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Sample records for roseobacter clade colonize

  1. 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.

  2. 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

  3. 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...

  4. 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...

  5. Antagonism of Roseobacter clade bacteria against pathogenic bacteria

    DEFF Research Database (Denmark)

    Porsby, Cisse Hedegaard

    Ph.d. projektet omhandler brug af probiotiske bakterier mod bakteriesygdomme i fiskeopdræt. Marine bakterier, der tilhører Roseobacter-gruppen, har vist sig at være lovende probiotiske bakterier. En del af bakteriernes probiotiske effekt skyldes sandsynligvis produktion af et antibakerielt stof, ...

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

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    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

  7. Investigation of the Genetics and Biochemistry of Roseobacticide Production in the Roseobacter Clade Bacterium Phaeobacter inhibens

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    Rurun Wang

    2016-03-01

    Full Text Available Roseobacter clade bacteria are abundant in surface waters and are among the most metabolically diverse and ecologically significant species. This group includes opportunistic symbionts that associate with micro- and macroalgae. We have proposed that one representative member, Phaeobacter inhibens, engages in a dynamic symbiosis with the microalga Emiliania huxleyi. In one phase, mutualistically beneficial molecules are exchanged, including the Roseobacter-produced antibiotic tropodithietic acid (TDA, which is thought to protect the symbiotic interaction. In an alternative parasitic phase, triggered by algal senescence, the bacteria produce potent algaecides, the roseobacticides, which kill the algal host. Here, we employed genetic and biochemical screens to identify the roseobacticide biosynthetic gene cluster. By using a transposon mutagenesis approach, we found that genes required for TDA synthesis—the tda operon and paa catabolon—are also necessary for roseobacticide production. Thus, in contrast to the one-cluster–one-compound paradigm, the tda gene cluster can generate two sets of molecules with distinct structures and bioactivities. We further show that roseobacticide production is quorum sensing regulated via an N-acyl homoserine lactone signal (3-OH–C10-HSL. To ensure tight regulation of algaecide production, and thus of a lifestyle switch from mutualism to parasitism, roseobacticide biosynthesis necessitates the presence of both an algal senescence molecule and a quorum sensing signal.

  8. Ecology, Inhibitory Activity, and Morphogenesis of a Marine Antagonistic Bacterium Belonging to the Roseobacter Clade

    DEFF Research Database (Denmark)

    Bruhn, Jesper Bartholin; Nielsen, Kristian Fog; Hjelm, Mette

    2005-01-01

    Roseobacter strain 27-4 has been isolated from a turbot larval rearing unit and is capable of reducing mortality in turbot egg yolk sac larvae. Here, we demonstrate that the supernatant of Roseobacter 27-4 is lethal to the larval pathogens Vibrio anguillarum and Vibrio splendidus in a buffer syst...

  9. Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade

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    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

  10. 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.

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

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    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

  12. Phaeobacter inhibens from the Roseobacter clade has an environmental niche as a surface colonizer in harbors

    DEFF Research Database (Denmark)

    Gram, Lone; Rasmussen, Bastian Barker; Wemheuer, Bernd

    2015-01-01

    in the environment is to date unknown. Here, we report on the repeated isolation of Phaeobacter inhibens strains from a marine environment (harbors) not related to aquaculture. Based on phenotype and 16S rRNA gene sequence similarity, a total of 64 P. inhibens strains were identified from 35 samples (eukaryotic...... and used for amplification of 16S rRNA. P. inhibens was detected in five of these samples, all of which were biofilm samples, by pyrotag-sequencing at a prevalence of 0.02–0.68% of the prokaryotic community. The results indicated that P. inhibens had a niche in biofilms of fouled surfaces in harbor areas...

  13. Phylogenomic analysis of marine Roseobacters.

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    Kai Tang

    2010-07-01

    Full Text Available Members of the Roseobacter clade which play a key role in the biogeochemical cycles of the ocean are diverse and abundant, comprising 10-25% of the bacterioplankton in most marine surface waters. The rapid accumulation of whole-genome sequence data for the Roseobacter clade allows us to obtain a clearer picture of its evolution.In this study about 1,200 likely orthologous protein families were identified from 17 Roseobacter bacteria genomes. Functional annotations for these genes are provided by iProClass. Phylogenetic trees were constructed for each gene using maximum likelihood (ML and neighbor joining (NJ. Putative organismal phylogenetic trees were built with phylogenomic methods. These trees were compared and analyzed using principal coordinates analysis (PCoA, approximately unbiased (AU and Shimodaira-Hasegawa (SH tests. A core set of 694 genes with vertical descent signal that are resistant to horizontal gene transfer (HGT is used to reconstruct a robust organismal phylogeny. In addition, we also discovered the most likely 109 HGT genes. The core set contains genes that encode ribosomal apparatus, ABC transporters and chaperones often found in the environmental metagenomic and metatranscriptomic data. These genes in the core set are spread out uniformly among the various functional classes and biological processes.Here we report a new multigene-derived phylogenetic tree of the Roseobacter clade. Of particular interest is the HGT of eleven genes involved in vitamin B12 synthesis as well as key enzynmes for dimethylsulfoniopropionate (DMSP degradation. These aquired genes are essential for the growth of Roseobacters and their eukaryotic partners.

  14. Does the colonization of new biogeographic regions influence the diversification and accumulation of clade richness among the Corvides (Aves: Passeriformes)?

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    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.

  15. Ecotype diversification of an abundant Roseobacter lineage.

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    Sun, Ying; Zhang, Yao; Hollibaugh, James T; Luo, Haiwei

    2017-04-01

    The Roseobacter DC5-80-3 cluster (also known as the RCA clade) is among the most abundant bacterial lineages in temperate and polar oceans. Previous studies revealed two phylotypes within this cluster that are distinctly distributed in the Antarctic and other ocean provinces. Here, we report a nearly complete genome co-assembly of three closely related single cells co-occurring in the Antarctic, and compare it to the available genomes of the other phylotype from ocean regions where iron is more accessible but phosphorus and nitrogen are less. The Antarctic phylotype exclusively contains an operon structure consisting of a dicitrate transporter fecBCDE and an upstream regulator likely for iron uptake, whereas the other phylotype consistently carry a high-affinity phosphate pst transporter and the phoB-phoR regulatory system, a high-affinity ammonium amtB transporter, urea and taurine utilization systems. Moreover, the Antarctic phylotype uses proteorhodopsin to acquire light, whereas the other uses bacteriochlorophyll-a and the sulfur-oxidizing sox cluster for energy acquisition. This is potentially an iron-saving strategy for the Antarctic phylotype because only the latter two pathways have iron-requiring cytochromes. Therefore, the two DC5-80-3 phylotypes, while diverging by only 1.1% in their 16S rRNA genes, have evolved systematic differences in metabolism to support their distinct ecologies. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. Regressive Evolution of Photosynthesis in the Roseobacter Clade

    Czech Academy of Sciences Publication Activity Database

    Koblížek, M.; Zeng, Y.; Horák, Aleš; Oborník, Miroslav

    2013-01-01

    Roč. 66, č. 2013 (2013), s. 385-405 ISSN 0065-2296 R&D Projects: GA MŠk ED2.1.00/03.0110; GA ČR GBP501/12/G055 Institutional support: RVO:60077344 Keywords : bacteriochlorophyll-a * bacteria * horizontal transfer Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.740, year: 2013

  17. Biofilm plasmids with a rhamnose operon are widely distributed determinants of the 'swim-or-stick' lifestyle in roseobacters.

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    Michael, Victoria; Frank, Oliver; Bartling, Pascal; Scheuner, Carmen; Göker, Markus; Brinkmann, Henner; Petersen, Jörn

    2016-10-01

    Alphaproteobacteria of the metabolically versatile Roseobacter group (Rhodobacteraceae) are abundant in marine ecosystems and represent dominant primary colonizers of submerged surfaces. Motility and attachment are the prerequisite for the characteristic 'swim-or-stick' lifestyle of many representatives such as Phaeobacter inhibens DSM 17395. It has recently been shown that plasmid curing of its 65-kb RepA-I-type replicon with >20 genes for exopolysaccharide biosynthesis including a rhamnose operon results in nearly complete loss of motility and biofilm formation. The current study is based on the assumption that homologous biofilm plasmids are widely distributed. We analyzed 33 roseobacters that represent the phylogenetic diversity of this lineage and documented attachment as well as swimming motility for 60% of the strains. All strong biofilm formers were also motile, which is in agreement with the proposed mechanism of surface attachment. We established transposon mutants for the four genes of the rhamnose operon from P. inhibens and proved its crucial role in biofilm formation. In the Roseobacter group, two-thirds of the predicted biofilm plasmids represent the RepA-I type and their physiological role was experimentally validated via plasmid curing for four additional strains. Horizontal transfer of these replicons was documented by a comparison of the RepA-I phylogeny with the species tree. A gene content analysis of 35 RepA-I plasmids revealed a core set of genes, including the rhamnose operon and a specific ABC transporter for polysaccharide export. Taken together, our data show that RepA-I-type biofilm plasmids are essential for the sessile mode of life in the majority of cultivated roseobacters.

  18. Horizontal transfers of two types of puf operons among phototrophic members of the Roseobacter clade

    Czech Academy of Sciences Publication Activity Database

    Koblížek, M.; Moulisová, V.; Muroňová, M.; Oborník, Miroslav

    2015-01-01

    Roč. 60, č. 1 (2015), s. 37-43 ISSN 0015-5632 R&D Projects: GA ČR GBP501/12/G055 Institutional support: RVO:60077344 Keywords : bacteria * diversity * sea Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.335, year: 2015

  19. Horizontal transfers of two types of puf operons among phototrophic members of the Roseobacter clade

    Czech Academy of Sciences Publication Activity Database

    Koblížek, Michal; Moulisová, Vladimíra; Muroňová, Markéta; Oborník, Miroslav

    2015-01-01

    Roč. 60, č. 1 (2015), s. 37-43 ISSN 0015-5632 R&D Projects: GA MŠk ED2.1.00/03.0110; GA ČR GAP501/10/0221; GA ČR GBP501/12/G055 Institutional support: RVO:61388971 Keywords : Rosebacter * horizontal transfer * puf operon s Subject RIV: EE - Microbiology, Virology Impact factor: 1.335, year: 2015

  20. VarR controls colonization and virulence in the marine macroalgal pathogen Nautella italica R11

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    Melissa eGardiner

    2015-10-01

    Full Text Available There is increasing evidence to suggest that macroalgae (seaweeds are susceptible to infectious disease. However, to date, little is known about the mechanisms that facilitate the colonization and virulence of microbial seaweed pathogens. One well-described example of a seaweed disease is the bleaching of the red alga Delisea pulchra, which can be caused by the bacterium Nautella italica R11, a member of the Roseobacter clade. This pathogen contains a unique luxR-type gene, varR, which we hypothesize controls its colonization and virulence. We show here that a varR knock-out strain is deficient in its ability to cause disease in D. pulchra and is defective in biofilm formation and attachment to a common algal polysaccharide. Moreover complementation of the varR gene in trans can restore these functions to the wild type levels. Proteomic analysis of bacterial cells in planktonic and biofilm growth highlight the potential importance of nitrogen scavenging, mobilization of energy reserves, and stress resistance in the biofilm lifestyle of N. italica R11. Moreover, we show that VarR regulates the expression of a specific subset of biofilm-associated proteins. Taken together these data suggest that VarR controls colonization and persistence of N. italica R11 on the surface of a macroalgal host and that it is an important regulator of virulence.

  1. Genetic Dissection of Tropodithietic Acid Biosynthesis by Marine Roseobacters

    DEFF Research Database (Denmark)

    Geng, Haifeng; Bruhn, Jesper Bartholin; Nielsen, Kristian Fog

    2008-01-01

    by the bacteria, and mutation in any one of these results in a loss of antibiotic activity (Tda(-)) and pigment production. Unexpectedly, six of the genes, referred to as tdaA-F, could not be found on the annotated TM1040 genome and were instead located on a previously unidentified plasmid (ca. 130 kb; pSTM3......The symbiotic association between the roseobacter Silicibacter sp. strain TM1040 and the dinoflagellate Pfiesteria piscicida involves bacterial chemotaxis to dinoflagellate-produced dimethylsulfoniopropionate (DMSP), DMSP demethylation, and ultimately a biofilm on the surface of the host. Biofilm...... formation is coincident with the production of an antibiotic and a yellow-brown pigment. In this report, we demonstrate that the antibiotic is a sulfur-containing compound, tropodithietic acid (TDA). Using random transposon insertion mutagenesis, 12 genes were identified as critical for TDA biosynthesis...

  2. Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis

    DEFF Research Database (Denmark)

    Sonnenschein, Eva; Nielsen, Kristian Fog; D'Alvise, Paul

    2017-01-01

    in the free-living fraction occurring in 40% and 6% of the samples, respectively. Our data and the TARA data, although lacking sufficient data from the polar regions, demonstrate that R. mobilis is a globally distributed marine bacterial species found primarily in the upper open oceans. It has preserved key....... Major genomic differences within the sub-clusters include prophages and toxin-antitoxin systems. In general, the genome of R. mobilis revealed adaptation to a particle-associated life style and querying TARA ocean data confirmed that R. mobilis is more abundant in the particle-associated fraction than...

  3. Ultrafast excited state processes in Roseobacter denitrificans antennae: comparison of isolated complexes and native membranes

    NARCIS (Netherlands)

    Ferretti, M.; Duquesne, K.; Sturgis, J.N.; van Grondelle, R.

    2014-01-01

    Roseobacter (Rsb.) denitrificans is a marine aerobic anoxygenic photosynthetic purple bacterium with an unusually high-800 nm absorption band. Ultrafast excited state processes have been intensively studied in the past in order to understand why the energy transfer efficiency between photosynthetic

  4. Roseobacter-Like Bacteria in Red and Mediterranean Sea Aerobic Anoxygenic Photosynthetic Populations

    Czech Academy of Sciences Publication Activity Database

    Oz, A.; Sabehi, G.; Koblížek, Michal; Massana, R.; Béja, O.

    2005-01-01

    Roč. 71, č. 1 (2005), s. 344-353 ISSN 0099-2240 R&D Projects: GA ČR GP206/03/P079; GA MŠk LN00A141 Institutional research plan: CEZ:AV0Z5020903 Keywords : Roseobacter * photosynthetic population Subject RIV: EE - Microbiology, Virology Impact factor: 3.818, year: 2005

  5. Culture conditions of Roseobacter strain 27-4 affect its attachment and biofilm formation as quantified by real-time PCR

    DEFF Research Database (Denmark)

    Bruhn, Jesper Bartholin; Haagensen, Janus Anders Juul; Bagge-Ravn, D.

    2006-01-01

    The fish probiotic bacterium Roseobacter strain 27-4 grows only as rosettes and produces its antibacterial compound under static growth conditions. It forms three-dimensional biofilms when precultured under static conditions. We quantified attachment of Roseobacter strain 27-4 using a direct real...

  6. Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage

    DEFF Research Database (Denmark)

    Billerbeck, Sara; Wemheuer, Bernd; Voget, Sonja

    2016-01-01

    The identification and functional characterization of microbial communities remains a prevailing topic in microbial oceanography as information on environmentally relevant pelagic prokaryotes is still limited. The Roseobacter group, an abundant lineage of marine Alphaproteobacteria, can constitute...... large proportions of the bacterioplankton. Roseobacters also occur associated with eukaryotic organisms and possess streamlined as well as larger genomes from 2.2 to >5 Mpb. Here, we show that one pelagic cluster of this group, CHAB-I-5, occurs globally from tropical to polar regions and accounts for up...

  7. Plasmid Transfer in the Ocean – A Case Study from the Roseobacter Group

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    Jörn Petersen

    2017-07-01

    Full Text Available Plasmid mediated horizontal gene transfer (HGT has been speculated to be one of the prime mechanisms for the adaptation of roseobacters (Rhodobacteraceae to their ecological niches in the marine habitat. Their plasmids contain ecologically crucial functional modules of up to ∼40-kb in size, e.g., for aerobic anoxygenic photosynthesis, flagellar formation and the biosynthesis of the antibiotic tropodithietic acid. Furthermore, the widely present type four secretion system (T4SS of roseobacters has been shown to mediate conjugation across genus barriers, albeit in the laboratory. Here we discovered that Confluentimicrobium naphthalenivorans NS6T, a tidal flat bacterium isolated in Korea, carries a 185-kb plasmid, which exhibits a long-range synteny with the conjugative 126-kb plasmid of Dinoroseobacter shibae DFL12T. Both replicons are stably maintained by RepABC operons of the same compatibility group (-2 and they harbor a homologous T4SS. Principal component analysis of the codon usage shows a large similarity between the two plasmids, while the chromosomes are very distinct, showing that neither of the two bacterial species represents the original host of those RepABC-2 type plasmids. The two species do not share a common habitat today and they are phylogenetically only distantly related. Our finding demonstrates the first clear-cut evidence for conjugational plasmid transfer across biogeographical and phylogenetic barriers in Rhodobacteraceae and documents the importance of conjugative HGT in the ocean.

  8. Structure and function of the tetraheme cytochrome associated to the reaction center of Roseobacter denitrificans.

    Science.gov (United States)

    Garcia, D; Richaud, P; Breton, J; Verméglio, A

    1994-01-01

    We have characterized the tetrahemic RC bound cytochrome isolated from the quasi-photosynthetic bacterium Roseobacter denitrificans in terms of absorption spectrum, redox property and orientation with respect to the membrane plane. The heme, designated H1, which possesses the highest redox midpoint potential (+290 mV), absorbs at 555 nm. Its plane makes an angle of 40 degrees with the membrane plane. The second high potential heme, H2 (+240 mV), peaks at 554 nm and makes a tilt of 55 degrees with the membrane. The two low potential hemes, L1 and L2, present a similar and rather high redox midpoint potential (+90 mV). They absorb at 553 nm and 550 nm. One of these hemes is oriented at 40 degrees while the other makes an angle of 90 degrees with the membrane plane. The soluble cytochrome c551 completes the cyclic electron transfer between the RC and the bc1 complex. Both the oxidation and the re-reduction of cytochrome c551 are diffusible processes. Under semi-aerobic conditions, one of the low potential hemes is photo-oxidized under illumination but only extremely slowly re-reduced. This explains the requirement of high aerobic conditions for growth of Roseobacter denitrificans cells in the light.

  9. 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

  10. Molecular origins and consequences of High-800 LH2 in Roseobacter denitrificans.

    Science.gov (United States)

    Duquesne, Katia; Blanchard, Cecile; Sturgis, James N

    2011-08-09

    Roseobacter denitrificans is a marine bacterium capable of using a wide variety of different metabolic schemes and in particular is an anoxygenic aerobic photosynthetic bacterium. In the work reported here we use a deletion mutant that we have constructed to investigate the structural origin of the unusual High-800 light-harvesting complex absorption in this bacterium. We suggest that the structure is essentially unaltered when compared to the usual nonameric complexes but that a change in the environment of the C(13:1) carbonyl group is responsible for the change in spectrum. We tentatively relate this change to the presence of a serine residue in the α-polypeptide. Surprisingly, the low spectral overlap between the peripheral and core light-harvesting systems appears not to compromise energy collection efficiency too severely. We suggest that this may be at the expense of maintaining a low antenna size. © 2011 American Chemical Society

  11. Colon cancer

    Science.gov (United States)

    Colorectal cancer; Cancer - colon; Rectal cancer; Cancer - rectum; Adenocarcinoma - colon; Colon - adenocarcinoma; Colon carcinoma ... eat may play a role in getting colon cancer. Colon cancer may be linked to a high-fat, ...

  12. Characterization and Complete Genome Sequences of Three N4-Like Roseobacter Phages Isolated from the South China Sea.

    Science.gov (United States)

    Li, Baolian; Zhang, Si; Long, Lijuan; Huang, Sijun

    2016-09-01

    Three bacteriophages (RD-1410W1-01, RD-1410Ws-07, and DS-1410Ws-06) were isolated from the surface water of Sanya Bay, northern South China Sea, on two marine bacteria type strains of the Roseobacter lineage. These phages have an isometric head and a short tail, morphologically belonging to the Podoviridae family. Two of these phages can infect four of seven marine roseobacter strains tested and the other one can infect three of them, showing relatively broader host ranges compared to known N4-like roseophages. One-step growth curves showed that these phages have similar short latent periods (1-2 h) but highly variable burst sizes (27-341 pfu cell(-1)). Their complete genomes show high level of similarities to known N4-like roseophages in terms of genome size, G + C content, gene content, and arrangement. The morphological and genomic features of these phages indicate that they belong to the N4likevirus genus. Moreover, comparative genomic analysis based on 43 N4-like phages (10 roseobacter phages and 33 phages infecting other lineages of bacteria) revealed a core genome of 18 genes shared by all the 43 phages and 38 genes shared by all the ten roseophages. The 38 core genes of N4-like roseophages nearly make up 70 % of each genome in length. Phylogenetic analysis based on the concatenated core gene products showed that our phage isolates represent two new phyletic branches, suggesting the broad genetic diversity of marine N4-like roseophages remains.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  15. Complete genome sequence of the bacteriochlorophyll a-containing Roseibacterium elongatum type strain (DSM 19469T), a representative of the Roseobacter group isolated from Australian coast sand

    Science.gov (United States)

    Riedel, Thomas; Fiebig, Anne; Göker, Markus; Klenk, Hans-Peter

    2014-01-01

    Roseibacterium elongatum Suzuki et al. 2006 is a pink-pigmented and bacteriochlorophyll a-producing representative of the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae. Representatives of the marine ‘Roseobacter group’ were found to be abundant in the ocean and play an important role in global and biogeochemical processes. In the present study we describe the features of R. elongatum strain OCh 323T together with its genome sequence and annotation. The 3,555,102 bp long genome consists of one circular chromosome with no extrachromosomal elements and is one of the smallest known Roseobacter genomes. It contains 3,540 protein-coding genes and 59 RNA genes. Genome analysis revealed the presence of a photosynthetic gene cluster, which putatively enables a photoheterotrophic lifestyle. Gene sequences associated with quorum sensing, motility, surface attachment, and thiosulfate and carbon monoxide oxidation could be detected. The genome was sequenced as part of the activities of the Transregional Collaborative Research Centre 51 (TRR51) funded by the German Research Foundation (DFG). PMID:25197467

  16. Complete genome sequence of the bacteriochlorophyll a-containing Roseibacterium elongatum type strain (DSM 19469(T)), a representative of the Roseobacter group isolated from Australian coast sand.

    Science.gov (United States)

    Riedel, Thomas; Fiebig, Anne; Göker, Markus; Klenk, Hans-Peter

    2014-06-15

    Roseibacterium elongatum Suzuki et al. 2006 is a pink-pigmented and bacteriochlorophyll a-producing representative of the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae. Representatives of the marine 'Roseobacter group' were found to be abundant in the ocean and play an important role in global and biogeochemical processes. In the present study we describe the features of R. elongatum strain OCh 323(T) together with its genome sequence and annotation. The 3,555,102 bp long genome consists of one circular chromosome with no extrachromosomal elements and is one of the smallest known Roseobacter genomes. It contains 3,540 protein-coding genes and 59 RNA genes. Genome analysis revealed the presence of a photosynthetic gene cluster, which putatively enables a photoheterotrophic lifestyle. Gene sequences associated with quorum sensing, motility, surface attachment, and thiosulfate and carbon monoxide oxidation could be detected. The genome was sequenced as part of the activities of the Transregional Collaborative Research Centre 51 (TRR51) funded by the German Research Foundation (DFG).

  17. 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 ...

  18. Co-Cultures of Pseudomonas aeruginosa and Roseobacter denitrificans Reveal Shifts in Gene Expression Levels Compared to Solo Cultures

    Directory of Open Access Journals (Sweden)

    Crystal A. Conway

    2012-01-01

    Full Text Available Consistent biosynthesis of desired secondary metabolites (SMs from pure microbial cultures is often unreliable. In a proof-of-principle study to induce SM gene expression and production, we describe mixed “co-culturing” conditions and monitoring of messages via quantitative real-time PCR (qPCR. Gene expression of model bacterial strains (Pseudomonas aeruginosa PAO1 and Roseobacter denitrificans Och114 was analyzed in pure solo and mixed cocultures to infer the effects of interspecies interactions on gene expression in vitro, Two P. aeruginosa genes (PhzH coding for portions of the phenazine antibiotic pathway leading to pyocyanin (PCN and the RhdA gene for thiosulfate: cyanide sulfurtransferase (Rhodanese and two R. denitrificans genes (BetaLact for metallo-beta-lactamase and the DMSP gene for dimethylpropiothetin dethiomethylase were assessed for differential expression. Results showed that R. denitrificans DMSP and BetaLact gene expression became elevated in a mixed culture. In contrast, P. aeruginosa co-cultures with R. denitrificans or a third species did not increase target gene expression above control levels. This paper provides insight for better control of target SM gene expression in vitro and bypass complex genetic engineering manipulations.

  19. 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.

  20. Colon interposition

    International Nuclear Information System (INIS)

    Isolauri, J.; Tampere Univ. Central Hospital; Paakkala, T.; Arajaervi, P.; Markkula, H.

    1987-01-01

    Colon interposition was carried out in 12 patients with oesophageal carcinoma and on 38 patients with benign oesophageal disease an average of 71 months before the radiographic examination. Various ischaemic changes including 'jejunization', loss of haustration and stricture formation were observed in 15 cases. In 12 patients one or several diverticula were seen in the colon graft. Reflux was observed in 17 cases in supine position. Double contrast technique in the examination of interposed colon is recommended. (orig.)

  1. Colonic lipoma

    International Nuclear Information System (INIS)

    Siddiqui, M.S.; Khatri, A.R.; Quraishy, M.S.; Fatima, L.; Muzaffar, S.

    2003-01-01

    Lipoma of the colon is rare and may lead to intestinal obstruct. We have presented two cases of colonic lipoma. Both were elderly females, one presented with diarrhea and the other with sub-acute intestinal obstruction. After colonoscopy surgical removal was done. Histopathology revealed lipoma. (author)

  2. Colonic angiodysplasia

    International Nuclear Information System (INIS)

    Vallee, C.; Legmann, P.; Garnier, T.; Levesque, M.

    1984-01-01

    The main clinical, endoscopic and radiographic findings in thirty documented cases of colonic angiodysplasia or vacular ectasia are described. We emphasise the association with colonic diverticulosis and cardiovascular pathology, describe the histological changes, summarize the present physiopathological hypothesis, and consider the various therapeutic approaches. (orig.)

  3. Colonic locomotion

    NARCIS (Netherlands)

    Dodou, D.

    2006-01-01

    The most effective screening method for colonic cancer is colonoscopy. However, colonoscopy cannot be easily embraced by the population because of the related pain intensity. Robotic devices that pull themselves forward through the colon are a possible alternative. The main challenge for such

  4. Cytogenetics of Legumes in the Phaseoloid Clade

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  6. Colon neoplasm

    International Nuclear Information System (INIS)

    Kimura F, K.

    1991-01-01

    The main aspects of colon neoplasms are described, including several factors that predispose the disease, the occurrence, the main biomedical radiography and the evaluation after the surgery. (C.G.C.)

  7. 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.

  8. increased specialisation causes the demise of animal clades

    OpenAIRE

    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...

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

    Science.gov (United States)

    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

  10. 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...

  11. Signature proteins for the major clades of Cyanobacteria

    Directory of Open Access Journals (Sweden)

    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

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. Colonic lymphoid follicles associated with colonic neoplasms

    International Nuclear Information System (INIS)

    Glick, S.N.; Teplick, S.K.; Ross, W.M.

    1986-01-01

    The authors prospectively evaluated 62 patients over 40 years old in whom lymphoid follicles were demonstrated on double-contrast enema examinations. Eighteen patients (29%) had no current radiographic evidence of, or history of, colonic neoplasms. Forty-four patients (71%) had an associated neoplasm. Fourteen patients had associated colonic carcinoma, and ten patients had a history of a previously resected colon cancer. One patient had previously undergone resection for ''polyps.'' Twenty-two patients had an associated ''polyp.'' There were no clinical or radiographic features that could reliably distinguish the neoplastic from the nonneoplastic groups. However, lymphoid follicles in the left colon or diffusely involving the colon were more likely to be associated with a colonic neoplasm. Lymphoid follicles were almost always identified near a malignant lesion

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

    Directory of Open Access Journals (Sweden)

    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.

  19. 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,...

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

    Science.gov (United States)

    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.

  1. Antegrade Colonic Lavage in Acute Colonic Obstruction

    OpenAIRE

    Foster, Michael E.; Johnson, Colin D.

    1986-01-01

    Conventional management of acute left sided colonic obstruction employs some form of proximal colostomy. Intraoperative antegrade colonic irrigation relieves proximal faecal loading and may permit safer primary resection and anastomosis. The results of a pilot study are presented, and are shown to be favourable.

  2. Management of Colonic Volvulus

    Science.gov (United States)

    Gingold, Daniel; Murrell, Zuri

    2012-01-01

    Colonic volvulus is a common cause of large bowel obstruction worldwide. It can affect all parts of the colon, but most commonly occurs in the sigmoid and cecal areas. This disease has been described for centuries, and was studied by Hippocrates himself. Currently, colonic volvulus is the third most common cause of large bowel obstruction worldwide, and is responsible for ∼15% of large bowel obstructions in the United States. This article will discuss the history of colonic volvulus, and the predisposing factors that lead to this disease. Moreover, the epidemiology and diagnosis of each type of colonic volvulus, along with the various treatment options will be reviewed. PMID:24294126

  3. Molecular Characterization of Natural Hybrids Formed between Five Related Indigenous Clade 6 Phytophthora Species

    Science.gov (United States)

    Burgess, Treena I.

    2015-01-01

    Most Phytophthora hybrids characterized to date have emerged from nurseries and managed landscapes, most likely generated as a consequence of biological invasions associated with the movement of living plants and germplasm for ornamental, horticultural and agricultural purposes. Presented here is evidence for natural hybridization among a group of five closely related indigenous clade 6 Phytophthora species isolated from waterways and riparian ecosystems in Western Australia. Molecular characterization of hybrids consisted of cloning and sequencing two nuclear genes (ITS and ASF), sequencing of two further nuclear loci (BT and HSP) and of two mitochondrial loci (COI and NADH). Additionally, phenotypic traits including morphology of sporangia and optima and maxima temperatures for growth were also determined. In most cases the nuclear genes were biparentally and in all cases the mtDNA were uniparentally inherited, indicating hybrid formation through sexual crosses. Some isolates bear the molecular signature of three parents suggesting additional hybrid events, although it cannot be determined from the data if these were sequential or simultaneous. These species and their hybrids co-exist in riparian ecosystems and waterways where their ability for rapid asexual proliferation would enable them to rapidly colonize green plant litter. The apparent ease of hybridization could eventually lead to the merging of species through introgression. However, at this point in time, species integrity has been maintained and a more likely scenario is that the hybrids are not stable evolutionary lineages, but rather transient hybrid clones. PMID:26248187

  4. Contrasting patterns of Andean diversification among three diverse clades of Neotropical clearwing butterflies.

    Science.gov (United States)

    Chazot, Nicolas; De-Silva, Donna Lisa; Willmott, Keith R; Freitas, André V L; Lamas, Gerardo; Mallet, James; Giraldo, Carlos E; Uribe, Sandra; Elias, Marianne

    2018-04-01

    The Neotropical region is the most biodiverse on Earth, in a large part due to the highly diverse tropical Andean biota. The Andes are a potentially important driver of diversification within the mountains and for neighboring regions. We compared the role of the Andes in diversification among three subtribes of Ithomiini butterflies endemic to the Neotropics, Dircennina, Oleriina, and Godyridina. The diversification patterns of Godyridina have been studied previously. Here, we generate the first time-calibrated phylogeny for the largest ithomiine subtribe, Dircennina, and we reanalyze a published phylogeny of Oleriina to test different biogeographic scenarios involving the Andes within an identical framework. We found common diversification patterns across the three subtribes, as well as major differences. In Dircennina and Oleriina, our results reveal a congruent pattern of diversification related to the Andes with an Andean origin, which contrasts with the Amazonian origin and multiple Andean colonizations of Godyridina. In each of the three subtribes, a clade diversified in the Northern Andes at a faster rate. Diversification within Amazonia occurred in Oleriina and Godyridina, while virtually no speciation occurred in Dircennina in this region. Dircennina was therefore characterized by higher diversification rates within the Andes compared to non-Andean regions, while in Oleriina and Godyridina, we found no difference between these regions. Our results and discussion highlight the importance of comparative approaches in biogeographic studies.

  5. Genotyping of Brucella species using clade specific SNPs

    Directory of Open Access Journals (Sweden)

    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.

  6. 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.

  7. 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.

    Directory of Open Access Journals (Sweden)

    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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. CT in colon cancer

    International Nuclear Information System (INIS)

    Fujita, Nobuyuki; Hasegawa, Takashi; Kubo, Kozo; Ogawa, Hajime; Sato, Yukihiko; Tomita, Masayoshi; Hanawa, Makoto; Matsuzawa, Tohru; Nishioka, Ken

    1990-01-01

    CT pictures from 59 lesions of advanced colon cancer including rectal cancer were reviewed to evaluate a role of CT in preoperative staging diagnosis. CT findings were recorded following general rules for clinical and pathological studies on cancer of colon rectum and anus, proposed by Japanese society for cancer of colon and rectum. Tumors were detected in 90% of advanced colon cancers. Sensitivity in local extension (S factor) was 58.0%. Sensitivity in lymphonode involvement (N factor) was 50.0%. Sensitivity in final staging diagnosis, dividing colon cancer into two groups below st II and above st III, was 63.3%. Further study should be necessitated to provide useful information for preoperative staging diagnosis of colon cancer. (author)

  14. An Act of Colonization

    DEFF Research Database (Denmark)

    Rasmussen, Anders Bo

    When Gideon Welles, U.S. Secretary of the Navy, sat down to write his diary entry on September 26, 1862, his thoughts turned once more to colonization. President Lincoln was an ardent proponent of colonization, “the government-promoted settlement of black Americans in Africa or some other location....... Croix. Thus, when the Lincoln administration seriously considered colonization plans in 1862, Danish Charge d’Affaires Waldemar Raasløff offered free transport for freedmen to the Caribbean island, where there was a “distinct lack of laborers.” As a small first step towards colonization, Denmark...

  15. Colon cancer screening

    Science.gov (United States)

    Screening for colon cancer; Colonoscopy - screening; Sigmoidoscopy - screening; Virtual colonoscopy - screening; Fecal immunochemical test; Stool DNA test; sDNA test; Colorectal cancer - screening; Rectal ...

  16. 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

  17. Ecological opportunity and incumbency in the diversification of repeated continental colonizations by muroid rodents.

    Science.gov (United States)

    Schenk, John J; Rowe, Kevin C; Steppan, Scott J

    2013-11-01

    Why some clades are more species-rich than others is a central question in macroevolution. Most hypotheses explaining exceptionally diverse clades involve the emergence of an ecological opportunity caused by a major biogeographic transition or evolution of a key innovation. The radiation of muroid rodents is an ideal model for testing theories of diversification rates in relation to biogeography and ecological opportunity because the group is exceptionally species-rich (comprising nearly one-third of all mammal species), it is ecologically diverse, and it has colonized every major landmass except New Zealand and Antarctica, thus providing multiple replicate radiations. We present an extension of the conventional ecological opportunity model to include a geographic incumbency effect, develop the largest muroid phylogeny to date, and use this phylogeny to test the new model. The nearly 300-species phylogeny based on four nuclear genes is robustly resolved throughout. Consistent with the fossil record, we identified Eurasia as the most likely origin of the group and reconstructed five to seven colonizations of Africa, five of North America, four of Southeast Asia, two of South America, two of Sahul, one of Madagascar, and eight to ten recolonizations of Eurasia. We accounted for incomplete taxon sampling by using multiple statistical methods and identified three corroborated regions of the tree with significant shifts in diversification rates. In several cases, higher rates were associated with the first colonization of a continental area, but most colonizations were not followed by bursts of speciation. We found strong evidence for diversification consistent with the ecological opportunity model (initial burst followed by density-dependent slowdown) in the first colonization of South America and partial support for this model in the first colonization of Sahul. Primary colonizers appear to inhibit the ultimate diversity of secondary colonizers, a pattern of

  18. CT Findings of Colonic Complications Associated with Colon Cancer

    International Nuclear Information System (INIS)

    Kim, Sang Won; Shin, Hyeong Cheol; Kim, Il Young; Kim, Young Tong; Kim, Chang Jin

    2010-01-01

    A broad spectrum of colonic complications can occur in patients with colon cancer. Clinically, some of these complications can obscure the presence of underlying malignancies in the colon and these complications may require emergency surgical management. The complications of the colon that can be associated with colon cancer include obstruction, perforation, abscess formation, acute appendicitis, ischemic colitis and intussusception. Although the majority of these complications only rarely occur, familiarity with the various manifestations of colon cancer complications will facilitate making an accurate diagnosis and administering prompt management in these situations. The purpose of this pictorial essay is to review the CT appearance of the colonic complications associated with colon cancer

  19. CT Findings of Colonic Complications Associated with Colon Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sang Won; Shin, Hyeong Cheol; Kim, Il Young; Kim, Young Tong; Kim, Chang Jin [Cheonan Hospital, Soonchunhyang University, Cheonan (Korea, Republic of)

    2010-04-15

    A broad spectrum of colonic complications can occur in patients with colon cancer. Clinically, some of these complications can obscure the presence of underlying malignancies in the colon and these complications may require emergency surgical management. The complications of the colon that can be associated with colon cancer include obstruction, perforation, abscess formation, acute appendicitis, ischemic colitis and intussusception. Although the majority of these complications only rarely occur, familiarity with the various manifestations of colon cancer complications will facilitate making an accurate diagnosis and administering prompt management in these situations. The purpose of this pictorial essay is to review the CT appearance of the colonic complications associated with colon cancer.

  20. Colon and rectal cancer

    International Nuclear Information System (INIS)

    Saldombide, L.; Cordoba, A.

    2010-01-01

    This study is about the diagnosis, therapy and monitoring of colon cancer. The techniques used are the endoscopy with biopsy in the pre and post operative colon surgery, abdominal ultrasound, chest X-ray studies of hemogram as well as liver and renal function

  1. Colon of the rat

    International Nuclear Information System (INIS)

    Lindstroem, C.G.; Rosengren, J.-E.; Fork, F.-T.

    1979-01-01

    The anatomy and radiologic appearance of the colon in rats are described on the basis of 300 animals treated with carcinogenic agents and 40 normal rats. The macroscopic and microscopic appearance of the mucosa varies in the different parts of the colon. Lymphoid plaques are normal structures. The results justify a new anatomic nomenclature. (Auth.)

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

    Directory of Open Access Journals (Sweden)

    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.

  3. 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...

  4. 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

  5. A Case of Sigmoid Colon Tuberculosis Mimicking Colon Cancer

    OpenAIRE

    Yu, Seong-Min; Park, Jong-Hwan; Kim, Min-Dae; Lee, Hee-Ryong; Jung, Peel; Ryu, Tae-Hyun; Choi, Seung-Ho; Lee, Il-Seon

    2012-01-01

    Tuberculosis of the sigmoid colon is a rare disorder. An 80-year-old man visited Bongseng Memorial Hospital for medical examination. A colonoscopy was performed, and a lesion in the sigmoid colon that was suspected to be colon cancer was found. A biopsy was performed, and tuberculous enteritis with chronic granulomatous inflammation was diagnosed. Intestinal tuberculosis is most frequent in the ileocecal area, followed by the ascending colon, transverse colon, duodenum, stomach, and sigmoid c...

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. 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.

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

    Science.gov (United States)

    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

  10. Bad Clade Deletion Supertrees: A Fast and Accurate Supertree Algorithm.

    Science.gov (United States)

    Fleischauer, Markus; Böcker, Sebastian

    2017-09-01

    Supertree methods merge a set of overlapping phylogenetic trees into a supertree containing all taxa of the input trees. The challenge in supertree reconstruction is the way of dealing with conflicting information in the input trees. Many different algorithms for different objective functions have been suggested to resolve these conflicts. In particular, there exist methods based on encoding the source trees in a matrix, where the supertree is constructed applying a local search heuristic to optimize the respective objective function. We present a novel heuristic supertree algorithm called Bad Clade Deletion (BCD) supertrees. It uses minimum cuts to delete a locally minimal number of columns from such a matrix representation so that it is compatible. This is the complement problem to Matrix Representation with Compatibility (Maximum Split Fit). Our algorithm has guaranteed polynomial worst-case running time and performs swiftly in practice. Different from local search heuristics, it guarantees to return the directed perfect phylogeny for the input matrix, corresponding to the parent tree of the input trees, if one exists. Comparing supertrees to model trees for simulated data, BCD shows a better accuracy (F1 score) than the state-of-the-art algorithms SuperFine (up to 3%) and Matrix Representation with Parsimony (up to 7%); at the same time, BCD is up to 7 times faster than SuperFine, and up to 600 times faster than Matrix Representation with Parsimony. Finally, using the BCD supertree as a starting tree for a combined Maximum Likelihood analysis using RAxML, we reach significantly improved accuracy (1% higher F1 score) and running time (1.7-fold speedup). © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  11. Carotenoids and colon cancer.

    Science.gov (United States)

    Slattery, M L; Benson, J; Curtin, K; Ma, K N; Schaeffer, D; Potter, J D

    2000-02-01

    Carotenoids have numerous biological properties that may underpin a role for them as chemopreventive agents. However, except for beta-carotene, little is known about how dietary carotenoids are associated with common cancers, including colon cancer. The objective of this study was to evaluate associations between dietary alpha-carotene, beta-carotene, lycopene, lutein, zeaxanthin, and beta-cryptoxanthin and the risk of colon cancer. Data were collected from 1993 case subjects with first primary incident adenocarcinoma of the colon and from 2410 population-based control subjects. Dietary data were collected from a detailed diet-history questionnaire and nutrient values for dietary carotenoids were obtained from the US Department of Agriculture-Nutrition Coordinating Center carotenoid database (1998 updated version). Lutein was inversely associated with colon cancer in both men and women [odds ratio (OR) for upper quintile of intake relative to lowest quintile of intake: 0.83; 95% CI: 0.66, 1.04; P = 0.04 for linear trend]. The greatest inverse association was observed among subjects in whom colon cancer was diagnosed when they were young (OR: 0.66; 95% CI: 0.48, 0.92; P = 0.02 for linear trend) and among those with tumors located in the proximal segment of the colon (OR: 0.65; 95% CI: 0.51, 0.91; P lettuce, tomatoes, oranges and orange juice, carrots, celery, and greens. These data suggest that incorporating these foods into the diet may help reduce the risk of developing colon cancer.

  12. 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

  13. 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

  14. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  16. CT findings of colonic diverticulitis

    International Nuclear Information System (INIS)

    Sasaki, Shigeru; Ohba, Satoru; Mizutani, Masaru

    1998-01-01

    Although colonic diverticulitis has no indication for operation, but in some mistaken cases were operated with a diagnosis of acute appendicitis. We evaluated the CT findings of colonic diverticulitis about 19 cases and of asymptomatic colonic diverticula about 15 cases retrospectively. Diagnosis was confirmed of barium enema and operation. CT are complementary methods of examination that can delineated the range of thickening of the colon and the extension of inflammatory changes around the colon. We also believe that CT findings of colonic diverticulitis are useful for differentiating from a diagnosis of appendicitis. (author)

  17. Complicated colonic intussusception

    Directory of Open Access Journals (Sweden)

    Justin James

    2012-01-01

    Full Text Available The manuscript deals with the case of a 53-year-old woman who developed large bowel obstruction. Per-rectal examination revealed a pedunculated lesion in the rectum; rigid sigmoidoscopy revealed a prolapsing pedunculated mass with a necrotic surface. The patient recovered well following anterior resection. Histology confirmed a pedunculated sub mucosal lipoma as the lead point for intussusception. Colonic intussusception is a rare cause of adult large bowel obstruction, and the preoperative clinical diagnosis of this condition can be difficult. Resection of the involved segment of the colon is the most appropriate choice of treatment in most such cases.

  18. Colonic potassium handling

    DEFF Research Database (Denmark)

    Sørensen, Mads Vaarby; Matos, Joana E.; Prætorius, Helle

    2010-01-01

    , intestinal K+ losses caused by activated ion secretion may become life threatening. This topical review provides an update of the molecular mechanisms and the regulation of mammalian colonic K+ absorption and secretion. It is motivated by recent results, which have identified the K+ secretory ion channel...... regulated by hormones and adapts readily to changes in dietary K+ intake, aldosterone and multiple local paracrine agonists. In chronic renal insufficiency, colonic K+ secretion is greatly enhanced and becomes an important accessory K+ excretory pathway. During severe diarrheal diseases of different causes...

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

    Directory of Open Access Journals (Sweden)

    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.

  20. 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....

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

    Directory of Open Access Journals (Sweden)

    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.

  2. Colonization, mouse-style

    Directory of Open Access Journals (Sweden)

    Searle Jeremy B

    2010-10-01

    Full Text Available Abstract Several recent papers, including one in BMC Evolutionary Biology, examine the colonization history of house mice. As well as background for the analysis of mouse adaptation, such studies offer a perspective on the history of movements of the humans that accidentally transported the mice. See research article: http://www.biomedcentral.com/1471-2148/10/325

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

    Directory of Open Access Journals (Sweden)

    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.

  4. 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

  5. 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...

  6. Schwannoma of the Colon

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    Ronaldo Nonose

    2009-09-01

    Full Text Available Schwannomas are neoplasms originating from Schwann cells, which are the cells forming nerve sheaths. These neoplasms generally involve peripheral nerves. They rarely affect the gastrointestinal tract and primary colon involvement is extremely rare. The objective of the present paper was to present a case of primary schwannoma of the sigmoid colon, unassociated with von Recklinghausen disease, that was histopathologically confirmed by means of an immunohistochemical panel. The patient was a 71-year-old woman who had had rectal bleeding when evacuating, with pain and tenesmus, for 4 months. She underwent colonoscopy, which identified a raised submucous lesion of 2.8 cm in diameter, located in the sigmoid colon, 30 cm from the anal margin. During examination, loop polypectomy with lesion excision was performed. Histopathological evaluation showed that this was a tumor of stromal origin. Its resection margins were compromised by neoplasia, and colon resection by means of videolaparoscopy was indicated. Conventional histopathological examination using the hematoxylin-eosin technique suggested that the neoplasm was of mesenchymal origin. An immunohistochemical panel was run for etiological confirmation, using anti-CD34 antibodies, desmin, cytokeratins (AE1/AE3, cKit, chromogranin and S-100 protein. The panel showed intense immunoexpression of S-100 protein. Investigation of the proliferative activity rate using Ki-67 antibodies showed that there was a low rate of mitotic activity, thus confirming the diagnosis of primary benign schwannoma of the colon. The patient’s postoperative evolution was uneventful and she remains in good health, without signs of tumor recurrence, 15 months after surgical excision.

  7. External coating of colonic anastomoses

    DEFF Research Database (Denmark)

    Pommergaard, Hans-Christian; Achiam, Michael Patrick; Rosenberg, Jacob

    2012-01-01

    Colon anastomotic leakage remains both a frequent and serious complication in gastrointestinal surgery. External coating of colonic anastomoses has been proposed as a means to lower the rate of this complication. The aim of this review was to evaluate existing studies on external coating of colonic...

  8. 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

    Directory of Open Access Journals (Sweden)

    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.

  9. Divergence times and colonization of the Canary Islands by Gallotia lizards.

    Science.gov (United States)

    Cox, Siobhan C; Carranza, Salvador; Brown, Richard P

    2010-08-01

    The Canary Islands have become a model region for evolutionary studies. We obtained 1.8 Kbp of mtDNA sequence from all known island forms of the endemic lizard genus Gallotia and from its sister taxon Psammodromus in order to reanalyze phylogenetic relationships within the archipelago, estimate lineage divergence times, and reconstruct the colonization history of this group. Well-supported phylogenies were obtained using maximum parsimony and Bayesian inference. Previous studies have been unable to establish the branching pattern at the base of the tree. We found evidence that G. stehlini (Gran Canaria) originated from the most basal Gallotia node and G. atlantica from the subsequent node. Divergence times were estimated under a global clock using Bayesian Markov Chain Monte Carlo methods implemented by three different programs: BEAST, MCMCTREE, MULTIDIVTIME. Node constraints were derived from subaerial island appearance data and were incorporated into the analyses as soft or hard maximal bounds. Posterior node ages differed slightly between programs, possibly due to different priors on divergence times. The most eastern Canary Islands first emerged just over 20 mya and their colonization appears to have taken place relatively quickly, around 17-20 mya. The subsequent node is consistent with cladogenesis due to colonization of Gran Canaria from the eastern islands about 11-13 mya. The western islands appear to have been colonized by a dispersal event from Lanzarote/Fuerteventura in the east to either La Gomera or one of the ancient edifices that subsequently formed Tenerife in the west, about 9-10 mya. Within the western islands, the most recent node that is ancestral to both the G. intermedia/G. gomerana/G. simonyi and the G.galloti/G. caesaris clades is dated at about 5-6 mya. Subsequent dispersal events between ancient Tenerife islands and La Gomera are dated at around 3 mya in both clades, although the direction of dispersal cannot be determined. Finally, we

  10. 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.

  11. 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.

  12. Outcomes of colon resection in patients with metastatic colon cancer.

    Science.gov (United States)

    Moghadamyeghaneh, Zhobin; Hanna, Mark H; Hwang, Grace; Mills, Steven; Pigazzi, Alessio; Stamos, Michael J; Carmichael, Joseph C

    2016-08-01

    Patients with advanced colorectal cancer have a high incidence of postoperative complications. We sought to identify outcomes of patients who underwent resection for colon cancer by cancer stage. The National Surgical Quality Improvement Program database was used to evaluate all patients who underwent colon resection with a diagnosis of colon cancer from 2012 to 2014. Multivariate logistic regression analysis was performed to investigate patient outcomes by cancer stage. A total of 7,786 colon cancer patients who underwent colon resection were identified. Of these, 10.8% had metastasis at the time of operation. Patients with metastatic disease had significantly increased risks of perioperative morbidity (adjusted odds ratio [AOR]: 1.44, P = .01) and mortality (AOR: 3.72, P = .01). Patients with metastatic disease were significantly younger (AOR: .99, P colon cancer have metastatic disease. Postoperative morbidity and mortality are significantly higher than in patients with localized disease. Published by Elsevier Inc.

  13. 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.

  14. 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

  15. Colonic motility and enema spreading

    International Nuclear Information System (INIS)

    Hardy, J.G.; Wood, E.; Clark, A.G.; Reynolds, J.R.; Queen's Medical Centre, Nottingham

    1986-01-01

    Radiolabelled enema solution was administered to eight healthy subjects, both in fasted and fed states. Enema spreading was monitored over a 4-h period using gamma scintigraphy and colonic motility was recorded simultaneously using a pressure sensitive radiotelemetry capsule. The rate and extent of enema dispersion were unaffected by eating. Spreading could be correlated with colonic motility and was inhibited by aboral propulsion of the colonic contents. (orig.)

  16. Vasohibin-1 suppresses colon cancer

    OpenAIRE

    Liu, Shuai; Han, Bing; Zhang, Qunyuan; Dou, Jie; Wang, Fang; Lin, Wenli; Sun, Yuping; Peng, Guangyong

    2015-01-01

    Vasohibin-1 (VASH1) is an endogenous angiogenesis inhibitor. However, the clinical relevance of VASH1 in colon cancer and its regulations on cancer angiogenesis and cancer cell biological characteristics are still unknown. Here we showed that stromal VASH1 levels were negatively correlated with tumor size, advanced clinical stage and distant metastases in colon cancer patients. Overexpression of VASH1 in colon cancer cells induced apoptosis and senescence, inhibiting cancer cell growth and co...

  17. Diffuse hemangioma of the colon

    International Nuclear Information System (INIS)

    Reis, J.; Caseiro-Alves, F.; Cruz, L.; Moreira, A.; Rebelo, O.

    1995-01-01

    We report two cases of diffuse hemangioma of the colon in adolescent patients. One patient had multiple phleboliths at the lower pelvis identified with plain radiographs of the abdomen. Several aspects were seen on double-contrast enema: luminal narrowing, colonic-wall thickening and submucosal colonic masses that changed in appearance with the degree of colonic distension. Angiography was inconclusive in one case. Use of CT and MR provided relevant information regarding the true extent of the disease, but MR was superior in demonstrating unequivocally the vascular nature of the lesions. (orig.)

  18. 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.

  19. MALToma of the Transverse colon, Ascending colon and Caecum: A ...

    African Journals Online (AJOL)

    TNHJOURNALPH

    RESULT. We herein report a case of a 40-year-old male with mucosa - associated lymphoid tissue. [MALT] lymphoma of the transverse colon, ascending colon and caecum. He presented with severe abdominal pains and a centrally located huge abdominal mass for which a surgical resection was done. Histologically.

  20. 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, ...

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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...

  7. 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

  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. 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

  10. 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

  11. 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

  12. 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

  13. Colonic duplication in an adult

    International Nuclear Information System (INIS)

    Baro, P.; Dario Casas, J.; Sanchez, D.

    1988-01-01

    A case of colonic duplication that was diagnosed radiologically in an adult is reported. A long duplicated segment below the normal transverse colon, with a wide anastomosis at the hepatic flexure level, was observed on barium enema. The rarity of this anomaly unassociated with other malformations is emphasized. (orig.)

  14. Prehistoric human colonization of India

    Indian Academy of Sciences (India)

    Unknown

    2. Earliest human colonization of south Asia. The early human colonization of south Asia is represented largely by an abundance of stone tool assemblages. The oldest known tools ..... component among finished tools is conspicuous in the hinterland riverine ...... sativum), green gram (Vigna radiata), gram/chicken pea.

  15. Colonic Diverticulitis in the Elderly

    Directory of Open Access Journals (Sweden)

    Chien-Kuo Liu

    2009-03-01

    Full Text Available Diverticular disease of the colon is a disease that mainly affects the elderly and presents in 50–70% of those aged 80 years or older. The most common complication is colonic diverticulitis. Eighty percent of patients who present with colonic diverticulitis are aged 50 years and older. Diagnosis and treatment of colonic diverticulitis in the elderly is more difficult and complicated owing to more comorbid conditions. Computed tomography is recommended for diagnosis when colonic diverticulitis is suspected. Most patients admitted with acute colonic diverticulitis respond to conservative treatment, but 15–30% of patients require surgery. Because surgery for acute colonic diverticulitis carries significant rates of morbidity and mortality, conservative treatment is recommended in the elderly. Conservative treatment of colonic diverticulitis with antibiotics, bowel rest, possibly including parenteral alimentation, is usually applied for 1–2 weeks. In the absence of a response to conservative treatment, frequent recurrence or complications (abscesses, fistulas, bowel obstructions, and free perforations, surgery is indicated.

  16. Colonic perforation following endoscopic retrograde ...

    African Journals Online (AJOL)

    She developed severe upper abdominal pain after the ... non-surgical management of pancreatitis and associated complications, colonic perforation should be considered in patients who deteriorate ... To our knowledge this is the first case of a secure pre-operative diagnosis of colonic perforation due to to pancreatitis.

  17. Diverticulosis of colon: Case report

    International Nuclear Information System (INIS)

    Han, Chang Yul

    1972-01-01

    The authors reports 2 cases of diverticulosis involving the sacending colon and cecum: one, 55 year old, 85 kg Korean male admitted to Paik Hospital because of abdominal palm, constipation and tenderness in the right lower abdomen. The other, 48 year old, 78 kg male visited to our hospital for the routine examination. According to late European and American statistics, the colonic diverticulosis was discovered in late middle life about 20%, however, the incidence of colonic diverticulosis is rare in Korea. This paper presents a brief review of literature on the etiology, incidence and symptom

  18. Vasohibin-1 suppresses colon cancer

    Science.gov (United States)

    Liu, Shuai; Han, Bing; Zhang, Qunyuan; Dou, Jie; Wang, Fang; Lin, Wenli; Sun, Yuping; Peng, Guangyong

    2015-01-01

    Vasohibin-1 (VASH1) is an endogenous angiogenesis inhibitor. However, the clinical relevance of VASH1 in colon cancer and its regulations on cancer angiogenesis and cancer cell biological characteristics are still unknown. Here we showed that stromal VASH1 levels were negatively correlated with tumor size, advanced clinical stage and distant metastases in colon cancer patients. Overexpression of VASH1 in colon cancer cells induced apoptosis and senescence, inhibiting cancer cell growth and colony formation in vitro and tumor growth in vivo. In addition, knockdown of VASH1 in cancer cells promoted cell growth, adhesion and migration in vitro, and enhanced tumorigenesis and metastasis in vivo. PMID:25797264

  19. Colonic motility in proctalgia fugax.

    Science.gov (United States)

    Harvey, R F

    1979-10-06

    Intraluminal pressure recordings were obtained from the rectum and sigmoid colon in two patients experiencing attacks of proctalgia fugax. In each patient the pain appeared to result from contractions of the sigmoid colon, and not from spasm of the levator ani, rectal wall muscle, or anal sphincters, all of which have previously been suggested as the source of such pain. Proctalgia fugax therefore appears, at least in some patients, to be an unusual variant of the irritable bowel syndrome, in which pain is referred from the sigmoid colon to the rectum.

  20. Vasohibin-1 suppresses colon cancer.

    Science.gov (United States)

    Liu, Shuai; Han, Bing; Zhang, Qunyuan; Dou, Jie; Wang, Fang; Lin, Wenli; Sun, Yuping; Peng, Guangyong

    2015-04-10

    Vasohibin-1 (VASH1) is an endogenous angiogenesis inhibitor.However, the clinical relevance of VASH1 in colon cancer and its regulations on cancer angiogenesis and cancer cell biological characteristics are still unknown. Here we showed that stromal VASH1 levels were negatively correlated with tumor size, advanced clinical stage and distant metastases in colon cancer patients. Overexpression of VASH1 in colon cancer cells induced apoptosis and senescence, inhibiting cancer cell growth and colony formation in vitro and tumor growth in vivo. In addition, knockdown of VASH1 in cancer cells promoted cell growth, adhesion and migration in vitro, and enhanced tumorigenesis and metastasis in vivo.

  1. Ancient lineage, young troglobites: recent colonization of caves by Nesticella spiders.

    Science.gov (United States)

    Zhang, Yuanyuan; Li, Shuqiang

    2013-09-04

    The evolution and origin of cave organisms is a recurring issue in evolutionary studies, but analyses are often hindered by the inaccessibility of caves, morphological convergence, and complex colonization processes. Here we investigated the evolutionary history of Nesticella cave spiders, which are mainly distributed in the Yunnan-Guizhou Plateau, China. With comprehensive sampling and phylogenetic and coalescent-based analyses, we investigated the tempo and mode of diversification and the origins of these troglobites. We also aimed to determine which factors have influenced the diversification of this little-known group. Coalescent-based species delimitation validated the 18 species recognized by morphological inspection and also suggested the existence of cryptic lineages. Divergence time estimates suggested that Nesticella cave spiders in the Yunnan-Guizhou Plateau constituted a monophyletic troglobite clade that originated in the middle Miocene (11.1-18.6 Ma). Although the Yunnan-Guizhou Plateau clade was composed exclusively of troglobite species, suggesting an ancient common subterranean ancestor, we favor multiple, independent cave colonizations during the Pleistocene over a single ancient cave colonization event to explain the origin of these cave faunas. The diversification of plateau Nesticella has been greatly influenced by the sequential uplift of the plateau and likely reflects multiple cave colonizations over time by epigean ancestors during Pleistocene glacial advances. We concluded that plateau cave Nesticella represent an ancient group of spiders, but with young troglobite lineages that invaded caves only recently. The absence of extant epigean relatives and nearly complete isolation among caves supported their relict status. Our work highlights the importance of comprehensive sampling for studies of subterranean diversity and the evolution of cave organisms. The existence of potentially cryptic species and the relict status of Nesticella

  2. Present diversity of Galápagos leaf-toed geckos (Phyllodactylidae: Phyllodactylus) stems from three independent colonization events.

    Science.gov (United States)

    Torres-Carvajal, Omar; Rodríguez-Guerra, Andrea; Chaves, Jaime A

    2016-10-01

    We re-examined the biogeography of the leaf-toed geckos (Phyllodactylus) endemic to the Galápagos Islands by analyzing for the first time samples of P. gilberti, a species endemic to Wolf island, in a phylogenetic framework. Our aim was to test the three-colonizations scenario previously proposed for these lizards and estimate the age of each colonization event. To achieve this we estimated simultaneously a species tree and divergence times with Bayesian methods. Our results supported the three-colonizations scenario. Similar to a previous hypothesis, the species tree obtained here showed that most species of Phyllodactylus are nested in a single clade with an age between 5.49 and 13.8Ma, whereas a second independent colonization corresponding to P. darwini from San Cristóbal island occurred 3.03Ma ago. The species from Wolf island, P. gilberti, stems from a more recent colonization event (0.69Ma). Thus, present diversity of Galápagos leaf-toed geckos stems from three independent, asynchronous colonization events. As with other Galápagos organisms, the Pacific coast of South America seems to be the source for the founders of P. gilberti. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. 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.

  4. 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.

  5. 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...

  6. 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.

  7. Colonization and environment

    International Nuclear Information System (INIS)

    Garcia Gutierrez, E.

    1999-01-01

    It stands out the man's paper in the deterioration of the soil and in the phenomenon of the desertization, the conflicts of the use of the soil in the country and the underestimate that it is made of this resource in the environmental analysis. The man's relationships are discussed with the earth and the problem of the soils of the Colombian Orinoquia is examined in terms of the excess of toxic elements as To the, Fe and Mn and the other elements like P, S, Ca, Mg, K, B, and Zn. It is examined the degradation and poverty of the organic complex of the soil, the physical degradation and chemistry and their susceptibility to the erosion, as well as the excess conditions and deficit of humidity. It is recognized that it lacks calibration of the analytic methods for the soils oxisoils of the Orinoquia and the Amazonia. The importance of the soils of the humid tropic is stood out as seat of colonization that have failed when not having an appropriate technology for its handling that it forces to undertake systems of migratory agriculture and to the transformation of the forest in prairie, phenomenon that comes accompanied by the degradation of the soils, illicit cultivations, social conflicts and alteration of the essential ecological processes for the survival

  8. Multidetector CT of the colon

    International Nuclear Information System (INIS)

    Luboldt, W.; Hoepffner, N.; Holzer, K.

    2003-01-01

    Multidetector technology, enabling faster imaging, higher spatial resolution and reduction in radiation dose, increases the role of CT in colonic diagnostic. The higher spatial resolution in the z-direction also changes the way to analyze the images. Instead of reading axial sections, now the colon can be systematically assessed in 3D by scrolling through multiplanar reconstructions or in CT colonography by virtual endoscopy. With ongoing improvements in computer-aided diagnosis CT colonography becomes an alternative to fiberoptic colonocopy for screening (http://www.multiorganscreening.org). In this article we propose a CT examination protocol for the colon, describe the typical imaging findings of different colonic diseases, and summarize the current status of CT colonography. (orig.)

  9. Understanding your colon cancer risk

    Science.gov (United States)

    ... for women and 2 drinks per day for men DO NOT smoke You can also have genetic testing done to assess your risk for colon cancer. If you have a strong family history of the disease, talk with your ...

  10. Colon Cleansing: Health or Hype?

    Science.gov (United States)

    ... cramps Dizziness Dehydration Bowel perforation Infection Depletion of probiotics, sodium and potassium Kidney damage Plus, colon cleansing ... goodbye to bacon, sausage, deli meats and hot dogs. Cancer-causing substances form when meats are preserved. ...

  11. 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 ...

  12. 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...

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  15. 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.

  16. Primary closure in colon trauma.

    Science.gov (United States)

    Salinas-Aragón, Luis Enrique; Guevara-Torres, Lorenzo; Vaca-Pérez, Enrique; Belmares-Taboada, Jaime Arístides; Ortiz-Castillo, Fátima de Guadalupe; Sánchez-Aguilar, Martín

    2009-01-01

    Primary repair of colon injuries is an accepted therapeutic option; however, controversy persists regarding its safety. Our objective was to report the evolution and presence of complications in patients with colon injury who underwent primary closure and to determine if the time interval (>6 h), degree of injury, contamination, anatomic site injured, PATI (Penetrating Abdominal Trauma Index) >25, and the presence of other injuries in colon trauma are associated with increased morbidity and mortality. This was a prospective, observational, longitudinal and descriptive study conducted at the Central Hospital "Dr. Ignacio Morones Prieto," San Luis Potosí, Mexico, from January 1, 2003 to December 31, 2007. We included patients with abdominal trauma with colon injury subjected to surgical treatment. chi(2) was used for basic statistical analysis. There were 481 patients with abdominal trauma who underwent surgery; 77(16.1%) had colon injury. Ninety percent (n = 69) were treated in the first 6 h; 91% (n = 70) were due to penetrating injuries, and gunshot wound accounted for 48% (n = 37). Transverse colon was the most frequently injured (38%) (n = 29). Grade I and II injuries accounted for 75.3% (n = 58). Procedures included primary repair (76.66 %) (n = 46); resection with anastomosis (8.3%) (n = 5); and colostomy (15%) (n = 9). Associated injuries were present in 76.6% (n = 59). There was some degree of contamination in 85.7% (n = 66); 82.8% (58) had PATI colon injury. Primary repair is a safe procedure for treatment of colon injuries. Patients with primary repair had lower morbidity (p <0.009). Surgery during the first 6 h (p <0.006) and in hemodynamically stable patients (p <0.014) had a lower risk of complications.

  17. Evolutionary relationships in the sand-dwelling cichlid lineage of lake tanganyika suggest multiple colonization of rocky habitats and convergent origin of biparental mouthbrooding.

    Science.gov (United States)

    Koblmüller, Stephan; Salzburger, Walter; Sturmbauer, Christian

    2004-01-01

    The cichlid species flock of Lake Tanganyika is comprised of seven seeding lineages that evolved in step with changes of the lake environment. One seeding lineage diversified into at least six lineages within a short period of time. Our study focuses on the diversification of one of these lineages, the Ectodini, comprising highly specialized, sand- and rock-dwelling species. They display two distinct breeding styles: maternal and biparental mouthbrooding. By analyzing three mtDNA gene segments in 30 species representing all 13 described genera, we show that the Ectodini rapidly diversified into four clades at the onset of their radiation. The monotypic genus Grammatotria is likely to represent the most ancestral split, followed by the almost contemporary origin of three additional clades, the first comprising the benthic genus Callochromis, the second comprising the benthic genera Asprotilapia, Xenotilapia, Enantiopus, and Microdontochromis, and the third comprising the semi-pelagic genera Ophthalmotilapia, Cardiopharynx, Cyathopharynx, Ectodus, Aulonocranus, Lestradea, and Cunningtonia. Our study confirms the benthic and sand-dwelling life-style as ancestral. Rocky habitats were colonized independently in the Xenotilapia- and Ophthalmotilapia-clade. The Xenotilapia-clade comprises both maternal and biparental mouthbrooders. Their mode of breeding appears to be highly plastic: biparental mouthbrooding either evolved once in the common ancestor of the clade, to be reverted at least three times, or evolved at least five times independently from a maternally mouthbrooding ancestor. Furthermore, the genera Xenotilapia, Microdontochromis, Lestradea, and Ophthalmotilapia appeared paraphyletic in our analyses, suggesting the need of taxonomic revision.

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

    Directory of Open Access Journals (Sweden)

    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.

  19. 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.

  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. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. Colon in acute intestinal infection.

    Science.gov (United States)

    Guarino, Alfredo; Buccigrossi, Vittoria; Armellino, Carla

    2009-04-01

    The colon is actively implicated in intestinal infections not only as a target of enteric pathogens and their products but also as a target organ for treatment. In the presence of diarrhea, both of osmotic and secretory nature, the colon reacts with homeostatic mechanisms to increase ion absorption. These mechanisms can be effectively exploited to decrease fluid discharge. A model of intestinal infections using rotavirus (RV) in colonic cells was set up and used to define a dual model of secretory and osmotic diarrhea in sequence. Using this model, antidiarrheal drugs were tested, namely zinc and the enkephalinase inhibitor racecadotril. Zinc was able to decrease the enterotoxic activity responsible for secretory diarrhea. It also inhibited the cytotoxic effect of RV. The mechanism of zinc was related at least in part to the activation of MAPK activity, but also a direct antiviral effect was observed. Racecadotril showed a potent and selective inhibition of active secretion, being particularly effective in the first phase of RV diarrhea. The use of drugs active at the colonic level, therefore, offers effective options to treat intestinal infections in childhood. In addition, the colon is the natural site of colonic microflora, a target of probiotic therapy, which is the first line of approach recommended by the European Society for Paediatric Gastroenterology, Hepatology and Nutrition to treat infectious diarrhea.

  10. Colonic diverticulosis is not a risk factor for colonic adenoma.

    Science.gov (United States)

    Hong, Wandong; Dong, Lemei; Zippi, Maddalena; Stock, Simon; Geng, Wujun; Xu, Chunfang; Zhou, Mengtao

    2018-01-01

    Colonic diverticulosis may represent a risk factor for colonic adenomas by virtue of the fact that evolving data suggest that these 2 conditions may share common risk factors such as Western dietary pattern and physical inactivity. This study aims to investigate the association between colonic diverticulosis and colonic adenomas in mainland China. We conducted a cross-sectional study on patients who underwent colonoscopic examination between October 2013 and December 2014 in a university hospital in mainland China. Age, gender, colonic adenomas, advanced adenomas, and distribution of diverticulosis were recorded during the procedures. Multivariate logistic regression and stratified analysis were used to evaluate the associations between the prevalence of diverticulosis and age, sex, and presence of colonic adenomas and advanced adenomas. A total of 17,456 subjects were enrolled. The prevalence of colonic diverticulosis and adenoma was 2.4% and 13.2%, respectively. With regard to distribution of diverticula, most (365/424, 86.1%) were right-sided. Multiple logistic regression analysis suggested that age and male gender were independent risk factors for adenoma and advanced adenoma. There was no relationship between diverticulosis or location of diverticulosis and presence of adenoma and advanced adenoma adjusting by age and gender. In a stratified analysis according to age and gender, similar results were also noted. There was no statistical relationship between diverticulosis and the risk of adenoma and advanced adenoma. Our results may not be generalized to the Western population due to the fact that left-sided diverticular cases were very small in our study.

  11. Colonization and environment

    International Nuclear Information System (INIS)

    Garcia Gutierrez, E.

    1999-01-01

    The environmental results of the colonization, process and their consequences are analyzed in the local, national and international order, the activities through which the acts on the means and the nature of these. It is examined the meaning of the sustainable development, the phenomenon of the exhaustion of the ecosystems and their responsible ones. It discusses the importance of the Orinoquia in the mark of the environmental problems in the international order, the region has been intensely exploded by means of intensive production systems, what has led to the exhaustion of these areas in the world environment. The colonist's paper is exposed in the environmental deterioration, in front of the function of the tropical humid forest and it confirms a focus that it approaches the environmental problem from a perspective that makes emphasis in the social component of that problem, in opposition to the conservators where the ecosystem is the only valid reason and the social groups that intervene him, they should simply disappear. It is necessary the necessity to focus of integral way, the colonist's nature like element of a social group, the list that completes in the mark of the nation and their development model, the political economic system and the nationality inside which makes their economic decisions and of production. It is recognized that they are not enough solutions of technical order to impact on the use and sustainable handling of the Orinoquia, but rather it should be contemplated the economic, social, environmental and political aspects of the problem simultaneously, as well as the growing and resolved participation of the social group in their group

  12. 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

  13. Enfermedad Diverticular del Colon

    Directory of Open Access Journals (Sweden)

    Gonzalo López Escobar

    1991-06-01

    Full Text Available

    Los divertículos del colon han sido reconocidos por varios observadores desde hace más de un siglo, pero en su mayor parte se trataba de casos aislados, hoy se la considera como la enfermedad del siglo XX, la de la era moderna y de los países industrializados y de avanzada tecnología (5,18,33.

    Según el diccionario de la Real Academia Española (11, divertículo, del latín, diverticulum, quiere decir desviación de un camino; y desde el punto de vista anatómico, apéndice hueco y terminado en fondo de saco. (Gráfica No. 1.

    Goligher (17 lo define como la “posada al borde del camino, probablemente un lugar, a menudo, de mala reputación”.

    Historia

    Según Hackford (18, el proceso fué descrito brevemente por Littre a comienzos del siglo XVIII; pero se le atribuye a Cruveilhier la primera descripción como proceso patológico en 1849, quien, además, mencionó: “encontramos, no rara vez, en el sigmoide, entre las bandas de fibras musculares longitudinales, una serie de pequeños tumores piriformes oscuros, que están formados por hernias de la mucosa a través de brechas en la capa muscular” (17.

    Fleischman en 1815 hizo la primera observación de la enfermedad y empleó el término divertículo (45.

    Rokitansky en 1.849, habló de una enfermedad adquirida y consideró que su causa consistía en la constipación (45.

    Virchowen 1853 describió la perisigmoiditis (45.

    En 1859 Sidney Jones informó de una fístula colo-vesical debida a diverticulitis (5,45.

    Loomis en 1870 describe una peritonitis como resultante de una diverticulitis (45.

    En 1877 Ball describió la anatomía patológica de la enfermedad y presentó dos casos de fístula colovesical debidas a diverticulitis (9. Cripps en 1.888 popularizó la colostomía de desviación como tratamiento para la fístula colovesical(18...

  14. Percutaneous drainage of colonic diverticular abscess: is colon resection necessary?

    Science.gov (United States)

    Gaertner, Wolfgang B; Willis, David J; Madoff, Robert D; Rothenberger, David A; Kwaan, Mary R; Belzer, George E; Melton, Genevieve B

    2013-05-01

    Recurrent diverticulitis has been reported in up to 30% to 40% of patients who recover from an episode of colonic diverticular abscess, so elective interval resection is traditionally recommended. The aim of this study was to review the outcomes of patients who underwent percutaneous drainage of colonic diverticular abscess without subsequent operative intervention. This was an observational study. This investigation was conducted at a tertiary care academic medical center and a single-hospital health system. Patients treated for symptomatic colonic diverticular abscess from 2002 through 2007 were included. The primary outcomes measured were complications, recurrence, and colectomy-free survival. Two hundred eighteen patients underwent percutaneous drainage of colonic diverticular abscesses. Thirty-two patients (15%) did not undergo subsequent colonic resection. Abscess location was pelvic (n = 9) and paracolic (n = 23), the mean abscess size was 4.2 cm, and the median duration of percutaneous drainage was 20 days. The comorbidities of this group of patients included severe cardiac disease (n = 16), immunodeficiency (n = 7), and severe pulmonary disease (n = 6). Freedom from recurrence at 7.4 years was 0.58 (95% CI 0.42-0.73). All recurrences were managed nonoperatively. Recurrence was significantly associated with an abscess size larger than 5 cm. Colectomy-free survival at 7.4 years was 0.17 (95% CI 0.13-0.21). This study was limited by its retrospective, nonexperimental design and short follow-up. In selected patients, observation after percutaneous drainage of colonic diverticular abscess appears to be a safe and low-risk management option.

  15. Complete colonic duplication in children.

    Science.gov (United States)

    Khaleghnejad Tabari, Ahmad; Mirshemirani, Alireza; Khaleghnejad Tabari, Nasibeh

    2012-01-01

    Complete colonic duplication is a very rare congenital anomaly that may have different presentations according to its location and size. Complete colonic duplication can occur in 15% of gastrointestinal duplication. We report two cases of complete colonic duplications, and their characteristics. We present two patients with complete colonic duplication with different types and presentations. Case 1: A 2- year old boy presented to the clinic with abdominal protrusion, difficulty to defecate, chronic constipation and mucosal prolaps covered bulging (rectocele) since he was 6 months old. The patient had palpable pelvic mass with doughy consistency. Rectal exam confirmed perirectal mass with soft consistency. The patient underwent a surgical operation that had total tubular colorectal duplication with one blind end and was treated with simple fenestration of distal end, and was discharged without complication. After two years follow up, he had normal defecation and good weight gain. Case 2: A 2 -day old infant was referred with imperforate anus and complete duplication of recto-sigmoid colon, diphallus, double bladder, and hypospadiasis. After clinical and paraclinical investigations, he underwent operations in several stages in different periods, and was discharged without complications. After four years follow up, he led a normal life. The patients with complete duplication have to be examined carefully because of the high incidence of other systemic anomalies. Treatment includes simple resection of distal common wall, fenestration, and repair other associated anomalies.

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

    Directory of Open Access Journals (Sweden)

    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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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...

  3. The Economics of Colon Cancer.

    Science.gov (United States)

    Orangio, Guy R

    2018-04-01

    The economic burden of cancer on the national health expenditure is billions of dollars. The economic cost is measured on direct and indirect medical costs, which vary depending on stage at diagnosis, patient age, type of medical services, and site of service. Costs vary by region, physician behavior, and patient preferences. When analyzing the economic burden of survivors of colon cancer, we cannot forget the societal burden. Post-acute care and readmissions are major economic burdens. People with colon cancer have to be followed for their lifetime. Economic models are being studied to give cost-effective solutions to this problem. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Neurological manifestation of colonic adenocarcinoma

    Directory of Open Access Journals (Sweden)

    Uzair Chaudhary

    2012-04-01

    Full Text Available Paraneoplastic neurologic disorders are extremely rare in cancer patients and are most commonly associated with certain tumors, such as ovarian cancer, small cell lung cancer, and breast cancer. We report here a paraneoplastic neurological syndrome in a 53-year-old man with colonic adenocarcinoma with a solitary liver metastasis. His paraneoplastic syndrome was successfully treated by methylprednisolone and primary oncologic therapies including neoadjuvant chemotherapy and definitive surgery. This is also the first documented case of simultaneous manifestation of a sensory neuropathy and limbic encephalitis with colon cancer.

  5. MALToma of the Transverse colon, Ascending colon and Caecum: A ...

    African Journals Online (AJOL)

    Background The stomach is the most common site formucosa - associated lymphoid tissue [MALT] lymphoma (MALToma). MALToma of the colon is a rare occurrence. It is on this background that we report this case. Methods The case records a patient with a MALT lymphoma and a review of the literature on the subject ...

  6. Speciation on a conveyor belt: sequential colonization of the hawaiian islands by Orsonwelles spiders (Araneae, Linyphiidae).

    Science.gov (United States)

    Hormiga, Gustavo; Arnedo, Miquel; Gillespie, Rosemary G

    2003-02-01

    Spiders of the recently described linyphiid genus Orsonwelles (Araneae, Linyphiidae) are one of the most conspicuous groups of terrestrial arthropods of Hawaiian native forests. There are 13 known Orsonwelles species, and all are single- island endemics. This radiation provides an excellent example of insular gigantism. We reconstructed the cladistic relationships of Orsonwelles species using a combination of morphological and molecular characters (both mitochondrial and nuclear sequences) within a parsimony framework. We explored and quantified the contribution of different character partitions and their sensitivity to changes in the traditional parameters (gap, transition, and transversion costs). The character data show a strong phylogenetic signal, robust to parameter changes. The monophyly of the genus Orsonwelles is strongly supported. The parsimony analysis of all character evidence combined recovered a clade with of all the non-Kauai Orsonwelles species; the species from Kauai form a paraphyletic assemblage with respect to the latter former clade. The biogeographic pattern of the Hawaiian Orsonwelles species is consistent with colonization by island progression, but alternative explanations for our data exist. Although the geographic origin of the radiation remains unknown, it appears that the ancestral colonizing species arrived first on Kauai (or an older island). The ambiguity in the area cladogram (i.e., post-Oahu colonization) is not derived from conflicting or unresolved phylogenetic signal among Orsonwelles species but rather from the number of taxa on the youngest islands. Speciation in Orsonwelles occurred more often within islands (8 of the 12 cladogenic events) than between islands. A molecular clock was rejected for the sequence data. Divergence times were estimated by using the nonparametric rate smoothing method of Sanderson (1997, Mol. Biol. Evol. 14:1218-1231) and the available geological data for calibration. The results suggest that the

  7. Evolving colon injury management: a review.

    Science.gov (United States)

    Greer, Lauren T; Gillern, Suzanne M; Vertrees, Amy E

    2013-02-01

    The colon is the second most commonly injured intra-abdominal organ in penetrating trauma. Management of traumatic colon injuries has evolved significantly over the past 200 years. Traumatic colon injuries can have a wide spectrum of severity, presentation, and management options. There is strong evidence that most non-destructive colon injuries can be successfully managed with primary repair or primary anastomosis. The management of destructive colon injuries remains controversial with most favoring resection with primary anastomosis and others favor colonic diversion in specific circumstances. The historical management of traumatic colon injuries, common mechanisms of injury, demographics, presentation, assessment, diagnosis, management, and complications of traumatic colon injuries both in civilian and military practice are reviewed. The damage control revolution has added another layer of complexity to management with continued controversy.

  8. Colon Trauma: Evidence-Based Practices.

    Science.gov (United States)

    Yamamoto, Ryo; Logue, Alicia J; Muir, Mark T

    2018-01-01

    Colon injury is not uncommon and occurs in about a half of patients with penetrating hollow viscus injuries. Despite major advances in the operative management of penetrating colon wounds, there remains discussion regarding the appropriate treatment of destructive colon injuries, with a significant amount of scientific evidence supporting segmental resection with primary anastomosis in most patients without comorbidities or large transfusion requirement. Although literature is sparse concerning the management of blunt colon injuries, some studies have shown operative decision based on an algorithm originally defined for penetrating wounds should be considered in blunt colon injuries. The optimal management of colonic injuries in patients requiring damage control surgery (DCS) also remains controversial. Studies have recently reported that there is no increased risk compared with patients treated without DCS if fascial closure is completed on the first reoperation, or that a management algorithm for penetrating colon wounds is probably efficacious for colon injuries in the setting of DCS as well.

  9. Conservative management of colonic injury during percutaneous ...

    African Journals Online (AJOL)

    M. Elghoneimy

    2016-02-22

    Feb 22, 2016 ... Patients' records were searched for the occurrence of colonic injury. Records were ... tion to opacify the system and the percutaneous renal access was .... identify the presence of a retrorenal colon, yet the rarity of such a.

  10. Continuous Exposure Of Vibrio Anguillarum To Tropodithietic Acid: Genetic Changes And Influence On Virulence

    DEFF Research Database (Denmark)

    Rasmussen, Bastian Barker; D'Alvise, Paul; Grotkjær, Torben

    2015-01-01

    Introduction: The fish pathogen Vibrio anguillarum is a major problem in aquaculture causing Vibriosis. Bacteria of the Roseobacter clade can antagonize pathogenic vibrios in cultures in live feed such as microalgae, rotifers and Artemia, as well as in fish larvae. Therefore, roseobacters could...

  11. Toxicity of Bioactive and Probiotic Marine Bacteria and Their Secondary Metabolites in Artemia sp. and Caenorhabditis elegans as Eukaryotic Model Organisms

    DEFF Research Database (Denmark)

    Neu, Anna; Månsson, Maria; Gram, Lone

    2014-01-01

    We have previously reported that some strains belonging to the marine Actinobacteria class, the Pseudoalteromonas genus, the Roseobacter clade, and the Photobacteriaceae and Vibrionaceae families produce both antibacterial and antivirulence compounds, and these organisms are interesting from......-producing Roseobacter bacteria as a promising group to be used as probiotics in aquaculture, whereas Actinobacteria, Pseudoalteromonas, Photobacteriaceae, and Vibrionaceae should be used with caution....

  12. 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).

  13. 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.

  14. 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.

  15. 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.

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  18. 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.

  19. Prehistoric human colonization of India

    Indian Academy of Sciences (India)

    Unknown

    J. Biosci. | Vol. 26 | No. 4 | Suppl. | November 2001. V N Misra. 492 ... humans differ from the other apes in their upright posture, ... characterized by Levallois flakes and blades and by the ... and the coastal region running parallel to them, northeast ..... November 2001. Prehistoric human colonization of India. 497. Figure 1.

  20. 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.

  1. 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

  2. Acute pseudo-obstruction of the colon

    International Nuclear Information System (INIS)

    Beese, M.; Heller, M.

    1988-01-01

    The radiological correlate to the pseudo-obstruction of the colon is not specific, but it does supply a pointer to the disease of it shows dilation of the caecum, colon ascendens and colon transversum with air-pockets and reflected imaging as well as a usually not dilated colon descendens with remarkably little air. To make the diagnosis quite sure we must exclude intestinal obstruction by using X-ray contrast media or by coloscopy. (orig./GDG) [de

  3. Laparoscopic colectomy for transverse colon carcinoma.

    Science.gov (United States)

    Zmora, O; Bar-Dayan, A; Khaikin, M; Lebeydev, A; Shabtai, M; Ayalon, A; Rosin, D

    2010-03-01

    Laparoscopic resection of transverse colon carcinoma is technically demanding and was excluded from most of the large trials of laparoscopic colectomy. The aim of this study was to assess the safety, feasibility, and outcome of laparoscopic resection of carcinoma of the transverse colon. A retrospective review was performed to identify patients who underwent laparoscopic resection of transverse colon carcinoma. These patients were compared to patients who had laparoscopic resection for right and sigmoid colon carcinoma. In addition, they were compared to a historical series of patients who underwent open resection for transverse colon cancer. A total of 22 patients underwent laparoscopic resection for transverse colon carcinoma. Sixty-eight patients operated for right colon cancer and 64 operated for sigmoid colon cancer served as comparison groups. Twenty-four patients were identified for the historical open group. Intraoperative complications occurred in 4.5% of patients with transverse colon cancer compared to 5.9% (P = 1.0) and 7.8% (P = 1.0) of patients with right and sigmoid colon cancer, respectively. The early postoperative complication rate was 45, 50 (P = 1.0), and 37.5% (P = 0.22) in the three groups, respectively. Conversion was required in 1 (5%) patient in the laparoscopic transverse colon group. The conversion rate and late complications were not significantly different in the three groups. There was no significant difference in the number of lymph nodes harvested in the laparoscopic and open groups. Operative time was significantly longer in the laparoscopic transverse colectomy group when compared to all other groups (P = 0.001, 0.008, and transverse colectomy, respectively). The results of laparoscopic colon resection for transverse colon carcinoma are comparable to the results of laparoscopic resection of right or sigmoid colon cancer and open resection of transverse colon carcinoma. These results suggest that laparoscopic resection of transverse

  4. CALCIUM AND THE PREVENTION OF COLON CANCER

    NARCIS (Netherlands)

    WELBERG, JWM; KLEIBEUKER, JH; VANDERMEER, R; MULDER, NH; DEVRIES, EGE

    1991-01-01

    Diet is a major determinant of colon cancer risk. Calcium may protect against colon cancer, presumably by binding cytotoxic bile acids and fatty acids. Numerous studies support this proposition. In subjects at risk for colon cancer oral calcium supplementation has been shown to reduce rectal

  5. Congenital Diverticular Disease of the Entire Colon

    Directory of Open Access Journals (Sweden)

    A. Patel

    2013-01-01

    Full Text Available Congenital or true colonic diverticulosis is a rare condition typified by the preservation of the colonic wall architecture within the diverticular outpouching. Cases of multiple jejunal diverticula have been reported as well as cases of solitary giant diverticula of the colon. There have been no reports in the literature of pancolonic congenital diverticulosis.

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

    Directory of Open Access Journals (Sweden)

    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.

  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. Control of Colon Cancer Progression by the Colon Microbiome

    Science.gov (United States)

    2015-08-01

    Award  Number:    W81XWH-­14-­1-­0235   TITLE:      Control of Colon Cancer Progression by the Colon Microbiome PRINCIPAL  INVESTIGATOR:    Frank  J... Microbiome Table  of  Contents   Page   1. Introduction………………………………………………………….4 2. Keywords…………………………………………………………….5 3. Accomplishments………..…………………………………………5

  10. 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

  11. 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

  12. Transverse loop colostomy and colonic motility.

    Science.gov (United States)

    Pucciani, F; Ringressi, M N; Maltinti, G; Bechi, P

    2014-11-01

    The motility of the defunctionalized colon, distal to transverse loop colostomy, has never been studied "in vivo." The aim of our study was to evaluate the influence of transverse loop colostomy on colonic motility. Thirteen patients were examined before stoma closure by means of clinical evaluation and colonic manometry; we studied both the right and distal colon in both fasting and fed patients in order to detect motor activity. Quantitative and qualitative manometric analyses showed that the diverted colon had motor activity even if no regular colonic motor pattern was observed. The spreading of aboral propagated contractions (PCs) was sometimes recorded from the right colon to the distal colon. The response of the proximal and distal colon to a standard meal, when compared to fasting values, increased more than 40 and 35 %, respectively. Stool and gas ejections from the colostomy were never related to a particular type of colonic motility: Motor quiescence such as PCs was chaotically related to stool escape. In conclusion, motility of the defunctionalized colon is preserved in patients with transverse loop colostomy.

  13. 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.

  14. Colonization of overlaying water by bacteria from dry river sediments.

    Science.gov (United States)

    Fazi, Stefano; Amalfitano, Stefano; Piccini, Claudia; Zoppini, Annamaria; Puddu, Alberto; Pernthaler, Jakob

    2008-10-01

    We studied the diversity, community composition and activity of the primary microbial colonizers of the water above freshly re-wetted sediments from a temporary river. Dried sediments, collected from Mulargia River (Sardinia, Italy), were covered with sterile freshwater in triplicate microcosms, and changes of the planktonic microbial assemblage were monitored over a 48 h period. During the first 9 h bacterial abundance was low (1.5 x 10(4) cells ml(-1)); it increased to 3.4 x 10(6) cells ml(-1) after 28 h and did not change thereafter. Approximately 20% of bacteria exhibited DNA de novo synthesis already after 9 h of incubation. Changes of the ratios of (3)H-leucine to (3)H-thymidine incorporation rates indicated a shift of growth patterns during the experiment. Extracellular enzyme activity showed a maximum at 48 h with aminopeptidase activity (430.8 +/- 22.6 nmol MCA l(-1) h(-1)) significantly higher than alkaline phosphatase (98.6 +/- 4.3 nmol MUF l(-1) h(-1)). The primary microbial colonizers of the overlaying water - as determined by 16S rRNA gene sequence analysis - were related to at least six different phylogenetic lineages of Bacilli and to Alphaproteobacteria (Brevundimonas spp. and Caulobacter spp.). Large bacterial cells affiliated to one clade of Bacillus sp. were rare in the dried sediments, but constituted the majority of the planktonic microbial assemblage and of cells with detectable DNA-synthesis until 28 h after re-wetting. Their community contribution decreased in parallel with a rise of flagellated and ciliated protists. Estimates based on cell production rates suggested that the rapidly enriched Bacillus sp. suffered disproportionally high loss rates from selective predation, thus favouring the establishment of a more heterogenic assemblage of microbes (consisting of Proteobacteria, Actinobacteria and Cytophaga-Flavobacteria). Our results suggest that the primary microbial colonizers of the water above dried sediments are passively released

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

    Directory of Open Access Journals (Sweden)

    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

  16. 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.

  17. Schwannoma of the sigmoid colon

    OpenAIRE

    Çakır, Tuğrul; Aslaner, Arif; Yaz, Müjgan; Gündüz, Umut rıza

    2015-01-01

    Colonic schwannomas are very rare gastrointestinal tumours originating from Schwann cells, which form the neural sheath. Primary schwannomas of the lower gastrointestinal tract are very rare and usually benign in nature. However, if they are not surgically removed, malign degeneration can occur. We report a case of a 79-year-old woman who presented to our clinic with rectal bleeding and constipation. She underwent a lower gastrointestinal tract endoscopy. A mass subtotally obstructing the lum...

  18. Oral yeast colonization throughout pregnancy

    OpenAIRE

    Rio, Rute; Sim?es-Silva, Liliana; Garro, Sofia; Silva, M?rio-Jorge; Azevedo, ?lvaro; Sampaio-Maia, Benedita

    2017-01-01

    Background Recent studies suggest that placenta may harbour a unique microbiome that may have origin in maternal oral microbiome. Although the major physiological and hormonal adjustments observed in pregnant women lead to biochemical and microbiological modifications of the oral environment, very few studies evaluated the changes suffered by the oral microbiota throughout pregnancy. So, the aim of our study was to evaluate oral yeast colonization throughout pregnancy and to compare it with n...

  19. 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.

  20. 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.

  1. 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.

  2. Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae based on sequence capture data

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    Alejandra Panzera

    2017-10-01

    Full Text Available The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenus Liolaemus sensu stricto, and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in the phylogeny, because only a few loci (nine were recovered for this species. Topologies or support values did not change dramatically upon exclusion of L. t. tenuis from analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships between L. fuscus, L. monticola, L. nigroviridis and L. nitidus, and L. platei and L. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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).

  9. Oral yeast colonization throughout pregnancy.

    Science.gov (United States)

    Rio, R; Simões-Silva, L; Garro, S; Silva, M-J; Azevedo, Á; Sampaio-Maia, B

    2017-03-01

    Recent studies suggest that placenta may harbour a unique microbiome that may have origin in maternal oral microbiome. Although the major physiological and hormonal adjustments observed in pregnant women lead to biochemical and microbiological modifications of the oral environment, very few studies evaluated the changes suffered by the oral microbiota throughout pregnancy. So, the aim of our study was to evaluate oral yeast colonization throughout pregnancy and to compare it with non-pregnant women. The oral yeast colonization was assessed in saliva of 30 pregnant and non-pregnant women longitudinally over a 6-months period. Demographic information was collected, a non-invasive intra-oral examination was performed and saliva flow and pH were determined. Pregnant and non-pregnant groups were similar regarding age and level of education. Saliva flow rate did not differ, but saliva pH was lower in pregnant than in non-pregnant women. Oral yeast prevalence was higher in pregnant than in non-pregnant women, either in the first or in the third trimester, but did not attain statistical significance. In individuals colonized with yeast, the total yeast quantification (Log10CFU/mL) increase from the 1st to the 3rd trimester in pregnant women, but not in non-pregnant women. Pregnancy may favour oral yeast growth that may be associated with an acidic oral environment.

  10. CT staging of colon cancer

    Energy Technology Data Exchange (ETDEWEB)

    Dighe, S. [Department of Radiology, Royal Marsden Hospital, Sutton SM5 2TT (United Kingdom); Swift, I. [Department of Surgery, Mayday University Hospital, Croydon CR7 7YE (United Kingdom); Brown, G. [Department of Radiology, Royal Marsden Hospital, Sutton SM5 2TT (United Kingdom)], E-mail: gina.brown@rmh.nhs.uk

    2008-12-15

    Computer tomography (CT) has been the principal investigation in the staging of colon cancers. The information obtained with routine CT has been limited to identifying the site of the tumour, size of the tumour, infiltration into surrounding structures and metastatic spread. The Foxtrot trial National Cancer Research Institute (NCRI) has been specifically designed to evaluate the efficacy of neoadjuvant treatment in colon cancers by using preoperative chemotherapy with or without an anti-Epidermal Growth Factor Receptor (EGFR) monoclonal antibody to improve outcome in high-risk operable colon cancer. Patients are selected based on their staging CT examination. The criteria for poor prognosis are T4 and T3 tumours with more than 5 mm extramural depth. Thus the success of the trial would depend upon the confidence of the radiologist to identify the patients that would receive the neoadjuvant treatment. The aim of this review is to explain the process of identifying high-risk features seen on the staging CT images. This will help to identify a cohort of patients that could truly benefit from neoadjuvant strategies.

  11. CT staging of colon cancer

    International Nuclear Information System (INIS)

    Dighe, S.; Swift, I.; Brown, G.

    2008-01-01

    Computer tomography (CT) has been the principal investigation in the staging of colon cancers. The information obtained with routine CT has been limited to identifying the site of the tumour, size of the tumour, infiltration into surrounding structures and metastatic spread. The Foxtrot trial National Cancer Research Institute (NCRI) has been specifically designed to evaluate the efficacy of neoadjuvant treatment in colon cancers by using preoperative chemotherapy with or without an anti-Epidermal Growth Factor Receptor (EGFR) monoclonal antibody to improve outcome in high-risk operable colon cancer. Patients are selected based on their staging CT examination. The criteria for poor prognosis are T4 and T3 tumours with more than 5 mm extramural depth. Thus the success of the trial would depend upon the confidence of the radiologist to identify the patients that would receive the neoadjuvant treatment. The aim of this review is to explain the process of identifying high-risk features seen on the staging CT images. This will help to identify a cohort of patients that could truly benefit from neoadjuvant strategies

  12. 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...

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

    Directory of Open Access Journals (Sweden)

    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

  14. The Neogene rise of the tropical Andes facilitated diversification of wax palms (Ceroxylon: Arecaceae) through geographical colonization and climatic niche separation

    DEFF Research Database (Denmark)

    Sanín, María José; Kissling, W. Daniel; Bacon, Christine D.

    2016-01-01

    The tropical Andes are a biodiversity hotspot, partly due to their rich and complex floristic composition. A fundamental question regarding this outstanding biodiversity is what role the Andean orogeny has played in species diversification. Ceroxylon is a genus of endemic Andean palms that stands...... gradients. Ancestral areas were reconstructed under a model allowing for founder-event speciation and climatic niches were inferred from climatic variables at present-day occurrences of all species. Niche evolution in a phylogenetic framework was evaluated by testing differences between the climatic niches...... of clades. Our analyses identified four main clades, with a general pattern of diversification through geographical colonization from south to north after the Pliocene uplift of the northern Andes. Adaptation to low temperatures was conserved at the generic level, with climatic niche differentiation among...

  15. Cell proliferation and ageing in mouse colon

    International Nuclear Information System (INIS)

    Hamilton, E.; Franks, L.M.

    1980-01-01

    Cell kinetic parameters in the descending colon of unirradiated mice, 3-30-months-old were compared with those in mice irradiated repeatedly from the age of 6 or 24 months. The latter animals were given 1250 rad local X-irradiation to the colon every 6 weeks. Dose-survival curves showed the colon crypts of 6 and 24-months-old mice were similarly radiosensitive. In unirradiated mice the number of crypts per colon section decreased significantly at 30 months, but no significant age-related changes were seen in crypt size or labelling index (LI). Cell proliferation returned to control levels within 6 weeks of each X-ray dose and remained at this level for 20 weeks after the final dose. Later, cell proliferation in the irradiated colon fell significantly below control. A total of 6 or 7 doses each of 1250 rad produced only 1 colon carcinoma amongst 50 mice kept until they died. (author)

  16. Historical and Current Trends in Colon Trauma

    Science.gov (United States)

    Causey, Marlin Wayne; Rivadeneira, David E.; Steele, Scott R.

    2012-01-01

    The authors discuss the evolution of the evaluation and management of colonic trauma, as well as the debate regarding primary repair versus fecal diversion. Their evidence-based review covers diagnosis, management, surgical approaches, and perioperative care of patients with colon-related trauma. The management of traumatic colon injuries has evolved significantly over the past 50 years; here the authors describe a practical approach to the treatment and management of traumatic injuries to the colon based on the most current research. However, management of traumatic colon injuries remains a challenge and continues to be associated with significant morbidity. Familiarity with the different methods to the approach and management of colonic injuries will allow surgeons to minimize unnecessary complications and mortality. PMID:24294119

  17. Complications of acromegaly: thyroid and colon.

    Science.gov (United States)

    Tirosh, Amit; Shimon, Ilan

    2017-02-01

    In acromegaly the long-term exposure to high growth hormone (GH) and insulin-like growth factor-1 (IGF-1) levels may result in specific complications in different human organs, including the thyroid gland and the colon. We will review here the evidence available regarding the characteristic thyroid and colon complications in acromegaly. This review summarizes the published data observing noncancerous structural abnormalities (thyroid nodules, colonic polyps) and thyroid and colon cancer in patients diagnosed with acromegaly. Thyroid micro-carcinomas are probably over-diagnosed among acromegalic patients. In regard to colon cancer, there is no sufficient data to suggest that colon cancer risk is higher in acromegaly compared to the general population.

  18. Image diagnostic of colonic diseases - controversial questions

    International Nuclear Information System (INIS)

    Pomakov, P.; Rizov, A.; Stancheva, I.

    2013-01-01

    In the system of colonic diseases' diagnostic algorithm, fibrocolonoscopy (FCS) is defined as 'Golden Standard'. By this reason some X-ray diagnostic methods - irrigography, etc. are currently not being used in a number of health institutions. The aim of this study is a comparative analysis of FCS and irrigography diagnostic efficacy in various colonic diseases. For 10-years period, in cooperation with a gastroenterologist-gastroscopist, 2151 patients with various colonic diseases were evaluated by FCS and irrigography with pharmaco-diagnostics/when necessary. Advantage of FCS was established in diagnosing diseases with patho-morfologic changes on the inner surface of the colon - benign and malignant neoplastic processes, chronic inflammatory diseases, etc. At the same time functional changes - irritated colon syndrome, changes in defecation act, etc., are not an object of diagnosis through FCS. Correction in colonic diseases diagnostic algorithm is necessary. FCS should be mandatory. If result is negative - irrigography with pharmaco-diagnostics should be done. (authors)

  19. 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

  20. 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

  1. 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....

  2. Historical and Current Trends in Colon Trauma

    OpenAIRE

    Causey, Marlin Wayne; Rivadeneira, David E.; Steele, Scott R.

    2012-01-01

    The authors discuss the evolution of the evaluation and management of colonic trauma, as well as the debate regarding primary repair versus fecal diversion. Their evidence-based review covers diagnosis, management, surgical approaches, and perioperative care of patients with colon-related trauma. The management of traumatic colon injuries has evolved significantly over the past 50 years; here the authors describe a practical approach to the treatment and management of traumatic injuries to th...

  3. Perforated Solitary Diverticulitis of the Ascending Colon

    Science.gov (United States)

    2005-06-01

    postoperative day 6. DISCUSSION Diverticuli of the right colon exist in approximately 1% to 5% of patients with diverticular disease .1-3 They are...ORIGINAL REPORTS Perforated Solitary Diverticulitis of the Ascending Colon CPT David S. Kauvar, MC, USA, MAJ, Jayson Aydelotte, MC, USA, and MAJ...Michael Harnisch, MC, USA Department of Surgery, Brooke Army Medical Center, Fort Sam Houston, Texas KEY WORDS: solitary colon diverticulum

  4. Volvulus of the Small Bowel and Colon

    Science.gov (United States)

    Kapadia, Muneera R.

    2017-01-01

    Volvulus of the intestines may involve either the small bowel or colon. In the pediatric population, small bowel volvulus is more common, while in the adult population, colonic volvulus is more often seen. The two most common types of colonic volvulus include sigmoid and cecal volvulus. Prompt diagnosis and treatment is imperative, otherwise bowel ischemia may ensue. Treatment often involves emergent surgical exploration and bowel resection. PMID:28144211

  5. Sigmoid colon vaginoplasty in children.

    Science.gov (United States)

    Ekinci, S; Karnak, I; Ciftci, A O; Senocak, M E; Tanyel, F C; Büyükpamukçu, N

    2006-06-01

    Vaginal construction is necessary for the patients with aplasia of Mullerian ducts, testicular feminisation and androgen insensitivity syndromes. Many methods of vaginal construction have been described. We report here the outcomes of six adolescent patients who underwent sigmoid colon vaginoplasty with special emphasis on the surgical technique and outcomes. Between 1990 and 2003, six patients underwent sigmoid vaginoplasty after a diagnosis of 5alpha-reductase deficiency (n = 3), testicular feminisation (n = 2) or vaginal atresia (n = 1). The mean age was 16 years (13 to 18). Wide spectrum antibiotics and whole-gut preparation were used in all cases. A 15-20 cm segment of sigmoid colon was pulled through the retrovesical tunnel. The proximal end was closed in two layers in patients with 5alpha-reductase deficiency and with testicular feminisation. A distal anastomosis was carried out to the opening made on the vaginal plate (5alpha-reductase deficiency) or on the tip of the shallow rudimentary vagina (testicular feminisation). The sigmoid segment was interposed between the blind end of the atretic vagina and the perineum in the patient with vaginal atresia. Patients were instructed to perform daily vaginal irrigation. The neovagina was examined and calibrated under anaesthesia. No routine vaginal dilatation was recommended. All but one patient had an uneventful postoperative period and were discharged within 7-8 days. All patients had an excellent cosmetic result with an appropriate vaginal length. One of the patients experienced late stenosis of the introitus which responded to dilatations. Mucus discharge was not a significant problem. The patient with vaginal atresia (Bardet-Biedl syndrome) experienced deep vein thrombosis, renal failure and sepsis, resulting in death. Sigmoid colon vaginoplasty is a special procedure which appears appropriate for the construction of a new vagina in children. A sigmoid colon neovagina meets all necessary criteria after a

  6. Colonic diseases: The value of US examination

    International Nuclear Information System (INIS)

    Hollerweger, Alois

    2007-01-01

    The colon is affected by a number of diseases, mainly inflammatory, ischemic, and neoplastic conditions. Depending upon clinical indications endoscopy, US, CT, or other radiological methods are used for evaluation. The fact that US is frequently used as the initial imaging method in patients with non-specific clinical symptoms allows for greater influence in further diagnostic evaluation and with treatment, provided the investigator is familiar with the features of different intestinal diseases. This article will describe the anatomical characteristics of the colon, the US technique for examination of the colon, and the typical US features of the more common diagnoses of the colon

  7. Muscarinic Receptor Signaling in Colon Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Rosenvinge, Erik C. von, E-mail: evonrose@medicine.umaryland.edu; Raufman, Jean-Pierre [University of Maryland School of Medicine, Division of Gastroenterology & Hepatology, 22 S. Greene Street, N3W62, Baltimore, MD 21201 (United States); Department of Veterans Affairs, VA Maryland Health Care System, 10 North Greene Street, Baltimore, MD 21201 (United States)

    2011-03-02

    According to the adenoma-carcinoma sequence, colon cancer results from accumulating somatic gene mutations; environmental growth factors accelerate and augment this process. For example, diets rich in meat and fat increase fecal bile acids and colon cancer risk. In rodent cancer models, increased fecal bile acids promote colon dysplasia. Conversely, in rodents and in persons with inflammatory bowel disease, low-dose ursodeoxycholic acid treatment alters fecal bile acid composition and attenuates colon neoplasia. In the course of elucidating the mechanism underlying these actions, we discovered that bile acids interact functionally with intestinal muscarinic receptors. The present communication reviews muscarinic receptor expression in normal and neoplastic colon epithelium, the role of autocrine signaling following synthesis and release of acetylcholine from colon cancer cells, post-muscarinic receptor signaling including the role of transactivation of epidermal growth factor receptors and activation of the ERK and PI3K/AKT signaling pathways, the structural biology and metabolism of bile acids and evidence for functional interaction of bile acids with muscarinic receptors on human colon cancer cells. In murine colon cancer models, deficiency of subtype 3 muscarinic receptors attenuates intestinal neoplasia; a proof-of-concept supporting muscarinic receptor signaling as a therapeutic target for colon cancer.

  8. Muscarinic Receptor Signaling in Colon Cancer

    International Nuclear Information System (INIS)

    Rosenvinge, Erik C. von; Raufman, Jean-Pierre

    2011-01-01

    According to the adenoma-carcinoma sequence, colon cancer results from accumulating somatic gene mutations; environmental growth factors accelerate and augment this process. For example, diets rich in meat and fat increase fecal bile acids and colon cancer risk. In rodent cancer models, increased fecal bile acids promote colon dysplasia. Conversely, in rodents and in persons with inflammatory bowel disease, low-dose ursodeoxycholic acid treatment alters fecal bile acid composition and attenuates colon neoplasia. In the course of elucidating the mechanism underlying these actions, we discovered that bile acids interact functionally with intestinal muscarinic receptors. The present communication reviews muscarinic receptor expression in normal and neoplastic colon epithelium, the role of autocrine signaling following synthesis and release of acetylcholine from colon cancer cells, post-muscarinic receptor signaling including the role of transactivation of epidermal growth factor receptors and activation of the ERK and PI3K/AKT signaling pathways, the structural biology and metabolism of bile acids and evidence for functional interaction of bile acids with muscarinic receptors on human colon cancer cells. In murine colon cancer models, deficiency of subtype 3 muscarinic receptors attenuates intestinal neoplasia; a proof-of-concept supporting muscarinic receptor signaling as a therapeutic target for colon cancer

  9. Muscarinic Receptor Signaling in Colon Cancer

    Directory of Open Access Journals (Sweden)

    Jean-Pierre Raufman

    2011-03-01

    Full Text Available According to the adenoma-carcinoma sequence, colon cancer results from accumulating somatic gene mutations; environmental growth factors accelerate and augment this process. For example, diets rich in meat and fat increase fecal bile acids and colon cancer risk. In rodent cancer models, increased fecal bile acids promote colon dysplasia. Conversely, in rodents and in persons with inflammatory bowel disease, low-dose ursodeoxycholic acid treatment alters fecal bile acid composition and attenuates colon neoplasia. In the course of elucidating the mechanism underlying these actions, we discovered that bile acids interact functionally with intestinal muscarinic receptors. The present communication reviews muscarinic receptor expression in normal and neoplastic colon epithelium, the role of autocrine signaling following synthesis and release of acetylcholine from colon cancer cells, post-muscarinic receptor signaling including the role of transactivation of epidermal growth factor receptors and activation of the ERK and PI3K/AKT signaling pathways, the structural biology and metabolism of bile acids and evidence for functional interaction of bile acids with muscarinic receptors on human colon cancer cells. In murine colon cancer models, deficiency of subtype 3 muscarinic receptors attenuates intestinal neoplasia; a proof-of-concept supporting muscarinic receptor signaling as a therapeutic target for colon cancer.

  10. Phylogenetic signal in the acoustic parameters of the advertisement calls of four clades of anurans.

    Science.gov (United States)

    Gingras, Bruno; Mohandesan, Elmira; Boko, Drasko; Fitch, W Tecumseh

    2013-07-01

    Anuran vocalizations, especially their advertisement calls, are largely species-specific and can be used to identify taxonomic affiliations. Because anurans are not vocal learners, their vocalizations are generally assumed to have a strong genetic component. This suggests that the degree of similarity between advertisement calls may be related to large-scale phylogenetic relationships. To test this hypothesis, advertisement calls from 90 species belonging to four large clades (Bufo, Hylinae, Leptodactylus, and Rana) were analyzed. Phylogenetic distances were estimated based on the DNA sequences of the 12S mitochondrial ribosomal RNA gene, and, for a subset of 49 species, on the rhodopsin gene. Mean values for five acoustic parameters (coefficient of variation of root-mean-square amplitude, dominant frequency, spectral flux, spectral irregularity, and spectral flatness) were computed for each species. We then tested for phylogenetic signal on the body-size-corrected residuals of these five parameters, using three statistical tests (Moran's I, Mantel, and Blomberg's K) and three models of genetic distance (pairwise distances, Abouheif's proximities, and the variance-covariance matrix derived from the phylogenetic tree). A significant phylogenetic signal was detected for most acoustic parameters on the 12S dataset, across statistical tests and genetic distance models, both for the entire sample of 90 species and within clades in several cases. A further analysis on a subset of 49 species using genetic distances derived from rhodopsin and from 12S broadly confirmed the results obtained on the larger sample, indicating that the phylogenetic signals observed in these acoustic parameters can be detected using a variety of genetic distance models derived either from a variable mitochondrial sequence or from a conserved nuclear gene. We found a robust relationship, in a large number of species, between anuran phylogenetic relatedness and acoustic similarity in the

  11. Brain structure evolution in a basal vertebrate clade: evidence from phylogenetic comparative analysis of cichlid fishes

    Directory of Open Access Journals (Sweden)

    Kolm Niclas

    2009-09-01

    Full Text Available Abstract Background The vertebrate brain is composed of several interconnected, functionally distinct structures and much debate has surrounded the basic question of how these structures evolve. On the one hand, according to the 'mosaic evolution hypothesis', because of the elevated metabolic cost of brain tissue, selection is expected to target specific structures mediating the cognitive abilities which are being favored. On the other hand, the 'concerted evolution hypothesis' argues that developmental constraints limit such mosaic evolution and instead the size of the entire brain varies in response to selection on any of its constituent parts. To date, analyses of these hypotheses of brain evolution have been limited to mammals and birds; excluding Actinopterygii, the basal and most diverse class of vertebrates. Using a combination of recently developed phylogenetic multivariate allometry analyses and comparative methods that can identify distinct rates of evolution, even in highly correlated traits, we studied brain structure evolution in a highly variable clade of ray-finned fishes; the Tanganyikan cichlids. Results Total brain size explained 86% of the variance in brain structure volume in cichlids, a lower proportion than what has previously been reported for mammals. Brain structures showed variation in pair-wise allometry suggesting some degree of independence in evolutionary changes in size. This result is supported by variation among structures on the strength of their loadings on the principal size axis of the allometric analysis. The rate of evolution analyses generally supported the results of the multivariate allometry analyses, showing variation among several structures in their evolutionary patterns. The olfactory bulbs and hypothalamus were found to evolve faster than other structures while the dorsal medulla presented the slowest evolutionary rate. Conclusion Our results favor a mosaic model of brain evolution, as certain

  12. 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

  13. Methods for the quantitative comparison of molecular estimates of clade age and the fossil record.

    Science.gov (United States)

    Clarke, Julia A; Boyd, Clint A

    2015-01-01

    Approaches quantifying the relative congruence, or incongruence, of molecular divergence estimates and the fossil record have been limited. Previously proposed methods are largely node specific, assessing incongruence at particular nodes for which both fossil data and molecular divergence estimates are available. These existing metrics, and other methods that quantify incongruence across topologies including entirely extinct clades, have so far not taken into account uncertainty surrounding both the divergence estimates and the ages of fossils. They have also treated molecular divergence estimates younger than previously assessed fossil minimum estimates of clade age as if they were the same as cases in which they were older. However, these cases are not the same. Recovered divergence dates younger than compared oldest known occurrences require prior hypotheses regarding the phylogenetic position of the compared fossil record and standard assumptions about the relative timing of morphological and molecular change to be incorrect. Older molecular dates, by contrast, are consistent with an incomplete fossil record and do not require prior assessments of the fossil record to be unreliable in some way. Here, we compare previous approaches and introduce two new descriptive metrics. Both metrics explicitly incorporate information on uncertainty by utilizing the 95% confidence intervals on estimated divergence dates and data on stratigraphic uncertainty concerning the age of the compared fossils. Metric scores are maximized when these ranges are overlapping. MDI (minimum divergence incongruence) discriminates between situations where molecular estimates are younger or older than known fossils reporting both absolute fit values and a number score for incompatible nodes. DIG range (divergence implied gap range) allows quantification of the minimum increase in implied missing fossil record induced by enforcing a given set of molecular-based estimates. These metrics are used

  14. 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

  15. Generation of an inducible colon-specific Cre enzyme mouse line for colon cancer research

    NARCIS (Netherlands)

    Tetteh, Paul W.; Kretzschmar, Kai; Begthel, Harry; Van Den Born, Maaike; Korving, Jeroen; Morsink, Folkert; Farin, Henner; Van Es, Johan H.; Offerhaus, G. Johan A; Clevers, Hans

    2016-01-01

    Current mouse models for colorectal cancer often differ significantly from human colon cancer, being largely restricted to the small intestine. Here, we aim to develop a colon-specific inducible mouse model that can faithfully recapitulate human colon cancer initiation and progression. Carbonic

  16. 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

  17. 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.

  18. Right colon cancer: Left behind.

    Science.gov (United States)

    Gervaz, P; Usel, M; Rapiti, E; Chappuis, P; Neyroud-Kaspar, I; Bouchardy, C

    2016-09-01

    Prognosis of colon cancer (CC) has steadily improved during the past three decades. This trend, however, may vary according to proximal (right) or distal (left) tumor location. We studied if improvement in survival was greater for left than for right CC. We included all CC recorded at the Geneva population-based registry between 1980 and 2006. We compared patients, tumor and treatment characteristics between left and right CC by logistic regression and compared CC specific survival by Cox models taking into account putative confounders. We also compared changes in survival between CC location in early and late years of observation. Among the 3396 CC patients, 1334 (39%) had right-sided and 2062 (61%) left-sided tumors. In the early 1980s, 5-year specific survival was identical for right and left CCs (49% vs. 48%). During the study period, a dramatic improvement in survival was observed for patients with left-sided cancers (Hazard ratio [HR]: 0.42, 95% confidence interval [CI]: 0.29-0.62, p colon cancer patients, those with right-sided lesions have by far the worse prognosis. Change of strategic management in this subgroup is warranted. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Dietary pattern and colonic diverticulosis.

    Science.gov (United States)

    Tursi, Antonio

    2017-09-01

    To assess the role of dietary pattern on the occurrence of colonic diverticulosis, diverticular disease and acute diverticulitis. High-fiber diet does not prevent diverticulosis occurrence, and results about prevention/treatment of diverticular disease and acute diverticulitis are still conflicting.No association was seen between nut, corn or popcorn consumption and occurrence of diverticulosis, diverticular disease and acute diverticulitis.It seems to be a mild association between high alcohol intake and diverticulosis occurrence, whereas alcohol dependence seems to show lower risk of in-hospital mortality due to acute diverticulitis.Higher red-meat consumption shows mild increased risk of acute diverticulitis, especially when consumed as unprocessed red meat (defined as consumption of 'beef or lamb as main dish', 'pork as main dish', 'hamburger' and 'beef, pork or lamb as a sandwich or mixed dish'); higher consumption of poultry (viz. white meat) was not associated with risk of acute diverticulitis.Finally, higher fish intake was associated with reduced risk of diverticulitis in age-adjusted model, but not after further adjustment for other potential confounders. Current literature data about the role of dietary pattern on the occurrence of colonic diverticulosis, diverticular disease and acute diverticulitis are still too conflicting.

  20. 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.

  1. Feeding ecology and sexual dimorphism in a speciose flower beetle clade (Hopliini: Scarabaeidae

    Directory of Open Access Journals (Sweden)

    Jonathan F. Colville

    2018-06-01

    Full Text Available The relationship between feeding ecology and sexual dimorphism is examined in a speciose South African monkey beetle clade. We test whether feeding and mating at a fixed site (embedding guild is associated with greater levels of sexual dimorphism and possibly sexual selection than species using unpredictable feeding resources (non-embedding guild. Sexual dimorphism was measured using a point scoring system for hind leg and colour across the two feeding guilds for >50% of the regional fauna. Quantification of hind leg dimorphism using a scoring system and allometric scaling were used to identify traits subject to sexual selection. Feeding guild had a significant effect on hind leg dimorphism, with embedders having high and non-embedders low scores. The sessile and defendable distribution of females on stable platform flowers may favour contests and associated hind leg weaponry. In contrast, degree of colour dimorphism between the sexes was not associated with any particular feeding guild, and may serve to reduce male conflict and combat. Embedder males had high proportions (∼76% of species with positive allometric slopes for almost all hind leg traits. For male non-embedders, only ∼37% of species showed positive scaling relationships. Phylogenetic data, in conjunction with behavioural data on the function of leg weaponry and visual signalling among males is needed to better understand the link between sexual dimorphism and sexual selection in the radiation of the monkey beetles.

  2. Sigma viruses from three species of Drosophila form a major new clade in the rhabdovirus phylogeny

    Science.gov (United States)

    Longdon, Ben; Obbard, Darren J.; Jiggins, Francis M.

    2010-01-01

    The sigma virus (DMelSV), which is a natural pathogen of Drosophila melanogaster, is the only Drosophila-specific rhabdovirus that has been described. We have discovered two new rhabdoviruses, D. obscura and D. affinis, which we have named DObsSV and DAffSV, respectively. We sequenced the complete genomes of DObsSV and DMelSV, and the L gene from DAffSV. Combining these data with sequences from a wide range of other rhabdoviruses, we found that the three sigma viruses form a distinct clade which is a sister group to the Dimarhabdovirus supergroup, and the high levels of divergence between these viruses suggest that they deserve to be recognized as a new genus. Furthermore, our analysis produced the most robustly supported phylogeny of the Rhabdoviridae to date, allowing us to reconstruct the major transitions that have occurred during the evolution of the family. Our data suggest that the bias towards research into plants and vertebrates means that much of the diversity of rhabdoviruses has been missed, and rhabdoviruses may be common pathogens of insects. PMID:19812076

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

    Science.gov (United States)

    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.

  5. Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome.

    Science.gov (United States)

    Anda, Mizue; Ohtsubo, Yoshiyuki; Okubo, Takashi; Sugawara, Masayuki; Nagata, Yuji; Tsuda, Masataka; Minamisawa, Kiwamu; Mitsui, Hisayuki

    2015-11-17

    rRNA is essential for life because of its functional importance in protein synthesis. The rRNA (rrn) operon encoding 16S, 23S, and 5S rRNAs is located on the "main" chromosome in all bacteria documented to date and is frequently used as a marker of chromosomes. Here, our genome analysis of a plant-associated alphaproteobacterium, Aureimonas sp. AU20, indicates that this strain has its sole rrn operon on a small (9.4 kb), high-copy-number replicon. We designated this unusual replicon carrying the rrn operon on the background of an rrn-lacking chromosome (RLC) as the rrn-plasmid. Four of 12 strains close to AU20 also had this RLC/rrn-plasmid organization. Phylogenetic analysis showed that those strains having the RLC/rrn-plasmid organization represented one clade within the genus Aureimonas. Our finding introduces a previously unaddressed viewpoint into studies of genetics, genomics, and evolution in microbiology and biology in general.

  6. A new clade, based on partial LSU rDNA sequences, of unarmoured dinoflagellates.

    Science.gov (United States)

    Reñé, Albert; de Salas, Miguel; Camp, Jordi; Balagué, Vanessa; Garcés, Esther

    2013-09-01

    The order Gymnodiniales comprises unarmoured dinoflagellates. However, the lack of sequences hindered determining the phylogenetic positions and systematic relationships of several gymnodinioid taxa. In this study, a monophyletic clade was defined for the species Ceratoperidinium margalefii Loeblich III, Gyrodinium falcatum Kofoid & Swezy, three Cochlodinium species, and two Gymnodinium-like dinoflagellates. Despite their substantial morphotypic differentiation, Cochlodinium cf. helix, G. falcatum and 'Gymnodinium' sp. 1 share a common shape of the acrobase. The phylogenetic data led to the following conclusions: (1) C. margalefii is closely related to several unarmoured dinoflagellates. Its sulcus shape has been observed for the first time. (2) G. falcatum was erroneously assigned to the genus Gyrodinium and is transferred to Ceratoperidinium (C. falcatum (Kofoid & Swezy) Reñé & de Salas comb. nov.). (3) The genus Cochlodinium is polyphyletic and thus artificial; our data support its separation into three different genera. (4) The two Gymnodinium-like species could not be morphologically or phylogenetically related to any other gymnodinioid species sequenced to date. While not all studied species have been definitively transferred to the correct genus, our study is a step forward in the classification of inconspicuous unarmoured dinoflagellates. The family Ceratoperidiniaeceae and the genus Ceratoperidinium are emended. Copyright © 2013 Elsevier GmbH. All rights reserved.

  7. 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.

  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. Diversification of the Genus Anopheles and a Neotropical Clade from the Late Cretaceous.

    Directory of Open Access Journals (Sweden)

    Lucas A Freitas

    Full Text Available The Anopheles genus is a member of the Culicidae family and consists of approximately 460 recognized species. The genus is composed of 7 subgenera with diverse geographical distributions. Despite its huge medical importance, a consensus has not been reached on the phylogenetic relationships among Anopheles subgenera. We assembled a comprehensive dataset comprising the COI, COII and 5.8S rRNA genes and used maximum likelihood and Bayesian inference to estimate the phylogeny and divergence times of six out of the seven Anopheles subgenera. Our analysis reveals a monophyletic group composed of the three exclusively Neotropical subgenera, Stethomyia, Kerteszia and Nyssorhynchus, which began to diversify in the Late Cretaceous, at approximately 90 Ma. The inferred age of the last common ancestor of the Anopheles genus was ca. 110 Ma. The monophyly of all Anopheles subgenera was supported, although we failed to recover a significant level of statistical support for the monophyly of the Anopheles genus. The ages of the last common ancestors of the Neotropical clade and the Anopheles and Cellia subgenera were inferred to be at the Late Cretaceous (ca. 90 Ma. Our analysis failed to statistically support the monophyly of the Anopheles genus because of an unresolved polytomy between Bironella and A. squamifemur.

  11. 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.

  12. Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade.

    Science.gov (United States)

    Tachibana, Shin-Ichiro; Sullivan, Steven A; Kawai, Satoru; Nakamura, Shota; Kim, Hyunjae R; Goto, Naohisa; Arisue, Nobuko; Palacpac, Nirianne M Q; Honma, Hajime; Yagi, Masanori; Tougan, Takahiro; Katakai, Yuko; Kaneko, Osamu; Mita, Toshihiro; Kita, Kiyoshi; Yasutomi, Yasuhiro; Sutton, Patrick L; Shakhbatyan, Rimma; Horii, Toshihiro; Yasunaga, Teruo; Barnwell, John W; Escalante, Ananias A; Carlton, Jane M; Tanabe, Kazuyuki

    2012-09-01

    P. cynomolgi, a malaria-causing parasite of Asian Old World monkeys, is the sister taxon of P. vivax, the most prevalent malaria-causing species in humans outside of Africa. Because P. cynomolgi shares many phenotypic, biological and genetic characteristics with P. vivax, we generated draft genome sequences for three P. cynomolgi strains and performed genomic analysis comparing them with the P. vivax genome, as well as with the genome of a third previously sequenced simian parasite, Plasmodium knowlesi. Here, we show that genomes of the monkey malaria clade can be characterized by copy-number variants (CNVs) in multigene families involved in evasion of the human immune system and invasion of host erythrocytes. We identify genome-wide SNPs, microsatellites and CNVs in the P. cynomolgi genome, providing a map of genetic variation that can be used to map parasite traits and study parasite populations. The sequencing of the P. cynomolgi genome is a critical step in developing a model system for P. vivax research and in counteracting the neglect of P. vivax.

  13. The first freshwater mosasauroid (Upper Cretaceous, Hungary and a new clade of basal mosasauroids.

    Directory of Open Access Journals (Sweden)

    László Makádi

    Full Text Available Mosasauroids are conventionally conceived of as gigantic, obligatorily aquatic marine lizards (1000s of specimens from marine deposited rocks with a cosmopolitan distribution in the Late Cretaceous (90-65 million years ago [mya] oceans and seas of the world. Here we report on the fossilized remains of numerous individuals (small juveniles to large adults of a new taxon, Pannoniasaurus inexpectatus gen. et sp. nov. from the Csehbánya Formation, Hungary (Santonian, Upper Cretaceous, 85.3-83.5 mya that represent the first known mosasauroid that lived in freshwater environments. Previous to this find, only one specimen of a marine mosasauroid, cf. Plioplatecarpus sp., is known from non-marine rocks in Western Canada. Pannoniasaurus inexpectatus gen. et sp. nov. uniquely possesses a plesiomorphic pelvic anatomy, a non-mosasauroid but pontosaur-like tail osteology, possibly limbs like a terrestrial lizard, and a flattened, crocodile-like skull. Cladistic analysis reconstructs P. inexpectatus in a new clade of mosasauroids: (Pannoniasaurus (Tethysaurus (Yaguarasaurus, Russellosaurus. P. inexpectatus is part of a mixed terrestrial and freshwater faunal assemblage that includes fishes, amphibians turtles, terrestrial lizards, crocodiles, pterosaurs, dinosaurs and birds.

  14. Imaging of total colonic Hirschsprung disease

    International Nuclear Information System (INIS)

    Stranzinger, Enno; DiPietro, Michael A.; Strouse, Peter J.; Teitelbaum, Daniel H.

    2008-01-01

    Hirschsprung disease (HD) is a functional obstruction of the bowel caused by the absence of intrinsic enteric ganglion cells. The diagnosis of total colonic HD (TCHD) based on contrast enemas is difficult in newborns because radiological findings vary. To evaluate the radiographic and contrast enema findings in patients with pathologically proven TCHD. From 1966 to 2007, 17 records from a total of 31 patients with TCHD were retrospectively evaluated for diameter and shape of the colon, diameter of the small bowel, bowel wall contour, ileal reflux, abdominal calcifications, pneumoperitoneum, filling defects, transitional zones and rectosigmoid index. Three colonic patterns of TCHD were found: microcolon, question-mark-shape colon and normal caliber colon. Additional findings included spasmodic colon, ileal reflux, delayed evacuation and abdominal calcifications. Colonic transitional zones were found in eight patients with TCHD. The diagnosis of TCHD is difficult to establish by contrast enema studies. The length of the aganglionic small bowel and the age of the patient can influence the radiological findings in TCHD. The transitional zone and the rectosigmoid index can be false-positive in TCHD. The colon can appear normal. Consider TCHD if the contrast enema study is normal but the patient remains symptomatic and other causes of distal bowel obstruction have been excluded. (orig.)

  15. Seat belt injuries and sigmoid colon trauma.

    OpenAIRE

    Eltahir, E M; Hamilton, D

    1997-01-01

    Colonic seat belt injuries are rare but carry higher mortality rates than small bowel injuries. The case of a 44 year old man is described who had severe sigmoid colon compression injury from his seat belt a few days after a road traffic accident.

  16. A Study Of Fungal Colonization In Newborn

    Directory of Open Access Journals (Sweden)

    S Rashid Husain

    1997-04-01

    Full Text Available Research Problem: What are the factors responsible for fungal colonization in newborns? Objective: To study the pattern of and predisposing fac­tors for the development of superficial candidiasis and fungal colonization in the newborns. Study Design: Prospective study. Setting: Neonatology unitof the Paediatrics department of a teaching hospital. Participants: Randomly selected pregnant mothers admit­ted to the maternity ward and the newborns delivered to them. Sample Size: 120 pregnant mothers and the newborns delivered. Study Variables: Candida, Site of colonization. Statistical Analysis: By tests of significance Results: Candida was isolated from 23 (19.16% infants on the first day increasing to 52 (43.33% infants on the sixth day. The most common site of colonization was oral cavity. Candida colonization was more common in prema­ture infants (p<0.05. Oral thrush was seen in 29 (24.17% infants during the study and a significant number of these infants showed colonization from the first day of life. Conclusions: Fungal colonization of the newborns due to Candida species is quite common, and in the first week of life predominantly occurred in the ora I cavity. Superficial clinical candidiasis, especially oral thrush is more common in those colonized on the first day of life.

  17. Role of neutral ceramidase in colon cancer.

    Science.gov (United States)

    García-Barros, Mónica; Coant, Nicolas; Kawamori, Toshihiko; Wada, Masayuki; Snider, Ashley J; Truman, Jean-Philip; Wu, Bill X; Furuya, Hideki; Clarke, Christopher J; Bialkowska, Agnieszka B; Ghaleb, Amr; Yang, Vincent W; Obeid, Lina M; Hannun, Yusuf A

    2016-12-01

    Alterations in sphingolipid metabolism, especially ceramide and sphingosine 1-phosphate, have been linked to colon cancer, suggesting that enzymes of sphingolipid metabolism may emerge as novel regulators and targets in colon cancer. Neutral ceramidase (nCDase), a key enzyme in sphingolipid metabolism that hydrolyzes ceramide into sphingosine, is highly expressed in the intestine; however, its role in colon cancer has not been defined. Here we show that molecular and pharmacological inhibition of nCDase in colon cancer cells increases ceramide, and this is accompanied by decreased cell survival and increased apoptosis and autophagy, with minimal effects on noncancerous cells. Inhibition of nCDase resulted in loss of β-catenin and inhibition of ERK, components of pathways relevant for colon cancer development. Furthermore, inhibition of nCDase in a xenograft model delayed tumor growth and increased ceramide while decreasing proliferation. It is noteworthy that mice lacking nCDase treated with azoxymethane were protected from tumor formation. Taken together, these studies show that nCDase is pivotal for regulating initiation and development of colon cancer, and these data suggest that this enzyme is a suitable and novel target for colon cancer therapy.-García-Barros, M., Coant, N., Kawamori, T., Wada, M., Snider, A. J., Truman, J.-P., Wu, B. X., Furuya, H., Clarke, C. J., Bialkowska, A. B., Ghaleb, A., Yang, V. W., Obeid, L. M., Hannun, Y. A. Role of neutral ceramidase in colon cancer. © FASEB.

  18. Congenital segmental dilatation of the colon

    African Journals Online (AJOL)

    Congenital segmental dilatation of the colon is a rare cause of intestinal obstruction in neonates. We report a case of congenital segmental dilatation of the colon and highlight the clinical, radiological, and histopathological features of this entity. Proper surgical treatment was initiated on the basis of preoperative radiological ...

  19. Incidence of retrorenal colon during percutaneous nephrolithotomy

    Directory of Open Access Journals (Sweden)

    Mehmet Balasar

    2015-04-01

    Full Text Available Objective The aim of this study was to investigate retrorenal colon incidence in percutaneous nephrolithotomy (PNL interventions made in our clinic. Materials and Methods Clinical data of 804 PNL patients, accumulated over a 7 year period (2006-2012, was surveyed. The patient files were reviewed retrospectively, and only those who had abdominal computed tomography (CT images before PNL intervention were included in the study. In the CT images, the position of both the ascending and descending colon in relation to the right and left kidneys were evaluated. Results According to our hospital reports, 394 patients with CT images were included in the present study 27 patients (6.9% had retrorenal colon, of which 18 (4.6% were on the left side, 4 (1.0% on the right side and 5 (1.3% had bilateral retrorenal colons. Colonic perforation complication was seen only in two patients and the colonic perforation rate was 0.3%. These two cases had no CT images. Conclusions PNL, in the process of becoming the standard treatment modality, is a safe and reliable technique for renal stone treatment. Colonic injury should be taken into consideration during PNL interventions of the lower pole of the kidney (especially on the left side due to the location of retrorenal colon.

  20. The colon shuffle : A modified urinary diversion

    NARCIS (Netherlands)

    Meijer, R. P.; Mertens, L. S.; Meinhardt, W.; Verwaal, V. J.; Dik, P.; Horenblas, S.

    2015-01-01

    Aim To assess the results of a urinary diversion in patients who already have a colostomy or simultaneously require a (rectum) colon resection. The diversion is created from the distal part of the transected colon with a simultaneously created new colostomy contra-laterally (if necessary). This

  1. Colonic ischemic necrosis following therapeutic embolization

    International Nuclear Information System (INIS)

    Shenoy, S.S.; Satchidanand, S.; Wesp, E.H.; State Univ. of New York, Buffalo

    1981-01-01

    Transcatheter embolization of the middle colic artery for diverticular bleeding was followed by ischemic necrosis in the transverse colon at the site of previous anastomosis and stricture formation. This is a potential complication of intra-arterial embolization for colonic bleeding. (orig.)

  2. Colonic ischemic necrosis following therapeutic embolization

    Energy Technology Data Exchange (ETDEWEB)

    Shenoy, S S; Satchidanand, S; Wesp, E H

    1981-07-15

    Transcatheter embolization of the middle colic artery for diverticular bleeding was followed by ischemic necrosis in the transverse colon at the site of previous anastomosis and stricture formation. This is a potential complication of intra-arterial embolization for colonic bleeding.

  3. A prognostic analysis of 895 cases of stage III colon cancer in different colon subsites.

    Science.gov (United States)

    Zhang, Yan; Ma, Junli; Zhang, Sai; Deng, Ganlu; Wu, Xiaoling; He, Jingxuan; Pei, Haiping; Shen, Hong; Zeng, Shan

    2015-09-01

    Stage III colon cancer is currently treated as an entity with a unified therapeutic principle. The aim of the retrospective study is to explore the clinicopathological characteristics and outcomes of site-specific stage III colon cancers and the influences of tumor location on prognosis. Eight hundred ninety-five patients with stage III colon cancer treated with radical operation and subsequent adjuvant chemotherapy (5-fluorouracil/oxaliplatin) were divided into seven groups according to colon segment (cecum, ascending colon, hepatic flexure, transverse colon, splenic flexure, descending colon, and sigmoid colon). Expression of excision repair cross-complementing group 1 (ERCC1) and thymidylate synthase (TS) was examined by immunohistochemistry. We assessed if differences exist in patient characteristics and clinic outcomes between the seven groups. There were significant differences in tumor differentiation (P Cancer (AJCC) tumor-node-metastasis (TNM) stage (P colon. Cox regression analyses identified that tumor location was an independent prognostic factor for RFS and OS. Stage III colon cancer located proximally carried a poorer survival than that located distally. Different efficacies of FOLFOX adjuvant chemotherapy may be an important factor affecting survival of site-specific stage III colon cancers.

  4. Association between colonic polyps and diverticular disease

    Institute of Scientific and Technical Information of China (English)

    Tetsuo Hirata; Yuko Kawakami; Nagisa Kinjo; Susumu Arakald; Tetsu Arakaki; Akira Hokama; Fukunori Kinjo; Jim Fujita

    2008-01-01

    AIM: TO evaluate the association between colonic polyps and diverticular disease in Japan.METHODS: We retrospectively reviewed the medical records of 672 consecutive patients who underwent total colonoscopy between August 2006 and April 2007 at Nishinjo Hospital, Okinawa, Japan. Patients with ahistory of any of the following were excluded from the study: previous polypectomy, colonic resection, and inflammatory bowel diseases. The association between colonic polyps and diverticular disease was analyzed by logistic regression analysis, adjusted for age and sex.RESULTS: Prevalence of colonic polyps in all patients with diverticular disease was significantly higher than that in those without diverticular disease (adjusted odds ratio 1.7).CONCLUSION: Our data showed that patients with diverticular disease have a higher risk of colonic polyps compared to those without.

  5. Duplication Cyst of the Sigmoid Colon

    Directory of Open Access Journals (Sweden)

    Bastian Domajnko

    2009-01-01

    Full Text Available A 21-year-old male with developmental delay presented with abdominal pain of two days' duration. He was afebrile and his abdomen was soft with mild diffuse tenderness. There were no peritoneal signs. Plain x-ray demonstrated a large air-filled structure in the right upper quadrant. Computed tomography of the abdomen revealed a 9×8 cm structure adjacent to the hepatic flexure containing an air-fluid level. It did not contain oral contrast and had no apparent communication with the colon. At operation, the cystic lesion was identified as a duplication cyst of the sigmoid colon that was adherent to the right upper quadrant. The cyst was excised with a segment of the sigmoid colon and a stapled colo-colostomy was performed. Recovery was uneventful. Final pathology was consistent with a duplication cyst of the sigmoid colon. The cyst was attached to the colon but did not communicate with the lumen.

  6. Association between colonic polyps and diverticular disease

    Science.gov (United States)

    Hirata, Tetsuo; Kawakami, Yuko; Kinjo, Nagisa; Arakaki, Susumu; Arakaki, Tetsu; Hokama, Akira; Kinjo, Fukunori; Fujita, Jiro

    2008-01-01

    AIM: To evaluate the association between colonic polyps and diverticular disease in Japan. METHODS: We retrospectively reviewed the medical records of 672 consecutive patients who underwent total colonoscopy between August 2006 and April 2007 at Nishinjo Hospital, Okinawa, Japan. Patients with a history of any of the following were excluded from the study: previous polypectomy, colonic resection, and inflammatory bowel diseases. The association between colonic polyps and diverticular disease was analyzed by logistic regression analysis, adjusted for age and sex. RESULTS: Prevalence of colonic polyps in all patients with diverticular disease was significantly higher than that in those without diverticular disease (adjusted odds ratio 1.7). CONCLUSION: Our data showed that patients with diverticular disease have a higher risk of colonic polyps compared to those without. PMID:18416471

  7. Immunological comparison of ovarian and colonic CEA

    International Nuclear Information System (INIS)

    Burtin, P.; Gendron, M.C.; Maunoury, M.T.; Lamerz, R.; Schnabel, G.

    1982-01-01

    Ovarian and colonic CEA were compared immunologically by means of antisera prepared against each of them. CEAs of both origins were found identical by immunodiffusion methods. In radioimmunological experiments, slight differences were observed between some but not all ovarian CEAs and colonic CEAs and also between different preparations of colonic CEA: no organ specificity of ovarian CEA could be demonstrated. Finally, CEA level was measured in 41 sera of patients with ovarian carcinoma by two radioimmunoassays, one using colonic CEA as tracer and standard and anti-colonic CEA serum, the other using ovarian CEA and anti-ovarian CEA serum: the values given by the two assays were highly correlated (rsub(s) = 0.8107), meaning that an organ specific assay for ovarian CEA is not needed. (Auth.)

  8. [Continent colostomy and colon irrigation].

    Science.gov (United States)

    Kostov, D; Temelkov, T; Kiriazov, E; Ivanov, K; Ignatov, V; Kobakov, G

    2000-01-01

    The authors have studied a functional activity of a continent colostomy at 20 patients, undergone an abdomeno-perineal extirpation of rectum and carried out periodic colonirrigations, during a period of 6 months. A conus type, closed irrigating system has been used. The degree of an incontinency at patients has been compared before and after the beginning of the colonirrigations. The irrigating procedures have reduced spontaneous defications at patients during a week 28 times and have improved the quality of life significantly. The application of colostomy bags has been restricted in 8 (40%) patients. An intraluminal ultrasonographic investigation has been done at 12 (60%) patients at the end of 6 month irrigating period. No changes of the ultrasonographic image of the precolostomic segment of colon has been observed.

  9. Magnetomotive colon elastography: preliminary assessment

    International Nuclear Information System (INIS)

    Bruno, A. Colello; Grillo, F.W.; Sampaio, D.R.T.; Carneiro, A.A.O.

    2015-01-01

    Colorectal cancer (CRC) is the third most common malignant neoplasm worldwide and early diagnosis reduces morbidity. The standard preventive exams methods are uncomfortable for the patient, invasive, and /or are ionizing. Here, we evaluate the potential of magneto-motive ultrasound (MMUS) as a new, minimally invasive CRC screening technique. We developed a hybrid transducer (comprised of an ultrasound probe and a magnetic coil system) to construct relative elastography maps in a paraffin phantom with isoechoic inclusions. The electromagnetic component of our system manipulated ferromagnetic fluid located inside of our synthetic colon, and the captured ultrasound images were used to produce relative elastography maps. The MMUS images reveal by otherwise invisible structures based on differences in stiffness. Ultrasound elastography (relative) images by MMUs technique complements usual preventive CRC exams, is minimally invasive, has relative low cost when compared with others image methods. Also is fast diagnose and more comfortable for patient which prevents withdrawal of the screening. (author)

  10. Colon and rectal cancer survival by tumor location and microsatellite instability: the Colon Cancer Family Registry.

    Science.gov (United States)

    Phipps, Amanda I; Lindor, Noralane M; Jenkins, Mark A; Baron, John A; Win, Aung Ko; Gallinger, Steven; Gryfe, Robert; Newcomb, Polly A

    2013-08-01

    Cancers in the proximal colon, distal colon, and rectum are frequently studied together; however, there are biological differences in cancers across these sites, particularly in the prevalence of microsatellite instability. We assessed the differences in survival by colon or rectal cancer site, considering the contribution of microsatellite instability to such differences. This is a population-based prospective cohort study for cancer survival. This study was conducted within the Colon Cancer Family Registry, an international consortium. Participants were identified from population-based cancer registries in the United States, Canada, and Australia. Information on tumor site, microsatellite instability, and survival after diagnosis was available for 3284 men and women diagnosed with incident invasive colon or rectal cancer between 1997 and 2002, with ages at diagnosis ranging from 18 to 74. Cox regression was used to calculate hazard ratios for the association between all-cause mortality and tumor location, overall and by microsatellite instability status. Distal colon (HR, 0.59; 95% CI, 0.49-0.71) and rectal cancers (HR, 0.68; 95% CI, 0.57-0.81) were associated with lower mortality than proximal colon cancer overall. Compared specifically with patients with proximal colon cancer exhibiting no/low microsatellite instability, patients with distal colon and rectal cancers experienced lower mortality, regardless of microsatellite instability status; patients with proximal colon cancer exhibiting high microsatellite instability had the lowest mortality. Study limitations include the absence of stage at diagnosis and cause-of-death information for all but a subset of study participants. Some patient groups defined jointly by tumor site and microsatellite instability status are subject to small numbers. Proximal colon cancer survival differs from survival for distal colon and rectal cancer in a manner apparently dependent on microsatellite instability status. These

  11. Necrotizing colitis associated with carcinoma of the colon

    International Nuclear Information System (INIS)

    Woo, Seong Ku; Lim, Jae Hoon; Kim, Soon Yong; Ahn, Chi Yul

    1982-01-01

    Necrotizing colitis associated with carcinoma of the colon, known also as obstructive colitis, is a disorder characterized by anulceration and inflammation of the colon proximal to an obstructive lesion, especially carcinoma of the rectosigmoid colon, and in rare instance, leads to acute gangrene of the colon. The authors analyzed radiologic findings in four cases of necrotizing colitis associated with carcinoma of the colon. Barium enema disclosed mucosal edema, nodular filling defects, irregularity of the colonic contour and typical thumbprinting appearance of involved colon proximal to an obstructing carcinoma of the colon. The mechanism of necrotizing colitis was briefly reviewed

  12. 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

  13. 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

  14. Fine scale mapping of genomic introgressions within the Drosophila yakuba clade.

    Science.gov (United States)

    Turissini, David A; Matute, Daniel R

    2017-09-01

    The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount of interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur. In west Africa, D. santomea and D. yakuba hybridize on the island of São Tomé, while D. yakuba and D. teissieri hybridize on the nearby island of Bioko. In this report, we quantify the genomic extent of introgression between the three species of the Drosophila yakuba clade (D. yakuba, D. santomea), D. teissieri). We sequenced the genomes of 86 individuals from all three species. We also developed and applied a new statistical framework, using a hidden Markov approach, to identify introgression. We found that introgression has occurred between both species pairs but most introgressed segments are small (on the order of a few kilobases). After ruling out the retention of ancestral polymorphism as an explanation for these similar regions, we find that the sizes of introgressed haplotypes indicate that genetic exchange is not recent (>1,000 generations ago). We additionally show that in both cases, introgression was rarer on X chromosomes than on autosomes which is consistent with sex chromosomes playing a large role in reproductive isolation. Even though the two species pairs have stable contemporary hybrid zones, providing the opportunity for ongoing gene flow, our results indicate that genetic exchange between these species is currently rare.

  15. Evaluating rare amino acid substitutions (RGC_CAMs in a yeast model clade.

    Directory of Open Access Journals (Sweden)

    Kenneth Polzin

    Full Text Available When inferring phylogenetic relationships, not all sites in a sequence alignment are equally informative. One recently proposed approach that takes advantage of this inequality relies on sites that contain amino acids whose replacement requires multiple substitutions. Identifying these so-called RGC_CAM substitutions (after Rare Genomic Changes as Conserved Amino acids-Multiple substitutions requires that, first, at any given site in the amino acid sequence alignment, there must be a minimum of two different amino acids; second, each amino acid must be present in at least two taxa; and third, the amino acids must require a minimum of two nucleotide substitutions to replace each other. Although theory suggests that RGC_CAM substitutions are expected to be rare and less likely to be homoplastic, the informativeness of RGC_CAM substitutions has not been extensively evaluated in biological data sets. We investigated the quality of RGC_CAM substitutions by examining their degree of homoplasy and internode certainty in nearly 2.7 million aligned amino acid sites from 5,261 proteins from five species belonging to the yeast Saccharomyces sensu stricto clade whose phylogeny is well-established. We identified 2,647 sites containing RGC_CAM substitutions, a number that contrasts sharply with the 100,887 sites containing RGC_non-CAM substitutions (i.e., changes between amino acids that require only a single nucleotide substitution. We found that RGC_CAM substitutions had significantly lower homoplasy than RGC_non-CAM ones; specifically RGC_CAM substitutions showed a per-site average homoplasy index of 0.100, whereas RGC_non-CAM substitutions had a homoplasy index of 0.215. Internode certainty values were also higher for sites containing RGC_CAM substitutions than for RGC_non-CAM ones. These results suggest that RGC_CAM substitutions possess a strong phylogenetic signal and are useful markers for phylogenetic inference despite their rarity.

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

    Science.gov (United States)

    Aflitos, Saulo; Schijlen, Elio; de Jong, Hans; de Ridder, Dick; Smit, Sandra; Finkers, Richard; Wang, Jun; Zhang, Gengyun; Li, Ning; Mao, Likai; Bakker, Freek; Dirks, Rob; Breit, Timo; Gravendeel, Barbara; Huits, Henk; Struss, Darush; Swanson-Wagner, Ruth; van Leeuwen, Hans; van Ham, Roeland C H J; Fito, Laia; Guignier, Laëtitia; Sevilla, Myrna; Ellul, Philippe; Ganko, Eric; Kapur, Arvind; Reclus, Emannuel; de Geus, Bernard; van de Geest, Henri; Te Lintel Hekkert, Bas; van Haarst, Jan; Smits, Lars; Koops, Andries; Sanchez-Perez, Gabino; van Heusden, Adriaan W; Visser, Richard; Quan, Zhiwu; Min, Jiumeng; Liao, Li; Wang, Xiaoli; Wang, Guangbiao; Yue, Zhen; Yang, Xinhua; Xu, Na; Schranz, Eric; Smets, Erik; Vos, Rutger; Rauwerda, Johan; Ursem, Remco; Schuit, Cees; Kerns, Mike; van den Berg, Jan; Vriezen, Wim; Janssen, Antoine; Datema, Erwin; Jahrman, Torben; Moquet, Frederic; Bonnet, Julien; Peters, Sander

    2014-10-01

    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 reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment revealed group-, species- and accession-specific polymorphisms, explaining characteristic fruit traits and growth habits in the various cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences in the ratio between non-synonymous and synonymous SNPs (dN/dS) in fruit diversification and plant growth genes compared to a random set of genes, indicating positive selection and differences in selection pressure between crop accessions and wild species. In wild species, the number of single-nucleotide polymorphisms (SNPs) exceeds 10 million, i.e. 20-fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, the highest levels of heterozygosity were found for allogamous self-incompatible wild species, while facultative and autogamous self-compatible species display a lower heterozygosity level. Using whole-genome SNP information for maximum-likelihood analysis, we achieved complete tree resolution, whereas maximum-likelihood trees based on SNPs from ten fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. Emergency management of acute colonic cancer obstruction.

    Science.gov (United States)

    Gainant, A

    2012-02-01

    Emergency management of obstructing colonic cancer depends on both tumor location and stage, general condition of the patient and surgeon's experience. Right sided or transverse colon obstructing cancers are usually treated by right hemicolectomy-extended if necessary to the transverse colon-with primary anastomosis. For left-sided obstructing cancer, in patients with low surgical risk, primary resection and anastomosis associated with on-table irrigation or manual decompression can be performed. It prevents the confection of a loop colostomy but presents the risk of anastomotic leakage. Subtotal or total colectomy allows the surgeon to encompass distended and fecal-loaded colon, and to perform one-stage resection and anastomosis. Its disadvantage is an increased daily frequency of stools. It must be performed only in cases of diastatic colon perforation or synchronous right colonic cancer. In patients with high surgical risk, Hartmann procedure must be preferred. It allows the treatment of both obstruction and cancer, and prevents anastomotic leakage but needs a second operation to reverse the colostomy. Colonic stenting is clinically successful in up to 90% in specialized groups. It is used as palliation in patients with disseminated disease or bridge to surgery in the others. If stent insertion is not possible, loop colostomy is still indicated in patients at high surgical risk. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  8. Massive Submucosal Ganglia in Colonic Inertia.

    Science.gov (United States)

    Naemi, Kaveh; Stamos, Michael J; Wu, Mark Li-Cheng

    2018-02-01

    - Colonic inertia is a debilitating form of primary chronic constipation with unknown etiology and diagnostic criteria, often requiring pancolectomy. We have occasionally observed massively enlarged submucosal ganglia containing at least 20 perikarya, in addition to previously described giant ganglia with greater than 8 perikarya, in cases of colonic inertia. These massively enlarged ganglia have yet to be formally recognized. - To determine whether such "massive submucosal ganglia," defined as ganglia harboring at least 20 perikarya, characterize colonic inertia. - We retrospectively reviewed specimens from colectomies of patients with colonic inertia and compared the prevalence of massive submucosal ganglia occurring in this setting to the prevalence of massive submucosal ganglia occurring in a set of control specimens from patients lacking chronic constipation. - Seven of 8 specimens affected by colonic inertia harbored 1 to 4 massive ganglia, for a total of 11 massive ganglia. One specimen lacked massive ganglia but had limited sampling and nearly massive ganglia. Massive ganglia occupied both superficial and deep submucosal plexus. The patient with 4 massive ganglia also had 1 mitotically active giant ganglion. Only 1 massive ganglion occupied the entire set of 10 specimens from patients lacking chronic constipation. - We performed the first, albeit distinctly small, study of massive submucosal ganglia and showed that massive ganglia may be linked to colonic inertia. Further, larger studies are necessary to determine whether massive ganglia are pathogenetic or secondary phenomena, and whether massive ganglia or mitotically active ganglia distinguish colonic inertia from other types of chronic constipation.

  9. Colon cancer associated transcripts in human cancers.

    Science.gov (United States)

    Chen, Yincong; Xie, Haibiao; Gao, Qunjun; Zhan, Hengji; Xiao, Huizhong; Zou, Yifan; Zhang, Fuyou; Liu, Yuchen; Li, Jianfa

    2017-10-01

    Long non-coding RNAs serve as important regulators in complicated cellular activities, including cell differentiation, proliferation and death. Dysregulation of long non-coding RNAs occurs in the formation and progression of cancers. The family of colon cancer associated transcripts, long non-coding RNAs colon cancer associated transcript-1 and colon cancer associated transcript-2 are known as oncogenes involved in various cancers. Colon cancer associated transcript-1 is a novel lncRNA located in 8q24.2, and colon cancer associated transcript-2 maps to the 8q24.21 region encompassing rs6983267. Colon cancer associated transcripts have close associations with clinical characteristics, such as lymph node metastasis, high TNM stage and short overall survival. Knockdown of them can reverse the malignant phenotypes of cancer cells, including proliferation, migration, invasion and apoptosis. Moreover, they can increase the expression level of c-MYC and oncogenic microRNAs via activating a series of complex mechanisms. In brief, the family of colon cancer associated transcripts may serve as potential biomarkers or therapeutic targets for human cancers. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  10. Nutrients and Risk of Colon Cancer

    Directory of Open Access Journals (Sweden)

    Les Mery

    2010-02-01

    Full Text Available Dietary fats are thought to be important in the etiology of colon cancer. However, the evidence linking them is inconclusive. Studies on dietary protein, cholesterol and carbohydrate and the risk of colon cancer are also inconsistent. This study examined the association between dietary intake of protein, fats, cholesterol and carbohydrates, and the risk of colon cancer. Mailed questionnaires were completed by 1731 individuals with histologically confirmed cases of colon cancer and 3097 population controls between 1994 and 1997 in seven Canadian provinces. Measurements included socio-economic status, lifestyle habits and diet. A 69-item food frequency questionnaire was used to provide data on eating habits from two years before the study. Odds ratios (OR and 95% confidence intervals (CI were computed using unconditional logistic regression. The nutrients were categorized by quartiles based on the distributions among the controls. Intake of polyunsaturated fat, trans-fat and cholesterol were significantly associated with the risk of colon cancer; the ORs for the highest quartiles were 1.36 (95% CI, 1.02–1.80, 1.37 (95% CI, 1.10–1.71 and 1.42 (95% CI, 1.10–1.84, respectively. The association was stronger with proximal colon cancer (PCC. An increased risk was also observed with increasing intake of sucrose for both proximal and distal colon cancers; the ORs for the highest quartiles were 1.67 (95% CI, 1.22–2.29 for PCC and 1.58 (95% CI, 1.18–2.10 for distal colon cancer (DCC. An elevated risk of PCC was also found with increased lactose intake. Our findings provide evidence that a diet low in fat and sucrose could reduce the risk of various colon cancers.

  11. Nutrients and Risk of Colon Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Jinfu, E-mail: Jinfu.hu@phac-aspc.gc.ca [Evidence and Risk Assessment Division, Centre for Chronic Disease Prevention and Control, Public Health Agency of Canada, 785 Carling Avenue, AL: 6807B, Ottawa, Ontario K1A 0K9 (Canada); La Vecchia, Carlo [Istituto di Ricerche Farmacologiche “Mario Negri,” Via La Masa, 19-20156 Milan (Italy); Istituto di Statistica Medica e Biometria, Università degli Studi di Milano, Via Venezian, 1, 20133 Milan (Italy); Negri, Eva [Istituto di Ricerche Farmacologiche “Mario Negri,” Via La Masa, 19-20156 Milan (Italy); Mery, Les [Evidence and Risk Assessment Division, Centre for Chronic Disease Prevention and Control, Public Health Agency of Canada, 785 Carling Avenue, AL: 6807B, Ottawa, Ontario K1A 0K9 (Canada)

    2010-02-10

    Dietary fats are thought to be important in the etiology of colon cancer. However, the evidence linking them is inconclusive. Studies on dietary protein, cholesterol and carbohydrate and the risk of colon cancer are also inconsistent. This study examined the association between dietary intake of protein, fats, cholesterol and carbohydrates, and the risk of colon cancer. Mailed questionnaires were completed by 1731 individuals with histologically confirmed cases of colon cancer and 3097 population controls between 1994 and 1997 in seven Canadian provinces. Measurements included socio-economic status, lifestyle habits and diet. A 69-item food frequency questionnaire was used to provide data on eating habits from two years before the study. Odds ratios (OR) and 95% confidence intervals (CI) were computed using unconditional logistic regression. The nutrients were categorized by quartiles based on the distributions among the controls. Intake of polyunsaturated fat, trans-fat and cholesterol were significantly associated with the risk of colon cancer; the ORs for the highest quartiles were 1.36 (95% CI, 1.02–1.80), 1.37 (95% CI, 1.10–1.71) and 1.42 (95% CI, 1.10–1.84), respectively. The association was stronger with proximal colon cancer (PCC). An increased risk was also observed with increasing intake of sucrose for both proximal and distal colon cancers; the ORs for the highest quartiles were 1.67 (95% CI, 1.22–2.29) for PCC and 1.58 (95% CI, 1.18–2.10) for distal colon cancer (DCC). An elevated risk of PCC was also found with increased lactose intake. Our findings provide evidence that a diet low in fat and sucrose could reduce the risk of various colon cancers.

  12. Nutrients and Risk of Colon Cancer

    International Nuclear Information System (INIS)

    Hu, Jinfu; La Vecchia, Carlo; Negri, Eva; Mery, Les

    2010-01-01

    Dietary fats are thought to be important in the etiology of colon cancer. However, the evidence linking them is inconclusive. Studies on dietary protein, cholesterol and carbohydrate and the risk of colon cancer are also inconsistent. This study examined the association between dietary intake of protein, fats, cholesterol and carbohydrates, and the risk of colon cancer. Mailed questionnaires were completed by 1731 individuals with histologically confirmed cases of colon cancer and 3097 population controls between 1994 and 1997 in seven Canadian provinces. Measurements included socio-economic status, lifestyle habits and diet. A 69-item food frequency questionnaire was used to provide data on eating habits from two years before the study. Odds ratios (OR) and 95% confidence intervals (CI) were computed using unconditional logistic regression. The nutrients were categorized by quartiles based on the distributions among the controls. Intake of polyunsaturated fat, trans-fat and cholesterol were significantly associated with the risk of colon cancer; the ORs for the highest quartiles were 1.36 (95% CI, 1.02–1.80), 1.37 (95% CI, 1.10–1.71) and 1.42 (95% CI, 1.10–1.84), respectively. The association was stronger with proximal colon cancer (PCC). An increased risk was also observed with increasing intake of sucrose for both proximal and distal colon cancers; the ORs for the highest quartiles were 1.67 (95% CI, 1.22–2.29) for PCC and 1.58 (95% CI, 1.18–2.10) for distal colon cancer (DCC). An elevated risk of PCC was also found with increased lactose intake. Our findings provide evidence that a diet low in fat and sucrose could reduce the risk of various colon cancers

  13. CT findings of early right colonic diverticulitis

    International Nuclear Information System (INIS)

    Lee, Jong Hwa; Ham, Su Yeon; Whang, Kang Ik

    1998-01-01

    The purpose of this study is to investigate the CT findings of acute right colonic diverticulitis, and to determine the difference between these and published reports describing left colonic, especially sigmoid, diverticulitis. Inflamed diverticula were visible in all cases, and were solitary. Nine cases occurred in the ascending colon and four in the cecum; in particular, eleven occurred around the ileocecal valve. In three cases, the inflamed diverticulum was less than 1 cm in diameter; in five cases, 1-2 cm; in three, 2-3 cm, and in two, 3-4 cm. These were able to be classified into two major forms. In three cases it was nodular with hyperattenuation and some inhomogeneity, and ten shows the target form with thick walls and a central cavity. In five of these target lesions, the wall pattern was partially or completely inhomogeneous, or multilayered. The material filling the central cavity were gas in five cases, fecalith in two, and fluid in three. Abnormal pericoloic fat infiltrations were seen in twelve cases (92%), segmental colonic wall thickening in eleven (85%), other not-inflamed diverticula in five (38%), mesenteric lymph node enlargement in three (23%), free pericecal fluid collection in three (23%), and perirenal fascial thickening in two (15%). The complications such as remote abscess cavity, colonic obstruction, fistula or perforation were not found. On barium colon study, diverticulitis was in all cases confirmed by the presence of barium in the deformed diversiculum. Among CT findings for acute right colonic diverticulitis, the most important and pathognomonic is inflamed diverticula; the forms of these vary, and include gangrenous diverticulitis. The CT findings of early right colonic diverticulitis in Koreans might not, however, reveal the complications which sigmoid diverticulitis frequently involves; in patients with right lower quadrant pain imaging studies are performed promptly, and for the mesentery, the anatomical base between right and

  14. Effect of complex polyphenols on colon carcinogenesis.

    Science.gov (United States)

    Caderni, G; Remy, S; Cheynier, V; Morozzi, G; Dolara, P

    1999-06-01

    Complex polyphenols and tannins from wine (WCPT) are being considered increasingly as potential cancer chemopreventive agents, since epidemiological studies suggest that populations consuming a high amount of polyphenols in the diet may have a lower incidence of some types of cancer. We studied the effect of WCPT on a series of parameters related to colon carcinogenesis in rats. WCPT were administered to F344 rats at a dose of 14 or 57 mg/kg/d, mixed with the diet. The higher dose is about ten times the exposure to polyphenols of a moderate drinker of red wine. In rats treated with WCPT, we measured fecal bile acids and long chain fatty acids, colon mucosa cell proliferation, apoptosis and, after administration of colon carcinogens, the number and size of aberrant crypt foci (ACF) and nuclear aberrations. Colon mucosa proliferation was not varied by chronic administration (90 d) of WCPT (14 or 57 mg/kg/d). The highest dose of WCPT decreased the number of cells in the colon crypts, but did not increase apoptosis. WCPT (57 mg/kg) administered before or after the administration of azoxymethane (AOM) did not vary the number or multiplicity of ACF in the colon. The number of nuclear aberrations (NA) in colon mucosa was studied after administration of 1,2-dimethylhydrazine (DMH) and 2-amino-3-methylimidazo (4,5-f)quinoline (IQ), colon-specific carcinogens which require metabolic activation. The effect of DMH and IQ was not varied by pre-feeding WCPT (57 mg/kg) for 10 d. Similarly, the levels of total, secondary bile acids and long chain fatty acids did not varied significantly in animals fed WCPT for 90 d. WCPT administration does not influence parameters related to colon carcinogenesis in the rat.

  15. 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.

  16. Marine worms (genus Osedax) colonize cow bones

    OpenAIRE

    Jones, William J; Johnson, Shannon B; Rouse, Greg W; Vrijenhoek, Robert C

    2007-01-01

    Bone-eating worms of the genus Osedax colonized and grew on cow bones deployed at depths ranging from 385 to 2893 m in Monterey Bay, California. Colonization occurred as rapidly as two months following deployment of the cow bones, similar to the time it takes to colonize exposed whalebones. Some Osedax females found on the cow bones were producing eggs and some hosted dwarf males in their tubes. Morphological and molecular examinations of these worms confirmed the presence of six Osedax speci...

  17. Neoadjuvant chemotherapy in locally advanced colon cancer

    DEFF Research Database (Denmark)

    Jakobsen, Anders; Andersen, Fahimeh; Fischer, Anders

    2015-01-01

    BACKGROUND: Neoadjuvant chemotherapy has proven valuable in several tumors, but it has not been elucidated in colon cancer. The present phase II trial addressed the issue in high-risk patients selected by computed tomography (CT) scan. MATERIAL AND METHODS: Patients with resectable colon cancer...... 32% (p = 0.005) translating into a three-year DFS of 94% versus 63% (p = 0.005). CONCLUSION: Neoadjuvant chemotherapy in colon cancer is feasible and the results suggest that a major part of the patients can be spared adjuvant chemotherapy. Validation in a randomized trial is warranted....

  18. 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

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

    Directory of Open Access Journals (Sweden)

    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

  20. 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

    be correctly moderating the node-age estimate based on the limited morphological divergence. Topologies are generally similar across analyses, but BEAST trees for crocodyliforms differ when clades are deeply nested but contain very old taxa. It appears that the constant-rate sampling assumption of the BDSS tree prior influences topology inference by disfavoring long, unsampled branches.

  1. Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification.

    Science.gov (United States)

    Schmedes, Sarah E; Woerner, August E; Novroski, Nicole M M; Wendt, Frank R; King, Jonathan L; Stephens, Kathryn M; Budowle, Bruce

    2018-01-01

    The human skin microbiome is comprised of diverse communities of bacterial, eukaryotic, and viral taxa and contributes millions of additional genes to the repertoire of human genes, affecting human metabolism and immune response. Numerous genetic and environmental factors influence the microbiome composition and as such contribute to individual-specific microbial signatures which may be exploited for forensic applications. Previous studies have demonstrated the potential to associate skin microbial profiles collected from touched items to their individual owner, mainly using unsupervised methods from samples collected over short time intervals. Those studies utilize either targeted 16S rRNA or shotgun metagenomic sequencing to characterize skin microbiomes; however, these approaches have limited species and strain resolution and susceptibility to stochastic effects, respectively. Clade-specific markers from the skin microbiome, using supervised learning, can predict individual identity using skin microbiomes from their respective donors with high accuracy. In this study the hidSkinPlex is presented, a novel targeted sequencing method using skin microbiome markers developed for human identification. The hidSkinPlex (comprised of 286 bacterial (and phage) family-, genus-, species-, and subspecies-level markers), initially was evaluated on three bacterial control samples represented in the panel (i.e., Propionibacterium acnes, Propionibacterium granulosum, and Rothia dentocariosa) to assess the performance of the multiplex. The hidSkinPlex was further evaluated for prediction purposes. The hidSkinPlex markers were used to attribute skin microbiomes collected from eight individuals from three body sites (i.e., foot (Fb), hand (Hp) and manubrium (Mb)) to their host donor. Supervised learning, specifically regularized multinomial logistic regression and 1-nearest-neighbor classification were used to classify skin microbiomes to their hosts with up to 92% (Fb), 96% (Mb

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

    Directory of Open Access Journals (Sweden)

    Alan H Turner

    -clock model appears to be correctly moderating the node-age estimate based on the limited morphological divergence. Topologies are generally similar across analyses, but BEAST trees for crocodyliforms differ when clades are deeply nested but contain very old taxa. It appears that the constant-rate sampling assumption of the BDSS tree prior influences topology inference by disfavoring long, unsampled branches.

  3. Drugs Approved for Colon and Rectal Cancer

    Science.gov (United States)

    This page lists cancer drugs approved by the Food and Drug Administration (FDA) for use in colon cancer and rectal cancer. The list includes generic names, brand names, and common drug combinations, which are shown in capital letters.

  4. Understanding Antegrade Colonic Enema (ACE) Surgery

    Science.gov (United States)

    ... Enema (ACE) Surgery Menu Overview Procedure Details Risks / Benefits What is antegrade colonic enema (ACE) surgery? Antegrade ... Accepted Insurance Make a Donation Refer a Patient Phone Directory Blog, News & Mobile Apps Consult QD Health Essentials Newsroom Mobile Apps ...

  5. Colon Cancer Risk Assessment - Gauss Program

    Science.gov (United States)

    An executable file (in GAUSS) that projects absolute colon cancer risk (with confidence intervals) according to NCI’s Colorectal Cancer Risk Assessment Tool (CCRAT) algorithm. GAUSS is not needed to run the program.

  6. Preventing Second Cancers in Colon Cancer Survivors

    Science.gov (United States)

    In this phase III trial, people who have had curative surgery for colon cancer will be randomly assigned to take sulindac and a placebo, eflornithine and a placebo, both sulindac and eflornithine, or two placebo pills for 36 months.

  7. Redefining Adjuvant Therapy for Colon Cancer

    Science.gov (United States)

    In this trial, patients with resected stage III colon cancer are being randomly assigned to receive FOLFOX chemotherapy for either 3 or 6 months and to take either a pill called celecoxib or a matching placebo pill for 3 years.

  8. Intestinal Colonization Dynamics of Vibrio cholerae.

    Directory of Open Access Journals (Sweden)

    Salvador Almagro-Moreno

    2015-05-01

    Full Text Available To cause the diarrheal disease cholera, Vibrio cholerae must effectively colonize the small intestine. In order to do so, the bacterium needs to successfully travel through the stomach and withstand the presence of agents such as bile and antimicrobial peptides in the intestinal lumen and mucus. The bacterial cells penetrate the viscous mucus layer covering the epithelium and attach and proliferate on its surface. In this review, we discuss recent developments and known aspects of the early stages of V. cholerae intestinal colonization and highlight areas that remain to be fully understood. We propose mechanisms and postulate a model that covers some of the steps that are required in order for the bacterium to efficiently colonize the human host. A deeper understanding of the colonization dynamics of V. cholerae and other intestinal pathogens will provide us with a variety of novel targets and strategies to avoid the diseases caused by these organisms.

  9. Neural control of colonic cell proliferation.

    Science.gov (United States)

    Tutton, P J; Barkla, D H

    1980-03-15

    The mitotic rate in rat colonic crypts and in dimethylhydrazine-induced colonic carcinomas was measured using a stathmokinetic technique. In sympathectomized animals cell proliferation was retarded in the crypts but not in the tumors, whereas in animals treated with Metaraminol, a drug which releases norepinephrine from nerve terminals, crypt cell but not tumor cell proliferation was accelerated. Blockade of alpha-adrenoceptors also inhibited crypt cell proliferation. However, stimulation of beta-adrenoceptors inhibited and blockade of beta-adrenoceptors accelerated tumor cell proliferation without influencing crypt cell proliferation. Injection of either serotonin or histamine stimulated tumor but not crypt cell proliferation and blockade or serotonin receptors or histamine H2-receptors inhibited tumor cell proliferation. It is postulated that cell proliferation in the colonic crypts, like that in the jejunal crypts, is under both endocrine and autonomic neural control whereas colonic tumor cell division is subject to endocrine regulation alone.

  10. Marine worms (genus Osedax) colonize cow bones.

    Science.gov (United States)

    Jones, William J; Johnson, Shannon B; Rouse, Greg W; Vrijenhoek, Robert C

    2008-02-22

    Bone-eating worms of the genus Osedax colonized and grew on cow bones deployed at depths ranging from 385 to 2893m in Monterey Bay, California. Colonization occurred as rapidly as two months following deployment of the cow bones, similar to the time it takes to colonize exposed whalebones. Some Osedax females found on the cow bones were producing eggs and some hosted dwarf males in their tubes. Morphological and molecular examinations of these worms confirmed the presence of six Osedax species, out of the eight species presently known from Monterey Bay. The ability of Osedax species to colonize, grow and reproduce on cow bones challenges previous notions that these worms are 'whale-fall specialists.'

  11. [Role of oral cavity colonization resistance in dental caries development].

    Science.gov (United States)

    Petrushanko, T A; Chereda, V V; Loban', G A

    2013-01-01

    Colonization resistance is one of local immunity mechanisms determined by a combination of factors that inhibit the adhesion and growth of mucous membrane bacteria. We examined patients with different levels of caries intensity assessing oral mucosa colonization resistance by our own method. Caries development resulted in changes of colonization resistance with the increased rate of inhibition of the oral mucosa colonization resistance barrier.

  12. Pancreatoduodenectomy with colon resection for cancer: A nationwide retrospective analysis

    NARCIS (Netherlands)

    Marsman, E. Madelief; de Rooij, Thijs; van Eijck, Casper H.; Boerma, Djamila; Bonsing, Bert A.; van Dam, Ronald M.; van Dieren, Susan; Erdmann, Joris I.; Gerhards, Michael F.; de Hingh, Ignace H.; Kazemier, Geert; Klaase, Joost; Molenaar, I. Quintus; Patijn, Gijs A.; Scheepers, Joris J.; Tanis, Pieter J.; Busch, Olivier R.; Besselink, Marc G.

    2016-01-01

    Microscopically radical (R0) resection of pancreatic, periampullary, or colon cancer may occasionally require a pancreatoduodenectomy with colon resection (PD-colon), but the benefits of this procedure have been disputed, and multicenter studies on morbidity and oncologic outcomes after PD-colon are

  13. Improving Outcomes Following Penetrating Colon Wounds

    Science.gov (United States)

    Miller, Preston R.; Fabian, Timothy C.; Croce, Martin A.; Magnotti, Louis J.; Elizabeth Pritchard, F.; Minard, Gayle; Stewart, Ronald M.

    2002-01-01

    Introduction During World War II, failure to treat penetrating colon injuries with diversion could result in court martial. Based on this wartime experience, colostomy for civilian colon wounds became the standard of care for the next 4 decades. Previous work from our institution demonstrated that primary repair was the optimal management for nondestructive colon wounds. Optimal management of destructive wounds requiring resection remains controversial. To address this issue, we performed a study that demonstrated risk factors (pre or intraoperative transfusion requirement of more than 6 units of packed red blood cells, significant comorbid diseases) that were associated with a suture line failure rate of 14%, and of whom 33% died. Based on these outcomes, a clinical pathway for management of destructive colon wounds was developed. The results of the implementation of this pathway are the focus of this report. Methods Patients with penetrating colon injury were identified from the registry of a level I trauma center over a 5-year period. Records were reviewed for demographics, injury characteristics, and outcome. Patients with nondestructive injuries underwent primary repair. Patients with destructive wounds but no comorbidities or large transfusion requirement underwent resection and anastomosis, while patients with destructive wounds and significant medical illness or transfusion requirements of more than 6 units/blood received end colostomy. The current patients (CP) were compared to the previous study (PS) to determine the impact of the clinical pathway. Outcomes examined included colon related mortality and morbidity (suture line leak and abscess). Results Over a 5.5-year period, 231 patients had penetrating colon wounds. 209 survived more 24 hours and comprise the study population. Primary repair was performed on 153 (73%) patients, and 56 patients had destructive injuries (27%). Of these, 40 (71%) had resection and anastomosis and 16 (29%) had diversion

  14. Generation of an inducible colon-specific Cre enzyme mouse line for colon cancer research.

    Science.gov (United States)

    Tetteh, Paul W; Kretzschmar, Kai; Begthel, Harry; van den Born, Maaike; Korving, Jeroen; Morsink, Folkert; Farin, Henner; van Es, Johan H; Offerhaus, G Johan A; Clevers, Hans

    2016-10-18

    Current mouse models for colorectal cancer often differ significantly from human colon cancer, being largely restricted to the small intestine. Here, we aim to develop a colon-specific inducible mouse model that can faithfully recapitulate human colon cancer initiation and progression. Carbonic anhydrase I (Car1) is a gene expressed uniquely in colonic epithelial cells. We generated a colon-specific inducible Car1 CreER knock-in (KI) mouse with broad Cre activity in epithelial cells of the proximal colon and cecum. Deletion of the tumor suppressor gene Apc using the Car1 CreER KI caused tumor formation in the cecum but did not yield adenomas in the proximal colon. Mutation of both Apc and Kras yielded microadenomas in both the cecum and the proximal colon, which progressed to macroadenomas with significant morbidity. Aggressive carcinomas with some invasion into lymph nodes developed upon combined induction of oncogenic mutations of Apc, Kras, p53, and Smad4 Importantly, no adenomas were observed in the small intestine. Additionally, we observed tumors from differentiated Car1-expressing cells with Apc/Kras mutations, suggesting that a top-down model of intestinal tumorigenesis can occur with multiple mutations. Our results establish the Car1 CreER KI as a valuable mouse model to study colon-specific tumorigenesis and metastasis as well as cancer-cell-of-origin questions.

  15. Colon Cancer After Acute Diverticulitis Treatment

    OpenAIRE

    Oh, Kwang Hoon; Han, Koon Hee; Kim, Eun Jung; Lee, Je Hoon; Choi, Kyu Un; Han, Myung Sik; Ahn, Jae Hong; Cheon, Gab Jin

    2013-01-01

    Diverticulitis is the most common clinical complication of diverticular disease, affecting 10-25% of the patients with diverticula. The prevalences of diverticulitis and colon cancer tend to increase with age and are higher in industrialized countries. Consequently, diverticulitis and colon cancer have been reported to have similar epidemiological characteristics. However, the relationship between these diseases remains controversial, as is the performance of routine colonoscopy after an epis...

  16. Echoendoscopic characterization of the human colon

    Directory of Open Access Journals (Sweden)

    Fernando M. Castro-Poças

    Full Text Available Purpose: To characterize colon and rectum walls, pericolic and perirectal spaces, using endoscopic ultrasonography miniprobes. Methods: Sixty individuals (50% males, aged 18-80, were included. Using 12 and 20 MHz endoscopic ultrasonography miniprobes, all different colon segments (ascending, transverse, descending, sigmoid and rectum were evaluated according to the number and thickness of the different layers in intestinal wall, to the presence and (largest diameter of vessels in the submucosa and of peri-intestinal nodes. Results: The 20 MHz miniprobe identified a higher number of layers than the 12 MHz miniprobe, with medians of 7 and 5 respectively (p < 0.001. The rectal wall (p = 0.001, its muscularis propria (p < 0.001 and mucosa (p = 0.01 were significantly thicker than the different segments of the colon, which had no significant differences between them. Patients aged 41-60 presented thicker colonic wall and muscularis propria in descending (p = 0.001 and p = 0.004 and rectum (p=0.01 and p=0.01. Submucosal vessels were identified in 30% of individuals in descending and rectum, and in 12% in ascending. Adenopathies were observed in 9% of the colon segments and 5% in rectum. Conclusions: A higher frequency enabled the identification of a higher number of layers. Rectal wall is thicker than the one from all the segments of the colon and there are no differences between these, namely in the ascending colon. Moreover, peri-intestinal adenopathies were rarely identified but present in asymptomatic individuals. All together, these results describe for the first time features which are relevant during staging and therapeutic management of colonic lesions.

  17. Effects of morphine and naloxone on feline colonic transit

    International Nuclear Information System (INIS)

    Krevsky, B.; Libster, B.; Maurer, A.H.; Chase, B.J.; Fisher, R.S.

    1989-01-01

    The effects of endogenous and exogenous opioid substances on feline colonic transit were evaluated using colonic transit scintigraphy. Naloxone accelerated emptying of the cecum and ascending colon, and filling of the transverse colon. Endogenous opioid peptides thus appear to play a significant role in the regulation of colonic transit. At a moderate dose of morphine cecum and ascending colon transit was accelerated, while at a larger dose morphine had no effect. Since naloxone, a relatively nonspecific opioid antagonist, and morphine, a principally mu opioid receptor agonist, both accelerate proximal colonic transit, a decelerating role for at least one of the other opioid receptors is inferred

  18. Effects of morphine and naloxone on feline colonic transit

    Energy Technology Data Exchange (ETDEWEB)

    Krevsky, B.; Libster, B.; Maurer, A.H.; Chase, B.J.; Fisher, R.S.

    1989-01-01

    The effects of endogenous and exogenous opioid substances on feline colonic transit were evaluated using colonic transit scintigraphy. Naloxone accelerated emptying of the cecum and ascending colon, and filling of the transverse colon. Endogenous opioid peptides thus appear to play a significant role in the regulation of colonic transit. At a moderate dose of morphine cecum and ascending colon transit was accelerated, while at a larger dose morphine had no effect. Since naloxone, a relatively nonspecific opioid antagonist, and morphine, a principally mu opioid receptor agonist, both accelerate proximal colonic transit, a decelerating role for at least one of the other opioid receptors is inferred.

  19. Synchronous colon and gastric advanced carcinomas

    International Nuclear Information System (INIS)

    Giuliani, A.; Demoro, M.; Corona, M.; Di Bari, M.; Ricciardulli, T.; Galati, G.; Ciardi, A.

    2005-01-01

    An unusual case of advanced synchronous colon and gastric carcinoma is described. A 36 year old female was admitted to our Department with a stenosing right colon cancer diagnosed at endoscopy which was performed for lower crampy abdominal pain and gross blood in the stool. Multiple colon polyps, distal to the tumor, were also detected. On preoperative abdominal computed tomography, a stenosing right colon cancer, without evidence of abdominal diffusion, was confirmed. At laparotomy, in addition to colon cancer, an antral gastric cancer was incidentally found. En bloc hemi gastrectomy and subtotal colectomy were performed. Digestive continuity was restored by gastrojejunal and ileosigmoid anastomoses. At histology, a poorly differentiated gastric adenocarcinoma with signet ring-cell component (pT2, pN0; stage IB) and a moderately differentiated colon adenocarcinoma with a tubulovillous component (pT3, pN1; stage III, Stage Dukes C) were revealed. Both tumors showed a low expression of p53 and c-erb2 oncoproteins. No genetic defect was identified in the APC and MMR genes. The patient is alive, without recurrence, two years after the operation

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

    Directory of Open Access Journals (Sweden)

    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

  1. 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

  2. Pectin-based colon-specific drug delivery

    OpenAIRE

    Shailendra Shukla; Deepak Jain; Kavita Verma; Shiddarth Verma

    2011-01-01

    Colon-specific drug delivery have a great importance in the delivery of drugs for the treatment of local colonic, as well as systemic diseases like Crohn′s disease, ulcerative colitis, colorectal cancer, amoebiasis, asthma, arthritis and inflammation which can be achieved by targeted delivery of drug to colon. Specific systemic absorption in the colon gave interesting possibilities for the delivery of protein and peptides. It contains relatively less proteolytic enzyme activities in the colon...

  3. Curative resection of transverse colon cancer via minilaparotomy.

    Science.gov (United States)

    Ishida, Hideyuki; Ishiguro, Tohru; Ishibashi, Keiichiro; Ohsawa, Tomonori; Okada, Norimichi; Kumamoto, Kensuke; Haga, Norihiro

    2011-01-01

    Minilaparotomy has been reported to be a minimally invasive alternative to laparoscopically assisted surgery. We retrospectively evaluated the usefulness of minilaparotomy for the resection of transverse colon cancer, which has generally been considered difficult to resect laparoscopically. Patients for whom curative resection was attempted for transverse colon cancer (n = 21) or sigmoid colon cancer (n = 81) via minilaparotomy (skin incision, transverse colon cancer as well as those with sigmoid colon cancer.

  4. 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.

  5. 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

  6. Systematics of the Madagascar Anelosimus spiders: remarkable local richness and endemism, and dual colonization from the Americas

    Directory of Open Access Journals (Sweden)

    Ingi Agnarsson

    2015-06-01

    Full Text Available Despite the alarming rates of deforestation and forest fragmentation, Madagascar still harbors extraordinary biodiversity. However, in many arthropod groups, such as spiders, this biodiversity remains mostly unexplored and undescribed. The first subsocial Madagascan species of the theridiid spider genus Anelosimus were described in 2005 when six new species were found to coexist in the Périnet forest fragment within Andasibe-Mantadia NP. However, this discovery was based only on a few specimens and the extent of this Madagascan radiation has remained unknown. We here report on a thorough survey of >350 colonies from Périnet, and three pilot surveys into additional Madagascar forests (Ambohitantely, Ranamofana, and Montagne d’Ambre. The morphological, molecular and natural history data from these surveys facilitated a revised taxonomy and phylogenetic hypothesis of Madagascan Anelosimus. This subsocial clade currently comprises six previously known (A. andasibe Agnarsson & Kuntner, 2005, A. may Agnarsson, 2005, A. nazariani Agnarsson & Kuntner, 2005, A. sallee Agnarsson & Kuntner, 2005, A. salut Agnarsson & Kuntner, 2005, A. vondrona Agnarsson & Kuntner, 2005 and 10 new species: A. ata sp. n., A. buffoni sp. n., A. darwini sp. n., A. hookeri sp. n., A. huxleyi sp. n., A. lamarcki sp. n., A. moramora sp. n., A. tita sp. n., A. torfi sp. n., A. wallacei sp. n.. With the exception of A. may and A. vondrona, all other species appear to be single forest endemics. While additional sampling is necessary, these data imply a much higher local richness and endemism in Madagascan forests than in any other comparable area globally. The phylogenetic results establish a sister clade relationship between the subsocial Anelosimus in Madagascar and the American ‘eximius group’, and between the solitary A. decaryi on Madagascar and a solitary American clade. These findings imply duplicate colonizations from America, an otherwise rare biogeographical

  7. A study of the colonic transit function by dual radionuclide colon scintigraphy

    International Nuclear Information System (INIS)

    Yang Weidong; Sun Buzhou; Song Changyi; Lu Jinyan; Wang Shejiao; Zheng Xianghong; Huang Lin; Lei Yamei

    1999-01-01

    Objective: To establish a new, simple and noninvasive method which can quantitatively analyze the colonic transit function by dual radionuclide colon scintigraphy. Methods: 24 patients with constipation and 32 normal controls were studied. Na 131 I was sealed into capsule made by polyvinylchloride which can not be digested and absorbed in gastrointestinal tract. Patients and normal volunteers swallow 131 I capsules and drink 99 Tc m labelled sulfur colloid solution at the same time. The static image was acquired at the regular time, then calculate the Geometric Center values (GC). Results: 1) The capsules can be clearly located through the colonic contour shown by 99 Tc m labeled sulfur colloid when it reached the large bowel. 2) The transiting time from mouth to cecum, through colon and through whole gastrointestinal in normal people were (6.61 +- 1.94), (36.61 +- 10.51) and (42.72 +- 10.02) h, respectively, in constipation group were (8.03 +- 3.63), (65.50 +- 28.40) and (74.05 +- 28.17) h, respectively. There was no significant difference (P > 0.05) in two groups compared with each other. But the transiting time through colon and whole gastrointestinal in constipation was slower than that in normal people, with significant difference (P < 0.01). 3) Through examination the colonic transit abnormality can be divided into three patterns: whole colon transit delay, right-colon transit delay and left-colon transit delay. Conclusions: This method is a simple, physiologic and quantitative in evaluating the colonic transit, it can also stage the colonic dyskinesia of the patients

  8. Matrilinear phylogeography of Atlantic salmon ( Salmo salar L.) in Europe and postglacial colonization of the Baltic Sea area

    DEFF Research Database (Denmark)

    Nilsson, J.; Gross, R.; Asplund, T.

    2001-01-01

    was analysed by RFLP of ND3/4/5/6. Representative RFLP haplotypes from different parts of the distribution area were sequenced and the phylogeny of European haplotypes and their relations to the North American lineage was described. The four common European haplotypes derive from the ancestral ND1-BBBA...... (rooting the European clade to the North American) by one-step substitutions: AAAA BBBB. The Swedish west- coast populations differ from the geographically close southern Baltic, indicating absence of inward and limited outward gene flow through the Danish straits during the last 8000 years....... Within the Baltic Sea, only three ND1 haplotypes were detected and there was no variation for ND3/4/5/6. In the whole southern Baltic and in lakes Vanern, Ladoga and Onega the haplotype AABA dominated. Proposed postglacial colonization routes to the Baltic Sea are discussed in relation to the haplotype...

  9. 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

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

    Science.gov (United States)

    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

  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. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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.

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

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    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.

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

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    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

  4. Melanosis coli in patients with colon cancer

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    Dorota Biernacka-Wawrzonek

    2016-12-01

    Full Text Available Intoduction: Melanosis coli is a benign lesion affecting the mucosa of the large intestine. There is a relationship between the presence of melanosis and anthraquinone laxative use. Melanosis coli is also observed in patients with colon cancer, but there is doubt whether these two conditions are related. Aim : To analyze the correlation between melanosis and colon cancer. Material and methods: We analyzed retrospectively 436 patients undergoing colon cancer surgery. There were 246 women and 190 men. Patients were divided into three age groups: under 50 years, between 51 and 65 years, and over 66 years. We analyzed sections of the cancer and intestinal mucosa from the tumor’s proximal (2–5 cm and distal (8–10 cm zone. Results : Melanosis coli was present in 52 patients, which represents 11.9% of patients with colon cancer. More often it was present in women. The most common location of melanosis and colon cancer was the terminal part of the large intestine. In patients below 50 years of age in both sexes melanosis coli did not occur. In men, melanosis was more common in the age group over 66 years. Intensity of pigmentation was higher in the tumor’s distal zone. Conclusions : The incidence of melanosis coli increases with age, similar to that of colon cancer. Melanosis was not present inside tumors, in almost half of the cases it was not present in the proximal zone, and the degree of pigmentation increased in distal zone. The cause-effect relationship between melanosis coli and colon cancer remains uncertain.

  5. The Usefulness of Intraoperative Colonic Irrigation and Primary Anastomosis in Patients Requiring a Left Colon Resection.

    Science.gov (United States)

    Hong, Youngki; Nam, Soomin; Kang, Jung Gu

    2017-06-01

    The aim of this study is to assess the short-term outcome of intraoperative colonic irrigation and primary anastomosis and to suggest the usefulness of the procedure when a preoperative mechanical bowel preparation is inappropriate. This retrospective study included 38 consecutive patients (19 male patients) who underwent intraoperative colonic irrigation and primary anastomosis for left colon disease between January 2010 and December 2016. The medical records of the patients were reviewed to evaluate the patients' characteristics, operative data, and postoperative short-term outcomes. Twenty-nine patients had colorectal cancer, 7 patients had perforated diverticulitis, and the remaining 2 patients included 1 with sigmoid volvulus and 1 with a perforated colon due to focal colonic ischemia. A diverting loop ileostomy was created in 4 patients who underwent a low anterior resection. Complications occurred in 15 patients (39.5%), and the majority was superficial surgical site infections (18.4%). Anastomotic leakage occurred in one patient (2.6%) who underwent an anterior resection due sigmoid colon cancer with obstruction. No significant difference in overall postoperative complications and superficial surgical site infections between patients with obstruction and those with peritonitis were noted. No mortality occurred during the first 30 postoperative days. The median hospital stay after surgery was 15 days (range, 8-39 days). Intraoperative colonic irrigation and primary anastomosis seem safe and feasible in selected patients. This procedure may reduce the burden of colostomy in patients requiring a left colon resection with an inappropriate preoperative mechanical bowel preparation.

  6. Fellow travellers: a concordance of colonization patterns between mice and men in the North Atlantic region

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    Jones EP

    2012-03-01

    Full Text Available Abstract Background House mice (Mus musculus are commensals of humans and therefore their phylogeography can reflect human colonization and settlement patterns. Previous studies have linked the distribution of house mouse mitochondrial (mt DNA clades to areas formerly occupied by the Norwegian Vikings in Norway and the British Isles. Norwegian Viking activity also extended further westwards in the North Atlantic with the settlement of Iceland, short-lived colonies in Greenland and a fleeting colony in Newfoundland in 1000 AD. Here we investigate whether house mouse mtDNA sequences reflect human history in these other regions as well. Results House mice samples from Iceland, whether from archaeological Viking Age material or from modern-day specimens, had an identical mtDNA haplotype to the clade previously linked with Norwegian Vikings. From mtDNA and microsatellite data, the modern-day Icelandic mice also share the low genetic diversity shown by their human hosts on Iceland. Viking Age mice from Greenland had an mtDNA haplotype deriving from the Icelandic haplotype, but the modern-day Greenlandic mice belong to an entirely different mtDNA clade. We found no genetic association between modern Newfoundland mice and the Icelandic/ancient Greenlandic mice (no ancient Newfoundland mice were available. The modern day Icelandic and Newfoundland mice belong to the subspecies M. m. domesticus, the Greenlandic mice to M. m. musculus. Conclusions In the North Atlantic region, human settlement history over a thousand years is reflected remarkably by the mtDNA phylogeny of house mice. In Iceland, the mtDNA data show the arrival and continuity of the house mouse population to the present day, while in Greenland the data suggest the arrival, subsequent extinction and recolonization of house mice - in both places mirroring the history of the European human host populations. If house mice arrived in Newfoundland with the Viking settlers at all, then, like the

  7. Hemangioma colorretal Colon rectal hemangioma

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    João Batista Pinheiro Barreto

    2007-06-01

    Full Text Available O hemangioma colorretal (HCR é uma lesão vascular benigna rara, com manifestação clínica geralmente entre 5 e 25 anos de idade. Faz parte do diagnóstico diferencial das causas de hemorragia digestiva baixa, sendo confundido, na maioria das vezes, com entidades mais comuns, como hemorróidas e doenças inflamatórias intestinais. O retardo do diagnóstico ocorre freqüentemente devido ao desconhecimento da doença, com taxas de mortalidade alcançando 40 a 50% na presença de sangramento importante. O caso relatado é de uma paciente de 17 anos de idade, admitida no Serviço de Colo-proctologia do Hospital Universitário - HUUFMA, em setembro de 2005, com anemia e sangramento retal, desde a infância, de forma intermitente e não dolorosa. Apresentado sua história clínica e propedêutica diagnóstica, realizada por meio de exames laboratoriais, endoscopia digestiva alta, colonoscopia e arteriografia de mesentéricas e ilíacas internas. O tratamento cirúrgico realizado foi retossigmoidectomia convencional com anastomose colorretal baixa, com boa evolução pós-operatória, tendo o exame histopatológico da peça cirúrgica ressecada, confirmado o diagnostico.The colon and rectum hemangioma is a rare benign vascular lesion, with clinical features usually between 5 and 25 years of age. It is included in the differential diagnose of the lower digestive bleeding causes, and has been frequently misdiagnosed with other more common entities, like hemorrhoids and bowel inflammatory disease. The late diagnose occurs usually because of the rarity of the disease, with mortality rates reaching 40 to 50% in presence of severe bleeding. We report a case of a 17 years old girl who was admitted at the Coloproctology Service of the Academic Hospital - HUUFMA, in September 2005, with anemia and intermittent rectal bleeding since childhood. Laboratorial findings included laboratorial exams, GI endoscopy, colonoscopy and arteriography of mesenteric and

  8. Ecology of root colonizing Massilia (Oxalobacteraceae.

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    Maya Ofek

    Full Text Available BACKGROUND: Ecologically meaningful classification of bacterial populations is essential for understanding the structure and function of bacterial communities. As in soils, the ecological strategy of the majority of root-colonizing bacteria is mostly unknown. Among those are Massilia (Oxalobacteraceae, a major group of rhizosphere and root colonizing bacteria of many plant species. METHODOLOGY/PRINCIPAL FINDINGS: The ecology of Massilia was explored in cucumber root and seed, and compared to that of Agrobacterium population, using culture-independent tools, including DNA-based pyrosequencing, fluorescence in situ hybridization and quantitative real-time PCR. Seed- and root-colonizing Massilia were primarily affiliated with other members of the genus described in soil and rhizosphere. Massilia colonized and proliferated on the seed coat, radicle, roots, and also on hyphae of phytopathogenic Pythium aphanidermatum infecting seeds. High variation in Massilia abundance was found in relation to plant developmental stage, along with sensitivity to plant growth medium modification (amendment with organic matter and potential competitors. Massilia absolute abundance and relative abundance (dominance were positively related, and peaked (up to 85% at early stages of succession of the root microbiome. In comparison, variation in abundance of Agrobacterium was moderate and their dominance increased at later stages of succession. CONCLUSIONS: In accordance with contemporary models for microbial ecology classification, copiotrophic and competition-sensitive root colonization by Massilia is suggested. These bacteria exploit, in a transient way, a window of opportunity within the succession of communities within this niche.

  9. Imaging analysis of colonic villous tumors

    International Nuclear Information System (INIS)

    Lee, Choon Hyeong; Lim, Joo Won; Lee, Dong Ho; Ko, Yung Tae; Yang, Ik

    1996-01-01

    To evaluate the CT and US features of the colonic villous tumors. We retrospectively reviewed the CT findings of 11 cases with histologically proved colonic villous tumor. CT parameters evaluated were morphological appearances and enhancing pattern (size, shape, margin, presence or absence of fronds, bowel wall thickening). CT features of six cases with malignant change were compared with five tumors without malignant change. US features available in 10 patients were also analyzed. On CT, the tumors showed irregular margin(n=9), presence of fronds(n=6), lobulated shape(n=11), with pericolonic invasion(n=1). Six cases with malignant change were larger(mean, 6.8 cm in diameter) than those without malignant change(mean, 3.3cm). US features in 10 cases were intraluminal mass(n=5), colonic wall thickening(n=5), with variable echogenicity. Colonic villous tumor appeared as a nonspecific mass on CT and US with a difficulty in distinguishing from colon carcinoma

  10. PREOPERATIVE ENDOSCOPIC MARKING OF UNPALPABLE COLONIC TUMORS

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    A. L. Goncharov

    2013-01-01

    Full Text Available The identification of small colon lesions is one of the major problems in laparoscopic colonic resection.Research objective: to develop a technique of visualization of small tumors of a colon by preoperative endoscopic marking of a tumor.Materials and methods. In one day prior to operation to the patient after bowel preparation the colonoscopy is carried out. In the planned point near tumor on antimesentery edge the submucous infiltration of marking solution (Micky Sharpz blue tattoo pigment, UK is made. The volume of entered solution of 1–3 ml. In only 5 months of use of a technique preoperative marking to 14 patients with small (the size of 1–3 cm malignant tumors of the left colon is performed.Results. The tattoo mark was well visualized by during operation at 13 of 14 patients. In all cases we recorded no complications. Time of operation with preoperative marking averaged 108 min, that is significantly less in comparison with average time of operation with an intra-operative colonoscopy – 155 min (р < 0.001.Conclusions. The first experience of preoperative endoscopic marking of non palpable small tumors of a colon is encouraging. Performance of a technique wasn't accompanied by complications and allowed to reduce significantly time of operation and to simplify conditions of performance of operation.

  11. Nuclear microscopy of rat colon epithelial cells

    Science.gov (United States)

    Ren, M.; Rajendran, Reshmi; Ng, Mary; Udalagama, Chammika; Rodrigues, Anna E.; Watt, Frank; Jenner, Andrew Michael

    2011-10-01

    Using Nuclear microscopy, we have investigated iron distributions in the colons of Sprague Dawley rats, in order to elucidate heme uptake. Four groups of five Sprague Dawley rats (mean weight 180 g) were fed different purified diets containing either heme diet (2.5% w/w hemoglobin), high fat diet (HFD) (18% w/w fat, 1% w/w cholesterol), 'western' diet (combination of hemoglobin 2.5% and 18% fat, 1% cholesterol) or control diet (7% w/w fat). After 4 weeks, animals were sacrificed by exsanguination after anaesthesia. Thin sections of frozen colon tissue were taken, freeze dried and scanned using nuclear microscopy utilising the techniques PIXE, RBS and STIM. The new data acquisition system (IonDaq) developed in CIBA was used to obtain high resolution images and line scans were used to map the iron distributions across the colon boundaries. The nuclear microscope results indicate that when HFD is given in addition to heme, the iron content of the epithelial cells that line the colon decreases, and the zinc in the smooth muscle wall increases. This implies that the level of heme and fat in diet has an important role in colon health, possibly by influencing epithelial cells directly or changing luminal composition such as bacterial flora or levels of metabolites and cytotoxins.

  12. Primary repair vs. colostomy in colon injuries.

    Science.gov (United States)

    Robles-Castillo, Javier; Murillo-Zolezzi, Adrián; Murakami, Pablo Daniel; Silva-Velasco, Jorge

    2009-01-01

    Colon trauma is frequent and its prevalence is difficult to establish because of the different factors that intervene in its origin. In Mexico, traumatic colon injuries, albeit stab wounds or gunshot wounds, are on the rise. Our objective was to evaluate the most appropriate management for traumatic colon injuries. We conducted a retrospective study of 178 case files of patients with abdominal trauma and colon lesions during a 5-year period from January 2003 to June 2008 from the General Hospital of Balbuena, Mexico City. The study compared the use of primary closure vs. colostomy, analyzing variables such as sex, age, type of wound, severity of lesion and mortality. There were a total of 178 patients; 156 were male (87.6%) and 22 were female (12.4%). The most affected age group was between 21 and 30 years; 74 patients (41.6%) had stab wounds and 104 patients (58.4%) had gunshot wounds. Management consisted mainly of primary closure in 92 cases (51.7%) vs. colostomy in 86 patients (48.3%). However, 64% of gunshot wounds were treated with colostomy. Reported mortality was 9.55% and this was due to different factors such as multiple organ injury. Treatment of traumatic colon injury should be case specific, taking into account the mechanism of the lesion, its severity and associated injuries.

  13. Space Colonization-Benefits for the World

    Science.gov (United States)

    Siegfried, W. H.

    2003-01-01

    We have begun to colonize space, even to the extent of early space tourism. Our early Vostok, Mercury, Gemini, Apollo, Skylab, Spacehab, Mir and now ISS are humankind's first ventures toward colonization. Efforts are underway to provide short space tours, and endeavors such as the X-Prize are encouraging entrepreneurs to provide new systems. Many believe that extended space travel (colonization) will do for the 21st century what aviation did for the 20th. Our current concerns including terrorism, hunger, disease, and problems of air quality, safe abundant water, poverty, and weather vagaries tend to overshadow long-term activities such as Space Colonization in the minds of many. Our leading ``think tanks'' such as the Woodrow Wilson International Center for Scholars and the Brookings Institute do not rate space travel high on lists of future beneficial undertakings even though many of the concerns listed above are prominently featured. It is the contention of this paper that Space Colonization will lead toward solutions to many of the emerging problems of our Earth, both technological and sociological. The breadth of the enterprise far exceeds the scope of our normal single-purpose missions and, therefore, its benefits will be greater.

  14. Ursodeoxycholic acid attenuates colonic epithelial secretory function

    Science.gov (United States)

    Kelly, Orlaith B; Mroz, Magdalena S; Ward, Joseph B J; Colliva, Carolina; Scharl, Michael; Pellicciari, Roberto; Gilmer, John F; Fallon, Padraic G; Hofmann, Alan F; Roda, Aldo; Murray, Frank E; Keely, Stephen J

    2013-01-01

    Dihydroxy bile acids, such as chenodeoxycholic acid (CDCA), are well known to promote colonic fluid and electrolyte secretion, thereby causing diarrhoea associated with bile acid malabsorption. However, CDCA is rapidly metabolised by colonic bacteria to ursodeoxycholic acid (UDCA), the effects of which on epithelial transport are poorly characterised. Here, we investigated the role of UDCA in the regulation of colonic epithelial secretion. Cl− secretion was measured across voltage-clamped monolayers of T84 cells and muscle-stripped sections of mouse or human colon. Cell surface biotinylation was used to assess abundance/surface expression of transport proteins. Acute (15 min) treatment of T84 cells with bilateral UDCA attenuated Cl− secretory responses to the Ca2+ and cAMP-dependent secretagogues carbachol (CCh) and forskolin (FSK) to 14.0 ± 3.8 and 40.2 ± 7.4% of controls, respectively (n= 18, P acid (LCA). Accordingly, LCA (50–200 μm) enhanced agonist-induced secretory responses in vitro and a metabolically stable UDCA analogue, 6α-methyl-UDCA, exerted anti-secretory actions in vitro and in vivo. In conclusion, UDCA exerts direct anti-secretory actions on colonic epithelial cells and metabolically stable derivatives of the bile acid may offer a new approach for treating intestinal diseases associated with diarrhoea. PMID:23507881

  15. Nuclear microscopy of rat colon epithelial cells

    International Nuclear Information System (INIS)

    Ren, M.; Rajendran, Reshmi; Ng, Mary; Udalagama, Chammika; Rodrigues, Anna E.; Watt, Frank; Jenner, Andrew Michael

    2011-01-01

    Using Nuclear microscopy, we have investigated iron distributions in the colons of Sprague Dawley rats, in order to elucidate heme uptake. Four groups of five Sprague Dawley rats (mean weight 180 g) were fed different purified diets containing either heme diet (2.5% w/w hemoglobin), high fat diet (HFD) (18% w/w fat, 1% w/w cholesterol), 'western' diet (combination of hemoglobin 2.5% and 18% fat, 1% cholesterol) or control diet (7% w/w fat). After 4 weeks, animals were sacrificed by exsanguination after anaesthesia. Thin sections of frozen colon tissue were taken, freeze dried and scanned using nuclear microscopy utilising the techniques PIXE, RBS and STIM. The new data acquisition system (IonDaq) developed in CIBA was used to obtain high resolution images and line scans were used to map the iron distributions across the colon boundaries. The nuclear microscope results indicate that when HFD is given in addition to heme, the iron content of the epithelial cells that line the colon decreases, and the zinc in the smooth muscle wall increases. This implies that the level of heme and fat in diet has an important role in colon health, possibly by influencing epithelial cells directly or changing luminal composition such as bacterial flora or levels of metabolites and cytotoxins.

  16. Ecology of root colonizing Massilia (Oxalobacteraceae).

    Science.gov (United States)

    Ofek, Maya; Hadar, Yitzhak; Minz, Dror

    2012-01-01

    Ecologically meaningful classification of bacterial populations is essential for understanding the structure and function of bacterial communities. As in soils, the ecological strategy of the majority of root-colonizing bacteria is mostly unknown. Among those are Massilia (Oxalobacteraceae), a major group of rhizosphere and root colonizing bacteria of many plant species. The ecology of Massilia was explored in cucumber root and seed, and compared to that of Agrobacterium population, using culture-independent tools, including DNA-based pyrosequencing, fluorescence in situ hybridization and quantitative real-time PCR. Seed- and root-colonizing Massilia were primarily affiliated with other members of the genus described in soil and rhizosphere. Massilia colonized and proliferated on the seed coat, radicle, roots, and also on hyphae of phytopathogenic Pythium aphanidermatum infecting seeds. High variation in Massilia abundance was found in relation to plant developmental stage, along with sensitivity to plant growth medium modification (amendment with organic matter) and potential competitors. Massilia absolute abundance and relative abundance (dominance) were positively related, and peaked (up to 85%) at early stages of succession of the root microbiome. In comparison, variation in abundance of Agrobacterium was moderate and their dominance increased at later stages of succession. In accordance with contemporary models for microbial ecology classification, copiotrophic and competition-sensitive root colonization by Massilia is suggested. These bacteria exploit, in a transient way, a window of opportunity within the succession of communities within this niche.

  17. Is diverticular disease associated with colonic malignancy?

    Science.gov (United States)

    Ekbom, Anders

    2012-01-01

    Colon cancer and diverticular disease have common characteristics; there are increases in the incidences in both disease entities and these diseases are more common in the westernized world. There is also an increase in the age-specific incidence with advancing age. Similar dietary features have been implicated for both diseases and already during the 1960s it was postulated by Burkitt that there is an association. Observational studies initially were able to demonstrate that patients with a history of diverticular disease of the colon had an increased risk of colon cancer, especially in the left side. However, the results from these studies have not been consistent, and problems like selection bias and confounding by indication have been major drawbacks in order to interpret the results and infer causality. Recent studies, which have had a better assessment of diverticular disease by new diagnostic methods, do not support such an association to the same extent as previously. Moreover, surveillance bias has become an increasing problem as patients with diverticular disease of the colon are subjected to a higher diagnostic intensity than other individuals in a population-based setting. A critical evaluation of the studies published so far therefore clearly indicates that the proposed association between diverticular disease and colonic malignancy is not evidence based, which should have an impact on clinical practice as well as on how to deal with these patient groups within the realms of a screening program. Copyright © 2012 S. Karger AG, Basel.

  18. Nuclear microscopy of rat colon epithelial cells

    Energy Technology Data Exchange (ETDEWEB)

    Ren, M., E-mail: phyrenmq@nus.edu.sg [Centre for Ion Beam Applications (CIBA), Department of Physics, National University of Singapore, Singapore 117542 (Singapore); Rajendran, Reshmi [Lab of Molecular Imaging, Singapore Bioimaging Consotium, 11 Biopolis Way, 02-02 Helios, Singapore 138667 (Singapore); Ng, Mary [Department of Pharmacology, National University of Singapore (Singapore); Udalagama, Chammika; Rodrigues, Anna E.; Watt, Frank [Centre for Ion Beam Applications (CIBA), Department of Physics, National University of Singapore, Singapore 117542 (Singapore); Jenner, Andrew Michael [Illawara Health and Medical Research Institute (IHMRI), University of Wollongong, NSW 2522 (Australia)

    2011-10-15

    Using Nuclear microscopy, we have investigated iron distributions in the colons of Sprague Dawley rats, in order to elucidate heme uptake. Four groups of five Sprague Dawley rats (mean weight 180 g) were fed different purified diets containing either heme diet (2.5% w/w hemoglobin), high fat diet (HFD) (18% w/w fat, 1% w/w cholesterol), 'western' diet (combination of hemoglobin 2.5% and 18% fat, 1% cholesterol) or control diet (7% w/w fat). After 4 weeks, animals were sacrificed by exsanguination after anaesthesia. Thin sections of frozen colon tissue were taken, freeze dried and scanned using nuclear microscopy utilising the techniques PIXE, RBS and STIM. The new data acquisition system (IonDaq) developed in CIBA was used to obtain high resolution images and line scans were used to map the iron distributions across the colon boundaries. The nuclear microscope results indicate that when HFD is given in addition to heme, the iron content of the epithelial cells that line the colon decreases, and the zinc in the smooth muscle wall increases. This implies that the level of heme and fat in diet has an important role in colon health, possibly by influencing epithelial cells directly or changing luminal composition such as bacterial flora or levels of metabolites and cytotoxins.

  19. Inverted Lymphoglandular Polyp in Descending Colon

    Directory of Open Access Journals (Sweden)

    Shengmei Zhou

    2015-01-01

    Full Text Available A 47-year-old male with a history of left colon cancer, status post left colon resection for 12 years, presented with rectal bleeding. Colonoscopic examination revealed an 8 mm sessile polyp in the proximal descending colon. Microscopic examination showed that the surface of this polyp was covered with a layer of normal colonic mucosa with focal surface erosion. In the submucosal layer, an intimate admixture of multiple cystically dilated glands and prominent lymphoid aggregates with germinal centers was seen. The glands were lined by columnar epithelium. Immunohistochemical staining showed the glands were positive for CK20 and CDX2 and negative for CK7, with a low proliferative index, mostly consistent with reactive colonic glands. The patient remained asymptomatic after one-year follow-up. A review of the literature shows very rare descriptions of similar lesions, but none fits exactly this pattern. We would designate this inverted lymphoglandular polyp and present this case to raise the awareness of recognizing this unusual histological entity.

  20. Clostridium difficile – From Colonization to Infection

    Science.gov (United States)

    Schäffler, Holger; Breitrück, Anne

    2018-01-01

    Clostridium difficile is the most frequent cause of nosocomial antibiotic-associated diarrhea. The incidence of C. difficile infection (CDI) has been rising worldwide with subsequent increases in morbidity, mortality, and health care costs. Asymptomatic colonization with C. difficile is common and a high prevalence has been found in specific cohorts, e.g., hospitalized patients, adults in nursing homes and in infants. However, the risk of infection with C. difficile differs significantly between these cohorts. While CDI is a clear indication for therapy, colonization with C. difficile is not believed to be a direct precursor for CDI and therefore does not require treatment. Antibiotic therapy causes alterations of the intestinal microbial composition, enabling C. difficile colonization and consecutive toxin production leading to disruption of the colonic epithelial cells. Clinical symptoms of CDI range from mild diarrhea to potentially life-threatening conditions like pseudomembranous colitis or toxic megacolon. While antibiotics are still the treatment of choice for CDI, new therapies have emerged in recent years such as antibodies against C. difficile toxin B and fecal microbial transfer (FMT). This specific therapy for CDI underscores the role of the indigenous bacterial composition in the prevention of the disease in healthy individuals and its role in the pathogenesis after alteration by antibiotic treatment. In addition to the pathogenesis of CDI, this review focuses on the colonization of C. difficile in the human gut and factors promoting CDI. PMID:29692762

  1. Nickel remediation by AM-colonized sunflower.

    Science.gov (United States)

    Ker, Keomany; Charest, Christiane

    2010-08-01

    This greenhouse study aimed to examine the contribution of arbuscular mycorrhizal (AM) colonization on the uptake of and tolerance to nickel (Ni) in sunflower (Helianthus annuus L.). We hypothesized that AM colonization increases Ni content and tolerance in sunflower grown under varying soil Ni concentrations. The combined effect of AM colonization and soil Ni input on the assimilation of nitrogen, in particular the activity of glutamine synthetase (GS), in sunflower plants was also investigated. A factorial experimental design was performed with sunflower cv. Lemon Queen, with or without the AM fungus, Glomus intraradices Schenck & Smith, and treated with 0, 100, 200, or 400 mg Ni kg(-1) dry soil (DS). The AM colonization significantly enhanced plant growth and Ni content, especially at the lower soil Ni treatments. Furthermore, the AM plants exposed to the highest soil Ni level of 400 mg Ni kg(-1) DS had a significantly higher shoot Ni extracted percentage than non-AM plants, suggesting that the AM symbiosis contributed to Ni uptake, then its translocation from roots to shoots. The AM colonization also significantly increased the GS activity in roots, this being likely an indicator of an enhanced Ni tolerance. These findings support the hypothesis that AM symbiosis contributes to an enhanced Ni plant uptake and tolerance and should be considered as part of phytoremediation strategies.

  2. A Study of Clinicopathological Differences Between Right-sided and Left-sided Colon Cancers

    OpenAIRE

    芳賀, 駿介; 遠藤, 俊吾; 加藤, 博之; 高橋, 直樹; 吉松, 和彦; 橋本, 雅彦; 石橋, 敬一郎; 梅原, 有弘; 横溝, 肇; 梶原, 哲郎; Shunsuke, HAGA; Shungo, ENDO; Hiroyuki, KATO; Naoki, TAKAHASHI; Kazuhiko, YOSHIMATSU

    1996-01-01

    The present study was aimed to determine the clinicopathological features of cancers of the right-sided colon (cecum, ascending colon, transverse colon) and left-sided colon (descending colon, sigmoid colon) in order to help improve the efficacy of their treatment. Excluding multiple cancer cases, 364 patients with primary colon cancer underwent surgey at our department between 1974 and 1994; they comprised 171 individuals with right-sided colon cancer and 193 with left-sided colon cancer. A ...

  3. PET-MRI in Diagnosing Patients With Colon or Rectal Cancer

    Science.gov (United States)

    2015-11-25

    Recurrent Colon Cancer; Recurrent Rectal Cancer; Stage IIA Colon Cancer; Stage IIA Rectal Cancer; Stage IIB Colon Cancer; Stage IIB Rectal Cancer; Stage IIC Colon Cancer; Stage IIC Rectal Cancer; Stage IIIA Colon Cancer; Stage IIIA Rectal Cancer; Stage IIIB Colon Cancer; Stage IIIB Rectal Cancer; Stage IIIC Colon Cancer; Stage IIIC Rectal Cancer; Stage IVA Colon Cancer; Stage IVA Rectal Cancer; Stage IVB Colon Cancer; Stage IVB Rectal Cancer

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. "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.

  12. 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.

  13. 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.

  14. 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

  15. The colon. Clinical radiology and endoscopy

    International Nuclear Information System (INIS)

    Rosenbusch, G.; Reeders, J.W.A.J.

    1993-01-01

    This comprehensive reference work presents in-depth information on the diagnostic radiology and endoscopy of the colon. After a brief review of the history of colon examinations, two chapters explain the anatomy, physiology and pharmacology of the large intestine as well as the methods and techniques applied for radiological examination of the colon. The pathology and characteristical findings and the diagnostic evaluation of the various types of disease are the main subject, with the chapters discussing inflammations and tumors consuming by far most of the space, but there is also valuable information on vascular lesions, traumata, latrogenous or post-surgery lesions, among others, and on the characteristical findings in children. Numerous tables, radiographs and endoscopic images together with drawings illustrate and accompany the textbook information. (orig.). 492 figs., 95 tabs [de

  16. A Higher-Order Colon Translation

    DEFF Research Database (Denmark)

    Danvy, Olivier; Nielsen, Lasse Reichstein

    2001-01-01

    A lambda-encoding such as the CPS transformation gives rise to administrative redexes. In his seminal article ``Call-by-name, call-by-value and the lambda-calculus'', 25 years ago, Plotkin tackled administrative reductions using a so-called ``colon translation.'' 10 years ago, Danvy and Filinski...... integrated administrative reductions in the CPS transformation, making it operate in one pass. The technique applies to other lambda-encodings (e.g., variants of CPS), but we do not see it used in practice--instead, Plotkin's colon translation appears to be favored. Therefore, in an attempt to link both...... techniques, we recast Plotkin's proof of Indifference and Simulation to the higher-order specification of the one-pass CPS transformation. To this end, we extend his colon translation from first order to higher order...

  17. Combinatorial nanomedicines for colon cancer therapy.

    Science.gov (United States)

    Anitha, A; Maya, S; Sivaram, Amal J; Mony, U; Jayakumar, R

    2016-01-01

    Colon cancer is one of the major causes of cancer deaths worldwide. Even after surgical resection and aggressive chemotherapy, 50% of colorectal carcinoma patients develop recurrent disease. Thus, the rationale of developing new therapeutic approaches to improve the current chemotherapeutic regimen would be highly recommended. There are reports on the effectiveness of combination chemotherapy in colon cancer and it has been practiced in clinics for long time. These approaches are associated with toxic side effects. Later, the drug delivery research had shown the potential of nanoencapsulation techniques and active targeting as an effective method to improve the effectiveness of chemotherapy with less toxicity. This current focus article provides a brief analysis of the ongoing research in the colon cancer area using the combinatorial nanomedicines and its outcome. © 2015 Wiley Periodicals, Inc.

  18. Pneumocystis jirovecii colonization in chronic pulmonary disease

    Directory of Open Access Journals (Sweden)

    Gutiérrez S.

    2011-05-01

    Full Text Available Pneumocystis jirovecii causes pneumonia in immunosuppressed individuals. However, it has been reported the detection of low levels of Pneumocystis DNA in patients without signs and symptoms of pneumonia, which likely represents colonization. Several studies performed in animals models and in humans have demonstrated that Pneumocystis induces a local and a systemic response in the host. Since P. jirovecii colonization has been found in patients with chronic pulmonary diseases it has been suggested that P. jirovecii may play a role in the physiopathology and progression of those diseases. In this report we revise P. jirovecii colonization in different chronic pulmonary diseases such us, chronic obstructive pulmonary disease, interstitial lung diseases, cystic fibrosis and lung cancer.

  19. Prehistoric human colonization of India.

    Science.gov (United States)

    Misra, V N

    2001-11-01

    Human colonization in India encompasses a span of at least half-a-million years and is divided into two broad periods, namely the prehistoric (before the emergence of writing) and the historic (after writing). The prehistoric period is divided into stone, bronze and iron ages. The stone age is further divided into palaeolithic, mesolithic and neolithic periods. As the name suggests, the technology in these periods was primarily based on stone. Economically, the palaeolithic and mesolithic periods represented a nomadic, hunting-gathering way of life, while the neolithic period represented a settled, food-producing way of life. Subsequently copper was introduced as a new material and this period was designated as the chalcolithic period. The invention of agriculture, which took place about 8000 years ago, brought about dramatic changes in the economy, technology and demography of human societies. Human habitat in the hunting-gathering stage was essentially on hilly, rocky and forested regions, which had ample wild plant and animal food resources. The introduction of agriculture saw it shifting to the alluvial plains which had fertile soil and perennial availability of water. Hills and forests, which had so far been areas of attraction, now turned into areas of isolation. Agriculture led to the emergence of villages and towns and brought with it the division of society into occupational groups. The first urbanization took place during the bronze age in the arid and semi-arid region of northwest India in the valleys of the Indus and the Saraswati rivers, the latter represented by the now dry Ghaggar-Hakra bed. This urbanization is known as the Indus or Harappan civilization which flourished during 3500-1500 B.C. The rest of India during this period was inhabited by neolithic and chalcolithic farmers and mesolithic hunter-gatherers. With the introduction of iron technology about 3000 years ago, the focus of development shifted eastward into the Indo-Gangetic divide and

  20. Human wound colonization by Lucilia eximia and Chrysomya rufifacies (Diptera: Calliphoridae): myiasis, perimortem, or postmortem colonization?

    Science.gov (United States)

    Sanford, Michelle R; Whitworth, Terry L; Phatak, Darshan R

    2014-05-01

    The infestation of human or animal tissues by fly larvae has been given distinctive terminology depending on the timing and location of colonization. Wounds and orifices colonized by Diptera in a living human or animal are typically referred to as myiasis. When the colonization occurs after death, it is referred to as postmortem colonization and can be used to estimate the minimum postmortem interval. What happens when the human, as in the case presented here, has a necrotic limb while the human remains alive, at least for a short period of time? The case presented here documents perimortem wound colonization by Lucilia eximia (Wiedemann) and Chrysomya rufifacies (Macquart) and the considerations for approximating development temperatures and estimating the time of colonization (TOC). This represents the first record of L. eximia in human myiasis in the United States and the first record of the co-occurrence of L. eximia and C. rufifacies in human myiasis in the United States. The TOC was estimated using both ambient and body temperature. Insect colonization before death complicates the estimation of TOC and minimum postmortem interval and illustrates the problem of temperature approximation in forensic entomology casework.

  1. Fungal colonization of air-conditioning systems

    Directory of Open Access Journals (Sweden)

    Ljaljević-Grbić Milica

    2008-01-01

    Full Text Available Fungi have been implicated as quantitatively the most important bioaerosol component of indoor air associated with contaminated air-conditioning systems. rarely, indoor fungi may cause human infections, but more commonly allergenic responses ranging from pneumonitis to asthma-like symptoms. From all air conditioner filters analyzed, 16 fungal taxa were isolated and identified. Aspergillus fumigatus causes more lethal infections worldwide than any other mold. Air-conditioning filters that adsorb moisture and volatile organics appear to provide suitable substrates for fungal colonization. It is important to stress that fungal colonization of air-conditioning systems should not be ignored, especially in hospital environments.

  2. Delirium in fast-track colonic surgery

    DEFF Research Database (Denmark)

    Kurbegovic, Sorel; Andersen, Jens; Krenk, Lene

    2015-01-01

    BACKGROUND: Postoperative delirium (PD) is a common but serious problem after major surgery with a multifactorial pathogenesis including age, pain, opioid use, sleep disturbances and the surgical stress response. These factors have been minimised by the "fast-track methodology" previously...... demonstrated to enhance recovery and reduce morbidity. METHODS: Clinical symptoms of PD were routinely collected three times daily from preoperatively until discharge in a well-defined enhanced recovery program after colonic surgery in 247 consecutive patients. RESULTS: Total median length of hospital stay...... postoperative recovery program may decrease the risk and duration of PD after colonic surgery....

  3. Inflammatory fibroid polyp of sigmoid colon.

    Science.gov (United States)

    Lifschitz, O; Lew, S; Witz, M; Reiss, R; Griffel, B

    1979-01-01

    A case of inflammatory fibroid polyp of the sigmoid colon is presented. This is the eight case of this type of polyp in the colon and, to the best of our knowledge, the first one involving the sigmoid and producing intussusception. Symptomatology of the inflamed fibroid polyp in this part of the gut closely simulates gastrointestinal malignancy. The treatment is surgical excision of the polyp, or colonoscopic resection when it is possible. Intraoperative colonoscopy helps the surgeon to localize the lesion and to role out the existence of other lesions.

  4. Cesarean section changes neonatal gut colonization

    DEFF Research Database (Denmark)

    Stokholm, Jakob; Thorsen, Jonathan; Chawes, Bo L

    2016-01-01

    BACKGROUND: Delivery by means of cesarean section has been associated with increased risk of childhood immune-mediated diseases, suggesting a role of early bacterial colonization patterns for immune maturation. OBJECTIVE: We sought to describe the influence of delivery method on gut and airway......-driven partial least squares analyses. The initial airway microbiota was unaffected by birth method. CONCLUSION: Delivery by means of cesarean section was associated with early colonization patterns of the neonatal gut but not of the airways. The differences normalized within the first year of life. We speculate...

  5. SPECIAL FEATURES OF CARCINOGENESIS OF COLON ADENOCARCINOMA

    Directory of Open Access Journals (Sweden)

    G. A. Raskin

    2015-01-01

    Full Text Available Colorectal cancer is one of the most common malignancies and the leading cause of cancer-related death. There are 4 basic colon carcinogenic steps: malignant transformation of adenoma into carcinoma; HNPCC (hereditary nonpolyposis colon cancer; cancer «de novo»; chronic colitis malignant transformation. All of them, except for Lynch syndrome, are increasingly focused on stem tissue-committed cells as mutation targets and the source of malignancies. Subsequently, cancer stem cells are considered as the cause of chemoresistance of tumors, metastases and relapses. Thus, the study of the cell population can dramatically change approaches to the treatment of patients with colorectal adenocarcinoma.

  6. The double contrast examination of the colon

    International Nuclear Information System (INIS)

    Welin, S.; Welin, G.

    1980-01-01

    The double contrast method has been modified in order to get a more detailed picture of the mucous membrane of the colon. The method has been employed at Malmoe hospital since 1953. The method and its diagnostic application in cases of adenoids, villiferous tumours, diverticula, Crohn's disease, ulcerating colitis, and deformation of the rectum/sigma junction due to external endometriosis and peritoneal carcinosis are described. The diagnostic values of the double contrast method and colposcopy/biopsy of the colon are compared. The two methods are found to be complementary. (MG) [de

  7. 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

  8. 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.

  9. The retrorenal colon in the supine and prone patient

    International Nuclear Information System (INIS)

    Hopper, K.D.; Sherman, J.L.; Luethke, J.M.; Ghaed, N.

    1986-01-01

    Ninety patients underwent CT in both supine and prone positions so that the orientation of the retroperitoneal colon about the kidneys could be determined. Particular attention was given to bowel found posterior to the kidneys, the so-called retrorenal colon. The frequency of retrorenal colon increased from 1.9% on supine studies to 10.7% on prone studies. Since most invasive renal procedures performed with the patient prone would miss retrorenal colon located behind the lateral one third of the kidney, the data were reevaluated, excluding these patients. The resulting frequency of significant retrorenal colon found on prone studies was 4.7%. Significant retrorenal colon was found exclusively at the level of the lower renal poles, and the involved colon in these patients was extensively distended with gas. Particular attention should be given, under fluoroscopic guidance, to detecting this unusual posteriorly positioned, air-filled colon before one undertakes any invasive renal procedure

  10. Colorectal (Colon) Cancer: What Are the Risk Factors?

    Science.gov (United States)

    ... The CDC Cancel Submit Search The CDC Colorectal (Colon) Cancer Note: Javascript is disabled or is not supported ... Risk Assessment Tool (National Cancer Institute) Learning About Colon Cancer Stay Informed Language: English Español (Spanish) File Formats ...

  11. Prune belly syndrome with pouch colon with scaphoid megalourethra

    African Journals Online (AJOL)

    We here report a rare association of megalourethra with pouch colon with prune belly syndrome. We also provide a newer embryological and prognostic perspective to this association. Keywords: megalourethra, prune belly syndrome pouch colon, scaphoid ...

  12. Cardiovascular and respiratory changes and convalescence in laparoscopic colonic surgery

    DEFF Research Database (Denmark)

    Schulze, S; Lyng, K M; Bugge, K

    1999-01-01

    Gasless laparoscopy produces smaller cardiopulmonary and systemic changes than carbon dioxide (CO2) laparoscopy during colonic surgery.......Gasless laparoscopy produces smaller cardiopulmonary and systemic changes than carbon dioxide (CO2) laparoscopy during colonic surgery....

  13. Dysphagia after Colon Interposition Graft for Esophageal Carcinoma

    Directory of Open Access Journals (Sweden)

    C. Spitali

    2012-01-01

    Full Text Available Colon interposition is an established technique for esophageal reconstruction. We describe the case of primary adenocarcinoma arising in a colonic interposition graft that was performed after total esophagectomy for recurrence adenocarcinoma derived from the Barrett esophagus.

  14. Clinicopathologic factors identify sporadic mismatch repair-defective colon cancers

    DEFF Research Database (Denmark)

    Halvarsson, Britta; Anderson, Harald; Domanska, Katarina

    2008-01-01

    Identification of sporadic mismatch repair (MMR)-defective colon cancers is increasingly demanded for decisions on adjuvant therapies. We evaluated clinicopathologic factors for the identification of these prognostically favorable tumors. Histopathologic features in 238 consecutive colon cancers...

  15. Enterobacter Strains Might Promote Colon Cancer.

    Science.gov (United States)

    Yurdakul, Dilşad; Yazgan-Karataş, Ayten; Şahin, Fikrettin

    2015-09-01

    Many studies have been performed to determine the interaction between bacterial species and cancer. However, there has been no attempts to demonstrate a possible relationship between Enterobacter spp. and colon cancer so far. Therefore, in the present study, it is aimed to investigate the effects of Enterobacter strains on colon cancer. Bacterial proteins were isolated from 11 Enterobacter spp., one Morganella morganii, and one Escherichia coli strains, and applied onto NCM460 (Incell) and CRL1790 (ATCC) cell lines. Cell viability and proliferation were determined in MTS assay. Flow Cytometry was used to detect CD24 level and apoptosis. Real-Time PCR studies were performed to determine NFKB and Bcl2 expression. Graphpad Software was used for statistical analysis. The results showed that proteins, isolated from the Enterobacter spp., have significantly increased cell viability and proliferation, while decreasing the apoptosis of the cell lines tested. The data in the present study indicated that Enterobacter strains might promote colon cancer. Moreover, Enterobacter spp. could be a clinically important factor for colon cancer initiation and progression. Studies can be extended on animal models in order to develop new strategies for treatment.

  16. Accuracy of colonoscopy in localizing colonic cancer.

    Science.gov (United States)

    Stanciu, C; Trifan, Anca; Khder, Saad Alla

    2007-01-01

    It is important to establish the precise localization of colonic cancer preoperatively; while colonoscopy is regarded as the diagnostic gold standard for colorectal cancer, its ability to localize the tumor is less reliable. To define the accuracy of colonoscopy in identifying the location of colonic cancer. All of the patients who had a colorectal cancer diagnosed by colonoscopy at the Institute of Gastroenterology and Hepatology, Iaşi and subsequently received a surgical intervention at three teaching hospitals in Iaşi, between January 2001 and December 2005, were included in this study. Endoscopic records and operative notes were carefully reviewed, and tumor localization was recorded. There were 161 patients (89 men, 72 women, aged 61.3 +/- 12.8 years) who underwent conventional surgery for colon cancer detected by colonoscopy during the study period. Twenty-two patients (13.66%) had erroneous colonoscopic localization of the tumors. The overall accuracy of preoperative colonoscopic localization was 87.58%. Colonoscopy is an accurate, reliable method for locating colon cancer, although additional techniques (i.e., endoscopic tattooing) should be performed at least for small lesions.

  17. Bacterial Endophyte Colonization and Distribution within Plants

    Directory of Open Access Journals (Sweden)

    Shyam L. Kandel

    2017-11-01

    Full Text Available The plant endosphere contains a diverse group of microbial communities. There is general consensus that these microbial communities make significant contributions to plant health. Both recently adopted genomic approaches and classical microbiology techniques continue to develop the science of plant-microbe interactions. Endophytes are microbial symbionts residing within the plant for the majority of their life cycle without any detrimental impact to the host plant. The use of these natural symbionts offers an opportunity to maximize crop productivity while reducing the environmental impacts of agriculture. Endophytes promote plant growth through nitrogen fixation, phytohormone production, nutrient acquisition, and by conferring tolerance to abiotic and biotic stresses. Colonization by endophytes is crucial for providing these benefits to the host plant. Endophytic colonization refers to the entry, growth and multiplication of endophyte populations within the host plant. Lately, plant microbiome research has gained considerable attention but the mechanism allowing plants to recruit endophytes is largely unknown. This review summarizes currently available knowledge about endophytic colonization by bacteria in various plant species, and specifically discusses the colonization of maize plants by Populus endophytes.

  18. TRANSVERSE COLON POUCH: AN ALTERNATIVE TO ...

    African Journals Online (AJOL)

    Objective Urinary diversion after pelvic irradiation is challenging. The use of irradiated bowel is mostly complicated and unsuccessful. Therefore, the use of an exclusively non-irradiated bowel segment, such as the transverse colon, is a good alternative in such situation. Patients and Methods Twenty-nine female patients ...

  19. Massive rectal bleeding from colonic diverticulosis

    African Journals Online (AJOL)

    ABEOLUGBENGAS

    barium enema studies have indicated increasing world prevalence ... Other diagnostic modalities include barium enema, computerised ... This is in contrast to the findings in our patient when colonoscopy was carried out, in which the diverticula were more at the descending colon-left sided, and were found to be bleeding.

  20. Pharmacological interventions for improved colonic anastomotic healing

    DEFF Research Database (Denmark)

    Oines, Mari Nanna; Krarup, Peter-Martin; Jorgensen, Lars Nannestad

    2014-01-01

    with the primary purpose of promoting healing of anastomoses made in the colon or rectum under uncomplicated conditions. We excluded studies on adverse events from interventions, nutritional interventions or in situ physical supporting biomaterials. The primary outcome was biomechanical strength or AL. We...

  1. Metabolic Syndrome X and Colon Cancer

    Czech Academy of Sciences Publication Activity Database

    Matoulek, M.; Svobodová, S.; Svačina, Š.; Plavcová, Marie; Zvárová, Jana; Visokai, V.; Lipská, M.

    2003-01-01

    Roč. 27, suppl. 1 (2003), s. 86 ISSN 0307-0565. [European Congress on Obesity /12./. 29.05.2003-01.06.2003, Helsinki] R&D Projects: GA MZd NB6635; GA MŠk LN00B107 Keywords : metabolic syndrome X * colon cancer Subject RIV: BB - Applied Statistics, Operational Research

  2. Diverticular Disease of the Colon in Korea

    Science.gov (United States)

    Kim, Byoung Ho; Lee, Sung Hoon; Lee, Seung Sei; Oh, Dong Joo; Chung, Eul Soon; Lee, Sang Jong

    1987-01-01

    This study is designed to determine the relative prevalence and characteristics of diverticular disease of the colon in Korea. We did a retrospective evaluation of 16,964 consecutive barium enemas performed at Koryo General Hospital between January 1971 and October 1986, and found 100 patients with diverticular disease of the colon. The results are as follows: 1) Colonic diverticula were found in 100 patients, and incidence of 0.59% in 16,964 consecutive barium enemas. The male to female ratio was 2.1:1.2) Incidence rose with advancing age from 0.45% in the second decade to 2.5% in the seventh decade.3) Patient age ranged from 19 to 77 years with more than 70% of the patients in the 5th, 6th and 7th decades.4) The greater majority (81%) of the diverticular disease the right colon.5) Fifty percent of the cases were classified as multiple diverticula.6) The mean age of patients with right sided diverticula was 47.5 years and that of patients with left sided diverticula was 57.7 years. The mean age of single diverticular patients was 50.4 years and that of multiple diverticular patients was 48.4 year.7) Associated diseases were hemorrhoids (18%), gall stones (12%) and previous appendectomy (11%). Among the 29 patients who had hemorrhoids and or a previous appendectomy, 28 of those had right sided diverticula. PMID:3154819

  3. Colonization of exopolysaccharide-producing Paenibacillus ...

    African Journals Online (AJOL)

    SERVER

    2007-07-04

    Jul 4, 2007 ... inhibitory effect against A. niger. Growth, protein and biopolymers production of bacteria were ... bacterium colonized plant roots and were able to migrate downward with the root as it elongated. Scanning electron ...... siderophores producing Pseudomonas fluorescence on crown rot. Haggag 1577 disease ...

  4. Management of the colonic volvulus in 2016.

    Science.gov (United States)

    Perrot, L; Fohlen, A; Alves, A; Lubrano, J

    2016-06-01

    Colonic volvulus is the third leading cause of colonic obstruction worldwide, occurring at two principal locations: the sigmoid colon and cecum. In Western countries, sigmoid volvulus preferentially affects elderly men whereas cecal volvulus affects younger women. Some risk factors, such as chronic constipation, high-fiber diet, frequent use of laxatives, personal past history of laparotomy and anatomic predispositions, are common to both locations. Clinical symptomatology is non-specific, including a combination of abdominal pain, gaseous distention, and bowel obstruction. Abdominopelvic computerized tomography is currently the gold standard examination, allowing positive diagnosis as well as detection of complications. Specific management depends on the location, patient comorbidities and colonic wall viability, but treatment is an emergency in every case. If clinical or radiological signs of gravity are present, emergency surgery is mandatory, but is associated with high morbidity and mortality rates. For sigmoid volvulus without criteria of gravity, the ideal strategy is an endoscopic detorsion procedure followed, within 2 to 5 days, by surgery that includes a sigmoid colectomy with primary anastomosis. Exclusively endoscopic therapy must be reserved for patients who are at excessive risk for surgical intervention. In cecal volvulus, endoscopy has no role and surgery is the rule. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  5. Colonic spirochetosis in animals and humans.

    Science.gov (United States)

    Smith, James L

    2005-07-01

    Colonic spirochetosis is a disease caused by the gram-negative bacteria Brachyspira aalborgi and Brachyspira pilosicoli. B. pilosicoli induces disease in both humans and animals, whereas B. aalborgi affects only humans and higher primates. Symptoms in humans include diarrhea, rectal bleeding, and abdominal cramps. Colonic spirochetosis is common in third world countries; however, in developed countries, the disease is observed mainly in homosexual males. Terminally ill patients infected with Brachyspira are particularly at risk for developing spirochetemia. Diarrhea, poor growth performance, and decreased feed-to-gain efficiency is seen in pigs with colonic spirochetosis. The disease in chickens is characterized by delayed and/or reduced egg production, diarrhea, poor feed conversion, and retarded growth. Thus, colonic spirochetosis can represent a serious economic loss in the swine and poultry industries. The organisms are transmitted by the fecal-oral route, and several studies have demonstrated that human, primate, pig, dog, or bird strains of B. pilosicoli can be transmitted to pigs, chickens, and mice. B. pilosicoli may be a zoonotic pathogen, and although it has not been demonstrated, there is a possibility that both B. pilosicoli and B. aalborgi can be transferred to humans via contact with the feces of infected animals, meat from infected animals, or food contaminated by food handlers. Neither B. pilosicoli nor B. aalborgi has been well characterized in terms of basic cellular functions, pathogenicity, or genetics. Studies are needed to more thoroughly understand these Brachyspira species and their disease mechanisms.

  6. A Higher-Order Colon Translation

    DEFF Research Database (Denmark)

    Danvy, Olivier; Nielsen, Lasse R.

    2000-01-01

    A lambda-encoding such as the CPS transformation gives rise to administrative redexes. In his seminal article ``Call-by-name, call-by-value and the lambda-calculus'', 25 years ago, Plotkin tackled administrative reductions using a so-called ``colon translation.'' 10 years ago, Danvy and Filinski...

  7. [Postoperative intraperitoneal complications in colon cancer surgery].

    Science.gov (United States)

    Erokhina, E A; Topuzov, É G; Topuzov, É É

    2014-01-01

    The authors studied the clinical characteristics and terms of the development of postoperative intraperitoneal complications in patients undergoing colon cancer surgery. It was stated, that the diversity of clinical data depended on complication characteristics. Results of investigation allowed defining of the most dangerous terms of intraperitoneal complications and risk factors.

  8. Therapeutic considerations in Dukes C colon cancer

    NARCIS (Netherlands)

    Bleeker, Willem Aldert

    2001-01-01

    Colon cancer is one of the main health issues in the western world. In the Netherlands more than 7000 patients are diagnosed yearly with this disease and half of them will die from it. Prognosis largely depends on tumor stage, which is estimated by radiological, clinical and histological

  9. Colon cancer: it's CIN or CIMP.

    Science.gov (United States)

    Issa, Jean-Pierre

    2008-10-01

    Combined genetic and epigenetic analysis of sporadic colon cancer suggest that it can no longer be viewed as a single disease. There are at least three different subsets with distinct clinico-pathologic features, with important implications for preventions, screening, and therapy.

  10. Types of planned agrarian colonization in Brazilian forests: Historical examples

    OpenAIRE

    Gerd Kohlhepp

    2015-01-01

    About 200 years ago state or privately controlled agrarian colonization in South Brazil began with immigrants from Central and Southern Europe. As the Brazilian campos had been occupied by extensive cattle ranching of large landholders, forests were systematically cleared by peasants, the new rural social middle class. Three examples of the most different types of agrarian colonization are presented, colonization of European small farmers in South Brazil in the 19th century; colonization of a...

  11. Laparoscopic colonic surgery in Denmark 2004-2007

    DEFF Research Database (Denmark)

    Schulze, S.; Iversen, M.G.; Bendixen, A.

    2008-01-01

    OBJECTIVE: Laparoscopic colonic surgery was introduced about 15 years ago and has together with the evidence-based 'fast-track' methodology improved early postoperative outcome. The purpose of this study was to asses the organization and early outcome after laparoscopic colonic surgery in Denmark...... of laparoscopic colonic surgery but probably performed in too many low volume departments. Laparoscopic colonic surgery should be monitored and further advances secured by adjustment of perioperative care to fast-track care Udgivelsesdato: 2008/11...

  12. [Brazilian colonization in the Paraguayan agricultural frontier].

    Science.gov (United States)

    Neupert, R F

    1991-04-01

    This work briefly describes Brazilian colonization of the Paraguayan agricultural frontier, analyzes factors responsible for expelling population from Brazil and for attracting Brazilians to Paraguay, and assesses the economic and social consequences of immigration to the area. Paraguay's vast and sparsely populated agricultural frontier in areas outside the Central subregion underwent a process of intense colonization from the early 1960s to the mid-1980s. The Paraguayan government initiated an ambitious colonization program in 1963 to increase production, relieve population pressure and subdivision of small parcels in the Central subregion, encourage agricultural modernization, and produce a more diversified agriculture. Paraguayan agriculture in the early 1960s suffered from excessive concentration of land in a few hands and resulting exclusion of around 3/4 of workers from ownership and from any possibility of obtaining credit to fund technological improvements. Results of studies 2 decades after implementation of the colonization plan suggest that it has failed in significant areas. Although a considerable population redistribution alleviated pressure in the Central subregion, it apparently resulted more from spontaneous movement of peasants outside the colonization areas than from the official program. Concentration of lands is now occurring in the colonization area. Assistance for agricultural modernization and diversification of production in the peasant sector has been minimal. On the other hand, production of soy, wheat, and cotton for export increased substantially, because of an entrepreneurial agriculture capitalized by foreign as well as national interests The unmet goals of the colonization program would have required structural reforms rather than simple spatial redistribution of the population. Many of the colonists in the 1970s were Brazilian families displaced by mechanized agriculture in the southern states of Parana, Santa Catarina, and Rio

  13. Diverticular disease of the right colon

    Directory of Open Access Journals (Sweden)

    Boutross-Tadross Odette

    2011-10-01

    Full Text Available Abstract Background The incidence of colonic diverticular disease varies with national origin, cultural background and diet. The frequency of this disease increases with advancing age. Right-sided diverticular disease is uncommon and reported to occur in 1-2% of surgical specimens in European and American series. In contrast the disease is more prevalent and reported in 43-50% of specimens in Asian series. Various lines of evidence suggest this variation may represent hereditary differences. The aim of the study is to report all cases of right sided diverticular disease underwent surgical resection or identified during pathological examination of right hemicoloectomy specimens Methods A retrospective review of all surgical specimens with right sided colonic diverticular disease selected from a larger database of all colonic diverticulosis and diverticulitis surgical specimen reported between January 1993 and December 2010 at the Pathology Department McMaster University Medical Centre Canada. The clinical and pathological features of these cases were reviewed Results The review identified 15 cases of right colon diverticulosis. The clinical diagnoses of these cases were appendicitis, diverticulitis or adenocarcinoma. Eight cases of single congenital perforated diverticuli were identified and seven cases were incidental multiple acquired diverticuli found in specimen resected for right side colonic carcinomas/large adenomas. Laparotomy or laparoscopic assisted haemicolectomies were done for all cases. Pathological examination showed caecal wall thickening with inflammation associated with perforated diverticuli. Histology confirmed true solitary diverticuli that exhibited in two cases thick walled vessels in the submucosa and muscular layer indicating vascular malformation/angiodysplasia. Acquired diverticuli tend to be multiple and are mostly seen in specimens resected for neoplastic right colon diseases. Conclusion Single true diverticular

  14. Diverticular disease of the right colon.

    Science.gov (United States)

    Radhi, Jasim M; Ramsay, Jennifer A; Boutross-Tadross, Odette

    2011-10-06

    The incidence of colonic diverticular disease varies with national origin, cultural background and diet. The frequency of this disease increases with advancing age. Right-sided diverticular disease is uncommon and reported to occur in 1-2% of surgical specimens in European and American series. In contrast the disease is more prevalent and reported in 43-50% of specimens in Asian series. Various lines of evidence suggest this variation may represent hereditary differences. The aim of the study is to report all cases of right sided diverticular disease underwent surgical resection or identified during pathological examination of right hemicoloectomy specimens A retrospective review of all surgical specimens with right sided colonic diverticular disease selected from a larger database of all colonic diverticulosis and diverticulitis surgical specimen reported between January 1993 and December 2010 at the Pathology Department McMaster University Medical Centre Canada. The clinical and pathological features of these cases were reviewed The review identified 15 cases of right colon diverticulosis. The clinical diagnoses of these cases were appendicitis, diverticulitis or adenocarcinoma. Eight cases of single congenital perforated diverticuli were identified and seven cases were incidental multiple acquired diverticuli found in specimen resected for right side colonic carcinomas/large adenomas. Laparotomy or laparoscopic assisted haemicolectomies were done for all cases. Pathological examination showed caecal wall thickening with inflammation associated with perforated diverticuli. Histology confirmed true solitary diverticuli that exhibited in two cases thick walled vessels in the submucosa and muscular layer indicating vascular malformation/angiodysplasia. Acquired diverticuli tend to be multiple and are mostly seen in specimens resected for neoplastic right colon diseases. Single true diverticular disease of the right colon is usually of congenital type and affects

  15. Chemoembolization Using Irinotecan in Treating Patients With Liver Metastases From Metastatic Colon or Rectal Cancer

    Science.gov (United States)

    2015-09-10

    Liver Metastases; Mucinous Adenocarcinoma of the Colon; Mucinous Adenocarcinoma of the Rectum; Recurrent Colon Cancer; Recurrent Rectal Cancer; Signet Ring Adenocarcinoma of the Colon; Signet Ring Adenocarcinoma of the Rectum; Stage IV Colon Cancer; Stage IV Rectal Cancer

  16. Functional anatomy of the colonic bioreactor: Impact of antibiotics and Saccharomyces boulardii on bacterial composition in human fecal cylinders.

    Science.gov (United States)

    Swidsinski, Alexander; Loening-Baucke, Vera; Schulz, Stefan; Manowsky, Julia; Verstraelen, Hans; Swidsinski, Sonja

    2016-02-01

    Sections of fecal cylinders were analyzed using fluorescence in situ hybridization targeting 180 bacterial groups. Samples were collected from three groups of women (N=20 each) treated for bacterial vaginosis with ciprofloxacin+metronidazole. Group A only received the combined antibiotic regimen, whereas the A/Sb group received concomitant Saccharomyces boulardii CNCM I-745 treatment, and the A_Sb group received S. boulardii prophylaxis following the 14-day antibiotic course. The number of stool cylinders analyzed was 188 out of 228 in group A, 170 out of 228 in group A/Sb, and 172 out of 216 in group A_Sb. The colonic biomass was organized into a separate mucus layer with no bacteria, a 10-30μm broad unstirred transitional layer enriched with bacteria, and a patchy fermentative area that mixed digestive leftovers with bacteria. The antibiotics suppressed bacteria mainly in the fermentative area, whereas abundant bacterial clades retreated to the transitional mucus and survived. As a result, the total concentration of bacteria decreased only by one order. These effects were lasting, since the overall recovery of the microbial mass, bacterial diversity and concentrations were still below pre-antibiotic values 4 months after the end of antibiotic treatment. Sb-prophylaxis markedly reduced antibiotic effects and improved the recovery rates. Since the colon is a sophisticated bioreactor, the study indicated that the spatial anatomy of its biomass was crucial for its function. Copyright © 2015 The Authors. Published by Elsevier GmbH.. All rights reserved.

  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. Three New Soil-inhabiting Species of Trichoderma in the Stromaticum Clade with Test of Their Antagonism to Pathogens.

    Science.gov (United States)

    Chen, Kai; Zhuang, Wen-Ying

    2017-09-01

    Trichoderma is a dominant component of the soil mycoflora. During the field investigations of northern, central, and southwestern China, three new species in the Stromaticum clade were encountered from soil, and named as T. hebeiense, T. sichuanense, and T. verticillatum. Their phylogenetic positions were determined by analyses of the combined two genes: partial sequences of translation elongation factor 1-alpha and the second largest RNA polymerase subunit-encoding genes. Distinctions between the new species and their close relatives were discussed. Trichoderma hebeiense appeared as a separate terminal branch. The species is distinctive by its oblong conidia and aggregated pustules in culture. Trichoderma sichuanense features in concentric colony and produces numerous clean exudates on aerial mycelium in culture. Trichoderma verticillatum is characterized by its verticillium-like synanamorph and production of abundant chlamydospores. In vitro antagonism towards the new species was tested by dual culture technique.

  19. A novel extracellular gut symbiont in the marine worm Priapulus caudatus (Priapulida reveals an alphaproteobacterial symbiont clade of the Ecdysozoa

    Directory of Open Access Journals (Sweden)

    Paul eKroer

    2016-04-01

    Full Text Available Priapulus caudatus (phylum Priapulida is a benthic marine predatory worm with a cosmopolitan distribution. In its digestive tract we detected symbiotic bacteria that were consistently present in specimens collected over eight years from three sites at the Swedish west coast. Based on their 16S rRNA gene sequence, these symbionts comprise a novel genus of the order Rickettsiales (Alphaproteobacteria. Electron microscopy and fluorescence in situ hybridization (FISH identified them as extracellular, elongate bacteria closely associated with the microvilli, for which we propose the name ‘Candidatus Tenuibacter priapulorum’. Within Rickettsiales, they form a phylogenetically well-defined, family-level clade with uncultured symbionts of marine, terrestrial, and freshwater arthropods. Cand. Tenuibacter priapulorum expands the host range of this candidate family from Arthropoda to the entire Ecdysozoa, which may indicate an evolutionary adaptation of this bacterial group to the microvilli-lined guts of the Ecdysozoa.

  20. A Novel Extracellular Gut Symbiont in the Marine Worm Priapulus caudatus (Priapulida) Reveals an Alphaproteobacterial Symbiont Clade of the Ecdysozoa.

    Science.gov (United States)

    Kroer, Paul; Kjeldsen, Kasper U; Nyengaard, Jens R; Schramm, Andreas; Funch, Peter

    2016-01-01

    Priapulus caudatus (phylum Priapulida) is a benthic marine predatory worm with a cosmopolitan distribution. In its digestive tract we detected symbiotic bacteria that were consistently present in specimens collected over 8 years from three sites at the Swedish west coast. Based on their 16S rRNA gene sequence, these symbionts comprise a novel genus of the order Rickettsiales (Alphaproteobacteria). Electron microscopy and fluorescence in situ hybridization (FISH) identified them as extracellular, elongate bacteria closely associated with the microvilli, for which we propose the name "Candidatus Tenuibacter priapulorum". Within Rickettsiales, they form a phylogenetically well-defined, family-level clade with uncultured symbionts of marine, terrestrial, and freshwater arthropods. Cand. Tenuibacter priapulorum expands the host range of this candidate family from Arthropoda to the entire Ecdysozoa, which may indicate an evolutionary adaptation of this bacterial group to the microvilli-lined guts of the Ecdysozoa.

  1. Screening for colorectal cancer in defunctioned colons.

    Science.gov (United States)

    Akbar, Fayyaz; Quyn, Aaron; Steele, Robert

    2018-01-01

    Objectives Population-based colorectal (bowel) cancer screening using faecal occult blood tests leads to a reduction in cause-specific mortality. However, in people where the colon is defunctioned, the use of standard faecal occult blood test is not appropriate. The aim of this study was to examine the current trends of clinical practice for colorectal cancer screening in people with defunctioned colons. Methods An online survey was performed using SurveyMonkey. All members of the Association of Coloproctology of Great Britain and Ireland were invited by email to participate. Reminders were sent to non-responders and partial responders till six weeks. All responses were included in our analysis. Results Of the 206 (34.59%) questionnaires completed, all questions were answered in 110 (55.8%). Among responders, 94 (85.4%) were colorectal consultant surgeons, 72% had worked in their current capacity for more than five years, and 105 (50.9%) had encountered colorectal cancer in defunctioned colons during their career. Some 72.2% of responders stated that a screening test for colorectal cancer in patients with defunctioned colons was currently not offered, or that they did not know whether or not it was offered in their area. Conclusions Bowel screening in the United Kingdom is currently not offered to 72.2% of the age appropriate population with defunctioned colons. Among responding colorectal surgeons, 50% had encountered colorectal cancer in such patients. There is considerable variability in clinical practice regarding the optimal age for onset of screening, time interval, and the optimal modality to offer for screening in such cases.

  2. The role of colonic metabolism in lactose intolerance

    NARCIS (Netherlands)

    He, T.; Venema, K.; Priebe, M. G.; Welling, G. W.; Brummer, R. -J. M.; Vonk, R. J.

    Lactose maldigestion and intolerance affect a large part of the world population. The underlying factors of lactose intolerance are not fully understood. In this review, the role of colonic metabolism is discussed, i.e. fermentation of lactose by the colonic microbiota, colonic processing of the

  3. Formulation, development and evaluation of colon-specific ketorolac ...

    African Journals Online (AJOL)

    The major intention to formulate and develop colon targeted tablets is to improve the therapeutic efficacy by increasing therapeutic drug concentrations in colon. The present study was aimed to develop guar gum compression coated tablets ketorolac tromethamine to achieve the colon-specific drug release. In this study ...

  4. Red meat and colon cancer : a possible role for heme

    NARCIS (Netherlands)

    Sesink, Aloysius Lambertus Antonia

    2000-01-01

    Sporadic colon cancer is a multifactorial aging disease affected by long-term exposure to environmental risk factors. Epidemiological studies have shown that risk for colon cancer is associated with diets high in red meat and/or animal fat. The mechanisms by which colonic tumors arise are, however,

  5. Clinicopathologic factors identify sporadic mismatch repair-defective colon cancers

    DEFF Research Database (Denmark)

    Halvarsson, Britta; Anderson, Harald; Domanska, Katarina

    2008-01-01

    Identification of sporadic mismatch repair (MMR)-defective colon cancers is increasingly demanded for decisions on adjuvant therapies. We evaluated clinicopathologic factors for the identification of these prognostically favorable tumors. Histopathologic features in 238 consecutive colon cancers...... and excluded 61.5% of the tumors from MMR testing. This clinicopathologic index thus successfully selects MMR-defective colon cancers. Udgivelsesdato: 2008-Feb...

  6. Preparation and Characterization of Colon-Specific Microspheres of ...

    African Journals Online (AJOL)

    Purpose: To prepare and evaluate colon specific drug delivery system of diclofenac sodium for highly localized delivery to the colon. Methods: The colon specific drug delivery system was prepared as matrix-type microspheres using Ethyl Cellulose (EC), Cellulose Acetate Phthalate (CAP), and Eudragit L 100-55 by the ...

  7. Isolation and in vitro expansion of human colonic stem cells

    NARCIS (Netherlands)

    Jung, P.; Sato, T.; Merlos-Suarez, A.; Barriga, F.M.; Iglesias, M.; Rossell, D.; Auer, H.; Gallardo, M.; Blasco, M.A.; Sancho, E.; Clevers, H.; Batlle, E.

    2011-01-01

    Here we describe the isolation of stem cells of the human colonic epithelium. Differential cell surface abundance of ephrin type-B receptor 2 (EPHB2) allows the purification of different cell types from human colon mucosa biopsies. The highest EPHB2 surface levels correspond to epithelial colonic

  8. The role of colonic metabolism in lactose intolerance

    NARCIS (Netherlands)

    He, T.; Venema, K.; Priebe, M.G.; Welling, G.W.; Brummer, R.J.M.; Vonk, R.J.

    2008-01-01

    Lactose maldigestion and intolerance affect a large part of the world population. The underlying factors of lactose intolerance are not fully understood. In this review, the role of colonic metabolism is discussed, i.e. fermentation of lactose by the colonic microbiota, colonic processing of the

  9. 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."

  10. 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.

  11. 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.

  12. 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

  13. Phylogenomic analysis of Candidatus ‘Izimaplasma’ species: free-living representatives from a Tenericutes clade found in methane seeps

    KAUST Repository

    Skennerton, Connor T.

    2016-04-08

    Tenericutes are a unique class of bacteria that lack a cell wall and are typically parasites or commensals of eukaryotic hosts. Environmental 16S rDNA surveys have identified a number of tenericute clades in diverse environments, introducing the possibility that these Tenericutes may represent non-host-associated, free-living microorganisms. Metagenomic sequencing of deep-sea methane seep sediments resulted in the assembly of two genomes from a Tenericutes-affiliated clade currently known as \\'NB1-n\\' (SILVA taxonomy) or \\'RF3\\' (Greengenes taxonomy). Metabolic reconstruction revealed that, like cultured members of the Mollicutes, these \\'NB1-n\\' representatives lack a tricarboxylic acid cycle and instead use anaerobic fermentation of simple sugars for substrate level phosphorylation. Notably, the genomes also contained a number of unique metabolic features including hydrogenases and a simplified electron transport chain containing an RNF complex, cytochrome bd oxidase and complex I. On the basis of the metabolic potential predicted from the annotated genomes, we devised an anaerobic enrichment media that stimulated the growth of these Tenericutes at 10 °C, resulting in a mixed culture where these organisms represented ∼60% of the total cells by targeted fluorescence in situ hybridization (FISH). Visual identification by FISH confirmed these organisms were not directly associated with Eukaryotes and electron cryomicroscopy of cells in the enrichment culture confirmed an ultrastructure consistent with the defining phenotypic property of Tenericutes, with a single membrane and no cell wall. On the basis of their unique gene content, phylogenetic placement and ultrastructure, we propose these organisms represent a novel class within the Tenericutes, and suggest the names Candidatus \\'Izimaplasma sp. HR1\\' and Candidatus \\'Izimaplasma sp. HR2\\' for the two genome representatives.

  14. 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.

  15. Spinning Gland Transcriptomics from Two Main Clades of Spiders (Order: Araneae) - Insights on Their Molecular, Anatomical and Behavioral Evolution

    Science.gov (United States)

    Prosdocimi, Francisco; Bittencourt, Daniela; da Silva, Felipe Rodrigues; Kirst, Matias; Motta, Paulo C.; Rech, Elibio L.

    2011-01-01

    Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium) to generate ∼80,000 reads from the spinning gland of Actinopus spp. (infraorder: Mygalomorphae) and Gasteracantha cancriformis (infraorder: Araneomorphae, Orbiculariae clade). Actinopus spp. retains primitive characteristics on web usage and presents a single undifferentiated spinning gland while the orbiculariae spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative transcriptomics. Genes related to spider silks were manually curated and analyzed. Although a single spidroin gene family was found in Actinopus spp., a vast repertoire of specialized spider silk proteins was encountered in orbiculariae. Astacin-like metalloproteases (meprin subfamily) were shown to be some of the most sampled unigenes and duplicated gene families in G. cancriformis since its evolutionary split from mygalomorphs. Our results confirm that the evolution of the molecular repertoire of silk proteins was accompanied by the (i) anatomical differentiation of spinning glands and (ii) behavioral complexification in the web usage. Finally, a phylogenetic tree was constructed to cluster most of the known spidroins in gene clades. This is the first large-scale, multi-organism transcriptome for spider spinning glands and a first step into a broad understanding of spider web systems biology and evolution. PMID:21738742

  16. 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.

  17. Spinning gland transcriptomics from two main clades of spiders (order: Araneae--insights on their molecular, anatomical and behavioral evolution.

    Directory of Open Access Journals (Sweden)

    Francisco Prosdocimi

    Full Text Available Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium to generate ∼80,000 reads from the spinning gland of Actinopus spp. (infraorder: Mygalomorphae and Gasteracantha cancriformis (infraorder: Araneomorphae, Orbiculariae clade. Actinopus spp. retains primitive characteristics on web usage and presents a single undifferentiated spinning gland while the orbiculariae spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative transcriptomics. Genes related to spider silks were manually curated and analyzed. Although a single spidroin gene family was found in Actinopus spp., a vast repertoire of specialized spider silk proteins was encountered in orbiculariae. Astacin-like metalloproteases (meprin subfamily were shown to be some of the most sampled unigenes and duplicated gene families in G. cancriformis since its evolutionary split from mygalomorphs. Our results confirm that the evolution of the molecular repertoire of silk proteins was accompanied by the (i anatomical differentiation of spinning glands and (ii behavioral complexification in the web usage. Finally, a phylogenetic tree was constructed to cluster most of the known spidroins in gene clades. This is the first large-scale, multi-organism transcriptome for spider spinning glands and a first step into a broad understanding of spider web systems biology and evolution.

  18. Mortality risk factor analysis in colonic perforation: would retroperitoneal contamination increase mortality in colonic perforation?

    Science.gov (United States)

    Yoo, Ri Na; Kye, Bong-Hyeon; Kim, Gun; Kim, Hyung Jin; Cho, Hyeon-Min

    2017-10-01

    Colonic perforation is a lethal condition presenting high morbidity and mortality in spite of urgent surgical treatment. This study investigated the surgical outcome of patients with colonic perforation associated with retroperitoneal contamination. Retrospective analysis was performed for 30 patients diagnosed with colonic perforation caused by either inflammation or ischemia who underwent urgent surgical treatment in our facility from January 2005 to December 2014. Patient characteristics were analyzed to find risk factors correlated with increased postoperative mortality. Using the Physiological and Operative Severity Score for the Enumeration of Mortality and Morbidity (POSSUM) audit system, the mortality and morbidity rates were estimated to verify the surgical outcomes. Patients with retroperitoneal contamination, defined by the presence of retroperitoneal air in the preoperative abdominopelvic CT, were compared to those without retroperitoneal contamination. Eight out of 30 patients (26.7%) with colonic perforation had died after urgent surgical treatment. Factors associated with mortality included age, American Society of Anesthesiologists (ASA) physical status classification, and the ischemic cause of colonic perforation. Three out of 6 patients (50%) who presented retroperitoneal contamination were deceased. Although the patients with retroperitoneal contamination did not show significant increase in the mortality rate, they showed significantly higher ASA physical status classification than those without retroperitoneal contamination. The mortality rate predicted from Portsmouth POSSUM was higher in the patients with retroperitoneal contamination. Patients presenting colonic perforation along with retroperitoneal contamination demonstrated severe comorbidity. However, retroperitoneal contamination was not found to be correlated with the mortality rate.

  19. 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.

  20. Parallel gigantism and complex colonization patterns in the Cape Verde scincid lizards Mabuya and Macroscincus (Reptilia: Scincidae) revealed by mitochondrial DNA sequences.

    Science.gov (United States)

    Carranza, S; Arnold, E N; Mateo, J A; López-Jurado, L F

    2001-08-07

    The scincid lizards of the Cape Verde islands comprise the extinct endemic giant Macroscincus coctei and at least five species of Mabuya, one of which, Mabuya vaillanti, also had populations with large body size. Phylogenetic analysis based on DNA sequences derived from the mitochondrial cytochrome b, cytochrome oxidase I and 12S rRNA genes (711, 498 and 378 base pairs (bp), respectively) corroborates morphological evidence that these species constitute a clade and that Macroscincus is unrelated to very large skinks in other areas. The relationships are ((M. vaillanti and Mabuya delalandii) (Mabuya spinalis and Macroscincus coctei (Mabuya fogoensis nicolauensis (Mabuya fogoensis antaoensis and Mabuya stangeri)))). The Cape Verde archipelago was colonized from West Africa, probably in the Late Miocene or Early Pliocene period. The north-eastern islands were probably occupied first, after which the ancestor of M. vaillanti and M. delalandii may have originated on Boavista, the ancestor of the latter species arriving on Santiago or Fogo later. The M. fogoensis--M. stangeri clade colonized the islands of Branco, Razo, Santa Luzia and São Vicente from São Nicolau and reached Santo Antão after this. Colonization of these northeastern islands was slow, perhaps because the recipient islands had not developed earlier or because colonization cut across the path of the Canary Current and the Northeast Trade Winds, the main dispersing agents in the region. Rapid extension of range into the southwestern islands occurred later in M. spinalis and then in M. vaillanti and M. delalandii. The long apparent delay between the origin of these species and their southwestern dispersal may have been because there were earlier colonizations of the southern islands which excluded later ones until the earlier inhabitants were exterminated by volcanic or climatic events. The evolution of large size in Macroscincus occurred in the northwestern islands and was paralleled in the eastern and

  1. The Hyalella (Crustacea: Amphipoda) species cloud of the ancient Lake Titicaca originated from multiple colonizations.

    Science.gov (United States)

    Adamowicz, Sarah J; Marinone, María Cristina; Menu-Marque, Silvina; Martin, Jeffrey W; Allen, Daniel C; Pyle, Michelle N; De Los Ríos, Patricio; Sobel, Crystal N; Ibañez, Carla; Pinto, Julio; Witt, Jonathan D S

    2018-08-01

    Ancient lakes are renowned for their exceptional diversity of endemic species. As model systems for the study of sympatric speciation, it is necessary to understand whether a given hypothesized species flock is of monophyletic or polyphyletic origin. Here, we present the first molecular characterization of the Hyalella (Crustacea: Amphipoda) species complex of Lake Titicaca, using COI and 28S DNA sequences, including samples from the connected Small and Large Lakes that comprise Lake Titicaca as well as from a broader survey of southern South American sites. At least five evolutionarily distant lineages are present within Lake Titicaca, which were estimated to have diverged from one another 12-20 MYA. These major lineages are dispersed throughout the broader South American Hyalella phylogeny, with each lineage representing at least one independent colonization of the lake. Moreover, complex genetic relationships are revealed between Lake Titicaca individuals and those from surrounding water bodies, which may be explained by repeated dispersal into and out of the lake, combined with parallel intralacustrine diversification within two separate clades. Although further work in deeper waters will be required to determine the number of species present and modes of diversification, our results strongly indicate that this amphipod species cloud is polyphyletic with a complex geographic history. Copyright © 2018 Elsevier Inc. All rights reserved.

  2. Eating patterns and risk of colon cancer.

    Science.gov (United States)

    Slattery, M L; Boucher, K M; Caan, B J; Potter, J D; Ma, K N

    1998-07-01

    Colon cancer has been associated with several nutrients and foods. The authors used data from a population-based study conducted in Northern California, Utah, and Minnesota to examine associations between dietary eating patterns and risk of developing colon cancer. Through factor analysis, detailed dietary intake data obtained from 1,993 cases (diagnosed in 1991-1994) and 2,410 controls were grouped into factors that were evaluated for relations with lifestyle characteristics and colon cancer risk. Several dietary patterns emerged. The dietary patterns with the most variation were labeled "Western," "prudent," "high fat/sugar dairy," "substituters," and "drinkers." The "Western" dietary pattern was associated with a higher body mass index and a greater intake of total energy and dietary cholesterol. The "prudent" pattern was associated with higher levels of vigorous leisure time physical activity, smaller body size, and higher intakes of dietary fiber and folate. Persons who had high scores on the "drinker" pattern were also more likely to smoke cigarettes. The "Western" dietary pattern was associated with an increased risk of colon cancer in both men and women. The association was strongest among people diagnosed prior to age 67 years (for men, odds ratio (OR)=1.96, 95% confidence interval (CI) 1.22-3.15; for women, OR=2.02, 95% CI 1.21-3.36) and among men with distal tumors (OR=2.25, 95% CI 1.47-3.46). The "prudent" diet was protective, with the strongest associations being observed among people diagnosed prior to age 67 years (men: OR=0.63, 95% CI 0.43-0.92; women: OR=0.58, 95% CI 0.38-0.87); associations with this dietary pattern were also strong among persons with proximal tumors (men: OR=0.55, 95% CI 0.38-0.80; women: OR=0.64, 95% CI 0.45-0.92). Although "substituters" (people who substituted low fat dairy products for high fat dairy products, margarine for butter, poultry for red meat, and whole grains for refined grains) were at reduced risk of colon cancer

  3. Does hyperbaric oxygen therapy reduce the effects of ischemia on colonic anastomosis in laparoscopic colon resection?

    Science.gov (United States)

    Emir, Seyfi; Gurdal, Sibel Ozkan; Sozen, Selim; Bali, Ilhan; Yesildag, Ebru; Celik, Atilla; Guzel, Savas; Sahin, Onder; Ay, Hakan; Topcu, Birol

    2016-01-01

    An increase in intra-abdominal pressure causes a decrease in the splanchnic blood flow and the intramucosal pH of the bowel, as well as increasing the risk of ischemia in the colon. The aim of the present study is to evaluate the effect of hyperbaric oxygen therapy (HBOT) on the ischemia caused by laparoscopy in colonic anastomosis in an experimental model of laparoscopic colonic surgery. We divided 30 male Wistar albino rats into three groups: Group A was the control (open colon anastomosis); Group B received LCA (laparoscopic colon anastomosis); while Group C received both LCA and HBOT. Each group contained ten animals. We placed Group C (LCA and HBOT) in an experimental hyperbaric chamber into which we administered pure oxygen at 2.1 atmospheres absolute 100% oxygen for 60 min for ten consecutive days. The anastomotic bursting pressure value was found to be higher in the open surgery group (226 ± 8.8) (Group A). The result for Group C (213 ± 27), which received HBOT, was better than that for Group B (197 ± 27). However, there was no statistically significant difference between Group B and Group C. Group A showed better healing than the other groups, while significant differences in the fibroblast proliferation scores were found between Groups A and B. In terms of tissue hydroxyproline levels, a significant difference was found between Groups A and B and between Groups A and C, but not between Groups B and C. HBOT increases the oxygen level in the injured tissue. Although HBOT might offer several advantages, it had only a limited effect on the healing of colonic anastomosis in rats with increased intra-abdominal pressure in our study. Anastomosis, Colon, Hyperbaric Oxygen Treatment, Oxidative Stress.

  4. Aspergillus fumigatus colonization of punctal plugs.

    Science.gov (United States)

    Tabbara, Khalid F

    2007-01-01

    Punctal plugs are used in patients with dry eye syndrome to preserve the tears. In this report, I present two cases of Aspergillus fumigatus colonization of punctal plugs. Observational series of two cases. Approval was obtained from the institutional review board. Two men aged 29 and 31 years developed black spots inside the hole of punctal plug, which looked like eyeliner deposits. The deposits inside the hole of the plug in each patient were removed and cultured. Cultures of the two punctal plugs black deposits grew A fumigatus. Bacterial cultures were negative. Colonization of the punctal plug hole with A fumigatus was observed in two cases. It is recommended that punctal plugs be removed in patients undergoing refractive or intraocular procedures or in patients who are receiving topical corticosteroids. Current punctal plugs should be redesigned to avoid the presence of an inserter hole.

  5. Colonization of bone matrices by cellular components

    Science.gov (United States)

    Shchelkunova, E. I.; Voropaeva, A. A.; Korel, A. V.; Mayer, D. A.; Podorognaya, V. T.; Kirilova, I. A.

    2017-09-01

    Practical surgery, traumatology, orthopedics, and oncology require bioengineered constructs suitable for replacement of large-area bone defects. Only rigid/elastic matrix containing recipient's bone cells capable of mitosis, differentiation, and synthesizing extracellular matrix that supports cell viability can comply with these requirements. Therefore, the development of the techniques to produce structural and functional substitutes, whose three-dimensional structure corresponds to the recipient's damaged tissues, is the main objective of tissue engineering. This is achieved by developing tissue-engineering constructs represented by cells placed on the matrices. Low effectiveness of carrier matrix colonization with cells and their uneven distribution is one of the major problems in cell culture on various matrixes. In vitro studies of the interactions between cells and material, as well as the development of new techniques for scaffold colonization by cellular components are required to solve this problem.

  6. Multifaceted Interpretation of Colon Cancer Stem Cells.

    Science.gov (United States)

    Hatano, Yuichiro; Fukuda, Shinya; Hisamatsu, Kenji; Hirata, Akihiro; Hara, Akira; Tomita, Hiroyuki

    2017-07-05

    Colon cancer is one of the leading causes of cancer-related deaths worldwide, despite recent advances in clinical oncology. Accumulating evidence sheds light on the existence of cancer stem cells and their role in conferring therapeutic resistance. Cancer stem cells are a minor fraction of cancer cells, which enable tumor heterogeneity and initiate tumor formation. In addition, these cells are resistant to various cytotoxic factors. Therefore, elimination of cancer stem cells is difficult but essential to cure the malignant foci completely. Herein, we review the recent evidence for intestinal stem cells and colon cancer stem cells, methods to detect the tumor-initiating cells, and clinical significance of cancer stem cell markers. We also describe the emerging problems of cancer stem cell theory, including bidirectional conversion and intertumoral heterogeneity of stem cell phenotype.

  7. Colonic complications following human bone marrow transplantation

    Directory of Open Access Journals (Sweden)

    Paulino Martínez Hernández-Magro

    2015-01-01

    Full Text Available Background: Human bone marrow transplantation (BMT becomes an accepted treatment of leukemia, aplastic anemia, immunodeficiency syndromes, and hematologic malignancies. Colorectal surgeons must know how to determine and manage the main colonic complications. Objective: To review the clinical features, clinical and pathological staging of graft vs host disease (GVHD, and treatment of patients suffering with colonic complications of human bone marrow transplantation. Patients and methods: We have reviewed the records of all patients that received an allogeneic bone marrow transplant and were evaluated at our Colon and Rectal Surgery department due to gastrointestinal symptoms, between January 2007 and January 2012. The study was carried out in patients who developed colonic complications, all of them with clinical, histopathological or laboratory diagnosis. Results: The study group was constituted by 77 patients, 43 male and 34 female patients. We identified colonic complications in 30 patients (38.9%; five patients developed intestinal toxicity due to pretransplant chemotherapy (6.4%; graft vs. host disease was present in 16 patients (20%; 13 patients (16.8% developed acute colonic GVHD, and 3 (3.8% chronic GVHD. Infection was identified in 9 patients (11.6%. Conclusions: The three principal colonic complications are the chemotherapy toxicity, GVHD, and superinfection; the onset of symptoms could help to suspect the type of complication (0–20 day chemotherapy toxicity, 20 and more GVHD, and infection could appear in any time of transplantation. Resumo: Experiência: O transplante de medula óssea humana (MOH passou a ser um tratamento adotado para leucemia, anemia aplástica, síndromes de imunodeficiência e neoplasias hematológicas. Cirurgiões colorretais devem saber como determinar e tratar as principais complicações do cólon. Objetivo: Revisar as características clínicas, estadiamentos clínico e patológico da doença do enxerto

  8. The radiographic examination of the colon

    International Nuclear Information System (INIS)

    Hendrix, T.R.; Saba, G.P. II.

    1980-01-01

    To provide medical and scientific background on certain selected technologies generally considered to be of particular significance, the National Center for Health Care Technology commissioned a series of overview papers, one of which is entitled 'The Radiographic Examination of the Colon.' These overviews are likely to be of most immediate interest to clinicians and biomedical scientists; they also may provide valuable background for assessments undertaken by the Center and for exploring the broad societal implications of health care technologies. Barium enema is the most available and widely used technique for examining the colon. It is often a routine part of the gastrointestinal work-up regardless of the suspected basis, anatomical or functional, of the patient's symptoms. Indeed, common practice is not to entertain a diagnosis of functional disorder before excluding all reasonable possibility of an anatomical abnormality. Barium enema is one of the most frequently ordered radiographic examinations

  9. Role of microsatellite instability in colon cancer

    Directory of Open Access Journals (Sweden)

    M. Yu. Fedyanin

    2012-01-01

    Full Text Available Coloncancer is among leading causes of cancer morbidity and mortality both inRussiaand worldwide. Development of molecular biology lead to decoding of carcinogenesis and tumor progression mechanisms. These processes require accumulation of genetic and epigenetic alterations in a tumor cell.Coloncancer carcinogenesis is characterized by mutations cumulation in genes controlling growth and differentiation of epithelial cells, which leads to their genetic instability. Microsatellite instability is a type of genetic instability characterized by deterioration of mismatch DNA repair. This leads to faster accumulation of mutations in DNA. Loss of mismatch repair mechanism can easily be diagnosed by length of DNA microsatellites. These alterations are termed microsatellite instability. They can be found both in hereditary and sporadic colon cancers. This review covers the questions of microsatellite instability, its prognostic and predictive value in colon cancer.

  10. Potassium secretion in mammalian distal colon

    DEFF Research Database (Denmark)

    Sørensen, Mads Vaarby

    2009-01-01

    Epithelial organs adjust the „inner milieu“ of the body and are crucial for all homeostatic processes. Epithelial transport of different solutes and water is regulated phenomena. The regulation processes include both long term hormonal regulation and short term local agonist mediated regulation....... This research project is the summary of 3 original papers addressing the functional role of different regulating factors on ion transport in mouse distal colon. The first paper addresses the effect of luminal nucleotides on electrogenic Na+ absorption. The distal colon, like the distal nephron is an aldosterone......-sensitive tissue and participates in the regulation of Na+ excretion. In the distal nephron it was found that luminal nucleotides inhibit ENaC-mediated Na+ absorption. Here it was addressed whether luminal nucleotides regulate Na+ absorption and if so, which of the known luminal P2 receptors are involved. Using...

  11. Melanocyte colonization and pigmentation of breast carcinoma

    DEFF Research Database (Denmark)

    Mele, Marco; Laurberg, Tinne; Engberg Damsgaard, Tine

    2012-01-01

    . The pathogenesis by which melanocyte migration takes place is not known, but a breached basement membrane is considered essential. Conclusion. Histological examination and additional staining of skin are essential to differentiate breast cancer melanosis from malignant melanoma.......Introduction. Melanocyte colonization of breast carcinoma by nonneoplastic melanocytes of epidermal origin is a rare and serious condition first described in 1977. We report on the exceptional clinical and pathological features of this migration phenomenon in a 74-year-old patient. Discussion...

  12. Peri-colonic haematoma following routine colonoscopy

    OpenAIRE

    Felicity Page; Olfunso Adedeji

    2016-01-01

    Introduction: We present a case of an extra-luminal haematoma following routine colonoscopy. This case highlights an uncommon but potentially life threatening complication in which there is little published literature to date. Presentation of case: A 73 year old male presented with abdominal pain and a reduction in haemoglobin following an uneventful colonoscopy. The imaging had been required as part of colorectal cancer follow up. Initial differential diagnosis included colonic perforatio...

  13. Synchronous colonic tumours of dual pathology.

    Science.gov (United States)

    Basu, S; Selvachandran, S N; Cade, D

    2001-05-01

    Synchronous colonic tumours of dual pathology are extremely rare. A review of the literature revealed that few cases have been reported to date. Because of their rarity and lack of specific symptoms, preoperative diagnosis is not easy and there is no protocol as yet for the ideal management of these cases. We present such a case which was treated by a combination of surgery and chemotherapy.

  14. Congenital pouch colon in female subjects

    Directory of Open Access Journals (Sweden)

    Sarin Y

    2007-01-01

    Full Text Available Over a period of 5-year (May 2000 to April 2005 29 patients of congenital pouch colon (CPC were managed by single pediatric surgeon in the Department of Pediatric Surgery of a tertiary hospital. Of these, 11 were girls (M: F: 1.6:1. Detailed anatomy could be studied in nine patients, were included in this study. Age of presentation in female subjects ranged 1 day to 8 years. On examination, eight of the nine patients had single perineal opening suggesting a very high incidence of association of cloaca in female subjects with CPC. Four had short urogenital sinus with colonic pouch opening in the posterior wall of urinary bladder. In other two patients, CPC terminated in short cloaca. Anomalies of mullerian structures such as uterus didelphus and septate vagina ware commonly encountered. Proximal diversion with or without pouch excision was done as the initial preliminary treatment for all those patients who presented in early life. Of the nine girls, two died after the preliminary surgery. Only five patients have undergone definitive surgery. Definitive surgery included abdomino-perineal pull-through of proximal normal colon ( n =2, tubularization of pouch with abdomino- posterior sagittal- pull through ( n =2 and abdomino-posterior sagittal urethra-vaginoanorectoplasty with pull through of tapered pouch colon in one patient. Two of these patients had concomitant bowel vaginoplasty. Three patients with tubularized pouches had constipation and spurious diarrhea. However, good pseudo-continence of bowel was achieved on regular bowel washes. The cosmetic appearance of perineum in all these three patients was acceptable. The patients in whom pouch excision was done had diarrhea and severe perineal excoriation resistant to conservative management.

  15. Urgent surgery for complicated colonic diverticula.

    Science.gov (United States)

    Funariu, Gheorghe; Binţinţan, Vasile; Seicean, Radu

    2006-03-01

    The AIM of this retrospective study was to evaluate the emergency surgical treatment of life-threatening complications of colonic diverticula. In the last 11 years, 22 of 101 patients with colonic diverticula (22.1%) underwent urgent surgery for acute complications: perforated gangrenous diverticulitis with generalized peritonitis (n=8) or pericolic abscess (n=8), acute bowel obstruction (n=4) and severe diverticular bleeding (n=2). In all patients with diffuse peritonitis or acute obstruction the indication for surgery was decided on clinical basis and the complicated diverticula were recognized only intra-operatively. Emergency surgical strategy differed according to the type of complication and the biologic condition of the patient: segmental colectomy and primary anastomosis for diverticular perforation (n=4), colonic stenosis (n=3) or diverticular bleeding (n=2); Hartmann resection with late reconnecting anastomosis in patients with diverticular perforation (n=5) or colonic obstruction (n=1); diverticulectomy with peritoneal drainage (n=2) and colostomy and drainage followed by secondary colectomy (n=5) for diverticular perforations in patients with poor general condition. Only one patient (4.5%) died post-operatively of multiple organ failure from generalized peritonitis. There was no anastomotic leakage in patients with primary anastomosis. Six patients (27.2%) developed wound infection. Hospital stay ranged between 11 and 60 days, significantly longer in cases with two-stage operations. Primary colectomy with immediate or delayed anastomosis is the best surgical procedure for acute divericular complications in patients with good biologic status. Two-stage operations such as colostomy and drainage coupled with late colectomy remain the viable alternative in patients with advanced disease and critical biologic condition.

  16. Managing Potentially Resectable Metastatic Colon Cancer

    OpenAIRE

    Marshall, John L.

    2008-01-01

    For patients with metastatic colon cancer, management has evolved from resecting a single liver metastasis and having only one chemotherapy medicine, to resecting multiple metastases including those outside the liver as well as using combination chemotherapy (based on recent supportive trials) to improve outcomes. This success has also raised many questions, including the role of adjuvant chemotherapy to downstage borderline resectable tumors, whether patients who receive preoperative chemoth...

  17. A surprise case of colonic interposition

    International Nuclear Information System (INIS)

    Law, Robert

    2006-01-01

    Blind nasogastric intubation failure as a result of changes to the normal anatomical pathway is not uncommon. This case report is of fluoroscopically guided intubation in a patient in whom blind intubation failed as a result of what was subsequently found to be a colonic interposition with associated late complications. Fluroscopically guided nasogastric intubation is a safe and effective procedure that should always be considered when blind intubation has failed

  18. Laparoscopic right colon resection with intracorporeal anastomosis.

    Science.gov (United States)

    Chang, Karen; Fakhoury, Mathew; Barnajian, Moshe; Tarta, Cristi; Bergamaschi, Roberto

    2013-05-01

    This study was performed to evaluate short-term clinical outcomes of laparoscopic intracorporeal ileocolic anastomosis following resection of the right colon. This was a retrospective study of selected patients who underwent laparoscopic intracorporeal ileocolic anastomosis following resection of the right colon for tumors or Crohn's disease by a single surgeon from July 2002 through June 2012. Data were retrieved from an Institutional Review Board-approved database. Study end point was postoperative adverse events, including mortality, complications, reoperations, and readmissions at 30 days. Antiperistaltic side-to-side anastomoses were fashioned laparoscopically with a 60-mm-long stapler cartridge and enterocolotomy was hand-sewn intracorporeally in two layers. Values were expressed as medians (ranges) for continuous variables. There were 243 patients (143 females) aged 61 (range = 19-96) years, with body mass index of 29 (18-43) kg/m(2) and ASA 1:2:3:4 of 52:110:77:4; 30 % had previous abdominal surgery and 38 % had a preexisting comorbidity. There were 84 ileocolic resections with ileo ascending anastomosis and 159 right colectomies with ileotransverse anastomosis. Operating time was 135 (60-220) min. Estimated blood loss was 50 (10-600) ml. Specimen extraction site incision length was 4.1 (3-4.4) cm. Conversion rate was 3 % and there was no mortality at 30 days, 15 complications (6.2 %), and 8 reoperations (3.3 %). Readmission rate was 8.7 %. Length of stay was 4 (2-32) days. Pathology confirmed Crohn's disease in 84 patients, adenocarcinoma in 152, and other tumors in 7 patients. Laparoscopic intracorporeal ileocolic anastomosis following resection of the right colon resulted in a favorable outcome in selected patients with Crohn's disease or tumors of the right colon.

  19. Distributed power sources for Mars colonization

    International Nuclear Information System (INIS)

    Miley, George H.; Shaban, Yasser

    2003-01-01

    One of the fundamental needs for Mars colonization is an abundant source of energy. The total energy system will probably use a mixture of sources based on solar energy, fuel cells, and nuclear energy. Here we concentrate on the possibility of developing a distributed system employing several unique new types of nuclear energy sources, specifically small fusion devices using inertial electrostatic confinement and portable 'battery type' proton reaction cells

  20. Sustainability: A Tedious Path to Galactic Colonization

    OpenAIRE

    Dutil, Y.; Dumas, S.

    2007-01-01

    Civilization cannot sustain an exponential growth for long time even when neglecting numerous laws of physics! In this paper, we examine what are fundamental obstacles to long term survival of a civilization and its possibility to colonize the Galaxy. Using the solar system as a reference, resources available for sustained growth are analyzed. Using this information, we will explore the probability of discovering a civilization at its different stage of energy evolution as estimating some pos...

  1. 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.

  2. 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...

  3. 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.

  4. 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

  5. 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...

  6. 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...

  7. 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.

  8. [Penetrant injuries of colon--our experience].

    Science.gov (United States)

    Lazović, R; Krivokapić, Z; Dobricanin, V

    2010-01-01

    In attemption to determine the place of primary repair in management of colon injuries, an open, non randomized clinical study was performed. Retrospective (RS) group of 62 patients according to exclusion criteria by Stone (S/F) and Flint (F1) was managed by one or two stage surgical procedure. Prospective (PR) group of 34 patients was managed using one stage repair non-selectively: two stage procedures were performed in 3 cases of advanced peritonitis and multi-segmental lacerations with impaired circulation of colon. In RS group 36 patients were managed by primary repair and in PR group, 31 were managed by primary repair. Both groups were of similar age/sex. Indexes of trauma severity were similar (TS, ISS, PATI). The latent time was shorter in PR group. Associated injuries to other body regions and abdominal organs were similar in both groups. S/F criteria and Flint grading in both (RS vs. PR) groups were similar. Comparison of attempted and successful primary repairs justifies the more liberal use of primary repair in early management of colon injuries.

  9. Transcatheter emboilization therapy of massive colonic bleeding

    International Nuclear Information System (INIS)

    Shin, G. H.; Oh, J. H.; Yoon, Y.

    1996-01-01

    To evaulate the efficacy and safety of emergent superselective transcatheter embolization for controlling massive colonic bleeding. Six of the seven patients who had symptom of massive gastrointestinal bleeding underwent emergent transcatheter embolization for control of the bleeding. Gastrointestinal bleeding in these patients was originated from various colonic diseases: rectal cancer(n=1), proctitis(n=1), benign ulcer(n=1), mucosal injury by ventriculoperitoneal shunt(n=1), and unknown(n=2). All patients except one with rectal cancer were critically ill. Superselective embolization were done by using Gelfoam particles and/or coils. The vessels embolized were ileocolic artery(n=1). superior rectal artery(n=2), inferior rectal artery (n=1), and middle and inferior rectal arteries(n=1). Hemostasis was successful immediately in all patients. Two underwnet surgery due to recurrent bleeding developed 3 days after the procedure(n=1) or in associalion with underlying rectal cancer(n=1). On surgical specimen of two cases, there was no mucosal ischemic change. Transcatheter embolization is a safe and effective treatment of method for the control of massive colonic bleeding

  10. Social Media, Delinguistification and Colonization of Lifeworld

    Directory of Open Access Journals (Sweden)

    Rob Heyman

    2015-12-01

    Full Text Available The article critically investigates, from an interdisciplinary perspective, how the current evolution of social media—like social network sites—interferes with the balance between private, commercial, and public space. We build on the concepts of lifeworld and systems, developed in Habermas’ theory of communicative action. The discussion is supported and enriched by the work of Feenberg and van Dijck, integrating insights from Science and Technology Studies and media studies. Technology philosopher and critical Science and Technology Studies scholar Feenberg introduces technology as a steering “medium” that delinguistifies and possibly colonizes the lifeworld by reinterpreting media sociological perspectives of Habermas, Marcuse, Latour, and Callon. In a similar way, media scholar van Dijck analyses the transition from human connectedness to automated connectivity in the context of social media. We then illustrate the delinguistification and the colonization of lifeworld with a systematic analysis of the contingent evolution of Facebook as one particular case in social media. We focus on three specific artifacts in Facebook, framed as obligatory passage points: EdgeRank, Sponsored Stories, and Gatekeeper. Each of them gives an idea how the private space is subsumed under the commercial space and how the colonization reconfigures the public space in social media like Facebook. In this sense, we complement the political economy analysis of prosumer commodity with the action-theoretical autonomist approach of immaterial labor, highlighting new potential threats of the current social media development.

  11. Importance of neural mechanisms in colonic mucosal and muscular dysfunction in adult rats following neonatal colonic irritation.

    Science.gov (United States)

    Chaloner, A; Rao, A; Al-Chaer, E D; Greenwood-Van Meerveld, B

    2010-02-01

    Previous studies have shown that early life trauma induced by maternal separation or colonic irritation leads to hypersensitivity to colorectal distension in adulthood. We tested the hypothesis that repetitive colorectal distension in neonates leads to abnormalities in colonic permeability and smooth muscle function in the adult rat. In neonatal rats, repetitive colorectal distension was performed on days 8, 10, and 12. As adults, stool consistency was graded from 0 (formed stool) to 3 (liquid stool). Colonic tissue was isolated for histology and myeloperoxidase levels. The colonic mucosa was placed in modified Ussing chambers for measurements of permeability and short-circuit current responses to forskolin, electrical field stimulation, and carbachol. Segments of colonic musculature were placed in organ baths and contractile response to potassium chloride, electrical field stimulation, and carbachol were determined. In adult rats that experienced neonatal colonic irritation, no significant changes in colonic histology or myeloperoxidase activity were observed; however, stool consistency scores were increased. Mucosal permeability, measured as an increase in basal conductance, was significantly increased but no changes in short-circuit current responses were observed. In adulthood, rats that underwent colorectal distension as neonates exhibited an elevated smooth muscle contractile response to potassium chloride, but no changes in response to electrical field stimulation or carbachol. In summary, neonatal colonic irritation, shown previously to produce colonic hypersensitivity, leads to significant alterations in colonic mucosal and smooth muscle function characterized by loose stools, increased mucosal permeability, and increased smooth muscle contractility in the absence of colon inflammation in adulthood. Published by Elsevier Ltd.

  12. Colon preneoplasia after carcinogen exposure is enhanced and colonic serotonergic system is suppressed by food deprivation.

    Science.gov (United States)

    Kannen, Vinicius; Fernandes, Cleverson R; Stopper, Helga; Zanette, Dalila L; Ferreira, Frederico R; Frajacomo, Fernando T; Carvalho, Milene C; Brandão, Marcus L; Elias Junior, Jorge; Jordão Junior, Alceu Afonso; Uyemura, Sérgio Akira; Waaga-Gasser, Ana Maria; Garcia, Sérgio B

    2013-10-04

    Calorie restriction regimens usually promote health and extend life-span in mammals. This is partially related to their preventive effects against malignancies. However, certain types of nutritional restriction failed to induce beneficial effects. The American Institute of Nutrition defines calorie restriction as diets which have only 40% fewer calories, but provide normal amounts of necessary food components such as protein, vitamins and minerals; whereas, food restriction means 40% less of all dietary ingredients plus 40% less calories. Our study aimed to test the hypothesis that the latter type of food deprivation (40% less food than consumed by standard fed rats) might increase cancer risk instead of reducing it, as is generally assumed for all dietary restrictive regimens. Since the endogenous modulation of the colon serotonergic system has been observed to play a role during the early steps of carcinogenesis we also investigated whether the serotoninergic system could be involved in the food intake modulation of cancer risk. For this, rats were exposed to a carcinogen and subjected to food deprivation for 56 days. Triglyceride levels and visceral adipose tissue were reduced while hepatic and colonic lipid peroxidation was increased. This dietary restriction also decreased serotonin levels in colon, and gene expression of its intestinal transporter and receptors. Finally, the numbers of preneoplastic lesions in the colon tissue of carcinogen-exposed rats were increased. Our data suggest that food deprivation enhances formation of early tumorigenic lesions by suppressing serotonergic activity in colon tissue. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  13. Colon cancer information as a source of exercise motivation for relatives of patients with colon cancer.

    Science.gov (United States)

    McGowan, Erin L; Prapavessis, Harry

    2010-12-01

    Using a Protection Motivation Theory (PMT) framework, this study examined whether factual colon cancer information is a meaningful source of exercise motivation for relatives of patients with colon cancer. One hundred sixty-six inactive relatives were randomly assigned to one of two treatment conditions: PMT group (intervention); and non-PMT group (attention control). At baseline (T1) participants completed demographic information, a questionnaire designed to assess their beliefs toward exercise and colon cancer as well as their exercise intentions. At T2 (one week following T1) participants watched one of two DVD videos that were created for the study. The intervention DVD contained exercise and colon cancer information that was yoked within the four major components of PMT: perceived vulnerability (PV); perceived severity (PS); response efficacy (RE); and self-efficacy (SE), while the attention control DVD contained general diet and cancer information. Immediately following watching the DVD, participants completed the same measures as in T1. Participants assigned to the PMT intervention group showed significant improvement in PV, RE, SE and exercise intentions, whereas participants assigned to the attention control group showed significant improvement only in RE. RE, SE, and PS made significant and unique contributions to prediction of exercise intention. Overall, the results of the present study demonstrate that a single exposure media intervention grounded in a PMT framework can change individuals' exercise and colon cancer beliefs, as well as change their exercise intentions. Implications of these findings and direction for future research are discussed.

  14. Malignant transformation of colonic epithelial cells by a colon-derived long noncoding RNA

    International Nuclear Information System (INIS)

    Franklin, Jeffrey L.; Rankin, Carl R.; Levy, Shawn; Snoddy, Jay R.; Zhang, Bing; Washington, Mary Kay; Thomson, J. Michael; Whitehead, Robert H.; Coffey, Robert J.

    2013-01-01

    Highlights: •Non-coding RNAs are found in the colonic crypt progenitor compartment. •Colonocytes transformed by ncNRFR are highly invasive and metastatic. •ncNRFR has a region similar to the miRNA, let-7 family. •ncNRFR expression alters let-7 activity as measured by reporter construct. •ncNRFR expression upregulates let-7b targets. -- Abstract: Recent progress has been made in the identification of protein-coding genes and miRNAs that are expressed in and alter the behavior of colonic epithelia. However, the role of long non-coding RNAs (lncRNAs) in colonic homeostasis is just beginning to be explored. By gene expression profiling of post-mitotic, differentiated tops and proliferative, progenitor-compartment bottoms of microdissected adult mouse colonic crypts, we identified several lncRNAs more highly expressed in crypt bottoms. One identified lncRNA, designated non-coding Nras functional RNA (ncNRFR), resides within the Nras locus but appears to be independent of the Nras coding transcript. Stable overexpression of ncNRFR in non-transformed, conditionally immortalized mouse colonocytes results in malignant transformation, as determined by growth in soft agar and formation of highly invasive tumors in nude mice. Moreover, ncNRFR appears to inhibit the function of the tumor suppressor let-7. These results suggest precise regulation of ncNRFR is necessary for proper cell growth in the colonic crypt, and its misregulation results in neoplastic transformation

  15. Selling space colonization and immortality: A psychosocial, anthropological critique of the rush to colonize Mars

    Science.gov (United States)

    Slobodian, Rayna Elizabeth

    2015-08-01

    Extensive media coverage regarding the proposal to send four people to Mars by 2025 has exploded recently. Private enterprise has taken the reins to venture into space, which has typically only been reserved for government agencies. I argue, that with this new direction comes less regulation, raising questions regarding the ethics of sending people into outer space to colonize Mars within a decade. Marketers selling colonization to the public include perspectives such as biological drives, species survival, inclusiveness and utopian ideals. I challenge these narratives by suggesting that much of our desire to colonize space within the next decade is motivated by ego, money and romanticism. More specifically, I will examine the roles that fear and stories of immortality play within selling space and how those stories are marketed. I am passionate about space and hope that one day humanity will colonize other worlds, but the rush to settle is dangerous and careless. I assert that humanity should first gain more experience and knowledge before colonizing outer space, using this research to mitigate the risk to astronauts and proceed with careful consideration for the lives of potential astronauts.

  16. 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

  17. 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

  18. Why do morphological phylogenies vary in quality? An investigation based on the comparative history of lizard clades.

    Science.gov (United States)

    Arnold, E N

    1990-05-22

    Phylogenies based on morphology vary considerably in their quality: some are robust and explicit with little conflict in the data set, whereas others are far more tenuous, with much conflict and many possible alternatives. The main primary reasons for untrue or inexplicit morphological phylogenies are: not enough characters developed between branching points, uncertain character polarity, poorly differentiated character states, homoplasy caused by parallelism or reversal, and extinction, which may remove species entirely from consideration and can make originally conflicting data sets misleadingly compatible, increasing congruence at the expense of truth. Extinction differs from other confounding factors in not being apparent either in the data set or in subsequent analysis. One possibility is that variation in the quality of morphological phylogenies has resulted from exposure to different ecological situations. To investigate this, it is necessary to compare the histories of the clades concerned. In the case of explicit morphological phylogenies, ecological and behavioural data can be integrated with them and it may then be possible to decide whether morphological characters are likely to have been elicited by the environments through which the clade has passed. The credibility of such results depends not only on the phylogeny being robust but also on its detailed topology: a pectinate phylogeny will often allow more certain and more explicit statements to be made about historical events. In the case of poor phylogenies, it is not possible to produce detailed histories, but they can be compared with robust phylogenies in the range of ecological situations occupied, and whether they occupy novel situations in comparison with their outgroups. LeQuesne testing can give information about niche homoplasy, and it may also be possible to see if morphological features are functionally associated with ecological parameters, even if the direction of change is unknown

  19. Multiple differences in calling songs and other traits between solitary and gregarious Mormon crickets from allopatric mtDNA clades

    Directory of Open Access Journals (Sweden)

    Bailey William V

    2007-01-01

    Full Text Available Abstract Background In acoustic species, traits such as male calling song are likely to diverge quickly between allopatric populations due to sexual selection, and divergence in parameters such as carrier frequency, chirp structure, and other important song characters can influence sexual isolation. Here we make use of two forms of Mormon crickets to examine differences in a broad suite of traits that have the potential to influence speciation via sexual isolation. Mormon crickets in "gregarious" populations aggregate into dense migratory bands, and females are the sexually competitive sex (sex-role reversal. There is also a non-outbreak "solitary" form. These two forms are largely but not perfectly correlated with a significant mtDNA subdivision within the species that is thought to have arisen in allopatry. Combined information about multiple, independently evolving traits, such as morphology and structural and behavioural differences in calling song, provides greater resolution of the overall differences between these allopatric populations, and allows us to assess their stage of divergence. We test two predictions, first that the forms differ in song and second that gregarious males are more reluctant to sing than solitary males due to sex role reversal. We also tested for a difference in the relationship between the size of the forewing resonator, the mirror, and carrier frequency, as most models of sound production in crickets indicate that mirror size should predict carrier frequency. Results Multivariate analyses showed that solitary and gregarious individuals from different populations representing the two mtDNA clades had almost non-overlapping distributions based on multiple song and morphological measurements. Carrier frequency differed between the two, and gregarious males were more reluctant to sing overall. Mirror size predicted carrier frequency; however, the relationship between mirror size and surface area varied between

  20. 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.