2011-08-01

    A simulation study of transmit ultrasound beams from several transducer configurations is conducted to compare second-harmonic imaging at 3.5 MHz and 11 MHz. Second- harmonic generation and the ability to suppress near field echoes are compared. Each transducer configuration is defined by a chosen f-number and focal depth, and the transmit pressure is estimated to not exceed a mechanical index of 1.2. The medium resembles homogeneous muscle tissue with nonlinear elasticity and power-law attenuation. To improve computational efficiency, the KZK equation is utilized, and all transducers are circular-symmetric. Previous literature shows that second-harmonic generation is proportional to the square of the transmit pressure, and that transducer configurations with different transmit frequencies, but equal aperture and focal depth in terms of wavelengths, generate identical second-harmonic fields in terms of shape. Results verify this for a medium with attenuation f1. For attenuation f1.1, deviations are found, and the high frequency subsequently performs worse than the low frequency. The results suggest that high frequencies are less able to suppress near-field echoes in the presence of a heterogeneous body wall than low frequencies.

  1. Evaluation of transmitted images by teleradiology system

    International Nuclear Information System (INIS)

    Hoshikawa, Yoshikazu

    1993-01-01

    Teleradiology system is a combination of digital data networks and computer systems, which is the electric transmission of radiographs and/or radiologic images from local to center radiological system. The author evaluated reproducibility of transmitted images using Photophone (Image Data Corporation) as teleradiology system. Proven cases of abdominal free air (38 plain films, 15 CT), pneumothorax (24 plain films, 20 CT) and small bowel obstruction (30 plain films, 8 CT) were transmitted. Findings could be identified on non-magnified plain films in 75.6%, 83.3% and 96.7% respectively and on magnified CT in 100%, 100% and 100%. Transmitted images of 57 cases of abdominal trauma were read for positive findings and diagnosis by three radiologists. Average positive ratio was 47.3% on plain films and 70.9% on CT. Diagnosis was correct in 66.7% on CT. Specificity and sensitivity were 81.9% and 61.6% respectively on plain film and 88.6% and 93.9% on CT. The accuracy of transmitted images appears to be unsatisfactory on this study. It is suggested that the system is useful for consultation of already identified findings on the original images. (author)

  2. Evaluation of transmitted images by teleradiology system

    Energy Technology Data Exchange (ETDEWEB)

    Hoshikawa, Yoshikazu (St. Marianna Univ., Kawasaki (Japan). School of Medicine)

    1993-12-01

    Teleradiology system is a combination of digital data networks and computer systems, which is the electric transmission of radiographs and/or radiologic images from local to center radiological system. The author evaluated reproducibility of transmitted images using Photophone (Image Data Corporation) as teleradiology system. Proven cases of abdominal free air (38 plain films, 15 CT), pneumothorax (24 plain films, 20 CT) and small bowel obstruction (30 plain films, 8 CT) were transmitted. Findings could be identified on non-magnified plain films in 75.6%, 83.3% and 96.7% respectively and on magnified CT in 100%, 100% and 100%. Transmitted images of 57 cases of abdominal trauma were read for positive findings and diagnosis by three radiologists. Average positive ratio was 47.3% on plain films and 70.9% on CT. Diagnosis was correct in 66.7% on CT. Specificity and sensitivity were 81.9% and 61.6% respectively on plain film and 88.6% and 93.9% on CT. The accuracy of transmitted images appears to be unsatisfactory on this study. It is suggested that the system is useful for consultation of already identified findings on the original images. (author).

  3. Seven wood-inhabiting new species of the genus Trichoderma (Fungi, Ascomycota) in Viride clade.

    Science.gov (United States)

    Qin, Wen-Tao; Zhuang, Wen-Ying

    2016-06-01

    More than 200 recent collections of Trichoderma from China were examined and 16 species belonging to the Viride clade were identified based on integrated studies of phenotypic and molecular data. Among them, seven wood-inhabiting new species, T. albofulvopsis, T. densum, T. laevisporum, T. sinokoningii, T. sparsum, T. sphaerosporum and T. subviride, are found. They form trichoderma- to verticillium-like conidiophores, lageniform to subulate phialides and globose to ellipsoidal conidia, but vary greatly in colony features, growth rates, and sizes of phialides and conidia. To explore their taxonomic positions, the phylogenetic tree including all the known species of the Viride clade is constructed based on sequence analyses of the combined RNA polymerase II subunit b and translation elongation factor 1 alpha exon genes. Our results indicated that the seven new species were well-located in the Koningii, Rogersonii and Neorufum subclades as well as a few independent terminal branches. They are clearly distinguishable from any existing species. Morphological distinctions and sequence divergences between the new species and their close relatives were discussed.

  4. Autecology of crenarchaeotal and bacterial clades in marine sediments and microbial mats

    OpenAIRE

    Kubo, Kyoko

    2011-01-01

    The focus of this thesis was the autecology of the Miscellaneous Crenarchaeotal Group (MCG), a phylum-level clade of Archaea occurring mostly in marine sediments. Sequences of MCG 16S rRNA genes have been retrieved from a wide range of marine and terrestrial habitats, such as deep subsurface sediments, hydrothermal sediments, mud volcanoes, estuaries, hot springs and freshwater lake sediments. MCG members seem to have no general preferences for a particular temperature or salinity. So far, no...

  5. Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms.

    Science.gov (United States)

    Anderson, Frank E; Williams, Bronwyn W; Horn, Kevin M; Erséus, Christer; Halanych, Kenneth M; Santos, Scott R; James, Samuel W

    2017-05-30

    Earthworms (Crassiclitellata) are a diverse group of annelids of substantial ecological and economic importance. Earthworms are primarily terrestrial infaunal animals, and as such are probably rather poor natural dispersers. Therefore, the near global distribution of earthworms reflects an old and likely complex evolutionary history. Despite a long-standing interest in Crassiclitellata, relationships among and within major clades remain unresolved. In this study, we evaluate crassiclitellate phylogenetic relationships using 38 new transcriptomes in combination with publicly available transcriptome data. Our data include representatives of nearly all extant earthworm families and a representative of Moniligastridae, another terrestrial annelid group thought to be closely related to Crassiclitellata. We use a series of differentially filtered data matrices and analyses to examine the effects of data partitioning, missing data, compositional and branch-length heterogeneity, and outgroup inclusion. We recover a consistent, strongly supported ingroup topology irrespective of differences in methodology. The topology supports two major earthworm clades, each of which consists of a Northern Hemisphere subclade and a Southern Hemisphere subclade. Divergence time analysis results are concordant with the hypothesis that these north-south splits are the result of the breakup of the supercontinent Pangaea. These results support several recently proposed revisions to the classical understanding of earthworm phylogeny, reveal two major clades that seem to reflect Pangaean distributions, and raise new questions about earthworm evolutionary relationships.

  6. Genomic differentiation among two strains of the PS1 clade isolated from geographically separated marine habitats

    KAUST Repository

    Jimenez Infante, Francy M.; Ngugi, David; Alam, Intikhab; Rashid, Mamoon; Ba Alawi, Wail; Kamau, Allan; Bajic, Vladimir B.; Stingl, Ulrich

    2014-01-01

    Using dilution-to-extinction cultivation, we isolated a strain affiliated with the PS1 clade from surface waters of the Red Sea. Strain RS24 represents the second isolate of this group of marine Alphaproteobacteria after IMCC14465 that was isolated

  7. Molecular-based rapid inventories of sympatric diversity: a comparison of DNA barcode clustering methods applied to geography-based vs clade-based sampling of amphibians.

    Science.gov (United States)

    Paz, Andrea; Crawford, Andrew J

    2012-11-01

    Molecular markers offer a universal source of data for quantifying biodiversity. DNA barcoding uses a standardized genetic marker and a curated reference database to identify known species and to reveal cryptic diversity within wellsampled clades. Rapid biological inventories, e.g. rapid assessment programs (RAPs), unlike most barcoding campaigns, are focused on particular geographic localities rather than on clades. Because of the potentially sparse phylogenetic sampling, the addition of DNA barcoding to RAPs may present a greater challenge for the identification of named species or for revealing cryptic diversity. In this article we evaluate the use of DNA barcoding for quantifying lineage diversity within a single sampling site as compared to clade-based sampling, and present examples from amphibians. We compared algorithms for identifying DNA barcode clusters (e.g. species, cryptic species or Evolutionary Significant Units) using previously published DNA barcode data obtained from geography-based sampling at a site in Central Panama, and from clade-based sampling in Madagascar. We found that clustering algorithms based on genetic distance performed similarly on sympatric as well as clade-based barcode data, while a promising coalescent-based method performed poorly on sympatric data. The various clustering algorithms were also compared in terms of speed and software implementation. Although each method has its shortcomings in certain contexts, we recommend the use of the ABGD method, which not only performs fairly well under either sampling method, but does so in a few seconds and with a user-friendly Web interface.

  8. Production of three symbiosis-related fatty acids by Symbiodinium types in clades A-F associated with marine invertebrate larvae

    Science.gov (United States)

    Mies, M.; Chaves-Filho, A. B.; Miyamoto, S.; Güth, A. Z.; Tenório, A. A.; Castro, C. B.; Pires, D. O.; Calderon, E. N.; Sumida, P. Y. G.

    2017-12-01

    Symbiodinium are dinoflagellates engaged in a mutualistic symbiosis with multiple coral reef taxa. They are divided in nine different clades (A-I), which typically associate with different hosts. However, very little information is available on metabolic differences in Symbiodinium types, especially when associated with metazoan larvae. We tested whether three ω3 fatty acids (stearidonic acid, SDA; docosapentaenoic acid, DPA; and docosahexaenoic acid, DHA) that are typically translocated from Symbiodinium to its host are produced by Symbiodinium types within clades A-F associated with Mussismilia hispida (scleractinian coral), Berghia stephanieae (nudibranch), and Tridacna crocea (giant clam) larvae. We acquired and spawned broodstock for each host, cultured their larvae, and offered Symbiodinium types belonging to clades A-F. Samples were taken during a 72-h window after the offer of Symbiodinium, and fatty acids were extracted and analyzed by gas chromatography. The concentrations of SDA and DPA for all host larvae-dinoflagellate associations were low and variable, without trends. However, M. hispida planula larvae associated with Symbiodinium A1 and C1 had a statistically significant higher amount of DHA. The veliger larvae of B. stephanieae digested the Symbiodinium, and the amount of DHA remained constant throughout the experiment. The veliger larvae of T. crocea associated with Symbiodinium A1 and C1 also presented a higher amount of DHA, although not statistically different from the other types. These results show that Symbiodinium A1 and C1, in the case of M. hispida and T. crocea (which usually harbor strains within clades A and C), may contribute a small amount of DHA to the larvae of these organisms and form a stronger mutualism than other strains.

  9. USACE AIS Transmit Technical Support Summary Report

    Science.gov (United States)

    2014-09-01

    the TAG block for the correct transmitters, and then send to the USACE AIS network. B. Outbound openings in the USCG firewall for the USCG Message...USACE AIS Transmit Technical Support Summary Report Distribution Statement A: Approved for public release; distribution is unlimited...September 2014 Report No. CD-D-09-15 USACE AIS Transmit Technical Support Summary Report ii UNCLAS//Public | CG-926 RDC | I. Gonin et al. Public

  10. Roseobacter-clade bacteria as probiotics in marine larvaeculture

    DEFF Research Database (Denmark)

    Grotkjær, Torben

    Disease caused by fish pathogenic bacteria can cause large scale crashes in marine fish larval rearing units. One of the biggest challenges for aquaculture is the management of these bacterial outbreaks. Vaccines can be admitted to fish but only the juvenile and the adult fish because they need...... to have a mature immune system. This means that the larvae of the fish, until they are 2-3 weeks old are more prone to bacterial infections. A short term solution is antibiotics but this leaves way for the selection for antibiotic resistance among the pathogenic bacteria, which again can be transferred...... to human pathogens. Alternatives are therefore needed and one could be the use of probiotic bacteria. Marine bacteria from the Roseobacter clade (Phaeobacter inhibens) have shown great potential as probiotic bacteria, and we have hypothesized that they could be used to antagonize pathogenic fish...

  11. Changing patterns in HIV-1 non-B clade prevalence and diversity in Italy over three decades

    DEFF Research Database (Denmark)

    Lai, A; Riva, C; Marconi, A

    2010-01-01

    HIV-1 non-B subtypes have recently entered Western Europe following immigration from other regions. The distribution of non-B clades and their association with demographic factors, over the entire course of the HIV-1 epidemic, have not been fully investigated in Italy....

  12. Genetic variation within Symbiodinium clade B from the coral genus Madracis in the Caribbean (Netherlands Antilles)

    NARCIS (Netherlands)

    Diekmann, O.E.; Olsen, J.L.; Stam, W.T.; Bak, R.P M

    The internal transcribed spacer (ITS) region was sequenced in symbiotic dinoflagellates (zooxanthellae) from five morphospecies in the genus Madracis. The phylogeny of the symbionts is congruent with a companion phylogeny of the coral host. Comparison with known clade B symbiont ITS types reveals

  13. Real-time PCR reveals a high incidence of Symbiodinium clade D at low levels in four scleractinian corals across the Great Barrier Reef : implications for symbiont shuffling

    NARCIS (Netherlands)

    Mieog, J. C.; van Oppen, M. J. H.; Cantin, N. E.; Stam, W. T.; Olsen, J. L.

    Reef corals form associations with an array of genetically and physiologically distinct endosymbionts from the genus Symbiodinium. Some corals harbor different clades of symbionts simultaneously, and over time the relative abundances of these clades may change through a process called symbiont

  14. A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies

    Directory of Open Access Journals (Sweden)

    Turmel Monique

    2007-01-01

    Full Text Available Abstract Background The Viridiplantae comprise two major phyla: the Streptophyta, containing the charophycean green algae and all land plants, and the Chlorophyta, containing the remaining green algae. Despite recent progress in unravelling phylogenetic relationships among major green plant lineages, problematic nodes still remain in the green tree of life. One of the major issues concerns the scaly biflagellate Mesostigma viride, which is either regarded as representing the earliest divergence of the Streptophyta or a separate lineage that diverged before the Chlorophyta and Streptophyta. Phylogenies based on chloroplast and mitochondrial genomes support the latter view. Because some green plant lineages are not represented in these phylogenies, sparse taxon sampling has been suspected to yield misleading topologies. Here, we describe the complete chloroplast DNA (cpDNA sequence of the early-diverging charophycean alga Chlorokybus atmophyticus and present chloroplast genome-based phylogenies with an expanded taxon sampling. Results The 152,254 bp Chlorokybus cpDNA closely resembles its Mesostigma homologue at the gene content and gene order levels. Using various methods of phylogenetic inference, we analyzed amino acid and nucleotide data sets that were derived from 45 protein-coding genes common to the cpDNAs of 37 green algal/land plant taxa and eight non-green algae. Unexpectedly, all best trees recovered a robust clade uniting Chlorokybus and Mesostigma. In protein trees, this clade was sister to all streptophytes and chlorophytes and this placement received moderate support. In contrast, gene trees provided unequivocal support to the notion that the Mesostigma + Chlorokybus clade represents the earliest-diverging branch of the Streptophyta. Independent analyses of structural data (gene content and/or gene order and of subsets of amino acid data progressively enriched in slow-evolving sites led us to conclude that the latter topology

  15. Broad antibody mediated cross-neutralization and preclinical immunogenicity of new codon-optimized HIV-1 clade CRF02_AG and G primary isolates.

    Directory of Open Access Journals (Sweden)

    Simon M Agwale

    Full Text Available Creation of an effective vaccine for HIV has been an elusive goal of the scientific community for almost 30 years. Neutralizing antibodies are assumed to be pivotal to the success of a prophylactic vaccine but previous attempts to make an immunogen capable of generating neutralizing antibodies to primary "street strain" isolates have resulted in responses of very limited breadth and potency. The objective of the study was to determine the breadth and strength of neutralizing antibodies against autologous and heterologous primary isolates in a cohort of HIV-1 infected Nigerians and to characterize envelopes from subjects with particularly broad or strong immune responses for possible use as vaccine candidates in regions predominated by HIV-1 CRF02_AG and G subtypes. Envelope vectors from a panel of primary Nigerian isolates were constructed and tested with plasma/sera from the same cohort using the PhenoSense HIV neutralizing antibody assay (Monogram Biosciences Inc, USA to assess the breadth and potency of neutralizing antibodies. The immediate goal of this study was realized by the recognition of three broadly cross-neutralizing sera: (NG2-clade CRF02_AG, NG3-clade CRF02_AG and NG9- clade G. Based on these findings, envelope gp140 sequences from NG2 and NG9, complemented with a gag sequence (Clade G and consensus tat (CRF02_AG and G antigens have been codon-optimized, synthesized, cloned and evaluated in BALB/c mice. The intramuscular administration of these plasmid DNA constructs, followed by two booster DNA immunizations, induced substantial specific humoral response against all constructs and strong cellular responses against the gag and tat constructs. These preclinical findings provide a framework for the design of candidate vaccine for use in regions where the HIV-1 epidemic is driven by clades CRF02_AG and G.

  16. Broad antibody mediated cross-neutralization and preclinical immunogenicity of new codon-optimized HIV-1 clade CRF02_AG and G primary isolates.

    Science.gov (United States)

    Agwale, Simon M; Forbi, Joseph C; Notka, Frank; Wrin, Terri; Wild, Jens; Wagner, Ralf; Wolf, Hans

    2011-01-01

    Creation of an effective vaccine for HIV has been an elusive goal of the scientific community for almost 30 years. Neutralizing antibodies are assumed to be pivotal to the success of a prophylactic vaccine but previous attempts to make an immunogen capable of generating neutralizing antibodies to primary "street strain" isolates have resulted in responses of very limited breadth and potency. The objective of the study was to determine the breadth and strength of neutralizing antibodies against autologous and heterologous primary isolates in a cohort of HIV-1 infected Nigerians and to characterize envelopes from subjects with particularly broad or strong immune responses for possible use as vaccine candidates in regions predominated by HIV-1 CRF02_AG and G subtypes. Envelope vectors from a panel of primary Nigerian isolates were constructed and tested with plasma/sera from the same cohort using the PhenoSense HIV neutralizing antibody assay (Monogram Biosciences Inc, USA) to assess the breadth and potency of neutralizing antibodies. The immediate goal of this study was realized by the recognition of three broadly cross-neutralizing sera: (NG2-clade CRF02_AG, NG3-clade CRF02_AG and NG9- clade G). Based on these findings, envelope gp140 sequences from NG2 and NG9, complemented with a gag sequence (Clade G) and consensus tat (CRF02_AG and G) antigens have been codon-optimized, synthesized, cloned and evaluated in BALB/c mice. The intramuscular administration of these plasmid DNA constructs, followed by two booster DNA immunizations, induced substantial specific humoral response against all constructs and strong cellular responses against the gag and tat constructs. These preclinical findings provide a framework for the design of candidate vaccine for use in regions where the HIV-1 epidemic is driven by clades CRF02_AG and G.

  17. Discourse on the values transmitted in universities Uganda ...

    African Journals Online (AJOL)

    The study delved into the values transmitted in Universities in Uganda. Data were collected from a sample of 850 respondents who were drawn from faith-based, for–profit and public universities in the country. It was found that material, social/ public, personal and religious values are transmitted to students in the selected ...

  18. Integrated Reconfigurable High-Voltage Transmitting Circuit for CMUTs

    DEFF Research Database (Denmark)

    Llimos Muntal, Pere; Larsen, Dennis Øland; Jørgensen, Ivan Harald Holger

    2014-01-01

    -out and measurements are performed on the integrated circuit. The transmitting circuit is reconfigurable externally making it able to drive a wide variety of CMUTs. The transmitting circuit can generate several pulse shapes, pulse voltages up to 100 V, maximum pulse range of 50 V and frequencies up to 5 MHz. The area...

  19. Emergence of multiple clade 2.3.2.1 influenza A (H5N1) virus subgroups in Vietnam and detection of novel reassortants.

    Science.gov (United States)

    Creanga, Adrian; Thi Nguyen, Diep; Gerloff, Nancy; Thi Do, Hoa; Balish, Amanda; Dang Nguyen, Hoang; Jang, Yunho; Thi Dam, Vui; Thor, Sharmi; Jones, Joyce; Simpson, Natosha; Shu, Bo; Emery, Shannon; Berman, LaShondra; Nguyen, Ha T; Bryant, Juliet E; Lindstrom, Steve; Klimov, Alexander; Donis, Ruben O; Davis, C Todd; Nguyen, Tung

    2013-09-01

    Phylogenetic analyses of 169 influenza A(H5N1) virus genomes were conducted for samples collected through active surveillance and outbreak responses in Vietnam between September 2010 and September 2012. While clade 1.1 viruses persisted in southern regions, three genetically distinct subgroups of clade 2.3.2.1 were found in northern and central Vietnam. The identification of each subgroup corresponded with detection of novel reassortants, likely due to their overlapping circulation throughout the country. While the previously identified clade 1.1 and A/Hubei/1/2010-like 2.3.2.1 genotypes remained the predominant viruses detected, four viruses were found to be reassortants between A/Hubei/1/2010-like (HA, NA, PB2, PB1, PA, NP) and A/duck/Vietnam/NCVD-885/2010-like (M, NS) viruses and one virus was identified as having A/duck/Vietnam/NCVD-885/2010-like HA, NA, PB1, and NP with A/Hubei/1/2010-like PB2 and PA genes. Additionally, clade 2.3.2.1 A/Hong Kong/6841/2010-like viruses, first detected in mid-2012, were identified as reassortants comprised of A/Hubei/1/2010-like PB2 and PA and A/duck/Vietnam/NCVD-885/2010-like PB1, NP, NA, M, NS genes. Published by Elsevier Inc.

  20. Note on transmitted complexity for quantum dynamical systems

    Science.gov (United States)

    Watanabe, Noboru; Muto, Masahiro

    2017-10-01

    Transmitted complexity (mutual entropy) is one of the important measures for quantum information theory developed recently in several ways. We will review the fundamental concepts of the Kossakowski, Ohya and Watanabe entropy and define a transmitted complexity for quantum dynamical systems. This article is part of the themed issue `Second quantum revolution: foundational questions'.

  1. Stigma and stereotypes: women and sexually transmitted infections.

    Science.gov (United States)

    East, Leah; Jackson, Debra; O'Brien, Louise; Peters, Kathleen

    2012-01-01

    Sexually transmitted infections have long been associated with stigma and stereotypes due to their very nature. Throughout history sexually transmitted infections have been associated with female prostitution and deviant immoral behaviour making women who contract these infections particularly vulnerable to being stigmatised and stereotyped. Although the stigma attached to such infections has previously been documented in the literature, the aim of this research was to gain in depth insight into young Australian women's experiences of having a sexually transmitted infection from a feminist perspective. Findings from this study provide insight into the onerous effects stigma can have on women with these infections and sheds light on how these effects can influence self-perceptions, fear of rejection and feelings of unworthiness. These findings can provide nurses with greater understanding and insight into the effects of stigma on women's experiences of having a sexually transmitted infection. Having this understanding and insight has the potential to promote therapeutic care and minimise the stigma that may be felt among women who have contracted this type of infection.

  2. Phylogenetic analysis of canine distemper virus in South America clade 1 reveals unique molecular signatures of the local epidemic.

    Science.gov (United States)

    Fischer, Cristine D B; Gräf, Tiago; Ikuta, Nilo; Lehmann, Fernanda K M; Passos, Daniel T; Makiejczuk, Aline; Silveira, Marcos A T; Fonseca, André S K; Canal, Cláudio W; Lunge, Vagner R

    2016-07-01

    Canine distemper virus (CDV) is a highly contagious pathogen for domestic dogs and several wild carnivore species. In Brazil, natural infection of CDV in dogs is very high due to the large non-vaccinated dog population, a scenario that calls for new studies on the molecular epidemiology. This study investigates the phylodynamics and amino-acid signatures of CDV epidemic in South America by analyzing a large dataset compiled from publicly available sequences and also by collecting new samples from Brazil. A population of 175 dogs with canine distemper (CD) signs was sampled, from which 89 were positive for CDV, generating 42 new CDV sequences. Phylogenetic analysis of the new and publicly available sequences revealed that Brazilian sequences mainly clustered in South America 1 (SA1) clade, which has its origin estimated to the late 1980's. The reconstruction of the demographic history in SA1 clade showed an epidemic expanding until the recent years, doubling in size every nine years. SA1 clade epidemic distinguished from the world CDV epidemic by the emergence of the R580Q strain, a very rare and potentially detrimental substitution in the viral genome. The R580Q substitution was estimated to have happened in one single evolutionary step in the epidemic history in SA1 clade, emerging shortly after introduction to the continent. Moreover, a high prevalence (11.9%) of the Y549H mutation was observed among the domestic dogs sampled here. This finding was associated (p<0.05) with outcome-death and higher frequency in mixed-breed dogs, the later being an indicator of a continuous exchange of CDV strains circulating among wild carnivores and domestic dogs. The results reported here highlight the diversity of the worldwide CDV epidemic and reveal local features that can be valuable for combating the disease. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Sentinel surveillance of HIV-1 transmitted drug resistance, acute infection and recent infection.

    Directory of Open Access Journals (Sweden)

    Hong-Ha M Truong

    Full Text Available HIV-1 acute infection, recent infection and transmitted drug resistance screening was integrated into voluntary HIV counseling and testing (VCT services to enhance the existing surveillance program in San Francisco. This study describes newly-diagnosed HIV cases and characterizes correlates associated with infection.A consecutive sample of persons presenting for HIV VCT at the municipal sexually transmitted infections (STI clinic from 2004 to 2006 (N = 9,868 were evaluated by standard enzyme-linked immunoassays (EIA. HIV antibody-positive specimens were characterized as recent infections using a less-sensitive EIA. HIV-RNA pooled testing was performed on HIV antibody-negative specimens to identify acute infections. HIV antibody-positive and acute infection specimens were evaluated for drug resistance by sequence analysis. Multivariable logistic regression was performed to evaluate associations. The 380 newly-diagnosed HIV cases included 29 acute infections, 128 recent infections, and 47 drug-resistant cases, with no significant increases or decreases in prevalence over the three years studied. HIV-1 transmitted drug resistance prevalence was 11.0% in 2004, 13.4% in 2005 and 14.9% in 2006 (p = 0.36. Resistance to non-nucleoside reverse transcriptase inhibitors (NNRTI was the most common pattern detected, present in 28 cases of resistance (59.6%. Among MSM, recent infection was associated with amphetamine use (AOR = 2.67; p<0.001, unprotected anal intercourse (AOR = 2.27; p<0.001, sex with a known HIV-infected partner (AOR = 1.64; p = 0.02, and history of gonorrhea (AOR = 1.62; p = 0.03.New HIV diagnoses, recent infections, acute infections and transmitted drug resistance prevalence remained stable between 2004 and 2006. Resistance to NNRTI comprised more than half of the drug-resistant cases, a worrisome finding given its role as the backbone of first-line antiretroviral therapy in San Francisco as well as worldwide. The integration of HIV-1 drug

  4. An Evaluation of Phylogenetic Methods for Reconstructing Transmitted HIV Variants using Longitudinal Clonal HIV Sequence Data

    Science.gov (United States)

    McCloskey, Rosemary M.; Liang, Richard H.; Harrigan, P. Richard; Brumme, Zabrina L.

    2014-01-01

    ABSTRACT A population of human immunodeficiency virus (HIV) within a host often descends from a single transmitted/founder virus. The high mutation rate of HIV, coupled with long delays between infection and diagnosis, make isolating and characterizing this strain a challenge. In theory, ancestral reconstruction could be used to recover this strain from sequences sampled in chronic infection; however, the accuracy of phylogenetic techniques in this context is unknown. To evaluate the accuracy of these methods, we applied ancestral reconstruction to a large panel of published longitudinal clonal and/or single-genome-amplification HIV sequence data sets with at least one intrapatient sequence set sampled within 6 months of infection or seroconversion (n = 19,486 sequences, median [interquartile range] = 49 [20 to 86] sequences/set). The consensus of the earliest sequences was used as the best possible estimate of the transmitted/founder. These sequences were compared to ancestral reconstructions from sequences sampled at later time points using both phylogenetic and phylogeny-naive methods. Overall, phylogenetic methods conferred a 16% improvement in reproducing the consensus of early sequences, compared to phylogeny-naive methods. This relative advantage increased with intrapatient sequence diversity (P reconstructing ancestral indel variation, especially within indel-rich regions of the HIV genome. Although further improvements are needed, our results indicate that phylogenetic methods for ancestral reconstruction significantly outperform phylogeny-naive alternatives, and we identify experimental conditions and study designs that can enhance accuracy of transmitted/founder virus reconstruction. IMPORTANCE When HIV is transmitted into a new host, most of the viruses fail to infect host cells. Consequently, an HIV infection tends to be descended from a single “founder” virus. A priority target for the vaccine research, these transmitted/founder viruses are

  5. A Middle Jurassic abelisaurid from Patagonia and the early diversification of theropod dinosaurs.

    Science.gov (United States)

    Pol, Diego; Rauhut, Oliver W M

    2012-08-22

    Abelisaurids are a clade of large, bizarre predatory dinosaurs, most notable for their high, short skulls and extremely reduced forelimbs. They were common in Gondwana during the Cretaceous, but exceedingly rare in the Northern Hemisphere. The oldest definitive abelisaurids so far come from the late Early Cretaceous of South America and Africa, and the early evolutionary history of the clade is still poorly known. Here, we report a new abelisaurid from the Middle Jurassic of Patagonia, Eoabelisaurus mefi gen. et sp. nov., which predates the so far oldest known secure member of this lineage by more than 40 Myr. The almost complete skeleton reveals the earliest evolutionary stages of the distinctive features of abelisaurids, such as the modification of the forelimb, which started with a reduction of the distal elements. The find underlines the explosive radiation of theropod dinosaurs in the Middle Jurassic and indicates an unexpected diversity of ceratosaurs at that time. The apparent endemism of abelisauroids to southern Gondwana during Pangean times might be due to the presence of a large, central Gondwanan desert. This indicates that, apart from continent-scale geography, aspects such as regional geography and climate are important to reconstruct the biogeographical history of Mesozoic vertebrates.

  6. Syndromes Associated with Sexually Transmitted Infections

    Directory of Open Access Journals (Sweden)

    Max Chernesky

    2005-01-01

    Full Text Available Excellent technologies have been developed to identify the specific microbial agents of chlamydia, gonorrhea, syphilis, herpes, chancroid, trichomoniasis, human papillomavirus and HIV infection. However, it is also crucial to recognize syndromes that may be caused by one or more sexually transmitted pathogens. When laboratory services are lacking or are inadequate to provide timely results to enable appropriate treatment, some patients must be managed and treated syndromically. Most Canadian laboratories should be able to provide diagnostic services to determine the etiology of syndromes such as cervicitis, urethritis, pelvic inflammatory disease, prostatitis, genital ulcers, sexually transmitted infection (STI-related enteric infections, epididymitis, hepatitis, ophthalmia neonatorum, vulvovaginitis and vaginosis.

  7. Evolutionary history of LINE-1 in the major clades of placental mammals.

    Directory of Open Access Journals (Sweden)

    Paul D Waters

    2007-01-01

    Full Text Available LINE-1 constitutes an important component of mammalian genomes. It has a dynamic evolutionary history characterized by the rise, fall and replacement of subfamilies. Most data concerning LINE-1 biology and evolution are derived from the human and mouse genomes and are often assumed to hold for all placentals.To examine LINE-1 relationships, sequences from the 3' region of the reverse transcriptase from 21 species (representing 13 orders across Afrotheria, Xenarthra, Supraprimates and Laurasiatheria were obtained from whole genome sequence assemblies, or by PCR with degenerate primers. These sequences were aligned and analysed.Our analysis reflects accepted placental relationships suggesting mostly lineage-specific LINE-1 families. The data provide clear support for several clades including Glires, Supraprimates, Laurasiatheria, Boreoeutheria, Xenarthra and Afrotheria. Within the afrotherian LINE-1 (AfroLINE clade, our tree supports Paenungulata, Afroinsectivora and Afroinsectiphillia. Xenarthran LINE-1 (XenaLINE falls sister to AfroLINE, providing some support for the Atlantogenata (Xenarthra+Afrotheria hypothesis.LINEs and SINEs make up approximately half of all placental genomes, so understanding their dynamics is an essential aspect of comparative genomics. Importantly, a tree of LINE-1 offers a different view of the root, as long edges (branches such as that to marsupials are shortened and/or broken up. Additionally, a robust phylogeny of diverse LINE-1 is essential in testing that site-specific LINE-1 insertions, often regarded as homoplasy-free phylogenetic markers, are indeed unique and not convergent.

  8. Tip of the clade on the top of the World—the first fossil Lophopidae (Hemiptera: Fulgoromorpha) from the Palaeocene of Tibet

    Science.gov (United States)

    Szwedo, Jacek; Stroiński, Adam; Lin, Qibin

    2015-06-01

    Lophopidae is a family of planthoppers (Hemiptera: Fulgoromorpha) present today in tropical and subtropical zones of the Old World. The most recent taxonomic studies and phylogeny of these insects do not include the extinct representatives. Therefore, each new discovery of a fossil lophopid is of high interest, giving new insights to their evolutionary history and enabling to test the proposed relationships. The recent findings of extinct Lophopidae in Europe, in various Palaeogene deposits, put in doubts their proposed evolutionary and biogeographic scenario. The new fossil from the Palaeocene of Northern Tibet is related to one of the Lophopidae clades, Apia+ group, believed to be the most advanced one, and recently distributed in the recent Sundaland-New Guinea-Queensland area. A new genus and species Gesaris gnapo gen. et sp. n. provide information on early lophopids diversity and relationships and demonstrates the necessity for a revision of the existing hypotheses for the initial diversification and distributional pattern of the Lophopidae.

  9. Analysis of Ecological Distribution and Genomic Content from a Clade of Bacteroidetes Endemic to Sulfidic Environments

    Science.gov (United States)

    Zhou, K.; Sylvan, J. B.; Hallam, S. J.

    2017-12-01

    The Bacteroidetes are a ubiquitous phylum of bacteria found in a wide variety of habitats. Marine Bacteroidetes are known to utilize complex carbohydrates and have a potentially important role in the global carbon cycle through processing these compounds, which are not digestible by many other microbes. Some members of the phylum are known to perform denitrification and are facultative anaerobes, but Bacteroidetes are not known to participate in sulfur redox cycling. Recently, it was shown that a clade of uncultured Bacteroidetes, including the VC2.1_Bac22 group, appears to be endemic to sulfidic environments, including hydrothermal vent sulfide chimneys, sediments and marine water column oxygen minimum zones (OMZs). This clade, dubbed the Sulfiphilic Bacteroidetes, is not detected in 16S rRNA amplicon studies from non-sulfidic environments. To test the hypothesis that the Sulphiphilic Bacteroidetes are involved in sulfur redox chemistry, we updated our meta-analysis of the clade using 16s rRNA sequences from public databases and employed single-cell genomics to survey their genomic potential using 19 single amplified genomes (SAGs) isolated from the seasonally anoxic Saanich Inlet, a seasonally hypoxic basin in British Columbia. Initial analysis of these SAGs indicates the Sulphiphilic Bacteroidetes may perform sulfur redox reactions using a three gene psrABC operon encoding the polysulfide reductase enzyme complex with a thiosulfate sulfurtransferase (rhodanese), which putatively uses cyanide to convert thiosulfate to sulfite, just upstream. Interestingly, this is the same configuration as discovered recently in some Marine Group A bacteria. Further aspects of the Sulphiphilic Bacteroidetes' genomic potential will be presented in light of their presence in sulfidic environments.

  10. Adaptive single-antenna transmit selection with interference suppression

    KAUST Repository

    Radaydeh, Redha Mahmoud Mesleh

    2011-10-01

    This paper studies the performance of adaptive transmit selection with co-channel interference suppression in multipath fading channels. The adaptive selection algorithms are configured for single-antenna bandwidth-efficient or power-efficient transmission with as low transmit channel estimations as possible. Due to the fact that the number of active co-channel interfering signals and their corresponding powers experience random behavior, the adaptation to channels conditions, assuming uniform buffer and traffic loading, is proposed to be jointly based on the transmit channels instantaneous signal-to-noise ratios (SNRs) and signal-to-interference-plus-noise ratios (SINRs). Two interference cancelation algorithms are considered. The first algorithm assumes that the receiver eliminates the impact of the strongest subset of interferers, whereas the second algorithm suggests random cancelation of interferers to further reduce processing complexity. The impact of outdated ordering of interferers powers on the efficiency of interference cancelation, and the effect of imperfect prediction of transmit channels for desired user adaptation are investigated. Analytical formulations for various performance measures and comparisons between the performance and processing complexity of different adaptation schemes are presented. © 2011 IEEE.

  11. Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

    Science.gov (United States)

    Feng, Yan-Jie; Liang, Dan; Hillis, David M.; Cannatella, David C.; Zhang, Peng

    2017-01-01

    Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous–Paleogene (K–Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K–Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation. PMID:28673970

  12. Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous-Paleogene boundary.

    Science.gov (United States)

    Feng, Yan-Jie; Blackburn, David C; Liang, Dan; Hillis, David M; Wake, David B; Cannatella, David C; Zhang, Peng

    2017-07-18

    Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous-Paleogene (K-Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K-Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation.

  13. Toward a comprehensive phylogenetic reconstruction of the evolutionary history of mitogen-activated protein kinases in the plant kingdom.

    Science.gov (United States)

    Janitza, Philipp; Ullrich, Kristian Karsten; Quint, Marcel

    2012-01-01

    The mitogen-activated protein kinase (MAPK) pathway is a three-tier signaling cascade that transmits cellular information from the plasma membrane to the cytoplasm where it triggers downstream responses. The MAPKs represent the last step in this cascade and are activated when both tyrosine and threonine residues in a conserved TxY motif are phosphorylated by MAPK kinases, which in turn are themselves activated by phosphorylation by MAPK kinase kinases. To understand the molecular evolution of MAPKs in the plant kingdom, we systematically conducted a Hidden-Markov-Model based screen to identify MAPKs in 13 completely sequenced plant genomes. In this analysis, we included green algae, bryophytes, lycophytes, and several mono- and eudicotyledonous species covering >800 million years of evolution. The phylogenetic relationships of the 204 identified MAPKs based on Bayesian inference facilitated the retraction of the sequence of emergence of the four major clades that are characterized by the presence of a TDY or TEY-A/TEY-B/TEY-C type kinase activation loop. We present evidence that after the split of TDY- and TEY-type MAPKs, initially the TEY-C clade emerged. This was followed by the TEY-B clade in early land plants until the TEY-A clade finally emerged in flowering plants. In addition to these well characterized clades, we identified another highly conserved clade of 45 MAPK-likes, members of which were previously described as Mak-homologous kinases. In agreement with their essential functions, molecular population genetic analysis of MAPK genes in Arabidopsis thaliana accessions reveal that purifying selection drove the evolution of the MAPK family, implying strong functional constraints on MAPK genes. Closely related MAPKs most likely subfunctionalized, a process in which differential transcriptional regulation of duplicates may be involved.

  14. Towards a comprehensive phylogenetic reconstruction of the evolutionary history of mitogen-activated protein kinases in the plant kingdom

    Directory of Open Access Journals (Sweden)

    Philipp eJanitza

    2012-12-01

    Full Text Available The mitogen-activated protein kinase (MAPK pathway is a three-tier signaling cascade that transmits cellular information from the plasma membrane to the cytoplasm where it triggers downstream responses. The MAPKs represent the last step in this cascade and are activated when both tyrosine and threonine residues in a conserved TxY motif are phosphorylated by MAPK kinases, which in turn are themselves activated by phosphorylation by MAPK kinase kinases. To understand the molecular evolution of MAPKs in the plant kingdom, we systematically conducted a Hidden-Markov-Model based screen to identify MAPKs in 13 completely sequenced plant genomes. In this analysis, we included green algae, bryophytes, lycophytes, and several mono- and dicotyledonous species covering >800 million years of evolution. The phylogenetic relationships of the 204 identified MAPKs based on Bayesian inference facilitated the retraction of the sequence of emergence of the four major clades that are characterized by the presence of a TDY or TEY-A/TEY-B/TEY-C type kinase activation loop. We present evidence that after the split of TDY- and TEY-type MAPKs, initially the TEY-C clade emerged. This was followed by the TEY-B clade in early land plants until the TEY-A clade finally emerged in flowering plants. In addition to these well characterized clades, we identified another highly conserved clade of 45 MAPK-likes, members of which were previously described as MHKs. In agreement with their essential functions, molecular population genetic analysis of MAPK genes in Arabidopsis thaliana accessions reveal that purifying selection drove the evolution of the MAPK family, implying strong functional constraints on MAPK genes. Closely related MAPKs most likely subfunctionalized, a process in which differential transcriptional regulation of duplicates may be involved.

  15. An Early Miocene bumble bee from northern Bohemia (Hymenoptera, Apidae

    Directory of Open Access Journals (Sweden)

    Jakub Prokop

    2017-10-01

    Full Text Available A new species of fossil bumble bee (Apinae: Bombini is described and figured from Early Miocene (Burdigalian deposits of the Most Basin at the Bílina Mine, Czech Republic. Bombus trophonius sp. n., is placed within the subgenus Cullumanobombus Vogt and distinguished from the several species groups therein. The species is apparently most similar to the Nearctic B. (Cullumanobombus rufocinctus Cresson, the earliest-diverging species within the clade and the two may be related only by symplesiomorphies. The age of the fossil is in rough accordance with divergence estimations for Cullumanobombus.

  16. HIV Controllers Exhibit Enhanced Frequencies of Major Histocompatibility Complex Class II Tetramer+ Gag-Specific CD4+ T Cells in Chronic Clade C HIV-1 Infection.

    Science.gov (United States)

    Laher, Faatima; Ranasinghe, Srinika; Porichis, Filippos; Mewalal, Nikoshia; Pretorius, Karyn; Ismail, Nasreen; Buus, Søren; Stryhn, Anette; Carrington, Mary; Walker, Bruce D; Ndung'u, Thumbi; Ndhlovu, Zaza M

    2017-04-01

    Immune control of viral infections is heavily dependent on helper CD4 + T cell function. However, the understanding of the contribution of HIV-specific CD4 + T cell responses to immune protection against HIV-1, particularly in clade C infection, remains incomplete. Recently, major histocompatibility complex (MHC) class II tetramers have emerged as a powerful tool for interrogating antigen-specific CD4 + T cells without relying on effector functions. Here, we defined the MHC class II alleles for immunodominant Gag CD4 + T cell epitopes in clade C virus infection, constructed MHC class II tetramers, and then used these to define the magnitude, function, and relation to the viral load of HIV-specific CD4 + T cell responses in a cohort of untreated HIV clade C-infected persons. We observed significantly higher frequencies of MHC class II tetramer-positive CD4 + T cells in HIV controllers than progressors ( P = 0.0001), and these expanded Gag-specific CD4 + T cells in HIV controllers showed higher levels of expression of the cytolytic proteins granzymes A and B. Importantly, targeting of the immunodominant Gag41 peptide in the context of HLA class II DRB1*1101 was associated with HIV control ( r = -0.5, P = 0.02). These data identify an association between HIV-specific CD4 + T cell targeting of immunodominant Gag epitopes and immune control, particularly the contribution of a single class II MHC-peptide complex to the immune response against HIV-1 infection. Furthermore, these results highlight the advantage of the use of class II tetramers in evaluating HIV-specific CD4 + T cell responses in natural infections. IMPORTANCE Increasing evidence suggests that virus-specific CD4 + T cells contribute to the immune-mediated control of clade B HIV-1 infection, yet there remains a relative paucity of data regarding the role of HIV-specific CD4 + T cells in shaping adaptive immune responses in individuals infected with clade C, which is responsible for the majority of HIV

  17. Nosocomial Infections Transmitted Via Computers : A Literature Review

    OpenAIRE

    Atanda, Angela Achieng; Nwaoha, Nkechi Naomi

    2010-01-01

    The purpose of this review was to discuss how current literature described nosocomial infections transmitted via computers in hospitals. It also described the various methods used to disinfect computers. The research questions in this study were; What are nosocomial infections? How do contaminated computer devices transmit nosocomial infections? and What infection control methods are applied to decontaminate computers within hospitals? The aim of conducting this study was to create an aw...

  18. 22 CFR 1203.735-214 - Transmitting communications and gifts.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 2 2010-04-01 2010-04-01 true Transmitting communications and gifts. 1203.735....735-214 Transmitting communications and gifts. (a) Correspondence. In corresponding with anyone other... it to be clearly in the public interest to do so. (c) Gifts. An employee shall not act as an agent...

  19. A Theater-Based Approach to Primary Prevention of Sexual Behavior for Early Adolescents

    Science.gov (United States)

    Lieberman, Lisa D.; Berlin, Cydelle; Palen, Lori-Ann; Ashley, Olivia Silber

    2012-01-01

    Early adolescence is a crucial period for preventing teen pregnancy and sexually transmitted infections. This study evaluated STAR LO, a theater-based intervention designed to affect antecedents of sexual activity among urban early adolescents (N = 1,143). Public elementary/middle schools received the intervention or served as a wait-listed…

  20. Decreasing Prevalence of Transfusion Transmitted Infection in Indian Scenario

    Directory of Open Access Journals (Sweden)

    Tulika Chandra

    2014-01-01

    Full Text Available Transfusion transmitted infections are major problem associated with blood transfusion. Accurate estimates of risk of TTIs are essential for monitoring the safety of blood supply and evaluating the efficacy of currently employed screening procedures. The present study was carried out to assess the percentage of voluntary donors and replacement donors and to find out prevalence and changing trends of various TTIs blood donors in recent years. A study was carried out on blood units of voluntary and replacement donors which were collected from January 2008 to December 2012. On screening of 180,371 replacement units, seropositivity of transfusion transmitted disease in replacement donors was 0.15% in HIV, 1.67% in hepatitis B surface antigen, 0.49% in hepatitis C virus, 0.01% in VDRL, and 0.009% in malaria. Of 11,977 voluntary units, seropositivity of transfusion transmitted disease in voluntary donors was 0.08% in HIV, 0.24% in hepatitis B surface antigen, 0.001% in hepatitis C virus, 0.008% in VDRL (sexually transmitted disease, and 0.01% in malaria. From results it has been concluded that prevalence of transfusion transmitted infection (HIV, HBV, HCV, VDRL, and malaria was more in replacement donors in comparison to voluntary donors. Extensive donor selection and screening procedures will help in improving the blood safety.

  1. Super-Orthogonal Space-Time Turbo Transmit Diversity for CDMA

    Directory of Open Access Journals (Sweden)

    Pieter G. W. van Rooyen

    2005-05-01

    Full Text Available Studies have shown that transmit and receive diversity employing a combination of multiple transmit-receive antennas (given ideal channel state information (CSI and independent fading between antenna pairs will potentially yield maximum achievable system capacity. In this paper, the concept of a layered super-orthogonal turbo transmit diversity (SOTTD for downlink direct-sequence code-division multiple-access (CDMA systems is explored. This open-loop transmit diversity technique improves the downlink performance by using a small number of antenna elements at the base station and a single antenna at the handset. In the proposed technique, low-rate super-orthogonal code-spread CDMA is married with code-division transmit diversity (CDTD. At the mobile receiver, space-time (ST RAKE CDTD processing is combined with iterative turbo code-spread decoding to yield large ST gains. The performance of the SOTTD system is compared with single- and multiantenna turbo-coded (TC CDTD systems evaluated over a frequency-selective Rayleigh fading channel. The evaluation is done both by means of analysis and computer simulations. The performance results illustrate the superior performance of SOTTD compared to TC CDTD systems over practically the complete useful capacity range of CDMA. It is shown that the performance degradation characteristic of TC CDTD at low system loads (due to the inherent TC error floor is alleviated by the SOTTD system.

  2. The mystery of clade X: Orciraptor gen. nov. and Viridiraptor gen. nov. are highly specialised, algivorous amoeboflagellates (Glissomonadida, Cercozoa).

    Science.gov (United States)

    Hess, Sebastian; Melkonian, Michael

    2013-09-01

    In freshwater ecosystems a vast diversity of elusive protists exists that specifically feed on microalgae. Due to difficulties in isolation and long-term maintenance, most of these are still poorly known. In this study stable, bacteria-free cultures of several limnetic, algivorous amoeboflagellates were investigated by light microscopy and molecular phylogenetic analyses. All strains represent naked, biflagellate cells, either occurring as rigid flagellates or as surface-attached amoebae. They perforate cell walls of certain Zygnematophyceae and Chlorophyceae (Viridiplantae) and phagocytose algal cell contents. Time-lapse microscopy revealed the feeding behaviour, locomotional processes and life histories of the amoeboflagellates. Clear differences in cell morphology and food range specificity led to the description of two new, monotypic genera Orciraptor and Viridiraptor, which occupy similar, but distinct ecological niches in aquatic ecosystems as 'necrophytophagous' and 'parasitoid' protists, respectively. Molecular phylogenetic analyses based on 18S rDNA sequence data demonstrated that Orciraptor and Viridiraptor belonged to 'clade X' within the order Glissomonadida (Cercozoa, Rhizaria). In conclusion, we established the phenotypic identity of a clade, which until now was exclusively known from environmental sequences, and erect the new family Viridiraptoridae for 'clade X'. Its algivorous members are compared with other glissomonads and nomenclatural, methodological and ecological aspects of these novel 'raptorial' amoeboflagellates are discussed. Copyright © 2013 Elsevier GmbH. All rights reserved.

  3. Fourier-Based Transmit Beampattern Design Using MIMO Radar

    KAUST Repository

    Lipor, John

    2014-05-01

    In multiple-input multiple-output (MIMO) radar settings, it is often desirable to transmit power only to a given location or set of locations defined by a beampattern. Transmit waveform design is a topic that has received much attention recently, involving synthesis of both the signal covariance matrix,, as well as the actual waveforms. Current methods involve a two-step process of designing via iterative solutions and then using to generate waveforms that fulfill practical constraints such as having a constant-envelope or drawing from a finite alphabet. In this paper, a closed-form method to design for a uniform linear array is proposed that utilizes the discrete Fourier transform (DFT) coefficients and Toeplitz matrices. The resulting covariance matrix fulfills the practical constraints such as positive semidefiniteness and the uniformelemental power constraint and provides performance similar to that of iterative methods, which require a much greater computation time. Next, a transmit architecture is presented that exploits the orthogonality of frequencies at discrete DFT values to transmit a sum of orthogonal signals from each antenna. The resulting waveforms provide a lower mean-square error than current methods at a much lower computational cost, and a simulated detection scenario demonstrates the performance advantages achieved.

  4. Characteristics of primary infection of a European human immunodeficiency virus type 1 clade B isolate in chimpanzees

    NARCIS (Netherlands)

    Bogers, W. M.; Koornstra, W. H.; Dubbes, R. H.; ten Haaft, P. J.; Verstrepen, B. E.; Jhagjhoorsingh, S. S.; Haaksma, A. G.; Niphuis, H.; Laman, J. D.; Norley, S.; Schuitemaker, H.; Goudsmit, J.; Hunsmann, G.; Heeney, J. L.; Wigzell, H.

    1998-01-01

    The aim of the study was to select, from a panel of candidate European human immunodeficiency virus type 1 (HIV-1) clade B primary virus isolates, one isolate based on replication properties in chimpanzee peripheral blood mononuclear cells (PBMC). Secondly, to evaluate the in vivo kinetics of

  5. Atomic force microscopy imaging reveals the formation of ASIC/ENaC cross-clade ion channels

    International Nuclear Information System (INIS)

    Jeggle, Pia; Smith, Ewan St. J.; Stewart, Andrew P.; Haerteis, Silke; Korbmacher, Christoph; Edwardson, J. Michael

    2015-01-01

    ASIC and ENaC are co-expressed in various cell types, and there is evidence for a close association between them. Here, we used atomic force microscopy (AFM) to determine whether ASIC1a and ENaC subunits are able to form cross-clade hybrid ion channels. ASIC1a and ENaC could be co-isolated from detergent extracts of tsA 201 cells co-expressing the two subunits. Isolated proteins were incubated with antibodies against ENaC and Fab fragments against ASIC1a. AFM imaging revealed proteins that were decorated by both an antibody and a Fab fragment with an angle of ∼120° between them, indicating the formation of ASIC1a/ENaC heterotrimers. - Highlights: • There is evidence for a close association between ASIC and ENaC. • We used AFM to test whether ASIC1a and ENaC subunits form cross-clade ion channels. • Isolated proteins were incubated with subunit-specific antibodies and Fab fragments. • Some proteins were doubly decorated at ∼120° by an antibody and a Fab fragment. • Our results indicate the formation of ASIC1a/ENaC heterotrimers

  6. Atomic force microscopy imaging reveals the formation of ASIC/ENaC cross-clade ion channels

    Energy Technology Data Exchange (ETDEWEB)

    Jeggle, Pia; Smith, Ewan St. J.; Stewart, Andrew P. [Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD (United Kingdom); Haerteis, Silke; Korbmacher, Christoph [Institut für Zelluläre und Molekulare Physiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Waldstrasse 6, 91054 Erlangen (Germany); Edwardson, J. Michael, E-mail: jme1000@cam.ac.uk [Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD (United Kingdom)

    2015-08-14

    ASIC and ENaC are co-expressed in various cell types, and there is evidence for a close association between them. Here, we used atomic force microscopy (AFM) to determine whether ASIC1a and ENaC subunits are able to form cross-clade hybrid ion channels. ASIC1a and ENaC could be co-isolated from detergent extracts of tsA 201 cells co-expressing the two subunits. Isolated proteins were incubated with antibodies against ENaC and Fab fragments against ASIC1a. AFM imaging revealed proteins that were decorated by both an antibody and a Fab fragment with an angle of ∼120° between them, indicating the formation of ASIC1a/ENaC heterotrimers. - Highlights: • There is evidence for a close association between ASIC and ENaC. • We used AFM to test whether ASIC1a and ENaC subunits form cross-clade ion channels. • Isolated proteins were incubated with subunit-specific antibodies and Fab fragments. • Some proteins were doubly decorated at ∼120° by an antibody and a Fab fragment. • Our results indicate the formation of ASIC1a/ENaC heterotrimers.

  7. Sealing of transmitted-heat lines at wall piercings; Abdichtung von Fernwaermeleitungen in Mauerdurchfuehrungen

    Energy Technology Data Exchange (ETDEWEB)

    Werner, A.; Ney, K. [Doyma GmbH und Co., Oyten (Germany)

    1998-04-01

    Flexible sealing systems are necessary to provide permanent protection of transmitted-heat pipe wall penetrations against the ingress of water. Unlike the rigid sealing methods in widespread use, flexible sealing systems are capable of absorbing thermally induced pipe movements and thus of preventing leaks around such piercings. The following article provides an introduction to the subject and offers practical suggestions for the ideal design of transmitted-heat pipe wall penetrations. Sealing system variants with a range of degrees of flexibility are discussed, in addition to measures which need to be taken into account as early as the installation of the pipe itself. Prime attention is devoted not to methods already practised, but to recent, potentially marketable developments. (orig.) [Deutsch] Um Mauerdurchfuehrungen von Fernwaermeleitungen dauerhaft gegen das Eindringen von Wasser zu schuetzen, sind flexible Abdichtsysteme notwendig. Im Gegensatz zu den verbreiteten starren Abdichtungsmethoden koennen flexible Systeme die thermisch bedingten Rohrbewegungen aufnehmen und damit Undichtigkeiten im Bereich der Durchfuehrungen verhindern. Der folgende Beitrag fuehrt in die Thematik ein und gibt praktische Hinweise, wie eine Mauerdurchfuehrung von Fernwaermeleitungen idealerweise gestaltet werden sollte. Neben Massnahmen, die bereits bei der Rohrverlegung zu beachten sind, werden Abdichtvarianten mit unterschiedlichem Flexibilitaetsgrad skizziert. Schwerpunkt der Untersuchung liegt hier nicht nur auf bereits bekannten Verfahren sondern auch auf marktfaehigen Neuentwicklungen. (orig.)

  8. Alfalfa Leaf Curl Virus: an Aphid-Transmitted Geminivirus.

    Science.gov (United States)

    Roumagnac, Philippe; Granier, Martine; Bernardo, Pauline; Deshoux, Maëlle; Ferdinand, Romain; Galzi, Serge; Fernandez, Emmanuel; Julian, Charlotte; Abt, Isabelle; Filloux, Denis; Mesléard, François; Varsani, Arvind; Blanc, Stéphane; Martin, Darren P; Peterschmitt, Michel

    2015-09-01

    The family Geminiviridae comprises seven genera differentiated by genome organization, sequence similarity, and insect vector. Capulavirus, an eighth genus, has been proposed to accommodate two newly discovered highly divergent geminiviruses that presently have no known vector. Alfalfa leaf curl virus, identified here as a third capulavirus, is shown to be transmitted by Aphis craccivora. This is the first report of an aphid-transmitted geminivirus. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  9. Differential clade-specific HLA-B*3501 association with HIV-1 disease outcome is linked to immunogenicity of a single Gag epitope

    DEFF Research Database (Denmark)

    Matthews, Philippa C; Koyanagi, Madoka; Kløverpris, Henrik N

    2012-01-01

    -clade sequences, which critically reduces recognition of the Gag NY10 epitope. These data suggest that in spite of any inherent HLA-linked T-cell receptor repertoire differences that may exist, maximizing the breadth of the Gag-specific CD8(+) T-cell response, by the addition of even a single epitope, may......The strongest genetic influence on immune control in HIV-1 infection is the HLA class I genotype. Rapid disease progression in B-clade infection has been linked to HLA-B*35 expression, in particular to the less common HLA-B*3502 and HLA-B*3503 subtypes but also to the most prevalent subtype, HLA...

  10. Transfusion-transmitted CMV infection - current knowledge and future perspectives.

    Science.gov (United States)

    Ziemann, M; Thiele, T

    2017-08-01

    Transmission of human cytomegalovirus (CMV) via transfusion (TT-CMV) may still occur and remains a challenge in the treatment of immunocompromised CMV-seronegative patients, e.g. after stem cell transplantation, and for low birthweight infants. Measures to reduce the risk of TT-CMV have been evaluated in clinical studies, including leucocyte depletion of cellular blood products and/or the selection of CMV-IgG-negative donations. Studies in large blood donor cohorts indicate that donations from newly CMV-IgG-positive donors should bear the highest risk for transmitting CMV infections because they contain the highest levels of CMV-DNA, and early CMV antibodies cannot neutralise CMV. Based on this knowledge, rational strategies to reduce the residual risk of TT-CMV using leucoreduced blood products could be designed. However, there is a lack of evidence that CMV is still transmitted by transfusion of leucoreduced units. In low birthweight infants, most (if not all) CMV infections are caused by breast milk feeding or congenital transmission rather than by transfusion of leucoreduced blood products. For other patients at risk, no definitive data exist about the relative importance of alternative transmission routes of CMV compared to blood transfusion. As a result, only the conduction of well-designed studies addressing strategies to prevent TT-CMV and the thorough examination of presumed cases of TT-CMV will achieve guidance for the best transfusion regimen in patients at risk. © 2017 British Blood Transfusion Society.

  11. Risk behaviors for sexually transmitted diseases among crack users

    Directory of Open Access Journals (Sweden)

    Rafael Alves Guimarães

    2015-08-01

    Full Text Available AbstractObjectives: to investigate the prevalence and risk behaviors by means of reporting of sexually transmitted diseases among crack users.Method: cross-sectional study carried out with 588 crack users in a referral care unit for the treatment of chemical dependency. Data were collected by means of face-to-face interview and analyzed using Stata statistical software, version 8.0.Results: of the total participants, 154 (26.2%; 95% CI: 22.8-29.9 reported antecedents of sexually transmitted diseases. Ages between 25 and 30 years (RP: 2.1; 95% CI: 1.0-4.0 and over 30 years (RP: 3.8; 95% CI: 2.1-6.8, alcohol consumption (RP: 1.9; 95% CI: 1.1-3.3, antecedents of prostitution (RP: 1.9; 95% CI: 1.3-2.9 and sexual intercourse with person living with human immunodeficiency virus/AIDS (RP: 2.7; 95% CI: 1.8-4.2 were independently associated with reporting of sexually transmitted diseases.Conclusion: the results of this study suggest high risk and vulnerability of crack users for sexually transmitted diseases.

  12. The Control of Transmitted Power in an Active Isolation System

    DEFF Research Database (Denmark)

    Elliott, S.J.; Gardonio, P.; Pinnington, R.J.

    1997-01-01

    The isolation of vibration through a system with multiple active mounts is discussed, in which each of the mounts can transmit vibration in several degrees of freedom. Theoretical models of the various parts of this system have been developed which include a flexible receiving structure and distr......The isolation of vibration through a system with multiple active mounts is discussed, in which each of the mounts can transmit vibration in several degrees of freedom. Theoretical models of the various parts of this system have been developed which include a flexible receiving structure...... and distributed active mounts, and these models can be connected together to produce an overall theoretical description of a realistic active isolation system. Total transmitted power has been found to be an excellent criterion to quantify the effect of various control strategies in this model in which...... the contributions to the transmitted power in the various degrees of freedom can be clearly understood. It has also been found, however, that an active control system which minimises a practical estimate of transmitted power, calculated from the product of the axial forces and velocities under the mounts, can give...

  13. Pelagic larval duration predicts extinction risk in a freshwater fish clade.

    Science.gov (United States)

    Douglas, Morgan; Keck, Benjamin P; Ruble, Crystal; Petty, Melissa; Shute, J R; Rakes, Patrick; Hulsey, C Darrin

    2013-01-01

    Pelagic larval duration (PLD) can influence evolutionary processes ranging from dispersal to extinction in aquatic organisms. Using estimates of PLD obtained from species of North American darters (Percidae: Etheostomatinae), we demonstrate that this freshwater fish clade exhibits surprising variation in PLD. Comparative analyses provide some evidence that higher stream gradients favour the evolution of shorter PLD. Additionally, similar to patterns in the marine fossil record in which lower PLD is associated with greater extinction probability, we found a reduced PLD in darter lineages was evolutionarily associated with extinction risk. Understanding the causes and consequences of PLD length could lead to better management and conservation of organisms in our increasingly imperiled aquatic environments.

  14. Diversification Patterns of Lanternfishes Reveal Multiple Rate Shifts in a Critical Mesopelagic Clade Targeted for Human Exploitation.

    Science.gov (United States)

    Denton, John S S

    2018-03-19

    The mesopelagic (midwater) and deep-sea environments together comprise over 90% of the volume of the world ocean [1] and provide services that are only recently becoming recognized [2]. One of the most significant of these services relates to midwater fish biomass, recently estimated to be two orders of magnitude larger than the current worldwide fisheries catch [3, 4]. Calls to exploit midwater fish biomass have increased despite warnings about the unknown recovery potential of such organisms [2] and despite existing data suggesting that deep-sea fishes could be classified as endangered [5]. Here, to provide a null model for the respondability of midwater fishes, I use lanternfishes-which comprise the majority of worldwide midwater fish biomass [6]-to examine the diversification response of a critical midwater clade to oceanic changes over evolutionary timescales, including several extinction and turnover events. Using a time-calibrated molecular phylogeny based on seven autosomal protein-coding loci, with over 50% species sampling and three ingroup node calibrations, I show that lanternfishes exhibit a continuously increasing diversification rate, consistent with nonequilibrium speciation dynamics, and three major evolutionary rate shift locations with timing that is similar to those of marine clades in more well-known environments. These results suggest that lanternfish diversification patterns overlapped with major events in the physical partitioning of the ocean volume and that the clade has responded positively to a range of pre-Anthropocene extinction drivers [7]. However, lanternfish respondability to modern extinction drivers-habitat loss and overexploitation-is best addressed with populational and ecological data and remains largely unknown. Copyright © 2018 Elsevier Ltd. All rights reserved.

  15. Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade.

    Science.gov (United States)

    Sorn, San; Sok, Touch; Ly, Sovann; Rith, Sareth; Tung, Nguyen; Viari, Alain; Gavotte, Laurent; Holl, Davun; Seng, Heng; Asgari, Nima; Richner, Beat; Laurent, Denis; Chea, Nora; Duong, Veasna; Toyoda, Tetsuya; Yasuda, Chadwick Y; Kitsutani, Paul; Zhou, Paul; Bing, Sun; Deubel, Vincent; Donis, Ruben; Frutos, Roger; Buchy, Philippe

    2013-04-01

    In Cambodia, the first detection of HPAI H5N1 virus in birds occurred in January 2004 and since then there have been 33 outbreaks in poultry while 21 human cases were reported. The origin and dynamics of these epizootics in Cambodia remain unclear. In this work we used a range of bioinformatics methods to analyze the Cambodian virus sequences together with those from neighboring countries. Six HA lineages belonging to clades 1 and 1.1 were identified since 2004. Lineage 1 shares an ancestor with viruses from Thailand and disappeared after 2005, to be replaced by lineage 2 originating from Vietnam and then by lineage 3. The highly adapted lineage 4 was seen only in Cambodia. Lineage 5 is circulating both in Vietnam and Cambodia since 2008 and was probably introduced in Cambodia through unregistered transboundary poultry trade. Lineage 6 is endemic to Cambodia since 2010 and could be classified as a new clade according to WHO/OIE/FAO criteria for H5N1 virus nomenclature. We propose to name it clade 1.1A. There is a direct filiation of lineages 2 to 6 with a temporal evolution and geographic differentiation for lineages 4 and 6. By the end of 2011, two lineages, i.e. lineages 5 and 6, with different transmission paths cocirculate in Cambodia. The presence of lineage 6 only in Cambodia suggests the existence of a transmission specific to this country whereas the presence of lineage 5 in both Cambodia and Vietnam indicates a distinct way of circulation of infected poultry. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. A novel strategy for efficient production of anti-V3 human scFvs against HIV-1 clade C

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    Kumar Rajesh

    2012-11-01

    Full Text Available Abstract Background Production of human monoclonal antibodies that exhibit broadly neutralizing activity is needed for preventing HIV-1 infection, however only a few such antibodies have been generated till date. Isolation of antibodies by the hybridoma technology is a cumbersome process with fewer yields. Further, the loss of unstable or slowly growing clones which may have unique binding specificities often occurs during cloning and propagation and the strongly positive clones are often lost. This has been avoided by the process described in this paper, wherein, by combining the strategy of EBV transformation and recombinant DNA technology, we constructed human single chain variable fragments (scFvs against the third variable region (V3 of the clade C HIV-1 envelope. Results An antigen specific phage library of 7000 clones was constructed from the enriched V3- positive antibody secreting EBV transformed cells. By ligation of the digested scFv DNA into phagemid vector and bio panning against the HIV-1 consensus C and B V3 peptides followed by random selection of 40 clones, we identified 15 clones that showed V3 reactivity in phage ELISA. DNA fingerprinting analysis and sequencing showed that 13 out of the 15 clones were distinct. Expression of the positive clones was tested by SDS-PAGE and Western blot. All the 13 anti-V3 scFvs showed cross-reactivity against both the clade C and B V3 peptides and did not show any reactivity against other unrelated peptides in ELISA. Preliminary neutralization assays indicated varying degrees of neutralization of clade C and B viruses. EBV transformation, followed by antigen selection of lines to identify specific binders, enabled the selection of phage from un-cloned lines for scFv generation, thus avoiding the problems of hybridoma technology. Moreover, as the clones were pretested for antigen binding, a comparatively small library sufficed for the selection of a considerable number of unique antigen binding

  17. Diversification rates indicate an early role of adaptive radiations at the origin of modern echinoid fauna.

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    Simon Boivin

    Full Text Available Evolutionary radiations are fascinating phenomena corresponding to a dramatic diversification of taxa and a burst of cladogenesis over short periods of time. Most evolutionary radiations have long been regarded as adaptive but this has seldom been demonstrated with large-scale comparative datasets including fossil data. Originating in the Early Jurassic, irregular echinoids are emblematic of the spectacular diversification of mobile marine faunas during the Mesozoic Marine Revolution. They diversified as they colonized various habitats, and now constitute the main component of echinoid fauna in modern seas. The evolutionary radiation of irregular echinoids has long been considered as adaptive but this hypothesis has never been tested. In the present work we analyze the evolution of echinoid species richness and morphological disparity over 37 million years based on an extensive fossil dataset. Our results demonstrate that morphological and functional diversifications in certain clades of irregular echinoids were exceptionally high compared to other clades and that they were associated with the evolution of new modes of life and so can be defined as adaptive radiations. The role played by ecological opportunities in the diversification of these clades was critical, with the evolution of the infaunal mode of life promoting the adaptive radiation of irregular echinoids.

  18. Signaling Architectures that Transmit Unidirectional Information Despite Retroactivity.

    Science.gov (United States)

    Shah, Rushina; Del Vecchio, Domitilla

    2017-08-08

    A signaling pathway transmits information from an upstream system to downstream systems, ideally in a unidirectional fashion. A key obstacle to unidirectional transmission is retroactivity, the additional reaction flux that affects a system once its species interact with those of downstream systems. This raises the fundamental question of whether signaling pathways have developed specialized architectures that overcome retroactivity and transmit unidirectional signals. Here, we propose a general procedure based on mathematical analysis that provides an answer to this question. Using this procedure, we analyze the ability of a variety of signaling architectures to transmit one-way (from upstream to downstream) signals, as key biological parameters are tuned. We find that single stage phosphorylation and phosphotransfer systems that transmit signals from a kinase show a stringent design tradeoff that hampers their ability to overcome retroactivity. Interestingly, cascades of these architectures, which are highly represented in nature, can overcome this tradeoff and thus enable unidirectional transmission. By contrast, phosphotransfer systems, and single and double phosphorylation cycles that transmit signals from a substrate, are unable to mitigate retroactivity effects, even when cascaded, and hence are not well suited for unidirectional information transmission. These results are largely independent of the specific reaction-rate constant values, and depend on the topology of the architectures. Our results therefore identify signaling architectures that, allowing unidirectional transmission of signals, embody modular processes that conserve their input/output behavior across multiple contexts. These findings can be used to decompose natural signal transduction networks into modules, and at the same time, they establish a library of devices that can be used in synthetic biology to facilitate modular circuit design. Copyright © 2017 Biophysical Society. Published by

  19. Influence of sexually transmitted infections in a horse breeding

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    Kosec Marjan

    2015-01-01

    Full Text Available The most frequent problems in horses reproduction are generally divided into those of infectious and non infectious etiology. Common causes of infectious diseases are usual­ly viruses and bacteria, and less frequently protozoa, mykoplasma and fungi. In this work there are presented the most important fact about sexually transmitted diseases, their clinical picture, risk factors, preventive measures as well as measures to prevent and eradicate the diseases. The biggest risk factor for sexually transmitted diseases in horses are breeding stallions, both in natural mating and in artificial insemination. Therefore, in order to prevent genital infections in horses, it is essential that the stallions used for breeding are healthy (non-infected. That can be determined with certainty only if the stallions are examined (tested just before the breeding season on most frequent sexually transmitted diseases (CEM,EAV. It is well known that in most cases the clinical picture of sexually transmitted diseses is not manifested on genitals. As well, variations in clinical picture can be expected also in mares, depending on the stage of the disease and its etiology. Harms arising from sexually transmitted diseases can be divided into direct and indirect. Direct damage occurs in the form of endometritis, miscarriage, stillbirths and births of weak foals, and indirect in restricting the traffic of infected and suspicios animals, isolation of the infected ones as well as medical treatment and interrupting mating.

  20. Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades?

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    Michel Tibayrenc

    2014-04-01

    Full Text Available An abundant literature dealing with the population genetics and taxonomy of Giardia duodenalis, Cryptosporidium spp., Pneumocystis spp., and Cryptococcus spp., pathogens of high medical and veterinary relevance, has been produced in recent years. We have analyzed these data in the light of new population genetic concepts dealing with predominant clonal evolution (PCE recently proposed by us. In spite of the considerable phylogenetic diversity that exists among these pathogens, we have found striking similarities among them. The two main PCE features described by us, namely highly significant linkage disequilibrium and near-clading (stable phylogenetic clustering clouded by occasional recombination, are clearly observed in Cryptococcus and Giardia, and more limited indication of them is also present in Cryptosporidium and Pneumocystis. Moreover, in several cases, these features still obtain when the near-clades that subdivide the species are analyzed separately ("Russian doll pattern". Lastly, several sets of data undermine the notion that certain microbes form clonal lineages simply owing to a lack of opportunity to outcross due to low transmission rates leading to lack of multiclonal infections ("starving sex hypothesis". We propose that the divergent taxonomic and population genetic inferences advanced by various authors about these pathogens may not correspond to true evolutionary differences and could be, rather, the reflection of idiosyncratic practices among compartmentalized scientific communities. The PCE model provides an opportunity to revise the taxonomy and applied research dealing with these pathogens and others, such as viruses, bacteria, parasitic protozoa, and fungi.

  1. An early geikiid dicynodont from the Tropidostoma Assemblage Zone (late Permian of South Africa

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    Christian F. Kammerer

    2017-01-01

    Full Text Available Based on specimens previously identified as Tropidostoma, a new taxon of dicynodont (Bulbasaurus phylloxyron gen. et sp. nov. from the Karoo Basin of South Africa is described. Bulbasaurus is a medium-sized dicynodont (maximum dorsal skull length 16.0 cm restricted to the Tropidostoma Assemblage Zone (early Lopingian of the Beaufort Group. Bulbasaurus can be distinguished from Tropidostoma by an array of characters including the presence of a tall, sharp premaxillary ridge, large, rugose, nearly-confluent nasal bosses, a nasofrontal ridge, massive tusks, robust pterygoids, prominently twisted subtemporal bar, and absence of a distinct postfrontal. Inclusion of Bulbasaurus in a phylogenetic analysis of anomodont therapsids recovers it as a member of Geikiidae, a clade of otherwise later Permian dicynodonts such as Aulacephalodon and Pelanomodon. Bulbasaurus exhibits many of the characters typical of adult Aulacephalodon, but at substantially smaller skull size (these characters are absent in comparably-sized Aulacephalodon juveniles, suggesting that the evolution of typical geikiid morphology preceded gigantism in the clade. Bulbasaurus is the earliest known geikiid and the only member of the group known from the Tropidostoma Assemblage Zone; discovery of this taxon shortens a perplexing ghost lineage and indicates that abundant clades from the later Permian of South Africa (e.g., Geikiidae, Dicynodontoidea may have originated as rare components of earlier Karoo assemblage zones.

  2. Spatial distribution of soil-transmitted helminths, including Strongyloides stercoralis, among children in Zanzibar

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    Stefanie Knopp

    2008-11-01

    Full Text Available A programme periodically distributing anthelminthic drugs to school-aged children for the control of soiltransmitted helminthiasis was launched in Zanzibar in the early 1990s. We investigated the spatial distribution of soiltransmitted helminth infections, including Strongyloides stercoralis, in 336 children from six districts in Unguja, Zanzibar, in 2007. One stool sample per child was examined with the Kato-Katz, Koga agar plate and Baermann methods. The point prevalence of the different helminth infections was compared to the geological characteristics of the study sites. The observed prevalences for Trichuris trichiura, Ascaris lumbricoides, hookworm and S. stercoralis were 35.5%, 12.2%, 11.9% and 2.2%, respectively, with considerable spatial heterogeneity. Whilst T. trichiura and hookworm infections were found in all six districts, no A. lumbricoides infections were recorded in the urban setting and only a low prevalence (2.2% was observed in the South district. S. stercoralis infections were found in four districts with the highest prevalence (4.0% in the West district. The prevalence of infection with any soil-transmitted helminth was highest in the North A district (69.6% and lowest in the urban setting (22.4%. A. lumbricoides, hookworm and, with the exception of the North B district, S. stercoralis infections were observed to be more prevalent in the settings north of Zanzibar Town, which are characterized by alluvial clayey soils, moist forest regions and a higher precipitation. After a decade of large-scale administration of anthelminthic drugs, the prevalence of soil-transmitted helminth infections across Unguja is still considerable. Hence, additional measures, such as improving access to adequate sanitation and clean water and continued health education, are warranted to successfully control soil-transmitted helminthiasis in Zanzibar.

  3. On reflectionless equi-transmitting matrices

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    Pavel Kurasov

    2014-01-01

    Full Text Available Reflectionless equi-transmitting unitary matrices are studied in connection to matching conditions in quantum graphs. All possible such matrices of size 6 are described explicitly. It is shown that such matrices form 30 six-parameter families intersected along 12 five-parameter families closely connected to conference matrices.

  4. Analysis of C. elegans NR2E nuclear receptors defines three conserved clades and ligand-independent functions

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    Weber Katherine P

    2012-06-01

    Full Text Available Abstract Background The nuclear receptors (NRs are an important class of transcription factors that are conserved across animal phyla. Canonical NRs consist of a DNA-binding domain (DBD and ligand-binding domain (LBD. While most animals have 20–40 NRs, nematodes of the genus Caenorhabditis have experienced a spectacular proliferation and divergence of NR genes. The LBDs of evolutionarily-conserved Caenorhabditis NRs have diverged sharply from their Drosophila and vertebrate orthologs, while the DBDs have been strongly conserved. The NR2E family of NRs play critical roles in development, especially in the nervous system. In this study, we explore the phylogenetics and function of the NR2E family of Caenorhabditis elegans, using an in vivo assay to test LBD function. Results Phylogenetic analysis reveals that the NR2E family of NRs consists of three broadly-conserved clades of orthologous NRs. In C. elegans, these clades are defined by nhr-67, fax-1 and nhr-239. The vertebrate orthologs of nhr-67 and fax-1 are Tlx and PNR, respectively. While the nhr-239 clade includes orthologs in insects (Hr83, an echinoderm, and a hemichordate, the gene appears to have been lost from vertebrate lineages. The C. elegans and C. briggsae nhr-239 genes have an apparently-truncated and highly-diverged LBD region. An additional C. elegans NR2E gene, nhr-111, appears to be a recently-evolved paralog of fax-1; it is present in C. elegans, but not C. briggsae or other animals with completely-sequenced genomes. Analysis of the relatively unstudied nhr-111 and nhr-239 genes demonstrates that they are both expressed—nhr-111 very broadly and nhr-239 in a small subset of neurons. Analysis of the FAX-1 LBD in an in vivo assay revealed that it is not required for at least some developmental functions. Conclusions Our analysis supports three conserved clades of NR2E receptors, only two of which are represented in vertebrates, indicating three ancestral NR2E genes in the

  5. Some models for epidemics of vector-transmitted diseases

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    Fred Brauer

    2016-10-01

    Full Text Available Vector-transmitted diseases such as dengue fever and chikungunya have been spreading rapidly in many parts of the world. The Zika virus has been known since 1947 and invaded South America in 2013. It can be transmitted not only by (mosquito vectors but also directly through sexual contact. Zika has developed into a serious global health problem because, while most cases are asymptomatic or very light, babies born to Zika - infected mothers may develop microcephaly and other very serious birth defects.We formulate and analyze two epidemic models for vector-transmitted diseases, one appropriate for dengue and chikungunya fever outbreaks and one that includes direct transmission appropriate for Zika virus outbreaks. This is especially important because the Zika virus is the first example of a disease that can be spread both indirectly through a vector and directly (through sexual contact. In both cases, we obtain expressions for the basic reproduction number and show how to use the initial exponential growth rate to estimate the basic reproduction number. However, for the model that includes direct transmission some additional data would be needed to identify the fraction of cases transmitted directly. Data for the 2015 Zika virus outbreak in Barranquilla, Colombia has been used to fit parameters to the model developed here and to estimate the basic reproduction number.

  6. The Australasian frog family Ceratobatrachidae in China, Myanmar and Thailand: discovery of a new Himalayan forest frog clade

    Science.gov (United States)

    YAN, Fang; JIANG, Ke; WANG, Kai; JIN, Jie-Qiong; SUWANNAPOOM, Chatmongkon; LI, Cheng; Jens, V. VINDUM; Rafe, M. BROWN; CHE, Jing

    2016-01-01

    In an effort to study the systematic affinities and specieslevel phylogenetic relationships of the enigmatic anurans variably assigned to the genera Ingerana or Limnonectes (family Dicroglossidae), we collected new molecular sequence data for five species including four Himalayan taxa, Limnonectes xizangensis, Lim. medogensis, Lim. alpine, Ingerana borealis and one southeast Asian species, I. tasanae, and analyzed these together with data from previous studies involving other ostensibly related taxa. Our surprising results demonstrate unequivocally that Lim. xizangensis, Lim. medogensis and Lim. alpine form a strongly supported clade, the sister-group of the family Australasian forest frog family Ceratobatrachidae. This discovery requires an expansion of the definition of Ceratobatrachidae and represents the first record of this family in China. These three species are distinguished from the species of Ingerana and Limnonectes by the: (1) absence of interdigital webbing of the foot, (2) absence of terminal discs on fingers and toes, (3) absence of circumarginal grooves on the fingers and toes, and (4) absence of tarsal folds. Given their phylogenetic and morphological distinctiveness, we assign them to the oldest available generic name for this clade, Liurana Dubois 1987, and transfer Liurana from Dicroglossidae to the family Ceratobatrachidae. In contrast, Ingerana tasanae was found to be clustered with strong support with the recently described genus Alcalus (Ceratobatrachidae), a small clade of otherwise Sundaic species; this constitutes a new record of the family Ceratobatrachidae for Myanmar and Thailand. Finally, Ingerana borealis clustered with the "true" Ingerana (family Dicroglossidae), for which the type species is I. tenasserimensis. PMID:26828029

  7. Some Models for Epidemics of Vector-Transmitted Diseases

    OpenAIRE

    Brauer, Fred; Castillo-Chavez, Carlos; Mubayi, Anuj; Towers, Sherry

    2016-01-01

    Vector-transmitted diseases such as dengue fever and chikungunya have been spreading rapidly in many parts of the world. The Zika virus has been known since 1947 and invaded South America in 2013. It can be transmitted not only by (mosquito) vectors but also directly through sexual contact. Zika has developed into a serious global health problem because, while most cases are asymptomatic or very light, babies born to Zika - infected mothers may develop microcephaly and other very serious birt...

  8. Modelling the geographical distribution of soil-transmitted helminth infections in Bolivia.

    Science.gov (United States)

    Chammartin, Frédérique; Scholte, Ronaldo G C; Malone, John B; Bavia, Mara E; Nieto, Prixia; Utzinger, Jürg; Vounatsou, Penelope

    2013-05-25

    The prevalence of infection with the three common soil-transmitted helminths (i.e. Ascaris lumbricoides, Trichuris trichiura, and hookworm) in Bolivia is among the highest in Latin America. However, the spatial distribution and burden of soil-transmitted helminthiasis are poorly documented. We analysed historical survey data using Bayesian geostatistical models to identify determinants of the distribution of soil-transmitted helminth infections, predict the geographical distribution of infection risk, and assess treatment needs and costs in the frame of preventive chemotherapy. Rigorous geostatistical variable selection identified the most important predictors of A. lumbricoides, T. trichiura, and hookworm transmission. Results show that precipitation during the wettest quarter above 400 mm favours the distribution of A. lumbricoides. Altitude has a negative effect on T. trichiura. Hookworm is sensitive to temperature during the coldest month. We estimate that 38.0%, 19.3%, and 11.4% of the Bolivian population is infected with A. lumbricoides, T. trichiura, and hookworm, respectively. Assuming independence of the three infections, 48.4% of the population is infected with any soil-transmitted helminth. Empirical-based estimates, according to treatment recommendations by the World Health Organization, suggest a total of 2.9 million annualised treatments for the control of soil-transmitted helminthiasis in Bolivia. We provide estimates of soil-transmitted helminth infections in Bolivia based on high-resolution spatial prediction and an innovative variable selection approach. However, the scarcity of the data suggests that a national survey is required for more accurate mapping that will govern spatial targeting of soil-transmitted helminthiasis control.

  9. Sexually Transmitted Diseases Surveillance, 2014: Syphilis

    Science.gov (United States)

    ... 2014 Sexually Transmitted Diseases Surveillance Table of Contents Introductory Section Foreword Preface Acronyms Figures- National Profile Figures – ... GISP Profiles Related Links STD Home STD Data & Statistics NCHHSTP Atlas Interactive STD Data – 1996-2013 STD ...

  10. Coalescent-based genome analyses resolve the early branches of the euarchontoglires.

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    Vikas Kumar

    Full Text Available Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides from all orders except Dermoptera (flying lemurs. Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods.

  11. Selective wave-transmitting electromagnetic absorber through composite metasurface

    Science.gov (United States)

    Sun, Zhiwei; Zhao, Junming; Zhu, Bo; Jiang, Tian; Feng, Yijun

    2017-11-01

    Selective wave-transmitting absorbers which have one or more narrow transmission bands inside a wide absorption band are often demanded in wireless communication and radome applications for reducing the coupling between different systems, improving anti-jamming capability, and reducing antennas' radar cross section. Here we propose a feasible method that utilizing composite of two metasurfaces with different polarization dependent characteristics, one works as electromagnetic polarization rotator and the other as a wideband polarization dependent electromagnetic wave absorber. The polarization rotator produces a cross polarization output in the wave-transmitting band, while preserves the polarization of the incidence outside the band. The metasurface absorber works for certain linear polarization with a much wider absorption band covering the wave-transmitting frequency. When combining these two metasurfaces properly, the whole structure behaves as a wideband absorber with a certain frequency transmission window. The proposal may be applied in radome designs to reduce the radar cross section of antenna or improving the electromagnetic compatibility in communication devices.

  12. Effect of backing material on the transmitting response level and bandwidth of a wideband underwater transmitting transducer using 1-3 piezocomposite

    CSIR Research Space (South Africa)

    Nicolaides, K

    2009-01-01

    Full Text Available : Transducer design The 1-3 piezocomposite (40% VF) active element was designed to resonate at around 300 kHz see figure 2. 1-3 piezocomposite material with 40% VF was selected due its excellent wide bandwidth and high transmitting response characteristics... is shown in figure 3(a). These results demonstrate the wide bandwidth characteristics for such a design. The transmitting response and acoustic characteristics (bandwidth and level) of this configuration will be used as our base line and all...

  13. GOOD HOMOSEXUAL BEHAVIOUR DECREASE PREVALENCE OF SEXUAL TRANSMITTED DISSEASE

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    Purwaningsih Purwaningsih

    2017-07-01

    Full Text Available Introduction: The homosexual behaviour were become indicators of sexually transmitted diseases’s (STDs prevalencies. Prevalence of sexually transmitted diseases in homosexual community was very high but until recently study it was conducted sporadically. The objective of this study was to analyze the correlation of homosexual behaviour with prevalence of sexually transmitted diseases (STDs in Mobile Clinic Community Centre of IGAMA collaborating with Public Health Centre Sumberpucung of Malang Regency. Method:  Analytic design with cross sectional methode was used in this study. The population were all visitors of Mobile Clinic Community Centre of IGAMA collaborating with Public Health Centre Sumberpucung of Malang Regency (353 people. Sample were 40 people who met to the inclusion criteria. The independent variable was homosexual behaviour and the dependent variable was prevalence of sexually transmitted diseases (STDs. Data for homosexual behaviour were collected by using questionnaire and indhept interview with content analyze and data for prevalence of sexually transmitted diseases (STDs were collected by using laboratorium test for STDs. Result: The research result was presented in the form diagram, table of cross tabulation and analyzed by using Spearman Rho with significance level ρ=0.005. The result showed that there was correlation of homosexual knowledge (ρ=0.001, attitude (ρ=0.000 and  practice (ρ=0.000 with prevalence of STDs. Dsicussion:  It can be concluded that the better knowledge, attitude and practice of homosexual could be decrease prevalence of STDs. Futher studies are recomended to analyze the correlation between homosexual behaviour and prevalence of STDs with Health Believe approach.

  14. Differing Roles of the Face and Voice in Early Human Communication: Roots of Language in Multimodal Expression

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    Yuna Jhang

    2017-09-01

    Full Text Available Seeking roots of language, we probed infant facial expressions and vocalizations. Both have roles in language, but the voice plays an especially flexible role, expressing a variety of functions and affect conditions with the same vocal categories—a word can be produced with many different affective flavors. This requirement of language is seen in very early infant vocalizations. We examined the extent to which affect is transmitted by early vocal categories termed “protophones” (squeals, vowel-like sounds, and growls and by their co-occurring facial expressions, and similarly the extent to which vocal type is transmitted by the voice and co-occurring facial expressions. Our coder agreement data suggest infant affect during protophones was most reliably transmitted by the face (judged in video-only, while vocal type was transmitted most reliably by the voice (judged in audio-only. Voice alone transmitted negative affect more reliably than neutral or positive affect, suggesting infant protophones may be used especially to call for attention when the infant is in distress. By contrast, the face alone provided no significant information about protophone categories. Indeed coders in VID could scarcely recognize the difference between silence and voice when coding protophones in VID. The results suggest that partial decoupling of communicative roles for face and voice occurs even in the first months of life. Affect in infancy appears to be transmitted in a way that audio and video aspects are flexibly interwoven, as in mature language.

  15. Differing Roles of the Face and Voice in Early Human Communication: Roots of Language in Multimodal Expression.

    Science.gov (United States)

    Jhang, Yuna; Franklin, Beau; Ramsdell-Hudock, Heather L; Oller, D Kimbrough

    2017-01-01

    Seeking roots of language, we probed infant facial expressions and vocalizations. Both have roles in language, but the voice plays an especially flexible role, expressing a variety of functions and affect conditions with the same vocal categories-a word can be produced with many different affective flavors. This requirement of language is seen in very early infant vocalizations. We examined the extent to which affect is transmitted by early vocal categories termed "protophones" (squeals, vowel-like sounds, and growls) and by their co-occurring facial expressions, and similarly the extent to which vocal type is transmitted by the voice and co-occurring facial expressions. Our coder agreement data suggest infant affect during protophones was most reliably transmitted by the face (judged in video-only), while vocal type was transmitted most reliably by the voice (judged in audio-only). Voice alone transmitted negative affect more reliably than neutral or positive affect, suggesting infant protophones may be used especially to call for attention when the infant is in distress. By contrast, the face alone provided no significant information about protophone categories. Indeed coders in VID could scarcely recognize the difference between silence and voice when coding protophones in VID. The results suggest that partial decoupling of communicative roles for face and voice occurs even in the first months of life. Affect in infancy appears to be transmitted in a way that audio and video aspects are flexibly interwoven, as in mature language.

  16. Early tumour detection: a transillumination, time-resolved technique

    International Nuclear Information System (INIS)

    Behin-Ain, S.; Van Doorn, T.; Patterson, J.

    2000-01-01

    Full text: Research into transillumination techniques for the detection of tumours in soft tissue has been ongoing for over 70 years. The resolution and contrast, however, remain severely limited by scatter. Single photon detection techniques, with ideally infinite extinction coefficients, have been proposed to accumulate sub-hertz photon transmitted frequencies in the early part of a transmitted pulse. Computer based simulations have been undertaken to examine the theoretical performance requirements of the detector and the resultant image qualities that may be expected with this imaging technique. This paper reports on the computational techniques required for implementing these simulations in an efficient manner. Controlled Monte Carlo (CMC) and Convolution of Layers (CL) techniques were employed to constrain the photon to those having more chance of detection and hence enhance the detection statistics. Extrapolation techniques are proposed to reconstruct the early part of the temporal profile. Computational methods were implemented to evaluate Path Integrals, which are otherwise overly complex to evaluate. CMC and CL reduce the computational time by more than 10 orders of magnitude by only tracking those photons more likely to reach the detector. In the case of an optically thick medium with high scattering coefficient, extrapolation techniques are used to reconstruct the early part of temporal profile. Analytical solutions were found to be too involved for the simplest geometries. However the CL and implementation of computational techniques make Path integrals a useful analytical tool to compliment full Monte Carlo techniques. Results have shown that these methods collectively enable detection of small inhomogeneites within soft tissues. Reduced computation times and full reconstruction of the temporal profile of transmitted photons through optically thick medium enable fast simulations of single photon detectors to be achieved with the above described

  17. A novel thymidylate synthase from the Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP) clade with altered nucleotide and folate binding sites.

    Science.gov (United States)

    Lopez-Zavala, Alonso A; Guevara-Hernandez, Eduardo; Vazquez-Lujan, Luz H; Sanchez-Paz, Arturo; Garcia-Orozco, Karina D; Contreras-Vergara, Carmen A; Lopez-Leal, Gamaliel; Arvizu-Flores, Aldo A; Ochoa-Leyva, Adrian; Sotelo-Mundo, Rogerio R

    2018-01-01

    Thymidylate synthase (TS, E.C. 2.1.1.45) is a crucial enzyme for de novo deoxythymidine monophosphate (dTMP) biosynthesis. The gene for this enzyme is thyA , which encodes the folate-dependent TS that converts deoxyuridine monophosphate group (dUMP) into (dTMP) using the cofactor 5,10-methylenetetrahydrofolate (mTHF) as a carbon donor. We identified the thyA gene in the genome of the Vibrio parahaemolyticus strain FIM-S1708+ that is innocuous to humans but pathogenic to crustaceans. Surprisingly, we found changes in the residues that bind the substrate dUMP and mTHF, previously postulated as invariant among all TSs known (Finer-Moore, Santi & Stroud, 2003). Interestingly, those amino acid changes were also found in a clade of microorganisms that contains Vibrionales , Alteromonadales , Aeromonadales , and Pasteurellales (VAAP) from the Gammaproteobacteria class. In this work, we studied the biochemical properties of recombinant TS from V. parahemolyticus FIM-S1708+ (VpTS) to address the natural changes in the TS amino acid sequence of the VAAP clade. Interestingly, the K m for dUMP was 27.3 ± 4.3 µM, about one-fold larger compared to other TSs. The K m for mTHF was 96.3 ± 18 µM, about three- to five-fold larger compared to other species, suggesting also loss of affinity. Thus, the catalytic efficiency was between one or two orders of magnitude smaller for both substrates. We used trimethoprim, a common antibiotic that targets both TS and DHFR for inhibition studies. The IC 50 values obtained were high compared to other results in the literature. Nonetheless, this molecule could be a lead for the design antibiotics towards pathogens from the VAAP clade. Overall, the experimental results also suggest that in the VAAP clade the nucleotide salvage pathway is important and should be investigated, since the de novo dTMP synthesis appears to be compromised by a less efficient thymidylate synthase.

  18. A novel thymidylate synthase from the Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP clade with altered nucleotide and folate binding sites

    Directory of Open Access Journals (Sweden)

    Alonso A. Lopez-Zavala

    2018-06-01

    Full Text Available Thymidylate synthase (TS, E.C. 2.1.1.45 is a crucial enzyme for de novo deoxythymidine monophosphate (dTMP biosynthesis. The gene for this enzyme is thyA, which encodes the folate-dependent TS that converts deoxyuridine monophosphate group (dUMP into (dTMP using the cofactor 5,10-methylenetetrahydrofolate (mTHF as a carbon donor. We identified the thyA gene in the genome of the Vibrio parahaemolyticus strain FIM-S1708+ that is innocuous to humans but pathogenic to crustaceans. Surprisingly, we found changes in the residues that bind the substrate dUMP and mTHF, previously postulated as invariant among all TSs known (Finer-Moore, Santi & Stroud, 2003. Interestingly, those amino acid changes were also found in a clade of microorganisms that contains Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP from the Gammaproteobacteria class. In this work, we studied the biochemical properties of recombinant TS from V. parahemolyticus FIM-S1708+ (VpTS to address the natural changes in the TS amino acid sequence of the VAAP clade. Interestingly, the Km for dUMP was 27.3 ± 4.3 µM, about one-fold larger compared to other TSs. The Km for mTHF was 96.3 ± 18 µM, about three- to five-fold larger compared to other species, suggesting also loss of affinity. Thus, the catalytic efficiency was between one or two orders of magnitude smaller for both substrates. We used trimethoprim, a common antibiotic that targets both TS and DHFR for inhibition studies. The IC50 values obtained were high compared to other results in the literature. Nonetheless, this molecule could be a lead for the design antibiotics towards pathogens from the VAAP clade. Overall, the experimental results also suggest that in the VAAP clade the nucleotide salvage pathway is important and should be investigated, since the de novo dTMP synthesis appears to be compromised by a less efficient thymidylate synthase.

  19. New euprimate postcrania from the early Eocene of Gujarat, India, and the strepsirrhine-haplorhine divergence.

    Science.gov (United States)

    Dunn, Rachel H; Rose, Kenneth D; Rana, Rajendra S; Kumar, Kishor; Sahni, Ashok; Smith, Thierry

    2016-10-01

    The oldest primates of modern aspect (euprimates) appear abruptly on the Holarctic continents during a brief episode of global warming known as the Paleocene-Eocene Thermal Maximum, at the beginning of the Eocene (∼56 Ma). When they first appear in the fossil record, they are already divided into two distinct clades, Adapoidea (basal members of Strepsirrhini, which includes extant lemurs, lorises, and bushbabies) and Omomyidae (basal Haplorhini, which comprises living tarsiers, monkeys, and apes). Both groups have recently been discovered in the early Eocene Cambay Shale Formation of Vastan lignite mine, Gujarat, India, where they are known mainly from teeth and jaws. The Vastan fossils are dated at ∼54.5 Myr based on associated dinoflagellates and isotope stratigraphy. Here, we describe new, exquisitely preserved limb bones of these Indian primates that reveal more primitive postcranial characteristics than have been previously documented for either clade, and differences between them are so minor that in many cases we cannot be certain to which group they belong. Nevertheless, the small distinctions observed in some elements foreshadow postcranial traits that distinguish the groups by the middle Eocene, suggesting that the Vastan primates-though slightly younger than the oldest known euprimates-may represent the most primitive known remnants of the divergence between the two great primate clades. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Mechanisms and consequences of paternally transmitted chromosomal abnormalities

    Energy Technology Data Exchange (ETDEWEB)

    Marchetti, F; Wyrobek, A J

    2005-04-05

    Paternally transmitted chromosomal damage has been associated with pregnancy loss, developmental and morphological defects, infant mortality, infertility, and genetic diseases in the offspring including cancer. There is epidemiological evidence linking paternal exposure to occupational or environmental agents with an increased risk of abnormal reproductive outcomes. There is also a large body of literature on germ cell mutagenesis in rodents showing that treatment of male germ cells with mutagens has dramatic consequences on reproduction producing effects such as those observed in human epidemiological studies. However, we know very little about the etiology, transmission and early embryonic consequences of paternally-derived chromosomal abnormalities. The available evidence suggests that: (1) there are distinct patterns of germ cell-stage differences in the sensitivity of induction of transmissible genetic damage with male postmeiotic cells being the most sensitive; (2) cytogenetic abnormalities at first metaphase after fertilization are critical intermediates between paternal exposure and abnormal reproductive outcomes; and, (3) there are maternally susceptibility factors that may have profound effects on the amount of sperm DNA damage that is converted into chromosomal aberrations in the zygote and directly affect the risk for abnormal reproductive outcomes.

  1. The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes

    Science.gov (United States)

    Danchin, Etienne G.J.; Perfus-Barbeoch, Laetitia; Rancurel, Corinne; Thorpe, Peter; Da Rocha, Martine; Bajew, Simon; Neilson, Roy; Sokolova (Guzeeva), Elena; Da Silva, Corinne; Guy, Julie; Labadie, Karine; Esmenjaud, Daniel; Helder, Johannes; Jones, John T.

    2017-01-01

    Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been implicated in the evolution of plant parasitism. We have used ribonucleic acid sequencing (RNAseq) to generate reference transcriptomes for two economically important nematode species, Xiphinema index and Longidorus elongatus, representative of two genera within the early-branching Clade 2 of the phylum Nematoda. We used a transcriptome-wide analysis to identify putative horizontal gene transfer events. This represents the first in-depth transcriptome analysis from any plant-parasitic nematode of this clade. For each species, we assembled ~30 million Illumina reads into a reference transcriptome. We identified 62 and 104 transcripts, from X. index and L. elongatus, respectively, that were putatively acquired via horizontal gene transfer. By cross-referencing horizontal gene transfer prediction with a phylum-wide analysis of Pfam domains, we identified Clade 2-specific events. Of these, a GH12 cellulase from X. index was analysed phylogenetically and biochemically, revealing a likely bacterial origin and canonical enzymatic function. Horizontal gene transfer was previously shown to be a phenomenon that has contributed to the evolution of plant parasitism among nematodes. Our findings underline the importance and the extensiveness of this phenomenon in the evolution of plant-parasitic life styles in this speciose and widespread animal phylum. PMID:29065523

  2. The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes.

    Science.gov (United States)

    Danchin, Etienne G J; Perfus-Barbeoch, Laetitia; Rancurel, Corinne; Thorpe, Peter; Da Rocha, Martine; Bajew, Simon; Neilson, Roy; Guzeeva, Elena Sokolova; Da Silva, Corinne; Guy, Julie; Labadie, Karine; Esmenjaud, Daniel; Helder, Johannes; Jones, John T; den Akker, Sebastian Eves-van

    2017-10-23

    Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been implicated in the evolution of plant parasitism. We have used ribonucleic acid sequencing (RNAseq) to generate reference transcriptomes for two economically important nematode species, Xiphinema index and Longidorus elongatus , representative of two genera within the early-branching Clade 2 of the phylum Nematoda. We used a transcriptome-wide analysis to identify putative horizontal gene transfer events. This represents the first in-depth transcriptome analysis from any plant-parasitic nematode of this clade. For each species, we assembled ~30 million Illumina reads into a reference transcriptome. We identified 62 and 104 transcripts, from X. index and L. elongatus , respectively, that were putatively acquired via horizontal gene transfer. By cross-referencing horizontal gene transfer prediction with a phylum-wide analysis of Pfam domains, we identified Clade 2-specific events. Of these, a GH12 cellulase from X. index was analysed phylogenetically and biochemically, revealing a likely bacterial origin and canonical enzymatic function. Horizontal gene transfer was previously shown to be a phenomenon that has contributed to the evolution of plant parasitism among nematodes. Our findings underline the importance and the extensiveness of this phenomenon in the evolution of plant-parasitic life styles in this speciose and widespread animal phylum.

  3. The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes

    Directory of Open Access Journals (Sweden)

    Etienne G.J. Danchin

    2017-10-01

    Full Text Available Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been implicated in the evolution of plant parasitism. We have used ribonucleic acid sequencing (RNAseq to generate reference transcriptomes for two economically important nematode species, Xiphinema index and Longidorus elongatus, representative of two genera within the early-branching Clade 2 of the phylum Nematoda. We used a transcriptome-wide analysis to identify putative horizontal gene transfer events. This represents the first in-depth transcriptome analysis from any plant-parasitic nematode of this clade. For each species, we assembled ~30 million Illumina reads into a reference transcriptome. We identified 62 and 104 transcripts, from X. index and L. elongatus, respectively, that were putatively acquired via horizontal gene transfer. By cross-referencing horizontal gene transfer prediction with a phylum-wide analysis of Pfam domains, we identified Clade 2-specific events. Of these, a GH12 cellulase from X. index was analysed phylogenetically and biochemically, revealing a likely bacterial origin and canonical enzymatic function. Horizontal gene transfer was previously shown to be a phenomenon that has contributed to the evolution of plant parasitism among nematodes. Our findings underline the importance and the extensiveness of this phenomenon in the evolution of plant-parasitic life styles in this speciose and widespread animal phylum.

  4. "cART intensification by the HIV-1 Tat B clade vaccine: progress to phase III efficacy studies".

    Science.gov (United States)

    Cafaro, Aurelio; Sgadari, Cecilia; Picconi, Orietta; Tripiciano, Antonella; Moretti, Sonia; Francavilla, Vittorio; Pavone Cossut, Maria Rosaria; Buttò, Stefano; Cozzone, Giovanni; Ensoli, Fabrizio; Monini, Paolo; Ensoli, Barbara

    2018-02-01

    In spite of its success at suppressing HIV replication, combination antiretroviral therapy (cART) only partially reduces immune dysregulation and loss of immune functions. These cART-unmet needs appear to be due to persistent virus replication and cell-to-cell transmission in reservoirs, and are causes of increased patients' morbidity and mortality. Up to now, therapeutic interventions aimed at cART-intensification by attacking the virus reservoir have failed. Areas covered: We briefly review the rationale and clinical development of Tat therapeutic vaccine in cART-treated subjects in Italy and South Africa (SA). Vaccination with clade-B Tat induced cross-clade neutralizing antibodies, immune restoration, including CD4 + T cell increase particularly in low immunological responders, and reduction of proviral DNA. Phase III efficacy trials in SA are planned both in adult and pediatric populations. Expert commentary: We propose the Tat therapeutic vaccine as a pathogenesis-driven intervention that effectively intensifies cART and may lead to a functional cure and provide new perspectives for prevention and virus eradication strategies.

  5. Analysis of Ultrasonic Transmitted Signal for Apple using Wavelet Transform

    International Nuclear Information System (INIS)

    Kim, Ki Bok; Lee, Sang Dae; Choi, Man Yong; Kim, Man Soo

    2005-01-01

    This study was conducted to analyze the ultrasonic transmitted signal for apple using wavelet transform. Fruit consists of nonlinear visco-elastic properties such as flesh, an ovary and rind and lienee most ultrasonic wave is attenuated and its frequency is shifted during passing the fruit. Thus it is not easy to evaluate the internal quality of the fruit using typical ultrasonic parameters such as wave velocity, attenuation, and frequency spectrum. The discrete wavelet transform was applied to the ultrasonic transmitted signal for apple. The magnitude of the first peak frequency of the wavelet basis from the ultrasonic transmitted signal showed a close correlation to the storage time of apple

  6. Inductive Reasoning about Causally Transmitted Properties

    Science.gov (United States)

    Shafto, Patrick; Kemp, Charles; Bonawitz, Elizabeth Baraff; Coley, John D.; Tenenbaum, Joshua B.

    2008-01-01

    Different intuitive theories constrain and guide inferences in different contexts. Formalizing simple intuitive theories as probabilistic processes operating over structured representations, we present a new computational model of category-based induction about causally transmitted properties. A first experiment demonstrates undergraduates'…

  7. Effects of a transmitted light device for pediatric peripheral venipuncture and intravenous cannulation

    Directory of Open Access Journals (Sweden)

    Yamazaki S

    2011-10-01

    Full Text Available Shinya Yamazaki1, Shu Tomita1, Masahiro Watanabe1, Hiroyoshi Kawaai1, Kazuhiro Shimamura2 1Department of Dental Anesthesiology; 2Department of Pediatric Dentistry, Ohu University Dental Hospital, Koriyama City, Fukushima Prefecture, Japan Abstract: Pediatric peripheral venipuncture and intravenous cannulation are difficult. However, successful venipuncture and intravenous cannulation are absolutely required for pediatric clinical risk management. This study assessed the success rate of venipuncture and intravenous cannulation when transmitted light was applied to the pediatric dorsum manus. The subjects included 100 young children who were scheduled for dental treatment or oral surgery under general anesthesia. Anesthesia was induced, and insertion of an intravenous catheter into the dorsum manus was attempted with or without using transmitted light. The patients were evaluated to determine whether the venipuncture was successful, and whether the intravenous cannulation of the external catheter was successful. The success rate of venipuncture was 100% when transmitted light was used, and 83% when the transmitted light was not used (P = 0.000016. In addition, the success rate of intravenous cannulation was 88% when transmitted light was used, and 55% when the transmitted light was not used (P = 0.0000002. The shape of the vein in the dorsum manus can be clearly recognized when transmitted light is used. The use of light significantly increased the success rate of intravenous cannulation, because it allowed direct confirmation of the direction to push the intravenous catheter forward. The use of transmitted light allows for more successful venipuncture and intravenous cannulation in young children. Keywords: transmitted light, pediatric peripheral venipuncture, pediatric peripheral intravenous cannulation

  8. United States Climate Reference Network (USCRN) Raw Data Transmitted from Satellite

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — USCRN Raw Transmitted Data is level 0 data received from the USCRN stations that are transmitted continuously. The data values are ingested with a unique 18-bit...

  9. Contrasting patterns of phylogenetic assemblage structure along the elevational gradient for major hummingbird clades

    DEFF Research Database (Denmark)

    Parra, Juan L.; Rahbek, Carsten; McGuire, Jimmy A.

    2011-01-01

    Aim We evaluated the hypothesis that, given niche conservatism, relatedness of co-occurring hummingbird species of a given clade will increase at greater distances from the elevation where it originated. We also used prior knowledge of flight biomechanics and feeding specialization of hummingbird...... specialization (hermits and brilliants) always included a vegetation-related variable as an important predictor of change in phylogenetic structure. Main conclusions We found no overall support for the conservatism and zone of origin hypotheses. Knowledge of each clade’s natural history proved useful...

  10. A diplodocid sauropod survivor from the early cretaceous of South America.

    Directory of Open Access Journals (Sweden)

    Pablo A Gallina

    Full Text Available Diplodocids are by far the most emblematic sauropod dinosaurs. They are part of Diplodocoidea, a vast clade whose other members are well-known from Jurassic and Cretaceous strata in Africa, Europe, North and South America. However, Diplodocids were never certainly recognized from the Cretaceous or in any other southern land mass besides Africa. Here we report a new sauropod, Leikupal laticauda gen. et sp. nov., from the early Lower Cretaceous (Bajada Colorada Formation of Neuquén Province, Patagonia, Argentina. This taxon differs from any other sauropod by the presence of anterior caudal transverse process extremely developed with lateroventral expansions reinforced by robust dorsal and ventral bars, very robust centroprezygapophyseal lamina in anterior caudal vertebra and paired pneumatic fossae on the postzygapophyses in anterior-most caudal vertebra. The phylogenetic analyses support its position not only within Diplodocidae but also as a member of Diplodocinae, clustering together with the African form Tornieria, pushing the origin of Diplodocoidea to the Middle Jurassic or even earlier. The new discovery represents the first record of a diplodocid for South America and the stratigraphically youngest record of this clade anywhere.

  11. Novel sequence types of extended-spectrum and acquired AmpC beta-lactamase producing Escherichia coli and Escherichia clade V isolated from wild mammals.

    Science.gov (United States)

    Alonso, Carla Andrea; Alcalá, Leticia; Simón, Carmen; Torres, Carmen

    2017-08-01

    The closer contact with wildlife due to the growing human population and the destruction of natural habitats emphasizes the need of gaining insight into the role of animals as source of antimicrobial resistance. Here, we aim at characterizing the antimicrobial resistance genes and phylogenetic distribution of commensal Escherichia coli from 62 wild mammals. Isolates exhibiting resistance to ≥1 antibiotic were detected in 25.8% of the animals and 6.4% carried an extended-spectrum beta-lactamase (ESBL)/AmpC-producing E. coli. Genetic mechanisms involved in third-generation cephalosporin resistance were as follows: (i) hyperproduction of chromosomal AmpC (hedgehog), (ii) production of acquired CMY-2 β-lactamase (hedgehog), (iii) production of SHV-12 and CTX-M-14 ESBLs (n = 2, mink and roe-deer). ESBL genes were transferable by conjugation, and blaCMY-2 was mobilized by a 95kb IncI1 plasmid. The distribution of the phylogenetic groups in the E. coli collection studied was B1 (44.6%), B2 (24.6%), E (15.4%), A (4.6%) and F (3.1%). Five isolates (7.7%) were cryptic Escherichia clades (clade IV, 4 mice; clade V, 1 mink). ESBL/AmpC-E. coli isolates showed different sequence types (STs): ST1128/B1, ST4564/B1 (new), ST4996/B1 (new) and a non-registered ST. This study contributes to better understand the E. coli population and antimicrobial resistance flow in wildlife and reports new AmpC-E. coli STs and a first described ESBL-producing Escherichia clade V isolate. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Early Communication System (ECOMM) for ISS

    Science.gov (United States)

    Gaylor, Kent; Tu, Kwei

    1999-01-01

    The International Space Station (ISS) Early Communications System (ECOMM) was a Johnson Space Center (JSC) Avionic Systems Division (ASD) in-house developed communication system to provide early communications between the ISS and the Mission Control Center-Houston (MCC-H). This system allows for low rate commands (link rate of 6 kbps) to be transmitted through the Tracking and Data Relay Satellite System (TDRSS) from MCC-H to the ISS using TDRSS's S-band Single Access Forward (SSA/) link service. This system also allows for low rate telemetry (link rate of 20.48 kbps) to be transmitted from ISS to MCC-H through the TDRSS using TDRSS's S-band Single Access Return (SSAR) link service. In addition this system supports a JSC developed Onboard Communications Adapter (OCA) that allows for a two-way data exchange of 128 kbps between MCC-H and the ISS through TDRSS. This OCA data can be digital video/audio (two-way videoconference), and/or file transfers, and/or "white board". The key components of the system, the data formats used by the system to insure compatibility with the future ISS S-Band System, as well as how other vehicles may be able to use this system for their needs are discussed in this paper.

  13. Glossina palpalis palpalis populations from Equatorial Guinea belong to distinct allopatric clades.

    Science.gov (United States)

    Cordon-Obras, Carlos; Cano, Jorge; Knapp, Jenny; Nebreda, Paloma; Ndong-Mabale, Nicolas; Ncogo-Ada, Policarpo Ricardo; Ndongo-Asumu, Pedro; Navarro, Miguel; Pinto, Joao; Benito, Agustin; Bart, Jean-Mathieu

    2014-01-17

    Luba is one of the four historical foci of Human African Trypanosomiasis (HAT) on Bioko Island, in Equatorial Guinea. Although no human cases have been detected since 1995, T. b. gambiense was recently observed in the vector Glossina palpalis palpalis. The existence of cryptic species within this vector taxon has been previously suggested, although no data are available regarding the evolutionary history of tsetse flies populations in Bioko. A phylogenetic analysis of 60 G. p. palpalis from Luba was performed sequencing three mitochondrial (COI, ND2 and 16S) and one nuclear (rDNA-ITS1) DNA markers. Phylogeny reconstruction was performed by Distance Based, Maximum Likelihood and Bayesian Inference methods. The COI and ND2 mitochondrial genes were concatenated and revealed 10 closely related haplotypes with a dominant one found in 61.1% of the flies. The sequence homology of the other 9 haplotypes compared to the former ranged from 99.6 to 99.9%. Phylogenetic analysis clearly clustered all island samples with flies coming from the Western African Clade (WAC), and separated from the flies belonging to the Central Africa Clade (CAC), including samples from Mbini and Kogo, two foci of mainland Equatorial Guinea. Consistent with mitochondrial data, analysis of the microsatellite motif present in the ITS1 sequence exhibited two closely related genotypes, clearly divergent from the genotypes previously identified in Mbini and Kogo. We report herein that tsetse flies populations circulating in Equatorial Guinea are composed of two allopatric subspecies, one insular and the other continental. The presence of these two G. p. palpalis cryptic taxa in Equatorial Guinea should be taken into account to accurately manage vector control strategy, in a country where trypanosomiasis transmission is controlled but not definitively eliminated yet.

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

    Science.gov (United States)

    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

  15. Coherent Code Tracking for Spatial Transmit Diversity DS-CDMA Systems

    Directory of Open Access Journals (Sweden)

    R. W. Stewart

    2005-09-01

    Full Text Available Spatial transmit diversity schemes are now well integrated into third-generation cellular mobile communication system specifications. When DS-CDMA-based technology is deployed in typical macro- and microcell environments, multipath diversity and spatial diversity may be exploited simultaneously by a 2D RAKE receiver. The work presented in this paper focuses on taking advantage of spatial transmit diversity in synchronising the 2D RAKE structure. We investigate the use of coherent and noncoherent techniques for tracking the timing parameters of each multipath component. It is shown that both noncoherent and coherent techniques benefit from transmit diversity. Additionally the performance gap between these two techniques increases with the number of antennas.

  16. Vector-transmitted disease vaccines: targeting salivary proteins in transmission (SPIT).

    Science.gov (United States)

    McDowell, Mary Ann

    2015-08-01

    More than half the population of the world is at risk for morbidity and mortality from vector-transmitted diseases, and emerging vector-transmitted infections are threatening new populations. Rising insecticide resistance and lack of efficacious vaccines highlight the need for novel control measures. One such approach is targeting the vector-host interface by incorporating vector salivary proteins in anti-pathogen vaccines. Debate remains about whether vector saliva exposure exacerbates or protects against more severe clinical manifestations, induces immunity through natural exposure or extends to all vector species and associated pathogens. Nevertheless, exploiting this unique biology holds promise as a viable strategy for the development of vaccines against vector-transmitted diseases. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Barcoding success as a function of phylogenetic relatedness in Viburnum, a clade of woody angiosperms

    Directory of Open Access Journals (Sweden)

    Clement Wendy L

    2012-05-01

    Full Text Available Abstract Background The chloroplast genes matK and rbcL have been proposed as a “core” DNA barcode for identifying plant species. Published estimates of successful species identification using these loci (70-80% may be inflated because they may have involved comparisons among distantly related species within target genera. To assess the ability of the proposed two-locus barcode to discriminate closely related species, we carried out a hierarchically structured set of comparisons within Viburnum, a clade of woody angiosperms containing ca. 170 species (some 70 of which are currently used in horticulture. For 112 Viburnum species, we evaluated rbcL + matK, as well as the chloroplast regions rpl32-trnL, trnH-psbA, trnK, and the nuclear ribosomal internal transcribed spacer region (nrITS. Results At most, rbcL + matK could discriminate 53% of all Viburnum species, with only 18% of the comparisons having genetic distances >1%. When comparisons were progressively restricted to species within major Viburnum subclades, there was a significant decrease in both the discriminatory power and the genetic distances. trnH-psbA and nrITS show much higher levels of variation and potential discriminatory power, and their use in plant barcoding should be reconsidered. As barcoding has often been used to discriminate species within local areas, we also compared Viburnum species within two regions, Japan and Mexico and Central America. Greater success in discriminating among the Japanese species reflects the deeper evolutionary history of Viburnum in that area, as compared to the recent radiation of a single clade into the mountains of Latin America. Conclusions We found very low levels of discrimination among closely related species of Viburnum, and low levels of variation in the proposed barcoding loci may limit success within other clades of long-lived woody plants. Inclusion of the supplementary barcodes trnH-psbA and nrITS increased discrimination rates but

  18. 47 CFR 25.220 - Non-conforming transmit/receive earth station operations.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 2 2010-10-01 2010-10-01 false Non-conforming transmit/receive earth station operations. 25.220 Section 25.220 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Technical Standards § 25.220 Non-conforming transmit/receive...

  19. Emergence of Arthropod Transmitted infections in Kennel Dogs

    Directory of Open Access Journals (Sweden)

    Javed Jameel

    Full Text Available Changing scenario of climate resulting from global warming and adversity of nature has also resulted in emergence and re-emergence of diseases transmitted by arthropods. Increasing trends of population growth of dogs has increased the chance of disease transmission due to readily available susceptible host. Babesiosis and Hepatozoonosis and Ehrlichiosis are the main arthropod borne diseases of dogs prevalent in India. The present article explains the importance of these arthropod transmitted infections in kennel dogs, research progress and reason for their emergence in the present scenario. [Vet. World 2011; 4(11.000: 522-528

  20. Transmit antenna selection based on shadowing side information

    KAUST Repository

    Yilmaz, Ferkan

    2011-05-01

    In this paper, we propose a new transmit antenna selection scheme based on shadowing side information. In the proposed scheme, single transmit antenna which has the highest shadowing coefficient is selected. By the proposed technique, usage of the feedback channel and channel estimation complexity at the receiver can be reduced. We consider independent but not identically distributed Generalized-K composite fading model, which is a general composite fading & shadowing channel model for wireless environments. Exact closed-form outage probability, moment generating function and symbol error probability expressions are derived. In addition, theoretical performance results are validated by Monte Carlo simulations. © 2011 IEEE.

  1. Transmit antenna selection based on shadowing side information

    KAUST Repository

    Yilmaz, Ferkan; Yilmaz, Ahmet Oǧuz; Alouini, Mohamed-Slim; Kucur, Oǧuz

    2011-01-01

    In this paper, we propose a new transmit antenna selection scheme based on shadowing side information. In the proposed scheme, single transmit antenna which has the highest shadowing coefficient is selected. By the proposed technique, usage of the feedback channel and channel estimation complexity at the receiver can be reduced. We consider independent but not identically distributed Generalized-K composite fading model, which is a general composite fading & shadowing channel model for wireless environments. Exact closed-form outage probability, moment generating function and symbol error probability expressions are derived. In addition, theoretical performance results are validated by Monte Carlo simulations. © 2011 IEEE.

  2. Integrated differential high-voltage transmitting circuit for CMUTs

    DEFF Research Database (Denmark)

    Llimos Muntal, Pere; Larsen, Dennis Øland; Farch, Kjartan

    2015-01-01

    In this paper an integrated differential high-voltage transmitting circuit for capacitive micromachined ultrasonic transducers (CMUTs) used in portable ultrasound scanners is designed and implemented in a 0.35 μm high-voltage process. Measurements are performed on the integrated circuit in order...... to assess its performance. The circuit generates pulses at differential voltage levels of 60V, 80V and 100 V, a frequency up to 5MHz and a measured driving strength of 1.75 V/ns with the CMUT connected. The total on-chip area occupied by the transmitting circuit is 0.18 mm2 and the power consumption...

  3. Analytical Model and Optimized Design of Power Transmitting Coil for Inductively Coupled Endoscope Robot.

    Science.gov (United States)

    Ke, Quan; Luo, Weijie; Yan, Guozheng; Yang, Kai

    2016-04-01

    A wireless power transfer system based on the weakly inductive coupling makes it possible to provide the endoscope microrobot (EMR) with infinite power. To facilitate the patients' inspection with the EMR system, the diameter of the transmitting coil is enlarged to 69 cm. Due to the large transmitting range, a high quality factor of the Litz-wire transmitting coil is a necessity to ensure the intensity of magnetic field generated efficiently. Thus, this paper builds an analytical model of the transmitting coil, and then, optimizes the parameters of the coil by enlarging the quality factor. The lumped model of the transmitting coil includes three parameters: ac resistance, self-inductance, and stray capacitance. Based on the exact two-dimension solution, the accurate analytical expression of ac resistance is derived. Several transmitting coils of different specifications are utilized to verify this analytical expression, being in good agreements with the measured results except the coils with a large number of strands. Then, the quality factor of transmitting coils can be well predicted with the available analytical expressions of self- inductance and stray capacitance. Owing to the exact estimation of quality factor, the appropriate coil turns of the transmitting coil is set to 18-40 within the restrictions of transmitting circuit and human tissue issues. To supply enough energy for the next generation of the EMR equipped with a Ø9.5×10.1 mm receiving coil, the coil turns of the transmitting coil is optimally set to 28, which can transfer a maximum power of 750 mW with the remarkable delivering efficiency of 3.55%.

  4. Phylogenetic analysis of Melon chlorotic leaf curl virus from Guatemala: Another emergent species in the Squash leaf curl virus clade

    KAUST Repository

    Brown, J.K.; Mills-Lujan, K.; Idris, Ali

    2011-01-01

    divergent owing in part to recombination, but also due to the accumulation of a substantial number of mutations. In addition they are differentially host-adapted, as has been documented for other cucurbit-infecting, bean-adapted, species in the SLCV clade

  5. Protection of White Leghorn chickens by U.S. emergency H5 vaccination against clade 2.3.4.4 H5N2 high pathogenicity avian influenza virus.

    Science.gov (United States)

    Bertran, Kateri; Balzli, Charles; Lee, Dong-Hun; Suarez, David L; Kapczynski, Darrell R; Swayne, David E

    2017-11-01

    During December 2014-June 2015, the U.S. experienced a high pathogenicity avian influenza (HPAI) outbreak caused by clade 2.3.4.4 H5Nx Goose/Guangdong lineage viruses with devastating consequences for the poultry industry. Three vaccines, developed based on updating existing registered vaccines or currently licensed technologies, were evaluated for possible use: an inactivated reverse genetics H5N1 vaccine (rgH5N1) and an RNA particle vaccine (RP-H5), both containing the hemagglutinin gene of clade 2.3.4.4 strain, and a recombinant herpesvirus turkey vectored vaccine (rHVT-H5) containing the hemagglutinin gene of clade 2.2 strain. The efficacy of the three vaccines, alone or in combination, was assessed in White Leghorn chickens against clade 2.3.4.4 H5N2 HPAI virus challenge. In Study 1, single (rHVT-H5) and prime-boost (rHVT-H5+rgH5N1 or rHVT-H5+RP-H5) vaccination strategies protected chickens with high levels of protective immunity and significantly reduced virus shedding. In Study 2, single vaccination with either rgH5N1 or RP-H5 vaccines provided clinical protection in adult chickens and significantly reduced virus shedding. In Study 3, double rgH5N1 vaccination protected adult chickens from clinical signs and mortality when challenged 20weeks post-boost, with high levels of long-lasting protective immunity and significantly reduced virus shedding. These studies support the use of genetically related vaccines, possibly in combination with a broad protective priming vaccine, for emergency vaccination programs against clade 2.3.4.4 H5Nx HPAI virus in young and adult layer chickens. Published by Elsevier Ltd.

  6. Divergent regulation of Arabidopsis SAUR genes: a focus on the SAUR10-clade.

    Science.gov (United States)

    van Mourik, Hilda; van Dijk, Aalt D J; Stortenbeker, Niek; Angenent, Gerco C; Bemer, Marian

    2017-12-19

    Small Auxin-Upregulated RNA (SAUR) genes encode growth regulators that induce cell elongation. Arabidopsis contains more than 70 SAUR genes, of which the growth-promoting function has been unveiled in seedlings, while their role in other tissues remained largely unknown. Here, we focus on the regulatory regions of Arabidopsis SAUR genes, to predict the processes in which they play a role, and understand the dynamics of plant growth. In this study, we characterized in detail the entire SAUR10-clade: SAUR8, SAUR9, SAUR10, SAUR12, SAUR16, SAUR50, SAUR51 and SAUR54. Overexpression analysis revealed that the different proteins fulfil similar functions, while the SAUR expression patterns were highly diverse, showing expression throughout plant development in a variety of tissues. In addition, the response to application of different hormones largely varied between the different genes. These tissue-specific and hormone-specific responses could be linked to transcription factor binding sites using in silico analyses. These analyses also supported the existence of two groups of SAURs in Arabidopsis: Class I genes can be induced by combinatorial action of ARF-BZR-PIF transcription factors, while Class II genes are not regulated by auxin. SAUR10-clade genes generally induce cell-elongation, but exhibit diverse expression patterns and responses to hormones. Our experimental and in silico analyses suggest that transcription factors involved in plant development determine the tissue specific expression of the different SAUR genes, whereas the amplitude of this expression can often be controlled by hormone response transcription factors. This allows the plant to fine tune growth in a variety of tissues in response to internal and external signals.

  7. Phylogeographic Patterns in Africa and High Resolution Delineation of Genetic Clades in the Lion (Panthera leo)

    Science.gov (United States)

    Bertola, L. D.; Jongbloed, H.; van der Gaag, K. J.; de Knijff, P.; Yamaguchi, N.; Hooghiemstra, H.; Bauer, H.; Henschel, P.; White, P. A.; Driscoll, C. A.; Tende, T.; Ottosson, U.; Saidu, Y.; Vrieling, K.; de Iongh, H. H.

    2016-08-01

    Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.

  8. Phylogeographic Patterns in Africa and High Resolution Delineation of Genetic Clades in the Lion (Panthera leo).

    Science.gov (United States)

    Bertola, L D; Jongbloed, H; van der Gaag, K J; de Knijff, P; Yamaguchi, N; Hooghiemstra, H; Bauer, H; Henschel, P; White, P A; Driscoll, C A; Tende, T; Ottosson, U; Saidu, Y; Vrieling, K; de Iongh, H H

    2016-08-04

    Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.

  9. Preliminary phylogenetic analysis of the Andean clade and the placement of new Colombian blueberries (Ericaceae, Vaccinieae

    Directory of Open Access Journals (Sweden)

    Paola Pedraza-Penalosa

    2015-04-01

    Full Text Available The blueberry tribe Vaccinieae (Ericaceae is particularly diverse in South America and underwent extensive radiation in Colombia where many endemics occur. Recent fieldwork in Colombia has resulted in valuable additions to the phylogeny and as well in the discovery of morphologically noteworthy new species that need to be phylogenetically placed before being named. This is particularly important, as the monophyly of many of the studied genera have not been confirmed. In order to advance our understanding of the relationships within neotropical Vaccinieae and advice the taxonomy of the new blueberry relatives, here we present the most comprehensive phylogenetic analysis for the Andean clade. Anthopterus, Demosthenesia, and Pellegrinia are among the putative Andean genera recovered as monophyletic, while other eight Andean genera were not. The analyses also showed that genera that have been traditionally widely defined are non-monophyletic and could be further split into more discrete groups. Four newly discovered Colombian Vaccinieae are placed in the monophyletic Satyria s.s. and the Psammisia I clade. Although these new species are endemic to the Colombian Western Cordillera and Chocó biogeographic region and three are not known outside of Las Orquídeas National Park, they do not form sister pairs.

  10. Mouse immature oocytes irradiated in vivo at 14-days of age and evaluated for transmitted effects using the aggregation embryo chimera assay

    International Nuclear Information System (INIS)

    Straume, T.; Raabe, O.G.; Walsh, K.J.; Wiley, L.M.

    1996-01-01

    A previous study using the mouse-preimplantation-embryo-chimera assay demonstrated a reproducible transmitted effect (proliferation disadvantage observed in early embryos) from females irradiated as 49-day-old adults using 0.15 Gy of gamma rays and then mated seven weeks later, i.e., embryos were from oocytes that were immature at time of irradiation. Because mouse immature oocytes are known to be much more radiosensitive to cell killing in juveniles than in adults, a follow-on study was performed here using 14-day-old juvenile mice. In contrast to adults, the exposure of juveniles to 0.15 Gy of gamma rays did not result in a detectable transmitted proliferation disadvantage when animals were mated 7 or 12 weeks later. This observation is discussed in light of previous studies on mouse immature oocytes and embryo chimeras

  11. CDC WONDER: Sexually Transmitted Disease (STD) morbidity

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sexually Transmitted Disease (STD) Morbidity online databases on CDC WONDER contain case reports reported from the 50 United States and D.C., Puerto Rico, Virgin...

  12. CDC WONDER: Sexually Transmitted Disease (STD) Morbidity

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sexually Transmitted Disease (STD) Morbidity online databases on CDC WONDER contain case reports reported from the 50 United States and D.C., Puerto Rico, Virgin...

  13. Comparisons of receive array interference reduction techniques under erroneous generalized transmit beamforming

    KAUST Repository

    Radaydeh, Redha Mahmoud; Alouini, Mohamed-Slim

    2014-01-01

    information for the desired user spatially uncorrelated transmit channels on the effectiveness of transmit beamforming for different interference reduction techniques is investigated. The case of over-loaded receive array with closely-spaced elements

  14. Plasmodium falciparum dolichol phosphate mannose synthase represents a novel clade

    International Nuclear Information System (INIS)

    Shams-Eldin, Hosam; Santos de Macedo, Cristiana; Niehus, Sebastian; Dorn, Caroline; Kimmel, Juergen; Azzouz, Nahid; Schwarz, Ralph T.

    2008-01-01

    Dolichol phosphate mannose synthase (DPM) catalyzes the reaction between dolichol phosphate (Dol-P) and guanosine diphosphate mannose (GDP-Man) to form dolichol-phosphate-mannose (Dol-P-Man). This molecule acts as mannose donor for N-glycosylation and glycosylphosphatidylinositol (GPI) biosynthesis. The Plasmodium falciparum DPM1 (Pfdpm1) possesses a single predicted transmembrane region near the N-, but not the C-terminus. Here we show that the cloned Pfdpm1 gene failed to complement a Saccharomyces cerevisiae mutant indicating that the parasite gene does not belong to the baker's yeast group, as was previously assumed. Furthermore, Pfdpm1 was unable to complement a mouse mutant deficient in DPM but efficiently complements the Schizosaccharomyces pombe fission yeast mutant, indicating a difference between fission yeast and mammalian DPM genes. Therefore, we reanalyzed the hydrophobicity scales of all known DPMs and consequently reclassify the DPM clade into six major novel subgroups. Furthermore, we show that Pfdpm1 represents a unique enzyme among these subgroups

  15. Knowledge of Sexually Transmitted Diseases among Secondary ...

    African Journals Online (AJOL)

    The study was carried out in three public secondary schools in Ogbondoroko and Laduba .... population live in the rural areas where information on sexually transmitted ..... Centers for Disease Control and Prevention (2009) Diagnoses of HIV ...

  16. Spatio-temporal distribution of soil-transmitted helminth infections in Brazil.

    Science.gov (United States)

    Chammartin, Frédérique; Guimarães, Luiz H; Scholte, Ronaldo Gc; Bavia, Mara E; Utzinger, Jürg; Vounatsou, Penelope

    2014-09-18

    In Brazil, preventive chemotherapy targeting soil-transmitted helminthiasis is being scaled-up. Hence, spatially explicit estimates of infection risks providing information about the current situation are needed to guide interventions. Available high-resolution national model-based estimates either rely on analyses of data restricted to a given period of time, or on historical data collected over a longer period. While efforts have been made to take into account the spatial structure of the data in the modelling approach, little emphasis has been placed on the temporal dimension. We extracted georeferenced survey data on the prevalence of infection with soil-transmitted helminths (i.e. Ascaris lumbricoides, hookworm and Trichuris trichiura) in Brazil from the Global Neglected Tropical Diseases (GNTD) database. Selection of the most important predictors of infection risk was carried out using a Bayesian geostatistical approach and temporal models that address non-linearity and correlation of the explanatory variables. The spatial process was estimated through a predictive process approximation. Spatio-temporal models were built on the selected predictors with integrated nested Laplace approximation using stochastic partial differential equations. Our models revealed that, over the past 20 years, the risk of soil-transmitted helminth infection has decreased in Brazil, mainly because of the reduction of A. lumbricoides and hookworm infections. From 2010 onwards, we estimate that the infection prevalences with A. lumbricoides, hookworm and T. trichiura are 3.6%, 1.7% and 1.4%, respectively. We also provide a map highlighting municipalities in need of preventive chemotherapy, based on a predicted soil-transmitted helminth infection risk in excess of 20%. The need for treatments in the school-aged population at the municipality level was estimated at 1.8 million doses of anthelminthic tablets per year. The analysis of the spatio-temporal aspect of the risk of infection

  17. Dental histology of Coelophysis bauri and the evolution of tooth attachment tissues in early dinosaurs.

    Science.gov (United States)

    Fong, Raymond K M; LeBlanc, Aaron R H; Berman, David S; Reisz, Robert R

    2016-07-01

    Studies of dinosaur teeth have focused primarily on external crown morphology and thus, use shed or in situ tooth crowns, and are limited to the enamel and dentine dental tissues. As a result, the full suites of periodontal tissues that attach teeth to the jaws remain poorly documented, particularly in early dinosaurs. These tissues are an integral part of the tooth and thus essential to a more complete understanding of dental anatomy, development, and evolution in dinosaurs. To identify the tooth attachment tissues in early dinosaurs, histological thin sections were prepared from the maxilla and dentary of a partial skull of the early theropod Coelophysis bauri from the Upper Triassic (Rhaetian- 209-201 Ma) Whitaker Quarry, New Mexico, USA. As one of the phylogenetically and geologically oldest dinosaurs, it is an ideal candidate for examining dental tissues near the base of the dinosaurian clade. The teeth of C. bauri exhibited a fibrous tooth attachment in which the teeth possessed five tissues: enamel, dentine, cementum, periodontal ligament (PDL), and alveolar bone. Our findings, coupled with those of more recent studies of ornithischian teeth, indicate that a tripartite periodontium, similar to that of crocodilians and mammals, is the plesiomorphic condition for dinosaurs. The occurrence of a tripartite periodontium in dinosaurs adds to the growing consensus that the presence of these tissues is the plesiomorphic condition for the major amniote clades. Furthermore, this study establishes the relative timing of tissue development and growth directions of periodontal tissues and provides the first comparative framework for future studies of dinosaur periodontal development, tooth replacement, and histology. J. Morphol. 277:916-924, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  18. High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade

    Directory of Open Access Journals (Sweden)

    Christie-Oleza Joseph A

    2012-02-01

    Full Text Available Abstract Background The structural and functional annotation of genomes is now heavily based on data obtained using automated pipeline systems. The key for an accurate structural annotation consists of blending similarities between closely related genomes with biochemical evidence of the genome interpretation. In this work we applied high-throughput proteogenomics to Ruegeria pomeroyi, a member of the Roseobacter clade, an abundant group of marine bacteria, as a seed for the annotation of the whole clade. Results A large dataset of peptides from R. pomeroyi was obtained after searching over 1.1 million MS/MS spectra against a six-frame translated genome database. We identified 2006 polypeptides, of which thirty-four were encoded by open reading frames (ORFs that had not previously been annotated. From the pool of 'one-hit-wonders', i.e. those ORFs specified by only one peptide detected by tandem mass spectrometry, we could confirm the probable existence of five additional new genes after proving that the corresponding RNAs were transcribed. We also identified the most-N-terminal peptide of 486 polypeptides, of which sixty-four had originally been wrongly annotated. Conclusions By extending these re-annotations to the other thirty-six Roseobacter isolates sequenced to date (twenty different genera, we propose the correction of the assigned start codons of 1082 homologous genes in the clade. In addition, we also report the presence of novel genes within operons encoding determinants of the important tricarboxylic acid cycle, a feature that seems to be characteristic of some Roseobacter genomes. The detection of their corresponding products in large amounts raises the question of their function. Their discoveries point to a possible theory for protein evolution that will rely on high expression of orphans in bacteria: their putative poor efficiency could be counterbalanced by a higher level of expression. Our proteogenomic analysis will increase

  19. The hidden epidemic: confronting sexually transmitted diseases

    National Research Council Canada - National Science Library

    Eng, Thomas R; Butler, William T

    .... In addition, STDs increase the risk of HIV transmission. The Hidden Epidemic examines the scope of sexually transmitted infections in the United States and provides a critical assessment of the nation's response to this public health crisis...

  20. A nearly modern amphibious bird from the Early Cretaceous of northwestern China.

    Science.gov (United States)

    You, Hai-Lu; Lamanna, Matthew C; Harris, Jerald D; Chiappe, Luis M; O'connor, Jingmai; Ji, Shu-An; Lü, Jun-Chang; Yuan, Chong-Xi; Li, Da-Qing; Zhang, Xing; Lacovara, Kenneth J; Dodson, Peter; Ji, Qiang

    2006-06-16

    Three-dimensional specimens of the volant fossil bird Gansus yumenensis from the Early Cretaceous Xiagou Formation of northwestern China demonstrate that this taxon possesses advanced anatomical features previously known only in Late Cretaceous and Cenozoic ornithuran birds. Phylogenetic analysis recovers Gansus within the Ornithurae, making it the oldest known member of the clade. The Xiagou Formation preserves the oldest known ornithuromorph-dominated avian assemblage. The anatomy of Gansus, like that of other non-neornithean (nonmodern) ornithuran birds, indicates specialization for an amphibious life-style, supporting the hypothesis that modern birds originated in aquatic or littoral niches.

  1. Resurrecting a subgenus to genus: molecular phylogeny of Euphyllia and Fimbriaphyllia (order Scleractinia; family Euphyllidae; clade V

    Directory of Open Access Journals (Sweden)

    Katrina S. Luzon

    2017-12-01

    Full Text Available Background The corallum is crucial in building coral reefs and in diagnosing systematic relationships in the order Scleractinia. However, molecular phylogenetic analyses revealed a paraphyly in a majority of traditional families and genera among Scleractinia showing that other biological attributes of the coral, such as polyp morphology and reproductive traits, are underutilized. Among scleractinian genera, the Euphyllia, with nine nominal species in the Indo-Pacific region, is one of the groups that await phylogenetic resolution. Multiple genetic markers were used to construct the phylogeny of six Euphyllia species, namely E. ancora, E. divisa, E. glabrescens, E. paraancora, E. paradivisa, and E. yaeyamaensis. The phylogeny guided the inferences on the contributions of the colony structure, polyp morphology, and life history traits to the systematics of the largest genus in Euphyllidae (clade V and, by extension, to the rest of clade V. Results Analyses of cytochrome oxidase 1 (cox1, cytochrome b (cytb, and β-tubulin genes of 36 colonies representing Euphyllia and a confamilial species, Galaxea fascicularis, reveal two distinct groups in the Euphyllia that originated from different ancestors. Euphyllia glabrescens formed a separate group. Euphyllia ancora, E. divisa, E. paraancora, E. paradivisa, and E. yaeyamaensis clustered together and diverged from the same ancestor as G. fascicularis. The 3′-end of the cox1 gene of Euphyllia was able to distinguish morphospecies. Discussion Species of Euphyllia were traditionally classified into two subgenera, Euphyllia and Fimbriaphyllia, which represented a dichotomy on colony structure. The paraphyletic groups retained the original members of the subgenera providing a strong basis for recognizing Fimbriaphyllia as a genus. However, colony structure was found to be a convergent trait between Euphyllia and Fimbriaphyllia, while polyp shape and length, sexuality, and reproductive mode defined the

  2. Using Piezoelectric Devices to Transmit Power through Walls

    Science.gov (United States)

    Sherrit, Stewart; Bar-Cohen, Yoseph; Bao, Xiaoqi

    2008-01-01

    A method denoted wireless acoustic-electric feed-through (WAEF) has been conceived for transmitting power and/or data signals through walls or other solid objects made of a variety of elastic materials that could be electrically conductive or nonconductive. WAEF would make it unnecessary to use wires, optical fibers, tubes, or other discrete wall-penetrating signal-transmitting components, thereby eliminating the potential for structural weakening or leakage at such penetrations. Avoidance of such penetrations could be essential in some applications in which maintenance of pressure, vacuum, or chemical or biological isolation is required. In a basic WAEF setup, a transmitting piezoelectric transducer on one side of a wall would be driven at resonance to excite ultrasonic vibrations in the wall. A receiving piezoelectric transducer on the opposite side of the wall would convert the vibrations back to an ultrasonic AC electric signal, which would then be detected and otherwise processed in a manner that would depend on the modulation (if any) applied to the signal and whether the signal was used to transmit power, data, or both. An electromechanical-network model has been derived as a computationally efficient means of analyzing and designing a WAEF system. This model is a variant of a prior model, known in the piezoelectric-transducer art as Mason's equivalent-circuit model, in which the electrical and mechanical dynamics, including electromechanical couplings, are expressed as electrical circuit elements that can include inductors, capacitors, and lumped-parameter complex impedances. The real parts of the complex impedances are used to account for dielectric, mechanical, and coupling losses in all components (including all piezoelectric-transducer, wall, and intermediate material layers). In an application to a three-layer piezoelectric structure, this model was shown to yield the same results as do solutions of the wave equations of piezoelectricity and acoustic

  3. The Affordability of Providing Sexually Transmitted Disease Services at a Safety-net Clinic.

    Science.gov (United States)

    Dean, Lorraine T; Montgomery, Madeline C; Raifman, Julia; Nunn, Amy; Bertrand, Thomas; Almonte, Alexi; Chan, Philip A

    2018-04-01

    Sexually transmitted diseases continue to increase in the U.S. There is a growing need for financially viable models to ensure the longevity of safety-net sexually transmitted disease clinics, which provide testing and treatment to high-risk populations. This micro-costing analysis estimated the number of visits required to balance cost and revenue of a sexually transmitted disease clinic in a Medicaid expansion state. In 2017, actual and projected cost and revenues were estimated from the Rhode Island sexually transmitted disease clinic in 2015. Projected revenues for a hypothetical clinic offering a standard set of sexually transmitted disease services were based on Medicaid; private ("commercial") insurance; and institutional ("list price") reimbursement rates. The number of visits needed to cover clinic costs at each rate was assessed. Total operating cost for 2,153 clinic visits was estimated at $255,769, or $119 per visit. Laboratory testing and salaries each accounted for 44% of operating costs, medications for treatment 7%, supplies 5%, and 28% of visits used insurance. For a standard clinic offering a basic set of sexually transmitted disease services to break even, a projected 73% of visits need to be covered at the Medicaid rate, 38% at private rate, or 11% at institutional rate. Sexually transmitted disease clinics may be financially viable when a majority of visits are billed at a Medicaid rate; however, mixed private/public models may be needed if not all visits are billed. In this manner, sexually transmitted disease clinics can be solvent even if not all visits are billed to insurance, thus ensuring access to uninsured or underinsured patients. Copyright © 2018 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

  4. Sexually Transmitted Diseases Treatment Guidelines, 2015

    Science.gov (United States)

    Workowski, Kimberly A.; Bolan, Gail A.

    2016-01-01

    Summary These guidelines for the treatment of persons who have or are at risk for sexually transmitted diseases (STDs) were updated by CDC after consultation with a group of professionals knowledgeable in the field of STDs who met in Atlanta on April 30–May 2, 2013. The information in this report updates the Sexually Transmitted Diseases Treatment Guidelines, 2010 (MMWR Recomm Rep 2010;59 [No. RR–12]). These updated guidelines discuss 1) alternative treatment regimens for Neisseria gonorrhoeae; 2) the use of nucleic acid amplification tests for the diagnosis of trichomoniasis; 3) alternative treatment options for genital warts; 4) the role of Mycoplasma genitalium in urethritis/cervicitis and treatment-related implications; 5) updated HPV vaccine recommendations and counseling messages; 6) the management of persons who are transgender; 7) annual testing for hepatitis C in persons with HIV infection; 8) updated recommendations for diagnostic evaluation of urethritis; and 9) retesting to detect repeat infection. Physicians and other health-care providers can use these guidelines to assist in the prevention and treatment of STDs. PMID:26042815

  5. Open source approaches to establishing Roseobacter clade bacteria as synthetic biology chassis for biogeoengineering

    Directory of Open Access Journals (Sweden)

    Yanika Borg

    2016-07-01

    Full Text Available Aim. The nascent field of bio-geoengineering stands to benefit from synthetic biologists’ efforts to standardise, and in so doing democratise, biomolecular research methods. Roseobacter clade bacteria comprise 15–20% of oceanic bacterio-plankton communities, making them a prime candidate for establishment of synthetic biology chassis for bio-geoengineering activities such as bioremediation of oceanic waste plastic. Developments such as the increasing affordability of DNA synthesis and laboratory automation continue to foster the establishment of a global ‘do-it-yourself’ research community alongside the more traditional arenas of academe and industry. As a collaborative group of citizen, student and professional scientists we sought to test the following hypotheses: (i that an incubator capable of cultivating bacterial cells can be constructed entirely from non-laboratory items, (ii that marine bacteria from the Roseobacter clade can be established as a genetically tractable synthetic biology chassis using plasmids conforming to the BioBrickTM standard and finally, (iii that identifying and subcloning genes from a Roseobacter clade species can readily by achieved by citizen scientists using open source cloning and bioinformatic tools. Method. We cultivated three Roseobacter species, Roseobacter denitrificans, Oceanobulbus indolifexand Dinoroseobacter shibae. For each species we measured chloramphenicol sensitivity, viability over 11 weeks of glycerol-based cryopreservation and tested the effectiveness of a series of electroporation and heat shock protocols for transformation using a variety of plasmid types. We also attempted construction of an incubator-shaker device using only publicly available components. Finally, a subgroup comprising citizen scientists designed and attempted a procedure for isolating the cold resistance anf1 gene from Oceanobulbus indolifexcells and subcloning it into a BioBrickTM formatted plasmid. Results. All

  6. Secure direct communication based on secret transmitting order of particles

    International Nuclear Information System (INIS)

    Zhu Aidong; Zhang Shou; Xia Yan; Fan Qiubo

    2006-01-01

    We propose the schemes of quantum secure direct communication based on a secret transmitting order of particles. In these protocols, the secret transmitting order of particles ensures the security of communication, and no secret messages are leaked even if the communication is interrupted for security. This strategy of security for communication is also generalized to a quantum dialogue. It not only ensures the unconditional security but also improves the efficiency of communication

  7. Imperfect generalized transmit beamforming with co-channel interference cancelation

    KAUST Repository

    Radaydeh, Redha Mahmoud Mesleh

    2010-10-01

    The performance of a generalized single-stream transmit beamforming scheme employing receive co-channel interference -steering algorithms in slowly varying and flat fading channels is analyzed. The impact of imperfect prediction of channel state information (CSI) for the desired user spatially uncorrelated transmit channels is considered. Both dominant interference cancelation and adaptive arbitrary interference cancelation algorithms for closely spaced receive antennas are used. The impact of outdated statistical ordering of the interferers instantaneous powers on the effectiveness of dominant interference cancelation is investigated against the less complex adaptive arbitrary cancelation scheme. For the system models described above, new exact formulas for the statistics of combined signal-to-interference-plus-noise ratio (SINR) are derived, from which results for conventional maximum ratio transmission (MRT) and best transmit channel selection schemes can be deduced as limiting cases. The results presented herein can be used to obtain quantitative measure for various performance metrics, and in addition to investigate the performance-complexity tradeoff for different multiple-antenna system models. © 2010 IEEE.

  8. Switch and examine transmit diversity for spectrum sharing systems

    KAUST Repository

    Abdallah, Mohamed M.

    2011-06-01

    In this paper, we develop a switch and examine transmit diversity algorithm for spectrum sharing cognitive networks. We consider a cognitive network composed of a primary link that employs constant rate and constant power transmission scheme with automatic-and-repeat request (ARQ) protocol, while the secondary link is composed of a fixed power multiple-antenna secondary transmitter and a single antenna receiver. Our objective is to develop a low complex transmit diversity algorithm at the secondary transmitter that maximizes the performance of the secondary link in terms of the effective throughput while maintaining a predetermined maximum loss in the packet rate of the primary link. In achieving this objective, we develop an algorithm that selects the best antenna, which maintains the quality of the secondary link in terms of signal-to-noise ratio above a specific threshold, based on overhearing the acknowledgment (ACK) and negative acknowledgment (NACK) feedback messages transmitted over the primary link. We also develop closed form expressions for the bit error rates and the effective throughput of the secondary link. © 2011 IEEE.

  9. Pair formation models for sexually transmitted infections: A primer

    Directory of Open Access Journals (Sweden)

    Mirjam Kretzschmar

    2017-08-01

    Full Text Available For modelling sexually transmitted infections, duration of partnerships can strongly influence the transmission dynamics of the infection. If partnerships are monogamous, pairs of susceptible individuals are protected from becoming infected, while pairs of infected individuals delay onward transmission of the infection as long as they persist. In addition, for curable infections re-infection from an infected partner may occur. Furthermore, interventions based on contact tracing rely on the possibility of identifying and treating partners of infected individuals. To reflect these features in a mathematical model, pair formation models were introduced to mathematical epidemiology in the 1980's. They have since been developed into a widely used tool in modelling sexually transmitted infections and the impact of interventions. Here we give a basic introduction to the concepts of pair formation models for a susceptible-infected-susceptible (SIS epidemic. We review some results and applications of pair formation models mainly in the context of chlamydia infection. Keywords: Pair formation, Mathematical model, Partnership duration, Sexually transmitted infections, Basic reproduction number

  10. Estimating Transmitted-Signal Phase Variations for Uplink Array Antennas

    Science.gov (United States)

    Paal, Leslie; Mukai, Ryan; Vilntrotter, Victor; Cornish, Timothy; Lee, Dennis

    2009-01-01

    A method of estimating phase drifts of microwave signals distributed to, and transmitted by, antennas in an array involves the use of the signals themselves as phase references. The method was conceived as part of the solution of the problem of maintaining precise phase calibration required for proper operation of an array of Deep Space Network (DSN) antennas on Earth used for communicating with distant spacecraft at frequencies between 7 and 8 GHz. The method could also be applied to purely terrestrial phased-array radar and other radio antenna array systems. In the DSN application, the electrical lengths (effective signal-propagation path lengths) of the various branches of the system for distributing the transmitted signals to the antennas are not precisely known, and they vary with time. The variations are attributable mostly to thermal expansion and contraction of fiber-optic and electrical signal cables and to a variety of causes associated with aging of signal-handling components. The variations are large enough to introduce large phase drifts at the signal frequency. It is necessary to measure and correct for these phase drifts in order to maintain phase calibration of the antennas. A prior method of measuring phase drifts involves the use of reference-frequency signals separate from the transmitted signals. A major impediment to accurate measurement of phase drifts over time by the prior method is the fact that although DSN reference-frequency sources separate from the transmitting signal sources are stable and accurate enough for most DSN purposes, they are not stable enough for use in maintaining phase calibrations, as required, to within a few degrees over times as long as days or possibly even weeks. By eliminating reliance on the reference-frequency subsystem, the present method overcomes this impediment. In a DSN array to which the present method applies (see figure), the microwave signals to be transmitted are generated by exciters in a signal

  11. How to handle speciose clades? Mass taxon-sampling as a strategy towards illuminating the natural history of Campanula (Campanuloideae.

    Directory of Open Access Journals (Sweden)

    Guilhem Mansion

    Full Text Available BACKGROUND: Speciose clades usually harbor species with a broad spectrum of adaptive strategies and complex distribution patterns, and thus constitute ideal systems to disentangle biotic and abiotic causes underlying species diversification. The delimitation of such study systems to test evolutionary hypotheses is difficult because they often rely on artificial genus concepts as starting points. One of the most prominent examples is the bellflower genus Campanula with some 420 species, but up to 600 species when including all lineages to which Campanula is paraphyletic. We generated a large alignment of petD group II intron sequences to include more than 70% of described species as a reference. By comparison with partial data sets we could then assess the impact of selective taxon sampling strategies on phylogenetic reconstruction and subsequent evolutionary conclusions. METHODOLOGY/PRINCIPAL FINDINGS: Phylogenetic analyses based on maximum parsimony (PAUP, PRAP, Bayesian inference (MrBayes, and maximum likelihood (RAxML were first carried out on the large reference data set (D680. Parameters including tree topology, branch support, and age estimates, were then compared to those obtained from smaller data sets resulting from "classification-guided" (D088 and "phylogeny-guided sampling" (D101. Analyses of D088 failed to fully recover the phylogenetic diversity in Campanula, whereas D101 inferred significantly different branch support and age estimates. CONCLUSIONS/SIGNIFICANCE: A short genomic region with high phylogenetic utility allowed us to easily generate a comprehensive phylogenetic framework for the speciose Campanula clade. Our approach recovered 17 well-supported and circumscribed sub-lineages. Knowing these will be instrumental for developing more specific evolutionary hypotheses and guide future research, we highlight the predictive value of a mass taxon-sampling strategy as a first essential step towards illuminating the detailed

  12. Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae and Lentisphaerae of Bacteria Provide Insights into their Evolutionary Relationships

    Directory of Open Access Journals (Sweden)

    Radhey S. Gupta

    2012-09-01

    Full Text Available The PVC superphylum is an amalgamation of species from the phyla Planctomycetes, Verrucomicrobia and Chlamydiae, along with the Lentisphaerae, Poribacteria and two other candidate divisions. The diverse species of this superphylum lack any significant marker that differentiates them from other bacteria. Recently, genome sequences for 37 species covering all of the main PVC groups of bacteria have become available. We have used these sequences to construct a phylogenetic tree based upon concatenated sequences for 16 proteins and identify molecular signatures in protein sequences that are specific for the species from these phyla or those providing molecular links among them. Of the useful molecular markers identified in the present work, 6 conserved signature indels (CSIs in the proteins Cyt c oxidase, UvrD helicase, urease and a helicase-domain containing protein are specific for the species from the Verrucomicrobia phylum; three other CSIs in an ABC transporter protein, cobyrinic acid ac-diamide synthase and SpoVG protein are specific for the Planctomycetes species. Additionally, a 3 aa insert in the RpoB protein is uniquely present in all sequenced Chlamydiae, Verrucomicrobia and Lentisphaerae species, providing evidence for the shared ancestry of the species from these three phyla. Lastly, we have also identified a conserved protein of unknown function that is exclusively found in all sequenced species from the phyla Chlamydiae, Verrucomicrobia, Lentisphaerae and Planctomycetes suggesting a specific linkage among them. The absence of this protein in Poribacteria, which branches separately from other members of the PVC clade, indicates that it is not specifically related to the PVC clade of bacteria. The molecular markers described here in addition to clarifying the evolutionary relationships among the PVC clade of bacteria also provide novel tools for their identification and for genetic and biochemical studies on these organisms.

  13. How to Handle Speciose Clades? Mass Taxon-Sampling as a Strategy towards Illuminating the Natural History of Campanula (Campanuloideae)

    Science.gov (United States)

    Mansion, Guilhem; Parolly, Gerald; Crowl, Andrew A.; Mavrodiev, Evgeny; Cellinese, Nico; Oganesian, Marine; Fraunhofer, Katharina; Kamari, Georgia; Phitos, Dimitrios; Haberle, Rosemarie; Akaydin, Galip; Ikinci, Nursel; Raus, Thomas; Borsch, Thomas

    2012-01-01

    Background Speciose clades usually harbor species with a broad spectrum of adaptive strategies and complex distribution patterns, and thus constitute ideal systems to disentangle biotic and abiotic causes underlying species diversification. The delimitation of such study systems to test evolutionary hypotheses is difficult because they often rely on artificial genus concepts as starting points. One of the most prominent examples is the bellflower genus Campanula with some 420 species, but up to 600 species when including all lineages to which Campanula is paraphyletic. We generated a large alignment of petD group II intron sequences to include more than 70% of described species as a reference. By comparison with partial data sets we could then assess the impact of selective taxon sampling strategies on phylogenetic reconstruction and subsequent evolutionary conclusions. Methodology/Principal Findings Phylogenetic analyses based on maximum parsimony (PAUP, PRAP), Bayesian inference (MrBayes), and maximum likelihood (RAxML) were first carried out on the large reference data set (D680). Parameters including tree topology, branch support, and age estimates, were then compared to those obtained from smaller data sets resulting from “classification-guided” (D088) and “phylogeny-guided sampling” (D101). Analyses of D088 failed to fully recover the phylogenetic diversity in Campanula, whereas D101 inferred significantly different branch support and age estimates. Conclusions/Significance A short genomic region with high phylogenetic utility allowed us to easily generate a comprehensive phylogenetic framework for the speciose Campanula clade. Our approach recovered 17 well-supported and circumscribed sub-lineages. Knowing these will be instrumental for developing more specific evolutionary hypotheses and guide future research, we highlight the predictive value of a mass taxon-sampling strategy as a first essential step towards illuminating the detailed evolutionary

  14. Evolution and functional insights of different ancestral orthologous clades of chitin synthase genes in the fungal tree of life

    Directory of Open Access Journals (Sweden)

    Mu eLi

    2016-02-01

    Full Text Available Chitin synthases (CHSs are key enzymes in the biosynthesis of chitin, an important structural component of fungal cell walls that can trigger innate immune responses in host plants and animals. Members of CHS gene family perform various functions in fungal cellular processes. Previous studies focused primarily on classifying diverse CHSs into different classes, regardless of their functional diversification, or on characterizing their functions in individual fungal species. A complete and systematic comparative analysis of CHS genes based on their orthologous relationships will be valuable for elucidating the evolution and functions of different CHS genes in fungi. Here, we identified and compared members of the CHS gene family across the fungal tree of life, including 18 divergent fungal lineages. Phylogenetic analysis revealed that the fungal CHS gene family is comprised of at least 10 ancestral orthologous clades, which have undergone multiple independent duplications and losses in different fungal lineages during evolution. Interestingly, one of these CHS clades (class III was expanded in plant or animal pathogenic fungi belonging to different fungal lineages. Two clades (classes VIb and VIc identified for the first time in this study occurred mainly in plant pathogenic fungi from Sordariomycetes and Dothideomycetes. Moreover, members of classes III and VIb were specifically up-regulated during plant infection, suggesting important roles in pathogenesis. In addition, CHS-associated networks conserved among plant pathogenic fungi are involved in various biological processes, including sexual reproduction and plant infection. We also identified specificity-determining sites, many of which are located at or adjacent to important structural and functional sites that are potentially responsible for functional divergence of different CHS classes. Overall, our results provide new insights into the evolution and function of members of CHS gene

  15. A high-temperature tolerant species in clade 9 of the genus Phytophthora: P. hydrogena sp. nov.

    Science.gov (United States)

    Yang, Xiao; Gallegly, Mannon E; Hong, Chuanxue

    2014-01-01

    A previously unknown Phytophthora species was isolated from irrigation water in Virginia, USA. This novel species produces abundant noncaducous and nonpapillate sporangia in soil water extract solution. It sometimes produces chlamydospores and hyphal swellings in aged cultures and in Petri's solution. This species has optimum vegetative growth at 30 C and grows well at 35 C. The lowest and highest temperatures for growth are 5 and 40 C. All isolates examined in this study are compatibility type A1 and produce mostly plerotic oospores when paired with an A2 mating-type tester of P. cinnamomi. Sequence analyses of the rDNA internal transcribed spacer (ITS) regions and the mitochondrially encoded cytochrome c oxidase 1 (cox 1) gene placed this species in clade 9 of the genus Phytophthora. These characteristics support the description of this taxon as a new species for which we propose the name P. hydrogena sp. nov. Further phylogenetic and physiological investigations of clade 9 species revealed a high-temperature tolerant cluster including P. hydrogena, P. aquimorbida, P. hydropathica, P. irrigata, P. chrysanthemi, P. insolita, P. polonica and P. parsiana. These species all grow well at 35 C. The monophyly of the species in this heat-tolerant cluster except P. insolita and P. polonica is highly supported by the maximum-likelihood analyses of the ITS and cox 1 sequences.

  16. Vulnerability and Knowledge of Sexually Transmitted Infections ...

    African Journals Online (AJOL)

    Vulnerability and Knowledge of Sexually Transmitted Infections Among Female Traders of Reproductive Age in Enugu, Nigeria. ... Conclusion: The inclusion of health education in schools' curricula to ensure that adolescents are adequately aware of STIs, their modes of transmission, prevention and treatment before ...

  17. Knowledge of sexually transmitted diseases among secondary ...

    African Journals Online (AJOL)

    Background: Sexually Transmitted Diseases (STDs) are a major health problem affecting mostly young people in both developed and developing countries. Insufficient knowledge about STDs is a major impediment to successfully prevent the diseases among adolescent populations in developing countries. Objective: To ...

  18. Coexistence of two clades of enterovirus D68 in pediatric Swedish patients in the summer and fall of 2014.

    Science.gov (United States)

    Dyrdak, Robert; Rotzén-Östlund, Maria; Samuelson, Agneta; Eriksson, Margareta; Albert, Jan

    2015-01-01

    In 2014, an outbreak of enterovirus D68 (EV-D68) was observed in North America, with cases of severe respiratory illness and a possible etiological link to cases of acute flaccid paralysis. EV-D68 has also been reported from European countries, but no data from Sweden are available. This study investigated respiratory specimens collected during July-October 2014 from 30 Swedish children aged 0-9 years who were positive for enterovirus and/or rhinovirus in routine clinical PCR. Seven samples were typed as EV-D68 by VP4/VP2 sequencing. Two genetically distinct EV-D68 variants coexisted. Six viruses belonged to clade B, the variant involved in the North American outbreak, and one virus belonged to clade A. Respiratory illness was the major symptom among EV-D68 infected patients and all fully recovered. This is the first report of EV-D68 in Sweden. Considering the current epidemiological situation, genotyping and specific EV-D68 testing should be considered in patients with severe respiratory illness who test positive for enterovirus or rhinovirus in routine diagnostics.

  19. Empirical and Bayesian approaches to fossil-only divergence times: A study across three reptile clades.

    Science.gov (United States)

    Turner, Alan H; Pritchard, Adam C; Matzke, Nicholas J

    2017-01-01

    Estimating divergence times on phylogenies is critical in paleontological and neontological studies. Chronostratigraphically-constrained fossils are the only direct evidence of absolute timing of species divergence. Strict temporal calibration of fossil-only phylogenies provides minimum divergence estimates, and various methods have been proposed to estimate divergences beyond these minimum values. We explore the utility of simultaneous estimation of tree topology and divergence times using BEAST tip-dating on datasets consisting only of fossils by using relaxed morphological clocks and birth-death tree priors that include serial sampling (BDSS) at a constant rate through time. We compare BEAST results to those from the traditional maximum parsimony (MP) and undated Bayesian inference (BI) methods. Three overlapping datasets were used that span 250 million years of archosauromorph evolution leading to crocodylians. The first dataset focuses on early Sauria (31 taxa, 240 chars.), the second on early Archosauria (76 taxa, 400 chars.) and the third on Crocodyliformes (101 taxa, 340 chars.). For each dataset three time-calibrated trees (timetrees) were calculated: a minimum-age timetree with node ages based on earliest occurrences in the fossil record; a 'smoothed' timetree using a range of time added to the root that is then averaged over zero-length internodes; and a tip-dated timetree. Comparisons within datasets show that the smoothed and tip-dated timetrees provide similar estimates. Only near the root node do BEAST estimates fall outside the smoothed timetree range. The BEAST model is not able to overcome limited sampling to correctly estimate divergences considerably older than sampled fossil occurrence dates. Conversely, the smoothed timetrees consistently provide node-ages far older than the strict dates or BEAST estimates for morphologically conservative sister-taxa when they sit on long ghost lineages. In this latter case, the relaxed-clock model appears to

  20. Empirical and Bayesian approaches to fossil-only divergence times: A study across three reptile clades.

    Directory of Open Access Journals (Sweden)

    Alan H Turner

    Full Text Available Estimating divergence times on phylogenies is critical in paleontological and neontological studies. Chronostratigraphically-constrained fossils are the only direct evidence of absolute timing of species divergence. Strict temporal calibration of fossil-only phylogenies provides minimum divergence estimates, and various methods have been proposed to estimate divergences beyond these minimum values. We explore the utility of simultaneous estimation of tree topology and divergence times using BEAST tip-dating on datasets consisting only of fossils by using relaxed morphological clocks and birth-death tree priors that include serial sampling (BDSS at a constant rate through time. We compare BEAST results to those from the traditional maximum parsimony (MP and undated Bayesian inference (BI methods. Three overlapping datasets were used that span 250 million years of archosauromorph evolution leading to crocodylians. The first dataset focuses on early Sauria (31 taxa, 240 chars., the second on early Archosauria (76 taxa, 400 chars. and the third on Crocodyliformes (101 taxa, 340 chars.. For each dataset three time-calibrated trees (timetrees were calculated: a minimum-age timetree with node ages based on earliest occurrences in the fossil record; a 'smoothed' timetree using a range of time added to the root that is then averaged over zero-length internodes; and a tip-dated timetree. Comparisons within datasets show that the smoothed and tip-dated timetrees provide similar estimates. Only near the root node do BEAST estimates fall outside the smoothed timetree range. The BEAST model is not able to overcome limited sampling to correctly estimate divergences considerably older than sampled fossil occurrence dates. Conversely, the smoothed timetrees consistently provide node-ages far older than the strict dates or BEAST estimates for morphologically conservative sister-taxa when they sit on long ghost lineages. In this latter case, the relaxed

  1. Successive Interference Cancellation for DS-CDMA Systems with Transmit Diversity

    Directory of Open Access Journals (Sweden)

    Li Wei

    2004-01-01

    Full Text Available We introduce a new successive interference cancellation (SIC technique for direct sequence code division multiple access (DS-CDMA systems with transmit diversity. The transmit diversity is achieved with a space-time block code (STBC. In our work we first consider hard decision SIC with an STBC, and then investigate the performance of soft decision SIC with an STBC. System performance over a Rayleigh fading channel is investigated and the analysis is confirmed by simulation.

  2. Evolution of extreme ontogenetic allometric diversity and heterochrony in pythons, a clade of giant and dwarf snakes.

    Science.gov (United States)

    Esquerré, Damien; Sherratt, Emma; Keogh, J Scott

    2017-12-01

    Ontogenetic allometry, how species change with size through their lives, and heterochony, a decoupling between shape, size, and age, are major contributors to biological diversity. However, macroevolutionary allometric and heterochronic trends remain poorly understood because previous studies have focused on small groups of closely related species. Here, we focus on testing hypotheses about the evolution of allometry and how allometry and heterochrony drive morphological diversification at the level of an entire species-rich and diverse clade. Pythons are a useful system due to their remarkably diverse and well-adapted phenotypes and extreme size disparity. We collected detailed phenotype data on 40 of the 44 species of python from 1191 specimens. We used a suite of analyses to test for shifts in allometric trajectories that modify morphological diversity. Heterochrony is the main driver of initial divergence within python clades, and shifts in the slopes of allometric trajectories make exploration of novel phenotypes possible later in divergence history. We found that allometric coefficients are highly evolvable and there is an association between ontogenetic allometry and ecology, suggesting that allometry is both labile and adaptive rather than a constraint on possible phenotypes. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  3. Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae (Cypriniformes.

    Directory of Open Access Journals (Sweden)

    Wenjing Tao

    Full Text Available Despite their great diversity and biological importance, evolutionary relationships among the endemic clade of East Asian Cyprinidae remain ambiguous. Understanding the phylogenetic history of this group involves many challenges. For instance, ecomorphological convergence may confound morphology-based phylogenetic inferences, and previous molecular phylogenetic studies based on single genes have often yielded contradictory and poorly supported trees. We assembled a comprehensive data matrix of 100 nuclear gene segments (∼ 71132 base pairs for representative species of the endemic East Asian cyprinid fauna and recovered a robust phylogeny from this genome-wide signal supported by multiple analytical methods, including maximum parsimony, maximum likelihood and Bayesian inference. Relaxed molecular clock analyses indicated species radiations of this clade concentrated at approximately 1.9-7.6 MYA. We provide evidence that the bursts of diversification in this fauna are directly linked to major paleoenvironmental events associated with monsoon evolution occurring from late Miocene to Pliocene. Ancestral state reconstruction reveals convergent morphological characters are hypothesized to be independent products of similar selective pressures in ecosystems. Our study is the first comprehensive phylogenetic study of the enigmatic East-Asian cyprinids. The explicit molecular phylogeny provides a valuable framework for future research in genome evolution, adaptation and speciation of cyprinids.

  4. Development and characterization of 79 nuclear markers amplifying in viviparous and oviparous clades of the European common lizard.

    Science.gov (United States)

    Horreo, J L; Peláez, M L; Suárez, T; Fitze, P S

    2018-02-01

    The European common lizard (Zootoca vivipara) is a widely distributed species across Europe and Asia exhibiting two reproductive modes (oviparity/viviparity), six major lineages and several sublineages. It has been used to tackle a large variety of research questions, nevertheless, few nuclear DNA sequence markers have been developed for this species. Here we developed 79 new nuclear DNA sequence markers using a clonation protocol. These markers were amplified in several oviparous and viviparous specimens including samples of all extant clades, to test the amplification success and their diversity. 49.4% of the markers were polymorphic and of those, 51.3% amplified in all and 94.9% amplified in 5-7 of the extant Z. vivipara clades. These new markers will be very useful for the study of the population structure, population dynamics, and micro/macro evolution of Z. vivipara. Cross-species amplification in four lizard species (Psammodromus edwardsianus, Podarcis muralis, Lacerta bilineata, and Takydromus sexlineatus) was positive in several of the markers, and six makers amplified in all five species. The large genetic distance between P. edwardsianus and Z. vivipara further suggests that these markers may as well be employed in many other species.

  5. A clade in the QUASIMODO2 family evolved with vascular plants and supports a role for cell wall composition in adaptation to environmental changes.

    Science.gov (United States)

    Fuentes, Sara; Pires, Nuno; Østergaard, Lars

    2010-08-01

    The evolution of plant vascular tissue is tightly linked to the evolution of specialised cell walls. Mutations in the QUASIMODO2 (QUA2) gene from Arabidopsis thaliana were previously shown to result in cell adhesion defects due to reduced levels of the cell wall component homogalacturonic acid. In this study, we provide additional information about the role of QUA2 and its closest paralogues, QUASIMODO2 LIKE1 (QUL1) and QUL2. Within the extensive QUA2 family, our phylogenetic analysis shows that these three genes form a clade that evolved with vascular plants. Consistent with a possible role of this clade in vasculature development, QUA2 is highly expressed in the vascular tissue of embryos and inflorescence stems and overexpression of QUA2 resulted in temperature-sensitive xylem collapse. Moreover, in-depth characterisation of qua2 qul1 qul2 triple mutant and 35S::QUA2 overexpression plants revealed contrasting temperature-dependent stem development with dramatic effects on stem width. Taken together, our results suggest that the QUA2-specific clade contributed to the evolution of vasculature and illustrate the important role that modification of cell wall composition plays in the adaptation to changing environmental conditions, including changes in temperature.

  6. Large-scale patterns of diversification in the widespread legume genus Senna and the evolutionary role of extrafloral nectaries.

    Science.gov (United States)

    Marazzi, Brigitte; Sanderson, Michael J

    2010-12-01

    Unraveling the diversification history of old, species-rich and widespread clades is difficult because of extinction, undersampling, and taxonomic uncertainty. In the context of these challenges, we investigated the timing and mode of lineage diversification in Senna (Leguminosae) to gain insights into the evolutionary role of extrafloral nectaries (EFNs). EFNs secrete nectar, attracting ants and forming ecologically important ant-plant mutualisms. In Senna, EFNs characterize one large clade (EFN clade), including 80% of its 350 species. Taxonomic accounts make Senna the largest caesalpinioid genus, but quantitative comparisons to other taxa require inferences about rates. Molecular dating analyses suggest that Senna originated in the early Eocene, and its major lineages appeared during early/mid Eocene to early Oligocene. EFNs evolved in the late Eocene, after the main radiation of ants. The EFN clade diversified faster, becoming significantly more species-rich than non-EFN clades. The shift in diversification rates associated with EFN evolution supports the hypothesis that EFNs represent a (relatively old) key innovation in Senna. EFNs may have promoted the colonization of new habitats appearing with the early uplift of the Andes. This would explain the distinctive geographic concentration of the EFN clade in South America. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

  7. A final size relation for epidemic models of vector-transmitted diseases

    OpenAIRE

    Fred Brauer

    2017-01-01

    We formulate and analyze an age of infection model for epidemics of diseases transmitted by a vector, including the possibility of direct transmission as well. We show how to determine a basic reproduction number. While there is no explicit final size relation as for diseases transmitted directly, we are able to obtain estimates for the final size of the epidemic.

  8. Comprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophs

    KAUST Repository

    Jimenez Infante, Francy M.; Ngugi, David; Vinu, Manikandan; Alam, Intikhab; Kamau, Allan; Blom, Jochen; Bajic, Vladimir B.; Stingl, Ulrich

    2015-01-01

    The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs playing important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (designated here as MBRS-H7) from the ultra-oligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species, which forms a distinct cluster together with isolate KB13 from Hawaii (H-RS cluster) that is separate from that represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S–23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low chlorophyll and/or high temperature provinces for the H-RS cluster, but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of H-RS include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely the existence of the NADH:quinone oxidoreductase NUO system in the H-RS and the non-homologous NQR system in HTCC2181, which might have implications on their overall energetic yields.

  9. Comprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophs

    KAUST Repository

    Jimenez Infante, Francy M.

    2015-12-11

    The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs playing important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (designated here as MBRS-H7) from the ultra-oligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species, which forms a distinct cluster together with isolate KB13 from Hawaii (H-RS cluster) that is separate from that represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S–23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low chlorophyll and/or high temperature provinces for the H-RS cluster, but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of H-RS include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely the existence of the NADH:quinone oxidoreductase NUO system in the H-RS and the non-homologous NQR system in HTCC2181, which might have implications on their overall energetic yields.

  10. Geospatial forecast model for tsetse-transmitted animal ...

    African Journals Online (AJOL)

    Results indicate that GIS model developed for parasitic diseases based on growing degree day (GDD) concept can be applied to tsetse-transmitted trypanosomosis. GIS for animal trypanosomosis was created using Food and Agriculture Organization – Crop Production System Zones (FAO-CPSZ) database and Normalized ...

  11. Soil transmitted helminths infections, malnutrition and anaemia ...

    African Journals Online (AJOL)

    Soil-transmitted helminths (STHs) are a major public health problem in many developing countries. Establishment of prevalence and intensity of infections is important in designing, implementating and evaluating control programs. This study aimed at determining the prevalence and intensity of STH infections, malnutrition ...

  12. Paradoxical associations between soil-transmitted helminths and Plasmodium falciparum infection.

    Science.gov (United States)

    Fernández-Niño, Julián A; Idrovo, Alvaro J; Cucunubá, Zulma M; Reyes-Harker, Patricia; Guerra, Ángela P; Moncada, Ligia I; López, Myriam C; Barrera, Sandra M; Cortés, Liliana J; Olivera, Mario; Nicholls, Rubén S

    2012-11-01

    Evidence on the comorbidity between soil-transmitted helminth infections and malaria is scarce and divergent. This study explored the interactions between soil-transmitted helminth infections and uncomplicated falciparum malaria in an endemic area of Colombia. A paired case-control study matched by sex, age and location in Tierralta, Cordoba, was done between January and September 2010. The incident cases were 68 patients with falciparum malaria and 178 asymptomatic controls. A questionnaire was used to gather information on sociodemographic variables. Additionally physical examinations were carried out, stool samples were analysed for intestinal parasites and blood samples for Ig E concentrations. We found associations between infection with hookworm (OR: 4.21; 95% CI: 1.68-11.31) and Ascaris lumbricoides (OR 0.43; 95% CI: 0.18-1.04) and the occurrence of falciparum malaria. The effects of soil-transmitted helminths on the occurrence of malaria were found to be paradoxical. While hookworm is a risk factor, A. lumbricoides has a protective effect. The findings suggest that, in addition to the comorbidity, the presence of common determinants of soil-transmitted helminth infections and malaria could also exist. While the biological mechanisms involved are not clear, public health policies aimed at the control of their common social and environmental determinants are suggested. Copyright © 2012 Royal Society of Tropical Medicine and Hygiene. Published by Elsevier Ltd. All rights reserved.

  13. Vegaviidae, a new clade of southern diving birds that survived the K/T boundary

    Science.gov (United States)

    Agnolín, Federico L.; Egli, Federico Brissón; Chatterjee, Sankar; Marsà, Jordi Alexis Garcia; Novas, Fernando E.

    2017-12-01

    The fossil record of Late Cretaceous-Paleogene modern birds in the Southern Hemisphere includes the Maastrichtian Neogaeornis wetzeli from Chile, Polarornis gregorii and Vegavis iaai from Antarctica, and Australornis lovei from the Paleogene of New Zealand. The recent finding of a new and nearly complete Vegavis skeleton constitutes the most informative source for anatomical comparisons among Australornis, Polarornis, and Vegavis. The present contribution includes, for the first time, Vegavis, Polarornis, and Australornis in a comprehensive phylogenetic analysis. This analysis resulted in the recognition of these taxa as a clade of basal Anseriformes that we call Vegaviidae. Vegaviids share a combination of characters related to diving adaptations, including compact and thickened cortex of hindlimb bones, femur with anteroposteriorly compressed and bowed shaft, deep and wide popliteal fossa delimited by a medial ridge, tibiotarsus showing notably proximally expanded cnemial crests, expanded fibular crest, anteroposterior compression of the tibial shaft, and a tarsometatarsus with a strong transverse compression of the shaft. Isolated bones coming from the Cretaceous and Paleogene of South America, Antarctica, and New Zealand are also referred to here to Vegaviidae and support the view that these basal anseriforms were abundant and diverse at high southern latitudes. Moreover, vegaviids represent the first avian lineage to have definitely crossed the K-Pg boundary, supporting the idea that some avian clades were not affected by the end Mesozoic mass extinction event, countering previous interpretations. Recognition of Vegaviidae indicates that modern birds were diversified in southern continents by the Cretaceous and reinforces the hypothesis indicating the important role of Gondwana for the evolutionary history of Anseriformes and Neornithes as a whole.

  14. Effect of Salt on the Metabolism of ‘Candidatus Accumulibacter’ Clade I and II

    KAUST Repository

    Wang, Zhongwei; Dunne, Aislinn; van Loosdrecht, Mark C. M.; Saikaly, Pascal

    2018-01-01

    Saline wastewater is known to affect the performance of phosphate-accumulating organisms (PAOs) in enhanced biological phosphorus removal (EBPR) process. However, studies comparing the effect of salinity on different PAO clades are lacking. In this study, 'Candidatus Accumulibacter phosphatis' Clade I and II (hereafter referred to as PAOI and PAOII) were highly enriched (~90% in relative abundance as determined by quantitative FISH) in the form of granules in two sequencing batch reactors. Anaerobic and aerobic batch experiments were conducted to evaluate the effect of salinity on the kinetics and stoichiometry of PAOI and PAOII. PAOI and PAOII communities showed different priority in using polyphosphate (poly-P) and glycogen to generate ATP in the anaerobic phase when exposed to salt, with PAOI depending more on intracellular poly-P degradation (e.g., the proportion of calculated ATP derived from poly-P increased by 5-6% at 0.256 mol/L NaCl or KCl) while PAOII on glycolysis of intracellularly stored glycogen (e.g., the proportion of calculated ATP derived from glycogen increased by 29-30% at 0.256 mol/L NaCl or KCl). In the aerobic phase, the loss of phosphate uptake capability was more pronounced in PAOII due to the higher energy cost to synthesize their larger glycogen pool compared to PAOI. For both PAOI and PAOII, aerobic conversion rates were more sensitive to salt than anaerobic conversion rates. Potassium (K) and sodium (Na) ions exhibited different effect regardless of the enriched PAO culture, suggesting that the composition of salt is an important factor to consider when studying the effect of salt on EBPR performance.

  15. Effect of Salt on the Metabolism of ‘Candidatus Accumulibacter’ Clade I and II

    Directory of Open Access Journals (Sweden)

    Zhongwei Wang

    2018-03-01

    Full Text Available Saline wastewater is known to affect the performance of phosphate-accumulating organisms (PAOs in enhanced biological phosphorus removal (EBPR process. However, studies comparing the effect of salinity on different PAO clades are lacking. In this study, ‘Candidatus Accumulibacter phosphatis’ Clade I and II (hereafter referred to as PAOI and PAOII were highly enriched (∼90% in relative abundance as determined by quantitative FISH in the form of granules in two sequencing batch reactors. Anaerobic and aerobic batch experiments were conducted to evaluate the effect of salinity on the kinetics and stoichiometry of PAOI and PAOII. PAOI and PAOII communities showed different priority in using polyphosphate (poly-P and glycogen to generate ATP in the anaerobic phase when exposed to salt, with PAOI depending more on intracellular poly-P degradation (e.g., the proportion of calculated ATP derived from poly-P increased by 5–6% at 0.256 mol/L NaCl or KCl while PAOII on glycolysis of intracellularly stored glycogen (e.g., the proportion of calculated ATP derived from glycogen increased by 29–30% at 0.256 mol/L NaCl or KCl. In the aerobic phase, the loss of phosphate uptake capability was more pronounced in PAOII due to the higher energy cost to synthesize their larger glycogen pool compared to PAOI. For both PAOI and PAOII, aerobic conversion rates were more sensitive to salt than anaerobic conversion rates. Potassium (K+ and sodium (Na+ ions exhibited different effect regardless of the enriched PAO culture, suggesting that the composition of salt is an important factor to consider when studying the effect of salt on EBPR performance.

  16. Effect of Salt on the Metabolism of ‘Candidatus Accumulibacter’ Clade I and II

    KAUST Repository

    Wang, Zhongwei

    2018-03-16

    Saline wastewater is known to affect the performance of phosphate-accumulating organisms (PAOs) in enhanced biological phosphorus removal (EBPR) process. However, studies comparing the effect of salinity on different PAO clades are lacking. In this study, \\'Candidatus Accumulibacter phosphatis\\' Clade I and II (hereafter referred to as PAOI and PAOII) were highly enriched (~90% in relative abundance as determined by quantitative FISH) in the form of granules in two sequencing batch reactors. Anaerobic and aerobic batch experiments were conducted to evaluate the effect of salinity on the kinetics and stoichiometry of PAOI and PAOII. PAOI and PAOII communities showed different priority in using polyphosphate (poly-P) and glycogen to generate ATP in the anaerobic phase when exposed to salt, with PAOI depending more on intracellular poly-P degradation (e.g., the proportion of calculated ATP derived from poly-P increased by 5-6% at 0.256 mol/L NaCl or KCl) while PAOII on glycolysis of intracellularly stored glycogen (e.g., the proportion of calculated ATP derived from glycogen increased by 29-30% at 0.256 mol/L NaCl or KCl). In the aerobic phase, the loss of phosphate uptake capability was more pronounced in PAOII due to the higher energy cost to synthesize their larger glycogen pool compared to PAOI. For both PAOI and PAOII, aerobic conversion rates were more sensitive to salt than anaerobic conversion rates. Potassium (K) and sodium (Na) ions exhibited different effect regardless of the enriched PAO culture, suggesting that the composition of salt is an important factor to consider when studying the effect of salt on EBPR performance.

  17. Reoccurrence of H5Nx clade 2.3.4.4 highly pathogenic avian influenza viruses in wild birds during 2016

    Science.gov (United States)

    The Asian-origin H5N1 A/goose/Guangdong/1/1996 (Gs/GD) lineage of high pathogenicity avian influenza viruses (HPAIV) has become widespread across four continents, affecting poultry, wild birds and humans. H5N1 HPAIV has evolved into multiple hemagglutinin (HA) genetic clades and reassorting with dif...

  18. Narrative Review: Sexually Transmitted Diseases and Homeless Youth-What Do We Know About Sexually Transmitted Disease Prevalence and Risk?

    Science.gov (United States)

    Caccamo, Alexandra; Kachur, Rachel; Williams, Samantha P

    2017-08-01

    Homelessness affects an estimated 1.6 million US youth annually. Compared with housed youth, homeless youth are more likely to engage in high-risk behaviors, including inconsistent condom use, multiple sex partners, survival sex, and alcohol/drug use, putting them at increased sexually transmitted disease (STD) risk. However, there is no national estimate of STD prevalence among this population. We identified 10 peer-reviewed articles (9 unique studies) reporting STD prevalence among homeless US youth (2000-2015). Descriptive and qualitative analyses identified STD prevalence ranges and risk factors among youth. Eight studies reported specific STD prevalence estimates, mainly chlamydia, gonorrhea, and syphilis. Overall STD prevalence among homeless youth ranged from 6% to 32%. STD rates for girls varied from 16.7% to 46%, and from 9% to 13.1% in boys. Most studies were conducted in the Western United States, with no studies from the Southeast or Northeast. Youths who experienced longer periods of homelessness were more likely to engage in high-risk sexual behaviors. Girls had lower rates of condom use and higher rates of STDs; boys were more likely to engage in anal and anonymous sex. Additionally, peer social networks contributed to protective effects on individual sexual risk behavior. Sexually transmitted disease prevalence estimates among homeless youth fluctuated greatly by study. Sexually transmitted disease risk behaviors are associated with unmet survival needs, length of homelessness, and influence of social networks. To promote sexual health and reduce STD rates, we need better estimates of STD prevalence, more geographic diversity of studies, and interventions addressing the behavioral associations identified in our review.

  19. EXPERIMENTAL STUDY ON LIGHT TRANSMITTING CONCRETE BY USING OPTICAL FIBRE

    OpenAIRE

    S. Suganya; S. Minu Gopika

    2017-01-01

    Light transmitting concrete is one of the fibre reinforced concrete which is mainly used for aesthetic application by incorporating the optical fibres in concrete. Optical fibres help to transmit the light through the fibres and the end-light type of fibre is used to increase the aesthetic appearance of the concrete which is like a transparent concrete. Fibres are arranged in different layers, to increase the load carrying capacity and also the pattern can be created to make the concrete deco...

  20. Multiple X-ray tomography using transmitted, scattered and fluorescent radiation

    International Nuclear Information System (INIS)

    Cesareo, R.; Brunetti, A.; Golosio, B.; Lopes, R.T.; Barroso, R.C.; Donativi, M.; Castellano, A.; Quarta, S.

    2003-01-01

    A multiple CT-scanner is described, which contemporaneously uses transmitted, scattered and fluorescent X-rays for Imaging. The scanner is characterized by a small size X-ray tube and by four detectors: a ''pencil'' X-ray NaI(Tl) for transmitted tomography, a larger size NaI(Tl) for 90 C o Compton tomography, a thermoelectrically cooled Si-PIN or CdZnTe for fluorescent imaging and a CdZnTe for Rayleigh (or diffraction) tomography. Examples of applications are shown

  1. Phylogenetics of Cucumis (Cucurbitaceae: Cucumber (C. sativus belongs in an Asian/Australian clade far from melon (C. melo

    Directory of Open Access Journals (Sweden)

    Schaefer Hanno

    2007-04-01

    Full Text Available Abstract Background Melon, Cucumis melo, and cucumber, C. sativus, are among the most widely cultivated crops worldwide. Cucumis, as traditionally conceived, is geographically centered in Africa, with C. sativus and C. hystrix thought to be the only Cucumis species in Asia. This taxonomy forms the basis for all ongoing Cucumis breeding and genomics efforts. We tested relationships among Cucumis and related genera based on DNA sequences from chloroplast gene, intron, and spacer regions (rbcL, matK, rpl20-rps12, trnL, and trnL-F, adding nuclear internal transcribed spacer sequences to resolve relationships within Cucumis. Results Analyses of combined chloroplast sequences (4,375 aligned nucleotides for 123 of the 130 genera of Cucurbitaceae indicate that the genera Cucumella, Dicaelospermum, Mukia, Myrmecosicyos, and Oreosyce are embedded within Cucumis. Phylogenetic trees from nuclear sequences for these taxa are congruent, and the combined data yield a well-supported phylogeny. The nesting of the five genera in Cucumis greatly changes the natural geographic range of the genus, extending it throughout the Malesian region and into Australia. The closest relative of Cucumis is Muellerargia, with one species in Australia and Indonesia, the other in Madagascar. Cucumber and its sister species, C. hystrix, are nested among Australian, Malaysian, and Western Indian species placed in Mukia or Dicaelospermum and in one case not yet formally described. Cucumis melo is sister to this Australian/Asian clade, rather than being close to African species as previously thought. Molecular clocks indicate that the deepest divergences in Cucumis, including the split between C. melo and its Australian/Asian sister clade, go back to the mid-Eocene. Conclusion Based on congruent nuclear and chloroplast phylogenies we conclude that Cucumis comprises an old Australian/Asian component that was heretofore unsuspected. Cucumis sativus evolved within this Australian

  2. Modernized Approach for Generating Reproducible Heterogeneity Using Transmitted-Light for Flow Visualization Experiments

    Science.gov (United States)

    Jones, A. A.; Holt, R. M.

    2017-12-01

    Image capturing in flow experiments has been used for fluid mechanics research since the early 1970s. Interactions of fluid flow between the vadose zone and permanent water table are of great interest because this zone is responsible for all recharge waters, pollutant transport and irrigation efficiency for agriculture. Griffith, et al. (2011) developed an approach where constructed reproducible "geologically realistic" sand configurations are deposited in sandfilled experimental chambers for light-transmitted flow visualization experiments. This method creates reproducible, reverse graded, layered (stratified) thin-slab sand chambers for point source experiments visualizing multiphase flow through porous media. Reverse-graded stratification of sand chambers mimic many naturally occurring sedimentary deposits. Sandfilled chambers use light as nonintrusive tools for measuring water saturation in two-dimensions (2-D). Homogeneous and heterogeneous sand configurations can be produced to visualize the complex physics of the unsaturated zone. The experimental procedure developed by Griffith, et al. (2011) was designed using now outdated and obsolete equipment. We have modernized this approach with new Parker Deadel linear actuator and programed projects/code for multiple configurations. We have also updated the Roper CCD software and image processing software with the latest in industry standards. Modernization of transmitted-light source, robotic equipment, redesigned experimental chambers, and newly developed analytical procedures have greatly reduced time and cost per experiment. We have verified the ability of the new equipment to generate reproducible heterogeneous sand-filled chambers and demonstrated the functionality of the new equipment and procedures by reproducing several gravity-driven fingering experiments conducted by Griffith (2008).

  3. The hidden epidemic: confronting sexually transmitted diseases

    National Research Council Canada - National Science Library

    Eng, Thomas R; Butler, William T

    ... of Sexually Transmitted Diseases INSTITUTE OF MEDICINE Division of Health Promotion and Disease Prevention NATIONAL ACADEMY PRESS Washington, D.C. 1997 Copyrightthe cannot be not from book, paper however, version for formatting, original authoritative the typesetting-specific the as from created publication files XML from other this ...

  4. Multiple routes transmitted epidemics on multiplex networks

    International Nuclear Information System (INIS)

    Zhao, Dawei; Li, Lixiang; Peng, Haipeng; Luo, Qun; Yang, Yixian

    2014-01-01

    This letter investigates the multiple routes transmitted epidemic process on multiplex networks. We propose detailed theoretical analysis that allows us to accurately calculate the epidemic threshold and outbreak size. It is found that the epidemic can spread across the multiplex network even if all the network layers are well below their respective epidemic thresholds. Strong positive degree–degree correlation of nodes in multiplex network could lead to a much lower epidemic threshold and a relatively smaller outbreak size. However, the average similarity of neighbors from different layers of nodes has no obvious effect on the epidemic threshold and outbreak size. -- Highlights: •We studies multiple routes transmitted epidemic process on multiplex networks. •SIR model and bond percolation theory are used to analyze the epidemic processes. •We derive equations to accurately calculate the epidemic threshold and outbreak size. •ASN has no effect on the epidemic threshold and outbreak size. •Strong positive DDC leads to a lower epidemic threshold and a smaller outbreak size.

  5. Multiple routes transmitted epidemics on multiplex networks

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Dawei [Information Security Center, State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, P.O. Box 145, Beijing 100876 (China); National Engineering Laboratory for Disaster Backup and Recovery, Beijing University of Posts and Telecommunications, Beijing 100876 (China); Shandong Provincial Key Laboratory of Computer Network, Shandong Computer Science Center, Jinan 250014 (China); Li, Lixiang [Information Security Center, State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, P.O. Box 145, Beijing 100876 (China); National Engineering Laboratory for Disaster Backup and Recovery, Beijing University of Posts and Telecommunications, Beijing 100876 (China); Peng, Haipeng, E-mail: penghaipeng@bupt.edu.cn [Information Security Center, State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, P.O. Box 145, Beijing 100876 (China); National Engineering Laboratory for Disaster Backup and Recovery, Beijing University of Posts and Telecommunications, Beijing 100876 (China); Luo, Qun; Yang, Yixian [Information Security Center, State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, P.O. Box 145, Beijing 100876 (China); National Engineering Laboratory for Disaster Backup and Recovery, Beijing University of Posts and Telecommunications, Beijing 100876 (China)

    2014-02-01

    This letter investigates the multiple routes transmitted epidemic process on multiplex networks. We propose detailed theoretical analysis that allows us to accurately calculate the epidemic threshold and outbreak size. It is found that the epidemic can spread across the multiplex network even if all the network layers are well below their respective epidemic thresholds. Strong positive degree–degree correlation of nodes in multiplex network could lead to a much lower epidemic threshold and a relatively smaller outbreak size. However, the average similarity of neighbors from different layers of nodes has no obvious effect on the epidemic threshold and outbreak size. -- Highlights: •We studies multiple routes transmitted epidemic process on multiplex networks. •SIR model and bond percolation theory are used to analyze the epidemic processes. •We derive equations to accurately calculate the epidemic threshold and outbreak size. •ASN has no effect on the epidemic threshold and outbreak size. •Strong positive DDC leads to a lower epidemic threshold and a smaller outbreak size.

  6. Information guided channel hopping with an arbitrary number of transmit antennas

    KAUST Repository

    Yang, Yuli; Aï ssa, Sonia

    2012-01-01

    In order to realize the information guided channel hopping, also known as spatial modulation, with more design flexibility, in this paper we propose a novel scheme that allows operation with an arbitrary number of transmit antennas. Once the number of transmit antennas is not a power of two, the antennas' symbols are mapped by different numbers of bits. Subsequently, constellations with different orders are exploited for the modulation of radiated symbols so as to guarantee that the total number of bits transmitted at each time slot remains the same. Furthermore, we introduce a decoding algorithm with low complexity for this design. Numerical results on bit error rate performance are provided and substantiate that the proposed scheme turns out to be a promising alternative to the design of information guided channel hopping. © 2012 IEEE.

  7. Information guided channel hopping with an arbitrary number of transmit antennas

    KAUST Repository

    Yang, Yuli

    2012-10-01

    In order to realize the information guided channel hopping, also known as spatial modulation, with more design flexibility, in this paper we propose a novel scheme that allows operation with an arbitrary number of transmit antennas. Once the number of transmit antennas is not a power of two, the antennas\\' symbols are mapped by different numbers of bits. Subsequently, constellations with different orders are exploited for the modulation of radiated symbols so as to guarantee that the total number of bits transmitted at each time slot remains the same. Furthermore, we introduce a decoding algorithm with low complexity for this design. Numerical results on bit error rate performance are provided and substantiate that the proposed scheme turns out to be a promising alternative to the design of information guided channel hopping. © 2012 IEEE.

  8. Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages

    OpenAIRE

    Karol, Kenneth G; Arumuganathan, Kathiravetpillai; Boore, Jeffrey L; Duffy, Aaron M; Everett, Karin DE; Hall, John D; Hansen, S Kellon; Kuehl, Jennifer V; Mandoli, Dina F; Mishler, Brent D; Olmstead, Richard G; Renzaglia, Karen S; Wolf, Paul G

    2010-01-01

    Abstract Background Despite considerable progress in our understanding of land plant phylogeny, several nodes in the green tree of life remain poorly resolved. Furthermore, the bulk of currently available data come from only a subset of major land plant clades. Here we examine early land plant evolution using complete plastome sequences including two previously unexamined and phylogenetically critical lineages. To better understand the evolution of land plants and their plastomes, we examined...

  9. 48 CFR 245.7206 - Transmitting DD Form 1342, DoD Property Record.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false Transmitting DD Form 1342... Instructions 245.7206 Transmitting DD Form 1342, DoD Property Record. As a minimum, the plant clearance officer will provide the following information in a letter forwarding DD Forms 1342 to DSCR— (a) Number of DD...

  10. Standard generalized markup language: A guide for transmitting encoded bibliographic records

    International Nuclear Information System (INIS)

    1994-09-01

    This document provides the guidance necessary to transmit to DOE's Office of Scientific and Technical Information (OSTI) an encoded bibliographic record that conforms to International Standard ISO 8879, Information Processing -- Text and office systems -- Standard Generalized Markup Language (SGML). Included in this document are element and attribute tag definitions, sample bibliographic records, the bibliographic document type definition, and instructions on how to transmit a bibliographic record electronically to OSTI

  11. Sexually transmitted parasites and host mating behavior in the decorated cricket

    OpenAIRE

    Lien T. Luong; Harry K. Kaya

    2005-01-01

    Sexually transmitted diseases play a potentially important role in the ecology and evolution of host mating behavior. Here, we use a sexually transmitted nematode-cricket (Mehdinema alii--Gryllodes sigillatus) system to examine the effects of parasitism on host mating activity and female choice. Previous work has shown that infected male crickets produce a significantly smaller nuptial gift (spermatophylax) than uninfected males. This is expected to result in reduced spermatophylax feeding du...

  12. Sexually transmitted nematodes affect spermatophylax production in the cricket, Gryllodes sigillatus

    OpenAIRE

    Lien T. Luong; Harry K. Kaya

    2005-01-01

    Parasites can influence various aspects of host reproduction and mating, including spermatophore production. In the cricket, Gryllodes sigillatus, males transfer to females a two-part spermatophore containing a sperm-filled ampulla and a gelatinous spermatophylax (nuptial gift). Here we investigate the effects of a sexually transmitted nematode on male spermatophylax production. Sexually transmitted diseases (STDs) have the potential to reduce host fertility or fecundity in insect hosts. To o...

  13. Standard generalized markup language: A guide for transmitting encoded bibliographic records

    Energy Technology Data Exchange (ETDEWEB)

    1994-09-01

    This document provides the guidance necessary to transmit to DOE`s Office of Scientific and Technical Information (OSTI) an encoded bibliographic record that conforms to International Standard ISO 8879, Information Processing -- Text and office systems -- Standard Generalized Markup Language (SGML). Included in this document are element and attribute tag definitions, sample bibliographic records, the bibliographic document type definition, and instructions on how to transmit a bibliographic record electronically to OSTI.

  14. Trypanosoma janseni n. sp. (Trypanosomatida: Trypanosomatidae) isolated from Didelphis aurita (Mammalia: Didelphidae) in the Atlantic Rainforest of Rio de Janeiro, Brazil: integrative taxonomy and phylogeography within the Trypanosoma cruzi clade.

    Science.gov (United States)

    Lopes, Camila Madeira Tavares; Menna-Barreto, Rubem Figueiredo Sadok; Pavan, Márcio Galvão; Pereira, Mirian Cláudia De Souza; Roque, André Luiz R

    2018-01-01

    Didelphis spp. are a South American marsupial species that are among the most ancient hosts for the Trypanosoma spp. We characterise a new species (Trypanosoma janseni n. sp.) isolated from the spleen and liver tissues of Didelphis aurita in the Atlantic Rainforest of Rio de Janeiro, Brazil. The parasites were isolated and a growth curve was performed in NNN and Schneider's media containing 10% foetal bovine serum. Parasite morphology was evaluated via light microscopy on Giemsa-stained culture smears, as well as scanning and transmission electron microscopy. Molecular taxonomy was based on a partial region (737-bp) of the small subunit (18S) ribosomal RNA gene and 708 bp of the nuclear marker, glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) genes. Maximum likelihood and Bayesian inference methods were used to perform a species coalescent analysis and to generate individual and concatenated gene trees. Divergence times among species that belong to the T. cruzi clade were also inferred. In vitro growth curves demonstrated a very short log phase, achieving a maximum growth rate at day 3 followed by a sharp decline. Only epimastigote forms were observed under light and scanning microscopy. Transmission electron microscopy analysis showed structures typical to Trypanosoma spp., except one structure that presented as single-membraned, usually grouped in stacks of three or four. Phylogeography analyses confirmed the distinct species status of T. janseni n. sp. within the T. cruzi clade. Trypanosoma janseni n. sp. clusters with T. wauwau in a well-supported clade, which is exclusive and monophyletic. The separation of the South American T. wauwau + T. janseni coincides with the separation of the Southern Super Continent. This clade is a sister group of the trypanosomes found in Australian marsupials and its discovery sheds light on the initial diversification process based on what we currently know about the T. cruzi clade.

  15. Phylogenetic position of Sphaerospora testicularis and Latyspora scomberomori n. gen. n. sp. (Myxozoa) within the marine urinary clade

    Czech Academy of Sciences Publication Activity Database

    Bartošová, Pavla; Freeman, M. A.; Yokoyama, H.; Caffara, M.; Fiala, Ivan

    2011-01-01

    Roč. 138, č. 3 (2011), 381-393 ISSN 0031-1820 R&D Projects: GA AV ČR KJB600960701; GA ČR GD524/03/H133; GA MŠk LC522 Institutional research plan: CEZ:AV0Z60220518 Keywords : Myxosporea * Sphaerospora * Latyspora * Scomberomorus * Dicentrarchus * SSU rDNA * sutural line * marine urinary clade Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 2.961, year: 2011

  16. Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade

    Directory of Open Access Journals (Sweden)

    Rabus Ralf

    2009-09-01

    Full Text Available Abstract Background In the present work the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis was studied at the level of metabolic fluxes. These two strains belong to the marine Roseobacter clade, a dominant bacterial group in various marine habitats, and represent surface-associated, biofilm-forming growth (P. gallaeciensis and symbiotic growth with eukaryotic algae (D. shibae. Based on information from recently sequenced genomes, a rich repertoire of pathways has been identified in the carbon core metabolism of these organisms, but little is known about the actual contribution of the various reactions in vivo. Results Using 13C labelling techniques in specifically designed experiments, it could be shown that glucose-grown cells of D. shibae catabolise the carbon source exclusively via the Entner-Doudoroff pathway, whereas alternative routes of glycolysis and the pentose phosphate pathway are obviously utilised for anabolic purposes only. Enzyme assays confirmed this flux pattern and link the lack of glycolytic flux to the absence of phosphofructokinase activity. The previously suggested formation of phosphoenolpyruvate from pyruvate during mixotrophic CO2 assimilation was found to be inactive under the conditions studied. Moreover, it could be shown that pyruvate carboxylase is involved in CO2 assimilation and that the cyclic respiratory mode of the TCA cycle is utilised. Interestingly, the use of intracellular pathways was highly similar for P. gallaeciensis. Conclusion The present study reveals the first insight into pathway utilisation within the Roseobacter group. Fluxes through major intracellular pathways of the central carbon metabolism, which are closely linked to the various important traits found for the Roseobacter clade, could be determined. The close similarity of fluxes between the two physiologically rather different species might provide the first indication of more general key properties among

  17. Double-transmitting and Sextuple-receiving Borehole Transient Electromagnetic Method and Experimental Study

    Directory of Open Access Journals (Sweden)

    Bo Wang

    2017-04-01

    Full Text Available With the continuous improvement of precision requirements for borehole geophysical exploration, the application of transient electromagnetic method (from now on referred to as TEM in a borehole has become a hot spot. The conventional borehole TEM can only determine the longitudinal depth of the geological anomaly, the radial azimuth and depth cannot be resolved. A double-transmitting and sextuple-receiving borehole TEM is proposed, through which the radial anomaly is excited by the electromagnetic field generated by the double-emitting loops, and the azimuth and depth of the anomaly will be identified by the difference characteristics of the six receiving loops signals. In this paper, the response equations of the transmitting-receiving mode of double-transmitting and sextuple-receiving borehole TEM are deduced, and the response characteristics of the induction segment and the attenuation segment of the receiving loops are obtained based on the response equations under ramp function turn-off condition, providing the basis for theoretical analysis. Due to the negative value of the double-transmitting and sextuple-receiving transient electromagnetic response signals, a negative transformation algorithm under the double logarithmic coordinate system is proposed to provide the essential method for the analysis of two kinds of physical simulation experimental data of the radial azimuth and radial depth detection of the anomaly. The results show that the double-transmitting and sextuple-receiving borehole TEM has decent resolution ability in detecting the radial azimuth of the anomaly, and the effective resolution is 30°. The geometric difference among induced voltages of different measuring points can be used to evaluate the radial depth of the anomaly qualitatively. It is expected that the double-transmitting and sextuple-receiving borehole TEM can provide technical guidance for little borehole geophysical exploration in the fields of oil, natural

  18. Transmitted wavefront testing with large dynamic range based on computer-aided deflectometry

    Science.gov (United States)

    Wang, Daodang; Xu, Ping; Gong, Zhidong; Xie, Zhongmin; Liang, Rongguang; Xu, Xinke; Kong, Ming; Zhao, Jun

    2018-06-01

    The transmitted wavefront testing technique is demanded for the performance evaluation of transmission optics and transparent glass, in which the achievable dynamic range is a key issue. A computer-aided deflectometric testing method with fringe projection is proposed for the accurate testing of transmitted wavefronts with a large dynamic range. Ray tracing of the modeled testing system is carried out to achieve the virtual ‘null’ testing of transmitted wavefront aberrations. The ray aberration is obtained from the ray tracing result and measured slope, with which the test wavefront aberration can be reconstructed. To eliminate testing system modeling errors, a system geometry calibration based on computer-aided reverse optimization is applied to realize accurate testing. Both numerical simulation and experiments have been carried out to demonstrate the feasibility and high accuracy of the proposed testing method. The proposed testing method can achieve a large dynamic range compared with the interferometric method, providing a simple, low-cost and accurate way for the testing of transmitted wavefronts from various kinds of optics and a large amount of industrial transmission elements.

  19. Power balance and loss mechanism analysis in RF transmit coil arrays.

    Science.gov (United States)

    Kuehne, Andre; Goluch, Sigrun; Waxmann, Patrick; Seifert, Frank; Ittermann, Bernd; Moser, Ewald; Laistler, Elmar

    2015-10-01

    To establish a framework for transmit array power balance calculations based on power correlation matrices to accurately quantify the loss contributions from different mechanisms such as coupling, lumped components, and radiation. Starting from Poynting's theorem, power correlation matrices are derived for all terms in the power balance, which is formulated as a matrix equation. Finite-difference time-domain simulations of two 7 T eight-channel head array coils at 297.2 MHz are used to verify the theoretical considerations and demonstrate their application. Care is taken to accurately incorporate all loss mechanisms. The power balance for static B1 phase shims as well as two-dimensional spatially selective transmit SENSE pulses is shown. The simulated power balance shows an excellent agreement with theory, with a maximum power imbalance of less than 0.11%. Power loss contributions from the different loss mechanisms vary significantly between the investigated setups, and depending on the excitation mode imposed on the coil. The presented approach enables a straightforward loss evaluation for an arbitrary excitation of transmit coil arrays. Worst-case power imbalance and losses are calculated in a straightforward manner. This allows for deeper insight into transmit array loss mechanisms, incorporation of radiated power components in specific absorption rate calculations and verification of electromagnetic simulations. © 2014 Wiley Periodicals, Inc.

  20. Individuality evaluation for paper based artifact-metrics using transmitted light image

    Science.gov (United States)

    Yamakoshi, Manabu; Tanaka, Junichi; Furuie, Makoto; Hirabayashi, Masashi; Matsumoto, Tsutomu

    2008-02-01

    Artifact-metrics is an automated method of authenticating artifacts based on a measurable intrinsic characteristic. Intrinsic characters, such as microscopic random-patterns made during the manufacturing process, are very difficult to copy. A transmitted light image of the distribution can be used for artifact-metrics, since the fiber distribution of paper is random. Little is known about the individuality of the transmitted light image although it is an important requirement for intrinsic characteristic artifact-metrics. Measuring individuality requires that the intrinsic characteristic of each artifact significantly differs, so having sufficient individuality can make an artifact-metric system highly resistant to brute force attack. Here we investigate the influence of paper category, matching size of sample, and image-resolution on the individuality of a transmitted light image of paper through a matching test using those images. More concretely, we evaluate FMR/FNMR curves by calculating similarity scores with matches using correlation coefficients between pairs of scanner input images, and the individuality of paper by way of estimated EER with probabilistic measure through a matching method based on line segments, which can localize the influence of rotation gaps of a sample in the case of large matching size. As a result, we found that the transmitted light image of paper has a sufficient individuality.

  1. 76 FR 75523 - Vessel Monitoring Systems; Approved Mobile Transmitting Units and Communications Service...

    Science.gov (United States)

    2011-12-02

    ... Monitoring Systems; Approved Mobile Transmitting Units and Communications Service Providers for Use in... relevant features of the enhanced mobile transmitting unit (E-MTU) VMS and communications service providers... with the Orbcomm mobile communications provider service. Skymate can be reached at 866-SKYMATE and...

  2. Phylogenetic analysis of the lux operon distinguishes two evolutionarily distinct clades of Photobacterium leiognathi.

    Science.gov (United States)

    Ast, Jennifer C; Dunlap, Paul V

    2004-05-01

    The luminous marine bacterium Photobacterium mandapamensis was synonymized several years ago with Photobacterium leiognathi based on a high degree of phenotypic and genetic similarity. To test the possibility that P. leiognathi as now formulated, however, actually contains two distinct bacterial groups reflecting the earlier identification of P. mandapamensis and P. leiognathi as separate species, we compared P. leiognathi strains isolated from light-organ symbiosis with leiognathid fishes (i.e., ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1) with strains from seawater originally described as P. mandapamensis and later synonymized as P. leiognathi (i.e., ATCC 27561(T) and ATCC 33981) and certain strains initially identified as P. leiognathi (i.e., PL-721, PL-741, 554). Analysis of the 16S rRNA and gyrB genes did not resolve distinct clades, affirming a close relationship among these strains. However, strains ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554 were found to bear a luxF gene in the lux operon ( luxABFE), whereas ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1 lack this gene ( luxABE). Phylogenetic analysis of the luxAB(F)E region confirmed this distinction. Furthermore, ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554 all produced a higher level of luminescence on high-salt medium, as previously described for PL-721, whereas ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1 all produced a higher level of luminescence on low-salt medium, a characteristic of P. leiognathi from leiognathid fish light organs. These results demonstrate that P. leiognathi contains two evolutionarily and phenotypically distinct clades, P. leiognathi subsp. leiognathi (strains ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1), and P. leiognathi subsp. mandapamensis (strains ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554).

  3. Adaptive single-antenna transmit selection with interference suppression

    KAUST Repository

    Radaydeh, Redha Mahmoud Mesleh; Alouini, Mohamed-Slim

    2011-01-01

    -efficient transmission with as low transmit channel estimations as possible. Due to the fact that the number of active co-channel interfering signals and their corresponding powers experience random behavior, the adaptation to channels conditions, assuming uniform buffer

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

    Science.gov (United States)

    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

  5. Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets.

    Science.gov (United States)

    Ilyushina, Natalia A; Seiler, Jon P; Rehg, Jerold E; Webster, Robert G; Govorkova, Elena A

    2010-05-27

    The acquisition of neuraminidase (NA) inhibitor resistance by H5N1 influenza viruses has serious clinical implications, as this class of drugs can be an essential component of pandemic control measures. The continuous evolution of the highly pathogenic H5N1 influenza viruses results in the emergence of natural NA gene variations whose impact on viral fitness and NA inhibitor susceptibility are poorly defined. We generated seven genetically stable recombinant clade 2.2 A/Turkey/15/06-like (H5N1) influenza viruses carrying NA mutations located either in the framework residues (E119A, H274Y, N294S) or in close proximity to the NA enzyme active site (V116A, I117V, K150N, Y252H). NA enzyme inhibition assays showed that NA mutations at positions 116, 117, 274, and 294 reduced susceptibility to oseltamivir carboxylate (IC(50)s increased 5- to 940-fold). Importantly, the E119A NA mutation (previously reported to confer resistance in the N2 NA subtype) was stable in the clade 2.2 H5N1 virus background and induced cross-resistance to oseltamivir carboxylate and zanamivir. We demonstrated that Y252H NA mutation contributed for decreased susceptibility of clade 2.2 H5N1 viruses to oseltamivir carboxylate as compared to clade 1 viruses. The enzyme kinetic parameters (V(max), K(m) and K(i)) of the avian-like N1 NA glycoproteins were highly consistent with their IC(50) values. None of the recombinant H5N1 viruses had attenuated virulence in ferrets inoculated with 10(6) EID(50) dose. Most infected ferrets showed mild clinical disease signs that differed in duration. However, H5N1 viruses carrying the E119A or the N294S NA mutation were lethal to 1 of 3 inoculated animals and were associated with significantly higher virus titers (Pinfluenza drugs that target different virus/host factors and can limit the emergence of resistance.

  6. Three Dimensional Energy Transmitting Boundary in the Time Domain

    Directory of Open Access Journals (Sweden)

    Naohiro eNakamura

    2015-11-01

    Full Text Available Although the energy transmitting boundary is accurate and efficient for the FEM earthquake response analysis, it could be applied in the frequency domain only. In the previous papers, the author proposed an earthquake response analysis method using the time domain energy transmitting boundary for two dimensional problems. In this paper, this technique is expanded for three dimensional problems. The inner field is supposed to be a hexahedron shape and the approximate time domain boundary is explained, first. Next, two dimensional anti-plane time domain boundary is studied for a part of the approximate three dimensional boundary method. Then, accuracy and efficiency of the proposed method are confirmed by example problems.

  7. Adaption of wild-bird origin H5Nx highly pathogenic avian influenza virus Clade 2.3.4.4 in vaccinated poultry

    Science.gov (United States)

    The 2014-2015 incursion of H5Nx clade 2.3.4.4 high pathogenicity avian influenza (HPAI) virus caused the largest animal health emergency in U.S. history and renewed interest in developing vaccines against these newly emergent viruses. Our previous research demonstrated several H5 vaccines with varyi...

  8. SVD-BASED TRANSMIT BEAMFORMING FOR VARIOUS MODULATIONS WITH CONVOLUTION ENCODING

    Directory of Open Access Journals (Sweden)

    M. Raja

    2011-09-01

    Full Text Available This paper present a new beamforming technique using singular value decomposition (SVD for closed loop Multiple-input, multiple-output (MIMO wireless systems with various modulation techniques such as BPSK, 16-QAM, 16-PSK, DPSK and PAM along with convolution encoder. The channel matrix is decomposed into a number of independent orthogonal modes of excitation, which refer to as eigenmodes of the channel. Transmit precoding is performed by multiplying the input symbols with unitary matrix to produce the transmit beamforming, and the precoded symbols are transmitted over Rayleigh fading channel. At the receiver, combining process is performed by using maximum ratio combiner (MRC, and the receiver shaping is performed to retrieve the original input symbols by multiplying the received signal with conjugate transpose of the unitary matrix. Furthermore, the expressions for average bit error rate (BER for M-PSK and average BER for M-QAM are derived. The superiority of the proposed work is proved by simulation results and the proposed work is compared to the other beamforming methods.

  9. Reduction of vibration forces transmitted from a radiator cooling fan to a vehicle body

    Science.gov (United States)

    Lim, Jonghyuk; Sim, Woojeong; Yun, Seen; Lee, Dongkon; Chung, Jintai

    2018-04-01

    This article presents methods for reducing transmitted vibration forces caused by mass unbalance of the radiator cooling fan during vehicle idling. To identify the effects of mass unbalance upon the vibration characteristics, vibration signals of the fan blades were experimentally measured both with and without an added mass. For analyzing the vibration forces transmitted to the vehicle body, a dynamic simulation model was established that reflected the vibration characteristics of the actual system. This process included a method described herein for calculating the equivalent stiffness and the equivalent damping of the shroud stators and rubber mountings. The dynamic simulation model was verified by comparing its results with experimental results of the radiator cooling fan. The dynamic simulation model was used to analyze the transmitted vibration forces at the rubber mountings. Also, a measure was established to evaluate the effects of varying the design parameters upon the transmitted vibration forces. We present design guidelines based on these analyses to reduce the transmitted vibration forces of the radiator cooling fan.

  10. Neuromuscular study of early branching Diuronotus aspetos (Paucitubulatina) yields insights into the evolution of organs systems in Gastrotricha

    DEFF Research Database (Denmark)

    Bekkouche, Nicolas Tarik; Worsaae, Katrine

    2016-01-01

    BACKGROUND: Diuronotus is one of the most recently described genera of Paucitubulatina, one of the three major clades in Gastrotricha. Its morphology suggests that Diuronotus is an early branch of Paucitubulatina, making it a key taxon for understanding the evolution of this morphologically...... constitute new apomorphies of Paucitubulatina, or even Gastrotricha. In order to test these new evolutionary hypotheses, comparable morphological data from other understudied gastrotrich branches and a better resolution of the basal nodes of the gastrotrich phylogeny are warranted. Nonetheless, the present...

  11. Southern rice black-streaked dwarf virus: a white-backed planthopper transmitted fijivirus threadening rice production in Asia

    Directory of Open Access Journals (Sweden)

    Guohui eZhou

    2013-09-01

    Full Text Available Southern rice black-streaked dwarf virus (SRBSDV, a nonenveloped icosahedral virus with a genome of 10 double-stranded RNA segments, is a novel species in the genus Fijivirus (family Reoviridae first recognized in 2008. Rice plants infected with this virus exhibit symptoms similar to those caused by Rice black-streaked dwarf virus. Since 2009, the virus has rapidly spread and caused serious rice losses in East and Southeast Asia. Significant progress has been made in recent years in understanding this disease, especially about the functions of the viral genes, rice–virus–insect interactions, and epidemiology and control measures. The virus can be efficiently transmitted by the white-backed planthopper (WBPH, Sogatella furcifera in a persistent circulative propagative manner but cannot be transmitted by the brown planthopper (Nilaparvata lugens and small brown planthopper (Laodelphax striatellus. Rice, maize, Chinese sorghum (Coix lacryma-jobi and other grass weeds can be infected via WBPH. However, only rice plays a major role in the virus infection cycle because of the vector's preference. In Southeast Asia, WBPH is a long-distance migratory rice pest. The disease cycle can be described as follows: SRBSDV and its WBPH vector overwinter in warm tropical or sub-tropical areas; viruliferous WBPH adults carry the virus from south to north via long-distance migration in early spring, transmit the virus to rice seedlings in the newly colonized areas, and lay eggs on the infected seedlings; the next generation of WBPHs propagate on infected seedlings, become viruliferous, disperse, and cause new disease outbreaks. Several molecular and serological methods have been developed to detect SRBSDV in plant tissues and individual insects. Control measures based on protection from WBPH, including seedbed coverage, chemical seed treatments, and chemical spraying of seedlings, have proven effective in China.

  12. Stochastic dynamics for reinfection by transmitted diseases

    Science.gov (United States)

    Barros, Alessandro S.; Pinho, Suani T. R.

    2017-06-01

    The use of stochastic models to study the dynamics of infectious diseases is an important tool to understand the epidemiological process. For several directly transmitted diseases, reinfection is a relevant process, which can be expressed by endogenous reactivation of the pathogen or by exogenous reinfection due to direct contact with an infected individual (with smaller reinfection rate σ β than infection rate β ). In this paper, we examine the stochastic susceptible, infected, recovered, infected (SIRI) model simulating the endogenous reactivation by a spontaneous reaction, while exogenous reinfection by a catalytic reaction. Analyzing the mean-field approximations of a site and pairs of sites, and Monte Carlo (MC) simulations for the particular case of exogenous reinfection, we obtained continuous phase transitions involving endemic, epidemic, and no transmission phases for the simple approach; the approach of pairs is better to describe the phase transition from endemic phase (susceptible, infected, susceptible (SIS)-like model) to epidemic phase (susceptible, infected, and removed or recovered (SIR)-like model) considering the comparison with MC results; the reinfection increases the peaks of outbreaks until the system reaches endemic phase. For the particular case of endogenous reactivation, the approach of pairs leads to a continuous phase transition from endemic phase (SIS-like model) to no transmission phase. Finally, there is no phase transition when both effects are taken into account. We hope the results of this study can be generalized for the susceptible, exposed, infected, and removed or recovered (SEIRIE) model, for which the state exposed (infected but not infectious), describing more realistically transmitted diseases such as tuberculosis. In future work, we also intend to investigate the effect of network topology on phase transitions when the SIRI model describes both transmitted diseases (σ social contagions (σ >1 ).

  13. 75 FR 63445 - Vessel Monitoring Systems; Approved Mobile Transmitting Units and Communications Service...

    Science.gov (United States)

    2010-10-15

    ... Monitoring Systems; Approved Mobile Transmitting Units and Communications Service Providers for Use in the... features of the VMS. ADDRESSES: To obtain copies of the list of NOAA-approved VMS mobile transmitting units and NOAA-approved VMS communications service providers, please contact the VMS Support Center at...

  14. Geostatistical modelling of soil-transmitted helminth infection in Cambodia: do socioeconomic factors improve predictions?

    Science.gov (United States)

    Karagiannis-Voules, Dimitrios-Alexios; Odermatt, Peter; Biedermann, Patricia; Khieu, Virak; Schär, Fabian; Muth, Sinuon; Utzinger, Jürg; Vounatsou, Penelope

    2015-01-01

    Soil-transmitted helminth infections are intimately connected with poverty. Yet, there is a paucity of using socioeconomic proxies in spatially explicit risk profiling. We compiled household-level socioeconomic data pertaining to sanitation, drinking-water, education and nutrition from readily available Demographic and Health Surveys, Multiple Indicator Cluster Surveys and World Health Surveys for Cambodia and aggregated the data at village level. We conducted a systematic review to identify parasitological surveys and made every effort possible to extract, georeference and upload the data in the open source Global Neglected Tropical Diseases database. Bayesian geostatistical models were employed to spatially align the village-aggregated socioeconomic predictors with the soil-transmitted helminth infection data. The risk of soil-transmitted helminth infection was predicted at a grid of 1×1km covering Cambodia. Additionally, two separate individual-level spatial analyses were carried out, for Takeo and Preah Vihear provinces, to assess and quantify the association between soil-transmitted helminth infection and socioeconomic indicators at an individual level. Overall, we obtained socioeconomic proxies from 1624 locations across the country. Surveys focussing on soil-transmitted helminth infections were extracted from 16 sources reporting data from 238 unique locations. We found that the risk of soil-transmitted helminth infection from 2000 onwards was considerably lower than in surveys conducted earlier. Population-adjusted prevalences for school-aged children from 2000 onwards were 28.7% for hookworm, 1.5% for Ascaris lumbricoides and 0.9% for Trichuris trichiura. Surprisingly, at the country-wide analyses, we did not find any significant association between soil-transmitted helminth infection and village-aggregated socioeconomic proxies. Based also on the individual-level analyses we conclude that socioeconomic proxies might not be good predictors at an

  15. Inter-Vehicle Communication System Utilizing Autonomous Distributed Transmit Power Control

    Science.gov (United States)

    Hamada, Yuji; Sawa, Yoshitsugu; Goto, Yukio; Kumazawa, Hiroyuki

    In ad-hoc network such as inter-vehicle communication (IVC) system, safety applications that vehicles broadcast the information such as car velocity, position and so on periodically are considered. In these applications, if there are many vehicles broadcast data in a communication area, congestion incurs a problem decreasing communication reliability. We propose autonomous distributed transmit power control method to keep high communication reliability. In this method, each vehicle controls its transmit power using feed back control. Furthermore, we design a communication protocol to realize the proposed method, and we evaluate the effectiveness of proposed method using computer simulation.

  16. An Accurate Transmitting Power Control Method in Wireless Communication Transceivers

    Science.gov (United States)

    Zhang, Naikang; Wen, Zhiping; Hou, Xunping; Bi, Bo

    2018-01-01

    Power control circuits are widely used in transceivers aiming at stabilizing the transmitted signal power to a specified value, thereby reducing power consumption and interference to other frequency bands. In order to overcome the shortcomings of traditional modes of power control, this paper proposes an accurate signal power detection method by multiplexing the receiver and realizes transmitting power control in the digital domain. The simulation results show that this novel digital power control approach has advantages of small delay, high precision and simplified design procedure. The proposed method is applicable to transceivers working at large frequency dynamic range, and has good engineering practicability.

  17. A Simple Differential Modulation Scheme for Quasi-Orthogonal Space-Time Block Codes with Partial Transmit Diversity

    Directory of Open Access Journals (Sweden)

    Lingyang Song

    2007-04-01

    Full Text Available We report a simple differential modulation scheme for quasi-orthogonal space-time block codes. A new class of quasi-orthogonal coding structures that can provide partial transmit diversity is presented for various numbers of transmit antennas. Differential encoding and decoding can be simplified for differential Alamouti-like codes by grouping the signals in the transmitted matrix and decoupling the detection of data symbols, respectively. The new scheme can achieve constant amplitude of transmitted signals, and avoid signal constellation expansion; in addition it has a linear signal detector with very low complexity. Simulation results show that these partial-diversity codes can provide very useful results at low SNR for current communication systems. Extension to more than four transmit antennas is also considered.

  18. Comparisons of receive array interference reduction techniques under erroneous generalized transmit beamforming

    KAUST Repository

    Radaydeh, Redha Mahmoud

    2014-02-01

    This paper studies generalized single-stream transmit beamforming employing receive array co-channel interference reduction algorithms under slow and flat fading multiuser wireless systems. The impact of imperfect prediction of channel state information for the desired user spatially uncorrelated transmit channels on the effectiveness of transmit beamforming for different interference reduction techniques is investigated. The case of over-loaded receive array with closely-spaced elements is considered, wherein it can be configured to specified interfering sources. Both dominant interference reduction and adaptive interference reduction techniques for statistically ordered and unordered interferers powers, respectively, are thoroughly studied. The effect of outdated statistical ordering of the interferers powers on the efficiency of dominant interference reduction is studied and then compared against the adaptive interference reduction. For the system models described above, new analytical formulations for the statistics of combined signal-to-interference-plus-noise ratio are presented, from which results for conventional maximum ratio transmission and single-antenna best transmit selection can be directly deduced as limiting cases. These results are then utilized to obtain quantitative measures for various performance metrics. They are also used to compare the achieved performance of various configuration models under consideration. © 1972-2012 IEEE.

  19. [Soil-transmitted helminth trends and prevalence in La Virgen, Colombia 1995-2005].

    Science.gov (United States)

    Fernández-Niño, Julián A; Reyes-Harker, Patricia; Moncada-Alvarez, Ligia I; López, Myriam C; Cháves, María Del Pilar; Knudson, Angélica; Ariza, Yoseth

    2007-01-01

    Describing soil-transmitted helminthiasis prevalence and trends in children aged less than 15 in the village of La Virgen, Cundinamarca. Three non-random surveys were carried out on school-children aged 0 to 15 years. Intestinal parasitism was determined In the three cross-sectional studies by direct examination of fecal samples and modified Ritchie-Frick concentration method. Intestinal parasitism distribution was analysed and the trend during 1995-2005 described. The prevalence of intestinal parasitism in children aged less than 5 increased from 62,5 % in 1995 to 66,7 % in 2001 and to 69 % in 2005; soil-transmitted helminthiasis prevalence in this age group was 37,5 % in 1995, 23,6 % in 2001 and 27,6 % in 2005. The prevalence of intestinal parasitism for children aged over 5 increased from 86,2 % in 1995 to 89,1 % in 2005; soil-transmitted helminthiasis prevalence was 62,9 % in 1995, 39,8 % in 2001 and 23,9 % in 2005. Soil-transmitted helminthiasis was endemic and presented high prevalence during the study period. Effective control measures are needed to prevent intestinal parasitism in pre-school and schoolchildren.

  20. Transmit-receive eddy current probes

    International Nuclear Information System (INIS)

    Obrutsky, L.S.; Sullivan, S.P.; Cecco, V.S.

    1997-01-01

    In the last two decades, due to increased inspection demands, eddy current instrumentation has advanced from single-frequency, single-output instruments to multifrequency, computer-aided systems. This has significantly increased the scope of eddy current testing, but, unfortunately, it has also increased the cost and complexity of inspections. In addition, this approach has not always improved defect detectability or signal-to-noise. Most eddy current testing applications are still performed with impedance probes, which have well known limitations. However, recent research at AECL has led to improved eddy current inspections through the design and development of transmit-receive (T/R) probes. T/R eddy current probes, with laterally displaced transmit and receive coils, present a number of advantages over impedance probes. They have improved signal-to-noise ratio in the presence of variable lift-off compared to impedance probes. They have strong directional properties, permitting probe optimization for circumferential or axial crack detection, and possess good phase discrimination to surface defects. They can significantly increase the scope of eddy current testing permitting reliable detection and sizing of cracks in heat exchanger tubing as well as in welded areas of both ferritic and non-ferromagnetic components. This presentation will describe the operating principles of T/R probes with the help of computer-derived normalized voltage diagrams. We will discuss their directional properties and analyze the advantages of using single and multiple T/R probes over impedance probes for specific inspection cases. Current applications to surface and tube testing and some typical inspection results will be described. (author)

  1. Behavioural risk factors for sexually transmitted infections and health ...

    African Journals Online (AJOL)

    Behavioural risk factors for sexually transmitted infections and health ... sharing of personal effects, malnourishment and sexual harassment. ... Development of risk reduction and appropriate sexual health interventions targeted at prevention ...

  2. Rates and modes of body size evolution in early carnivores and herbivores: a case study from Captorhinidae

    Directory of Open Access Journals (Sweden)

    Neil Brocklehurst

    2016-01-01

    Full Text Available Body size is an extremely important characteristic, impacting on a variety of ecological and life-history traits. It is therefore important to understand the factors which may affect its evolution, and diet has attracted much interest in this context. A recent study which examined the evolution of the earliest terrestrial herbivores in the Late Carboniferous and Early Permian concluded that in the four herbivorous clades examined there was a trend towards increased body size, and that this increase was more substantial than that observed in closely related carnivorous clades. However, this hypothesis was not based on quantitative examination, and phylogenetic comparative methods provide a more robust means of testing such hypotheses. Here, the evolution of body size within different dietary regimes is examined in Captorhinidae, the most diverse and longest lived of these earliest high fibre herbivores. Evolutionary models were fit to their phylogeny to test for variation in rate and mode of evolution between the carnivorous and herbivorous members of this clade, and an analysis of rate variation throughout the tree was carried out. Estimates of ancestral body sizes were calculated in order to compare the rates and direction of evolution of lineages with different dietary regimes. Support for the idea that the high fibre herbivores within captorhinids are being drawn to a higher adaptive peak in body size than the carnivorous members of this clade is weak. A shift in rates of body size evolution is identified, but this does not coincide with the evolution of high-fibre herbivory, instead occurring earlier in time and at a more basal node. Herbivorous lineages which show an increase in size are not found to evolve at a faster rate than those which show a decrease; in fact, it is those which experience a size decrease which evolve at higher rates. It is possible the shift in rates of evolution is related to the improved food processing ability of

  3. Simultaneous Transmit and Receive Performance of an 8-channel Digital Phased Array

    Science.gov (United States)

    2017-01-16

    hardware. An 8-channel ALSTAR array prototype was constructed and demonstrated to achieve 125.5 dB effective isotropic isolation between broadside...transmit and receive beams over a 100 MHz instantaneous band centered at 2.45 GHz. I. INTRODUCTION A phased array capable of Simultaneous Transmit and...Receive (STAR) could provide significant benefits for many applications including communications, radar, spectral sens- ing, and multifunctional systems

  4. Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages

    Directory of Open Access Journals (Sweden)

    Mandoli Dina F

    2010-10-01

    Full Text Available Abstract Background Despite considerable progress in our understanding of land plant phylogeny, several nodes in the green tree of life remain poorly resolved. Furthermore, the bulk of currently available data come from only a subset of major land plant clades. Here we examine early land plant evolution using complete plastome sequences including two previously unexamined and phylogenetically critical lineages. To better understand the evolution of land plants and their plastomes, we examined aligned nucleotide sequences, indels, gene and nucleotide composition, inversions, and gene order at the boundaries of the inverted repeats. Results We present the plastome sequences of Equisetum arvense, a horsetail, and of Isoetes flaccida, a heterosporous lycophyte. Phylogenetic analysis of aligned nucleotides from 49 plastome genes from 43 taxa supported monophyly for the following clades: embryophytes (land plants, lycophytes, monilophytes (leptosporangiate ferns + Angiopteris evecta + Psilotum nudum + Equisetum arvense, and seed plants. Resolution among the four monilophyte lineages remained moderate, although nucleotide analyses suggested that P. nudum and E. arvense form a clade sister to A. evecta + leptosporangiate ferns. Results from phylogenetic analyses of nucleotides were consistent with the distribution of plastome gene rearrangements and with analysis of sequence gaps resulting from insertions and deletions (indels. We found one new indel and an inversion of a block of genes that unites the monilophytes. Conclusions Monophyly of monilophytes has been disputed on the basis of morphological and fossil evidence. In the context of a broad sampling of land plant data we find several new pieces of evidence for monilophyte monophyly. Results from this study demonstrate resolution among the four monilophytes lineages, albeit with moderate support; we posit a clade consisting of Equisetaceae and Psilotaceae that is sister to the "true ferns

  5. Experimental infection of clade 1.1.2 (H5N1), clade 2.3.2.1c (H5N1) and clade 2.3.4.4 (H5N6) highly pathogenic avian influenza viruses in dogs.

    Science.gov (United States)

    Lyoo, K S; Na, W; Phan, L V; Yoon, S W; Yeom, M; Song, D; Jeong, D G

    2017-12-01

    Since the emergence of highly pathogenic avian influenza (HPAI) H5N1 in Asia, the haemagglutinin (HA) gene of this virus lineage has continued to evolve in avian populations, and H5N1 lineage viruses now circulate concurrently worldwide. Dogs may act as an intermediate host, increasing the potential for zoonotic transmission of influenza viruses. Virus transmission and pathologic changes in HPAI clade 1.1.2 (H5N1)-, 2.3.2.1c (H5N1)- and 2.3.4.4 (H5N6)-infected dogs were investigated. Mild respiratory signs and antibody response were shown in dogs intranasally infected with the viruses. Lung histopathology showed lesions that were associated with moderate interstitial pneumonia in the infected dogs. In this study, HPAI H5N6 virus replication in dogs was demonstrated for the first time. Dogs have been suspected as a "mixing vessel" for reassortments between avian and human influenza viruses to occur. The replication of these three subtypes of the H5 lineage of HPAI viruses in dogs suggests that dogs could serve as intermediate hosts for avian-human influenza virus reassortment if they are also co-infected with human influenza viruses. © 2017 Blackwell Verlag GmbH.

  6. Cooperative Spatial Reuse with Transmit Beamforming in Multi-rate Wireless Networks

    DEFF Research Database (Denmark)

    Lu, Chenguang; Fitzek, Frank; Eggers, Patrick Claus F.

    2009-01-01

    We present a cooperative spatial reuse (CSR) scheme as a cooperative extension of the current TDMA-based MAC to enable spatial reuse in multi-rate wireless networks. We model spatial reuse as a cooperation problem on utilizing the time slots obtained from the TDMA-based MAC. In CSR, there are two...... operation modes. One is TDMA mode while the other is spatial reuse mode in which links transmit simultaneously. Links contribute their own time slots to form a cooperative group to do spatial reuse. Each link joins the group only if it can benefit in capacity or energy efficiency. Otherwise, the link...... will leave spatial reuse mode and switch back to TDMA. In this work, we focus on the transmit beamforming techniques to enable CSR by interference cancellation on MISO (Multiple Input Single Output) links. We compare the CSR scheme using zero-forcing (ZF) transmit beamforming, namely ZF-CSR, to the TDMA...

  7. High Levels of Transmitted HIV Drug Resistance in a Study in Papua New Guinea.

    Science.gov (United States)

    Lavu, Evelyn; Kave, Ellan; Mosoro, Euodia; Markby, Jessica; Aleksic, Eman; Gare, Janet; Elsum, Imogen A; Nano, Gideon; Kaima, Petronia; Dala, Nick; Gurung, Anup; Bertagnolio, Silvia; Crowe, Suzanne M; Myatt, Mark; Hearps, Anna C; Jordan, Michael R

    2017-01-01

    Papua New Guinea is a Pacific Island nation of 7.3 million people with an estimated HIV prevalence of 0.8%. ART initiation and monitoring are guided by clinical staging and CD4 cell counts, when available. Little is known about levels of transmitted HIV drug resistance in recently infected individuals in Papua New Guinea. Surveillance of transmitted HIV drug resistance in a total of 123 individuals recently infected with HIV and aged less than 30 years was implemented in Port Moresby (n = 62) and Mount Hagen (n = 61) during the period May 2013-April 2014. HIV drug resistance testing was performed using dried blood spots. Transmitted HIV drug resistance was defined by the presence of one or more drug resistance mutations as defined by the World Health Organization surveillance drug resistance mutations list. The prevalence of non-nucleoside reverse transcriptase inhibitor transmitted HIV drug resistance was 16.1% (95% CI 8.8%-27.4%) and 8.2% (95% CI 3.2%-18.2%) in Port Moresby and Mount Hagen, respectively. The prevalence of nucleoside reverse transcriptase inhibitor transmitted HIV drug resistance was 3.2% (95% CI 0.2%-11.7%) and 3.3% (95% CI 0.2%-11.8%) in Port Moresby and Mount Hagen, respectively. No protease inhibitor transmitted HIV drug resistance was observed. The level of non-nucleoside reverse transcriptase inhibitor drug resistance in antiretroviral drug naïve individuals recently infected with HIV in Port Moresby is amongst the highest reported globally. This alarming level of transmitted HIV drug resistance in a young sexually active population threatens to limit the on-going effective use of NNRTIs as a component of first-line ART in Papua New Guinea. To support the choice of nationally recommended first-line antiretroviral therapy, representative surveillance of HIV drug resistance among antiretroviral therapy initiators in Papua New Guinea should be urgently implemented.

  8. Nurses stigmatization of sufferers of sexually transmitted diseases ...

    African Journals Online (AJOL)

    This study's objective is to assess nurses' stigmatization of sufferers of sexual transmitted diseases and its implications on treatment options. The study's method was the survey research through structured questionnaire and interview technique for selected sample of students and nurses. The multistage random sampling ...

  9. Prevalence and distribution of avian influenza a(H5N1) virus clade variants in live bird markets of Vietnam, 2011-2013.

    Science.gov (United States)

    Nguyen, Diep T; Bryant, Juliet E; Davis, C Todd; Nguyen, Long V; Pham, Long T; Loth, Leo; Inui, Ken; Nguyen, Tung; Jang, Yunho; To, Thanh L; Nguyen, Tho D; Hoang, Diep T; Do, Hoa T; Nguyen, Trang T; Newman, Scott; Jennifer Siembieda; Pham, Dong V

    2014-12-01

    Active surveillance for avian influenza (Al) viruses in poultry sold at live bird markets (LBMs) was conducted in 44 of 63 provinces throughout Vietnam over two periods from September 2011 to February 2012 and October 2012 to June 2013. The study objectives were to assess the prevalence of avian influenza type A, H5, and H5N1 subtype viruses and characterize the geographical and temporal distribution of H5N1 virus genetic variants across the country. Monthly sampling was conducted in 394 LBMs located in 372 communes. A total of 9790 oropharyngeal swabs from poultry were screened for influenza A virus by real-time reverse-transcriptase PCR Virus isolation was attempted on all positive samples in embryonated chicken eggs, and the HA1 region of each H5 virus isolate was sequenced. Market prevalence of H5 subtype virus was 32.2% (127/394) over the cumulative 15 mo of surveillance. Phylogenetic analyses indicated that clade 1.1 viruses persisted in the south, whereas three genetically distinct subgroups of dade 2.3.2.1 were found simultaneously in northern, central, and southern Vietnam. Clade 2.3.2.1c viruses first appeared in July 2012 and spread rapidly to the center and south of Vietnam in late 2012, where they were predominant among clade 2.3.2.1 viruses and were detected in both active LBM surveillance and poultry outbreaks. Given the overlapping geographic distribution of dade variants and the antigenic divergence previously described for these dades, current AI poultry vaccines used in Vietnam may require bivalent formulations containing representatives of both dade 1.1 and dade 2.3.2.1 viruses.

  10. Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs

    Science.gov (United States)

    Jimenez-Infante, Francy; Ngugi, David Kamanda; Vinu, Manikandan; Alam, Intikhab; Kamau, Allan Anthony; Blom, Jochen; Bajic, Vladimir B.

    2015-01-01

    The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs that play important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields. PMID:26655752

  11. 75 FR 79006 - Submission for OMB Review; Comment Request; Transfusion-Transmitted Retrovirus and Hepatitis...

    Science.gov (United States)

    2010-12-17

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health Submission for OMB Review; Comment Request; Transfusion- Transmitted Retrovirus and Hepatitis Virus Rates and Risk Factors: Improving... control number. Proposed Collection: Title: Transfusion-transmitted retrovirus and hepatitis virus rates...

  12. Two New Mylagaulid Rodents from the Early Miocene of China.

    Directory of Open Access Journals (Sweden)

    Xiaoyu Lu

    Full Text Available Mylagaulid fossorial rodents are a common component of North American Miocene fossil faunas. However outside of North America, only three species are known from Asia. Here we report two new mylagaulids, Irtyshogaulus minor gen. et sp. nov. and Irtyshogaulus major gen. et sp. nov., recovered from early Miocene sediments in the Junggar Basin in northwestern China. The two new taxa are small-sized, high-crowned promylagauline rodents. Their lower molars possess high metastylid crests, small mesostylids, broad and posterolingually expanded labial inflections, and transversely extending metalophid IIs. The mesoconid is absent in both species. The anterior and posterior fossettids are large and equally developed. Their upper M1-2s possess a square occlusal surface with five deep fossettes. The two new taxa are distinguished from each other mainly by their size, the morphology of fossettes and fossettids, development of mesial and distal lophs, posterior reduction of M3, and the orientation of m2 hypolophid. Our phylogenetic analysis indicates that Irtyshogaulus and Lamugaulus (another early Miocene Asian mylagaulid are sister taxa. The two genera are nested among the North American promylagaulines, and share a common ancestor from North America, indicating early Miocene intercontinental dispersal within this clade of rodents.

  13. MIMO Radar Transmit Beampattern Design Without Synthesising the Covariance Matrix

    KAUST Repository

    Ahmed, Sajid

    2013-10-28

    Compared to phased-array, multiple-input multiple-output (MIMO) radars provide more degrees-offreedom (DOF) that can be exploited for improved spatial resolution, better parametric identifiability, lower side-lobe levels at the transmitter/receiver, and design variety of transmit beampatterns. The design of the transmit beampattern generally requires the waveforms to have arbitrary auto- and crosscorrelation properties. The generation of such waveforms is a two step complicated process. In the first step a waveform covariance matrix is synthesised, which is a constrained optimisation problem. In the second step, to realise this covariance matrix actual waveforms are designed, which is also a constrained optimisation problem. Our proposed scheme converts this two step constrained optimisation problem into a one step unconstrained optimisation problem. In the proposed scheme, in contrast to synthesising the covariance matrix for the desired beampattern, nT independent finite-alphabet constantenvelope waveforms are generated and pre-processed, with weight matrix W, before transmitting from the antennas. In this work, two weight matrices are proposed that can be easily optimised for the desired symmetric and non-symmetric beampatterns and guarantee equal average power transmission from each antenna. Simulation results validate our claims.

  14. Trypanosoma janseni n. sp. (Trypanosomatida: Trypanosomatidae isolated from Didelphis aurita (Mammalia: Didelphidae in the Atlantic Rainforest of Rio de Janeiro, Brazil: integrative taxonomy and phylogeography within the Trypanosoma cruzi clade

    Directory of Open Access Journals (Sweden)

    Camila Madeira Tavares Lopes

    Full Text Available BACKGROUND Didelphis spp. are a South American marsupial species that are among the most ancient hosts for the Trypanosoma spp. OBJECTIVES We characterise a new species (Trypanosoma janseni n. sp. isolated from the spleen and liver tissues of Didelphis aurita in the Atlantic Rainforest of Rio de Janeiro, Brazil. METHODS The parasites were isolated and a growth curve was performed in NNN and Schneider's media containing 10% foetal bovine serum. Parasite morphology was evaluated via light microscopy on Giemsa-stained culture smears, as well as scanning and transmission electron microscopy. Molecular taxonomy was based on a partial region (737-bp of the small subunit (18S ribosomal RNA gene and 708 bp of the nuclear marker, glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH genes. Maximum likelihood and Bayesian inference methods were used to perform a species coalescent analysis and to generate individual and concatenated gene trees. Divergence times among species that belong to the T. cruzi clade were also inferred. FINDINGS In vitro growth curves demonstrated a very short log phase, achieving a maximum growth rate at day 3 followed by a sharp decline. Only epimastigote forms were observed under light and scanning microscopy. Transmission electron microscopy analysis showed structures typical to Trypanosoma spp., except one structure that presented as single-membraned, usually grouped in stacks of three or four. Phylogeography analyses confirmed the distinct species status of T. janseni n. sp. within the T. cruzi clade. Trypanosoma janseni n. sp. clusters with T. wauwau in a well-supported clade, which is exclusive and monophyletic. The separation of the South American T. wauwau + T. janseni coincides with the separation of the Southern Super Continent. CONCLUSIONS This clade is a sister group of the trypanosomes found in Australian marsupials and its discovery sheds light on the initial diversification process based on what we currently

  15. [Dutch Institute for Health Care Improvement revised guideline, 'Sexually transmitted diseases and neonatal herpes'

    NARCIS (Netherlands)

    Bleker, O.P.; Meijden, W.I. van der; Wittenberg, J.; Bergen, J.E. van; Boeke, A.J.; Doornum, G.J.J. van; Henquet, C.J.; Galama, J.M.D.; Postma, M.J.; Prins, J.M.; Voorst Vader, P.C. van

    2003-01-01

    The Dutch Institute for Health Care Improvement revised guideline, 'Sexually transmitted diseases and neonatal herpes' summarises the current scientific position on the diagnosis and treatment of a great number of sexually transmitted diseases (STD) and neonatal herpes. Symptomatic treatment of

  16. Transmitted/Founder Viruses Rapidly Escape from CD8+ T Cell Responses in Acute Hepatitis C Virus Infection.

    Science.gov (United States)

    Bull, Rowena A; Leung, Preston; Gaudieri, Silvana; Deshpande, Pooja; Cameron, Barbara; Walker, Melanie; Chopra, Abha; Lloyd, Andrew R; Luciani, Fabio

    2015-05-01

    The interaction between hepatitis C virus (HCV) and cellular immune responses during very early infection is critical for disease outcome. To date, the impact of antigen-specific cellular immune responses on the evolution of the viral population establishing infection and on potential escape has not been studied. Understanding these early host-virus dynamics is important for the development of a preventative vaccine. Three subjects who were followed longitudinally from the detection of viremia preseroconversion until disease outcome were analyzed. The evolution of transmitted/founder (T/F) viruses was undertaken using deep sequencing. CD8(+) T cell responses were measured via enzyme-linked immunosorbent spot (ELISpot) assay using HLA class I-restricted T/F epitopes. T/F viruses were rapidly extinguished in all subjects associated with either viral clearance (n = 1) or replacement with viral variants leading to establishment of chronic infection (n = 2). CD8(+) T cell responses against 11 T/F epitopes were detectable by 33 to 44 days postinfection, and 5 of these epitopes had not previously been reported. These responses declined rapidly in those who became chronically infected and were maintained in the subject who cleared infection. Higher-magnitude CD8(+) T cell responses were associated with rapid development of immune escape variants at a rate of up to 0.1 per day. Rapid escape from CD8(+) T cell responses has been quantified for the first time in the early phase of primary HCV infection. These rapid escape dynamics were associated with higher-magnitude CD8(+) T cell responses. These findings raise questions regarding optimal selection of immunogens for HCV vaccine development and suggest that detailed analysis of individual epitopes may be required. A major limitation in our detailed understanding of the role of immune response in HCV clearance has been the lack of data on very early primary infection when the transmitted viral variants successfully establish

  17. Sexually transmitted infection incidence among adolescents in Ireland.

    LENUS (Irish Health Repository)

    Davoren, Martin P

    2014-10-01

    The burden of sexually transmitted infections (STIs) rests with young people, yet in Ireland there has been very little research into this population. The purpose of this study was to determine the incidence rate and establish risk factors that predict STI occurrence among adolescents in Ireland.

  18. Sexually transmitted infections and mate-finding Allee effects

    Czech Academy of Sciences Publication Activity Database

    Berec, Luděk; Janoušková, E.; Theuer, M.

    2017-01-01

    Roč. 114, APR 01 (2017), s. 59-69 ISSN 0040-5809 Institutional support: RVO:60077344 Keywords : Allee effect * mating * sexually transmitted disease Subject RIV: EH - Ecology, Behaviour OBOR OECD: Ecology Impact factor: 1.613, year: 2016 http://www.sciencedirect.com/science/article/pii/S0040580916301186

  19. Multielement Synthetic Transmit Aperture Imaging Using Temporal Encoding

    DEFF Research Database (Denmark)

    Gammelmark, Kim; Jensen, Jørgen Arendt

    2003-01-01

    A new method to increase the signal-to-noise ratio (SNR) of synthetic transmit aperture imaging is investigated. The approach utilizes multiple elements to emulate a spherical wave, and the conventional short excitation pulse is replaced by a linear frequency-modulated (FM) signal. The approach i...

  20. A 16-channel receive, forced current excitation dual-transmit coil for breast imaging at 7T.

    Directory of Open Access Journals (Sweden)

    Samantha By

    Full Text Available To enable high spatial and temporal breast imaging resolution via combined use of high field MRI, array coils, and forced current excitation (FCE multi channel transmit.A unilateral 16-channel receive array insert was designed for use in a transmit volume coil optimized for quadrature operation with dual-transmit RF shimming at 7 T. Signal-to-noise ratio (SNR maps, g-factor maps, and high spatial and temporal resolution in vivo images were acquired to demonstrate the utility of the coil architecture.The dual-transmit FCE coil provided homogeneous excitation and the array provided an increase in average SNR of 3.3 times (max 10.8, min 1.5 compared to the volume coil in transmit/receive mode. High resolution accelerated in vivo breast imaging demonstrated the ability to achieve isotropic spatial resolution of 0.5 mm within clinically relevant 90 s scan times, as well as the ability to perform 1.0 mm isotropic resolution imaging, 7 s per dynamics, with the use of bidirectional SENSE acceleration of up to R = 9.The FCE design of the transmit coil easily accommodates the addition of a sixteen channel array coil. The improved spatial and temporal resolution provided by the high-field array coil with FCE dual-channel transmit will ultimately be beneficial in lesion detection and characterization.

  1. Early cenozoic differentiation of polar marine faunas.

    Directory of Open Access Journals (Sweden)

    J Alistair Crame

    Full Text Available The widespread assumption that the origin of polar marine faunas is linked to the onset of major global cooling in the Late Eocene-Early Oligocene is being increasingly challenged. The Antarctic fossil record in particular is suggesting that some modern Southern Ocean taxa may have Early Eocene or even Paleocene origins, i.e. well within the Early Cenozoic greenhouse world. A global analysis of one of the largest marine clades at the present day, the Neogastropoda, indicates that not only is there a decrease in the number of species from the tropics to the poles but also a decrease in the evenness of their distribution. A small number of neogastropod families with predominantly generalist trophic strategies at both poles points to the key role of seasonality in structuring the highest latitude marine assemblages. A distinct latitudinal gradient in seasonality is temperature-invariant and would have operated through periods of global warmth such as the Early Cenozoic. To test this concept a second global analysis was undertaken of earliest Cenozoic (Paleocene neogastropods and this does indeed show a certain degree of faunal differentiation at both poles. The Buccinidae, s.l. is especially well developed at this time, and this is a major generalist taxon at the present day. There is an element of asymmetry associated with this development of Paleocene polar faunas in that those in the south are more strongly differentiated than their northern counterparts; this can in turn be linked to the already substantial isolation of the southern high latitudes. The key role of seasonality in the formation of polar marine faunas has implications for contemporary ecosystem structure and stability.

  2. Controlling the transmitted information of a multi-photon interacting with a single-Cooper pair box

    International Nuclear Information System (INIS)

    Kadry, Heba; Abdel-Aty, Abdel-Haleem; Zakaria, Nordin; Cheong, Lee Yen

    2014-01-01

    We study a model of a multi-photon interaction of a single Cooper pair box with a cavity field. The exchange of the information using this system is studied. We quantify the fidelity of the transmitted information. The effect of the system parameters (detuning parameter, field photons, state density and mean photon number) in the fidelity of the transmitted information is investigated. We found that the fidelity of the transmitted information can be controlled using the system parameters

  3. Controlling the transmitted information of a multi-photon interacting with a single-Cooper pair box

    Energy Technology Data Exchange (ETDEWEB)

    Kadry, Heba, E-mail: hkadry1@yahoo.com; Abdel-Aty, Abdel-Haleem, E-mail: hkadry1@yahoo.com; Zakaria, Nordin, E-mail: hkadry1@yahoo.com [Computer and Information Science Department, Universiti Teknologi Petronas, Seri Iskandar, 31750 Tronoh, Perak (Malaysia); Cheong, Lee Yen [Fundamental and Applied Science Department, Universiti Teknologi Petronas, Seri Iskandar, 31750 Tronoh, Perak (Malaysia)

    2014-10-24

    We study a model of a multi-photon interaction of a single Cooper pair box with a cavity field. The exchange of the information using this system is studied. We quantify the fidelity of the transmitted information. The effect of the system parameters (detuning parameter, field photons, state density and mean photon number) in the fidelity of the transmitted information is investigated. We found that the fidelity of the transmitted information can be controlled using the system parameters.

  4. A Study Of Sexually Transmitted Diseases With Application Of Syndromic Approach

    Directory of Open Access Journals (Sweden)

    Choudhury Hasan Hana

    2000-01-01

    Full Text Available The pattern of sexually transmitted diseases in Assam Medical College was studied for a period of one year. The incidence of sexually transmitted diseases was 1.43%. Out of 150 patients the number of patients with genitoulcerative diseases was syphilis 27 (18%, herpes genitalis 26(17.33%, condyloma acuminate 30 (20%, chancroid 11 (7.33%, donovanosis 2(1.33% and LGV 1(0.67%. Patients with urethral or vaginal discharge comprised of gonorrhoea 4(2.67% Vulvovaginitis 14 (9.33%, NGU 12(8.00%, trichomoniasis 2(1.33%, balanoposthitis 17(11.33%.

  5. Knowledge and practices related to sexually transmitted infections ...

    African Journals Online (AJOL)

    Background: Sexually transmitted infections (STIs) still stand as one of the commonest health problems affecting women of reproductive age. The knowledge and .... With the help of local leaders, one of 4 in- terview teams approached ... Ethical clearance to conduct the study was sought from the Makerere University School ...

  6. Comparative Costs of Antibacterial Usage in Sexually Transmitted ...

    African Journals Online (AJOL)

    Erah

    Purpose: To evaluate the cost of antibacterial usage to patients in a tertiary health facility in Nigeria. Methods: Drug utilization evaluation was carried out retrospectively among patients with sexually transmitted infections (STIs) over a one-year period between 2005 and 2006 in Lagos University. Teaching Hospital (LUTH) ...

  7. Switch and examine transmit diversity for spectrum sharing systems

    KAUST Repository

    Abdallah, Mohamed M.; Alouini, Mohamed-Slim; Qaraqe, Khalid A.

    2011-01-01

    In this paper, we develop a switch and examine transmit diversity algorithm for spectrum sharing cognitive networks. We consider a cognitive network composed of a primary link that employs constant rate and constant power transmission scheme

  8. Characterization of Clade 2.3.2.1 H5N1 Highly Pathogenic Avian Influenza Viruses Isolated from Wild Birds (Mandarin Duck and Eurasian Eagle Owl in 2010 in Korea

    Directory of Open Access Journals (Sweden)

    Youn-Jeong Lee

    2013-04-01

    Full Text Available Starting in late November 2010, the H5N1 highly pathogenic avian influenza (HPAI virus was isolated from many types of wild ducks and raptors and was subsequently isolated from poultry in Korea. We assessed the genetic and pathogenic properties of the HPAI viruses isolated from a fecal sample from a mandarin duck and a dead Eurasian eagle owl, the most affected wild bird species during the 2010/2011 HPAI outbreak in Korea. These viruses have similar genetic backgrounds and exhibited the highest genetic similarity with recent Eurasian clade 2.3.2.1 HPAI viruses. In animal inoculation experiments, regardless of their originating hosts, the two Korean isolates produced highly pathogenic characteristics in chickens, ducks and mice without pre-adaptation. These results raise concerns about veterinary and public health. Surveillance of wild birds could provide a good early warning signal for possible HPAI infection in poultry as well as in humans.

  9. Pair formation models for sexually transmitted infections : A primer

    NARCIS (Netherlands)

    Kretzschmar, MEE; Heijne, Janneke C M

    For modelling sexually transmitted infections, duration of partnerships can strongly influence the transmission dynamics of the infection. If partnerships are monogamous, pairs of susceptible individuals are protected from becoming infected, while pairs of infected individuals delay onward

  10. ABO, rhesus blood groups and transfusion-transmitted infections ...

    African Journals Online (AJOL)

    Background: Few studies focused on the study of blood groups in Gabon. This study aimed to determine the phenotypic frequency of ABO and Rhesus antigens in blood donors of Libreville and to assess the association between ABO blood groups and transfusion-transmitted infections. Materials and Methods: The study of ...

  11. The initial antibody response to HIV-1: induction of ineffective early B cell responses against GP41 by the transmitted/founder virus

    Energy Technology Data Exchange (ETDEWEB)

    Chavez, Leslie L [Los Alamos National Laboratory; Perelson, Alan [Los Alamos National Laboratory

    2008-01-01

    A window of opportunity for immune responses to extinguish HIV -1 exists from the moment of transmission through establishment of the latent pool of HIV -I-infected cells. A critical time to study the initial immune responses to the transmitted/founder virus is the eclipse phase of HIV-1 infection (time from transmission to the first appearance of plasma virus) but, to date, this period has been logistically difficult to analyze. Studies in non-human primates challenged with chimeric simianhuman immunodeficiency virus have shown that neutralizing antibodies, when present at the time of infection, can prevent virus infection.

  12. A non-persistently transmitted-virus induces a pull-push strategy in its aphid vector to optimize transmission and spread.

    Science.gov (United States)

    Carmo-Sousa, Michele; Moreno, Aranzazu; Garzo, Elisa; Fereres, Alberto

    2014-06-24

    Plant viruses are known to modify the behaviour of their insect vectors, both directly and indirectly, generally adapting to each type of virus-vector relationship in a way that enhances transmission efficiency. Here, we report results of three different studies showing how a virus transmitted in a non-persistent (NP) manner (Cucumber mosaic virus; CMV, Cucumovirus) can induce changes in its host plant, cucumber (Cucumis sativus cv. Marumba) that modifies the behaviour of its aphid vector (Aphis gossypii Glover; Hemiptera: Aphididae) in a way that enhances virus transmission and spread non-viruliferous aphids changed their alighting, settling and probing behaviour activities over time when exposed to CMV-infected and mock-inoculated cucumber plants. Aphids exhibited no preference to migrate from CMV-infected to mock-inoculated plants at short time intervals (1, 10 and 30 min after release), but showed a clear shift in preference to migrate from CMV-infected to mock-inoculated plants 60 min after release. Our free-choice preference assays showed that A. gossypii alates preferred CMV-infected over mock-inoculated plants at an early stage (30 min), but this behaviour was reverted at a later stage and aphids preferred to settle and reproduce on mock-inoculated plants. The electrical penetration graph (EPG) technique revealed a sharp change in aphid probing behaviour over time when exposed to CMV-infected plants. At the beginning (first 15 min) aphid vectors dramatically increased the number of short superficial probes and intracellular punctures when exposed to CMV-infected plants. At a later stage (second hour of recording) aphids diminished their feeding on CMV-infected plants as indicated by much less time spent in phloem salivation and ingestion (E1 and E2). This particular probing behaviour including an early increase in the number of short superficial probes and intracellular punctures followed by a phloem feeding deterrence is known to enhance the transmission

  13. Open cup nests evolved from roofed nests in the early passerines.

    Science.gov (United States)

    Price, J Jordan; Griffith, Simon C

    2017-02-08

    The architectural diversity of nests in the passerine birds (order Passeriformes) is thought to have played an important role in the adaptive radiation of this group, which now comprises more than half of avian species and occupies nearly all terrestrial ecosystems. Here, we present an extensive survey and ancestral state reconstruction of nest design across the passerines, focusing on early Australian lineages and including members of nearly all passerine families worldwide. Most passerines build open cup-shaped nests, whereas a minority build more elaborate domed structures with roofs. We provide strong evidence that, despite their relative rarity today, domed nests were constructed by the common ancestor of all modern passerines. Open cup nests evolved from enclosed domes at least four times independently during early passerine evolution, at least three of which occurred on the Australian continent, yielding several primarily cup-nesting clades that are now widespread and numerically dominant among passerines. Our results show that the ubiquitous and relatively simple cup-shaped nests of many birds today evolved multiple times convergently, suggesting adaptive benefits over earlier roofed designs. © 2017 The Author(s).

  14. High-voltage integrated transmitting circuit with differential driving for CMUTs

    DEFF Research Database (Denmark)

    Llimos Muntal, Pere; Larsen, Dennis Øland; Færch, Kjartan Ullitz

    2016-01-01

    In this paper, a high-voltage integrated differential transmitting circuit for capacitive micromachined ultrasonic transducers (CMUTs) used in portable ultrasound scanners is presented. Due to its application, area and power consumption are critical and need to be minimized. The circuitry...... is designed and implemented in AMS 0.35 μ m high-voltage process. Measurements are performed on the fabricated integrated circuit in order to assess its performance. The transmitting circuit consists of a low-voltage control logic, pulse-triggered level shifters and a differential output stage that generates...... conditions is 0.936 mW including the load. The integrated circuits measured prove to be consistent and robust to local process variations by measurements....

  15. Interaction of the tick immune system with transmitted pathogens

    Directory of Open Access Journals (Sweden)

    Ondrej eHajdusek

    2013-07-01

    Full Text Available Ticks are hematophagous arachnids transmitting a wide variety of pathogens including viruses, bacteria, and protozoans to their vertebrate hosts. The tick vector competence has to be intimately linked to the ability of transmitted pathogens to evade tick defense mechanisms encountered on their route through the tick body comprising midgut, hemolymph, salivary glands or ovaries. Tick innate immunity is, like in other invertebrates, based on an orchestrated action of humoral and cellular immune responses. The direct antimicrobial defense in ticks is accomplished by a variety of small molecules such as defensins, lysozymes or by tick-specific antimicrobial compounds such as microplusin/hebraein or 5.3-kDa family proteins. Phagocytosis of the invading microbes by tick hemocytes seems to be mediated by the primordial complement-like system composed of thioester-containing proteins, fibrinogen-related lectins and convertase-like factors. Moreover, an important role in survival of the ingested microbes seems to be played by host proteins and redox balance maintenance in the tick midgut. Here, we summarize recent knowledge about the major components of tick immune system and focus on their interaction with the relevant tick-transmitted pathogens, represented by spirochetes (Borrelia, rickettsiae (Anaplasma, and protozoans (Babesia. Availability of the tick genomic database and feasibility of functional genomics based on RNA interference greatly contribute to the understanding of molecular and cellular interplay at the tick-pathogen interface and may provide new targets for blocking the transmission of tick pathogens.

  16. A genetic polymorphism evolving in parallel in two cell compartments and in two clades

    Directory of Open Access Journals (Sweden)

    Watt Ward B

    2013-01-01

    Full Text Available Abstract Background The enzyme phosphoenolpyruvate carboxykinase, PEPCK, occurs in its guanosine-nucleotide-using form in animals and a few prokaryotes. We study its natural genetic variation in Colias (Lepidoptera, Pieridae. PEPCK offers a route, alternative to pyruvate kinase, for carbon skeletons to move between cytosolic glycolysis and mitochondrial Krebs cycle reactions. Results PEPCK is expressed in both cytosol and mitochondrion, but differently in diverse animal clades. In vertebrates and independently in Drosophila, compartment-specific paralogous genes occur. In a contrasting expression strategy, compartment-specific PEPCKs of Colias and of the silkmoth, Bombyx, differ only in their first, 5′, exons; these are alternatively spliced onto a common series of following exons. In two Colias species from distinct clades, PEPCK sequence is highly variable at nonsynonymous and synonymous sites, mainly in its common exons. Three major amino acid polymorphisms, Gly 335 ↔ Ser, Asp 503 ↔ Glu, and Ile 629 ↔ Val occur in both species, and in the first two cases are similar in frequency between species. Homology-based structural modelling shows that the variants can alter hydrogen bonding, salt bridging, or van der Waals interactions of amino acid side chains, locally or at one another′s sites which are distant in PEPCK′s structure, and thus may affect its enzyme function. We ask, using coalescent simulations, if these polymorphisms′ cross-species similarities are compatible with neutral evolution by genetic drift, but find the probability of this null hypothesis is 0.001 ≤ P ≤ 0.006 under differing scenarios. Conclusion Our results make the null hypothesis of neutrality of these PEPCK polymorphisms quite unlikely, but support an alternative hypothesis that they are maintained by natural selection in parallel in the two species. This alternative can now be justifiably tested further via studies of PEPCK genotypes′ effects

  17. Sexually transmitted infections: prevalence, knowledge and treatment practices among female sex workers in a cosmopolitan city in Nigeria.

    Science.gov (United States)

    Sekoni, Adekemi O; Odukoya, Oluwakemi O; Onajole, Adebayo T; Odeyemi, Kofoworola A

    2013-03-01

    Sexually transmitted infections constitute economic burden for developing countries, exposure to causative agents is an occupational hazard for female sex workers. Targeted interventions for this population can reduce the incidence and prevalence of sexually transmitted infections including human immunodeficiency virus, but barriers exists which can hinder effective implementation of such programs. This descriptive cross sectional study sought to assess the prevalence, knowledge and treatment practices of sexually transmitted infections among brothel based female sex workers. Three hundred and twenty three consenting female sex workers were surveyed using pre tested, interviewer administered questionnaires. More than half of the respondents (54.2%) had poor knowledge of symptoms of sexually transmitted infections. Only 13.9% were aware that sexually transmitted infections could be asymptomatic. The self reported prevalence of symptomatic sexually transmitted infections was 36.5%. About half of those with sexually transmitted infectionss sought treatment in a hospital or health centre while 32.5% from a patent medicine vendor. Most respondents (53.8%) mentioned the perceived quality of care as the main reason for seeking treatment in their chosen place. More of the respondents with good knowledge of sexually transmitted infections reported symptoms compared to those with fair and poor knowledge. The knowledge of sexually transmitted infections among these female sex workers is poor and the prevalence is relatively high. Efforts to improve knowledge promote and encourage preventive as well as effective treatment practices must be made for this population.

  18. Speaking American: Comparing Supreme Court and Hollywood Racial Interpretation in the Early Twenty-First Century

    Science.gov (United States)

    Hawkins, Paul Henry

    2010-01-01

    Apprehending that race is social, not biological, this study examines U.S. racial formation in the early twenty-first century. In particular, Hollywood and Supreme Court texts are analyzed as media for gathering, shaping and transmitting racial ideas. Representing Hollywood, the 2004 film "Crash" is analyzed. Representing the Supreme Court, the…

  19. Deep divergences and extensive phylogeographic structure in a clade of lowland tropical salamanders

    Directory of Open Access Journals (Sweden)

    Rovito Sean M

    2012-12-01

    Full Text Available Abstract Background The complex geological history of Mesoamerica provides the opportunity to study the impact of multiple biogeographic barriers on population differentiation. We examine phylogeographic patterns in a clade of lowland salamanders (Bolitoglossa subgenus Nanotriton using two mitochondrial genes and one nuclear gene. We use several phylogeographic analyses to infer the history of this clade and test hypotheses regarding the geographic origin of species and location of genetic breaks within species. We compare our results to those for other taxa to determine if historical events impacted different species in a similar manner. Results Deep genetic divergence between species indicates that they are relatively old, and two of the three widespread species show strong phylogeographic structure. Comparison of mtDNA and nuclear gene trees shows no evidence of hybridization or introgression between species. Isolated populations of Bolitoglossa rufescens from Los Tuxtlas region constitute a separate lineage based on molecular data and morphology, and divergence between Los Tuxtlas and other areas appears to predate the arrival of B. rufescens in other areas west of the Isthmus of Tehuantepec. The Isthmus appears responsible for Pliocene vicariance within B. rufescens, as has been shown for other taxa. The Motagua-Polochic fault system does not appear to have caused population vicariance, unlike in other systems. Conclusions Species of Nanotriton have responded to some major geological events in the same manner as other taxa, particularly in the case of the Isthmus of Tehuantepec. The deep divergence of the Los Tuxtlas populations of B. rufescens from other populations highlights the contribution of this volcanic system to patterns of regional endemism, and morphological differences observed in the Los Tuxtlas populations suggests that they may represent an undescribed species of Bolitoglossa. The absence of phylogeographic structure in B

  20. Mechanical transport and dissemination of soil-transmitted helminth ...

    African Journals Online (AJOL)

    In previous studies, helminth eggs were isolated from wild-caught Musca domestica L. (Diptera: Muscidae). This laboratory study investigated the potential of the fly for mechanical transport and transmission of soil-transmitted helminths. Naïve, 2-3 day old, laboratory-reared adult flies were exposed to a mixture of Ascaris ...

  1. Recreational Drug Use During Sex and Sexually Transmitted Infections Among Clients of a City Sexually Transmitted Infections Clinic in Amsterdam, The Netherlands

    NARCIS (Netherlands)

    Heiligenberg, Marlies; Wermeling, Paulien R.; van Rooijen, Martijn S.; Urbanus, Anouk T.; Speksnijder, Arjen G. C. L.; Heijman, Titia; Prins, Maria; Coutinho, Roel A.; Schim van der Loeff, Maarten F.

    2012-01-01

    Background: Recreational drug use is associated with high-risk sexual behavior and sexually transmitted infections (STIs). We assessed the prevalence of drug use during sex and the associations between such use and STI (chlamydia, gonorrhea, or syphilis). Methods: During 3 periods in 2008 and 2009,

  2. Tuber aztecorum sp. nov., a truffle species from Mexico belonging to the Maculatum clade (Tuberaceae, Pezizales

    Directory of Open Access Journals (Sweden)

    Gonzalo Guevara-Guerrero

    2018-02-01

    Full Text Available A new species of truffle, T. aztecorum, is described from central Mexico. Tuber aztecorum can be distinguished from other related Tuber species synoptically by a combination of morphological features including ascospore size, pellis cells with irregular thickness, cystidia, ascoma colour and associated host (Abies religiosa an endemic Abies species from central Mexico; sequence variation on the ITS rDNA also distinguishes T. aztecorum from related species. A phylogenetic analysis of the ITS rDNA demonstrates that T. aztecorum belongs to the Maculatum clade and is unique from other similar small, white-cream coloured Tuber species distributed in north-eastern Mexico such as T. castilloi and T. guevarai.

  3. Preliminary In-vivo Results For Spatially Coded Synthetic Transmit Aperture Ultrasound Based On Frequency Division

    DEFF Research Database (Denmark)

    Gran, Fredrik; Hansen, Kristoffer Lindskov; Jensen, Jørgen Arendt

    2006-01-01

    This paper investigates the possibility of using spatial coding based on frequency division for in-vivo synthetic transmit aperture (STA) ultrasound imaging. When using spatial encoding for STA, it is possible to use several transmitters simultaneously and separate the signals at the receiver....... This increases the maximum transmit power compared to conventional STA, where only one transmitter can be active. The signal-to-noise-ratio can therefore he increased and better penetration can be obtained. For frequency division, the coding is achieved by designing a number of transmit waveforms with disjoint...... spectral support, spanning the passband of the ultrasound transducer. The signals can therefore he separated at the receiver using matched filtering. The method is tested using a commercial linear array transducer with a center frequency of 9 MHz and 68% fractional bandwidth. In this paper, the transmit...

  4. Evaluation of the NucliSens EasyQ v2.0 assay in comparison with the Roche Amplicor v1.5 and the Roche CAP/CTM HIV-1 Test v2.0 in quantification of C-clade HIV-1 in plasma.

    Directory of Open Access Journals (Sweden)

    Maximilian Muenchhoff

    Full Text Available Human immunodeficiency virus type 1 (HIV-1 genetic diversity poses a challenge to reliable viral load monitoring. Discrepancies between different testing platforms have been observed, especially for non-clade-B virus. Therefore we compare, in antiretroviral therapy (ART-naïve South African subjects predominantly infected with HIV-1 clade-C, three commercially available assays: the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test version 2.0 by Roche (CAP/CTM v2.0, the BioMérieux NucliSens Version 2.0 Easy Q/Easy Mag (NucliSens v2.0 and the Roche COBAS Amplicor HIV-1 Monitor Test Version 1.5 (Amplicor v1.5. Strong linear correlation was observed and Bland-Altman analyses showed overall good agreement between the assays with mean viral load differences of 0.078 log cp/ml (NucliSens v2.0 - Amplicor v1.5, 0.260 log cp/ml (CAP/CTM v2.0 - Amplicor v1.5 and 0.164 log cp/ml (CAP/CTM v2.0 - NucliSens v2.0, indicating lower mean viral load results for the Amplicor v1.5 and higher mean readings for the CAP/CTM v2.0. Consistent with observations following previous comparisons of CAP/CTM v2.0 versus Amplicor v1.5, the CAP/CTM v2.0 assay detected low-level viremia (median 65 cp/ml in more than one-third of those in whom viremia had been undetectable (<20 cp/ml in assays using the NucliSens platform. These levels of viremia are of uncertain clinical significance but may be of importance in early detection of ART resistance in those on treatment. Overall the three assays showed good comparability of results but with consistent, albeit relatively small, discrepancies for HIV-1 clade-C samples, especially in the low-viremic range that should be taken into account when interpreting viral load data.

  5. partner notification in the management of sexually transmitted

    African Journals Online (AJOL)

    hi-tech

    2003-12-12

    Dec 12, 2003 ... Objective: To assess utilization of partner notification as a tool in prevention and control of Sexually transmitted ... being out of town (44.6%) fear of quarrels and violence from partners (32.5%) and ..... More than half of the men in this study reported ... patients give reasons that justify their actions. Such.

  6. A New Resource for STD Clinical Providers: The Sexually Transmitted Diseases Clinical Consultation Network.

    Science.gov (United States)

    Caragol, Laura A; Wendel, Karen A; Anderson, Teri S; Burnside, Helen C; Finkenbinder, Allison; Fitch, John D; Kelley, Destiny H; Stewart, Terry W; Thrun, Mark; Rietmeijer, Cornelis A

    2017-08-01

    An online consultation tool, the Sexually Transmitted Diseases Clinical Consultation Network is a new resource for sexually transmitted disease clinicians and clinic managers. An initial evaluation shows that most requests (29%) were from medical doctors, followed by nurse practitioners (22%). Syphilis queries comprised 39% of consults followed by gonorrhea (12%) and chlamydia (11%).

  7. Soil-transmitted Helminthiasis in the United States: a systematic review--1940-2010.

    Science.gov (United States)

    Starr, Michelle C; Montgomery, Susan P

    2011-10-01

    The epidemiology of soil-transmitted helminth infections (hookworm, Trichuris trichiura, Ascaris lumbricoides, and Strongyloides stercoralis) in the United States is poorly understood. To gain understanding of the status of disease, a systematic review was performed to assess the prevalence of soil-transmitted helminth infections in the United States. Of all studies reviewed, 14 were designated as high-quality. High-quality studies were published from 1942 to 1982 and showed that infection was prevalent throughout the southern United States and Appalachia as recently as 1982, finding that hookworm (19.6%), T. trichiura (55.2%), A. lumbricoides (49.4%), and S. stercoralis (3.8%) affected significant percentages of the population. However, because the most recent high-quality studies were published over 25 years ago, the literature does not provide sufficient data to assess current endemic transmission. Because the status of disease remains unclear, there is a need for additional studies to determine if soil-transmitted helminths remain endemic in the United States.

  8. An unexpected clade of South American ground beetles (Coleoptera, Carabidae, Bembidion).

    Science.gov (United States)

    Maddison, David R

    2014-01-01

    Phylogenetic relationships of the Antiperyphanes Complex of the genus Bembidion are inferred using DNA sequences from seven genes (two nuclear ribosomal, four nuclear protein coding, and one mitochondrial protein coding). Redefined subgenera within the complex are each well-supported as monophyletic. Most striking was the discovery that a small set of morphologically and ecologically heterogeneous species formed a clade, here called subgenus Nothonepha. This unexpected result was corroborated by the discovery of deep pits in the lateral body wall (in the mesepisternum) of all Nothonepha, a trait unique within Bembidion. These pits are filled with a waxy substance in ethanol-preserved specimens. In one newly discovered species (Bembidion tetrapholeon sp. n., described here), these pits are so deep that their projections into the body cavity from the two sides touch each other internally. These structures in Bembidion (Nothonepha) are compared to very similar mesepisternal pits which have convergently evolved in two other groups of carabid beetles. The function of these thoracic pits is unknown. Most members of subgenus Nothonepha have in addition similar but smaller pits in the abdomen. A revised classification is proposed for the Antiperyphanes Complex.

  9. An unexpected clade of South American ground beetles (Coleoptera, Carabidae, Bembidion

    Directory of Open Access Journals (Sweden)

    David Maddison

    2014-06-01

    Full Text Available Phylogenetic relationships of the Antiperyphanes Complex of the genus Bembidion are inferred using DNA sequences from seven genes (two nuclear ribosomal, four nuclear protein coding, and one mitochondrial protein coding. Redefined subgenera within the complex are each well-supported as monophyletic. Most striking was the discovery that a small set of morphologically and ecologically heterogeneous species formed a clade, here called subgenus Nothonepha. This unexpected result was corroborated by the discovery of deep pits in the lateral body wall (in the mesepisternum of all Nothonepha, a trait unique within Bembidion. These pits are filled with a waxy substance in ethanol-preserved specimens. In one newly discovered species (Bembidion tetrapholeon sp. n., described here, these pits are so deep that their projections into the body cavity from the two sides touch each other internally. These structures in Bembidion (Nothonepha are compared to very similar mesepisternal pits which have convergently evolved in two other groups of carabid beetles. The function of these thoracic pits is unknown. Most members of subgenus Nothonepha have in addition similar but smaller pits in the abdomen. A revised classification is proposed for the Antiperyphanes Complex.

  10. [Diseases transmitted through water for human consumption].

    Science.gov (United States)

    Franco, E; Dentamaro, M

    2003-01-01

    The water for human consumption maintains a biological risk and can transmit diseases. The classical waterborne and the presently frequent diseases caused by protozoi Giardia and Cryptosporidium are considered and Arcobacter butzleri, a new waterborne pathogen, is described. Many measures have been adopted by institutions to ensure the quality of the drinking water. Managers and public health operators is working in order to verify the efficiency of more suitable indicators for its monitoring.

  11. Prevalence of Sexually Transmitted Infection in Teenage Pregnancy in Rajavithi Hospital, Thailand.

    Science.gov (United States)

    Asavapiriyanont, Suvanna; Chaovarindr, Udom; Kaoien, Surasak; Chotigeat, Uraiwan; Kovavisarach, Ekachai

    2016-02-01

    Behavioral and social changes in the modern era have triggered an increase in the incidence of early sexual contact and teenage pregnancy. Since there is no routine Gonococcal & Chlamydial (GC & CT) screening in teens in antenatal clinics in Thailand, the present study was performed to find the prevalence of STI, especially Chlamydial infection, in teenage pregnancy. To evaluate the prevalence of sexually transmitted infections (STIs), especially Chlamydial infection (CT), in teenage pregnancy and its related factors. One hundred and twenty-one teenage pregnancies were recruited at the ANC in Rajavithi Hospital from October 2006 to May 2007. After signing informed consent forms, they were asked to answer questionnaires about baseline data, sexual information and risk factors, after which urine specimens were collected for screening for GC and CT using the PCR technique (AMPLICOR by Roche). Later, pelvic examination was per formed by the gynecologist at the STD (sexually transmitted disease) clinic. All the data and LAB results were recorded and analyzed by the SPSS program. Numbers, percentages, means with SD, Chi-squared test, Fisher's exact test and odds ratio were used. Potential risk factors were analyzed using binary logistic regression. The prevalence of STI in pregnant teenagers was 28.1% (CT = 19.8%, GC = 1.7%, hepatitis B = 3.3%, trichomoniasis 1.7%, Herpes simplex = 0.8% and condyloma acuminata = 0.8%). No Syphilis, chancroid or HIV were found in the present study Other non-STI like candidiasis and bacterial vaginosis were found in 45.5% of participants (candidiasis and bacterial vaginosis at 19.0% and 24.8%, respectively). The risk of CT infection was significantly related (6.9 times higher) to having previous sexual contact before the current partner (95% CI, 1.8-27.0). STI, especially Chlamydial infection, was found in a significant number of teenage pregnancies. Measures should be taken to prevent this resulting in complicated outcomes in the future.

  12. Simplified methods for estimating gamma exposure fields transmitted through straight rectangular ducts

    International Nuclear Information System (INIS)

    Shultis, J.K.; Thompson, K.R.; Faw, R.E.

    1986-01-01

    Approximate computational models are developed to describe the spatial variation in the radiation field transmitted through a straight reactangular duct obliquely illuminated by monoenergetic gamma photons. These models account for single and multiple scattering from the duct walls and lips as well as for direct penetration by the photons. Results of calculations are compared to results from a recent benchmark duct streaming experiment, and empirical correction factors are obtained which enable the models to predict the transmitted exposure rates to within 20% of the experimental values

  13. Maryland Alcohol Sales Tax and Sexually Transmitted Infections: A Natural Experiment.

    Science.gov (United States)

    Staras, Stephanie A S; Livingston, Melvin D; Wagenaar, Alexander C

    2016-03-01

    Sexually transmitted infections are common causes of morbidity and mortality, including infertility and certain types of cancer. Alcohol tax increases may decrease sexually transmitted infection rates overall and differentially across population subgroups by decreasing alcohol consumption in general and prior to sex, thus decreasing sexual risk taking and sexually transmitted infection acquisition. This study investigated the effects of a Maryland increase in alcohol beverage sales tax on statewide gonorrhea and chlamydia rates overall and within age, gender, and race/ethnicity subpopulations. This study used an interrupted time series design, including multiple cross-state comparisons, to examine the effects of the 2011 alcohol tax increase in Maryland on chlamydia and gonorrhea cases reported to the U.S. National Notifiable Disease Surveillance System for January 2003 to December 2012 (N=120 repeated monthly observations, analyzed in 2015). Effects were assessed with Box-Jenkins autoregressive moving average models with structural parameters. After the alcohol-specific sales tax increase, gonorrhea rates decreased 24% (95% CI=11%, 37%), resulting in 1,600 fewer statewide gonorrhea cases annually. Cohen's d indicated a substantial effect of the tax increase on gonorrhea rates (range across control group models, -1.25 to -1.42). The study did not find evidence of an effect on chlamydia or differential effects across age, race/ethnicity, or gender subgroups. Results strengthen the evidence from prior studies of alcohol taxes influencing gonorrhea rates and extend health prevention effects from alcohol excise to sales taxes. Alcohol tax increases may be an efficient strategy for reducing sexually transmitted infections. Copyright © 2016 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

  14. High rate of teenage pregnancy and sexually transmitted infections ...

    African Journals Online (AJOL)

    There is increased in teenage pregnancy despite the presence of dual protection practice and health care awareness programmes related to health and sexuality education in South Africa. The present study explores the underlying causes of high teenage pregnancy and sexually transmitted diseases rates, including HIV ...

  15. AN EARLY JURASSIC SAUROPOD TOOTH FROM PATAGONIA (CAÑADÓN ASFALTO FORMATION: IMPLICATIONS FOR SAUROPOD DIVERSITY

    Directory of Open Access Journals (Sweden)

    Carballido, José L

    2017-12-01

    Full Text Available Eusauropods were a group of herbivorous dinosaurs that evolved during the Early Jurassic and dominated the terrestrial ecosystems throughout the Jurassic and Cretaceous. A peak of diversity is represented by the Late Jurassic, when most of the lineages of the derived clade, Neosauropoda, are represented. Different lineages of eusauropods differ in several morphological aspects, including a great diversity in gathering strategies, inferred by their dentition morphology and wear facets. Here we describe a new tooth morphotype that can be well differentiated from any other tooth recovered from the Cañadón Asfalto Formation (Lower Jurassic-Middle-Jurassic. Therefore this new tooth morphology increase the evidence of a high diversity of sauropods during that time as well as providing evidence of advanced characters in the dentition of some Early Jurassic sauropods (e.g., subcylindrical and narrow crowns with single apical wear facet.

  16. Population genetic structure of the major malaria vector Anopheles funestus s.s. and allied species in southern Africa

    Directory of Open Access Journals (Sweden)

    Choi Kwang Shik

    2012-12-01

    Full Text Available Abstract Background Anopheles funestus s.s., one of the major malaria vectors in sub-Saharan Africa, belongs to a group of eleven African species that are morphologically similar at the adult stage, most of which do not transmit malaria. The population structure of An. funestus based on mitochondrial DNA data led to the description of two cryptic subdivisions, clade I widespread throughout Africa and clade II known only from Mozambique and Madagascar. In this study, we investigated five common members of the Anopheles funestus group in southern Africa in order to determine relationships within and between species. Methods A total of 155 specimens of An. funestus, An. parensis, An. vaneedeni, An. funestus-like and An. rivulorum from South Africa, Mozambique and Malawi were used for the study. The population genetic structure was assessed within and between populations using mitochondrial DNA. Results The phylogenetic trees revealed three main lineages: 1 An. rivulorum; 2 An. funestus-like clade I and An. parensis clade II; and 3 An. funestus clades I and II, An. funestus-like clade II, An. parensis clade I and An. vaneedeni clades I and II. Within An. funestus, 32 specimens from Mozambique consisted of 40.6% clade I and 59.4% clade II while all 21 individuals from Malawi were clade I. In the analysis of mitochondrial DNA sequences, there were 37 polymorphic sites and 9 fixed different nucleotides for ND5 and 21 polymorphic sites and 6 fixed different nucleotides for COI between the two An. funestus clades. The results for COI supported the ND5 analysis. Conclusion This is the first report comparing An. funestus group species including An. funestus clades I and II and the new species An. funestus-like. Anopheles funestus clade I is separated from the rest of the members of the An. funestus subgroup and An. funestus-like is distinctly distributed from the other species in this study. However, there were two clades for An. funestus-like, An

  17. Sexually transmitted diseases: educational intervention among teenagers in a technical-professional teaching center

    Directory of Open Access Journals (Sweden)

    Roberto Dair García de la Rosa

    2014-02-01

    Full Text Available Introduction. Sexually transmitted diseases are among the leading health problems of humankind. They are highly prevalent diseases that cause distress, disability and significant severe complications. These infections do not have high mortality rates in general, with the exception of Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome, and Hepatitis B that cause a significant number of deaths. Objective. To improve the level of knowledge about sexually transmitted diseases among a group of teenagers of Bernabé Boza Technical School, county of Camagüey, and assess the effectiveness of the intervention. Methods. Knowledge assessments were conducted before and after the intervention in Bernabé Boza Technical School between January and June 2012. The sample universe was 120 students who comprised the complete second year enrollment. Results. There was a predominance of female sixteen-year-old teenagers. The knowledge level about features of sexually transmitted diseases increased significantly after the intervention among the teenagers in the study (71.7% versus 95.8% p<0.0001, route of infection (74.2% versus 100% p<0.0001, and prevention (20% versus 91.7% p<0.0001. Conclusion. The educational intervention increased significantly the level of knowledge about sexually transmitted diseases among the teenagers, Thus, this is an important educational tool in this age group.

  18. Modeling the transmitted and stored energy in multilayer protective clothing under low-level radiant exposure

    International Nuclear Information System (INIS)

    Su, Yun; He, Jiazhen; Li, Jun

    2016-01-01

    Highlights: • A numerical model from heating source to skin tissues through multilayer fabric system is developed. • The numerical model is comprehensively validated with experimental data. • The model is used to investigate the relationship between the transmitted and stored energy and the influencing factors. - Abstract: A finite difference model was introduced to simulate the transmitted and stored energy in firefighters' protective clothing exposed to low-level thermal radiation. The model domain consists of a three-layer fire-resistant fabric system (outer shell, moisture barrier, and thermal liner), the human skin, and the air gap between clothing and the skin. The model accounted for the relationship between the transmitted heat during the exposure and the discharged heat during the cooling-down period. The numerical model predictions were compared with experimental data. Additionally, the parameters that affect the transmitted and stored energy of protective clothing were investigated. The results demonstrate that for the typical multilayer firefighter protective clothing, the transmitted heat during exposure and the discharged heat after exposure totally determine the skin burn under low-level heat exposure, especially for third-degree skin burns. The findings obtained in this study can be used to engineer fabric systems that provide better protection for the stored thermal burn.

  19. Elevated Extinction Rates as a Trigger for Diversification Rate Shifts: Early Amniotes as a Case Study

    Science.gov (United States)

    Brocklehurst, Neil; Ruta, Marcello; Müller, Johannes; Fröbisch, Jörg

    2015-01-01

    Tree shape analyses are frequently used to infer the location of shifts in diversification rate within the Tree of Life. Many studies have supported a causal relationship between shifts and temporally coincident events such as the evolution of “key innovations”. However, the evidence for such relationships is circumstantial. We investigated patterns of diversification during the early evolution of Amniota from the Carboniferous to the Triassic, subjecting a new supertree to analyses of tree balance in order to infer the timing and location of diversification shifts. We investigated how uneven origination and extinction rates drive diversification shifts, and use two case studies (herbivory and an aquatic lifestyle) to examine whether shifts tend to be contemporaneous with evolutionary novelties. Shifts within amniotes tend to occur during periods of elevated extinction, with mass extinctions coinciding with numerous and larger shifts. Diversification shifts occurring in clades that possess evolutionary innovations do not coincide temporally with the appearance of those innovations, but are instead deferred to periods of high extinction rate. We suggest such innovations did not cause increases in the rate of cladogenesis, but allowed clades to survive extinction events. We highlight the importance of examining general patterns of diversification before interpreting specific shifts. PMID:26592209

  20. Flying lemurs – The 'flying tree shrews'? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade

    Directory of Open Access Journals (Sweden)

    Volobouev Vitaly

    2008-05-01

    Full Text Available Abstract Background Flying lemurs or Colugos (order Dermoptera represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires, the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous. Results To search for cytogenetic signatures that could help to clarify the evolutionary affinities within this superordinal group, we have established a genome-wide comparative map between human and the Malayan flying lemur (Galeopterus variegatus by reciprocal chromosome painting using both human and G. variegatus chromosome-specific probes. The 22 human autosomal paints and the X chromosome paint defined 44 homologous segments in the G. variegatus genome. A putative inversion on GVA 11 was revealed by the hybridization patterns of human chromosome probes 16 and 19. Fifteen associations of human chromosome segments (HSA were detected in the G. variegatus genome: HSA1/3, 1/10, 2/21, 3/21, 4/8, 4/18, 7/15, 7/16, 7/19, 10/16, 12/22 (twice, 14/15, 16/19 (twice. Reverse painting of G. variegatus chromosome-specific paints onto human chromosomes confirmed the above results, and defined the origin of the homologous human chromosomal segments in these associations. In total, G. variegatus paints revealed 49 homologous chromosomal segments in the HSA genome. Conclusion Comparative analysis of our map with published maps from representative species of other placental orders, including Scandentia, Primates, Lagomorpha and Rodentia, suggests a signature rearrangement (HSA2q/21 association that links Scandentia and Dermoptera to one sister clade. Our results thus provide new evidence for the hypothesis that Scandentia and Dermoptera have a closer phylogenetic relationship to each other than either of them has to Primates.

  1. Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2 clade.

    Science.gov (United States)

    Schreiber, Lars; Holler, Thomas; Knittel, Katrin; Meyerdierks, Anke; Amann, Rudolf

    2010-08-01

    The anaerobic oxidation of methane (AOM) with sulfate as terminal electron acceptor is mediated by consortia of methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). Whereas three clades of ANME have been repeatedly studied with respect to phylogeny, key genes and genomic capabilities, little is known about their sulfate-reducing partner. In order to identify the partner of anaerobic methanotrophs of the ANME-2 clade, bacterial 16S rRNA gene libraries were constructed from cultures highly enriched for ANME-2a and ANME-2c in consortia with Deltaproteobacteria of the Desulfosarcina/Desulfococcus group (DSS). Phylogenetic analysis of those and publicly available sequences from AOM sites supported the hypothesis by Knittel and colleagues that the DSS partner belongs to the diverse SEEP-SRB1 cluster. Six subclusters of SEEP-SRB1, SEEP-SRB1a to SEEP-SRB1f, were proposed and specific oligonucleotide probes were designed. Using fluorescence in situ hybridization on samples from six different AOM sites, SEEP-SRB1a was identified as sulfate-reducing partner in up to 95% of total ANME-2 consortia. SEEP-SRB1a cells exhibited a rod-shaped, vibrioid, or coccoid morphology and were found to be associated with subgroups ANME-2a and ANME-2c. Moreover, SEEP-SRB1a was also detected in 8% to 23% of ANME-3 consortia in Haakon Mosby Mud Volcano sediments, previously described to be predominantly associated with SRB of the Desulfobulbus group. SEEP-SRB1a contributed to only 0.3% to 0.7% of all single cells in almost all samples indicating that these bacteria are highly adapted to a symbiotic relationship with ANME-2. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

  2. [Anorectal manifestations of sexually transmitted infections].

    Science.gov (United States)

    Lautenschlager, Stephan

    2013-07-01

    The incidence of sexually transmitted infections is rising in Europe and in Switzerland since the beginning of the third millenium. Many organisms may affect the perianal skin and the anorectum. While some of these infections are a result of contigous spread from genital infection, most result from receptive anal intercourse affecting males who have sex with males but is seen increasingly in females as well since there is evidence of the increasing popularity of anal sex among heterosexuals. The symptoms of specific infections are largely dependent on the route and site of inoculation. Organisms that cause typical genital symptoms - such as syphilis, chancroid, herpes simplex or HPV-infection - result in similar symptoms when the perianal skin, the anoderm or the distal anal canal are the site of infection. Patients with proctitis may have unspecific signs in various degrees including mucous discharge, rectal bleeding, anorectal pain, superficial ulcers and sometimes generalized lymphadenopathy and fever. It is of utmost importance to include STIs (e. g. lymphogranuloma venereum, gonorrhea, non-LGV-chlamydia and herpes simplex) in the differential diagnosis in these patients. Unfortunately rectal infection with chlamydia and gonorrhea is asymptomatic in the majority of cases of men having sex with men and in high-risk females. A careful history and physical examination is essential in establishing a correct diagnosis, usually supported by proctoscopy, culture, PCR, serology and histology. Certain organisms, more commonly thought of as food- or water-borne disease may be sexually transmitted by direct or indirect fecal-oral contact from various sexual practices.

  3. Synchrotron scanning reveals amphibious ecomorphology in a new clade of bird-like dinosaurs

    Science.gov (United States)

    Cau, Andrea; Beyrand, Vincent; Voeten, Dennis F. A. E.; Fernandez, Vincent; Tafforeau, Paul; Stein, Koen; Barsbold, Rinchen; Tsogtbaatar, Khishigjav; Currie, Philip J.; Godefroit, Pascal

    2017-12-01

    Maniraptora includes birds and their closest relatives among theropod dinosaurs. During the Cretaceous period, several maniraptoran lineages diverged from the ancestral coelurosaurian bauplan and evolved novel ecomorphologies, including active flight, gigantism, cursoriality and herbivory. Propagation X-ray phase-contrast synchrotron microtomography of a well-preserved maniraptoran from Mongolia, still partially embedded in the rock matrix, revealed a mosaic of features, most of them absent among non-avian maniraptorans but shared by reptilian and avian groups with aquatic or semiaquatic ecologies. This new theropod, Halszkaraptor escuilliei gen. et sp. nov., is related to other enigmatic Late Cretaceous maniraptorans from Mongolia in a novel clade at the root of Dromaeosauridae. This lineage adds an amphibious ecomorphology to those evolved by maniraptorans: it acquired a predatory mode that relied mainly on neck hyperelongation for food procurement, it coupled the obligatory bipedalism of theropods with forelimb proportions that may support a swimming function, and it developed postural adaptations convergent with short-tailed birds.

  4. Digital Receiver Design for Transmitted Reference Ultra-Wideband Systems

    NARCIS (Netherlands)

    Wang, Y.; Leus, G.; Van der Veen, A.J.

    2009-01-01

    A complete detection, channel estimation, synchronization, and equalization scheme for a transmitted reference (TR) ultra-wideband (UWB) system is proposed in this paper. The scheme is based on a data model which admits a moderate data rate and takes both the interframe interference (IFI) and the

  5. Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1 influenza virus in ferrets.

    Directory of Open Access Journals (Sweden)

    Natalia A Ilyushina

    2010-05-01

    Full Text Available The acquisition of neuraminidase (NA inhibitor resistance by H5N1 influenza viruses has serious clinical implications, as this class of drugs can be an essential component of pandemic control measures. The continuous evolution of the highly pathogenic H5N1 influenza viruses results in the emergence of natural NA gene variations whose impact on viral fitness and NA inhibitor susceptibility are poorly defined. We generated seven genetically stable recombinant clade 2.2 A/Turkey/15/06-like (H5N1 influenza viruses carrying NA mutations located either in the framework residues (E119A, H274Y, N294S or in close proximity to the NA enzyme active site (V116A, I117V, K150N, Y252H. NA enzyme inhibition assays showed that NA mutations at positions 116, 117, 274, and 294 reduced susceptibility to oseltamivir carboxylate (IC(50s increased 5- to 940-fold. Importantly, the E119A NA mutation (previously reported to confer resistance in the N2 NA subtype was stable in the clade 2.2 H5N1 virus background and induced cross-resistance to oseltamivir carboxylate and zanamivir. We demonstrated that Y252H NA mutation contributed for decreased susceptibility of clade 2.2 H5N1 viruses to oseltamivir carboxylate as compared to clade 1 viruses. The enzyme kinetic parameters (V(max, K(m and K(i of the avian-like N1 NA glycoproteins were highly consistent with their IC(50 values. None of the recombinant H5N1 viruses had attenuated virulence in ferrets inoculated with 10(6 EID(50 dose. Most infected ferrets showed mild clinical disease signs that differed in duration. However, H5N1 viruses carrying the E119A or the N294S NA mutation were lethal to 1 of 3 inoculated animals and were associated with significantly higher virus titers (P<0.01 and inflammation in the lungs compared to the wild-type virus. Our results suggest that highly pathogenic H5N1 variants carrying mutations within the NA active site that decrease susceptibility to NA inhibitors may possess increased

  6. Spectrally efficient switched transmit diversity for spectrum sharing systems

    KAUST Repository

    Bouida, Zied; Abdallah, Mohamed M.; Qaraqe, Khalid A.; Alouini, Mohamed-Slim

    2011-01-01

    Under the scenario of an underlay cognitive radio network, we propose in this paper an adaptive scheme using switched transmit diversity and adaptive modulation in order to increase the spectral efficiency of the secondary link. The proposed bandwidth efficient scheme (BES) uses the scan and wait (SWC) combining technique where a transmission occurs only when a branch with an acceptable performance is found, otherwise data is buffered. In our scheme, the modulation constellation size and the used transmit branch are determined to achieve the highest spectral efficiency given the fading channel conditions, the required error rate performance, and a peak interference constraint to the primary receiver. Selected numerical examples show that the BES scheme increases the capacity of the secondary link when compared to an existing switching efficient scheme (SES). This spectral efficiency comes at the expense of an increased average number of switched branches and thus an increased average delay. © 2011 IEEE.

  7. Environmental pollution with soil-transmitted helminths in Sanliurfa, Turkey

    Directory of Open Access Journals (Sweden)

    Ulukanligil Mustafa

    2001-01-01

    Full Text Available Soil transmitted helminth (STH infection are endemic in developing countries. A study was carried out of sewage farms, streams and vegetables to determine the sources and routes of STH infection in Sanliurfa, Turkey. Stool samples from farmhouse inhabitants as well as soil and vegetable samples from the gardens were collected and examined. In addition, water samples from streams and vegetable samples from the city market were collected and examined. One hundred and eighty-seven (59.5% of a total of 314 samples, including 88.4% of the stool samples, 60.8% of the water samples, 84.4% of the soil samples and 14% of the vegetable samples, were found to be positive for STH eggs. These results indicate that the water, soil and vegetables are heavily contaminated, and suggest a vicious circle between humans and the environment. Improving environmental sanitation is imperative for the control of soil-transmitted helminthiasis in Sanliurfa.

  8. Spectrally efficient switched transmit diversity for spectrum sharing systems

    KAUST Repository

    Bouida, Zied

    2011-09-01

    Under the scenario of an underlay cognitive radio network, we propose in this paper an adaptive scheme using switched transmit diversity and adaptive modulation in order to increase the spectral efficiency of the secondary link. The proposed bandwidth efficient scheme (BES) uses the scan and wait (SWC) combining technique where a transmission occurs only when a branch with an acceptable performance is found, otherwise data is buffered. In our scheme, the modulation constellation size and the used transmit branch are determined to achieve the highest spectral efficiency given the fading channel conditions, the required error rate performance, and a peak interference constraint to the primary receiver. Selected numerical examples show that the BES scheme increases the capacity of the secondary link when compared to an existing switching efficient scheme (SES). This spectral efficiency comes at the expense of an increased average number of switched branches and thus an increased average delay. © 2011 IEEE.

  9. Trichomonas vaginalis infection in Nigerian pregnant women and risk factors associated with sexually transmitted infections.

    Science.gov (United States)

    Oyeyemi, Oyetunde T; Fadipe, Olamide; Oyeyemi, Ifeoluwa T

    2016-11-01

    Trichomoniasis poses a public health threat to pregnant women and neonatal health. This study evaluated Trichomonas vaginalis and other common sexually transmitted infections (STIs) status in pregnant women, and risk factors associated with them. The study was cross-sectional and descriptive and a total of 198 pregnant women were recruited for T. vaginalis screening by microscopic examination. Questionnaires were also administered to 108 pregnant women to access information related to socio-demography and other factors associated with STI transmission. The overall prevalence of T. vaginalis was 18.7%. While prevalence of T. vaginalis was neither age nor parity dependent (p > 0.05), women in their first trimester showed significantly higher prevalence of trichomoniasis compared to women in their second and third trimesters (p vaginalis in pregnant women, with those at an early gestational age at greater risk. The improved education of women on safe sex and the need to know partners' STI status are advocated. © The Author(s) 2015.

  10. Prevalence of Sexually Transmitted Diseases and Blood-Borne Transmitted Infections among Male Patients with Antisocial Personality Disorder

    Directory of Open Access Journals (Sweden)

    Hamza Yıldız

    2015-03-01

    Full Text Available Objective: The aim of this study was to compare the patients who have antisocial personality disorder (ASPD and the healthy individuals in terms of sexually transmitted diseases (STDs and Blood-Borne Transmitted Infections (BTIs prevalences. Methods: This study is a prospective, single-center, open-label, non-randomized controlled clinical study. There were two groups in the study. The patient group consistsed of 100 males who were diagnosed as ASPD with a clinical interview form. The control group consisted of 98 healthy males who did not have any psychiatric disorder. Dermatologic examination was performed, and clinical findings were recorded. Results: The mean age of the patient group was 21.96±2.40 (range 20-37 years. The mean age of the control group was 24.20±2.88 (21-36 years. The most common disease was gonorrhea (25% followed by genital wart (11%, molluskum contagiosum (5%, HBsAg (4%, and HSV-2 seropositivity (4% in the patients group. In the control group, HSV-2 seropositivity (4.08%, genital wart (3.06%, molluskum contagiosum (3.06%, and gonorrhe (1.02% were commonly seen in the control group. STDs and/or BVTIs were found more common in the patients group (82% than that in the control group (45.91% (X2=30.62, p=0.000. Conclusions: The patients with ASPD are at greater risk than normal population to catch a STDs or BTIs because of their lower educational levels and riskier behaviors. This condition entertains a risk in the general population and the patients themselves.

  11. Genetic Structure and Antimicrobial Resistance of Escherichia coli and Cryptic Clades in Birds with Diverse Human Associations.

    Science.gov (United States)

    Blyton, Michaela D J; Pi, Hongfei; Vangchhia, Belinda; Abraham, Sam; Trott, Darren J; Johnson, James R; Gordon, David M

    2015-08-01

    The manner and extent to which birds associate with humans may influence the genetic attributes and antimicrobial resistance of their commensal Escherichia communities through strain transmission and altered selection pressures. In this study, we determined whether the distribution of the different Escherichia coli phylogenetic groups and cryptic clades, the occurrence of 49 virulence associated genes, and/or the prevalence of resistance to 12 antimicrobials differed between four groups of birds from Australia with contrasting types of human association. We found that birds sampled in suburban and wilderness areas had similar Escherichia communities. The Escherichia communities of backyard domestic poultry were phylogenetically distinct from the Escherichia communities sourced from all other birds, with a large proportion (46%) of poultry strains belonging to phylogenetic group A and a significant minority (17%) belonging to the cryptic clades. Wild birds sampled from veterinary and wildlife rehabilitation centers (in-care birds) carried Escherichia isolates that possessed particular virulence-associated genes more often than Escherichia isolates from birds sampled in suburban and wilderness areas. The Escherichia isolates from both the backyard poultry and in-care birds were more likely to be multidrug resistant than the Escherichia isolates from wild birds. We also detected a multidrug-resistant E. coli strain circulating in a wildlife rehabilitation center, reinforcing the importance of adequate hygiene practices when handling and caring for wildlife. We suggest that the relatively high frequency of antimicrobial resistance in the in-care birds and backyard poultry is due primarily to the use of antimicrobials in these animals, and we recommend that the treatment protocols used for these birds be reviewed. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  12. MVA-based H5N1 vaccine affords cross-clade protection in mice against influenza A/H5N1 viruses at low doses and after single immunization.

    Directory of Open Access Journals (Sweden)

    Joost H C M Kreijtz

    Full Text Available Human infections with highly pathogenic avian influenza viruses of the H5N1 subtype, frequently reported since 2003, result in high morbidity and mortality. It is feared that these viruses become pandemic, therefore the development of safe and effective vaccines is desirable. MVA-based H5N1 vaccines already proved to be effective when two immunizations with high doses were used. Dose-sparing strategies would increase the number of people that can be vaccinated when the amount of vaccine preparations that can be produced is limited. Furthermore, protective immunity is induced ideally after a single immunization. Therefore the minimal requirements for induction of protective immunity with a MVA-based H5N1 vaccine were assessed in mice. To this end, mice were vaccinated once or twice with descending doses of a recombinant MVA expressing the HA gene of influenza virus A/Vietnam/1194/04. The protective efficacy was determined after challenge infection with the homologous clade 1 virus and a heterologous virus derived from clade 2.1, A/Indonesia/5/05 by assessing weight loss, virus replication and histopathological changes. It was concluded that MVA-based vaccines allowed significant dose-sparing and afford cross-clade protection, also after a single immunization, which are favorable properties for an H5N1 vaccine candidate.

  13. Separate introns gained within short and long soluble peridinin-chlorophyll a-protein genes during radiation of Symbiodinium (Dinophyceae) clade A and B lineages - PLoS One

    Science.gov (United States)

    Here we document introns in two Symbiodinium clades that were most likely gained following divergence of this genus from other peridinin-containing dinoflagellate lineages. Soluble peridinin-chlorophyll a-proteins (sPCP) occur in short and long forms in different species, and all...

  14. Recommendation on vectors and vector-transmitted diseases

    OpenAIRE

    Netherlands Food and Consumer Product Safety Authority

    2009-01-01

    In view of their increasing risk of introduction and their possible implications in causing major disease outbreaks, vectors, as well as vector-transmitted diseases like dengue, West Nile disease, Lyme disease and bluetongue need to be recognised as a threat to public and animal health and to the economy, also in the Netherlands. There has been an increase in the incidence of these diseases in the past two to three decades. Climate changes and changes in the use of land, water managemen...

  15. Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome.

    Science.gov (United States)

    Durham, Bryndan P; Grote, Jana; Whittaker, Kerry A; Bender, Sara J; Luo, Haiwei; Grim, Sharon L; Brown, Julia M; Casey, John R; Dron, Antony; Florez-Leiva, Lennin; Krupke, Andreas; Luria, Catherine M; Mine, Aric H; Nigro, Olivia D; Pather, Santhiska; Talarmin, Agathe; Wear, Emma K; Weber, Thomas S; Wilson, Jesse M; Church, Matthew J; DeLong, Edward F; Karl, David M; Steward, Grieg F; Eppley, John M; Kyrpides, Nikos C; Schuster, Stephan; Rappé, Michael S

    2014-06-15

    Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.

  16. Can environmental conditions experienced in early life influence future generations?

    Science.gov (United States)

    Burton, Tim; Metcalfe, Neil B

    2014-06-22

    The consequences of early developmental conditions for performance in later life are now subjected to convergent interest from many different biological sub-disciplines. However, striking data, largely from the biomedical literature, show that environmental effects experienced even before conception can be transmissible to subsequent generations. Here, we review the growing evidence from natural systems for these cross-generational effects of early life conditions, showing that they can be generated by diverse environmental stressors, affect offspring in many ways and can be transmitted directly or indirectly by both parental lines for several generations. In doing so, we emphasize why early life might be so sensitive to the transmission of environmentally induced effects across generations. We also summarize recent theoretical advancements within the field of developmental plasticity, and discuss how parents might assemble different 'internal' and 'external' cues, even from the earliest stages of life, to instruct their investment decisions in offspring. In doing so, we provide a preliminary framework within the context of adaptive plasticity for understanding inter-generational phenomena that arise from early life conditions.

  17. Atomic force microscopy imaging reveals the formation of ASIC/ENaC cross-clade ion channels.

    Science.gov (United States)

    Jeggle, Pia; Smith, Ewan St J; Stewart, Andrew P; Haerteis, Silke; Korbmacher, Christoph; Edwardson, J Michael

    2015-08-14

    ASIC and ENaC are co-expressed in various cell types, and there is evidence for a close association between them. Here, we used atomic force microscopy (AFM) to determine whether ASIC1a and ENaC subunits are able to form cross-clade hybrid ion channels. ASIC1a and ENaC could be co-isolated from detergent extracts of tsA 201 cells co-expressing the two subunits. Isolated proteins were incubated with antibodies against ENaC and Fab fragments against ASIC1a. AFM imaging revealed proteins that were decorated by both an antibody and a Fab fragment with an angle of ∼120° between them, indicating the formation of ASIC1a/ENaC heterotrimers. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Knowledge and attitude of sexually transmitted diseases among adolescents in Ikeji-Arakeji, Osun State, in South-Western Nigeria.

    Science.gov (United States)

    Akokuwebe, M E; Daini, B; Falayi, E O; Oyebade, O

    2016-09-01

    Globally, sexually transmitted disease (STD) is a public health problem. In Nigeria, adolescents form a substantial proportion (22%) of the population and are particularly prone to STDs because of the influence of peer pressure and urge to experiment sexual activity. The study examined the knowledge and attitude of adolescents towards the prevention of sexually transmitted diseases. The survey study was descriptive cross- sectional and carried out among consenting secondary school students aged 10-24 years completing a self- administered questionnaire on knowledge and attitude in relation to sexually transmitted diseases in Ikeji- Arakeji, Oriade Local government, Osun State, Nigeria. The proportionate sampling technique was used to recruit 341 participants into the study. Data were analyzed using descriptive and inferential statistics. Male-Female distributions were 46.3% and 53.7% respectively. Mean age at first sex (sex initiation) was 16.8 years (approximately 17years) and about 97% of the respondents knew about STDs. The media/ magazine was the major source of information about STDs, accounting for more than half (57%) of the responses on sources of STD information followed closely from that from friends with 31%. Parent's source of information was about 11%. Knowledge of STDs centred mainly on HIV/AIDS with 83% and there was a poor knowledge (78%) of its symptoms. About 40% of all respondents had initiated sex at the time of the study and 46% of the adolescents, as against 54%, thought it was bad to initiate sex before marriage. There was a significant association between perception about initiating sex before marriage and ever having sex using bivariate analysis x(2)=268.4, Psex initiation (F=318.47 and P=0.000). Post-hoc analysis showed that each of the different groups (sources of information) was distinct. Adolescents' knowledge of STDs generally limited to HIV/AIDS and perception about sex significantly influenced the decision to initiate sex. There is

  19. Intervention for the control of Soil -transmitted helminthiasis in the community

    Science.gov (United States)

    Albonico, Marco; Montresor, Antonio; Crompton, DWT; Savioli, Lorenzo

    2017-01-01

    The global strategy for the control of soil-transmitted helminthiasis, based on regular anthelminthic treatment, health education, and improved sanitation standards, is reviewed. The reasons for the development of a control strategy based on population intervention rather than on individual treatment are explained. The evidence and experience from control programmes that created the basis for i) the definition of the intervention package, ii) the identification of the groups at risk, iii) the standardization of the community diagnosis, and iv) the selection of the appropriate intervention for each category in the community are discussed. How to best deliver the appropriate intervention, the impact of the control measures on morbidity and on indicators such as school attendance, cognitive development and productivity are presented. The factors influencing the cost-benefits of helminth control are also considered. The recent progress on the control of soil-transmitted helminth infections is illustrated. Research needs are analysed in relation to the most recent perceptions from private-public partnerships involved in helminth control. The way forward for the control of soil-transmitted helminth infections is described as a multi-disease approach that goes beyond deworming and fosters a pro-poor strategy that supports the aims of the Millennium Development Goals. PMID:16735168

  20. New insights on the phylogenetic relationships among the traditional Philodendron subgenera and the other groups of the Homalomena clade (Araceae).

    Science.gov (United States)

    Vasconcelos, Santelmo; Soares, Maria de Lourdes; Sakuragui, Cássia M; Croat, Thomas B; Oliveira, Guilherme; Benko-Iseppon, Ana M

    2018-05-19

    Philodendron (Araceae) is one of the largest Neotropical plant genera, with approximately 500 species and at least 1000 species predicted. There is a considerable ecological diversity in the group, although most species occur in the humid forests of tropical America. Despite being relatively well-studied in taxonomic analyses, the relationships among the traditional morphological groups of the genus are not well-established, mainly regarding the three traditional subgenera, referred here as Philodendron sensu lato (s.l.), P. subg. Pteromischum, P. subg. Philodendron and P. subg. Meconostigma, which was recently recognized as a separate genus, Thaumatophyllum. Therefore, the present work evaluates the phylogenetic position and the monophyly of Philodendron s.l. and its three main subdivisions, and the sister groups within the Homalomena clade, which also includes the Neotropical genus Adelonema, the two Asian genera Homalomena and Furtadoa, and the two African genera Cercestis and Culcasia, by means of molecular phylogenetic approaches including chloroplast DNA (atpF-atpH, rpl32-trnL, trnQ-5'-rps16 and trnV-ndhC) and nuclear (ITS2) markers. The monophyly of Philodendron s.l. and its three lineages is confirmed and our analyses corroborate previous morphologic data indicating Thaumatophyllum as sister to the clade formed by P. subg. Pteromischum and P. subg. Philodendron. Copyright © 2018 Elsevier Inc. All rights reserved.

  1. Does the colonization of new biogeographic regions influence the diversification and accumulation of clade richness among the Corvides (Aves: Passeriformes)?

    Science.gov (United States)

    Kennedy, Jonathan D; Borregaard, Michael K; Jønsson, Knud A; Holt, Ben; Fjeldså, Jon; Rahbek, Carsten

    2017-01-01

    Regional variation in clade richness can be vast, reflecting differences in the dynamics of historical dispersal and diversification among lineages. Although it has been proposed that dispersal into new biogeographic regions may facilitate diversification, to date there has been limited assessment of the importance of this process in the generation, and maintenance, of broad-scale biodiversity gradients. To address this issue, we analytically derive biogeographic regions for a global radiation of passerine birds (the Corvides, c. 790 species) that are highly variable in the geographic and taxonomic distribution of species. Subsequently, we determine rates of historical dispersal between regions, the dynamics of diversification following regional colonization, and spatial variation in the distribution of species that differ in their rates of lineage diversification. The results of these analyses reveal spatiotemporal differences in the build-up of lineages across regions. The number of regions occupied and the rate of transition between regions both predict family richness well, indicating that the accumulation of high clade richness is associated with repeated expansion into new geographic areas. However, only the largest family (the Corvidae) had significantly heightened rates of both speciation and regional transition, implying that repeated regional colonization is not a general mechanism promoting lineage diversification among the Corvides. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  2. Protective Efficacy of Recombinant Turkey Herpes Virus (rHVT-H5) and Inactivated H5N1 Vaccines in Commercial Mulard Ducks against the Highly Pathogenic Avian Influenza (HPAI) H5N1 Clade 2.2.1 Virus.

    Science.gov (United States)

    Kilany, Walid H; Safwat, Marwa; Mohammed, Samy M; Salim, Abdullah; Fasina, Folorunso Oludayo; Fasanmi, Olubunmi G; Shalaby, Azhar G; Dauphin, Gwenaelle; Hassan, Mohammed K; Lubroth, Juan; Jobre, Yilma M

    2016-01-01

    In Egypt, ducks kept for commercial purposes constitute the second highest poultry population, at 150 million ducks/year. Hence, ducks play an important role in the introduction and transmission of avian influenza (AI) in the Egyptian poultry population. Attempts to control outbreaks include the use of vaccines, which have varying levels of efficacy and failure. To date, the effects of vaccine efficacy has rarely been determined in ducks. In this study, we evaluated the protective efficacy of a live recombinant vector vaccine based on a turkey Herpes Virus (HVT) expressing the H5 gene from a clade 2.2 H5N1 HPAIV strain (A/Swan/Hungary/499/2006) (rHVT-H5) and a bivalent inactivated H5N1 vaccine prepared from clade 2.2.1 and 2.2.1.1 H5N1 seeds in Mulard ducks. A 0.3ml/dose subcutaneous injection of rHVT-H5 vaccine was administered to one-day-old ducklings (D1) and another 0.5ml/dose subcutaneous injection of the inactivated MEFLUVAC was administered at 7 days (D7). Four separate challenge experiments were conducted at Days 21, 28, 35 and 42, in which all the vaccinated ducks were challenged with 106EID50/duck of H5N1 HPAI virus (A/chicken/Egypt/128s/2012(H5N1) (clade 2.2.1) via intranasal inoculation. Maternal-derived antibody regression and post-vaccination antibody immune responses were monitored weekly. Ducks vaccinated at 21, 28, 35 and 42 days with the rHVT-H5 and MEFLUVAC vaccines were protected against mortality (80%, 80%, 90% and 90%) and (50%, 70%, 80% and 90%) respectively, against challenges with the H5N1 HPAI virus. The amount of viral shedding and shedding rates were lower in the rHVT-H5 vaccine groups than in the MEFLUVAC groups only in the first two challenge experiments. However, the non-vaccinated groups shed significantly more of the virus than the vaccinated groups. Both rHVT-H5 and MEFLUVAC provide early protection, and rHVT-H5 vaccine in particular provides protection against HPAI challenge.

  3. The chloroplast genome of a symbiodinium sp. clade C3 isolate

    KAUST Repository

    Barbrook, Adrian C.

    2014-01-01

    Dinoflagellate algae of the genus Symbiodinium form important symbioses within corals and other benthic marine animals. Dinoflagellates possess an extremely reduced plastid genome relative to those examined in plants and other algae. In dinoflagellates the plastid genes are located on small plasmids, commonly referred to as \\'minicircles\\'. However, the chloroplast genomes of dinoflagellates have only been extensively characterised from a handful of species. There is also evidence of considerable variation in the chloroplast genome organisation across those species that have been examined. We therefore characterised the chloroplast genome from an environmental coral isolate, in this case containing a symbiont belonging to the Symbiodinium sp. clade C3. The gene content of the genome is well conserved with respect to previously characterised genomes. However, unlike previously characterised dinoflagellate chloroplast genomes we did not identify any \\'empty\\' minicircles. The sequences of this chloroplast genome show a high rate of evolution relative to other algal species. Particularly notable was a surprisingly high level of sequence divergence within the core polypeptides of photosystem I, the reasons for which are currently unknown. This chloroplast genome also possesses distinctive codon usage and GC content. These features suggest that chloroplast genomes in Symbiodinium are highly plastic. © 2013 Adrian C. Barbrook.

  4. The chloroplast genome of a symbiodinium sp. clade C3 isolate

    KAUST Repository

    Barbrook, Adrian C.; Voolstra, Christian R.; Howe, Christopher J.

    2014-01-01

    Dinoflagellate algae of the genus Symbiodinium form important symbioses within corals and other benthic marine animals. Dinoflagellates possess an extremely reduced plastid genome relative to those examined in plants and other algae. In dinoflagellates the plastid genes are located on small plasmids, commonly referred to as 'minicircles'. However, the chloroplast genomes of dinoflagellates have only been extensively characterised from a handful of species. There is also evidence of considerable variation in the chloroplast genome organisation across those species that have been examined. We therefore characterised the chloroplast genome from an environmental coral isolate, in this case containing a symbiont belonging to the Symbiodinium sp. clade C3. The gene content of the genome is well conserved with respect to previously characterised genomes. However, unlike previously characterised dinoflagellate chloroplast genomes we did not identify any 'empty' minicircles. The sequences of this chloroplast genome show a high rate of evolution relative to other algal species. Particularly notable was a surprisingly high level of sequence divergence within the core polypeptides of photosystem I, the reasons for which are currently unknown. This chloroplast genome also possesses distinctive codon usage and GC content. These features suggest that chloroplast genomes in Symbiodinium are highly plastic. © 2013 Adrian C. Barbrook.

  5. Voice-band Modem: A Device to Transmit Data over Telephone ...

    Indian Academy of Sciences (India)

    over Telephone Networks. 2. Advanced Ideas ... transmitted signal power and No is the noise power spec- ... power distribution over all frequencies, and the samples of noise .... Figure 3, dmin=2fl, and average signal energy, assum- ing that ...

  6. Prevalence and Associated Factors of Genital and Sexually Transmitted Infections in Married Women of Iran

    Directory of Open Access Journals (Sweden)

    Elahe Ahmadnia

    2016-11-01

    Full Text Available Objectives: This study aimed to determine the prevalence of genital and sexually transmitted infections and its related factors in married women in Iran. Methods: We conducted a cross-sectional study of 4 274 married women living in urban and rural areas of the Zanjan province from 2012 to 2013. We used stratified cluster sampling to select the participants. Data collection included demographic characteristics, reproductive status, and cervical cytology results. Results: The prevalence of lower genital infections and sexually transmitted infections were 20.1% and 7.4%, respectively. The most common vaginal infection was bacterial vaginosis with a prevalence of 8.5%, and the most common sexually transmitted infection was Trichomonas vaginalis (1.4%. The use of the intrauterine device (IUD as a contraceptive, living in an urban area, and experiencing vaginal discharge were significantly related to genital tract and sexually transmitted infections. Conclusions: There was a high prevalence of genital infection among women living in Zanjab. Screening and treatment of genital infection are necessary to prevent adverse consequences in women who use an IUD or live in urban areas.

  7. The prevalence of transfusion-transmitted virus (TTV) infection in ...

    African Journals Online (AJOL)

    Transfusion-transmitted virus (TTV) is an unenveloped circular single-stranded DNA virus with a diameter of 30 to 32 nm that was first described in 1997 in Japan. TTV was detected in various populations without proven pathology, including blood donors and in patients with chronic hepatitis B virus (HBV) and hepatitis C ...

  8. Transfusion transmitted malaria in three major blood banks of ...

    African Journals Online (AJOL)

    This study estimates the risk of acquiring malaria from a single unit of blood in North of Pakistan. A prospective study was conducted to investigate transfusion transmitted malaria in three major blood banks of Peshawar, Pakistan. A total of 1558 (1534 males and 24 females) healthy volunteer blood donors were screened for ...

  9. Transfusion transmitted infections – A retrospective analysis from the ...

    African Journals Online (AJOL)

    Background: The emergence of transfusion transmitted infection (TTI) especially HIV/AIDS has created a huge obstacle in ensuring blood safety. To assess the situation in Eritrea, we carried out a retrospective study of 29,501 blood donors for the prevalence of TTI's i.e. HIV, HBV, HCV and Syphilis. Methods: The study ...

  10. Profile Of Sexually Transmitted Diseases In And Around Lucknow

    Directory of Open Access Journals (Sweden)

    Jaiswal A K

    2002-01-01

    Full Text Available A retrospective study was undertaken from the year 1988 to 1998 to study the pattern of sexually transmitted diseases in and around Lucknow. Among 1890 patients examined, chancroid predominated followed by syphilis, gonorrhoea, genital warts, herpes genitalis, LGV and non-specific urethritis. The incidence of donovanosis was the lowest.

  11. [Sexually transmitted infections in Germany : The current epidemiological situation].

    Science.gov (United States)

    Bremer, Viviane; Dudareva-Vizule, Sandra; Buder, Susanne; An der Heiden, Matthias; Jansen, Klaus

    2017-09-01

    Sexually transmitted infections (STIs) can impair sexual health. Surveillance and study data were used to provide an overview over STIs in Germany. We estimated 3900 new HIV diagnoses in 2015. Of newly diagnosed infections, 57% were attributed to men who have sex with men (MSM). It was further estimated that there were 3200 new HIV infections and 84,700 people living with HIV in 2015. A total of 6834 syphilis infections were recorded in 2015, which corresponds to an increase of 149% since 2009. The incidence in men was 16-times higher than in women. Of syphilis infections, 85% could be attributed to MSM. Antimicrobial resistance of gonococci against the broad-spectrum antibiotic cefixime decreased between 2014 and 2016 after a change of therapy guidelines and remained stable on a low level regarding the antibiotic ceftriaxone. After an increase of resistance against the antibiotic azithromycin to 11.3% in 2015, we observed a decreasing trend in 2016. Between 2013 and 2015, 2,355,336 chlamydia tests were reported through the chlamydia sentinel network. Of these, 92.5% of samples were from women. Uptake for screening for women human papilloma virus (HPV) of 38.1% was observed. A total of 30.5% of 15-year-old women were vaccinated against HPV in 2014. Data suggest that STIs represent a high burden of disease. Knowledge of STI prevention should be improved by targeted education campaigns. Extending existing offers for counselling and testing through cooperation between different health sectors would improve early diagnosis and treatment of STIs.

  12. [Current situation of soil-transmitted nematodiasis monitoring in China and working keys in future].

    Science.gov (United States)

    Chen, Ying-dan; Zang, Wei

    2015-04-01

    Soil-transmitted nematodiasis is widely epidemic in rural areas in China. It was showed that the infection rate of soil-transmitted nematodes was 19.56% while the overall number of persons infected was 129,000,000, which was supported by the results of the National Survey of Current Situation of Major Human Parasitic Diseases in China in 2005 published by former Ministry of Health. Therefore, soil-transmitted nematodiasis was included in the national infectious diseases and pathogenic media monitoring system by Chinese Center for Disease Control and Prevention in 2006, and subsequently 22 monitoring spots were established nationwide. From 2006 to 2013, the human infection rate of intestinal nematodes in national monitoring spots decreased from 20.88% to 3.12%, which showed a declining trend year by year. Meanwhile, the infection rates of Ascaris lumbricoides, Trichuris trichiura, hookworm, Enterobius vermicularis decreased from 10.10%, 5.88%, 8.88%, 10.00% in 2006 to 0.76%, 0.42%, 2.04%, 6.78% in 2013 respectively. In this paper, the current situation of soil-transmitted nematodiasis is overviewed based on a summary of the 8 years' monitoring work, as well as the experiences, challenges and key of monitoring work in the future.

  13. Indigenous Healers’ beliefs and practices concerning sexually transmitted diseases

    Directory of Open Access Journals (Sweden)

    FM Mulaudzi

    2006-09-01

    Full Text Available A Grounded Theory study has been used, based on its Theory of Symbolic Interactionism, to explore indigenous healers’ beliefs and practices concerning sexually transmitted diseases amongst the Vhavenda. Initial data collection has been done, using purposive sampling and when categories started emerging, theoretical sampling was then used. Data were analysed by using three basic types of coding namely, open coding, axial coding and selective coding. The findings of the study revealed a variety of terms used to identify STDs. It then also became evident that there are similarities between gonorrhoea, syphilis and condylomata as shown in the orthodox Sexually transmitted diseases posters used in orthodox medicine with some of the STDs that the indigenous healers are familiar with. In accordance with the Grounded Theory, the description of types of diseases, disease patterns as well as signs and symptoms culminated in the emergence of the Dirt Theory. Based on the above findings, it was recommended that guidelines for designing a module for teaching health professionals be formulated to assist nurses in understanding the beliefs and practices of the people they serve.

  14. Low-Complexity Transmit Antenna Selection and Beamforming for Large-Scale MIMO Communications

    Directory of Open Access Journals (Sweden)

    Kun Qian

    2014-01-01

    Full Text Available Transmit antenna selection plays an important role in large-scale multiple-input multiple-output (MIMO communications, but optimal large-scale MIMO antenna selection is a technical challenge. Exhaustive search is often employed in antenna selection, but it cannot be efficiently implemented in large-scale MIMO communication systems due to its prohibitive high computation complexity. This paper proposes a low-complexity interactive multiple-parameter optimization method for joint transmit antenna selection and beamforming in large-scale MIMO communication systems. The objective is to jointly maximize the channel outrage capacity and signal-to-noise (SNR performance and minimize the mean square error in transmit antenna selection and minimum variance distortionless response (MVDR beamforming without exhaustive search. The effectiveness of all the proposed methods is verified by extensive simulation results. It is shown that the required antenna selection processing time of the proposed method does not increase along with the increase of selected antennas, but the computation complexity of conventional exhaustive search method will significantly increase when large-scale antennas are employed in the system. This is particularly useful in antenna selection for large-scale MIMO communication systems.

  15. [Investigation on prevalence of soil-transmitted nematode infections and influencing factors for children in southwest areas of China].

    Science.gov (United States)

    Wang, Xiao-Bing; Wang, Guo-Fei; Zhang, Lin-Xiu; Luo, Ren-Fu; Tian, Hong-Chun; Tang, Li-Na; Wang, Ju-Jun; Medina, Alexis; Wise, Paul; Rozelle, Scott

    2012-06-01

    To understand the infection status and main risk factors of soil-transmitted nematodes in southwest China so as to provide the evidence for making the control programs for soil-transmitted nematodiasis. The prevalence of soil-transmitted nematode infections was determined by Kato-Katz technique and influencing factors were surveyed by using a standardized questionnaire, and in part of the children, the examination of Enterobius vermicularis eggs was performed by using the cellophane swab method. The relationship between soil-transmitted nematode infections and influencing factors was analyzed by the multiple probit estimated method. A total of 1 707 children were examined, with a soil-transmitted nematode infection rate of 22.2%, the crowd infection rates ofAscaris lumbricoides, hookworm, and Trichuris trichiura were 16.0%, 3.8% and 6.6% respectively and 495 children were examined on Enterobius vermicularis eggs, with the infection rate of 5.1%. The results of probit estimated analysis suggested that the effects of 4 factors on soil-transmitted nematode infections were significant (all P values were less than 0.05), namely the number of sib, educational level of mother, drinking unboiled water and raising livestock and poultry. Among the factors above, the educational level of mother could reduce the probability of infection (ME = -0.074), while the number of sib, drinking unboiled water and raising livestock and poultry could increase the probability of the infections (with ME of 0.028, -0.112 and 0.080, respectively). Soil-transmitted nematode infection rates are still in a high level for children in southwest poor areas of China, with Ascaris lumbricoides as a priority. The changes of children's bad health habits, raising livestock and poultry habits, and implementing the health education about parasitic diseases in mothers would be of great significance for the prevention and control of soil-transmitted nematodiasis.

  16. A 32-channel lattice transmission line array for parallel transmit and receive MRI at 7 tesla.

    Science.gov (United States)

    Adriany, Gregor; Auerbach, Edward J; Snyder, Carl J; Gözübüyük, Ark; Moeller, Steen; Ritter, Johannes; Van de Moortele, Pierre-François; Vaughan, Tommy; Uğurbil, Kâmil

    2010-06-01

    Transmit and receive RF coil arrays have proven to be particularly beneficial for ultra-high-field MR. Transmit coil arrays enable such techniques as B(1) (+) shimming to substantially improve transmit B(1) homogeneity compared to conventional volume coil designs, and receive coil arrays offer enhanced parallel imaging performance and SNR. Concentric coil arrangements hold promise for developing transceiver arrays incorporating large numbers of coil elements. At magnetic field strengths of 7 tesla and higher where the Larmor frequencies of interest can exceed 300 MHz, the coil array design must also overcome the problem of the coil conductor length approaching the RF wavelength. In this study, a novel concentric arrangement of resonance elements built from capacitively-shortened half-wavelength transmission lines is presented. This approach was utilized to construct an array with whole-brain coverage using 16 transceiver elements and 16 receive-only elements, resulting in a coil with a total of 16 transmit and 32 receive channels. (c) 2010 Wiley-Liss, Inc.

  17. Enrichment of Multilocus Sequence Typing Clade 1 with Oral Candida albicans Isolates in Patients with Untreated Periodontitis

    Science.gov (United States)

    McManus, Brenda A.; Maguire, Rory; Cashin, Phillipa J.; Claffey, Noel; Flint, Stephen; Abdulrahim, Mohammed H.

    2012-01-01

    This study investigated the prevalence and cell density of Candida species in periodontal pockets, healthy subgingival sites, and oral rinse samples of patients with untreated periodontitis. Twenty-one periodontitis patients underwent sampling at two periodontitis sites, and 19/21 of these patients underwent sampling at one periodontally healthy site. Both paper point and curette sampling techniques were employed. The periodontitis patients and 50 healthy subjects were also sampled by oral rinse. Candida isolates were recovered on CHROMagar Candida medium, and representative isolates were identified. Candida spp. were recovered from 10/21 (46.7%) periodontitis patients and from 16/50 (32%) healthy subjects. C. albicans predominated in both groups and was recovered from all Candida-positive subjects. Candida-positive periodontitis patients yielded Candida from periodontal pockets with average densities of 3,528 and 3,910 CFU/sample from curette and paper point samples, respectively, and 1,536 CFU/ml from oral rinse samples. The majority (18/19) of the healthy sites sampled from periodontitis patients were Candida negative. The 16 Candida-positive healthy subjects yielded an average of 279 CFU/ml from oral rinse samples. C. albicans isolates were investigated by multilocus sequence typing (MLST) to determine if specific clonal groups were associated with periodontitis. MLST analysis of 31 C. albicans isolates from periodontitis patients yielded 19 sequence types (STs), 13 of which were novel. Eleven STs belonged to MLST clade 1. In contrast, 16 C. albicans isolates from separate healthy subjects belonged to 16 STs, with 4 isolates belonging to clade 1. The distributions of STs between both groups were significantly different (P = 0.04) and indicated an enrichment of C. albicans isolates in periodontal pockets, which warrants a larger study. PMID:22875886

  18. Generation and Characterization of HIV-1 Transmitted and Founder Virus Consensus Sequence from Intravenous Drug Users in Xinjiang, China.

    Science.gov (United States)

    Li, Fan; Ma, Liying; Feng, Yi; Hu, Jing; Ni, Na; Ruan, Yuhua; Shao, Yiming

    2017-06-01

    HIV-1 transmission in intravenous drug users (IDUs) has been characterized by high genetic multiplicity and suggests a greater challenge for HIV-1 infection blocking. We investigated a total of 749 sequences of full-length gp160 gene obtained by single genome sequencing (SGS) from 22 HIV-1 early infected IDUs in Xinjiang province, northwest China, and generated a transmitted and founder virus (T/F virus) consensus sequence (IDU.CON). The T/F virus was classified as subtype CRF07_BC and predicted to be CCR5-tropic virus. The variable region (V1, V2, and V4 loop) of IDU.CON showed length variation compared with the heterosexual T/F virus consensus sequence (HSX.CON) and homosexual T/F virus consensus sequence (MSM.CON). A total of 26 N-linked glycosylation sites were discovered in the IDU.CON sequence, which is less than that of MSM.CON and HSX.CON. Characterization of T/F virus from IDUs highlights the genetic make-up and complexity of virus near the moment of transmission or in early infection preceding systemic dissemination and is important toward the development of an effective HIV-1 preventive methods, including vaccines.

  19. Management of whitefly-transmitted viruses in open-field production systems.

    Science.gov (United States)

    Lapidot, Moshe; Legg, James P; Wintermantel, William M; Polston, Jane E

    2014-01-01

    Whiteflies are a key pest of crops in open-field production throughout the tropics and subtropics. This is due in large part to the long and diverse list of devastating plant viruses transmitted by these vectors. Open-field production provides many challenges to manage these viruses and in many cases adequate management has not been possible. Diseases caused by whitefly-transmitted viruses have become limiting factors in open-field production of a wide range of crops, i.e., bean golden mosaic disease in beans, tomato yellow leaf curl disease in tomato, cassava mosaic disease and cassava brown streak disease in cassava, and cotton leaf crumple disease in cotton. While host resistance has proven to be the most cost-effective management solution, few examples of host resistance have been developed to date. The main strategy to limit the incidence of virus-infected plants has been the application of insecticides to reduce vector populations aided to some extent by the use of selected cultural practices. However, due to concerns about the effect of insecticides on pollinators, consumer demand for reduced pesticide use, and the ability of the whitefly vectors to develop insecticide-resistance, there is a growing need to develop and deploy strategies that do not rely on insecticides. The reduction in pesticide use will greatly increase the need for genetic resistance to more viruses in more crop plants. Resistance combined with selected IPM strategies could become a viable means to increase yields in crops produced in open fields despite the presence of whitefly-transmitted viruses.

  20. Climate Chage in Spain and its Influence on Vector-Transmitted Diseases

    Directory of Open Access Journals (Sweden)

    Andres Iriso Calle

    2017-06-01

    Full Text Available In the past few decades Spain has experienced a resurgence of some vector-transmitted diseases which were thought to be under control and the appearance of new ones. Likewise, the arrival of new vectors and, in some cases, their establishment and expansion is creating to new public health risks. In general, these phenomena have been associated with complex ecological and climate-driven changes which have favored and increased the densities of vectors and their reservoirs, but they have also been affected by processes that have been triggered or accelerated by man such as globalization, urban development, deforestation and land-use changes.Changes in the distribution of vectors and their capacity to transmit pathogens owing to climate change will become more evident in areas that lie within their distribution limits, as is Spain’s case.This is compounded by Spain’s proximity to Africa and the potential entry of new vectors and pathogens from this continent.This scenario necessitates setting up action programs aimed at both identifying risks posed by vectors and preventing vector-borne diseases, and efficiently managing possible outbreaks that could occur in the future.We have reviewed the scenarios which Spain is expected to experience in connection with climate change and its impact on the incidence of diseases transmitted by mosquitoes, phlebotomine sand flies, ticks and other arthropods, and rodents.