Ancestral genes can control the ability of horizontally acquired loci to confer new traits.

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H Deborah Chen

2011-07-01

Full Text Available Horizontally acquired genes typically function as autonomous units conferring new abilities when introduced into different species. However, we reasoned that proteins preexisting in an organism might constrain the functionality of a horizontally acquired gene product if it operates on an ancestral pathway. Here, we determine how the horizontally acquired pmrD gene product activates the ancestral PmrA/PmrB two-component system in Salmonella enterica but not in the closely related bacterium Escherichia coli. The Salmonella PmrD protein binds to the phosphorylated PmrA protein (PmrA-P, protecting it from dephosphorylation by the PmrB protein. This results in transcription of PmrA-dependent genes, including those conferring polymyxin B resistance. We now report that the E. coli PmrD protein can activate the PmrA/PmrB system in Salmonella even though it cannot do it in E. coli, suggesting that these two species differ in an additional component controlling PmrA-P levels. We establish that the E. coli PmrB displays higher phosphatase activity towards PmrA-P than the Salmonella PmrB, and we identified a PmrB subdomain responsible for this property. Replacement of the E. coli pmrB gene with the Salmonella homolog was sufficient to render E. coli resistant to polymyxin B under PmrD-inducing conditions. Our findings provide a singular example whereby quantitative differences in the biochemical activities of orthologous ancestral proteins dictate the ability of a horizontally acquired gene product to confer species-specific traits. And they suggest that horizontally acquired genes can potentiate selection at ancestral loci.

Horizontally Acquired Biosynthesis Genes Boost Coxiella burnetii's Physiology.

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Moses, Abraham S; Millar, Jess A; Bonazzi, Matteo; Beare, Paul A; Raghavan, Rahul

2017-01-01

Coxiella burnetii , the etiologic agent of acute Q fever and chronic endocarditis, has a unique biphasic life cycle, which includes a metabolically active intracellular form that occupies a large lysosome-derived acidic vacuole. C. burnetii is the only bacterium known to thrive within such an hostile intracellular niche, and this ability is fundamental to its pathogenicity; however, very little is known about genes that facilitate Coxiella 's intracellular growth. Recent studies indicate that C. burnetii evolved from a tick-associated ancestor and that the metabolic capabilities of C. burnetii are different from that of Coxiella -like bacteria found in ticks. Horizontally acquired genes that allow C. burnetii to infect and grow within mammalian cells likely facilitated the host shift; however, because of its obligate intracellular replication, C. burnetii would have lost most genes that have been rendered redundant due to the availability of metabolites within the host cell. Based on these observations, we reasoned that horizontally derived biosynthetic genes that have been retained in the reduced genome of C. burnetii are ideal candidates to begin to uncover its intracellular metabolic requirements. Our analyses identified a large number of putative foreign-origin genes in C. burnetii , including tRNA Glu 2 that is potentially required for heme biosynthesis, and genes involved in the production of lipopolysaccharide-a virulence factor, and of critical metabolites such as fatty acids and biotin. In comparison to wild-type C. burnetii , a strain that lacks tRNA Glu 2 exhibited reduced growth, indicating its importance to Coxiella 's physiology. Additionally, by using chemical agents that block heme and biotin biosyntheses, we show that these pathways are promising targets for the development of new anti- Coxiella therapies.

Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses

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Ogata Hiroyuki

2007-12-01

Full Text Available Abstract Background DNA viruses have a wide range of genome sizes (5 kb up to 1.2 Mb, compared to 0.16 Mb to 1.5 Mb for obligate parasitic bacteria that do not correlate with their virulence or the taxonomic distribution of their hosts. The reasons for such large variation are unclear. According to the traditional view of viruses as gifted "gene pickpockets", large viral genome sizes could originate from numerous gene acquisitions from their hosts. We investigated this hypothesis by studying 67 large DNA viruses with genome sizes larger than 150 kb, including the recently characterized giant mimivirus. Given that horizontally transferred DNA often have anomalous nucleotide compositions differing from the rest of the genome, we conducted a detailed analysis of the inter- and intra-genome compositional properties of these viruses. We then interpreted their compositional heterogeneity in terms of possible causes, including strand asymmetry, gene function/expression, and horizontal transfer. Results We first show that the global nucleotide composition and nucleotide word usage of viral genomes are species-specific and distinct from those of their hosts. Next, we identified compositionally anomalous (cA genes in viral genomes, using a method based on Bayesian inference. The proportion of cA genes is highly variable across viruses and does not exhibit a significant correlation with genome size. The vast majority of the cA genes were of unknown function, lacking homologs in the databases. For genes with known homologs, we found a substantial enrichment of cA genes in specific functional classes for some of the viruses. No significant association was found between cA genes and compositional strand asymmetry. A possible exogenous origin for a small fraction of the cA genes could be confirmed by phylogenetic reconstruction. Conclusion At odds with the traditional dogma, our results argue against frequent genetic transfers to large DNA viruses from their

Horizontal Gene Transfer Contributes to the Evolution of Arthropod Herbivory.

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Wybouw, Nicky; Pauchet, Yannick; Heckel, David G; Van Leeuwen, Thomas

2016-06-27

Within animals, evolutionary transition toward herbivory is severely limited by the hostile characteristics of plants. Arthropods have nonetheless counteracted many nutritional and defensive barriers imposed by plants and are currently considered as the most successful animal herbivores in terrestrial ecosystems. We gather a body of evidence showing that genomes of various plant feeding insects and mites possess genes whose presence can only be explained by horizontal gene transfer (HGT). HGT is the asexual transmission of genetic information between reproductively isolated species. Although HGT is known to have great adaptive significance in prokaryotes, its impact on eukaryotic evolution remains obscure. Here, we show that laterally transferred genes into arthropods underpin many adaptations to phytophagy, including efficient assimilation and detoxification of plant produced metabolites. Horizontally acquired genes and the traits they encode often functionally diversify within arthropod recipients, enabling the colonization of more host plant species and organs. We demonstrate that HGT can drive metazoan evolution by uncovering its prominent role in the adaptations of arthropods to exploit plants. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Horizontal gene transfer and the evolution of transcriptionalregulation in Escherichia coli

Energy Technology Data Exchange (ETDEWEB)

Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.

2007-12-20

Background: Most bacterial genes were acquired by horizontalgene transfer from other bacteria instead of being inherited bycontinuous vertical descent from an ancient ancestor}. To understand howthe regulation of these {acquired} genes evolved, we examined theevolutionary histories of transcription factors and of regulatoryinteractions from the model bacterium Escherichia coli K12. Results:Although most transcription factors have paralogs, these usually arose byhorizontal gene transfer rather than by duplication within the E. colilineage, as previously believed. In general, most neighbor regulators --regulators that are adjacent to genes that they regulate -- were acquiredby horizontal gene transfer, while most global regulators evolvedvertically within the gamma-Proteobacteria. Neighbor regulators wereoften acquired together with the adjacent operon that they regulate, sothe proximity might be maintained by repeated transfers (like "selfishoperons"). Many of the as-yet-uncharacterized (putative) regulators havealso been acquired together with adjacent genes, so we predict that theseare neighbor regulators as well. When we analyzed the histories ofregulatory interactions, we found that the evolution of regulation byduplication was rare, and surprisingly, many of the regulatoryinteractions that are shared between paralogs result from convergentevolution. Another surprise was that horizontally transferred genes aremore likely than other genes to be regulated by multiple regulators, andmost of this complex regulation probably evolved after the transfer.Conclusions: Our results highlight the rapid evolution of niche-specificgene regulation in bacteria.

Incorporation of a horizontally transferred gene into an operon during cnidarian evolution.

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Catherine E Dana

Full Text Available Genome sequencing has revealed examples of horizontally transferred genes, but we still know little about how such genes are incorporated into their host genomes. We have previously reported the identification of a gene (flp that appears to have entered the Hydra genome through horizontal transfer. Here we provide additional evidence in support of our original hypothesis that the transfer was from a unicellular organism, and we show that the transfer occurred in an ancestor of two medusozoan cnidarian species. In addition we show that the gene is part of a bicistronic operon in the Hydra genome. These findings identify a new animal phylum in which trans-spliced leader addition has led to the formation of operons, and define the requirements for evolution of an operon in Hydra. The identification of operons in Hydra also provides a tool that can be exploited in the construction of transgenic Hydra strains.

Horizontal gene transfer in an acid mine drainage microbial community.

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Guo, Jiangtao; Wang, Qi; Wang, Xiaoqi; Wang, Fumeng; Yao, Jinxian; Zhu, Huaiqiu

2015-07-04

Horizontal gene transfer (HGT) has been widely identified in complete prokaryotic genomes. However, the roles of HGT among members of a microbial community and in evolution remain largely unknown. With the emergence of metagenomics, it is nontrivial to investigate such horizontal flow of genetic materials among members in a microbial community from the natural environment. Because of the lack of suitable methods for metagenomics gene transfer detection, microorganisms from a low-complexity community acid mine drainage (AMD) with near-complete genomes were used to detect possible gene transfer events and suggest the biological significance. Using the annotation of coding regions by the current tools, a phylogenetic approach, and an approximately unbiased test, we found that HGTs in AMD organisms are not rare, and we predicted 119 putative transferred genes. Among them, 14 HGT events were determined to be transfer events among the AMD members. Further analysis of the 14 transferred genes revealed that the HGT events affected the functional evolution of archaea or bacteria in AMD, and it probably shaped the community structure, such as the dominance of G-plasma in archaea in AMD through HGT. Our study provides a novel insight into HGT events among microorganisms in natural communities. The interconnectedness between HGT and community evolution is essential to understand microbial community formation and development.

The Bacterium That Got Infected by a Cow! - Horizontal Gene

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 12; Issue 1. The Bacterium That Got Infected by a Cow! - Horizontal Gene Transfer and Evolution. Saurabh Dhawan Tomás John Ryan. General Article Volume 12 Issue 1 January 2007 pp 49-59 ...

Involvement of β-carbonic anhydrase (β-CA) genes in bacterial genomic islands and horizontal transfer to protists.

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Zolfaghari Emameh, Reza; Barker, Harlan R; Hytönen, Vesa P; Parkkila, Seppo

2018-05-25

Genomic islands (GIs) are a type of mobile genetic element (MGE) that are present in bacterial chromosomes. They consist of a cluster of genes which produce proteins that contribute to a variety of functions, including, but not limited to, regulation of cell metabolism, anti-microbial resistance, pathogenicity, virulence, and resistance to heavy metals. The genes carried in MGEs can be used as a trait reservoir in times of adversity. Transfer of genes using MGEs, occurring outside of reproduction, is called horizontal gene transfer (HGT). Previous literature has shown that numerous HGT events have occurred through endosymbiosis between prokaryotes and eukaryotes.Beta carbonic anhydrase (β-CA) enzymes play a critical role in the biochemical pathways of many prokaryotes and eukaryotes. We have previously suggested horizontal transfer of β-CA genes from plasmids of some prokaryotic endosymbionts to their protozoan hosts. In this study, we set out to identify β-CA genes that might have transferred between prokaryotic and protist species through HGT in GIs. Therefore, we investigated prokaryotic chromosomes containing β-CA-encoding GIs and utilized multiple bioinformatics tools to reveal the distinct movements of β-CA genes among a wide variety of organisms. Our results identify the presence of β-CA genes in GIs of several medically and industrially relevant bacterial species, and phylogenetic analyses reveal multiple cases of likely horizontal transfer of β-CA genes from GIs of ancestral prokaryotes to protists. IMPORTANCE The evolutionary process is mediated by mobile genetic elements (MGEs), such as genomic islands (GIs). A gene or set of genes in the GIs are exchanged between and within various species through horizontal gene transfer (HGT). Based on the crucial role that GIs can play in bacterial survival and proliferation, they were introduced as the environmental- and pathogen-associated factors. Carbonic anhydrases (CAs) are involved in many critical

An allele of an ancestral transcription factor dependent on a horizontally acquired gene product.

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Chen, H Deborah; Jewett, Mollie W; Groisman, Eduardo A

2012-01-01

Changes in gene regulatory circuits often give rise to phenotypic differences among closely related organisms. In bacteria, these changes can result from alterations in the ancestral genome and/or be brought about by genes acquired by horizontal transfer. Here, we identify an allele of the ancestral transcription factor PmrA that requires the horizontally acquired pmrD gene product to promote gene expression. We determined that a single amino acid difference between the PmrA proteins from the human adapted Salmonella enterica serovar Paratyphi B and the broad host range S. enterica serovar Typhimurium rendered transcription of PmrA-activated genes dependent on the PmrD protein in the former but not the latter serovar. Bacteria harboring the serovar Typhimurium allele exhibited polymyxin B resistance under PmrA- or under PmrA- and PmrD-inducing conditions. By contrast, isogenic strains with the serovar Paratyphi B allele displayed PmrA-regulated polymyxin B resistance only when experiencing activating conditions for both PmrA and PmrD. We establish that the two PmrA orthologs display quantitative differences in several biochemical properties. Strains harboring the serovar Paratyphi B allele showed enhanced biofilm formation, a property that might promote serovar Paratyphi B's chronic infection of the gallbladder. Our findings illustrate how subtle differences in ancestral genes can impact the ability of horizontally acquired genes to confer new properties.

CRISPR-cas-mediated phage resistance enhances horizontal gene transfer by transduction

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Watson, Bridget N.J.; Staals, Raymond H.J.; Fineran, Peter C.

2018-01-01

A powerful contributor to prokaryotic evolution is horizontal gene transfer (HGT) through transformation, conjugation, and transduction, which can be advantageous, neutral, or detrimental to fitness. Bacteria and archaea control HGT and phage infection through CRISPR-Cas (clustered regularly

Horizontal gene transfer and mobile genetic elements in marine systems.

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Sobecky, Patricia A; Hazen, Tracy H

2009-01-01

The pool of mobile genetic elements (MGE) in microbial communities consists of viruses, plasmids, and associated elements (insertion sequences, transposons, and integrons) that are either self-transmissible or use mobile plasmids and viruses as vehicles for their dissemination. This mobilome facilitates the horizontal transfer of genes that promote the evolution and adaptation of microbial communities. Efforts to characterize MGEs from microbial populations resident in a variety of ecological habitats have revealed a surprisingly novel and seemingly untapped biodiversity. To better understand the impact of horizontal gene transfer (HGT), as well as the agents that promote HGT in marine ecosystems and to determine whether or not environmental parameters can effect the composition and structure of the mobilome in marine microbial communities, information on the distribution, diversity, and ecological traits of the marine mobilome is presented. In this chapter we discuss recent insights gained from different methodological approaches used to characterize the biodiversity and ecology of MGE in marine environments and their contributions to HGT. In addition, we present case studies that highlight specific HGT examples in coastal, open-ocean, and deep-sea marine ecosystems.

Horizontal gene transfer in silkworm, Bombyx mori

Science.gov (United States)

2011-01-01

Background The domesticated silkworm, Bombyx mori, is the model insect for the order Lepidoptera, has economically important values, and has gained some representative behavioral characteristics compared to its wild ancestor. The genome of B. mori has been fully sequenced while function analysis of BmChi-h and BmSuc1 genes revealed that horizontal gene transfer (HGT) maybe bestow a clear selective advantage to B. mori. However, the role of HGT in the evolutionary history of B. mori is largely unexplored. In this study, we compare the whole genome of B. mori with those of 382 prokaryotic and eukaryotic species to investigate the potential HGTs. Results Ten candidate HGT events were defined in B. mori by comprehensive sequence analysis using Maximum Likelihood and Bayesian method combining with EST checking. Phylogenetic analysis of the candidate HGT genes suggested that one HGT was plant-to- B. mori transfer while nine were bacteria-to- B. mori transfer. Furthermore, functional analysis based on expression, coexpression and related literature searching revealed that several HGT candidate genes have added important characters, such as resistance to pathogen, to B. mori. Conclusions Results from this study clearly demonstrated that HGTs play an important role in the evolution of B. mori although the number of HGT events in B. mori is in general smaller than those of microbes and other insects. In particular, interdomain HGTs in B. mori may give rise to functional, persistent, and possibly evolutionarily significant new genes. PMID:21595916

Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer.

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Jaramillo, Vinicio D Armijos; Sukno, Serenella A; Thon, Michael R

2015-01-02

Horizontal gene transfer (HGT) is the stable transmission of genetic material between organisms by means other than vertical inheritance. HGT has an important role in the evolution of prokaryotes but is relatively rare in eukaryotes. HGT has been shown to contribute to virulence in eukaryotic pathogens. We studied the importance of HGT in plant pathogenic fungi by identifying horizontally transferred genes in the genomes of three members of the genus Colletotrichum. We identified eleven HGT events from bacteria into members of the genus Colletotrichum or their ancestors. The HGT events include genes involved in amino acid, lipid and sugar metabolism as well as lytic enzymes. Additionally, the putative minimal dates of transference were calculated using a time calibrated phylogenetic tree. This analysis reveals a constant flux of genes from bacteria to fungi throughout the evolution of subphylum Pezizomycotina. Genes that are typically transferred by HGT are those that are constantly subject to gene duplication and gene loss. The functions of some of these genes suggest roles in niche adaptation and virulence. We found no evidence of a burst of HGT events coinciding with major geological events. In contrast, HGT appears to be a constant, albeit rare phenomenon in the Pezizomycotina, occurring at a steady rate during their evolution.

Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi.

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Ropars, Jeanne; Rodríguez de la Vega, Ricardo C; López-Villavicencio, Manuela; Gouzy, Jérôme; Sallet, Erika; Dumas, Émilie; Lacoste, Sandrine; Debuchy, Robert; Dupont, Joëlle; Branca, Antoine; Giraud, Tatiana

2015-10-05

Domestication is an excellent model for studies of adaptation because it involves recent and strong selection on a few, identified traits [1-5]. Few studies have focused on the domestication of fungi, with notable exceptions [6-11], despite their importance to bioindustry [12] and to a general understanding of adaptation in eukaryotes [5]. Penicillium fungi are ubiquitous molds among which two distantly related species have been independently selected for cheese making-P. roqueforti for blue cheeses like Roquefort and P. camemberti for soft cheeses like Camembert. The selected traits include morphology, aromatic profile, lipolytic and proteolytic activities, and ability to grow at low temperatures, in a matrix containing bacterial and fungal competitors [13-15]. By comparing the genomes of ten Penicillium species, we show that adaptation to cheese was associated with multiple recent horizontal transfers of large genomic regions carrying crucial metabolic genes. We identified seven horizontally transferred regions (HTRs) spanning more than 10 kb each, flanked by specific transposable elements, and displaying nearly 100% identity between distant Penicillium species. Two HTRs carried genes with functions involved in the utilization of cheese nutrients or competition and were found nearly identical in multiple strains and species of cheese-associated Penicillium fungi, indicating recent selective sweeps; they were experimentally associated with faster growth and greater competitiveness on cheese and contained genes highly expressed in the early stage of cheese maturation. These findings have industrial and food safety implications and improve our understanding of the processes of adaptation to rapid environmental changes. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

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

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

2017-01-01

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

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

Science.gov (United States)

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

2017-10-23

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

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

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Etienne G.J. Danchin

2017-10-01

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

Cellular automata-based artificial life system of horizontal gene transfer

Directory of Open Access Journals (Sweden)

Ji-xin Liu

2016-02-01

Full Text Available Mutation and natural selection is the core of Darwin's idea about evolution. Many algorithms and models are based on this idea. However, in the evolution of prokaryotes, more and more researches have indicated that horizontal gene transfer (HGT would be much more important and universal than the authors had imagined. Owing to this mechanism, the prokaryotes not only become adaptable in nearly any environment on Earth, but also form a global genetic bank and a super communication network with all the genes of the prokaryotic world. Under this background, they present a novel cellular automata model general gene transfer to simulate and study the vertical gene transfer and HGT in the prokaryotes. At the same time, they use Schrodinger's life theory to formulate some evaluation indices and to discuss the intelligence and cognition of prokaryotes which is derived from HGT.

Drop deformation and breakup in a partially filled horizontal rotating cylinder

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White, Andrew; Pereira, Caroline; Hyacinthe, Hyaquino; Ward, Thomas

2014-11-01

Drop deformation and breakup due to shear flow has been studied extensively in Couette devices as well as in gravity-driven flows. In these cases shear is generated either by the moving wall or the drop's motion. For such flows the drop shape remains unperturbed at low capillary number (Ca), deforms at moderate Ca , and can experience breakup as Ca --> 1 and larger. Here single drops of NaOH(aq) will be placed in a horizontal cylindrical rotating tank partially filled with vegetable oil resulting in 10-2 saponification, can yield lower minimum surface tensions and faster adsorption than non-reactive surfactant systems. Oil films between the wall and drop as well as drop shape will be observed as rotation rates and NaOH(aq) concentration are varied. Results will be presented in the context of previous work on bubble and drop shapes and breakup. NSF CBET #1262718.

Risks from GMOs due to horizontal gene transfer.

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Keese, Paul

2008-01-01

Horizontal gene transfer (HGT) is the stable transfer of genetic material from one organism to another without reproduction or human intervention. Transfer occurs by the passage of donor genetic material across cellular boundaries, followed by heritable incorporation to the genome of the recipient organism. In addition to conjugation, transformation and transduction, other diverse mechanisms of DNA and RNA uptake occur in nature. The genome of almost every organism reveals the footprint of many ancient HGT events. Most commonly, HGT involves the transmission of genes on viruses or mobile genetic elements. HGT first became an issue of public concern in the 1970s through the natural spread of antibiotic resistance genes amongst pathogenic bacteria, and more recently with commercial production of genetically modified (GM) crops. However, the frequency of HGT from plants to other eukaryotes or prokaryotes is extremely low. The frequency of HGT to viruses is potentially greater, but is restricted by stringent selection pressures. In most cases the occurrence of HGT from GM crops to other organisms is expected to be lower than background rates. Therefore, HGT from GM plants poses negligible risks to human health or the environment.

Bioinformatics approach of three partial polyprenol reductase genes in Kandelia obovata

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Basyuni, M.; Wati, R.; Sagami, H.; Oku, H.; Baba, S.

2018-03-01

This present study describesthe bioinformatics approach to analyze three partial polyprenol reductase genes from mangrove plant, Kandeliaobovataas well aspredictedphysical and chemical properties, potential peptide, subcellular localization, and phylogenetic. The diversity was noted in the physical and chemical properties of three partial polyprenol reductase genes. The values of chloroplast were relatively high, showed that chloroplast transit peptide occurred in mangrove polyprenol reductase. The target peptide value of mitochondria varied from 0.088 to 0.198 indicated it was possible to be present. These results suggested the importance of understanding the diversity of physicochemical properties of the different amino acids in polyprenol reductase. The subcellular localization of two partial genes located in the plasma membrane. To confirm the homology among the polyprenol reductase in the database, a dendrogram was drawn. The phylogenetic tree depicts that there are three clusters, the partial genes of K. obovata joined the largest one: C23157 was close to Ricinus communis polyprenol reductase. Whereas, C23901 and C24171 were grouped with Ipomoea nil polyprenol reductase, suggested that these polyprenol reductase genes form distinct separation into tropical habitat plants.

A Preliminary List of Horizontally Transferred Genes in Prokaryotes Determined by Tree Reconstruction and Reconciliation

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Hyeonsoo Jeong

2017-08-01

Full Text Available Genome-wide global detection of genes involved in horizontal gene transfer (HGT remains an active area of research in medical microbiology and evolutionary genomics. Utilizing the explicit evolutionary method of comparing topologies of a total of 154,805 orthologous gene trees against corresponding 16S rRNA “reference” trees, we previously detected a total of 660,894 candidate HGT events in 2,472 completely-sequenced prokaryotic genomes. Here, we report an HGT-index for each individual gene-reference tree pair reconciliation, representing the total number of detected HGT events on the gene tree divided by the total number of genomes (taxa member of that tree. HGT-index is thus a simple measure indicating the sensitivity of prokaryotic genes to participate (or not participate in HGT. Our preliminary list provides HGT-indices for a total of 69,365 genes (detected in >10 and <50% available prokaryotic genomes that are involved in a wide range of biological processes such as metabolism, information, and bacterial response to environment. Identification of horizontally-derived genes is important to combat antibiotic resistance and is a step forward toward reconstructions of improved phylogenies describing the history of life. Our effort is thus expected to benefit ongoing research in the fields of clinical microbiology and evolutionary biology.

Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer.

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Yahara, Koji; Fukuyo, Masaki; Sasaki, Akira; Kobayashi, Ichizo

2009-11-03

Homing endonuclease genes are "selfish" mobile genetic elements whose endonuclease promotes the spread of its own gene by creating a break at a specific target site and using the host machinery to repair the break by copying and inserting the gene at this site. Horizontal transfer across the boundary of a species or population within which mating takes place has been thought to be necessary for their evolutionary persistence. This is based on the assumption that they will become fixed in a host population, where opportunities of homing will disappear, and become susceptible to degeneration. To test this hypothesis, we modeled behavior of a homing endonuclease gene that moves during meiosis through double-strand break repair. We mathematically explored conditions for persistence of the homing endonuclease gene and elucidated their parameter dependence as phase diagrams. We found that, if the cost of the pseudogene is lower than that of the homing endonuclease gene, the 2 forms can persist in a population through autonomous periodic oscillation. If the cost of the pseudogene is higher, 2 types of dynamics appear that enable evolutionary persistence: bistability dependent on initial frequency or fixation irrespective of initial frequency. The prediction of long persistence in the absence of horizontal transfer was confirmed by stochastic simulations in finite populations. The average time to extinction of the endonuclease gene was found to be thousands of meiotic generations or more based on realistic parameter values. These results provide a solid theoretical basis for an understanding of these and other extremely selfish elements.

Role of Horizontal Gene Transfer in the Evolution of Plant Parasitism Among Nematodes

NARCIS (Netherlands)

Mitreva, M.; Smant, G.; Helder, J.

2009-01-01

Horizontal gene transfer (HGT) implies the non-sexual exchange of genetic material between species ¿ in some cases even across kingdoms. Although common among Bacteria and Archaea, HGTs from pro- to eukaryotes and between eukaryotes were thought to be extremely rare. Recent studies on intracellular

Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer

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Vidal-Russell Romina

2004-10-01

Full Text Available Abstract Background The phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizanthes and Sapria (Rafflesiaceae s. str. in the angiosperm order Malpighiales and Mitrastema (Mitrastemonaceae in Ericales. These phylogenetic studies did not, however, sample two additional groups traditionally classified within Rafflesiales (Apodantheaceae and Cytinaceae. Here we provide molecular phylogenetic evidence using DNA sequence data from mitochondrial and nuclear genes for representatives of all genera in Rafflesiales. Results Our analyses indicate that the phylogenetic affinities of the large-flowered clade and Mitrastema, ascertained using mitochondrial matR, are congruent with results from nuclear SSU rDNA when these data are analyzed using maximum likelihood and Bayesian methods. The relationship of Cytinaceae to Malvales was recovered in all analyses. Relationships between Apodanthaceae and photosynthetic angiosperms varied depending upon the data partition: Malvales (3-gene, Cucurbitales (matR or Fabales (atp1. The latter incongruencies suggest that horizontal gene transfer (HGT may be affecting the mitochondrial gene topologies. The lack of association between Mitrastema and Ericales using atp1 is suggestive of HGT, but greater sampling within eudicots is needed to test this hypothesis further. Conclusions Rafflesiales are not monophyletic but composed of three or four independent lineages (families: Rafflesiaceae, Mitrastemonaceae, Apodanthaceae and Cytinaceae. Long-branch attraction appears to be misleading parsimony analyses of nuclear small-subunit rDNA data, but model-based methods (maximum likelihood and Bayesian analyses recover a topology that is congruent with the mitochondrial matR gene tree, thus providing compelling evidence for organismal relationships. Horizontal gene transfer appears to

Horizontal gene transfers with or without cell fusions in all categories of the living matter.

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Sinkovics, Joseph G

2011-01-01

This article reviews the history of widespread exchanges of genetic segments initiated over 3 billion years ago, to be part of their life style, by sphero-protoplastic cells, the ancestors of archaea, prokaryota, and eukaryota. These primordial cells shared a hostile anaerobic and overheated environment and competed for survival. "Coexist with, or subdue and conquer, expropriate its most useful possessions, or symbiose with it, your competitor" remain cellular life's basic rules. This author emphasizes the role of viruses, both in mediating cell fusions, such as the formation of the first eukaryotic cell(s) from a united crenarchaeon and prokaryota, and the transfer of host cell genes integrated into viral (phages) genomes. After rising above the Darwinian threshold, rigid rules of speciation and vertical inheritance in the three domains of life were established, but horizontal gene transfers with or without cell fusions were never abolished. The author proves with extensive, yet highly selective documentation, that not only unicellular microorganisms, but the most complex multicellular entities of the highest ranks resort to, and practice, cell fusions, and donate and accept horizontally (laterally) transferred genes. Cell fusions and horizontally exchanged genetic materials remain the fundamental attributes and inherent characteristics of the living matter, whether occurring accidentally or sought after intentionally. These events occur to cells stagnating for some 3 milliard years at a lower yet amazingly sophisticated level of evolution, and to cells achieving the highest degree of differentiation, and thus functioning in dependence on the support of a most advanced multicellular host, like those of the human brain. No living cell is completely exempt from gene drains or gene insertions.

Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers.

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Jan Janouškovec

Full Text Available Red algae have the most gene-rich plastid genomes known, but despite their evolutionary importance these genomes remain poorly sampled. Here we characterize three complete and one partial plastid genome from a diverse range of florideophytes. By unifying annotations across all available red algal plastid genomes we show they all share a highly compact and slowly-evolving architecture and uniquely rich gene complements. Both chromosome structure and gene content have changed very little during red algal diversification, and suggest that plastid-to nucleus gene transfers have been rare. Despite their ancient character, however, the red algal plastids also contain several unprecedented features, including a group II intron in a tRNA-Met gene that encodes the first example of red algal plastid intron maturase - a feature uniquely shared among florideophytes. We also identify a rare case of a horizontally-acquired proteobacterial operon, and propose this operon may have been recruited for plastid function and potentially replaced a nucleus-encoded plastid-targeted paralogue. Plastid genome phylogenies yield a fully resolved tree and suggest that plastid DNA is a useful tool for resolving red algal relationships. Lastly, we estimate the evolutionary rates among more than 200 plastid genes, and assess their usefulness for species and subspecies taxonomy by comparison to well-established barcoding markers such as cox1 and rbcL. Overall, these data demonstrates that red algal plastid genomes are easily obtainable using high-throughput sequencing of total genomic DNA, interesting from evolutionary perspectives, and promising in resolving red algal relationships at evolutionarily-deep and species/subspecies levels.

Two Horizontally Transferred Xenobiotic Resistance Gene Clusters Associated with Detoxification of Benzoxazolinones by Fusarium Species

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Glenn, Anthony E.; Davis, C. Britton; Gao, Minglu; Gold, Scott E.; Mitchell, Trevor R.; Proctor, Robert H.; Stewart, Jane E.; Snook, Maurice E.

2016-01-01

Microbes encounter a broad spectrum of antimicrobial compounds in their environments and often possess metabolic strategies to detoxify such xenobiotics. We have previously shown that Fusarium verticillioides, a fungal pathogen of maize known for its production of fumonisin mycotoxins, possesses two unlinked loci, FDB1 and FDB2, necessary for detoxification of antimicrobial compounds produced by maize, including the γ-lactam 2-benzoxazolinone (BOA). In support of these earlier studies, microarray analysis of F. verticillioides exposed to BOA identified the induction of multiple genes at FDB1 and FDB2, indicating the loci consist of gene clusters. One of the FDB1 cluster genes encoded a protein having domain homology to the metallo-β-lactamase (MBL) superfamily. Deletion of this gene (MBL1) rendered F. verticillioides incapable of metabolizing BOA and thus unable to grow on BOA-amended media. Deletion of other FDB1 cluster genes, in particular AMD1 and DLH1, did not affect BOA degradation. Phylogenetic analyses and topology testing of the FDB1 and FDB2 cluster genes suggested two horizontal transfer events among fungi, one being transfer of FDB1 from Fusarium to Colletotrichum, and the second being transfer of the FDB2 cluster from Fusarium to Aspergillus. Together, the results suggest that plant-derived xenobiotics have exerted evolutionary pressure on these fungi, leading to horizontal transfer of genes that enhance fitness or virulence. PMID:26808652

Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer

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Lewis M. Ward

2018-02-01

Full Text Available The evolutionary mechanisms behind the extant distribution of photosynthesis is a point of substantial contention. Hypotheses range from the presence of phototrophy in the last universal common ancestor and massive gene loss in most lineages, to a later origin in Cyanobacteria followed by extensive horizontal gene transfer into the extant phototrophic clades, with intermediate scenarios that incorporate aspects of both end-members. Here, we report draft genomes of 11 Chloroflexi: the phototrophic Chloroflexia isolate Kouleothrix aurantiaca as well as 10 genome bins recovered from metagenomic sequencing of microbial mats found in Japanese hot springs. Two of these metagenome bins encode photrophic reaction centers and several of these bins form a metabolically diverse, monophyletic clade sister to the Anaerolineae class that we term Candidatus Thermofonsia. Comparisons of organismal (based on conserved ribosomal and phototrophy (reaction center and bacteriochlorophyll synthesis protein phylogenies throughout the Chloroflexi demonstrate that two new lineages acquired phototrophy independently via horizontal gene transfer (HGT from different ancestral donors within the classically phototrophic Chloroflexia class. These results illustrate a complex history of phototrophy within this group, with metabolic innovation tied to HGT. These observations do not support simple hypotheses for the evolution of photosynthesis that require massive character loss from many clades; rather, HGT appears to be the defining mechanic for the distribution of phototrophy in many of the extant clades in which it appears.

Phylogenetic study of Geitlerinema and Microcystis (Cyanobacteria) using PC-IGS and 16S-23S ITS as markers: investigation of horizontal gene transfer.

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Piccin-Santos, Viviane; Brandão, Marcelo Mendes; Bittencourt-Oliveira, Maria Do Carmo

2014-08-01

Selection of genes that have not been horizontally transferred for prokaryote phylogenetic inferences is regarded as a challenging task. The markers internal transcribed spacer of ribosomal genes (16S-23S ITS) and phycocyanin intergenic spacer (PC-IGS), based on the operons of ribosomal and phycocyanin genes respectively, are among the most used markers in cyanobacteria. The region of the ribosomal genes has been considered stable, whereas the phycocyanin operon may have undergone horizontal transfer. To investigate the occurrence of horizontal transfer of PC-IGS, phylogenetic trees of Geitlerinema and Microcystis strains were generated using PC-IGS and 16S-23S ITS and compared. Phylogenetic trees based on the two markers were mostly congruent for Geitlerinema and Microcystis, indicating a common evolutionary history among ribosomal and phycocyanin genes with no evidence for horizontal transfer of PC-IGS. Thus, PC-IGS is a suitable marker, along with 16S-23S ITS for phylogenetic studies of cyanobacteria. © 2014 Phycological Society of America.

Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients.

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Noon, Jason B; Baum, Thomas J

2016-04-12

Hoplolaimina plant-parasitic nematodes (PPN) are a lineage of animals with many documented cases of horizontal gene transfer (HGT). In a recent study, we reported on three likely HGT candidate genes in the soybean cyst nematode Heterodera glycines, all of which encode secreted candidate effectors with putative functions in the host plant. Hg-GLAND1 is a putative GCN5-related N-acetyltransferase (GNAT), Hg-GLAND13 is a putative invertase (INV), and Hg-GLAND16 is a putative chorismate mutase (CM), and blastp searches of the non-redundant database resulted in highest similarity to bacterial sequences. Here, we searched nematode and non-nematode sequence databases to identify all the nematodes possible that contain these three genes, and to formulate hypotheses about when they most likely appeared in the phylum Nematoda. We then performed phylogenetic analyses combined with model selection tests of alternative models of sequence evolution to determine whether these genes were horizontally acquired from bacteria. Mining of nematode sequence databases determined that GNATs appeared in Hoplolaimina PPN late in evolution, while both INVs and CMs appeared before the radiation of the Hoplolaimina suborder. Also, Hoplolaimina GNATs, INVs and CMs formed well-supported clusters with different rhizosphere bacteria in the phylogenetic trees, and the model selection tests greatly supported models of HGT over descent via common ancestry. Surprisingly, the phylogenetic trees also revealed additional, well-supported clusters of bacterial GNATs, INVs and CMs with diverse eukaryotes and archaea. There were at least eleven and eight well-supported clusters of GNATs and INVs, respectively, from different bacteria with diverse eukaryotes and archaea. Though less frequent, CMs from different bacteria formed supported clusters with multiple different eukaryotes. Moreover, almost all individual clusters containing bacteria and eukaryotes or archaea contained species that inhabit very similar

Phylogeographic support for horizontal gene transfer involving sympatric bruchid species

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Grill Andrea

2006-07-01

Full Text Available Abstract Background We report on the probable horizontal transfer of a mitochondrial gene, cytb, between species of Neotropical bruchid beetles, in a zone where these species are sympatric. The bruchid beetles Acanthoscelides obtectus, A. obvelatus, A. argillaceus and Zabrotes subfasciatus develop on various bean species in Mexico. Whereas A. obtectus and A. obvelatus develop on Phaseolus vulgaris in the Mexican Altiplano, A. argillaceus feeds on P. lunatus in the Pacific coast. The generalist Z. subfasciatus feeds on both bean species, and is sympatric with A. obtectus and A. obvelatus in the Mexican Altiplano, and with A. argillaceus in the Pacific coast. In order to assess the phylogenetic position of these four species, we amplified and sequenced one nuclear (28S rRNA and two mitochondrial (cytb, COI genes. Results Whereas species were well segregated in topologies obtained for COI and 28S rRNA, an unexpected pattern was obtained in the cytb phylogenetic tree. In this tree, individuals from A. obtectus and A. obvelatus, as well as Z. subfasciatus individuals from the Mexican Altiplano, clustered together in a unique little variable monophyletic unit. In contrast, A. argillaceus and Z. subfasciatus individuals from the Pacific coast clustered in two separated clades, identically to the pattern obtained for COI and 28S rRNA. An additional analysis showed that Z. subfasciatus individuals from the Mexican Altiplano also possessed the cytb gene present in individuals of this species from the Pacific coast. Zabrotes subfasciatus individuals from the Mexican Altiplano thus demonstrated two cytb genes, an "original" one and an "infectious" one, showing 25% of nucleotide divergence. The "infectious" cytb gene seems to be under purifying selection and to be expressed in mitochondria. Conclusion The high degree of incongruence of the cytb tree with patterns for other genes is discussed in the light of three hypotheses: experimental contamination

Phylogeographic support for horizontal gene transfer involving sympatric bruchid species.

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Alvarez, Nadir; Benrey, Betty; Hossaert-McKey, Martine; Grill, Andrea; McKey, Doyle; Galtier, Nicolas

2006-07-27

We report on the probable horizontal transfer of a mitochondrial gene, cytb, between species of Neotropical bruchid beetles, in a zone where these species are sympatric. The bruchid beetles Acanthoscelides obtectus, A. obvelatus, A. argillaceus and Zabrotes subfasciatus develop on various bean species in Mexico. Whereas A. obtectus and A. obvelatus develop on Phaseolus vulgaris in the Mexican Altiplano, A. argillaceus feeds on P. lunatus in the Pacific coast. The generalist Z. subfasciatus feeds on both bean species, and is sympatric with A. obtectus and A. obvelatus in the Mexican Altiplano, and with A. argillaceus in the Pacific coast. In order to assess the phylogenetic position of these four species, we amplified and sequenced one nuclear (28S rRNA) and two mitochondrial (cytb, COI) genes. Whereas species were well segregated in topologies obtained for COI and 28S rRNA, an unexpected pattern was obtained in the cytb phylogenetic tree. In this tree, individuals from A. obtectus and A. obvelatus, as well as Z. subfasciatus individuals from the Mexican Altiplano, clustered together in a unique little variable monophyletic unit. In contrast, A. argillaceus and Z. subfasciatus individuals from the Pacific coast clustered in two separated clades, identically to the pattern obtained for COI and 28S rRNA. An additional analysis showed that Z. subfasciatus individuals from the Mexican Altiplano also possessed the cytb gene present in individuals of this species from the Pacific coast. Zabrotes subfasciatus individuals from the Mexican Altiplano thus demonstrated two cytb genes, an "original" one and an "infectious" one, showing 25% of nucleotide divergence. The "infectious" cytb gene seems to be under purifying selection and to be expressed in mitochondria. The high degree of incongruence of the cytb tree with patterns for other genes is discussed in the light of three hypotheses: experimental contamination, hybridization, and pseudogenisation. However, none of these

Operon Formation is Driven by Co-Regulation and Not by Horizontal Gene Transfer

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Price, Morgan N.; Huang, Katherine H.; Arkin, Adam P.; Alm, Eric J.

2005-04-12

Although operons are often subject to horizontal gene transfer (HGT), non-HGT genes are particularly likely to be in operons. To resolve this apparent discrepancy and to determine whether HGT is involved in operon formation, we examined the evolutionary history of the genes and operons in Escherichia coli K12. We show that genes that have homologs in distantly related bacteria but not in close relatives of E. coli (indicating HGTi) form new operons at about the same rates as native genes. Furthermore, genes in new operons are no more likely than other genes to have phylogenetic trees that are inconsistent with the species tree. In contrast, essential genes and ubiquitous genes without paralogs (genes believed to undergo HGT rarely) often form new operons. We conclude that HGT is not associated with operon formation, but instead promotes the prevalence of pre-existing operons. To explain operon formation, we propose that new operons reduce the amount of regulatory information required to specify optimal expression patterns. Consistent with this hypothesis, operons have greater amounts of conserved regulatory sequences than do individually transcribed genes.

Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment

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Takenaka Akio

2006-02-01

Full Text Available Abstract Background The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants was studied using ciliate Expressed Sequence Tags (ESTs. More than 4000 ESTs were sequenced from representatives of the two major groups of rumen Cilates: the order Entodiniomorphida (Entodinium simplex, Entodinium caudatum, Eudiplodinium maggii, Metadinium medium, Diploplastron affine, Polyplastron multivesiculatum and Epidinium ecaudatum and the order Vestibuliferida, previously called Holotricha (Isotricha prostoma, Isotricha intestinalis and Dasytricha ruminantium. Results A comparison of the sequences with the completely sequenced genomes of Eukaryotes and Prokaryotes, followed by large-scale construction and analysis of phylogenies, identified 148 ciliate genes that specifically cluster with genes from the Bacteria and Archaea. The phylogenetic clustering with bacterial genes, coupled with the absence of close relatives of these genes in the Ciliate Tetrahymena thermophila, indicates that they have been acquired via Horizontal Gene Transfer (HGT after the colonization of the gut by the rumen Ciliates. Conclusion Among the HGT candidates, we found an over-representation (>75% of genes involved in metabolism, specifically in the catabolism of complex carbohydrates, a rich food source in the rumen. We propose that the acquisition of these genes has greatly facilitated the Ciliates' colonization of the rumen providing evidence for the role of HGT in the adaptation to new niches.

Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment.

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Ricard, Guénola; McEwan, Neil R; Dutilh, Bas E; Jouany, Jean-Pierre; Macheboeuf, Didier; Mitsumori, Makoto; McIntosh, Freda M; Michalowski, Tadeusz; Nagamine, Takafumi; Nelson, Nancy; Newbold, Charles J; Nsabimana, Eli; Takenaka, Akio; Thomas, Nadine A; Ushida, Kazunari; Hackstein, Johannes H P; Huynen, Martijn A

2006-02-10

The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants) was studied using ciliate Expressed Sequence Tags (ESTs). More than 4000 ESTs were sequenced from representatives of the two major groups of rumen Cilates: the order Entodiniomorphida (Entodinium simplex, Entodinium caudatum, Eudiplodinium maggii, Metadinium medium, Diploplastron affine, Polyplastron multivesiculatum and Epidinium ecaudatum) and the order Vestibuliferida, previously called Holotricha (Isotricha prostoma, Isotricha intestinalis and Dasytricha ruminantium). A comparison of the sequences with the completely sequenced genomes of Eukaryotes and Prokaryotes, followed by large-scale construction and analysis of phylogenies, identified 148 ciliate genes that specifically cluster with genes from the Bacteria and Archaea. The phylogenetic clustering with bacterial genes, coupled with the absence of close relatives of these genes in the Ciliate Tetrahymena thermophila, indicates that they have been acquired via Horizontal Gene Transfer (HGT) after the colonization of the gut by the rumen Ciliates. Among the HGT candidates, we found an over-representation (>75%) of genes involved in metabolism, specifically in the catabolism of complex carbohydrates, a rich food source in the rumen. We propose that the acquisition of these genes has greatly facilitated the Ciliates' colonization of the rumen providing evidence for the role of HGT in the adaptation to new niches.

Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract

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Maguin Emmanuelle

2007-08-01

Full Text Available Abstract Background While genes that are conserved between related bacterial species are usually thought to have evolved along with the species, phylogenetic trees reconstructed for individual genes may contradict this picture and indicate horizontal gene transfer. Individual trees are often not resolved with high confidence, however, and in that case alternative trees are generally not considered as contradicting the species tree, although not confirming it either. Here we conduct an in-depth analysis of 401 protein phylogenetic trees inferred with varying levels of confidence for three lactobacilli from the acidophilus complex. At present the relationship between these bacteria, isolated from environments as diverse as the gastrointestinal tract (Lactobacillus acidophilus and Lactobacillus johnsonii and yogurt (Lactobacillus delbrueckii ssp. bulgaricus, is ambiguous due to contradictory phenotypical and 16S rRNA based classifications. Results Among the 401 phylogenetic trees, those that could be reconstructed with high confidence support the 16S-rRNA tree or one alternative topology in an astonishing 3:2 ratio, while the third possible topology is practically absent. Lowering the confidence threshold for trees to be taken into consideration does not significantly affect this ratio, and therefore suggests that gene transfer may have affected as much as 40% of the core genome genes. Gene function bias suggests that the 16S rRNA phylogeny of the acidophilus complex, which indicates that L. acidophilus and L. delbrueckii ssp. bulgaricus are the closest related of these three species, is correct. A novel approach of comparison of interspecies protein divergence data employed in this study allowed to determine that gene transfer most likely took place between the lineages of the two species found in the gastrointestinal tract. Conclusion This case-study reports an unprecedented level of phylogenetic incongruence, presumably resulting from extensive

Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus

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Monier, Adam; Pagarete, António; de Vargas, Colomban; Allen, Michael J.; Read, Betsy; Claverie, Jean-Michel; Ogata, Hiroyuki

2009-01-01

Interactions between viruses and phytoplankton, the main primary producers in the oceans, affect global biogeochemical cycles and climate. Recent studies are increasingly revealing possible cases of gene transfers between cyanobacteria and phages, which might have played significant roles in the evolution of cyanobacteria/phage systems. However, little has been documented about the occurrence of horizontal gene transfer in eukaryotic phytoplankton/virus systems. Here we report phylogenetic evidence for the transfer of seven genes involved in the sphingolipid biosynthesis pathway between the cosmopolitan eukaryotic microalga Emiliania huxleyi and its large DNA virus EhV. PCR assays indicate that these genes are prevalent in E. huxleyi and EhV strains isolated from different geographic locations. Patterns of protein and gene sequence conservation support that these genes are functional in both E. huxleyi and EhV. This is the first clear case of horizontal gene transfer of multiple functionally linked enzymes in a eukaryotic phytoplankton–virus system. We examine arguments for the possible direction of the gene transfer. The virus-to-host direction suggests the existence of ancient viruses that controlled the complex metabolic pathway in order to infect primitive eukaryotic cells. In contrast, the host-to-virus direction suggests that the serial acquisition of genes involved in the same metabolic pathway might have been a strategy for the ancestor of EhVs to stay ahead of their closest relatives in the great evolutionary race for survival. PMID:19451591

Horizontal Transfer of Tetracycline Resistance Genes in the Subsurface of a Poultry Farm

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You, Y.; Ward, M.; Hilpert, M.

2008-12-01

Concentrated animal feeding operations (CAFOs) are considered to be important man-made reservoirs of antibiotic resistant bacteria and antibiotic resistance genes. At a poultry farm, we, together with Mr.~James Doolittle from USDA, measured the apparent subsurface electrical conductivity (ECa) using a EM38 meter. The resulting ECaR) associated with the poultry farm due to the fact that tetracycline (Tc) is one of the most frequently used antibiotics in food animal production and therefore is probably used at this farm. Soil and aquifer samples were taken from the farm. TcR bacteria were detected, with higher concentrations in the top layer of soil than in the aquifer. TcR bacteria were then enriched from a soil sample, and two classes of TcR genes were detected: tet(M) genes encoding ribosomal protection proteins and tet(L) genes encoding tet efflux pumps. Sequences of the PCR products were compared to known tet(M) and tet(L) genes in GenBank using BLASTN. Phylogenetic trees were also built based on the sequence information. The tet(M) genes found in our soil sample were highly similar to those located on transposons. In a soil microcosm experiment, we used the aforementioned soil sample as incubation medium as well as genetic donor (TcR soil bacteria), and a green fluorescent strain of E. coli as a model genetic recipient to study horizontal transfer of TcR genes from soil bacteria to naïve bacteria. Concentrations of inoculated E. coli were continuously monitored for 15 days, TcR E. coli isolated, and colony PCR performed. The tet(M) genes were found to be transferred to naïve E. coli. The highest horizontal transfer ratio, 0.62 transconjugant per recipient, was observed when Tc was supplemented to a soil microcosm at a concentration of 140 μg/kg soil. Modeling is also ongoing to obtain a better understanding of this complex phenomenon.

Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australis obtained Brassicaceae-specific strictosidine synthase-like genes by horizontal gene transfer.

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Zhang, Dale; Qi, Jinfeng; Yue, Jipei; Huang, Jinling; Sun, Ting; Li, Suoping; Wen, Jian-Fan; Hettenhausen, Christian; Wu, Jinsong; Wang, Lei; Zhuang, Huifu; Wu, Jianqiang; Sun, Guiling

2014-01-13

Besides gene duplication and de novo gene generation, horizontal gene transfer (HGT) is another important way of acquiring new genes. HGT may endow the recipients with novel phenotypic traits that are important for species evolution and adaption to new ecological niches. Parasitic systems expectedly allow the occurrence of HGT at relatively high frequencies due to their long-term physical contact. In plants, a number of HGT events have been reported between the organelles of parasites and the hosts, but HGT between host and parasite nuclear genomes has rarely been found. A thorough transcriptome screening revealed that a strictosidine synthase-like (SSL) gene in the root parasitic plant Orobanche aegyptiaca and the shoot parasitic plant Cuscuta australis showed much higher sequence similarities with those in Brassicaceae than with those in their close relatives, suggesting independent gene horizontal transfer events from Brassicaceae to these parasites. These findings were strongly supported by phylogenetic analysis and their identical unique amino acid residues and deletions. Intriguingly, the nucleus-located SSL genes in Brassicaceae belonged to a new member of SSL gene family, which were originated from gene duplication. The presence of introns indicated that the transfer occurred directly by DNA integration in both parasites. Furthermore, positive selection was detected in the foreign SSL gene in O. aegyptiaca but not in C. australis. The expression of the foreign SSL genes in these two parasitic plants was detected in multiple development stages and tissues, and the foreign SSL gene was induced after wounding treatment in C. australis stems. These data imply that the foreign genes may still retain certain functions in the recipient species. Our study strongly supports that parasitic plants can gain novel nuclear genes from distantly related host species by HGT and the foreign genes may execute certain functions in the new hosts.

CysQ of , a Protozoa, May Have Been Acquired from Bacteria by Horizontal Gene Transfer

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Ji Young Lee

2012-03-01

Full Text Available Horizontal gene transfer (HGT is the movement of genetic material between kingdoms and is considered to play a positive role in adaptation. Cryptosporidium parvum is a parasitic protozoan that causes an infectious disease. Its genome sequencing reported 14 bacteria-like proteins in the nuclear genome. Among them, cgd2_1810, which has been annotated as CysQ, a sulfite synthesis pathway protein, is listed as one of the candidates of genes horizontally transferred from bacterial origin. In this report, we examined this issue using phylogenetic analysis. Our BLAST search showed that C. parvum CysQ protein had the highest similarity with that of proteobacteria. Analysis with NCBI's Conserved Domain Tree showed phylogenetic incongruence, in that C. parvum CysQ protein was located within a branch of proteobacteria in the cd01638 domain, a bacterial member of the inositol monophosphatase family. According to Kyoto Encyclopedia of Genes and Genomes (KEGG pathway, the sulfate assimilation pathway, where CysQ plays an important role, is well conserved in most eukaryotes as well as prokaryotes. However, the Apicomplexa, including C. parvum, largely lack orthologous genes of the pathway, suggesting its loss in those protozoan lineages. Therefore, we conclude that C. parvum regained cysQ from proteobacteria by HGT, although its functional role is elusive.

What tangled web: barriers to rampant horizontal gene transfer.

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Kurland, Charles G

2005-07-01

Dawkins in his The Selfish Gene(1) quite aptly applies the term "selfish" to parasitic repetitive DNA sequences endemic to eukaryotic genomes, especially vertebrates. Doolittle and Sapienza(2) as well as Orgel and Crick(3) enlivened this notion of selfish DNA with the identification of such repetitive sequences as remnants of mobile elements such as transposons. In addition, Orgel and Crick(3) associated parasitic DNA with a potential to outgrow their host genomes by propagating both vertically via conventional genome replication as well as infectiously by horizontal gene transfer (HGT) to other genomes. Still later, Doolittle(4) speculated that unchecked HGT between unrelated genomes so complicates phylogeny that the conventional representation of a tree of life would have to be replaced by a thicket or a web of life.(4) In contrast, considerable data now show that reconstructions based on whole genome sequences are consistent with the conventional "tree of life".(5-10) Here, we identify natural barriers that protect modern genome populations from the inroads of rampant HGT. Copyright (c) 2005 Wiley Periodicals, Inc.

Soliton wave model for simulating the slug formation in vertical-to-horizontal partially blocked pipes

International Nuclear Information System (INIS)

Nihan Onder; Alberto Teyssedou; Danila Roubtsov

2005-01-01

Full text of publication follows: In CANDU reactors the fuel channels are connected to inlet and outlet headers by feeder-pipes that consist of vertical and horizontal legs. In some feeders, orifices are installed for flow adjustment. During a postulated Loss of Coolant Accidents, the emergency cooling water injected into the inlet and outlet headers enters the fuel channels through the feeder pipes. Steam produced in the feeders and in the fuel channels may flow in the direction opposite to that of the water, thereby creating vertical to horizontal Counter-Current Flow (CCF). The rate at which the cooling water enters the fuel channel may be substantially limited by the flooding phenomena that entrains the water in the same direction as the steam flow. Steam flowing in the direction opposite to the cooling water can bring about the formation of slug flow. Long slugs of liquid moving at relatively high speed are transported back towards the headers by the steam. This phenomenon substantially reduces the amount of cooling water that can reach the reactor core. We conducted CCF experiments using a vertical-to-horizontal test section connected by 90 deg. elbows, with an orifice installed in the horizontal leg. Four different orifices were used to carry out the experiments. We have observed that soliton-type waves generated close to the elbow propagate in the horizontal leg towards the orifice, where a partial reflection takes place. Without an orifice, the soliton waves are reflected from the second elbow. The reflected waves move in the opposite direction to that of the incident wave. Since soliton-type waves are periodically generated, the incident and reflected waves interfere at some place in the horizontal leg. If the amplitude of the interference wave is high enough, the bridging of the tubes occur, which generates the slugs. During the experiments the water and air flow rates, pressures and void fraction distributions were measured. The slug propagation

Single-leaf partial meniscectomy in extensive horizontal tears of the discoid lateral meniscus: Does decreased peripheral meniscal thickness affect outcomes? (Mean four-year follow-up).

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Lee, Se-Won; Chun, Yong-Min; Choi, Chong-Hyuk; Kim, Sung-Jae; Jung, Min; Han, Joon-Woo; Kim, Sung-Hwan

2016-06-01

To evaluate whether single-leaf partial meniscectomy in horizontal tears along the entire discoid lateral meniscus has any advantages in clinical and radiological results compared with other meniscectomies in discoid lateral meniscus. A total of 145 patients with a horizontal tear pattern in symptomatic lateral discoid meniscus were retrospectively reviewed. Twenty-seven patients had undergone full-extent single-leaf partial meniscectomy (group A), 60 had undergone conventional partial meniscectomy (saucerization) maintaining peripheral meniscal height (group B), and 58 patients had undergone total meniscectomy (group C). Each patient was evaluated with the Lysholm knee score, International Knee Documentation Committee (IKDC) subjective grading, and modified Kellgren-Lawrence grade in plain radiography at their last follow-up. Group C had inferior functional results to groups A and B on the Lysholm knee score and IKDC subjective score. There was no significant difference between groups A and B. Group C fared significantly worse than groups A and B (p=0.003, pmeniscus tears, the full-extent single-leaf partial meniscectomy group had no adverse results compared with the total meniscectomy group and was not significantly different compared to the conventional partial meniscectomy group. Cohort study. Level III, therapeutic study. See Guidelines for Authors for a complete description of levels of evidence. Copyright © 2015 Elsevier B.V. All rights reserved.

Survival of Antibiotic Resistant Bacteria and Horizontal Gene Transfer Control Antibiotic Resistance Gene Content in Anaerobic Digesters.

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Miller, Jennifer H; Novak, John T; Knocke, William R; Pruden, Amy

2016-01-01

Understanding fate of antibiotic resistant bacteria (ARB) vs. their antibiotic resistance genes (ARGs) during wastewater sludge treatment is critical in order to reduce the spread of antibiotic resistance through process optimization. Here, we spiked high concentrations of tetracycline-resistant bacteria, isolated from mesophilic (Iso M1-1-a Pseudomonas sp.) and thermophilic (Iso T10-a Bacillus sp.) anaerobic digested sludge, into batch digesters and monitored their fate by plate counts and quantitative polymerase chain reaction (QPCR) of their corresponding tetracycline ARGs. In batch studies, spiked ARB plate counts returned to baseline (thermophilic) or 1-log above baseline (mesophilic) while levels of the ARG present in the spiked isolate [tet(G)] remained high in mesophilic batch reactors. To compare results under semi-continuous flow conditions with natural influent variation, tet(O), tet(W), and sul1 ARGs, along with the intI1 integrase gene, were monitored over a 9-month period in the raw feed sludge and effluent sludge of lab-scale thermophilic and mesophilic anaerobic digesters. sul1 and intI1 in mesophilic and thermophilic digesters correlated positively (Spearman rho = 0.457-0.829, P < 0.05) with the raw feed sludge. There was no correlation in tet(O) or tet(W) ratios in raw sludge and mesophilic digested sludge or thermophilic digested sludge (Spearman rho = 0.130-0.486, P = 0.075-0.612). However, in the thermophilic digester, the tet(O) and tet(W) ratios remained consistently low over the entire monitoring period. We conclude that the influent sludge microbial composition can influence the ARG content of a digester, apparently as a result of differential survival or death of ARBs or horizontal gene transfer of genes between raw sludge ARBs and the digester microbial community. Notably, mesophilic digestion was more susceptible to ARG intrusion than thermophilic digestion, which may be attributed to a higher rate of ARB survival and/or horizontal gene

Detection of horizontal transfer of individual genes by anomalous oligomer frequencies

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Elhai Jeff

2012-06-01

Full Text Available Abstract Background Understanding the history of life requires that we understand the transfer of genetic material across phylogenetic boundaries. Detecting genes that were acquired by means other than vertical descent is a basic step in that process. Detection by discordant phylogenies is computationally expensive and not always definitive. Many have used easily computed compositional features as an alternative procedure. However, different compositional methods produce different predictions, and the effectiveness of any method is not well established. Results The ability of octamer frequency comparisons to detect genes artificially seeded in cyanobacterial genomes was markedly increased by using as a training set those genes that are highly conserved over all bacteria. Using a subset of octamer frequencies in such tests also increased effectiveness, but this depended on the specific target genome and the source of the contaminating genes. The presence of high frequency octamers and the GC content of the contaminating genes were important considerations. A method comprising best practices from these tests was devised, the Core Gene Similarity (CGS method, and it performed better than simple octamer frequency analysis, codon bias, or GC contrasts in detecting seeded genes or naturally occurring transposons. From a comparison of predictions with phylogenetic trees, it appears that the effectiveness of the method is confined to horizontal transfer events that have occurred recently in evolutionary time. Conclusions The CGS method may be an improvement over existing surrogate methods to detect genes of foreign origin.

Study on kinetic degradation in soil and horizontal transfer of bt gene by 35S isotopic tracing method

International Nuclear Information System (INIS)

Wang Haiyan; Zhang Yanfei; Ye Qingfu

2012-01-01

In this study, 35 S isotopic tracing method was applied to investigate kinetic degradation of bt gene from Bt transgenic rice TT51 in two different soil and possibility of its horizontal transfer into soil bacteria as well. Results showed that, during 30 d of aerobic incubation, it was indicated that 35 S-Bt gene was not horizontally transferred into soil microorganisms. The aerobic soil degradation dynamics significantly followed a first-order dissipation pattern for bt gene. After 30 d of incubation, the amount of bt gene reached 9.32% of applied radioactivity for the fluvio-marine yellow loamy soil and 9.92% for the fluvio-aquatic soil, respectively. The half-lives in two soils were 3.53 d for the former soil and 5. 77 d for the latter soil, which means that bt gene was more easily degradable in the weak acidic soil. The use of 35 S labeling proved to be valuable; it served the purpose of validating the rigorousness of experimental protocols, and provided insights into the soil environmental safety assessment for Bt transgenic rice. (authors)

Horizontal transfer of a eukaryotic plastid-targeted protein gene to cyanobacteria

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Keeling Patrick J

2007-06-01

Full Text Available Abstract Background Horizontal or lateral transfer of genetic material between distantly related prokaryotes has been shown to play a major role in the evolution of bacterial and archaeal genomes, but exchange of genes between prokaryotes and eukaryotes is not as well understood. In particular, gene flow from eukaryotes to prokaryotes is rarely documented with strong support, which is unusual since prokaryotic genomes appear to readily accept foreign genes. Results Here, we show that abundant marine cyanobacteria in the related genera Synechococcus and Prochlorococcus acquired a key Calvin cycle/glycolytic enzyme from a eukaryote. Two non-homologous forms of fructose bisphosphate aldolase (FBA are characteristic of eukaryotes and prokaryotes respectively. However, a eukaryotic gene has been inserted immediately upstream of the ancestral prokaryotic gene in several strains (ecotypes of Synechococcus and Prochlorococcus. In one lineage this new gene has replaced the ancestral gene altogether. The eukaryotic gene is most closely related to the plastid-targeted FBA from red algae. This eukaryotic-type FBA once replaced the plastid/cyanobacterial type in photosynthetic eukaryotes, hinting at a possible functional advantage in Calvin cycle reactions. The strains that now possess this eukaryotic FBA are scattered across the tree of Synechococcus and Prochlorococcus, perhaps because the gene has been transferred multiple times among cyanobacteria, or more likely because it has been selectively retained only in certain lineages. Conclusion A gene for plastid-targeted FBA has been transferred from red algae to cyanobacteria, where it has inserted itself beside its non-homologous, functional analogue. Its current distribution in Prochlorococcus and Synechococcus is punctate, suggesting a complex history since its introduction to this group.

Horizontal gene transfer versus biostimulation: A strategy for bioremediation in Goa.

Science.gov (United States)

Pasumarthi, Rajesh; Mutnuri, Srikanth

2016-12-15

Bioaugmentation, Biostimulation and Horizontal gene transfer (HGT) of catabolic genes have been proven for their role in bioremediation of hydrocarbons. It also has been proved that selection of either biostimulation or bioremediation varies for every contaminated site. The reliability of HGT compared to biostimulation and bioremediation was not tested. The present study focuses on reliability of biostimulatiion, bioaugmentation and HGT during biodegradation of Diesel oil and Non aqueous phase liquids (NAPL). Pseudomonas aeruginosa (AEBBITS1) having alkB and NDO genes was used for bioaugmentation and the experiment was conducted using seawater as medium. Based on Gas chromatography results diesel was found to be degraded to 100% in both presence and absence of AEBBITS1. Denturing gradient gel electrophoresis result showed same pattern in presence and absence of AEBBITS1 indicating no HGT. NAPL degradation was found to be more by Biostimulated Bioaugmentation compared to biostimulation and bioaugmentation alone. This proves that biostimulated bioaugmentation is better strategy for oil contamination (tarabll) in Velsao beach, Goa. Copyright © 2016 Elsevier Ltd. All rights reserved.

Horizontal transfer of a nitrate assimilation gene cluster and ecological transitions in fungi: a phylogenetic study.

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Jason C Slot

Full Text Available High affinity nitrate assimilation genes in fungi occur in a cluster (fHANT-AC that can be coordinately regulated. The clustered genes include nrt2, which codes for a high affinity nitrate transporter; euknr, which codes for nitrate reductase; and NAD(PH-nir, which codes for nitrite reductase. Homologs of genes in the fHANT-AC occur in other eukaryotes and prokaryotes, but they have only been found clustered in the oomycete Phytophthora (heterokonts. We performed independent and concatenated phylogenetic analyses of homologs of all three genes in the fHANT-AC. Phylogenetic analyses limited to fungal sequences suggest that the fHANT-AC has been transferred horizontally from a basidiomycete (mushrooms and smuts to an ancestor of the ascomycetous mold Trichoderma reesei. Phylogenetic analyses of sequences from diverse eukaryotes and eubacteria, and cluster structure, are consistent with a hypothesis that the fHANT-AC was assembled in a lineage leading to the oomycetes and was subsequently transferred to the Dikarya (Ascomycota+Basidiomycota, which is a derived fungal clade that includes the vast majority of terrestrial fungi. We propose that the acquisition of high affinity nitrate assimilation contributed to the success of Dikarya on land by allowing exploitation of nitrate in aerobic soils, and the subsequent transfer of a complete assimilation cluster improved the fitness of T. reesei in a new niche. Horizontal transmission of this cluster of functionally integrated genes supports the "selfish operon" hypothesis for maintenance of gene clusters.

Horizontal Acquisition and Transcriptional Integration of Novel Genes in Mosquito-Associated Spiroplasma.

Science.gov (United States)

Lo, Wen-Sui; Kuo, Chih-Horng

2017-12-01

Genetic differentiation among symbiotic bacteria is important in shaping biodiversity. The genus Spiroplasma contains species occupying diverse niches and is a model system for symbiont evolution. Previous studies have established that two mosquito-associated species have diverged extensively in their carbohydrate metabolism genes despite having a close phylogenetic relationship. Notably, although the commensal Spiroplasma diminutum lacks identifiable pathogenicity factors, the pathogenic Spiroplasma taiwanense was found to have acquired a virulence factor glpO and its associated genes through horizontal transfer. However, it is unclear if these acquired genes have been integrated into the regulatory network. In this study, we inferred the gene content evolution in these bacteria, as well as examined their transcriptomes in response to glucose availability. The results indicated that both species have many more gene acquisitions from the Mycoides-Entomoplasmataceae clade, which contains several important pathogens of ruminants, than previously thought. Moreover, several acquired genes have higher expression levels than the vertically inherited homologs, indicating possible functional replacement. Finally, the virulence factor and its functionally linked genes in S. taiwanense were up-regulated in response to glucose starvation, suggesting that these acquired genes are under expression regulation and the pathogenicity may be a stress response. In summary, although differential gene losses are a major process for symbiont divergence, gene gains are critical in counteracting genome degradation and driving diversification among facultative symbionts. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Plant nodulation inducers enhance horizontal gene transfer of Azorhizobium caulinodans symbiosis island.

Science.gov (United States)

Ling, Jun; Wang, Hui; Wu, Ping; Li, Tao; Tang, Yu; Naseer, Nawar; Zheng, Huiming; Masson-Boivin, Catherine; Zhong, Zengtao; Zhu, Jun

2016-11-29

Horizontal gene transfer (HGT) of genomic islands is a driving force of bacterial evolution. Many pathogens and symbionts use this mechanism to spread mobile genetic elements that carry genes important for interaction with their eukaryotic hosts. However, the role of the host in this process remains unclear. Here, we show that plant compounds inducing the nodulation process in the rhizobium-legume mutualistic symbiosis also enhance the transfer of symbiosis islands. We demonstrate that the symbiosis island of the Sesbania rostrata symbiont, Azorhizobium caulinodans, is an 87.6-kb integrative and conjugative element (ICE Ac ) that is able to excise, form a circular DNA, and conjugatively transfer to a specific site of gly-tRNA gene of other rhizobial genera, expanding their host range. The HGT frequency was significantly increased in the rhizosphere. An ICE Ac -located LysR-family transcriptional regulatory protein AhaR triggered the HGT process in response to plant flavonoids that induce the expression of nodulation genes through another LysR-type protein, NodD. Our study suggests that rhizobia may sense rhizosphere environments and transfer their symbiosis gene contents to other genera of rhizobia, thereby broadening rhizobial host-range specificity.

In silico prediction of horizontal gene transfer events in Lactobacillus bulgaricus and Streptococcus thermophilus reveals protocooperation in yogurt manufacturing.

Science.gov (United States)

Liu, Mengjin; Siezen, Roland J; Nauta, Arjen

2009-06-01

Lactobacillus bulgaricus and Streptococcus thermophilus, used in yogurt starter cultures, are well known for their stability and protocooperation during their coexistence in milk. In this study, we show that a close interaction between the two species also takes place at the genetic level. We performed an in silico analysis, combining gene composition and gene transfer mechanism-associated features, and predicted horizontally transferred genes in both L. bulgaricus and S. thermophilus. Putative horizontal gene transfer (HGT) events that have occurred between the two bacterial species include the transfer of exopolysaccharide (EPS) biosynthesis genes, transferred from S. thermophilus to L. bulgaricus, and the gene cluster cbs-cblB(cglB)-cysE for the metabolism of sulfur-containing amino acids, transferred from L. bulgaricus or Lactobacillus helveticus to S. thermophilus. The HGT event for the cbs-cblB(cglB)-cysE gene cluster was analyzed in detail, with respect to both evolutionary and functional aspects. It can be concluded that during the coexistence of both yogurt starter species in a milk environment, agonistic coevolution at the genetic level has probably been involved in the optimization of their combined growth and interactions.

Effect of genomic location on horizontal transfer of a recombinant gene cassette between Pseudomonas strains in the rhizosphere and spermosphere of barley seedlings

DEFF Research Database (Denmark)

Sengelov, G.; Kristensen, K. J.; Sørensen, Anders Morten Hay

2001-01-01

, horizontal transfer of a recombinant gene cassette inserted into the chromosome of a Pseudomonas strutzeri strain, into a mobilizable plasmid (pAGM42), and into a conjugative plasmid (pKJK5) isolated from barley rhizosphere was investigated. Horizontal transfer efficiencies of the gene cassette inserted...... efficiencies were up to 4.36 x 10(-3) transconjugants/(donors x recipients)(1/2). Transfer of chromosomal encoded genes could not be detected in the microcosms by conjugation or transformation. However, transformation did occur by using the same bacterial strains under laboratory conditions. The rhizosphere...

Real-time PCR detection of Fe-type nitrile hydratase genes from environmental isolates suggests horizontal gene transfer between multiple genera.

Science.gov (United States)

Coffey, Lee; Owens, Erica; Tambling, Karen; O'Neill, David; O'Connor, Laura; O'Reilly, Catherine

2010-11-01

Nitriles are widespread in the environment as a result of biological and industrial activity. Nitrile hydratases catalyse the hydration of nitriles to the corresponding amide and are often associated with amidases, which catalyze the conversion of amides to the corresponding acids. Nitrile hydratases have potential as biocatalysts in bioremediation and biotransformation applications, and several successful examples demonstrate the advantages. In this work a real-time PCR assay was designed for the detection of Fe-type nitrile hydratase genes from environmental isolates purified from nitrile-enriched soils and seaweeds. Specific PCR primers were also designed for amplification and sequencing of the genes. Identical or highly homologous nitrile hydratase genes were detected from isolates of numerous genera from geographically diverse sites, as were numerous novel genes. The genes were also detected from isolates of genera not previously reported to harbour nitrile hydratases. The results provide further evidence that many bacteria have acquired the genes via horizontal gene transfer. The real-time PCR assay should prove useful in searching for nitrile hydratases that could have novel substrate specificities and therefore potential in industrial applications.

Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment.

NARCIS (Netherlands)

Ricard, G.N.S.; McEwan, N.R.; Dutilh, B.E.; Jouany, J.P.; Macheboeuf, D.; Mitsumori, M.; McIntosh, F.M.; Michalowski, T.; Nagamine, T.; Nelson, N.; Newbold, C.J.; Nsabimana, E.; Takenaka, A; Thomas, N.A.; Ushida, K.; Hackstein, J.H.P.; Huynen, M.A.

2006-01-01

BACKGROUND: The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants) was studied using ciliate Expressed Sequence Tags (ESTs). More than 4000 ESTs were sequenced from representatives of the two major

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

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Gouy Manolo

2008-10-01

Full Text Available Abstract Background Despite a large agreement between ribosomal RNA and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its deepest nodes. For instance, the position of the hyperthermophilic Aquificales is debated, as their commonly observed position close to Thermotogales may proceed from horizontal gene transfers, long branch attraction or compositional biases, and may not represent vertical descent. Indeed, another view, based on the analysis of rare genomic changes, places Aquificales close to epsilon-Proteobacteria. Results To get a whole genome view of Aquifex relationships, all trees containing sequences from Aquifex in the HOGENOM database were surveyed. This study revealed that Aquifex is most often found as a neighbour to Thermotogales. Moreover, informational genes, which appeared to be less often transferred to the Aquifex lineage than non-informational genes, most often placed Aquificales close to Thermotogales. To ensure these results did not come from long branch attraction or compositional artefacts, a subset of carefully chosen proteins from a wide range of bacterial species was selected for further scrutiny. Among these genes, two phylogenetic hypotheses were found to be significantly more likely than the others: the most likely hypothesis placed Aquificales as a neighbour to Thermotogales, and the second one with epsilon-Proteobacteria. We characterized the genes that supported each of these two hypotheses, and found that differences in rates of evolution or in amino-acid compositions could not explain the presence of two incongruent phylogenetic signals in the alignment. Instead, evidence for a large Horizontal Gene Transfer between Aquificales and epsilon-Proteobacteria was found. Conclusion Methods based on concatenated informational proteins and methods based on character cladistics led to different conclusions regarding the position of Aquificales because this lineage

Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes

Science.gov (United States)

2010-01-01

Background Horizontal gene transfer (HGT) is relatively common in plant mitochondrial genomes but the mechanisms, extent and consequences of transfer remain largely unknown. Previous results indicate that parasitic plants are often involved as either transfer donors or recipients, suggesting that direct contact between parasite and host facilitates genetic transfer among plants. Results In order to uncover the mechanistic details of plant-to-plant HGT, the extent and evolutionary fate of transfer was investigated between two groups: the parasitic genus Cuscuta and a small clade of Plantago species. A broad polymerase chain reaction (PCR) survey of mitochondrial genes revealed that at least three genes (atp1, atp6 and matR) were recently transferred from Cuscuta to Plantago. Quantitative PCR assays show that these three genes have a mitochondrial location in the one species line of Plantago examined. Patterns of sequence evolution suggest that these foreign genes degraded into pseudogenes shortly after transfer and reverse transcription (RT)-PCR analyses demonstrate that none are detectably transcribed. Three cases of gene conversion were detected between native and foreign copies of the atp1 gene. The identical phylogenetic distribution of the three foreign genes within Plantago and the retention of cytidines at ancestral positions of RNA editing indicate that these genes were probably acquired via a single, DNA-mediated transfer event. However, samplings of multiple individuals from two of the three species in the recipient Plantago clade revealed complex and perplexing phylogenetic discrepancies and patterns of sequence divergence for all three of the foreign genes. Conclusions This study reports the best evidence to date that multiple mitochondrial genes can be transferred via a single HGT event and that transfer occurred via a strictly DNA-level intermediate. The discovery of gene conversion between co-resident foreign and native mitochondrial copies suggests

Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes

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Hao Weilong

2010-12-01

Full Text Available Abstract Background Horizontal gene transfer (HGT is relatively common in plant mitochondrial genomes but the mechanisms, extent and consequences of transfer remain largely unknown. Previous results indicate that parasitic plants are often involved as either transfer donors or recipients, suggesting that direct contact between parasite and host facilitates genetic transfer among plants. Results In order to uncover the mechanistic details of plant-to-plant HGT, the extent and evolutionary fate of transfer was investigated between two groups: the parasitic genus Cuscuta and a small clade of Plantago species. A broad polymerase chain reaction (PCR survey of mitochondrial genes revealed that at least three genes (atp1, atp6 and matR were recently transferred from Cuscuta to Plantago. Quantitative PCR assays show that these three genes have a mitochondrial location in the one species line of Plantago examined. Patterns of sequence evolution suggest that these foreign genes degraded into pseudogenes shortly after transfer and reverse transcription (RT-PCR analyses demonstrate that none are detectably transcribed. Three cases of gene conversion were detected between native and foreign copies of the atp1 gene. The identical phylogenetic distribution of the three foreign genes within Plantago and the retention of cytidines at ancestral positions of RNA editing indicate that these genes were probably acquired via a single, DNA-mediated transfer event. However, samplings of multiple individuals from two of the three species in the recipient Plantago clade revealed complex and perplexing phylogenetic discrepancies and patterns of sequence divergence for all three of the foreign genes. Conclusions This study reports the best evidence to date that multiple mitochondrial genes can be transferred via a single HGT event and that transfer occurred via a strictly DNA-level intermediate. The discovery of gene conversion between co-resident foreign and native

Beyond Agrobacterium-Mediated Transformation: Horizontal Gene Transfer from Bacteria to Eukaryotes.

Science.gov (United States)

Lacroix, Benoît; Citovsky, Vitaly

2018-03-03

Besides the massive gene transfer from organelles to the nuclear genomes, which occurred during the early evolution of eukaryote lineages, the importance of horizontal gene transfer (HGT) in eukaryotes remains controversial. Yet, increasing amounts of genomic data reveal many cases of bacterium-to-eukaryote HGT that likely represent a significant force in adaptive evolution of eukaryotic species. However, DNA transfer involved in genetic transformation of plants by Agrobacterium species has traditionally been considered as the unique example of natural DNA transfer and integration into eukaryotic genomes. Recent discoveries indicate that the repertoire of donor bacterial species and of recipient eukaryotic hosts potentially are much wider than previously thought, including donor bacterial species, such as plant symbiotic nitrogen-fixing bacteria (e.g., Rhizobium etli) and animal bacterial pathogens (e.g., Bartonella henselae, Helicobacter pylori), and recipient species from virtually all eukaryotic clades. Here, we review the molecular pathways and potential mechanisms of these trans-kingdom HGT events and discuss their utilization in biotechnology and research.

In Silico Prediction of Horizontal Gene Transfer Events in Lactobacillus bulgaricus and Streptococcus thermophilus Reveals Protocooperation in Yogurt Manufacturing▿ †

Science.gov (United States)

Liu, Mengjin; Siezen, Roland J.; Nauta, Arjen

2009-01-01

Lactobacillus bulgaricus and Streptococcus thermophilus, used in yogurt starter cultures, are well known for their stability and protocooperation during their coexistence in milk. In this study, we show that a close interaction between the two species also takes place at the genetic level. We performed an in silico analysis, combining gene composition and gene transfer mechanism-associated features, and predicted horizontally transferred genes in both L. bulgaricus and S. thermophilus. Putative horizontal gene transfer (HGT) events that have occurred between the two bacterial species include the transfer of exopolysaccharide (EPS) biosynthesis genes, transferred from S. thermophilus to L. bulgaricus, and the gene cluster cbs-cblB(cglB)-cysE for the metabolism of sulfur-containing amino acids, transferred from L. bulgaricus or Lactobacillus helveticus to S. thermophilus. The HGT event for the cbs-cblB(cglB)-cysE gene cluster was analyzed in detail, with respect to both evolutionary and functional aspects. It can be concluded that during the coexistence of both yogurt starter species in a milk environment, agonistic coevolution at the genetic level has probably been involved in the optimization of their combined growth and interactions. PMID:19395564

Diagnosis of partial body radiation exposure in mice using peripheral blood gene expression profiles.

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Sarah K Meadows

2010-07-01

Full Text Available In the event of a terrorist-mediated attack in the United States using radiological or improvised nuclear weapons, it is expected that hundreds of thousands of people could be exposed to life-threatening levels of ionizing radiation. We have recently shown that genome-wide expression analysis of the peripheral blood (PB can generate gene expression profiles that can predict radiation exposure and distinguish the dose level of exposure following total body irradiation (TBI. However, in the event a radiation-mass casualty scenario, many victims will have heterogeneous exposure due to partial shielding and it is unknown whether PB gene expression profiles would be useful in predicting the status of partially irradiated individuals. Here, we identified gene expression profiles in the PB that were characteristic of anterior hemibody-, posterior hemibody- and single limb-irradiation at 0.5 Gy, 2 Gy and 10 Gy in C57Bl6 mice. These PB signatures predicted the radiation status of partially irradiated mice with a high level of accuracy (range 79-100% compared to non-irradiated mice. Interestingly, PB signatures of partial body irradiation were poorly predictive of radiation status by site of injury (range 16-43%, suggesting that the PB molecular response to partial body irradiation was anatomic site specific. Importantly, PB gene signatures generated from TBI-treated mice failed completely to predict the radiation status of partially irradiated animals or non-irradiated controls. These data demonstrate that partial body irradiation, even to a single limb, generates a characteristic PB signature of radiation injury and thus may necessitate the use of multiple signatures, both partial body and total body, to accurately assess the status of an individual exposed to radiation.

Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer

Science.gov (United States)

2011-01-01

Background Brachyspira spp. colonize the intestines of some mammalian and avian species and show different degrees of enteropathogenicity. Brachyspira intermedia can cause production losses in chickens and strain PWS/AT now becomes the fourth genome to be completed in the genus Brachyspira. Results 15 classes of unique and shared genes were analyzed in B. intermedia, B. murdochii, B. hyodysenteriae and B. pilosicoli. The largest number of unique genes was found in B. intermedia and B. murdochii. This indicates the presence of larger pan-genomes. In general, hypothetical protein annotations are overrepresented among the unique genes. A 3.2 kb plasmid was found in B. intermedia strain PWS/AT. The plasmid was also present in the B. murdochii strain but not in nine other Brachyspira isolates. Within the Brachyspira genomes, genes had been translocated and also frequently switched between leading and lagging strands, a process that can be followed by different AT-skews in the third positions of synonymous codons. We also found evidence that bacteriophages were being remodeled and genes incorporated into them. Conclusions The accessory gene pool shapes species-specific traits. It is also influenced by reductive genome evolution and horizontal gene transfer. Gene-transfer events can cross both species and genus boundaries and bacteriophages appear to play an important role in this process. A mechanism for horizontal gene transfer appears to be gene translocations leading to remodeling of bacteriophages in combination with broad tropism. PMID:21816042

The advantages and disadvantages of horizontal gene transfer and the emergence of the first species

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Higgs Paul G

2011-01-01

Full Text Available Abstract Background Horizontal Gene Transfer (HGT is beneficial to a cell if the acquired gene confers a useful function, but is detrimental if the gene has no function, if it is incompatible with existing genes, or if it is a selfishly replicating mobile element. If the balance of these effects is beneficial on average, we would expect cells to evolve high rates of acceptance of horizontally transferred genes, whereas if it is detrimental, cells should reduce the rate of HGT as far as possible. It has been proposed that the rate of HGT was very high in the early stages of prokaryotic evolution, and hence there were no separate lineages of organisms. Only when the HGT rate began to fall, would lineages begin to emerge with their own distinct sets of genes. Evolution would then become more tree-like. This phenomenon has been called the Darwinian Threshold. Results We study a model for genome evolution that incorporates both beneficial and detrimental effects of HGT. We show that if rate of gene loss during genome replication is high, as was probably the case in the earliest genomes before the time of the last universal common ancestor, then a high rate of HGT is favourable. HGT leads to the rapid spread of new genes and allows the build-up of larger, fitter genomes than could be achieved by purely vertical inheritance. In contrast, if the gene loss rate is lower, as in modern prokaryotes, then HGT is, on average, unfavourable. Conclusions Modern cells should therefore evolve to reduce HGT if they can, although the prevalence of independently replicating mobile elements and viruses may mean that cells cannot avoid HGT in practice. In the model, natural selection leads to gradual improvement of the replication accuracy and gradual decrease in the optimal rate of HGT. By clustering genomes based on gene content, we show that there are no separate lineages of organisms when the rate of HGT is high; however, as the rate of HGT decreases, a tree

Plasmid transfer by conjugation as a possible route of horizontal gene transfer and recombination in Xylella fastidiosa

Science.gov (United States)

Horizontal gene transfer is an important component of evolution and adaptation of bacterial species. Xylella fastidiosa has the ability to incorporate exogenous DNA into its genome by homologous recombination at relatively high rates. This genetic recombination is believed to play a role in adaptati...

Role of horizontal gene transfer as a control on the coevolution of ribosomal proteins and the genetic code

Energy Technology Data Exchange (ETDEWEB)

Woese, Carl R.; Goldenfeld, Nigel; Luthey-Schulten, Zaida

2011-03-31

Our main goal is to develop the conceptual and computational tools necessary to understand the evolution of the universal processes of translation and replication and to identify events of horizontal gene transfer that occurred within the components. We will attempt to uncover the major evolutionary transitions that accompanied the development of protein synthesis by the ribosome and associated components of the translation apparatus. Our project goes beyond standard genomic approaches to explore homologs that are represented at both the structure and sequence level. Accordingly, use of structural phylogenetic analysis allows us to probe further back into deep evolutionary time than competing approaches, permitting greater resolution of primitive folds and structures. Specifically, our work focuses on the elements of translation, ranging from the emergence of the canonical genetic code to the evolution of specific protein folds, mediated by the predominance of horizontal gene transfer in early life. A unique element of this study is the explicit accounting for the impact of phenotype selection on translation, through a coevolutionary control mechanism. Our work contributes to DOE mission objectives through: (1) sophisticated computer simulation of protein dynamics and evolution, and the further refinement of techniques for structural phylogeny, which complement sequence information, leading to improved annotation of genomic databases; (2) development of evolutionary approaches to exploring cellular function and machinery in an integrated way; and (3) documentation of the phenotype interaction with translation over evolutionary time, reflecting the system response to changing selection pressures through horizontal gene transfer.

Horizontal Gene Acquisitions, Mobile Element Proliferation, and Genome Decay in the Host-Restricted Plant Pathogen Erwinia Tracheiphila

Science.gov (United States)

Shapiro, Lori R.; Scully, Erin D.; Straub, Timothy J.; Park, Jihye; Stephenson, Andrew G.; Beattie, Gwyn A.; Gleason, Mark L.; Kolter, Roberto; Coelho, Miguel C.; De Moraes, Consuelo M.; Mescher, Mark C.; Zhaxybayeva, Olga

2016-01-01

Modern industrial agriculture depends on high-density cultivation of genetically similar crop plants, creating favorable conditions for the emergence of novel pathogens with increased fitness in managed compared with ecologically intact settings. Here, we present the genome sequence of six strains of the cucurbit bacterial wilt pathogen Erwinia tracheiphila (Enterobacteriaceae) isolated from infected squash plants in New York, Pennsylvania, Kentucky, and Michigan. These genomes exhibit a high proportion of recent horizontal gene acquisitions, invasion and remarkable amplification of mobile genetic elements, and pseudogenization of approximately 20% of the coding sequences. These genome attributes indicate that E. tracheiphila recently emerged as a host-restricted pathogen. Furthermore, chromosomal rearrangements associated with phage and transposable element proliferation contribute to substantial differences in gene content and genetic architecture between the six E. tracheiphila strains and other Erwinia species. Together, these data lead us to hypothesize that E. tracheiphila has undergone recent evolution through both genome decay (pseudogenization) and genome expansion (horizontal gene transfer and mobile element amplification). Despite evidence of dramatic genomic changes, the six strains are genetically monomorphic, suggesting a recent population bottleneck and emergence into E. tracheiphila’s current ecological niche. PMID:26992913

Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction.

Science.gov (United States)

Beiko, Robert G; Ragan, Mark A

2009-01-01

Phylogenomic methods can be used to investigate the tangled evolutionary relationships among genomes. Building 'all the trees of all the genes' can potentially identify common pathways of horizontal gene transfer (HGT) among taxa at varying levels of phylogenetic depth. Phylogenetic affinities can be aggregated and merged with the information about genetic linkage and biochemical function to examine hypotheses of adaptive evolution via HGT. Additionally, the use of many genetic data sets increases the power of statistical tests for phylogenetic artifacts. However, large-scale phylogenetic analyses pose several challenges, including the necessary abandonment of manual validation techniques, the need to translate inferred phylogenetic discordance into inferred HGT events, and the challenges involved in aggregating results from search-based inference methods. In this chapter we describe a tree search procedure to recover the most parsimonious pathways of HGT, and examine some of the assumptions that are made by this method.

Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer

Directory of Open Access Journals (Sweden)

Christian Johannes Hendrik Von Wintersdorff

2016-02-01

Full Text Available The emergence and spread of antibiotic resistance among pathogenic bacteria has been a rising problem for public health in recent decades. It is becoming increasingly recognized that not only antibiotic resistance genes (ARGs encountered in clinical pathogens are of relevance, but rather, all pathogenic, commensal as well as environmental bacteria – and also mobile genetic elements and bacteriophages – form a reservoir of ARGs (the resistome from which pathogenic bacteria can acquire resistance via horizontal gene transfer (HGT. HGT has caused antibiotic resistance to spread from commensal and environmental species to pathogenic ones, as has been shown for some clinically important ARGs. Of the three canonical mechanisms of HGT, conjugation is thought to have the greatest influence on the dissemination of ARGs. While transformation and transduction are deemed less important, recent discoveries suggest their role may be larger than previously thought. Understanding the extent of the resistome and how its mobilization to pathogenic bacteria takes place is essential for efforts to control the dissemination of these genes. Here, we will discuss the concept of the resistome, provide examples of HGT of clinically relevant ARGs and present an overview of the current knowledge of the contributions the various HGT mechanisms make to the spread of antibiotic resistance.

Horizontal gene transfer confers adaptive advantages to phytopathogenic fungi: a case study of catalase-peroxidase in Fusarium verticillioides

Science.gov (United States)

Horizontal gene transfer (HGT), the exchange and stable integration of genetic material between different evolutionary lineages, is widely observed in fungi. We hypothesize that successful stabilization of HGT elements provides adaptive advantages (e.g., virulence). Catalase/peroxidases (KatGs) are ...

AS3MT-mediated tolerance to arsenic evolved by multiple independent horizontal gene transfers from bacteria to eukaryotes

DEFF Research Database (Denmark)

Palmgren, Michael; Engström, Karin; Hallström, Björn M.

2017-01-01

the evolutionary origin of AS3MT and assessed the ability of different genotypes to produce methylated arsenic metabolites. Phylogenetic analysis suggests that multiple, independent horizontal gene transfers between different bacteria, and from bacteria to eukaryotes, increased tolerance to environmental arsenic...

PPARγ partial agonist GQ-16 strongly represses a subset of genes in 3T3-L1 adipocytes

Energy Technology Data Exchange (ETDEWEB)

Milton, Flora Aparecida [Faculdade de Ciências da Saúde, Laboratório de Farmacologia Molecular, Universidade de Brasília (Brazil); Genomic Medicine, Houston Methodist Research Institute, Houston, TX (United States); Cvoro, Aleksandra [Genomic Medicine, Houston Methodist Research Institute, Houston, TX (United States); Amato, Angelica A. [Faculdade de Ciências da Saúde, Laboratório de Farmacologia Molecular, Universidade de Brasília (Brazil); Sieglaff, Douglas H.; Filgueira, Carly S.; Arumanayagam, Anithachristy Sigamani [Genomic Medicine, Houston Methodist Research Institute, Houston, TX (United States); Caro Alves de Lima, Maria do; Rocha Pitta, Ivan [Laboratório de Planejamento e Síntese de Fármacos – LPSF, Universidade Federal de Pernambuco (Brazil); Assis Rocha Neves, Francisco de [Faculdade de Ciências da Saúde, Laboratório de Farmacologia Molecular, Universidade de Brasília (Brazil); Webb, Paul, E-mail: pwebb@HoustonMethodist.org [Genomic Medicine, Houston Methodist Research Institute, Houston, TX (United States)

2015-08-28

Thiazolidinediones (TZDs) are peroxisome proliferator-activated receptor gamma (PPARγ) agonists that improve insulin resistance but trigger side effects such as weight gain, edema, congestive heart failure and bone loss. GQ-16 is a PPARγ partial agonist that improves glucose tolerance and insulin sensitivity in mouse models of obesity and diabetes without inducing weight gain or edema. It is not clear whether GQ-16 acts as a partial agonist at all PPARγ target genes, or whether it displays gene-selective actions. To determine how GQ-16 influences PPARγ activity on a gene by gene basis, we compared effects of rosiglitazone (Rosi) and GQ-16 in mature 3T3-L1 adipocytes using microarray and qRT-PCR. Rosi changed expression of 1156 genes in 3T3-L1, but GQ-16 only changed 89 genes. GQ-16 generally showed weak effects upon Rosi induced genes, consistent with partial agonist actions, but a subset of modestly Rosi induced and strongly repressed genes displayed disproportionately strong GQ-16 responses. PPARγ partial agonists MLR24 and SR1664 also exhibit disproportionately strong effects on transcriptional repression. We conclude that GQ-16 displays a continuum of weak partial agonist effects but efficiently represses some negatively regulated PPARγ responsive genes. Strong repressive effects could contribute to physiologic actions of GQ-16. - Highlights: • GQ-16 is an insulin sensitizing PPARγ ligand with reduced harmful side effects. • GQ-16 displays a continuum of weak partial agonist activities at PPARγ-induced genes. • GQ-16 exerts strong repressive effects at a subset of genes. • These inhibitor actions should be evaluated in models of adipose tissue inflammation.

PPARγ partial agonist GQ-16 strongly represses a subset of genes in 3T3-L1 adipocytes

International Nuclear Information System (INIS)

Milton, Flora Aparecida; Cvoro, Aleksandra; Amato, Angelica A.; Sieglaff, Douglas H.; Filgueira, Carly S.; Arumanayagam, Anithachristy Sigamani; Caro Alves de Lima, Maria do; Rocha Pitta, Ivan; Assis Rocha Neves, Francisco de; Webb, Paul

2015-01-01

Thiazolidinediones (TZDs) are peroxisome proliferator-activated receptor gamma (PPARγ) agonists that improve insulin resistance but trigger side effects such as weight gain, edema, congestive heart failure and bone loss. GQ-16 is a PPARγ partial agonist that improves glucose tolerance and insulin sensitivity in mouse models of obesity and diabetes without inducing weight gain or edema. It is not clear whether GQ-16 acts as a partial agonist at all PPARγ target genes, or whether it displays gene-selective actions. To determine how GQ-16 influences PPARγ activity on a gene by gene basis, we compared effects of rosiglitazone (Rosi) and GQ-16 in mature 3T3-L1 adipocytes using microarray and qRT-PCR. Rosi changed expression of 1156 genes in 3T3-L1, but GQ-16 only changed 89 genes. GQ-16 generally showed weak effects upon Rosi induced genes, consistent with partial agonist actions, but a subset of modestly Rosi induced and strongly repressed genes displayed disproportionately strong GQ-16 responses. PPARγ partial agonists MLR24 and SR1664 also exhibit disproportionately strong effects on transcriptional repression. We conclude that GQ-16 displays a continuum of weak partial agonist effects but efficiently represses some negatively regulated PPARγ responsive genes. Strong repressive effects could contribute to physiologic actions of GQ-16. - Highlights: • GQ-16 is an insulin sensitizing PPARγ ligand with reduced harmful side effects. • GQ-16 displays a continuum of weak partial agonist activities at PPARγ-induced genes. • GQ-16 exerts strong repressive effects at a subset of genes. • These inhibitor actions should be evaluated in models of adipose tissue inflammation

Characterization of five partial deletions of the factor VIII gene

International Nuclear Information System (INIS)

Youssoufian, H.; Antonarakis, S.E.; Aronis, S.; Tsiftis, G.; Phillips, D.G.; Kazazian, H.H. Jr.

1987-01-01

Hemophilia A is an X-linked disorder of coagulation caused by a deficiency of factor VIII. By using cloned DNA probes, the authors have characterized the following five different partial deletions of the factor VIII gene from a panel of 83 patients with hemophilia A: (i) a 7-kilobase (kb) deletion that eliminates exon 6; (ii) a 2.5-kb deletion that eliminates 5' sequences of exon 14; (iii) a deletion of at least 7 kb that eliminates exons 24 and 25; (iv) a deletion of at least 16 kb that eliminates exons 23-25; and (v) a 5.5-kb deletion that eliminates exon 22. The first four deletions are associated with severe hemophilia A. By contrast, the last deletion is associated with moderate disease, possibly because of in-frame splicing from adjacent exons. None of those patients with partial gene deletions had circulating inhibitors to factor VIII. One deletion occurred de novo in a germ cell of the maternal grandmother, while a second deletion occurred in a germ cell of the maternal grandfather. These observations demonstrate that de novo deletions of X-linked genes can occur in either male or female gametes

Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers.

Science.gov (United States)

Park, Seongjun; Grewe, Felix; Zhu, Andan; Ruhlman, Tracey A; Sabir, Jamal; Mower, Jeffrey P; Jansen, Robert K

2015-10-01

The exchange of genetic material between cellular organelles through intracellular gene transfer (IGT) or between species by horizontal gene transfer (HGT) has played an important role in plant mitochondrial genome evolution. The mitochondrial genomes of Geraniaceae display a number of unusual phenomena including highly accelerated rates of synonymous substitutions, extensive gene loss and reduction in RNA editing. Mitochondrial DNA sequences assembled for 17 species of Geranium revealed substantial reduction in gene and intron content relative to the ancestor of the Geranium lineage. Comparative analyses of nuclear transcriptome data suggest that a number of these sequences have been functionally relocated to the nucleus via IGT. Evidence for rampant HGT was detected in several Geranium species containing foreign organellar DNA from diverse eudicots, including many transfers from parasitic plants. One lineage has experienced multiple, independent HGT episodes, many of which occurred within the past 5.5 Myr. Both duplicative and recapture HGT were documented in Geranium lineages. The mitochondrial genome of Geranium brycei contains at least four independent HGT tracts that are absent in its nearest relative. Furthermore, G. brycei mitochondria carry two copies of the cox1 gene that differ in intron content, providing insight into contrasting hypotheses on cox1 intron evolution. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

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

NARCIS (Netherlands)

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

2017-01-01

Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been

Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment

OpenAIRE

Ricard, Guénola; McEwan, Neil R; Dutilh, Bas E; Jouany, Jean-Pierre; Macheboeuf, Didier; Mitsumori, Makoto; McIntosh, Freda M; Michalowski, Tadeusz; Nagamine, Takafumi; Nelson, Nancy; Newbold, Charles J; Nsabimana, Eli; Takenaka, Akio; Thomas, Nadine A; Ushida, Kazunari

2006-01-01

Abstract Background The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants) was studied using ciliate Expressed Sequence Tags (ESTs). More than 4000 ESTs were sequenced from representatives of the two major groups of rumen Cilates: the order Entodiniomorphida (Entodinium simplex, Entodinium caudatum, Eudiplodinium maggii, Metadinium medium, Diploplastron affine, Polyplastron multivesiculatum and...

Partial characterization of three β-defensin gene transcripts in river ...

African Journals Online (AJOL)

In this study, the tracheal tissues from Egyptian river buffalo and cattle were screened for the presence of three bovine β-defensin gene transcripts. Three primer pairs were designed on the basis of published Bos taurus sequences for partial amplification of β-defensin 4, β-defensin 10 and β-defensin 11 complementary DNA ...

Et tu, Brute? Not Even Intracellular Mutualistic Symbionts Escape Horizontal Gene Transfer

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Sergio López-Madrigal

2017-09-01

Full Text Available Many insect species maintain mutualistic relationships with endosymbiotic bacteria. In contrast to their free-living relatives, horizontal gene transfer (HGT has traditionally been considered rare in long-term endosymbionts. Nevertheless, meta-omics exploration of certain symbiotic models has unveiled an increasing number of bacteria-bacteria and bacteria-host genetic transfers. The abundance and function of transferred loci suggest that HGT might play a major role in the evolution of the corresponding consortia, enhancing their adaptive value or buffering detrimental effects derived from the reductive evolution of endosymbionts’ genomes. Here, we comprehensively review the HGT cases recorded to date in insect-bacteria mutualistic consortia, and discuss their impact on the evolutionary success of these associations.

Mainstreams of horizontal gene exchange in enterobacteria: consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011.

Directory of Open Access Journals (Sweden)

Oliver Bezuidt

Full Text Available BACKGROUND: Escherichia coli O104:H4 caused a severe outbreak in Europe in 2011. The strain TY-2482 sequenced from this outbreak allowed the discovery of its closest relatives but failed to resolve ways in which it originated and evolved. On account of the previous statement, may we expect similar upcoming outbreaks to occur recurrently or spontaneously in the future? The inability to answer these questions shows limitations of the current comparative and evolutionary genomics methods. PRINCIPAL FINDINGS: The study revealed oscillations of gene exchange in enterobacteria, which originated from marine γ-Proteobacteria. These mobile genetic elements have become recombination hotspots and effective 'vehicles' ensuring a wide distribution of successful combinations of fitness and virulence genes among enterobacteria. Two remarkable peculiarities of the strain TY-2482 and its relatives were observed: i retaining the genetic primitiveness by these strains as they somehow avoided the main fluxes of horizontal gene transfer which effectively penetrated other enetrobacteria; ii acquisition of antibiotic resistance genes in a plasmid genomic island of β-Proteobacteria origin which ontologically is unrelated to the predominant genomic islands of enterobacteria. CONCLUSIONS: Oscillations of horizontal gene exchange activity were reported which result from a counterbalance between the acquired resistance of bacteria towards existing mobile vectors and the generation of new vectors in the environmental microflora. We hypothesized that TY-2482 may originate from a genetically primitive lineage of E. coli that has evolved in confined geographical areas and brought by human migration or cattle trade onto an intersection of several independent streams of horizontal gene exchange. Development of a system for monitoring the new and most active gene exchange events was proposed.

H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes.

OpenAIRE

Koichi Higashi; Toru Tobe; Akinori Kanai; Ebru Uyar; Shu Ishikawa; Yutaka Suzuki; Naotake Ogasawara; Ken Kurokawa; Taku Oshima

2016-01-01

Bacteria can acquire new traits through horizontal gene transfer. Inappropriate expression of transferred genes, however, can disrupt the physiology of the host bacteria. To reduce this risk, Escherichia coli expresses the nucleoid-associated protein, H-NS, which preferentially binds to horizontally transferred genes to control their expression. Once expression is optimized, the horizontally transferred genes may actually contribute to E. coli survival in new habitats. Therefore, we investiga...

Counter-current flow in a vertical to horizontal tube with obstructions

Energy Technology Data Exchange (ETDEWEB)

Tye, P.; Matuszkiewicz, A.; Teyssedou, A. [Institut de Genie Nucleaire, Quebec (Canada)] [and others

1995-09-01

This paper presents experimental results on counter-current flow and flooding in an elbow between a vertical and a horizontal run. The experimental technique used allowed not only the flooding limit to be determined, but also the entire partial delivery region to be studied as well. The influence that various size orifices placed in the horizontal run have on both the delivered liquid flow rates and on the flooding limits is also examined. It is observed that both the flooding limits and the delivered liquid flow rates decrease with decreasing orifice size. Further, it is also observed that the mechanisms that govern the partial delivery of the liquid are significantly different when an orifice is present in the horizontal leg as compared to the case when no orifice is present.

Recombination and horizontal transfer of nodulation and ACC deaminase (acdS) genes within Alpha- and Betaproteobacteria nodulating legumes of the Cape Fynbos biome.

Science.gov (United States)

Lemaire, Benny; Van Cauwenberghe, Jannick; Chimphango, Samson; Stirton, Charles; Honnay, Olivier; Smets, Erik; Muasya, A Muthama

2015-11-01

The goal of this work is to study the evolution and the degree of horizontal gene transfer (HGT) within rhizobial genera of both Alphaproteobacteria (Mesorhizobium, Rhizobium) and Betaproteobacteria (Burkholderia), originating from South African Fynbos legumes. By using a phylogenetic approach and comparing multiple chromosomal and symbiosis genes, we revealed conclusive evidence of high degrees of horizontal transfer of nodulation genes among closely related species of both groups of rhizobia, but also among species with distant genetic backgrounds (Rhizobium and Mesorhizobium), underscoring the importance of lateral transfer of symbiosis traits as an important evolutionary force among rhizobia of the Cape Fynbos biome. The extensive exchange of symbiosis genes in the Fynbos is in contrast with a lack of significant events of HGT among Burkholderia symbionts from the South American Cerrado and Caatinga biome. Furthermore, homologous recombination among selected housekeeping genes had a substantial impact on sequence evolution within Burkholderia and Mesorhizobium. Finally, phylogenetic analyses of the non-symbiosis acdS gene in Mesorhizobium, a gene often located on symbiosis islands, revealed distinct relationships compared to the chromosomal and symbiosis genes, suggesting a different evolutionary history and independent events of gene transfer. The observed events of HGT and incongruence between different genes necessitate caution in interpreting topologies from individual data types. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer

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Kujin Tang

2018-04-01

Full Text Available Horizontal gene transfer (HGT plays an important role in the evolution of microbial organisms including bacteria. Alignment-free methods based on single genome compositional information have been used to detect HGT. Currently, Manhattan and Euclidean distances based on tetranucleotide frequencies are the most commonly used alignment-free dissimilarity measures to detect HGT. By testing on simulated bacterial sequences and real data sets with known horizontal transferred genomic regions, we found that more advanced alignment-free dissimilarity measures such as CVTree and d2* that take into account the background Markov sequences can solve HGT detection problems with significantly improved performance. We also studied the influence of different factors such as evolutionary distance between host and donor sequences, size of sliding window, and host genome composition on the performances of alignment-free methods to detect HGT. Our study showed that alignment-free methods can predict HGT accurately when host and donor genomes are in different order levels. Among all methods, CVTree with word length of 3, d2* with word length 3, Markov order 1 and d2* with word length 4, Markov order 1 outperform others in terms of their highest F1-score and their robustness under the influence of different factors.

Comparative videostroboscopic analysis after different external partial laryngectomies

Directory of Open Access Journals (Sweden)

Mumović Gordana M.

2014-01-01

Full Text Available Background/Aim. After external partial laryngectomias, videostroborscopy is very usefull in evaluation of postoperative phonatory mehanisms showing the “slow motion” of the vibrations of the remaining laryngeal structures. The aim of this paper was to compare the videostroboscopic characteristics of the vibration and to establish the differences in the phonation mechanisms depending on the type of external partial laryngectomy performed. Methods. This prospective study was conducted during the period 2003-2009 at the Ear, Nose and Throat Clinic, Clinical Center of Vojvodina, Novi Sad, including 99 patients with laryngeal carcinoma, treated with open surgical approach using different types of vertical and horizontal partial laryngectomy. Videostroboscopy was used to analyse vibrations of the remaining laryngeal structures. Results. The dominant vibration structure after partial horizontal laryngectomy, chordectomy, frontolateral laryngectomy and three quarter laryngectomy was the remaining vocal fold, after hemilaryngectomy it was the false vocal fold and after subtotal and near total laryngectomy it was the arythenoid. In patients with supracricoid hemilaryngopharyngectomy performed, many different structures were involved in the vibration. After most of the partial laryngectomies, vibrations can be found in the reconstructed part of the defect. In both horizontal and vertical partial laryngectomies movements of the larynx during phonation were mostly medial, while in cricohyoidoglottopexies they were anterior-posterior. Most of the operated patients (72.7% had insufficient occlusion of the neoglottis during the phonation. Conclusion. Videostroboscopy is a useful method in examining the phonation mechanisms of reconstructed laryngeal structures after partial laryngectomy as well as in planning postoperative voice therapy.

Phylogenetic detection of horizontal gene transfer during the step-wise genesis of Mycobacterium tuberculosis

Directory of Open Access Journals (Sweden)

Turenne Christine

2009-08-01

Full Text Available Abstract Background In the past decade, the availability of complete genome sequence data has greatly facilitated comparative genomic research aimed at addressing genetic variability within species. More recently, analysis across species has become feasible, especially in genera where genome sequencing projects of multiple species have been initiated. To understand the genesis of the pathogen Mycobacterium tuberculosis within a genus where the majority of species are harmless environmental organisms, we have used genome sequence data from 16 mycobacteria to look for evidence of horizontal gene transfer (HGT associated with the emergence of pathogenesis. First, using multi-locus sequence analysis (MLSA of 20 housekeeping genes across these species, we derived a phylogeny that serves as the basis for HGT assignments. Next, we performed alignment searches for the 3989 proteins of M. tuberculosis H37Rv against 15 other mycobacterial genomes, generating a matrix of 59835 comparisons, to look for genetic elements that were uniquely found in M. tuberculosis and closely-related pathogenic mycobacteria. To assign when foreign genes were likely acquired, we designed a bioinformatic program called mycoHIT (mycobacterial homologue investigation tool to analyze these data in conjunction with the MLSA-based phylogeny. Results The bioinformatic screen predicted that 137 genes had been acquired by HGT at different phylogenetic strata; these included genes coding for metabolic functions and modification of mycobacterial lipids. For the majority of these genes, corroborating evidence of HGT was obtained, such as presence of phage or plasmid, and an aberrant GC%. Conclusion M. tuberculosis emerged through vertical inheritance along with the step-wise addition of genes acquired via HGT events, a process that may more generally describe the evolution of other pathogens.

Insights into horizontal acquisition patterns of dormancy and ...

Indian Academy of Sciences (India)

2016-07-22

Jul 22, 2016 ... ed the horizontal acquisition of fatty acid synthesis genes from α-proteobacteria .... of the genes related to fatty acid, polyketide or lipoprotein metabolism in M. ..... Basic local alignment search tool. J. Mol. Biol. 215 403–410.

Partial Gene Cloning and Enzyme Structure Modeling of Exolevanase Fragment from Bacillus subtilis

Science.gov (United States)

Azhar, M.; Natalia, D.; Syukur, S.; Andriani, N.; Jamsari, J.

2018-04-01

Inulin hydrolysis thermophilic and thermotolerant bacteria are potential sources of inulin hydrolysis enzymes. Partial gene that encodes inulin hydrolysis enzymes had been isolated from Bacillus subtilis using polymerase chain reaction (PCR) method with the DPE.slFandDPE.eR degenerative primers. The partial gene was cloned into pGEM-T Easy vector with E. coli as host cells and analyzed using BLASTx, CrustalW2, and Phyre2 programs. Size of thepartial gene had been found539 bp that encoded 179aminoacid residues of protein fragment. The sequences of protein fragment was more similar to exolevanase than exoinulinase. The protein fragment had conserved motif FSGS, and specific hits GH32 β-fructosidase. It had three residues of active site and five residues of substrate binding. The active site on the protein fragment were D (1-WLNDP-5), D (125-FRDPK-129) and E (177-WEC-179). Substrate binding on the protein fragment were ND (1-WLNDP-5), Q (18-FYQY-21), FS (60-FSGS-63) RD (125-FRDPK-129) and E (177-WEC-179).

Análisis de transferencia horizontal de genes en ensayos de biorremediación con grasas recalcitrantes

Directory of Open Access Journals (Sweden)

Catalina Rozo

2010-01-01

Full Text Available El empleo de microorganismos como herramienta para la mineralización de contaminantes orgánicos es una práctica que ha tomado mucha fuerza gracias a su eficiencia y bajo costo. La transferencia horizontal vía conjugación de genes es un requerimiento básico para optimizar procesos de biorremediación, por esta razón, además de conocer la diversidad metabólica es fundamental entender las interacciones que ocurren en una comunidad bacteriana para potenciar los procesos de biorremediación en campo. En este estudio se busca evaluar el potencial de transferencia horizontal (TH, tanto in vitro como en microcosmos de suelo, de aislamientos de bacterias obtenidas de un pasivo ambiental de grasas provenientes de la explotación carbonífera del Cerrejón. Inicialmente se agruparon los aislamientos de acuerdo con sus patrones de resistencia a antibióticos: ampicilina, cloramfenicol, gentamicina, tetraciclina y kanamicina. El potencial de TH de las cepas Vlf4, Ot3, Ot6, Pgt4, Blf11 y Vlf13 fue evaluado in vitro en medio sólido Luria-Bertani (LB donde se obtuvieron nuevos fenotipos a partir de los cruces Vlf13xOt6 y Pgt4xOt6, el nuevo fenotipo indica resistencia a los dos marcadores (ampR, kanR y su morfología sugiere que el receptor, en los dos casos, es la cepa Ot6. Los parentales Vlf13, Pgt4 y Ot6 fueron identificados por amplificación del gen RNAr 16S como Pseudomonas sp., Pseudomonas sp. y Chryseobacterium sp., respectivamente, y los transconjugantes como Chryseobacterium sp. Posteriormente, estos dos cruces fueron sometidos a ensayos de transferencia horizontal en microcosmos de suelos, donde se hizo evidente nuevamente la presencia de TH a una menor tasa. Los resultados obtenidos indican la posibilidad de un potencial de transferencia horizontal de genes entre los aislamientos seleccionados, dando lugar a la probabilidad de formular en futuros estudios un consorcio de bacterias que demuestran tener esta ventaja adaptativa.

Horizontal drilling assessment in Western Canada

International Nuclear Information System (INIS)

Catania, Peter; Wilson, Malcolm

1999-01-01

least partially responsible for every significant benefit to the provincial economy. In Saskatchewan, horizontal wells have (i) paid over CDN $400 million in royalties since 1990, (ii) annually generated CDN $525 million in investment and (iii) sustained 4350 jobs. Details pertaining to the Winter Cummings Sand Pool and others as examples of the success of the horizontal well program in Saskatchewan are discussed in this paper. (Author)

Sequence diversities of serine-aspartate repeat genes among Staphylococcus aureus isolates from different hosts presumably by horizontal gene transfer.

Directory of Open Access Journals (Sweden)

Huping Xue

Full Text Available BACKGROUND: Horizontal gene transfer (HGT is recognized as one of the major forces for bacterial genome evolution. Many clinically important bacteria may acquire virulence factors and antibiotic resistance through HGT. The comparative genomic analysis has become an important tool for identifying HGT in emerging pathogens. In this study, the Serine-Aspartate Repeat (Sdr family has been compared among different sources of Staphylococcus aureus (S. aureus to discover sequence diversities within their genomes. METHODOLOGY/PRINCIPAL FINDINGS: Four sdr genes were analyzed for 21 different S. aureus strains and 218 mastitis-associated S. aureus isolates from Canada. Comparative genomic analyses revealed that S. aureus strains from bovine mastitis (RF122 and mastitis isolates in this study, ovine mastitis (ED133, pig (ST398, chicken (ED98, and human methicillin-resistant S. aureus (MRSA (TCH130, MRSA252, Mu3, Mu50, N315, 04-02981, JH1 and JH9 were highly associated with one another, presumably due to HGT. In addition, several types of insertion and deletion were found in sdr genes of many isolates. A new insertion sequence was found in mastitis isolates, which was presumably responsible for the HGT of sdrC gene among different strains. Moreover, the sdr genes could be used to type S. aureus. Regional difference of sdr genes distribution was also indicated among the tested S. aureus isolates. Finally, certain associations were found between sdr genes and subclinical or clinical mastitis isolates. CONCLUSIONS: Certain sdr gene sequences were shared in S. aureus strains and isolates from different species presumably due to HGT. Our results also suggest that the distributional assay of virulence factors should detect the full sequences or full functional regions of these factors. The traditional assay using short conserved regions may not be accurate or credible. These findings have important implications with regard to animal husbandry practices that may

Comparative genomics reveals cotton-specific virulence factors in flexible genomic regions in Verticillium dahliae and evidence of horizontal gene transfer from Fusarium.

Science.gov (United States)

Chen, Jie-Yin; Liu, Chun; Gui, Yue-Jing; Si, Kai-Wei; Zhang, Dan-Dan; Wang, Jie; Short, Dylan P G; Huang, Jin-Qun; Li, Nan-Yang; Liang, Yong; Zhang, Wen-Qi; Yang, Lin; Ma, Xue-Feng; Li, Ting-Gang; Zhou, Lei; Wang, Bao-Li; Bao, Yu-Ming; Subbarao, Krishna V; Zhang, Geng-Yun; Dai, Xiao-Feng

2018-01-01

Verticillium dahliae isolates are most virulent on the host from which they were originally isolated. Mechanisms underlying these dominant host adaptations are currently unknown. We sequenced the genome of V. dahliae Vd991, which is highly virulent on its original host, cotton, and performed comparisons with the reference genomes of JR2 (from tomato) and VdLs.17 (from lettuce). Pathogenicity-related factor prediction, orthology and multigene family classification, transcriptome analyses, phylogenetic analyses, and pathogenicity experiments were performed. The Vd991 genome harbored several exclusive, lineage-specific (LS) genes within LS regions (LSRs). Deletion mutants of the seven genes within one LSR (G-LSR2) in Vd991 were less virulent only on cotton. Integration of G-LSR2 genes individually into JR2 and VdLs.17 resulted in significantly enhanced virulence on cotton but did not affect virulence on tomato or lettuce. Transcription levels of the seven LS genes in Vd991 were higher during the early stages of cotton infection, as compared with other hosts. Phylogenetic analyses suggested that G-LSR2 was acquired from Fusarium oxysporum f. sp. vasinfectum through horizontal gene transfer. Our results provide evidence that horizontal gene transfer from Fusarium to Vd991 contributed significantly to its adaptation to cotton and may represent a significant mechanism in the evolution of an asexual plant pathogen. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Insights on the Horizontal Gene Transfer of Carbapenemase Determinants in the Opportunistic Pathogen Acinetobacter baumannii

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Da Silva, Gabriela Jorge; Domingues, Sara

2016-01-01

Horizontal gene transfer (HGT) is a driving force to the evolution of bacteria. The fast emergence of antimicrobial resistance reflects the ability of genetic adaptation of pathogens. Acinetobacter baumannii has emerged in the last few decades as an important opportunistic nosocomial pathogen, in part due to its high capacity of acquiring resistance to diverse antibiotic families, including to the so-called last line drugs such as carbapenems. The rampant selective pressure and genetic exchange of resistance genes hinder the effective treatment of resistant infections. A. baumannii uses all the resistance mechanisms to survive against carbapenems but production of carbapenemases are the major mechanism, which may act in synergy with others. A. baumannii appears to use all the mechanisms of gene dissemination. Beyond conjugation, the mostly reported recent studies point to natural transformation, transduction and outer membrane vesicles-mediated transfer as mechanisms that may play a role in carbapenemase determinants spread. Understanding the genetic mobilization of carbapenemase genes is paramount in preventing their dissemination. Here we review the carbapenemases found in A. baumannii and present an overview of the current knowledge of contributions of the various HGT mechanisms to the molecular epidemiology of carbapenem resistance in this relevant opportunistic pathogen. PMID:27681923

Fluorescence recovery allows theimplementation of a fluorescence reporter gene platform applicable for the detection and quantification of horizontal gene transfer in anoxic environments

DEFF Research Database (Denmark)

Pinilla-Redondo, Rafael; Riber, Leise; Sørensen, Søren Johannes

2018-01-01

H limitations, and provide experimental tools that will help broaden its horizon of application to other fields.IMPORTANCEMany anaerobic environments, like the gastrointestinal tract, anaerobic digesters, and the interiors of dense biofilms, have been shown to be hotspots for horizontal gene transfer (HGT......). Despite the increasing wealth of reports warning about the alarming spread of antibiotic resistance determinants, to date, HGT studies mainly rely on cultivation-based methods. Unfortunately, the relevance of these studies is often questionable, as only a minor fraction of bacteria can be cultivated...

Modeling horizontal gene transfer (HGT in the gut of the Chagas disease vector Rhodnius prolixus

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Durvasula Ravi V

2011-05-01

Full Text Available Abstract Background Paratransgenesis is an approach to reducing arthropod vector competence using genetically modified symbionts. When applied to control of Chagas disease, the symbiont bacterium Rhodococcus rhodnii, resident in the gut lumen of the triatomine vector Rhodnius prolixus (Hemiptera: Reduviidae, is transformed to export cecropin A, an insect immune peptide. Cecropin A is active against Trypanosoma cruzi, the causative agent of Chagas disease. While proof of concept has been achieved in laboratory studies, a rigorous and comprehensive risk assessment is required prior to consideration of field release. An important part of this assessment involves estimating probability of transgene horizontal transfer to environmental organisms (HGT. This article presents a two-part risk assessment methodology: a theoretical model predicting HGT in the gut of R. prolixus from the genetically transformed symbiont R. rhodnii to a closely related non-target bacterium, Gordona rubropertinctus, in the absence of selection pressure, and a series of laboratory trials designed to test the model. Results The model predicted an HGT frequency of less than 1.14 × 10-16 per 100,000 generations at the 99% certainty level. The model was iterated twenty times, with the mean of the ten highest outputs evaluated at the 99% certainty level. Laboratory trials indicated no horizontal gene transfer, supporting the conclusions of the model. Conclusions The model treats HGT as a composite event, the probability of which is determined by the joint probability of three independent events: gene transfer through the modalities of transformation, transduction, and conjugation. Genes are represented in matrices and Monte Carlo method and Markov chain analysis are used to simulate and evaluate environmental conditions. The model is intended as a risk assessment instrument and predicts HGT frequency of less than 1.14 × 10-16 per 100,000 generations. With laboratory studies that

Polygalacturonase from Sitophilus oryzae: Possible horizontal transfer of a pectinase gene from fungi to weevils

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Zhicheng Shen

2003-08-01

Full Text Available Endo-polygalacturonase, one of the group of enzymes known collectively as pectinases, is widely distributed in bacteria, plants and fungi. The enzyme has also been found in several weevil species and a few other insects, such as aphids, but not in Drosophila melanogaster, Anopheles gambiae, or Caenorhabditis elegans or, as far as is known, in any more primitive animal species. What, then, is the genetic origin of the polygalacturonases in weevils? Since some weevil species harbor symbiotic microorganisms, it has been suggested, reasonably, that the symbionts' genomes of both aphids and weevils, rather than the insects' genomes, could encode polygalacturonase. We report here the cloning of a cDNA that encodes endo-polygalacturonase in the rice weevil, Sitophilus oryzae (L., and investigations based on the cloned cDNA. Our results, which include analysis of genes in antibiotic-treated rice weevils, indicate that the enzyme is, in fact, encoded by the insect genome. Given the apparent absence of the gene in much of the rest of the animal kingdom, it is therefore likely that the rice weevil polygalacturonase gene was incorporated into the weevil's genome by horizontal transfer, possibly from a fungus.

An acyltransferase gene that putatively functions in anthocyanin modification was horizontally transferred from Fabaceae into the genus Cuscuta

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Ting Sun

2016-06-01

Full Text Available Horizontal gene transfer (HGT refers to the flow of genetic materials to non-offspring, and occasionally HGT in plants can improve the adaptation of organisms in new niches due to expanded metabolic capability. Anthocyanins are an important group of water-soluble red, purple, or blue secondary metabolites, whose diversity results from modification after the main skeleton biosynthesis. Cuscuta is a stem holoparasitic genus, whose members form direct connection with hosts to withdraw water, nutrients, and macromolecules. Such intimate association is thought to increase the frequency of HGT. By transcriptome screening for foreign genes in Cuscuta australis, we discovered that one gene encoding a putative anthocyanin acyltransferase gene of the BAHD family, which is likely to be involved in anthocyanin modification, was acquired by C. australis from Fabaceae through HGT. The anthocyanin acyltransferase-like (AT-like gene was confirmed to be present in the genome assembly of C. australis and the transcriptomes of Cuscuta pentagona. The higher transcriptional level in old stems is consistent with its putative function in secondary metabolism by stabilizing anthocyanin at neutral pH and thus HGT of this AT-like gene may have improved biotic and abiotic resistance of Cuscuta.

Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi.

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Richards, Thomas A; Soanes, Darren M; Foster, Peter G; Leonard, Guy; Thornton, Christopher R; Talbot, Nicholas J

2009-07-01

Horizontal gene transfer (HGT) describes the transmission of genetic material across species boundaries and is an important evolutionary phenomenon in the ancestry of many microbes. The role of HGT in plant evolutionary history is, however, largely unexplored. Here, we compare the genomes of six plant species with those of 159 prokaryotic and eukaryotic species and identify 1689 genes that show the highest similarity to corresponding genes from fungi. We constructed a phylogeny for all 1689 genes identified and all homolog groups available from the rice (Oryza sativa) genome (3177 gene families) and used these to define 14 candidate plant-fungi HGT events. Comprehensive phylogenetic analyses of these 14 data sets, using methods that account for site rate heterogeneity, demonstrated support for nine HGT events, demonstrating an infrequent pattern of HGT between plants and fungi. Five HGTs were fungi-to-plant transfers and four were plant-to-fungi HGTs. None of the fungal-to-plant HGTs involved angiosperm recipients. These results alter the current view of organismal barriers to HGT, suggesting that phagotrophy, the consumption of a whole cell by another, is not necessarily a prerequisite for HGT between eukaryotes. Putative functional annotation of the HGT candidate genes suggests that two fungi-to-plant transfers have added phenotypes important for life in a soil environment. Our study suggests that genetic exchange between plants and fungi is exceedingly rare, particularly among the angiosperms, but has occurred during their evolutionary history and added important metabolic traits to plant lineages.

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

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Wolf Yuri I

2012-12-01

Full Text Available Abstract Background Collections of Clusters of Orthologous Genes (COGs provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs. Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. Results The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major ‘highways’ of horizontal gene transfer. Conclusions The updated collection

A method for evaluating horizontal well pumping tests.

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Langseth, David E; Smyth, Andrew H; May, James

2004-01-01

Predicting the future performance of horizontal wells under varying pumping conditions requires estimates of basic aquifer parameters, notably transmissivity and storativity. For vertical wells, there are well-established methods for estimating these parameters, typically based on either the recovery from induced head changes in a well or from the head response in observation wells to pumping in a test well. Comparable aquifer parameter estimation methods for horizontal wells have not been presented in the ground water literature. Formation parameter estimation methods based on measurements of pressure in horizontal wells have been presented in the petroleum industry literature, but these methods have limited applicability for ground water evaluation and are based on pressure measurements in only the horizontal well borehole, rather than in observation wells. This paper presents a simple and versatile method by which pumping test procedures developed for vertical wells can be applied to horizontal well pumping tests. The method presented here uses the principle of superposition to represent the horizontal well as a series of partially penetrating vertical wells. This concept is used to estimate a distance from an observation well at which a vertical well that has the same total pumping rate as the horizontal well will produce the same drawdown as the horizontal well. This equivalent distance may then be associated with an observation well for use in pumping test algorithms and type curves developed for vertical wells. The method is shown to produce good results for confined aquifers and unconfined aquifers in the absence of delayed yield response. For unconfined aquifers, the presence of delayed yield response increases the method error.

Cloning and sequence analysis of a partial CDS of leptospiral ligA gene in pET-32a - Escherichia coli DH5α system

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Manju Soman

2018-04-01

Full Text Available Aim: This study aims at cloning, sequencing, and phylogenetic analysis of a partial CDS of ligA gene in pET-32a - Escherichia coli DH5α system, with the objective of identifying the conserved nature of the ligA gene in the genus Leptospira. Materials and Methods: A partial CDS (nucleotide 1873 to nucleotide 3363 of the ligA gene was amplified from genomic DNA of Leptospira interrogans serovar Canicola by polymerase chain reaction (PCR. The PCR-amplified DNA was cloned into pET-32a vector and transformed into competent E. coli DH5α bacterial cells. The partial ligA gene insert was sequenced and the nucleotide sequences obtained were aligned with the published ligA gene sequences of other Leptospira serovars, using nucleotide BLAST, NCBI. Phylogenetic analysis of the gene sequence was done by maximum likelihood method using Mega 6.06 software. Results: The PCR could amplify the 1491 nucleotide sequence spanning from nucleotide 1873 to nucleotide 3363 of the ligA gene and the partial ligA gene could be successfully cloned in E. coli DH5α cells. The nucleotide sequence when analyzed for homology with the reported gene sequences of other Leptospira serovars was found to have 100% homology to the 1910 bp to 3320 bp sequence of ligA gene of L. interrogans strain Kito serogroup Canicola. The predicted protein consisted of 470 aminoacids. Phylogenetic analysis revealed that the ligA gene was conserved in L. interrogans species. Conclusion: The partial ligA gene could be successfully cloned and sequenced from E. coli DH5α cells. The sequence showed 100% homology to the published ligA gene sequences. The phylogenetic analysis revealed the conserved nature of the ligA gene. Further studies on the expression and immunogenicity of the partial LigA protein need to be carried out to determine its competence as a subunit vaccine candidate.

No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales.

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Gophna, Uri; Kristensen, David M; Wolf, Yuri I; Popa, Ovidiu; Drevet, Christine; Koonin, Eugene V

2015-09-01

The CRISPR (clustered, regularly, interspaced, short, palindromic repeats)-Cas (CRISPR-associated genes) systems of archaea and bacteria provide adaptive immunity against viruses and other selfish elements and are believed to curtail horizontal gene transfer (HGT). Limiting acquisition of new genetic material could be one of the sources of the fitness cost of CRISPR-Cas maintenance and one of the causes of the patchy distribution of CRISPR-Cas among bacteria, and across environments. We sought to test the hypothesis that the activity of CRISPR-Cas in microbes is negatively correlated with the extent of recent HGT. Using three independent measures of HGT, we found no significant dependence between the length of CRISPR arrays, which reflects the activity of the immune system, and the estimated number of recent HGT events. In contrast, we observed a significant negative dependence between the estimated extent of HGT and growth temperature of microbes, which could be explained by the lower genetic diversity in hotter environments. We hypothesize that the relevant events in the evolution of resistance to mobile elements and proclivity for HGT, to which CRISPR-Cas systems seem to substantially contribute, occur on the population scale rather than on the timescale of species evolution.

Contribution of horizontal gene transfer to the emergence of VIM-4 carbapenemase producer Enterobacteriaceae in Kuwait

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Sonnevend Á

2017-12-01

Full Text Available Ágnes Sonnevend,1 Nour Yahfoufi,1,2 Akela Ghazawi,1 Wafaa Jamal,3 Vincent Rotimi,3 Tibor Pál1 1Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, UAE; 2Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada; 3Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait Abstract: Carbapenem-resistant Enterobacteriaceae encountered in countries of the Arabian Peninsula usually produce OXA-48-like and New Delhi metallo-beta-lactamases (NDM carbapenemases. However, a temporary increase in VIM-4-producing, clonally unrelated Enterobacteriaceae strains was described earlier in a Kuwaiti hospital. We investigated the genetic support of blaVIM-4 in six Klebsiella pneumoniae strains, one Escherichia coli, and one Enterobacter cloacae strain and compared it to that of VIM-4-producing isolates from other countries of the region. Five K. pneumoniae strains and the E. coli strain from Kuwait carried an ~165 kb IncA/C-type plasmid indistinguishable by restriction fragment length polymorphism. The complete sequence of one of them (pKKp4-VIM was established. pKKp4-VIM exhibited extensive similarities to episomes pKP-Gr642 carrying blaVIM-19 encountered in Greece and to the partially sequenced pCC416 harboring blaVIM-4 detected in Italy. In other countries of the region, the only similar plasmid was the one detected in the isolate from the UAE. In all Kuwaiti strains, irrespective of the species and their VIM plasmids, the blaVIM-4 gene was located within the same integron structure (In416, different from those of other countries of the region. Our data show that the spread of this IncA/C plasmid and particularly that of the In416 integron caused a considerable, albeit temporary, increase in the rate of mostly clonally unrelated VIM-producing Enterobacteriaceae strains of multiple species

Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes.

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Todd J Treangen

2011-01-01

Full Text Available Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. While there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families. We analyzed closely related prokaryote strains or species with small genomes (Helicobacter, Neisseria, Streptococcus, Sulfolobus, average-sized genomes (Bacillus, Enterobacteriaceae, and large genomes (Pseudomonas, Bradyrhizobiaceae to untangle the effects of duplication and horizontal transfer. After removing the effects of transposable elements and phages, we show that the vast majority of expansions of protein families are due to transfer, even among large genomes. Transferred genes--xenologs--persist longer in prokaryotic lineages possibly due to a higher/longer adaptive role. On the other hand, duplicated genes--paralogs--are expressed more, and, when persistent, they evolve slower. This suggests that gene transfer and gene duplication have very different roles in shaping the evolution of biological systems: transfer allows the acquisition of new functions and duplication leads to higher gene dosage. Accordingly, we show that paralogs share most protein-protein interactions and genetic regulators, whereas xenologs share very few of them. Prokaryotes invented most of life's biochemical diversity. Therefore, the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families.

Outbreak tracking of Aleutian mink disease virus (AMDV) using partial NS1 gene sequencing

DEFF Research Database (Denmark)

Ryt-Hansen, Pia; Hjulsager, Charlotte Kristiane; Hagberg, E. E.

2017-01-01

. However, in 2015, several outbreaks of AMDV occurred at mink farms throughout Denmark, and the sources of these outbreaks were not known. Partial NS1 gene sequencing, phylogenetic analyses data were utilized along with epidemiological to determine the origin of the outbreaks. The phylogenetic analyses...... not be excluded. This study confirmed that partial NS1 sequencing can be used in outbreak tracking to determine major viral clusters of AMDV. Using this method, two new distinct AMDV clusters with low intra-cluster sequence diversity were identified, and epidemiological data helped to reveal possible ways...

Changes in Gene Expression of Arabidopsis Thaliana Cell Cultures Upon Exposure to Real and Simulated Partial- g Forces

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Fengler, Svenja; Spirer, Ina; Neef, Maren; Ecke, Margret; Hauslage, Jens; Hampp, Rüdiger

2016-06-01

Cell cultures of the plant model organism Arabidopsis thaliana were exposed to partial- g forces during parabolic flight and clinostat experiments (0.16 g, 0.38 g and 0.5 g were tested). In order to investigate gravity-dependent alterations in gene expression, samples were metabolically quenched by the fixative RNA later Ⓡ to stabilize nucleic acids and used for whole-genome microarray analysis. An attempt to identify the potential threshold acceleration for the gravity-dependent response showed that the smaller the experienced g-force, the greater was the susceptibility of the cell cultures. Compared to short-term μ g during a parabolic flight, the number of differentially expressed genes under partial- g was lower. In addition, the effect on the alteration of amounts of transcripts decreased during partial- g parabolic flight due to the sequence of the different parabolas (0.38 g, 0.16 g and μ g). A time-dependent analysis under simulated 0.5 g indicates that adaptation occurs within minutes. Differentially expressed genes (at least 2-fold up- or down-regulated in expression) under real flight conditions were to some extent identical with those affected by clinorotation. The highest number of homologuous genes was detected within seconds of exposure to 0.38 g (both flight and clinorotation). To a considerable part, these genes deal with cell wall properties. Additionally, responses specific for clinorotation were observed.

Directed partial correlation: inferring large-scale gene regulatory network through induced topology disruptions.

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Yinyin Yuan

Full Text Available Inferring regulatory relationships among many genes based on their temporal variation in transcript abundance has been a popular research topic. Due to the nature of microarray experiments, classical tools for time series analysis lose power since the number of variables far exceeds the number of the samples. In this paper, we describe some of the existing multivariate inference techniques that are applicable to hundreds of variables and show the potential challenges for small-sample, large-scale data. We propose a directed partial correlation (DPC method as an efficient and effective solution to regulatory network inference using these data. Specifically for genomic data, the proposed method is designed to deal with large-scale datasets. It combines the efficiency of partial correlation for setting up network topology by testing conditional independence, and the concept of Granger causality to assess topology change with induced interruptions. The idea is that when a transcription factor is induced artificially within a gene network, the disruption of the network by the induction signifies a genes role in transcriptional regulation. The benchmarking results using GeneNetWeaver, the simulator for the DREAM challenges, provide strong evidence of the outstanding performance of the proposed DPC method. When applied to real biological data, the inferred starch metabolism network in Arabidopsis reveals many biologically meaningful network modules worthy of further investigation. These results collectively suggest DPC is a versatile tool for genomics research. The R package DPC is available for download (http://code.google.com/p/dpcnet/.

Integrating Horizontal Gene Transfer and Common Descent to Depict Evolution and Contrast It with “Common Design”1

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GUILLERMO PAZ-Y-MIÑO-C; ESPINOSA, AVELINA

2016-01-01

Horizontal gene transfer (HGT) and common descent interact in space and time. Because events of HGT co-occur with phylogenetic evolution, it is difficult to depict evolutionary patterns graphically. Tree-like representations of life’s diversification are useful, but they ignore the significance of HGT in evolutionary history, particularly of unicellular organisms, ancestors of multicellular life. Here we integrate the reticulated-tree model, ring of life, symbiogenesis whole-organism model, and eliminative pattern pluralism to represent evolution. Using Entamoeba histolytica alcohol dehydrogenase 2 (EhADH2), a bifunctional enzyme in the glycolytic pathway of amoeba, we illustrate how EhADH2 could be the product of both horizontally acquired features from ancestral prokaryotes (i.e. aldehyde dehydrogenase [ALDH] and alcohol dehydrogenase [ADH]), and subsequent functional integration of these enzymes into EhADH2, which is now inherited by amoeba via common descent. Natural selection has driven the evolution of EhADH2 active sites, which require specific amino acids (cysteine 252 in the ALDH domain; histidine 754 in the ADH domain), iron- and NAD+ as cofactors, and the substrates acetyl-CoA for ALDH and acetaldehyde for ADH. Alternative views invoking “common design” (i.e. the non-naturalistic emergence of major taxa independent from ancestry) to explain the interaction between horizontal and vertical evolution are unfounded. PMID:20021546

Horizontal gene acquisition of Liberibacter plant pathogens from a bacteriome-confined endosymbiont of their psyllid vector.

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Atsushi Nakabachi

Full Text Available he Asian citrus psyllid Diaphorina citri is a notorious agricultural pest that transmits the phloem-inhabiting alphaproteobacterial 'Candidatus Liberibacter asiaticus' and allied plant pathogens, which cause the devastating citrus disease called Huanglongbing or greening disease. D. citri harbors two distinct bacterial mutualists in the symbiotic organ called bacteriome: the betaproteobacterium 'Candidatus Profftella armatura' in the syncytial cytoplasm at the center of the bacteriome, and the gammaproteobacterium 'Candidatus Carsonella ruddii' in uninucleate bacteriocytes. Here we report that a putative amino acid transporter LysE of Profftella forms a highly supported clade with proteins of L. asiaticus, L. americanus, and L. solanacearum. L. crescens, the most basal Liberibacter lineage currently known, lacked the corresponding gene. The Profftella-Liberibacter subclade of LysE formed a clade with proteins from betaproteobacteria of the order Burkholderiales, to which Profftella belongs. This phylogenetic pattern favors the hypothesis that the Liberibacter lineage acquired the gene from the Profftella lineage via horizontal gene transfer (HGT after L. crescens diverged from other Liberibacter lineages. K A/K S analyses further supported the hypothesis that the genes encoded in the Liberibacter genomes are functional. These findings highlight the possible evolutionary importance of HGT between plant pathogens and their insect vector's symbionts that are confined in the symbiotic organ and seemingly sequestered from external microbial populations.

Horizontal gene transfer from macrophages to ischemic muscles upon delivery of naked DNA with Pluronic block copolymers.

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Mahajan, Vivek; Gaymalov, Zagit; Alakhova, Daria; Gupta, Richa; Zucker, Irving H; Kabanov, Alexander V

2016-01-01

Intramuscular administration of plasmid DNA (pDNA) with non-ionic Pluronic block copolymers increases gene expression in injected muscles and lymphoid organs. We studied the role of immune cells in muscle transfection upon inflammation. Local inflammation in murine hind limb ischemia model (MHLIM) drastically increased DNA, RNA and expressed protein levels in ischemic muscles injected with pDNA/Pluronic. The systemic inflammation (MHLIM or peritonitis) also increased expression of pDNA/Pluronic in the muscles. When pDNA/Pluronic was injected in ischemic muscles the reporter gene, Green Fluorescent Protein (GFP) co-localized with desmin(+) muscle fibers and CD11b(+) macrophages (MØs), suggesting transfection of MØs along with the muscle cells. P85 enhanced (∼ 4 orders) transfection of MØs with pDNA in vitro. Moreover, adoptively transferred MØs were shown to pass the transgene to inflamed muscle cells in MHLIM. Using a co-culture of myotubes (MTs) and transfected MØs expressing a reporter gene under constitutive (cmv-luciferase) or muscle specific (desmin-luciferase) promoter we demonstrated that P85 enhances horizontal gene transfer from MØ to MTs. Therefore, MØs can play an important role in muscle transfection with pDNA/Pluronic during inflammation, with both inflammation and Pluronic contributing to the increased gene expression. pDNA/Pluronic has potential for therapeutic gene delivery in muscle pathologies that involve inflammation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

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Corinne Rancurel

2017-09-01

Full Text Available Horizontal gene transfer (HGT is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr. Alienness parses BLAST results against public libraries to rapidly identify candidate HGT in any genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any National Center for Biotechnology Information (NCBI protein library. The user defines recipient (e.g., Metazoa and donor (e.g., bacteria, fungi branches of interest in the NCBI taxonomy. Based on the best BLAST E-values of candidate donor and recipient taxa, Alienness calculates an Alien Index (AI for each query protein. An AI > 0 indicates a better hit to candidate donor than recipient taxa and a possible HGT. Higher AI represent higher gap of E-values between candidate donor and recipient and a more likely HGT. We confirmed the accuracy of Alienness on phylogenetically confirmed HGT of non-metazoan origin in plant-parasitic nematodes. Alienness scans whole proteomes to rapidly identify possible HGT in any species of interest and thus fosters exploration of HGT more easily and largely across the tree of life.

In situ detection of horizontal transfer of mobile genetic elements

DEFF Research Database (Denmark)

Haagensen, Janus Anders Juul; Hansen, Susse Kirkelund; Johansen, Tove

2002-01-01

. The obtained data show that the several different types of fluorescent reporters, which are now available, allow more informative in situ investigations of horizontal gene transfer to be carried out, and by combining these genes with various expression systems it is possible to simultaneously monitor donor...

Changes in Contact Area in Meniscus Horizontal Cleavage Tears Subjected to Repair and Resection.

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Beamer, Brandon S; Walley, Kempland C; Okajima, Stephen; Manoukian, Ohan S; Perez-Viloria, Miguel; DeAngelis, Joseph P; Ramappa, Arun J; Nazarian, Ara

2017-03-01

To assess the changes in tibiofemoral contact pressure and contact area in human knees with a horizontal cleavage tear before and after treatment. Ten human cadaveric knees were tested. Pressure sensors were placed under the medial meniscus and the knees were loaded at twice the body weight for 20 cycles at 0°, 10°, and 20° of flexion. Contact area and pressure were recorded for the intact meniscus, the meniscus with a horizontal cleavage tear, after meniscal repair, after partial meniscectomy (single leaflet), and after subtotal meniscectomy (double leaflet). The presence of a horizontal cleavage tear significantly increased average peak contact pressure and reduced effective average tibiofemoral contact area at all flexion angles tested compared with the intact state (P contact pressure after creation of the horizontal cleavage tear. Repairing the horizontal cleavage tear restored peak contact pressures and areas to within 15% of baseline, statistically similar to the intact state at all angles tested (P contact pressure and reduced average contact area at all degrees of flexion compared with the intact state (P contact area and a significant elevation in contact pressure. These changes may accelerate joint degeneration. A suture-based repair of these horizontal cleavage tears returns the contact area and contact pressure to nearly normal, whereas both partial and subtotal meniscectomy lead to significant reductions in contact area and significant elevations in contact pressure within the knee. Repairing horizontal cleavage tears may lead to improved clinical outcomes by preserving meniscal tissue and the meniscal function. Understanding contact area and peak contact pressure resulting from differing strategies for treating horizontal cleavage tears will allow the surgeon to evaluate the best strategy for treating his or her patients who present with this meniscal pathology. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier

[On the recurrence risk with partial larynx resections (author's transl)].

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Flach, M

1978-06-01

28 cases of recurrences after 127 vertical and horizontal partial larynx resections (22 per cent) were analysed. Unfavourable preconditions for partial resections are the affliction of the ary cartilage and arrest of vocal chord movility. The hemiresections according to Hautant have the heighest recidivation percentage (40 per cent) judging from the observations available. Radical operations after failured partial resections are uncertain as to their prognoses.

A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land.

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Emiliani, Giovanni; Fondi, Marco; Fani, Renato; Gribaldo, Simonetta

2009-02-16

The pioneering ancestor of land plants that conquered terrestrial habitats around 500 million years ago had to face dramatic stresses including UV radiation, desiccation, and microbial attack. This drove a number of adaptations, among which the emergence of the phenylpropanoid pathway was crucial, leading to essential compounds such as flavonoids and lignin. However, the origin of this specific land plant secondary metabolism has not been clarified. We have performed an extensive analysis of the taxonomic distribution and phylogeny of Phenylalanine Ammonia Lyase (PAL), which catalyses the first and essential step of the general phenylpropanoid pathway, leading from phenylalanine to p-Coumaric acid and p-Coumaroyl-CoA, the entry points of the flavonoids and lignin routes. We obtained robust evidence that the ancestor of land plants acquired a PAL via horizontal gene transfer (HGT) during symbioses with soil bacteria and fungi that are known to have established very early during the first steps of land colonization. This horizontally acquired PAL represented then the basis for further development of the phenylpropanoid pathway and plant radiation on terrestrial environments. Our results highlight a possible crucial role of HGT from soil bacteria in the path leading to land colonization by plants and their subsequent evolution. The few functional characterizations of sediment/soil bacterial PAL (production of secondary metabolites with powerful antimicrobial activity or production of pigments) suggest that the initial advantage of this horizontally acquired PAL in the ancestor of land plants might have been either defense against an already developed microbial community and/or protection against UV.

Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions [version 1; referees: 2 approved

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Eugene V. Koonin

2016-07-01

Full Text Available The wide spread of gene exchange and loss in the prokaryotic world has prompted the concept of ‘lateral genomics’ to the point of an outright denial of the relevance of phylogenetic trees for evolution. However, the pronounced coherence congruence of the topologies of numerous gene trees, particularly those for (nearly universal genes, translates into the notion of a statistical tree of life (STOL, which reflects a central trend of vertical evolution. The STOL can be employed as a framework for reconstruction of the evolutionary processes in the prokaryotic world. Quantitatively, however, horizontal gene transfer (HGT dominates microbial evolution, with the rate of gene gain and loss being comparable to the rate of point mutations and much greater than the duplication rate. Theoretical models of evolution suggest that HGT is essential for the survival of microbial populations that otherwise deteriorate due to the Muller’s ratchet effect. Apparently, at least some bacteria and archaea evolved dedicated vehicles for gene transfer that evolved from selfish elements such as plasmids and viruses. Recent phylogenomic analyses suggest that episodes of massive HGT were pivotal for the emergence of major groups of organisms such as multiple archaeal phyla as well as eukaryotes. Similar analyses appear to indicate that, in addition to donating hundreds of genes to the emerging eukaryotic lineage, mitochondrial endosymbiosis severely curtailed HGT. These results shed new light on the routes of evolutionary transitions, but caution is due given the inherent uncertainty of deep phylogenies.

Impaired expression of mitochondrial and adipogenic genes in adipose tissue from a patient with acquired partial lipodystrophy (Barraquer-Simons syndrome: a case report

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Guallar Jordi P

2008-08-01

Full Text Available Abstract Introduction Acquired partial lipodystrophy or Barraquer-Simons syndrome is a rare form of progressive lipodystrophy. The etiopathogenesis of adipose tissue atrophy in these patients is unknown. Case presentation This is a case report of a 44-year-old woman with acquired partial lipodystrophy. To obtain insight into the molecular basis of lipoatrophy in acquired partial lipodystrophy, we examined gene expression in adipose tissue from this patient newly diagnosed with acquired partial lipodystrophy. A biopsy of subcutaneous adipose tissue was obtained from the patient, and DNA and RNA were extracted in order to evaluate mitochondrial DNA abundance and mRNA expression levels. Conclusion The expression of marker genes of adipogenesis and adipocyte metabolism, including the master regulator PPARγ, was down-regulated in subcutaneous adipose tissue from this patient. Adiponectin mRNA expression was also reduced but leptin mRNA levels were unaltered. Markers of local inflammatory status were unaltered. Expression of genes related to mitochondrial function was reduced despite unaltered levels of mitochondrial DNA. It is concluded that adipogenic and mitochondrial gene expression is impaired in adipose tissue in this patient with acquired partial lipodystrophy.

An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters

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Palmer Jeffrey D

2006-09-01

Full Text Available Abstract Background Horizontal gene transfer (HGT to the plant mitochondrial genome has recently been shown to occur at a surprisingly high rate; however, little evidence has been found for HGT to the plastid genome, despite extensive sequencing. In this study, we analyzed all genes from sequenced plastid genomes to unearth any neglected cases of HGT and to obtain a measure of the overall extent of HGT to the plastid. Results Although several genes gave strongly supported conflicting trees under certain conditions, we are confident of HGT in only a single case beyond the rubisco HGT already reported. Most of the conflicts involved near neighbors connected by long branches (e.g. red algae and their secondary hosts, where phylogenetic methods are prone to mislead. However, three genes – clpP, ycf2, and rpl36 – provided strong support for taxa moving far from their organismal position. Further taxon sampling of clpP and ycf2 resulted in rejection of HGT due to long-branch attraction and a serious error in the published plastid genome sequence of Oenothera elata, respectively. A single new case, a bacterial rpl36 gene transferred into the ancestor of the cryptophyte and haptophyte plastids, appears to be a true HGT event. Interestingly, this rpl36 gene is a distantly related paralog of the rpl36 type found in other plastids and most eubacteria. Moreover, the transferred gene has physically replaced the native rpl36 gene, yet flanking genes and intergenic regions show no sign of HGT. This suggests that gene replacement somehow occurred by recombination at the very ends of rpl36, without the level and length of similarity normally expected to support recombination. Conclusion The rpl36 HGT discovered in this study is of considerable interest in terms of both molecular mechanism and phylogeny. The plastid acquisition of a bacterial rpl36 gene via HGT provides the first strong evidence for a sister-group relationship between haptophyte and

An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters

Science.gov (United States)

Rice, Danny W; Palmer, Jeffrey D

2006-01-01

Background Horizontal gene transfer (HGT) to the plant mitochondrial genome has recently been shown to occur at a surprisingly high rate; however, little evidence has been found for HGT to the plastid genome, despite extensive sequencing. In this study, we analyzed all genes from sequenced plastid genomes to unearth any neglected cases of HGT and to obtain a measure of the overall extent of HGT to the plastid. Results Although several genes gave strongly supported conflicting trees under certain conditions, we are confident of HGT in only a single case beyond the rubisco HGT already reported. Most of the conflicts involved near neighbors connected by long branches (e.g. red algae and their secondary hosts), where phylogenetic methods are prone to mislead. However, three genes – clpP, ycf2, and rpl36 – provided strong support for taxa moving far from their organismal position. Further taxon sampling of clpP and ycf2 resulted in rejection of HGT due to long-branch attraction and a serious error in the published plastid genome sequence of Oenothera elata, respectively. A single new case, a bacterial rpl36 gene transferred into the ancestor of the cryptophyte and haptophyte plastids, appears to be a true HGT event. Interestingly, this rpl36 gene is a distantly related paralog of the rpl36 type found in other plastids and most eubacteria. Moreover, the transferred gene has physically replaced the native rpl36 gene, yet flanking genes and intergenic regions show no sign of HGT. This suggests that gene replacement somehow occurred by recombination at the very ends of rpl36, without the level and length of similarity normally expected to support recombination. Conclusion The rpl36 HGT discovered in this study is of considerable interest in terms of both molecular mechanism and phylogeny. The plastid acquisition of a bacterial rpl36 gene via HGT provides the first strong evidence for a sister-group relationship between haptophyte and cryptophyte plastids to the

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.

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Raquel Bromberg

2016-06-01

Full Text Available Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz.

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

Science.gov (United States)

Grishin, Nick V.; Otwinowski, Zbyszek

2016-01-01

Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz. PMID:27336403

Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria.

Science.gov (United States)

Bershtein, Shimon; Serohijos, Adrian W R; Bhattacharyya, Sanchari; Manhart, Michael; Choi, Jeong-Mo; Mu, Wanmeng; Zhou, Jingwen; Shakhnovich, Eugene I

2015-10-01

Horizontal gene transfer (HGT) plays a central role in bacterial evolution, yet the molecular and cellular constraints on functional integration of the foreign genes are poorly understood. Here we performed inter-species replacement of the chromosomal folA gene, encoding an essential metabolic enzyme dihydrofolate reductase (DHFR), with orthologs from 35 other mesophilic bacteria. The orthologous inter-species replacements caused a marked drop (in the range 10-90%) in bacterial growth rate despite the fact that most orthologous DHFRs are as stable as E.coli DHFR at 37°C and are more catalytically active than E. coli DHFR. Although phylogenetic distance between E. coli and orthologous DHFRs as well as their individual molecular properties correlate poorly with growth rates, the product of the intracellular DHFR abundance and catalytic activity (kcat/KM), correlates strongly with growth rates, indicating that the drop in DHFR abundance constitutes the major fitness barrier to HGT. Serial propagation of the orthologous strains for ~600 generations dramatically improved growth rates by largely alleviating the fitness barriers. Whole genome sequencing and global proteome quantification revealed that the evolved strains with the largest fitness improvements have accumulated mutations that inactivated the ATP-dependent Lon protease, causing an increase in the intracellular DHFR abundance. In one case DHFR abundance increased further due to mutations accumulated in folA promoter, but only after the lon inactivating mutations were fixed in the population. Thus, by apparently distinguishing between self and non-self proteins, protein homeostasis imposes an immediate and global barrier to the functional integration of foreign genes by decreasing the intracellular abundance of their products. Once this barrier is alleviated, more fine-tuned evolution occurs to adjust the function/expression of the transferred proteins to the constraints imposed by the intracellular

Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria.

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Shimon Bershtein

2015-10-01

Full Text Available Horizontal gene transfer (HGT plays a central role in bacterial evolution, yet the molecular and cellular constraints on functional integration of the foreign genes are poorly understood. Here we performed inter-species replacement of the chromosomal folA gene, encoding an essential metabolic enzyme dihydrofolate reductase (DHFR, with orthologs from 35 other mesophilic bacteria. The orthologous inter-species replacements caused a marked drop (in the range 10-90% in bacterial growth rate despite the fact that most orthologous DHFRs are as stable as E.coli DHFR at 37°C and are more catalytically active than E. coli DHFR. Although phylogenetic distance between E. coli and orthologous DHFRs as well as their individual molecular properties correlate poorly with growth rates, the product of the intracellular DHFR abundance and catalytic activity (kcat/KM, correlates strongly with growth rates, indicating that the drop in DHFR abundance constitutes the major fitness barrier to HGT. Serial propagation of the orthologous strains for ~600 generations dramatically improved growth rates by largely alleviating the fitness barriers. Whole genome sequencing and global proteome quantification revealed that the evolved strains with the largest fitness improvements have accumulated mutations that inactivated the ATP-dependent Lon protease, causing an increase in the intracellular DHFR abundance. In one case DHFR abundance increased further due to mutations accumulated in folA promoter, but only after the lon inactivating mutations were fixed in the population. Thus, by apparently distinguishing between self and non-self proteins, protein homeostasis imposes an immediate and global barrier to the functional integration of foreign genes by decreasing the intracellular abundance of their products. Once this barrier is alleviated, more fine-tuned evolution occurs to adjust the function/expression of the transferred proteins to the constraints imposed by the

Evidence of recent interspecies horizontal gene transfer regarding nucleopolyhedrovirus infection of Spodoptera frugiperda.

Science.gov (United States)

Barrera, Gloria Patricia; Belaich, Mariano Nicolás; Patarroyo, Manuel Alfonso; Villamizar, Laura Fernanda; Ghiringhelli, Pablo Daniel

2015-11-25

Baculoviruses are insect-associated viruses carrying large, circular double-stranded-DNA genomes with significant biotechnological applications such as biological pest control, recombinant protein production, gene delivery in mammals and as a model of DNA genome evolution. These pathogens infect insects from the orders Lepidoptera, Hymenoptera and Diptera, and have high species diversity which is expressed in their diverse biological properties including morphology, virulence or pathogenicity. Spodoptera frugiperda (Lepidoptera: Noctuidae), the fall armyworm, represents a significant pest for agriculture in America; it is a host for baculoviruses such as the Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) (Colombia strain, genotype A) having been classified as a Group II alphabaculovirus making it a very attractive target for bioinsecticidal use. Genome analysis by pyrosequencing revealed that SfMNPV ColA has 145 ORFs, 2 of which were not present in the other sequenced genotypes of the virus (SfMNPV-NicB, SfMNPV-NicG, SfMNPV-19 and SfMNPV-3AP2). An in-depth bioinformatics study showed that ORF023 and ORF024 were acquired by a recent homologous recombination process between Spodoptera frugiperda and Spodoptera litura (the Oriental leafworm moth) nucleopolyhedroviruses. Auxiliary genes are numerous in the affected locus which has a homologous region (hr3), a repetitive sequence associated with genome replication which became lost in SfColA along with 1 ORF. Besides, the mRNAs associated with two acquired genes appeared in the virus' life-cycle during the larval stage. Predictive studies concerning the theoretical proteins identified that ORF023 protein would be a phosphatase involved in DNA repair and that the ORF024 protein would be a membrane polypeptide associated with cell transport. The SfColA genome was thus revealed to be a natural recombinant virus showing evidence of recent horizontal gene transfer between different baculovirus species occurring

Gene loss and horizontal gene transfer contributed to the genome evolution of the extreme acidophile Ferrovum

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Sophie Roxana Ullrich

2016-05-01

Full Text Available Acid mine drainage (AMD, associated with active and abandoned mining sites, is a habitat for acidophilic microorganisms that gain energy from the oxidation of reduced sulfur compounds and ferrous iron and that thrive at pH below 4. Members of the recently proposed genus Ferrovum are the first acidophilic iron oxidizers to be described within the Betaproteobacteria. Although they have been detected as typical community members in AMD habitats worldwide, knowledge of their phylogenetic and metabolic diversity is scarce. Genomics approaches appear to be most promising in addressing this lacuna since isolation and cultivation of Ferrovum has proven to be extremely difficult and has so far only been successful for the designated type strain Ferrovum myxofaciens P3G. In this study, the genomes of two novel strains of Ferrovum (PN-J185 and Z-31 derived from water samples of a mine water treatment plant were sequenced. These genomes were compared with those of Ferrovum sp. JA12 that also originated from the mine water treatment plant, and of the type strain (P3G. Phylogenomic scrutiny suggests that the four strains represent three Ferrovum species that cluster in two groups (1 and 2. Comprehensive analysis of their predicted metabolic pathways revealed that these groups harbor characteristic metabolic profiles, notably with respect to motility, chemotaxis, nitrogen metabolism, biofilm formation and their potential strategies to cope with the acidic environment. For example, while the F. myxofaciens strains (group 1 appear to be motile and diazotrophic, the non-motile group 2 strains have the predicted potential to use a greater variety of fixed nitrogen sources. Furthermore, analysis of their genome synteny provides first insights into their genome evolution, suggesting that horizontal gene transfer and genome reduction in the group 2 strains by loss of genes encoding complete metabolic pathways or physiological features contributed to the observed

Horizontal vibrations of piles in a centrifuge

International Nuclear Information System (INIS)

Bourdin, B.

1987-01-01

The aim of the thesis is the study of soil dynamics for important structures like nuclear power plants, offshore platforms, dams etc. Experimental results of horizontal vibrations on a pile partially anchored in a soil scale model put into a centrifuge are presented. Mechanical similitude conditions from equilibrium equations or rheologic laws are described. After a description of testing equipment (centrifuge, electrodynamic excitator) experimental results are interpreted with a model. Non-linearities on frequency response curves are characterized [fr

Response of horizontal magnetic field variation to partial counter electrojet

International Nuclear Information System (INIS)

Mukunda Rao, M.; Alamelu, V.

1985-01-01

The partial counter electrojet events seen through backscatter observations are examined in terms of the parameter ΔH'sub(CEJ)=(Hsub(equator)-Hsub(low lat.))sub(CEJday)-(Hsub(equator)-Hsub(low lat.))sub(mean 1Qday). It is found that the parameter indicates most of the changes in the electrojet observed through the backscatter observations. (author)

Transcriptome analysis highlights defense and signaling pathways mediated by rice pi21 gene with partial resistance to Magnaporthe oryzae

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Yu Zhang

2016-12-01

Full Text Available Rice blast disease is one of the most destructive rice diseases worldwide. The pi21 gene confers partial and durable resistance to Magnaporthe oryzae. However, little is known regarding the molecular mechanisms of resistance mediated by the loss-of-function of Pi21. In this study, comparative transcriptome profiling of the Pi21-RNAi transgenic rice line and Nipponbare with M. oryzae infection at different time points (0, 12, 24, 48, and 72 hpi were investigated using RNA sequencing. The results generated 43,222 unique genes mapped to the rice genome. In total, 1,109 differentially expressed genes (DEGs were identified between the Pi21-RNAi line and Nipponbare with M. oryzae infection, with 103, 281, 209, 69, and 678 DEGs at 0, 12, 24, 48, and 72 hpi, respectively. Functional analysis showed that most of the DEGs were involved in metabolism, transport, signaling, and defense. Among the genes assigned to plant–pathogen interaction, we identified 43 receptor kinase genes associated with pathogen-associated molecular pattern recognition and calcium ion influx. The expression levels of brassinolide-insensitive 1, flagellin sensitive 2 and elongation factor Tu receptor, ethylene (ET biosynthesis and signaling genes, were higher in the Pi21-RNAi line than Nipponbare. This suggested that there was a more robust PTI response in Pi21-RNAi plants and that ET signaling was important to rice blast resistance. We also identified 53 transcription factor genes, including WRKY, NAC, DOF, and ERF families that show differential expression between the two genotypes. This study highlights possible candidate genes that may serve a function in the partial rice blast resistance mediated by the loss-of-function of Pi21 and increase our understanding of the molecular mechanisms involved in partial resistance against M. oryzae.

Assessment of the horizontal transfer of functional genes as a suitable approach for evaluation of the bioremediation potential of petroleum-contaminated sites: a mini-review.

Science.gov (United States)

Shahi, Aiyoub; Ince, Bahar; Aydin, Sevcan; Ince, Orhan

2017-06-01

Petroleum sludge contains recalcitrant residuals. These compounds because of being toxic to humans and other organism are of the major concerns. Therefore, petroleum sludge should be safely disposed. Physicochemical methods which are used by this sector are mostly expensive and need complex devices. Bioremediation methods because of being eco-friendly and cost-effective overcome most of the limitations of physicochemical treatments. Microbial strains capable to degrade petroleum hydrocarbons are practically present in all soils and sediments and their population density increases in contact with contaminants. Bacterial strains cannot degrade alone all kinds of petroleum hydrocarbons, rather microbial consortium should collaborate with each other for degradation of petroleum hydrocarbon mixtures. Horizontal transfer of functional genes between bacteria plays an important role in increasing the metabolic potential of the microbial community. Therefore, selecting a suitable degrading gene and tracking its horizontal transfer would be a useful approach to evaluate the bioremediation process and to assess the bioremediation potential of contaminated sites.

Wetting phase permeability in a partially saturated horizontal fracture

International Nuclear Information System (INIS)

Nicholl, M.J.; Glass, R.J.

1994-01-01

Fractures within geologic media can dominate the hydraulic properties of the system. Therefore, conceptual models used to assess the potential for radio-nuclide migration in unsaturated fractured rock such as that composing Yucca Mountain, Nevada, must be consistent with flow processes in individual fractures. A major obstacle to the understanding and simulation of unsaturated fracture flow is the paucity of physical data on both fracture aperture structure and relative permeability. An experimental procedure is developed for collecting detailed data on aperture and phase structure from a transparent analog fracture. To facilitate understanding of basic processes and provide a basis for development of effective property models, the simplest possible rough-walled fracture is used. Stable phase structures of varying complexity are created within the horizontal analog fracture. Wetting phase permeability is measured under steady-state conditions. A process based model for wetting phase relative permeability is then explored. Contributions of the following processes to reduced wetting phase permeability under unsaturated conditions are considered: reduction in cross-sectional flow area, increased path length, localized flow restriction, and preferential occupation of large apertures by the non-wetting phase

H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes.

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Koichi Higashi

2016-01-01

Full Text Available Bacteria can acquire new traits through horizontal gene transfer. Inappropriate expression of transferred genes, however, can disrupt the physiology of the host bacteria. To reduce this risk, Escherichia coli expresses the nucleoid-associated protein, H-NS, which preferentially binds to horizontally transferred genes to control their expression. Once expression is optimized, the horizontally transferred genes may actually contribute to E. coli survival in new habitats. Therefore, we investigated whether and how H-NS contributes to this optimization process. A comparison of H-NS binding profiles on common chromosomal segments of three E. coli strains belonging to different phylogenetic groups indicated that the positions of H-NS-bound regions have been conserved in E. coli strains. The sequences of the H-NS-bound regions appear to have diverged more so than H-NS-unbound regions only when H-NS-bound regions are located upstream or in coding regions of genes. Because these regions generally contain regulatory elements for gene expression, sequence divergence in these regions may be associated with alteration of gene expression. Indeed, nucleotide substitutions in H-NS-bound regions of the ybdO promoter and coding regions have diversified the potential for H-NS-independent negative regulation among E. coli strains. The ybdO expression in these strains was still negatively regulated by H-NS, which reduced the effect of H-NS-independent regulation under normal growth conditions. Hence, we propose that, during E. coli evolution, the conservation of H-NS binding sites resulted in the diversification of the regulation of horizontally transferred genes, which may have facilitated E. coli adaptation to new ecological niches.

H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes.

Science.gov (United States)

Higashi, Koichi; Tobe, Toru; Kanai, Akinori; Uyar, Ebru; Ishikawa, Shu; Suzuki, Yutaka; Ogasawara, Naotake; Kurokawa, Ken; Oshima, Taku

2016-01-01

Bacteria can acquire new traits through horizontal gene transfer. Inappropriate expression of transferred genes, however, can disrupt the physiology of the host bacteria. To reduce this risk, Escherichia coli expresses the nucleoid-associated protein, H-NS, which preferentially binds to horizontally transferred genes to control their expression. Once expression is optimized, the horizontally transferred genes may actually contribute to E. coli survival in new habitats. Therefore, we investigated whether and how H-NS contributes to this optimization process. A comparison of H-NS binding profiles on common chromosomal segments of three E. coli strains belonging to different phylogenetic groups indicated that the positions of H-NS-bound regions have been conserved in E. coli strains. The sequences of the H-NS-bound regions appear to have diverged more so than H-NS-unbound regions only when H-NS-bound regions are located upstream or in coding regions of genes. Because these regions generally contain regulatory elements for gene expression, sequence divergence in these regions may be associated with alteration of gene expression. Indeed, nucleotide substitutions in H-NS-bound regions of the ybdO promoter and coding regions have diversified the potential for H-NS-independent negative regulation among E. coli strains. The ybdO expression in these strains was still negatively regulated by H-NS, which reduced the effect of H-NS-independent regulation under normal growth conditions. Hence, we propose that, during E. coli evolution, the conservation of H-NS binding sites resulted in the diversification of the regulation of horizontally transferred genes, which may have facilitated E. coli adaptation to new ecological niches.

Isolation, cloning, and characterization of a partial novel aro A gene in common reed (Phragmites australis).

Science.gov (United States)

Taravat, Elham; Zebarjadi, Alireza; Kahrizi, Danial; Yari, Kheirollah

2015-05-01

Among the essential amino acids, phenylalanine, tryptophan, and tyrosine are aromatic amino acids which are synthesized by the shikimate pathway in plants and bacteria. Herbicide glyphosate can inhibit the biosynthesis of these amino acids. So, identification of the gene tolerant to glyphosate is very important. It has been shown that the common reed or Phragmites australis Cav. (Poaceae) is relatively tolerant to glyphosate. The aim of the current research is identification, cloning, sequencing, and registering of partial aro A gene of the common reed P. australis. The partial aro A gene of common reed (P. australis) was cloned in Escherichia coli and the amino acid sequence was identified/determined for the first time. This is the first report for isolation, cloning, and sequencing of a part of aro A gene from the common reed. A 670 bp fragment including two introns (86 bp and 289 bp) was obtained. The open reading frame (ORF) region in part of gene was encoded for 98 amino acids. Alignment showed high similarity among this region with Zea mays (L.) (Poaceae) (94.6%), Eleusine indica L. Gaertn (Poaceae) (94.2%), and Zoysia japonica Steud. (Poaceae) (94.2%). The alignment of amino acid sequence of the investigated part of the gene showed a homology with aro A from several other plants. This conserved region forms the enzyme active site. The alignment results of nucleotide and amino acid residues with related sequences showed that there are some differences among them. The relative glyphosate tolerance in the common reed may be related to these differences.

The Widespread Multidrug-Resistant Serotype O12 Pseudomonas aeruginosa Clone Emerged through Concomitant Horizontal Transfer of Serotype Antigen and Antibiotic Resistance Gene Clusters

DEFF Research Database (Denmark)

Thrane, Sandra Wingaard; Taylor, Véronique L.; Freschi, Luca

2015-01-01

. aeruginosa O12 OSA gene cluster, an antibiotic resistance determinant (gyrAC248T), and other genes that have been transferred between P. aeruginosa strains with distinct core genome architectures. We showed that these genes were likely acquired from an O12 serotype strain that is closely related to P...... in clinical settings and outbreaks. These serotype O12 isolates exhibit high levels of resistance to various classes of antibiotics. Here, we explore how the P. aeruginosa OSA biosynthesis gene clusters evolve in the population by investigating the association between the phylogenetic relationships among 83 P....... aeruginosa strains and their serotypes. While most serotypes were closely linked to the core genome phylogeny, we observed horizontal exchange of OSA biosynthesis genes among phylogenetically distinct P. aeruginosa strains. Specifically, we identified a "serotype island" ranging from 62 kb to 185 kb containing the P...

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

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Galperin Michael Y

2003-01-01

Full Text Available Abstract Background Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT, at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task. Results We addressed the problem of constructing parsimonious scenarios for individual sets of orthologous genes given a species tree. The orthologous sets were taken from the database of Clusters of Orthologous Groups of proteins (COGs. We show that the phyletic patterns (patterns of presence-absence in completely sequenced genomes of almost 90% of the COGs are inconsistent with the hypothetical species tree. Algorithms were developed to reconcile the phyletic patterns with the species tree by postulating gene loss, COG emergence and HGT (the latter two classes of events were collectively treated as gene gains. We prove that each of these algorithms produces a parsimonious evolutionary scenario, which can be represented as mapping of loss and gain events on the species tree. The distribution of the evolutionary events among the tree nodes substantially depends on the underlying assumptions of the reconciliation algorithm, e.g. whether or not independent gene gains (gain after loss after gain are permitted. Biological considerations suggest that, on average, gene loss might be a more likely event than gene gain. Therefore different gain penalties were used and the resulting series of reconstructed gene sets for the last universal common ancestor (LUCA of the extant life forms were analysed. The number of genes in the reconstructed LUCA gene sets grows as the gain penalty increases. However, qualitative examination of the LUCA versions reconstructed with different gain penalties

Experimental study on heat transfer enhancement of laminar ferrofluid flow in horizontal tube partially filled porous media under fixed parallel magnet bars

Energy Technology Data Exchange (ETDEWEB)

Sheikhnejad, Yahya; Hosseini, Reza, E-mail: hoseinir@aut.ac.ir; Saffar Avval, Majid

2017-02-15

In this study, steady state laminar ferroconvection through circular horizontal tube partially filled with porous media under constant heat flux is experimentally investigated. Transverse magnetic fields were applied on ferrofluid flow by two fixed parallel magnet bar positioned on a certain distance from beginning of the test section. The results show promising notable enhancement in heat transfer as a consequence of partially filled porous media and magnetic field, up to 2.2 and 1.4 fold enhancement were observed in heat transfer coefficient respectively. It was found that presence of both porous media and magnetic field simultaneously can highly improve heat transfer up to 2.4 fold. Porous media of course plays a major role in this configuration. Virtually, application of Magnetic field and porous media also insert higher pressure loss along the pipe which again porous media contribution is higher that magnetic field. - Highlights: • Porous media can improve the coefficient of heat transfer up to 2.2 fold. • Both porous media and Nano particles have undesired pressure drop effect. • Application of both porous media and magnetic field in ferrofluid flow will result in significant enhancement in heat transfer up to 2.4 fold. • Magnet bar effect is mainly restricted to approximately one fourth of the test section. • Diluted Ferrofluids 2%, results in over 1.4 fold enhancement in heat transfer coefficient.

A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes.

Science.gov (United States)

Tsirigos, Aristotelis; Rigoutsos, Isidore

2005-01-01

In earlier work, we introduced and discussed a generalized computational framework for identifying horizontal transfers. This framework relied on a gene's nucleotide composition, obviated the need for knowledge of codon boundaries and database searches, and was shown to perform very well across a wide range of archaeal and bacterial genomes when compared with previously published approaches, such as Codon Adaptation Index and C + G content. Nonetheless, two considerations remained outstanding: we wanted to further increase the sensitivity of detecting horizontal transfers and also to be able to apply the method to increasingly smaller genomes. In the discussion that follows, we present such a method, Wn-SVM, and show that it exhibits a very significant improvement in sensitivity compared with earlier approaches. Wn-SVM uses a one-class support-vector machine and can learn using rather small training sets. This property makes Wn-SVM particularly suitable for studying small-size genomes, similar to those of viruses, as well as the typically larger archaeal and bacterial genomes. We show experimentally that the new method results in a superior performance across a wide range of organisms and that it improves even upon our own earlier method by an average of 10% across all examined genomes. As a small-genome case study, we analyze the genome of the human cytomegalovirus and demonstrate that Wn-SVM correctly identifies regions that are known to be conserved and prototypical of all beta-herpesvirinae, regions that are known to have been acquired horizontally from the human host and, finally, regions that had not up to now been suspected to be horizontally transferred. Atypical region predictions for many eukaryotic viruses, including the alpha-, beta- and gamma-herpesvirinae, and 123 archaeal and bacterial genomes, have been made available online at http://cbcsrv.watson.ibm.com/HGT_SVM/.

Distribution of tetracycline resistance genes in anaerobic treatment of waste sludge: The role of pH in regulating tetracycline resistant bacteria and horizontal gene transfer.

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Huang, Haining; Chen, Yinguang; Zheng, Xiong; Su, Yinglong; Wan, Rui; Yang, Shouye

2016-10-01

Although pH value has been widely regarded as an important factor that affects resource recovery of waste sludge, the potential influence of diverse pHs on the distribution of tetracycline resistance genes (TRGs) during sludge anaerobic treatment is largely unknown. Here we reported that in the range of pH 4-10, 0.58-1.18 log unit increase of target TRGs was observed at pH 4, compared with that at pH 7, while 0.70-1.31 log unit further removal were obtained at pH 10. Mechanism study revealed that varied pHs not only altered the community structures of tetracycline resistant bacteria (TRB), but also changed their relative abundances, benefitting the propagation (acidic pHs) or attenuation (alkaline pHs) of TRB. Further investigation indicated that the amount and gene-possessing abilities of key genetic vectors for horizontal TRGs transfer were greatly promoted at acidic pHs but restricted under alkaline conditions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Globicatella sanguinis bacteraemia identified by partial 16S rRNA gene sequencing

DEFF Research Database (Denmark)

Abdul-Redha, Rawaa Jalil; Balslew, Ulla; Christensen, Jens Jørgen

2007-01-01

Globicatella sanguinis is a gram-positive coccus, resembling non-haemolytic streptococci. The organism has been isolated infrequently from normally sterile sites of humans. Three isolates obtained by blood culture could not be identified by Rapid 32 ID Strep, but partial sequencing of the 16S r......RNA gene revealed the identity of the isolated bacteria, and supplementary biochemical tests confirmed the species identification. The cases histories illustrate the dilemma of finding relevant, newly recognized, opportunistic pathogens and the identification achievement (s) that can be obtained by using...

In Vivo Gene Therapy of Hemophilia B: Sustained Partial Correction in Factor IX-Deficient Dogs

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Kay, Mark A.; Rothenberg, Steven; Landen, Charles N.; Bellinger, Dwight A.; Leland, Frances; Toman, Carol; Finegold, Milton; Thompson, Arthur R.; Read, M. S.; Brinkhous, Kenneth M.; Woo, Savio L. C.

1993-10-01

The liver represents a model organ for gene therapy. A method has been developed for hepatic gene transfer in vivo by the direct infusion of recombinant retroviral vectors into the portal vasculature, which results in the persistent expression of exogenous genes. To determine if these technologies are applicable for the treatment of hemophilia B patients, preclinical efficacy studies were done in a hemophilia B dog model. When the canine factor IX complementary DNA was transduced directly into the hepatocytes of affected dogs in vivo, the animals constitutively expressed low levels of canine factor IX for more than 5 months. Persistent expression of the clotting. factor resulted in reductions of whole blood clotting and partial thromboplastin times of the treated animals. Thus, long-term treatment of hemophilia B patients may be feasible by direct hepatic gene therapy in vivo.

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population

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Jessica eLabonté

2015-04-01

Full Text Available A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a three km-deep fracture water in the 2.9 Ga-old Witwatersrand Basin of South Africa. Between 0 and 32 % of genes recovered from single cells were not present in the original, metagenomic assembly of Desulforudis, which was obtained from a neighboring subsurface fracture. We found a transposable prophage, a retron, multiple clustered regularly interspaced short palindromic repeats (CRISPRs and restriction-modification systems, and an unusually high frequency of transposases in the analyzed single cell genomes. This indicates that recombination, HGT and viral infections are prevalent evolutionary events in the studied population of microorganisms inhabiting a highly stable deep subsurface environment.

Insights into horizontal acquisition patterns of dormancy and ...

Indian Academy of Sciences (India)

Horizontal Gene Transfer (HGT) events, initially thought to be rare in Mycobacterium tuberculosis, have recentlybeen shown to be involved in the acquisition of virulence operons in M. tuberculosis. We have developed a newpartitioning framework based HGT prediction algorithm, called Grid3M, and applied the same for the ...

Partial least squares based gene expression analysis in estrogen receptor positive and negative breast tumors.

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Ma, W; Zhang, T-F; Lu, P; Lu, S H

2014-01-01

Breast cancer is categorized into two broad groups: estrogen receptor positive (ER+) and ER negative (ER-) groups. Previous study proposed that under trastuzumab-based neoadjuvant chemotherapy, tumor initiating cell (TIC) featured ER- tumors response better than ER+ tumors. Exploration of the molecular difference of these two groups may help developing new therapeutic strategies, especially for ER- patients. With gene expression profile from the Gene Expression Omnibus (GEO) database, we performed partial least squares (PLS) based analysis, which is more sensitive than common variance/regression analysis. We acquired 512 differentially expressed genes. Four pathways were found to be enriched with differentially expressed genes, involving immune system, metabolism and genetic information processing process. Network analysis identified five hub genes with degrees higher than 10, including APP, ESR1, SMAD3, HDAC2, and PRKAA1. Our findings provide new understanding for the molecular difference between TIC featured ER- and ER+ breast tumors with the hope offer supports for therapeutic studies.

A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land

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Gribaldo Simonetta

2009-02-01

Full Text Available Abstract Background The pioneering ancestor of land plants that conquered terrestrial habitats around 500 million years ago had to face dramatic stresses including UV radiation, desiccation, and microbial attack. This drove a number of adaptations, among which the emergence of the phenylpropanoid pathway was crucial, leading to essential compounds such as flavonoids and lignin. However, the origin of this specific land plant secondary metabolism has not been clarified. Results We have performed an extensive analysis of the taxonomic distribution and phylogeny of Phenylalanine Ammonia Lyase (PAL, which catalyses the first and essential step of the general phenylpropanoid pathway, leading from phenylalanine to p-Coumaric acid and p-Coumaroyl-CoA, the entry points of the flavonoids and lignin routes. We obtained robust evidence that the ancestor of land plants acquired a PAL via horizontal gene transfer (HGT during symbioses with soil bacteria and fungi that are known to have established very early during the first steps of land colonization. This horizontally acquired PAL represented then the basis for further development of the phenylpropanoid pathway and plant radiation on terrestrial environments. Conclusion Our results highlight a possible crucial role of HGT from soil bacteria in the path leading to land colonization by plants and their subsequent evolution. The few functional characterizations of sediment/soil bacterial PAL (production of secondary metabolites with powerful antimicrobial activity or production of pigments suggest that the initial advantage of this horizontally acquired PAL in the ancestor of land plants might have been either defense against an already developed microbial community and/or protection against UV. Reviewers This article was reviewed by Purificación López-García, Janet Siefert, and Eugene Koonin.

Dissection of two soybean QTL conferring partial resistance to Phytophthora sojae through sequence and gene expression analysis

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Wang Hehe

2012-08-01

Full Text Available Abstract Background Phytophthora sojae is the primary pathogen of soybeans that are grown on poorly drained soils. Race-specific resistance to P. sojae in soybean is gene-for-gene, although in many areas of the US and worldwide there are populations that have adapted to the most commonly deployed resistance to P. sojae ( Rps genes. Hence, this system has received increased attention towards identifying mechanisms and molecular markers associated with partial resistance to this pathogen. Several quantitative trait loci (QTL have been identified in the soybean cultivar ‘Conrad’ that contributes to the expression of partial resistance to multiple P. sojae isolates. Results In this study, two of the Conrad QTL on chromosome 19 were dissected through sequence and expression analysis of genes in both resistant (Conrad and susceptible (‘Sloan’ genotypes. There were 1025 single nucleotide polymorphisms (SNPs in 87 of 153 genes sequenced from Conrad and Sloan. There were 304 SNPs in 54 genes sequenced from Conrad compared to those from both Sloan and Williams 82, of which 11 genes had SNPs unique to Conrad. Eleven of 19 genes in these regions analyzed with qRT-PCR had significant differences in fold change of transcript abundance in response to infection with P. sojae in lines with QTL haplotype from the resistant parent compared to those with the susceptible parent haplotype. From these, 8 of the 11 genes had SNPs in the upstream, untranslated region, exon, intron, and/or downstream region. These 11 candidate genes encode proteins potentially involved in signal transduction, hormone-mediated pathways, plant cell structural modification, ubiquitination, and basal resistance. Conclusions These findings may indicate a complex defense network with multiple mechanisms underlying these two soybean QTL conferring resistance to P. sojae. SNP markers derived from these candidate genes can contribute to fine mapping of QTL and marker assisted breeding for

Horizontal transfer of a subtilisin gene from plants into an ancestor of the plant pathogenic fungal genus Colletotrichum.

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Armijos Jaramillo, Vinicio Danilo; Vargas, Walter Alberto; Sukno, Serenella Ana; Thon, Michael R

2013-01-01

The genus Colletotrichum contains a large number of phytopathogenic fungi that produce enormous economic losses around the world. The effect of horizontal gene transfer (HGT) has not been studied yet in these organisms. Inter-Kingdom HGT into fungal genomes has been reported in the past but knowledge about the HGT between plants and fungi is particularly limited. We describe a gene in the genome of several species of the genus Colletotrichum with a strong resemblance to subtilisins typically found in plant genomes. Subtilisins are an important group of serine proteases, widely distributed in all of the kingdoms of life. Our hypothesis is that the gene was acquired by Colletotrichum spp. through (HGT) from plants to a Colletotrichum ancestor. We provide evidence to support this hypothesis in the form of phylogenetic analyses as well as a characterization of the similarity of the subtilisin at the primary, secondary and tertiary structural levels. The remarkable level of structural conservation of Colletotrichum plant-like subtilisin (CPLS) with plant subtilisins and the differences with the rest of Colletotrichum subtilisins suggests the possibility of molecular mimicry. Our phylogenetic analysis indicates that the HGT event would have occurred approximately 150-155 million years ago, after the divergence of the Colletotrichum lineage from other fungi. Gene expression analysis shows that the gene is modulated during the infection of maize by C. graminicola suggesting that it has a role in plant disease. Furthermore, the upregulation of the CPLS coincides with the downregulation of several plant genes encoding subtilisins. Based on the known roles of subtilisins in plant pathogenic fungi and the gene expression pattern that we observed, we postulate that the CPLSs have an important role in plant infection.

Horizontal transfer of short and degraded DNA has evolutionary implications for microbes and eukaryotic sexual reproduction.

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Overballe-Petersen, Søren; Willerslev, Eske

2014-10-01

Horizontal gene transfer in the form of long DNA fragments has changed our view of bacterial evolution. Recently, we discovered that such processes may also occur with the massive amounts of short and damaged DNA in the environment, and even with truly ancient DNA. Although it presently remains unclear how often it takes place in nature, horizontal gene transfer of short and damaged DNA opens up the possibility for genetic exchange across distinct species in both time and space. In this essay, we speculate on the potential evolutionary consequences of this phenomenon. We argue that it may challenge basic assumptions in evolutionary theory; that it may have distant origins in life's history; and that horizontal gene transfer should be viewed as an evolutionary strategy not only preceding but causally underpinning the evolution of sexual reproduction. © 2014 The Authors. BioEssays Published by WILEY Periodicals, Inc.

Partial Least Squares Based Gene Expression Analysis in EBV- Positive and EBV-Negative Posttransplant Lymphoproliferative Disorders.

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Wu, Sa; Zhang, Xin; Li, Zhi-Ming; Shi, Yan-Xia; Huang, Jia-Jia; Xia, Yi; Yang, Hang; Jiang, Wen-Qi

2013-01-01

Post-transplant lymphoproliferative disorder (PTLD) is a common complication of therapeutic immunosuppression after organ transplantation. Gene expression profile facilitates the identification of biological difference between Epstein-Barr virus (EBV) positive and negative PTLDs. Previous studies mainly implemented variance/regression analysis without considering unaccounted array specific factors. The aim of this study is to investigate the gene expression difference between EBV positive and negative PTLDs through partial least squares (PLS) based analysis. With a microarray data set from the Gene Expression Omnibus database, we performed PLS based analysis. We acquired 1188 differentially expressed genes. Pathway and Gene Ontology enrichment analysis identified significantly over-representation of dysregulated genes in immune response and cancer related biological processes. Network analysis identified three hub genes with degrees higher than 15, including CREBBP, ATXN1, and PML. Proteins encoded by CREBBP and PML have been reported to be interact with EBV before. Our findings shed light on expression distinction of EBV positive and negative PTLDs with the hope to offer theoretical support for future therapeutic study.

Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae: Unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer

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Lemieux Claude

2008-06-01

Full Text Available Abstract Background To gain insight into the branching order of the five main lineages currently recognized in the green algal class Chlorophyceae and to expand our understanding of chloroplast genome evolution, we have undertaken the sequencing of chloroplast DNA (cpDNA from representative taxa. The complete cpDNA sequences previously reported for Chlamydomonas (Chlamydomonadales, Scenedesmus (Sphaeropleales, and Stigeoclonium (Chaetophorales revealed tremendous variability in their architecture, the retention of only few ancestral gene clusters, and derived clusters shared by Chlamydomonas and Scenedesmus. Unexpectedly, our recent phylogenies inferred from these cpDNAs and the partial sequences of three other chlorophycean cpDNAs disclosed two major clades, one uniting the Chlamydomonadales and Sphaeropleales (CS clade and the other uniting the Oedogoniales, Chaetophorales and Chaetopeltidales (OCC clade. Although molecular signatures provided strong support for this dichotomy and for the branching of the Oedogoniales as the earliest-diverging lineage of the OCC clade, more data are required to validate these phylogenies. We describe here the complete cpDNA sequence of Oedogonium cardiacum (Oedogoniales. Results Like its three chlorophycean homologues, the 196,547-bp Oedogonium chloroplast genome displays a distinctive architecture. This genome is one of the most compact among photosynthetic chlorophytes. It has an atypical quadripartite structure, is intron-rich (17 group I and 4 group II introns, and displays 99 different conserved genes and four long open reading frames (ORFs, three of which are clustered in the spacious inverted repeat of 35,493 bp. Intriguingly, two of these ORFs (int and dpoB revealed high similarities to genes not usually found in cpDNA. At the gene content and gene order levels, the Oedogonium genome most closely resembles its Stigeoclonium counterpart. Characters shared by these chlorophyceans but missing in members

Trans-kingdom horizontal DNA transfer from bacteria to yeast is highly plastic due to natural polymorphisms in auxiliary nonessential recipient genes.

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Kazuki Moriguchi

Full Text Available With the rapid accumulation of genomic information from various eukaryotes in the last decade, genes proposed to have been derived from recent horizontal gene transfer (HGT events have been reported even in non-phagotrophic unicellular and multicellular organisms, but the molecular pathways underlying HGT remain to be explained. The development of in vitro HGT detection systems, which permit the molecular and genetic analyses of donor and recipient organisms and quantify HGT, are helpful in order to gain insight into mechanisms that may contribute to contemporary HGT events or may have contributed to past HGT events. We applied a horizontal DNA transfer system model based on conjugal gene transfer called trans-kingdom conjugation (TKC from the prokaryote Escherichia coli to the eukaryote Saccharomyces cerevisiae, and assessed whether and to what extent genetic variations in the eukaryotic recipient affect its receptivity to TKC. Strains from a collection of 4,823 knock-out mutants of S. cerevisiae MAT-α haploids were tested for their individual TKC receptivity. Two types of mutants, an ssd1 mutant and respiratory mutants, which are also found in experimental strains and in nature widely, were identified as highly receptive mutants. The TKC efficiency for spontaneously accrued petite (rho (-/0 mutants of the functional allele (SSD1-V strain showed increased receptivity. The TKC efficiency of the ssd1Δ mutant was 36% for bacterial conjugation, while that of the petite/ssd1Δ double mutants was even higher (220% in average compared to bacterial conjugation. This increased TKC receptivity was also observed when other conjugal transfer systems were applied and the donor bacterium was changed to Agrobacterium tumefaciens. These results support the idea that the genomes of certain eukaryotes have been exposed to exogenous DNA more frequently and continuously than previously thought.

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

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Sergio eLópez-Madrigal

2014-08-01

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

Evolutionary novelty in gravity sensing through horizontal gene transfer and high-order protein assembly.

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Tu Anh Nguyen

2018-04-01

Full Text Available Horizontal gene transfer (HGT can promote evolutionary adaptation by transforming a species' relationship to the environment. In most well-understood cases of HGT, acquired and donor functions appear to remain closely related. Thus, the degree to which HGT can lead to evolutionary novelties remains unclear. Mucorales fungi sense gravity through the sedimentation of vacuolar protein crystals. Here, we identify the octahedral crystal matrix protein (OCTIN. Phylogenetic analysis strongly supports acquisition of octin by HGT from bacteria. A bacterial OCTIN forms high-order periplasmic oligomers, and inter-molecular disulphide bonds are formed by both fungal and bacterial OCTINs, suggesting that they share elements of a conserved assembly mechanism. However, estimated sedimentation velocities preclude a gravity-sensing function for the bacterial structures. Together, our data suggest that HGT from bacteria into the Mucorales allowed a dramatic increase in assembly scale and emergence of the gravity-sensing function. We conclude that HGT can lead to evolutionary novelties that emerge depending on the physiological and cellular context of protein assembly.

Horizontal gene transfer and bacterial diversity

Indian Academy of Sciences (India)

Unknown

This review discusses how the recent influx of complete chromosomal sequences of various ... enteric bacteria, a great deal of phenotypic diversity among species is ..... E V 1998 Evidence for massive gene exchange between archaeal and ...

Striking similarity in the gene expression levels of individual Myc module members among ESCs, EpiSCs, and partial iPSCs.

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Masataka Hirasaki

Full Text Available Predominant transcriptional subnetworks called Core, Myc, and PRC modules have been shown to participate in preservation of the pluripotency and self-renewality of embryonic stem cells (ESCs. Epiblast stem cells (EpiSCs are another cell type that possesses pluripotency and self-renewality. However, the roles of these modules in EpiSCs have not been systematically examined to date. Here, we compared the average expression levels of Core, Myc, and PRC module genes between ESCs and EpiSCs. EpiSCs showed substantially higher and lower expression levels of PRC and Core module genes, respectively, compared with those in ESCs, while Myc module members showed almost equivalent levels of average gene expression. Subsequent analyses revealed that the similarity in gene expression levels of the Myc module between these two cell types was not just overall, but striking similarities were evident even when comparing the expression of individual genes. We also observed equivalent levels of similarity in the expression of individual Myc module genes between induced pluripotent stem cells (iPSCs and partial iPSCs that are an unwanted byproduct generated during iPSC induction. Moreover, our data demonstrate that partial iPSCs depend on a high level of c-Myc expression for their self-renewal properties.

Horizontal transmission of malignancy: in-vivo fusion of human lymphomas with hamster stroma produces tumors retaining human genes and lymphoid pathology.

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David M Goldenberg

Full Text Available We report the in-vivo fusion of two Hodgkin lymphomas with golden hamster cheek pouch cells, resulting in serially-transplanted (over 5-6 years GW-532 and GW-584 heterosynkaryon tumor cells displaying both human and hamster DNA (by FISH, lymphoma-like morphology, aggressive metastasis, and retention of 7 human genes (CD74, CXCR4, CD19, CD20, CD71, CD79b, and VIM out of 24 tested by PCR. The prevalence of B-cell restricted genes (CD19, CD20, and CD79b suggests that this uniform population may be the clonal initiating (malignant cells of Hodgkin lymphoma, despite their not showing translation to their respective proteins by immunohistochemical analysis. This is believed to be the first report of in-vivo cell-cell fusion of human lymphoma and rodent host cells, and may be a method to disclose genes regulating both organoid and metastasis signatures, suggesting that the horizontal transfer of tumor DNA to adjacent stromal cells may be implicated in tumor heterogeneity and progression. The B-cell gene signature of the hybrid xenografts suggests that Hodgkin lymphoma, or its initiating cells, is a B-cell malignancy.

Reversible effects of oxygen partial pressure on genes associated with placental angiogenesis and differentiation in primary-term cytotrophoblast cell culture.

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Debiève, F; Depoix, C; Gruson, D; Hubinont, C

2013-09-01

Timely regulated changes in oxygen partial pressure are important for placental formation. Disturbances could be responsible for pregnancy-related diseases like preeclampsia and intrauterine growth restriction. We aimed to (i) determine the effect of oxygen partial pressure on cytotrophoblast differentiation; (ii) measure mRNA expression and protein secretion from genes associated with placental angiogenesis; and (iii) determine the reversibility of these effects at different oxygen partial pressures. Term cytotrophoblasts were incubated at 21% and 2.5% O2 for 96 hr, or were switched between the two oxygen concentrations after 48 hr. Real-time PCR and enzyme-linked immunosorbent assays (ELISAs) were used to evaluate cell fusion and differentiation, measuring transcript levels for those genes involved in cell fusion and placental angiogenesis, including VEGF, PlGF, VEGFR1, sVEGFR1, sENG, INHA, and GCM1. Cytotrophoblasts underwent fusion and differentiation in 2.5% O2 . PlGF expression was inhibited while sVEGFR1 expression increased. VEGF and sENG mRNA expressions increased in 2.5% compared to 21% O2 , but no protein was detected in the cell supernatants. Finally, GCM1 mRNA expression increased during trophoblast differentiation at 21% O2 , but was inhibited at 2.5% O2 . These mRNA expression effects were reversed by returning the cells to 21% O2 . Thus, low-oxygen partial pressure does not inhibit term-cytotrophoblast cell fusion and differentiation in vitro. Lowering the oxygen partial pressure from 21% to 2.5% caused normal-term trophoblasts to reversibly modify their expression of genes associated with placental angiogenesis. This suggests that modifications observed in pregnancy diseases such as preeclampsia or growth retardation are probably due to an extrinsic effect on trophoblasts. Copyright © 2013 Wiley Periodicals, Inc.

EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer detection in eukaryotes.

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Clasen, Frederick Johannes; Pierneef, Rian Ewald; Slippers, Bernard; Reva, Oleg

2018-05-03

Genomic islands (GIs) are inserts of foreign DNA that have potentially arisen through horizontal gene transfer (HGT). There are evidences that GIs can contribute significantly to the evolution of prokaryotes. The acquisition of GIs through HGT in eukaryotes has, however, been largely unexplored. In this study, the previously developed GI prediction tool, SeqWord Gene Island Sniffer (SWGIS), is modified to predict GIs in eukaryotic chromosomes. Artificial simulations are used to estimate ratios of predicting false positive and false negative GIs by inserting GIs into different test chromosomes and performing the SWGIS v2.0 algorithm. Using SWGIS v2.0, GIs are then identified in 36 fungal, 22 protozoan and 8 invertebrate genomes. SWGIS v2.0 predicts GIs in large eukaryotic chromosomes based on the atypical nucleotide composition of these regions. Averages for predicting false negative and false positive GIs were 20.1% and 11.01% respectively. A total of 10,550 GIs were identified in 66 eukaryotic species with 5299 of these GIs coding for at least one functional protein. The EuGI web-resource, freely accessible at http://eugi.bi.up.ac.za , was developed that allows browsing the database created from identified GIs and genes within GIs through an interactive and visual interface. SWGIS v2.0 along with the EuGI database, which houses GIs identified in 66 different eukaryotic species, and the EuGI web-resource, provide the first comprehensive resource for studying HGT in eukaryotes.

Lightning-triggered electroporation and electrofusion as possible contributors to natural horizontal gene transfer.

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Kotnik, Tadej

2013-09-01

Phylogenetic studies show that horizontal gene transfer (HGT) is a significant contributor to genetic variability of prokaryotes, and was perhaps even more abundant during the early evolution. Hitherto, research of natural HGT has mainly focused on three mechanisms of DNA transfer: conjugation, natural competence, and viral transduction. This paper discusses the feasibility of a fourth such mechanism--cell electroporation and/or electrofusion triggered by atmospheric electrostatic discharges (lightnings). A description of electroporation as a phenomenon is followed by a review of experimental evidence that electroporation of prokaryotes in aqueous environments can result in release of non-denatured DNA, as well as uptake of DNA from the surroundings and transformation. Similarly, a description of electrofusion is followed by a review of experiments showing that prokaryotes devoid of cell wall can electrofuse into hybrids expressing the genes of their both precursors. Under sufficiently fine-tuned conditions, electroporation and electrofusion are efficient tools for artificial transformation and hybridization, respectively, but the quantitative analysis developed here shows that conditions for electroporation-based DNA release, DNA uptake and transformation, as well as for electrofusion are also present in many natural aqueous environments exposed to lightnings. Electroporation is thus a plausible contributor to natural HGT among prokaryotes, and could have been particularly important during the early evolution, when the other mechanisms might have been scarcer or nonexistent. In modern prokaryotes, natural absence of the cell wall is rare, but it is reasonable to assume that the wall has formed during a certain stage of evolution, and at least prior to this, electrofusion could also have contributed to natural HGT. The concluding section outlines several guidelines for assessment of the feasibility of lightning-triggered HGT. © 2013 Elsevier B.V. All rights

Partial Sequence Analysis of Merozoite Surface Proteine-3α Gene in Plasmodium vivax Isolates from Malarious Areas of Iran

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H Mirhendi

2008-12-01

Full Text Available Background: Approximately 85-90% of malaria infections in Iran are attributed to Plasmodium vivax, while little is known about the genetic of the parasite and its strain types in this region. This study was designed and performed for describing genetic characteristics of Plasmodium vivax population of Iran based on the merozoite surface protein-3α gene sequence. Methods: Through a descriptive study we analyzed partial P. vivax merozoite surface protein-3α gene sequences from 17 clinical P. vivax isolates collected from malarious areas of Iran. Genomic DNA was extracted by Q1Aamp® DNA blood mini kit, amplified through nested PCR for a partial nucleotide sequence of PvMSP-3 gene in P. vivax. PCR-amplified products were sequenced with an ABI Prism Perkin-Elmer 310 sequencer machine and the data were analyzed with clustal W software. Results: Analysis of PvMSP-3 gene sequences demonstrated extensive polymorphisms, but the sequence identity between isolates of same types was relatively high. We identified specific insertions and deletions for the types A, B and C variants of P. vivax in our isolates. In phylogenetic comparison of geographically separated isolates, there was not a significant geo­graphical branching of the parasite populations. Conclusion: The highly polymorphic nature of isolates suggests that more investigations of the PvMSP-3 gene are needed to explore its vaccine potential.

Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species.

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Baker, Kate S; Dallman, Timothy J; Field, Nigel; Childs, Tristan; Mitchell, Holly; Day, Martin; Weill, François-Xavier; Lefèvre, Sophie; Tourdjman, Mathieu; Hughes, Gwenda; Jenkins, Claire; Thomson, Nicholas

2018-04-13

Horizontal gene transfer has played a role in developing the global public health crisis of antimicrobial resistance (AMR). However, the dynamics of AMR transfer through bacterial populations and its direct impact on human disease is poorly elucidated. Here, we study parallel epidemic emergences of multiple Shigella species, a priority AMR organism, in men who have sex with men to gain insight into AMR emergence and spread. Using genomic epidemiology, we show that repeated horizontal transfer of a single AMR plasmid among Shigella enhanced existing and facilitated new epidemics. These epidemic patterns contrasted with slighter, slower increases in disease caused by organisms with vertically inherited (chromosomally encoded) AMR. This demonstrates that horizontal transfer of AMR directly affects epidemiological outcomes of globally important AMR pathogens and highlights the need for integration of genomic analyses into all areas of AMR research, surveillance and management.

Antibiotic Resistance Genetic Markers and Integrons in White Soft Cheese: Aspects of Clinical Resistome and Potentiality of Horizontal Gene Transfer.

Science.gov (United States)

de Paula, Ana Caroline L; Medeiros, Julliane D; de Azevedo, Analice C; de Assis Chagas, Jéssica M; da Silva, Vânia L; Diniz, Cláudio G

2018-02-19

Antibiotic resistance poses an important threat to global public health and has become a challenge to modern medicine. The occurrence of antibiotic-resistant bacteria in a broad range of foods has led to a growing concern about the impact that food may have as a reservoir of antibiotic resistance genes. Considering Minas Frescal Cheese (MFC)-a typical Brazilian white soft cheese-and its economic and cultural values, in this study, medically relevant antimicrobial-resistance genetic markers (AR genes) were screened, and the occurrence of integrons were evaluated in manufactured MFC using culture-independent approaches. Through a fingerprinting analysis, the tested MFCs were brand-clustered, indicating reproducibility along the production chain. A common core of resistance markers in all brands evaluated and related antimicrobials such as β-lactams, tetracyclines, quinolones, and sulfonamide was detected. Several other markers, including efflux pumps and aminoglycosides-resistance were distributed among brands. Class 1 and 2 integrons were observed, respectively, in 77% and 97% of the samples. The presence of AR genes is of special interest due to their clinical relevance. Taken together, the data may suggest that the production chain of MFC might contribute to the spread of putative drug-resistant bacteria, which could greatly impact human health. Furthermore, detection of class 1 and class 2 integrons in MFC has led to discussions about resistance gene spread in this traditional cheese, providing evidence of potential horizontal transfer of AR genes to human gut microbiota.

Antibiotic Resistance Genetic Markers and Integrons in White Soft Cheese: Aspects of Clinical Resistome and Potentiality of Horizontal Gene Transfer

Directory of Open Access Journals (Sweden)

Ana Caroline L. de Paula

2018-02-01

Full Text Available Antibiotic resistance poses an important threat to global public health and has become a challenge to modern medicine. The occurrence of antibiotic-resistant bacteria in a broad range of foods has led to a growing concern about the impact that food may have as a reservoir of antibiotic resistance genes. Considering Minas Frescal Cheese (MFC—a typical Brazilian white soft cheese—and its economic and cultural values, in this study, medically relevant antimicrobial-resistance genetic markers (AR genes were screened, and the occurrence of integrons were evaluated in manufactured MFC using culture-independent approaches. Through a fingerprinting analysis, the tested MFCs were brand-clustered, indicating reproducibility along the production chain. A common core of resistance markers in all brands evaluated and related antimicrobials such as β-lactams, tetracyclines, quinolones, and sulfonamide was detected. Several other markers, including efflux pumps and aminoglycosides-resistance were distributed among brands. Class 1 and 2 integrons were observed, respectively, in 77% and 97% of the samples. The presence of AR genes is of special interest due to their clinical relevance. Taken together, the data may suggest that the production chain of MFC might contribute to the spread of putative drug-resistant bacteria, which could greatly impact human health. Furthermore, detection of class 1 and class 2 integrons in MFC has led to discussions about resistance gene spread in this traditional cheese, providing evidence of potential horizontal transfer of AR genes to human gut microbiota.

Ballasting pipeline moving in horizontal well as method of control sticking phenomenon

Science.gov (United States)

Toropov, V. S.; Toropov, E. S.

2018-05-01

The mechanism of the phenomenon of sticking a pipeline moving in a well while pulled by the facility horizontal directional drilling is investigated. A quantitative evaluation of the force arising from sticking is given. At the same time, the working hypothesis takes a view of the combined effect of adhesion and friction interactions as the reasons that cause this phenomenon. As a measure to control the occurrence of sticking and to reduce the resistance force to movement of the pipeline in the well, several methods of ballasting the working pipeline are proposed, depending on the profile of the well and the ratio of the length of the curved sections of the inlet and outlet and the straight horizontal sections of the profile. It is shown that for crossings, which profile contains an extended horizontal section, it is possible to partially fill the pipeline with water to achieve zero buoyancy, and for crossings with curvature along the entire profile, the ballasting efficiency will be minimal.

Accuracy of CAD-CAM-fabricated removable partial dentures.

Science.gov (United States)

Arnold, Christin; Hey, Jeremias; Schweyen, Ramona; Setz, Jürgen M

2018-04-01

The conventional fabrication of removable partial dentures (RPDs) is a complex, error-prone, time-consuming, and expensive process. The use of computer-aided design and computer-aided manufacturing (CAD-CAM) techniques, especially rapid prototyping, promises a more effective method for fabricating RPD frameworks. The purpose of this in vitro study was to evaluate the fit of RPD clasps fabricated by means of 4 different CAD-CAM-systems and to compare those fittings with that of the conventional lost-wax casting technique (LWT). A master model of a partially edentulous maxilla with the canines and second molars as the remaining teeth was fabricated. After the model was optically scanned, we designed a quadrangularly supported RPD with 4 clasps and a palatal strap major connector. A standard tessellation language data set was used to fabricate 12 identical RPDs by using 4 different CAD-CAM techniques: indirect rapid prototyping (wax inject printing combined with LWT), direct rapid prototyping (selective laser melting), indirect milling (wax milling with LWT), and direct milling (resin milling [polyetheretherketone]). Three conventionally cast RPDs (LWT) served as the control group. The fit accuracy of the clasps (n=12 for each group) was determined in both the horizontal and vertical dimensions by using light microscopy. Indirectly milled RPDs (117 ±34 μm horizontal and 45 ±21 μm vertical) and directly milled RPDs (43 ±23 μm horizontal, and 38 ±21 μm vertical) showed significantly better (P<.05) fit than did conventionally fabricated LWT RPDs (133 ±59 μm horizontal; 73 ±25 μm vertical). The worst fit was found for RPDs fabricated using indirect rapid prototyping (323 ±188 μm horizontal and 112 ±60 μm vertical) or direct rapid prototyping (365 ±205 μm horizontal and 363 ±133 μm vertical), which were unstable on the master model, making them unsuitable for clinical use. Most RPDs exhibited smaller vertical measuring distances. Compared with the LWT

Sobre el papel del sistema SOS, la recombinación y el intercambio horizontal de genes en la evolución bacteriana

OpenAIRE

Rodríguez Beltrán, Jerónimo

2015-01-01

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 06-11-2015 El principal objetivo de esta tesis ha sido cuantificar y ampliar el conocimiento sobre los diferentes sistemas evolutivos implicados en el control de la tasa adaptativa en los seres vivos, usando para ello la bacteria modelo E. coli. La mutación, la recombinación y la transferencia horizontal de genes son los mecanismos más prominentes d...

Genome Comparison of Erythromycin Resistant Campylobacter from Turkeys Identifies Hosts and Pathways for Horizontal Spread of erm(B Genes

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Diego Florez-Cuadrado

2017-11-01

Full Text Available Pathogens in the genus Campylobacter are the most common cause of food-borne bacterial gastro-enteritis. Campylobacteriosis, caused principally by Campylobacter jejuni and Campylobacter coli, is transmitted to humans by food of animal origin, especially poultry. As for many pathogens, antimicrobial resistance in Campylobacter is increasing at an alarming rate. Erythromycin prescription is the treatment of choice for clinical cases requiring antimicrobial therapy but this is compromised by mobility of the erythromycin resistance gene erm(B between strains. Here, we evaluate resistance to six antimicrobials in 170 Campylobacter isolates (133 C. coli and 37 C. jejuni from turkeys. Erythromycin resistant isolates (n = 85; 81 C. coli and 4 C. jejuni were screened for the presence of the erm(B gene, that has not previously been identified in isolates from turkeys. The genomes of two positive C. coli isolates were sequenced and in both isolates the erm(B gene clustered with resistance determinants against aminoglycosides plus tetracycline, including aad9, aadE, aph(2″-IIIa, aph(3′-IIIa, and tet(O genes. Comparative genomic analysis identified identical erm(B sequences among Campylobacter from turkeys, Streptococcus suis from pigs and Enterococcus faecium and Clostridium difficile from humans. This is consistent with multiple horizontal transfer events among different bacterial species colonizing turkeys. This example highlights the potential for dissemination of antimicrobial resistance across bacterial species boundaries which may compromise their effectiveness in antimicrobial therapy.

The long-term outcome of boys with partial androgen insensitivity syndrome and a mutation in the androgen receptor gene

NARCIS (Netherlands)

Lucas-Herald, A.; S. Bertelloni (Silvano); A. Juul (Anders); J. Bryce (Jillian); Jiang, J.; M. Rodie (Martina); R. Sinnott (Richard); Boroujerdi, M.; Lindhardt Johansen, M.; O. Hiort (Olaf); P-M. Holterhus (Paul-Martin); M.L. Cools (Martine); Guaragna-Filho, G.; Guerra-Junior, G.; N. Weintrob (Naomi); S.E. Hannema (Sabine); S.L.S. Drop (Stenvert); T. Guran (Tulay); F. Darendeliler (Feyza); A. Nordenström (Anna); I.A. Hughes (Ieuan A.); Acerini, C.; Tadokoro-Cuccaro, R.; S.F. Ahmed (Faisal)

2016-01-01

textabstractBackground: In boys with suspected partial androgen insensitivity syndrome (PAIS), systematic evidence that supports the long-term prognostic value of identifying a mutation in the androgen receptor gene (AR) is lacking. Objective: To assess the clinical characteristics and long-term

Genomic Evidence of Chemotrophic Metabolisms in Deep-Dwelling Chloroflexi Conferred by Ancient Horizontal Gene Transfer Events

Science.gov (United States)

Momper, L. M.; Magnabosco, C.; Amend, J.; Osburn, M. R.; Fournier, G. P.

2017-12-01

The marine and terrestrial subsurface biospheres represent quite likely the largest reservoirs for life on Earth, directly impacting surface processes and global cycles throughout Earth's history. In the deep subsurface biosphere (DSB) organic carbon and energy are often extremely scarce. However, archaea and bacteria are able to persist in the DSB to at least 3.5 km below surface [1]. Understanding how they persist, and by what metabolisms they subsist, are key questions in this biosphere. To address these questions we investigated 5 global DSB environments: one legacy mine in South Dakota, USA, 3 mines in South Africa and marine fluids circulating beneath the Juan de Fuca Ridge. Boreholes within these mines provided access to fluids buried beneath the earth's surface and sampled depths down to 3.1 km. Geochemical data were collected concomitantly with DNA for metagenomic sequencing. We examined genomes of the ancient and deeply branching Chloroflexi for metabolic capabilities and interrogated the geochemical drivers behind those metabolisms with in situ thermodynamic modeling of reaction energetics. In total, 23 Chloroflexi genomes were identified and analyzed from the 5 subsurface sites. Genes for nitrate reduction (nar) and sulfite reduction (dsr) were found in many of the South Africa Chloroflexi but were absent from genomes collected in South Dakota. Indeed, nitrate reduction was among the most energetically favorable reactions in South African fluids (10-14 kJ cell-1 sec -1 per mol of reactant) and sulfur reduction with Fe2+ or H2 was also exergonic [2]. Conversely, genes for nitrite and nitrous oxide reduction (nrf, nir and nos) were found in genomes collected in South Dakota and Juan de Fuca, but not South Africa. We examined the origin of genes conferring these metabolisms in the Chloroflexi genomes. We discovered evidence for horizontal gene transfer (HGT) for all of these putative metabolisms. Retention of these genes in Chloroflexi lineages indicates

Recurrent invasion and extinction of a selfish gene.

Science.gov (United States)

Goddard, M R; Burt, A

1999-11-23

Homing endonuclease genes show super-Mendelian inheritance, which allows them to spread in populations even when they are of no benefit to the host organism. To test the idea that regular horizontal transmission is necessary for the long-term persistence of these genes, we surveyed 20 species of yeasts for the omega-homing endonuclease gene and associated group I intron. The status of omega could be categorized into three states (functional, nonfunctional, or absent), and status was not clustered on the host phylogeny. Moreover, the phylogeny of omega differed significantly from that of the host, strong evidence of horizontal transmission. Further analyses indicate that horizontal transmission is more common than transposition, and that it occurs preferentially between closely related species. Parsimony analysis and coalescent theory suggest that there have been 15 horizontal transmission events in the ancestry of our yeast species, through simulations indicate that this value is probably an underestimate. Overall, the data support a cyclical model of invasion, degeneration, and loss, followed by reinvasion, and each of these transitions is estimated to occur about once every 2 million years. The data are thus consistent with the idea that frequent horizontal transmission is necessary for the long-term persistence of homing endonuclease genes, and further, that this requirement limits these genes to organisms with easily accessible germ lines. The data also show that mitochondrial DNA sequences are transferred intact between yeast species; if other genes do not show such high levels of horizontal transmission, it would be due to lack of selection, rather than lack of opportunity.

Phylogenetic relationships of seven previously unclassified viruses within the family Rhabdoviridae using partial nucleoprotein gene sequences.

Science.gov (United States)

Kuzmin, I V; Hughes, G J; Rupprecht, C E

2006-08-01

Partial nucleoprotein (N) gene sequences of the rhabdoviruses Obodhiang (OBOV), Kotonkon (KOTV), Rochambeau (RBUV), Kern canyon (KCV), Mount Elgon bat (MEBV), Kolongo (KOLV) and Sandjimba (SJAV) were generated and their phylogenetic positions within the family Rhabdoviridae were determined. Both OBOV and KOTV were placed within the genus Ephemerovirus. RBUV was joined to the same cluster, but more distantly. MEBV and KCV were grouped into a monophyletic cluster (putative genus) with Oita virus (OITAV). These three viruses, originating from different regions of the world, were all isolated from insectivorous bats and may be specific for these mammals. African avian viruses KOLV and SJAV were joined to each other and formed another clade at the genus level. Further, they were grouped with the recently characterized rhabdovirus Tupaia virus (TRV). Although the genetic distance was great, the grouping was supported by consistent bootstrap values. This observation suggests that viruses of this group may be distributed widely in the Old World. Non-synonymous/synonymous substitution ratio estimations (dN/dS) using a partial N gene fragment (241 codons) for the three rhabdovirus genera revealed contrasting patterns of evolution, where dN/dS values follow the pattern Ephemerovirus > Vesiculovirus > Lyssavirus. The magnitude of this ratio corresponds well with the number of negatively selected codons. The accumulation of dS appears evenly distributed along the gene fragment for all three genera. These estimations demonstrated clearly that lyssaviruses are subjected to the strongest constraints against amino acid substitutions, probably related to their particular niche and unique pathobiology.

Fastidious Gram-Negatives: Identification by the Vitek 2 Neisseria-Haemophilus Card and by Partial 16S rRNA Gene Sequencing Analysis.

Science.gov (United States)

Sönksen, Ute Wolff; Christensen, Jens Jørgen; Nielsen, Lisbeth; Hesselbjerg, Annemarie; Hansen, Dennis Schrøder; Bruun, Brita

2010-12-31

Taxonomy and identification of fastidious Gram negatives are evolving and challenging. We compared identifications achieved with the Vitek 2 Neisseria-Haemophilus (NH) card and partial 16S rRNA gene sequence (526 bp stretch) analysis with identifications obtained with extensive phenotypic characterization using 100 fastidious Gram negative bacteria. Seventy-five strains represented 21 of the 26 taxa included in the Vitek 2 NH database and 25 strains represented related species not included in the database. Of the 100 strains, 31 were the type strains of the species. Vitek 2 NH identification results: 48 of 75 database strains were correctly identified, 11 strains gave `low discrimination´, seven strains were unidentified, and nine strains were misidentified. Identification of 25 non-database strains resulted in 14 strains incorrectly identified as belonging to species in the database. Partial 16S rRNA gene sequence analysis results: For 76 strains phenotypic and sequencing identifications were identical, for 23 strains the sequencing identifications were either probable or possible, and for one strain only the genus was confirmed. Thus, the Vitek 2 NH system identifies most of the commonly occurring species included in the database. Some strains of rarely occurring species and strains of non-database species closely related to database species cause problems. Partial 16S rRNA gene sequence analysis performs well, but does not always suffice, additional phenotypical characterization being useful for final identification.

Association between NLPR1, NLPR3, and P2X7R Gene Polymorphisms with Partial Seizures

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Haidong Wang

2017-01-01

Full Text Available Objectives. Clinical and experimental evidence has clarified that the inflammatory processes within the brain play a pivotal role in the pathophysiology of seizures and epilepsy. Inflammasomes and P2X7 purinergic receptor (P2X7R are important mediators during the inflammatory process. Therefore, we investigated the possible association between partial seizures and inflammasomes NLPR1, NLRP3, and P2X7R gene polymorphisms in the present study. Method. A total of 163 patients and 201 health controls were enrolled in this study and polymorphisms of NLPR1, NLRP3, and P2X7R genes were detected using polymerase chain reaction- (PCR- ligase detection reaction method. Result. The frequency of rs878329 (G>C genotype with C (CG + CC was significantly lower among patients with partial seizures relative to controls (OR = 2.033, 95% CI = 1.290–3.204, p=0.002 for GC + CC versus GG. Intriguingly, we found that the significant difference of rs878329 (G>C genotype and allele frequency only existed among males (OR = 2.542, 95% CI = 1.344–4.810, p=0.004 for GC + CC versus GG, while there was no statistically significant difference among females. However, no significant results were presented for the genotype distributions of rs8079034, rs4612666, rs10754558, rs2027432, rs3751143, and rs208294 polymorphisms between patients and controls. Conclusion. Our study demonstrated the potentially significant role of NLRP1 rs878329 (G>C in developing susceptibility to the partial seizures in a Chinese Han population.

Absence of association between major vault protein (MVP) gene polymorphisms and drug resistance in Chinese Han patients with partial epilepsy.

Science.gov (United States)

Zhou, Luo; Zhang, Mengqi; Long, Hongyu; Long, Lili; Xie, Yuanyuan; Liu, Zhaoqian; Kang, Jin; Chen, Qihua; Feng, Li; Xiao, Bo

2015-11-15

Drug resistance in epilepsy is common despite many antiepileptic drugs (AEDs) available for treatment. The development of drug resistant epilepsy may be a result of multiple factors. Several previous studies reported that the major vault protein (MVP) was significantly increased in epileptogenic brain tissues resected from patients with partial-onset seizures, indicating the possible involvement of MVP in drug resistance. In this article, we aimed to identify the association between single nucleotide polymorphisms (SNPs) of MVP gene and drug resistance of partial epilepsy in a Chinese Han population. A total of 510 patients with partial-onset seizures and 206 healthy controls were recruited. Among the patients, 222 were drug resistant and 288 were responsive. The selection of tagging SNPs was based on the Hapmap database and Haploview software and the genotyping was conducted on the Sequenom MassARRAY iPLEX platform. For the selected loci rs12149746, rs9938630 and rs4788186 in the MVP gene, there was no significant difference in allele or genotype distribution between the drug resistant and responsive groups, or between all of the patients and healthy controls. Linkage disequilibrium between any two loci was detected but there was no significant difference in haplotype frequency between the drug resistant and responsive groups. Our results suggest that MVP genetic polymorphisms and haplotypes may not be associated with drug resistance of partial epilepsy in the Chinese Han population. Copyright © 2015 Elsevier B.V. All rights reserved.

Heavy crude production from shallow formations: long horizontal wells versus horizontal fractures

Energy Technology Data Exchange (ETDEWEB)

Valko, P.; Economides, M. J. [Texas A and M Univ., TX (United States)

1998-12-31

The feasibility of producing heavy oil from shallow formations using either horizontal wells or short horizontal wells fractured horizontally is demonstrated. The problem of optimum proppant placement is solved in two steps. In step one, the finite productivity performance is considered in general terms showing that the performance is a function of two dimensionless parameters. Following derivation of optimum conditions, the solution is applied to the horizontal fracture consideration. The limiting factor is that to create an effective finite conductivity fracture, the dimensionless fracture conductivity must be on the order of unity, a fracture that is difficult to realize in higher permeability formations. The best candidates for the suggested configuration are shallow or moderate formations, or formations otherwise proven to accept horizontal fractures, and formations with low permeability/viscosity ratio. 7 refs., 2 tabs., 10 figs., 2 appendices.

A Horizontally Transferred Autonomous Helitron Became a Full Polydnavirus Segment in Cotesia vestalis

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Pedro Heringer

2017-12-01

Full Text Available Bracoviruses associate symbiotically with thousands of parasitoid wasp species in the family Braconidae, working as virulence gene vectors, and allowing the development of wasp larvae within hosts. These viruses are composed of multiple DNA circles that are packaged into infective particles, and injected together with wasp’s eggs during parasitization. One of the viral segments of Cotesia vestalis bracovirus contains a gene that has been previously described as a helicase of unknown origin. Here, we demonstrate that this gene is a Rep/Helicase from an intact Helitron transposable element that covers the viral segment almost entirely. We also provide evidence that this element underwent at least two horizontal transfers, which appear to have occurred consecutively: first from a Drosophila host ancestor to the genome of the parasitoid wasp C. vestalis and its bracovirus, and then from C. vestalis to a lepidopteran host (Bombyx mori. Our results reinforce the idea of parasitoid wasps as frequent agents of horizontal transfers in eukaryotes. Additionally, this Helitron-bracovirus segment is the first example of a transposable element that effectively became a whole viral circle.

Sub-inhibitory concentrations of heavy metals facilitate the horizontal transfer of plasmid-mediated antibiotic resistance genes in water environment.

Science.gov (United States)

Zhang, Ye; Gu, April Z; Cen, Tianyu; Li, Xiangyang; He, Miao; Li, Dan; Chen, Jianmin

2018-06-01

Although widespread antibiotic resistance has been mostly attributed to the selective pressure generated by overuse and misuse of antibiotics, recent growing evidence suggests that chemicals other than antibiotics, such as certain metals, can also select and stimulate antibiotic resistance via both co-resistance and cross-resistance mechanisms. For instance, tetL, merE, and oprD genes are resistant to both antibiotics and metals. However, the potential de novo resistance induced by heavy metals at environmentally-relevant low concentrations (much below theminimum inhibitory concentrations [MICs], also referred as sub-inhibitory) has hardly been explored. This study investigated and revealed that heavy metals, namely Cu(II), Ag(I), Cr(VI), and Zn(II), at environmentally-relevant and sub-inhibitory concentrations, promoted conjugative transfer of antibiotic resistance genes (ARGs) between E. coli strains. The mechanisms of this phenomenon were further explored, which involved intracellular reactive oxygen species (ROS) formation, SOS response, increased cell membrane permeability, and altered expression of conjugation-relevant genes. These findings suggest that sub-inhibitory levels of heavy metals that widely present in various environments contribute to the resistance phenomena via facilitating horizontal transfer of ARGs. This study provides evidence from multiple aspects implicating the ecological effect of low levels of heavy metals on antibiotic resistance dissemination and highlights the urgency of strengthening efficacious policy and technology to control metal pollutants in the environments. Copyright © 2018 Elsevier Ltd. All rights reserved.

Computing the partial volume of pressure vessels

Energy Technology Data Exchange (ETDEWEB)

Wiencke, Bent [Nestle USA, Corporate Engineering, 800 N. Brand Blvd, Glendale, CA 91203 (United States)

2010-06-15

The computation of the partial and total volume of pressure vessels with various type of head profiles requires detailed knowledge of the head profile geometry. Depending on the type of head profile the derivation of the equations can become very complex and the calculation process cumbersome. Certain head profiles require numerical methods to obtain the partial volume, which for most application is beyond the scope of practicability. This paper suggests a unique method that simplifies the calculation procedure for the various types of head profiles by using one common set of equations without the need for numerical or complex computation methods. For ease of use, all equations presented in this paper are summarized in a single table format for horizontal and vertical vessels. (author)

Analysis of pumping tests of partially penetrating wells in an unconfined aquifer using inverse numerical optimization

Science.gov (United States)

Hvilshøj, S.; Jensen, K. H.; Barlebo, H. C.; Madsen, B.

1999-08-01

Inverse numerical modeling was applied to analyze pumping tests of partially penetrating wells carried out in three wells established in an unconfined aquifer in Vejen, Denmark, where extensive field investigations had previously been carried out, including tracer tests, mini-slug tests, and other hydraulic tests. Drawdown data from multiple piezometers located at various horizontal and vertical distances from the pumping well were included in the optimization. Horizontal and vertical hydraulic conductivities, specific storage, and specific yield were estimated, assuming that the aquifer was either a homogeneous system with vertical anisotropy or composed of two or three layers of different hydraulic properties. In two out of three cases, a more accurate interpretation was obtained for a multi-layer model defined on the basis of lithostratigraphic information obtained from geological descriptions of sediment samples, gammalogs, and flow-meter tests. Analysis of the pumping tests resulted in values for horizontal hydraulic conductivities that are in good accordance with those obtained from slug tests and mini-slug tests. Besides the horizontal hydraulic conductivity, it is possible to determine the vertical hydraulic conductivity, specific yield, and specific storage based on a pumping test of a partially penetrating well. The study demonstrates that pumping tests of partially penetrating wells can be analyzed using inverse numerical models. The model used in the study was a finite-element flow model combined with a non-linear regression model. Such a model can accommodate more geological information and complex boundary conditions, and the parameter-estimation procedure can be formalized to obtain optimum estimates of hydraulic parameters and their standard deviations.

Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes.

Science.gov (United States)

Lawrence, J

1999-12-01

The Selfish Operon Model postulates that the organization of bacterial genes into operons is beneficial to the constituent genes in that proximity allows horizontal cotransfer of all genes required for a selectable phenotype; eukaryotic operons formed for very different reasons. Horizontal transfer of selfish operons most probably promotes bacterial diversification.

Horizontal wells in subsurface remediation

International Nuclear Information System (INIS)

Losonsky, G.; Beljin, M.S.

1992-01-01

This paper reports on horizontal wells which offer an effective alternative to vertical wells in various environmental remediation technologies. Hydrogeological advantages of horizontal wells over vertical wells include a larger zone of influence, greater screen length, higher specific capacity and lower groundwater screen entrance velocity. Because of these advantages, horizontal wells can reduce treatment time and costs of groundwater recovery (pump-and-treat), in situ groundwater aeration (sparging) and soil gas extraction (vacuum extraction). Horizontal wells are also more effective than vertical wells in landfill leachate collection (under-drains), bioremediation, and horizontal grout injection

Phylogenetic diversity of Pasteurellaceae and horizontal gene transfer of leukotoxin in wild and domestic sheep.

Science.gov (United States)

Kelley, Scott T; Cassirer, E Frances; Weiser, Glen C; Safaee, Shirin

2007-01-01

Wild and domestic animal populations are known to be sources and reservoirs of emerging diseases. There is also a growing recognition that horizontal genetic transfer (HGT) plays an important role in bacterial pathogenesis. We used molecular phylogenetic methods to assess diversity and cross-transmission rates of Pasteurellaceae bacteria in populations of bighorn sheep, Dall's sheep, domestic sheep and domestic goats. Members of the Pasteurellaceae cause an array of deadly illnesses including bacterial pneumonia known as "pasteurellosis", a particularly devastating disease for bighorn sheep. A phylogenetic analysis of a combined dataset of two RNA genes (16S ribosomal RNA and RNAse P RNA) revealed remarkable evolutionary diversity among Pasteurella trehalosi and Mannheimia (Pasteurella) haemolytica bacteria isolated from sheep and goats. Several phylotypes appeared to associate with particular host species, though we found numerous instances of apparent cross-transmission among species and populations. Statistical analyses revealed that host species, geographic locale and biovariant classification, but not virulence, correlated strongly with Pasteurellaceae phylogeny. Sheep host species correlated with P. trehalosi isolates phylogeny (PTP test; P=0.002), but not with the phylogeny of M. haemolytica isolates, suggesting that P. trehalosi bacteria may be more host specific. With regards to populations within species, we also discovered a strong correlation between geographic locale and isolate phylogeny in the Rocky Mountain bighorn sheep (PTP test; P=0.001). We also investigated the potential for HGT of the leukotoxin A (lktA) gene, which produces a toxin that plays an integral role in causing disease. Comparative analysis of the combined RNA gene phylogeny and the lktA phylogenies revealed considerable incongruence between the phylogenies, suggestive of HGT. Furthermore, we found identical lktA alleles in unrelated bacterial species, some of which had been isolated

In Silico Gene-Level Evolution Explains Microbial Population Diversity through Differential Gene Mobility

NARCIS (Netherlands)

van Dijk, Bram; Hogeweg, P.

2016-01-01

Microbial communities can show astonishing ecological and phylogenetic diversity. What is the role of pervasive horizontal gene transfer (HGT) in shaping this diversity in the presence of clonally expanding "killer strains"? Does HGT of antibiotic production and resistance genes erase phylogenetic

Nitrogen removal and its relationship with the nitrogen-cycle genes and microorganisms in the horizontal subsurface flow constructed wetlands with different design parameters.

Science.gov (United States)

Chen, Jun; Ying, Guang-Guo; Liu, You-Sheng; Wei, Xiao-Dong; Liu, Shuang-Shuang; He, Liang-Ying; Yang, Yong-Qiang; Chen, Fan-Rong

2017-07-03

This study aims to investigate nitrogen removal and its relationship with the nitrogen-cycle genes and microorganisms in the horizontal subsurface flow constructed wetlands (CWs) with different design parameters. Twelve mesocosm-scale CWs with four substrates and three hydraulic loading rates were set up in the outdoor. The result showed the CWs with zeolite as substrate and HLR of 20 cm/d were selected as the best choice for the TN and NH 3 -N removal. It was found that the single-stage mesocosm-scale CWs were incapable to achieve high removals of TN and NH 3 -N due to inefficient nitrification process in the systems. This was demonstrated by the lower abundance of the nitrification genes (AOA and AOB) than the denitrification genes (nirK and nirS), and the less diverse nitrification microorganisms than the denitrification microorganisms in the CWs. The results also show that microorganism community structure including nitrogen-cycle microorganisms in the constructed wetland systems was affected by the design parameters especially the substrate type. These findings show that nitrification is a limiting factor for the nitrogen removal by CWs.

Genetic classification and distinguishing of Staphylococcus species based on different partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf gene sequences.

Science.gov (United States)

Ghebremedhin, B; Layer, F; König, W; König, B

2008-03-01

The analysis of 16S rRNA gene sequences has been the technique generally used to study the evolution and taxonomy of staphylococci. However, the results of this method do not correspond to the results of polyphasic taxonomy, and the related species cannot always be distinguished from each other. Thus, new phylogenetic markers for Staphylococcus spp. are needed. We partially sequenced the gap gene (approximately 931 bp), which encodes the glyceraldehyde-3-phosphate dehydrogenase, for 27 Staphylococcus species. The partial sequences had 24.3 to 96% interspecies homology and were useful in the identification of staphylococcal species (F. Layer, B. Ghebremedhin, W. König, and B. König, J. Microbiol. Methods 70:542-549, 2007). The DNA sequence similarities of the partial staphylococcal gap sequences were found to be lower than those of 16S rRNA (approximately 97%), rpoB (approximately 86%), hsp60 (approximately 82%), and sodA (approximately 78%). Phylogenetically derived trees revealed four statistically supported groups: S. hyicus/S. intermedius, S. sciuri, S. haemolyticus/S. simulans, and S. aureus/epidermidis. The branching of S. auricularis, S. cohnii subsp. cohnii, and the heterogeneous S. saprophyticus group, comprising S. saprophyticus subsp. saprophyticus and S. equorum subsp. equorum, was not reliable. Thus, the phylogenetic analysis based on the gap gene sequences revealed similarities between the dendrograms based on other gene sequences (e.g., the S. hyicus/S. intermedius and S. sciuri groups) as well as differences, e.g., the grouping of S. arlettae and S. kloosii in the gap-based tree. From our results, we propose the partial sequencing of the gap gene as an alternative molecular tool for the taxonomical analysis of Staphylococcus species and for decreasing the possibility of misidentification.

Genetic Classification and Distinguishing of Staphylococcus Species Based on Different Partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf Gene Sequences▿

Science.gov (United States)

Ghebremedhin, B.; Layer, F.; König, W.; König, B.

2008-01-01

The analysis of 16S rRNA gene sequences has been the technique generally used to study the evolution and taxonomy of staphylococci. However, the results of this method do not correspond to the results of polyphasic taxonomy, and the related species cannot always be distinguished from each other. Thus, new phylogenetic markers for Staphylococcus spp. are needed. We partially sequenced the gap gene (∼931 bp), which encodes the glyceraldehyde-3-phosphate dehydrogenase, for 27 Staphylococcus species. The partial sequences had 24.3 to 96% interspecies homology and were useful in the identification of staphylococcal species (F. Layer, B. Ghebremedhin, W. König, and B. König, J. Microbiol. Methods 70:542-549, 2007). The DNA sequence similarities of the partial staphylococcal gap sequences were found to be lower than those of 16S rRNA (∼97%), rpoB (∼86%), hsp60 (∼82%), and sodA (∼78%). Phylogenetically derived trees revealed four statistically supported groups: S. hyicus/S. intermedius, S. sciuri, S. haemolyticus/S. simulans, and S. aureus/epidermidis. The branching of S. auricularis, S. cohnii subsp. cohnii, and the heterogeneous S. saprophyticus group, comprising S. saprophyticus subsp. saprophyticus and S. equorum subsp. equorum, was not reliable. Thus, the phylogenetic analysis based on the gap gene sequences revealed similarities between the dendrograms based on other gene sequences (e.g., the S. hyicus/S. intermedius and S. sciuri groups) as well as differences, e.g., the grouping of S. arlettae and S. kloosii in the gap-based tree. From our results, we propose the partial sequencing of the gap gene as an alternative molecular tool for the taxonomical analysis of Staphylococcus species and for decreasing the possibility of misidentification. PMID:18174295

Vertical and horizontal distribution of sediment nitrite-dependent methane-oxidizing organisms in a mesotrophic freshwater reservoir.

Science.gov (United States)

Long, Yan; Liu, Changbao; Lin, Hengliang; Li, Ningning; Guo, Qingwei; Xie, Shuguang

2017-06-01

In the present study, we investigated the spatial change of sediment nitrite-dependent anaerobic methane-oxidizing (n-damo) organisms in the mesotrophic freshwater Gaozhou Reservoir (6 different sampling locations and 2 sediment depths (0-5 cm, 5-10 cm)), one of the largest drinking water reservoirs in China. The abundance of sediment n-damo bacteria was quantified using quantitative polymerase chain reaction assay, while the richness, diversity, and composition of n-damo pmoA gene sequences were characterized using clone library analysis. Vertical and horizontal changes in sediment n-damo bacterial abundance occurred in Gaozhou Reservoir, with 1.37 × 10 5 to 8.24 × 10 5 n-damo 16S rRNA gene copies per gram of dry sediment. Considerable horizontal and vertical variations of n-damo pmoA gene diversity (Shannon index = 0.32-2.50) and composition also occurred in this reservoir. Various types of sediment n-damo pmoA genes existed in Gaozhou Reservoir. A small proportion of n-damo pmoA gene sequences (19.1%) were related to those recovered from "Candidatus Methylomirabilis oxyfera". Our results suggested that sediment n-damo pmoA gene diversity might be regulated by nitrite, while n-damo pmoA gene richness might be governed by multiple environmental factors, including total organic carbon, total phosphorus, nitrite, and total nitrogen.

Molecular analysis of the androgen-receptor gene in a family with receptor-positive partial androgen insensitivity: an unusual type of intronic mutation

NARCIS (Netherlands)

H.T. Brüggenwirth (Hennie); A.L.M. Boehmer (Annemie); S. Ramnarain; M.C. Verleun-Mooijman; D.P.E. Satijn (David); J. Trapman (Jan); J.A. Grootegoed (Anton); A.O. Brinkmann (Albert)

1997-01-01

textabstractIn the coding part and the intron-exon boundaries of the androgen-receptor gene of a patient with partial androgen insensitivity, no mutation was found. The androgen receptor of this patient displayed normal ligand-binding parameters and migrated as a

Gene features selection for three-class disease classification via multiple orthogonal partial least square discriminant analysis and S-plot using microarray data.

Science.gov (United States)

Yang, Mingxing; Li, Xiumin; Li, Zhibin; Ou, Zhimin; Liu, Ming; Liu, Suhuan; Li, Xuejun; Yang, Shuyu

2013-01-01

DNA microarray analysis is characterized by obtaining a large number of gene variables from a small number of observations. Cluster analysis is widely used to analyze DNA microarray data to make classification and diagnosis of disease. Because there are so many irrelevant and insignificant genes in a dataset, a feature selection approach must be employed in data analysis. The performance of cluster analysis of this high-throughput data depends on whether the feature selection approach chooses the most relevant genes associated with disease classes. Here we proposed a new method using multiple Orthogonal Partial Least Squares-Discriminant Analysis (mOPLS-DA) models and S-plots to select the most relevant genes to conduct three-class disease classification and prediction. We tested our method using Golub's leukemia microarray data. For three classes with subtypes, we proposed hierarchical orthogonal partial least squares-discriminant analysis (OPLS-DA) models and S-plots to select features for two main classes and their subtypes. For three classes in parallel, we employed three OPLS-DA models and S-plots to choose marker genes for each class. The power of feature selection to classify and predict three-class disease was evaluated using cluster analysis. Further, the general performance of our method was tested using four public datasets and compared with those of four other feature selection methods. The results revealed that our method effectively selected the most relevant features for disease classification and prediction, and its performance was better than that of the other methods.

Co-evolution of secondary metabolite gene clusters and their host

DEFF Research Database (Denmark)

Kjærbølling, Inge; Vesth, Tammi Camilla; Frisvad, Jens Christian

Secondary metabolite gene cluster evolution is mainly driven by two events: gene duplication and annexation and horizontal gene transfer. Here we use comparative genomics of Aspergillus species to investigate the evolution of secondary metabolite (SM) gene clusters across a wide spectrum of speci....... We investigate the dynamic evolutionary relationship between the cluster and the host by examining the genes within the cluster and the number of homologous genes found within the host and in closely related species.......Secondary metabolite gene cluster evolution is mainly driven by two events: gene duplication and annexation and horizontal gene transfer. Here we use comparative genomics of Aspergillus species to investigate the evolution of secondary metabolite (SM) gene clusters across a wide spectrum of species...

Comparative genomic analysis of the arthropod muscle myosin heavy chain genes allows ancestral gene reconstruction and reveals a new type of 'partially' processed pseudogene

Directory of Open Access Journals (Sweden)

Kollmar Martin

2008-02-01

Full Text Available Abstract Background Alternative splicing of mutually exclusive exons is an important mechanism for increasing protein diversity in eukaryotes. The insect Mhc (myosin heavy chain gene produces all different muscle myosins as a result of alternative splicing in contrast to most other organisms of the Metazoa lineage, that have a family of muscle genes with each gene coding for a protein specialized for a functional niche. Results The muscle myosin heavy chain genes of 22 species of the Arthropoda ranging from the waterflea to wasp and Drosophila have been annotated. The analysis of the gene structures allowed the reconstruction of an ancient muscle myosin heavy chain gene and showed that during evolution of the arthropods introns have mainly been lost in these genes although intron gain might have happened in a few cases. Surprisingly, the genome of Aedes aegypti contains another and that of Culex pipiens quinquefasciatus two further muscle myosin heavy chain genes, called Mhc3 and Mhc4, that contain only one variant of the corresponding alternative exons of the Mhc1 gene. Mhc3 transcription in Aedes aegypti is documented by EST data. Mhc3 and Mhc4 inserted in the Aedes and Culex genomes either by gene duplication followed by the loss of all but one variant of the alternative exons, or by incorporation of a transcript of which all other variants have been spliced out retaining the exon-intron structure. The second and more likely possibility represents a new type of a 'partially' processed pseudogene. Conclusion Based on the comparative genomic analysis of the alternatively spliced arthropod muscle myosin heavy chain genes we propose that the splicing process operates sequentially on the transcript. The process consists of the splicing of the mutually exclusive exons until one exon out of the cluster remains while retaining surrounding intronic sequence. In a second step splicing of introns takes place. A related mechanism could be responsible for

Horizontal transfer generates genetic variation in an asexual pathogen

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Xiaoqiu Huang

2014-10-01

Full Text Available There are major gaps in the understanding of how genetic variation is generated in the asexual pathogen Verticillium dahliae. On the one hand, V. dahliae is a haploid organism that reproduces clonally. On the other hand, single-nucleotide polymorphisms and chromosomal rearrangements were found between V. dahliae strains. Lineage-specific (LS regions comprising about 5% of the genome are highly variable between V. dahliae strains. Nonetheless, it is unknown whether horizontal gene transfer plays a major role in generating genetic variation in V. dahliae. Here, we analyzed a previously sequenced V. dahliae population of nine strains from various geographical locations and hosts. We found highly homologous elements in LS regions of each strain; LS regions of V. dahliae strain JR2 are much richer in highly homologous elements than the core genome. In addition, we discovered, in LS regions of JR2, several structural forms of nonhomologous recombination, and two or three homologous sequence types of each form, with almost each sequence type present in an LS region of another strain. A large section of one of the forms is known to be horizontally transferred between V. dahliae strains. We unexpectedly found that 350 kilobases of dynamic LS regions were much more conserved than the core genome between V. dahliae and a closely related species (V. albo-atrum, suggesting that these LS regions were horizontally transferred recently. Our results support the view that genetic variation in LS regions is generated by horizontal transfer between strains, and by chromosomal reshuffling reported previously.

Vertical and horizontal subsidiarity

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Ivan V. Daniluk

2016-02-01

Full Text Available This article makes an attempt to analyze the principle of subsidiarity in its two main manifestations, namely vertical and horizontal, to outline the principles of relations between the state and regions within the vertical subsidiarity, and features a collaboration of the government and civil society within the horizontal subsidiarity. Scientists identify two types, or two levels of the subsidiarity principle: vertical subsidiarity and horizontal subsidiarity. First, vertical subsidiarity (or territorial concerning relations between the state and other levels of subnational government, such as regions and local authorities; second, horizontal subsidiarity (or functional concerns the relationship between state and citizen (and civil society. Vertical subsidiarity expressed in the context of the distribution of administrative responsibilities to the appropriate higher level lower levels relative to the state structure, ie giving more powers to local government. However, state intervention has subsidiary-lower action against local authorities in cases of insolvency last cope on their own, ie higher organisms intervene only if the duties are less authority is insufficient to achieve the goals. Horizontal subsidiarity is within the relationship between power and freedom, and is based on the assumption that the concern for the common good and the needs of common interest community, able to solve community members (as individuals and citizens’ associations and role of government, in accordance horizontal subsidiarity comes to attracting features subsidiarity assistance, programming, coordination and possibly control.

Improved waterflooding efficiency by horizontal wells

Energy Technology Data Exchange (ETDEWEB)

Popa, C. G. [Petroleum and Gas Univ., Ploesti (Romania); Clipea, M. [SNP Petrom SA, ICPT Campina (Romania)

1998-12-31

The influence of well pattern involving the use of horizontal wells on the overall efficiency of the waterflooding process was analyzed. Three different scenarios were examined: (1) a pattern of using two parallel horizontal wells, one for injection, the other for production, (2) a pattern of one horizontal well for water injection and several vertical wells for production, and (3) a pattern of using vertical wells for injection and one horizontal well for production. In each case, the waterflooding process was simulated using a two phase two dimensional numerical model. Results showed that the pressure loss along the horizontal section had a large influence on the sweep efficiency whether the horizontal well was used for injection or production. Overall, the most successful combination appeared to be using vertical wells for injection and horizontal wells for production. 4 refs., 1 tab., 15 figs.

Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability. | Office of Cancer Genomics

Science.gov (United States)

Genomic instability is a hallmark of human cancer, and results in widespread somatic copy number alterations. We used a genome-scale shRNA viability screen in human cancer cell lines to systematically identify genes that are essential in the context of particular copy-number alterations (copy-number associated gene dependencies). The most enriched class of copy-number associated gene dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes, and spliceosome components were the most prevalent.

DNA methylation dynamics in the rat EGF gene promoter after partial hepatectomy

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Deming Li

2014-06-01

Full Text Available Epidermal growth factor (EGF, a multifunctional growth factor, is a regulator in a wide variety of physiological processes. EGF plays an important role in the regulation of liver regeneration. This study was aimed at investigating the methylation level of EGF gene throughout liver regeneration. DNA of liver tissue from control rats and partial hepatectomy (PH rats at 10 time points was extracted and a 354 bp fragment including 10 CpG sites from the transcription start was amplified after DNA was modified by sodium bisulfate. The result of sequencing suggested that methylation ratio of four CpG sites was found to be significantly changed when PH group was compared to control group, in particular two of them were extremely striking. mRNA expression of EGF was down-regulated in total during liver regeneration. We think that the rat EGF promoter region is regulated by variation in DNA methylation during liver regeneration.

Groundwater flow to a horizontal or slanted well in an unconfined aquifer

Science.gov (United States)

Zhan, Hongbin; Zlotnik, Vitaly A.

2002-07-01

New semianalytical solutions for evaluation of the drawdown near horizontal and slanted wells with finite length screens in unconfined aquifers are presented. These fully three-dimensional solutions consider instantaneous drainage or delayed yield and aquifer anisotropy. As a basis, solution for the drawdown created by a point source in a uniform anisotropic unconfined aquifer is derived in Laplace domain. Using superposition, the point source solution is extended to the cases of the horizontal and slanted wells. The previous solutions for vertical wells can be described as a special case of the new solutions. Numerical Laplace inversion allows effective evaluation of the drawdown in real time. Examples illustrate the effects of well geometry and the aquifer parameters on drawdown. Results can be used to generate type curves from observations in piezometers and partially or fully penetrating observation wells. The proposed solutions and software are useful for the parameter identification, design of remediation systems, drainage, and mine dewatering.

The patterning of retinal horizontal cells: normalizing the regularity index enhances the detection of genomic linkage

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Patrick W. Keeley

2014-10-01

Full Text Available Retinal neurons are often arranged as non-random distributions called mosaics, as their somata minimize proximity to neighboring cells of the same type. The horizontal cells serve as an example of such a mosaic, but little is known about the developmental mechanisms that underlie their patterning. To identify genes involved in this process, we have used three different spatial statistics to assess the patterning of the horizontal cell mosaic across a panel of genetically distinct recombinant inbred strains. To avoid the confounding effect cell density, which varies two-fold across these different strains, we computed the real/random regularity ratio, expressing the regularity of a mosaic relative to a randomly distributed simulation of similarly sized cells. To test whether this latter statistic better reflects the variation in biological processes that contribute to horizontal cell spacing, we subsequently compared the genetic linkage for each of these two traits, the regularity index and the real/random regularity ratio, each computed from the distribution of nearest neighbor (NN distances and from the Voronoi domain (VD areas. Finally, we compared each of these analyses with another index of patterning, the packing factor. Variation in the regularity indexes, as well as their real/random regularity ratios, and the packing factor, mapped quantitative trait loci (QTL to the distal ends of Chromosomes 1 and 14. For the NN and VD analyses, we found that the degree of linkage was greater when using the real/random regularity ratio rather than the respective regularity index. Using informatic resources, we narrow the list of prospective genes positioned at these two intervals to a small collection of six genes that warrant further investigation to determine their potential role in shaping the patterning of the horizontal cell mosaic.

To migrate, or not to migrate: partial diel horizontal migration of fish in a temperate freshwater reservoir

Czech Academy of Sciences Publication Activity Database

Muška, Milan; Tušer, Michal; Frouzová, Jaroslava; Draštík, Vladislav; Čech, Martin; Jůza, Tomáš; Kratochvíl, Michal; Mrkvička, T.; Peterka, Jiří; Prchalová, Marie; Říha, Milan; Vašek, Mojmír; Kubečka, Jan

2013-01-01

Roč. 707, č. 1 (2013), s. 17-28 ISSN 0018-8158. [Česká ichtyologická konference /13./. Červená nad Vltavou, 24.10.2012-26.10.2012] R&D Projects: GA MZe(CZ) QH81046; GA MŠk(CZ) EE2.3.20.0204 Institutional support: RVO:60077344 Keywords : diel activity * diurnal migration * individual decision making * horizontal hydroacoustics * purse seining * cyprinids Subject RIV: EH - Ecology, Behaviour Impact factor: 2.212, year: 2013

Theoretical study of evaporation heat transfer in horizontal microfin tubes: stratified flow model

Energy Technology Data Exchange (ETDEWEB)

Honda, H; Wang, Y S [Kyushu Univ., Inst. for Materials Chemistry and Engineering, Kasuga, Fukuoka (Japan)

2004-08-01

The stratified flow model of evaporation heat transfer in helically grooved, horizontal microfin tubes has been developed. The profile of stratified liquid was determined by a theoretical model previously developed for condensation in horizontal microfin tubes. For the region above the stratified liquid, the meniscus profile in the groove between adjacent fins was determined by a force balance between the gravity and surface tension forces. The thin film evaporation model was applied to predict heat transfer in the thin film region of the meniscus. Heat transfer through the stratified liquid was estimated by using an empirical correlation proposed by Mori et al. The theoretical predictions of the circumferential average heat transfer coefficient were compared with available experimental data for four tubes and three refrigerants. A good agreement was obtained for the region of Fr{sub 0}<2.5 as long as partial dry out of tube surface did not occur. (Author)

Mobilisation and remobilisation of a large archetypal pathogenicity island of uropathogenic Escherichia coli in vitro support the role of conjugation for horizontal transfer of genomic islands

Directory of Open Access Journals (Sweden)

Hochhut Bianca

2011-09-01

Full Text Available Abstract Background A substantial amount of data has been accumulated supporting the important role of genomic islands (GEIs - including pathogenicity islands (PAIs - in bacterial genome plasticity and the evolution of bacterial pathogens. Their instability and the high level sequence similarity of different (partial islands suggest an exchange of PAIs between strains of the same or even different bacterial species by horizontal gene transfer (HGT. Transfer events of archetypal large genomic islands of enterobacteria which often lack genes required for mobilisation or transfer have been rarely investigated so far. Results To study mobilisation of such large genomic regions in prototypic uropathogenic E. coli (UPEC strain 536, PAI II536 was supplemented with the mobRP4 region, an origin of replication (oriVR6K, an origin of transfer (oriTRP4 and a chloramphenicol resistance selection marker. In the presence of helper plasmid RP4, conjugative transfer of the 107-kb PAI II536 construct occured from strain 536 into an E. coli K-12 recipient. In transconjugants, PAI II536 existed either as a cytoplasmic circular intermediate (CI or integrated site-specifically into the recipient's chromosome at the leuX tRNA gene. This locus is the chromosomal integration site of PAI II536 in UPEC strain 536. From the E. coli K-12 recipient, the chromosomal PAI II536 construct as well as the CIs could be successfully remobilised and inserted into leuX in a PAI II536 deletion mutant of E. coli 536. Conclusions Our results corroborate that mobilisation and conjugal transfer may contribute to evolution of bacterial pathogens through horizontal transfer of large chromosomal regions such as PAIs. Stabilisation of these mobile genetic elements in the bacterial chromosome result from selective loss of mobilisation and transfer functions of genomic islands.

Comparative Screening of Digestion Tract Toxic Genes in Proteus mirabilis.

Science.gov (United States)

Shi, Xiaolu; Lin, Yiman; Qiu, Yaqun; Li, Yinghui; Jiang, Min; Chen, Qiongcheng; Jiang, Yixiang; Yuan, Jianhui; Cao, Hong; Hu, Qinghua; Huang, Shenghe

2016-01-01

Proteus mirabilis is a common urinary tract pathogen, and may induce various inflammation symptoms. Its notorious ability to resist multiple antibiotics and to form urinary tract stones makes its treatment a long and painful process, which is further challenged by the frequent horizontal gene transferring events in P. mirabilis genomes. Three strains of P. mirabilis C02011/C04010/C04013 were isolated from a local outbreak of a food poisoning event in Shenzhen, China. Our hypothesis is that new genes may have been acquired horizontally to exert the digestion tract infection and toxicity. The functional characterization of these three genomes shows that each of them independently acquired dozens of virulent genes horizontally from the other microbial genomes. The representative strain C02011 induces the symptoms of both vomit and diarrhea, and has recently acquired a complete type IV secretion system and digestion tract toxic genes from the other bacteria.

Modelling and control of growing slugs in horizontal multiphase pipe flows

Directory of Open Access Journals (Sweden)

Steinar M. Elgsæter

2006-07-01

Full Text Available In this paper, the use of active control to restrict the length of growing slugs in horizontal pipelines is investigated. Specifically, the paper attempts to determine if such control can be attained with realistic measurements and actuators. Simulations in OLGA2000 show that a feedback controller can use measurements or estimates of slug length to control the growth of a slug in a horizontal pipeline by partially closing inlet or outlet chokes. A control-volume approach is used to develop a low-order model of inlet choke-slug growth dynamics based on mass- and impulse balances. The resulting model is a system of nonlinear differential-algebraic equations, which is suitable for observer-design. The tuned model is found to be in good agreement with experiments and OLGA2000-simulations. Linearizations of the model are found to be observable around realistic trajectories when rates and pressures at the inlet and outlet are measured. An extended Luenberger-observer is shown to give good estimates of slug length and -position in simulations even under model uncertainty.

Massive gene swamping among cheese-making Penicillium fungi

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Jeanne Ropars

2015-03-01

Full Text Available Horizontal gene transfers (HGT, i.e., the transmission of genetic material between species not directly attributable to meiotic gene exchange, have long been acknowledged as a major driver of prokaryotic evolution and is increasingly recognized as an important source of adaptation in eukaryotes. In fungi in particular, many convincing examples of HGT have been reported to confer selective advantages on the recipient fungal host, either promoting fungal pathogenicity on plants or increasing their toxicity by the acquisition of secondary metabolic clusters, resulting in adaptation to new niches and in some cases eventually even in speciation. These horizontal gene transfers involve single genes, complete metabolic pathways or even entire chromosomes. A recent study has uncovered multiple recent horizontal transfers of a 575 kb genomic island in cheese Penicillium fungi, representing ca. 2% of the Penicillium roqueforti’s genome, that may confer selective advantage in the competing cheese environment where bacteria and fungi occur. Novel phylogenomic methods are being developed, revealing massive HGT among fungi. Altogether, these recent studies indicate that HGT is a crucial mechanism of rapid adaptation, even among eukaryotes.

Deep sequencing revealed molecular signature of horizontal gene transfer of plant like transcripts in the mosquito Anopheles culicifacies: an evolutionary puzzle [version 1; referees: 2 approved

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Punita Sharma

2015-12-01

Full Text Available In prokaryotes, horizontal gene transfer (HGT has been regarded as an important evolutionary drive to acquire and retain beneficial genes for their survival in diverse ecologies. However, in eukaryotes, the functional role of HGTs remains questionable, although current genomic tools are providing increased evidence of acquisition of novel traits within non-mating metazoan species. Here, we provide another transcriptomic evidence for the acquisition of massive plant genes in the mosquito, Anopheles culicifacies. Our multiple experimental validations including genomic PCR, RT-PCR, real-time PCR, immuno-blotting and immuno-florescence microscopy, confirmed that plant like transcripts (PLTs are of mosquito origin and may encode functional proteins. A comprehensive molecular analysis of the PLTs and ongoing metagenomic analysis of salivary microbiome provide initial clues that mosquitoes may have survival benefits through the acquisition of nuclear as well as chloroplast encoded plant genes. Our findings of PLTs further support the similar questionable observation of HGTs in other higher organisms, which is still a controversial and debatable issue in the community of evolutionists. We believe future understanding of the underlying mechanism of the feeding associated molecular responses may shed new insights in the functional role of PLTs in the mosquito.

Experimental and Simulation for the Effect of Partial Shading on Solar Panel Performance

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Emad Talib Hahsim

2016-06-01

Full Text Available Partial shading is one of the problems that affects the power production and the efficiency of photovoltaic module. A series of experimental work have been done of partial shading of monocrystalline PV module; 50W, Isc: 3.1A, Voc: 22V with 36 cells in series is achieved. Non-linear power output responses of the module are observed by applying various cases of partial shading (vertical and horizontal shading of solar cells in the module. Shading a single cell (corner cell has the greatest impact on output energy. Horizontal shading or vertical shading reduced the power from 41W to 18W at constant solar radiation 1000W/m2 and steady state condition. Vertical blocking a column of cells (9 cells in a module reduces the power from 41W to 18W (53% power reduction; while, blocking one or two cell in the row reduces the power from 41 W to 18W (53% power reduction. Shading three or four cells in the same row reduces the power from 41W to 1W or 0.006W (94% power reduction. A complete Matlab / Simulink model are achieved to simulate the effect of partial shading on power output of module. It is found that shading a single cell reduces the power from 50 W to 25 W (50% using Matlab/Simulink model. Comparisons have been made between the I-V and P-V characteristic curves from the simulation with the practical (experimental curves. The results showed that the percentage of error between the Simulink results and the corresponding experimental measurement are 22% without shading effect and, 32% with partial shading.

Partial correction of a severe molecular defect in hemophilia A, because of errors during expression of the factor VIII gene

Energy Technology Data Exchange (ETDEWEB)

Young, M.; Antonarakis, S.E. [Univ. of Geneva (Switzerland); Inaba, Hiroshi [Tokyo Medical College (Japan)] [and others

1997-03-01

Although the molecular defect in patients in a Japanese family with mild to moderately severe hemophilia A was a deletion of a single nucleotide T within an A{sub 8}TA{sub 2} sequence of exon 14 of the factor VIII gene, the severity of the clinical phenotype did not correspond to that expected of a frameshift mutation. A small amount of functional factor VIII protein was detected in the patient`s plasma. Analysis of DNA and RNA molecules from normal and affected individuals and in vitro transcription/translation suggested a partial correction of the molecular defect, because of the following: (i) DNA replication/RNA transcription errors resulting in restoration of the reading frame and/or (ii) {open_quotes}ribosomal frameshifting{close_quotes} resulting in the production of normal factor VIII polypeptide and, thus, in a milder than expected hemophilia A. All of these mechanisms probably were promoted by the longer run of adenines, A{sub 10} instead of A{sub 8}TA{sub 2}, after the delT. Errors in the complex steps of gene expression therefore may partially correct a severe frameshift defect and ameliorate an expected severe phenotype. 36 refs., 6 figs.

Partial Sequencing of 16S rRNA Gene of Selected Staphylococcus aureus Isolates and its Antibiotic Resistance

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Harsi Dewantari Kusumaningrum

2016-08-01

Full Text Available The choice of primer used in 16S rRNA sequencing for identification of Staphylococcus species found in food is important. This study aimed to characterize Staphylococcus aureus isolates by partial sequencing based on 16S rRNA gene employing primers 16sF, 63F or 1387R. The isolates were isolated from milk, egg dishes and chicken dishes and selected based on the presence of sea gene that responsible for formation of enterotoxin-A. Antibiotic susceptibility of the isolates towards six antibiotics was also tested. The use of 16sF resulted generally in higher identity percentage and query coverage compared to the sequencing by 63F or 1387R. BLAST results of all isolates, sequenced by 16sF, showed 99% homology to complete genome of four S. aureus strains, with different characteristics on enterotoxin production and antibiotic resistance. Considering that all isolates were carrying sea gene, indicated by the occurence of 120 bp amplicon after PCR amplification using primer SEA1/SEA2,  the isolates were most in agreeing to S. aureus subsp. aureus ST288. This study indicated that 4 out of 8 selected isolates were resistant towards streptomycin. The 16S rRNA gene sequencing using 16sF is useful for identification of S. aureus. However, additional analysis such as PCR employing specific gene target, should give a valuable supplementary information, when specific characteristic is expected.

Evolutionary Significance of Wolbachia-to-Animal Horizontal Gene Transfer: Female Sex Determination and the f Element in the Isopod Armadillidium vulgare.

Science.gov (United States)

Cordaux, Richard; Gilbert, Clément

2017-07-21

An increasing number of horizontal gene transfer (HGT) events from bacteria to animals have been reported in the past years, many of which involve Wolbachia bacterial endosymbionts and their invertebrate hosts. Most transferred Wolbachia genes are neutrally-evolving fossils embedded in host genomes. A remarkable case of Wolbachia HGT for which a clear evolutionary significance has been demonstrated is the " f element", a nuclear Wolbachia insert involved in female sex determination in the terrestrial isopod Armadillidium vulgare . The f element represents an instance of bacteria-to-animal HGT that has occurred so recently that it was possible to infer the donor (feminizing Wolbachia closely related to the w VulC Wolbachia strain of A. vulgare ) and the mechanism of integration (a nearly complete genome inserted by micro-homology-mediated recombination). In this review, we summarize our current knowledge of the f element and discuss arising perspectives regarding female sex determination, unstable inheritance, population dynamics and the molecular evolution of the f element. Overall, the f element unifies three major areas in evolutionary biology: symbiosis, HGT and sex determination. Its characterization highlights the tremendous impact sex ratio distorters can have on the evolution of sex determination mechanisms and sex chromosomes in animals and plants.

Evolutionary Significance of Wolbachia-to-Animal Horizontal Gene Transfer: Female Sex Determination and the f Element in the Isopod Armadillidium vulgare

Directory of Open Access Journals (Sweden)

Richard Cordaux

2017-07-01

Full Text Available An increasing number of horizontal gene transfer (HGT events from bacteria to animals have been reported in the past years, many of which involve Wolbachia bacterial endosymbionts and their invertebrate hosts. Most transferred Wolbachia genes are neutrally-evolving fossils embedded in host genomes. A remarkable case of Wolbachia HGT for which a clear evolutionary significance has been demonstrated is the “f element”, a nuclear Wolbachia insert involved in female sex determination in the terrestrial isopod Armadillidium vulgare. The f element represents an instance of bacteria-to-animal HGT that has occurred so recently that it was possible to infer the donor (feminizing Wolbachia closely related to the wVulC Wolbachia strain of A. vulgare and the mechanism of integration (a nearly complete genome inserted by micro-homology-mediated recombination. In this review, we summarize our current knowledge of the f element and discuss arising perspectives regarding female sex determination, unstable inheritance, population dynamics and the molecular evolution of the f element. Overall, the f element unifies three major areas in evolutionary biology: symbiosis, HGT and sex determination. Its characterization highlights the tremendous impact sex ratio distorters can have on the evolution of sex determination mechanisms and sex chromosomes in animals and plants.

Cell-specific cre recombinase expression allows selective ablation of glutamate receptors from mouse horizontal cells.

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Sebastian Ströh

Full Text Available In the mouse retina, horizontal cells form an electrically coupled network and provide feedback signals to photoreceptors and feedforward signals to bipolar cells. Thereby, horizontal cells contribute to gain control at the first visual synapse and to the antagonistic organization of bipolar and ganglion cell receptive fields. However, the nature of horizontal cell output remains a matter of debate, just as the exact contribution of horizontal cells to center-surround antagonism. To facilitate studying horizontal cell function, we developed a knockin mouse line which allows ablating genes exclusively in horizontal cells. This knockin line expresses a Cre recombinase under the promoter of connexin57 (Cx57, a gap junction protein only expressed in horizontal cells. Consistently, in Cx57+/Cre mice, Cre recombinase is expressed in almost all horizontal cells (>99% and no other retinal neurons. To test Cre activity, we crossbred Cx57+/Cre mice with a mouse line in which exon 11 of the coding sequence for the ionotropic glutamate receptor subunit GluA4 was flanked by two loxP sites (GluA4fl/fl. In GluA4fl/fl:Cx57+/Cre mice, GluA4 immunoreactivity was significantly reduced (∼ 50% in the outer retina where horizontal cells receive photoreceptor inputs, confirming the functionality of the Cre/loxP system. Whole-cell patch-clamp recordings from isolated horizontal cell somata showed a reduction of glutamate-induced inward currents by ∼ 75%, suggesting that the GluA4 subunit plays a major role in mediating photoreceptor inputs. The persistent current in GluA4-deficient cells is mostly driven by AMPA and to a very small extent by kainate receptors as revealed by application of the AMPA receptor antagonist GYKI52466 and concanavalin A, a potentiator of kainate receptor-mediated currents. In summary, the Cx57+/Cre mouse line provides a versatile tool for studying horizontal cell function. GluA4fl/fl:Cx57+/Cre mice, in which horizontal cells receive less

Cell-Specific Cre Recombinase Expression Allows Selective Ablation of Glutamate Receptors from Mouse Horizontal Cells

Science.gov (United States)

Janssen-Bienhold, Ulrike; Schultz, Konrad; Cimiotti, Kerstin; Weiler, Reto; Willecke, Klaus; Dedek, Karin

2013-01-01

In the mouse retina, horizontal cells form an electrically coupled network and provide feedback signals to photoreceptors and feedforward signals to bipolar cells. Thereby, horizontal cells contribute to gain control at the first visual synapse and to the antagonistic organization of bipolar and ganglion cell receptive fields. However, the nature of horizontal cell output remains a matter of debate, just as the exact contribution of horizontal cells to center-surround antagonism. To facilitate studying horizontal cell function, we developed a knockin mouse line which allows ablating genes exclusively in horizontal cells. This knockin line expresses a Cre recombinase under the promoter of connexin57 (Cx57), a gap junction protein only expressed in horizontal cells. Consistently, in Cx57+/Cre mice, Cre recombinase is expressed in almost all horizontal cells (>99%) and no other retinal neurons. To test Cre activity, we crossbred Cx57+/Cre mice with a mouse line in which exon 11 of the coding sequence for the ionotropic glutamate receptor subunit GluA4 was flanked by two loxP sites (GluA4fl/fl). In GluA4fl/fl:Cx57+/Cre mice, GluA4 immunoreactivity was significantly reduced (∼50%) in the outer retina where horizontal cells receive photoreceptor inputs, confirming the functionality of the Cre/loxP system. Whole-cell patch-clamp recordings from isolated horizontal cell somata showed a reduction of glutamate-induced inward currents by ∼75%, suggesting that the GluA4 subunit plays a major role in mediating photoreceptor inputs. The persistent current in GluA4-deficient cells is mostly driven by AMPA and to a very small extent by kainate receptors as revealed by application of the AMPA receptor antagonist GYKI52466 and concanavalin A, a potentiator of kainate receptor-mediated currents. In summary, the Cx57+/Cre mouse line provides a versatile tool for studying horizontal cell function. GluA4fl/fl:Cx57+/Cre mice, in which horizontal cells receive less excitatory input

Identification of small secreted peptides (SSPs) in maize and expression analysis of partial SSP genes in reproductive tissues.

Science.gov (United States)

Li, Ye Long; Dai, Xin Ren; Yue, Xun; Gao, Xin-Qi; Zhang, Xian Sheng

2014-10-01

Maize 1,491 small secreted peptides were identified, which were classified according to the character of peptide sequences. Partial SSP gene expressions in reproductive tissues were determined by qRT-PCR. Small secreted peptides (SSPs) are important cell-cell communication messengers in plants. Most information on plant SSPs come from Arabidopsis thaliana and Oryza sativa, while little is known about the SSPs of other grass species such as maize (Zea mays). In this study, we identified 1,491 SSP genes from maize genomic sequences. These putative SSP genes were distributed throughout the ten maize chromosomes. Among them, 611 SSPs were classified into 198 superfamilies according to their conserved domains, and 725 SSPs with four or more cysteines at their C-termini shared similar cysteine arrangements with their counterparts in other plant species. Moreover, the SSPs requiring post-translational modification, as well as defensin-like (DEFL) proteins, were identified. Further, the expression levels of 110 SSP genes were analyzed in reproductive tissues, including male flower, pollen, silk, and ovary. Most of the genes encoding basal-layer antifungal peptide-like, small coat proteins-like, thioredoxin-like proteins, γ-thionins-like, and DEFL proteins showed high expression levels in the ovary and male flower compared with their levels in silk and mature pollen. The rapid alkalinization factor-like genes were highly expressed only in the mature ovary and mature pollen, and pollen Ole e 1-like genes showed low expression in silk. The results of this study provide basic information for further analysis of SSP functions in the reproductive process of maize.

Partial IGF-1 deficiency is sufficient to reduce heart contractibility, angiotensin II sensibility, and alter gene expression of structural and functional cardiac proteins.

Science.gov (United States)

González-Guerra, José Luis; Castilla-Cortazar, Inma; Aguirre, Gabriel A; Muñoz, Úrsula; Martín-Estal, Irene; Ávila-Gallego, Elena; Granado, Miriam; Puche, Juan E; García-Villalón, Ángel Luis

2017-01-01

Circulating levels of IGF-1 may decrease under several circumstances like ageing, metabolic syndrome, and advanced cirrhosis. This reduction is associated with insulin resistance, dyslipidemia, progression to type 2 diabetes, and increased risk for cardiovascular diseases. However, underlying mechanisms between IGF-1 deficiency and cardiovascular disease remain elusive. The specific aim of the present work was to study whether the partial IGF-1 deficiency influences heart and/or coronary circulation, comparing vasoactive factors before and after of ischemia-reperfusion (I/R). In addition, histology of the heart was performed together with cardiac gene expression for proteins involved in structure and function (extracellular matrix, contractile proteins, active peptides); carried out using microarrays, followed by RT-qPCR confirmation of the three experimental groups. IGF-1 partial deficiency is associated to a reduction in contractility and angiotensin II sensitivity, interstitial fibrosis as well as altered expression pattern of genes involved in extracellular matrix proteins, calcium dynamics, and cardiac structure and function. Although this work is descriptive, it provides a clear insight of the impact that partial IGF-1 deficiency on the heart and establishes this experimental model as suitable for studying cardiac disease mechanisms and exploring therapeutic options for patients under IGF-1 deficiency conditions.

Partial IGF-1 deficiency is sufficient to reduce heart contractibility, angiotensin II sensibility, and alter gene expression of structural and functional cardiac proteins.

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José Luis González-Guerra

Full Text Available Circulating levels of IGF-1 may decrease under several circumstances like ageing, metabolic syndrome, and advanced cirrhosis. This reduction is associated with insulin resistance, dyslipidemia, progression to type 2 diabetes, and increased risk for cardiovascular diseases. However, underlying mechanisms between IGF-1 deficiency and cardiovascular disease remain elusive. The specific aim of the present work was to study whether the partial IGF-1 deficiency influences heart and/or coronary circulation, comparing vasoactive factors before and after of ischemia-reperfusion (I/R. In addition, histology of the heart was performed together with cardiac gene expression for proteins involved in structure and function (extracellular matrix, contractile proteins, active peptides; carried out using microarrays, followed by RT-qPCR confirmation of the three experimental groups. IGF-1 partial deficiency is associated to a reduction in contractility and angiotensin II sensitivity, interstitial fibrosis as well as altered expression pattern of genes involved in extracellular matrix proteins, calcium dynamics, and cardiac structure and function. Although this work is descriptive, it provides a clear insight of the impact that partial IGF-1 deficiency on the heart and establishes this experimental model as suitable for studying cardiac disease mechanisms and exploring therapeutic options for patients under IGF-1 deficiency conditions.

Biochemical diversification through foreign gene expression in bdelloid rotifers.

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Chiara Boschetti

Full Text Available Bdelloid rotifers are microinvertebrates with unique characteristics: they have survived tens of millions of years without sexual reproduction; they withstand extreme desiccation by undergoing anhydrobiosis; and they tolerate very high levels of ionizing radiation. Recent evidence suggests that subtelomeric regions of the bdelloid genome contain sequences originating from other organisms by horizontal gene transfer (HGT, of which some are known to be transcribed. However, the extent to which foreign gene expression plays a role in bdelloid physiology is unknown. We address this in the first large scale analysis of the transcriptome of the bdelloid Adineta ricciae: cDNA libraries from hydrated and desiccated bdelloids were subjected to massively parallel sequencing and assembled transcripts compared against the UniProtKB database by blastx to identify their putative products. Of ~29,000 matched transcripts, ~10% were inferred from blastx matches to be horizontally acquired, mainly from eubacteria but also from fungi, protists, and algae. After allowing for possible sources of error, the rate of HGT is at least 8%-9%, a level significantly higher than other invertebrates. We verified their foreign nature by phylogenetic analysis and by demonstrating linkage of foreign genes with metazoan genes in the bdelloid genome. Approximately 80% of horizontally acquired genes expressed in bdelloids code for enzymes, and these represent 39% of enzymes in identified pathways. Many enzymes encoded by foreign genes enhance biochemistry in bdelloids compared to other metazoans, for example, by potentiating toxin degradation or generation of antioxidants and key metabolites. They also supplement, and occasionally potentially replace, existing metazoan functions. Bdelloid rotifers therefore express horizontally acquired genes on a scale unprecedented in animals, and foreign genes make a profound contribution to their metabolism. This represents a potential

Partial nucleotide sequence analysis of 18S ribosomal RNA gene of the four genotypes of Trypanosoma congolense

International Nuclear Information System (INIS)

Osanya, A.; Majiwa, P.A.O.; Kinyanjui, P.W.

2006-01-01

Specific oligonucleotide primers based on conserved nucleotide sequences of 18s ribisomal RNA (18s rRNA) gene of Trypanosoma brucei, Leishmania donovani, Triponema aequale and Lagenidium gigantum have been designed and used in the ploymerase chain reaction (PCR) to amplify genomic DNA from four different clones each representing a different genotypic group of T. congolence. PCR products of approximately 1Kb were generated using as template DNA from each of the trypanosomes. The PCR products cross-hybridized with genomic DNA from T.brucei, T. simiae and the four genotypes of T.congolense implying significant sequence homology of 18S rRNA gene among trypanosomes. The nucleotide sequence of a segment of the PCR products were determined by direct sequencing to provide partial nucleotide sequence of the 18s rRNA gene in each T.congolense genotypic group. The sequences obtained together with those that have been published for T.brucei reveals that although most regions show inter and intra species nucleotide identity, there are several sites where deletions, insertions and base changes have occured in nucleotide sequence of of T.brucei and the four genotypes of T.congolense.(author)

An Experimental Investigation on the Ultimate Strength of Partially Infilled: Braced Steel Frames

Science.gov (United States)

Dubey, Shailendra Kumar Damodar; Kute, Sunil Y.

2017-12-01

Infilled walls are usually, considered as non-structural elements. However, these walls are effective in carrying lateral loads. In this regard, an experimental investigation was planned and conducted to study the effect of braced and partially infilled steel frames with cement mortar and concrete in comparison to the bare frames. All these frames were tested up to collapse and subjected only to horizontal loads to obtain an effective and possible solution for soft storey which are generally not infilled. In comparison to bare steel frames, partially infilled frames have an increase of lateral load capacity by 45-60%. Central bracing is more effective than that of the corner bracing. For the same load partially infilled frames have significantly less deflection than that of the bare frames. A reduced load factor is suggested for the design of soft storey columns with the partial infills. A mathematical model has been proposed to calculate the theoretical ultimate load for the braced, cement mortar and concrete partial infilled frames.

Ecological Origins of Freedom: Pathogens, Heat Stress, and Frontier Topography Predict More Vertical but Less Horizontal Governmental Restriction.

Science.gov (United States)

Conway, Lucian Gideon; Bongard, Kate; Plaut, Victoria; Gornick, Laura Janelle; Dodds, Daniel P; Giresi, Thomas; Tweed, Roger G; Repke, Meredith A; Houck, Shannon C

2017-10-01

What kinds of physical environments make for free societies? The present research investigates the effect of three different types of ecological stressors (climate stress, pathogen stress, and frontier topography) on two measurements of governmental restriction: Vertical restriction involves select persons imposing asymmetrical laws on others, while horizontal restriction involves laws that restrict most members of a society equally. Investigation 1 validates our measurements of vertical and horizontal restriction. Investigation 2 demonstrates that, across both U.S. states and a sample of nations, ecological stressors tend to cause more vertically restrictive societies but less horizontally restrictive societies. Investigation 3 demonstrates that assortative sociality partially mediates ecological stress→restriction relationships across nations, but not in U.S. states. Although some stressor-specific effects emerged (most notably, cold stress consistently showed effects in the opposite direction), these results in the main suggest that ecological stress simultaneously creates opposing pressures that push freedom in two different directions.

Partial Androgen Insensitivity Syndrome Presenting with Gynecomastia

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Sung Won Lee

2015-06-01

Full Text Available Gynecomastia is a benign enlargement of the male breast caused by the proliferation of glandular breast tissue. Determining the various causes of gynecomastia such as physiological causes, drugs, systemic diseases, and endocrine disorders is important. Androgen insensitivity syndrome (AIS is a rare endocrine disorder presenting with gynecomastia and is a disorder of male sexual differentiation caused by mutations within the androgen receptor gene. All individuals with AIS have the 46 XY karyotype, although AIS phenotypes can be classified as mild, partial or complete and can differ among both males and females including ambiguous genitalia or infertility in males. We experienced a case of partial AIS presenting with gynecomastia and identified the androgen receptor gene mutation.

Horizontal Accelerator

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Federal Laboratory Consortium — The Horizontal Accelerator (HA) Facility is a versatile research tool available for use on projects requiring simulation of the crash environment. The HA Facility is...

Molecular characterization of partial fusion gene and C-terminus extension length of haemagglutinin-neuraminidase gene of recently isolated Newcastle disease virus isolates in Malaysia

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Berhanu Ayalew

2010-08-01

Full Text Available Abstract Background Newcastle disease (ND, caused by Newcastle disease virus (NDV, is a highly contagious disease of birds and has been one of the major causes of economic losses in the poultry industry. Despite routine vaccination programs, sporadic cases have occasionally occurred in the country and remain a constant threat to commercial poultry. Hence, the present study was aimed to characterize NDV isolates obtained from clinical cases in various locations of Malaysia between 2004 and 2007 based on sequence and phylogenetic analysis of partial F gene and C-terminus extension length of HN gene. Results The coding region of eleven NDV isolates fusion (F gene and carboxyl terminal region of haemagglutinin-neuraminidase (HN gene including extensions were amplified by reverse transcriptase PCR and directly sequenced. All the isolates have shown to have non-synonymous to synonymous base substitution rate ranging between 0.081 - 0.264 demonstrating presence of negative selection. Analysis based on F gene showed the characterized isolates possess three different types of protease cleavage site motifs; namely 112RRQKRF117, 112RRRKRF117 and 112GRQGRL117 and appear to show maximum identities with isolates in the region such as cockatoo/14698/90 (Indonesia, Ch/2000 (China, local isolate AF2240 indicating the high similarity of isolates circulating in the South East Asian countries. Meanwhile, one of the isolates resembles commonly used lentogenic vaccine strains. On further characterization of the HN gene, Malaysian isolates had C-terminus extensions of 0, 6 and 11 amino acids. Analysis of the phylogenetic tree revealed that the existence of three genetic groups; namely, genotype II, VII and VIII. Conclusions The study concluded that the occurrence of three types of NDV genotypes and presence of varied carboxyl terminus extension lengths among Malaysian isolates incriminated for sporadic cases.

Molecular characterization of partial fusion gene and C-terminus extension length of haemagglutinin-neuraminidase gene of recently isolated Newcastle disease virus isolates in Malaysia.

Science.gov (United States)

Berhanu, Ayalew; Ideris, Aini; Omar, Abdul R; Bejo, Mohd Hair

2010-08-08

Newcastle disease (ND), caused by Newcastle disease virus (NDV), is a highly contagious disease of birds and has been one of the major causes of economic losses in the poultry industry. Despite routine vaccination programs, sporadic cases have occasionally occurred in the country and remain a constant threat to commercial poultry. Hence, the present study was aimed to characterize NDV isolates obtained from clinical cases in various locations of Malaysia between 2004 and 2007 based on sequence and phylogenetic analysis of partial F gene and C-terminus extension length of HN gene. The coding region of eleven NDV isolates fusion (F) gene and carboxyl terminal region of haemagglutinin-neuraminidase (HN) gene including extensions were amplified by reverse transcriptase PCR and directly sequenced. All the isolates have shown to have non-synonymous to synonymous base substitution rate ranging between 0.081 - 0.264 demonstrating presence of negative selection. Analysis based on F gene showed the characterized isolates possess three different types of protease cleavage site motifs; namely 112RRQKRF117, 112RRRKRF117 and 112GRQGRL117 and appear to show maximum identities with isolates in the region such as cockatoo/14698/90 (Indonesia), Ch/2000 (China), local isolate AF2240 indicating the high similarity of isolates circulating in the South East Asian countries. Meanwhile, one of the isolates resembles commonly used lentogenic vaccine strains. On further characterization of the HN gene, Malaysian isolates had C-terminus extensions of 0, 6 and 11 amino acids. Analysis of the phylogenetic tree revealed that the existence of three genetic groups; namely, genotype II, VII and VIII. The study concluded that the occurrence of three types of NDV genotypes and presence of varied carboxyl terminus extension lengths among Malaysian isolates incriminated for sporadic cases.

Middle frontal horizontal partial laryngectomy (MFHPL: a treatment for stage T1b squamous cell carcinoma of the glottic larynx involving anterior vocal commissure.

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Wen-bin Lei

Full Text Available OBJECTIVE: The therapeutic effect of middle frontal horizontal partial laryngectomy (MFHPL in treating stage T1b squamous cell carcinoma of the glottic larynx involving anterior vocal commissure (AVC was compared with that of the anterior frontolateral vertical partial laryngectomy (AFVPL. The feasibility and practical significance of MFHPL in clinical application was discussed in the present study. METHODS: From January 1996 to January 2010, a total of 65 patients diagnosed with stage T1bN0M0 glottic laryngeal cancer were treated with MFHPL or AFVPL. The postoperative complications, glottic reconstruction, recurrence rate, voice quality and survival rates were evaluated and compared between two treatments. RESULTS: AFVPL and MFHPL were performed in 34 and 31 patients, respectively. Flexible fiberoptic laryngoscopy revealed that in the MFHPL-treated patients the reconstructed glottis was spacious and symmetric. In contrast, AFVPL treatment resulted in irregular glottic area with poor symmetry and tubular glottis. The incidence of postoperative laryngeal stenosis significantly differed between the MFHPL- and AFVPL-treated groups (P = 0.025. No significant difference was detected in the 3- and 5-year overall- or tumor-free survival rates between two treatments. The Voice Handicap Index (VHI and maximum phonation time (MPT after surgery were 51.0±12.99 and 12.42±3.44 sec in the AFVPL-treated group; while in the MFHPL-treated patients they were 31.81±7.48 and 7.65±1.98 sec, respectively. Both differences in VHI (P = 0.012 and MPT (P = 0.024 were significant between two treatments. CONCLUSIONS: MFHPL was comparable to AFVPL with respect to postoperative complications, recurrence rate and survival rates, but possessed advantages over AFVPL in terms of the incidence of laryngeal stenosis and voice quality. Our study indicated that MFHPL has a potential value in clinical practice of treating stage T1b squamous cell carcinoma of the

What can we learn from tobacco and other Solanaceae about horizontal DNA transfer?

Czech Academy of Sciences Publication Activity Database

Talianová, Martina; Janoušek, Bohuslav

2011-01-01

Roč. 98, č. 8 (2011), s. 1231-1242 ISSN 0002-9122 R&D Projects: GA ČR(CZ) GA521/08/0932; GA ČR(CZ) GD204/09/H002 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : Agrobacterium * grafting * horizontal gene transfer Subject RIV: BO - Biophysics Impact factor: 2.664, year: 2011

Infective Endocarditis: Identification of Catalase-Negative, Gram-Positive Cocci from Blood Cultures by Partial 16S rRNA Gene Analysis and by Vitek 2 Examination

DEFF Research Database (Denmark)

Abdul-Redha, Rawaa Jalil; Kemp, Michael; Bangsborg, Jette M

2010-01-01

Streptococci, enterococci and Streptococcus-like bacteria are frequent etiologic agents of infective endocarditis and correct species identification can be a laboratory challenge. Viridans streptococci (VS) not seldomly cause contamination of blood cultures. Vitek 2 and partial sequencing of the 16......S rRNA gene were applied in order to compare the results of both methods. STRAINS ORIGINATED FROM TWO GROUPS OF PATIENTS: 149 strains from patients with infective endocarditis and 181 strains assessed as blood culture contaminants. Of the 330 strains, based on partial 16S rRNA gene sequencing......-agreeing identifications with the two methods with respect to allocation to the same VS group. Non-agreeing species identification mostly occurred among strains in the contaminant group, while for endocarditis strains notably fewer disagreeing results were observed.Only 67 of 150 strains in the mitis group strains...

Partial protoporphyrinogen oxidase (PPOX gene deletions, due to different Alu-mediated mechanisms, identified by MLPA analysis in patients with variegate porphyria

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Barbaro Michela

2013-01-01

Full Text Available Abstract Variegate porphyria (VP is an autosomal dominantly inherited hepatic porphyria. The genetic defect in the PPOX gene leads to a partial defect of protoporphyrinogen oxidase, the penultimate enzyme of heme biosynthesis. Affected individuals can develop cutaneous symptoms in sun-exposed areas of the skin and/or neuropsychiatric acute attacks. The identification of the genetic defect in VP families is of crucial importance to detect the carrier status which allows counseling to prevent potentially life threatening neurovisceral attacks, usually triggered by factors such as certain drugs, alcohol or fasting. In a total of 31 Swedish VP families sequence analysis had identified a genetic defect in 26. In the remaining five families an extended genetic investigation was necessary. After the development of a synthetic probe set, MLPA analysis to screen for single exon deletions/duplications was performed. We describe here, for the first time, two partial deletions within the PPOX gene detected by MLPA analysis. One deletion affects exon 5 and 6 (c.339-197_616+320del1099 and has been identified in four families, most probably after a founder effect. The other extends from exon 5 to exon 9 (c.339-350_987+229del2609 and was found in one family. We show that both deletions are mediated by Alu repeats. Our findings emphasize the usefulness of MLPA analysis as a complement to PPOX gene sequencing analysis for comprehensive genetic diagnostics in patients with VP.

Partial duplication of the APBA2 gene in chromosome 15q13 corresponds to duplicon structures

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Kesterson Robert A

2003-04-01

Full Text Available Abstract Background Chromosomal abnormalities affecting human chromosome 15q11-q13 underlie multiple genomic disorders caused by deletion, duplication and triplication of intervals in this region. These events are mediated by highly homologous segments of DNA, or duplicons, that facilitate mispairing and unequal cross-over in meiosis. The gene encoding an amyloid precursor protein-binding protein (APBA2 was previously mapped to the distal portion of the interval commonly deleted in Prader-Willi and Angelman syndromes and duplicated in cases of autism. Results We show that this gene actually maps to a more telomeric location and is partially duplicated within the broader region. Two highly homologous copies of an interval containing a large 5' exon and downstream sequence are located ~5 Mb distal to the intact locus. The duplicated copies, containing the first coding exon of APBA2, can be distinguished by single nucleotide sequence differences and are transcriptionally inactive. Adjacent to APBA2 maps a gene termed KIAA0574. The protein encoded by this gene is weakly homologous to a protein termed X123 that in turn maps adjacent to APBA1 on 9q21.12; APBA1 is highly homologous to APBA2 in the C-terminal region and is distinguished from APBA2 by the N-terminal region encoded by this duplicated exon. Conclusion The duplication of APBA2 sequences in this region adds to a complex picture of different low copy repeats present across this region and elsewhere on the chromosome.

Environmental Bacteriophages of the Emerging Enterobacterial Phytopathogen, Dickeya solani, Show Genomic Conservation and Capacity for Horizontal Gene Transfer between Their Bacterial Hosts

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Andrew Day

2017-08-01

Full Text Available Dickeya solani is an economically important phytopathogen widespread in mainland Europe that can reduce potato crop yields by 25%. There are no effective environmentally-acceptable chemical systems available for diseases caused by Dickeya. Bacteriophages have been suggested for use in biocontrol of this pathogen in the field, and limited field trials have been conducted. To date only a small number of bacteriophages capable of infecting D. solani have been isolated and characterized, and so there is a need to expand the repertoire of phages that may have potential utility in phage therapy strategies. Here we describe 67 bacteriophages from environmental sources, the majority of which are members of the viral family Myoviridae. Full genomic sequencing of two isolates revealed a high degree of DNA identity with D. solani bacteriophages isolated in Europe in the past 5 years, suggesting a wide ecological distribution of this phage family. Transduction experiments showed that the majority of the new environmental bacteriophages are capable of facilitating efficient horizontal gene transfer. The possible risk of unintentional transfer of virulence or antibiotic resistance genes between hosts susceptible to transducing phages cautions against their environmental use for biocontrol, until specific phages are fully tested for transduction capabilities.

Horizontal drilling under Lake Erie

Energy Technology Data Exchange (ETDEWEB)

Meller, R.

2001-07-01

Drilling oil wells under Lake Erie calls for horizontal drilling wells to be drilled from shore out into the pay-zone under the lake. The nature and characteristics of horizontal wells as compared to vertical wells are explored. Considerations that have to be taken into account in drilling horizontal wells are explained (the degree of curvature, drilling fluid quality, geosteering in the pay-zone, steering instrumentation, measurements while drilling (MWD), logging while drilling (LWD)). The concept and reasons for extended reach wells are outlined, along with characteristic features of multilateral wells.

Natural Frequencies Evaluation on Partially Damaged Building using Ambient Vibration Technique

Science.gov (United States)

Kamarudin, A. F.; Zainal Abidin, M. H.; Daud, M. E.; Noh, M. S. Md; Madun, A.; Ibrahim, A.; Matarul, J.; Mokhatar, S. N.

2018-04-01

Severe damages observed on the school blocks, roads, retaining walls and drainage within the compound of SMK Kundasang Sabah possibly due to the ground movements triggered by the Ranau earthquake in 1991. Ambient vibration measurements were carried on the remaining demolished 3-storey building which partially damaged in order to measure the predominant building frequencies using tri-axial 1 Hz seismometer sensors. Popular methods of Horizontal-to-vertical spectral ratios (HVSR) and Fourier amplitude spectra (FAS) were used to compute the ambient vibration wave fields of each building axes (Transverse or North-South (NS), Longitudinal or East-West (EW) and vertical) into Fourier spectra. Two main modes of translation and torsion were observed from the peaks frequencies obtained at 2.99 to 3.10 Hz (1st mode), 4.85 Hz (2nd mode) and 5.63 to 5.85 Hz (3rd mode). The building experiencing translation modes of bending and shear in the NS and EW directions. It could be seen when the amplitudes tends to increase when the floor are increased. Meanwhile, the torsional bending mode is expected to occur when the deformation amplitudes are found to be increasing horizontally, when moving into partially structural damaged section located on the East wing of building.

Fully developed laminar flow of two immiscible liquids through horizontal pipes: a variational approach

Energy Technology Data Exchange (ETDEWEB)

Kurban, Adib Paulo Abdalla [PETROBRAS, Rio de Janeiro (Brazil). Centro de Pesquisas; Bannwart, Antonio Carlos [Universidade Estadual de Campinas, SP (Brazil). Faculdade de Engenharia Mecanica

1990-12-31

The fully developed laminar flow of two immiscible liquids with both different viscosities and densities through a horizontal round pipe is studied. The interface between the fluids as well as their flow fields are determined by the use of a variational principle: the so called viscous dissipation principle: The results foreseen by this paper are in agreement with the physical observation (e.g. Southern and Ballman) that the more viscous fluid is total or partially encapsulated by the less viscous one. (author) 8 refs., 4 figs.

Fully developed laminar flow of two immiscible liquids through horizontal pipes: a variational approach

Energy Technology Data Exchange (ETDEWEB)

Kurban, Adib Paulo Abdalla [PETROBRAS, Rio de Janeiro (Brazil). Centro de Pesquisas; Bannwart, Antonio Carlos [Universidade Estadual de Campinas, SP (Brazil). Faculdade de Engenharia Mecanica

1991-12-31

The fully developed laminar flow of two immiscible liquids with both different viscosities and densities through a horizontal round pipe is studied. The interface between the fluids as well as their flow fields are determined by the use of a variational principle: the so called viscous dissipation principle: The results foreseen by this paper are in agreement with the physical observation (e.g. Southern and Ballman) that the more viscous fluid is total or partially encapsulated by the less viscous one. (author) 8 refs., 4 figs.

Partial Correlation Matrix Estimation using Ridge Penalty Followed by Thresholding and Reestimation

Science.gov (United States)

2014-01-01

Summary Motivated by the problem of construction gene co-expression network, we propose a statistical framework for estimating high-dimensional partial correlation matrix by a three-step approach. We first obtain a penalized estimate of a partial correlation matrix using ridge penalty. Next we select the non-zero entries of the partial correlation matrix by hypothesis testing. Finally we reestimate the partial correlation coefficients at these non-zero entries. In the second step, the null distribution of the test statistics derived from penalized partial correlation estimates has not been established. We address this challenge by estimating the null distribution from the empirical distribution of the test statistics of all the penalized partial correlation estimates. Extensive simulation studies demonstrate the good performance of our method. Application on a yeast cell cycle gene expression data shows that our method delivers better predictions of the protein-protein interactions than the Graphic Lasso. PMID:24845967

Horizontal Transfer of Small RNAs To and From Plants

Directory of Open Access Journals (Sweden)

Lu eHan

2015-12-01

Full Text Available Genetic information is traditionally thought to be transferred from parents to offspring. However, there is evidence indicating that gene transfer can also occur from microbes to higher species, such as plants, invertebrates and vertebrates. This horizontal transfer can be carried out by small RNAs (sRNAs. sRNAs have been recently reported to move across kingdoms as mobile signals, spreading silencing information toward targeted genes. sRNAs, especially microRNAs (miRNAs and small interfering RNAs (siRNAs, are non-coding molecules that control gene expression at the transcriptional or post-transcriptional level. Some sRNAs act in a cross-kingdom manner between animals and their parasites, but little is known about such sRNAs associated with plants. In this report, we provide a brief introduction to miRNAs that are transferred from plants to mammals/viruses and siRNAs that are transferred from microbes to plants. Both miRNAs and siRNAs can exert corresponding functions in the target organisms. Additionally, we provide information concerning a host-induced gene silencing (HIGS system as a potential application that utilizes the transgenic trafficking of RNA molecules to silence the genes of interacting organisms. Moreover, we lay out the controversial views regarding cross-kingdom miRNAs and call for better methodology and experimental design to confirm this unique function of miRNAs.

The emergence and fate of horizontally acquired genes in Escherichia coli

NARCIS (Netherlands)

Passel, van M.W.J.; Marri, P.R.; Ochman, H.

2008-01-01

Bacterial species, and even strains within species, can vary greatly in their gene contents and metabolic capabilities. We examine the evolution of this diversity by assessing the distribution and ancestry of each gene in 13 sequenced isolates of Escherichia coli and Shigella. We focus on the

Penetrating particles in horizontal air showers

International Nuclear Information System (INIS)

Wohlenberg, J.; Boehm, E.

1975-01-01

Particle density and arrival time of muons has been measured in Horizontal Air Showers. 5,600 showers have been recorded in 7,800 hours. Using stringent selection criteria 155 showers have been found horizontal (zenith angle larger 70 0 ) in the size range 4.1 > lg N > 5.5. The muons observed in these showers can be explained by purely electromagnetic origin of horizontal showers. (orig.) [de

Hydraulic reliability of a horizontal wetland for wastewater treatment in Sicily.

Science.gov (United States)

Marzo, A; Ventura, D; Cirelli, G L; Aiello, R; Vanella, D; Rapisarda, R; Barbagallo, S; Consoli, S

2018-09-15

The purpose of this study was to evaluate how the hydraulic behavior of a horizontal subsurface wetland (HF), that is part of the hybrid wetland (hybrid-TW) of the IKEA® store in Eastern Sicily (Italy), influences the overall wastewater treatment performance. The HF unit experiences frequent overloading peaks due to the extreme variability in the number of visitors at the store, and after 2 years of operation it showed signals of partial clogging at the inlet area. The hydraulics of the HF unit has been monitored through measurements of hydraulic conductivity at saturation (Ks), tracer tests, and geophysical (i.e. electrical resistivity tomography-ERT) measurements carried out during the years 2016 and 2017. Results indicated a general good agreement between the performed measurement techniques, thus their combination, if adequately performed and calibrated, might be a reliable tool for detecting those wetland areas mainly affected by clogging conditions. The results also indicated that partial clogging had no significant effect on the quality of the discharged water. Copyright © 2018 Elsevier B.V. All rights reserved.

The chimeric gene CHRFAM7A, a partial duplication of the CHRNA7 gene, is a dominant negative regulator of α7*nAChR function.

Science.gov (United States)

Araud, Tanguy; Graw, Sharon; Berger, Ralph; Lee, Michael; Neveu, Estele; Bertrand, Daniel; Leonard, Sherry

2011-10-15

The human α7 neuronal nicotinic acetylcholine receptor gene (CHRNA7) is a candidate gene for schizophrenia and an important drug target for cognitive deficits in the disorder. Activation of the α7*nAChR, results in opening of the channel and entry of mono- and divalent cations, including Ca(2+), that presynaptically participates to neurotransmitter release and postsynaptically to down-stream changes in gene expression. Schizophrenic patients have low levels of α7*nAChR, as measured by binding of the ligand [(125)I]-α-bungarotoxin (I-BTX). The structure of the gene, CHRNA7, is complex. During evolution, CHRNA7 was partially duplicated as a chimeric gene (CHRFAM7A), which is expressed in the human brain and elsewhere in the body. The association between a 2bp deletion in CHRFAM7A and schizophrenia suggested that this duplicate gene might contribute to cognitive impairment. To examine the putative contribution of CHRFAM7A on receptor function, co-expression of α7 and the duplicate genes was carried out in cell lines and Xenopus oocytes. Expression of the duplicate alone yielded protein expression but no functional receptor and co-expression with α7 caused a significant reduction of the amplitude of the ACh-evoked currents. Reduced current amplitude was not correlated with a reduction of I-BTX binding, suggesting the presence of non-functional (ACh-silent) receptors. This hypothesis is supported by a larger increase of the ACh-evoked current by the allosteric modulator 1-(5-chloro-2,4-dimethoxy-phenyl)-3-(5-methyl-isoxazol-3-yl)-urea (PNU-120596) in cells expressing the duplicate than in the control. These results suggest that CHRFAM7A acts as a dominant negative modulator of CHRNA7 function and is critical for receptor regulation in humans. Copyright © 2011 Elsevier Inc. All rights reserved.

Pseudo Boolean Programming for Partially Ordered Genomes

Science.gov (United States)

Angibaud, Sébastien; Fertin, Guillaume; Thévenin, Annelyse; Vialette, Stéphane

Comparing genomes of different species is a crucial problem in comparative genomics. Different measures have been proposed to compare two genomes: number of common intervals, number of adjacencies, number of reversals, etc. These measures are classically used between two totally ordered genomes. However, genetic mapping techniques often give rise to different maps with some unordered genes. Starting from a partial order between genes of a genome, one method to find a total order consists in optimizing a given measure between a linear extension of this partial order and a given total order of a close and well-known genome. However, for most common measures, the problem turns out to be NP-hard. In this paper, we propose a (0,1)-linear programming approach to compute a linear extension of one genome that maximizes the number of common intervals (resp. the number of adjacencies) between this linear extension and a given total order. Next, we propose an algorithm to find linear extensions of two partial orders that maximize the number of adjacencies.

Horizontal violence in Nursing

Directory of Open Access Journals (Sweden)

Tsimoulaki Evangelia

2017-01-01

Full Text Available One’s effort to clarify the definition of horizontal labour violence is of great importance, due to the variety of definitions that are mentioned in the worldwide scientific literature. Furthermore, the reference of multiple forms of such violence herein the nurse professional group is challenging, as well. Another fact of great importance is that, any form of professional violence (horizontal violence, horizontal mobbing in the work place environment can be possibly escalated and include even physical abuse (Bullying, besides the psychological and emotional impact for the victim. The definitions of Horizontal violence, Mobbing and Bullying, include a repeated negative behaviour emanating from at least one “predator” towards at least one “victim”, with work status differences and the existence or lack of physical abuse (Bullying. Horizontal violence is a hostile, aggressive and harmful behaviour which is either overt or concealed and is pointed from an individual to another individual of the same working rank and causes intense emotional pain at the victim. The manifestations vary from humiliating tasks assignment or the victim’s efforts undermining to clearly aggressive behaviors (criticism, intimidation, sarcasm etc.. The reason behind this phenomenon is multifactorial extended not only towards the working environment but also to the personal characteristics of the “predator” as well as the possible “victim”. The researchers emphasize the high incidence of the phenomenon, as well as the cost that is induced by the violent behaviors to both the health professionals and the hospital. Finally, they point out the paradox of the presence of violence inside a system that is designed to promote health.

Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea.

Science.gov (United States)

Schneider, Rhiannon; Rolling, William; Song, Qijian; Cregan, Perry; Dorrance, Anne E; McHale, Leah K

2016-08-11

Phytophthora root and stem rot is one of the most yield-limiting diseases of soybean [Glycine max (L.) Merr], caused by the oomycete Phytophthora sojae. Partial resistance is controlled by several genes and, compared to single gene (Rps gene) resistance to P. sojae, places less selection pressure on P. sojae populations. Thus, partial resistance provides a more durable resistance against the pathogen. In previous work, plant introductions (PIs) originating from the Republic of Korea (S. Korea) have shown to be excellent sources for high levels of partial resistance against P. sojae. Resistance to two highly virulent P. sojae isolates was assessed in 1395 PIs from S. Korea via a greenhouse layer test. Lines exhibiting possible Rps gene immunity or rot due to other pathogens were removed and the remaining 800 lines were used to identify regions of quantitative resistance using genome-wide association mapping. Sixteen SNP markers on chromosomes 3, 13 and 19 were significantly associated with partial resistance to P. sojae and were grouped into seven quantitative trait loci (QTL) by linkage disequilibrium blocks. Two QTL on chromosome 3 and three QTL on chromosome 19 represent possible novel loci for partial resistance to P. sojae. While candidate genes at QTL varied in their predicted functions, the coincidence of QTLs 3-2 and 13-1 on chromosomes 3 and 13, respectively, with Rps genes and resistance gene analogs provided support for the hypothesized mechanism of partial resistance involving weak R-genes. QTL contributing to partial resistance towards P. sojae in soybean germplasm originating from S. Korea were identified. The QTL identified in this study coincide with previously reported QTL, Rps genes, as well as novel loci for partial resistance. Molecular markers associated with these QTL can be used in the marker-assisted introgression of these alleles into elite cultivars. Annotations of genes within QTL allow hypotheses on the possible mechanisms of partial

Horizontal steam generator thermal-hydraulics

Energy Technology Data Exchange (ETDEWEB)

Ubra, O. [SKODA Praha Company, Prague (Czechoslovakia); Doubek, M. [Czech Technical Univ., Prague (Czechoslovakia)

1995-09-01

Horizontal steam generators are typical components of nuclear power plants with pressure water reactor type VVER. Thermal-hydraulic behavior of horizontal steam generators is very different from the vertical U-tube steam generator, which has been extensively studied for several years. To contribute to the understanding of the horizontal steam generator thermal-hydraulics a computer program for 3-D steady state analysis of the PGV-1000 steam generator has been developed. By means of this computer program, a detailed thermal-hydraulic and thermodynamic study of the horizontal steam generator PGV-1000 has been carried out and a set of important steam generator characteristics has been obtained. The 3-D distribution of the void fraction and 3-D level profile as functions of load and secondary side pressure have been investigated and secondary side volumes and masses as functions of load and pressure have been evaluated. Some of the interesting results of calculations are presented in the paper.

A horizontally gene transferred copper resistance locus confers hyper‐resistance to antibacterial copper toxicity and enables survival of community acquired methicillin resistant Staphylococcus aureus USA300 in macrophages

Science.gov (United States)

Purves, Joanne; Thomas, Jamie; Riboldi, Gustavo P.; Zapotoczna, Marta; Tarrant, Emma; Andrew, Peter W.; Londoño, Alejandra; Planet, Paul J.; Geoghegan, Joan A.; Waldron, Kevin J.

2018-01-01

Summary Excess copper is highly toxic and forms part of the host innate immune system's antibacterial arsenal, accumulating at sites of infection and acting within macrophages to kill engulfed pathogens. We show for the first time that a novel, horizontally gene transferred copper resistance locus (copXL), uniquely associated with the SCCmec elements of the highly virulent, epidemic, community acquired methicillin resistant Staphylococcus aureus (CA‐MRSA) USA300, confers copper hyper‐resistance. These genes are additional to existing core genome copper resistance mechanisms, and are not found in typical S. aureus lineages, but are increasingly identified in emerging pathogenic isolates. Our data show that CopX, a putative P1B‐3‐ATPase efflux transporter, and CopL, a novel lipoprotein, confer copper hyper‐resistance compared to typical S. aureus strains. The copXL genes form an operon that is tightly repressed in low copper environments by the copper regulator CsoR. Significantly, CopX and CopL are important for S. aureus USA300 intracellular survival within macrophages. Therefore, the emergence of new S. aureus clones with the copXL locus has significant implications for public health because these genes confer increased resistance to antibacterial copper toxicity, enhancing bacterial fitness by altering S. aureus interaction with innate immunity. PMID:29521441

Study of the Local Horizon. (Spanish Title: Estudio del Horizonte Local.) Estudo do Horizonte Local

Science.gov (United States)

Ros, Rosa M.

2009-12-01

The study of the horizon is fundamental to easy the first observations of the students at any education center. A simple model, to be developed in each center, allows to easy the study and comprehension of the rudiments of astronomy. The constructed model is presented in turn as a simple equatorial clock, other models (horizontal and vertical) may be constructed starting from it. El estudio del horizonte es fundamental para poder facilitar las primeras observaciones de los alumnos en un centro educativo. Un simple modelo, que debe realizarse para cada centro, nos permite facilitar el estudio y la comprensión de los primeros rudimentos astronómicos. El modelo construido se presenta a su vez como un sencillo modelo de reloj ecuatorial y a partir de él se pueden construir otros modelos (horizontal y vertical). O estudo do horizonte é fundamental para facilitar as primeiras observações dos alunos num centro educativo. Um modelo simples, que deve ser feito para cada centro, permite facilitar o estudo e a compreensão dos primeiros rudimentos astronômicos. O modelo construído apresenta-se, por sua vez, como um modelo simples de relógio equatorial e a partir dele pode-se construir outros modelos (horizontal e vertical)

Fastidious Gram-Negatives: Identification by the Vitek 2 Neisseria-Haemophilus Card and by Partial 16S rRNA Gene Sequencing Analysis

DEFF Research Database (Denmark)

Wolff Sönksen, Ute; Christensen, Jens Jørgen; Nielsen, Lisbeth

2010-01-01

Taxonomy and identification of fastidious Gram negatives are evolving and challenging. We compared identifications achieved with the Vitek 2 Neisseria-Haemophilus (NH) card and partial 16S rRNA gene sequence (526 bp stretch) analysis with identifications obtained with extensive phenotypic...... characterization using 100 fastidious Gram negative bacteria. Seventy-five strains represented 21 of the 26 taxa included in the Vitek 2 NH database and 25 strains represented related species not included in the database. Of the 100 strains, 31 were the type strains of the species. Vitek 2 NH identification...... results: 48 of 75 database strains were correctly identified, 11 strains gave `low discrimination´, seven strains were unidentified, and nine strains were misidentified. Identification of 25 non-database strains resulted in 14 strains incorrectly identified as belonging to species in the database. Partial...

Horizontal acquisition of a hypoxia-responsive molybdenum cofactor biosynthesis pathway contributed to Mycobacterium tuberculosis pathoadaptation.

Science.gov (United States)

Levillain, Florence; Poquet, Yannick; Mallet, Ludovic; Mazères, Serge; Marceau, Michael; Brosch, Roland; Bange, Franz-Christoph; Supply, Philip; Magalon, Axel; Neyrolles, Olivier

2017-11-01

The unique ability of the tuberculosis (TB) bacillus, Mycobacterium tuberculosis, to persist for long periods of time in lung hypoxic lesions chiefly contributes to the global burden of latent TB. We and others previously reported that the M. tuberculosis ancestor underwent massive episodes of horizontal gene transfer (HGT), mostly from environmental species. Here, we sought to explore whether such ancient HGT played a part in M. tuberculosis evolution towards pathogenicity. We were interested by a HGT-acquired M. tuberculosis-specific gene set, namely moaA1-D1, which is involved in the biosynthesis of the molybdenum cofactor. Horizontal acquisition of this gene set was striking because homologues of these moa genes are present all across the Mycobacterium genus, including in M. tuberculosis. Here, we discovered that, unlike their paralogues, the moaA1-D1 genes are strongly induced under hypoxia. In vitro, a M. tuberculosis moaA1-D1-null mutant has an impaired ability to respire nitrate, to enter dormancy and to survive in oxygen-limiting conditions. Conversely, heterologous expression of moaA1-D1 in the phylogenetically closest non-TB mycobacterium, Mycobacterium kansasii, which lacks these genes, improves its capacity to respire nitrate and grants it with a marked ability to survive oxygen depletion. In vivo, the M. tuberculosis moaA1-D1-null mutant shows impaired survival in hypoxic granulomas in C3HeB/FeJ mice, but not in normoxic lesions in C57BL/6 animals. Collectively, our results identify a novel pathway required for M. tuberculosis resistance to host-imposed stress, namely hypoxia, and provide evidence that ancient HGT bolstered M. tuberculosis evolution from an environmental species towards a pervasive human-adapted pathogen.

Partial characterization of nif genes from the bacterium Azospirillum amazonense

Directory of Open Access Journals (Sweden)

D.P. Potrich

2001-09-01

Full Text Available Azospirillum amazonense revealed genomic organization patterns of the nitrogen fixation genes similar to those of the distantly related species A. brasilense. Our work suggests that A. brasilense nifHDK, nifENX, fixABC operons and nifA and glnB genes may be structurally homologous to the counterpart genes of A. amazonense. This is the first analysis revealing homology between A. brasilense nif genes and the A. amazonense genome. Sequence analysis of PCR amplification products revealed similarities between the amino acid sequences of the highly conserved nifD and glnB genes of A. amazonense and related genes of A. brasilense and other bacteria. However, the A. amazonense non-coding regions (the upstream activator sequence region and the region between the nifH and nifD genes differed from related regions of A. brasilense even in nitrogenase structural genes which are highly conserved among diazotrophic bacteria. The feasibility of the 16S ribosomal RNA gene-based PCR system for specific detection of A. amazonense was shown. Our results indicate that the PCR primers for 16S rDNA defined in this article are highly specific to A. amazonense and can distinguish this species from A. brasilense.

Relationship Between Preoperative Extrusion of the Medial Meniscus and Surgical Outcomes After Partial Meniscectomy.

Science.gov (United States)

Kim, Sung-Jae; Choi, Chong Hyuk; Chun, Yong-Min; Kim, Sung-Hwan; Lee, Su-Keon; Jang, Jinyoung; Jeong, Howon; Jung, Min

2017-07-01

No previous study has examined arthritic change after meniscectomy with regard to extrusion of the medial meniscus. (1) To determine the factors related to preoperative meniscal extrusion; (2) to investigate the relationship between medial meniscal extrusion and postoperative outcomes of partial meniscectomy, and to identify a cutoff point of meniscal extrusion that contributes to arthritic change after partial meniscectomy in nonosteoarthritic knees. Cohort study; Level of evidence, 3. A total of 208 patients who underwent partial meniscectomy of the medial meniscus between January 2000 and September 2006 were retrospectively reviewed. The extent of extrusion and severity of degeneration of the medial meniscus as shown on preoperative MRI were evaluated. The minimum follow-up duration was 7 years. Clinical function was assessed with the Lysholm knee scoring scale, the International Knee Documentation Committee (IKDC) subjective knee evaluation form, and the Tapper and Hoover grading system. Radiological evaluation was conducted by use of the IKDC radiographic assessment scale. Regression analysis was performed to identify factors affecting preoperative extrusion of the medial meniscus and factors influencing follow-up results after partial meniscectomy. Receiver operating characteristic curve was used to identify a cutoff point for the extent of meniscal extrusion that was associated with arthritic change. The mean ± SD preoperative Lysholm knee score was 65.0 ± 6.3 and the mean IKDC subjective score was 60.1 ± 7.5. The mean follow-up functional scores were 93.2 ± 5.1 ( P meniscus showed a tendency to increase as the extent of intrameniscal degeneration increased, and the medial meniscus was extruded more in patients with horizontal, horizontal flap, and complex tears. The preoperative extent of meniscal extrusion had a statistically significant correlation with follow-up Lysholm knee score (coefficient = -0.10, P = .002), IKDC subjective score (coefficient

Plant-mediated horizontal transmission of Rickettsia endosymbiont between different whitefly species.

Science.gov (United States)

Li, Yi-Han; Ahmed, Muhammad Z; Li, Shao-Jian; Lv, Ning; Shi, Pei-Qiong; Chen, Xiao-Sheng; Qiu, Bao-Li

2017-12-01

A growing number of studies have revealed the presence of closely related endosymbionts in phylogenetically distant arthropods, indicating horizontal transmission of these bacteria. Here we investigated the interspecific horizontal transmission of Rickettsia between two globally invasive whitefly species, Bemisia tabaci MEAM1 and B. tabaci MED, via cotton plants. We found both scattered and confined distribution patterns of Rickettsia in these whiteflies. After entering cotton leaves, Rickettsia was restricted to the leaf phloem vessels and could be taken up by both species of the Rickettsia-free whitefly adults, but only the scattered pattern was observed in the recipient whiteflies. Both the relative quantity of Rickettsia and the efficiency of transmitting Rickettsia into cotton leaves were significantly higher in MEAM1 females than in MED females. The retention time of Rickettsia transmitted from MEAM1 into cotton leaves was at least 5 days longer than that of MED. Phylogenetic analysis based on 16S rRNA and gltA genes confirmed that the Rickettsia extracted from the donor MEAM1, the cotton leaves, the recipient MEAM1 and the recipient MED were all identical. We conclude that cotton plants can mediate horizontal transmission of Rickettsia between different insect species, and that the transmission dynamics of Rickettsia vary with different host whitefly species. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Horizontal transfer of potential mobile units in phytoplasmas.

Science.gov (United States)

Ku, Chuan; Lo, Wen-Sui; Kuo, Chih-Horng

2013-09-01

Phytoplasmas are uncultivated phytopathogenic bacteria that cause diseases in a wide range of economically important plants. Through secretion of effector proteins, they are able to manipulate their plant hosts to facilitate their multiplication and dispersal by insect vectors. The genome sequences of several phytoplasmas have been characterized to date and a group of putative composite transposons called potential mobile units (PMUs) are found in these highly reduced genomes. Recently, our team reported the genome sequence and comparative analysis of a peanut witches' broom (PnWB) phytoplasma, the first representative of the phytoplasma 16SrII group. Comparisons between the species phylogeny and the phylogenies of the PMU genes revealed that the PnWB PMU is likely to have been transferred from the 16SrI group. This indicates that PMUs are not only the DNA unit for transposition within a genome, but also for horizontal transfer among divergent phytoplasma lineages. Given the association of PMUs with effector genes, the mobility of PMUs across genomes has important implications for phytoplasma ecology and evolution.

Similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission

DEFF Research Database (Denmark)

Sipkema, Detmer; de Caralt, Sònia; Morillo, Jose A

2015-01-01

Marine sponges host diverse communities of microorganisms that are often vertically transmitted from mother to oocyte or embryo. Horizontal transmission has often been proposed to co-occur in marine sponges, but the mechanism is poorly understood. To assess the impact of the mode of transmission...... on the microbial assemblages of sponges, we analysed the microbiota in sympatric sponges that have previously been reported to acquire bacteria via either vertical (Corticium candelabrum and Crambe crambe) or horizontal transmission (Petrosia ficiformis). The comparative study was performed by PCR......-DGGE and pyrosequencing of barcoded PCR-amplified 16S rRNA gene fragments. We found that P. ficiformis and C. candelabrum each harbor their own species-specific bacteria, but they are similar to other high-microbial-abundance sponges, while the low-microbial-abundance sponge C. crambe hosts microbiota of a very different...

Multiclass Prediction with Partial Least Square Regression for Gene Expression Data: Applications in Breast Cancer Intrinsic Taxonomy

Directory of Open Access Journals (Sweden)

Chi-Cheng Huang

2013-01-01

Full Text Available Multiclass prediction remains an obstacle for high-throughput data analysis such as microarray gene expression profiles. Despite recent advancements in machine learning and bioinformatics, most classification tools were limited to the applications of binary responses. Our aim was to apply partial least square (PLS regression for breast cancer intrinsic taxonomy, of which five distinct molecular subtypes were identified. The PAM50 signature genes were used as predictive variables in PLS analysis, and the latent gene component scores were used in binary logistic regression for each molecular subtype. The 139 prototypical arrays for PAM50 development were used as training dataset, and three independent microarray studies with Han Chinese origin were used for independent validation (n=535. The agreement between PAM50 centroid-based single sample prediction (SSP and PLS-regression was excellent (weighted Kappa: 0.988 within the training samples, but deteriorated substantially in independent samples, which could attribute to much more unclassified samples by PLS-regression. If these unclassified samples were removed, the agreement between PAM50 SSP and PLS-regression improved enormously (weighted Kappa: 0.829 as opposed to 0.541 when unclassified samples were analyzed. Our study ascertained the feasibility of PLS-regression in multi-class prediction, and distinct clinical presentations and prognostic discrepancies were observed across breast cancer molecular subtypes.

HORIZONTAL WELL DRILL-IN FLUIDS

Directory of Open Access Journals (Sweden)

Nediljka Gaurina-Međimurec

1998-12-01

Full Text Available Main objective of horizontal driling is to place a drain-hole for a long distance within the pay zone to enhance productivity or injectivity. In drilling horizontal wells, more serious problems appear than in drilling vertical wells. These problems are: poor hole cleaning, excessive torque and drag, hole filling, pipe stucking, wellbore instability, loss of circulation, formation damage, poor cement job, and difficulties at logging jobs. From that reason, successful drilling and production of horizontal well depends largely on the fluid used during drilling and completion phases. Several new fluids, that fulfill some or all of required properties (hole cleaning, cutting suspension, good lubrication, and relative low formation damage, are presented in this paper.

Productivity and injectivity of horizontal wells

Energy Technology Data Exchange (ETDEWEB)

Aziz, Khalid

2000-03-06

One of the key issues addressed was pressure drop in long horizontal wells and its influence on well performance. Very little information is available in the literature on flow in pipes with influx through pipe walls. Virtually all of this work has been in small diameter pipes and with single-phase flow. In order to address this problem new experimental data on flow in horizontal and near horizontal wells have been obtained. Experiments were conducted at an industrial facility on typical 6 1/8 ID, 100 feet long horizontal well model. The new data along with available information in the literature have been used to develop new correlations and mechanistic models. Thus it is now possible to predict, within reasonable accuracy, the effect of influx through the well on pressure drop in the well.

Partial correlation matrix estimation using ridge penalty followed by thresholding and re-estimation.

Science.gov (United States)

Ha, Min Jin; Sun, Wei

2014-09-01

Motivated by the problem of construction of gene co-expression network, we propose a statistical framework for estimating high-dimensional partial correlation matrix by a three-step approach. We first obtain a penalized estimate of a partial correlation matrix using ridge penalty. Next we select the non-zero entries of the partial correlation matrix by hypothesis testing. Finally we re-estimate the partial correlation coefficients at these non-zero entries. In the second step, the null distribution of the test statistics derived from penalized partial correlation estimates has not been established. We address this challenge by estimating the null distribution from the empirical distribution of the test statistics of all the penalized partial correlation estimates. Extensive simulation studies demonstrate the good performance of our method. Application on a yeast cell cycle gene expression data shows that our method delivers better predictions of the protein-protein interactions than the Graphic Lasso. © 2014, The International Biometric Society.

Indication of Horizontal DNA Gene Transfer by Extracellular Vesicles.

Directory of Open Access Journals (Sweden)

Stefanie Fischer

Full Text Available The biological relevance of extracellular vesicles (EV in intercellular communication has been well established. Thus far, proteins and RNA were described as main cargo. Here, we show that EV released from human bone marrow derived mesenchymal stromal cells (BM-hMSC also carry high-molecular DNA in addition. Extensive EV characterization revealed this DNA mainly associated with the outer EV membrane and to a smaller degree also inside the EV. Our EV purification protocol secured that DNA is not derived from apoptotic or necrotic cells. To analyze the relevance of EV-associated DNA we lentivirally transduced Arabidopsis thaliana-DNA (A.t.-DNA as indicator into BM-hMSC and generated EV. Using quantitative polymerase chain reaction (qPCR techniques we detected high copy numbers of A.t.-DNA in EV. In recipient hMSC incubated with tagged EV for two weeks we identified A.t.-DNA transferred to recipient cells. Investigation of recipient cell DNA using quantitative PCR and verification of PCR-products by sequencing suggested stable integration of A.t.-DNA. In conclusion, for the first time our proof-of-principle experiments point to horizontal DNA transfer into recipient cells via EV. Based on our results we assume that eukaryotic cells are able to exchange genetic information in form of DNA extending the known cargo of EV by genomic DNA. This mechanism might be of relevance in cancer but also during cell evolution and development.

Entropy Generation on Nanofluid Flow through a Horizontal Riga Plate

Directory of Open Access Journals (Sweden)

Tehseen Abbas

2016-06-01

Full Text Available In this article, entropy generation on viscous nanofluid through a horizontal Riga plate has been examined. The present flow problem consists of continuity, linear momentum, thermal energy, and nanoparticle concentration equation which are simplified with the help of Oberbeck-Boussinesq approximation. The resulting highly nonlinear coupled partial differential equations are solved numerically by means of the shooting method (SM. The expression of local Nusselt number and local Sherwood number are also taken into account and discussed with the help of table. The physical influence of all the emerging parameters such as Brownian motion parameter, thermophoresis parameter, Brinkmann number, Richardson number, nanoparticle flux parameter, Lewis number and suction parameter are demonstrated graphically. In particular, we conferred their influence on velocity profile, temperature profile, nanoparticle concentration profile and Entropy profile.

Performance of horizontal versus vertical vapor extraction wells

International Nuclear Information System (INIS)

Birdsell, K.H.; Roseberg, N.D.; Edlund, K.M.

1994-06-01

Vapor extraction wells used for site remediation of volatile organic chemicals in the vadose zone are typically vertical wells. Over the past few years, there has been an increased interest in horizontal wells for environmental remediation. Despite the interest and potential benefits of horizontal wells, there has been little study of the relative performance of horizontal and vertical vapor extraction wells. This study uses numerical simulations to investigate the relative performance of horizontal versus vertical vapor extraction wells under a variety of conditions. The most significant conclusion that can be drawn from this study is that in a homogeneous medium, a single, horizontal vapor extraction well outperforms a single, vertical vapor extraction well (with surface capping) only for long, linear plumes. Guidelines are presented regarding the use of horizontal wells

Implications of Nash Bargaining for Horizontal Industry Integration

OpenAIRE

Richard E. Just; Siddhartha Mitra; Sinaia Netanyahu

2005-01-01

This article shows how horizontal industry integration can arise from transferable asymmetry of technologies and endowments. The Nash bargaining solution suggests that greater technological diversity among coordinating parties yields greater gains from horizontal integration. The framework fits the case where a firm with a superior technology franchises the technology by horizontal integration. The results appear to fit hog production where integration has been primarily horizontal and, in pa...

Evolutionary acquisition and loss of saxitoxin biosynthesis in dinoflagellates: the second "core" gene, sxtG.

Science.gov (United States)

Orr, Russell J S; Stüken, Anke; Murray, Shauna A; Jakobsen, Kjetill S

2013-04-01

Saxitoxin and its derivatives are potent neurotoxins produced by several cyanobacteria and dinoflagellate species. SxtA is the initial enzyme in the biosynthesis of saxitoxin. The dinoflagellate full mRNA and partial genomic sequences have previously been characterized, and it appears that sxtA originated in dinoflagellates through a horizontal gene transfer from a bacterium. So far, little is known about the remaining genes involved in this pathway in dinoflagellates. Here we characterize sxtG, an amidinotransferase enzyme gene that putatively encodes the second step in saxitoxin biosynthesis. In this study, the entire sxtG transcripts from Alexandrium fundyense CCMP1719 and Alexandrium minutum CCMP113 were amplified and sequenced. The transcripts contained typical dinoflagellate spliced leader sequences and eukaryotic poly(A) tails. In addition, partial sxtG transcript fragments were amplified from four additional Alexandrium species and Gymnodinium catenatum. The phylogenetic inference of dinoflagellate sxtG, congruent with sxtA, revealed a bacterial origin. However, it is not known if sxtG was acquired independently of sxtA. Amplification and sequencing of the corresponding genomic sxtG region revealed noncanonical introns. These introns show a high interspecies and low intraspecies variance, suggesting multiple independent acquisitions and losses. Unlike sxtA, sxtG was also amplified from Alexandrium species not known to synthesize saxitoxin. However, amplification was not observed for 22 non-saxitoxin-producing dinoflagellate species other than those of the genus Alexandrium or G. catenatum. This result strengthens our hypothesis that saxitoxin synthesis has been secondarily lost in conjunction with sxtA for some descendant species.

A Partial Least Square Approach for Modeling Gene-gene and Gene-environment Interactions When Multiple Markers Are Genotyped

Science.gov (United States)

Wang, Tao; Ho, Gloria; Ye, Kenny; Strickler, Howard; Elston, Robert C.

2008-01-01

Genetic association studies achieve an unprecedented level of resolution in mapping disease genes by genotyping dense SNPs in a gene region. Meanwhile, these studies require new powerful statistical tools that can optimally handle a large amount of information provided by genotype data. A question that arises is how to model interactions between two genes. Simply modeling all possible interactions between the SNPs in two gene regions is not desirable because a greatly increased number of degrees of freedom can be involved in the test statistic. We introduce an approach to reduce the genotype dimension in modeling interactions. The genotype compression of this approach is built upon the information on both the trait and the cross-locus gametic disequilibrium between SNPs in two interacting genes, in such a way as to parsimoniously model the interactions without loss of useful information in the process of dimension reduction. As a result, it improves power to detect association in the presence of gene-gene interactions. This approach can be similarly applied for modeling gene-environment interactions. We compare this method with other approaches: the corresponding test without modeling any interaction, that based on a saturated interaction model, that based on principal component analysis, and that based on Tukey’s 1-df model. Our simulations suggest that this new approach has superior power to that of the other methods. In an application to endometrial cancer case-control data from the Women’s Health Initiative (WHI), this approach detected AKT1 and AKT2 as being significantly associated with endometrial cancer susceptibility by taking into account their interactions with BMI. PMID:18615621

A partial least-square approach for modeling gene-gene and gene-environment interactions when multiple markers are genotyped.

Science.gov (United States)

Wang, Tao; Ho, Gloria; Ye, Kenny; Strickler, Howard; Elston, Robert C

2009-01-01

Genetic association studies achieve an unprecedented level of resolution in mapping disease genes by genotyping dense single nucleotype polymorphisms (SNPs) in a gene region. Meanwhile, these studies require new powerful statistical tools that can optimally handle a large amount of information provided by genotype data. A question that arises is how to model interactions between two genes. Simply modeling all possible interactions between the SNPs in two gene regions is not desirable because a greatly increased number of degrees of freedom can be involved in the test statistic. We introduce an approach to reduce the genotype dimension in modeling interactions. The genotype compression of this approach is built upon the information on both the trait and the cross-locus gametic disequilibrium between SNPs in two interacting genes, in such a way as to parsimoniously model the interactions without loss of useful information in the process of dimension reduction. As a result, it improves power to detect association in the presence of gene-gene interactions. This approach can be similarly applied for modeling gene-environment interactions. We compare this method with other approaches, the corresponding test without modeling any interaction, that based on a saturated interaction model, that based on principal component analysis, and that based on Tukey's one-degree-of-freedom model. Our simulations suggest that this new approach has superior power to that of the other methods. In an application to endometrial cancer case-control data from the Women's Health Initiative, this approach detected AKT1 and AKT2 as being significantly associated with endometrial cancer susceptibility by taking into account their interactions with body mass index.

Hemichannel-mediated and pH-based feedback from horizontal cells to cones in the vertebrate retina.

Directory of Open Access Journals (Sweden)

Iris Fahrenfort

2009-06-01

Full Text Available Recent studies designed to identify the mechanism by which retinal horizontal cells communicate with cones have implicated two processes. According to one account, horizontal cell hyperpolarization induces an increase in pH within the synaptic cleft that activates the calcium current (Ca(2+-current in cones, enhancing transmitter release. An alternative account suggests that horizontal cell hyperpolarization increases the Ca(2+-current to promote transmitter release through a hemichannel-mediated ephaptic mechanism.To distinguish between these mechanisms, we interfered with the pH regulating systems in the retina and studied the effects on the feedback responses of cones and horizontal cells. We found that the pH buffers HEPES and Tris partially inhibit feedback responses in cones and horizontal cells and lead to intracellular acidification of neurons. Application of 25 mM acetate, which does not change the extracellular pH buffer capacity, does lead to both intracellular acidification and inhibition of feedback. Because intracellular acidification is known to inhibit hemichannels, the key experiment used to test the pH hypothesis, i.e. increasing the extracellular pH buffer capacity, does not discriminate between a pH-based feedback system and a hemichannel-mediated feedback system. To test the pH hypothesis in a manner independent of artificial pH-buffer systems, we studied the effect of interfering with the endogenous pH buffer, the bicarbonate/carbonic anhydrase system. Inhibition of carbonic anhydrase allowed for large changes in pH in the synaptic cleft of bipolar cell terminals and cone terminals, but the predicted enhancement of the cone feedback responses, according to the pH-hypothesis, was not observed. These experiments thus failed to support a proton mediated feedback mechanism. The alternative hypothesis, the hemichannel-mediated ephaptic feedback mechanism, was therefore studied experimentally, and its feasibility was buttressed

Visualization of Two Phase Flow in a Horizontal Flow with Electrical Resistance Tomography based on Extended Kalman Filter

International Nuclear Information System (INIS)

Lee, Jeong Seong; Malik, Nauman Muhammad; Khambampati, Anil Kumar; Rashid, Ahmar; Kim, Sin; Kim, Kyung Youn

2008-01-01

For the visualization of the phase distribution in two phase flows, the electrical resistance tomography (ERT) technique is introduced. In ERT, the internal resistivity distribution is reconstructed based on the known sets of the injected currents and measured voltages on the surface of the object. The physical relationship between the internal resistivity and the surface voltages is governed by a partial differential equation with appropriate boundary conditions. This paper considers the estimation of the phase distribution with ERT in two phase flow in a horizontal flow using extended Kalman filter. To evaluate the reconstruction performance of the proposed algorithm, the experiments simulated two phase flows in a horizontal flow were carried out. The experiments with two phase flow phantom were done to suggest a practical implication of this research in detecting gas bubble in a feed water pipe of heat transfer systems

In situ bioremediation via horizontal wells

International Nuclear Information System (INIS)

Hazen, T.C.; Looney, B.B.; Enzien, M.; Dougherty, J.M.; Wear, J.; Fliermans, C.B.; Eddy, C.A.

1993-01-01

The test consisted of methane mixed with air into the contaminated aquifer via a horizontal well and extraction from the vadose zone via a parallel horizontal well. This configuration has the advantage of simultaneously stimulating methanotrophic activity in both the groundwater and vadose zone, and inhibiting spread of the contaminant plume. Groundwater was monitored biweekly from 13 wells for a variety of chemical and microbiological parameters. Groundwater from wells in affected areas showed increases in methanotrophs of more than 1 order of magnitude every 2 weeks for several weeks after 1% methane-in-air injection was started. Some wells had increases as much as 7 orders of magnitude. Simultaneous with the increase in methanotrophs was a decrease in water and soil gas concentrations of trichloroethylene (TCE) and tetrachloroethane (PCE). Two wells declined in TCE/PCE concentration in the water by more than 90% to below 2 ppb. All of the wells in the affected zone showed significant decreases in contaminants in less than one month. Chloride concentrations in the water were inversely correlated with TCE/PCE concentration. Four of five vadose zone piezometers declined from concentration as high as 10,000 ppm to less than 5 ppm in less than 6 weeks. The fifth cluster also declined by more than 95%. After only three months on injection, a decline in TCE/PCE in the sediment of more than 30% was also observed, with TCE/PCE being undetectable in most sediments at the end of the 14-month test. Gene probes and direct isolation from the water and sediment revealed that the right types of methanotrophs were being stimulated and that isolates could degrade TCE at a high rate

Accidental genetic engineers: horizontal sequence transfer from parasitoid wasps to their Lepidopteran hosts.

Directory of Open Access Journals (Sweden)

Sean E Schneider

Full Text Available We show here that 105 regions in two Lepidoptera genomes appear to derive from horizontally transferred wasp DNA. We experimentally verified the presence of two of these sequences in a diverse set of silkworm (Bombyx mori genomes. We hypothesize that these horizontal transfers are made possible by the unusual strategy many parasitoid wasps employ of injecting hosts with endosymbiotic polydnaviruses to minimize the host's defense response. Because these virus-like particles deliver wasp DNA to the cells of the host, there has been much interest in whether genetic information can be permanently transferred from the wasp to the host. Two transferred sequences code for a BEN domain, known to be associated with polydnaviruses and transcriptional regulation. These findings represent the first documented cases of horizontal transfer of genes between two organisms by a polydnavirus. This presents an interesting evolutionary paradigm in which host species can acquire new sequences from parasitoid wasps that attack them. Hymenoptera and Lepidoptera diverged ∼300 MYA, making this type of event a source of novel sequences for recipient species. Unlike many other cases of horizontal transfer between two eukaryote species, these sequence transfers can be explained without the need to invoke the sequences 'hitchhiking' on a third organism (e.g. retrovirus capable of independent reproduction. The cellular machinery necessary for the transfer is contained entirely in the wasp genome. The work presented here is the first such discovery of what is likely to be a broader phenomenon among species affected by these wasps.

Horizontal transmission of the Leningrad-Zagreb mumps vaccine strain: a report of six symptomatic cases of parotitis and one case of meningitis.

Science.gov (United States)

Atrasheuskaya, Alina; Kulak, Mikhail; Fisenko, Elena G; Karpov, Igor; Ignatyev, George; Atrasheuskaya, Alena

2012-08-03

Here we report horizontal symptomatic transmission of the Leningrad-Zagreb (L-Zagreb) mumps vaccine virus. Children who were the source of transmission had been vaccinated with the MMR vaccine (Serum Institute of India) contained L-Zagreb mumps virus. This is the first report of horizontal symptomatic transmission of this vaccine. The etiology of all seven contact cases was confirmed by epidemiological linking, serology and by F, SH, NP and HN mumps virus genes sequencing. Copyright © 2012 Elsevier Ltd. All rights reserved.

What tangled web: barriers to rampant horizontal gene transfer

OpenAIRE

Kurland, Charles

2005-01-01

Dawkins in his The Selfish Gene(1) quite aptly applies the term "selfish" to parasitic repetitive DNA sequences endemic to eukaryotic genomes, especially vertebrates. Doolittle and Sapienza (2) as well as Orgel and Crick (3) enlivened this notion of selfish DNA with the identification of such repetitive sequences as remnants of mobile elements such as transposons. In addition, Orgel and Crick (3) associated parasitic DNA with a potential to outgrow their host genomes by propagating ...

Small horizontal emittance in the TESLA damping ring

International Nuclear Information System (INIS)

Decking, W.

2001-01-01

The present TESLA damping ring is designed for a normalized horizontal emittance of 8x10 -6 m. γ-γ collisions at the TESLA linear collider will benefit from a further decrease of the horizontal emittance. This paper reviews the processes which limit the horizontal emittance in the damping ring. Preliminary estimates on the smallest horizontal emittance for the present TESLA damping ring design as well as an ultimate limit of the emittance reachable with the TESLA damping ring concept will be given

Reconciliation of Gene and Species Trees

Directory of Open Access Journals (Sweden)

L. Y. Rusin

2014-01-01

Full Text Available The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree.

A status report on artificial lift systems and challenges in North Dakota horizontal completions

Energy Technology Data Exchange (ETDEWEB)

Fangmeier, K. [Amerada Hess Corp., ND (United States)

2005-07-01

Partially pressure depleted reservoirs and unfavorable horizontal flow geometries can impact artificial lift designs and diagnostics. In addition, terrain slugging, drilling fines, high gas volume fractions, H{sub 2}S gas and high bottom hole temperatures also pose challenges. This paper provides an overview of various systems utilized by Amerada Hess, a company which examines methods of reducing gas lift gas volumes to achieve maximum flow. A description of naturally fractured reservoirs and limited natural fractures was provided. A comparison was presented between the original conditions at Beaver Lodge Madison and existing conditions with horizontal development. Various artificial lift challenges were examined. It was suggested that high volume lift utilizing gas lift was the preferred artificial lift system for high volume wells. It was noted that downhole sensors can be used as an indicator of potential run life. However, reliability is limited by downhole operating temperatures and electrical ground faults. A comparison of friendly and unfriendly flow systems was presented, as well as a gas lift pressure chart. A summary of average gas volume systems was provided as well as an example of a response to increase drawdown. Examples of downhole Electric Submersible Pump (ESP) sensors were provided, as well as possible flowing pressure profiles in horizontal completion because of the constraints of lift capacity. It was concluded that a single point injection and proven gas lift system is the next step in high volume lift strategy. 2 tabs, 16 figs.

Evolutionary Acquisition and Loss of Saxitoxin Biosynthesis in Dinoflagellates: the Second “Core” Gene, sxtG

Science.gov (United States)

Orr, Russell J. S.; Stüken, Anke; Murray, Shauna A.

2013-01-01

Saxitoxin and its derivatives are potent neurotoxins produced by several cyanobacteria and dinoflagellate species. SxtA is the initial enzyme in the biosynthesis of saxitoxin. The dinoflagellate full mRNA and partial genomic sequences have previously been characterized, and it appears that sxtA originated in dinoflagellates through a horizontal gene transfer from a bacterium. So far, little is known about the remaining genes involved in this pathway in dinoflagellates. Here we characterize sxtG, an amidinotransferase enzyme gene that putatively encodes the second step in saxitoxin biosynthesis. In this study, the entire sxtG transcripts from Alexandrium fundyense CCMP1719 and Alexandrium minutum CCMP113 were amplified and sequenced. The transcripts contained typical dinoflagellate spliced leader sequences and eukaryotic poly(A) tails. In addition, partial sxtG transcript fragments were amplified from four additional Alexandrium species and Gymnodinium catenatum. The phylogenetic inference of dinoflagellate sxtG, congruent with sxtA, revealed a bacterial origin. However, it is not known if sxtG was acquired independently of sxtA. Amplification and sequencing of the corresponding genomic sxtG region revealed noncanonical introns. These introns show a high interspecies and low intraspecies variance, suggesting multiple independent acquisitions and losses. Unlike sxtA, sxtG was also amplified from Alexandrium species not known to synthesize saxitoxin. However, amplification was not observed for 22 non-saxitoxin-producing dinoflagellate species other than those of the genus Alexandrium or G. catenatum. This result strengthens our hypothesis that saxitoxin synthesis has been secondarily lost in conjunction with sxtA for some descendant species. PMID:23335767

Spondylolysis and the sacro-horizontal angle in athletes

International Nuclear Information System (INIS)

Swaerd, L.; Hellstroem, M.; Jacobsson, B.; Peterson, L.; Sahlgrenska Sjukhuset, Goeteborg; King Faisal Specialist Hospital and Research Centre, Riyadh

1989-01-01

The frequency of spondylolysis and the relationship between spondylolysis and the sacro-horizontal angle in 143 athletes and 30 non-athletes is reported. Athletes had a larger sacro-horizontal angle than non-athletes. The sacro-horizontal angle was larger in athletes with spondylolysis as compared with those without. An increased incidence of spondylolysis with an increased angle was demonstrated. It is suggested that an increased sacro-horizontal angle may predispose to spondylolysis, especially in combination with the high mechanical loads sustained in certain sports. (orig.)

Spondylolysis and the sacro-horizontal angle in athletes

Energy Technology Data Exchange (ETDEWEB)

Swaerd, L.; Hellstroem, M.; Jacobsson, B.; Peterson, L. (Oestra Sjukhuset, Goeteborg (Sweden). Dept. of Orthopaedics; Sahlgrenska Sjukhuset, Goeteborg (Sweden). Dept. of Diagnostic Radiology; King Faisal Specialist Hospital and Research Centre, Riyadh (Saudi Arabia). Dept. of Radiology)

The frequency of spondylolysis and the relationship between spondylolysis and the sacro-horizontal angle in 143 athletes and 30 non-athletes is reported. Athletes had a larger sacro-horizontal angle than non-athletes. The sacro-horizontal angle was larger in athletes with spondylolysis as compared with those without. An increased incidence of spondylolysis with an increased angle was demonstrated. It is suggested that an increased sacro-horizontal angle may predispose to spondylolysis, especially in combination with the high mechanical loads sustained in certain sports. (orig.).

Retinal genes are differentially expressed in areas of primary versus secondary degeneration following partial optic nerve injury.

Directory of Open Access Journals (Sweden)

Wissam Chiha

Full Text Available Partial transection (PT of the optic nerve is an established experimental model of secondary degeneration in the central nervous system. After a dorsal transection, retinal ganglion cells (RGCs with axons in ventral optic nerve are intact but vulnerable to secondary degeneration, whereas RGCs in dorsal retina with dorsal axons are affected by primary and secondary injuries. Using microarray, we quantified gene expression changes in dorsal and ventral retina at 1 and 7 days post PT, to characterize pathogenic pathways linked to primary and secondary degeneration.In comparison to uninjured retina Cryba1, Cryba2 and Crygs, were significantly downregulated in injured dorsal retina at days 1 and 7. While Ecel1, Timp1, Mt2A and CD74, which are associated with reducing excitotoxicity, oxidative stress and inflammation, were significantly upregulated. Genes associated with oxygen binding pathways, immune responses, cytokine receptor activity and apoptosis were enriched in dorsal retina at day 1 after PT. Oxygen binding and apoptosis remained enriched at day 7, as were pathways involved in extracellular matrix modification. Fewer changes were observed in ventral retina at day 1 after PT, most associated with the regulation of protein homodimerization activity. By day 7, apoptosis, matrix organization and signal transduction pathways were enriched. Discriminant analysis was also performed for specific functional gene groups to compare expression intensities at each time point. Altered expression of selected genes (ATF3, GFAP, Ecel1, TIMP1, Tp53 and proteins (GFAP, ECEL1 and ATF3 were semi-quantitatively assessed by qRT-PCR and immunohistochemistry respectively.There was an acute and complex primary injury response in dorsal retina indicative of a dynamic interaction between neuroprotective and neurodegenerative events; ventral retina vulnerable to secondary degeneration showed a delayed injury response. Both primary and secondary injury resulted in the

Horizontal alveolar bone loss: A periodontal orphan

Science.gov (United States)

Jayakumar, A.; Rohini, S.; Naveen, A.; Haritha, A.; Reddy, Krishnanjeneya

2010-01-01

Background: Attempts to successfully regenerate lost alveolar bone have always been a clinician’s dream. Angular defects, at least, have a fairer chance, but the same cannot be said about horizontal bone loss. The purpose of the present study was to evaluate the prevalence of horizontal alveolar bone loss and vertical bone defects in periodontal patients; and later, to correlate it with the treatment modalities available in the literature for horizontal and vertical bone defects. Materials and Methods: The study was conducted in two parts. Part I was the radiographic evaluation of 150 orthopantomographs (OPGs) (of patients diagnosed with chronic periodontitis and seeking periodontal care), which were digitized and read using the AutoCAD 2006 software. All the periodontitis-affected teeth were categorized as teeth with vertical defects (if the defect angle was ≤45° and defect depth was ≥3 mm) or as having horizontal bone loss. Part II of the study comprised search of the literature on treatment modalities for horizontal and vertical bone loss in four selected periodontal journals. Results: Out of the 150 OPGs studied, 54 (36%) OPGs showed one or more vertical defects. Totally, 3,371 teeth were studied, out of which horizontal bone loss was found in 3,107 (92.2%) teeth, and vertical defects were found only in 264 (7.8%) of the teeth, which was statistically significant (P<.001). Search of the selected journals revealed 477 papers have addressed the treatment modalities for vertical and horizontal types of bone loss specifically. Out of the 477 papers, 461 (96.3%) have addressed vertical bone loss, and 18 (3.7%) have addressed treatment options for horizontal bone loss. Two papers have addressed both types of bone loss and are included in both categories. Conclusion: Horizontal bone loss is more prevalent than vertical bone loss but has been sidelined by researchers as very few papers have been published on the subject of regenerative treatment modalities for

16S partial gene mitochondrial DNA and internal transcribed spacers ribosomal DNA as differential markers of Trichuris discolor populations.

Science.gov (United States)

Callejón, R; Halajian, A; de Rojas, M; Marrugal, A; Guevara, D; Cutillas, C

2012-05-25

Comparative morphological, biometrical and molecular studies of Trichuris discolor isolated from Bos taurus from Spain and Iran was carried out. Furthermore, Trichuris ovis isolated from B. taurus and Capra hircus from Spain has been, molecularly, analyzed. Morphological studies revealed clear differences between T. ovis and T. discolor isolated from B. taurus but differences were not observed between populations of T. discolor isolated from different geographical regions. Nevertheless, the molecular studies based on the amplification and sequencing of the internal transcribed spacers 1 and 2 ribosomal DNA and 16S partial gene mitochondrial DNA showed clear differences between both populations of T. discolor from Spain and Iran suggesting two cryptic species. Phylogenetic studies corroborated these data. Thus, phylogenetic trees based on ITS1, ITS2 and 16S partial gene sequences showed that individuals of T. discolor from B. taurus from Iran clustered together and separated, with high bootstrap values, of T. discolor isolated from B. taurus from Spain, while populations of T. ovis from B. taurus and C. hircus from Spain clustered together but separated with high bootstrap values of both populations of T. discolor. Furthermore, a comparative phylogenetic study has been carried out with the ITS1and ITS2 sequences of Trichuris species from different hosts. Three clades were observed: the first clustered all the species of Trichuris parasitizing herbivores (T. discolor, T. ovis, Trichuris leporis and Trichuris skrjabini), the second clustered all the species of Trichuris parasitizing omnivores (Trichuris trichiura and Trichuris suis) and finally, the third clustered species of Trichuris parasitizing carnivores (Trichuris muris, Trichuris arvicolae and Trichuris vulpis). Copyright © 2011 Elsevier B.V. All rights reserved.

comparative evaluation of pressure distribution between horizontal

African Journals Online (AJOL)

user

This paper presents comparative analysis between the pressure behavior of ... Green and source function were used to evaluate the performance of horizontal well and ..... Superscript. ' derivative. D = dimensionless. h = horizontal. = change.

Numerical analysis of the flow field in a sloshing tank with a horizontal perforated plate

Science.gov (United States)

Jin, Heng; Liu, Yong; Li, Huajun; Fu, Qiang

2017-08-01

Liquid sloshing is a type of free surface flow inside a partially filled water tank. Sloshing exerts a significant effect on the safety of liquid transport systems; in particular, it may cause large hydrodynamic loads when the frequency of the tank motion is close to the natural frequency of the tank. Perforated plates have recently been used to suppress the violent movement of liquids in a sloshing tank at resonant conditions. In this study, a numerical model based on OpenFOAM (Open Source Field Operation and Manipulation), an open source computed fluid dynamic code, is used to investigate resonant sloshing in a swaying tank with a submerged horizontal perforated plate. The numerical results of the free surface elevations are first verified using experimental data, and then the flow characteristics around the perforated plate and the fluid velocity distribution in the entire tank are examined using numerical examples. The results clearly show differences in sloshing motions under first-order and third-order resonant frequencies. This study provides a better understanding of the energy dissipation mechanism of a horizontal perforated plate in a swaying tank.

Behavior of water jet horizontally discharged from a small circular hole set on a circular pipe-surface into air

International Nuclear Information System (INIS)

Tsuyuki, Koji; Igarashi, Saburo; Sudo, Seiichi; Yamabe, Masahiro; Kikuchi, Akira; Oba, Risaburo

2001-01-01

In order to clarify the behavior of the water jet horizontally discharged from a small circular hole set on a circular pipe surface into air, in this paper, for the first step, we systematically observed the jet aspects, the efflux angle, the discharge coefficient and so on, when the hole diameter d is much smaller than the pipe diameter D. Since the upstream kinetic energy from the hole is somewhat higher than the downstream counterpart, the upstream partial jet with higher efflux angle crashes into the downstream partial jet and drives out the latter into up- and down-side, resulting in a marked pair of vortices, so that resulting in a three-dimensional spiral flow accompanying with marked surface waves. (author)

The development of Canadian leadership in horizontal drilling technology

Energy Technology Data Exchange (ETDEWEB)

Hawkins, J R

1989-01-01

Horizontal wells are of increasing interest in the oil and gas industry, as is evident from the increase in the numbers of such wells being drilled. Horizontal well technology is used to improve production rates, notably in low permeability formations; to capture reserves if a reservoir is not economic using non-horizontal wells; to manage breakthrough of sweep fluids and increase sweep efficiency; and to extend the areal reach from a single surface location, especially in offshore production. The types of horizontal wells, differentiated on the basis of how quickly the well becomes horizontal, are briefly outlined and a short history of horizontal wells is presented. Canadian accomplishments in this field are then described, including steerable drilling systems, measurement-while-drilling systems, management of hole drag and torque, and well completion techniques. About 25 horizontal wells are forecast to be drilled in Canada in 1989, indicating the favorable future of this technology. 2 figs., 5 tabs.

Influence of gravity on the spatial orientation of eye nystagmus induced by unilateral lesion of horizontal semicircular canal.

Science.gov (United States)

Pettorossi, V E; Ermanno, M; Pierangelo, E; Silvarosa, G

2000-03-01

The influence of gravity in the orientation and slow phase eye velocity of the ocular nystagmus following unilateral damage of the cupula in the ampulla of the horizontal semicircular canal (UHCD) was investigated. The nystagmus was analysed at different sagittal head positions using the x-y infrared eye monitor technique. The nystagmus was almost horizontal at 0 degrees head pitch angle and remained partially fixed in space when the head was pitched upward or downward. The reorientation gain of the slow and quick phases was high (about 0.75) within +/- 45 degrees of head pitch angle, but beyond this range, it decreased greatly. The gain value depended on the lesion extension to otolithic receptors. The absolute value of the slow phase eye velocity of UHCD nystagmus was also modified systematically by the head pitch, showing a reduction in the upward and an increase in the downward.

Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis

Directory of Open Access Journals (Sweden)

Butler Geraldine

2008-06-01

Full Text Available Abstract Background To date very few incidences of interdomain gene transfer into fungi have been identified. Here, we used the emerging genome sequences of Candida albicans WO-1, Candida tropicalis, Candida parapsilosis, Clavispora lusitaniae, Pichia guilliermondii, and Lodderomyces elongisporus to identify recent interdomain HGT events. We refer to these as CTG species because they translate the CTG codon as serine rather than leucine, and share a recent common ancestor. Results Phylogenetic and syntenic information infer that two C. parapsilosis genes originate from bacterial sources. One encodes a putative proline racemase (PR. Phylogenetic analysis also infers that there were independent transfers of bacterial PR enzymes into members of the Pezizomycotina, and protists. The second HGT gene in C. parapsilosis belongs to the phenazine F (PhzF superfamily. Most CTG species also contain a fungal PhzF homolog. Our phylogeny suggests that the CTG homolog originated from an ancient HGT event, from a member of the proteobacteria. An analysis of synteny suggests that C. parapsilosis has lost the endogenous fungal form of PhzF, and subsequently reacquired it from a proteobacterial source. There is evidence that Schizosaccharomyces pombe and Basidiomycotina also obtained a PhzF homolog through HGT. Conclusion Our search revealed two instances of well-supported HGT from bacteria into the CTG clade, both specific to C. parapsilosis. Therefore, while recent interkingdom gene transfer has taken place in the CTG lineage, its occurrence is rare. However, our analysis will not detect ancient gene transfers, and we may have underestimated the global extent of HGT into CTG species.

The horizontal plane appearances of scoliosis

DEFF Research Database (Denmark)

Illés, Tamás S.; Burkus, Máté; Somoskeőy, Szabolcs

2017-01-01

Purpose: A posterior-anterior vertebral vector is proposed to facilitate visualization and understanding of scoliosis. The aim of this study was to highlight the interest of using vertebral vectors, especially in the horizontal plane, in clinical practice. Methods: We used an EOS two-/three-dimen......Purpose: A posterior-anterior vertebral vector is proposed to facilitate visualization and understanding of scoliosis. The aim of this study was to highlight the interest of using vertebral vectors, especially in the horizontal plane, in clinical practice. Methods: We used an EOS two...... cases of a normal spine and a thoracic scoliosis are presented. Results: For a normal spine, vector projections in the transverse plane are aligned with the posterior-anterior anatomical axis. For a scoliotic spine, vector projections in the horizontal plane provide information on the lateral...... decompensation of the spine and the lateral displacement of vertebrae. In the horizontal plane view, vertebral rotation and projections of the sagittal curves can also be analyzed simultaneously. Conclusions: The use of posterior-anterior vertebral vector facilitates the understanding of the 3D nature...

Horizontal gaze palsy and progressive scoliosis in a patient with congenital esotropia and inability to abduct. A case report.

Science.gov (United States)

Fernández-Vega Cueto, A; Rodríguez-Ezcurra, J J; Rodríguez-Maiztegui, I

2016-12-01

The case is presented on a 4- year-old child with congenital esotropia, limitation of abduction, cross-fixation, and thoracolumbar scoliosis. Genetic testing of ROBO3 gene confirmed the diagnosis of horizontal gaze palsy and scoliosis (HGPSS) DISCUSSION: HGPPS is a rare congenital disorder characterised by absence of conjugate horizontal eye movements and progressive scoliosis developed in childhood and adolescence. We highlight this motility disorder as a part of the differential diagnosis of early childhood esotropia with cross- fixation and limitation of abduction. Copyright © 2016 Sociedad Española de Oftalmología. Publicado por Elsevier España, S.L.U. All rights reserved.

Fastidious Gram-Negatives: Identification by the Vitek 2 Neisseria-Haemophilus Card and by Partial 16S rRNA Gene Sequencing Analysis

DEFF Research Database (Denmark)

Wolff Sönksen, Ute; Christensen, Jens Jørgen; Nielsen, Lisbeth

2010-01-01

Taxonomy and identification of fastidious Gram negatives are evolving and challenging. We compared identifications achieved with the Vitek 2 Neisseria-Haemophilus (NH) card and partial 16S rRNA gene sequence (526 bp stretch) analysis with identifications obtained with extensive phenotypic...... characterization using 100 fastidious Gram negative bacteria. Seventy-five strains represented 21 of the 26 taxa included in the Vitek 2 NH database and 25 strains represented related species not included in the database. Of the 100 strains, 31 were the type strains of the species. Vitek 2 NH identification...

The removable acrylic partial denture in primary care: the experience and satisfaction of dental surgeons

OpenAIRE

Rita de Cássia SILVA; Raquel Conceição FERREIRA; Denise Vieira TRAVASSOS; Andréa Maria Duarte VARGAS

2017-01-01

Abstract Introduction The guidelines of the National Politics of Oral Health have led to the inclusion of elemental prostheses in the list of Primary Care procedures. Objective This paper aimed to evaluate the performance and satisfaction of dental surgeons with the implementation of Acrylic Partial Dentures. Metodology The sample was composed by 159 dental surgeons (sample calculation), in Belo Horizonte, MG, Brazil, selected via raffle (simple random sampling). A structured questionnaire...

MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum

NARCIS (Netherlands)

Schmidt, S.M.; Houterman, P.M.; Schreiver, I.; Ma, L.; Amyotte, S.; Chellappan, B.; Boeren, S.; Takken, F.L.W.; Rep, M.

2013-01-01

Background The plant-pathogenic fungus Fusarium oxysporum f.sp.lycopersici (Fol) has accessory, lineage-specific (LS) chromosomes that can be transferred horizontally between strains. A single LS chromosome in the Fol4287 reference strain harbors all known Fol effector genes. Transfer of this

Horizontal drilling in Miocene thin sand of Lake Maracaibo

Energy Technology Data Exchange (ETDEWEB)

Partidas, C. [PDVSA Exploration and Production (Venezuela)

1998-12-31

Horizontal drilling in the mature Lake Maracaibo field in Venezuela as a means of stimulating production are discussed. The Miocene sand where the horizontal well technology was applied, presented a number of intervals of unconsolidated sand of varied continuity, pay intervals at ten to twenty feet thickness, and reservoir pressures mostly at hydrostatic or below hydrostatic values. This paper evaluates a horizontal drilling program in the Lagunallis Lago Production Unit of Maracaibo, involving 91 wells to date (since 1995). When assessed in economic terms, results indicate that horizontal wells are a better economic alternative than vertical wells. The same results also showed that drainage from thin sand reservoirs resulted in better production with horizontal well technology than production from vertical wells. Payout was less than two years for 50 per cent of the horizontal wells while 40 per cent had payouts of between two and four years. Profit to investment ratio was greater than two in the case of about 70 per cent of the horizontal wells drilled in 1996. 2 tabs., 10 figs.

Actin gene identification from selected medicinal plants for their use as internal controls for gene expression studies

International Nuclear Information System (INIS)

Mufti, F.U.D.; Banaras, S.

2015-01-01

Internal control genes are the constitutive genes which maintain the basic cellular functions and regularly express in both normal and stressed conditions in living organisms. They are used in normalization of gene expression studies in comparative analysis of target genes, as their expression remains comparatively unchanged in all varied conditions. Among internal control genes, actin is considered as a candidate gene for expression studies due to its vital role in shaping cytoskeleton and plant physiology. Unfortunately most of such knowledge is limited to only model plants or crops, not much is known about important medicinal plants. Therefore, we selected seven important medicinal wild plants for molecular identification of actin gene. We used gene specific primers designed from the conserved regions of several known orthologues or homologues of actin genes from other plants. The amplified products of 370-380 bp were sequenced and submitted to GeneBank after their confirmation using different bioinformatics tools. All the novel partial sequences of putative actin genes were submitted to GeneBank (Parthenium hysterophorus (KJ774023), Fagonia indica (KJ774024), Rhazya stricta (KJ774025), Whithania coagulans (KJ774026), Capparis decidua (KJ774027), Verbena officinalis (KJ774028) and Aerva javanica (KJ774029)). The comparisons of these partial sequences by Basic Local Alignment Search Tool (BLAST) and phylogenetic trees demonstrated high similarity with known actin genes of other plants. Our findings illustrated highly conserved nature of actin gene among these selected plants. These novel partial fragments of actin genes from these wild medicinal plants can be used as internal controls for future gene expression studies of these important plants after precise validations of their stable expression in such plants. (author)

Benefits of a horizontal well in sandstone waterflood

International Nuclear Information System (INIS)

Hansen, K.L.

1992-01-01

This is a case study which describes the planning and results of a horizontal well in a shallow Wilcox sandstone waterflood unit in central Louisiana. The Tremont H-13-1 was OXY USA Inc.'s first horizontal well. Analysis will include examination of the selection criteria, planning, execution, completion, and production. A variety of well and field data is presented and reviewed to access the value of this information as it applies towards other applications. The Cruse Waterflood Unit is a 2100 ft. Wilcox formation in central Louisiana. Production improvements have been 500% or greater for the horizontal well versus adjacent vertical wells. The horizontal well paid out in less than 4 months Results from this well indicate that not only was this project an economic success, but that other fields will similar conditions can be produced in a more profitable manner with horizontal wells

Partial Portal Vein Arterialization Attenuates Acute Bile Duct Injury Induced by Hepatic Dearterialization in a Rat Model.

Science.gov (United States)

Jiang, Jun; Wei, Jishu; Wu, Junli; Gao, Wentao; Li, Qiang; Jiang, Kuirong; Miao, Yi

2016-01-01

Hepatic infarcts or abscesses occur after hepatic artery interruption. We explored the mechanisms of hepatic deprivation-induced acute liver injury and determine whether partial portal vein arterialization attenuated this injury in rats. Male Sprague-Dawley rats underwent either complete hepatic arterial deprivation or partial portal vein arterialization, or both. Hepatic ischemia was evaluated using biochemical analysis, light microscopy, and transmission electron microscopy. Hepatic ATP levels, the expression of hypoxia- and inflammation-associated genes and proteins, and the expression of bile transporter genes were assessed. Complete dearterialization of the liver induced acute liver injury, as evidenced by the histological changes, significantly increased serum biochemical markers, decreased ATP content, increased expression of hypoxia- and inflammation-associated genes and proteins, and decreased expression of bile transporter genes. These detrimental changes were extenuated but not fully reversed by partial portal vein arterialization, which also attenuated ductular reaction and fibrosis in completely dearterialized rat livers. Collectively, complete hepatic deprivation causes severe liver injury, including bile infarcts and biloma formation. Partial portal vein arterialization seems to protect against acute ischemia-hypoxia-induced liver injury.

Partial Portal Vein Arterialization Attenuates Acute Bile Duct Injury Induced by Hepatic Dearterialization in a Rat Model

Directory of Open Access Journals (Sweden)

Jun Jiang

2016-01-01

Full Text Available Hepatic infarcts or abscesses occur after hepatic artery interruption. We explored the mechanisms of hepatic deprivation-induced acute liver injury and determine whether partial portal vein arterialization attenuated this injury in rats. Male Sprague-Dawley rats underwent either complete hepatic arterial deprivation or partial portal vein arterialization, or both. Hepatic ischemia was evaluated using biochemical analysis, light microscopy, and transmission electron microscopy. Hepatic ATP levels, the expression of hypoxia- and inflammation-associated genes and proteins, and the expression of bile transporter genes were assessed. Complete dearterialization of the liver induced acute liver injury, as evidenced by the histological changes, significantly increased serum biochemical markers, decreased ATP content, increased expression of hypoxia- and inflammation-associated genes and proteins, and decreased expression of bile transporter genes. These detrimental changes were extenuated but not fully reversed by partial portal vein arterialization, which also attenuated ductular reaction and fibrosis in completely dearterialized rat livers. Collectively, complete hepatic deprivation causes severe liver injury, including bile infarcts and biloma formation. Partial portal vein arterialization seems to protect against acute ischemia-hypoxia-induced liver injury.

Horizontal transfer of DNA from the mitochondrial to the plastid genome and its subsequent evolution in milkweeds (Apocynaceae)

Science.gov (United States)

Shannon C.K. Straub; Richard C. Cronn; Christopher Edwards; Mark Fishbein; Aaron. Liston

2013-01-01

Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT. We sequenced the 158 kb plastome and the 690 kb mitochondrial genome of common milkweed (Asclepias syriaca [Apocynaceae...

The Process of Horizontal Differentiation: Two Models.

Science.gov (United States)

Daft, Richard L.; Bradshaw, Patricia J.

1980-01-01

Explores the process of horizontal differentiation by examining events leading to the establishment of 30 new departments in five universities. Two types of horizontal differentiation processes--administrative and academic--were observed and each was associated with different organizational conditions. (Author/IRT)

Cloning and selection of reference genes for gene expression ...

African Journals Online (AJOL)

Full length mRNA sequences of Ac-β-actin and Ac-gapdh, and partial mRNA sequences of Ac-18SrRNA and Ac-ubiquitin were cloned from pineapple in this study. The four genes were tested as housekeeping genes in three experimental sets. GeNorm and NormFinder analysis revealed that β-actin was the most ...

Evolving chromosomes and gene regulatory networks

Indian Academy of Sciences (India)

Aswin

Genes under H NS control can be. (a) regulated by H NS. (b) regulated by H NS and StpA. Because backup by StpA is partial. Page 19. Gene expression level. H NS regulated xenogenes. Other genes. Page 20 ... recollect: H&NS silences highl transcribable genes. Gene expression level unilateral. Other genes epistatic ...

Simulated self-motion in a visual gravity field: sensitivity to vertical and horizontal heading in the human brain.

Science.gov (United States)

Indovina, Iole; Maffei, Vincenzo; Pauwels, Karl; Macaluso, Emiliano; Orban, Guy A; Lacquaniti, Francesco

2013-05-01

Multiple visual signals are relevant to perception of heading direction. While the role of optic flow and depth cues has been studied extensively, little is known about the visual effects of gravity on heading perception. We used fMRI to investigate the contribution of gravity-related visual cues on the processing of vertical versus horizontal apparent self-motion. Participants experienced virtual roller-coaster rides in different scenarios, at constant speed or 1g-acceleration/deceleration. Imaging results showed that vertical self-motion coherent with gravity engaged the posterior insula and other brain regions that have been previously associated with vertical object motion under gravity. This selective pattern of activation was also found in a second experiment that included rectilinear motion in tunnels, whose direction was cued by the preceding open-air curves only. We argue that the posterior insula might perform high-order computations on visual motion patterns, combining different sensory cues and prior information about the effects of gravity. Medial-temporal regions including para-hippocampus and hippocampus were more activated by horizontal motion, preferably at constant speed, consistent with a role in inertial navigation. Overall, the results suggest partially distinct neural representations of the cardinal axes of self-motion (horizontal and vertical). Copyright © 2013 Elsevier Inc. All rights reserved.

Quantitative assessment of human exposure to extended spectrum and AmpC β-lactamases bearing E. coli in lettuce attributable to irrigation water and subsequent horizontal gene transfer

DEFF Research Database (Denmark)

Njage, Patrick Murigu Kamau; Buys, E. M.

2017-01-01

and irrigation water E. coli isolates was previously reported. This stochastic modeling was aimed at quantitatively assessing human exposure to ESBL/AmpC bearing E. coli through lettuce attributable to irrigation water and subsequent horizontal gene transfer. Modular process risk approach was used.......15), and prevalence of E. coli in irrigation water (ρ=0.16) had highest influence on consumer exposure. The most effective single methods in reducing consumer exposure were reduction in irrigation water microbial quality variation (87.4% reduction), storage period (49.9-87.4% reduction) and growth rate reduction...... irrigation water quality variation. The exposure levels may impose higher consumer risk than acceptable for irrigation water risk. E. coli contamination and growth related measures, as well as measures to reduce contamination with antimicrobial resistant E. coli from lettuce production environment...

Partial recovery of hemiparesis following hemispherectomy in infant monkeys.

Science.gov (United States)

Burke, Mark W; Zangenehpour, Shahin; Ptito, Maurice

2010-01-22

Hemiparesis, unilateral weakness or partial paralysis, is a common outcome following hemispherectomy in humans. We use the non-human primate as an invaluable translational model for our understanding of developmental plasticity in response to hemispherectomy. Three infant vervet monkeys (Chlorocebus sabeus) underwent hemispherectomy at a median age of 9 weeks and two additional monkeys at 48 months. Gross motor assessment was conducted in a large open field that contained a horizontal bar spanning the width of the cage. Subjects were assessed yearly following surgery in infantile lesions for a period of 3 years. Adult-lesioned subjects were assessed 40 months following surgery. Shortly after surgery both infant and adult-lesioned subjects were unable to move the contralateral side of their body, but all subjects were able to walk within 6 months following surgery. At each time point the lower limb gait was normal in infant-lesioned subjects with no apparent limp or dragging, however the upper limb demonstrated significant impairment. Horizontal bar crossing was significantly impaired during the first 24 months following surgery. Adult-lesioned subjects also displayed upper limb movement impairments similar to infant-lesioned subjects. In addition the adult-lesioned subjects displayed a noticeable lower limb limp, which was not observed in the infant-lesioned group. Both groups at each time point showed a propensity for ipsiversive turning. The upper limb gait impairment and horizontal bar crossing of lesioned subjects are reminiscent of hemiparesis seen in hemisperectomized humans with the young-lesioned subjects showing a greater propensity for recovery. (c) 2009 Elsevier Ireland Ltd. All rights reserved.

Applicability of petroleum horizontal drilling technology to hazardous waste site characterization and remediation

International Nuclear Information System (INIS)

Goranson, C.

1992-09-01

Horizontal wells have the potential to become an important tool for use in characterization, remediation and monitoring operations at hazardous waste disposal, chemical manufacturing, refining and other sites where subsurface pollution may develop from operations or spills. Subsurface pollution of groundwater aquifers can occur at these sites by leakage of surface disposal ponds, surface storage tanks, underground storage tanks (UST), subsurface pipelines or leakage from surface operations. Characterization and remediation of aquifers at or near these sites requires drilling operations that are typically shallow, less than 500-feet in depth. Due to the shallow nature of polluted aquifers, waste site subsurface geologic formations frequently consist of unconsolidated materials. Fractured, jointed and/or layered high compressive strength formations or compacted caliche type formations can also be encountered. Some formations are unsaturated and have pore spaces that are only partially filled with water. Completely saturated underpressured aquifers may be encountered in areas where the static ground water levels are well below the ground surface. Each of these subsurface conditions can complicate the drilling and completion of wells needed for monitoring, characterization and remediation activities. This report describes some of the equipment that is available from petroleum drilling operations that has direct application to groundwater characterization and remediation activities. A brief discussion of petroleum directional and horizontal well drilling methodologies is given to allow the reader to gain an understanding of the equipment needed to drill and complete horizontal wells. Equipment used in river crossing drilling technology is also discussed. The final portion of this report is a description of the drilling equipment available and how it can be applied to groundwater characterization and remediation activities

Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer.

Directory of Open Access Journals (Sweden)

Michael J Bryan

Full Text Available BACKGROUND: S-PM2 is a phage capable of infecting strains of unicellular cyanobacteria belonging to the genus Synechococcus. S-PM2, like other myoviruses infecting marine cyanobacteria, encodes a number of bacterial-like genes. Amongst these genes is one encoding a MazG homologue that is hypothesized to be involved in the adaption of the infected host for production of progeny phage. METHODOLOGY/PRINCIPAL FINDINGS: This study focuses on establishing the occurrence of mazG homologues in other cyanophages isolated from different oceanic locations. Degenerate PCR primers were designed using the mazG gene of S-PM2. The mazG gene was found to be widely distributed and highly conserved among Synechococcus myoviruses and podoviruses from diverse oceanic provinces. CONCLUSIONS/SIGNIFICANCE: This study provides evidence of a globally connected cyanophage gene pool, the cyanophage mazG gene having a small effective population size indicative of rapid lateral gene transfer despite being present in a substantial fraction of cyanophage. The Prochlorococcus and Synechococcus phage mazG genes do not cluster with the host mazG gene, suggesting that their primary hosts are not the source of the mazG gene.

Variability of the inclination of anatomic horizontal reference planes of the craniofacial complex in relation to the true horizontal line in orthognathic patients.

Science.gov (United States)

Zebeib, Ameen M; Naini, Farhad B

2014-12-01

The purpose of this study was to assess the reliability of the Frankfort horizontal (FH), sella-nasion horizontal, and optic planes in terms of their variabilities in relation to a true horizontal line in orthognathic surgery patients. Thirty-six consecutive presurgical orthognathic patients (13 male, 23 female; age range, 16-35 years; 30 white, 6 African Caribbean) had lateral cephalometric radiographs taken in natural head position, with a plumb line orientating the true vertical line, and the true horizontal line perpendicular to the true vertical. The inclinations of the anatomic reference planes were compared with the true horizontal. The FH plane was found to be on average closest to the true horizontal, with a mean of -1.6° (SD, 3.4°), whereas the sella-nasion horizontal and the optic plane had means of 2.1° (SD, 5.1°) and 3.2° (SD, 4.7°), respectively. The FH showed the least variability of the 3 anatomic planes. The ranges of variability were high for all anatomic planes: -8° to 8° for the FH, -8° to 15° for the sella-nasion horizontal, and -6° to 13° for the optic plane. No significant differences were found in relation to patients' sex, skeletal patterns, or ethnic backgrounds. The clinically significant variability in the inclinations of anatomic reference planes in relation to the true horizontal plane makes their use unreliable in orthognathic patients. Copyright © 2014 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

Horizontal well impact on heavy oil supply

International Nuclear Information System (INIS)

Bowers, B.; Bielecki, J.; Hu, J.; Wall, B.; Drummond, K.

1993-01-01

Horizontal wells can take advantage of gravity drainage mechanisms, which can be important in conventional heavy oil and bitumen recovery. Horizontal drilling will impact on the development of established conventional heavy oil pools by infill drilling and application of enhanced recovery techniques. There will also be an impact on the development of extensions to established and newly discovered heavy oil pools, as well as a major impact on development of bitumen resources. To assess the impact of horizontal drilling on heavy oil supply, high-impact and low-impact scenarios were evaluated under specified oil-price assumptions for four heavy oil areas in Saskatchewan and Alberta. Horizontal well potential for infill drilling, waterflood projects, and thermal projects was assessed and estimates were made of such developments as reserves additions and heavy oil development wells under the two scenarios. In the low case, projected supply of conventional heavy oil and bitumen stabilizes at a level in the 90,000-94,000 m 3 /d after 1994. In the high case, overall supply continuously grows from 80,000 m 3 /d in 1992 to 140,000 m 3 /d in 2002. Through application of horizontal drilling, reserves additions in western Canada could be improved by ca 100 million m 3 by 2002. 14 figs., 6 tabs

Horizontal bridges in polar dielectric liquids

Science.gov (United States)

Woisetschläger, Jakob; Wexler, Adam D.; Holler, Gert; Eisenhut, Mathias; Gatterer, Karl; Fuchs, Elmar C.

2012-01-01

When a high-voltage direct-current is applied to two beakers filled with polar liquid dielectrica like water or methanol, a horizontal bridge forms between the two beakers. By repeating a version of Pellat's experiment, it is shown that a horizontal bridge is stable by the action of electrohydrodynamic pressure. Thus, the static and dynamic properties of the phenomenon called a `floating water bridge' can be explained by the gradient of Maxwell pressure, replenishing the liquid within the bridge against any drainage mechanism. It is also shown that a number of liquids can form stable and long horizontal bridges. The stability of such a connection, and the asymmetry in mass flow through such bridges caused by the formation of ion clouds in the vicinity of the electrodes, is also discussed by two further experiments.

Delineation of the genus Actinobacillus by comparison of partial infB sequences

DEFF Research Database (Denmark)

Nørskov-Lauritsen, Niels; Christensen, H; Okkels, H.

2004-01-01

A 426 bp fragment of infB, a housekeeping gene that encodes translation initiation factor 2, was sequenced from 59 clinical isolates and type strains of Actinobacillus species and sequences were compared. Partial sequences of 16S rRNA genes were also obtained. By comparing infB sequences, Actinob...

Vertical-horizontal wells for depletion and sweep

Energy Technology Data Exchange (ETDEWEB)

Muraikhi, A. J.; Pham, T. R.; Liu, J. S.; Khatib, M. R.; Muhaish, A. S. [Saudi Aramco (Saudi Arabia)

1998-12-31

A well completion scheme currently in use in a thick, large, elongated carbonate anticline Middle-East oil reservoir is described. This method of well completion calls for a combination of an open hole horizontal section penetrating the top 10 feet of the reservoir and a cased or undisturbed vertical segment through the thick formation. The horizontal section is used for producing and the vertical segment is used for monitoring purposes. Field experience and supported reservoir simulation exercises have shown that the horizontal application is superior to conventional vertical completion both from the economic and from the sweep point of view. 4 refs., 12 figs.

Horizontal bridges in polar dielectric liquids

Energy Technology Data Exchange (ETDEWEB)

Woisetschlaeger, Jakob [Graz University of Technology, Experimental Turbomachinery Research and Optical Measurement Group, Institute for Thermal Turbomachinery and Machine Dynamics, Graz (Austria); Wexler, Adam D.; Fuchs, Elmar C. [Wetsus, Center of Excellence for Sustainable Water Technology, Leeuwarden (Netherlands); Holler, Gert [Graz University of Technology, Institute of Electrical Measurement and Measurement Signal Processing, Graz (Austria); Eisenhut, Mathias [Graz University of Technology, Institute of Analytical Chemistry and Food Chemistry, Graz (Austria); Gatterer, Karl [Graz University of Technology, Institute of Physical and Theoretical Chemistry, Graz (Austria)

2012-01-15

When a high-voltage direct-current is applied to two beakers filled with polar liquid dielectrica like water or methanol, a horizontal bridge forms between the two beakers. By repeating a version of Pellat's experiment, it is shown that a horizontal bridge is stable by the action of electrohydrodynamic pressure. Thus, the static and dynamic properties of the phenomenon called a 'floating water bridge' can be explained by the gradient of Maxwell pressure, replenishing the liquid within the bridge against any drainage mechanism. It is also shown that a number of liquids can form stable and long horizontal bridges. The stability of such a connection, and the asymmetry in mass flow through such bridges caused by the formation of ion clouds in the vicinity of the electrodes, is also discussed by two further experiments. (orig.)

Identification of five partial ABC genes in the liver of the Antarctic fish Trematomus bernacchii and sensitivity of ABCB1 and ABCC2 to Cd exposure

Energy Technology Data Exchange (ETDEWEB)

Zucchi, Sara, E-mail: zucchi2@unisi.i [Department of Environmental Sciences ' G. Sarfatti' , University of Siena, Via Mattioli 4, 53100 Siena (Italy); Corsi, Ilaria [Department of Environmental Sciences ' G. Sarfatti' , University of Siena, Via Mattioli 4, 53100 Siena (Italy); Luckenbach, Till [UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig (Germany); Bard, Shannon Mala [Environmental Programmes, Dalhousie University, 1355 Oxford Street, Life Science Centre, Room 820, Halifax, Nova Scotia, Canada B3H 4J1 (Canada); Regoli, Francesco [Department of Biochemistry, Biology and Genetics, Polytechnic University of Marches, Ancona (Italy); Focardi, Silvano [Department of Environmental Sciences ' G. Sarfatti' , University of Siena, Via Mattioli 4, 53100 Siena (Italy)

2010-08-15

Several ABC transporters have been characterized from many aquatic organisms, but no information is yet available for Antarctic fish. The aim of this work was to identify the expression of genes for ABC proteins in Trematomus bernacchii, a bioindicator species of the Southern Ocean. Partial cDNA sequences of ABCB1, ABCC1, ABCC2, ABCC4 and ABCC9 were cloned from liver. Using RACE technology, 3.5 and 2.2 kb contigs were obtained for ABCB1 and ABCC2. Considering the elevated natural bioavailability of cadmium at Terra Nova Bay, responsiveness of ABCB1 and ABCC2 to this element was investigated under laboratory conditions. ABCB1 and ABCC2 mRNA levels were approximately four-fold higher in Cd-exposed fish compared to the controls. Induction of ABCB1 protein was also found by western blot. This study provides the first identification of five ABC genes in the liver of an Antarctic key species, some of which may be involved in cellular detoxification. - The presence of five partial sequences showing homology with ABC transporters and the sensitivity of ABCB1 and ABCC2 toward cadmium were determined in the liver of T. bernacchii.

Comparison of growth on mannitol salt agar, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, VITEK® 2 with partial sequencing of 16S rRNA gene for identification of coagulase-negative staphylococci.

Science.gov (United States)

Ayeni, Funmilola A; Andersen, Camilla; Nørskov-Lauritsen, Niels

2017-04-01

Mannitol salt agar (MSA) is often used in resources' limited laboratories for identification of S. aureus however, coagulase-negative staphylococci (CoNS) grows and ferments mannitol on MSA. 171 strains of CoNS which have been previously misidentified as S. aureus due to growth on MSA were collected from different locations in Nigeria and two methods for identification of CoNS were compared i.e. ViTEK 2 and MALDI-TOF MS with partial 16S rRNA gene sequencing as gold standard. Partial tuf gene sequencing was used for contradicting identification. All 171 strains (13 species) grew on MSA and ferments mannitol. All tested strains of S. epidermidis, S. haemolyticus, S. nepalensis, S. pasteuri, S. sciuri,, S. warneri, S. xylosus, S. capitis were correctly identified by MALDI-TOF while variable identification were observed in S. saprophyticus and S. cohnii (90%, 81%). There was low identification of S. arlettae (14%) while all strains of S. kloosii and S. gallinarum were misidentified. There is absence of S. gallinarum in the MALDI-TOF database at the period of this study. All tested strains of S. epidermidis, S. gallinarum, S. haemolyticus, S. sciuri,, S. warneri, S. xylosus and S. capitis were correctly identified by ViTEK while variable identification were observed in S. saprophyticus, S. arlettae, S. cohnii, S. kloosii, (84%, 86%, 75%, 60%) and misidentification of S. nepalensis, S. pasteuri. Partial sequencing of 16S rRNA gene was used as gold standard for most strains except S. capitis and S. xylosus where the two species were misidentified by partial sequencing of 16S rRNA contrary to MALDI-TOF and ViTEK identification. Tuf gene sequencing was used for correct identification. Characteristic growth on MSA for CoNS is also identical to S. aureus growth on the media and therefore, MSA could not differentiate between S. aureus and CoNS. The percentage accuracy of ViTEK was better than MALDI-TOF in identification of CoNS. Although partial sequencing of

Bubble shape in horizontal and near horizontal intermittent flow

International Nuclear Information System (INIS)

Gu, Hanyang; Guo, Liejin

2015-01-01

Highlights: • The bubble shapes in intermittent flows are presented experimentally. • The nose-tail inversion phenomenon appears at a low Froude number in downward pipe. • Transition from plug to slug flow occurs when the bubble tail changes from staircase pattern to hydraulic jump. - Abstract: This paper presents an experimental study of the shape of isolated bubbles in horizontal and near horizontal intermittent flows. It is found that the shapes of the nose and body of bubble depend on the Froude number defined by gas/liquid mixture velocity in a pipe, whereas the shape of the back of bubble region depends on both the Froude number and bubble length. The photographic studies show that the transition from plug to slug flow occurs when the back of the bubble changes from staircase pattern to hydraulic jump with the increase of the Froude number and bubble length. The effect of pipe inclination on characteristics of bubble is significant: The bubble is inversely located in a downwardly inclined pipe when the Froude number is low, and the transition from plug flow to slug flow in an upward inclined pipe is more ready to occur compared with that in a downwardly inclined pipe

Gain and loss of phototrophic genes revealed by comparison of two Citromicrobium bacterial genomes.

Directory of Open Access Journals (Sweden)

Qiang Zheng

Full Text Available Proteobacteria are thought to have diverged from a phototrophic ancestor, according to the scattered distribution of phototrophy throughout the proteobacterial clade, and so the occurrence of numerous closely related phototrophic and chemotrophic microorganisms may be the result of the loss of genes for phototrophy. A widespread form of bacterial phototrophy is based on the photochemical reaction center, encoded by puf and puh operons that typically are in a 'photosynthesis gene cluster' (abbreviated as the PGC with pigment biosynthesis genes. Comparison of two closely related Citromicrobial genomes (98.1% sequence identity of complete 16S rRNA genes, Citromicrobium sp. JL354, which contains two copies of reaction center genes, and Citromicrobium strain JLT1363, which is chemotrophic, revealed evidence for the loss of phototrophic genes. However, evidence of horizontal gene transfer was found in these two bacterial genomes. An incomplete PGC (pufLMC-puhCBA in strain JL354 was located within an integrating conjugative element, which indicates a potential mechanism for the horizontal transfer of genes for phototrophy.

Horizontal biases in rats’ use of three-dimensional space

Science.gov (United States)

Jovalekic, Aleksandar; Hayman, Robin; Becares, Natalia; Reid, Harry; Thomas, George; Wilson, Jonathan; Jeffery, Kate

2011-01-01

Rodent spatial cognition studies allow links to be made between neural and behavioural phenomena, and much is now known about the encoding and use of horizontal space. However, the real world is three dimensional, providing cognitive challenges that have yet to be explored. Motivated by neural findings suggesting weaker encoding of vertical than horizontal space, we examined whether rats show a similar behavioural anisotropy when distributing their time freely between vertical and horizontal movements. We found that in two- or three-dimensional environments with a vertical dimension, rats showed a prioritization of horizontal over vertical movements in both foraging and detour tasks. In the foraging tasks, the animals executed more horizontal than vertical movements and adopted a “layer strategy” in which food was collected from one horizontal level before moving to the next. In the detour tasks, rats preferred the routes that allowed them to execute the horizontal leg first. We suggest three possible reasons for this behavioural bias. First, as suggested by Grobety and Schenk [5], it allows minimisation of energy expenditure, inasmuch as costly vertical movements are minimised. Second, it may be a manifestation of the temporal discounting of effort, in which animals value delayed effort as less costly than immediate effort. Finally, it may be that at the neural level rats encode the vertical dimension less precisely, and thus prefer to bias their movements in the more accurately encoded horizontal dimension. We suggest that all three factors are related, and all play a part. PMID:21419172

Partial loss of heterozygosity events at the mutated gene in tumors from MLH1/MSH2 large genomic rearrangement carriers

Energy Technology Data Exchange (ETDEWEB)

Zavodna, Katarina; Krivulcik, Tomas; Bujalkova, Maria Gerykova [Laboratory of Cancer Genetics, Cancer Research Institute of Slovak Academy of Sciences, Vlarska 7, 833 91 Bratislava (Slovakia); Slamka, Tomas; Martinicky, David; Ilencikova, Denisa [National Cancer Institute, Department of Oncologic Genetics, Klenova 1, 833 01 Bratislava (Slovakia); Bartosova, Zdena [Laboratory of Cancer Genetics, Cancer Research Institute of Slovak Academy of Sciences, Vlarska 7, 833 91 Bratislava (Slovakia)

2009-11-20

microsatellite) is a novel finding and can be regarded as a partial LOH. The conversion begins within the gene, and the details of conversion tracts are discussed for each case.

Partial loss of heterozygosity events at the mutated gene in tumors from MLH1/MSH2 large genomic rearrangement carriers

Directory of Open Access Journals (Sweden)

Ilencikova Denisa

2009-11-01

or MSH2 gene (heterozygous LGR region, SNP, or microsatellite is a novel finding and can be regarded as a partial LOH. The conversion begins within the gene, and the details of conversion tracts are discussed for each case.

Partial loss of heterozygosity events at the mutated gene in tumors from MLH1/MSH2 large genomic rearrangement carriers

International Nuclear Information System (INIS)

Zavodna, Katarina; Krivulcik, Tomas; Bujalkova, Maria Gerykova; Slamka, Tomas; Martinicky, David; Ilencikova, Denisa; Bartosova, Zdena

2009-01-01

microsatellite) is a novel finding and can be regarded as a partial LOH. The conversion begins within the gene, and the details of conversion tracts are discussed for each case

On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.

Science.gov (United States)

Kordi, Misagh; Bansal, Mukul S

2017-01-01

Duplication-Transfer-Loss (DTL) reconciliation has emerged as a powerful technique for studying gene family evolution in the presence of horizontal gene transfer. DTL reconciliation takes as input a gene family phylogeny and the corresponding species phylogeny, and reconciles the two by postulating speciation, gene duplication, horizontal gene transfer, and gene loss events. Efficient algorithms exist for finding optimal DTL reconciliations when the gene tree is binary. However, gene trees are frequently non-binary. With such non-binary gene trees, the reconciliation problem seeks to find a binary resolution of the gene tree that minimizes the reconciliation cost. Given the prevalence of non-binary gene trees, many efficient algorithms have been developed for this problem in the context of the simpler Duplication-Loss (DL) reconciliation model. Yet, no efficient algorithms exist for DTL reconciliation with non-binary gene trees and the complexity of the problem remains unknown. In this work, we resolve this open question by showing that the problem is, in fact, NP-hard. Our reduction applies to both the dated and undated formulations of DTL reconciliation. By resolving this long-standing open problem, this work will spur the development of both exact and heuristic algorithms for this important problem.

Alteration of a recombinant protein N-glycan structure in silkworms by partial suppression of N-acetylglucosaminidase gene expression.

Science.gov (United States)

Kato, Tatsuya; Kikuta, Kotaro; Kanematsu, Ayumi; Kondo, Sachiko; Yagi, Hirokazu; Kato, Koichi; Park, Enoch Y

2017-09-01

To synthesize complex type N-glycans in silkworms, shRNAs against the fused lobe from Bombyx mori (BmFDL), which codes N-acetylglucosaminidase (GlcNAcase) in the Golgi, was expressed by recombinant B. mori nucleopolyhedrovirus (BmNPV) in silkworm larvae. Expression was under the control of the actin promoter of B. mori or the U6-2 and i.e.-2 promoters from Orgyia pseudotsugata multiple nucleopolyhedrovirus (OpMNPV). The reduction of specific GlcNAcase activity was observed in Bm5 cells and silkworm larvae using the U6-2 promoter. In silkworm larvae, the partial suppression of BmFDL gene expression was observed. When shRNA against BmFDL was expressed under the control of U6-2 promoter, the Man 3 GlcNAc(Fuc)GlcNAc structure appeared in a main N-glycans of recombinant human IgG. These results suggested that the control of BmFDL expression by its shRNA in silkworms caused the modification of its N-glycan synthetic pathway, which may lead to the alteration of N-glycans in the expressed recombinant proteins. Suppression of BmFDL gene expression by shRNA is not sufficient to synthesize complex N-glycans in silkworm larvae but can modify the N-glycan synthetic pathway.

New Insight into Inter-kingdom Communication: Horizontal Transfer of Mobile Small RNAs.

Science.gov (United States)

Zhou, Geyu; Zhou, Yu; Chen, Xi

2017-01-01

Small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs), are conventionally regarded as critical molecular regulators of various intracellular processes. However, recent accumulating evidence indicates that sRNAs can be transferred within cells and tissues and even across species. In plants, nematodes and microbes, these mobile sRNAs can mediate inter-kingdom communication, environmental sensing, gene expression regulation, host-parasite defense and many other biological functions. Strikingly, a recent study by our group suggested that ingested plant miRNAs are transferred to blood, accumulate in tissues and regulate transcripts in consuming animals. While our and other independent groups' subsequent studies further explored the emerging field of sRNA-mediated crosstalk between species, some groups reported negative results and questioned its general applicability. Thus, further studies carefully evaluating the horizontal transfer of exogenous sRNAs and its potential biological functions are urgently required. Here, we review the current state of knowledge in the field of the horizontal transfer of mobile sRNAs, suggest its future directions and key points for examination and discuss its potential mechanisms and application prospects in nutrition, agriculture and medicine.

New Insight into Inter-kingdom Communication: Horizontal Transfer of Mobile Small RNAs

Directory of Open Access Journals (Sweden)

Xi Chen

2017-05-01

Full Text Available Small RNAs (sRNAs, including small interfering RNAs (siRNAs and microRNAs (miRNAs, are conventionally regarded as critical molecular regulators of various intracellular processes. However, recent accumulating evidence indicates that sRNAs can be transferred within cells and tissues and even across species. In plants, nematodes and microbes, these mobile sRNAs can mediate inter-kingdom communication, environmental sensing, gene expression regulation, host-parasite defense and many other biological functions. Strikingly, a recent study by our group suggested that ingested plant miRNAs are transferred to blood, accumulate in tissues and regulate transcripts in consuming animals. While our and other independent groups’ subsequent studies further explored the emerging field of sRNA-mediated crosstalk between species, some groups reported negative results and questioned its general applicability. Thus, further studies carefully evaluating the horizontal transfer of exogenous sRNAs and its potential biological functions are urgently required. Here, we review the current state of knowledge in the field of the horizontal transfer of mobile sRNAs, suggest its future directions and key points for examination and discuss its potential mechanisms and application prospects in nutrition, agriculture and medicine.

Children's conceptions of physical events: explicit and tacit understanding of horizontal motion.

Science.gov (United States)

Howe, Christine; Taylor Tavares, Joana; Devine, Amy

2014-06-01

The conceptual understanding that children display when predicting physical events has been shown to be inferior to the understanding they display when recognizing whether events proceed naturally. This has often been attributed to differences between the explicit engagement with conceptual knowledge required for prediction and the tacit engagement that suffices for recognition, and contrasting theories have been formulated to characterize the differences. Focusing on a theory that emphasizes omission at the explicit level of conceptual elements that are tacitly understood, the paper reports two studies that attempt clarification. The studies are concerned with 6- to 10-year-old children's understanding of, respectively, the direction (141 children) and speed (132 children) of motion in a horizontal direction. Using computer-presented billiards scenarios, the children predicted how balls would move (prediction task) and judged whether or not simulated motion was correct (recognition task). Results indicate that the conceptions underpinning prediction are sometimes interpretable as partial versions of the conceptions underpinning recognition, as the omission hypothesis would imply. However, there are also qualitative differences, which suggest partial dissociation between explicit and tacit understanding. It is suggested that a theoretical perspective that acknowledges this dissociation would provide the optimal framework for future research. © 2013 The British Psychological Society.

Characteristics of Buoyancy Driven Natural Ventilation through Horizontal Openings

DEFF Research Database (Denmark)

Li, Zhigang

through horizontal openings. Two cases of full-scale measurements of buoyancy driven natural ventilation through horizontal openings are performed: one horizontal opening and one horizontal opening combined with one vertical opening. For the case of one horizontal opening, the measurements are made....... Computational fluid dynamics (CFD) are used to study these two air flow cases. The air flow rate and air flow pattern are predicted and compared with the full-scale measurements. The measurement data are used to compare two CFD models: standard k- ε model and large eddy simulation (LES) model. The cases...... transient, unstable and complex, and the air flow rates oscillate with time. Correlations between the Froude number Fr and the opening ratio L/D are obtained, which is reasonable agreement with Epstein's formula derived from brine-water measurements, but the obtained Fr values show considerable deviations...

Experimental testing of anchoring devices for bottom rails in partially anchored timber frame shear walls

OpenAIRE

Caprolu, Giuseppe

2011-01-01

Källsner and Girhammar have presented a new plastic design method of wood-framed shear walls at ultimate limit state. This method allows the designer to calculate the load-carrying capacity of shear walls partially anchored, where the leading stud is not anchored against the uplift.The anchorage system of shear walls is provided from anchor bolts and hold downs. Anchor bolts provide horizontal shear continuity between the bottom rail and the foundation. Hold downs are directly connected from ...

Analysis of boundary layer flow over a porous nonlinearly stretching sheet with partial slip at

Directory of Open Access Journals (Sweden)

Swati Mukhopadhyay

2013-12-01

Full Text Available The boundary layer flow of a viscous incompressible fluid toward a porous nonlinearly stretching sheet is considered in this analysis. Velocity slip is considered instead of no-slip condition at the boundary. Similarity transformations are used to convert the partial differential equation corresponding to the momentum equation into nonlinear ordinary differential equation. Numerical solution of this equation is obtained by shooting method. It is found that the horizontal velocity decreases with increasing slip parameter.

Characteristic Value Method of Well Test Analysis for Horizontal Gas Well

Directory of Open Access Journals (Sweden)

Xiao-Ping Li

2014-01-01

Full Text Available This paper presents a study of characteristic value method of well test analysis for horizontal gas well. Owing to the complicated seepage flow mechanism in horizontal gas well and the difficulty in the analysis of transient pressure test data, this paper establishes the mathematical models of well test analysis for horizontal gas well with different inner and outer boundary conditions. On the basis of obtaining the solutions of the mathematical models, several type curves are plotted with Stehfest inversion algorithm. For gas reservoir with closed outer boundary in vertical direction and infinite outer boundary in horizontal direction, while considering the effect of wellbore storage and skin effect, the pseudopressure behavior of the horizontal gas well can manifest four characteristic periods: pure wellbore storage period, early vertical radial flow period, early linear flow period, and late horizontal pseudoradial flow period. For gas reservoir with closed outer boundary both in vertical and horizontal directions, the pseudopressure behavior of the horizontal gas well adds the pseudosteady state flow period which appears after the boundary response. For gas reservoir with closed outer boundary in vertical direction and constant pressure outer boundary in horizontal direction, the pseudopressure behavior of the horizontal gas well adds the steady state flow period which appears after the boundary response. According to the characteristic lines which are manifested by pseudopressure derivative curve of each flow period, formulas are developed to obtain horizontal permeability, vertical permeability, skin factor, reservoir pressure, and pore volume of the gas reservoir, and thus the characteristic value method of well test analysis for horizontal gas well is established. Finally, the example study verifies that the new method is reliable. Characteristic value method of well test analysis for horizontal gas well makes the well test analysis

Horizontal and vertical seismic isolation of a nuclear power plant

International Nuclear Information System (INIS)

Ikonomou, A.S.

1983-01-01

This paper presents a study for the horizontal and vertical seismic isolation of a nuclear power plant with a base isolation system, developed by the author, called the Alexisismon. This system -- which comprises different schemes for horizontal or vertical or both horizontal and vertical isolation -- is a linear system based on the principle of separation of functions. That is, horizontal and vertical isolation are realized through different components and act independently from each other. As far as horizontal isolation is concerned, the role of transmitting vertical loads is uncoupled from the role of inducing horizontal restoring forces so that both functions can be performed without instability. It is possible either to provide both horizontal and vertical isolation to the whole nuclear plant or to isolate the whole plant horizontally and to provide vertical isolation to sensitive and costly equipment only. When the fundamental period of the plant or equipment is 2 seconds and when the vertical displacements are of the order of + or - 20 inches, the structure or equipment are protected against earthquakes up to 1.10 and 1.30 g for actual and 0.60 and 1.50 g for artificial accelerograms. In both cases all the isolation elements behave elastically up to these acceleration limits as well as the superstructure and equipment

Annotation of a hybrid partial genome of the Coffee Rust (Hemileia vastatrix contributes to the gene repertoire catalogue of the Pucciniales

Directory of Open Access Journals (Sweden)

Marco Aurelio Cristancho

2014-10-01

Full Text Available Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333Mb was built based on the 8 isolates; this assembly was used for subsequent analyses.Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3,921 families were uncovered; a considerable proportion of the predicted proteins (73.8% were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish

Topological properties of the limited penetrable horizontal visibility graph family

Science.gov (United States)

Wang, Minggang; Vilela, André L. M.; Du, Ruijin; Zhao, Longfeng; Dong, Gaogao; Tian, Lixin; Stanley, H. Eugene

2018-05-01

The limited penetrable horizontal visibility graph algorithm was recently introduced to map time series in complex networks. In this work, we extend this algorithm to create a directed-limited penetrable horizontal visibility graph and an image-limited penetrable horizontal visibility graph. We define two algorithms and provide theoretical results on the topological properties of these graphs associated with different types of real-value series. We perform several numerical simulations to check the accuracy of our theoretical results. Finally, we present an application of the directed-limited penetrable horizontal visibility graph to measure real-value time series irreversibility and an application of the image-limited penetrable horizontal visibility graph that discriminates noise from chaos. We also propose a method to measure the systematic risk using the image-limited penetrable horizontal visibility graph, and the empirical results show the effectiveness of our proposed algorithms.

FunGene: the functional gene pipeline and repository.

Science.gov (United States)

Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

2013-01-01

Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

FunGene: the Functional Gene Pipeline and Repository

Directory of Open Access Journals (Sweden)

Jordan A. Fish

2013-10-01

Full Text Available Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer.While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/ offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

Vertical vs. Horizontal Integration: Pre-emptive Merging.

OpenAIRE

Colangelo, Giuseppe

1995-01-01

Preemption plays a crucial role in arms merger decisions. The author studies whether and under which circumstances preemptive merging occurs in vertically related industries. He finds that vertical mergers often preempt horizontal mergers and are dominant outcomes. Preempting the threat of a detrimental horizontal integration may be the main reason for vertically integrating. Copyright 1995 by Blackwell Publishing Ltd.

GABA sensitivity of spectrally classified horizontal cells in goldfish retina

NARCIS (Netherlands)

Verweij, J.; Kamermans, M.; Negishi, K.; Spekreijse, H.

1998-01-01

We studied the GABA sensitivity of horizontal cells in the isolated goldfish retina. After the glutamatergic input to the horizontal cells was blocked with DNQX, GABA depolarized the monophasic and biphasic horizontal cells. The pharmacology of these GABA-induced depolarizations was tested with the

Electroluminescence from completely horizontally oriented dye molecules

Energy Technology Data Exchange (ETDEWEB)

Komino, Takeshi [Education Center for Global Leaders in Molecular System for Devices, Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan); Center for Organic Photonics and Electronics Research, Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan); Japan Science and Technology Agency, ERATO, Adachi Molecular Exciton Engineering Project, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan); Sagara, Yuta [Center for Organic Photonics and Electronics Research, Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan); Tanaka, Hiroyuki [Center for Organic Photonics and Electronics Research, Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan); Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan); Oki, Yuji [Japan Science and Technology Agency, ERATO, Adachi Molecular Exciton Engineering Project, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan); Department of Electronics, Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan); Nakamura, Nozomi [Center for Organic Photonics and Electronics Research, Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan); International Institute for Carbon Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan); Fujimoto, Hiroshi [Center for Organic Photonics and Electronics Research, Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan); Fukuoka i" 3-Center for Organic Photonics and Electronics Research (i3-OPERA), Fukuoka 819-0388 (Japan); and others

2016-06-13

A complete horizontal molecular orientation of a linear-shaped thermally activated delayed fluorescent guest emitter 2,6-bis(4-(10Hphenoxazin-10-yl)phenyl)benzo[1,2-d:5,4-d′] bis(oxazole) (cis-BOX2) was obtained in a glassy host matrix by vapor deposition. The orientational order of cis-BOX2 depended on the combination of deposition temperature and the type of host matrix. Complete horizontal orientation was obtained when a thin film with cis-BOX2 doped in a 4,4′-bis(N-carbazolyl)-1,1′-biphenyl (CBP) host matrix was fabricated at 200 K. The ultimate orientation of guest molecules originates from not only the kinetic relaxation but also the kinetic stability of the deposited guest molecules on the film surface during film growth. Utilizing the ultimate orientation, a highly efficient organic light-emitting diode with the external quantum efficiency of 33.4 ± 2.0% was realized. The thermal stability of the horizontal orientation of cis-BOX2 was governed by the glass transition temperature (T{sub g}) of the CBP host matrix; the horizontal orientation was stable unless the film was annealed above T{sub g}.

Molecular typing of canine parvovirus from Sulaimani, Iraq and phylogenetic analysis using partial VP2 gene

Directory of Open Access Journals (Sweden)

M.O.Baba Sheikh

2017-09-01

Full Text Available Canine parvovirus (CPV remains the most significant viral cause of haemorrhagic enteritis and bloody diarrhoea in puppies over the age of 12 weeks. The objective of the present study was to detect and genotype CPV-2 by polymerase chain reaction (PCR and to perform phylogenetic analysis using partial VP2 gene sequences. We analysed eight faecal samples of unvaccinated dogs with signs of vomiting and bloody diarrhoea during the period from December 2013 to May 2014 in different locations in Sulaimani, Kurdistan, Iraq. After PCR detection, we found that all viral sequences in our study were CPV-2b variants, which differed genetically by 0.8% to 3.6% from five commercially available vaccines. Alignment between eight nucleotides of field virus sequences showed 95% to 99.5% similarity. The phylogenetic analysis for the 8 field sequences formed two distinct clusters with two sequences belonging to strains from China and Thailand and the other six – with a strain from Egypt. Molecular characterisation and CPV typing are crucial in epidemiological studies for future prevention and control of the disease.

Some effects of horizontal discretization on linear baroclinic and symmetric instabilities

Science.gov (United States)

Barham, William; Bachman, Scott; Grooms, Ian

2018-05-01

The effects of horizontal discretization on linear baroclinic and symmetric instabilities are investigated by analyzing the behavior of the hydrostatic Eady problem in ocean models on the B and C grids. On the C grid a spurious baroclinic instability appears at small wavelengths. This instability does not disappear as the grid scale decreases; instead, it simply moves to smaller horizontal scales. The peak growth rate of the spurious instability is independent of the grid scale as the latter decreases. It is equal to cf /√{Ri} where Ri is the balanced Richardson number, f is the Coriolis parameter, and c is a nondimensional constant that depends on the Richardson number. As the Richardson number increases c increases towards an upper bound of approximately 1/2; for large Richardson numbers the spurious instability is faster than the Eady instability. To suppress the spurious instability it is recommended to use fourth-order centered tracer advection along with biharmonic viscosity and diffusion with coefficients (Δx) 4 f /(32√{Ri}) or larger where Δx is the grid scale. On the B grid, the growth rates of baroclinic and symmetric instabilities are too small, and converge upwards towards the correct values as the grid scale decreases; no spurious instabilities are observed. In B grid models at eddy-permitting resolution, the reduced growth rate of baroclinic instability may contribute to partially-resolved eddies being too weak. On the C grid the growth rate of symmetric instability is better (larger) than on the B grid, and converges upwards towards the correct value as the grid scale decreases.

The stability and degradation of dietary DNA in the gastrointestinal tract of mammals: implications for horizontal gene transfer and the biosafety of GMOs.

Science.gov (United States)

Rizzi, Aurora; Raddadi, Noura; Sorlini, Claudia; Nordgrd, Lise; Nielsen, Kaare Magne; Daffonchio, Daniele

2012-01-01

The fate of dietary DNA in the gastrointestinal tract (GIT) of animals has gained renewed interest after the commercial introduction of genetically modified organisms (GMO). Among the concerns regarding GM food, are the possible consequences of horizontal gene transfer (HGT) of recombinant dietary DNA to bacteria or animal cells. The exposure of the GIT to dietary DNA is related to the extent of food processing, food composition, and to the level of intake. Animal feeding studies have demonstrated that a minor amount of fragmented dietary DNA may resist the digestive process. Mammals have been shown to take up dietary DNA from the GIT, but stable integration and expression of internalized DNA has not been demonstrated. Despite the ability of several bacterial species to acquire external DNA by natural transformation, in vivo transfer of dietary DNA to bacteria in the intestine has not been detected in the few experimental studies conducted so far. However, major methodological limitations and knowledge gaps of the mechanistic aspects of HGT calls for methodological improvements and further studies to understand the fate of various types of dietary DNA in the GIT.

Generation of genic diversity among Streptococcus pneumoniae strains via horizontal gene transfer during a chronic polyclonal pediatric infection.

Directory of Open Access Journals (Sweden)

N Luisa Hiller

2010-09-01

Full Text Available Although there is tremendous interest in understanding the evolutionary roles of horizontal gene transfer (HGT processes that occur during chronic polyclonal infections, to date there have been few studies that directly address this topic. We have characterized multiple HGT events that most likely occurred during polyclonal infection among nasopharyngeal strains of Streptococcus pneumoniae recovered from a child suffering from chronic upper respiratory and middle-ear infections. Whole genome sequencing and comparative genomics were performed on six isolates collected during symptomatic episodes over a period of seven months. From these comparisons we determined that five of the isolates were genetically highly similar and likely represented a dominant lineage. We analyzed all genic and allelic differences among all six isolates and found that all differences tended to occur within contiguous genomic blocks, suggestive of strain evolution by homologous recombination. From these analyses we identified three strains (two of which were recovered on two different occasions that appear to have been derived sequentially, one from the next, each by multiple recombination events. We also identified a fourth strain that contains many of the genomic segments that differentiate the three highly related strains from one another, and have hypothesized that this fourth strain may have served as a donor multiple times in the evolution of the dominant strain line. The variations among the parent, daughter, and grand-daughter recombinant strains collectively cover greater than seven percent of the genome and are grouped into 23 chromosomal clusters. While capturing in vivo HGT, these data support the distributed genome hypothesis and suggest that a single competence event in pneumococci can result in the replacement of DNA at multiple non-adjacent loci.

Sidewall containment of liquid metal with horizontal alternating magnetic fields

Science.gov (United States)

Pareg, Walter F.

1990-01-01

An apparatus for confining molten metal with a horizontal alternating magnetic field. In particular, this invention employs a magnet that can produce a horizontal alternating magnetic field to confine a molten metal at the edges of parallel horizontal rollers as a solid metal sheet is cast by counter-rotation of the rollers.

A horizontal well analysis from a view of its productivity

Directory of Open Access Journals (Sweden)

Lucia Sciranková

2006-10-01

Full Text Available The 1990s may become known in the oil field as the decade of the horizontal well. Horizontal wells can increase the production rate and the ultimate recovery, and can reduce the number of platforms on wells required to develop a reservoir.An empirical equation to calculate the inflow performance of two-phase flow for a vertical and a horizontal well in regime of dissolved gas presented by Vogel in 1968. His equation was based on the results of reservoir simulation. The created model whore result (output is the ratio of the productivity of a horizontal well to the productivity of a vertical well for a given area expressed by anumber of vertical wells the replaced by one horizontal well. The model is applied for a concrete ideological model.

[Phylogenetic analysis of closely related Leuconostoc citreum species based on partial housekeeping genes].

Science.gov (United States)

Lv, Qiang; Chen, Ming; Xu, Haiyan; Song, Yuqin; Sun, Zhihong; Dan, Tong; Sun, Tiansong

2013-07-04

Using the 16S rRNA, dnaA, murC and pyrG gene sequences, we identified the phylogenetic relationship among closely related Leuconostoc citreum species. Seven Leu. citreum strains originally isolated from sourdough were characterized by PCR methods to amplify the dnaA, murC and pyrG gene sequences, which were determined to assess the suitability as phylogenetic markers. Then, we estimated the genetic distance and constructed the phylogenetic trees including 16S rRNA and above mentioned three housekeeping genes combining with published corresponding sequences. By comparing the phylogenetic trees, the topology of three housekeeping genes trees were consistent with that of 16S rRNA gene. The homology of closely related Leu. citreum species among dnaA, murC, pyrG and 16S rRNA gene sequences were different, ranged from75.5% to 97.2%, 50.2% to 99.7%, 65.0% to 99.8% and 98.5% 100%, respectively. The phylogenetic relationship of three housekeeping genes sequences were highly consistent with the results of 16S rRNA gene sequence, while the genetic distance of these housekeeping genes were extremely high than 16S rRNA gene. Consequently, the dnaA, murC and pyrG gene are suitable for classification and identification closely related Leu. citreum species.

Horizontal and Vertical Rule Bases Method in Fuzzy Controllers

OpenAIRE

Aminifar, Sadegh; bin Marzuki, Arjuna

2013-01-01

Concept of horizontal and vertical rule bases is introduced. Using this method enables the designers to look for main behaviors of system and describes them with greater approximations. The rules which describe the system in first stage are called horizontal rule base. In the second stage, the designer modulates the obtained surface by describing needed changes on first surface for handling real behaviors of system. The rules used in the second stage are called vertical rule base. Horizontal...

Condensation Analysis of Steam/Air Mixtures in Horizontal Tubes

International Nuclear Information System (INIS)

Lee, Kwon Yeong; Bae, Sung Won; Kim, Moo Hwan

2008-01-01

Perhaps the most common flow configuration in which a convective condensation occurs is a flow in a horizontal circular tube. This configuration is encountered in air-conditioning and refrigeration condensers as well as condensers in Rankine power cycles. Although a convective condensation is also sometimes contrived to occur in a co-current vertical downward flow, a horizontal flow is often preferred because the flow can be repeatedly passed through the heat exchanger core in a serpentine fashion without trapping liquid or vapor in the return bends. Many researchers have investigated a in-tube condensation for horizontal heat exchangers. However, almost all of them obtained tube section-averaged data without a noncondensable gas. Recently, Wu and Vierow have experimentally studied the condensation of steam in a horizontal heat exchanger with air present. In order to measure the condenser tube inner surface temperatures and to calculate the local heat fluxes, they developed an innovative thermocouple design that allowed for nonintrusive measurements. Here we developed a theoretical model using the heat and mass analogy to analyze a steam condensation with a noncondensable gas in horizontal tubes

Efficiency of a Horizontal Sub-Surface Flow Constructed Wetland Treatment System in an Arid Area

Directory of Open Access Journals (Sweden)

Abeer Albalawneh

2016-02-01

Full Text Available The main objective of this study was to evaluate the performance and treatment efficiency of the Horizontal Sub-Surface Flow Constructed Wetland treatment system (HSF-CW in an arid climate. Seventeen sub-surface, horizontal-flow HSF-CW units have been operated for approximately three years to improve the quality of partially-treated municipal wastewater. The studied design parameters included two sizes of volcanic tuff media (i.e., fine or coarse, two different bed dimensions (i.e., long and short, and three plantation types (i.e., reed, kenaf, or no vegetation as a control. The effluent Biological Oxygen Demand (BOD5, Chemical Oxygen Demand (COD, Total Suspended Solid (TSS, and phosphorus from all of the treatments were significantly lower as compared to the influent and demonstrated a removal efficiency of 55%, 51%, 67%, and 55%, respectively. There were significant increases in Electrical Conductivity (EC, sulfate, and calcium in the effluent of most HSF-CWs due to evaporative concentration and mineral dissolution from the media. The study suggests that unplanted beds with either fine or coarse media are the most suitable combinations among all of the studied designs based on their treatment efficiency and less water loss in arid conditions.

Influence of pavement condition on horizontal curve safety.

Science.gov (United States)

Buddhavarapu, Prasad; Banerjee, Ambarish; Prozzi, Jorge A

2013-03-01

Crash statistics suggest that horizontal curves are the most vulnerable sites for crash occurrence. These crashes are often severe and many involve at least some level of injury due to the nature of the collisions. Ensuring the desired pavement surface condition is one potentially effective strategy to reduce the occurrence of severe accidents on horizontal curves. This study sought to develop crash injury severity models by integrating crash and pavement surface condition databases. It focuses on developing a causal relationship between pavement condition indices and severity level of crashes occurring on two-lane horizontal curves in Texas. In addition, it examines the suitability of the existing Skid Index for safety maintenance of two-lane curves. Significant correlation is evident between pavement condition and crash injury severity on two-lane undivided horizontal curves in Texas. Probability of a crash becoming fatal is appreciably sensitive to certain pavement indices. Data suggested that road facilities providing a smoother and more comfortable ride are vulnerable to severe crashes on horizontal curves. In addition, the study found that longitudinal skid measurement barely correlates with injury severity of crashes occurring on curved portions. The study recommends exploring the option of incorporating lateral friction measurement into Pavement Management System (PMS) databases specifically at curved road segments. Copyright © 2012 Elsevier Ltd. All rights reserved.

Partial status epilepticus - rapid genetic diagnosis of Alpers' disease.

LENUS (Irish Health Repository)

McCoy, Bláthnaid

2011-11-01

We describe four children with a devastating encephalopathy characterised by refractory focal seizures and variable liver dysfunction. We describe their electroencephalographic, radiologic, genetic and pathologic findings. The correct diagnosis was established by rapid gene sequencing. POLG1 based Alpers\\' disease should be considered in any child presenting with partial status epilepticus.

Surgical treatment for paralytic horizontal strabismus

Directory of Open Access Journals (Sweden)

Feng Zhou*

2015-08-01

Full Text Available AIM: To observe the effect of surgery for paralytic horizontal strabismus and the paralytic horizontal strabismus performed by Jensen procedure with antagonist muscle of paralytic muscle recession and medial or lateral rectus extra large resection/recession.METHODS: Fifteen cases(17 eyeswith complete or nearly complete paralytic horizontal strabismus from January 2005 to August. 2014 in our hospital were assessed retrospectively,7 eyes of 7 cases with treatment group A were performed Jensen procedure combined antagonist muscle of paralytic muscle recession, 10 eyes of 8 cases with treatment group B were performed medial or lateral rectus extra large resection/recession. seventeen eyes of 15 cases with an average of 21±8.71mo follow-up were observed.RESULTS: All 17 eyes of 15 cases after the operation obtained satisfied effects, 16 eyes of 14 cases obtained ideal long-term effect. One eye of a patient with a 6mo follow-up was undercorrected of 30△. We found a varying degree of postoperative improvement in visual function. There was a significant reduction in the strabismus angle for distance and near(t=28.71, Pt=36.21, Pt=17.96, Pt=9.20,PCONCLUSION: Jensen procedure combined antagonist muscle of paralytic muscle recession and medial or lateral rectus extra large resection/recession is a safe and successful method of treatment in complete or nearly complete paralysis horizontal strabismus. Patients achieve orthophoria, improvement of the motor ability, and larger field of binocular single vision for long time.

Analytical Solution for Time-drawdown Response to Constant Pumping from a Homogeneous, Confined Horizontal Aquifer with Unidirectional Flow

Science.gov (United States)

Parrish, K. E.; Zhang, J.; Teasdale, E.

2007-12-01

An exact analytical solution to the ordinary one-dimensional partial differential equation is derived for transient groundwater flow in a homogeneous, confined, horizontal aquifer using Laplace transformation. The theoretical analysis is based on the assumption that the aquifer is homogeneous and one-dimensional (horizontal); confined between impermeable formations on top and bottom; and of infinite horizontal extent and constant thickness. It is also assumed that there is only a single pumping well penetrating the entire aquifer; flow is everywhere horizontal within the aquifer to the well; the well is pumping with a constant discharge rate; the well diameter is infinitesimally small; and the hydraulic head is uniform throughout the aquifer before pumping. Similar to the Theis solution, this solution is suited to determine transmissivity and storativity for a two- dimensional, vertically confined aquifer, such as a long vertically fractured zone of high permeability within low permeable rocks or a long, high-permeability trench inside a low-permeability porous media. In addition, it can be used to analyze time-drawdown responses to pumping and injection in similar settings. The solution can also be used to approximate the groundwater flow for unconfined conditions if (1) the variation of transmissivity is negligible (groundwater table variation is small in comparison to the saturated thickness); and (2) the unsaturated flow is negligible. The errors associated with the use of the solution to unconfined conditions depend on the accuracies of the above two assumptions. The solution can also be used to assess the impacts of recharge from a seasonal river or irrigation canal on the groundwater system by assuming uniform, time- constant recharge along the river or canal. This paper presents the details for derivation of the analytical solution. The analytical solution is compared to numerical simulation results with example cases. Its accuracy is also assessed and

Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool

Science.gov (United States)

Schmidt, Johanna; Jezberová, Jitka; Koll, Ulrike; Hahn, Martin W.

2016-01-01

ABSTRACT Microdiversification of a planktonic freshwater bacterium was studied by comparing 37 Polynucleobacter asymbioticus strains obtained from three geographically separated sites in the Austrian Alps. Genome comparison of nine strains revealed a core genome of 1.8 Mb, representing 81% of the average genome size. Seventy-five percent of the remaining flexible genome is clustered in genomic islands (GIs). Twenty-four genomic positions could be identified where GIs are potentially located. These positions are occupied strain specifically from a set of 28 GI variants, classified according to similarities in their gene content. One variant, present in 62% of the isolates, encodes a pathway for the degradation of aromatic compounds, and another, found in 78% of the strains, contains an operon for nitrate assimilation. Both variants were shown in ecophysiological tests to be functional, thus providing the potential for microniche partitioning. In addition, detected interspecific horizontal exchange of GIs indicates a large gene pool accessible to Polynucleobacter species. In contrast to core genes, GIs are spread more successfully across spatially separated freshwater habitats. The mobility and functional diversity of GIs allow for rapid evolution, which may be a key aspect for the ubiquitous occurrence of Polynucleobacter bacteria. IMPORTANCE Assessing the ecological relevance of bacterial diversity is a key challenge for current microbial ecology. The polyphasic approach which was applied in this study, including targeted isolation of strains, genome analysis, and ecophysiological tests, is crucial for the linkage of genetic and ecological knowledge. Particularly great importance is attached to the high number of closely related strains which were investigated, represented by genome-wide average nucleotide identities (ANI) larger than 97%. The extent of functional diversification found on this narrow phylogenetic scale is compelling. Moreover, the transfer of

Demonstration of a utility industry horizontal drilling system: Horizontal well AMH-5 installation report

International Nuclear Information System (INIS)

1992-01-01

The Department of Energy's Office of Technology Development initiated an integrated demonstration of innovative technologies and systems for cleanup of VOCs in soils and groundwater at the Savannah River Site (SRS) in 1989. The overall goal of the program is demonstration of multiple technologies and systems in the fields of drilling, characterization, monitoring, and remediation at a single test bed. Innovative technologies are compared to one another and to baseline technologies in terms of technical performance and cost effectiveness. Transfer of successfully demonstrated technologies and systems to DOE environmental restoration organizations, to other government agencies, and to industry is a critical part of the program. Directional drilling has been shown to be a successful technique for enhancing access to the subsurface, thus improving remediation systems, especially remediation systems which perform in situ. Demonstration of an innovative directional drilling system at the Integrated Demonstration Site at the SRS, was initiated in June of 1992. The directional drilling system was designed to install an in situ remediation system. The drilling system is an experimental compaction/dry drilling technique developed by Charles Machine Works (Ditch Witch reg-sign) of Perry, Oklahoma. A horizontal well was installed in the M Area of the SRS below and parallel to an abandoned tile process sewer line. The installation of the horizontal well was a two-part process. Part one consisted of drilling the borehole, and part two was the horizontal well completion

Expression of isgylation related genes in regenerating rat liver

Directory of Open Access Journals (Sweden)

Kuklin A. V.

2015-10-01

Full Text Available Our recent studies have revealed the early up-regulated expression of interferon alpha (IFNα in the liver, induced by partial hepatectomy. The role of this cytokine of innate immune response in liver regeneration is still controversial. Aim. To analyze expression of canonical interferon-stimulated genes Ube1l, Ube2l6, Trim25, Usp18 and Isg15 during the liver transition from quiescence to proliferation induced by partial hepatectomy, and acute phase response induced by laparotomy. These genes are responsible for posttranslational modification of proteins by ISGylation. The expression of genes encoding TATA binding protein (TBP and 18S rRNA served as indirect general markers of transcriptional and translational activities. Methods. The abundance of investigated RNAs was assessed in total liver RNA by real time RT–qPCR. Results. Partial hepatecomy induced steady upregulation of the Tbp and 18S rRNA genes expression during 12 hours post-surgery and downregulation or no change in expression of ISGylation-related genes during the first 3 hours followed by slight upregulation at 12 hours. The level of Isg15 transcripts was permanently below that of the control during the prereplicative period. Laparotomy induced a continuous downregulation of Tbp and 18S rRNA expression and early (1–3h upregulation of ISGylation–related transcripts followed by a sharp drop at 6 hours and slight increase/decrease at 12 hours. The changes in the abundance of Ifnα and ISGylation-related mRNAs were oppositely directed at each stage of the response to partial hepatectomy and laparotomy. Conclusion. We suggest that the expression of ISGylation-related genes does not depend on the expression of Ifnα gene after both surgeries. The indirect indices of transcription and translation as well as the expression of ISGylation-relaled genes are principally different in response to partial hepatectomy and laparotomy and argue for the high specificity of innate immune response.

Vacuum horizontal drainage for depressurization of uranium tailings

International Nuclear Information System (INIS)

Pakalnis, R.; Chedsey, G.; Robertson, A.M.; Follin, S.

1985-01-01

A recent advance in tailings slope depressurization is the application of vacuum assist horizontal drainage. Horizontal drains have been used for several decades to reduce water pressures in slopes in order to improve stability. The benefit from vacuum assist arises from an increased hydraulic gradient caused by induced negative atmospheric pressures. The vacuum assist system has, since its inception in 1982, been successfully employed at two soil and four rock slope projects located in Western Canada. This paper describes the first application of this system in the United States. The technical feasibility of employing vacuum assisted horizontal drains to depressurize a uranium tailings dam near Riverton, Wyoming has been evaluated. Two horizontal drains (300 ft.) were installed and their effect monitored by nine piezometers. The study was conducted over a three-week internal with vacuum being applied for three and four day periods. The drawdowns achieved through vacuum drainage was found to be approximately double that obtained by gravity alone. The volume of water exhausted under vacuum during the seven day interval was approximately double that obtained by gravity alone

Should tsunami simulations include a nonzero initial horizontal velocity?

Science.gov (United States)

Lotto, Gabriel C.; Nava, Gabriel; Dunham, Eric M.

2017-08-01

Tsunami propagation in the open ocean is most commonly modeled by solving the shallow water wave equations. These equations require initial conditions on sea surface height and depth-averaged horizontal particle velocity or, equivalently, horizontal momentum. While most modelers assume that initial velocity is zero, Y.T. Song and collaborators have argued for nonzero initial velocity, claiming that horizontal displacement of a sloping seafloor imparts significant horizontal momentum to the ocean. They show examples in which this effect increases the resulting tsunami height by a factor of two or more relative to models in which initial velocity is zero. We test this claim with a "full-physics" integrated dynamic rupture and tsunami model that couples the elastic response of the Earth to the linearized acoustic-gravitational response of a compressible ocean with gravity; the model self-consistently accounts for seismic waves in the solid Earth, acoustic waves in the ocean, and tsunamis (with dispersion at short wavelengths). Full-physics simulations of subduction zone megathrust ruptures and tsunamis in geometries with a sloping seafloor confirm that substantial horizontal momentum is imparted to the ocean. However, almost all of that initial momentum is carried away by ocean acoustic waves, with negligible momentum imparted to the tsunami. We also compare tsunami propagation in each simulation to that predicted by an equivalent shallow water wave simulation with varying assumptions regarding initial velocity. We find that the initial horizontal velocity conditions proposed by Song and collaborators consistently overestimate the tsunami amplitude and predict an inconsistent wave profile. Finally, we determine tsunami initial conditions that are rigorously consistent with our full-physics simulations by isolating the tsunami waves from ocean acoustic and seismic waves at some final time, and backpropagating the tsunami waves to their initial state by solving the

Comparison of partial and full nitrification processes applied for treating high-strength nitrogen wastewaters: microbial ecology through nitrous oxide production.

Science.gov (United States)

Ahn, Joon Ho; Kwan, Tiffany; Chandran, Kartik

2011-04-01

The goal of this study was to compare the microbial ecology, gene expression, biokinetics, and N2O emissions from a lab-scale bioreactor operated sequentially in full-nitrification and partial-nitrification modes. Based on sequencing of 16S rRNA and ammonia monooxygenase subunit A (amoA) genes, ammonia oxidizing bacteria (AOB) populations during full- and partial-nitrification modes were distinct from one another. The concentrations of AOB (XAOB) and their respiration rates during full- and partial-nitrification modes were statistically similar, whereas the concentrations of nitrite oxidizing bacteria (XNOB) and their respiration rates declined significantly after the switch from full- to partial-nitrification. The transition from full-nitrification to partial nitrification resulted in a protracted transient spike of nitrous oxide (N2O) and nitric oxide (NO) emissions, which later stabilized. The trends in N2O and NO emissions correlated well with trends in the expression of nirK and norB genes that code for the production of these gases in AOB. Both the transient and stabilized N2O and NO emissions during partial nitrification were statistically higher than those during steady-state full-nitrification. Based on these results, partial nitrification strategies for biological nitrogen removal, although attractive for their reduced operating costs and energy demand, may need to be optimized against the higher carbon foot-print attributed to their N2O emissions.

Horizontal Multinational Firms, Vertical Multinational Firms and Domestic Investment

NARCIS (Netherlands)

J. Emami Namini (Julian); H.P.G. Pennings (Enrico)

2009-01-01

textabstractWe build a dynamic general equilibrium model with 2 countries, horizontal and vertical multinational activity and endogenous domestic and foreign investment. It is found that horizontal multinational activity always leads to a complementary relationship between domestic and foreign

Overproduction and partial purification of the Norrie disease gene product, norrin, from a recombinant baculovirus.

Science.gov (United States)

Shastry, Barkur S; Trese, Michael T

2003-12-05

Abnormal vascularization of the peripheral retina and retinal detachment are common clinical characteristics of Norrie disease (ND), familial exudative vitreoretinopathy, Coats' disease, and retinopathy of prematurity. Although little is known about the molecular basis of these diseases, studies have shown that all of these diseases are associated with mutations in the ND gene. In spite of this, little is known about norrin, its molecular mechanism of action, and its functional relationship with the development of abnormal retinal vasculature. To obtain a large quantity of norrin for structural and functional studies, we have overproduced it in insect cells. For this purpose, a cDNA fragment (869 bp) was isolated from a human retinal cDNA library by amplification and was cloned into an expression vector. The purified plasmid was co-transfected with wild-type linearized Bac-N-Blue DNA into S. frugiperda Sf21 insect cells. The recombinant virus plaques were purified and clones were selected based on the level of recombinant protein expressed in Sf21 cells infected with a purified recombinant virus. From these, a high-titer stock was generated and subsequently used to prepare a fused protein on a large scale. The protein was partially purified by the process of immobilized metal affinity chromatography and the use of ion exchange chromatography

Antibiotics and common antibacterial biocides stimulate horizontal transfer of resistance at low concentrations.

Science.gov (United States)

Jutkina, J; Marathe, N P; Flach, C-F; Larsson, D G J

2018-03-01

There is a rising concern that antibiotics, and possibly other antimicrobial agents, can promote horizontal transfer of antibiotic resistance genes. For most types of antimicrobials their ability to induce conjugation below minimal inhibitory concentrations (MICs) is still unknown. Our aim was therefore to explore the potential of commonly used antibiotics and antibacterial biocides to induce horizontal transfer of antibiotic resistance. Effects of a wide range of sub-MIC concentrations of the antibiotics cefotaxime, ciprofloxacin, gentamicin, erythromycin, sulfamethoxazole, trimethoprim and the antibacterial biocides chlorhexidine digluconate, hexadecyltrimethylammoniumchloride and triclosan were investigated using a previously optimized culture-based assay with a complex bacterial community as a donor of mobile resistance elements and a traceable Escherichia coli strain as a recipient. Chlorhexidine (24.4μg/L), triclosan (0.1mg/L), gentamicin (0.1mg/L) and sulfamethoxazole (1mg/L) significantly increased the frequencies of transfer of antibiotic resistance whereas similar effects were not observed for any other tested antimicrobial compounds. This corresponds to 200 times below the MIC of the recipient for chlorhexidine, 1/20 of the MIC for triclosan, 1/16 of the MIC for sulfamethoxazole and right below the MIC for gentamicin. To our best knowledge, this is the first study showing that triclosan and chlorhexidine could stimulate the horizontal transfer of antibiotic resistance. Together with recent research showing that tetracycline is a potent inducer of conjugation, our results indicate that several antimicrobials including both common antibiotics and antibacterial biocides at low concentrations could contribute to antibiotic resistance development by facilitating the spread of antibiotic resistance between bacteria. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of horizontal plyometric training volume on soccer players' performance.

Science.gov (United States)

Yanci, Javier; Los Arcos, Asier; Camara, Jesús; Castillo, Daniel; García, Alberto; Castagna, Carlo

2016-01-01

The aim of this study was to examine the dose response effect of strength and conditioning programmes, involving horizontally oriented plyometric exercises, on relevant soccer performance variables. Sixteen soccer players were randomly allocated to two 6-week plyometric training groups (G1 and G2) differing by imposed (twice a week) training volume. Post-training G1 (4.13%; d = 0.43) and G2 (2.45%; d = 0.53) moderately improved their horizontal countermovement jump performance. Significant between-group differences (p  0.05, d = trivial or small) post-training improvements in sprint, change of direction ability (CODA) and horizontal arm swing countermovement jump were reported in either group. Horizontal plyometric training was effective in promoting improvement in injury prevention variables. Doubling the volume of a horizontal plyometric training protocol was shown to have no additional effect over functional aspects of soccer players' performance.

Evaluation of horizontal magnification on panoramic images

Directory of Open Access Journals (Sweden)

Maryam Raoof

2013-01-01

Full Text Available Aims: This study evaluated the horizontal magnification of images taken from adults and pediatrics with PM 2002 CC Planmeca analogue machine. Materials and Methods: A series of 120 panoramic radiographs were obtained of 60 adults and 60 pediatrics. For all patients, negative impressions were used to make positive casts of the teeth. A caliper was used to measure the maximum mesiodistal length of the buccal surface of all teeth except canines on both casts and radiographs. The horizontal magnification factor was calculated for incisor, premolar, and molar regions by dividing the values obtained from the casts by the values obtained from the radiographs. Statistical Analysis: Independent t-test and one-way analysis of variance (ANOVA were used. Results: The results indicated that with regard to adults, maxillary and mandibular incisor regions, unlike the other two sessions, didn′t show significant difference of the mean magnification of horizontal dimension (P = 0.5. In pediatrics, the comparison between mean magnification factors of all subgroups showed significant difference (P < 0.0001. Despite the adults′ radiographs, the results of pediatrics′ radiographs showed significantly higher magnification than the index listed by the manufacturer of the radiographic machine used. Conclusion: The present study results point to the fact that PM 2002 CC Proline panoramic machine makes possible precise measurements on radiographs of adults′ jaws in the horizontal dimension.

Horizontal-Longitudinal Correlations of Acoustic Field in Deep Water

International Nuclear Information System (INIS)

Li Jun; Li Zheng-Lin; Ren Yun; Li Wen; Zhang Ren-He

2015-01-01

The horizontal-longitudinal correlations of the acoustic field in deep water are investigated based on the experimental data obtained in the South China Sea. It is shown that the horizontal-longitudinal correlation coefficients in the convergence zone are high, and the correlation length is consistent with the convergence zone width, which depends on the receiver depth and range. The horizontal-longitudinal correlation coefficients in the convergence zone also have a division structure for the deeper receiver. The signals from the second part of the convergence zone are still correlated with the reference signal in the first part. The horizontal-longitudinal correlation coefficients in the shadow zone are lower than that in the convergence zone, and the correlation length in the shadow zone is also much shorter than that in the convergence zone. The numerical simulation results by using the normal modes theory are qualitatively consistent with the experimental results. (paper)

Two fundamentally different classes of microbial genes.

Science.gov (United States)

Wolf, Yuri I; Makarova, Kira S; Lobkovsky, Alexander E; Koonin, Eugene V

2016-11-07

The evolution of bacterial and archaeal genomes is highly dynamic and involves extensive horizontal gene transfer and gene loss 1-4 . Furthermore, many microbial species appear to have open pangenomes, where each newly sequenced genome contains more than 10% ORFans, that is, genes without detectable homologues in other species 5,6 . Here, we report a quantitative analysis of microbial genome evolution by fitting the parameters of a simple, steady-state evolutionary model to the comparative genomic data on the gene content and gene order similarity between archaeal genomes. The results reveal two sharply distinct classes of microbial genes, one of which is characterized by effectively instantaneous gene replacement, and the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of the size of the prokaryotic genomic universe, which appears to consist of at least a billion distinct genes. Furthermore, the same distribution of constraints is shown to govern the evolution of gene complement and gene order, without the need to invoke long-range conservation or the selfish operon concept 7 .

Logging while drilling keeps horizontal well on small target

International Nuclear Information System (INIS)

Leake, J.; Shray, F.

1991-01-01

This paper reports that the logging-while-drilling (LWD) measurement to two resistivities of different characteristics had led to a new interpretation method for the analysis of horizontal wells. By logging deep and shallow resistivity in real-time, marker beds were identified to help maintain well bore trajectory. The resistivity measurements were split into vertical and horizontal components to provide additional information of formation evaluation. In 1945, Ark Fuel Co. discovered and began developing the Olla field on the crest of the La Salle arch in La Salle Parish, La. Oil production comes from the Wilcox formation from alluvial sand packages that range in thickness from 3 ft to 120 ft. Now operated by Oxy U.S.A. Inc., Olla field was chosen in 1990 for a horizontal well pilot project. It was hoped that a horizontal well could alleviate water coming in one of the field's more productive sand packages- the 40-ft Cruse sand

Effectiveness of Horizontal Rebar on Concrete Block Retaining Wall Strength

OpenAIRE

Krishpersad Manohar; Rikhi Ramkissoon

2016-01-01

The effectiveness of including a horizontal rebar compared to only a vertical rebar in concrete filled core interlocking concrete block retaining wall sections was investigated with respect to the horizontal retaining force. Experimental results for three specimens of interlocking blocks with vertical rebar and concrete filled cores showed an average horizontal retaining force of 24546 N ± 5.7% at an average wall deflection of 13.3 mm. Experimental results for three wall specimens of interloc...

Fancy a gene? A surprisingly complex evolutionary history/nof peroxiredoxins

Czech Academy of Sciences Publication Activity Database

Zíková, Alena; Oborník, Miroslav; Lukeš, Julius

2015-01-01

Roč. 2, č. 2 (2015), s. 33-37 E-ISSN 2311-2638 EU Projects: European Commission(XE) 316304 Institutional support: RVO:60077344 Keywords : horizontal gene transfer * Apicomplexa * endosymbiont * Plasmodium * Chromera * peroxiredoxin * oxidative stress Subject RIV: EB - Genetics ; Molecular Biology

Regulatory role of tetR gene in a novel gene cluster of Acidovorax avenae subsp. avenae RS-1 under oxidative stress

OpenAIRE

Liu, He; Yang, Chun-Lan; Ge, Meng-Yu; Ibrahim, Muhammad; Li, Bin; Zhao, Wen-Jun; Chen, Gong-You; Zhu, Bo; Xie, Guan-Lin

2014-01-01

Acidovorax avenae subsp. avenae is the causal agent of bacterial brown stripe disease in rice. In this study, we characterized a novel horizontal transfer of a gene cluster, including tetR, on the chromosome of A. avenae subsp. avenae RS-1 by genome-wide analysis. TetR acted as a repressor in this gene cluster and the oxidative stress resistance was enhanced in tetR-deletion mutant strain. Electrophoretic mobility shift assay demonstrated that TetR regulator bound directly to the promoter of ...

Horizontal gene transfer of a ColV plasmid has resulted in a dominant avian clonal type of Salmonella enterica serovar Kentucky.

Directory of Open Access Journals (Sweden)

Timothy J Johnson

Full Text Available Salmonella enterica continues to be a significant cause of foodborne gastrointestinal illness in humans. A wide variety of Salmonella serovars have been isolated from production birds and from retail poultry meat. Recently, though, S. enterica subsp. enterica serovar Kentucky has emerged as one of the prominent Salmonella serovars isolated from broiler chickens. Recent work suggests that its emergence apparently coincides with its acquisition of a ColV virulence plasmid. In the present study, we examined 902 Salmonella isolates belonging to 59 different serovars for the presence of this plasmid. Of the serovars examined, the ColV plasmid was found only among isolates belonging to the serovars Kentucky (72.9%, Typhimurium (15.0% and Heidelberg (1.7%. We demonstrated that a single PFGE clonal type of S. Kentucky harbors this plasmid, and acquisition of this plasmid by S. Kentucky significantly increased its ability to colonize the chicken cecum and cause extraintestinal disease. Comparison of the completed sequences of three ColV plasmids from S. Kentucky isolated from different geographical locales, timepoints and sources revealed a nearly identical genetic structure with few single nucleotide changes or insertions/deletions. Overall, it appears that the ColV plasmid was recently acquired by a single clonal type S. Kentucky and confers to its host enhanced colonization and fitness capabilities. Thus, the potential for horizontal gene transfer of virulence and fitness factors to Salmonella from other enteric bacteria exists in poultry, representing a potential human health hazard.

Improving steamflood effectiveness by horizontal producers

Energy Technology Data Exchange (ETDEWEB)

Leonhardt, B. [Wintershall AG, Barnstorf (Germany)

2001-12-01

The Emlichheim oilfield is located in North-West-Germany on the Dutch-German border being the Southern downdip part of the Schoonebeek anticline. The field was discovered in 1943 and came on production in 1944. Since production startup, Wintershall operates the field as owner of the concession (90% share of interest) in a joint venture with Mobil Erdgas-Erdoel GmbH (10%). For more than 50 years an average crude oil production of 150.000 t/year has been maintained. Starting with huff ''n'' puff and hot water flooding in the late 60's, the first steam flood project was implemented in 1981. Further steamflood projects started in 1989, 1992, 1993, 1994 and 1998 in different areas of the field. Until 1997, only vertical production wells were drilled in the field. Wellbore stability seemed to be a major problem for drilling horizontal wells in the unconsolidated sandstone reservoir at that time. In 1999 an innovative steamflood project was started with three newly drilled horizontal producers surrounding a vertical steam injector. First results are showing a significant improvement in the performance as compared to the earlier projects and offer new chances for further development of the field. Today, the field could no longer be operated without the steam projects as roughly 95% of the field production is coming from thermal EOR. This paper gives a brief overview of the field and its production history, the planning and realization of a current steamflood project using horizontal well technology as well as its performance compared to the earlier projects. It also describes the experience of drilling horizontal wells in the unconsolidated sandstone. A brief outlook to the future field development is given. (orig.)

Numerical Investigation of Deviation of Phase Change Characteristics of Horizontal and Vertical Flat Heat Pipe Configurations

Directory of Open Access Journals (Sweden)

Rakesh Hari

2015-12-01

Full Text Available The flow characteristics in the porous wick of a flat heat pipe subjected to boiling and condensation are analysed here using two-phase mixture model. Steady laminar boundary layer flow in the capillary wick structure is considered for both vertical and horizontal orientations. The governing boundary layer partial differential equations are simplified using similarity transformation. The transformed equations are then solved numerically by using shooting iterative technique. Investigation was carried out for the effects of the involved parameters such as saturation and temperature across the boundary layer. The behaviour of non-dimensional numbers due to the orientation of the heat pipe is also discussed. The study confirms that orientation plays a significant role in flow and temperature field.

Horizontal Stratification in Access to Danish University Programmes

DEFF Research Database (Denmark)

Munk, Martin D.; Thomsen, Jens Peter

2018-01-01

a relatively detailed classification of parents’ occupations to determine how students are endowed with different forms of capital, even when their parents would typically be characterised as belonging to the same social group. Second, we distinguish among disciplines and among university institutions...... to explain the dynamics of horizontal stratification in the Danish university system. Using unique and exhaustive register data, including all higher education institutions and the entire 1984 cohort as of the age of 24, we uncover distinct differences in the magnitude and type of horizontal stratification...... in different fields of study and university institutions. Most importantly, we find distinct patterns of horizontal stratification by field of study and parental occupation that would have remained hidden had we used more aggregated classifications for field of study and social origin....

Cassette structures associated with antibiotic resistance genes in Salmonella enterica isolated from processing plants, food animals, and retail meats

Science.gov (United States)

Slowing the spread of antibiotic resistance (AR) is one of the most urgent tasks currently facing the field of microbiology. Mobile genetic elements, like plasmids and integrons, allow AR genes to transfer horizontally, thus increasing the spread of AR genes. Determining which AR genes are found on ...

Horizontol dissemination of TEM- and SHV-typr beta-lactamase genes-carrying resistance plasmids amongst clonical isolates of Enterobacteriaceae Disseminação horizontal de plasmídios de resistência contendo genes de beta-lactamase dos tipos TEM e SHV entre isolados clínicos de Enterobacteriaceae

Directory of Open Access Journals (Sweden)

Osman Birol Ozgumus

2008-12-01

Full Text Available The extended-spectrum β-lactamase (ESBL-producing bacteria have been isolated at increasing frequency worldwide. Expression of ESBL is often associated with multidrug resistance and dissemination by resistance plasmids. During a two-month period in 2000, 133 clinical isolates of enterobacterial strains were randomly collected from outpatients and inpatients at a university hospital in Turkey. The ESBL producing strains were determined by double-disk synergy (DDS testing. Twenty ESBL producing strains (15% including Escherichia coli (n = 9, Klebsiella pneumoniae (n = 7, Klebsiella oxytoca (n = 2 and Enterobacter aerogenes (n = 2 were detected and further analyzed for their resistance transfer features, plasmid profile and nature of the resistance genes. Plasmid transfer assays were performed using broth mating techniques. TEM- and SHV- genes were analyzed by polymerase chain reaction (PCR and hybridization using specific probes. EcoRI restriction enzyme analyses of R plasmids were used in the detection of epidemic plasmids. Fourteen plasmid profiles (A, B1, B2, C1, and C2 to L were obtained with EcoRI restriction enzyme analysis. Most of these plasmids were detected to carry both TEM- and SHV-derived genes by PCR, and confirmed by localizing each gene by hybridization assay. Epidemiological evidence indicated that there was an apparent horizontal dissemination of conjugative R plasmids among multidrug-resistant enterobacterial genera and species in this hospitalO isolamento de bactérias produtoras de beta-lactamases de espectro expandido (ESBL está aumentando no mundo todo. Freqüentemente, a expressão de ESBL está associada com resistência a múltiplas drogas e disseminação por plasmídios de resistência. Durante um período de dois meses em 2000, 133 isolados clínicos de cepas de enterobactérias foram obtidos aleatoriamente de pacientes internos e externos de um hospital universitário na Turquia. As cepas produtoras de ESBL foram

Remediation of a contaminated thin aquifer by horizontal wells

Energy Technology Data Exchange (ETDEWEB)

Breh, W.; Suttheimer, J.; Hoetzl, H. [Univ. of Karlsruhe (Germany); Frank, K. [GEO-Service GmbH, Rheinmuenster (Germany)

1997-12-31

At an industrial site in Bruchsal (Germany) a huge trichloroethene contamination was found. After common remedial actions proved to be widely ineffective, new investigations led to a highly contaminated thin aquifer above the main aquifer. The investigation and the beginning of the remediation of the thin aquifer by two horizontal wells is described in this paper. Special attention was given to the dependence between precipitation and the flow direction in the thin aquifer and to hydraulic connections between the thin and the main aquifer. Also a short introduction into a new remedial technique by horizontal wells and first results of the test phase of the horizontal wells are given.

Two hAT transposon genes were transferred from Brassicaceae to broomrapes and are actively expressed in some recipients

Science.gov (United States)

Sun, Ting; Renner, Susanne S.; Xu, Yuxing; Qin, Yan; Wu, Jianqiang; Sun, Guiling

2016-01-01

A growing body of evidence is pointing to an important role of horizontal gene transfer (HGT) in the evolution of higher plants. However, reports of HGTs of transposable elements (TEs) in plants are still scarce, and only one case is known of a class II transposon horizontally transferred between grasses. To investigate possible TE transfers in dicots, we performed transcriptome screening in the obligate root parasite Phelipanche aegyptiaca (Orobanchaceae), data-mining in the draft genome assemblies of four other Orobanchaceae, gene cloning, gene annotation in species with genomic information, and a molecular phylogenetic analysis. We discovered that the broomrape genera Phelipanche and Orobanche acquired two related nuclear genes (christened BO transposase genes), a new group of the hAT superfamily of class II transposons, from Asian Sisymbrieae or a closely related tribe of Brassicaceae, by HGT. The collinearity of the flanking genes, lack of a classic border structure, and low expression levels suggest that BO transposase genes cannot transpose in Brassicaceae, whereas they are highly expressed in P. aegyptiaca. PMID:27452947

prokaryote genome annotation with GeneScan and GLIMMER

Indian Academy of Sciences (India)

Unknown

The number of false predictions (both positive and negative) is higher for GeneScan as compared to GLIMMER, but in a ... on whether they need to be trained on a set of genes in order to ..... FP has partial matches to the kdpA gene in C. jejuni.

Numerical method for wave forces acting on partially perforated caisson

Science.gov (United States)

Jiang, Feng; Tang, Xiao-cheng; Jin, Zhao; Zhang, Li; Chen, Hong-zhou

2015-04-01

The perforated caisson is widely applied to practical engineering because of its great advantages in effectively wave energy consumption and cost reduction. The attentions of many scientists were paid to the fluid-structure interaction between wave and perforated caisson studies, but until now, most concerns have been put on theoretical analysis and experimental model set up. In this paper, interaction between the wave and the partial perforated caisson in a 2D numerical wave flume is investigated by means of the renewed SPH algorithm, and the mathematical equations are in the form of SPH numerical approximation based on Navier-Stokes equations. The validity of the SPH mathematical method is examined and the simulated results are compared with the results of theoretical models, meanwhile the complex hydrodynamic characteristics when the water particles flow in or out of a wave absorbing chamber are analyzed and the wave pressure distribution of the perforated caisson is also addressed here. The relationship between the ratio of total horizontal force acting on caisson under regular waves and its influence factors is examined. The data show that the numerical calculation of the ratio of total horizontal force meets the empirical regression equation very well. The simulations of SPH about the wave nonlinearity and breaking are briefly depicted in the paper, suggesting that the advantages and great potentiality of the SPH method is significant compared with traditional methods.

A massive incorporation of microbial genes into the genome of Tetranychus urticae, a polyphagous arthropod herbivore.

Science.gov (United States)

Wybouw, N; Van Leeuwen, T; Dermauw, W

2018-06-01

A number of horizontal gene transfers (HGTs) have been identified in the spider mite Tetranychus urticae, a chelicerate herbivore. However, the genome of this mite species has at present not been thoroughly mined for the presence of HGT genes. Here, we performed a systematic screen for HGT genes in the T. urticae genome using the h-index metric. Our results not only validated previously identified HGT genes but also uncovered 25 novel HGT genes. In addition to HGT genes with a predicted biochemical function in carbohydrate, lipid and folate metabolism, we also identified the horizontal transfer of a ketopantoate hydroxymethyltransferase and a pantoate β-alanine ligase gene. In plants and bacteria, both genes are essential for vitamin B5 biosynthesis and their presence in the mite genome strongly suggests that spider mites, similar to Bemisia tabaci and nematodes, can synthesize their own vitamin B5. We further show that HGT genes were physically embedded within the mite genome and were expressed in different life stages. By screening chelicerate genomes and transcriptomes, we were able to estimate the evolutionary histories of these HGTs during chelicerate evolution. Our study suggests that HGT has made a significant and underestimated impact on the metabolic repertoire of plant-feeding spider mites. © 2018 The Royal Entomological Society.

Partial structure of the phylloxin gene from the giant monkey frog, Phyllomedusa bicolor: parallel cloning of precursor cDNA and genomic DNA from lyophilized skin secretion.

Science.gov (United States)

Chen, Tianbao; Gagliardo, Ron; Walker, Brian; Zhou, Mei; Shaw, Chris

2005-12-01

Phylloxin is a novel prototype antimicrobial peptide from the skin of Phyllomedusa bicolor. Here, we describe parallel identification and sequencing of phylloxin precursor transcript (mRNA) and partial gene structure (genomic DNA) from the same sample of lyophilized skin secretion using our recently-described cloning technique. The open-reading frame of the phylloxin precursor was identical in nucleotide sequence to that previously reported and alignment with the nucleotide sequence derived from genomic DNA indicated the presence of a 175 bp intron located in a near identical position to that found in the dermaseptins. The highly-conserved structural organization of skin secretion peptide genes in P. bicolor can thus be extended to include that encoding phylloxin (plx). These data further reinforce our assertion that application of the described methodology can provide robust genomic/transcriptomic/peptidomic data without the need for specimen sacrifice.

Principal permeability determination from multiple horizontal well tests

Energy Technology Data Exchange (ETDEWEB)

Economides, M. [Texas A and M Univ., TX (United States); Munoz, A.; Ehlig-Economides, C.

1998-12-31

A method for obtaining principal permeability magnitudes and direction that requires only the linear flow regime from transient tests in three horizontal wells oriented in three distinct and arbitrary directions, is described. Well design optimization strategies require knowledge of both the principal permeability orientation as well as the horizontal permeability magnitudes. When the degree of horizontal permeability anisotropy (i.e. permeability in the bedding plane with respect to direction) is significant, the productivity of a long horizontal well will depend greatly on its direction, especially when the well is first brought into production. Productivities have been found to deviate substantially among wells in the same reservoir and this deviation has been attributed to differences in well orientation. In view of this fact, measuring permeability anisotropy becomes a compelling necessity. The success of the proposed method is illustrated by a case study in which the principal permeability magnitudes and direction from three wells were used to predict the productivity of a fourth well within 10 per cent. Use of the computed principal permeabilities from the case study, it was possible to forecast the cumulative production to show the significance of well trajectory optimization on the discounted cash flow and the net present value. 20 refs., 3 figs.

Estimation of network parameters with consideration of the horizontal refraction influence

Directory of Open Access Journals (Sweden)

Ján Ježko

2007-06-01

Full Text Available The proposed paper is focused on reviewing the horizontal refraction during measurement in local geodetic networks. Based on elaborated theoretical assumptions the refraction model was arranged in a way that the questions were solved by the identity of the horizontal refraction. The necessary part of the application of the refraction model is the problem of optimizing the geodetic networks and deducting the method of the variance components, which play a major role in the precision of results. The independent acquisition of the thesis lies in the area of modeling the horizontal refraction with a stochastic approach, where the values of the refraction are gained through the measured data of the horizontal direction. In the model, it is necessary to identify the parameters according to the entire measurements and between two points. According to the attained results, I can state that the horizontal refraction was identified mainly on the measurements that were confirmed near the dam in most of the measured experiments. The experimented measurements were confirmed based on the assumptions that are in theoretical capitol, where the assumptions of the effect of the horizontal refraction are measured near the dam, river, shores, and valleys.

Demonstration of in situ-constructed horizontal soil containment barrier at Fernald

International Nuclear Information System (INIS)

Pettit, P.J.; Ridenour, D.; Walker, J.; Saugier, K.

1994-01-01

A new design of jet grouting tool that can be guided by horizontal well casings and that operates in the horizontal plane has been used for the in situ placement of grout and construction of a prototype horizontal barrier that is free of windows. Jet grouting techniques have been advanced to permit construction of horizontal barriers underneath contaminated soil without having to excavate or disturb the waste. The paper describes progress on the Fernald Environmental Restoration Management Corporation (FERMCO) In Situ Land Containment Project which is sponsored by the US Department of Energy's (DOE) Office of Technology Development (OTD) for DOE's Fernald Environmental Management Project (FEMP). The Fernald project is to demonstrate a novel, enabling technology for the controlled underground placement of horizontal panels of grout, and the joining of adjacent panels to construct practical, extensive barriers. Construction strategy, equipment mechanics and operating details of this new method are described

Business models for horizontal collaboration : a practical case study with reusable crates

NARCIS (Netherlands)

Brandi, Teresa

2012-01-01

This project is centered in the topic of horizontal collaboration. The first part focuses on finding business models for horizontal collaboration. The second part is a practical case study at Kuehne + Nagel. Horizontal collaboration consists of two or more independent companies that plan and execute

Cloning of partial cry1Ac gene from an indigenous isolate of Bacillus ...

African Journals Online (AJOL)

The discoveries of novel cry genes of Bacillus thuringiensis (Bt) with higher toxicity are important for the development of new products. The cry1 family genes are more toxic to the lepidopteran insects according to the previous reports. In the present study, nine indigenous isolates of Bt were used for screening of cry1 genes ...

Dose-dependent effects of calorie restriction on gene expression, metabolism, and tumor progression are partially mediated by insulin-like growth factor-1

International Nuclear Information System (INIS)

Nogueira, Leticia M; Lavigne, Jackie A; Chandramouli, Gadisetti V R; Lui, Huaitian; Barrett, J Carl; Hursting, Stephen D

2012-01-01

. Exogenous IGF-1 rescued the hepatic expression of several metabolic genes and pathways affected by CR. Exogenous IGF-1 also rescued the expression of several metabolism- and cancer-related genes affected by CR in the mammary gland. Furthermore, exogenous IGF-1 partially reversed the mammary tumor inhibitory effects of 30% CR. We conclude that several genes and pathways, particularly those associated with macronutrient and steroid hormone metabolism, are associated with the anticancer effects of CR, and that reduced IGF-1 levels can account, at least in part, for many of the effects of CR on gene expression and mammary tumor burden

beta. -Amyloid gene dosage in Alzheimer's disease

Energy Technology Data Exchange (ETDEWEB)

Murdoch, G H; Manuelidis, L; Kim, J H; Manuelidis, E E

1988-01-11

The 4-5 kd amyloid ..beta..-peptide is a major constituent of the characteristic amyloid plaque of Alzheimer's disease. It has been reported that some cases of sporatic Alzheimer's disease are associated with at least a partial duplication of chromosome 21 containing the gene corresponding to the 695 residue precursor of this peptide. To contribute to an understanding of the frequency to such a duplication event in the overall Alzheimer's population, the authors have determined the gene dosage of the ..beta..-amyloid gene in this collection of cases. All cases had a clinical diagnosis of Alzheimer's confirmed neuropathologically. Each Alzheimer's case had an apparent normal diploid ..beta..-amyloid gene dosage, while control Down's cases had the expected triploid dosage. Thus partial duplication of chromosome 21 may be a rare finding in Alzheimer's disease. Similar conclusions were just reported in several studies of the Harvard Alzheimer collection.

Partial Granger causality--eliminating exogenous inputs and latent variables.

Science.gov (United States)

Guo, Shuixia; Seth, Anil K; Kendrick, Keith M; Zhou, Cong; Feng, Jianfeng

2008-07-15

Attempts to identify causal interactions in multivariable biological time series (e.g., gene data, protein data, physiological data) can be undermined by the confounding influence of environmental (exogenous) inputs. Compounding this problem, we are commonly only able to record a subset of all related variables in a system. These recorded variables are likely to be influenced by unrecorded (latent) variables. To address this problem, we introduce a novel variant of a widely used statistical measure of causality--Granger causality--that is inspired by the definition of partial correlation. Our 'partial Granger causality' measure is extensively tested with toy models, both linear and nonlinear, and is applied to experimental data: in vivo multielectrode array (MEA) local field potentials (LFPs) recorded from the inferotemporal cortex of sheep. Our results demonstrate that partial Granger causality can reveal the underlying interactions among elements in a network in the presence of exogenous inputs and latent variables in many cases where the existing conditional Granger causality fails.

Horizontal H 2-air turbulent buoyant jet resulting from hydrogen leakage

KAUST Repository

El-Amin, Mohamed

2012-02-01

The current article is devoted to introducing mathematical and physical analyses with numerical investigation of a buoyant jet resulting from hydrogen leakage in air from a horizontal round source. H 2-air jet is an example of the non-Boussinesq buoyant jet in which a low-density gas jet is injected/leak into a high-density ambient. The density of the mixture is a function of the concentration only, the binary gas mixture is assumed to be of a linear mixing type and the rate of entrainment is assumed to be a function of the plume centerline velocity and the ratio of the mean plume and ambient densities. On the other hand, the local rate of entrainment consists of two components; one is the component of entrainment due to jet momentum while the other is the component of entrainment due to buoyancy. The top-hat profile assumption is used to obtain the mean centerline velocity, width, density and concentration of the H 2-air horizontal jet in addition to kinematic relations which govern the jet trajectories. A set of ordinary differential equations is obtained and solved numerically using Runge-Kutta method. In the second step, the mean axial velocity, mean concentration and mean density of the jet are obtained based on Gaussian model. Finally, several quantities of interest, including the cross-stream velocity, Reynolds stress, velocity-concentration correlation (radial flux), turbulent eddy viscosity and turbulent eddy diffusivity, are obtained by solving the governing partial differential equations. Additionally, the turbulent Schmidt number is estimated and the normalized jet-feed material density and the normalized momentum flux density are correlated. © 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

Two-phase flow patterns in horizontal rectangular minichannel

Directory of Open Access Journals (Sweden)

Ron’shin Fedor

2016-01-01

Full Text Available The two-phase flow in a short horizontal channel of rectangular cross-section of 1 × 19 mm2 has been studied experimentally. Five conventional two-phase flow patterns have been detected (bubble, churn, stratified, annular and jet and transitions between them have been determined. It is shown that a change in the width of the horizontal channels has a substantial effect on the boundaries between the flow regimes.

The vertical, the horizontal and the rest: anatomy of the middle cohomology of Calabi-Yau fourfolds and F-theory applications

Energy Technology Data Exchange (ETDEWEB)

Braun, A.P. [Department of Mathematics, King’s College,London WC2R 2LS (United Kingdom); Watari, T. [Kavli Institute for the Physics and Mathematics of the Universe, University of Tokyo,Kashiwano-ha 5-1-5, 277-8583 (Japan)

2015-01-12

The four-form field strength in F-theory compactifications on Calabi-Yau fourfolds takes its value in the middle cohomology group H{sup 4}. The middle cohomology is decomposed into a vertical, a horizontal and a remaining component, all three of which are present in general. We argue that a flux along the remaining or vertical component may break some symmetry, while a purely horizontal flux does not influence the unbroken part of the gauge group or the net chirality of charged matter fields. This makes the decomposition crucial to the counting of flux vacua in the context of F-theory GUTs. We use mirror symmetry to derive a combinatorial formula for the dimensions of these components applicable to any toric Calabi-Yau hypersurface, and also make a partial attempt at providing a geometric characterization of the four-cycles Poincaré dual to the remaining component of H{sup 4}. It is also found in general elliptic Calabi-Yau fourfolds supporting SU(5) gauge symmetry that a remaining component can be present, for example, in a form crucial to the symmetry breaking SU(5)⟶SU(3){sub C}×SU(2){sub L}×U(1){sub Y}. The dimension of the horizontal component is used to derive an estimate of the statistical distribution of the number of generations and the rank of 7-brane gauge groups in the landscape of F-theory flux vacua.

Real-time horizontal position control for Aditya-upgrade tokamak

International Nuclear Information System (INIS)

Kumar, Rohit; Ghosh, Joydeep; Tanna, Rakesh L.

2015-01-01

Position of plasma column is required to be controlled in real time for improved operation of any tokamak. A PID based system for real-time horizontal plasma position control has been designed for Aditya Upgrade tokamak. Modelling of transfer functions of actuators, plasma and diagnostic system are carried out for ADITYA-U tokamak. The PID controller is optimized using MATLAB-SIMULINK for horizontal position control. Further feed-forward loop is implemented where disturbance due to density variation is suppressed, which results in improved performance as compared to conventional PID operation. In this paper the detailed design of the whole system for real time control of plasma horizontal position in Aditya Upgrade tokamak is presented. (author)

Heat transfer by natural convection into an horizontal cavity; Transferencia de calor por conveccion natural en una cavidad horizontal

Energy Technology Data Exchange (ETDEWEB)

Arevalo J, P

1998-12-31

At this thesis it is studied the heat transfer by natural convection in an horizontal cavity, it is involved a boiling`s part that is described the regimes and correlations differences for boiling`s curve. It is designed a horizontal cavity for realize the experimental part and it`s mention from equipment or instrumentation to succeed in a experimentation that permits to realize the analysis of heat transfer, handling as water fluid at atmospheric pressure and where it`s present process from natural convection involving part boiling`s subcooled. The system consists of heater zone submerged in a horizontal cavity with water. Once part finished experimental with information to obtained it`s proceeded to obtain a correlation, realized starting from analysis dimensionless such as: Jakob, Bond and Grasoft (Boiling) besides of knows in natural convection: Prandtl and Nusselt. The mathematical model explains the behavior for natural convection continued part boiling`s subcooled. It is realize analysis graphics too where it`s show comparing with Globe Dropkin and Catton equations by natural convection with bottom heating. (Author)

Heat transfer by natural convection into an horizontal cavity; Transferencia de calor por conveccion natural en una cavidad horizontal

Energy Technology Data Exchange (ETDEWEB)

Arevalo J, P

1999-12-31

At this thesis it is studied the heat transfer by natural convection in an horizontal cavity, it is involved a boiling`s part that is described the regimes and correlations differences for boiling`s curve. It is designed a horizontal cavity for realize the experimental part and it`s mention from equipment or instrumentation to succeed in a experimentation that permits to realize the analysis of heat transfer, handling as water fluid at atmospheric pressure and where it`s present process from natural convection involving part boiling`s subcooled. The system consists of heater zone submerged in a horizontal cavity with water. Once part finished experimental with information to obtained it`s proceeded to obtain a correlation, realized starting from analysis dimensionless such as: Jakob, Bond and Grasoft (Boiling) besides of knows in natural convection: Prandtl and Nusselt. The mathematical model explains the behavior for natural convection continued part boiling`s subcooled. It is realize analysis graphics too where it`s show comparing with Globe Dropkin and Catton equations by natural convection with bottom heating. (Author)

Experimental measurements of the cavitating flow after horizontal water entry

Energy Technology Data Exchange (ETDEWEB)

Nguyen, Thang Tat; Thai, Nguyen Quang; Phuong, Truong Thi [Institute of Mechanics (IMECH), Vietnam Academy of Science and Technology (VAST), 264—Doi Can, Ba Dinh, Hanoi (Viet Nam); Hai, Duong Ngoc, E-mail: ntthang@imech.vast.vn, E-mail: dnhai@vast.vn, E-mail: nqthai@imech.vast.vn, E-mail: ttphuong@imech.vast.vn [Graduate University of Science and Technology (GUST), VAST, 18—Hoang Quoc Viet, Cau Giay, Hanoi (Viet Nam)

2017-10-15

Water-entry cavitating flow is of considerable importance in underwater high-speed applications. That is because of the drag-reduction effect that concerns the presence of a cavity around moving objects. Though the study of the flow has long been carried out, little data are documented in literature so far. Besides, currently, in the case of unsteady flow, experimental measurements of some flow parameters such as the cavity pressure still encounter difficulties. Hence continuing research efforts are of important significance. The objective of this study is to investigate experimentally the unsteady cavitating flow after the horizontal water entry of projectiles. An experimental apparatus has been developed. Qualitative and quantitative optical visualizations of the flow have been carried out by using high-speed videography. Digital image processing has been applied to analyzing the recorded flow images. Based on the known correlations between the ellipsoidal super-cavity’s size and the corresponding cavitation number, the cavity pressure has been measured by utilizing the data of image processing. A comparison between the partial- and super-cavitating flow regimes is reported. The received results can be useful for the design of high-speed underwater projectiles. (paper)

New transient-flow modelling of a multiple-fractured horizontal well

International Nuclear Information System (INIS)

Jia, Yong-Lu; Wang, Ben-Cheng; Nie, Ren-Shi; Wang, Dan-Ling

2014-01-01

A new transient-flow modelling of a multiple-fractured horizontal well is presented. Compared to conventional modelling, the new modelling considered more practical physical conditions, such as various inclined angles for different fractures, different fracture intervals, different fracture lengths and partially penetrating fractures to formation. A kind of new mathematical method, including a three-dimensional eigenvalue and orthogonal transform, was created to deduce the exact analytical solutions of pressure transients for constant-rate production in real space. In order to consider a wellbore storage coefficient and skin factor, we used a Laplace-transform approach to convert the exact analytical solutions to the solutions in Laplace space. Then the numerical solutions of pressure transients in real space were gained using a Stehfest numerical inversion. Standard type curves were plotted to describe the transient-flow characteristics. Flow regimes were clearly identified from type curves. Furthermore, the differences between the new modelling and the conventional modelling in pressure transients were especially compared and discussed. Finally, an example application to show the accordance of the new modelling with real conditions was implemented. Our new modelling is different from, but more practical than, conventional modelling. (paper)

Fourth international seminar on horizontal steam generators

Energy Technology Data Exchange (ETDEWEB)

Tuomisto, H. [ed.] [IVO Group, Vantaa (Finland); Purhonen, H. [ed.] [VTT, Espoo (Finland); Kouhia, V. [ed.] [Lappeenranta Univ. of Technology (Finland)

1997-12-31

The general objective of the International Seminars of Horizontal Steam Generator Modelling has been the improvement in understanding of realistic thermal hydraulic behaviour of the generators when performing safety analyses for VVER reactors. The main topics presented in the fourth seminar were: thermal hydraulic experiments and analyses, primary collector integrity, feedwater distributor replacement, management of primary-to-secondary leakage accidents and new developments in the VVER safety technology. The number of participants, representing designers and manufacturers of the horizontal steam generators, plant operators, engineering companies, research organizations, universities and regulatory authorities, was 70 from 10 countries.

Fourth international seminar on horizontal steam generators

Energy Technology Data Exchange (ETDEWEB)

Tuomisto, H [ed.; IVO Group, Vantaa (Finland); Purhonen, H [ed.; VTT, Espoo (Finland); Kouhia, V [ed.; Lappeenranta Univ. of Technology (Finland)

1998-12-31

The general objective of the International Seminars of Horizontal Steam Generator Modelling has been the improvement in understanding of realistic thermal hydraulic behaviour of the generators when performing safety analyses for VVER reactors. The main topics presented in the fourth seminar were: thermal hydraulic experiments and analyses, primary collector integrity, feedwater distributor replacement, management of primary-to-secondary leakage accidents and new developments in the VVER safety technology. The number of participants, representing designers and manufacturers of the horizontal steam generators, plant operators, engineering companies, research organizations, universities and regulatory authorities, was 70 from 10 countries.

Fourth international seminar on horizontal steam generators

International Nuclear Information System (INIS)

Tuomisto, H.; Purhonen, H.; Kouhia, V.

1997-01-01

The general objective of the International Seminars of Horizontal Steam Generator Modelling has been the improvement in understanding of realistic thermal hydraulic behaviour of the generators when performing safety analyses for VVER reactors. The main topics presented in the fourth seminar were: thermal hydraulic experiments and analyses, primary collector integrity, feedwater distributor replacement, management of primary-to-secondary leakage accidents and new developments in the VVER safety technology. The number of participants, representing designers and manufacturers of the horizontal steam generators, plant operators, engineering companies, research organizations, universities and regulatory authorities, was 70 from 10 countries

Prediction of evaporation heat transfer coefficient based on gas-liquid two-phase annular flow regime in horizontal microfin tubes

International Nuclear Information System (INIS)

Wang Yueshe; Wang Yanling; Wang, G.-X.; Honda, Hiroshi

2009-01-01

A physical model of gas-liquid two-phase annular flow regime is presented for predicting the enhanced evaporation heat transfer characteristics in horizontal microfin tubes. The model is based on the equivalence of a periodical distortion of the disturbance wave in the substrate layer. Corresponding to the stratified flow model proposed previously by authors, the dimensionless quantity Fr 0 = G/[gd e ρ v (ρ l - ρ v )] 0.5 may be used as a measure for determining the applicability of the present theoretical model, which was used to restrict the transition boundary between the stratified-wavy flow and the annular/intermittent flows. Comparison of the prediction of the circumferential average heat transfer coefficient with available experimental data for four tubes and three refrigerants reveals that a good agreement is obtained or the trend is better than that of the previously developed stratified flow model for Fr 0 > 4.0 as long as the partial dry out of tube does not occur. Obviously, the developed annular model is applicable and reliable for evaporation in horizontal microfin tubes under the case of high heat flux and high mass flux.

Prediction of evaporation heat transfer coefficient based on gas-liquid two-phase annular flow regime in horizontal microfin tubes

Energy Technology Data Exchange (ETDEWEB)

Wang Yueshe, E-mail: wangys@mail.xjtu.edu.cn [State Key Laboratory of Multiphase Flow in Power Engineering, Xi' an Jiaotong University, Xi' an 710049 (China); Yanling, Wang [State Key Laboratory of Multiphase Flow in Power Engineering, Xi' an Jiaotong University, Xi' an 710049 (China); Wang, G -X [Mechanical Engineering Department, The University of Akron, Akron, OH 44325-3903 (United States); Honda, Hiroshi [Kyushu University, 337 Kasuya-machi, Kasuya-gun, Kukuoka 811-2307 (Japan)

2009-10-15

A physical model of gas-liquid two-phase annular flow regime is presented for predicting the enhanced evaporation heat transfer characteristics in horizontal microfin tubes. The model is based on the equivalence of a periodical distortion of the disturbance wave in the substrate layer. Corresponding to the stratified flow model proposed previously by authors, the dimensionless quantity Fr{sub 0} = G/[gd{sub e}{rho}{sub v}({rho}{sub l} - {rho}{sub v})]{sup 0.5} may be used as a measure for determining the applicability of the present theoretical model, which was used to restrict the transition boundary between the stratified-wavy flow and the annular/intermittent flows. Comparison of the prediction of the circumferential average heat transfer coefficient with available experimental data for four tubes and three refrigerants reveals that a good agreement is obtained or the trend is better than that of the previously developed stratified flow model for Fr{sub 0} > 4.0 as long as the partial dry out of tube does not occur. Obviously, the developed annular model is applicable and reliable for evaporation in horizontal microfin tubes under the case of high heat flux and high mass flux.

Potential for horizontal well technology in the U.S

International Nuclear Information System (INIS)

Biglarbigi, K.; Mohan, H.; Ray, R.M.; Meehan, D.N.

2000-01-01

In the past decade, the use of horizontal well technology has increased significantly in the U.S., contributing to the drilling of 600 to 1000 horizontal oil wells annually. A total of 86 per cent of the existing horizontal wells have been drilled in three formations, the Austin chalk in Texas, the Bakken shale in North Dakota, and the Niobrara in Colorado and Wyoming. A unique analytical system has been developed by the United States Department of Energy, National Petroleum Technology Office (USDOE/NPTO) to assess the potential for greater use of horizontal well technology for other oil resources in other geological formations. The analytical system is designed to be used in association with other enhanced recovery methods that make up the DOE's Total Oil Recovery Information System (TORIS). The DOE/NPTO collaborated with industry to identify the target resource for horizontal well technology and to evaluate its future recovery potential under different economic and technological conditions. This paper provides a national summary of the potential for additional production and reserves with more diverse application of horizontal wells in various types of U.S. oil resources, including the rest of the fractured reservoirs in the Austin chalk, other fractured reservoirs in the north and northwestern states, thin-bed reservoirs, and mature waterflood field. The results were presented in terms of production, reserves and national economic benefits with a full cash-flow analysis at oil prices in the range of $16 to $24 U.S. per bbl. It is estimated that 541 million to 1 billion bbls of new reserves are economically producible at these prices. The reserves estimates pertain to future horizontal wells in known fields only and are in addition to the reserves for the existing wells as of 1 January 1998. Potential production is substantial, ranging from 50 million to 85 million bbl per year by 2004 and then declining at a rate of 8 per cent per year in the following years

Congenital Hypothyroidism Caused by a PAX8 Gene Mutation Manifested as Sodium/Iodide Symporter Gene Defect

Directory of Open Access Journals (Sweden)

Wakako Jo

2010-01-01

Full Text Available Loss-of-function mutations of the PAX8 gene are considered to mainly cause congenital hypothyroidism (CH due to thyroid hypoplasia. However, some patients with PAX8 mutation have demonstrated a normal-sized thyroid gland. Here we report a CH patient caused by a PAX8 mutation, which manifested as iodide transport defect (ITD. Hypothyroidism was detected by neonatal screening and L-thyroxine replacement was started immediately. Although 123I scintigraphy at 5 years of age showed that the thyroid gland was in the normal position and of small size, his iodide trapping was low. The ratio of the saliva/plasma radioactive iodide was low. He did not have goiter; however laboratory findings suggested that he had partial ITD. Gene analyses showed that the sodium/iodide symporter (NIS gene was normal; instead, a mutation in the PAX8 gene causing R31H substitution was identified. The present report demonstrates that individuals with defective PAX8 can have partial ITD, and thus genetic analysis is useful for differential diagnosis.

Characterization of horizontal air–water two-phase flow

Energy Technology Data Exchange (ETDEWEB)

Kong, Ran; Kim, Seungjin, E-mail: skim@psu.edu

2017-02-15

Highlights: • A visualization study is performed to develop flow regime map in horizontal flow. • Database in horizontal bubbly flow is extended using a local conductivity probe. • Frictional pressure drop analysis is performed in horizontal bubbly flow. • Drift flux analysis is performed in horizontal bubbly flow. - Abstract: This paper presents experimental studies performed to characterize horizontal air–water two-phase flow in a round pipe with an inner diameter of 3.81 cm. A detailed flow visualization study is performed using a high-speed video camera in a wide range of two-phase flow conditions to verify previous flow regime maps. Two-phase flows are classified into bubbly, plug, slug, stratified, stratified-wavy, and annular flow regimes. While the transition boundaries identified in the present study compare well with the existing ones (Mandhane et al., 1974) in general, some discrepancies are observed for bubbly-to-plug/slug, and plug-to-slug transition boundaries. Based on the new transition boundaries, three additional test conditions are determined in horizontal bubbly flow to extend the database by Talley et al. (2015a). Various local two-phase flow parameters including void fraction, interfacial area concentration, bubble velocity, and bubble Sauter mean diameter are obtained. The effects of increasing gas flow rate on void fraction, bubble Sauter mean diameter, and bubble velocity are discussed. Bubbles begin to coalesce near the gas–liquid layer instead of in the highly packed region when gas flow rate increases. Using all the current experimental data, two-phase frictional pressure loss analysis is performed using the Lockhart–Martinelli method. It is found that the coefficient C = 24 yields the best agreement with the data with the minimum average difference. Moreover, drift flux analysis is performed to predict void-weighted area-averaged bubble velocity and area-averaged void fraction. Based on the current database, functional

A horizontal vane radiometer: experiment, theory and simulation

OpenAIRE

Wolfe, David; Lazarra, Andres; Garcia, Alejandro

2015-01-01

The existence of two motive forces on a Crookes radiometer has complicated the investigation of either force independently. The thermal creep shear force in particular has been subject to differing interpretations of the direction in which it acts and its order of magnitude. In this article we provide a horizontal vane radiometer design which isolates the thermal creep shear force. The horizontal vane radiometer is explored through experiment, kinetic theory, and the Direct Simulation Monte C...

Molecular analysis of partial VP-2 gene amplified from rectal swab samples of diarrheic dogs in Pakistan confirms the circulation of canine parvovirus genetic variant CPV-2a and detects sequences of feline panleukopenia virus (FPV).

Science.gov (United States)

Ahmed, Nisar; Riaz, Adeel; Zubair, Zahra; Saqib, Muhammad; Ijaz, Sehrish; Nawaz-Ul-Rehman, Muhammad Shah; Al-Qahtani, Ahmed; Mubin, Muhammad

2018-03-15

The infection in dogs due to canine parvovirus (CPV), is a highly contagious one with high mortality rate. The present study was undertaken for a detailed genetic analysis of partial VP2 gene i.e., 630 bp isolated from rectal swab samples of infected domestic and stray dogs from all areas of district Faisalabad. Monitoring of viruses is important, as continuous prevalence of viral infection might be associated with emergence of new virulent strains. In the present study, 40 rectal swab samples were collected from diarrheic dogs from different areas of district Faisalabad, Pakistan, in 2014-15 and screened for the presence of CPV by immunochromatography. Most of these dogs were stray dogs showing symptoms of diarrhea. Viral DNA was isolated and partial VP2 gene was amplified using gene specific primer pair Hfor/Hrev through PCR. Amplified fragments were cloned in pTZ57R/T (Fermentas) and completely sequenced. Sequences were analyzed and assembled by the Lasergene DNA analysis package (v8; DNAStar Inc., Madison, WI, USA). The results with immunochromatography showed that 33/40 (82%) of dogs were positive for CPV. We were able to amplify a fragment of 630 bp from 25 samples. In 25 samples the sequences of CPV-2a were detected showing the amino acid substitution Ser297Ala and presence of amino acid (426-Asn) in partial VP2 protein. Interestingly the BLAST analysis showed the of feline panleukopenia virus (FPV) sequences in 3 samples which were already positive for new CPV-2a, with 99% sequence homology to other FPV sequences present in GenBank. Phylogenetic analysis showed clustering of partial CPV-VP-2 gene with viruses from China, India, Japan and Uruguay identifying a new variant, whereas the 3 FPV sequences showed immediate ancestral relationship with viruses from Portugal, South Africa and USA. Interesting observation was that CPV are clustering away from the commercial vaccine strains. In this work we provide a better understanding of CPV prevailing in Pakistan

Survey of horizontal stresses in coal mines from available measurements and mapping.

CSIR Research Space (South Africa)

Frith, R

2002-09-01

Full Text Available of work for the project was outlined in the proposal submitted to SIMRAC in mid-2000 and is summarised as follows: (i) to undertake a peer review of available in-situ stress measurements relating to the Witbank and Highveld coalfields in South Africa... OF HORIZONTAL STRESS IN THE WITBANK AND HIGHVELD COALFIELDS 21 4.1 Is Horizontal Stress at Work in Roadway Roof Behaviour? 21 4.2 Summary of Measured Horizontal Stresses 24 4.3 Proposed Model for the Origin of Horizontal Stress Within the Coalfields 27 4...

Biomechanical effects of two different collar implant structures on stress distribution under cantilever fixed partial dentures.

Science.gov (United States)

Merıç, Gökçe; Erkmen, Erkan; Kurt, Ahmet; Eser, Atilim; özden, Ahmet Utku

2011-11-01

The purpose of the study was to compare the effects of two distinct collar geometries of implants on stress distribution in the bone around the implants supporting cantilever fixed partial dentures (CFPDs) as well as in the implant-abutment complex and superstructures. The three-dimensional finite element method was selected to evaluate the stress distribution. CFPDs which was supported by microthread collar structured (MCS) and non-microthread collar structured (NMCS) implants was modeled; 300 N vertical, 150 N oblique and 60 N horizontal forces were applied to the models separately. The stress values in the bone, implant-abutment complex and superstructures were calculated. In the MCS model, higher stresses were located in the cortical bone and implant-abutment complex in the case of vertical load while decreased stresses in cortical bone and implant-abutment complex were noted within horizontal and oblique loading. In the case of vertical load, decreased stresses have been noted in cancellous bone and framework. Upon horizontal and oblique loading, a MCS model had higher stress in cancellous bone and framework than the NMCS model. Higher von Mises stresses have been noted in veneering material for NMCS models. It has been concluded that stress distribution in implant-supported CFPDs correlated with the macro design of the implant collar and the direction of applied force.

Cast Partial Denture versus Acrylic Partial Denture for Replacement of Missing Teeth in Partially Edentulous Patients

Directory of Open Access Journals (Sweden)

Pramita Suwal

2017-03-01

Full Text Available Aim: To compare the effects of cast partial denture with conventional all acrylic denture in respect to retention, stability, masticatory efficiency, comfort and periodontal health of abutments. Methods: 50 adult partially edentulous patient seeking for replacement of missing teeth having Kennedy class I and II arches with or without modification areas were selected for the study. Group-A was treated with cast partial denture and Group-B with acrylic partial denture. Data collected during follow-up visit of 3 months, 6 months, and 1 year by evaluating retention, stability, masticatory efficiency, comfort, periodontal health of abutment. Results: Chi-square test was applied to find out differences between the groups at 95% confidence interval where p = 0.05. One year comparison shows that cast partial denture maintained retention and stability better than acrylic partial denture (p< 0.05. The masticatory efficiency was significantly compromising from 3rd month to 1 year in all acrylic partial denture groups (p< 0.05. The comfort of patient with cast partial denture was maintained better during the observation period (p< 0.05. Periodontal health of abutment was gradually deteriorated in all acrylic denture group (p

Wake of inertial waves of a horizontal cylinder in horizontal translation

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Machicoane, Nathanaël; Labarre, Vincent; Voisin, Bruno; Moisy, Frédéric; Cortet, Pierre-Philippe

2018-03-01

We analyze theoretically and experimentally the wake behind a horizontal cylinder of diameter d horizontally translated at constant velocity U in a fluid rotating about the vertical axis at a rate Ω . Using particle image velocimetry measurements in the rotating frame, we show that the wake is stabilized by rotation for Reynolds number Re =U d /ν much larger than in a nonrotating fluid. Over the explored range of parameters, the limit of stability is Re ≃(275 ±25 )/Ro , with Ro =U /2 Ω d the Rossby number, indicating that the stabilizing process is governed by the Ekman pumping in the boundary layer. At low Rossby number, the wake takes the form of a stationary pattern of inertial waves, similar to the wake of surface gravity waves behind a ship. We compare this steady wake pattern to a model, originally developed by Johnson [E. R. Johnson, J. Fluid Mech. 120, 359 (1982), 10.1017/S0022112082002808], assuming a free-slip boundary condition and a weak streamwise perturbation. Our measurements show quantitative agreement with this model for Ro ≲0.3 . At larger Rossby number, the phase pattern of the wake is close to the prediction for an infinitely small line object. However, the wake amplitude and phase origin are not correctly described by the weak-streamwise-perturbation model, calling for an alternative model for the boundary condition at moderate rotation rate.

HORIZONTE Y ESTRUCTURA DE LA PREGUNTA PEDAGÓGICA

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Arturo G. Rillo

2011-01-01

Full Text Available En este artículo se abren caminos para la reflexión y la investigación de la pregunta pedagógica como un problema hermenéutico sustentado en la dialéctica de la pregunta y la respuesta. El punto de partida se construyó mediante las coordenadas propuestas por Heidegger (punto de mira, dirección de la mirada y horizonte de la mira y los prejuicios que subyacen en la tradición educativa contemporánea. El análisis se proyecta hacia la identificación de la estructura y el horizonte de la pregunta pedagógica confrontando los aportes de Heidegger, Gadamer y Freire en la elaboración de una pedagogía de la pregunta. La estructura de la pregunta incluye lo puesto en cuestión, lo preguntado y lo interrogado, lo que posibilita construir un horizonte para comprender la pregunta pedagógica desde la aproximación del estudiante a los saberes desde una praxis liberadora. Se concluye que la estructura y el horizonte de la pregunta pedagógica se sustentan en la lógica concreta del trabajo hermenéutico, donde la apertura del estudiante a las experiencias y vivencias desvela la construcción de su conocimiento mediante el arte de pensar que deriva de la praxis transformadora.

Edible Safety Assessment of Genetically Modified Rice T1C-1 for Sprague Dawley Rats through Horizontal Gene Transfer, Allergenicity and Intestinal Microbiota.

Science.gov (United States)

Zhao, Kai; Ren, Fangfang; Han, Fangting; Liu, Qiwen; Wu, Guogan; Xu, Yan; Zhang, Jian; Wu, Xiao; Wang, Jinbin; Li, Peng; Shi, Wei; Zhu, Hong; Lv, Jianjun; Zhao, Xiao; Tang, Xueming

2016-01-01

In this study, assessment of the safety of transgenic rice T1C-1 expressing Cry1C was carried out by: (1) studying horizontal gene transfer (HGT) in Sprague Dawley rats fed transgenic rice for 90 d; (2) examining the effect of Cry1C protein in vitro on digestibility and allergenicity; and (3) studying the changes of intestinal microbiota in rats fed with transgenic rice T1C-1 in acute and subchronic toxicity tests. Sprague Dawley rats were fed a diet containing either 60% GM Bacillus thuringiensis (Bt) rice T1C-1 expressing Cry1C protein, the parental rice Minghui 63, or a basic diet for 90 d. The GM Bt rice T1C-1 showed no evidence of HGT between rats and transgenic rice. Sequence searching of the Cry1C protein showed no homology with known allergens or toxins. Cry1C protein was rapidly degraded in vitro with simulated gastric and intestinal fluids. The expressed Cry1C protein did not induce high levels of specific IgG and IgE antibodies in rats. The intestinal microbiota of rats fed T1C-1 was also analyzed in acute and subchronic toxicity tests by DGGE. Cluster analysis of DGGE profiles revealed significant individual differences in the rats' intestinal microbiota.

Edible Safety Assessment of Genetically Modified Rice T1C-1 for Sprague Dawley Rats through Horizontal Gene Transfer, Allergenicity and Intestinal Microbiota.

Directory of Open Access Journals (Sweden)

Kai Zhao

Full Text Available In this study, assessment of the safety of transgenic rice T1C-1 expressing Cry1C was carried out by: (1 studying horizontal gene transfer (HGT in Sprague Dawley rats fed transgenic rice for 90 d; (2 examining the effect of Cry1C protein in vitro on digestibility and allergenicity; and (3 studying the changes of intestinal microbiota in rats fed with transgenic rice T1C-1 in acute and subchronic toxicity tests. Sprague Dawley rats were fed a diet containing either 60% GM Bacillus thuringiensis (Bt rice T1C-1 expressing Cry1C protein, the parental rice Minghui 63, or a basic diet for 90 d. The GM Bt rice T1C-1 showed no evidence of HGT between rats and transgenic rice. Sequence searching of the Cry1C protein showed no homology with known allergens or toxins. Cry1C protein was rapidly degraded in vitro with simulated gastric and intestinal fluids. The expressed Cry1C protein did not induce high levels of specific IgG and IgE antibodies in rats. The intestinal microbiota of rats fed T1C-1 was also analyzed in acute and subchronic toxicity tests by DGGE. Cluster analysis of DGGE profiles revealed significant individual differences in the rats' intestinal microbiota.

Ongoing Horizontal and Vertical Transmission of Virulence Genes and papA Alleles among Escherichia coli Blood Isolates from Patients with Diverse-Source Bacteremia

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Johnson, James R.; O'Bryan, Timothy T.; Kuskowski, Michael; Maslow, Joel N.

2001-01-01

The phylogenetic distributions of multiple putative virulence factors (VFs) and papA (P fimbrial structural subunit) alleles among 182 Escherichia coli blood isolates from patients with diverse-source bacteremia were defined. Phylogenetic correspondence among these strains, the E. coli Reference (ECOR) collection, and other collections of extraintestinal pathogenic E. coli (ExPEC) was assessed. Although among the 182 bacteremia isolates phylogenetic group B2 predominated, exhibited the greatest concentration of individual VFs, and contained the largest number of familiar virulent clones, other phylogenetic groups exhibited greater concentrations of certain VFs than did group B2 and included several additional virulent clones. Certain of the newly detected VF genes, e.g., fyuA (yersiniabactin; 76%) and focG (F1C fimbriae; 25%), were as prevalent or more prevalent than their more familiar traditional counterparts, e.g., iut (aerobactin; 57%) and sfaS (S fimbriae; 14%), thus possibly offering additional useful targets for preventive interventions. Considerable diversity of VF profiles was observed at every level within the phylogenetic tree, including even within individual lineages. This suggested that many different pathways can lead to extraintestinal virulence in E. coli and that the evolution of ExPEC, which involves extensive horizontal transmission of VFs and continuous remodeling of pathogenicity-associated islands, is a highly active, ongoing process. PMID:11500406

Partial androgen insensitivity syndrome due to somatic mosaicism of the androgen receptor.

Science.gov (United States)

Batista, Rafael Loch; Rodrigues, Andresa De Santi; Machado, Aline Zamboni; Nishi, Mirian Yumie; Cunha, Flávia Siqueira; Silva, Rosana Barbosa; Costa, Elaine M F; Mendonca, Berenice B; Domenice, Sorahia

2018-01-26

Androgen insensitivity syndrome (AIS) is the most frequent etiology of 46,XY disorders of sex development (DSDs), and it is an X-linked disorder caused by mutations in the androgen receptor (AR) gene. AIS patients present a broad phenotypic spectrum and individuals with a partial phenotype present with different degrees of undervirilized external genitalia. There are more than 500 different AR gene allelic variants reported to be linked to AIS, but the presence of somatic mosaicisms has been rarely identified. In the presence of a wild-type AR gene, a significant degree of spontaneous virilization at puberty can be observed, and it could influence the gender assignment, genetic counseling and the clinical and psychological management of these patients and the psychosexual outcomes of these patients are not known. In this study, we report two patients with AR allelic variants in heterozygous (c.382G>T and c.1769-1G>C) causing a partial AIS (PAIS) phenotype. The first patient was raised as female and she had undergone a gonadectomy at puberty. In both patients there was congruency between gender of rearing and gender identity and gender role. Somatic mosaicism is rare in AIS and nonsense AR variant allelic can cause partial AIS phenotype in this situation. Despite the risk of virilization and prenatal androgen exposure, the gender identity and gender role was concordant with sex of rearing in both cases. A better testosterone response can be expected in male individuals and this should be considered in the clinical management.

The Mycobacterium leprae antigen 85 complex gene family: identification of the genes for the 85A, 85C, and related MPT51 proteins

NARCIS (Netherlands)

Rinke de Wit, T. F.; Bekelie, S.; Osland, A.; Wieles, B.; Janson, A. A.; Thole, J. E.

1993-01-01

The genes for two novel members (designated 85A and 85C) of the Mycobacterium leprae antigen 85 complex family of proteins and the gene for the closely related M. leprae MPT51 protein were isolated. The complete DNA sequence of the M. leprae 85C gene and partial sequences of the 85A and MPT51 genes

The Interplay of Different Types of Governance in Horizontal Cooperations

DEFF Research Database (Denmark)

Raue, Jan Simon; Wieland, Andreas

2015-01-01

Purpose – Over the last decades, horizontal cooperations between logistics service providers (LSPs) have become a well-established organizational form and their use is expected to grow even further in the future. In spite of this increasing importance of horizontal LSP cooperations, little research...

Assessment of the perception of verticality and horizontality with self-paced saccades.