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Sample records for horizontally transferred regulators

  1. Global Regulation by Horizontally Transferred Regulators Establishes the Pathogenicity of Escherichia coli

    PubMed Central

    Abe, Hiroyuki; Miyahara, Akira; Oshima, Taku; Tashiro, Kosuke; Ogura, Yoshitoshi; Kuhara, Satoru; Ogasawara, Naotake; Hayashi, Tetsuya; Tobe, Toru

    2008-01-01

    Enterohemorrhagic Escherichia coli is an emerging pathogen that causes diarrhea and hemolytic uremic syndrome. Much of the genomic information that affects virulence is acquired by horizontal transfer. Genes necessary for attaching and effacing lesions are located in the locus for enterocyte effacement (LEE) pathogenicity island. LEE gene transcription is positively regulated by Ler, which is also encoded by the LEE, and by Pch regulators, which are encoded at other loci. Here we identified genes whose transcription profiles were similar to those of the LEE genes, by comparing the effects of altering ler and pch transcript levels. We assigned these genes into two classes, according to their transcription profiles. By determining the binding profiles for Ler and Pch, we showed that both were involved in regulating one class of genes, but only Pch was involved in regulating the other class. Binding sites were found in the coding region as well as the promoter region of regulated genes, which include genes common to K12 strains as well as 0157-specific genes, suggesting that both act as a global regulator. These results indicate that Ler and Pch orchestrate the transcription of virulence genes, which are captured by horizontal transfer and scattered throughout the chromosome. PMID:18222925

  2. Regulation, Integrase-Dependent Excision, and Horizontal Transfer of Genomic Islands in Legionella pneumophila

    PubMed Central

    Lautner, Monika; Schunder, Eva; Herrmann, Vroni

    2013-01-01

    Legionella pneumophila is a Gram-negative freshwater agent which multiplies in specialized nutrient-rich vacuoles of amoebae. When replicating in human alveolar macrophages, Legionella can cause Legionnaires' disease. Recently, we identified a new type of conjugation/type IVA secretion system (T4ASS) in L. pneumophila Corby (named trb-tra). Analogous versions of trb-tra are localized on the genomic islands Trb-1 and Trb-2. Both can exist as an episomal circular form, and Trb-1 can be transferred horizontally to other Legionella strains by conjugation. In our current work, we discovered the importance of a site-specific integrase (Int-1, lpc2818) for the excision and conjugation process of Trb-1. Furthermore, we identified the genes lvrRABC (lpc2813 to lpc2816) to be involved in the regulation of Trb-1 excision. In addition, we demonstrated for the first time that a Legionella genomic island (LGI) of L. pneumophila Corby (LpcGI-2) encodes a functional type IV secretion system. The island can be transferred horizontally by conjugation and is integrated site specifically into the genome of the transconjugants. LpcGI-2 generates three different episomal forms. The predominant episomal form, form A, is generated integrase dependently (Lpc1833) and transferred by conjugation in a pilT-dependent manner. Therefore, the genomic islands Trb-1 and LpcGI-2 should be classified as integrative and conjugative elements (ICEs). Coculture studies of L. pneumophila wild-type and mutant strains revealed that the int-1 and lvrRABC genes (located on Trb-1) as well as lpc1833 and pilT (located on LpcGI-2) do not influence the in vivo fitness of L. pneumophila in Acanthamoeba castellanii. PMID:23354744

  3. Inferring Horizontal Gene Transfer

    PubMed Central

    Lassalle, Florent; Dessimoz, Christophe

    2015-01-01

    Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages [1]. Computational identification of HGT events relies upon the investigation of sequence composition or evolutionary history of genes. Sequence composition-based ("parametric") methods search for deviations from the genomic average, whereas evolutionary history-based ("phylogenetic") approaches identify genes whose evolutionary history significantly differs from that of the host species. The evaluation and benchmarking of HGT inference methods typically rely upon simulated genomes, for which the true history is known. On real data, different methods tend to infer different HGT events, and as a result it can be difficult to ascertain all but simple and clear-cut HGT events. PMID:26020646

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

    SciTech Connect

    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.

  5. Panspermia and horizontal gene transfer

    NASA Astrophysics Data System (ADS)

    Klyce, Brig

    2009-08-01

    Evidence that extremophiles are hardy and ubiquitous is helping to make panspermia a respectable theory. But even if life on Earth originally came from space, biologists assume that the subsequent evolution of life is still governed by the darwinian paradigm. In this review we show how panspermia could amend darwinism and point to a cosmic source for, not only extremophiles but, all of life. This version of panspermia can be called "strong panspermia." To support this theory we will discuss recent evidence pertaining to horizontal gene transfer, viruses, genes apparently older than the Earthly evolution of the features they encode, and primate-specific genes without identifiable precursors.

  6. Widespread horizontal transfer of retrotransposons

    PubMed Central

    Walsh, Ali Morton; Kortschak, R. Daniel; Gardner, Michael G.; Bertozzi, Terry; Adelson, David L.

    2013-01-01

    In higher organisms such as vertebrates, it is generally believed that lateral transfer of genetic information does not readily occur, with the exception of retroviral infection. However, horizontal transfer (HT) of protein coding repetitive elements is the simplest way to explain the patchy distribution of BovB, a long interspersed element (LINE) about 3.2 kb long, that has been found in ruminants, marsupials, squamates, monotremes, and African mammals. BovB sequences are a major component of some of these genomes. Here we show that HT of BovB is significantly more widespread than believed, and we demonstrate the existence of two plausible arthropod vectors, specifically reptile ticks. A phylogenetic tree built from BovB sequences from species in all of these groups does not conform to expected evolutionary relationships of the species, and our analysis indicates that at least nine HT events are required to explain the observed topology. Our results provide compelling evidence for HT of genetic material that has transformed vertebrate genomes. PMID:23277587

  7. Detecting Highways of Horizontal Gene Transfer

    NASA Astrophysics Data System (ADS)

    Bansal, Mukul S.; Gogarten, J. Peter; Shamir, Ron

    In a horizontal gene transfer (HGT) event a gene is transferred between two species that do not share an ancestor-descendant relationship. Typically, no more than a few genes are horizontally transferred between any two species. However, several studies identified pairs of species between which many different genes were horizontally transferred. Such a pair is said to be linked by a highway of gene sharing. We present a method for inferring such highways. Our method is based on the fact that the evolutionary histories of horizontally transferred genes disagree with the corresponding species phylogeny. Specifically, given a set of gene trees and a trusted rooted species tree, each gene tree is first decomposed into its constituent quartet trees and the quartets that are inconsistent with the species tree are identified. Our method finds a pair of species such that a highway between them explains the largest (normalized) fraction of inconsistent quartets. For a problem on n species, our method requires O(n 4) time, which is optimal with respect to the quartets input size. An application of our method to a dataset of 1128 genes from 11 cyanobacterial species, as well as to simulated datasets, illustrates the efficacy of our method.

  8. Detecting highways of horizontal gene transfer.

    PubMed

    Bansal, Mukul S; Banay, Guy; Gogarten, J Peter; Shamir, Ron

    2011-09-01

    In a horizontal gene transfer (HGT) event, a gene is transferred between two species that do not have an ancestor-descendant relationship. Typically, no more than a few genes are horizontally transferred between any two species. However, several studies identified pairs of species between which many different genes were horizontally transferred. Such a pair is said to be linked by a highway of gene sharing. We present a method for inferring such highways. Our method is based on the fact that the evolutionary histories of horizontally transferred genes disagree with the corresponding species phylogeny. Specifically, given a set of gene trees and a trusted rooted species tree, each gene tree is first decomposed into its constituent quartet trees and the quartets that are inconsistent with the species tree are identified. Our method finds a pair of species such that a highway between them explains the largest (normalized) fraction of inconsistent quartets. For a problem on n species and m input quartet trees, we give an efficient O(m + n(2))-time algorithm for detecting highways, which is optimal with respect to the quartets input size. An application of our method to a dataset of 1128 genes from 11 cyanobacterial species, as well as to simulated datasets, illustrates the efficacy of our method.

  9. Horizontal gene transfer in parasitic plants.

    PubMed

    Davis, Charles C; Xi, Zhenxiang

    2015-08-01

    Horizontal gene transfer (HGT) between species has been a major focus of plant evolutionary research during the past decade. Parasitic plants, which establish a direct connection with their hosts, have provided excellent examples of how these transfers are facilitated via the intimacy of this symbiosis. In particular, phylogenetic studies from diverse clades indicate that parasitic plants represent a rich system for studying this phenomenon. Here, HGT has been shown to be astonishingly high in the mitochondrial genome, and appreciable in the nuclear genome. Although explicit tests remain to be performed, some transgenes have been hypothesized to be functional in their recipient species, thus providing a new perspective on the evolution of novelty in parasitic plants.

  10. Horizontal gene transfer: A critical view

    PubMed Central

    Kurland, C. G.; Canback, B.; Berg, Otto G.

    2003-01-01

    It has been suggested that horizontal gene transfer (HGT) is the “essence of phylogeny.” In contrast, much data suggest that this is an exaggeration resulting in part from a reliance on inadequate methods to identify HGT events. In addition, the assumption that HGT is a ubiquitous influence throughout evolution is questionable. Instead, rampant global HGT is likely to have been relevant only to primitive genomes. In modern organisms we suggest that both the range and frequencies of HGT are constrained most often by selective barriers. As a consequence those HGT events that do occur most often have little influence on genome phylogeny. Although HGT does occur with important evolutionary consequences, classical Darwinian lineages seem to be the dominant mode of evolution for modern organisms. PMID:12902542

  11. Horizontal Gene Transfer, Dispersal and Haloarchaeal Speciation

    PubMed Central

    Papke, R. Thane; Corral, Paulina; Ram-Mohan, Nikhil; de la Haba, Rafael R.; Sánchez-Porro, Cristina; Makkay, Andrea; Ventosa, Antonio

    2015-01-01

    The Halobacteria are a well-studied archaeal class and numerous investigations are showing how their diversity is distributed amongst genomes and geographic locations. Evidence indicates that recombination between species continuously facilitates the arrival of new genes, and within species, it is frequent enough to spread acquired genes amongst all individuals in the population. To create permanent independent diversity and generate new species, barriers to recombination are probably required. The data support an interpretation that rates of evolution (e.g., horizontal gene transfer and mutation) are faster at creating geographically localized variation than dispersal and invasion are at homogenizing genetic differences between locations. Therefore, we suggest that recurrent episodes of dispersal followed by variable periods of endemism break the homogenizing forces of intrapopulation recombination and that this process might be the principal stimulus leading to divergence and speciation in Halobacteria. PMID:25997110

  12. Horizontal gene transfer from Agrobacterium to plants

    PubMed Central

    Matveeva, Tatiana V.; Lutova, Ludmila A.

    2014-01-01

    Most genetic engineering of plants uses Agrobacterium mediated transformation to introduce novel gene content. In nature, insertion of T-DNA in the plant genome and its subsequent transfer via sexual reproduction has been shown in several species in the genera Nicotiana and Linaria. In these natural examples of horizontal gene transfer from Agrobacterium to plants, the T-DNA donor is assumed to be a mikimopine strain of A. rhizogenes. A sequence homologous to the T-DNA of the Ri plasmid of Agrobacterium rhizogenes was found in the genome of untransformed Nicotiana glauca about 30 years ago, and was named “cellular T-DNA” (cT-DNA). It represents an imperfect inverted repeat and contains homologs of several T-DNA oncogenes (NgrolB, NgrolC, NgORF13, NgORF14) and an opine synthesis gene (Ngmis). A similar cT-DNA has also been found in other species of the genus Nicotiana. These presumably ancient homologs of T-DNA genes are still expressed, indicating that they may play a role in the evolution of these plants. Recently T-DNA has been detected and characterized in Linaria vulgaris and L. dalmatica. In Linaria vulgaris the cT-DNA is present in two copies and organized as a tandem imperfect direct repeat, containing LvORF2, LvORF3, LvORF8, LvrolA, LvrolB, LvrolC, LvORF13, LvORF14, and the Lvmis genes. All L. vulgaris and L. dalmatica plants screened contained the same T-DNA oncogenes and the mis gene. Evidence suggests that there were several independent T-DNA integration events into the genomes of these plant genera. We speculate that ancient plants transformed by A. rhizogenes might have acquired a selective advantage in competition with the parental species. Thus, the events of T-DNA insertion in the plant genome might have affected their evolution, resulting in the creation of new plant species. In this review we focus on the structure and functions of cT-DNA in Linaria and Nicotiana and discuss their possible evolutionary role. PMID:25157257

  13. Horizontal functional gene transfer from bacteria to fishes

    PubMed Central

    Sun, Bao-Fa; Li, Tong; Xiao, Jin-Hua; Jia, Ling-Yi; Liu, Li; Zhang, Peng; Murphy, Robert W.; He, Shun-Min; Huang, Da-Wei

    2015-01-01

    Invertebrates can acquire functional genes via horizontal gene transfer (HGT) from bacteria but fishes are not known to do so. We provide the first reliable evidence of one HGT event from marine bacteria to fishes. The HGT appears to have occurred after emergence of the teleosts. The transferred gene is expressed and regulated developmentally. Its successful integration and expression may change the genetic and metabolic repertoire of fishes. In addition, this gene contains conserved domains and similar tertiary structures in fishes and their putative donor bacteria. Thus, it may function similarly in both groups. Evolutionary analyses indicate that it evolved under purifying selection, further indicating its conserved function. We document the first likely case of HGT of functional gene from prokaryote to fishes. This discovery certifies that HGT can influence vertebrate evolution. PMID:26691285

  14. Horizontal functional gene transfer from bacteria to fishes.

    PubMed

    Sun, Bao-Fa; Li, Tong; Xiao, Jin-Hua; Jia, Ling-Yi; Liu, Li; Zhang, Peng; Murphy, Robert W; He, Shun-Min; Huang, Da-Wei

    2015-12-22

    Invertebrates can acquire functional genes via horizontal gene transfer (HGT) from bacteria but fishes are not known to do so. We provide the first reliable evidence of one HGT event from marine bacteria to fishes. The HGT appears to have occurred after emergence of the teleosts. The transferred gene is expressed and regulated developmentally. Its successful integration and expression may change the genetic and metabolic repertoire of fishes. In addition, this gene contains conserved domains and similar tertiary structures in fishes and their putative donor bacteria. Thus, it may function similarly in both groups. Evolutionary analyses indicate that it evolved under purifying selection, further indicating its conserved function. We document the first likely case of HGT of functional gene from prokaryote to fishes. This discovery certifies that HGT can influence vertebrate evolution.

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

    PubMed

    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.

  16. 13. DETAIL OF BEVEL GEAR TRANSFERRING HORIZONTAL DRIVE FROM MAIN ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    13. DETAIL OF BEVEL GEAR TRANSFERRING HORIZONTAL DRIVE FROM MAIN WATERWHEEL SHAFT TO VERTICAL SHAFT DRIVING COFFEE HUSKING MILL ON SECOND FLOOR - Hacienda Cafetalera Santa Clara, Coffee Mill, KM 19, PR Route 372, Hacienda La Juanita, Yauco Municipio, PR

  17. Horizontal gene transfer and the evolution of transcriptionalregulation in Escherichia coli

    SciTech Connect

    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.

  18. The interconnection between biofilm formation and horizontal gene transfer.

    PubMed

    Madsen, Jonas Stenløkke; Burmølle, Mette; Hansen, Lars Hestbjerg; Sørensen, Søren Johannes

    2012-07-01

    Recent research has revealed that horizontal gene transfer and biofilm formation are connected processes. Although published research investigating this interconnectedness is still limited, we will review this subject in order to highlight the potential of these observations because of their believed importance in the understanding of the adaptation and subsequent evolution of social traits in bacteria. Here, we discuss current evidence for such interconnectedness centred on plasmids. Horizontal transfer rates are typically higher in biofilm communities compared with those in planktonic states. Biofilms, furthermore, promote plasmid stability and may enhance the host range of mobile genetic elements that are transferred horizontally. Plasmids, on the other hand, are very well suited to promote the evolution of social traits such as biofilm formation. This, essentially, transpires because plasmids are independent replicons that enhance their own success by promoting inter-bacterial interactions. They typically also carry genes that heighten their hosts' direct fitness. Furthermore, current research shows that the so-called mafia traits encoded on mobile genetic elements can enforce bacteria to maintain stable social interactions. It also indicates that horizontal gene transfer ultimately enhances the relatedness of bacteria carrying the mobile genetic elements of the same origin. The perspective of this review extends to an overall interconnectedness between horizontal gene transfer, mobile genetic elements and social evolution of bacteria.

  19. International transferability of accident modification functions for horizontal curves.

    PubMed

    Elvik, Rune

    2013-10-01

    Studies of the relationship between characteristics of horizontal curves and accident rate have been reported in several countries. The characteristic most often studied is the radius of a horizontal curve. Functions describing the relationship between the radius of horizontal curves and accident rate have been developed in Australia, Canada, Denmark, Germany, Great Britain, New Zealand, Norway, Portugal, Sweden, and the United States. Other characteristics of horizontal curves that have been studied include deflection angle, curve length, the presence of transition curves, super-elevation in curves and distance to adjacent curves. This paper assesses the international transferability of mathematical functions (accident modification functions) that have been developed to relate the radius of horizontal curves to their accident rate. The main research problem is whether these functions are similar, which enhances international transferability, or dissimilar, which reduces international transferability. Accident modification functions for horizontal curve radius developed in the countries listed above are synthesised. The sensitivity of the functions to other characteristics of curves than radius is examined. Accident modification functions developed in different countries have important similarities. The functions diverge with respect to accident rate in the sharpest curves.

  20. Evolution of and horizontal gene transfer in the Endornavirus genus.

    PubMed

    Song, Dami; Cho, Won Kyong; Park, Sang-Ho; Jo, Yeonhwa; Kim, Kook-Hyung

    2013-01-01

    The transfer of genetic information between unrelated species is referred to as horizontal gene transfer. Previous studies have demonstrated that both retroviral and non-retroviral sequences have been integrated into eukaryotic genomes. Recently, we identified many non-retroviral sequences in plant genomes. In this study, we investigated the evolutionary origin and gene transfer of domains present in endornaviruses which are double-stranded RNA viruses. Using the available sequences for endornaviruses, we found that Bell pepper endornavirus-like sequences homologous to the glycosyltransferase 28 domain are present in plants, fungi, and bacteria. The phylogenetic analysis revealed the glycosyltransferase 28 domain of Bell pepper endornavirus may have originated from bacteria. In addition, two domains of Oryza sativa endornavirus, a glycosyltransferase sugar-binding domain and a capsular polysaccharide synthesis protein, also exhibited high similarity to those of bacteria. We found evidence that at least four independent horizontal gene transfer events for the glycosyltransferase 28 domain have occurred among plants, fungi, and bacteria. The glycosyltransferase sugar-binding domains of two proteobacteria may have been horizontally transferred to the genome of Thalassiosira pseudonana. Our study is the first to show that three glycome-related viral genes in the genus Endornavirus have been acquired from marine bacteria by horizontal gene transfer.

  1. Evolution of and Horizontal Gene Transfer in the Endornavirus Genus

    PubMed Central

    Park, Sang-Ho; Jo, Yeonhwa; Kim, Kook-Hyung

    2013-01-01

    The transfer of genetic information between unrelated species is referred to as horizontal gene transfer. Previous studies have demonstrated that both retroviral and non-retroviral sequences have been integrated into eukaryotic genomes. Recently, we identified many non-retroviral sequences in plant genomes. In this study, we investigated the evolutionary origin and gene transfer of domains present in endornaviruses which are double-stranded RNA viruses. Using the available sequences for endornaviruses, we found that Bell pepper endornavirus-like sequences homologous to the glycosyltransferase 28 domain are present in plants, fungi, and bacteria. The phylogenetic analysis revealed the glycosyltransferase 28 domain of Bell pepper endornavirus may have originated from bacteria. In addition, two domains of Oryza sativa endornavirus, a glycosyltransferase sugar-binding domain and a capsular polysaccharide synthesis protein, also exhibited high similarity to those of bacteria. We found evidence that at least four independent horizontal gene transfer events for the glycosyltransferase 28 domain have occurred among plants, fungi, and bacteria. The glycosyltransferase sugar-binding domains of two proteobacteria may have been horizontally transferred to the genome of Thalassiosira pseudonana. Our study is the first to show that three glycome-related viral genes in the genus Endornavirus have been acquired from marine bacteria by horizontal gene transfer. PMID:23667703

  2. Horizontal transfers of transposable elements in eukaryotes: The flying genes.

    PubMed

    Panaud, Olivier

    2016-01-01

    Transposable elements (TEs) are the major components of eukaryotic genomes. Their propensity to densely populate and in some cases invade the genomes of plants and animals is in contradiction with the fact that transposition is strictly controlled by several molecular pathways acting at either transcriptional or post-transcriptional levels. Horizontal transfers, defined as the transmission of genetic material between sexually isolated species, have long been considered as rare phenomena. Here, we show that the horizontal transfers of transposable elements (HTTs) are very frequent in ecosystems. The exact mechanisms of such transfers are not well understood, but species involved in close biotic interactions, like parasitism, show a propensity to exchange genetic material horizontally. We propose that HTTs allow TEs to escape the silencing machinery of their host genome and may therefore be an important mechanism for their survival and their dissemination in eukaryotes.

  3. Horizontal transfer of methoprene in Tribolium castaneum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aerosol applications of reduced risk insecticides such as pyrethrins, pyrethroids, and insect growth regulators are becoming more commonly used to manage stored-product insects in food facilities. However, these applications have a limited ability to penetrate into hidden refugia, where the majorit...

  4. A heat transfer model of a horizontal ground heat exchanger

    NASA Astrophysics Data System (ADS)

    Mironov, R. E.; Shtern, Yu. I.; Shtern, M. Yu.; Rogachev, M. S.

    2016-04-01

    Ground-source heat pumps are gaining popularity in Eastern Europe, especially those which are using the horizontal ground heat exchanger (GHX). Due to the difficulty of accessing GHX after the installation, materials and the quality of the installation must satisfy the very high requirements. An inaccurate calculation of GHX can be the reason of a scarcity of heat power in a crucial moment. So far, there isn't any appropriate mathematical description of the horizontal GHX which takes into account the mutual influence of GHX pipes on each other. To solve this problem we used the temperature wave approach. As a result, a mathematical model which describes the dependence of the heat transfer rate per unit length of the horizontal GHX pipe on the thermal properties of soil, operating time of GHX and the distance between pipes was obtained. Using this model, heat transfer rates per unit length of a horizontal GHX were plotted as functions of the distance between pipes and operating time. The modeling shows that heat transfer rates decreases rapidly with the distance between pipes lower then 2 meters. After the launch of heat pump, heat power of GHX is reduced during the first 20 - 30 days and get steady after that. The obtained results correlate with experimental data. Therefore the proposed mathematical model can be used to design a horizontal GHX with the optimal characteristics, and predict its capability during operation.

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

    PubMed

    Schneider, Sean E; Thomas, James H

    2014-01-01

    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.

  6. Quasispecies theory for horizontal gene transfer and recombination

    NASA Astrophysics Data System (ADS)

    Muñoz, Enrique; Park, Jeong-Man; Deem, Michael W.

    2008-12-01

    We introduce a generalization of the parallel, or Crow-Kimura, and Eigen models of molecular evolution to represent the exchange of genetic information between individuals in a population. We study the effect of different schemes of genetic recombination on the steady-state mean fitness and distribution of individuals in the population, through an analytic field theoretic mapping. We investigate both horizontal gene transfer from a population and recombination between pairs of individuals. Somewhat surprisingly, these nonlinear generalizations of quasispecies theory to modern biology are analytically solvable. For two-parent recombination, we find two selected phases, one of which is spectrally rigid. We present exact analytical formulas for the equilibrium mean fitness of the population, in terms of a maximum principle, which are generally applicable to any permutation invariant replication rate function. For smooth fitness landscapes, we show that when positive epistatic interactions are present, recombination or horizontal gene transfer introduces a mild load against selection. Conversely, if the fitness landscape exhibits negative epistasis, horizontal gene transfer or recombination introduces an advantage by enhancing selection towards the fittest genotypes. These results prove that the mutational deterministic hypothesis holds for quasispecies models. For the discontinuous single sharp peak fitness landscape, we show that horizontal gene transfer has no effect on the fitness, while recombination decreases the fitness, for both the parallel and the Eigen models. We present numerical and analytical results as well as phase diagrams for the different cases.

  7. Global Analysis of Horizontal Gene Transfer in Fusarium verticillioides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The co-occurrence of microbes within plants and other specialized niches may facilitate horizontal gene transfer (HGT) affecting host-pathogen interactions. We recently identified fungal-to-fungal HGTs involving metabolic gene clusters. For a global analysis of HGTs in the maize pathogen Fusarium ve...

  8. The power of phylogenetic approaches to detect horizontally transferred genes

    PubMed Central

    Poptsova, Maria S; Gogarten, J Peter

    2007-01-01

    Background Horizontal gene transfer plays an important role in evolution because it sometimes allows recipient lineages to adapt to new ecological niches. High genes transfer frequencies were inferred for prokaryotic and early eukaryotic evolution. Does horizontal gene transfer also impact phylogenetic reconstruction of the evolutionary history of genomes and organisms? The answer to this question depends at least in part on the actual gene transfer frequencies and on the ability to weed out transferred genes from further analyses. Are the detected transfers mainly false positives, or are they the tip of an iceberg of many transfer events most of which go undetected by current methods? Results Phylogenetic detection methods appear to be the method of choice to infer gene transfers, especially for ancient transfers and those followed by orthologous replacement. Here we explore how well some of these methods perform using in silico transfers between the terminal branches of a gamma proteobacterial, genome based phylogeny. For the experiments performed here on average the AU test at a 5% significance level detects 90.3% of the transfers and 91% of the exchanges as significant. Using the Robinson-Foulds distance only 57.7% of the exchanges and 60% of the donations were identified as significant. Analyses using bipartition spectra appeared most successful in our test case. The power of detection was on average 97% using a 70% cut-off and 94.2% with 90% cut-off for identifying conflicting bipartitions, while the rate of false positives was below 4.2% and 2.1% for the two cut-offs, respectively. For all methods the detection rates improved when more intervening branches separated donor and recipient. Conclusion Rates of detected transfers should not be mistaken for the actual transfer rates; most analyses of gene transfers remain anecdotal. The method and significance level to identify potential gene transfer events represent a trade-off between the frequency of erroneous

  9. Plasmid and clonal interference during post horizontal gene transfer evolution.

    PubMed

    Bedhomme, S; Perez Pantoja, D; Bravo, I G

    2017-02-16

    Plasmids are nucleic acid molecules that can drive their own replication in a living cell. They can be transmitted horizontally and can thrive in the host cell to high-copy numbers. Plasmid replication and gene expression consume cellular resources and cells carrying plasmids incur fitness costs. But many plasmids carry genes that can be beneficial under certain conditions, allowing the cell to endure in the presence of antibiotics, toxins, competitors or parasites. Horizontal transfer of plasmid-encoded genes can thus instantaneously confer differential adaptation to local or transient selection conditions. This conflict between cellular fitness and plasmid spread sets the scene for multilevel selection processes. We have engineered a system to study the short-term evolutionary impact of different synonymous versions of a plasmid-encoded antibiotic resistance gene. Applying experimental evolution under different selection conditions and deep sequencing allowed us to show rapid local adaptation to the presence of antibiotic and to the specific version of the resistance gene transferred. We describe the presence of clonal interference at two different levels: at the within-cell level, because a single cell can carry several plasmids, and at the between-cell level, because a bacterial population may contain several clones carrying different plasmids and displaying different fitness in the presence/absence of antibiotic. Understanding the within-cell and between-cell dynamics of plasmids after horizontal gene transfer is essential to unravel the dense network of mobile elements underlying the worldwide threat to public health of antibiotic resistance.

  10. Horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal Amanita.

    PubMed

    Chaib De Mares, Maryam; Hess, Jaqueline; Floudas, Dimitrios; Lipzen, Anna; Choi, Cindy; Kennedy, Megan; Grigoriev, Igor V; Pringle, Anne

    2015-03-01

    The genus Amanita encompasses both symbiotic, ectomycorrhizal fungi and asymbiotic litter decomposers; all species are derived from asymbiotic ancestors. Symbiotic species are no longer able to degrade plant cell walls. The carbohydrate esterases family 1 (CE1s) is a diverse group of enzymes involved in carbon metabolism, including decomposition and carbon storage. CE1 genes of the ectomycorrhizal A. muscaria appear diverged from all other fungal homologues, and more similar to CE1s of bacteria, suggesting a horizontal gene transfer (HGT) event. In order to test whether AmanitaCE1s were acquired horizontally, we built a phylogeny of CE1s collected from across the tree of life, and describe the evolution of CE1 genes among Amanita and relevant lineages of bacteria. CE1s of symbiotic Amanita were very different from CE1s of asymbiotic Amanita, and are more similar to bacterial CE1s. The protein structure of one CE1 gene of A. muscaria matched a depolymerase that degrades the carbon storage molecule poly((R)-3-hydroxybutyrate) (PHB). Asymbiotic Amanita do not carry sequence or structural homologues of these genes. The CE1s acquired through HGT may enable novel metabolisms, or play roles in signaling or defense. This is the first evidence for the horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal fungi.

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

    PubMed Central

    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. PMID:26789284

  12. Heat transfer during intermittent/slug flow in horizontal tubes

    SciTech Connect

    Shoham, O.; Dukler, A.E.; Taitel, Y.

    1982-08-01

    Heat transfer characteristics for two-phase gas-liquid slug flow in a horizontal pipe have been measured. The time variation of temperature, heat transfer coefficients, and heat flux is reported for the different zones of slug flow: the mixing region at the nose, the body of the slug, the liquid film, and the gas bubble behind the slug. Substantial differences in heat transfer coefficient exist between the bottom and top of the slug. This results from the fact that each slug is effectively a thermally developing entry region caused by the presence of a hot upper wall just upstream of each slug. A qualitative theory is presented which explains this behavior. 18 refs.

  13. High frequency of horizontal gene transfer in the oceans.

    PubMed

    McDaniel, Lauren D; Young, Elizabeth; Delaney, Jennifer; Ruhnau, Fabian; Ritchie, Kim B; Paul, John H

    2010-10-01

    Oceanic bacteria perform many environmental functions, including biogeochemical cycling of many elements, metabolizing of greenhouse gases, functioning in oceanic food webs (microbial loop), and producing valuable natural products and viruses. We demonstrate that the widespread capability of marine bacteria to participate in horizontal gene transfer (HGT) in coastal and oceanic environments may be the result of gene transfer agents (GTAs), viral-like particles produced by α-Proteobacteria. We documented GTA-mediated gene transfer frequencies a thousand to a hundred million times higher than prior estimates of HGT in the oceans, with as high as 47% of the culturable natural microbial community confirmed as gene recipients. These findings suggest a plausible mechanism by which marine bacteria acquire novel traits, thus ensuring resilience in the face of environmental change.

  14. Horizontal gene transfer and the evolution of methanogenic pathways.

    PubMed

    Fournier, Greg

    2009-01-01

    Horizontal gene transfer (HGT) is a driving force in the evolution of metabolic pathways, allowing novel enzymatic functions that provide a selective advantage to be rapidly incorporated into an organism's physiology. Here, the role of two HGT events in the evolution of methanogenesis is described. First, the acetoclastic sub-pathway of methanogenesis is shown to have evolved via a transfer of the ackA and pta genes from a cellulolytic clostridia to a family of methanogenic archaea. Second, the system for encoding the amino acid pyrrolysine, used for the synthesis of enzymes for methanogenesis from methylamines, is shown to likely have evolved via transfer from an ancient, unknown, deeply branching organismal lineage.

  15. Role of Vibrio cholerae exochitinase ChiA2 in horizontal gene transfer.

    PubMed

    Mondal, Moumita; Chatterjee, Nabendu Sekhar

    2016-03-01

    Vibrio cholerae exochitinase ChiA2 plays a key role in acquisition of nutrients by chitin hydrolysis in the natural environment as well as in pathogenesis in the intestinal milieu. In this study we demonstrate the importance of ChiA2 in horizontal gene transfer in the natural environment. We found that the expression of ChiA2 and TfoX, the central regulator of V. cholerae horizontal gene transfer, varied with changes in environmental conditions. The activity of ChiA2 was also dependent on these conditions. In 3 different environmental conditions tested here, we observed that the supporting environmental condition for maximum expression and activity of ChiA2 was 20 °C, pH 5.5, and 100 mmol/L salinity in the presence of chitin. The same condition also induced TfoX expression and was favorable for horizontal gene transfer in V. cholerae. High-performance liquid chromatography analysis showed that ChiA2 released a significant amount of (GlcNAc)2 from chitin hydrolysis under the favorable condition. We hypothesized that under the favorable environmental condition, ChiA2 was upregulated and maximally active to produce a significant amount of (GlcNAc)2 from chitin. The same environmental condition also induced tfoX expression, followed by its translational activation by the (GlcNAc)2 produced, leading to efficient horizontal gene transfer.

  16. Dynamic monitoring of horizontal gene transfer in soil

    NASA Astrophysics Data System (ADS)

    Cheng, H. Y.; Masiello, C. A.; Silberg, J. J.; Bennett, G. N.

    2015-12-01

    Soil microbial gene expression underlies microbial behaviors (phenotypes) central to many aspects of C, N, and H2O cycling. However, continuous monitoring of microbial gene expression in soils is challenging because genetically-encoded reporter proteins widely used in the lab are difficult to deploy in soil matrices: for example, green fluorescent protein cannot be easily visualized in soils, even in the lab. To address this problem we have developed a reporter protein that releases small volatile gases. Here, we applied this gas reporter in a proof-of-concept soil experiment, monitoring horizontal gene transfer, a microbial activity that alters microbial genotypes and phenotypes. Horizontal gene transfer is central to bacterial evolution and adaptation and is relevant to problems such as the spread of antibiotic resistance, increasing metal tolerance in superfund sites, and bioremediation capability of bacterial consortia. This process is likely to be impacted by a number of matrix properties not well-represented in the petri dish, such as microscale variations in water, nutrients, and O2, making petri-dish experiments a poor proxy for environmental processes. We built a conjugation system using synthetic biology to demonstrate the use of gas-reporting biosensors in safe, lab-based biogeochemistry experiments, and here we report the use of these sensors to monitor horizontal gene transfer in soils. Our system is based on the F-plasmid conjugation in Escherichia coli. We have found that the gas signal reports on the number of cells that acquire F-plasmids (transconjugants) in a loamy Alfisol collected from Kellogg Biological Station. We will report how a gas signal generated by transconjugants varies with the number of F-plasmid donor and acceptor cells seeded in a soil, soil moisture, and soil O2 levels.

  17. Horizontal gene transfer and recombination in Streptococcus dysgalactiae subsp. equisimilis

    PubMed Central

    McNeilly, Celia L.; McMillan, David J.

    2014-01-01

    Streptococcus dysgalactiae subsp. equisimilis (SDSE) is a human pathogen that colonizes the skin or throat, and causes a range of diseases from relatively benign pharyngitis to potentially fatal invasive diseases. While not as virulent as the close relative Streptococcus pyogenes the two share a number of virulence factors and are known to coexist in a human host. Both pre- and post-genomic studies have revealed that horizontal gene transfer (HGT) and recombination occurs between these two organisms and plays a major role in shaping the population structure of SDSE. This review summarizes our current knowledge of HGT and recombination in the evolution of SDSE. PMID:25566202

  18. Ecological networks to unravel the routes to horizontal transposon transfers

    PubMed Central

    Venner, Samuel; Miele, Vincent; Biémont, Christian; Daubin, Vincent; Feschotte, Cédric; Pontier, Dominique

    2017-01-01

    Transposable elements (TEs) represent the single largest component of numerous eukaryotic genomes, and their activity and dispersal constitute an important force fostering evolutionary innovation. The horizontal transfer of TEs (HTT) between eukaryotic species is a common and widespread phenomenon that has had a profound impact on TE dynamics and, consequently, on the evolutionary trajectory of many species' lineages. However, the mechanisms promoting HTT remain largely unknown. In this article, we argue that network theory combined with functional ecology provides a robust conceptual framework and tools to delineate how complex interactions between diverse organisms may act in synergy to promote HTTs. PMID:28199335

  19. Heat Transfer from a Horizontal Cylinder Rotating in Oil

    NASA Technical Reports Server (NTRS)

    Seban, R. A.; Johnson, H. A.

    1959-01-01

    Measurements of the heat transfer from a horizontal cylinder rotating about its axis have been made with oil as the surrounding fluid to provide an addition to the heat-transfer results for this system heretofore available only for air. The results embrace a Prandtl number range from about 130 to 660, with Reynolds numbers up to 3 x 10(exp 4), and show an increasing dependence of free-convection heat transfer on rotation as the Prandtl number is increased by reducing the oil temperature. Some correlation of this effect, which agrees with the prior results for air, has been achieved. At higher rotative speeds the flow becomes turbulent, the free- convection effect vanishes, and the results with oil can be correlated generally with those for air and with mass-transfer results for even higher Prandtl numbers. For this system, however, the analogy calculations which have successfully related the heat transfer to the friction for pipe flows at high Prandtl numbers fail.

  20. Horizontal Transfer of Small RNAs to and from Plants

    PubMed Central

    Han, Lu; Luan, Yu-Shi

    2015-01-01

    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 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. PMID:26697056

  1. Natural convection heat transfer within horizontal spent nuclear fuel assemblies

    SciTech Connect

    Canaan, R.E.

    1995-12-01

    Natural convection heat transfer is experimentally investigated in an enclosed horizontal rod bundle, which characterizes a spent nuclear fuel assembly during dry storage and/or transport conditions. The basic test section consists of a square array of sixty-four stainless steel tubular heaters enclosed within a water-cooled rectangular copper heat exchanger. The heaters are supplied with a uniform power generation per unit length while the surrounding enclosure is maintained at a uniform temperature. The test section resides within a vacuum/pressure chamber in order to subject the assembly to a range of pressure statepoints and various backfill gases. The objective of this experimental study is to obtain convection correlations which can be used in order to easily incorporate convective effects into analytical models of horizontal spent fuel systems, and also to investigate the physical nature of natural convection in enclosed horizontal rod bundles in general. The resulting data consist of: (1) measured temperatures within the assembly as a function of power, pressure, and backfill gas; (2) the relative radiative contribution for the range of observed temperatures; (3) correlations of convective Nusselt number and Rayleigh number for the rod bundle as a whole; and (4) correlations of convective Nusselt number as a function of Rayleigh number for individual rods within the array.

  2. Condensation heat transfer of steam on a single horizontal tube

    NASA Astrophysics Data System (ADS)

    Graber, K. A.

    1983-06-01

    An experimental apparatus was designed, constructed and instrumented in an effort to systematically and carefully study the condensation heat-transfer coefficient on a single, horizontal tube. A smooth, thick-walled copper tube of length 133.5 mm, with an outside diameter of 15.9 mm and an inside diameter of 12.7 mm was instrumented with six wall thermocouples. The temperature rise across the test section was measured accurately using quartz crystal thermometers. The inside heat-transfer coefficient was determined using the Sieder-Tate correlation with leading coefficient of 0.029. Initial steam side data were taken at atmospheric pressure to test the data acquisition/reduction computer programs.

  3. Rampant horizontal transfer of SPIN transposons in squamate reptiles.

    PubMed

    Gilbert, Clément; Hernandez, Sharon S; Flores-Benabib, Jaime; Smith, Eric N; Feschotte, Cédric

    2012-02-01

    Transposable elements (TEs) are highly abundant in the genome and capable of mobility, two properties that make them particularly prone to transfer horizontally between organisms. Although the impact of horizontal transfer (HT) of TEs is well recognized in prokaryotes, the frequency of this phenomenon and its contribution to genome evolution in eukaryotes remain poorly appreciated. Here, we provide evidence that a DNA transposon called SPIN has colonized the genome of 17 species of reptiles representing nearly every major lineage of squamates, including 14 families of lizards, snakes, and amphisbaenians. Slot blot analyses indicate that SPIN has amplified to high copy numbers in most of these species, ranging from 2,000-28,000 copies per haploid genome. In contrast, we could not detect the presence of SPIN in any of the turtles (seven species from seven families) and crocodiles (four species) examined. Genetic distances between SPIN sequences from species belonging to different squamate families are consistently very low (average = 0.1), considering the deep evolutionary divergence of the families investigated (most are >100 My diverged). Furthermore, these distances fall below interfamilial distances calculated for two genes known to have evolved under strong functional constraint in vertebrates (RAG1, average = 0.24 and C-mos, average = 0.27). These data, combined with phylogenetic analyses, indicate that the widespread distribution of SPIN among squamates is the result of at least 13 independent events of HTs. Molecular dating and paleobiogeographical data suggest that these transfers took place during the last 50 My on at least three different continents (North America, South America and, Africa). Together, these results triple the number of known SPIN transfer events among tetrapods, provide evidence for a previously hypothesized transoceanic movement of SPIN transposons during the Cenozoic, and further underscore the role of HT in the evolution of vertebrate

  4. Rampant Horizontal Transfer of SPIN Transposons in Squamate Reptiles

    PubMed Central

    Gilbert, Clément; Hernandez, Sharon S.; Flores-Benabib, Jaime; Smith, Eric N.; Feschotte, Cédric

    2012-01-01

    Transposable elements (TEs) are highly abundant in the genome and capable of mobility, two properties that make them particularly prone to transfer horizontally between organisms. Although the impact of horizontal transfer (HT) of TEs is well recognized in prokaryotes, the frequency of this phenomenon and its contribution to genome evolution in eukaryotes remain poorly appreciated. Here, we provide evidence that a DNA transposon called SPIN has colonized the genome of 17 species of reptiles representing nearly every major lineage of squamates, including 14 families of lizards, snakes, and amphisbaenians. Slot blot analyses indicate that SPIN has amplified to high copy numbers in most of these species, ranging from 2,000–28,000 copies per haploid genome. In contrast, we could not detect the presence of SPIN in any of the turtles (seven species from seven families) and crocodiles (four species) examined. Genetic distances between SPIN sequences from species belonging to different squamate families are consistently very low (average = 0.1), considering the deep evolutionary divergence of the families investigated (most are >100 My diverged). Furthermore, these distances fall below interfamilial distances calculated for two genes known to have evolved under strong functional constraint in vertebrates (RAG1, average = 0.24 and C-mos, average = 0.27). These data, combined with phylogenetic analyses, indicate that the widespread distribution of SPIN among squamates is the result of at least 13 independent events of HTs. Molecular dating and paleobiogeographical data suggest that these transfers took place during the last 50 My on at least three different continents (North America, South America and, Africa). Together, these results triple the number of known SPIN transfer events among tetrapods, provide evidence for a previously hypothesized transoceanic movement of SPIN transposons during the Cenozoic, and further underscore the role of HT in the evolution of

  5. Complexity of genetic sequences modified by horizontal gene transfer and degraded-DNA uptake

    NASA Astrophysics Data System (ADS)

    Tremberger, George; Dehipawala, S.; Nguyen, A.; Cheung, E.; Sullivan, R.; Holden, T.; Lieberman, D.; Cheung, T.

    2015-09-01

    Horizontal gene transfer has been a major vehicle for efficient transfer of genetic materials among living species and could be one of the sources for noncoding DNA incorporation into a genome. Our previous study of lnc- RNA sequence complexity in terms of fractal dimension and information entropy shows a tight regulation among the studied genes in numerous diseases. The role of sequence complexity in horizontal transferred genes was investigated with Mealybug in symbiotic relation with a 139K genome microbe and Deinococcus radiodurans as examples. The fractal dimension and entropy showed correlation R-sq of 0.82 (N = 6) for the studied Deinococcus radiodurans sequences. For comparison the Deinococcus radiodurans oxidative stress tolerant catalase and superoxide dismutase genes under extracellular dGMP growth condition showed R-sq ~ 0.42 (N = 6); and the studied arsenate reductase horizontal transferred genes for toxicity survival in several microorganisms showed no correlation. Simulation results showed that R-sq < 0.4 would be improbable at less than one percent chance, suggestive of additional selection pressure when compared to the R-sq ~ 0.29 (N = 21) in the studied transferred genes in Mealybug. The mild correlation of R-sq ~ 0.5 for fractal dimension versus transcription level in the studied Deinococcus radiodurans sequences upon extracellular dGMP growth condition would suggest that lower fractal dimension with less electron density fluctuation favors higher transcription level.

  6. Horizontal Gene Transfer Contributes to the Evolution of Arthropod Herbivory.

    PubMed

    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.

  7. Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi.

    PubMed

    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.

  8. Horizontal Gene Transfer Contributes to the Evolution of Arthropod Herbivory

    PubMed Central

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

    2016-01-01

    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. PMID:27307274

  9. Condensation heat transfer of actual flue gas on horizontal tubes

    SciTech Connect

    Osakabe, Masahiro; Itoh, Tugue; Yagi, Kiyoyuki

    1999-07-01

    In order to improve the boiler efficiency, latent heat recovery from an exhaust flue gas is a very important concept. Condensation heat transfer on horizontal stainless steel tubes was investigated experimentally using an actual flue gas from a natural gas boiler. The experiment was conducted at different air ratios and steam mass concentrations of the flue gas, and in a wide range of tube wall temperature. The condensation pattern was similar to the dropwise condensation near the dew point. As the wall temperature was decreased, the wall region covered with a thin liquid film increased. The heat and mass transfer behavior were well predicted with the simple analogy correlation in the high wall temperature region. But in the low wall temperature region, the total heat transfer rate was higher than that predicted by the simple analogy correlation. At a high steam mass concentration artificially generated with steam injection, the total heat transfer rate was higher than that predicted by the simple analogy correlation. The analogy correlation using the modified Sherwood number taking account of the mass absorption effect was proposed. The modified correlation gave a good prediction of the heat flux at the high steam mass concentration.

  10. Horizontal transfer of transposons between and within crustaceans and insects

    PubMed Central

    2014-01-01

    Background Horizontal transfer of transposable elements (HTT) is increasingly appreciated as an important source of genome and species evolution in eukaryotes. However, our understanding of HTT dynamics is still poor in eukaryotes because the diversity of species for which whole genome sequences are available is biased and does not reflect the global eukaryote diversity. Results In this study we characterized two Mariner transposable elements (TEs) in the genome of several terrestrial crustacean isopods, a group of animals particularly underrepresented in genome databases. The two elements have a patchy distribution in the arthropod tree and they are highly similar (>93% over the entire length of the element) to insect TEs (Diptera and Hymenoptera), some of which were previously described in Ceratitis rosa (Crmar2) and Drosophila biarmipes (Mariner-5_Dbi). In addition, phylogenetic analyses and comparisons of TE versus orthologous gene distances at various phylogenetic levels revealed that the taxonomic distribution of the two elements is incompatible with vertical inheritance. Conclusions We conclude that the two Mariner TEs each underwent at least three HTT events. Both elements were transferred once between isopod crustaceans and insects and at least once between isopod crustacean species. Crmar2 was also transferred between tephritid and drosophilid flies and Mariner-5 underwent HT between hymenopterans and dipterans. We demonstrate that these various HTTs took place recently (most likely within the last 3 million years), and propose iridoviruses and/or Wolbachia endosymbionts as potential vectors of these transfers. PMID:24472097

  11. Enhanced boiling heat transfer in horizontal test bundles

    SciTech Connect

    Trewin, R.R.; Jensen, M.K.; Bergles, A.E.

    1994-08-01

    Two-phase flow boiling from bundles of horizontal tubes with smooth and enhanced surfaces has been investigated. Experiments were conducted in pure refrigerant R-113, pure R-11, and mixtures of R-11 and R-113 of approximately 25, 50, and 75% of R-113 by mass. Tests were conducted in two staggered tube bundles consisting of fifteen rows and five columns laid out in equilateral triangular arrays with pitch-to-diameter ratios of 1.17 and 1.5. The enhanced surfaces tested included a knurled surface (Wolverine`s Turbo-B) and a porous surface (Linde`s High Flux). Pool boiling tests were conducted for each surface so that reference values of the heat transfer coefficient could be obtained. Boiling heat transfer experiments in the tube bundles were conducted at pressures of 2 and 6 bar, heat flux values from 5 to 80 kW/m{sup 2}s, and qualities from 0% to 80%, Values of the heat transfer coefficients for the enhanced surfaces were significantly larger than for the smooth tubes and were comparable to the values obtained in pool boiling. It was found that the performance of the enhanced tubes could be predicted using the pool boiling results. The degradation in the smooth tube heat transfer coefficients obtained in fluid mixtures was found to depend on the difference between the molar concentration in the liquid and vapor.

  12. Risks from GMOs due to horizontal gene transfer.

    PubMed

    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.

  13. Horizontal gene transfer: building the web of life.

    PubMed

    Soucy, Shannon M; Huang, Jinling; Gogarten, Johann Peter

    2015-08-01

    Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a parent-offspring relationship. HGT is a widely recognized mechanism for adaptation in bacteria and archaea. Microbial antibiotic resistance and pathogenicity are often associated with HGT, but the scope of HGT extends far beyond disease-causing organisms. In this Review, we describe how HGT has shaped the web of life using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes. We discuss replacement and additive HGT, the proposed mechanisms of HGT, selective forces that influence HGT, and the evolutionary impact of HGT on ancestral populations and existing populations such as the human microbiome.

  14. HGTree: database of horizontally transferred genes determined by tree reconciliation.

    PubMed

    Jeong, Hyeonsoo; Sung, Samsun; Kwon, Taehyung; Seo, Minseok; Caetano-Anollés, Kelsey; Choi, Sang Ho; Cho, Seoae; Nasir, Arshan; Kim, Heebal

    2016-01-04

    The HGTree database provides putative genome-wide horizontal gene transfer (HGT) information for 2472 completely sequenced prokaryotic genomes. This task is accomplished by reconstructing approximate maximum likelihood phylogenetic trees for each orthologous gene and corresponding 16S rRNA reference species sets and then reconciling the two trees under parsimony framework. The tree reconciliation method is generally considered to be a reliable way to detect HGT events but its practical use has remained limited because the method is computationally intensive and conceptually challenging. In this regard, HGTree (http://hgtree.snu.ac.kr) represents a useful addition to the biological community and enables quick and easy retrieval of information for HGT-acquired genes to better understand microbial taxonomy and evolution. The database is freely available and can be easily scaled and updated to keep pace with the rapid rise in genomic information.

  15. HGTree: database of horizontally transferred genes determined by tree reconciliation

    PubMed Central

    Jeong, Hyeonsoo; Sung, Samsun; Kwon, Taehyung; Seo, Minseok; Caetano-Anollés, Kelsey; Choi, Sang Ho; Cho, Seoae; Nasir, Arshan; Kim, Heebal

    2016-01-01

    The HGTree database provides putative genome-wide horizontal gene transfer (HGT) information for 2472 completely sequenced prokaryotic genomes. This task is accomplished by reconstructing approximate maximum likelihood phylogenetic trees for each orthologous gene and corresponding 16S rRNA reference species sets and then reconciling the two trees under parsimony framework. The tree reconciliation method is generally considered to be a reliable way to detect HGT events but its practical use has remained limited because the method is computationally intensive and conceptually challenging. In this regard, HGTree (http://hgtree.snu.ac.kr) represents a useful addition to the biological community and enables quick and easy retrieval of information for HGT-acquired genes to better understand microbial taxonomy and evolution. The database is freely available and can be easily scaled and updated to keep pace with the rapid rise in genomic information. PMID:26578597

  16. Quartet analysis of putative horizontal gene transfer in Crenarchaeota.

    PubMed

    Ching, Travers H; Yoza, Brandon A; Li, Qing X

    2014-02-01

    Horizontal gene transfers (HGT) between four Crenarchaeota species (Metallosphaera cuprina Ar-4T, Acidianus hospitalis W1T, Vulcanisaeta moutnovskia 768-28T, and Pyrobaculum islandicum DSM 4184T) were investigated with quartet analysis. Strong support was found for individual genes that disagree with the phylogeny of the majority, implying genomic mosaicism. One such gene, a ferredoxin-related gene, was investigated further and incorporated into a larger phylogeny, which provided evidence for HGT of this gene from the Vulcanisaeta lineage to the Acidianus lineage. This is the first application of quartet analysis of HGT for the phylum Crenarchaeota. The results have shown that quartet analysis is a powerful technique to screen homologous sequences for putative HGTs and is useful in visually describing genomic mosaicism and HGT within four taxa.

  17. Horizontal gene transfer in eukaryotes: The weak-link model

    PubMed Central

    Huang, Jinling

    2013-01-01

    The significance of horizontal gene transfer (HGT) in eukaryotic evolution remains controversial. Although many eukaryotic genes are of bacterial origin, they are often interpreted as being derived from mitochondria or plastids. Because of their fixed gene pool and gene loss, however, mitochondria and plastids alone cannot adequately explain the presence of all, or even the majority, of bacterial genes in eukaryotes. Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In addition, the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution. A model of HGT is proposed that suggests both unicellular and early developmental stages as likely entry points for foreign genes into multicellular eukaryotes. PMID:24037739

  18. Horizontal gene transfer in eukaryotes: the weak-link model.

    PubMed

    Huang, Jinling

    2013-10-01

    The significance of horizontal gene transfer (HGT) in eukaryotic evolution remains controversial. Although many eukaryotic genes are of bacterial origin, they are often interpreted as being derived from mitochondria or plastids. Because of their fixed gene pool and gene loss, however, mitochondria and plastids alone cannot adequately explain the presence of all, or even the majority, of bacterial genes in eukaryotes. Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In addition, the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution. A model of HGT is proposed that suggests both unicellular and early developmental stages as likely entry points for foreign genes into multicellular eukaryotes.

  19. Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi

    PubMed Central

    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

    2015-01-01

    Summary 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. PMID:26412136

  20. Phylogeographic support for horizontal gene transfer involving sympatric bruchid species

    PubMed Central

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

    2006-01-01

    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, hybridization, and

  1. Replacing and Additive Horizontal Gene Transfer in Streptococcus

    PubMed Central

    Choi, Sang Chul; Rasmussen, Matthew D.; Hubisz, Melissa J.; Gronau, Ilan; Stanhope, Michael J.; Siepel, Adam

    2012-01-01

    The prominent role of Horizontal Gene Transfer (HGT) in the evolution of bacteria is now well documented, but few studies have differentiated between evolutionary events that predominantly cause genes in one lineage to be replaced by homologs from another lineage (“replacing HGT”) and events that result in the addition of substantial new genomic material (“additive HGT”). Here in, we make use of the distinct phylogenetic signatures of replacing and additive HGTs in a genome-wide study of the important human pathogen Streptococcus pyogenes (SPY) and its close relatives S. dysgalactiae subspecies equisimilis (SDE) and S. dysgalactiae subspecies dysgalactiae (SDD). Using recently developed statistical models and computational methods, we find evidence for abundant gene flow of both kinds within each of the SPY and SDE clades and of reduced levels of exchange between SPY and SDD. In addition, our analysis strongly supports a pronounced asymmetry in SPY–SDE gene flow, favoring the SPY-to-SDE direction. This finding is of particular interest in light of the recent increase in virulence of pathogenic SDE. We find much stronger evidence for SPY–SDE gene flow among replacing than among additive transfers, suggesting a primary influence from homologous recombination between co-occurring SPY and SDE cells in human hosts. Putative virulence genes are correlated with transfer events, but this correlation is found to be driven by additive, not replacing, HGTs. The genes affected by additive HGTs are enriched for functions having to do with transposition, recombination, and DNA integration, consistent with previous findings, whereas replacing HGTs seen to influence a more diverse set of genes. Additive transfers are also found to be associated with evidence of positive selection. These findings shed new light on the manner in which HGT has shaped pathogenic bacterial genomes. PMID:22617954

  2. Synthetic Fatty Acids Prevent Plasmid-Mediated Horizontal Gene Transfer

    PubMed Central

    Getino, María; Sanabria-Ríos, David J.; Fernández-López, Raúl; Campos-Gómez, Javier; Sánchez-López, José M.; Fernández, Antonio; Carballeira, Néstor M.

    2015-01-01

    ABSTRACT Bacterial conjugation constitutes a major horizontal gene transfer mechanism for the dissemination of antibiotic resistance genes among human pathogens. Antibiotic resistance spread could be halted or diminished by molecules that interfere with the conjugation process. In this work, synthetic 2-alkynoic fatty acids were identified as a novel class of conjugation inhibitors. Their chemical properties were investigated by using the prototype 2-hexadecynoic acid and its derivatives. Essential features of effective inhibitors were the carboxylic group, an optimal long aliphatic chain of 16 carbon atoms, and one unsaturation. Chemical modification of these groups led to inactive or less-active derivatives. Conjugation inhibitors were found to act on the donor cell, affecting a wide number of pathogenic bacterial hosts, including Escherichia, Salmonella, Pseudomonas, and Acinetobacter spp. Conjugation inhibitors were active in inhibiting transfer of IncF, IncW, and IncH plasmids, moderately active against IncI, IncL/M, and IncX plasmids, and inactive against IncP and IncN plasmids. Importantly, the use of 2-hexadecynoic acid avoided the spread of a derepressed IncF plasmid into a recipient population, demonstrating the feasibility of abolishing the dissemination of antimicrobial resistances by blocking bacterial conjugation. PMID:26330514

  3. Indication of Horizontal DNA Gene Transfer by Extracellular Vesicles

    PubMed Central

    Speiseder, Thomas; Badbaran, Anita; Reimer, Rudolph; Indenbirken, Daniela; Grundhoff, Adam; Brunswig-Spickenheier, Bärbel; Alawi, Malik; Lange, Claudia

    2016-01-01

    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. PMID:27684368

  4. Horizontal Transfer and Death of a Fungal Secondary Metabolic Gene Cluster

    PubMed Central

    Campbell, Matthew A.; Rokas, Antonis; Slot, Jason C.

    2012-01-01

    A cluster composed of four structural and two regulatory genes found in several species of the fungal genus Fusarium (class Sordariomycetes) is responsible for the production of the red pigment bikaverin. We discovered that the unrelated fungus Botrytis cinerea (class Leotiomycetes) contains a cluster of five genes that is highly similar in sequence and gene order to the Fusarium bikaverin cluster. Synteny conservation, nucleotide composition, and phylogenetic analyses of the cluster genes indicate that the B. cinerea cluster was acquired via horizontal transfer from a Fusarium donor. Upon or subsequent to the transfer, the B. cinerea gene cluster became inactivated; one of the four structural genes is missing, two others are pseudogenes, and the fourth structural gene shows an accelerated rate of nonsynonymous substitutions along the B. cinerea lineage, consistent with relaxation of selective constraints. Interestingly, the bik4 regulatory gene is still intact and presumably functional, whereas bik5, which is a pathway-specific regulator, also shows a mild but significant acceleration of evolutionary rate along the B. cinerea lineage. This selective preservation of the bik4 regulator suggests that its conservation is due to its likely involvement in other non–bikaverin-related biological processes in B. cinerea. Thus, in addition to novel metabolism, horizontal transfer of wholesale metabolic gene clusters might also be contributing novel regulation. PMID:22294497

  5. Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen

    DOE PAGES

    Dhillon, Braham; Feau, Nicolas; Aerts, Andrea L.; ...

    2015-03-02

    Some of the most damaging tree diseases are caused by pathogens that induce cankers, a stem deformation often lethal. To investigate the cause of this adaptation, we sequenced the genomes of poplar pathogens that do and do not cause cankers. We found a unique cluster of genes that produce secondary metabolites and are co-activated when the canker pathogen is grown on poplar wood and leaves. The gene genealogy is discordant with the species phylogeny, showing a signature of horizontal transfer from fungi associated with wood decay. Furthermore, genes encoding hemicellulose-degrading enzymes are up-regulated on poplar wood chips, with some havingmore » been acquired horizontally. In conclusion, we propose that adaptation to colonize poplar woody stems is the result of acquisition of these genes.« less

  6. Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen

    SciTech Connect

    Dhillon, Braham; Feau, Nicolas; Aerts, Andrea L.; Beauseigle, Stéphanie; Bernier, Louis; Copeland, Alex; Foster, Adam; Gill, Navdeep; Henrissat, Bernard; Herath, Padmini; LaButti, Kurt M.; Levasseur, Anthony; Lindquist, Erika A.; Majoor, Eline; Ohm, Robin A.; Pangilinan, Jasmyn L.; Pribowo, Amadeus; Saddler, John N.; Sakalidis, Monique L.; de Vries, Ronald P.; Grigoriev, Igor V.; Goodwin, Stephen B.; Tanguay, Philippe; Hamelin, Richard C.

    2015-03-02

    Some of the most damaging tree diseases are caused by pathogens that induce cankers, a stem deformation often lethal. To investigate the cause of this adaptation, we sequenced the genomes of poplar pathogens that do and do not cause cankers. We found a unique cluster of genes that produce secondary metabolites and are co-activated when the canker pathogen is grown on poplar wood and leaves. The gene genealogy is discordant with the species phylogeny, showing a signature of horizontal transfer from fungi associated with wood decay. Furthermore, genes encoding hemicellulose-degrading enzymes are up-regulated on poplar wood chips, with some having been acquired horizontally. In conclusion, we propose that adaptation to colonize poplar woody stems is the result of acquisition of these genes.

  7. Novel "Superspreader" Bacteriophages Promote Horizontal Gene Transfer by Transformation.

    PubMed

    Keen, Eric C; Bliskovsky, Valery V; Malagon, Francisco; Baker, James D; Prince, Jeffrey S; Klaus, James S; Adhya, Sankar L

    2017-01-17

    Bacteriophages infect an estimated 10(23) to 10(25) bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub "superspreaders," releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation. Two novel Escherichia coli phage superspreaders, SUSP1 and SUSP2, liberated four evolutionarily distinct plasmids with equal efficiency, including two close relatives of prominent antibiotic resistance vectors in natural environments. SUSP2 also mediated the extensive lateral transfer of antibiotic resistance in unbiased communities of soil bacteria from Maryland and Wyoming. Furthermore, the addition of SUSP2 to cocultures of kanamycin-resistant E. coli and kanamycin-sensitive Bacillus sp. bacteria resulted in roughly 1,000-fold more kanamycin-resistant Bacillus sp. bacteria than arose in phage-free controls. Unlike many other lytic phages, neither SUSP1 nor SUSP2 encodes homologs to known hydrolytic endonucleases, suggesting a simple potential mechanism underlying the superspreading phenotype. Consistent with this model, the deletion of endonuclease IV and the nucleoid-disrupting protein ndd from coliphage T4, a phage known to extensively degrade chromosomal DNA, significantly increased its ability to promote plasmid transformation. Taken together, our results suggest that phage superspreaders may play key roles in microbial evolution and ecology but should be avoided in phage therapy and other medical applications.

  8. Horizontal transfer of expressed genes in a parasitic flowering plant

    PubMed Central

    2012-01-01

    Background Recent studies have shown that plant genomes have potentially undergone rampant horizontal gene transfer (HGT). In plant parasitic systems HGT appears to be facilitated by the intimate physical association between the parasite and its host. HGT in these systems has been invoked when a DNA sequence obtained from a parasite is placed phylogenetically very near to its host rather than with its closest relatives. Studies of HGT in parasitic plants have relied largely on the fortuitous discovery of gene phylogenies that indicate HGT, and no broad systematic search for HGT has been undertaken in parasitic systems where it is most expected to occur. Results We analyzed the transcriptomes of the holoparasite Rafflesia cantleyi Solms-Laubach and its obligate host Tetrastigma rafflesiae Miq. using phylogenomic approaches. Our analyses show that several dozen actively transcribed genes, most of which appear to be encoded in the nuclear genome, are likely of host origin. We also find that hundreds of vertically inherited genes (VGT) in this parasitic plant exhibit codon usage properties that are more similar to its host than to its closest relatives. Conclusions Our results establish for the first time a substantive number of HGTs in a plant host-parasite system. The elevated rate of unidirectional host-to- parasite gene transfer raises the possibility that HGTs may provide a fitness benefit to Rafflesia for maintaining these genes. Finally, a similar convergence in codon usage of VGTs has been shown in microbes with high HGT rates, which may help to explain the increase of HGTs in these parasitic plants. PMID:22681756

  9. Microbial Evolution Is in the Cards: Horizontal Gene Transfer in the Classroom

    ERIC Educational Resources Information Center

    Kagle, Jeanne; Hay, Anthony G.

    2007-01-01

    Horizontal gene transfer, the exchange of genetic material between bacteria, is a potentially important factor in the degradation of synthetic compounds introduced to the environment and in the acquisition of other characteristics including antibiotic resistance. This game-based activity illustrates the role of horizontal gene transfer in the…

  10. Lack of evidence for horizontal transfer of the lac operon into Escherichia coli.

    PubMed

    Stoebel, Daniel M

    2005-03-01

    The idea that Escherichia coli gained the lac operon via horizontal transfer, allowing it to invade a new niche and form a new species, has become a paradigmatic example of bacterial nonpathogenic adaptation and speciation catalyzed by horizontal transfer. Surprisingly, empirical evidence for this event is essentially nonexistent. To see whether horizontal transfer occurred, I compared a phylogeny of 14 Enterobacteriaceae based on two housekeeping genes to a phylogeny of a part of their lac operon. Although several species in this clade appear to have acquired some or all of the operon via horizontal transfer, there is no evidence of horizontal transfer into E. coli. It is not clear whether the horizontal transfer events for which there is evidence were adaptive because those species which have acquired the operon are not thought to live in high lactose environments. I propose that vertical transmission from the common ancestor of the Enterobacteriaceae, with subsequent loss of these genes in many species can explain much of the patchy distribution of lactose use in this clade. Finally, I argue that we need new, well-supported examples of horizontal transfer spurring niche expansion and speciation, particularly in nonpathogenic cases, before we can accept claims that horizontal transfer is a hallmark of bacterial adaptation.

  11. Horizontal gene transfer in the acquisition of novel traits by metazoans

    PubMed Central

    Boto, Luis

    2014-01-01

    Horizontal gene transfer is accepted as an important evolutionary force modulating the evolution of prokaryote genomes. However, it is thought that horizontal gene transfer plays only a minor role in metazoan evolution. In this paper, I critically review the rising evidence on horizontally transferred genes and on the acquisition of novel traits in metazoans. In particular, I discuss suspected examples in sponges, cnidarians, rotifers, nematodes, molluscs and arthropods which suggest that horizontal gene transfer in metazoans is not simply a curiosity. In addition, I stress the scarcity of studies in vertebrates and other animal groups and the importance of forthcoming studies to understand the importance and extent of horizontal gene transfer in animals. PMID:24403327

  12. Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes.

    PubMed

    Gilbert, Clément; Cordaux, Richard

    2013-01-01

    Horizontal transfer (HT) of transposable elements (TEs) plays a key role in prokaryotic evolution, and mounting evidence suggests that it has also had an important impact on eukaryotic evolution. Although many prokaryote-to-prokaryote and eukaryote-to-eukaryote HTs of TEs have been characterized, only few cases have been reported between prokaryotes and eukaryotes. Here, we carried out a comprehensive search for all major groups of prokaryotic insertion sequences (ISs) in 430 eukaryote genomes. We uncovered a total of 80 sequences, all deriving from the IS607 family, integrated in the genomes of 14 eukaryote species belonging to four distinct phyla (Amoebozoa, Ascomycetes, Basidiomycetes, and Stramenopiles). Given that eukaryote IS607-like sequences are most closely related to cyanobacterial IS607 and that their phylogeny is incongruent with that of their hosts, we conclude that the presence of IS607-like sequences in eukaryotic genomes is the result of several HT events. Selection analyses further suggest that our ability to detect these prokaryote TEs today in eukaryotes is because HT of these sequences occurred recently and/or some IS607 elements were domesticated after HT, giving rise to new eukaryote genes. Supporting the recent age of some of these HTs, we uncovered intact full-length, potentially active IS607 copies in the amoeba Acanthamoeba castellani. Overall, our study shows that prokaryote-to-eukaryote HT of TEs occurred at relatively low frequency during recent eukaryote evolution and it sets IS607 as the most widespread TE (being present in prokaryotes, eukaryotes, and viruses).

  13. Horizontal DNA transfer from bacteria to eukaryotes and a lesson from experimental transfers.

    PubMed

    Suzuki, Katsunori; Moriguchi, Kazuki; Yamamoto, Shinji

    2015-12-01

    Horizontal gene transfer (HGT) is widespread among bacteria and plays a key role in genome dynamics. HGT is much less common in eukaryotes, but is being reported with increasing frequency in eukaryotes. The mechanism as to how eukaryotes acquired genes from distantly related organisms remains obscure yet. This paper cites examples of bacteria-derived genes found in eukaryotic organisms, and then describes experimental DNA transports to eukaryotes by bacterial type 4 secretion systems in optimized conditions. The mechanisms of the latter are efficient, quite reproducible in vitro and predictable, and thereby would provide insight into natural HGT and to the development of new research tools.

  14. Horizontal gene transfers and cell fusions in microbiology, immunology and oncology (Review).

    PubMed

    Sinkovics, Joseph G

    2009-09-01

    Evolving young genomes of archaea, prokaryota and unicellular eukaryota were wide open for the acceptance of alien genomic sequences, which they often preserved and vertically transferred to their descendants throughout three billion years of evolution. Established complex large genomes, although seeded with ancestral retroelements, have come to regulate strictly their integrity. However, intruding retroelements, especially the descendents of Ty3/Gypsy, the chromoviruses, continue to find their ways into even the most established genomes. The simian and hominoid-Homo genomes preserved and accommodated a large number of endogenous retroviral genomic segments. These retroelements may mature into exogenous retroviruses, or into functional new genes. Phages and viruses have been instrumental in incorporating and transferring host cell genes. These events profoundly influenced and altered the course of evolution. Horizontal (lateral) gene transfers (HGT) overwhelmed the genomes of the ancient protocells and the evolving unicellular microorganisms, actually leading to their Cambrian explosion. While the rigidly organized genomes of multicellular organisms increasingly resist H/LGT, de-differentiated cells assuming the metabolism of their onto- or phylogenetic ancestors, open up widely to the practice of H/LGT by direct transfer, or to transfers mediated by viruses, or by cell fusions. This activity is intensified in malignantly transformed cells, thus rendering these subjects receptive to therapy with oncolytic viruses and with viral vectors of tumor-suppressive or immunogenic genetic materials. Naturally formed hybrids of dendritic and tumor cells are often tolerogenic, whereas laboratory products of these unisons may be immunogenic in the hosts of origin. As human breast cancer stem cells are induced by a treacherous class of CD8+ T cells to undergo epithelial to mesenchymal (ETM) transition and to yield to malignant transformation by the omnipresent proto

  15. Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences.

    PubMed

    Wagner, Andreas; de la Chaux, Nicole

    2008-11-01

    Horizontal gene transfer in prokaryotes is rampant on short and intermediate evolutionary time scales. It poses a fundamental problem to our ability to reconstruct the evolutionary tree of life. Is it also frequent over long evolutionary distances? To address this question, we analyzed the evolution of 2,091 insertion sequences from all 20 major families in 438 completely sequenced prokaryotic genomes. Specifically, we mapped insertion sequence occurrence on a 16S rDNA tree of the genomes we analyzed, and we also constructed phylogenetic trees of the insertion sequence transposase coding sequences. We found only 30 cases of likely horizontal transfer among distantly related prokaryotic clades. Most of these horizontal transfer events are ancient. Only seven events are recent. Almost all of these transfer events occur between pairs of human pathogens or commensals. If true also for other, non-mobile DNA, the rarity of distant horizontal transfer increases the odds of reliable phylogenetic inference from sequence data.

  16. Widespread impact of horizontal gene transfer on plant colonization of land

    PubMed Central

    Yue, Jipei; Hu, Xiangyang; Sun, Hang; Yang, Yongping; Huang, Jinling

    2012-01-01

    In complex multicellular eukaryotes such as animals and plants, horizontal gene transfer is commonly considered rare with very limited evolutionary significance. Here we show that horizontal gene transfer is a dynamic process occurring frequently in the early evolution of land plants. Our genome analyses of the moss Physcomitrella patens identified 57 families of nuclear genes that were acquired from prokaryotes, fungi or viruses. Many of these gene families were transferred to the ancestors of green or land plants. Available experimental evidence shows that these anciently acquired genes are involved in some essential or plant-specific activities such as xylem formation, plant defence, nitrogen recycling as well as the biosynthesis of starch, polyamines, hormones and glutathione. These findings suggest that horizontal gene transfer had a critical role in the transition of plants from aquatic to terrestrial environments. On the basis of these findings, we propose a model of horizontal gene transfer mechanism in nonvascular and seedless vascular plants. PMID:23093189

  17. Widespread impact of horizontal gene transfer on plant colonization of land.

    PubMed

    Yue, Jipei; Hu, Xiangyang; Sun, Hang; Yang, Yongping; Huang, Jinling

    2012-01-01

    In complex multicellular eukaryotes such as animals and plants, horizontal gene transfer is commonly considered rare with very limited evolutionary significance. Here we show that horizontal gene transfer is a dynamic process occurring frequently in the early evolution of land plants. Our genome analyses of the moss Physcomitrella patens identified 57 families of nuclear genes that were acquired from prokaryotes, fungi or viruses. Many of these gene families were transferred to the ancestors of green or land plants. Available experimental evidence shows that these anciently acquired genes are involved in some essential or plant-specific activities such as xylem formation, plant defence, nitrogen recycling as well as the biosynthesis of starch, polyamines, hormones and glutathione. These findings suggest that horizontal gene transfer had a critical role in the transition of plants from aquatic to terrestrial environments. On the basis of these findings, we propose a model of horizontal gene transfer mechanism in nonvascular and seedless vascular plants.

  18. Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes

    PubMed Central

    Huddleston, Jennifer R

    2014-01-01

    Bacterial infections are becoming increasingly difficult to treat due to widespread antibiotic resistance among pathogens. This review aims to give an overview of the major horizontal transfer mechanisms and their evolution and then demonstrate the human lower gastrointestinal tract as an environment in which horizontal gene transfer of resistance determinants occurs. Finally, implications for antibiotic usage and the development of resistant infections and persistence of antibiotic resistance genes in populations as a result of horizontal gene transfer in the large intestine will be discussed. PMID:25018641

  19. Health Considerations Regarding Horizontal Transfer of Microbial Transgenes Present in Genetically Modified Crops

    PubMed Central

    Kleter, Gijs A.

    2005-01-01

    The potential effects of horizontal gene transfer on human health are an important item in the safety assessment of genetically modified organisms. Horizontal gene transfer from genetically modified crops to gut microflora most likely occurs with transgenes of microbial origin. The characteristics of microbial transgenes other than antibiotic-resistance genes in market-approved genetically modified crops are reviewed. These characteristics include the microbial source, natural function, function in genetically modified crops, natural prevalence, geographical distribution, similarity to other microbial genes, known horizontal transfer activity, selective conditions and environments for horizontally transferred genes, and potential contribution to pathogenicity and virulence in humans and animals. The assessment of this set of data for each of the microbial genes reviewed does not give rise to health concerns. We recommend including the above-mentioned items into the premarket safety assessment of genetically modified crops carrying transgenes other than those reviewed in the present study. PMID:16489267

  20. Genome-wide identification of horizontal gene transfer in Fusarium verticillioides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Horizontal gene transfer (HGT), the exchange and stable integration of genetic material between different lineages, breaks species boundaries and generates new biological diversity. In eukaryotes, despite potential barriers, like the nuclear envelope and multicellularity, HGT may be facilitated by t...

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

    PubMed

    Talianova, Martina; Janousek, Bohuslav

    2011-08-01

    In eukaryotic organisms, horizontal gene transfer (HGT) is regarded as an important though infrequent source of reticulate evolution. Many confirmed instances of natural HGT involving multicellular eukaryotes come from flowering plants. This review intends to provide a synthesis of present knowledge regarding HGT in higher plants, with an emphasis on tobacco and other species in the Solanaceae family because there are numerous detailed reports concerning natural HGT events, involving various donors, in this family. Moreover, in-depth experimental studies using transgenic tobacco are of great importance for understanding this process. Valuable insights are offered concerning the mechanisms of HGT, the adaptive role and regulation of natural transgenes, and new routes for gene trafficking. With an increasing amount of data on HGT, a synthetic view is beginning to emerge.

  2. A new computational method for the detection of horizontal gene transfer events.

    PubMed

    Tsirigos, Aristotelis; Rigoutsos, Isidore

    2005-01-01

    In recent years, the increase in the amounts of available genomic data has made it easier to appreciate the extent by which organisms increase their genetic diversity through horizontally transferred genetic material. Such transfers have the potential to give rise to extremely dynamic genomes where a significant proportion of their coding DNA has been contributed by external sources. Because of the impact of these horizontal transfers on the ecological and pathogenic character of the recipient organisms, methods are continuously sought that are able to computationally determine which of the genes of a given genome are products of transfer events. In this paper, we introduce and discuss a novel computational method for identifying horizontal transfers that relies on a gene's nucleotide composition and obviates the need for knowledge of codon boundaries. In addition to being applicable to individual genes, the method can be easily extended to the case of clusters of horizontally transferred genes. With the help of an extensive and carefully designed set of experiments on 123 archaeal and bacterial genomes, we demonstrate that the new method exhibits significant improvement in sensitivity when compared to previously published approaches. In fact, it achieves an average relative improvement across genomes of between 11 and 41% compared to the Codon Adaptation Index method in distinguishing native from foreign genes. Our method's horizontal gene transfer predictions for 123 microbial genomes are available online at http://cbcsrv.watson.ibm.com/HGT/.

  3. Mechanisms of Horizontal Cell-to-Cell Transfer of Wolbachia spp. in Drosophila melanogaster.

    PubMed

    White, Pamela M; Pietri, Jose E; Debec, Alain; Russell, Shelbi; Patel, Bhavin; Sullivan, William

    2017-04-01

    Wolbachia is an intracellular endosymbiont present in most arthropod and filarial nematode species. Transmission between hosts is primarily vertical, taking place exclusively through the female germ line, although horizontal transmission has also been documented. The results of several studies indicate that Wolbachia spp. can undergo transfer between somatic and germ line cells during nematode development and in adult flies. However, the mechanisms underlying horizontal cell-to-cell transfer remain largely unexplored. Here, we establish a tractable system for probing horizontal transfer of Wolbachia cells between Drosophila melanogaster cells in culture using fluorescence in situ hybridization (FISH). First, we show that horizontal transfer is independent of cell-to-cell contact and can efficiently take place through the culture medium within hours. Further, we demonstrate that efficient transfer utilizes host cell phagocytic and clathrin/dynamin-dependent endocytic machinery. Lastly, we provide evidence that this process is conserved between species, showing that horizontal transfer from mosquito to Drosophila cells takes place in a similar fashion. Altogether, our results indicate that Wolbachia utilizes host internalization machinery during infection, and this mechanism is conserved across insect species.IMPORTANCE Our work has broad implications for the control and treatment of tropical diseases. Wolbachia can confer resistance against a variety of human pathogens in mosquito vectors. Elucidating the mechanisms of horizontal transfer will be useful for efforts to more efficiently infect nonnatural insect hosts with Wolbachia as a biological control agent. Further, as Wolbachia is essential for the survival of filarial nematodes, understanding horizontal transfer might provide new approaches to treating human infections by targeting Wolbachia Finally, this work provides a key first step toward the genetic manipulation of Wolbachia.

  4. Condensation Heat Transfer of Steam on a Single Horizontal Tube.

    DTIC Science & Technology

    1983-06-01

    thermometers. The inside heat-transfer coefficient was determined using the Sieder - Tate correlation with leading coefficient of 0.029. Initial...measured accurately using quartz crystal thermometers. The inside heat-transfer coefficient was determined using the Sieder -Tate correlation with...ACQUISITION/REDUCTION 34 A. DATA ACQUISITION AND STORAGE 34 3. DATA REDUCTION 34 C. STEPWISE SOLUTION PROCEDURE 35 1 . Program SIEDER 35

  5. Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach

    PubMed Central

    2008-01-01

    Background Poxviruses are important pathogens of humans, livestock and wild animals. These large dsDNA viruses have a set of core orthologs whose gene order is extremely well conserved throughout poxvirus genera. They also contain many genes with sequence and functional similarity to host genes which were probably acquired by horizontal gene transfer. Although phylogenetic trees can indicate the occurrence of horizontal gene transfer and even uncover multiple events, their use may be hampered by uncertainties in both the topology and the rooting of the tree. We propose to use synteny conservation around the horizontally transferred gene (HTgene) to distinguish between single and multiple events. Results Here we devise a method that incorporates comparative genomic information into the investigation of horizontal gene transfer, and we apply this method to poxvirus genomes. We examined the synteny conservation around twenty four pox genes that we identified, or which were reported in the literature, as candidate HTgenes. We found support for multiple independent transfers into poxviruses for five HTgenes. Three of these genes are known to be important for the survival of the virus in or out of the host cell and one of them increases susceptibility to some antiviral drugs. Conclusion In related genomes conserved synteny information can provide convincing evidence for multiple independent horizontal gene transfer events even in the absence of a robust phylogenetic tree for the HTgene. PMID:18304319

  6. Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events

    PubMed Central

    Zhaxybayeva, Olga; Gogarten, J. Peter; Charlebois, Robert L.; Doolittle, W. Ford; Papke, R. Thane

    2006-01-01

    Using 1128 protein-coding gene families from 11 completely sequenced cyanobacterial genomes, we attempt to quantify horizontal gene transfer events within cyanobacteria, as well as between cyanobacteria and other phyla. A novel method of detecting and enumerating potential horizontal gene transfer events within a group of organisms based on analyses of “embedded quartets” allows us to identify phylogenetic signal consistent with a plurality of gene families, as well as to delineate cases of conflict to the plurality signal, which include horizontally transferred genes. To infer horizontal gene transfer events between cyanobacteria and other phyla, we added homologs from 168 available genomes. We screened phylogenetic trees reconstructed for each of these extended gene families for highly supported monophyly of cyanobacteria (or lack of it). Cyanobacterial genomes reveal a complex evolutionary history, which cannot be represented by a single strictly bifurcating tree for all genes or even most genes, although a single completely resolved phylogeny was recovered from the quartets’ plurality signals. We find more conflicts within cyanobacteria than between cyanobacteria and other phyla. We also find that genes from all functional categories are subject to transfer. However, in interphylum as compared to intraphylum transfers, the proportion of metabolic (operational) gene transfers increases, while the proportion of informational gene transfers decreases. PMID:16899658

  7. Evidence for horizontal transfer of Wolbachia by a Drosophila mite.

    PubMed

    Brown, Amy N; Lloyd, Vett K

    2015-07-01

    Mites are common ectoparasites of Drosophila and have been implicated in bacterial and mobile element invasion of Drosophila stocks. The obligate endobacterium, Wolbachia, has widespread effects on gene expression in their arthropod hosts and alters host reproduction to enhance its survival and propagation, often with deleterious effects in Drosophila hosts. To determine whether Wolbachia could be transferred between Drosophila melanogaster laboratory stocks by the mite Tyrophagus putrescentiae, mites were introduced to Wolbachia-infected Drosophila vials. These vials were kept adjacent to mite-free and Wolbachia-uninfected Drosophila stock vials. The Wolbachia infection statuses of the infected and uninfected flies were checked from generation 1 to 5. Results indicate that Wolbachia DNA could be amplified from mites infesting Wolbachia-infected fly stocks and infection in the previously uninfected stocks arose within generation 1 or 2, concomitant with invasion of mites from the Wolbachia-infected stock. A possible mechanism for the transfer of Wolbachia from flies to mites and vice versa, can be inferred from time-lapse photography of fly and mite interactions. We demonstrated that mites ingest Drosophila corpses, including Wolbachia-infected corpses, and Drosophila larva ingest mites, providing possible sources of Wolbachia infection and transfer. This research demonstrated that T. putrescentiae white mites can facilitate Wolbachia transfer between Drosophila stocks and that this may occur by ingestion of infected corpses. Mite-vectored Wolbachia transfer allows for rapid establishment of Wolbachia infection within a new population. This mode of Wolbachia introduction may be relevant in nature as well as in the laboratory, and could have a variety of biological consequences.

  8. Boiling heat transfer in a small horizontal rectangular channel

    SciTech Connect

    Tran, T.N.; Wambsganss, M.W.; Jendrzejczyk, J.A.; France, D.M.

    1993-08-01

    Compact heat exchangers have traditionally found wide application in the transportation industry, where they are used as evaporators and condensers in vapor compression cycles for air conditioning and refrigeration. Such heat exchangers possess numerous attractive features including high thermal effectiveness, small size, low weight, design flexibility, and pure counterflow, and they can accommodate multiple streams. Today, there is a widespread interest in expanding the range of application of compact heat exchangers to include phase-change heat transfer in the process industries, among others. An overall objective of this effort is to provide the basis for establishing design technology in this area. In the present study, small channel flow boiling heat transfer was extended to a rectangular channel (4.06 {times} 1.70 mm) using refrigerant 12 (R-12). As with the circular tube studies, the flow channel wall was electrically heated providing a constant heat flux. Tests were performed over a quality range of 0.15 to 0.80, and large ranges of mass fluxes (50 to 400 kg/m{sup 2}s) and heat flux (4 to 34 kW/m{sup 2}). Heat transfer was measured and results are compared with correlation predictions.

  9. Horizontal transfer of iturin A operon, itu, to Bacillus subtilis 168 and conversion into an iturin A producer.

    PubMed

    Tsuge, Kenji; Inoue, Satoka; Ano, Takashi; Itaya, Mitsuhiro; Shoda, Makoto

    2005-11-01

    Iturin A and its derivatives are lipopeptide antibiotics produced by Bacillus subtilis and several closely related bacteria. Three iturin group operons (i.e., iturin A, mycosubtilin, and bacillomycin D) of those antibiotic-producing strains have been cloned and sequenced thus far, strongly implying the horizontal transfer of these operons. To examine the nature of such horizontal transfer in terms of antibiotic production, a 42-kb region of the B. subtilis RB14 genome, which contains a complete 38-kb iturin A operon, was transferred via competent cell transformation to the genome of a non-iturin A producer, B. subtilis 168, using a method based on double-crossover homologous recombination with two short landing pad sequences (LPSs) in the genome. The recombinant was positively selected by confirming the elimination of the cI repressor gene, which was localized between the two LPSs and substituted by the transferred segment. The iturin A operon-transferred strain 168 was then converted into an iturin A producer by the introduction of an sfp gene, which encodes 4'-phosphopantetheinyl transferase and is mutated in strain 168. By inserting the pleiotropic regulator degQ, the productivity of iturin A increased sevenfold and was restored to about half that of the donor strain RB14, without the transfer of additional genes, such as regulatory or self-resistance genes.

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

    PubMed Central

    Overballe-Petersen, Søren; Willerslev, Eske

    2014-01-01

    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. PMID:25143190

  11. Statistical Mechanics of Horizontal Gene Transfer in Evolutionary Ecology

    NASA Astrophysics Data System (ADS)

    Chia, Nicholas; Goldenfeld, Nigel

    2011-04-01

    The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living cells communicate genetically through transferred genes, as well as the ways in which they can reorganize their genomes in response to environmental pressure. We discuss how genome evolution can be thought of as related to the physical phenomenon of annealing, and describe the sense in which genomes can be said to exhibit an analogue of information entropy. As a direct application of these ideas, we analyze the variation with ocean depth of transposons in marine microbial genomes, predicting trends that are consistent with recent observations using metagenomic surveys.

  12. Genome-wide experimental determination of barriers to horizontal gene transfer

    SciTech Connect

    Rubin, Edward; Sorek, Rotem; Zhu, Yiwen; Creevey, Christopher J.; Francino, M. Pilar; Bork, Peer; Rubin, Edward M.

    2007-09-24

    Horizontal gene transfer, in which genetic material is transferred from the genome of one organism to another, has been investigated in microbial species mainly through computational sequence analyses. To address the lack of experimental data, we studied the attempted movement of 246,045 genes from 79 prokaryotic genomes into E. coli and identified genes that consistently fail to transfer. We studied the mechanisms underlying transfer inhibition by placing coding regions from different species under the control of inducible promoters. Their toxicity to the host inhibited transfer regardless of the species of origin and our data suggest that increased gene dosage and associated increased expression is a predominant cause for transfer failure. While these experimental studies examined transfer solely into E. coli, a computational analysis of gene transfer rates across available bacterial and archaeal genomes indicates that the barriers observed in our study are general across the tree of life.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  14. Horizontal transfer of methoprene by Tribolium castaneum (Herbst) and T. confusum Jacquelin du Val

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In food facilities the majority of insect populations typically occur within hidden locations with limited direct exposure to insecticides, but there is potential for dispersing insects to transport insecticides into hidden areas and transfer insecticide to other individuals (i.e., horizontal transf...

  15. Mechanisms for horizontal transfer of methoprene from treated to untreated Tribolium castaneum (Herbst)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Experiments were performed to determine the relative impact of different mechanisms of horizontal transfer of methoprene by Tribolium castaneum (Herbst), the red flour beetle. Insects exposed to 5 methoprene treated developmental stages (late-stage larvae, pupae, or adults) resulted in 100% mortalit...

  16. Evolution of Acetoclastic Methanogenesis in Methanosarcina via Horizontal Gene Transfer from Cellulolytic Clostridia▿ †

    PubMed Central

    Fournier, Gregory P.; Gogarten, J. Peter

    2008-01-01

    Phylogenetic analysis confirmed that two genes required for acetoclastic methanogenesis, ackA and pta, were horizontally transferred to the ancestor of Methanosarcina from a derived cellulolytic organism in the class Clostridia. This event likely occurred within the last 475 million years, causing profound changes in planetary methane biogeochemistry. PMID:18055595

  17. Horizontal Gene Transfer among Bacteria and Its Role in Biological Evolution

    PubMed Central

    Arber, Werner

    2014-01-01

    This is a contribution to the history of scientific advance in the past 70 years concerning the identification of genetic information, its molecular structure, the identification of its functions and the molecular mechanisms of its evolution. Particular attention is thereby given to horizontal gene transfer among microorganisms, as well as to biosafety considerations with regard to beneficial applications of acquired scientific knowledge. PMID:25370194

  18. Horizontal transfer of a non-autonomous Helitron among insect and viral genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The movement of genetic material among species by horizontal transfer (HT) influences genome evolution through the modification of structure and function. Helitrons are a relatively new lineage of DNA-based (class II) transposable elements (TEs) that propagate by rolling-circle replication and are ...

  19. Horizontally transferred genes in the genome of Pacific white shrimp, Litopenaeus vannamei

    PubMed Central

    2013-01-01

    Background In recent years, as the development of next-generation sequencing technology, a growing number of genes have been reported as being horizontally transferred from prokaryotes to eukaryotes, most of them involving arthropods. As a member of the phylum Arthropoda, the Pacific white shrimp Litopenaeus vannamei has to adapt to the complex water environments with various symbiotic or parasitic microorganisms, which provide a platform for horizontal gene transfer (HGT). Results In this study, we analyzed the genome-wide HGT events in L. vannamei. Through homology search and phylogenetic analysis, followed by experimental PCR confirmation, 14 genes with HGT event were identified: 12 of them were transferred from bacteria and two from fungi. Structure analysis of these genes showed that the introns of the two fungi-originated genes were substituted by shrimp DNA fragment, two genes transferred from bacteria had shrimp specific introns inserted in them. Furthermore, around other three bacteria-originated genes, there were three large DNA segments inserted into the shrimp genome. One segment was a transposon that fully transferred, and the other two segments contained only coding regions of bacteria. Functional prediction of these 14 genes showed that 6 of them might be related to energy metabolism, and 4 others related to defense of the organism. Conclusions HGT events from bacteria or fungi were happened in the genome of L. vannamei, and these horizontally transferred genes can be transcribed in shrimp. This is the first time to report the existence of horizontally transferred genes in shrimp. Importantly, most of these genes are exposed to a negative selection pressure and appeared to be functional. PMID:23914989

  20. Investigation of horizontal gene transfer in poplar/Amanita muscaria ectomycorrhizas.

    PubMed

    Zhang, Chi; Hampp, Rüdiger; Nehls, Uwe

    2005-01-01

    Fine roots of forest trees form together with certain soil fungi symbiotic structures (ectomycorrhizas), where fungal hyphae are in intimate contact with plant cells. Due to root cell degeneration, plant DNA is released and could be taken up by the fungus. The possibility that horizontal gene transfer might result in a risk for the environment should be evaluated before a massive release of genetically engineered trees into nature occurs, even though only a few convincing examples of horizontal gene transfer are known. Transgenic poplars containing a construct of the Streptomyces hygroscopicus bar gene under the control of the Cochliobolus heterostrophus GPD (glyceraldehyde-3-phosphate dehydrogenase) promoter were generated by Agrobacterium-mediated transformation. The functionality of this construct in the ectomycorrhizal model fungus Amanita muscaria was previously verified by protoplast-based fungal transformation. 35,000 ectomycorrhizas, formed between transgenic poplars and non-transgenic A. muscaria hyphae, were isolated and transferred to selective agar plates. Putative herbicide-resistant fungal colonies were obtained after the first round of selection. However, none of these colonies survived a transfer onto fresh selection medium, nor did they contain the bar gene, indicating that no horizontal gene transfer from poplar to A. muscaria occurred during symbiosis under axenic conditions. However, since ectomycorrhizas are associated under natural conditions with viruses, bacteria and other fungi, these additional associations should be evaluated in future.

  1. Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen.

    PubMed

    Dhillon, Braham; Feau, Nicolas; Aerts, Andrea L; Beauseigle, Stéphanie; Bernier, Louis; Copeland, Alex; Foster, Adam; Gill, Navdeep; Henrissat, Bernard; Herath, Padmini; LaButti, Kurt M; Levasseur, Anthony; Lindquist, Erika A; Majoor, Eline; Ohm, Robin A; Pangilinan, Jasmyn L; Pribowo, Amadeus; Saddler, John N; Sakalidis, Monique L; de Vries, Ronald P; Grigoriev, Igor V; Goodwin, Stephen B; Tanguay, Philippe; Hamelin, Richard C

    2015-03-17

    Some of the most damaging tree pathogens can attack woody stems, causing lesions (cankers) that may be lethal. To identify the genomic determinants of wood colonization leading to canker formation, we sequenced the genomes of the poplar canker pathogen, Mycosphaerella populorum, and the closely related poplar leaf pathogen, M. populicola. A secondary metabolite cluster unique to M. populorum is fully activated following induction by poplar wood and leaves. In addition, genes encoding hemicellulose-degrading enzymes, peptidases, and metabolite transporters were more abundant and were up-regulated in M. populorum growing on poplar wood-chip medium compared with M. populicola. The secondary gene cluster and several of the carbohydrate degradation genes have the signature of horizontal transfer from ascomycete fungi associated with wood decay and from prokaryotes. Acquisition and maintenance of the gene battery necessary for growth in woody tissues and gene dosage resulting in gene expression reconfiguration appear to be responsible for the adaptation of M. populorum to infect, colonize, and cause mortality on poplar woody stems.

  2. Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen

    PubMed Central

    Dhillon, Braham; Feau, Nicolas; Aerts, Andrea L.; Beauseigle, Stéphanie; Bernier, Louis; Copeland, Alex; Foster, Adam; Gill, Navdeep; Henrissat, Bernard; Herath, Padmini; LaButti, Kurt M.; Levasseur, Anthony; Lindquist, Erika A.; Majoor, Eline; Ohm, Robin A.; Pangilinan, Jasmyn L.; Pribowo, Amadeus; Saddler, John N.; Sakalidis, Monique L.; de Vries, Ronald P.; Grigoriev, Igor V.; Goodwin, Stephen B.; Tanguay, Philippe; Hamelin, Richard C.

    2015-01-01

    Some of the most damaging tree pathogens can attack woody stems, causing lesions (cankers) that may be lethal. To identify the genomic determinants of wood colonization leading to canker formation, we sequenced the genomes of the poplar canker pathogen, Mycosphaerella populorum, and the closely related poplar leaf pathogen, M. populicola. A secondary metabolite cluster unique to M. populorum is fully activated following induction by poplar wood and leaves. In addition, genes encoding hemicellulose-degrading enzymes, peptidases, and metabolite transporters were more abundant and were up-regulated in M. populorum growing on poplar wood-chip medium compared with M. populicola. The secondary gene cluster and several of the carbohydrate degradation genes have the signature of horizontal transfer from ascomycete fungi associated with wood decay and from prokaryotes. Acquisition and maintenance of the gene battery necessary for growth in woody tissues and gene dosage resulting in gene expression reconfiguration appear to be responsible for the adaptation of M. populorum to infect, colonize, and cause mortality on poplar woody stems. PMID:25733908

  3. Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis.

    PubMed

    Husnik, Filip; Nikoh, Naruo; Koga, Ryuichi; Ross, Laura; Duncan, Rebecca P; Fujie, Manabu; Tanaka, Makiko; Satoh, Nori; Bachtrog, Doris; Wilson, Alex C C; von Dohlen, Carol D; Fukatsu, Takema; McCutcheon, John P

    2013-06-20

    The smallest reported bacterial genome belongs to Tremblaya princeps, a symbiont of Planococcus citri mealybugs (PCIT). Tremblaya PCIT not only has a 139 kb genome, but possesses its own bacterial endosymbiont, Moranella endobia. Genome and transcriptome sequencing, including genome sequencing from a Tremblaya lineage lacking intracellular bacteria, reveals that the extreme genomic degeneracy of Tremblaya PCIT likely resulted from acquiring Moranella as an endosymbiont. In addition, at least 22 expressed horizontally transferred genes from multiple diverse bacteria to the mealybug genome likely complement missing symbiont genes. However, none of these horizontally transferred genes are from Tremblaya, showing that genome reduction in this symbiont has not been enabled by gene transfer to the host nucleus. Our results thus indicate that the functioning of this three-way symbiosis is dependent on genes from at least six lineages of organisms and reveal a path to intimate endosymbiosis distinct from that followed by organelles.

  4. Measurement of convective heat transfer coefficient for a horizontal cylinder rotating in quiescent air

    SciTech Connect

    Oezerdem, B.

    2000-04-01

    Heat transfer from a rotating cylinder is one of the problems, which is drawing attention due to its wide range of engineering applications. The present paper deals with convective heat transfer from a horizontal cylinder rotating in quiescent air, experimentally. The average convective heat transfer coefficients have been measured by using radiation pyrometer, which offers a new method. According to the experimental results, a correlation in terms of the average Nusselt number and rotating Reynolds number has been established. The average Nusselt number increased with an increase in the rotating speed. Comparison of the results, with previous studies, have been showed a good agreement with each other.

  5. Unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes

    PubMed Central

    Kordis, Dusan; Gubensek, Franc

    1998-01-01

    We have shown previously by Southern blot analysis that Bov-B long interspersed nuclear elements (LINEs) are present in different Viperidae snake species. To address the question as to whether Bov-B LINEs really have been transmitted horizontally between vertebrate classes, the analysis has been extended to a larger number of vertebrate, invertebrate, and plant species. In this paper, the evolutionary origin of Bov-B LINEs is shown unequivocally to be in Squamata. The previously proposed horizontal transfer of Bov-B LINEs in vertebrates has been confirmed by their discontinuous phylogenetic distribution in Squamata (Serpentes and two lizard infra-orders) as well as in Ruminantia, by the high level of nucleotide identity, and by their phylogenetic relationships. The horizontal transfer of Bov-B LINEs from Squamata to the ancestor of Ruminantia is evident from the genetic distances and discontinuous phylogenetic distribution. The ancestor of Colubroidea snakes is a possible donor of Bov-B LINEs to Ruminantia. The timing of horizontal transfer has been estimated from the distribution of Bov-B LINEs in Ruminantia and the fossil data of Ruminantia to be 40–50 My ago. The phylogenetic relationships of Bov-B LINEs from the various Squamata species agrees with that of the species phylogeny, suggesting that Bov-B LINEs have been maintained stably by vertical transmission since the origin of Squamata in the Mesozoic era. PMID:9724768

  6. Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers.

    PubMed

    Grilli, Jacopo; Romano, Mariacristina; Bassetti, Federico; Cosentino Lagomarsino, Marco

    2014-06-01

    Prokaryotes vary their protein repertoire mainly through horizontal transfer and gene loss. To elucidate the links between these processes and the cross-species gene-family statistics, we perform a large-scale data analysis of the cross-species variability of gene-family abundance (the number of members of the family found on a given genome). We find that abundance fluctuations are related to the rate of horizontal transfers. This is rationalized by a minimal theoretical model, which predicts this link. The families that are not captured by the model show abundance profiles that are markedly peaked around a mean value, possibly because of specific abundance selection. Based on these results, we define an abundance variability index that captures a family's evolutionary behavior (and thus some of its relevant functional properties) purely based on its cross-species abundance fluctuations. Analysis and model, combined, show a quantitative link between cross-species family abundance statistics and horizontal transfer dynamics, which can be used to analyze genome 'flux'. Groups of families with different values of the abundance variability index correspond to genome sub-parts having different plasticity in terms of the level of horizontal exchange allowed by natural selection.

  7. A case of horizontal gene transfer from Wolbachia to Aedes albopictus C6/36 cell line

    PubMed Central

    Hou, Qing; He, Ji; Yu, Jing; Ye, Yuting; Zhou, Dan; Sun, Yan; Zhang, Donghui; Ma, Lei; Shen, Bo; Zhu, Changliang

    2014-01-01

    Horizontal gene transfer plays an essential role in evolution and ecological adaptation, yet this phenomenon has remained controversial, particularly where it occurs between prokaryotes and eukaryotes. There are a handful of reported examples of horizontal gene transfer occurring between prokaryotes and eukaryotes in the literature, with most of these documented cases pertaining to invertebrates and endosymbionts. However, the vast majority of these horizontally transferred genes were either eventually excluded or rapidly became nonfunctional in the recipient genome. In this study, we report the discovery of a horizontal gene transfer from the endosymbiont Wolbachia in the C6/36 cell line derived from the mosquito Aedes albopictus. Moreover, we report that this horizontally transferred gene displayed high transcription level. This finding and the results of further experimentation strongly suggest this gene is functional and has been expressed and translated into a protein in the mosquito host cells. PMID:24812591

  8. Horizontal transfers of Tc1 elements between teleost fishes and their vertebrate parasites, lampreys.

    PubMed

    Kuraku, Shigehiro; Qiu, Huan; Meyer, Axel

    2012-01-01

    Horizontal gene transfer (HGT) has been recognized to be an important mechanism that shaped the evolution and genomes of prokaryotes and unicellular eukaryotes. However, HGT is regarded to be exceedingly rare among eukaryotes. We discovered massive transfers of a DNA transposon, a Tc1 element encoding a transposase, between multiple teleost fishes and lampreys that last shared a common ancestor over 500 Ma. Members of this group of Tc1 elements were found to exhibit a mosaic phylogenetic distribution, yet their sequences were highly similar even between distantly related lineages (95%-99% identity). Our molecular phylogenetic analyses suggested that horizontal transfers of this element happened repeatedly, involving multiple teleost fishes that are phylogenetically only distantly related. Interestingly, almost all the affected teleost lineages are also known to be subject to lamprey parasitism, suggesting that the horizontal transfers between vertebrates might have occurred through parasite-host interaction. The genomes of several northern hemisphere lamprey species, including that of the sea lamprey (Petromyzon marinus), were found to contain thousands of copies of the foreign elements. Impact of this event is discussed in relation to other peculiar genomic features of lampreys.

  9. Prediction of condensation heat transfer of low GWP refrigerants inside smooth horizontal tube

    NASA Astrophysics Data System (ADS)

    Hossain, Md. Anowar; Afroz, Hasan M. M.; Talukder, Shaon; Miyara, Akio

    2016-07-01

    The present research work observed the experimental and analytical results of two phase condensation heat transfer of the refrigerants R1234ze(E), R32, R410A, and R1234ze(E)/R32 mixtures inside a smooth horizontal tube. A water heated double tube horizontal heat exchanger with effective length of 3.6m and inner diameter of 4.35mm is used to take place the experiment. Mass flux and the saturation temperature are the design variables under which the experiment is carried out whose values varying from the range 160 to 400 Kg m-2s-1 and 30°C to 45°C, respectively. A new correlation for pure refrigerant has been proposed to predict the heat transfer inside a smooth horizontal tube by investigating the experimental data. The newly proposed correlation and some other existing correlations of condensation heat transfer for pure refrigerant have been used to predict the condensation heat transfer of R1234ze(E), R32, R410A and dimethyl ether (DME) and compared the results. The comparison allows that the proposed model of pure refrigerant offered a better performance for all the refrigerants. All the experimental data can be predicted within a 10.2% mean deviation by using the proposed correlation.

  10. An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers.

    PubMed

    Lin, Xuan; Faridi, Nurul; Casola, Claudio

    2016-05-02

    Comparative genomics analyses empowered by the wealth of sequenced genomes have revealed numerous instances of horizontal DNA transfers between distantly related species. In eukaryotes, repetitive DNA sequences known as transposable elements (TEs) are especially prone to move across species boundaries. Such horizontal transposon transfers, or HTTs, are relatively common within major eukaryotic kingdoms, including animals, plants, and fungi, while rarely occurring across these kingdoms. Here, we describe the first case of HTT from animals to plants, involving TEs known as Penelope-like elements, or PLEs, a group of retrotransposons closely related to eukaryotic telomerases. Using a combination of in situ hybridization on chromosomes, polymerase chain reaction experiments, and computational analyses we show that the predominant PLE lineage, EN(+)PLEs, is highly diversified in loblolly pine and other conifers, but appears to be absent in other gymnosperms. Phylogenetic analyses of both protein and DNA sequences reveal that conifers EN(+)PLEs, or Dryads, form a monophyletic group clustering within a clade of primarily arthropod elements. Additionally, no EN(+)PLEs were detected in 1,928 genome assemblies from 1,029 nonmetazoan and nonconifer genomes from 14 major eukaryotic lineages. These findings indicate that Dryads emerged following an ancient horizontal transfer of EN(+)PLEs from arthropods to a common ancestor of conifers approximately 340 Ma. This represents one of the oldest known interspecific transmissions of TEs, and the most conspicuous case of DNA transfer between animals and plants.

  11. An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers

    PubMed Central

    Lin, Xuan; Faridi, Nurul; Casola, Claudio

    2016-01-01

    Comparative genomics analyses empowered by the wealth of sequenced genomes have revealed numerous instances of horizontal DNA transfers between distantly related species. In eukaryotes, repetitive DNA sequences known as transposable elements (TEs) are especially prone to move across species boundaries. Such horizontal transposon transfers, or HTTs, are relatively common within major eukaryotic kingdoms, including animals, plants, and fungi, while rarely occurring across these kingdoms. Here, we describe the first case of HTT from animals to plants, involving TEs known as Penelope-like elements, or PLEs, a group of retrotransposons closely related to eukaryotic telomerases. Using a combination of in situ hybridization on chromosomes, polymerase chain reaction experiments, and computational analyses we show that the predominant PLE lineage, EN(+)PLEs, is highly diversified in loblolly pine and other conifers, but appears to be absent in other gymnosperms. Phylogenetic analyses of both protein and DNA sequences reveal that conifers EN(+)PLEs, or Dryads, form a monophyletic group clustering within a clade of primarily arthropod elements. Additionally, no EN(+)PLEs were detected in 1,928 genome assemblies from 1,029 nonmetazoan and nonconifer genomes from 14 major eukaryotic lineages. These findings indicate that Dryads emerged following an ancient horizontal transfer of EN(+)PLEs from arthropods to a common ancestor of conifers approximately 340 Ma. This represents one of the oldest known interspecific transmissions of TEs, and the most conspicuous case of DNA transfer between animals and plants. PMID:27190138

  12. Horizontal Gene Transfers from Bacteria to Entamoeba Complex: A Strategy for Dating Events along Species Divergence

    PubMed Central

    Romero, Miguel; Ximenez, Cecilia

    2016-01-01

    Horizontal gene transfer has proved to be relevant in eukaryotic evolution, as it has been found more often than expected and related to adaptation to certain niches. A relatively large list of laterally transferred genes has been proposed and evaluated for the parasite Entamoeba histolytica. The goals of this work were to elucidate the importance of lateral gene transfer along the evolutionary history of some members of the genus Entamoeba, through identifying donor groups and estimating the divergence time of some of these events. In order to estimate the divergence time of some of the horizontal gene transfer events, the dating of some Entamoeba species was necessary, following an indirect dating strategy based on the fossil record of plausible hosts. The divergence between E. histolytica and E. nuttallii probably occurred 5.93 million years ago (Mya); this lineage diverged from E. dispar 9.97 Mya, while the ancestor of the latter separated from E. invadens 68.18 Mya. We estimated times for 22 transferences; the most recent occurred 31.45 Mya and the oldest 253.59 Mya. Indeed, the acquisition of genes through lateral transfer may have triggered a period of adaptive radiation, thus playing a major role in the evolution of the Entamoeba genus. PMID:27239333

  13. Genome-Wide Survey of Gut Fungi (Harpellales) Reveals the First Horizontally Transferred Ubiquitin Gene from a Mosquito Host

    PubMed Central

    Wang, Yan; White, Merlin M.; Kvist, Sebastian; Moncalvo, Jean-Marc

    2016-01-01

    Harpellales, an early-diverging fungal lineage, is associated with the digestive tracts of aquatic arthropod hosts. Concurrent with the production and annotation of the first four Harpellales genomes, we discovered that Zancudomyces culisetae, one of the most widely distributed Harpellales species, encodes an insect-like polyubiquitin chain. Ubiquitin and ubiquitin-like proteins are universally involved in protein degradation and regulation of immune response in eukaryotic organisms. Phylogenetic analyses inferred that this polyubiquitin variant has a mosquito origin. In addition, its amino acid composition, animal-like secondary structure, as well as the fungal nature of flanking genes all further support this as a horizontal gene transfer event. The single-copy polyubiquitin gene from Z. culisetae has lower GC ratio compared with homologs of insect taxa, which implies homogenization of the gene since its putatively ancient transfer. The acquired polyubiquitin gene may have served to improve important functions within Z. culisetae, by perhaps exploiting the insect hosts’ ubiquitin-proteasome systems in the gut environment. Preliminary comparisons among the four Harpellales genomes highlight the reduced genome size of Z. culisetae, which corroborates its distinguishable symbiotic lifestyle. This is the first record of a horizontally transferred ubiquitin gene from disease-bearing insects to the gut-dwelling fungal endobiont and should invite further exploration in an evolutionary context. PMID:27343289

  14. Horizontal Gene Transfer and the Evolution of Bacterial and Archaeal Population Structure

    PubMed Central

    Alm, Eric J.; Hanage, William P.

    2013-01-01

    Many bacterial and archaeal lineages have a history of extensive and ongoing horizontal gene transfer and loss, as evidenced by the large differences in genome content even among otherwise closely related isolates. How ecologically cohesive populations might evolve and be maintained under such conditions of rapid gene turnover has remained controversial. Here we synthesize recent literature demonstrating the importance of habitat and niche in structuring horizontal gene transfer. This leads to a model of ecological speciation via gradual genetic isolation triggered by differential habitat association of nascent populations. Further, we hypothesize that subpopulations can evolve through local gene exchange networks by tapping into a gene pool that is adaptive towards local, continuously changing organismic interactions and is, to a large degree, responsible for the observed rapid gene turnover. Overall, these insights help explain how bacteria and archaea form populations that display both ecological cohesion and high genomic diversity. PMID:23332119

  15. Collective evolution of cyanobacteria and cyanophages mediated by horizontal gene transfer

    NASA Astrophysics Data System (ADS)

    Shih, Hong-Yan; Rogers, Tim; Goldenfeld, Nigel

    We describe a model for how antagonistic predator-prey coevolution can lead to mutualistic adaptation to an environment, as a result of horizontal gene transfer. Our model is a simple description of ecosystems such as marine cyanobacteria and their predator cyanophages, which carry photosynthesis genes. These genes evolve more rapidly in the virosphere than the bacterial pan-genome, and thus the bacterial population could potentially benefit from phage predation. By modeling both the barrier to predation and horizontal gene transfer, we study this balance between individual sacrifice and collective benefits. The outcome is an emergent mutualistic coevolution of improved photosynthesis capability, benefiting both bacteria and phage. This form of multi-level selection can contribute to niche stratification in the cyanobacteria-phage ecosystem. This work is supported in part by a cooperative agreement with NASA, Grant NNA13AA91A/A0018.

  16. Parallel Evolution and Horizontal Gene Transfer of the pst Operon in Firmicutes from Oligotrophic Environments

    PubMed Central

    Moreno-Letelier, Alejandra; Olmedo, Gabriela; Eguiarte, Luis E.; Martinez-Castilla, Leon; Souza, Valeria

    2011-01-01

    The high affinity phosphate transport system (pst) is crucial for phosphate uptake in oligotrophic environments. Cuatro Cienegas Basin (CCB) has extremely low P levels and its endemic Bacillus are closely related to oligotrophic marine Firmicutes. Thus, we expected the pst operon of CCB to share the same evolutionary history and protein similarity to marine Firmicutes. Orthologs of the pst operon were searched in 55 genomes of Firmicutes and 13 outgroups. Phylogenetic reconstructions were performed for the pst operon and 14 concatenated housekeeping genes using maximum likelihood methods. Conserved domains and 3D structures of the phosphate-binding protein (PstS) were also analyzed. The pst operon of Firmicutes shows two highly divergent clades with no correlation to the type of habitat nor a phylogenetic congruence, suggesting horizontal gene transfer. Despite sequence divergence, the PstS protein had a similar 3D structure, which could be due to parallel evolution after horizontal gene transfer events. PMID:21461370

  17. Evidence for Horizontal Gene Transfer as Origin of Putrescine Production in Oenococcus oeni RM83▿

    PubMed Central

    Marcobal, Ángela; de las Rivas, Blanca; Moreno-Arribas, M. Victoria; Muñoz, Rosario

    2006-01-01

    The nucleotide sequence of a 17.2-kb chromosomal DNA fragment containing the odc gene encoding ornithine decarboxylase has been determined in the putrescine producer Oenococcus oeni RM83. This DNA fragment contains 13 open reading frames, including genes coding for five transposases and two phage proteins. This description might represent the first evidence of a horizontal gene transfer event as the origin of a biogenic amine biosynthetic locus. PMID:17056681

  18. How much does horizontal gene transfer affect the phylogenetic tree of bacteria?

    NASA Astrophysics Data System (ADS)

    Tang, Bin; Boisvert, Philippe; Higgs, Paul

    2004-03-01

    Ribosomal RNA sequences are frequently used in bacterial phylogenetics. We have developed RNA-specific phylogenetic methods that take account of the conserved secondary structure of these sequences. Our method uses Monte Carlo simulations to generate a representative sample of evolutionary trees (analogous to an equilibrium ensemble in physics). It is known that horizontal transfer of genes can occur between bacterial species, although the frequency and implications of this are not fully understood. If horizontal transfer were frequent, there would be no consistent evolutionary tree for bacteria. We compared trees for 16S rRNA, 23S rRNA and tRNA genes from Proteobacteria (a diverse group for which many complete genome sequences are available). The gene trees are consistent with one another in most respects. Minor differences can almost all be attributed to uncertainties and unreliabilities in the phylogenetic method. We therefore conclude that these genes all give a coherent picture of the phylogeny of the organisms, and that horizontal transfer of these genes is too rare to obscure the signal of the organismal tree.

  19. Evidence for horizontal transfer of mitochondrial DNA to the plastid genome in a bamboo genus.

    PubMed

    Ma, Peng-Fei; Zhang, Yu-Xiao; Guo, Zhen-Hua; Li, De-Zhu

    2015-06-23

    In flowering plants, three genomes (nuclear, mitochondrial, and plastid) coexist and intracellular horizontal transfer of DNA is prevalent, especially from the plastid to the mitochondrion genome. However, the plastid genomes are generally conserved in evolution and have long been considered immune to foreign DNA. Recently, the opposite direction of DNA transfer from the mitochondrial to the plastid genome has been reported in two eudicot lineages. Here we sequenced 6 plastid genomes of bamboos, three of which are neotropical woody species and three are herbaceous ones. Several unusual features were found, including the duplication of trnT-GGU and loss of one copy of rps19 due to contraction of inverted repeats (IRs). The most intriguing was the ~2.7 kb insertion in the plastid IR regions in the three herbaceous bamboos. Furthermore, the insertion was documented to be horizontally transferred from the mitochondrial to the plastid genome. Our study provided evidence of the mitochondrial-to-plastid DNA transfer in the monocots, demonstrating again that this rare event does occur in other angiosperm lineages. However, the mechanism underlying the transfer remains obscure, and more studies in other plants may elucidate it in the future.

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

    PubMed Central

    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

  1. Evidence for horizontal transfer of mitochondrial DNA to the plastid genome in a bamboo genus

    PubMed Central

    Ma, Peng-Fei; Zhang, Yu-Xiao; Guo, Zhen-Hua; Li, De-Zhu

    2015-01-01

    In flowering plants, three genomes (nuclear, mitochondrial, and plastid) coexist and intracellular horizontal transfer of DNA is prevalent, especially from the plastid to the mitochondrion genome. However, the plastid genomes are generally conserved in evolution and have long been considered immune to foreign DNA. Recently, the opposite direction of DNA transfer from the mitochondrial to the plastid genome has been reported in two eudicot lineages. Here we sequenced 6 plastid genomes of bamboos, three of which are neotropical woody species and three are herbaceous ones. Several unusual features were found, including the duplication of trnT-GGU and loss of one copy of rps19 due to contraction of inverted repeats (IRs). The most intriguing was the ~2.7 kb insertion in the plastid IR regions in the three herbaceous bamboos. Furthermore, the insertion was documented to be horizontally transferred from the mitochondrial to the plastid genome. Our study provided evidence of the mitochondrial-to-plastid DNA transfer in the monocots, demonstrating again that this rare event does occur in other angiosperm lineages. However, the mechanism underlying the transfer remains obscure, and more studies in other plants may elucidate it in the future. PMID:26100509

  2. Horizontal transfer of bait in the German cockroach: indoxacarb causes secondary and tertiary mortality.

    PubMed

    Buczkowski, Grzegorz; Scherer, Clay W; Bennett, Gary W

    2008-06-01

    Horizontal transfer of indoxacarb in the German cockroach, Blattella germanica (L.), was examined under laboratory conditions. Results show that a single bait-fed adult cockroach (i.e., the donor) transferred indoxacarb to numerous primary recipients (secondary mortality),which then became secondary donors. These recipients subsequently became donors to other cockroaches and caused significant mortality in other members of the aggregation, resulting in tertiary kill. Indoxacarb was effectively transferred among adult cockroaches and resulted in significant secondary mortality. When adult males served as donors and vectored the insecticide to adult males, the donor:recipient ratio affected the mortality of the recipients and the rate of secondary mortality increased with increasing the ratio of donors to recipients. Furthermore, secondary mortality in the untreated cockroaches was significantly affected by the freshness of excretions from the donors, the presence of alternative food, and the duration of contact between the donors and the recipients. Ingested indoxacarb was most effectively translocated when the recipients interacted with freshly symptomatic donors in the absence of alternative food. The transfer of indoxacarb continued beyond secondary mortality and resulted in significant tertiary mortality. Excretions from a single bait-fed adult killed 38/50 (76%) nymphs within 72 h. The dead nymphs then vectored indoxacarb to 20 adult males and killed 16/20 (81%) recipients within 72 h. Behavioral mechanisms involved in the horizontal transfer of indoxacarb may include: contact with excretions, necrophagy, emetophagy, and ingestion of other excretions that originate from the donors.

  3. Radiative and free-convective heat transfer from a finite horizontal plate inside an enclosure

    NASA Technical Reports Server (NTRS)

    Hrycak, Peter; Sandman, D. J.

    1986-01-01

    An experimental and analytical investigation of heat transfer from a horizontal, thin, square plate inside of an enclosure was carried out. Experimental results were obtained from both the upward-facing and the downward-facing sides of the heated plate. Starting with the integrated momentum and energy equations, approximate solutions were obtained for heat transfer in the laminar and the turbulent regime that correlate well with experimental data. Radiative heat transfer correction was given special attention. Effects of the enclosure-related recirculation of the test fluid, as well as effects of simultaneous heat transfer on both sides of the plate, caused an early transition, and indicated a high level of internal turbulence.

  4. Bacteriophage WO Can Mediate Horizontal Gene Transfer in Endosymbiotic Wolbachia Genomes

    PubMed Central

    Wang, Guan H.; Sun, Bao F.; Xiong, Tuan L.; Wang, Yan K.; Murfin, Kristen E.; Xiao, Jin H.; Huang, Da W.

    2016-01-01

    Phage-mediated horizontal gene transfer (HGT) is common in free-living bacteria, and many transferred genes can play a significant role in their new bacterial hosts. However, there are few reports concerning phage-mediated HGT in endosymbionts (obligate intracellular bacteria within animal or plant hosts), such as Wolbachia. The Wolbachia-infecting temperate phage WO can actively shift among Wolbachia genomes and has the potential to mediate HGT between Wolbachia strains. In the present study, we extend previous findings by validating that the phage WO can mediate transfer of non-phage genes. To do so, we utilized bioinformatic, phylogenetic, and molecular analyses based on all sequenced Wolbachia and phage WO genomes. Our results show that the phage WO can mediate HGT between Wolbachia strains, regardless of whether the transferred genes originate from Wolbachia or other unrelated bacteria. PMID:27965627

  5. Horizontal Gene Transfer of Pectinases from Bacteria Preceded the Diversification of Stick and Leaf Insects

    PubMed Central

    Shelomi, Matan; Danchin, Etienne G. J.; Heckel, David; Wipfler, Benjamin; Bradler, Sven; Zhou, Xin; Pauchet, Yannick

    2016-01-01

    Genes acquired by horizontal transfer are increasingly being found in animal genomes. Understanding their origin and evolution requires knowledge about the phylogenetic relationships from both source and recipient organisms. We used RNASeq data and respective assembled transcript libraries to trace the evolutionary history of polygalacturonase (pectinase) genes in stick insects (Phasmatodea). By mapping the distribution of pectinase genes on a Polyneoptera phylogeny, we identified the transfer of pectinase genes from known phasmatodean gut microbes into the genome of an early euphasmatodean ancestor that took place between 60 and 100 million years ago. This transfer preceded the rapid diversification of the suborder, enabling symbiont-free pectinase production that would increase the insects’ digestive efficiency and reduce dependence on microbes. Bacteria-to-insect gene transfer was thought to be uncommon, however the increasing availability of large-scale genomic data may change this prevailing notion. PMID:27210832

  6. Saturated pool-boiling heat transfer of toluene-solvent magnetic fluid on a horizontal surface

    SciTech Connect

    Takahashi, Minoru; Inoue, Akiro; Matsuzaki, Mitsuo; Ohkawa, Riichiro . Research Lab. for Nuclear Reactors)

    1994-07-01

    Saturated pool-boiling heat transfer of a toluene-solvent magnetic fluid containing magnetite particles of 0--36.5 wt% was investigated on a horizontal surface in a vertical magnetic field at pressures of 0.021--0.061 MPa. In the absence of a magnetic field gradient, the heat transfer was enhanced significantly using a magnetic fluid with dilute magnetite particles, while it was reduced for the case of dense particles. As the magnetic field gradient was increased up to 3.9 [times] 10[sup 5] A/m[sup 2], the heat transfer of the dense magnetic fluid was enhanced significantly in the heat flux region, although it slowly began to show a reduced heat-transfer curve again at a certain transition heat flux. The transition heat flux increased as the magnetic field gradient became larger, the magnetic concentration, lower, and the pressure, higher.

  7. Numerical investigation of supercritical LNG convective heat transfer in a horizontal serpentine tube

    NASA Astrophysics Data System (ADS)

    Han, Chang-Liang; Ren, Jing-Jie; Dong, Wen-Ping; Bi, Ming-Shu

    2016-09-01

    The submerged combustion vaporizer (SCV) is indispensable general equipment for liquefied natural gas (LNG) receiving terminals. In this paper, numerical simulation was conducted to get insight into the flow and heat transfer characteristics of supercritical LNG on the tube-side of SCV. The SST model with enhanced wall treatment method was utilized to handle the coupled wall-to-LNG heat transfer. The thermal-physical properties of LNG under supercritical pressure were used for this study. After the validation of model and method, the effects of mass flux, outer wall temperature and inlet pressure on the heat transfer behaviors were discussed in detail. Then the non-uniformity heat transfer mechanism of supercritical LNG and effect of natural convection due to buoyancy change in the tube was discussed based on the numerical results. Moreover, different flow and heat transfer characteristics inside the bend tube sections were also analyzed. The obtained numerical results showed that the local surface heat transfer coefficient attained its peak value when the bulk LNG temperature approached the so-called pseudo-critical temperature. Higher mass flux could eliminate the heat transfer deteriorations due to the increase of turbulent diffusion. An increase of outer wall temperature had a significant influence on diminishing heat transfer ability of LNG. The maximum surface heat transfer coefficient strongly depended on inlet pressure. Bend tube sections could enhance the heat transfer due to secondary flow phenomenon. Furthermore, based on the current simulation results, a new dimensionless, semi-theoretical empirical correlation was developed for supercritical LNG convective heat transfer in a horizontal serpentine tube. The paper provided the mechanism of heat transfer for the design of high-efficiency SCV.

  8. Lines of evidence for horizontal gene transfer of a phenazine producing operon into multiple bacterial species.

    PubMed

    Fitzpatrick, David A

    2009-02-01

    Phenazines are secondary metabolites with broad-spectrum antibiotic activity against bacteria, fungi, and eukaryotes. In pseudomonad species, a conserved seven-gene phenazine operon (phzABCDEFG) is required for the conversion of chorismic acid to the broad-spectrum antibiotic phenazine-1-carboxylate. Previous analyses of genes involved in phenazine production from nonpseudomonad species uncovered a high degree of sequence similarity to pseudomonad homologues. The analyses undertaken in this study wished to eluciadate the evolutionary history of genes involved in the production of phenazines. Furthermore, I wanted to determine if the phenazine operon has been transferred through horizontal gene transfer. Analyses of GC content, codon usage patterns, frequency of 3:1 dinucleotides, sequence similarities, and phylogenetic reconstructions were undertaken to map the evolutionary history of phenazine genes from multiple bacterial species. Patchy phyletic distribution, high sequence similarities, and phylogenetic evidence infer that pseudomonad, Streptomyces cinnamonensis, Pantoea agglomerans, Burkholderia cepacia, Pectobacterium atrosepticum, Brevibacterium linens, and Mycobacterium abscessus species all contain a phenazine operon which has most likely been transferred among these species through horizontal gene transfer. The acquisition of an antibiotic-associated operon is significant, as it may increase the relative fitness of the recipient species.

  9. Natural convection heat transfer from a horizontal wavy surface in a porous enclosure

    SciTech Connect

    Murthy, P.V.S.N.; Kumar, B.V.R.; Singh, P.

    1997-02-07

    The effect of surface undulations on the natural convection heat transfer from an isothermal surface in a Darcian fluid-saturated porous enclosure has been numerically analyzed using the finite element method on a graded nonuniform mesh system. The flow-driving Rayleigh number Ra together with the geometrical parameters of wave amplitude a, wave phase {phi}, and the number of waves N considered in the horizontal dimension of the cavity are found to influence the flow and heat transfer process in the enclosure. For Ra around 50 and above, the phenomenon of flow separation and reattachment is noticed on the walls of the enclosure. A periodic shift in the reattachment point from the bottom wall to the adjacent walls in the clockwise direction, leading to the manifestation of cycles of unicellular and bicellular clockwise and counterclockwise flows, is observed, with the phase varying between 0{degree} and 350{degree}. The counterflow in the secondary circulation zone is intensified with the increase in the value of Ra. The counterflow on the wavy wall hinders the heat transfer into the system. An increase in either wave amplitude or the number of waves considered per unit length decreases the global heat flux into the system. Only marginal changes in global heat flux are noticed with increasing Ra. On the whole, the comparison of global heat flux results in the wavy wall case with those of the horizontal flat wall case shows that, in a porous enclosure, the wavy wall reduces the heat transfer into the system.

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

    PubMed Central

    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

  11. Horizontal transfer of fipronil is enhanced with increased group size in Coptotermes formosanus (Isoptera: Rhinotermitidae).

    PubMed

    Wang, Cai; Henderson, Gregg; Chen, Xuan; Gautam, Bal K

    2013-12-01

    Fipronil is a widely used insecticide for termite control. Although transfer of fipronil among termite cohorts has been investigated in previous studies, no study has yet focused on the influence of termite group size (density) on horizontal transfer. In this study, the mortality of donor and recipient Coptotermes formosanus Shiraki (Isoptera: Rhinotermitidae) was compared among groups of 10, 25, and 50 workers. Most donor termites were dead within 20 h. There was a significantly higher mortality of recipient termites starting at 44 h when in bigger groups. LT50 and LT90 of recipient termites decreased with increase in group size, being significantly shorter in groups of 50 termites compared with groups of 10 termites. Moreover, the variance (within-group difference) of recipient mortality and lethal time estimations was lowest in the groups of 50 termites, indicating a more uniform horizontal transfer of fipronil by termites in bigger groups. Our findings suggest that group size has an influence on fipronil transfer among C. formosanus workers and should be considered as a variable of importance.

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

    PubMed

    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.

  13. Recurrent Horizontal Transfers of Chapaev Transposons in Diverse Invertebrate and Vertebrate Animals

    PubMed Central

    Zhang, Hua-Hao; Feschotte, Cédric; Han, Min-Jin; Zhang, Ze

    2014-01-01

    Horizontal transfer (HT) of a transposable element (TE) into a new genome is regarded as an important force to drive genome variation and biological innovation. In addition, HT also plays an important role in the persistence of TEs in eukaryotic genomes. Here, we provide the first documented example for the repeated HT of three families of Chapaev transposons in a wide range of animal species, including mammals, reptiles, jawed fishes, lampreys, insects, and in an insect bracovirus. Multiple alignments of the Chapaev transposons identified in these species revealed extremely high levels of nucleotide sequence identity (79–99%), which are inconsistent with vertical evolution given the deep divergence time separating these host species. Rather, the discontinuous distribution amongst species and lack of purifying selection acting on these transposons strongly suggest that they were independently and horizontally transferred into these species lineages. The detection of Chapaev transposons in an insect bracovirus indicated that these viruses might act as a possible vector for the horizontal spread of Chapaev transposons. One of the Chapaev families was also shared by lampreys and some of their common hosts (such as sturgeon and paddlefish), which suggested that parasite–host interaction might facilitate HTs. PMID:24868016

  14. Recurrent horizontal transfers of Chapaev transposons in diverse invertebrate and vertebrate animals.

    PubMed

    Zhang, Hua-Hao; Feschotte, Cédric; Han, Min-Jin; Zhang, Ze

    2014-05-27

    Horizontal transfer (HT) of a transposable element (TE) into a new genome is regarded as an important force to drive genome variation and biological innovation. In addition, HT also plays an important role in the persistence of TEs in eukaryotic genomes. Here, we provide the first documented example for the repeated HT of three families of Chapaev transposons in a wide range of animal species, including mammals, reptiles, jawed fishes, lampreys, insects, and in an insect bracovirus. Multiple alignments of the Chapaev transposons identified in these species revealed extremely high levels of nucleotide sequence identity (79-99%), which are inconsistent with vertical evolution given the deep divergence time separating these host species. Rather, the discontinuous distribution amongst species and lack of purifying selection acting on these transposons strongly suggest that they were independently and horizontally transferred into these species lineages. The detection of Chapaev transposons in an insect bracovirus indicated that these viruses might act as a possible vector for the horizontal spread of Chapaev transposons. One of the Chapaev families was also shared by lampreys and some of their common hosts (such as sturgeon and paddlefish), which suggested that parasite-host interaction might facilitate HTs.

  15. A horizontally transferred nuclear gene is associated with microhabitat variation in a natural plant population

    PubMed Central

    Tunlid, Anders; Ghatnekar, Lena

    2015-01-01

    Horizontal gene transfer involves the non-sexual interspecific transmission of genetic material. Even if they are initially functional, horizontally transferred genes are expected to deteriorate into non-expressed pseudogenes, unless they become adaptively relevant in the recipient organism. However, little is known about the distributions of natural transgenes within wild species or the adaptive significance of natural transgenes within wild populations. Here, we examine the distribution of a natural plant-to-plant nuclear transgene in relation to environmental variation within a wild population. Festuca ovina is polymorphic for an extra (second) expressed copy of the nuclear gene (PgiC) encoding cytosolic phosphoglucose isomerase, with the extra PgiC locus having been acquired horizontally from the distantly related grass genus Poa. We investigated variation at PgiC in samples of F. ovina from a fine-scale, repeating patchwork of grassland microhabitats, replicated within spatially separated sites. Even after accounting for spatial effects, the distributions of F. ovina individuals carrying the additional PgiC locus, and one of the enzyme products encoded by the locus, are significantly associated with fine-scale habitat variation. Our results suggest that the PgiC transgene contributes, together with the unlinked ‘native’ PgiC locus, to local adaptation to a fine-scale mosaic of edaphic and biotic grassland microhabitats. PMID:26674953

  16. Evaporation heat transfer of carbon dioxide at low temperature inside a horizontal smooth tube

    NASA Astrophysics Data System (ADS)

    Yoon, Jung-In; Son, Chang-Hyo; Jung, Suk-Ho; Jeon, Min-Ju; Yang, Dong-Il

    2016-10-01

    In this paper, the evaporation heat transfer coefficient of carbon dioxide at low temperature of -30 to -20 °C in a horizontal smooth tube was investigated experimentally. The test devices consist of mass flowmeter, pre-heater, magnetic gear pump, test section (evaporator), condenser and liquid receiver. Test section is made of cooper tube. Inner and outer diameter of the test section is 8 and 9.52 mm, respectively. The experiment is conducted at mass fluxes from 100 to 300 kg/m2 s, saturation temperature from -30 to -20 °C. The main results are summarized as follows: In case that the mass flux of carbon dioxide is 100 kg/m2 s, the evaporation heat transfer coefficient is almost constant regardless of vapor quality. In case of 200 and 300 kg/m2 s, the evaporation heat transfer coefficient increases steadily with increasing vapor quality. For the same mass flux, the evaporation heat transfer coefficient increases as the evaporation temperature of the refrigerant decreases. In comparison of heat transfer correlations with the experimental result, the evaporation heat transfer correlations do not predict them exactly. Therefore, more accurate heat transfer correlation than the previous one is required.

  17. The effect of magnetic field on nanofluids heat transfer through a uniformly heated horizontal tube

    NASA Astrophysics Data System (ADS)

    Hatami, N.; Kazemnejad Banari, A.; Malekzadeh, A.; Pouranfard, A. R.

    2017-02-01

    In this study, the effects of magnetic field on forced convection heat transfer of Fe3O4-water nanofluid with laminar flow regime in a horizontal pipe under constant heat flux conditions were studied, experimentally. The convective heat transfer of magnetic fluid flow inside the heated pipe with uniform magnetic field was measured. Fe3O4 nanoparticles with diameters less than 100 nm dispersed in water with various volume concentrations are used as the test fluid. The effect of the external magnetic field (Ha = 33.4 ×10-4 to 136.6 ×10-4) and nanoparticle concentrations (φ = 0, 0.1, 0.5, 1%) on heat transfer characteristics were investigated. Results showed that by the presence of a magnetic field, increase in nanoparticle concentration caused reduction of convection heat transfer coefficient. In this condition, heat transfer decreased up to 25%. Where, in the absence of an external magnetic field, adding magnetic nanoparticles increased convection heat transfer more than 60%. It was observed that the Nusselt number decreased by increasing the Hartmann number at a specified concentration of magnetic nanofluids, that reduction about 25% in heat transfer rate could be found.

  18. Ribonucleotide reduction - horizontal transfer of a required function spans all three domains

    PubMed Central

    2010-01-01

    Background Ribonucleotide reduction is the only de novo pathway for synthesis of deoxyribonucleotides, the building blocks of DNA. The reaction is catalysed by ribonucleotide reductases (RNRs), an ancient enzyme family comprised of three classes. Each class has distinct operational constraints, and are broadly distributed across organisms from all three domains, though few class I RNRs have been identified in archaeal genomes, and classes II and III likewise appear rare across eukaryotes. In this study, we examine whether this distribution is best explained by presence of all three classes in the Last Universal Common Ancestor (LUCA), or by horizontal gene transfer (HGT) of RNR genes. We also examine to what extent environmental factors may have impacted the distribution of RNR classes. Results Our phylogenies show that the Last Eukaryotic Common Ancestor (LECA) possessed a class I RNR, but that the eukaryotic class I enzymes are not directly descended from class I RNRs in Archaea. Instead, our results indicate that archaeal class I RNR genes have been independently transferred from bacteria on two occasions. While LECA possessed a class I RNR, our trees indicate that this is ultimately bacterial in origin. We also find convincing evidence that eukaryotic class I RNR has been transferred to the Bacteroidetes, providing a stunning example of HGT from eukaryotes back to Bacteria. Based on our phylogenies and available genetic and genomic evidence, class II and III RNRs in eukaryotes also appear to have been transferred from Bacteria, with subsequent within-domain transfer between distantly-related eukaryotes. Under the three-domains hypothesis the RNR present in the last common ancestor of Archaea and eukaryotes appears, through a process of elimination, to have been a dimeric class II RNR, though limited sampling of eukaryotes precludes a firm conclusion as the data may be equally well accounted for by HGT. Conclusions Horizontal gene transfer has clearly played an

  19. Horizontal transfer of archaeal genes into the deinococcaceae: detection by molecular and computer-based approaches

    NASA Technical Reports Server (NTRS)

    Olendzenski, L.; Liu, L.; Zhaxybayeva, O.; Murphey, R.; Shin, D. G.; Gogarten, J. P.

    2000-01-01

    Members of the Deinococcaceae (e.g., Thermus, Meiothermus, Deinococcus) contain A/V-ATPases typically found in Archaea or Eukaryotes which were probably acquired by horizontal gene transfer. Two methods were used to quantify the extent to which archaeal or eukaryotic genes have been acquired by this lineage. Screening of a Meiothermus ruber library with probes made against Thermoplasma acidophilum DNA yielded a number of clones which hybridized more strongly than background. One of these contained the prolyl tRNA synthetase (RS) gene. Phylogenetic analysis shows the M. ruber and D. radiodurans prolyl RS to be more closely related to archaeal and eukaryal forms of this gene than to the typical bacterial type. Using a bioinformatics approach, putative open reading frames (ORFs) from the prerelease version of the D. radiodurans genome were screened for genes more closely related to archaeal or eukaryotic genes. Putative ORFs were searched against representative genomes from each of the three domains using automated BLAST. ORFs showing the highest matches against archaeal and eukaryotic genes were collected and ranked. Among the top-ranked hits were the A/V-ATPase catalytic and noncatalytic subunits and the prolyl RS genes. Using phylogenetic methods, ORFs were analyzed and trees assessed for evidence of horizontal gene transfer. Of the 45 genes examined, 20 showed topologies in which D. radiodurans homologues clearly group with eukaryotic or archaeal homologues, and 17 additional trees were found to show probable evidence of horizontal gene transfer. Compared to the total number of ORFs in the genome, those that can be identified as having been acquired from Archaea or Eukaryotes are relatively few (approximately 1%), suggesting that interdomain transfer is rare.

  20. Measurements of mixed convective heat transfer to low temperature helium in a horizontal channel

    NASA Technical Reports Server (NTRS)

    Yeroshenko, V. M.; Kuznetsov, Y. V.; Shevchenko, O. A.; Hendricks, R. C.; Daney, D. E.

    1979-01-01

    A horizontal 2.85 m long, 19 mm i.d. stainless steel heated circular channel was employed to measure coefficients of heat transfer to low temperature helium flow. Experimental parameters range from 6.5 to 15 K, from 0.12 to 0.3 MPa at heat fluxes up to 1000 W/m square and Reynolds numbers from 9,000 to 20,000. A significantly nonuniform distribution of heat transfer coefficients over the tube periphery is observed. Difference between temperatures on the upper and lower surfaces of the stainless steel channel wall was found to reach 9 K. It was noted that the highest temperature on the wall outer surface is displaced from its uppermost point. Measurements of local flow temperatures revealed vortical structure of the flow. The displacement of the point with the highest temperature is attributable to the effect of vortices. The relationships for calculating local and averaged coefficients of heat transfer are proposed.

  1. Numerical Study on the Heat Transfer of Carbon Dioxide in Horizontal Straight Tubes under Supercritical Pressure

    PubMed Central

    Yang, Mei

    2016-01-01

    Cooling heat transfer of supercritical CO2 in horizontal straight tubes with wall is numerically investigated by using FLUENT. The results show that almost all models are able to present the trend of heat transfer qualitatively, and the stand k−ε with enhanced wall treatment model shows the best agreement with the experimental data, followed by LB low Re turbulence model. Then further studies are discussed on velocity, temperature and turbulence distributions. The parameters which are defined as the criterion of buoyancy effect on convection heat transfer are introduced to judge the condition of the fluid. The relationships among the inlet temperature, outlet temperature, the mass flow rate, the heat flux and the diameter are discussed and the difference between the cooling and heating of CO2 are compared. PMID:27458729

  2. Multiple recent horizontal transfers of a large genomic region in cheese making fungi.

    PubMed

    Cheeseman, Kevin; Ropars, Jeanne; Renault, Pierre; Dupont, Joëlle; Gouzy, Jérôme; Branca, Antoine; Abraham, Anne-Laure; Ceppi, Maurizio; Conseiller, Emmanuel; Debuchy, Robert; Malagnac, Fabienne; Goarin, Anne; Silar, Philippe; Lacoste, Sandrine; Sallet, Erika; Bensimon, Aaron; Giraud, Tatiana; Brygoo, Yves

    2014-01-01

    While the extent and impact of horizontal transfers in prokaryotes are widely acknowledged, their importance to the eukaryotic kingdom is unclear and thought by many to be anecdotal. Here we report multiple recent transfers of a huge genomic island between Penicillium spp. found in the food environment. Sequencing of the two leading filamentous fungi used in cheese making, P. roqueforti and P. camemberti, and comparison with the penicillin producer P. rubens reveals a 575 kb long genomic island in P. roqueforti--called Wallaby--present as identical fragments at non-homologous loci in P. camemberti and P. rubens. Wallaby is detected in Penicillium collections exclusively in strains from food environments. Wallaby encompasses about 250 predicted genes, some of which are probably involved in competition with microorganisms. The occurrence of multiple recent eukaryotic transfers in the food environment provides strong evidence for the importance of this understudied and probably underestimated phenomenon in eukaryotes.

  3. Foreign Plastid Sequences in Plant Mitochondria are Frequently Acquired Via Mitochondrion-to-Mitochondrion Horizontal Transfer

    PubMed Central

    Gandini, C. L.; Sanchez-Puerta, M. V.

    2017-01-01

    Angiosperm mitochondrial genomes (mtDNA) exhibit variable quantities of alien sequences. Many of these sequences are acquired by intracellular gene transfer (IGT) from the plastid. In addition, frequent events of horizontal gene transfer (HGT) between mitochondria of different species also contribute to their expanded genomes. In contrast, alien sequences are rarely found in plastid genomes. Most of the plant-to-plant HGT events involve mitochondrion-to-mitochondrion transfers. Occasionally, foreign sequences in mtDNAs are plastid-derived (MTPT), raising questions about their origin, frequency, and mechanism of transfer. The rising number of complete mtDNAs allowed us to address these questions. We identified 15 new foreign MTPTs, increasing significantly the number of those previously reported. One out of five of the angiosperm species analyzed contained at least one foreign MTPT, suggesting a remarkable frequency of HGT among plants. By analyzing the flanking regions of the foreign MTPTs, we found strong evidence for mt-to-mt transfers in 65% of the cases. We hypothesize that plastid sequences were initially acquired by the native mtDNA via IGT and then transferred to a distantly-related plant via mitochondrial HGT, rather than directly from a foreign plastid to the mitochondrial genome. Finally, we describe three novel putative cases of mitochondrial-derived sequences among angiosperm plastomes. PMID:28262720

  4. Foreign Plastid Sequences in Plant Mitochondria are Frequently Acquired Via Mitochondrion-to-Mitochondrion Horizontal Transfer.

    PubMed

    Gandini, C L; Sanchez-Puerta, M V

    2017-03-06

    Angiosperm mitochondrial genomes (mtDNA) exhibit variable quantities of alien sequences. Many of these sequences are acquired by intracellular gene transfer (IGT) from the plastid. In addition, frequent events of horizontal gene transfer (HGT) between mitochondria of different species also contribute to their expanded genomes. In contrast, alien sequences are rarely found in plastid genomes. Most of the plant-to-plant HGT events involve mitochondrion-to-mitochondrion transfers. Occasionally, foreign sequences in mtDNAs are plastid-derived (MTPT), raising questions about their origin, frequency, and mechanism of transfer. The rising number of complete mtDNAs allowed us to address these questions. We identified 15 new foreign MTPTs, increasing significantly the number of those previously reported. One out of five of the angiosperm species analyzed contained at least one foreign MTPT, suggesting a remarkable frequency of HGT among plants. By analyzing the flanking regions of the foreign MTPTs, we found strong evidence for mt-to-mt transfers in 65% of the cases. We hypothesize that plastid sequences were initially acquired by the native mtDNA via IGT and then transferred to a distantly-related plant via mitochondrial HGT, rather than directly from a foreign plastid to the mitochondrial genome. Finally, we describe three novel putative cases of mitochondrial-derived sequences among angiosperm plastomes.

  5. Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene.

    PubMed

    Taghavi, Safiyh; Barac, Tanja; Greenberg, Bill; Borremans, Brigitte; Vangronsveld, Jaco; van der Lelie, Daniel

    2005-12-01

    Poplar, a plant species frequently used for phytoremediation of groundwater contaminated with organic solvents, was inoculated with the endophyte Burkholderia cepacia VM1468. This strain, whose natural host is yellow lupine, contains the pTOM-Bu61 plasmid coding for constitutively expressed toluene degradation. Noninoculated plants or plants inoculated with the soil bacterium B. cepacia Bu61(pTOM-Bu61) were used as controls. Inoculation of poplar had a positive effect on plant growth in the presence of toluene and reduced the amount of toluene released via evapotranspiration. These effects were more dramatic for VM1468, the endophytic strain, than for Bu61. Remarkably, none of the strains became established at detectable levels in the endophytic community, but there was horizontal gene transfer of pTOM-Bu61 to different members of the endogenous endophytic community, both in the presence and in the absence of toluene. This work is the first report of in planta horizontal gene transfer among plant-associated endophytic bacteria and demonstrates that such transfer could be used to change natural endophytic microbial communities in order to improve the remediation of environmental insults.

  6. Procedure for Horizontal Transfer of Patient-Derived Xenograft Tumors to Eliminate Corynebacterium bovis.

    PubMed

    Manuel, Christopher; Bagby, Stacey; Reisinger, Julie; Pugazhenthi, Umarani; Pitts, Todd; Keysar, Stephen; Arcaroli, John; Leszczynski, Jori

    2017-02-16

    Human patient-derived xenograft (PDX) tumors, propagated in immunodeficient mice, are rapidly growing in use as amodelfor cancer research. Horizontal transfer between mice, without in vitro cell culture, allows these tumors to retainmany of their unique characteristics from their individual patient of origin. However, the immunodeficient mouse strainsused to grow these tumors are susceptible to numerous opportunistic pathogens, including Corynebacterium bovis. At ourinstitution, 2 in vivo tumor banks of PDX tumors had been maintained within nude mouse colonies enzootically infectedwith C. bovis. Elimination of C. bovis from these colonies required the aseptic harvest and horizontal transfer of tumor tissue between infected and naïve recipient mice without cross-contamination. Out of necessity, we developed a standard operating procedure using enhancements to traditional aseptic surgical technique with concurrent application of both procedural and physical barriers to prevent C. bovis transmission. By using these methods, all 61 unique PDX tumor models were successfullyharvested from C. bovis-infected mice and transferred into recipient mice without transmission of infection. Our datademonstrate that, in situations where C. bovis-free colonies can be established and maintained, this procedure can successfullybe used to eliminate C. bovis from an in vivo tumor bank of valuable PDX tumors.

  7. Procedure for Horizontal Transfer of Patient-Derived Xenograft Tumors to Eliminate Corynebacterium bovis.

    PubMed

    Manuel, Christopher A; Bagby, Stacey M; Reisinger, Julie A; Pugazhenthi, Umarani; Pitts, Todd M; Keysar, Stephen B; Arcaroli, John J; Leszczynski, Jori K

    2017-03-01

    Human patient-derived xenograft (PDX) tumors, propagated in immunodeficient mice, are rapidly growing in use as a model for cancer research. Horizontal transfer between mice, without in vitro cell culture, allows these tumors to retain many of their unique characteristics from their individual patient of origin. However, the immunodeficient mouse strains used to grow these tumors are susceptible to numerous opportunistic pathogens, including Corynebacterium bovis. At our institution, 2 in vivo tumor banks of PDX tumors had been maintained within nude mouse colonies enzootically infected with C. bovis. Elimination of C. bovis from these colonies required the aseptic harvest and horizontal transfer of tumor tissue between infected and naïve recipient mice without cross-contamination. Out of necessity, we developed a standard operating procedure using enhancements to traditional aseptic surgical technique with concurrent application of both procedural and physical barriers to prevent C. bovis transmission. By using these methods, all 61 unique PDX tumor models were successfully harvested from C. bovis-infected mice and transferred into recipient mice without transmission of infection. Our data demonstrate that, in situations where C. bovis-free colonies can be established and maintained, this procedure can successfully be used to eliminate C. bovis from an in vivo tumor bank of valuable PDX tumors.

  8. Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence

    PubMed Central

    Juhas, Mario; Crook, Derrick W; Hood, Derek W

    2008-01-01

    Type IV secretion systems (T4SSs) are multisubunit cell-envelope-spanning structures, ancestrally related to bacterial conjugation machines, which transfer proteins and nucleoprotein complexes across membranes. T4SSs mediate horizontal gene transfer, thus contributing to genome plasticity and the evolution of pathogens through dissemination of antibiotic resistance and virulence genes. Moreover, T4SSs are also used for the delivery of bacterial effector proteins across the bacterial membrane and the plasmatic membrane of eukaryotic host cell, thus contributing directly to pathogenicity. T4SSs are usually encoded by multiple genes organized into a single functional unit. Based on a number of features, the organization of genetic determinants, shared homologies and evolutionary relationships, T4SSs have been divided into several groups. Type F and P (type IVA) T4SSs resembling the archetypal VirB/VirD4 system of Agrobacterium tumefaciens are considered to be the paradigm of type IV secretion, while type I (type IVB) T4SSs are found in intracellular bacterial pathogens, Legionella pneumophila and Coxiella burnetii. Several novel T4SSs have been identified recently and their functions await investigation. The most recently described GI type T4SSs play a key role in the horizontal transfer of a wide variety of genomic islands derived from a broad spectrum of bacterial strains. PMID:18549454

  9. Natural convection heat transfer for a staggered array of heated, horizontal cylinders within a rectangular enclosure

    SciTech Connect

    Triplett, C.E.

    1996-12-01

    This thesis presents the results of an experimental investigation of natural convection heat transfer in a staggered array of heated cylinders, oriented horizontally within a rectangular enclosure. The main purpose of this research was to extend the knowledge of heat transfer within enclosed bundles of spent nuclear fuel rods sealed within a shipping or storage container. This research extends Canaan`s investigation of an aligned array of heated cylinders that thermally simulated a boiling water reactor (BWR) spent fuel assembly sealed within a shipping or storage cask. The results are presented in terms of piecewise Nusselt-Rayleigh number correlations of the form Nu = C(Ra){sup n}, where C and n are constants. Correlations are presented both for individual rods within the array and for the array as a whole. The correlations are based only on the convective component of the heat transfer. The radiative component was calculated with a finite-element code that used measured surface temperatures, rod array geometry, and measured surface emissivities as inputs. The correlation results are compared to Canaan`s aligned array results and to other studies of natural convection in horizontal tube arrays.

  10. Reduction in horizontal transfer of conjugative plasmid by UV irradiation and low-level chlorination.

    PubMed

    Lin, Wenfang; Li, Shuai; Zhang, Shuting; Yu, Xin

    2016-03-15

    The widespread presence of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the drinking water system facilitates their horizontal gene transfer among microbiota. In this study, the conjugative gene transfer of RP4 plasmid after disinfection including ultraviolet (UV) irradiation and low-level chlorine treatment was investigated. It was found that both UV irradiation and low-level chlorine treatment reduced the conjugative gene transfer frequency. The transfer frequency gradually decreased from 2.75 × 10(-3) to 2.44 × 10(-5) after exposure to UV doses ranging from 5 to 20 mJ/cm(2). With higher UV dose of 50 and 100 mJ/cm(2), the transfer frequency was reduced to 1.77 × 10(-6) and 2.44 × 10(-8). The RP4 plasmid transfer frequency was not significantly affected by chlorine treatment at dosages ranging from 0.05 to 0.2 mg/l, but treatment with 0.3-0.5 mg/l chlorine induced a decrease in conjugative transfer to 4.40 × 10(-5) or below the detection limit. The mechanisms underlying these phenomena were also explored, and the results demonstrated that UV irradiation and chlorine treatment (0.3 and 0.5 mg/l) significantly reduced the viability of bacteria, thereby lowering the conjugative transfer frequency. Although the lower chlorine concentrations tested (0.05-0.2 mg/l) were not sufficient to damage the cells, exposure to these concentrations may still depress the expression of a flagellar gene (FlgC), an outer membrane porin gene (ompF), and a DNA transport-related gene (TraG). Additionally, fewer pili were scattered on the bacteria after chlorine treatment. These findings are important in assessing and controlling the risk of ARG transfer and dissemination in the drinking water system.

  11. Systematic Search for Evidence of Interdomain Horizontal Gene Transfer from Prokaryotes to Oomycete Lineages

    PubMed Central

    McCarthy, Charley G. P.

    2016-01-01

    ABSTRACT While most commonly associated with prokaryotes, horizontal gene transfer (HGT) can also have a significant influence on the evolution of microscopic eukaryotes. Systematic analysis of HGT in the genomes of the oomycetes, filamentous eukaryotic microorganisms in the Stramenopiles-Alveolates-Rhizaria (SAR) supergroup, has to date focused mainly on intradomain transfer events between oomycetes and fungi. Using systematic whole-genome analysis followed by phylogenetic reconstruction, we have investigated the extent of interdomain HGT between bacteria and plant-pathogenic oomycetes. We report five putative instances of HGT from bacteria into the oomycetes. Two transfers were found in Phytophthora species, including one unique to the cucurbit pathogen Phytophthora capsici. Two were found in Pythium species only, and the final transfer event was present in Phytopythium and Pythium species, the first reported bacterium-inherited genes in these genera. Our putative transfers included one protein that appears to be a member of the Pythium secretome, metabolic proteins, and enzymes that could potentially break down xenobiotics within the cell. Our findings complement both previous reports of bacterial genes in oomycete and SAR genomes and the growing body of evidence suggesting that interdomain transfer from prokaryotes into eukaryotes occurs more frequently than previously thought. IMPORTANCE Horizontal gene transfer (HGT) is the nonvertical inheritance of genetic material by transfer between different species. HGT is an important evolutionary mechanism for prokaryotes and in some cases is responsible for the spread of antibiotic resistance from resistant to benign species. Genome analysis has shown that examples of HGT are not as frequent in eukaryotes, but when they do occur they may have important evolutionary consequences. For example, the acquisition of fungal genes by an ancestral Phytophthora (plant destroyer) species is responsible for the large repertoire

  12. Phylogenetic analysis of the incidence of lux gene horizontal transfer in Vibrionaceae.

    PubMed

    Urbanczyk, Henryk; Ast, Jennifer C; Kaeding, Allison J; Oliver, James D; Dunlap, Paul V

    2008-05-01

    Horizontal gene transfer (HGT) is thought to occur frequently in bacteria in nature and to play an important role in bacterial evolution, contributing to the formation of new species. To gain insight into the frequency of HGT in Vibrionaceae and its possible impact on speciation, we assessed the incidence of interspecies transfer of the lux genes (luxCDABEG), which encode proteins involved in luminescence, a distinctive phenotype. Three hundred three luminous strains, most of which were recently isolated from nature and which represent 11 Aliivibrio, Photobacterium, and Vibrio species, were screened for incongruence of phylogenies based on a representative housekeeping gene (gyrB or pyrH) and a representative lux gene (luxA). Strains exhibiting incongruence were then subjected to detailed phylogenetic analysis of horizontal transfer by using multiple housekeeping genes (gyrB, recA, and pyrH) and multiple lux genes (luxCDABEG). In nearly all cases, housekeeping gene and lux gene phylogenies were congruent, and there was no instance in which the lux genes of one luminous species had replaced the lux genes of another luminous species. Therefore, the lux genes are predominantly vertically inherited in Vibrionaceae. The few exceptions to this pattern of congruence were as follows: (i) the lux genes of the only known luminous strain of Vibrio vulnificus, VVL1 (ATCC 43382), were evolutionarily closely related to the lux genes of Vibrio harveyi; (ii) the lux genes of two luminous strains of Vibrio chagasii, 21N-12 and SB-52, were closely related to those of V. harveyi and Vibrio splendidus, respectively; (iii) the lux genes of a luminous strain of Photobacterium damselae, BT-6, were closely related to the lux genes of the lux-rib(2) operon of Photobacterium leiognathi; and (iv) a strain of the luminous bacterium Photobacterium mandapamensis was found to be merodiploid for the lux genes, and the second set of lux genes was closely related to the lux genes of the lux-rib(2

  13. Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae▿ †

    PubMed Central

    Urbanczyk, Henryk; Ast, Jennifer C.; Kaeding, Allison J.; Oliver, James D.; Dunlap, Paul V.

    2008-01-01

    Horizontal gene transfer (HGT) is thought to occur frequently in bacteria in nature and to play an important role in bacterial evolution, contributing to the formation of new species. To gain insight into the frequency of HGT in Vibrionaceae and its possible impact on speciation, we assessed the incidence of interspecies transfer of the lux genes (luxCDABEG), which encode proteins involved in luminescence, a distinctive phenotype. Three hundred three luminous strains, most of which were recently isolated from nature and which represent 11 Aliivibrio, Photobacterium, and Vibrio species, were screened for incongruence of phylogenies based on a representative housekeeping gene (gyrB or pyrH) and a representative lux gene (luxA). Strains exhibiting incongruence were then subjected to detailed phylogenetic analysis of horizontal transfer by using multiple housekeeping genes (gyrB, recA, and pyrH) and multiple lux genes (luxCDABEG). In nearly all cases, housekeeping gene and lux gene phylogenies were congruent, and there was no instance in which the lux genes of one luminous species had replaced the lux genes of another luminous species. Therefore, the lux genes are predominantly vertically inherited in Vibrionaceae. The few exceptions to this pattern of congruence were as follows: (i) the lux genes of the only known luminous strain of Vibrio vulnificus, VVL1 (ATCC 43382), were evolutionarily closely related to the lux genes of Vibrio harveyi; (ii) the lux genes of two luminous strains of Vibrio chagasii, 21N-12 and SB-52, were closely related to those of V. harveyi and Vibrio splendidus, respectively; (iii) the lux genes of a luminous strain of Photobacterium damselae, BT-6, were closely related to the lux genes of the lux-rib2 operon of Photobacterium leiognathi; and (iv) a strain of the luminous bacterium Photobacterium mandapamensis was found to be merodiploid for the lux genes, and the second set of lux genes was closely related to the lux genes of the lux-rib2

  14. Security camera resolution measurements: Horizontal TV lines versus modulation transfer function measurements.

    SciTech Connect

    Birch, Gabriel Carisle; Griffin, John Clark

    2015-01-01

    The horizontal television lines (HTVL) metric has been the primary quantity used by division 6000 related to camera resolution for high consequence security systems. This document shows HTVL measurements are fundamen- tally insufficient as a metric to determine camera resolution, and propose a quantitative, standards based methodology by measuring the camera system modulation transfer function (MTF), the most common and accepted metric of res- olution in the optical science community. Because HTVL calculations are easily misinterpreted or poorly defined, we present several scenarios in which HTVL is frequently reported, and discuss their problems. The MTF metric is discussed, and scenarios are presented with calculations showing the application of such a metric.

  15. The impact of horizontal gene transfer on the biology of Clostridium difficile.

    PubMed

    Roberts, Adam P; Allan, Elaine; Mullany, Peter

    2014-01-01

    Clostridium difficile infection (CDI) is now recognised as the main cause of healthcare associated diarrhoea. Over the recent years there has been a change in the epidemiology of CDI with certain related strains dominating infection. These strains have been termed hyper-virulent and have successfully spread across the globe. Many C. difficile strains have had their genomes completely sequenced allowing researchers to build up a very detailed picture of the contribution of horizontal gene transfer to the adaptive potential, through the acquisition of mobile DNA, of this organism. Here, we review and discuss the contribution of mobile genetic elements to the biology of this clinically important pathogen.

  16. Bacterial Transport and Fate and Its Effect on Horizontal Gene Transfer in Soil

    NASA Astrophysics Data System (ADS)

    Lv, N.; Massoudieh, A.; Nguyen, T. H.; Kamai, T.; Zilles, J. L.; Ginn, T. R.; Liang, X.

    2013-12-01

    Biogeochemical cycling in ecosystems relies heavily on soil bacterial communities. Bacterial communities adapt to natural or anthropogenic disruptions through mutation and horizontal gene transfer. Horizontal gene transfer alters bacterial communities rapidly by transferring DNA across species. A systematic understanding of bacterial transport and fate and its effects on horizontal gene transfer is critical for predicting and harnessing bacterial adaption and evolution in soil. In this work, a multi-scale approach was applied to study the effects of both flagella and motility on transport and fate of the soil bacterium Azotobacter vinelandii in porous media. Both micromodel and column experiments showed decreasing deposition over time, suggesting that both flagellated and non-flagellated cells were blocked from deposition by previously deposited cells. In later stages, ripening effects were also observed, and they appeared earlier for the non-flagellated strain. Based on the overall clean collector removal efficiencies determined from micromodel and column experiments, the non-motile and non-flagellated strain DJNM deposited the most, while the motile, wild-type strain DJ showed the least deposition. The overall clean collector removal efficiencies was due to decreased deposition of motile cells on the front sides of the collectors (relative to the flow direction). The horizontal gene transfer of extracellular DNA, known as natural transformation, was evaluated with both dissolved and adsorbed extracellular DNA and with motile and non-motile but flagellated strains (DJ and DJ77, respectively). The distinct transport mechanisms of these strains resulted in different natural transformation rates and relationships to the concentration of cells and dissolved extracellular DNA. A modified mass action type relationship with power relationships was established to model the differences in natural transformation between DJ and DJ77. A cell-DNA pairing hypothesis was

  17. Exploration of horizontal gene transfer between transplastomic tobacco and plant-associated bacteria.

    PubMed

    Demanèche, Sandrine; Monier, Jean-Michel; Dugat-Bony, Eric; Simonet, Pascal

    2011-10-01

    The likelihood of gene transfer from transgenic plants to bacteria is dependent on the transgene copy number and on the presence of homologous sequences for recombination. The large number of chloroplast genomes in a plant cell as well as the prokaryotic origin of the transgene may thus significantly increase the likelihood of gene transfer from transplastomic plants to bacteria. In order to assess the probability of such a transfer, bacterial isolates, screened for their ability to colonize decaying tobacco plant tissue and possessing DNA sequence similarity to the chloroplastic genes accD and rbcL flanking the transgene (aadA), were tested for their ability to take up extracellular DNA (broad host-range pBBR1MCS-3-derived plasmid, transplastomic plant DNA and PCR products containing the genes accD-aadA-rbcL) by natural or electrotransformation. The results showed that among the 16 bacterial isolates tested, six were able to accept foreign DNA and acquire the spectinomycin resistance conferred by the aadA gene on plasmid, but none of them managed to integrate transgenic DNA in their chromosome. Our results provide no indication that the theoretical gene transfer-enhancing properties of transplastomic plants cause horizontal gene transfer at rates above those found in other studies with nuclear transgenes.

  18. Plant expansins in bacteria and fungi: evolution by horizontal gene transfer and independent domain fusion.

    PubMed

    Nikolaidis, Nikolas; Doran, Nicole; Cosgrove, Daniel J

    2014-02-01

    Horizontal gene transfer (HGT) has been described as a common mechanism of transferring genetic material between prokaryotes, whereas genetic transfers from eukaryotes to prokaryotes have been rarely documented. Here we report a rare case of HGT in which plant expansin genes that code for plant cell-wall loosening proteins were transferred from plants to bacteria, fungi, and amoebozoa. In several cases, the species in which the expansin gene was found is either in intimate association with plants or is a known plant pathogen. Our analyses suggest that at least two independent genetic transfers occurred from plants to bacteria and fungi. These events were followed by multiple HGT events within bacteria and fungi. We have also observed that in bacteria expansin genes have been independently fused to DNA fragments that code for an endoglucanase domain or for a carbohydrate binding module, pointing to functional convergence at the molecular level. Furthermore, the functional similarities between microbial expansins and their plant xenologs suggest that these proteins mediate microbial-plant interactions by altering the plant cell wall and therefore may provide adaptive advantages to these species. The evolution of these nonplant expansins represents a unique case in which bacteria and fungi have found innovative and adaptive ways to interact with and infect plants by acquiring genes from their host. This evolutionary paradigm suggests that despite their low frequency such HGT events may have significantly contributed to the evolution of prokaryotic and eukaryotic species.

  19. Effects of observed horizontal inhomogeneities within cirrus clouds on solar radiative transfer

    NASA Astrophysics Data System (ADS)

    Buschmann, Nicole; McFarquhar, Greg M.; Heymsfield, Andrew J.

    2002-10-01

    In situ microphysical and combined radar and radiometer measurements of 11 cirrus clouds from Central Equatorial Pacific Experiment (CEPEX), European Cloud and Radiation Experiment (EUCREX), investigation of Clouds by Ground-Based and Airborne Radar and Lidar (CARL), and First International Satellite Cloud Climatology Project (ISCCP) Regional Experiment (FIRE) are used to investigate effects of horizontal cloud inhomogeneities on solar radiative transfer. A three-dimensional ray-tracing model (GRIMALDI), based on the Monte Carlo method, is used to calculate upward and downward flux densities and absorption for the spectral range from 0.38 to 4.0 μm. Radiative flux densities are calculated using the inhomogeneous clouds derived from the observations and for horizontally and vertically averaged homogeneous clouds. Horizontally averaged values of radiative flux densities and absorption for heterogeneous clouds can differ by up to 30% from those calculated for the homogeneous clouds for convectively induced tropical cirrus clouds. The midlatitude cases examined tended to be more homogeneous, and hence differences between radiative properties for the homogeneous and heterogeneous clouds did not exceed 10%. For cirrus clouds with mean optical thicknesses smaller than 5 and with relative variances of optical thickness smaller than 0.2, errors caused by the homogeneous assumption are smaller than ±10%.

  20. Natural convective heat transfer within nanofluid-filled hemispherical horizontal enclosure

    NASA Astrophysics Data System (ADS)

    Haddad, O.; Baïri, A.

    2016-10-01

    This survey deals with some steady-state natural convection taking place in a hemispherical enclosure filled with nanofluid consisting of water based metallic nanoparticles, with volumetric fraction ranging between 0% (pure water) and 20%. The hot active wall of the cavity is its horizontal disk subjected to a wide range of constant heat fluxes. The 3D numerical approach is done by means of the finite volume method based on a mixture model. Temperature and velocity distributions are presented for some typical cases and the heat transfer is quantified by means of the Nusselt number versus Rayleigh number. A comparison done between the results with the water and the nanofluid clearly confirms enhancement of the convective heat transfer with the nanoparticles.

  1. Convective Heat Transfer from Castings of Ice Roughened Surfaces in Horizontal Flight

    NASA Technical Reports Server (NTRS)

    Dukhan, Nihad; Vanfossen, G. James, Jr.; Masiulaniec, K. Cyril; Dewitt, Kenneth J.

    1995-01-01

    A technique was developed to cast frozen ice shapes that had been grown on a metal surface. This technique was applied to a series of ice shapes that were grown in the NASA Lewis Icing Research Tunnel on flat plates. Eight different types of ice growths, characterizing different types of roughness, were obtained from these plates, from which aluminum castings were made. Test strips taken from these castings were outfitted with heat flux gages, such that when placed in a dry wind tunnel, they could be used to experimentally map out the convective heat transfer coefficient in the direction of flow from the roughened surfaces. The effects on the heat transfer coefficient for parallel flow, which simulates horizontal flight, were studied. The results of this investigation can be used to help size heaters for wings, helicopter rotor blades, jet engine intakes, etc., or de-icing for anti-icing applications where the flow is parallel to the iced surface.

  2. A gene horizontally transferred from bacteria protects arthropods from host plant cyanide poisoning

    PubMed Central

    Wybouw, Nicky; Dermauw, Wannes; Tirry, Luc; Stevens, Christian; Grbić, Miodrag; Feyereisen, René; Van Leeuwen, Thomas

    2014-01-01

    Cyanogenic glucosides are among the most widespread defense chemicals of plants. Upon plant tissue disruption, these glucosides are hydrolyzed to a reactive hydroxynitrile that releases toxic hydrogen cyanide (HCN). Yet many mite and lepidopteran species can thrive on plants defended by cyanogenic glucosides. The nature of the enzyme known to detoxify HCN to β-cyanoalanine in arthropods has remained enigmatic. Here we identify this enzyme by transcriptome analysis and functional expression. Phylogenetic analysis showed that the gene is a member of the cysteine synthase family horizontally transferred from bacteria to phytophagous mites and Lepidoptera. The recombinant mite enzyme had both β-cyanoalanine synthase and cysteine synthase activity but enzyme kinetics showed that cyanide detoxification activity was strongly favored. Our results therefore suggest that an ancient horizontal transfer of a gene originally involved in sulfur amino acid biosynthesis in bacteria was co-opted by herbivorous arthropods to detoxify plant produced cyanide. DOI: http://dx.doi.org/10.7554/eLife.02365.001 PMID:24843024

  3. Recent Origin of the Methacrylate Redox System in Geobacter sulfurreducens AM-1 through Horizontal Gene Transfer.

    PubMed

    Arkhipova, Oksana V; Meer, Margarita V; Mikoulinskaia, Galina V; Zakharova, Marina V; Galushko, Alexander S; Akimenko, Vasilii K; Kondrashov, Fyodor A

    2015-01-01

    The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome с (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1.

  4. Horizontal Gene Transfer is a Significant Driver of Gene Innovation in Dinoflagellates

    PubMed Central

    Wisecaver, Jennifer H.; Brosnahan, Michael L.; Hackett, Jeremiah D.

    2013-01-01

    The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314–1,563 depending on inference method) relative to all other organisms in the analysis (0–782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT. PMID:24259313

  5. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns.

    PubMed

    Li, Fay-Wei; Villarreal, Juan Carlos; Kelly, Steven; Rothfels, Carl J; Melkonian, Michael; Frangedakis, Eftychios; Ruhsam, Markus; Sigel, Erin M; Der, Joshua P; Pittermann, Jarmila; Burge, Dylan O; Pokorny, Lisa; Larsson, Anders; Chen, Tao; Weststrand, Stina; Thomas, Philip; Carpenter, Eric; Zhang, Yong; Tian, Zhijian; Chen, Li; Yan, Zhixiang; Zhu, Ying; Sun, Xiao; Wang, Jun; Stevenson, Dennis W; Crandall-Stotler, Barbara J; Shaw, A Jonathan; Deyholos, Michael K; Soltis, Douglas E; Graham, Sean W; Windham, Michael D; Langdale, Jane A; Wong, Gane Ka-Shu; Mathews, Sarah; Pryer, Kathleen M

    2014-05-06

    Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor--neochrome--that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.

  6. A role for host-parasite interactions in the horizontal transfer of transposons across phyla.

    PubMed

    Gilbert, Clément; Schaack, Sarah; Pace, John K; Brindley, Paul J; Feschotte, Cédric

    2010-04-29

    Horizontal transfer (HT), or the passage of genetic material between non-mating species, is increasingly recognized as an important force in the evolution of eukaryotic genomes. Transposons, with their inherent ability to mobilize and amplify within genomes, may be especially prone to HT. However, the means by which transposons can spread across widely diverged species remain elusive. Here we present evidence that host-parasite interactions have promoted the HT of four transposon families between invertebrates and vertebrates. We found that Rhodnius prolixus, a triatomine bug feeding on the blood of various tetrapods and vector of Chagas' disease in humans, carries in its genome four distinct transposon families that also invaded the genomes of a diverse, but overlapping, set of tetrapods. The bug transposons are approximately 98% identical and cluster phylogenetically with those of the opossum and squirrel monkey, two of its preferred mammalian hosts in South America. We also identified one of these transposon families in the pond snail Lymnaea stagnalis, a cosmopolitan vector of trematodes infecting diverse vertebrates, whose ancestral sequence is nearly identical and clusters with those found in Old World mammals. Together these data provide evidence for a previously hypothesized role of host-parasite interactions in facilitating HT among animals. Furthermore, the large amount of DNA generated by the amplification of the horizontally transferred transposons supports the idea that the exchange of genetic material between hosts and parasites influences their genomic evolution.

  7. Horizontal gene transfer events reshape the global landscape of arm race between viruses and homo sapiens

    PubMed Central

    Chen, Dong-Sheng; Wu, Yi-Quan; Zhang, Wei; Jiang, San-Jie; Chen, Shan-Ze

    2016-01-01

    Horizontal gene transfer (HGT) drives the evolution of recipient organism particularly if it provides a novel function which enhances the fitness or its adaption to the environment. Virus-host co-evolution is attractive for studying co-evolutionary processes, since viruses strictly replicate inside of the host cells and thus their evolution is inexorably tangled with host biology. HGT, as a mechanism of co-evolution between human and viruses, has been widely documented, however, the roles HGT play during the interaction between human and viruses are still in their infancy. In this study, we performed a comprehensive analysis on the genes horizontally transferred between viruses and their corresponding human hosts. Our study suggests that the HGT genes in human are predominantly enriched in immune related GO terms while viral HGT genes are tend to be encoded by viruses which promote the invasion of immune system of hosts. Based on our results, it gives us a hint about the evolution trajectory of HGT events. Overall, our study suggests that the HGT between human and viruses are highly relevant to immune interaction and probably reshaped the arm race between hosts and viruses. PMID:27270140

  8. Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes.

    PubMed

    Dunning Hotopp, Julie C; Grifantini, Renata; Kumar, Nikhil; Tzeng, Yih Ling; Fouts, Derrick; Frigimelica, Elisabetta; Draghi, Monia; Giuliani, Marzia Monica; Rappuoli, Rino; Stephens, David S; Grandi, Guido; Tettelin, Hervé

    2006-12-01

    To better understand Neisseria meningitidis genomes and virulence, microarray comparative genome hybridization (mCGH) data were collected from one Neisseria cinerea, two Neisseria lactamica, two Neisseria gonorrhoeae and 48 Neisseria meningitidis isolates. For N. meningitidis, these isolates are from diverse clonal complexes, invasive and carriage strains, and all major serogroups. The microarray platform represented N. meningitidis strains MC58, Z2491 and FAM18, and N. gonorrhoeae FA1090. By comparing hybridization data to genome sequences, the core N. meningitidis genome and insertions/deletions (e.g. capsule locus, type I secretion system) related to pathogenicity were identified, including further characterization of the capsule locus, bioinformatics analysis of a type I secretion system, and identification of some metabolic pathways associated with intracellular survival in pathogens. Hybridization data clustered meningococcal isolates from similar clonal complexes that were distinguished by the differential presence of six distinct islands of horizontal transfer. Several of these islands contained prophage or other mobile elements, including a novel prophage and a transposon carrying portions of a type I secretion system. Acquisition of some genetic islands appears to have occurred in multiple lineages, including transfer between N. lactamica and N. meningitidis. However, island acquisition occurs infrequently, such that the genomic-level relationship is not obscured within clonal complexes. The N. meningitidis genome is characterized by the horizontal acquisition of multiple genetic islands; the study of these islands reveals important sets of genes varying between isolates and likely to be related to pathogenicity.

  9. Heat and mass transfer characteristics of absorption of R134a into DMAC in a horizontal tube absorber

    NASA Astrophysics Data System (ADS)

    Harikrishnan, L.; Maiya, M. P.; Tiwari, S.; Wohlfeil, A.; Ziegler, F.

    2009-10-01

    In this paper the heat and mass transfer characteristics of a horizontal tube absorber for the mixture R134a/DMAC in terms of experimentally gained heat and mass transfer coefficients are presented. The heat transfer coefficient is mainly dependent on the solution’s mass flow rate. The mass transfer coefficient is strongly related to the subcooling of the solution. The data are compared to experimental absorption characteristics of water into aqueous lithium bromide in an absorption chiller. The mass transfer coefficients are of similar size whereas the heat transfer coefficients are about one order of magnitude smaller for R134a-DMAC.

  10. Multilevel populations and the evolution of antibiotic resistance through horizontal gene transfer.

    PubMed

    Andam, Cheryl P; Fournier, Gregory P; Gogarten, Johann Peter

    2011-09-01

    Horizontal gene transfer (HGT) can create diversity in the genetic repertoire of a lineage. Successful gene transfer likely occurs more frequently between more closely related organisms, leading to the formation of higher-level exchange groups that in some respects are comparable to single-species populations. Genes that appear fixed in a single species can be replaced through distant homologs or iso-functional analogs acquired through HGT. These genes may originate from other species or they may be acquired by an individual strain from the species pan-genome. Because of their similarity to alleles in a population, we label these gene variants that are exchanged between related species as homeoalleles. In a case study, we show that biased gene transfer plays an important role in the evolution of aminoacyl-tRNA synthetases (aaRS). Many microorganisms make use of these genes against naturally occurring antibiotics. We suggest that the resistance against naturally occurring antibiotics is the likely driving force behind the frequent switching between divergent aaRS types and the reason for the maintenance of these homeoalleles in higher-level exchange groups. Resistance to naturally occurring antibiotics may lead to the maintenance of different types of aminoacyl-tRNA synthetases in Bacteria through gene transfer.

  11. Effects of confining walls on heat transfer from a vertical array of isothermal horizontal elliptic cylinders

    SciTech Connect

    Yousefi, T.; Paknezhad, M.; Ashjaee, M.; Yazdani, S.

    2009-09-15

    Steady state two-dimensional natural convection heat transfer from the vertical array of five horizontal isothermal elliptic cylinders with vertical major axis which confined between two adiabatic walls has been studied experimentally. Experiments were carried out using a Mach-Zehnder interferometer. The Rayleigh number based on cylinder major axis was in the range 10{sup 3}{<=}Ra{<=}2.5 x 10{sup 3}, and dimensionless wall spacing 1.5{<=} t/b{<=}9 and infinity. The effect of wall spacing and Rayleigh number on the heat transfer from the individual cylinder and the array were investigated. Experiments are performed for ratio wall spacing to major diameter t/b = 1.5, 2, 2.5, 3, 3.5, 4, 5, 6, 7, 8, 9 and infinity. A correlation based on the experimental data for the average Nusselt number of the array as a function of Ra and t/b is presented in the aforementioned ranges. A relation has been derived for optimum wall spacing at which the Nusselt number of the array attains its maximum value. At optimum wall spacing, approximately 10% increase in the heat transfer from the confined array of elliptic cylinders has been observed as compared to the unconfined case. Also, a heat transfer correlation has been proposed for a single elliptic cylinder with vertical major axis and has been compared with earlier works. (author)

  12. Heat and mass transfer prediction of binary refrigerant mixtures condensing in a horizontal microfin tube

    SciTech Connect

    Koyama, Shigeru; Yu, Jian; Ishibashi, Akira

    1999-07-01

    In the face of the phase-out of HCFC22 for its effect on globe environment, the alternative refrigerant has been paid attention in the refrigeration and heat pump industry. In the present stage, it is found that any pure refrigerant is not a good substitute of HCFC22 for the system in use. The authors have to use binary or ternary refrigerant mixtures as the substitute to meet industrial requirement. But until now, although the heat transfer characteristics of the refrigerant mixtures can be measured in experiments and predicted in some degree, the mass transfer characteristics in condensation process, which is a main part in most systems, can not be clarified by both experimental and theoretical methods. In the present study a non-equilibrium model for condensation of binary refrigerant mixtures inside a horizontal microfin tube is proposed. In this model it is assumed that the phase equilibrium is only established at the vapor-liquid interface, while the bulk vapor and the bulk liquid are in non-equilibrium in the same cross section. The mass transfer characteristic in vapor core is obtained from the analogy between mass and momentum transfer. In the liquid layer, the mass fraction distribution is neglected, but the mass transfer coefficient is treated as infinite that can keep a finite value for the mass transfer rate in liquid phase. From the calculation results compared with the experimental ones for the condensation of HFC134a/HCFC123 and HCFC22/CFC114 mixtures, it is found that the calculated heat flux distribution along the tube axis is in good agreement with that of experiment, and the calculated values of condensing length agree well with the experimental ones. Using the present model, the local mass faction distribution, the diffusion mass transfer rate and the mass transfer characteristics in both vapor and liquid phase are demonstrated. From these results, the effect of mass transfer resistance on condensation heat transfer characteristics for binary

  13. Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes

    PubMed Central

    2011-01-01

    Background Legionella pneumophila is an intracellular pathogen of environmental protozoa. When humans inhale contaminated aerosols this bacterium may cause a severe pneumonia called Legionnaires' disease. Despite the abundance of dozens of Legionella species in aquatic reservoirs, the vast majority of human disease is caused by a single serogroup (Sg) of a single species, namely L. pneumophila Sg1. To get further insights into genome dynamics and evolution of Sg1 strains, we sequenced strains Lorraine and HL 0604 1035 (Sg1) and compared them to the available sequences of Sg1 strains Paris, Lens, Corby and Philadelphia, resulting in a comprehensive multigenome analysis. Results We show that L. pneumophila Sg1 has a highly conserved and syntenic core genome that comprises the many eukaryotic like proteins and a conserved repertoire of over 200 Dot/Icm type IV secreted substrates. However, recombination events and horizontal gene transfer are frequent. In particular the analyses of the distribution of nucleotide polymorphisms suggests that large chromosomal fragments of over 200 kbs are exchanged between L. pneumophila strains and contribute to the genome dynamics in the natural population. The many secretion systems present might be implicated in exchange of these fragments by conjugal transfer. Plasmids also play a role in genome diversification and are exchanged among strains and circulate between different Legionella species. Conclusion Horizontal gene transfer among bacteria and from eukaryotes to L. pneumophila as well as recombination between strains allows different clones to evolve into predominant disease clones and others to replace them subsequently within relatively short periods of time. PMID:22044686

  14. Natural convection heat transfer on two horizontal cylinders in liquid sodium

    SciTech Connect

    Hata, K.; Shiotsu, M.; Takeuchi, Y.

    1995-09-01

    Natural convection heat transfer on two horizontal 7.6 mm diameter test cylinders assembled with the ratio of the distance between each cylinder axis to the cylinder diameter, S/D, of 2 in liquid sodium was studied experimentally and theoretically. The heat transfer coefficients on the cylinder surface due to the same heat inputs ranging from 1.0 X 10{sup 7} to 1.0 x 10{sup 9} W/m{sup 3} were obtained experimentally for various setting angeles, {gamma}, between vertical direction and the plane including both of these cylinder axis over the range of zero to 90{degrees}. Theoretical equations for laminar natural convection heat transfer from the two horizontal cylinders were numerically solved for the same conditions as the experimental ones considering the temperature dependence of thermophysical properties concerned. The average Nusselt numbers, Nu, values on the Nu versus modified Rayleigh number, R{sub f}, graph. The experimental values of Nu for the upper cylinder are about 20% lower than those for the lower cylinder at {gamma} = 0{degrees} for the range of R{sub f} tested here. The value of Nu for the upper cylinder becomes higher and approaches that for the lower cylinder with the increase in {gamma} over range of 0 to 90{degrees}. The values of Nu for the lower cylinder at each {gamma} are almost in agreement with those for a single cylinder. The theoretical values of Nu on two cylinders except those for R{sub f}<4 at {gamma} = 0{degrees} are in agreement with the experimental data at each {gamma} with the deviations less than 15%. Correlations for Nu on the upper and lower cylinders were obtained as functions of S/D and {gamma} based n the theoretical solutions for the S/D ranged over 1.5 to 4.0.

  15. Bacteriophages Isolated from Chicken Meat and the Horizontal Transfer of Antimicrobial Resistance Genes

    PubMed Central

    Shousha, Amira; Awaiwanont, Nattakarn; Sofka, Dmitrij; Smulders, Frans J. M.; Paulsen, Peter; Szostak, Michael P.; Humphrey, Tom

    2015-01-01

    Antimicrobial resistance in microbes poses a global and increasing threat to public health. The horizontal transfer of antimicrobial resistance genes was thought to be due largely to conjugative plasmids or transposons, with only a minor part being played by transduction through bacteriophages. However, whole-genome sequencing has recently shown that the latter mechanism could be highly important in the exchange of antimicrobial resistance genes between microorganisms and environments. The transfer of antimicrobial resistance genes by phages could underlie the origin of resistant bacteria found in food. We show that chicken meat carries a number of phages capable of transferring antimicrobial resistance. Of 243 phages randomly isolated from chicken meat, about a quarter (24.7%) were able to transduce resistance to one or more of the five antimicrobials tested into Escherichia coli ATCC 13706 (DSM 12242). Resistance to kanamycin was transduced the most often, followed by that to chloramphenicol, with four phages transducing tetracycline resistance and three transducing ampicillin resistance. Phages able to transduce antimicrobial resistance were isolated from 44% of the samples of chicken meat that we tested. The statistically significant (P = 0.01) relationship between the presence of phages transducing kanamycin resistance and E. coli isolates resistant to this antibiotic suggests that transduction may be an important mechanism for transferring kanamycin resistance to E. coli. It appears that the transduction of resistance to certain antimicrobials, e.g., kanamycin, not only is widely distributed in E. coli isolates found on meat but also could represent a major mechanism for resistance transfer. The result is of high importance for animal and human health. PMID:25934615

  16. Bacteriophages Isolated from Chicken Meat and the Horizontal Transfer of Antimicrobial Resistance Genes.

    PubMed

    Shousha, Amira; Awaiwanont, Nattakarn; Sofka, Dmitrij; Smulders, Frans J M; Paulsen, Peter; Szostak, Michael P; Humphrey, Tom; Hilbert, Friederike

    2015-07-01

    Antimicrobial resistance in microbes poses a global and increasing threat to public health. The horizontal transfer of antimicrobial resistance genes was thought to be due largely to conjugative plasmids or transposons, with only a minor part being played by transduction through bacteriophages. However, whole-genome sequencing has recently shown that the latter mechanism could be highly important in the exchange of antimicrobial resistance genes between microorganisms and environments. The transfer of antimicrobial resistance genes by phages could underlie the origin of resistant bacteria found in food. We show that chicken meat carries a number of phages capable of transferring antimicrobial resistance. Of 243 phages randomly isolated from chicken meat, about a quarter (24.7%) were able to transduce resistance to one or more of the five antimicrobials tested into Escherichia coli ATCC 13706 (DSM 12242). Resistance to kanamycin was transduced the most often, followed by that to chloramphenicol, with four phages transducing tetracycline resistance and three transducing ampicillin resistance. Phages able to transduce antimicrobial resistance were isolated from 44% of the samples of chicken meat that we tested. The statistically significant (P = 0.01) relationship between the presence of phages transducing kanamycin resistance and E. coli isolates resistant to this antibiotic suggests that transduction may be an important mechanism for transferring kanamycin resistance to E. coli. It appears that the transduction of resistance to certain antimicrobials, e.g., kanamycin, not only is widely distributed in E. coli isolates found on meat but also could represent a major mechanism for resistance transfer. The result is of high importance for animal and human health.

  17. Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

    PubMed Central

    Stecher, Bärbel; Denzler, Rémy; Maier, Lisa; Bernet, Florian; Sanders, Mandy J.; Pickard, Derek J.; Barthel, Manja; Westendorf, Astrid M.; Krogfelt, Karen A.; Walker, Alan W.; Ackermann, Martin; Dobrindt, Ulrich; Thomson, Nicholas R.; Hardt, Wolf-Dietrich

    2012-01-01

    The mammalian gut harbors a dense microbial community interacting in multiple ways, including horizontal gene transfer (HGT). Pangenome analyses established particularly high levels of genetic flux between Gram-negative Enterobacteriaceae. However, the mechanisms fostering intraenterobacterial HGT are incompletely understood. Using a mouse colitis model, we found that Salmonella-inflicted enteropathy elicits parallel blooms of the pathogen and of resident commensal Escherichia coli. These blooms boosted conjugative HGT of the colicin-plasmid p2 from Salmonella enterica serovar Typhimurium to E. coli. Transconjugation efficiencies of ∼100% in vivo were attributable to high intrinsic p2-transfer rates. Plasmid-encoded fitness benefits contributed little. Under normal conditions, HGT was blocked by the commensal microbiota inhibiting contact-dependent conjugation between Enterobacteriaceae. Our data show that pathogen-driven inflammatory responses in the gut can generate transient enterobacterial blooms in which conjugative transfer occurs at unprecedented rates. These blooms may favor reassortment of plasmid-encoded genes between pathogens and commensals fostering the spread of fitness-, virulence-, and antibiotic-resistance determinants. PMID:22232693

  18. Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes.

    PubMed

    Richards, Thomas A; Soanes, Darren M; Jones, Meredith D M; Vasieva, Olga; Leonard, Guy; Paszkiewicz, Konrad; Foster, Peter G; Hall, Neil; Talbot, Nicholas J

    2011-09-13

    Horizontal gene transfer (HGT) can radically alter the genomes of microorganisms, providing the capacity to adapt to new lifestyles, environments, and hosts. However, the extent of HGT between eukaryotes is unclear. Using whole-genome, gene-by-gene phylogenetic analysis we demonstrate an extensive pattern of cross-kingdom HGT between fungi and oomycetes. Comparative genomics, including the de novo genome sequence of Hyphochytrium catenoides, a free-living sister of the oomycetes, shows that these transfers largely converge within the radiation of oomycetes that colonize plant tissues. The repertoire of HGTs includes a large number of putatively secreted proteins; for example, 7.6% of the secreted proteome of the sudden oak death parasite Phytophthora ramorum has been acquired from fungi by HGT. Transfers include gene products with the capacity to break down plant cell walls and acquire sugars, nucleic acids, nitrogen, and phosphate sources from the environment. Predicted HGTs also include proteins implicated in resisting plant defense mechanisms and effector proteins for attacking plant cells. These data are consistent with the hypothesis that some oomycetes became successful plant parasites by multiple acquisitions of genes from fungi.

  19. Effects of Adding Nanoparticles on Boiling and Condensing Heat Transfer inside a horizontal round tube

    NASA Astrophysics Data System (ADS)

    Sheikholeslami, Mohsen; Sadoughi, Mohammadkazem; Shariatmadar, Hamed; Akhavan-Behabadi, Mohammad Ali

    2015-11-01

    An experimental investigation is performed on heat transfer evaluation of a nano-refrigerant flow during condensation and evaporation inside a horizontal round tube. Experiments are carried out for three working fluid types including: i) pure refrigerant (R600a); ii) refrigerant/lubricant (R600a/oil); and iii) nano-refrigerant: refrigerant/lubricant/nanoparticles (R600a/oil/CuO). Nanoparticles are added to the lubricant and their mixture is mixed with pure refrigerant. Therefore, nano-refrigerants (R600a/oil/CuO) are prepared by dispersing CuO nanoparticles with different fractions of 0.5%, 1% and 1.5% in the baseline mixture (R600a/oil). Effects of different factors including vapor quality, mass flux, and nanoparticles on the heat transfer coefficient are examined for both of condensation and evaporation flows, separately. The results shows that maximum heat transfer augmentation of 79% and 83% are achieved by using the refrigerant/lubricant/nanoparticles mixture, in comparison with the pure refrigerant case in condensation and evaporation, respectively which are occurred for nano-refrigerant with 1.5% mass fraction in both of them.

  20. Horizontal Transfer of Diatomaceous Earth and Botanical Insecticides in the Common Bed Bug, Cimex lectularius L.; Hemiptera: Cimicidae

    PubMed Central

    Akhtar, Yasmin; Isman, Murray B.

    2013-01-01

    Background Horizontal transfer of insecticide occurs when insects contact or ingest an insecticide, return to an aggregation or a nest, and transfer the insecticide to other conspecific insects through contact. This phenomenon has been reported in a number of insects including social insects, however it has not been reported in bed bugs. Since horizontal transfer can facilitate the spread of insecticide into hard to reach spaces, it could contribute greatly to the management of these public health pests. Methodology/Results To demonstrate horizontal transfer of diatomaceous earth and botanical insecticides in C. lectularius, an exposed (donor) bed bug, following a 10-minute acquisition period, was placed with unexposed (recipient) bed bugs. Mortality data clearly demonstrates that diatomaceous earth (DE 51) was actively transferred from a single exposed bug to unexposed bugs in a concentration dependent manner. LC50 values varied from 24.4 mg at 48 h to 5.1 mg at 216 h when a single exposed bed bug was placed with 5 unexposed bed bugs. LT50 values also exhibited a concentration response. LT50 values varied from 1.8 days to 8.4 days when a ‘donor’ bug exposed to 20 and 5 mg of dust respectively was placed with 5 ‘recipient’ bugs. Dust was also actively transferred from adult bed bugs to the nymphs. In addition we observed horizontal transfer of botanical insecticides including neem, ryania, and rotenone to varying degrees. Conclusion/Significance Our data clearly demonstrate horizontal transfer of diatomaceous earth and botanical insecticides in the common bed bug, C. lectularius. Use of a fluorescent dust provided visual confirmation that contaminated bed bugs transfer dust to untreated bed bugs in harborage. This result is important because bedbugs live in hard-to-reach places and interaction between conspecifics can be exploited for delivery and dissemination of management products directed at this public health pest. PMID:24086593

  1. A horizontal gene transfer supported the evolution of an early metazoan biomineralization strategy

    PubMed Central

    2011-01-01

    Background The synchronous and widespread adoption of the ability to biomineralize was a defining event for metazoan evolution during the late Precambrian/early Cambrian 545 million years ago. However our understanding on the molecular level of how animals first evolved this capacity is poor. Because sponges are the earliest branching phylum of biomineralizing metazoans, we have been studying how biocalcification occurs in the coralline demosponge Astrosclera willeyana. Results We have isolated and characterized a novel protein directly from the calcified spherulites of A. willeyana. Using three independent lines of evidence (genomic architecture of the gene in A. willeyana, spatial expression of the gene product in A. willeyana and genomic architecture of the gene in the related demosponge Amphimedon queenslandica), we show that the gene that encodes this protein was horizontally acquired from a bacterium, and is now highly and exclusively expressed in spherulite forming cells. Conclusions Our findings highlight the ancient and close association that exists between sponges and bacteria, and provide support for the notion that horizontal gene transfer may have been an important mechanism that supported the evolution of this early metazoan biomineralisation strategy. PMID:21838889

  2. Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods.

    PubMed

    Pace, John K; Gilbert, Clément; Clark, Marlena S; Feschotte, Cédric

    2008-11-04

    Horizontal transfer (HT) is central to the evolution of prokaryotic species. Selfish and mobile genetic elements, such as phages, plasmids, and transposons, are the primary vehicles for HT among prokaryotes. In multicellular eukaryotes, the prevalence and evolutionary significance of HT remain unclear. Here, we identified a set of DNA transposon families dubbed SPACE INVADERS (or SPIN) whose consensus sequences are approximately 96% identical over their entire length (2.9 kb) in the genomes of murine rodents (rat/mouse), bushbaby (prosimian primate), little brown bat (laurasiatherian), tenrec (afrotherian), opossum (marsupial), and two non-mammalian tetrapods (anole lizard and African clawed frog). In contrast, SPIN elements were undetectable in other species represented in the sequence databases, including 19 other mammals with draft whole-genome assemblies. This patchy distribution, coupled with the extreme level of SPIN identity in widely divergent tetrapods and the overall lack of selective constraint acting on these elements, is incompatible with vertical inheritance, but strongly indicative of multiple horizontal introductions. We show that these germline infiltrations likely occurred around the same evolutionary time (15-46 mya) and spawned some of the largest bursts of DNA transposon activity ever recorded in any species lineage (nearly 100,000 SPIN copies per haploid genome in tenrec). The process also led to the emergence of a new gene in the murine lineage derived from a SPIN transposase. In summary, HT of DNA transposons has contributed significantly to shaping and diversifying the genomes of multiple mammalian and tetrapod species.

  3. Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods

    PubMed Central

    Pace, John K.; Gilbert, Clément; Clark, Marlena S.; Feschotte, Cédric

    2008-01-01

    Horizontal transfer (HT) is central to the evolution of prokaryotic species. Selfish and mobile genetic elements, such as phages, plasmids, and transposons, are the primary vehicles for HT among prokaryotes. In multicellular eukaryotes, the prevalence and evolutionary significance of HT remain unclear. Here, we identified a set of DNA transposon families dubbed SPACE INVADERS (or SPIN) whose consensus sequences are ≈96% identical over their entire length (2.9 kb) in the genomes of murine rodents (rat/mouse), bushbaby (prosimian primate), little brown bat (laurasiatherian), tenrec (afrotherian), opossum (marsupial), and two non-mammalian tetrapods (anole lizard and African clawed frog). In contrast, SPIN elements were undetectable in other species represented in the sequence databases, including 19 other mammals with draft whole-genome assemblies. This patchy distribution, coupled with the extreme level of SPIN identity in widely divergent tetrapods and the overall lack of selective constraint acting on these elements, is incompatible with vertical inheritance, but strongly indicative of multiple horizontal introductions. We show that these germline infiltrations likely occurred around the same evolutionary time (15–46 mya) and spawned some of the largest bursts of DNA transposon activity ever recorded in any species lineage (nearly 100,000 SPIN copies per haploid genome in tenrec). The process also led to the emergence of a new gene in the murine lineage derived from a SPIN transposase. In summary, HT of DNA transposons has contributed significantly to shaping and diversifying the genomes of multiple mammalian and tetrapod species. PMID:18936483

  4. Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life

    PubMed Central

    Fournier, Gregory P.; Huang, Jinling; Gogarten, J. Peter

    2009-01-01

    Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the ‘true’ evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history. PMID:19571243

  5. Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes

    PubMed Central

    Suh, Alexander; Witt, Christopher C.; Menger, Juliana; Sadanandan, Keren R.; Podsiadlowski, Lars; Gerth, Michael; Weigert, Anne; McGuire, Jimmy A.; Mudge, Joann; Edwards, Scott V.; Rheindt, Frank E.

    2016-01-01

    Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83–99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25–22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20–17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity. PMID:27097561

  6. Horizontal transfer of aligned Si nanowire arrays and their photoconductive performance

    PubMed Central

    2014-01-01

    An easy and low-cost method to transfer large-scale horizontally aligned Si nanowires onto a substrate is reported. Si nanowires prepared by metal-assisted chemical etching were assembled and anchored to fabricate multiwire photoconductive devices with standard Si technology. Scanning electron microscopy images showed highly aligned and successfully anchored Si nanowires. Current-voltage tests showed an approximately twofold change in conductivity between the devices in dark and under laser irradiation. Fully reversible light switching ON/OFF response was also achieved with an ION/IOFF ratio of 230. Dynamic response measurement showed a fast switching feature with response and recovery times of 10.96 and 19.26 ms, respectively. PMID:25520603

  7. Experimental and theoretical study of horizontal tube bundle for passive condensation heat transfer

    NASA Astrophysics Data System (ADS)

    Song, Yong Jae

    The research in this thesis supports the design of a horizontal tube bundle condenser for passive heat removal system in nuclear reactors. From nuclear power plant containment, condensation of steam from a steam/noncondensable gas occurs on the primary side and boiling occurs on the secondary side; thus, heat exchanger modeling is a challenge. For the purpose of this experimental study, a six-tube bundle is used, where the outer diameter, inner diameter, and length of each stainless steel tube measures 38.10mm (1.5 inches), 31.75mm (1.25 inches) and 3.96m (156 inches), respectively. The pitch to diameter ratio was determined based on information gathered from literature surveys, and the dimensions were determined from calculations and experimental data. The objective of the calculations, correlations, and experimental data was to obtain complete condensation within the tube bundle. Experimental conditions for the tests in this thesis work were determined from Design Basis Accident (DBA). The applications are for an actual Passive Containment Cooling Systems (PCCS) condenser under postulated accident conditions in future light water reactors. In this research, steady state and transient experiments were performed to investigate the effect of noncondensable gas on steam condensation inside and boiling outside a tube bundle heat exchanger. The condenser tube inlet steam mass flow rate varied from 18.0 to 48.0 g/s, the inlet pressure varied from 100 kPa to 400 kPa, and the inlet noncondensable gas mass fraction varied from 1% to 10%. The effect of the noncondensable gas was examined by comparing the tube centerline temperatures for various inlet and system conditions. As a result, it was determined that the noncondensable gas accumulated near the condensate film causing a decrease of mass and energy transfer. In addition, the effect of the inlet steam flow rate gas was investigated by comparing the tube centerline temperatures, the conclusion being that, as the inlet

  8. Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation

    PubMed Central

    Kondrashov, Fyodor A; Koonin, Eugene V; Morgunov, Igor G; Finogenova, Tatiana V; Kondrashova, Marie N

    2006-01-01

    Background The glyoxylate cycle is thought to be present in bacteria, protists, plants, fungi, and nematodes, but not in other Metazoa. However, activity of the glyoxylate cycle enzymes, malate synthase (MS) and isocitrate lyase (ICL), in animal tissues has been reported. In order to clarify the status of the MS and ICL genes in animals and get an insight into their evolution, we undertook a comparative-genomic study. Results Using sequence similarity searches, we identified MS genes in arthropods, echinoderms, and vertebrates, including platypus and opossum, but not in the numerous sequenced genomes of placental mammals. The regions of the placental mammals' genomes expected to code for malate synthase, as determined by comparison of the gene orders in vertebrate genomes, show clear similarity to the opossum MS sequence but contain stop codons, indicating that the MS gene became a pseudogene in placental mammals. By contrast, the ICL gene is undetectable in animals other than the nematodes that possess a bifunctional, fused ICL-MS gene. Examination of phylogenetic trees of MS and ICL suggests multiple horizontal gene transfer events that probably went in both directions between several bacterial and eukaryotic lineages. The strongest evidence was obtained for the acquisition of the bifunctional ICL-MS gene from an as yet unknown bacterial source with the corresponding operonic organization by the common ancestor of the nematodes. Conclusion The distribution of the MS and ICL genes in animals suggests that either they encode alternative enzymes of the glyoxylate cycle that are not orthologous to the known MS and ICL or the animal MS acquired a new function that remains to be characterized. Regardless of the ultimate solution to this conundrum, the genes for the glyoxylate cycle enzymes present a remarkable variety of evolutionary events including unusual horizontal gene transfer from bacteria to animals. Reviewers Arcady Mushegian (Stowers Institute for Medical

  9. A 55-kilodalton immunodominant antigen of Porphyromonas gingivalis W50 has arisen via horizontal gene transfer.

    PubMed

    Hanley, S A; Aduse-Opoku, J; Curtis, M A

    1999-03-01

    A 55-kDa outer membrane protein of Porphyromonas gingivalis W50 is a significant target of the serum immunoglobulin G antibody response of periodontal disease patients and hence may play an important role in host-bacterium interactions in periodontal disease. The gene encoding the 55-kDa antigen (ragB, for receptor antigen B) was isolated on a 9.5-kb partial Sau3AI fragment of P. gingivalis W50 chromosomal DNA in pUC18 by immunoscreening with a monoclonal antibody to this antigen. The 1.6-kb open reading frame (ORF) encoding RagB was located via subcloning and nested-deletion analysis. Sequence analysis demonstrated the presence of an upstream 3.1-kb ORF (ragA) which is cotranscribed with ragB. A number of genetic characteristics suggest that the ragAB locus was acquired by a horizontal gene transfer event. These include a significantly reduced G+C content relative to that of the P. gingivalis chromosome (42 versus 48%) and the presence of mobility elements flanking this locus in P. gingivalis W50. Furthermore, Southern blotting and PCR analyses showed a restricted distribution of this locus in laboratory and clinical isolates of this bacterium. The association of ragAB+ P. gingivalis with clinical status was examined by PCR analysis of subgingival samples. ragAB+ was not detected in P. gingivalis-positive shallow pockets from periodontal disease patients but was present in 36% of the P. gingivalis-positive samples from deep pockets. These data suggest that the ragAB locus was acquired by certain P. gingivalis strains via horizontal gene transfer and that the acquisition of this locus may facilitate the survival of these strains at sites of periodontal destruction.

  10. Extensive Intra-Kingdom Horizontal Gene Transfer Converging on a Fungal Fructose Transporter Gene

    PubMed Central

    Coelho, Marco A.; Gonçalves, Carla; Sampaio, José Paulo; Gonçalves, Paula

    2013-01-01

    Comparative genomics revealed in the last decade a scenario of rampant horizontal gene transfer (HGT) among prokaryotes, but for fungi a clearly dominant pattern of vertical inheritance still stands, punctuated however by an increasing number of exceptions. In the present work, we studied the phylogenetic distribution and pattern of inheritance of a fungal gene encoding a fructose transporter (FSY1) with unique substrate selectivity. 109 FSY1 homologues were identified in two sub-phyla of the Ascomycota, in a survey that included 241 available fungal genomes. At least 10 independent inter-species instances of horizontal gene transfer (HGT) involving FSY1 were identified, supported by strong phylogenetic evidence and synteny analyses. The acquisition of FSY1 through HGT was sometimes suggestive of xenolog gene displacement, but several cases of pseudoparalogy were also uncovered. Moreover, evidence was found for successive HGT events, possibly including those responsible for transmission of the gene among yeast lineages. These occurrences do not seem to be driven by functional diversification of the Fsy1 proteins because Fsy1 homologues from widely distant lineages, including at least one acquired by HGT, appear to have similar biochemical properties. In summary, retracing the evolutionary path of the FSY1 gene brought to light an unparalleled number of independent HGT events involving a single fungal gene. We propose that the turbulent evolutionary history of the gene may be linked to the unique biochemical properties of the encoded transporter, whose predictable effect on fitness may be highly variable. In general, our results support the most recent views suggesting that inter-species HGT may have contributed much more substantially to shape fungal genomes than heretofore assumed. PMID:23818872

  11. Exosomes derived from alcohol-treated hepatocytes horizontally transfer liver specific miRNA-122 and sensitize monocytes to LPS.

    PubMed

    Momen-Heravi, Fatemeh; Bala, Shashi; Kodys, Karen; Szabo, Gyongyi

    2015-05-14

    Hepatocyte damage and inflammation in monocytes/macrophages are central to the pathogenesis of alcoholic hepatitis (AH). MicroRNAs (miRNAs) regulate all of these processes. MiRNA-122 is abundantly expressed in hepatocytes while monocytes/macrophages have low levels. The role of exosomes in AH and possible cross talk between hepatocyte-derived exosomes and immune cells is not explored yet. Here, we show that the number of exosomes significantly increases in the sera of healthy individuals after alcohol binge drinking and in mice after binge or chronic alcohol consumption. Exosomes isolated from sera after alcohol consumption or from in vitro ethanol-treated hepatocytes contained miRNA-122. Exosomes derived from ethanol-treated Huh7.5 cells were taken up by the recipients THP1 monocytes and horizontally transferred a mature form of liver-specific miRNA-122. In vivo, liver mononuclear cells and Kupffer cells from alcohol-fed mice had increased miRNA-122 levels. In monocytes, miRNA-122 transferred via exosomes inhibited the HO-1 pathway and sensitized to LPS stimulation and increased levels of pro-inflammatory cytokines. Finally, inflammatory effects of exosomes from ethanol-treated hepatocytes were prevented by using RNA interference via exosome-mediated delivery of a miRNA-122 inhibitor. These results demonstrate that first, exosomes mediate communication between hepatocytes and monocytes/macrophages and second, hepatocyte-derived miRNA-122 can reprogram monocytes inducing sensitization to LPS.

  12. Mycelia as a focal point for horizontal gene transfer among soil bacteria

    PubMed Central

    Berthold, Tom; Centler, Florian; Hübschmann, Thomas; Remer, Rita; Thullner, Martin; Harms, Hauke; Wick, Lukas Y.

    2016-01-01

    Horizontal gene transfer (HGT) is a main mechanism of bacterial evolution endowing bacteria with new genetic traits. The transfer of mobile genetic elements such as plasmids (conjugation) requires the close proximity of cells. HGT between genetically distinct bacteria largely depends on cell movement in water films, which are typically discontinuous in natural systems like soil. Using laboratory microcosms, a bacterial reporter system and flow cytometry, we here investigated if and to which degree mycelial networks facilitate contact of and HGT between spatially separated bacteria. Our study shows that the network structures of mycelia promote bacterial HGT by providing continuous liquid films in which bacterial migration and contacts are favoured. This finding was confirmed by individual-based simulations, revealing that the tendency of migrating bacteria to concentrate in the liquid film around hyphae is a key factor for improved HGT along mycelial networks. Given their ubiquity, we propose that hyphae can act as focal point for HGT and genetic adaptation in soil. PMID:27811990

  13. Potential for horizontal gene transfer in microbial communities of the terrestrial subsurface.

    PubMed

    Coombs, Jonna M

    2009-01-01

    The deep terrestrial subsurface is a vast, largely unexplored environment that is oligotrophic, highly heterogeneous, and may contain extremes of both physical and chemical factors. In spite of harsh conditions, subsurface studies at several widely distributed geographic sites have revealed diverse communities of viable organisms, which have provided evidence of low but detectable metabolic activity. Although much of the terrestrial subsurface may be considered to be distant and isolated, the concept of horizontal gene transfer (HGT) in this environment has far-reaching implications for bioremediation efforts and groundwater quality, industrial harvesting of subsurface natural resources such as petroleum, and accurate assessment of the risks associated with DNA release and transport from genetically modified organisms. This chapter will explore what is known about some of the major mechanisms of HGT, and how the information gained from surface organisms might apply to conditions in the terrestrial subsurface. Evidence for the presence of mobile elements in subsurface bacteria and limited retrospective studies examining genetic signatures of potential past gene transfer events will be discussed.

  14. Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events.

    PubMed

    Gophna, Uri; Ron, Eliora Z; Graur, Dan

    2003-07-17

    Type III secretion systems (TTSS) are unique bacterial mechanisms that mediate elaborate interactions with their hosts. The fact that several of the TTSS proteins are closely related to flagellar export proteins has led to the suggestion that TTSS had evolved from flagella. Here we reconstruct the evolutionary history of four conserved type III secretion proteins and their phylogenetic relationships with flagellar paralogs. Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another. The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted. A comparison of the species tree, as deduced from 16S rDNA sequences, to the protein phylogenetic trees has led to the identification of several major lateral transfer events involving clusters of TTSS genes. It is hypothesized that horizontal gene transfer has occurred much earlier and more frequently than previously inferred for TTSS genes and is, consequently, a major force shaping the evolution of species that harbor type III secretion systems.

  15. Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi.

    PubMed

    Slot, Jason C; Rokas, Antonis

    2011-01-25

    Genes involved in intermediary and secondary metabolism in fungi are frequently physically linked or clustered. For example, in Aspergillus nidulans the entire pathway for the production of sterigmatocystin (ST), a highly toxic secondary metabolite and a precursor to the aflatoxins (AF), is located in a ∼54 kb, 23 gene cluster. We discovered that a complete ST gene cluster in Podospora anserina was horizontally transferred from Aspergillus. Phylogenetic analysis shows that most Podospora cluster genes are adjacent to or nested within Aspergillus cluster genes, although the two genera belong to different taxonomic classes. Furthermore, the Podospora cluster is highly conserved in content, sequence, and microsynteny with the Aspergillus ST/AF clusters and its intergenic regions contain 14 putative binding sites for AflR, the transcription factor required for activation of the ST/AF biosynthetic genes. Examination of ∼52,000 Podospora expressed sequence tags identified transcripts for 14 genes in the cluster, with several expressed at multiple life cycle stages. The presence of putative AflR-binding sites and the expression evidence for several cluster genes, coupled with the recent independent discovery of ST production in Podospora [1], suggest that this HGT event probably resulted in a functional cluster. Given the abundance of metabolic gene clusters in fungi, our finding that one of the largest known metabolic gene clusters moved intact between species suggests that such transfers might have significantly contributed to fungal metabolic diversity. PAPERFLICK:

  16. The case of horizontal gene transfer from bacteria to the peculiar dinoflagellate plastid genome

    PubMed Central

    Mackiewicz, Paweł; Bodył, Andrzej; Moszczyński, Krzysztof

    2013-01-01

    Organelle genomes lose their genes by transfer to host nuclear genomes, but only occasionally are enriched by foreign genes from other sources. In contrast to mitochondria, plastid genomes are especially resistant to such horizontal gene transfer (HGT), and thus every gene acquired in this way is notable. An exceptional case of HGT was recently recognized in the peculiar peridinin plastid genome of dinoflagellates, which is organized in plasmid-like minicircles. Genomic and phylogenetic analyses of Ceratium horridum and Pyrocystis lunula minicircles revealed four genes and one unannotated open reading frame that probably were gained from bacteria belonging to the Bacteroidetes. Such bacteria seem to be a good source of genes because close endosymbiotic associations between them and dinoflagellates have been observed. The HGT-acquired genes are involved in plastid functions characteristic of other photosynthetic eukaryotes, and their arrangement resembles bacterial operons. These studies indicate that the peridinin plastid genome, usually regarded as having resulted from reduction and fragmentation of a typical plastid genome derived from red algae, may have a chimeric origin that includes bacterial contributions. Potential contamination of the Ceratium and Pyrocystis plastid genomes by bacterial sequences and the controversial localization of their minicircles in the nucleus are also discussed. PMID:24195014

  17. Birth of a W sex chromosome by horizontal transfer of Wolbachia bacterial symbiont genome

    PubMed Central

    Leclercq, Sébastien; Thézé, Julien; Chebbi, Mohamed Amine; Giraud, Isabelle; Moumen, Bouziane; Ernenwein, Lise; Grève, Pierre; Cordaux, Richard

    2016-01-01

    Sex determination is a fundamental developmental pathway governing male and female differentiation, with profound implications for morphology, reproductive strategies, and behavior. In animals, sex differences between males and females are generally determined by genetic factors carried by sex chromosomes. Sex chromosomes are remarkably variable in origin and can differ even between closely related species, indicating that transitions occur frequently and independently in different groups of organisms. The evolutionary causes underlying sex chromosome turnover are poorly understood, however. Here we provide evidence indicating that Wolbachia bacterial endosymbionts triggered the evolution of new sex chromosomes in the common pillbug Armadillidium vulgare. We identified a 3-Mb insert of a feminizing Wolbachia genome that was recently transferred into the pillbug nuclear genome. The Wolbachia insert shows perfect linkage to the female sex, occurs in a male genetic background (i.e., lacking the ancestral W female sex chromosome), and is hemizygous. Our results support the conclusion that the Wolbachia insert is now acting as a female sex-determining region in pillbugs, and that the chromosome carrying the insert is a new W sex chromosome. Thus, bacteria-to-animal horizontal genome transfer represents a remarkable mechanism underpinning the birth of sex chromosomes. We conclude that sex ratio distorters, such as Wolbachia endosymbionts, can be powerful agents of evolutionary transitions in sex determination systems in animals. PMID:27930295

  18. Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade

    PubMed Central

    Boothby, Thomas C.; Tenlen, Jennifer R.; Smith, Frank W.; Wang, Jeremy R.; Patanella, Kiera A.; Osborne Nishimura, Erin; Tintori, Sophia C.; Li, Qing; Jones, Corbin D.; Yandell, Mark; Glasscock, Jarret; Goldstein, Bob

    2015-01-01

    Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini. Tardigrades are microscopic eight-legged animals that are famous for their ability to survive extreme conditions. Genome sequencing, direct confirmation of physical linkage, and phylogenetic analysis revealed that a large fraction of the H. dujardini genome is derived from diverse bacteria as well as plants, fungi, and Archaea. We estimate that approximately one-sixth of tardigrade genes entered by HGT, nearly double the fraction found in the most extreme cases of HGT into animals known to date. Foreign genes have supplemented, expanded, and even replaced some metazoan gene families within the tardigrade genome. Our results demonstrate that an unexpectedly large fraction of an animal genome can be derived from foreign sources. We speculate that animals that can survive extremes may be particularly prone to acquiring foreign genes. PMID:26598659

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

    PubMed Central

    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

  20. Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade.

    PubMed

    Boothby, Thomas C; Tenlen, Jennifer R; Smith, Frank W; Wang, Jeremy R; Patanella, Kiera A; Nishimura, Erin Osborne; Tintori, Sophia C; Li, Qing; Jones, Corbin D; Yandell, Mark; Messina, David N; Glasscock, Jarret; Goldstein, Bob

    2015-12-29

    Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini. Tardigrades are microscopic eight-legged animals that are famous for their ability to survive extreme conditions. Genome sequencing, direct confirmation of physical linkage, and phylogenetic analysis revealed that a large fraction of the H. dujardini genome is derived from diverse bacteria as well as plants, fungi, and Archaea. We estimate that approximately one-sixth of tardigrade genes entered by HGT, nearly double the fraction found in the most extreme cases of HGT into animals known to date. Foreign genes have supplemented, expanded, and even replaced some metazoan gene families within the tardigrade genome. Our results demonstrate that an unexpectedly large fraction of an animal genome can be derived from foreign sources. We speculate that animals that can survive extremes may be particularly prone to acquiring foreign genes.

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

    PubMed

    Da Silva, Gabriela Jorge; Domingues, Sara

    2016-08-23

    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.

  2. Effect of different magnetic field distributions on laminar ferroconvection heat transfer in horizontal tube

    NASA Astrophysics Data System (ADS)

    Sheikhnejad, Yahya; Hosseini, Reza; Saffar-avval, Majid

    2015-09-01

    The forced convection heat transfer of ferrofluid steady state laminar flow through a circular axisymmetric horizontal pipe under different magnetic field is the focus of this study. The pipe is under constant heat flux while different linear axial magnetic fields were applied on the ferrofluid with equal magnetic energy. In this scenario, viscosity of ferrofluid is temperature dependent, to capture ferrofluid real behavior a nonlinear Langevin equation was considered for equilibrium magnetization. For this purpose, the set of nonlinear governing PDEs was solved using proper CFD techniques: the finite volume method and SIMPLE algorithm were used to discretize and numerically solve the governing equation in order to obtain thermohydrodynamic flow characteristics. The numerical results show a promising enhancement of up to 135.7% in heat transfer as a consequence of the application of magnetic field. The magnetic field also increases pressure loss of up to 77% along the pipe; but effectiveness (favorable to unfavorable effect ratio) of the magnetic field as a performance index economically justifies its application such that higher magnetic field intensity causes higher effectiveness of up to 1.364.

  3. Applying horizontal gene transfer phenomena to enhance non-viral gene therapy

    PubMed Central

    Elmer, Jacob J.; Christensen, Matthew D.; Rege, Kaushal

    2014-01-01

    Horizontal gene transfer (HGT) is widespread amongst prokaryotes, but eukaryotes tend to be far less promiscuous with their genetic information. However, several examples of HGT from pathogens into eukaryotic cells have been discovered and mimicked to improve non-viral gene delivery techniques. For example, several viral proteins and DNA sequences have been used to significantly increase cytoplasmic and nuclear gene delivery. Plant genetic engineering is routinely performed with the pathogenic bacterium Agrobacterium tumefaciens and similar pathogens (e.g. Bartonella henselae) may also be able to transform human cells. Intracellular parasites like Trypanosoma cruzi may also provide new insights into overcoming cellular barriers to gene delivery. Finally, intercellular nucleic acid transfer between host cells will also be briefly discussed. This article will review the unique characteristics of several different viruses and microbes and discuss how their traits have been successfully applied to improve non-viral gene delivery techniques. Consequently, pathogenic traits that originally caused diseases may eventually be used to treat many genetic diseases. PMID:23994344

  4. Horizontal gene transfer of chlamydial-like tRNA genes into early vascular plant mitochondria.

    PubMed

    Knie, Nils; Polsakiewicz, Monika; Knoop, Volker

    2015-03-01

    Mitochondrial genomes of lycophytes are surprisingly diverse, including strikingly different transfer RNA (tRNA) gene complements: No mitochondrial tRNA genes are present in the spikemoss Selaginella moellendorffii, whereas 26 tRNAs are encoded in the chondrome of the clubmoss Huperzia squarrosa. Reinvestigating the latter we found that trnL(gag) and trnS(gga) had never before been identified in any other land plant mitochondrial DNA. Sensitive sequence comparisons showed these two tRNAs as well as trnN(guu) and trnS(gcu) to be very similar to their respective counterparts in chlamydial bacteria. We identified homologs of these chlamydial-type tRNAs also in other lycophyte, fern, and gymnosperm DNAs, suggesting horizontal gene transfer (HGT) into mitochondria in the early vascular plant stem lineages. These findings extend plant mitochondrial HGT to affect individual tRNA genes, to include bacterial donors, and suggest that Chlamydiae on top of their recently proposed key role in primary chloroplast establishment may also have participated in early tracheophyte genome evolution.

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

    PubMed Central

    2011-01-01

    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 support the predictions of

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

    NASA Astrophysics Data System (ADS)

    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.

  7. Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers

    PubMed Central

    Pang, Tin Yau; Lercher, Martin J.

    2017-01-01

    Adaptation of bacteria occurs predominantly via horizontal gene transfer (HGT). While it is widely recognized that horizontal acquisitions frequently encompass multiple genes, it is unclear what the size distribution of successfully transferred DNA segments looks like and what evolutionary forces shape this distribution. Here, we identified 1790 gene family pairs that were consistently co-gained on the same branches across a phylogeny of 53 E. coli strains. We estimated a lower limit of their genomic distances at the time they were transferred to their host genomes; this distribution shows a sharp upper bound at 30 kb. The same gene-pairs can have larger distances (up to 70 kb) in other genomes. These more distant pairs likely represent recent acquisitions via transduction that involve the co-transfer of excised prophage genes, as they are almost always associated with intervening phage-associated genes. The observed distribution of genomic distances of co-transferred genes is much broader than expected from a model based on the co-transfer of genes within operons; instead, this distribution is highly consistent with the size distribution of supra-operonic clusters (SOCs), groups of co-occurring and co-functioning genes that extend beyond operons. Thus, we propose that SOCs form a basic unit of horizontal gene transfer. PMID:28067311

  8. Horizontal Transfer of Antibiotic Resistance Genes on Abiotic Touch Surfaces: Implications for Public Health

    PubMed Central

    Warnes, Sarah L.; Highmore, Callum J.; Keevil, C. William

    2012-01-01

    ABSTRACT Horizontal gene transfer (HGT) is largely responsible for increasing the incidence of antibiotic-resistant infections worldwide. While studies have focused on HGT in vivo, this work investigates whether the ability of pathogens to persist in the environment, particularly on touch surfaces, may also play an important role. Escherichia coli, virulent clone ST131, and Klebsiella pneumoniae harboring extended-spectrum-β-lactamase (ESBL) blaCTX-M-15 and metallo-β-lactamase blaNDM-1, respectively, exhibited prolonged survival on stainless steel, with approximately 104 viable cells remaining from an inoculum of 107 CFU per cm2 after 1 month at 21°C. HGT of bla to an antibiotic-sensitive but azide-resistant recipient E. coli strain occurred on stainless steel dry touch surfaces and in suspension but not on dry copper. The conjugation frequency was approximately 10 to 50 times greater and occurred immediately, and resulting transconjugants were more stable with ESBL E. coli as the donor cell than with K. pneumoniae, but blaNDM-1 transfer increased with time. Transconjugants also exhibited the same resistance profile as the donor, suggesting multiple gene transfer. Rapid death, inhibition of respiration, and destruction of genomic and plasmid DNA of both pathogens occurred on copper alloys accompanied by a reduction in bla copy number. Naked E. coli DNA degraded on copper at 21°C and 37°C but slowly at 4°C, suggesting a direct role for the metal. Persistence of viable pathogenic bacteria on touch surfaces may not only increase the risk of infection transmission but may also contribute to the spread of antibiotic resistance by HGT. The use of copper alloys as antimicrobial touch surfaces may help reduce infection and HGT. PMID:23188508

  9. Heat transfer to small horizontal cylinders immersed in a fluidized bed

    SciTech Connect

    Friedman, J.; Koundakjian, P.; Naylor, D.; Rosero, D.

    2006-10-15

    Heat transfer to horizontal cylinders immersed in fluidized beds has been extensively studied, but mainly in the context of heat transfer to boiler tubes in coal-fired beds. As a result, most correlations in the literature have been derived for cylinders of 25-50 mm diameter in vigorously fluidizing beds. In recent years, fluidized bed heat treating furnaces fired by natural gas have become increasingly popular, particularly in the steel wire manufacturing industry. These fluidized beds typically operate at relatively low fluidizing rates and with small diameter wires (1-6 mm). Nusselt number correlations developed based on boiler tube studies do not extrapolate down to these small size ranges and low fluidizing rates. In order to obtain reliable Nusselt number data for these size ranges, an experimental investigation has been undertaken using two heat treating fluidized beds; one a pilot-scale industrial unit and the other a lab-scale (300 mm diameter) unit. Heat transfer measurements were obtained using resistively heated cylindrical samples ranging from 1.3 to 9.5 mm in diameter at fluidizing rates ranging from approximately 0.5 x G{sub mf} (packed bed condition) to over 10 x G{sub mf} using aluminum oxide sand particles ranging from d{sub p}=145-330 {mu}m (50-90 grit). It has been found that for all cylinder sizes tested, the Nusselt number reaches a maximum near 2 x G{sub mf}, then remains relatively steady ({+-}5-10%) to the maximum fluidizing rate tested, typically 8-12xG{sub mf}. A correlation for maximum Nusselt number is developed.

  10. Transient Hypermutagenesis Accelerates the Evolution of Legume Endosymbionts following Horizontal Gene Transfer

    PubMed Central

    Remigi, Philippe; Capela, Delphine; Clerissi, Camille; Tasse, Léna; Torchet, Rachel; Bouchez, Olivier; Batut, Jacques; Cruveiller, Stéphane; Rocha, Eduardo P. C.; Masson-Boivin, Catherine

    2014-01-01

    Horizontal gene transfer (HGT) is an important mode of adaptation and diversification of prokaryotes and eukaryotes and a major event underlying the emergence of bacterial pathogens and mutualists. Yet it remains unclear how complex phenotypic traits such as the ability to fix nitrogen with legumes have successfully spread over large phylogenetic distances. Here we show, using experimental evolution coupled with whole genome sequencing, that co-transfer of imuABC error-prone DNA polymerase genes with key symbiotic genes accelerates the evolution of a soil bacterium into a legume symbiont. Following introduction of the symbiotic plasmid of Cupriavidus taiwanensis, the Mimosa symbiont, into pathogenic Ralstonia solanacearum we challenged transconjugants to become Mimosa symbionts through serial plant-bacteria co-cultures. We demonstrate that a mutagenesis imuABC cassette encoded on the C. taiwanensis symbiotic plasmid triggered a transient hypermutability stage in R. solanacearum transconjugants that occurred before the cells entered the plant. The generated burst in genetic diversity accelerated symbiotic adaptation of the recipient genome under plant selection pressure, presumably by improving the exploration of the fitness landscape. Finally, we show that plasmid imuABC cassettes are over-represented in rhizobial lineages harboring symbiotic plasmids. Our findings shed light on a mechanism that may have facilitated the dissemination of symbiotic competency among α- and β-proteobacteria in natura and provide evidence for the positive role of environment-induced mutagenesis in the acquisition of a complex lifestyle trait. We speculate that co-transfer of complex phenotypic traits with mutagenesis determinants might frequently enhance the ecological success of HGT. PMID:25181317

  11. Evolution of substrate specificity in a recipient's enzyme following horizontal gene transfer.

    PubMed

    Noda-García, Lianet; Camacho-Zarco, Aldo R; Medina-Ruíz, Sofía; Gaytán, Paul; Carrillo-Tripp, Mauricio; Fülöp, Vilmos; Barona-Gómez, Francisco

    2013-09-01

    Despite the prominent role of horizontal gene transfer (HGT) in shaping bacterial metabolism, little is known about the impact of HGT on the evolution of enzyme function. Specifically, what is the influence of a recently acquired gene on the function of an existing gene? For example, certain members of the genus Corynebacterium have horizontally acquired a whole l-tryptophan biosynthetic operon, whereas in certain closely related actinobacteria, for example, Mycobacterium, the trpF gene is missing. In Mycobacterium, the function of the trpF gene is performed by a dual-substrate (βα)8 phosphoribosyl isomerase (priA gene) also involved in l-histidine (hisA gene) biosynthesis. We investigated the effect of a HGT-acquired TrpF enzyme upon PriA's substrate specificity in Corynebacterium through comparative genomics and phylogenetic reconstructions. After comprehensive in vivo and enzyme kinetic analyses of selected PriA homologs, a novel (βα)8 isomerase subfamily with a specialized function in l-histidine biosynthesis, termed subHisA, was confirmed. X-ray crystallography was used to reveal active-site mutations in subHisA important for narrowing of substrate specificity, which when mutated to the naturally occurring amino acid in PriA led to gain of function. Moreover, in silico molecular dynamic analyses demonstrated that the narrowing of substrate specificity of subHisA is concomitant with loss of ancestral protein conformational states. Our results show the importance of HGT in shaping enzyme evolution and metabolism.

  12. Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: involvement of an ancient horizontal gene transfer

    SciTech Connect

    Scholten, Johannes C.; Culley, David E.; Brockman, Fred J.; Wu, Gang; Zhang, Weiwen

    2007-01-05

    The sulfate reducing bacteria Desulfovibrio vulgaris and the methanogenic archaea Methanosarcina barkeri can grow syntrophically on lactate. In this study, three functionally unknown genes of D. vulgaris, DVU2103, DVU2104 and DVU2108, were found to be up-regulated 2-4 fold following the lifestyle shift from syntroph to sulfatereducer; moreover, none of these genes were regulated when D. vulgaris was grown alone in various pure culture conditions. These results suggest that these genes may play roles related to the lifestyle change of D. vulgaris from syntroph to sulfate reducer. This hypothesis is further supported by phylogenomic analyses showing that homologies of these genes were only narrowly present in several groups of bacteria, most of which are restricted to a syntrophic life-style, such as Pelobacter carbinolicus, Syntrophobacter fumaroxidans, Syntrophomonas wolfei and Syntrophus aciditrophicus. Phylogenetic analysis showed that the genes tended to be clustered with archaeal genera, and they were rooted on archaeal species in the phylogenetic trees, suggesting that they originated from an archaeal methanogen and were horizontally transferred to a common ancestor of delta- Proteobacteria, Clostridia and Thermotogae. While lost in most species during evolution, these genes appear to have been retained in bacteria capable of syntrophic relationships, probably due to their providing a selective advantage. In addition, no significant bias in codon and amino acid usages was detected between these genes and the rest of the D. vulgaris genome, suggesting these gene transfers may have occurred early in the evolutionary history so that sufficient time has elapsed to allow an adaptation to the codon and amino acid usages of D. vulgaris. This report provides novel insights into the origin and evolution of bacterial genes involved in the syntrophic lifestyle.

  13. Retinoblastoma (Rb) regulates laminar dendritic arbor reorganization in retinal horizontal neurons

    SciTech Connect

    Martins, Rodrigo; Davis, Denise; Dyer, Michael; Kerekes, Ryan A; Zhang, Jiakun; Bayazitov, Ildar; Hiler, Daniel; Karakaya, Mahmut; Frase, Sharon; Gleason, Shaun Scott; Zakharenko, Stanislav S; Johnson, Dianna

    2011-01-01

    Neuronal differentiation with respect to the acquisition of synaptic competence needs to be regulated precisely during neurogenesis to ensure proper formation of circuits at the right place and time in development.This regulation is particularly important for synaptic triads among photoreceptors, horizontal cells (HCs), and bipolar cells in the retina, because HCs are among the rst cell types produced during development, and bipolar cells are among thel ast.HCs undergo a dramatic transition from vertically oriented neurites that form columnar arbors to overlapping laminar dendritic arbors with differentiation.However, how this process is regulated and coordinated with differentiation of photoreceptors and bipolar cells remains unknown. Previous studies have suggested that there tino-blastoma(Rb) tumor suppressor gene may play a role in horizontal cell differentiation and synaptogenesis. By combining genetic mosaic analysis of individual synaptictriads with neuroanatomic analyses and multiphoton live imaging of developing HCs, we found that Rb plays a cell-autonomous role in there organization of horizontal cell neurites as they differentiate. Aberrant vertical processes in Rb-de cient HCs form ectopic synapses with rods in the outer nuclear layer but lack bipolar dendrites. Although previous reports indicate that photoreceptor abnormalities can trigger formation of ectopic synapses, our studies now demonstrate that defects in a post synaptic partner contribute to the formation of ectopic photoreceptor synapses in the mammalian retina.

  14. Influence of exogenous melatonin on horizontal transfer of Escherichia coli O157:H7 in experimentally infected sheep

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of the current research was to determine if exogenous melatonin would exert a “protective” effect on the gastrointestinal tract of sheep and prevent or reduce the horizontal transfer of E. coli O157:H7 from experimentally-infected to non-infected or “naïve” sheep. Sixteen crossbred ewe...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  16. Horizontal transfer and gene conversion as an important driving force in shaping the landscape of mitochondrial introns.

    PubMed

    Wu, Baojun; Hao, Weilong

    2014-04-16

    Group I introns are highly dynamic and mobile, featuring extensive presence-absence variation and widespread horizontal transfer. Group I introns can invade intron-lacking alleles via intron homing powered by their own encoded homing endonuclease gene (HEG) after horizontal transfer or via reverse splicing through an RNA intermediate. After successful invasion, the intron and HEG are subject to degeneration and sequential loss. It remains unclear whether these mechanisms can fully address the high dynamics and mobility of group I introns. Here, we found that HEGs undergo a fast gain-and-loss turnover comparable with introns in the yeast mitochondrial 21S-rRNA gene, which is unexpected, as the intron and HEG are generally believed to move together as a unit. We further observed extensively mosaic sequences in both the introns and HEGs, and evidence of gene conversion between HEG-containing and HEG-lacking introns. Our findings suggest horizontal transfer and gene conversion can accelerate HEG/intron degeneration and loss, or rescue and propagate HEG/introns, and ultimately result in high HEG/intron turnover rate. Given that up to 25% of the yeast mitochondrial genome is composed of introns and most mitochondrial introns are group I introns, horizontal transfer and gene conversion could have served as an important mechanism in introducing mitochondrial intron diversity, promoting intron mobility and consequently shaping mitochondrial genome architecture.

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

    PubMed

    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.

  18. Toxicity and horizontal transfer of 0.5% fipronil dust against Formosan subterranean termites.

    PubMed

    Gautam, Bal K; Henderson, Gregg; Davis, Robert W

    2012-10-01

    The toxicity and horizontal transfer of a new formulation of fipronil, 0.5% fipronil dust, was tested against Coptotermes formosanus Shiraki in the laboratory. The formulation was applied in three different ways: 1) Directly applied to termites (donors) and mixed with untreated termites (recipients) at three ratios, viz., 50 donors: 50 recipients, 20 donors: 80 recipients and 10 donors: 90 recipients. 2) Applied onto the surface of 3 mm thick sand or soil substrate in a petri dish and then topped with another 3 mm thick sand or soil layer whereupon termites were released. 3) Applied to the inner surface of a tube (either 5 cm or 15 cm long) that connected two foraging dishes, one containing dry sand and the other moist sand plus a wood block and termites were released into the dry sand dish. All donors and >93% of the recipients were dead by 42 h after treatment in the direct treatment experiment. Significant mortalities of both donors and recipients were observed at 5 h after treatment at all donor: recipient ratios. During this period, the mortality of the recipients (but not donors) at 10:90 was significantly lower than those at the other two ratios. All termites were dead at 65 h after exposure (HAE) on the sand treatment and at 190 HAE on soil treatment. More than 96% mortality was observed at 40 HAE on the sand treatment as compared with only 6% mortality onsoil treatment during the same time period. In the tube treatment experiment, > 97% mortality was observed at 90 h after release for both tube lengths as compared with < 3% mortality in controls. About half of the termites were dead by 15 h after release regardless of the tube length. Our results showed that 0.5% fipronil dust is nonrepellent and readily transferred from treated to nontreated termites.

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

    PubMed Central

    Bhattacharyya, Sanchari; Manhart, Michael; Choi, Jeong-Mo; Mu, Wanmeng; Zhou, Jingwen; Shakhnovich, Eugene I.

    2015-01-01

    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 (k cat/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

  20. Novel “Superspreader” Bacteriophages Promote Horizontal Gene Transfer by Transformation

    PubMed Central

    Bliskovsky, Valery V.; Malagon, Francisco; Baker, James D.; Prince, Jeffrey S.; Klaus, James S.; Adhya, Sankar L.

    2017-01-01

    ABSTRACT Bacteriophages infect an estimated 1023 to 1025 bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub “superspreaders,” releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation. Two novel Escherichia coli phage superspreaders, SUSP1 and SUSP2, liberated four evolutionarily distinct plasmids with equal efficiency, including two close relatives of prominent antibiotic resistance vectors in natural environments. SUSP2 also mediated the extensive lateral transfer of antibiotic resistance in unbiased communities of soil bacteria from Maryland and Wyoming. Furthermore, the addition of SUSP2 to cocultures of kanamycin-resistant E. coli and kanamycin-sensitive Bacillus sp. bacteria resulted in roughly 1,000-fold more kanamycin-resistant Bacillus sp. bacteria than arose in phage-free controls. Unlike many other lytic phages, neither SUSP1 nor SUSP2 encodes homologs to known hydrolytic endonucleases, suggesting a simple potential mechanism underlying the superspreading phenotype. Consistent with this model, the deletion of endonuclease IV and the nucleoid-disrupting protein ndd from coliphage T4, a phage known to extensively degrade chromosomal DNA, significantly increased its ability to promote plasmid transformation. Taken together, our results suggest that phage superspreaders may play key roles in microbial evolution and ecology but should be avoided in phage therapy and other medical applications. PMID:28096488

  1. Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer.

    PubMed

    Goremykin, Vadim V; Salamini, Francesco; Velasco, Riccardo; Viola, Roberto

    2009-01-01

    The mitochondrial genome of grape (Vitis vinifera), the largest organelle genome sequenced so far, is presented. The genome is 773,279 nt long and has the highest coding capacity among known angiosperm mitochondrial DNAs (mtDNAs). The proportion of promiscuous DNA of plastid origin in the genome is also the largest ever reported for an angiosperm mtDNA, both in absolute and relative terms. In all, 42.4% of chloroplast genome of Vitis has been incorporated into its mitochondrial genome. In order to test if horizontal gene transfer (HGT) has also contributed to the gene content of the grape mtDNA, we built phylogenetic trees with the coding sequences of mitochondrial genes of grape and their homologs from plant mitochondrial genomes. Many incongruent gene tree topologies were obtained. However, the extent of incongruence between these gene trees is not significantly greater than that observed among optimal trees for chloroplast genes, the common ancestry of which has never been in doubt. In both cases, we attribute this incongruence to artifacts of tree reconstruction, insufficient numbers of characters, and gene paralogy. This finding leads us to question the recent phylogenetic interpretation of Bergthorsson et al. (2003, 2004) and Richardson and Palmer (2007) that rampant HGT into the mtDNA of Amborella best explains phylogenetic incongruence between mitochondrial gene trees for angiosperms. The only evidence for HGT into the Vitis mtDNA found involves fragments of two coding sequences stemming from two closteroviruses that cause the leaf roll disease of this plant. We also report that analysis of sequences shared by both chloroplast and mitochondrial genomes provides evidence for a previously unknown gene transfer route from the mitochondrion to the chloroplast.

  2. Think laterally: horizontal gene transfer from symbiotic microbes may extend the phenotype of marine sessile hosts

    PubMed Central

    Degnan, Sandie M.

    2014-01-01

    Since the origin of the animal kingdom, marine animals have lived in association with viruses, prokaryotes and unicellular eukaryotes, often as symbionts. This long and continuous interaction has provided ample opportunity not only for the evolution of intimate interactions such as sharing of metabolic pathways, but also for horizontal gene transfer (HGT) of non-metazoan genes into metazoan genomes. The number of demonstrated cases of inter-kingdom HGT is currently small, such that it is not yet widely appreciated as a significant player in animal evolution. Sessile marine invertebrates that vertically inherit bacterial symbionts, that have no dedicated germ line, or that bud or excise pluripotent somatic cells during their life history may be particularly receptive to HGT from their symbionts. Closer scrutiny of the growing number of genomes being accrued for these animals may thus reveal HGT as a regular source of novel variation that can function to extend the host phenotype metabolically, morphologically, or even behaviorally. Taxonomic identification of symbionts will help to address the intriguing question of whether past HGT events may constrain contemporary symbioses. PMID:25477875

  3. No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini

    PubMed Central

    Koutsovoulos, Georgios; Laetsch, Dominik R.; Stevens, Lewis; Daub, Jennifer; Conlon, Claire; Maroon, Habib; Thomas, Fran; Aboobaker, Aziz A.

    2016-01-01

    Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper [Boothby TC, et al. (2015) Proc Natl Acad Sci USA 112(52):15976–15981], the authors concluded that the tardigrade Hypsibius dujardini had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT) and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of H. dujardini. As expected from whole-organism DNA sampling, our raw data contained reads from nontarget genomes. Filtering using metagenomics approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria and 0.2% strong candidates for fHGT from nonmetazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby et al. genome derived from contaminants. We conclude that fHGT into H. dujardini accounts for at most 1–2% of genes and that the proposal that one-sixth of tardigrade genes originate from functional HGT events is an artifact of undetected contamination. PMID:27035985

  4. TRT, a Vertebrate and Protozoan Tc1-Like Transposon: Current Activity and Horizontal Transfer.

    PubMed

    Zhang, Hua-Hao; Li, Guo-Yin; Xiong, Xiao-Min; Han, Min-Jin; Zhang, Xiao-Gu; Dai, Fang-Yin

    2016-10-05

    We report a Danio rerio transposon named DrTRT, for D. rerio Transposon Related to Tc1 The complete sequence of the DrTRT transposon is 1,563 base pairs (bp) in length, and its transposase putatively encodes a 338-amino acid protein that harbors a DD37E motif in its catalytic domain. We present evidence based on searches of publicly available genomes that TRT elements commonly occur in vertebrates and protozoa. Phylogenetic and functional domain comparisons confirm that TRT constitutes a new subfamily within the Tc1 family. Hallmark features of having no premature termination codons within the transposase, the presence of all expected functional domains, and its occurrence in the bony fish transcriptome suggest that TRT might have current or recent activity in these species. Further analysis showed that the activity of TRT elements in these species might have arisen about between 4 and 19 Ma. Interestingly, our results also implied that the widespread distribution of TRT among fishes, frog, and snakes is the result of multiple independent HT events, probably from bony fishes to snakes or frog. Finally, the mechanisms underlying horizontal transfer of TRT elements are discussed.

  5. Family of Tc1-like elements from fish genomes and horizontal transfer.

    PubMed

    Pocwierz-Kotus, Anita; Burzynski, Artur; Wenne, Roman

    2007-04-01

    The involvement of horizontal transfer (HT) in the evolution of vertebrate transposable elements (TEs) is a matter of an ongoing debate. The phylogenetic relationships between Tc1 TEs, based on limited dataset have been previously used to infer a case of Tc1 HT between the genomes of fish and frogs. Here this hypothesis has been critically evaluated by the experimental approach including comparative data on the range of fish species available today. The distribution of a Tc1 subfamily of TE in selected fish species was investigated by PCR with a single primer complementary to ITRs and showed that they are widespread in the studied 17 fish species. They belong to five different subfamilies of Tc1 TEs, as revealed by the comparison with current genomic data for fish and amphibians. The original hypothesis would get much weaker support from the current data, although at least one novel potential and more convincing case of HT was identified between genomes of Perciformes fish. An interesting case of recombination-driven mobilisation of a degenerated TE by distantly related TE from different subfamily was discovered in the genome of pike. The occurrence of such cases widens the range of TE elements identifiable with the employed experimental approach. Further similar studies would help to explain the evolution of the multiple Tc1 lineages including species for which full genome sequences will not be available soon.

  6. Achromobacter xylosoxidans: an emerging pathogen carrying different elements involved in horizontal genetic transfer.

    PubMed

    Traglia, German Matías; Almuzara, Marisa; Merkier, Andrea Karina; Adams, Christina; Galanternik, Laura; Vay, Carlos; Centrón, Daniela; Ramírez, María Soledad

    2012-12-01

    In the last few years, numerous cases of multidrug-resistant Achromobacter xylosoxidans infections have been documented in immunocompromised and cystic fibrosis patients. To gain insights into the molecular mechanisms and mobile elements related to multidrug resistance in this bacterium, we studied 24 non-epidemiological A. xylosoxidans clinical isolates from Argentina. Specific primers for plasmids, transposons, insertion sequences, bla(ampC), intI1, and intI2 genes were used in PCR reactions. The obtained results showed the presence of wide host range IncP plasmids in ten isolates and a high dispersion of class 1 integrons (n = 10) and class 2 integrons (n = 3). Four arrays in the variable region (vr) of class 1 integrons were identified carrying different gene cassettes as the aminoglycoside resistance aac(6')-Ib and aadA1, the trimethoprim resistance dfrA1 and dfrA16, and the β-lactamase bla(OXA-2). In only one of the class 2 integrons, a vr was amplified that includes sat2-aadA1. The bla(ampC) gene was found in all isolates, confirming its ubiquitous nature. Our results show that A. xylosoxidans clinical isolates contain a rich variety of genetic elements commonly associated with resistance genes and their dissemination. This supports the hypothesis that A. xylosoxidans is becoming a reservoir of horizontal genetic transfer elements commonly involved in spreading antibiotic resistance.

  7. Heat transfer enhancement of PCM melting in 2D horizontal elliptical tube using metallic porous matrix

    NASA Astrophysics Data System (ADS)

    Jourabian, Mahmoud; Farhadi, Mousa; Rabienataj Darzi, Ahmad Ali

    2016-12-01

    In this study, the melting process of ice as a phase-change material (PCM) saturated with a nickel-steel porous matrix inside a horizontal elliptical tube is investigated. Due to the low thermal conductivity of the PCM, it is motivated to augment the heat transfer performance of the system simultaneously by finding an optimum value of the aspect ratio and impregnating a metallic porous matrix into the base PCM. The lattice Boltzmann method with a double distribution function formulated based on the enthalpy method, is applied at the representative elementary volume scale under the local thermal equilibrium assumption between the PCM and porous matrix in the composite. While reducing or increasing the aspect ratio of the circular tubes leads to the expedited melting, the 90° inclination of each elliptical tube in the case of the pure PCM melting does not affect the melting rate. With the reduction in the porosity, the effective thermal conductivity and melting rate in all tubes promoted. Although the natural convection is fully suppressed due to the significant flow blockage in the porous structure, the melting rates are generally increased in all cases.

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

    PubMed

    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.

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

    PubMed Central

    Labonté, Jessica M.; Field, Erin K.; Lau, Maggie; Chivian, Dylan; Van Heerden, Esta; Wommack, K. Eric; Kieft, Thomas L.; Onstott, Tullis C.; Stepanauskas, Ramunas

    2015-01-01

    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 3 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. PMID:25954269

  10. The role of horizontal gene transfer in kleptoplastidy and the establishment of photosynthesis in the eukaryotes

    PubMed Central

    Pillet, Loïc

    2013-01-01

    Found in different eukaryotic lineages, kleptoplastidy is the ability to sequester chloroplasts from algal preys that are ingested and partially digested. While most of the genetic information required for the activity and maintenance of the kleptoplastids disappeared with the digestion of the algal nuclei, the photosynthetic organelles remain active during extended period of time. Many different hypotheses have been proposed to explain the longevity of the kleptoplastids within their host. The most popular one involves Horizontal Gene Transfer (HGT) from the algal genome to the host nucleus. In order to test this hypothesis, transcriptome-based analyses have been performed on different kleptoplastidic organisms during the past few years. However, the variability of the results obtained does not allow drawing a convincing conclusion regarding the precise role of HGT in kleptoplastidy. Understanding the mechanism that allow persistence of the plastids is crucial, not only for the characterization of kleptoplastidy, but also for important evolutionary questions surrounding endosymbiotic events and the emergence and spread of photosynthesis in the eukaryotes. Here, I discuss alternative theories that could explain the longevity of sequestered plastids in their host, with special focus on the simplest chloroplast stability hypothesis. PMID:23914312

  11. The Genetic Analysis of an Acinetobacter johnsonii Clinical Strain Evidenced the Presence of Horizontal Genetic Transfer.

    PubMed

    Montaña, Sabrina; Schramm, Sareda T J; Traglia, German Matías; Chiem, Kevin; Parmeciano Di Noto, Gisela; Almuzara, Marisa; Barberis, Claudia; Vay, Carlos; Quiroga, Cecilia; Tolmasky, Marcelo E; Iriarte, Andrés; Ramírez, María Soledad

    2016-01-01

    Acinetobacter johnsonii rarely causes human infections. While most A. johnsonii isolates are susceptible to virtually all antibiotics, strains harboring a variety of β-lactamases have recently been described. An A. johnsonii Aj2199 clinical strain recovered from a hospital in Buenos Aires produces PER-2 and OXA-58. We decided to delve into its genome by obtaining the whole genome sequence of the Aj2199 strain. Genome comparison studies on Aj2199 revealed 240 unique genes and a close relation to strain WJ10621, isolated from the urine of a patient in China. Genomic analysis showed evidence of horizontal genetic transfer (HGT) events. Forty-five insertion sequences and two intact prophages were found in addition to several resistance determinants such as blaPER-2, blaOXA-58, blaTEM-1, strA, strB, ereA, sul1, aacC2 and a new variant of blaOXA-211, called blaOXA-498. In particular, blaPER-2 and blaTEM-1 are present within the typical contexts previously described in the Enterobacteriaceae family. These results suggest that A. johnsonii actively acquires exogenous DNA from other bacterial species and concomitantly becomes a reservoir of resistance genes.

  12. Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee

    PubMed Central

    Acuña, Ricardo; Padilla, Beatriz E.; Flórez-Ramos, Claudia P.; Rubio, José D.; Herrera, Juan C.; Benavides, Pablo; Lee, Sang-Jik; Yeats, Trevor H.; Egan, Ashley N.; Doyle, Jeffrey J.; Rose, Jocelyn K. C.

    2012-01-01

    Horizontal gene transfer (HGT) involves the nonsexual transmission of genetic material across species boundaries. Although often detected in prokaryotes, examples of HGT involving animals are relatively rare, and any evolutionary advantage conferred to the recipient is typically obscure. We identified a gene (HhMAN1) from the coffee berry borer beetle, Hypothenemus hampei, a devastating pest of coffee, which shows clear evidence of HGT from bacteria. HhMAN1 encodes a mannanase, representing a class of glycosyl hydrolases that has not previously been reported in insects. Recombinant HhMAN1 protein hydrolyzes coffee berry galactomannan, the major storage polysaccharide in this species and the presumed food of H. hampei. HhMAN1 was found to be widespread in a broad biogeographic survey of H. hampei accessions, indicating that the HGT event occurred before radiation of the insect from West Africa to Asia and South America. However, the gene was not detected in the closely related species H. obscurus (the tropical nut borer or “false berry borer”), which does not colonize coffee beans. Thus, HGT of HhMAN1 from bacteria represents a likely adaptation to a specific ecological niche and may have been promoted by intensive agricultural practices. PMID:22371593

  13. No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini.

    PubMed

    Koutsovoulos, Georgios; Kumar, Sujai; Laetsch, Dominik R; Stevens, Lewis; Daub, Jennifer; Conlon, Claire; Maroon, Habib; Thomas, Fran; Aboobaker, Aziz A; Blaxter, Mark

    2016-05-03

    Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper [Boothby TC, et al. (2015) Proc Natl Acad Sci USA 112(52):15976-15981], the authors concluded that the tardigrade Hypsibius dujardini had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT) and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of H. dujardini As expected from whole-organism DNA sampling, our raw data contained reads from nontarget genomes. Filtering using metagenomics approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria and 0.2% strong candidates for fHGT from nonmetazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby et al. genome derived from contaminants. We conclude that fHGT into H. dujardini accounts for at most 1-2% of genes and that the proposal that one-sixth of tardigrade genes originate from functional HGT events is an artifact of undetected contamination.

  14. Horizontal gene transfer drives adaptive colonization of apple trees by the fungal pathogen Valsa mali

    PubMed Central

    Yin, Zhiyuan; Zhu, Baitao; Feng, Hao; Huang, Lili

    2016-01-01

    Horizontal gene transfer (HGT) often has strong benefits for fungi. In a study of samples from apple canker in Shaanxi Province, China, diverse microbes, along with the necrotrophic pathogen Valsa mali, were found to colonize the apple bark, thus providing ample opportunity for HGT to occur. In the present study, we identified 32 HGT events in V. mali by combining phyletic distribution-based methods with phylogenetic analyses. Most of these HGTs were from bacteria, whereas several others were from eukaryotes. Three HGTs putatively functioned in competition with actinomycetes, some of which showed a significant inhibitory effect on V. mali. Three HGTs that were probably involved in nitrogen uptake were also identified. Ten HGTs were thought to be involved in pathogenicity because they were related to known virulence factors, including cell wall-degrading enzymes and candidate effector proteins. HGT14, together with HGT32, was shown to contribute to bleomycin resistance of V. mali.These results suggest that HGT drives the adaptive evolution of V. mali. The HGTs identified here provide new clues for unveiling the adaptation mechanisms and virulence determinants of V. mali. PMID:27634406

  15. The Genetic Analysis of an Acinetobacter johnsonii Clinical Strain Evidenced the Presence of Horizontal Genetic Transfer

    PubMed Central

    Montaña, Sabrina; Schramm, Sareda T. J.; Traglia, German Matías; Chiem, Kevin; Parmeciano Di Noto, Gisela; Almuzara, Marisa; Barberis, Claudia; Vay, Carlos; Quiroga, Cecilia; Tolmasky, Marcelo E.; Iriarte, Andrés; Ramírez, María Soledad

    2016-01-01

    Acinetobacter johnsonii rarely causes human infections. While most A. johnsonii isolates are susceptible to virtually all antibiotics, strains harboring a variety of β-lactamases have recently been described. An A. johnsonii Aj2199 clinical strain recovered from a hospital in Buenos Aires produces PER-2 and OXA-58. We decided to delve into its genome by obtaining the whole genome sequence of the Aj2199 strain. Genome comparison studies on Aj2199 revealed 240 unique genes and a close relation to strain WJ10621, isolated from the urine of a patient in China. Genomic analysis showed evidence of horizontal genetic transfer (HGT) events. Forty-five insertion sequences and two intact prophages were found in addition to several resistance determinants such as blaPER-2, blaOXA-58, blaTEM-1, strA, strB, ereA, sul1, aacC2 and a new variant of blaOXA-211, called blaOXA-498. In particular, blaPER-2 and blaTEM-1 are present within the typical contexts previously described in the Enterobacteriaceae family. These results suggest that A. johnsonii actively acquires exogenous DNA from other bacterial species and concomitantly becomes a reservoir of resistance genes. PMID:27548264

  16. Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer

    PubMed Central

    von Wintersdorff, Christian J. H.; Penders, John; van Niekerk, Julius M.; Mills, Nathan D.; Majumder, Snehali; van Alphen, Lieke B.; Savelkoul, Paul H. M.; Wolffs, Petra F. G.

    2016-01-01

    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. PMID:26925045

  17. Horizontal Gene Transfer of Phytochelatin Synthases from Bacteria to Extremophilic Green Algae.

    PubMed

    Olsson, Sanna; Penacho, Vanessa; Puente-Sánchez, Fernando; Díaz, Silvia; Gonzalez-Pastor, José Eduardo; Aguilera, Angeles

    2017-01-01

    Transcriptomic sequencing together with bioinformatic analyses and an automated annotation process led us to identify novel phytochelatin synthase (PCS) genes from two extremophilic green algae (Chlamydomonas acidophila and Dunaliella acidophila). These genes are of intermediate length compared to known PCS genes from eukaryotes and PCS-like genes from prokaryotes. A detailed phylogenetic analysis gives new insight into the complicated evolutionary history of PCS genes and provides evidence for multiple horizontal gene transfer events from bacteria to eukaryotes within the gene family. A separate subgroup containing PCS-like genes within the PCS gene family is not supported since the PCS genes are monophyletic only when the PCS-like genes are included. The presence and functionality of the novel genes in the organisms were verified by genomic sequencing and qRT-PCR. Furthermore, the novel PCS gene in Chlamydomonas acidophila showed very strong induction by cadmium. Cloning and expression of the gene in Escherichia coli clearly improves its cadmium resistance. The gene in Dunaliella was not induced, most likely due to gene duplication.

  18. Comparative analysis of magnetosome gene clusters in magnetotactic bacteria provides further evidence for horizontal gene transfer.

    PubMed

    Jogler, Christian; Kube, Michael; Schübbe, Sabrina; Ullrich, Susanne; Teeling, Hanno; Bazylinski, Dennis A; Reinhardt, Richard; Schüler, Dirk

    2009-05-01

    The organization of magnetosome genes was analysed in all available complete or partial genomic sequences of magnetotactic bacteria (MTB), including the magnetosome island (MAI) of the magnetotactic marine vibrio strain MV-1 determined in this study. The MAI was found to differ in gene content and organization between Magnetospirillum species and strains MV-1 or MC-1. Although a similar organization of magnetosome genes was found in all MTB, distinct variations in gene order and sequence similarity were uncovered that may account for the observed diversity of biomineralization, cell biology and magnetotaxis found in various MTB. While several magnetosome genes were present in all MTB, others were confined to Magnetospirillum species, indicating that the minimal set of genes required for magnetosome biomineralization might be smaller than previously suggested. A number of novel candidate genes were implicated in magnetosome formation by gene cluster comparison. Based on phylogenetic and compositional evidence we present a model for the evolution of magnetotaxis within the Alphaproteobacteria, which suggests the independent horizontal transfer of magnetosome genes from an unknown ancestor of magnetospirilla into strains MC-1 and MV-1.

  19. Multiple horizontal transfers of nuclear ribosomal genes between phylogenetically distinct grass lineages

    PubMed Central

    Mahelka, Václav; Krak, Karol; Kopecký, David; Fehrer, Judith; Šafář, Jan; Bartoš, Jan; Hobza, Roman; Blavet, Nicolas; Blattner, Frank R.

    2017-01-01

    The movement of nuclear DNA from one vascular plant species to another in the absence of fertilization is thought to be rare. Here, nonnative rRNA gene [ribosomal DNA (rDNA)] copies were identified in a set of 16 diploid barley (Hordeum) species; their origin was traceable via their internal transcribed spacer (ITS) sequence to five distinct Panicoideae genera, a lineage that split from the Pooideae about 60 Mya. Phylogenetic, cytogenetic, and genomic analyses implied that the nonnative sequences were acquired between 1 and 5 Mya after a series of multiple events, with the result that some current Hordeum sp. individuals harbor up to five different panicoid rDNA units in addition to the native Hordeum rDNA copies. There was no evidence that any of the nonnative rDNA units were transcribed; some showed indications of having been silenced via pseudogenization. A single copy of a Panicum sp. rDNA unit present in H. bogdanii had been interrupted by a native transposable element and was surrounded by about 70 kbp of mostly noncoding sequence of panicoid origin. The data suggest that horizontal gene transfer between vascular plants is not a rare event, that it is not necessarily restricted to one or a few genes only, and that it can be selectively neutral. PMID:28137844

  20. Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee.

    PubMed

    Acuña, Ricardo; Padilla, Beatriz E; Flórez-Ramos, Claudia P; Rubio, José D; Herrera, Juan C; Benavides, Pablo; Lee, Sang-Jik; Yeats, Trevor H; Egan, Ashley N; Doyle, Jeffrey J; Rose, Jocelyn K C

    2012-03-13

    Horizontal gene transfer (HGT) involves the nonsexual transmission of genetic material across species boundaries. Although often detected in prokaryotes, examples of HGT involving animals are relatively rare, and any evolutionary advantage conferred to the recipient is typically obscure. We identified a gene (HhMAN1) from the coffee berry borer beetle, Hypothenemus hampei, a devastating pest of coffee, which shows clear evidence of HGT from bacteria. HhMAN1 encodes a mannanase, representing a class of glycosyl hydrolases that has not previously been reported in insects. Recombinant HhMAN1 protein hydrolyzes coffee berry galactomannan, the major storage polysaccharide in this species and the presumed food of H. hampei. HhMAN1 was found to be widespread in a broad biogeographic survey of H. hampei accessions, indicating that the HGT event occurred before radiation of the insect from West Africa to Asia and South America. However, the gene was not detected in the closely related species H. obscurus (the tropical nut borer or "false berry borer"), which does not colonize coffee beans. Thus, HGT of HhMAN1 from bacteria represents a likely adaptation to a specific ecological niche and may have been promoted by intensive agricultural practices.

  1. Horizontal gene transfer among microorganisms in food: current knowledge and future perspectives.

    PubMed

    Rossi, Franca; Rizzotti, Lucia; Felis, Giovanna E; Torriani, Sandra

    2014-09-01

    The possibility of horizontal gene transfer (HGT) among microorganisms in food matrices has been specifically targeted in a few investigations, though most current knowledge has been obtained indirectly or derived from genome sequence analyses. In this review, we have assembled reported examples of the HGT events that probably occurred in food matrices since the bacterial partners involved are commonly found in association in a food matrix or are specifically adapted to it. Exchanged genes include those encoding for substrate utilization, bacteriocin, exopolysaccharide and biogenic amine (BA) production, immunity to bacteriophages and antibiotic resistance (AR). While the acquisition of new traits involved in substrate utilization led to the natural genetic improvement of the microbial cultures for food production, the acquisition of hazardous traits, e.g., AR, virulence or BA production genes, can give rise to health concerns in otherwise innocuous species. Available evidence suggests that it would be opportune to determine what conditions favour HGT among bacteria in food ecosystems in order to naturally obtain improved starter or adjunct cultures, and also to prevent the propagation of hazardous traits.

  2. Viridans Group Streptococci Are Donors in Horizontal Transfer of Topoisomerase IV Genes to Streptococcus pneumoniae

    PubMed Central

    Balsalobre, Luz; Ferrándiz, María José; Liñares, Josefina; Tubau, Fe; de la Campa, Adela G.

    2003-01-01

    A total of 46 ciprofloxacin-resistant (Cipr) Streptococcus pneumoniae strains were isolated from 1991 to 2001 at the Hospital of Bellvitge. Five of these strains showed unexpectedly high rates of nucleotide variations in the quinolone resistance-determining regions (QRDRs) of their parC, parE, and gyrA genes. The nucleotide sequence of the full-length parC, parE, and gyrA genes of one of these isolates revealed a mosaic structure compatible with an interspecific recombination origin. Southern blot analysis and nucleotide sequence determinations showed the presence of an ant-like gene in the intergenic parE-parC regions of the S. pneumoniae Cipr isolates with high rates of variations in their parE and parC QRDRs. The ant-like gene was absent from typical S. pneumoniae strains, whereas it was present in the intergenic parE-parC regions of the viridans group streptococci (Streptococcus mitis and Streptococcus oralis). These results suggest that the viridans group streptococci are acting as donors in the horizontal transfer of fluoroquinolone resistance genes to S. pneumoniae. PMID:12821449

  3. Ancient horizontal transfer of transaldolase-like protein gene and its role in plant vascular development.

    PubMed

    Yang, Zefeng; Zhou, Yong; Huang, Jinling; Hu, Yunyun; Zhang, Enying; Xie, Zhengwen; Ma, Sijia; Gao, Yun; Song, Song; Xu, Chenwu; Liang, Guohua

    2015-04-01

    A major event in land plant evolution is the origin of vascular tissues, which ensure the long-distance transport of water, nutrients and organic compounds. However, the molecular basis for the origin and evolution of plant vascular tissues remains largely unknown. Here, we investigate the evolution of the land plant TAL-type transaldolase (TAL) gene and its potential function in rice (Oryza sativa) based on phylogenetic analyses and transgenic experiments, respectively. TAL genes are only present in land plants and bacteria. Phylogenetic analyses suggest that land plant TAL genes are derived from Actinobacteria through an ancient horizontal gene transfer (HGT) event. Further evidence reveals that land plant TAL genes have undergone positive selection and gained several introns following its acquisition by the most recent common ancestor of land plants. Transgenic plant experiments show that rice TAL is specifically expressed in vascular tissues and that knockdown of TAL expression leads to changes in both the number and pattern of vascular bundles. Our findings show that the ancient HGT of TAL from bacteria probably plays an important role in plant vascular development and adaptation to land environments.

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

    PubMed Central

    López-Madrigal, Sergio; Beltrà, Aleixandre; Resurrección, Serena; Soto, Antonia; Latorre, Amparo; Moya, Andrés; Gil, Rosario

    2014-01-01

    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. PMID:25206351

  5. Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer

    PubMed Central

    Mosig, Gisela; Gewin, John; Luder, Andreas; Colowick, Nancy; Vo, Daniel

    2001-01-01

    Two major pathways of recombination-dependent DNA replication, “join-copy” and “join-cut-copy,” can be distinguished in phage T4: join-copy requires only early and middle genes, but two late proteins, endonuclease VII and terminase, are uniquely important in the join-cut-copy pathway. In wild-type T4, timing of these pathways is integrated with the developmental program and related to transcription and packaging of DNA. In primase mutants, which are defective in origin-dependent lagging-strand DNA synthesis, the late pathway can bypass the lack of primers for lagging-strand DNA synthesis. The exquisitely regulated synthesis of endo VII, and of two proteins from its gene, explains the delay of recombination-dependent DNA replication in primase (as well as topoisomerase) mutants, and the temperature-dependence of the delay. Other proteins (e.g., the single-stranded DNA binding protein and the products of genes 46 and 47) are important in all recombination pathways, but they interact differently with other proteins in different pathways. These homologous recombination pathways contribute to evolution because they facilitate acquisition of any foreign DNA with limited sequence homology during horizontal gene transfer, without requiring transposition or site-specific recombination functions. Partial heteroduplex repair can generate what appears to be multiple mutations from a single recombinational intermediate. The resulting sequence divergence generates barriers to formation of viable recombinants. The multiple sequence changes can also lead to erroneous estimates in phylogenetic analyses. PMID:11459968

  6. A Complete Set of Flagellar Genes Acquired by Horizontal Transfer Coexists with the Endogenous Flagellar System in Rhodobacter sphaeroides▿ †

    PubMed Central

    Poggio, Sebastian; Abreu-Goodger, Cei; Fabela, Salvador; Osorio, Aurora; Dreyfus, Georges; Vinuesa, Pablo; Camarena, Laura

    2007-01-01

    Bacteria swim in liquid environments by means of a complex rotating structure known as the flagellum. Approximately 40 proteins are required for the assembly and functionality of this structure. Rhodobacter sphaeroides has two flagellar systems. One of these systems has been shown to be functional and is required for the synthesis of the well-characterized single subpolar flagellum, while the other was found only after the genome sequence of this bacterium was completed. In this work we found that the second flagellar system of R. sphaeroides can be expressed and produces a functional flagellum. In many bacteria with two flagellar systems, one is required for swimming, while the other allows movement in denser environments by producing a large number of flagella over the entire cell surface. In contrast, the second flagellar system of R. sphaeroides produces polar flagella that are required for swimming. Expression of the second set of flagellar genes seems to be positively regulated under anaerobic growth conditions. Phylogenic analysis suggests that the flagellar system that was initially characterized was in fact acquired by horizontal transfer from a γ-proteobacterium, while the second flagellar system contains the native genes. Interestingly, other α-proteobacteria closely related to R. sphaeroides have also acquired a set of flagellar genes similar to the set found in R. sphaeroides, suggesting that a common ancestor received this gene cluster. PMID:17293429

  7. Polymorphism of CRISPR shows separated natural groupings of Shigella subtypes and evidence of horizontal transfer of CRISPR.

    PubMed

    Yang, Chaojie; Li, Peng; Su, Wenli; Li, Hao; Liu, Hongbo; Yang, Guang; Xie, Jing; Yi, Shengjie; Wang, Jian; Cui, Xianyan; Wu, Zhihao; Wang, Ligui; Hao, Rongzhang; Jia, Leili; Qiu, Shaofu; Song, Hongbin

    2015-01-01

    Clustered, regularly interspaced, short palindromic repeats (CRISPR) act as an adaptive RNA-mediated immune mechanism in bacteria. They can also be used for identification and evolutionary studies based on polymorphisms within the CRISPR locus. We amplified and analyzed 6 CRISPR loci from 237 Shigella strains belonging to the 4 species groups, as well as 13 Escherichia coli strains. The CRISPR-associated (cas) gene sequence arrays of these strains were screened and compared. The CRISPR sequences from Shigella were conserved among subtypes, suggesting that CRISPR may represent a new identification tool for the detection and discrimination of Shigella species. Secondary structure analysis showed a different stem-loop structure at the terminal repeat, suggesting a distinct recognition mechanism in the formation of crRNA. In addition, the presence of "self-target" spacers and polymorphisms within CRISPR in Shigella indicated a selective pressure for inhibition of this system, which has the potential to damage "self DNA." Homology analysis of spacers showed that CRISPR might be involved in the regulation of virulence transmission. Phylogenetic analysis based on CRISPR sequences from Shigella and E. coli indicated that although phenotypic properties maintain convergent evolution, the 4 Shigella species do not represent natural groupings. Surprisingly, comparative analysis of Shigella repeats with other species provided new evidence for CRISPR horizontal transfer. Our results suggested that CRISPR analysis is applicable for the detection of Shigella species and for investigation of evolutionary relationships.

  8. Stagnation point flow and heat transfer behavior of Cu-water nanofluid towards horizontal and exponentially stretching/shrinking cylinders

    NASA Astrophysics Data System (ADS)

    Sulochana, C.; Sandeep, N.

    2016-03-01

    In this study we analyzed the stagnation point flow and heat transfer behavior of Cu-water nanofluid towards horizontal and exponentially permeable stretching/shrinking cylinders in presence of suction/injection, heat source and shape of nanoparticles. The governing boundary layer equations are transformed to nonlinear ordinary differential equations using similarity transformation which are then solved numerically using bvp4c Matlab package. The influence of non-dimensional governing parameters on the flow field and heat transfer characteristics are discussed and presented through graphs and tables. The study indicates that the solutions for the horizontal and exponential cylinders are non-unique and shape of nanoparticles also influences the rate of heat transfer. Comparisons of the present results with existed studies are presented. Present study has an excellent agreement with the existed studies under some special conditions.

  9. Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori

    PubMed Central

    Saunders, Nigel J; Boonmee, Prawit; Peden, John F; Jarvis, Stephen A

    2005-01-01

    Background Horizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism as a whole. In this study we describe a new methodology combining aspects of established signature analysis with textual analysis approaches. This approach has been used to analyze the two available genome sequences of H. pylori. Results This gene-by-gene analysis reveals a wide range of genes related to both virulence behaviour and the strain differences that have been relatively recently acquired from other sequence backgrounds. These frequently involve single genes or small numbers of genes that are not associated with transposases or bacteriophage genes, nor with inverted repeats typically used as markers for horizontal transfer. In addition, clear examples of horizontal exchange in genes associated with 'core' metabolic functions were identified, supported by differences between the sequenced strains, including: ftsK, xerD and polA. In some cases it was possible to determine which strain represented the 'parent' and 'altered' states for insertion-deletion events. Different signature component lengths showed different sensitivities for the detection of some horizontally transferred genes, which may reflect different amelioration rates of sequence components. Conclusion New implementations of signature analysis that can be applied on a gene-by-gene basis for the identification of horizontally acquired sequences are described. These findings highlight the central role of the availability of homologous substrates in evolution mediated by horizontal exchange, and suggest that some components of the supposedly stable 'core genome' may actually be favoured targets for integration of foreign sequences because of their degree of conservation. PMID:15676066

  10. Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict

    PubMed Central

    Croucher, Nicholas J.; Mostowy, Rafal; Wymant, Christopher; Turner, Paul; Bentley, Stephen D.; Fraser, Christophe

    2016-01-01

    Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell–cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing “arms race.” Reduced rates of transformation have also been observed in cells infected by MGEs that

  11. Aerodynamic study of a stall regulated horizontal-axis wind turbine

    NASA Astrophysics Data System (ADS)

    Constantinescu, S. G.; Crunteanu, D. E.; Niculescu, M. L.

    2013-10-01

    The wind energy is deemed as one of the most durable energetic variants of the future because the wind resources are immense. Furthermore, one predicts that the small wind turbines will play a vital role in the urban environment. Unfortunately, the complexity and the price of pitch regulated small horizontal-axis wind turbines represent ones of the main obstacles to widespread the use in populated zones. Moreover, the energetic efficiency of small stall regulated wind turbines has to be high even at low and medium wind velocities because, usually the cities are not windy places. During the running stall regulated wind turbines, due to the extremely broad range of the wind velocity, the angle of attack can reach high values and some regions of the blade will show stall and post-stall behavior. This paper deals with stall and post-stall regimes because they can induce significant vibrations, fatigue and even the wind turbine failure.

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

    PubMed Central

    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

  13. Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum".

    PubMed

    Ullrich, Sophie R; González, Carolina; Poehlein, Anja; Tischler, Judith S; Daniel, Rolf; Schlömann, Michael; Holmes, David S; Mühling, Martin

    2016-01-01

    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

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

    PubMed Central

    2009-01-01

    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. PMID:19664275

  15. Multiple Inter-Kingdom Horizontal Gene Transfers in the Evolution of the Phosphoenolpyruvate Carboxylase Gene Family

    PubMed Central

    Wang, Wen; Su, Bing

    2012-01-01

    Pepcase is a gene encoding phosphoenolpyruvate carboxylase that exists in bacteria, archaea and plants,playing an important role in plant metabolism and development. Most plants have two or more pepcase genes belonging to two gene sub-families, while only one gene exists in other organisms. Previous research categorized one plant pepcase gene as plant-type pepcase (PTPC) while the other as bacteria-type pepcase (BTPC) because of its similarity with the pepcase gene found in bacteria. Phylogenetic reconstruction showed that PTPC is the ancestral lineage of plant pepcase, and that all bacteria, protistpepcase and BTPC in plants are derived from a lineage of pepcase closely related with PTPC in algae. However, their phylogeny contradicts the species tree and traditional chronology of organism evolution. Because the diversification of bacteria occurred much earlier than the origin of plants, presumably all bacterialpepcase derived from the ancestral PTPC of algal plants after divergingfrom the ancestor of vascular plant PTPC. To solve this contradiction, we reconstructed the phylogeny of pepcase gene family. Our result showed that both PTPC and BTPC are derived from an ancestral lineage of gamma-proteobacteriapepcases, possibly via an ancient inter-kingdom horizontal gene transfer (HGT) from bacteria to the eukaryotic common ancestor of plants, protists and cellular slime mold. Our phylogenetic analysis also found 48other pepcase genes originated from inter-kingdom HGTs. These results imply that inter-kingdom HGTs played important roles in the evolution of the pepcase gene family and furthermore that HGTsare a more frequent evolutionary event than previouslythought. PMID:23251445

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

    PubMed

    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.

  17. An evaluation of the ecological relationship between Drosophila species and their parasitoid wasps as an opportunity for horizontal transposon transfer.

    PubMed

    Ortiz, Mauro Freitas; Wallau, Gabriel Luz; Graichen, Daniel Ângelo Sganzela; Loreto, Elgion Lucio Silva

    2015-02-01

    Evidences of horizontal transfer, the exchange of genetic material between reproductively isolated species, have accumulated over the last decades, including for multicellular eukaryotic organisms. However, the mechanisms and ecological relationships that promote such phenomenon is still poorly known. Host-parasite interaction is one type of relationship usually pointed in the literature that could potentially increase the probability of the horizontal transfer between species, because the species involved in such relationships are generally in close contact. Transposable elements, which are well-known genomic parasites, are DNA entities that tend to be involved in horizontal transfer due to their ability to mobilize between different genomic locations. Using Drosophila species and their parasitoid wasps as a host-parasite model, we evaluated the hypothesis that horizontal transposon transfers (HTTs) are more frequent in this set of species than in species that do not exhibit a close ecological and phylogenetic relationship. For this purpose, we sequenced two sets of species using a metagenomic and single-species genomic sampling approach through next-generation DNA sequencing. The first set was composed of five generalist Drosophila (D. maculifrons, D. bandeirantorum, D. polymorpha, D. mercatorum and D. willistoni) species and their associated parasitoid wasps, whereas the second set was composed of D. incompta, which is a flower specialist species, and its parasitoid wasp. We did not find strong evidence of HTT in the two sets of Drosophila and wasp parasites. However, at least five cases of HTT were observed between the generalist and specialist Drosophila species. Moreover, we detected an HT event involving a Wolbachia lineage between generalist and specialist species, indicating that these endosymbiotic bacteria could play a role as HTT vectors. In summary, our results do not support the hypothesis of prevalent HTT between species with a host

  18. Finite population analysis of the effect of horizontal gene transfer on the origin of an universal and optimal genetic code

    NASA Astrophysics Data System (ADS)

    Aggarwal, Neha; Vishwa Bandhu, Ashutosh; Sengupta, Supratim

    2016-06-01

    The origin of a universal and optimal genetic code remains a compelling mystery in molecular biology and marks an essential step in the origin of DNA and protein based life. We examine a collective evolution model of genetic code origin that allows for unconstrained horizontal transfer of genetic elements within a finite population of sequences each of which is associated with a genetic code selected from a pool of primordial codes. We find that when horizontal transfer of genetic elements is incorporated in this more realistic model of code-sequence coevolution in a finite population, it can increase the likelihood of emergence of a more optimal code eventually leading to its universality through fixation in the population. The establishment of such an optimal code depends on the probability of HGT events. Only when the probability of HGT events is above a critical threshold, we find that the ten amino acid code having a structure that is most consistent with the standard genetic code (SGC) often gets fixed in the population with the highest probability. We examine how the threshold is determined by factors like the population size, length of the sequences and selection coefficient. Our simulation results reveal the conditions under which sharing of coding innovations through horizontal transfer of genetic elements may have facilitated the emergence of a universal code having a structure similar to that of the SGC.

  19. Finite population analysis of the effect of horizontal gene transfer on the origin of an universal and optimal genetic code.

    PubMed

    Aggarwal, Neha; Bandhu, Ashutosh Vishwa; Sengupta, Supratim

    2016-05-27

    The origin of a universal and optimal genetic code remains a compelling mystery in molecular biology and marks an essential step in the origin of DNA and protein based life. We examine a collective evolution model of genetic code origin that allows for unconstrained horizontal transfer of genetic elements within a finite population of sequences each of which is associated with a genetic code selected from a pool of primordial codes. We find that when horizontal transfer of genetic elements is incorporated in this more realistic model of code-sequence coevolution in a finite population, it can increase the likelihood of emergence of a more optimal code eventually leading to its universality through fixation in the population. The establishment of such an optimal code depends on the probability of HGT events. Only when the probability of HGT events is above a critical threshold, we find that the ten amino acid code having a structure that is most consistent with the standard genetic code (SGC) often gets fixed in the population with the highest probability. We examine how the threshold is determined by factors like the population size, length of the sequences and selection coefficient. Our simulation results reveal the conditions under which sharing of coding innovations through horizontal transfer of genetic elements may have facilitated the emergence of a universal code having a structure similar to that of the SGC.

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

    SciTech Connect

    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.

  1. 77 FR 40459 - Electronic Fund Transfers (Regulation E); Correction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-10

    ... 1005 RIN 3170-AA15 Electronic Fund Transfers (Regulation E); Correction AGENCY: Bureau of Consumer..., the Bureau published the Final Rule (77 FR 6194), which implements the Electronic Fund Transfer Act... made to Sec. 1005.3(a) in the interim final rule, Electronic Fund Transfers (Regulation E),...

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

    PubMed

    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

  3. Noncognitive Predictors of Academic Performance and Persistence in Horizontal and Vertical Transfer Students by Academic Level

    ERIC Educational Resources Information Center

    Davis, Christopher A.

    2010-01-01

    College students increasingly are transferring among institutions of higher education in pursuit of their educational goals. The existing research on transfer students, however, does not adequately explore the unique characteristics of this heterogeneous population. The literature on transfer students suggests that transfer students are at-risk…

  4. Horizontal and trophic transfer of diflubenzuron and fipronil among grasshoppers (Melanoplus sanguinipes) and between grasshoppers and darkling beetles (Tenebrionidae).

    PubMed

    Smith, D I; Lockwood, J A

    2003-04-01

    The possibility of horizontal transmission of diflubenzuron and fipronil was assessed in rangeland grasshoppers. Laboratory studies of Melanoplus sanguinipes demonstrated that fipronil was horizontally transferred at lethal levels (p < 0.05) via cannibalism through four passages when the initial dose applied to a food source was 250 times the label rate for rangeland grasshopper and locust control (label rate is 4 g AI/ha). Mortality was 100% on the first three passages through cannibalism. At 25 and 1 times the label rate, fipronil was lethal (p < 0.05) only on the first cannibalistic passage. Diflubenzuron generated significant (p < 0.05) mortality via horizontal transmission through two passages when the initial dose applied to a food source was 2,000 times the label rate for rangeland grasshopper control (label rate is 8.71 g AI/ha). There was 100% mortality in the first passage via cannibalism. At 250 and 25 times the label rate, diflubenzuron was lethal only on the first cannibalistic passage. Field applications of these two acridicides followed by collection of cadavers (Amphitornus coloradus and Ageneotettix deorum) that were fed to M. sanguinipes in the laboratory revealed that fipronil (25 times the label rate) generated significant (p < 0.05) mortality through two passages and diflubenzuron (label rate) caused no mortality via necrophagy. Tenebrionid beetles fed grasshopper cadavers collected from the field application of fipronil yielded 45% mortality, compared with 25% mortality in the controls. These findings suggest that horizontal and trophic transfer probably play a nominal ecotoxicological role in rangeland grasshopper control programs with diflubenzuron, but the transfer of fipronil to grasshoppers, scavengers, and natural enemies via necrophagy may increase both the efficacy of control programs and their environmental affects.

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

    PubMed

    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/.

  6. VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to the Mariner Family within Drosophila.

    PubMed

    Wallau, Gabriel Luz; Capy, Pierre; Loreto, Elgion; Le Rouzic, Arnaud; Hua-Van, Aurélie

    2016-04-01

    Transposable elements (TEs) are genomic repeated sequences that display complex evolutionary patterns. They are usually inherited vertically, but can occasionally be transmitted between sexually independent species, through so-called horizontal transposon transfers (HTTs). Recurrent HTTs are supposed to be essential in life cycle of TEs, which are otherwise destined for eventual decay. HTTs also impact the host genome evolution. However, the extent of HTTs in eukaryotes is largely unknown, due to the lack of efficient, statistically supported methods that can be applied to multiple species sequence data sets. Here, we developed a new automated method available as a R package "vhica" that discriminates whether a given TE family was vertically or horizontally transferred, and potentially infers donor and receptor species. The method is well suited for TE sequences extracted from complete genomes, and applicable to multiple TEs and species at the same time. We first validated our method using Drosophila TE families with well-known evolutionary histories, displaying both HTTs and vertical transmission. We then tested 26 different lineages of mariner elements recently characterized in 20 Drosophila genomes, and found HTTs in 24 of them. Furthermore, several independent HTT events could often be detected within the same mariner lineage. The VHICA (Vertical and Horizontal Inheritance Consistence Analysis) method thus appears as a valuable tool to analyze the evolutionary history of TEs across a large range of species.

  7. Transient Duplication-Dependent Divergence and Horizontal Transfer Underlie the Evolutionary Dynamics of Bacterial Cell–Cell Signaling

    PubMed Central

    Pollak, Shaul; Eldar, Avigdor

    2016-01-01

    Evolutionary expansion of signaling pathway families often underlies the evolution of regulatory complexity. Expansion requires the acquisition of a novel homologous pathway and the diversification of pathway specificity. Acquisition can occur either vertically, by duplication, or through horizontal transfer, while divergence of specificity is thought to occur through a promiscuous protein intermediate. The way by which these mechanisms shape the evolution of rapidly diverging signaling families is unclear. Here, we examine this question using the highly diversified Rap-Phr cell–cell signaling system, which has undergone massive expansion in the genus Bacillus. To this end, genomic sequence analysis of >300 Bacilli genomes was combined with experimental analysis of the interaction of Rap receptors with Phr autoinducers and downstream targets. Rap-Phr expansion is shown to have occurred independently in multiple Bacillus lineages, with >80 different putative rap-phr alleles evolving in the Bacillius subtilis group alone. The specificity of many rap-phr alleles and the rapid gain and loss of Rap targets are experimentally demonstrated. Strikingly, both horizontal and vertical processes were shown to participate in this expansion, each with a distinct role. Horizontal gene transfer governs the acquisition of already diverged rap-phr alleles, while intralocus duplication and divergence of the phr gene create the promiscuous intermediate required for the divergence of Rap-Phr specificity. Our results suggest a novel role for transient gene duplication and divergence during evolutionary shifts in specificity. PMID:28033323

  8. VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to the Mariner Family within Drosophila

    PubMed Central

    Wallau, Gabriel Luz; Capy, Pierre; Loreto, Elgion; Le Rouzic, Arnaud; Hua-Van, Aurélie

    2016-01-01

    Transposable elements (TEs) are genomic repeated sequences that display complex evolutionary patterns. They are usually inherited vertically, but can occasionally be transmitted between sexually independent species, through so-called horizontal transposon transfers (HTTs). Recurrent HTTs are supposed to be essential in life cycle of TEs, which are otherwise destined for eventual decay. HTTs also impact the host genome evolution. However, the extent of HTTs in eukaryotes is largely unknown, due to the lack of efficient, statistically supported methods that can be applied to multiple species sequence data sets. Here, we developed a new automated method available as a R package “vhica” that discriminates whether a given TE family was vertically or horizontally transferred, and potentially infers donor and receptor species. The method is well suited for TE sequences extracted from complete genomes, and applicable to multiple TEs and species at the same time. We first validated our method using Drosophila TE families with well-known evolutionary histories, displaying both HTTs and vertical transmission. We then tested 26 different lineages of mariner elements recently characterized in 20 Drosophila genomes, and found HTTs in 24 of them. Furthermore, several independent HTT events could often be detected within the same mariner lineage. The VHICA (Vertical and Horizontal Inheritance Consistence Analysis) method thus appears as a valuable tool to analyze the evolutionary history of TEs across a large range of species. PMID:26685176

  9. Horizontal gene transfer of epigenetic machinery and evolution of parasitism in the malaria parasite Plasmodium falciparum and other apicomplexans

    PubMed Central

    2013-01-01

    Background The acquisition of complex transcriptional regulatory abilities and epigenetic machinery facilitated the transition of the ancestor of apicomplexans from a free-living organism to an obligate parasite. The ability to control sophisticated gene expression patterns enabled these ancient organisms to evolve several differentiated forms, invade multiple hosts and evade host immunity. How these abilities were acquired remains an outstanding question in protistan biology. Results In this work, we study SET domain bearing genes that are implicated in mediating immune evasion, invasion and cytoadhesion pathways of modern apicomplexans, including malaria parasites. We provide the first conclusive evidence of a horizontal gene transfer of a Histone H4 Lysine 20 (H4K20) modifier, Set8, from an animal host to the ancestor of apicomplexans. Set8 is known to contribute to the coordinated expression of genes involved in immune evasion in modern apicomplexans. We also show the likely transfer of a H3K36 methyltransferase (Ashr3 from plants), possibly derived from algal endosymbionts. These transfers appear to date to the transition from free-living organisms to parasitism and coincide with the proposed horizontal acquisition of cytoadhesion domains, the O-glycosyltransferase that modifies these domains, and the primary family of transcription factors found in apicomplexan parasites. Notably, phylogenetic support for these conclusions is robust and the genes clearly are dissimilar to SET sequences found in the closely related parasite Perkinsus marinus, and in ciliates, the nearest free-living organisms with complete genome sequences available. Conclusions Animal and plant sources of epigenetic machinery provide new insights into the evolution of parasitism in apicomplexans. Along with the horizontal transfer of cytoadhesive domains, O-linked glycosylation and key transcription factors, the acquisition of SET domain methyltransferases marks a key transitional event in

  10. Horizontal lifelines - review of regulations and simple design method considering anchorage rigidity.

    PubMed

    Galy, Bertrand; Lan, André

    2017-03-28

    Among the many occupational risks construction workers encounter every day falling from a height is the most dangerous. The objective of this article is to propose a simple analytical design method for horizontal lifelines (HLLs) that considers anchorage flexibility. The article presents a short review of the standards and regulations/acts/codes concerning HLLs in Canada the USA and Europe. A static analytical approach is proposed considering anchorage flexibility. The analytical results are compared with a series of 42 dynamic fall tests and a SAP2000 numerical model. The experimental results show that the analytical method is a little conservative and overestimates the line tension in most cases with a maximum of 17%. The static SAP2000 results show a maximum 2.1% difference with the analytical method. The analytical method is accurate enough to safely design HLLs and quick design abaci are provided to allow the engineer to make quick on-site verification if needed.

  11. ToxR Antagonizes H-NS Regulation of Horizontally Acquired Genes to Drive Host Colonization

    PubMed Central

    Kazi, Misha I.; Conrado, Aaron R.; Mey, Alexandra R.; Payne, Shelley M.; Davies, Bryan W.

    2016-01-01

    The virulence regulator ToxR initiates and coordinates gene expression needed by Vibrio cholerae to colonize the small intestine and cause disease. Despite its prominence in V. cholerae virulence, our understanding of the direct ToxR regulon is limited to four genes: toxT, ompT, ompU and ctxA. Here, we determine ToxR’s genome-wide DNA-binding profile and demonstrate that ToxR is a global regulator of both progenitor genome-encoded genes and horizontally acquired islands that encode V. cholerae’s major virulence factors and define pandemic lineages. We show that ToxR shares more than a third of its regulon with the histone-like nucleoid structuring protein H-NS, and antagonizes H-NS binding at shared binding locations. Importantly, we demonstrate that this regulatory interaction is the critical function of ToxR in V. cholerae colonization and biofilm formation. In the absence of H-NS, ToxR is no longer required for V. cholerae to colonize the infant mouse intestine or for robust biofilm formation. We further illustrate a dramatic difference in regulatory scope between ToxR and other prominent virulence regulators, despite similar predicted requirements for DNA binding. Our results suggest that factors in addition to primary DNA structure influence the ability of ToxR to recognize its target promoters. PMID:27070545

  12. ToxR Antagonizes H-NS Regulation of Horizontally Acquired Genes to Drive Host Colonization.

    PubMed

    Kazi, Misha I; Conrado, Aaron R; Mey, Alexandra R; Payne, Shelley M; Davies, Bryan W

    2016-04-01

    The virulence regulator ToxR initiates and coordinates gene expression needed by Vibrio cholerae to colonize the small intestine and cause disease. Despite its prominence in V. cholerae virulence, our understanding of the direct ToxR regulon is limited to four genes: toxT, ompT, ompU and ctxA. Here, we determine ToxR's genome-wide DNA-binding profile and demonstrate that ToxR is a global regulator of both progenitor genome-encoded genes and horizontally acquired islands that encode V. cholerae's major virulence factors and define pandemic lineages. We show that ToxR shares more than a third of its regulon with the histone-like nucleoid structuring protein H-NS, and antagonizes H-NS binding at shared binding locations. Importantly, we demonstrate that this regulatory interaction is the critical function of ToxR in V. cholerae colonization and biofilm formation. In the absence of H-NS, ToxR is no longer required for V. cholerae to colonize the infant mouse intestine or for robust biofilm formation. We further illustrate a dramatic difference in regulatory scope between ToxR and other prominent virulence regulators, despite similar predicted requirements for DNA binding. Our results suggest that factors in addition to primary DNA structure influence the ability of ToxR to recognize its target promoters.

  13. The ancestor of modern Holozoa acquired the CCA-adding enzyme from Alphaproteobacteria by horizontal gene transfer.

    PubMed

    Betat, Heike; Mede, Tobias; Tretbar, Sandy; Steiner, Lydia; Stadler, Peter F; Mörl, Mario; Prohaska, Sonja J

    2015-08-18

    Transfer RNAs (tRNAs) require the absolutely conserved sequence motif CCA at their 3'-ends, representing the site of aminoacylation. In the majority of organisms, this trinucleotide sequence is not encoded in the genome and thus has to be added post-transcriptionally by the CCA-adding enzyme, a specialized nucleotidyltransferase. In eukaryotic genomes this ubiquitous and highly conserved enzyme family is usually represented by a single gene copy. Analysis of published sequence data allows us to pin down the unusual evolution of eukaryotic CCA-adding enzymes. We show that the CCA-adding enzymes of animals originated from a horizontal gene transfer event in the stem lineage of Holozoa, i.e. Metazoa (animals) and their unicellular relatives, the Choanozoa. The tRNA nucleotidyltransferase, acquired from an α-proteobacterium, replaced the ancestral enzyme in Metazoa. However, in Choanoflagellata, the group of Choanozoa that is closest to Metazoa, both the ancestral and the horizontally transferred CCA-adding enzymes have survived. Furthermore, our data refute a mitochondrial origin of the animal tRNA nucleotidyltransferases.

  14. The Evolutionary Fate of the Horizontally Transferred Agrobacterial Mikimopine Synthase Gene in the Genera Nicotiana and Linaria

    PubMed Central

    Talianova, Martina; Vyskot, Boris

    2014-01-01

    Few cases of spontaneously horizontally transferred bacterial genes into plant genomes have been described to date. The occurrence of horizontally transferred genes from the T-DNA of Agrobacterium rhizogenes into the plant genome has been reported in the genus Nicotiana and in the species Linaria vulgaris. Here we compare patterns of evolution in one of these genes (a gene encoding mikimopine synthase, mis) following three different events of horizontal gene transfer (HGT). As this gene plays an important role in Agrobacterium, and there are known cases showing that genes from pathogens can acquire plant protection function, we hypothesised that in at least some of the studied species we will find signs of selective pressures influencing mis sequence. The mikimopine synthase (mis) gene evolved in a different manner in the branch leading to Nicotiana tabacum and N. tomentosiformis, in the branch leading to N. glauca and in the genus Linaria. Our analyses of the genus Linaria suggest that the mis gene began to degenerate soon after the HGT. In contrast, in the case of N. glauca, the mis gene evolved under significant selective pressures. This suggests a possible role of mikimopine synthase in current N. glauca and its ancestor(s). In N. tabacum and N. tomentosiformis, the mis gene has a common frameshift mutation that disrupted its open reading frame. Interestingly, our results suggest that in spite of the frameshift, the mis gene could evolve under selective pressures. This sequence may still have some regulatory role at the RNA level as suggested by coverage of this sequence by small RNAs in N. tabacum. PMID:25420106

  15. Evaluation of correlations of flow boiling heat transfer of R22 in horizontal channels.

    PubMed

    Zhou, Zhanru; Fang, Xiande; Li, Dingkun

    2013-01-01

    The calculation of two-phase flow boiling heat transfer of R22 in channels is required in a variety of applications, such as chemical process cooling systems, refrigeration, and air conditioning. A number of correlations for flow boiling heat transfer in channels have been proposed. This work evaluates the existing correlations for flow boiling heat transfer coefficient with 1669 experimental data points of flow boiling heat transfer of R22 collected from 18 published papers. The top two correlations for R22 are those of Liu and Winterton (1991) and Fang (2013), with the mean absolute deviation of 32.7% and 32.8%, respectively. More studies should be carried out to develop better ones. Effects of channel dimension and vapor quality on heat transfer are analyzed, and the results provide valuable information for further research in the correlation of two-phase flow boiling heat transfer of R22 in channels.

  16. 78 FR 49365 - Electronic Fund Transfers (Regulation E); Correction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-14

    ... From the Federal Register Online via the Government Publishing Office ] BUREAU OF CONSUMER FINANCIAL PROTECTION 12 CFR Part 1005 RIN 3170-AA33 Electronic Fund Transfers (Regulation E); Correction... rules \\1\\ implements the Electronic Fund Transfer Act's provisions regarding remittance transfers...

  17. High Rayleigh number heat transfer in a horizontal cylinder with adiabatic wall

    NASA Technical Reports Server (NTRS)

    Schiroky, G. H.; Rosenberger, F.

    1984-01-01

    The present investigation is concerned with an experimentally guided approach to the estimation of Nusselt numbers (Nu) at high Rayleigh numbers (Ra) for a cylinder with an adiabatic side wall. The Rayleigh number dependence of the Nusselt number for a horizontal cylinder with an adiabatic wall is presented in a graph. The obtained data are compared with results reported by Shih (1981). Shih has extended a three-term expansion for velocity and temperature distributions reported by Bejan and Tien (1978).

  18. Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes

    PubMed Central

    Naranjo-Ortíz, Miguel A.; Brock, Matthias; Brunke, Sascha; Hube, Bernhard; Marcet-Houben, Marina; Gabaldón, Toni

    2016-01-01

    Analysis of the growing number of available fully-sequenced genomes has shown that Horizontal Gene Transfer (HGT) in eukaryotes is more common than previously thought. It has been proposed that genes with certain functions may be more prone to HGT than others, but we still have a very poor understanding of the selective forces driving eukaryotic HGT. Recent work uncovered that d-amino acid racemases have been commonly transferred from bacteria to fungi, but their role in the receiving organisms is currently unknown. Here, we set out to assess whether d-amino acid racemases are commonly transferred to and between eukaryotic groups. For this we performed a global survey that used a novel automated phylogeny-based HGT-detection algorithm (Abaccus). Our results revealed that at least 7.0% of the total eukaryotic racemase repertoire is the result of inter- or intra-domain HGT. These transfers are significantly enriched in plant-associated fungi. For these, we hypothesize a possible role for the acquired racemases allowing to exploit minoritary nitrogen sources in plant biomass, a nitrogen-poor environment. Finally, we performed experiments on a transferred aspartate-glutamate racemase in the fungal human pathogen Candida glabrata, which however revealed no obvious biological role. PMID:28066338

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

    PubMed Central

    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

  20. Thermal Regulation of Heat Transfer Processes

    DTIC Science & Technology

    2014-10-02

    Besides thermal regulation, we also develop an electrochemical method to regulate thermal conductivity in battery materials. Both experiments and modeling...potential applications including power generation, desalination, waste water treatment, and hygiene systems. 4. Electrochemical regulation of...We also develop electrochemical regulation of thermal conductivity in battery materials, which opens new direction for exploration. Both

  1. Augmentation of heat transfer by twisted tape inserts during condensation of R-134a inside a horizontal tube

    NASA Astrophysics Data System (ADS)

    Akhavan-Behabadi, M. A.; Kumar, Ravi; Rajabi-Najar, A.

    2008-04-01

    An experimental investigation has been carried out to find the heat transfer coefficient during condensation of R-134a vapor inside a horizontal tube. Experiments were conducted for the condensation of R-134a inside a plain tube and tubes with different twisted tape inserts. Twisted tapes with different twisted ratios of 6, 9, 12 and 15 were inserted in the refrigerant side, one by one, in the full length of test-condenser. For each inserted tube and the plain tube, test runs were carried out for the mass velocities of 92, 110, 128 and 147 kg/s-m2. An empirical correlation has also been developed to predict the enhanced heat transfer coefficient.

  2. The animal food supplement sepiolite promotes a direct horizontal transfer of antibiotic resistance plasmids between bacterial species.

    PubMed

    Rodríguez-Beltrán, Jerónimo; Rodríguez-Rojas, Alexandro; Yubero, Elva; Blázquez, Jesús

    2013-06-01

    Animal fodder is routinely complemented with antibiotics together with other food supplements to improve growth. For instance, sepiolite is currently used as a dietary coadjuvant in animal feed, as it increases animal growth parameters and improves meat and derived final product quality. This type of food additive has so far been considered innocuous for the development and spread of antibiotic resistance. In this study, we demonstrate that sepiolite promotes the direct horizontal transfer of antibiotic resistance plasmids between bacterial species. The conditions needed for plasmid transfer (sepiolite and friction forces) occur in the digestive tracts of farm animals, which routinely receive sepiolite as a food additive. Furthermore, this effect may be aggravated by the use of antibiotics supplied as growth promoters.

  3. Two-phase heat transfer and pressure drop of LNG during saturated flow boiling in a horizontal tube

    NASA Astrophysics Data System (ADS)

    Chen, Dongsheng; Shi, Yumei

    2013-12-01

    Two-phase heat transfer and pressure drop of LNG (liquefied natural gas) have been measured in a horizontal smooth tube with an inner diameter of 8 mm. The experiments were conducted at inlet pressures from 0.3 to 0.7 MPa with a heat flux of 8-36 kW m-2, and mass flux of 49.2-201.8 kg m-2 s-1. The effect of vapor quality, inlet pressure, heat flux and mass flux on the heat transfer characteristic are discussed. The comparisons of the experimental data with the predicted value by existing correlations are analyzed. Zou et al. (2010) correlation shows the best accuracy with 24.1% RMS deviation among them. Moreover four frictional pressure drop methods are also chosen to compare with the experimental database.

  4. Development and applications of a DNA labeling method with magnetic nanoparticles to study the role of horizontal gene transfer events between bacteria in soil pollutant bioremediation processes.

    PubMed

    Pivetal, J; Frénéa-Robin, M; Haddour, N; Vézy, C; Zanini, L F; Ciuta, G; Dempsey, N M; Dumas-Bouchiat, F; Reyne, G; Bégin-Colin, S; Felder-Flesh, D; Ghobril, C; Pourroy, G; Simonet, P

    2015-12-01

    Horizontal gene transfers are critical mechanisms of bacterial evolution and adaptation that are involved to a significant level in the degradation of toxic molecules such as xenobiotic pesticides. However, understanding how these mechanisms are regulated in situ and how they could be used by man to increase the degradation potential of soil microbes is compromised by conceptual and technical limitations. This includes the physical and chemical complexity and heterogeneity in such environments leading to an extreme bacterial taxonomical diversity and a strong redundancy of genes and functions. In addition, more than 99 % of soil bacteria fail to develop colonies in vitro, and even new DNA-based investigation methods (metagenomics) are not specific and sensitive enough to consider lysis recalcitrant bacteria and those belonging to the rare biosphere. The objective of the ANR funded project “Emergent” was to develop a new culture independent approach to monitor gene transfer among soil bacteria by labeling plasmid DNA with magnetic nanoparticles in order to specifically capture and isolate recombinant cells using magnetic microfluidic devices. We showed the feasibility of the approach by using electrotransformation to transform a suspension of Escherichia coli cells with biotin-functionalized plasmid DNA molecules linked to streptavidin-coated superparamagnetic nanoparticles. Our results have demonstrated that magnetically labeled cells could be specifically retained on micromagnets integrated in a microfluidic channel and that an efficient selective separation can be achieved with the microfluidic device. Altogether, the project offers a promising alternative to traditional culture-based approaches for deciphering the extent of horizontal gene transfer events mediated by electro or natural genetic transformation mechanisms in complex environments such as soil.

  5. New flow boiling heat transfer model for hydrocarbons evaporating inside horizontal tubes

    SciTech Connect

    Chen, G. F.; Gong, M. Q.; Wu, J. F.; Zou, X.; Wang, S.

    2014-01-29

    Hydrocarbons have high thermodynamic performances, belong to the group of natural refrigerants, and they are the main components in mixture Joule-Thomson low temperature refrigerators (MJTR). New evaluations of nucleate boiling contribution and nucleate boiling suppression factor in flow boiling heat transfer have been proposed for hydrocarbons. A forced convection heat transfer enhancement factor correlation incorporating liquid velocity has also been proposed. In addition, the comparisons of the new model and other classic models were made to evaluate its accuracy in heat transfer prediction.

  6. Phase Diagrams of Quasispecies Theory with Recombination and Horizontal Gene Transfer

    NASA Astrophysics Data System (ADS)

    Park, J.-M.; Deem, M. W.

    2007-02-01

    We consider how transfer of genetic information between individuals influences the phase diagram and mean fitness of both the Eigen and the parallel, or Crow-Kimura, models of evolution. In the absence of genetic transfer, these physical models of evolution consider the replication and point mutation of the genomes of independent individuals in a large population. A phase transition occurs, such that below a critical mutation rate an identifiable quasispecies forms. We show how transfer of genetic information changes the phase diagram and mean fitness and introduces metastability in quasispecies theory, via an analytic field theoretic mapping.

  7. Horizontal transfer of PAH catabolism genes in Mycobacterium: evidence from comparative genomics and isolated pyrene-degrading bacteria.

    PubMed

    DeBruyn, Jennifer M; Mead, Thomas J; Sayler, Gary S

    2012-01-03

    Biodegradation of high molecular weight polycyclic aromatic hydrocarbons (PAHs), such as pyrene and benzo[a]pyrene, has only been observed in a few genera, namely fast-growing Mycobacterium and Rhodococcus. In M. vanbaalenii PYR-1, multiple aromatic ring hydroxylating dioxygenase (ARHDOs) genes including pyrene dioxygenases nidAB and nidA3B3 are localized in one genomic region. Here we examine the homologous genomic regions in four other PAH-degrading Mycobacterium (strains JLS, KMS, and MCS, and M. gilvum PYR-GCK), presenting evidence for past horizontal gene transfer events. Seven distinct types of ARHDO genes are present in all five genomes, and display conserved syntenic architecture with respect to gene order, orientation, and association with other genes. Duplications and putative integrase and transposase genes suggest past gene shuffling. To corroborate these observations, pyrene-degrading strains were isolated from two PAH-contaminated sediments: Chattanooga Creek (Tennessee) and Lake Erie (western basin). Some were related to fast-growing Mycobacterium spp. and carried both nidA and nidA3 genes. Other isolates belonged to Microbacteriaceae and Intrasporangiaceae presenting the first evidence of pyrene degradation in these families. These isolates had nidA (and some, nidA3) genes that were homologous to Mycobacterial ARHDO genes, suggesting that horizontal gene transfer events have occurred.

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

    PubMed Central

    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 HP; Huynen, Martijn 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 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. PMID:16472398

  9. Coupled heat and mass transfer by natural convection adjacent to a permeable horizontal cylinder in a saturated porous medium

    SciTech Connect

    Yih, K.A.

    1999-04-01

    Coupled heat and mass transfer (or double-diffusion) driven by buoyancy, due to temperature and concentration variations in a saturated porous medium, has several important applications in geothermal and geophysical engineering such as the migration of moisture through the air contained in fibrous insulation, the extraction of geothermal energy, underground disposal of nuclear wastes, and the spreading of chemical contaminants through water-saturated soil. Here, the heat and mass transfer characteristics of free convection about a permeable horizontal cylinder embedded in porous media under the coupled effects of thermal and mass diffusion are numerically analyzed. The surface of the horizontal cylinder is maintained at a uniform wall temperature and uniform wall concentration. The transformed governing equations are obtained and solved by Keller box method. Numerical results for the dimensionless temperature profiles, the dimensionless concentration profiles, the Nusselt number and the Sherwood number are presented. Increasing the buoyancy ratio N and the transpiration parameter f{sub w} increases the Nusselt number and the Sherwood number. For thermally assisting flow, when Lewis number Le increases, the Nusselt (Sherwood) number decreases (increases). Whereas, for thermally opposing flow, both the Nusselt number and the Sherwood number increase with increasing the Lewis number.

  10. The Role of Vertical and Horizontal Transfer in the Evolutionary Dynamics of PIF-Like Transposable Elements in Triticeae

    PubMed Central

    Markova, Dragomira N.; Mason-Gamer, Roberta J.

    2015-01-01

    PIF-like transposable elements are members of the PIF/Harbinger superfamily of DNA transposons found in the genomes of many plants, animals, and fungi. The evolution of the gene that encodes the transposase responsible for mobilizing PIF-like elements has been studied in both plants and animals, but the elements' history in flowering plants remains poorly known. In this work, we describe the phylogenetic distribution and evolution of PIF-like elements in the genomes of 21 diploid species from the wheat tribe, Triticeae, and we present the first convincing evidence of horizontal transfer of PIF elements in plant genomes. A phylogenetic analysis of 240 PIF sequences based on the conserved region of the transposase domain revealed at least four main transposase lineages. Their complex evolutionary history can be best explained by a combination of vertical transmission with differential evolutionary success among lineages, and occasional horizontal transfer between phylogenetically distant Triticeae genera. In addition, we identified 127 potentially functional transposase sequences indicating possible recent activity of PIF. PMID:26355747

  11. Horizontal Gene Transfer of PIB-Type ATPases among Bacteria Isolated from Radionuclide- and Metal-Contaminated Subsurface Soils

    PubMed Central

    Martinez, Robert J.; Wang, Yanling; Raimondo, Melanie A.; Coombs, Jonna M.; Barkay, Tamar; Sobecky, Patricia A.

    2006-01-01

    Aerobic heterotrophs were isolated from subsurface soil samples obtained from the U.S. Department of Energy's (DOE) Field Research Center (FRC) located at Oak Ridge, Tenn. The FRC represents a unique, extreme environment consisting of highly acidic soils with cooccurring heavy metals, radionuclides, and high nitrate concentrations. Four hundred isolates obtained from contaminated soil were assayed for heavy metal resistance, and a smaller subset was assayed for tolerance to uranium. The vast majority of the isolates were gram-positive bacteria and belonged to the high-G+C- and low-G+C-content genera Arthrobacter and Bacillus, respectively. Genomic DNA from a randomly chosen subset of 50 Pb-resistant (Pbr) isolates was amplified with PCR primers specific for PIB-type ATPases (i.e., pbrA/cadA/zntA). A total of 10 pbrA/cadA/zntA loci exhibited evidence of acquisition by horizontal gene transfer. A remarkable dissemination of the horizontally acquired PIB-type ATPases was supported by unusual DNA base compositions and phylogenetic incongruence. Numerous Pbr PIB-type ATPase-positive FRC isolates belonging to the genus Arthrobacter tolerated toxic concentrations of soluble U(VI) (UO22+) at pH 4. These unrelated, yet synergistic, physiological traits observed in Arthrobacter isolates residing in the contaminated FRC subsurface may contribute to the survival of the organisms in such an extreme environment. This study is, to the best of our knowledge, the first study to report broad horizontal transfer of PIB-type ATPases in contaminated subsurface soils and is among the first studies to report uranium tolerance of aerobic heterotrophs obtained from the acidic subsurface at the DOE FRC. PMID:16672448

  12. Study on solid liquid interface heat transfer of PCM under simultaneous charging and discharging (SCD) in horizontal cylinder annulus

    NASA Astrophysics Data System (ADS)

    Omojaro, Adebola Peter; Breitkopf, Cornelia

    2017-01-01

    Heat transfer performance during the simultaneous charging and discharging (SCD) operation process for phase change materials (PCM) contained inside the annulus of concentric horizontal cylinder was investigated. In the experimental set-up, the PCM inside the annulus serves as the heat sink along with an externally imposed forced cooling air. The obtained time wise temperature profile was used to determine the effects of different heat fluxes and the imposed forced convection cooling on the melt fraction values and the transition shift time from the observed conduction to natural convection heat transfer patterns. Furthermore, non-dimensional analysis was presented for the heat transfer at the interface to enable generalizing the result. Comparison of the results show that the SCD operation mode establish the condition that enables much PCM phase transition time and thus longer time of large latent heat transfer effect than the Partial and non simultaneous operations. Analysis results show that the variation of the heat flux for the SCD mode did not change the dominance of the natural convection over conduction heat transfers in the PCM. However, it significantly influences the commencement/transition shift time and melting rate while higher heat fluxes yields melt fraction that was 38-63% more for investigated process time. Variation with different cooling air flow rate shows more influences on the melt fraction than on the mode of heat transfer occurring in the PCM during melting. Available non-SCD modes correlation was shown to be insufficient to accurately predict interface heat transfer for the SCD modes.

  13. Frequency of horizontal gene transfer of a large catabolic plasmid (pJP4) in soil.

    PubMed

    Neilson, J W; Josephson, K L; Pepper, I L; Arnold, R B; Di Giovanni, G D; Sinclair, N A

    1994-11-01

    Limited work has been done to assess the bioremediation potential of transfer of plasmid-borne degradative genes from introduced to indigenous organisms in the environment. Here we demonstrate the transfer by conjugation of the catabolic plasmid pJP4, using a model system with donor and recipient organisms. The donor organism was Alcaligenes eutrophus JMP134 and the recipient organism was Variovorax paradoxus isolated from a toxic waste site. Plasmid pJP4 contains genes for mercury resistance and 2,4-dichlorophenoxyacetic (2,4-D) acid degradation. A transfer frequency of approximately 1/10(3) donor and recipient cells (parent cells) was observed on solid agar media, decreasing to 1/10(5) parent cells in sterile soil and finally 1/10(6) parent cells in 2,4-D-amended, nonsterile soil. Presumptive transconjugants were confirmed to be resistant to Hg, to be capable of degrading 2,4-D, and to contain a plasmid of size comparable to that of pJP4. In addition, we confirmed the transfer through PCR amplifications of the tfdB gene. Although transfer of pJP4 did occur at a high frequency in pure culture, the rate was significantly decreased by the introduction of abiotic (sterile soil) and biotic (nonsterile soil) stresses. An evaluation of the data from this model system implies that the reliance on plasmid transfer from a donor organism as a remediative strategy has limited potential.

  14. Heat transfer from a horizontal finned tube bundle in bubbling fluidized beds of small and large particles

    SciTech Connect

    Devaru, C.B.; Kolar, A.K.

    1995-12-31

    Steady state average heat transfer coefficient measurements were made by the local thermal simulation technique in a cold, square, bubbling air-fluidized bed (0.305 m x 0.305 m) with immersed horizontal finned tube bundles (in-line and staggered) with integral 60{degree} V-thread. Studies were conducted using beds of small (average particle diameter less than 1 mm) sand particles and of large (average particle diameter greater thin 1 mm) particles (raagi, mustard, millet and coriander). The fin pitch varied from 0.8 to 5.0 mm and the fin height varied from 0.69 to 4.4 mm. The tube pitch ratios used were 1.75 and 3.5. The influence of bed particle diameter, fluidizing velocity, fin pitch, and tube pitch ratio on average heat transfer coefficient was studied. Fin pitch and bed particle diameter are the most significant parameters affecting heat transfer coefficient within the range of experimental conditions. Bed pressure drop depends only on static bed height. New direct correlations, incorporating easily measurable quantities, for average heat transfer coefficient for finned tube bundles (in-line and staggered) are proposed.

  15. A genetic algorithm-based optimization model for pool boiling heat transfer on horizontal rod heaters at isolated bubble regime

    NASA Astrophysics Data System (ADS)

    Alavi Fazel, S. Ali

    2017-03-01

    A new optimized model which can predict the heat transfer in the nucleate boiling at isolated bubble regime is proposed for pool boiling on a horizontal rod heater. This model is developed based on the results of direct observations of the physical boiling phenomena. Boiling heat flux, wall temperature, bubble departing diameter, bubble generation frequency and bubble nucleation site density have been experimentally measured. Water and ethanol have been used as two different boiling fluids. Heating surface was made by several metals and various degrees of roughness. The mentioned model considers various mechanisms such as latent heat transfer due to micro-layer evaporation, transient conduction due to thermal boundary layer reformation, natural convection, heat transfer due to the sliding bubbles and bubble super-heating. The fractional contributions of individual mentioned heat transfer mechanisms have been calculated by genetic algorithm. The results show that at wall temperature difference more that about 3 K, bubble sliding transient conduction, non-sliding transient conduction, micro-layer evaporation, natural convection, radial forced convection and bubble super-heating have higher to lower fractional contributions respectively. The performance of the new optimized model has been verified by comparison of the existing experimental data.

  16. Contribution of Multiple Inter-Kingdom Horizontal Gene Transfers to Evolution and Adaptation of Amphibian-Killing Chytrid, Batrachochytrium dendrobatidis

    PubMed Central

    Sun, Baofa; Li, Tong; Xiao, Jinhua; Liu, Li; Zhang, Peng; Murphy, Robert W.; He, Shunmin; Huang, Dawei

    2016-01-01

    Amphibian populations are experiencing catastrophic declines driven by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Although horizontal gene transfer (HGT) facilitates the evolution and adaptation in many fungi by conferring novel function genes to the recipient fungi, inter-kingdom HGT in Bd remains largely unexplored. In this study, our investigation detects 19 bacterial genes transferred to Bd, including metallo-beta-lactamase and arsenate reductase that play important roles in the resistance to antibiotics and arsenates. Moreover, three probable HGT gene families in Bd are from plants and one gene family coding the ankyrin repeat-containing protein appears to come from oomycetes. The observed multi-copy gene families associated with HGT are probably due to the independent transfer events or gene duplications. Five HGT genes with extracellular locations may relate to infection, and some other genes may participate in a variety of metabolic pathways, and in doing so add important metabolic traits to the recipient. The evolutionary analysis indicates that all the transferred genes evolved under purifying selection, suggesting that their functions in Bd are similar to those of the donors. Collectively, our results indicate that HGT from diverse donors may be an important evolutionary driver of Bd, and improve its adaptations for infecting and colonizing host amphibians. PMID:27630622

  17. Multiple recent horizontal transfers of the cox1 intron in Solanaceae and extended co-conversion of flanking exons

    PubMed Central

    2011-01-01

    Background The most frequent case of horizontal transfer in plants involves a group I intron in the mitochondrial gene cox1, which has been acquired via some 80 separate plant-to-plant transfer events among 833 diverse angiosperms examined. This homing intron encodes an endonuclease thought to promote the intron's promiscuous behavior. A promising experimental approach to study endonuclease activity and intron transmission involves somatic cell hybridization, which in plants leads to mitochondrial fusion and genome recombination. However, the cox1 intron has not yet been found in the ideal group for plant somatic genetics - the Solanaceae. We therefore undertook an extensive survey of this family to find members with the intron and to learn more about the evolutionary history of this exceptionally mobile genetic element. Results Although 409 of the 426 species of Solanaceae examined lack the cox1 intron, it is uniformly present in three phylogenetically disjunct clades. Despite strong overall incongruence of cox1 intron phylogeny with angiosperm phylogeny, two of these clades possess nearly identical intron sequences and are monophyletic in intron phylogeny. These two clades, and possibly the third also, contain a co-conversion tract (CCT) downstream of the intron that is extended relative to all previously recognized CCTs in angiosperm cox1. Re-examination of all published cox1 genes uncovered additional cases of extended co-conversion and identified a rare case of putative intron loss, accompanied by full retention of the CCT. Conclusions We infer that the cox1 intron was separately and recently acquired by at least three different lineages of Solanaceae. The striking identity of the intron and CCT from two of these lineages suggests that one of these three intron captures may have occurred by a within-family transfer event. This is consistent with previous evidence that horizontal transfer in plants is biased towards phylogenetically local events. The discovery

  18. Phylogeny of chitinases and its implications for estimating horizontal gene transfer from chitinase-transgenic silver birch (Betula pendula).

    PubMed

    Lohtander, Katileena; Pasonen, Hanna-Leena; Aalto, Markku K; Palva, Tapio; Pappinen, Ari; Rikkinen, Jouko

    2008-01-01

    Chitinases are hydrolytic enzymes that have been employed in biotechnology in attempts to increase plants' resistance against fungal pathogens. Genetically modified plants have given rise to concerns of the spreading of transgenes into the environment through vertical or horizontal gene transfer (HGT). In this study, chitinase-like sequences from silver birch (Betula pendula) EST-libraries were identified and their phylogenetic relationships to other chitinases were studied. Phylogenetic analyses were used to estimate the frequency of historical gene transfer events of chitinase genes between plants and other organisms, and the usefulness of phylogenetic analyses as a source of information for the risk assessment of transgenic silver birch carrying a sugar beet chitinase IV gene was evaluated. Thirteen partial chitinase-like sequences, with an approximate length of 600 bp, were obtained from the EST-libraries. The sequences belonged to five chitinase classes. Some bacterial chitinases from Streptomyces and Burkholderia, as well as a chitinase from an oomycete, Phytophthora infestans, grouped together with the class IV chitinases of plants, supporting the hypothesis that some class IV chitinases in bacteria have evolved from eukaryotic chitinases via horizontal gene transfer. According to our analyses, HGT of a chitinase IV gene from eukaryotes to bacteria has presumably occurred only once. Based on this, the likelihood for the HGT of chitinase IV gene from transgenic birch to other organisms is extremely low. However, as risk is a function of both the likelihood and consequences of an event, the effects of rare HGT event(s) will finally determine the level of the risk.

  19. Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota.

    PubMed

    Deschamps, Philippe; Zivanovic, Yvan; Moreira, David; Rodriguez-Valera, Francisco; López-García, Purificación

    2014-06-12

    Horizontal gene transfer (HGT) is an important force in evolution, which may lead, among other things, to the adaptation to new environments by the import of new metabolic functions. Recent studies based on phylogenetic analyses of a few genome fragments containing archaeal 16S rRNA genes and fosmid-end sequences from deep-sea metagenomic libraries have suggested that marine planktonic archaea could be affected by high HGT frequency. Likewise, a composite genome of an uncultured marine euryarchaeote showed high levels of gene sequence similarity to bacterial genes. In this work, we ask whether HGT is frequent and widespread in genomes of these marine archaea, and whether HGT is an ancient and/or recurrent phenomenon. To answer these questions, we sequenced 997 fosmid archaeal clones from metagenomic libraries of deep-Mediterranean waters (1,000 and 3,000 m depth) and built comprehensive pangenomes for planktonic Thaumarchaeota (Group I archaea) and Euryarchaeota belonging to the uncultured Groups II and III Euryarchaeota (GII/III-Euryarchaeota). Comparison with available reference genomes of Thaumarchaeota and a composite marine surface euryarchaeote genome allowed us to define sets of core, lineage-specific core, and shell gene ortholog clusters for the two archaeal lineages. Molecular phylogenetic analyses of all gene clusters showed that 23.9% of marine Thaumarchaeota genes and 29.7% of GII/III-Euryarchaeota genes had been horizontally acquired from bacteria. HGT is not only extensive and directional but also ongoing, with high HGT levels in lineage-specific core (ancient transfers) and shell (recent transfers) genes. Many of the acquired genes are related to metabolism and membrane biogenesis, suggesting an adaptive value for life in cold, oligotrophic oceans. We hypothesize that the acquisition of an important amount of foreign genes by the ancestors of these archaeal groups significantly contributed to their divergence and ecological success.

  20. Parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects.

    PubMed

    Sloan, Daniel B; Nakabachi, Atsushi; Richards, Stephen; Qu, Jiaxin; Murali, Shwetha Canchi; Gibbs, Richard A; Moran, Nancy A

    2014-04-01

    Bacteria confined to intracellular environments experience extensive genome reduction. In extreme cases, insect endosymbionts have evolved genomes that are so gene-poor that they blur the distinction between bacteria and endosymbiotically derived organelles such as mitochondria and plastids. To understand the host's role in this extreme gene loss, we analyzed gene content and expression in the nuclear genome of the psyllid Pachypsylla venusta, a sap-feeding insect that harbors an ancient endosymbiont (Carsonella) with one of the most reduced bacterial genomes ever identified. Carsonella retains many genes required for synthesis of essential amino acids that are scarce in plant sap, but most of these biosynthetic pathways have been disrupted by gene loss. Host genes that are upregulated in psyllid cells housing Carsonella appear to compensate for endosymbiont gene losses, resulting in highly integrated metabolic pathways that mirror those observed in other sap-feeding insects. The host contribution to these pathways is mediated by a combination of native eukaryotic genes and bacterial genes that were horizontally transferred from multiple donor lineages early in the evolution of psyllids, including one gene that appears to have been directly acquired from Carsonella. By comparing the psyllid genome to a recent analysis of mealybugs, we found that a remarkably similar set of functional pathways have been shaped by independent transfers of bacterial genes to the two hosts. These results show that horizontal gene transfer is an important and recurring mechanism driving coevolution between insects and their bacterial endosymbionts and highlight interesting similarities and contrasts with the evolutionary history of mitochondria and plastids.

  1. Parallel Histories of Horizontal Gene Transfer Facilitated Extreme Reduction of Endosymbiont Genomes in Sap-Feeding Insects

    PubMed Central

    Sloan, Daniel B.; Nakabachi, Atsushi; Richards, Stephen; Qu, Jiaxin; Murali, Shwetha Canchi; Gibbs, Richard A.; Moran, Nancy A.

    2014-01-01

    Bacteria confined to intracellular environments experience extensive genome reduction. In extreme cases, insect endosymbionts have evolved genomes that are so gene-poor that they blur the distinction between bacteria and endosymbiotically derived organelles such as mitochondria and plastids. To understand the host’s role in this extreme gene loss, we analyzed gene content and expression in the nuclear genome of the psyllid Pachypsylla venusta, a sap-feeding insect that harbors an ancient endosymbiont (Carsonella) with one of the most reduced bacterial genomes ever identified. Carsonella retains many genes required for synthesis of essential amino acids that are scarce in plant sap, but most of these biosynthetic pathways have been disrupted by gene loss. Host genes that are upregulated in psyllid cells housing Carsonella appear to compensate for endosymbiont gene losses, resulting in highly integrated metabolic pathways that mirror those observed in other sap-feeding insects. The host contribution to these pathways is mediated by a combination of native eukaryotic genes and bacterial genes that were horizontally transferred from multiple donor lineages early in the evolution of psyllids, including one gene that appears to have been directly acquired from Carsonella. By comparing the psyllid genome to a recent analysis of mealybugs, we found that a remarkably similar set of functional pathways have been shaped by independent transfers of bacterial genes to the two hosts. These results show that horizontal gene transfer is an important and recurring mechanism driving coevolution between insects and their bacterial endosymbionts and highlight interesting similarities and contrasts with the evolutionary history of mitochondria and plastids. PMID:24398322

  2. Horizontal gene transfer of chromosomal Type II toxin-antitoxin systems of Escherichia coli.

    PubMed

    Ramisetty, Bhaskar Chandra Mohan; Santhosh, Ramachandran Sarojini

    2016-02-01

    Type II toxin-antitoxin systems (TAs) are small autoregulated bicistronic operons that encode a toxin protein with the potential to inhibit metabolic processes and an antitoxin protein to neutralize the toxin. Most of the bacterial genomes encode multiple TAs. However, the diversity and accumulation of TAs on bacterial genomes and its physiological implications are highly debated. Here we provide evidence that Escherichia coli chromosomal TAs (encoding RNase toxins) are 'acquired' DNA likely originated from heterologous DNA and are the smallest known autoregulated operons with the potential for horizontal propagation. Sequence analyses revealed that integration of TAs into the bacterial genome is unique and contributes to variations in the coding and/or regulatory regions of flanking host genome sequences. Plasmids and genomes encoding identical TAs of natural isolates are mutually exclusive. Chromosomal TAs might play significant roles in the evolution and ecology of bacteria by contributing to host genome variation and by moderation of plasmid maintenance.

  3. Anaerobic Growth, a Property Horizontally Transferred by an Hfr-Like Mechanism among Extreme Thermophiles

    PubMed Central

    Ramírez-Arcos, Sandra; Fernández-Herrero, Luis A.; Marín, Irma; Berenguer, José

    1998-01-01

    Despite the fact that the extreme thermophilic bacteria belonging to the genus Thermus are classified as strict aerobes, we have shown that Thermus thermophilus HB8 (ATCC 27634) can grow anaerobically when nitrate is present in the growth medium. This strain-specific property is encoded by a respiratory nitrate reductase gene cluster (nar) whose expression is induced by anoxia and nitrate (S. Ramírez-Arcos, L. A. Fernández-Herrero, and J. Berenguer, Biochim. Biophys. Acta, 1396:215–1997). We show here that this nar operon can be transferred by conjugation to an aerobic Thermus strain, enabling it to grow under anaerobic conditions. We show that this transfer takes place through a DNase-insensitive mechanism which, as for the Hfr (high frequency of recombination) derivatives of Escherichia coli, can also mobilize other chromosomal markers in a time-dependent way. Three lines of evidence are presented to support a genetic linkage between nar and a conjugative plasmid integrated into the chromosome. First, the nar operon is absent from a plasmid-free derivative and from a closely related strain. Second, we have identified an origin for autonomous replication (oriV) overlapping the last gene of the nar cluster. Finally, the mating time required for the transfer of the nar operon is in good agreement with the time expected if the transfer origin (oriT) were located nearby and downstream of nar. PMID:9620963

  4. Root growth and exudate production define the frequency of horizontal plasmid transfer in the Rhizosphere.

    PubMed

    Mølbak, Lars; Molin, Søren; Kroer, Niels

    2007-01-01

    To identify the main drivers of plasmid transfer in the rhizosphere, conjugal transfer was studied in the rhizospheres of pea and barley. The donor Pseudomonas putida KT2442, containing plasmid pKJK5::gfp, was coated onto the seeds, while the recipient P. putida LM24, having a chromosomal insertion of dsRed, was inoculated into the growth medium. Mean transconjugant-to-donor ratios in vermiculite were 4.0+/-0.8 x 10(-2) in the pea and 5.9+/-1.4 x 10(-3) in the barley rhizospheres. In soil, transfer ratios were about 10 times lower. As a result of a 2-times higher root exudation rate in pea, donor densities in pea (1 x 10(6)-2 x 10(9) CFU g(-1) root) were about 10 times higher than in barley. No difference in recipient densities was observed. In situ visualization of single cells on the rhizoplane and macroscopic visualization of the colonization pattern showed that donors and transconjugants were ubiquitously distributed in the pea rhizosphere, while they were only located on the upper parts of the barley roots. Because the barley root elongated about 10 times faster than the pea root, donors were probably outgrown by the elongating barley root. Thus by affecting the cell density and distribution, exudation and root growth appear to be key parameters controlling plasmid transfer in the rhizosphere.

  5. Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships

    PubMed Central

    2011-01-01

    Background Halophilic bacteria have shown their significance in industrial production of polyhydroxyalkanoates (PHA) and are gaining more attention for genetic engineering modification. Yet, little information on the genomics and PHA related genes from halophilic bacteria have been disclosed so far. Results The draft genome of moderately halophilic bacterium, Halomonas sp. TD01, a strain of great potential for industrial production of short-chain-length polyhydroxyalkanoates (PHA), was analyzed through computational methods to reveal the osmoregulation mechanism and the evolutionary relationship of the enzymes relevant to PHA and ectoine syntheses. Genes involved in the metabolism of PHA and osmolytes were annotated and studied in silico. Although PHA synthase, depolymerase, regulator/repressor and phasin were all involved in PHA metabolic pathways, they demonstrated different horizontal gene transfer (HGT) events between the genomes of different strains. In contrast, co-occurrence of ectoine genes in the same genome was more frequently observed, and ectoine genes were more likely under coincidental horizontal gene transfer than PHA related genes. In addition, the adjacent organization of the homologues of PHA synthase phaC1 and PHA granule binding protein phaP was conserved in the strain TD01, which was also observed in some halophiles and non-halophiles exclusively from γ-proteobacteria. In contrast to haloarchaea, the proteome of Halomonas sp. TD01 did not show obvious inclination towards acidity relative to non-halophilic Escherichia coli MG1655, which signified that Halomonas sp. TD01 preferred the accumulation of organic osmolytes to ions in order to balance the intracellular osmotic pressure with the environment. Conclusions The accessibility of genome information would facilitate research on the genetic engineering of halophilic bacteria including Halomonas sp. TD01. PMID:22040376

  6. Genomic study of the Type IVC secretion system in Clostridium difficile: understanding C. difficile evolution via horizontal gene transfer.

    PubMed

    Zhang, Wen; Cheng, Ying; Du, Pengcheng; Zhang, Yuanyuan; Jia, Hongbing; Li, Xianping; Wang, Jing; Han, Na; Qiang, Yujun; Chen, Chen; Lu, Jinxing

    2017-01-01

    Clostridium difficile, the etiological agent of Clostridium difficile infection (CDI), is a gram-positive, spore-forming bacillus that is responsible for ∼20% of antibiotic-related cases of diarrhea and nearly all cases of pseudomembranous colitis. Previous data have shown that a substantial proportion (11%) of the C. difficile genome consists of mobile genetic elements, including seven conjugative transposons. However, the mechanism underlying the formation of a mosaic genome in C. difficile is unknown. The type-IV secretion system (T4SS) is the only secretion system known to transfer DNA segments among bacteria. We searched genome databases to identify a candidate T4SS in C. difficile that could transfer DNA among different C. difficile strains. All T4SS gene clusters in C. difficile are located within genomic islands (GIs), which have variable lengths and structures and are all conjugative transposons. During the horizontal-transfer process of T4SS GIs within the C. difficile population, the excision sites were altered, resulting in different short-tandem repeat sequences among the T4SS GIs, as well as different chromosomal insertion sites and additional regions in the GIs.

  7. An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales

    PubMed Central

    2012-01-01

    Background Horizontal gene transfer (HGT) is considered to be a major force driving the evolutionary history of prokaryotes. HGT is widespread in prokaryotes, contributing to the genomic repertoire of prokaryotic organisms, and is particularly apparent in Rickettsiales genomes. Gene gains from both distantly and closely related organisms play crucial roles in the evolution of bacterial genomes. In this work, we focus on genes transferred from distantly related species into Rickettsiales species. Results We developed an automated approach for the detection of HGT from other organisms (excluding alphaproteobacteria) into Rickettsiales genomes. Our systematic approach consisted of several specialized features including the application of a parsimony method for inferring phyletic patterns followed by blast filter, automated phylogenetic reconstruction and the application of patterns for HGT detection. We identified 42 instances of HGT in 31 complete Rickettsiales genomes, of which 38 were previously unidentified instances of HGT from Anaplasma, Wolbachia, Candidatus Pelagibacter ubique and Rickettsia genomes. Additionally, putative cases with no phylogenetic support were assigned gene ontology terms. Overall, these transfers could be characterized as “rhizome-like”. Conclusions Our analysis provides a comprehensive, systematic approach for the automated detection of HGTs from several complete proteome sequences that can be applied to detect instances of HGT within other genomes of interest. PMID:23234643

  8. Effect of diffusional mass transfer on the performance of horizontal subsurface flow constructed wetlands in tropical climate conditions.

    PubMed

    Njau, K N; Gastory, L; Eshton, B; Katima, J H Y; Minja, R J A; Kimwaga, R; Shaaban, M

    2011-01-01

    The effect of mass transfer on the removal rate constants of BOD5, NH3, NO3 and TKN has been investigated in a Horizontal Subsurface Flow Constructed Wetland (HSSFCW) planted with Phragmites mauritianus. The plug flow model was assumed and the inlet and outlet concentrations were used to determine the observed removal rate constants. Mass transfer effects were studied by assessing the influence of interstitial velocity on pollutant removal rates in CW cells of different widths. The flow velocities varied between 3-46 m/d. Results indicate that the observed removal rate constants are highly influenced by the flow velocity. Correlation of dimensionless groups namely Reynolds Number (Re), Sherwood Number (Sh) and Schmidt Number (Sc) were applied and log-log plots of rate constants against velocity yielded straight lines with values beta = 0.87 for BOD5, 1.88 for NH3, 1.20 for NO3 and 0.94 for TKN. The correlation matched the expected for packed beds although the constant beta was higher than expected for low Reynolds numbers. These results indicate that the design values of rate constants used to size wetlands are influenced by flow velocity. This paper suggests the incorporation of mass transfer into CW design procedures in order to improve the performance of CW systems and reduce land requirements.

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

    PubMed Central

    2008-01-01

    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. PMID:18577206

  10. Origin of the plant Tm-1-like gene via two independent horizontal transfer events and one gene fusion event

    PubMed Central

    Yang, Zefeng; Liu, Li; Fang, Huimin; Li, Pengcheng; Xu, Shuhui; Cao, Wei; Xu, Chenwu; Huang, Jinling; Zhou, Yong

    2016-01-01

    The Tomato mosaic virus (ToMV) resistance gene Tm-1 encodes a direct inhibitor of ToMV RNA replication to protect tomato from infection. The plant Tm-1-like (Tm-1L) protein is predicted to contain an uncharacterized N-terminal UPF0261 domain and a C-terminal TIM-barrel signal transduction (TBST) domain. Homologous searches revealed that proteins containing both of these two domains are mainly present in charophyte green algae and land plants but absent from glaucophytes, red algae and chlorophyte green algae. Although Tm-1 homologs are widely present in bacteria, archaea and fungi, UPF0261- and TBST-domain-containing proteins are generally encoded by different genes in these linages. A co-evolution analysis also suggested a putative interaction between UPF0261- and TBST-domain-containing proteins. Phylogenetic analyses based on homologs of these two domains revealed that plants have acquired UPF0261- and TBST-domain-encoding genes through two independent horizontal gene transfer (HGT) events before the origin of land plants from charophytes. Subsequently, gene fusion occurred between these two horizontally acquired genes and resulted in the origin of the Tm-1L gene in streptophytes. Our results demonstrate a novel evolutionary mechanism through which the recipient organism may acquire genes with functional interaction through two different HGT events and further fuse them into one functional gene. PMID:27647002

  11. Horizontal transfer of whole mitochondria restores tumorigenic potential in mitochondrial DNA-deficient cancer cells

    PubMed Central

    Dong, Lan-Feng; Kovarova, Jaromira; Bajzikova, Martina; Bezawork-Geleta, Ayenachew; Svec, David; Endaya, Berwini; Sachaphibulkij, Karishma; Coelho, Ana R; Sebkova, Natasa; Ruzickova, Anna; Tan, An S; Kluckova, Katarina; Judasova, Kristyna; Zamecnikova, Katerina; Rychtarcikova, Zuzana; Gopalan, Vinod; Andera, Ladislav; Sobol, Margarita; Yan, Bing; Pattnaik, Bijay; Bhatraju, Naveen; Truksa, Jaroslav; Stopka, Pavel; Hozak, Pavel; Lam, Alfred K; Sedlacek, Radislav; Oliveira, Paulo J; Kubista, Mikael; Agrawal, Anurag; Dvorakova-Hortova, Katerina; Rohlena, Jakub; Berridge, Michael V; Neuzil, Jiri

    2017-01-01

    Recently, we showed that generation of tumours in syngeneic mice by cells devoid of mitochondrial (mt) DNA (ρ0 cells) is linked to the acquisition of the host mtDNA. However, the mechanism of mtDNA movement between cells remains unresolved. To determine whether the transfer of mtDNA involves whole mitochondria, we injected B16ρ0 mouse melanoma cells into syngeneic C57BL/6Nsu9-DsRed2 mice that express red fluorescent protein in their mitochondria. We document that mtDNA is acquired by transfer of whole mitochondria from the host animal, leading to normalisation of mitochondrial respiration. Additionally, knockdown of key mitochondrial complex I (NDUFV1) and complex II (SDHC) subunits by shRNA in B16ρ0 cells abolished or significantly retarded their ability to form tumours. Collectively, these results show that intact mitochondria with their mtDNA payload are transferred in the developing tumour, and provide functional evidence for an essential role of oxidative phosphorylation in cancer. DOI: http://dx.doi.org/10.7554/eLife.22187.001 PMID:28195532

  12. Neisseria infection of rhesus macaques as a model to study colonization, transmission, persistence, and horizontal gene transfer

    PubMed Central

    Weyand, Nathan J.; Wertheimer, Anne M.; Hobbs, Theodore R.; Sisko, Jennifer L.; Taku, Nyiawung A.; Gregston, Lindsay D.; Clary, Susan; Higashi, Dustin L.; Biais, Nicolas; Brown, Lewis M.; Planer, Shannon L.; Legasse, Alfred W.; Axthelm, Michael K.; Wong, Scott W.; So, Magdalene

    2013-01-01

    The strict tropism of many pathogens for man hampers the development of animal models that recapitulate important microbe–host interactions. We developed a rhesus macaque model for studying Neisseria–host interactions using Neisseria species indigenous to the animal. We report that Neisseria are common inhabitants of the rhesus macaque. Neisseria isolated from the rhesus macaque recolonize animals after laboratory passage, persist in the animals for at least 72 d, and are transmitted between animals. Neisseria are naturally competent and acquire genetic markers from each other in vivo, in the absence of selection, within 44 d after colonization. Neisseria macacae encodes orthologs of known or presumed virulence factors of human-adapted Neisseria, as well as current or candidate vaccine antigens. We conclude that the rhesus macaque model will allow studies of the molecular mechanisms of Neisseria colonization, transmission, persistence, and horizontal gene transfer. The model can potentially be developed further for preclinical testing of vaccine candidates. PMID:23382234

  13. Flow and heat transfer characteristics of graphene oxide nanofluids in a horizontal tube

    NASA Astrophysics Data System (ADS)

    Nunna, Maheshwar Rao

    This thesis presents a fundamental study conducted on heat transfer and decrease in flow through a straight copper tube of a graphene oxide (GO) nanofluid developed in-house. The GO particles were synthesized using the modified Hummers method. The physicochemical properties of the fabricated GO were characterized using X-ray diffraction analysis (XRD), a scanning electron microscope (SEM), and UV-Vis spectrophotometry, and the particle size distribution was investigated using dynamic light scattering. GO nanofluids of 0.01 wt. % and 0.1 wt. % were prepared by dispersing GO sheets in de-ionized water. Thermo-physical properties of GO nanofluids were also measured at different temperatures. An experimental setup was developed to find the heat transfer characteristics and pressure drop of nanofluids in the test section. A flexible heater was used to provide the constant heat flux condition at the wall of the tube for all the experiments. In this study, the experimental investigations of flow regime, flowrates, pressure drop and heat transfer characteristics were performed by considering three different heat flux conditions (7.38 kW/m2, 9.08 kW/m2, and 12.55 kW/m2) at three different set points of variable frequency drive (VFD), 15, 20, and 25, connected to the pump. Due to the increase in viscosity, there was a decrease in flowrate and Reynolds number from 0.01 wt. % to 0.1 wt. % of GO nanofluids at constant pump frequency. Experimental data obtained for water was validated with available data from the literature, and the correlations were formulated for the Nusselt number and Reynolds number by considering the multiple regression analysis. Convective heat transfer coefficient and dimensionless wall temperature for water and GO nanofluids were investigated. A rise in dimensionless wall temperature with the increase of velocity and particle concentration was observed. The convective heat transfer coefficient for GO 0.01 wt. % was higher when compared to GO 0.1 wt

  14. Type III effector diversification via both pathoadaptation and horizontal transfer in response to a coevolutionary arms race.

    PubMed

    Ma, Wenbo; Dong, Frederick F T; Stavrinides, John; Guttman, David S

    2006-12-01

    The concept of the coevolutionary arms race holds a central position in our understanding of pathogen-host interactions. Here we identify the molecular mechanisms and follow the stepwise progression of an arms race in a natural system. We show how the evolution and function of the HopZ family of type III secreted effector proteins carried by the plant pathogen Pseudomonas syringae are influenced by a coevolutionary arms race between pathogen and host. We surveyed 96 isolates of P. syringae and identified three homologs (HopZ1, HopZ2, and HopZ3) distributed among approximately 45% of the strains. All alleles were sequenced and their expression was confirmed. Evolutionary analyses determined that the diverse HopZ1 homologs are ancestral to P. syringae, and have diverged via pathoadaptive mutational changes into three functional and two degenerate forms, while HopZ2 and HopZ3 have been brought into P. syringae via horizontal transfer from other ecologically similar bacteria. A PAML selection analysis revealed that the C terminus of HopZ1 is under strong positive selection. Despite the extensive genetic variation observed in this family, all three homologs have cysteine-protease activity, although their substrate specificity may vary. The introduction of the ancestral hopZ1 allele into strains harboring alternate alleles results in a resistance protein-mediated defense response in their respective hosts, which is not observed with the endogenous allele. These data indicate that the P. syringae HopZ family has undergone allelic diversification via both pathoadaptive mutational changes and horizontal transfer in response to selection imposed by the host defense system. This genetic diversity permits the pathogen to avoid host defenses while still maintaining a virulence-associated protease, thereby allowing it to thrive on its current host, while simultaneously impacting its host range.

  15. Phylogenetic evidence for extensive horizontal gene transfer of type III secretion system genes among enterobacterial plant pathogens.

    PubMed

    Naum, Marianna; Brown, Eric W; Mason-Gamer, Roberta J

    2009-10-01

    This study uses sequences from four genes, which are involved in the formation of the type III secretion apparatus, to determine the role of horizontal gene transfer in the evolution of virulence genes for the enterobacterial plant pathogens. Sequences of Erwinia, Brenneria, Pectobacterium, Dickeya and Pantoea were compared (a) with one another, (b) with sequences of enterobacterial animal pathogens, and (c) with sequences of plant pathogenic gamma and beta proteobacteria, to evaluate probable paths of lateral exchange leading to the current distribution of virulence determinants among these micro-organisms. Phylogenies were reconstructed based on hrcC, hrcR, hrcJ and hrcV gene sequences using parsimony and maximum-likelihood algorithms. Virulence gene phylogenies were also compared with several housekeeping gene loci in order to evaluate patterns of lateral versus vertical acquisition. The resulting phylogenies suggest that multiple horizontal gene transfer events have occurred both within and among the enterobacterial plant pathogens and plant pathogenic gamma and beta proteobacteria. hrcJ sequences are the most similar, exhibiting anywhere from 2 to 50 % variation at the nucleotide level, with the highest degree of variation present between plant and animal pathogen sequences. hrcV sequences are conserved among plant and animal pathogens at the N terminus. The C-terminal domain is conserved only among the enterobacterial plant pathogens, as are the hrcC and hrcR sequences. Additionally, hrcJ and hrcV sequence phylogenies suggest that at least some type III secretion system virulence genes from enterobacterial plant pathogens are related more closely to those of the genus Pseudomonas, a conclusion neither supported nor refuted by hrcC or hrcR.

  16. Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota

    PubMed Central

    Loy, Alexander; Pfann, Carina; Steinberger, Michaela; Hanson, Buck; Herp, Simone; Brugiroux, Sandrine; Gomes Neto, João Carlos; Boekschoten, Mark V.; Schwab, Clarissa; Urich, Tim; Ramer-Tait, Amanda E.; Rattei, Thomas; Stecher, Bärbel

    2017-01-01

    ABSTRACT Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem. IMPORTANCE Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our

  17. Comparative analysis of the peanut witches'-broom phytoplasma genome reveals horizontal transfer of potential mobile units and effectors.

    PubMed

    Chung, Wan-Chia; Chen, Ling-Ling; Lo, Wen-Sui; Lin, Chan-Pin; Kuo, Chih-Horng

    2013-01-01

    Phytoplasmas are a group of bacteria that are associated with hundreds of plant diseases. Due to their economical importance and the difficulties involved in the experimental study of these obligate pathogens, genome sequencing and comparative analysis have been utilized as powerful tools to understand phytoplasma biology. To date four complete phytoplasma genome sequences have been published. However, these four strains represent limited phylogenetic diversity. In this study, we report the shotgun sequencing and evolutionary analysis of a peanut witches'-broom (PnWB) phytoplasma genome. The availability of this genome provides the first representative of the 16SrII group and substantially improves the taxon sampling to investigate genome evolution. The draft genome assembly contains 13 chromosomal contigs with a total size of 562,473 bp, covering ∼90% of the chromosome. Additionally, a complete plasmid sequence is included. Comparisons among the five available phytoplasma genomes reveal the differentiations in gene content and metabolic capacity. Notably, phylogenetic inferences of the potential mobile units (PMUs) in these genomes indicate that horizontal transfer may have occurred between divergent phytoplasma lineages. Because many effectors are associated with PMUs, the horizontal transfer of these transposon-like elements can contribute to the adaptation and diversification of these pathogens. In summary, the findings from this study highlight the importance of improving taxon sampling when investigating genome evolution. Moreover, the currently available sequences are inadequate to fully characterize the pan-genome of phytoplasmas. Future genome sequencing efforts to expand phylogenetic diversity are essential in improving our understanding of phytoplasma evolution.

  18. Comparative Analysis of the Peanut Witches'-Broom Phytoplasma Genome Reveals Horizontal Transfer of Potential Mobile Units and Effectors

    PubMed Central

    Lo, Wen-Sui; Lin, Chan-Pin; Kuo, Chih-Horng

    2013-01-01

    Phytoplasmas are a group of bacteria that are associated with hundreds of plant diseases. Due to their economical importance and the difficulties involved in the experimental study of these obligate pathogens, genome sequencing and comparative analysis have been utilized as powerful tools to understand phytoplasma biology. To date four complete phytoplasma genome sequences have been published. However, these four strains represent limited phylogenetic diversity. In this study, we report the shotgun sequencing and evolutionary analysis of a peanut witches'-broom (PnWB) phytoplasma genome. The availability of this genome provides the first representative of the 16SrII group and substantially improves the taxon sampling to investigate genome evolution. The draft genome assembly contains 13 chromosomal contigs with a total size of 562,473 bp, covering ∼90% of the chromosome. Additionally, a complete plasmid sequence is included. Comparisons among the five available phytoplasma genomes reveal the differentiations in gene content and metabolic capacity. Notably, phylogenetic inferences of the potential mobile units (PMUs) in these genomes indicate that horizontal transfer may have occurred between divergent phytoplasma lineages. Because many effectors are associated with PMUs, the horizontal transfer of these transposon-like elements can contribute to the adaptation and diversification of these pathogens. In summary, the findings from this study highlight the importance of improving taxon sampling when investigating genome evolution. Moreover, the currently available sequences are inadequate to fully characterize the pan-genome of phytoplasmas. Future genome sequencing efforts to expand phylogenetic diversity are essential in improving our understanding of phytoplasma evolution. PMID:23626855

  19. Indirect Measurement of Local Condensing Heat-Transfer Coefficient Around Horizontal Finned Tubes

    DTIC Science & Technology

    1987-09-01

    5.9 Effect of Tube Insulation on Sieder -Tate-Type Coefficient (C ) and Modified Coefficient (C.) for All Tubes •t Atmospheric Pressure...specific tube C Sleder-Tate-type coefficient in eqn. (4.2) C Modified Sieder -Tate-type coefficient in eqn. (5.2) D Tube diameter (m) D Equivalent diameter...an outside diameter equal to the fin root diameter). The Inside heat-transfer coefficent is given by a Sieder -Tate-type equation (4.2) and is

  20. Horizontal Transfer of the Salmonella enterica Serovar Infantis Resistance and Virulence Plasmid pESI to the Gut Microbiota of Warm-Blooded Hosts

    PubMed Central

    Aviv, Gili; Rahav, Galia

    2016-01-01

    ABSTRACT Salmonella enterica serovar Infantis is one of the prevalent salmonellae worldwide. Recently, we showed that the emergence of S. Infantis in Israel was facilitated by the acquisition of a unique megaplasmid (pESI) conferring multidrug resistance and increased virulence phenotypes. Here we elucidate the ecology, transmission properties, and regulation of pESI. We show that despite its large size (~280 kb), pESI does not impose a significant metabolic burden in vitro and that it has been recently fixed in the domestic S. Infantis population. pESI conjugation and the transcription of its pilus (pil) genes are inhibited at the ambient temperature (27°C) and by ≥1% bile but increased under temperatures of 37 to 41°C, oxidative stress, moderate osmolarity, and the microaerobic conditions characterizing the intestinal environment of warm-blooded animals. The pESI-encoded protein TraB and the oxygen homeostasis regulator Fnr were identified as transcriptional regulators of pESI conjugation. Using the mouse model, we show that following S. Infantis infection, pESI can be horizontally transferred to the gut microbiota, including to commensal Escherichia coli strains. Possible transfer, but not persistence, of pESI was also observed into Gram-positive mouse microbiota species, especially Lactobacillus reuteri. Moreover, pESI was demonstrated to further disseminate from gut microbiota to S. enterica serovar Typhimurium, in the context of gastrointestinal infection. These findings exhibit the ability of a selfish clinically relevant megaplasmid to distribute to and from the microbiota and suggest an overlooked role of the microbiota as a reservoir of mobile genetic elements and intermediator in the spread of resistance and virulence genes between commensals and pathogenic bacteria. PMID:27601577

  1. The Synergism Between Heat and Mass Transfer Additive and Advanced Surfaces in Aqueous LiBr Horizontal Tube Absorbers

    SciTech Connect

    Miller, W.A.

    1999-03-24

    Experiments were conducted in a laboratory to investigate the absorption of water vapor into a falling-film of aqueous lithium bromide (LiBr). A mini-absorber test stand was used to test smooth tubes and a variety of advanced tube surfaces placed horizontally in a single-row bundle. The bundle had six copper tubes; each tube had an outside diameter of 15.9-mm and a length of 0.32-m. A unique feature of the stand is its ability to operate continuously and support testing of LiBr brine at mass fractions {ge} 0.62. The test stand can also support testing to study the effect of the failing film mass flow rate, the coolant mass flow rate, the coolant temperature, the absorber pressure and the tube spacing. Manufacturers of absorption chillers add small quantities of a heat and mass transfer additive to improve the performance of the absorbers. The additive causes surface stirring which enhances the transport of absorbate into the bulk of the film. Absorption may also be enhanced with advanced tube surfaces that mechanically induce secondary flows in the falling film without increasing the thickness of the film. Several tube geometry's were identified and tested with the intent of mixing the film and renewing the interface with fresh solution from the tube wall. Testing was completed on a smooth tube and several different externally enhanced tube surfaces. Experiments were conducted over the operating conditions of 6.5 mm Hg absorber pressure, coolant temperatures ranging from 20 to 35 C and LiBr mass fractions ranging from 0.60 through 0.62. Initially the effect of tube spacing was investigated for the smooth tube surface, tested with no heat and mass transfer additive. Test results showed the absorber load and the mass absorbed increased as the tube spacing increased because of the improved wetting of the tube bundle. However, tube spacing was not a critical factor if heat and mass transfer additive was active in the mini-absorber. The additive dramatically affected

  2. Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer

    PubMed Central

    Novais, Carla; Tedim, Ana P.; Lanza, Val F.; Freitas, Ana R.; Silveira, Eduarda; Escada, Ricardo; Roberts, Adam P.; Al-Haroni, Mohammed; Baquero, Fernando; Peixe, Luísa; Coque, Teresa M.

    2016-01-01

    Ampicillin resistance has greatly contributed to the recent dramatic increase of a cluster of human adapted Enterococcus faecium lineages (ST17, ST18, and ST78) in hospital-based infections. Changes in the chromosomal pbp5 gene have been associated with different levels of ampicillin susceptibility, leading to protein variants (designated as PBP5 C-types to keep the nomenclature used in previous works) with diverse degrees of reduction in penicillin affinity. Our goal was to use a comparative genomics approach to evaluate the relationship between the diversity of PBP5 among E. faecium isolates of different phylogenomic groups as well as to assess the pbp5 transferability among isolates of disparate clonal lineages. The analyses of 78 selected E. faecium strains as well as published E. faecium genomes, suggested that the diversity of pbp5 mirrors the phylogenomic diversification of E. faecium. The presence of identical PBP5 C-types as well as similar pbp5 genetic environments in different E. faecium lineages and clones from quite different geographical and environmental origin was also documented and would indicate their horizontal gene transfer among E. faecium populations. This was supported by experimental assays showing transfer of large (≈180–280 kb) chromosomal genetic platforms containing pbp5 alleles, ponA (transglycosilase) and other metabolic and adaptive features, from E. faecium donor isolates to suitable E. faecium recipient strains. Mutation profile analysis of PBP5 from available genomes and strains from this study suggests that the spread of PBP5 C-types might have occurred even in the absence of a significant ampicillin resistance phenotype. In summary, genetic platforms containing pbp5 sequences were stably maintained in particular E. faecium lineages, but were also able to be transferred among E. faecium clones of different origins, emphasizing the growing risk of further spread of ampicillin resistance in this nosocomial pathogen. PMID

  3. Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer.

    PubMed

    Novais, Carla; Tedim, Ana P; Lanza, Val F; Freitas, Ana R; Silveira, Eduarda; Escada, Ricardo; Roberts, Adam P; Al-Haroni, Mohammed; Baquero, Fernando; Peixe, Luísa; Coque, Teresa M

    2016-01-01

    Ampicillin resistance has greatly contributed to the recent dramatic increase of a cluster of human adapted Enterococcus faecium lineages (ST17, ST18, and ST78) in hospital-based infections. Changes in the chromosomal pbp5 gene have been associated with different levels of ampicillin susceptibility, leading to protein variants (designated as PBP5 C-types to keep the nomenclature used in previous works) with diverse degrees of reduction in penicillin affinity. Our goal was to use a comparative genomics approach to evaluate the relationship between the diversity of PBP5 among E. faecium isolates of different phylogenomic groups as well as to assess the pbp5 transferability among isolates of disparate clonal lineages. The analyses of 78 selected E. faecium strains as well as published E. faecium genomes, suggested that the diversity of pbp5 mirrors the phylogenomic diversification of E. faecium. The presence of identical PBP5 C-types as well as similar pbp5 genetic environments in different E. faecium lineages and clones from quite different geographical and environmental origin was also documented and would indicate their horizontal gene transfer among E. faecium populations. This was supported by experimental assays showing transfer of large (≈180-280 kb) chromosomal genetic platforms containing pbp5 alleles, ponA (transglycosilase) and other metabolic and adaptive features, from E. faecium donor isolates to suitable E. faecium recipient strains. Mutation profile analysis of PBP5 from available genomes and strains from this study suggests that the spread of PBP5 C-types might have occurred even in the absence of a significant ampicillin resistance phenotype. In summary, genetic platforms containing pbp5 sequences were stably maintained in particular E. faecium lineages, but were also able to be transferred among E. faecium clones of different origins, emphasizing the growing risk of further spread of ampicillin resistance in this nosocomial pathogen.

  4. 77 FR 30923 - Electronic Fund Transfers (Regulation E)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-24

    ... Part 1005 [Docket No. CFPB-2012-0019] RIN 3170-AA22 Electronic Fund Transfers (Regulation E) AGENCY... interested in learning more about this product, including its costs, benefits, and risks to consumers. The Bureau intends to issue a proposal to extend the Regulation E protections to GPR cards. Your comments,...

  5. Experimental and numerical simulations of heat transfers between flowing water and a horizontal frozen porous medium

    NASA Astrophysics Data System (ADS)

    Roux, N.; Costard, F.; Grenier, C. F.

    2013-12-01

    In permafrost-affected regions, hydrological changes due to global warming are still under investigation. But yet, we can already foresee from recent studies that for example, the variability and intensity of surface/subsurface flow are likely to be affected by permafrost degradation. And the feedback induced by such changes on permafrost degradation is still not clearly assessed. Of particular interest are lake and river-taliks. A talik is a permanently unfrozen zone that lies below rivers or lake. They should play a key role in these interactions given that they are the only paths for groundwater flow in permafrost regions. Thus heat transfers on a regional scale are potentially influenced by groundwater circulation. The aim of our study is therefore to investigate the evolution of river taliks. We developed a multidisciplinary approach coupling field investigation, experimental studies in a cold room and numerical modeling. In Central Yakutia, Siberia, where permafrost is continuous, we recently installed instruments to monitor ground temperature and water pressure in a river talik between two thermokarst lakes. We present here the coupling of numerical modeling and laboratory experiments in order to look after the main parameters controlling river-talik installation. In a cold room at IDES, where a metric scale channel is filled with sand as a porous medium, we are able to control air, water and permafrost temperature, but also water flow, so that we can test various parameter sets for a miniaturized river. These results are confronted with a numerical model developed at the LSCE with Cast3m (www-cast3m.cea.fr), that couples heat and water transfer. In particular, expressions for river-talik heat exchange terms are investigated. A further step will come in the near future with results from field investigation providing the full complexity of a natural system. Keywords: Talik, River, Numerical Modeling, Cold Room, Permafrost.

  6. Widespread horizontal transfer of the cerato-ulmin gene between Ophiostoma novo-ulmi and Geosmithia species.

    PubMed

    Bettini, Priscilla P; Frascella, Arcangela; Kolařík, Miroslav; Comparini, Cecilia; Pepori, Alessia L; Santini, Alberto; Scala, Felice; Scala, Aniello

    2014-08-01

    Previous work had shown that a sequence homologous to the gene encoding class II hydrophobin cerato-ulmin from the fungus Ophiostoma novo-ulmi, the causal agent of Dutch Elm Disease (DED), was present in a strain of the unrelated species Geosmithia species 5 (Ascomycota: Hypocreales) isolated from Ulmus minor affected by DED. As both fungi occupy the same habitat, even if different ecological niches, the occurrence of horizontal gene transfer was proposed. In the present work we have analysed for the presence of the cerato-ulmin gene 70 Geosmithia strains representing 29 species, isolated from different host plants and geographic locations. The gene was found in 52.1 % of the strains derived from elm trees, while none of those isolated from nonelms possessed it. The expression of the gene in Geosmithia was also assessed by real time PCR in different growth conditions (liquid culture, solid culture, elm sawdust, dual culture with O. novo-ulmi), and was found to be extremely low in all conditions tested. On the basis of these results we propose that the cerato-ulmin gene is not functional in Geosmithia, but can be considered instead a marker of more extensive transfers of genetic material as shown in other fungi.

  7. Horizontal gene transfer from a flowering plant to the insular pine Pinus canariensis (Chr. Sm. Ex DC in Buch)

    PubMed Central

    Wang, B; Climent, J; Wang, X-R

    2015-01-01

    Horizontal gene transfer (HGT) is viewed as very common in the plant mitochondrial (mt) genome, but, to date, only one case of HGT has been found in gymnosperms. Here we report a new case of HGT, in which a mt nad5-1 fragment was transferred from an angiosperm to Pinus canariensis. Quantitative assay and sequence analyses showed that the foreign nad5-1 is located in the mt genome of P. canariensis and is nonfunctional. An extensive survey in the genus Pinus revealed that the angiosperm-derived nad5-1 is restricted to P. canariensis and present across the species' range. Molecular dating based on chloroplast DNA suggested that the HGT event occurred in the late Miocene after P. canariensis split from its closest relatives, and that the foreign copy became fixed in P. canariensis owing to drift during its colonization of the Canary Islands. The mechanism of this HGT is unclear but it was probably achieved through either direct cell–cell contact or external vectors. Our discovery provides evidence for an important role of HGT in plant mt genome evolution. PMID:25604946

  8. Evolution of genes and organisms: the tree/web of life in light of horizontal gene transfer.

    PubMed

    Olendzenski, Lorraine; Gogarten, J Peter

    2009-10-01

    Gene exchange necessitates expanding the model of the tree of life, impacts the notion of organismal and molecular most recent common ancestors, and provides examples of natural selection working at multiple levels. Gene exchange, whether by horizontal gene transfer (HGT), hybridization of species, or symbiosis, modifies the organismal tree of life into a web. Darwin suggested the tree of life was like a coral, where living surface branches were supported by masses of dead branches. In phylogenetic trees, organismal or molecular lineages coalesce back to a lucky universal ancestor whose descendents are found in current lineages and which coexisted with other, now-extinct lineages. HGT complicates the reconstruction of a universal ancestor; genes in a genome can have different evolutionary histories, and even infrequent gene transfer will cause different molecular lineages to coalesce to molecular ancestors that existed in different organismal lineages and at different times. HGT, as well as symbiosis, provides a mechanism for integrating and expanding the organizational level on which natural selection acts, contributing to selection at the group and community level.

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

    PubMed

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

    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]) and found evidence of intracellular HGT for a 2.4-kb segment of mitochondrial DNA to the rps2-rpoC2 intergenic spacer of the plastome. The transferred region contains an rpl2 pseudogene and is flanked by plastid sequence in the mitochondrial genome, including an rpoC2 pseudogene, which likely provided the mechanism for HGT back to the plastome through double-strand break repair involving homologous recombination. The plastome insertion is restricted to tribe Asclepiadeae of subfamily Asclepiadoideae, whereas the mitochondrial rpoC2 pseudogene is present throughout the subfamily, which confirms that the plastid to mitochondrial HGT event preceded the HGT to the plastome. Although the plastome insertion has been maintained in all lineages of Asclepiadoideae, it shows minimal evidence of transcription in A. syriaca and is likely nonfunctional. Furthermore, we found recent gene conversion of the mitochondrial rpoC2 pseudogene in Asclepias by the plastid gene, which reflects continued interaction of these genomes.

  10. Horizontal Transfer of DNA from the Mitochondrial to the Plastid Genome and Its Subsequent Evolution in Milkweeds (Apocynaceae)

    PubMed Central

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

    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]) and found evidence of intracellular HGT for a 2.4-kb segment of mitochondrial DNA to the rps2–rpoC2 intergenic spacer of the plastome. The transferred region contains an rpl2 pseudogene and is flanked by plastid sequence in the mitochondrial genome, including an rpoC2 pseudogene, which likely provided the mechanism for HGT back to the plastome through double-strand break repair involving homologous recombination. The plastome insertion is restricted to tribe Asclepiadeae of subfamily Asclepiadoideae, whereas the mitochondrial rpoC2 pseudogene is present throughout the subfamily, which confirms that the plastid to mitochondrial HGT event preceded the HGT to the plastome. Although the plastome insertion has been maintained in all lineages of Asclepiadoideae, it shows minimal evidence of transcription in A. syriaca and is likely nonfunctional. Furthermore, we found recent gene conversion of the mitochondrial rpoC2 pseudogene in Asclepias by the plastid gene, which reflects continued interaction of these genomes. PMID:24029811

  11. Multiple Horizontal Transfers of Bacteriophage WO and Host Wolbachia in Fig Wasps in a Closed Community

    PubMed Central

    Wang, Ningxin; Jia, Sisi; Xu, Heng; Liu, Yong; Huang, Dawei

    2016-01-01

    Wolbachia-bacteriophage WO is a good model system for studying interactions between bacteria and viruses. Previous surveys of insect hosts have been conducted via sampling from open or semi-open communities; however, no studies have reported the infection patterns of phage WO of insects living in a closed community. Figs and fig wasps form a peculiar closed community in which the Ficus tree provides a compact syconium habitat for a variety of fig wasp. Therefore, in this study, we performed a thorough survey of Wolbachia and bacteriophage WO infection patterns in a total of 1406 individuals from 23 fig wasps species living on three different fig tree species. The infection rates of Wolbachia and phage WO were 82.6% (19/23) and 39.1% (9/23), respectively. Additionally, phage WO from fig wasps showed strong insect host specificity based on orf7 sequences from fig wasps and 21 other insect species. Probably due to the physical barrier of fig syconium, most phage WO from fig wasps form a specific clade. Phylogenetic analysis showed the absence of congruence between WO and host Wolbachia, WO and insect host, as well as Wolbachia and fig wasps, suggesting that both Wolbachia and phage WO exchanged frequently and independently within the closed syconium. Thus, the infection pattern of bacteriophage WO from fig wasps appeared quite different from that in other insects living outside, although the effect and the transfer routes of phage WO are unclear, which need to be investigated in the future. PMID:26913026

  12. Saturated flow boiling heat transfer correlation for carbon dioxide for horizontal smooth tubes

    NASA Astrophysics Data System (ADS)

    Turgut, Oguz Emrah; Asker, Mustafa

    2017-01-01

    Literature comprises fewer studies about flow boiling modelling of refrigerants for in tube flows. In addition, researches on two phase flow heat transfer are based on the mathematical models which were derived in a very limited operational condition and correlated for their own measurements. In this study, a new flow boiling model including the superposed effects of nucleate and convective boiling mechanisms is proposed through the minimization of the cumulative error between the proposed mathematical model and actual data by means of artificial cooperative search algorithm and applied to the database of R-744 (carbon dioxide), available from different studies in the literature. Predictions obtained from the proposed model have been compared with those of retained from the literature correlations developed for flow boiling in tubes. The comparison results indicate that the new model outperforms the literature correlations in terms of prediction accuracy. Results of the comparisons reveal that the proposed flow boiling mathematical model has a mean absolute relative error of 14.6% and predicts 76.7% of the experimental data within ±20.0%.

  13. Multiple Horizontal Transfers of Bacteriophage WO and Host Wolbachia in Fig Wasps in a Closed Community.

    PubMed

    Wang, Ningxin; Jia, Sisi; Xu, Heng; Liu, Yong; Huang, Dawei

    2016-01-01

    Wolbachia-bacteriophage WO is a good model system for studying interactions between bacteria and viruses. Previous surveys of insect hosts have been conducted via sampling from open or semi-open communities; however, no studies have reported the infection patterns of phage WO of insects living in a closed community. Figs and fig wasps form a peculiar closed community in which the Ficus tree provides a compact syconium habitat for a variety of fig wasp. Therefore, in this study, we performed a thorough survey of Wolbachia and bacteriophage WO infection patterns in a total of 1406 individuals from 23 fig wasps species living on three different fig tree species. The infection rates of Wolbachia and phage WO were 82.6% (19/23) and 39.1% (9/23), respectively. Additionally, phage WO from fig wasps showed strong insect host specificity based on orf7 sequences from fig wasps and 21 other insect species. Probably due to the physical barrier of fig syconium, most phage WO from fig wasps form a specific clade. Phylogenetic analysis showed the absence of congruence between WO and host Wolbachia, WO and insect host, as well as Wolbachia and fig wasps, suggesting that both Wolbachia and phage WO exchanged frequently and independently within the closed syconium. Thus, the infection pattern of bacteriophage WO from fig wasps appeared quite different from that in other insects living outside, although the effect and the transfer routes of phage WO are unclear, which need to be investigated in the future.

  14. Biotechnology regulation: is policy transfer an appropriate answer?

    PubMed

    Cárdenas-Gómez, Olga Carolina; Létourneau, Lyne

    2010-01-01

    In the world of biotechnology regulation, one often encounters the suggestion that the legislation of other countries should be consulted. Known as "policy transfer" in the field of public policy analysis, the purpose of such a recommendation is for policymakers to use the experiences of other States as a basis for developing appropriate regulatory frameworks in a timely manner. This paper examines whether policy transfer is relevant as an instrument for biotechnology regulation, and if it is, to what extent. Our analysis uses the example of Assisted Reproductive Technologies (ART), and unfolds according to the following argumentative steps. We will begin by discussing policy transfer as a recognized feature of policymaking in the literature pertaining to public policy analysis. We will then introduce a distinction between the technical dimension of policymaking and its political component. We will refer to "morality policy" as an illustration of policymaking directed toward its political component. We will show that, in the case of morality policy, States have moved away from a policy transfer approach. We will then establish that ART qualifies as morality policy, suggesting that policy transfer is most likely not the optimal policymaking tool for dealing with biotechnology regulation. Moving beyond the issue of ART in order to expand our reasoning to biotechnology regulation as a whole, we will conclude that, although the experiences of other States may be useful, policy transfer does not suffice in terms of informing policymaking in the case of biotechnology advances.

  15. Vitamin B(12) synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales.

    PubMed

    Swithers, Kristen S; Petrus, Amanda K; Secinaro, Michael A; Nesbø, Camilla L; Gogarten, J Peter; Noll, Kenneth M; Butzin, Nicholas C

    2012-01-01

    The availability of genome sequences of Thermotogales species from across the order allows an examination of the evolutionary origins of phenotypic characteristics in this lineage. Several studies have shown that the Thermotogales have acquired large numbers of genes from distantly related lineages, particularly Firmicutes and Archaea. Here, we report the finding that some Thermotogales acquired the ability to synthesize vitamin B(12) by acquiring the requisite genes from these distant lineages. Thermosipho species, uniquely among the Thermotogales, contain genes that encode the means to synthesize vitamin B(12) de novo from glutamate. These genes are split into two gene clusters: the corrinoid synthesis gene cluster, that is unique to the Thermosipho and the cobinamide salvage gene cluster. The corrinoid synthesis cluster was acquired from the Firmicutes lineage, whereas the salvage pathway is an amalgam of bacteria- and archaea-derived proteins. The cobinamide salvage gene cluster has a patchy distribution among Thermotogales species, and ancestral state reconstruction suggests that this pathway was present in the common Thermotogales ancestor. We show that Thermosipho africanus can grow in the absence of vitamin B(12), so its de novo pathway is functional. We detected vitamin B(12) in the extracts of T. africanus cells to verify the synthetic pathway. Genes in T. africanus with apparent B(12) riboswitches were found to be down-regulated in the presence of vitamin B(12) consistent with their roles in B(12) synthesis and cobinamide salvage.

  16. Vitamin B12 Synthesis and Salvage Pathways Were Acquired by Horizontal Gene Transfer to the Thermotogales

    PubMed Central

    Swithers, Kristen S.; Petrus, Amanda K.; Secinaro, Michael A.; Nesbø, Camilla L.; Gogarten, J. Peter; Noll, Kenneth M.; Butzin, Nicholas C.

    2012-01-01

    The availability of genome sequences of Thermotogales species from across the order allows an examination of the evolutionary origins of phenotypic characteristics in this lineage. Several studies have shown that the Thermotogales have acquired large numbers of genes from distantly related lineages, particularly Firmicutes and Archaea. Here, we report the finding that some Thermotogales acquired the ability to synthesize vitamin B12 by acquiring the requisite genes from these distant lineages. Thermosipho species, uniquely among the Thermotogales, contain genes that encode the means to synthesize vitamin B12 de novo from glutamate. These genes are split into two gene clusters: the corrinoid synthesis gene cluster, that is unique to the Thermosipho and the cobinamide salvage gene cluster. The corrinoid synthesis cluster was acquired from the Firmicutes lineage, whereas the salvage pathway is an amalgam of bacteria- and archaea-derived proteins. The cobinamide salvage gene cluster has a patchy distribution among Thermotogales species, and ancestral state reconstruction suggests that this pathway was present in the common Thermotogales ancestor. We show that Thermosipho africanus can grow in the absence of vitamin B12, so its de novo pathway is functional. We detected vitamin B12 in the extracts of T. africanus cells to verify the synthetic pathway. Genes in T. africanus with apparent B12 riboswitches were found to be down-regulated in the presence of vitamin B12 consistent with their roles in B12 synthesis and cobinamide salvage. PMID:22798452

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

    PubMed Central

    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

  18. An investigation of horizontal transfer of feed introduced DNA to the aerobic microbiota of the gastrointestinal tract of rats

    PubMed Central

    2012-01-01

    Background Horizontal gene transfer through natural transformation of members of the microbiota of the lower gastrointestinal tract (GIT) of mammals has not yet been described. Insufficient DNA sequence similarity for homologous recombination to occur has been identified as the major barrier to interspecies transfer of chromosomal DNA in bacteria. In this study we determined if regions of high DNA similarity between the genomes of the indigenous bacteria in the GIT of rats and feed introduced DNA could lead to homologous recombination and acquisition of antibiotic resistance genes. Results Plasmid DNA with two resistance genes (nptI and aadA) and regions of high DNA similarity to 16S rRNA and 23S rRNA genes present in a broad range of bacterial species present in the GIT, were constructed and added to standard rat feed. Six rats, with a normal microbiota, were fed DNA containing pellets daily over four days before sampling of the microbiota from the different GI compartments (stomach, small intestine, cecum and colon). In addition, two rats were included as negative controls. Antibiotic resistant colonies growing on selective media were screened for recombination with feed introduced DNA by PCR targeting unique sites in the putatively recombined regions. No transformants were identified among 441 tested isolates. Conclusions The analyses showed that extensive ingestion of DNA (100 μg plasmid) per day did not lead to increased proportions of kanamycin resistant bacteria, nor did it produce detectable transformants among the aerobic microbiota examined for 6 rats (detection limit < 1 transformant per 1,1 × 108 cultured bacteria). The key methodological challenges to HGT detection in animal feedings trials are identified and discussed. This study is consistent with other studies suggesting natural transformation is not detectable in the GIT of mammals. PMID:22463741

  19. The genome of the mustard leaf beetle encodes two active xylanases originally acquired from bacteria through horizontal gene transfer

    PubMed Central

    Pauchet, Yannick; Heckel, David G.

    2013-01-01

    The primary plant cell wall comprises the most abundant polysaccharides on the Earth and represents a rich source of energy for organisms which have evolved the ability to digest them. Enzymes able to degrade plant cell wall polysaccharides are widely distributed in micro-organisms but are generally absent in animals, although their presence in insects, especially phytophagous beetles from the superfamilies Chrysomeloidea and Curculionoidea, has recently begun to be appreciated. The observed patchy distribution of endogenous genes encoding these enzymes in animals has raised questions about their evolutionary origins. Recent evidence suggests that endogenous plant cell wall degrading enzymes-encoding genes have been acquired by animals through a mechanism known as horizontal gene transfer (HGT). HGT describes how genetic material is moved by means other than vertical inheritance from a parent to an offspring. Here, we provide evidence that the mustard leaf beetle, Phaedon cochleariae, possesses in its genome genes encoding active xylanases from the glycoside hydrolase family 11 (GH11). We also provide evidence that these genes were originally acquired by P. cochleariae from a species of gammaproteobacteria through HGT. This represents the first example of the presence of genes from the GH11 family in animals. PMID:23698014

  20. A genome-wide association study identifies a horizontally transferred bacterial surface adhesin gene associated with antimicrobial resistant strains

    PubMed Central

    Suzuki, Masato; Shibayama, Keigo; Yahara, Koji

    2016-01-01

    Carbapenems are a class of last-resort antibiotics; thus, the increase in bacterial carbapenem-resistance is a serious public health threat. Acinetobacter baumannii is one of the microorganisms that can acquire carbapenem-resistance; it causes severe nosocomial infection, and is notoriously difficult to control in hospitals. Recently, a machine-learning approach was first used to analyze the genome sequences of hundreds of susceptible and resistant A. baumannii strains, including those carrying commonly acquired resistant mechanisms, to build a classifier that can predict strain resistance. A complementary approach is to explore novel genetic elements that could be associated with the antimicrobial resistance of strains, independent of known mechanisms. Therefore, we carefully selected A. baumannii strains, spanning various genotypes, from public genome databases, and conducted the first genome-wide association study (GWAS) of carbapenem resistance. We employed a recently developed method, capable of identifying any kind of genetic variation and accounting for bacterial population structure, and evaluated its effectiveness. Our study identified a surface adhesin gene that had been horizontally transferred to an ancestral branch of A. baumannii, as well as a specific region of that gene that appeared to accumulate multiple individual variations across the different branches of carbapenem-resistant A. baumannii strains. PMID:27892531

  1. Genetic Diversity and Horizontal Transfer of Genes Involved in Oxidation of Reduced Phosphorus Compounds by Alcaligenes faecalis WM2072

    PubMed Central

    Wilson, Marlena M.; Metcalf, William W.

    2005-01-01

    Enrichment was performed to isolate organisms that could utilize reduced phosphorus compounds as their sole phosphorus sources. One isolate that grew well with either hypophosphite or phosphite was identified by 16S rRNA gene analysis as a strain of Alcaligenes faecalis. The genes required for oxidation of hypophosphite and phosphite by this organism were identified by using transposon mutagenesis and include homologs of the ptxD and htxA genes of Pseudomonas stutzeri WM88, which encode an NAD-dependent phosphite dehydrogenase (PtxD) and 2-oxoglutarate-dependent hypophosphite dioxygenase (HtxA). This organism also has the htxB, htxC, and htxD genes that comprise an ABC-type transporter, presumably for hypophosphite and phosphite transport. The role of these genes in reduced phosphorus metabolism was confirmed by analyzing the growth of mutants in which these genes were deleted. Sequencing data showed that htxA, htxB, htxC, and htxD are virtually identical to their homologs in P. stutzeri at the DNA level, indicating that horizontal gene transfer occurred. However, A. faecalis ptxD is very different from its P. stutzeri homolog and represents a new ptxD lineage. Therefore, this gene has ancient evolutionary roots in bacteria. These data suggest that there is strong evolutionary selection for the ability of microorganisms to oxidize hypophosphite and phosphite. PMID:15640200

  2. Regions of Unusual Statistical Properties as Tools in the Search for Horizontally Transferred Genes in Escherichia coli

    NASA Astrophysics Data System (ADS)

    Putonti, Catherine; Chumakov, Sergei; Chavez, Arturo; Luo, Yi; Graur, Dan; Fox, George E.; Fofanov, Yuriy

    2006-09-01

    The observed diversity of statistical characteristics along genomic sequences is the result of the influences of a variety of ongoing processes including horizontal gene transfer, gene loss, genome rearrangements, and evolution. The rate at which various processes affect the genome typically varies between different genomic regions. Thus, variations in statistical properties seen in different regions of a genome are often associated with its evolution and functional organization. Analysis of such properties is therefore relevant to many ongoing biomedical research efforts. Similarity Plot or S-plot is a Windows-based application for large-scale comparisons and 2D visualization of similarities between genomic sequences. This application combines two approaches wildly used in genomics: window analysis of statistical characteristics along genomes and dot-plot visual representation. S-plot is effective in detecting highly similar regions between two genomes. Within a single genome, S-plot has the ability to identify highly dissimilar regions displaying unusual compositional properties. The application was used to perform a comparative analysis of 50+ microbial genomes as well as many eukaryote genomes including human, rat, mouse, and drosophila. We illustrate the uses of S-Plot in a comparison involving Escherichia coli K12 and E. coli O157:H7.

  3. Fluoroquinolone resistance in atypical pneumococci and oral streptococci: evidence of horizontal gene transfer of fluoroquinolone resistance determinants from Streptococcus pneumoniae.

    PubMed

    Ip, Margaret; Chau, Shirley S L; Chi, Fang; Tang, Julian; Chan, Paul K

    2007-08-01

    Atypical strains, presumed to be pneumococcus, with ciprofloxacin MICs of > or =4.0 microg/ml and unique sequence variations within the quinolone resistance-determining regions (QRDRs) of the gyrase and topoisomerase genes in comparison with the Streptococcus pneumoniae R6 strain, were examined. These strains were reidentified using phenotypic methods, including detection of optochin susceptibility, bile solubility, and agglutination by serotype-specific antisera, and genotypic methods, including detection of pneumolysin and autolysin genes by PCR, 16S rRNA sequencing, and multilocus sequence typing (MLST). The analysis based on concatenated sequences of the six MLST loci distinguished the "atypical" strains from pneumococci, and these strains clustered closely with S. mitis. However, all these strains and five of nine strains from the viridans streptococcal group possessed one to three gyrA, gyrB, parC, and parE genes whose QRDR sequences clustered with those of S. pneumoniae, providing evidence of horizontal transfer of the QRDRs of the gyrase and topoisomerase genes from pneumococci into viridans streptococci. These genes also conferred fluoroquinolone resistance to viridans streptococci. In addition, the fluoroquinolone resistance determinants of 32 well-characterized Streptococcus mitis and Streptococcus oralis strains from bacteremic patients were also compared. These strains have unique amino acid substitutions in GyrA and ParC that were distinguishable from those in fluoroquinolone-resistant pneumococci and the "atypical" isolates. Both recombinational events and de novo mutations play an important role in the development of fluoroquinolone resistance.

  4. Genetic diversity and horizontal transfer of genes involved in oxidation of reduced phosphorus compounds by Alcaligenes faecalis WM2072.

    PubMed

    Wilson, Marlena M; Metcalf, William W

    2005-01-01

    Enrichment was performed to isolate organisms that could utilize reduced phosphorus compounds as their sole phosphorus sources. One isolate that grew well with either hypophosphite or phosphite was identified by 16S rRNA gene analysis as a strain of Alcaligenes faecalis. The genes required for oxidation of hypophosphite and phosphite by this organism were identified by using transposon mutagenesis and include homologs of the ptxD and htxA genes of Pseudomonas stutzeri WM88, which encode an NAD-dependent phosphite dehydrogenase (PtxD) and 2-oxoglutarate-dependent hypophosphite dioxygenase (HtxA). This organism also has the htxB, htxC, and htxD genes that comprise an ABC-type transporter, presumably for hypophosphite and phosphite transport. The role of these genes in reduced phosphorus metabolism was confirmed by analyzing the growth of mutants in which these genes were deleted. Sequencing data showed that htxA, htxB, htxC, and htxD are virtually identical to their homologs in P. stutzeri at the DNA level, indicating that horizontal gene transfer occurred. However, A. faecalis ptxD is very different from its P. stutzeri homolog and represents a new ptxD lineage. Therefore, this gene has ancient evolutionary roots in bacteria. These data suggest that there is strong evolutionary selection for the ability of microorganisms to oxidize hypophosphite and phosphite.

  5. Horizontal gene transfer of a bacterial insect toxin gene into the Epichloë fungal symbionts of grasses

    PubMed Central

    Ambrose, Karen V.; Koppenhöfer, Albrecht M.; Belanger, Faith C.

    2014-01-01

    Horizontal gene transfer is recognized as an important factor in genome evolution, particularly when the newly acquired gene confers a new capability to the recipient species. We identified a gene similar to the makes caterpillars floppy (mcf1 and mcf2) insect toxin genes in Photorhabdus, bacterial symbionts of nematodes, in the genomes of the Epichloë fungi, which are intercellular symbionts of grasses. Infection by Epichloë spp. often confers insect resistance to the grass hosts, largely due to the production of fungal alkaloids. A mcf-like gene is present in all of the Epichloë genome sequences currently available but in no other fungal genomes. This suggests the Epichloë genes were derived from a single lineage-specific HGT event. Molecular dating was used to estimate the time of the HGT event at between 7.2 and 58.8 million years ago. The mcf-like coding sequence from Epichloë typhina subsp. poae was cloned and expressed in Escherichia coli. E. coli cells expressing the Mcf protein were toxic to black cutworms (Agrotis ipsilon), whereas E. coli cells containing the vector only were non-toxic. These results suggest that the Epichloë mcf-like genes may be a component, in addition to the fungal alkaloids, of the insect resistance observed in Epichloë-infected grasses. PMID:24990771

  6. Evidence of horizontal transfer of non-autonomous Lep1 Helitrons facilitated by host-parasite interactions.

    PubMed

    Guo, Xuezhu; Gao, Jingkun; Li, Fei; Wang, Jianjun

    2014-05-30

    Horizontal transfer (HT) of transposable elements has been recognized to be a major force driving genomic variation and biological innovation of eukaryotic organisms. However, the mechanisms of HT in eukaryotes remain poorly appreciated. The non-autonomous Helitron family, Lep1, has been found to be widespread in lepidopteran species, and showed little interspecific sequence similarity of acquired sequences at 3' end, which makes Lep1 a good candidate for the study of HT. In this study, we describe the Lep1-like elements in multiple non-lepidopteran species, including two aphids, Acyrthosiphon pisum and Aphis gossypii, two parasitoid wasps, Cotesia vestalis, and Copidosoma floridanum, one beetle, Anoplophora glabripennis, as well as two bracoviruses in parasitoid wasps, and one intracellular microsporidia parasite, Nosema bombycis. The patchy distribution and high sequence similarity of Lep1-like elements among distantly related lineages as well as incongruence of Lep1-like elements and host phylogeny suggest the occurrence of HT. Remarkably, the acquired sequences of both NbLep1 from N. bombycis and CfLep1 from C. floridanum showed over 90% identity with their lepidopteran host Lep1. Thus, our study provides evidence of HT facilitated by host-parasite interactions. Furthermore, in the context of these data, we discuss the putative directions and vectors of HT of Lep1 Helitrons.

  7. Evidence for Natural Horizontal Transfer of the pcpB Gene in the Evolution of Polychlorophenol-Degrading Sphingomonads

    PubMed Central

    Tiirola, Marja A.; Wang, Hong; Paulin, Lars; Kulomaa, Markku S.

    2002-01-01

    The chlorophenol degradation pathway in Sphingobium chlorophenolicum is initiated by the pcpB gene product, pentachlorophenol-4-monooxygenase. The distribution of the gene was studied in a phylogenetically diverse group of polychlorophenol-degrading bacteria isolated from contaminated groundwater in Kärkölä, Finland. All the sphingomonads isolated were shown to share pcpB gene homologs with 98.9 to 100% sequence identity. The gene product was expressed when the strains were induced by 2,3,4,6-tetrachlorophenol. A comparative analysis of the 16S rDNA and pcpB gene trees suggested that a recent horizontal transfer of the pcpB gene was involved in the evolution of the catabolic pathway in the Kärkölä sphingomonads. The full-length Kärkölä pcpB gene allele had approximately 70% identity with the three pcpB genes previously sequenced from sphingomonads. It was very closely related to the environmental clones obtained from chlorophenol-enriched soil samples (M. Beaulieu, V. Becaert, L. Deschenes, and R. Villemur, Microbiol. Ecol. 40:345-355, 2000). The gene was not present in polychlorophenol-degrading nonsphingomonads isolated from the Kärkölä source. PMID:12200305

  8. Evolution of a Sigma Factor: An All-In-One of Gene Duplication, Horizontal Gene Transfer, Purifying Selection, and Promoter Differentiation

    PubMed Central

    López-Leal, Gamaliel; Cevallos, Miguel A.; Castillo-Ramírez, Santiago

    2016-01-01

    Sigma factors are an essential part of bacterial gene regulation and have been extensively studied as far as their molecular mechanisms and protein structure are concerned. However, their molecular evolution, especially for the alternative sigma factors, is poorly understood. Here, we analyze the evolutionary forces that have shaped the rpoH sigma factors within the alphaproteobacteria. We found that an ancient duplication gave rise to two major groups of rpoH sigma factors and that after this event horizontal gene transfer (HGT) occurred in rpoH1 group. We also noted that purifying selection has differentially affected distinct parts of the gene; singularly, the gene segment that encodes the region 4.2, which interacts with the −35 motif of the RpoH-dependent genes, has been under relaxed purifying selection. Furthermore, these two major groups are clearly differentiated from one another regarding their promoter selectivity, as rpoH1 is under the transcriptional control of σ70 and σ32, whereas rpoH2 is under the transcriptional control of σ24. Our results suggest a scenario in which HGT, gene loss, variable purifying selection and clear promoter specialization occurred after the ancestral duplication event. More generally, our study offers insights into the molecular evolution of alternative sigma factors and highlights the importance of analyzing not only the coding regions but also the promoter regions. PMID:27199915

  9. 76 FR 81019 - Electronic Fund Transfers (Regulation E)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-27

    ...Title X of the Dodd-Frank Wall Street Reform and Consumer Protection Act (Dodd-Frank Act) transferred rulemaking authority for a number of consumer financial protection laws from seven Federal agencies to the Bureau of Consumer Financial Protection (Bureau) as of July 21, 2011. The Bureau is in the process of republishing the regulations implementing those laws with technical and conforming......

  10. 77 FR 77187 - Electronic Fund Transfers (Regulation E)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-31

    ... From the Federal Register Online via the Government Publishing Office ] Vol. 77 Monday, No. 250 December 31, 2012 Part II Bureau of Consumer Financial Protection 12 CFR Part 1005 Electronic Fund Transfers (Regulation E); Proposed Rule #0;#0;Federal Register / Vol. 77 , No. 250 / Monday, December...

  11. Two-Dimensional Computational Fluid Dynamics and Conduction Simulations of Heat Transfer in Horizontal Window Frames with Internal Cavities

    SciTech Connect

    Gustavsen, Arlid; Kohler, Christian; Dalehaug, Arvid; Arasteh, Dariush

    2008-12-01

    compared, at selected locations on the frames. Small differences was found in the results from model to model. Finally, the effectiveness of the ISO cavity radiation algorithms was examined by comparing results from these algorithms to detailed radiation calculations (from both programs). Our results suggest that improvements in cavity heat transfer calculations can be obtained by using detailed radiation modeling (i.e. view-factor or ray-tracing models), and that incorporation of these strategies may be more important for improving the accuracy of results than the use of CFD modeling for horizontal cavities.

  12. A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences.

    PubMed

    Putonti, Catherine; Luo, Yi; Katili, Charles; Chumakov, Sergey; Fox, George E; Graur, Dan; Fofanov, Yuriy

    2006-10-01

    Similarity Plot (S-plot) is a Windows-based application for large-scale comparisons and 2-dimensional visualization of compositional similarities between genomic sequences. This application combines 2 approaches widely used in genomics: window analysis of statistical characteristics along genomes and dot-plot visual representation. S-plot is effective in identifying highly similar regions between genomes as well as regions with unusual compositional properties (RUCPs) within a single genome, which may be indicative of horizontal gene transfer or of locus-specific selective forces. We use S-plot to identify regions that may have originated through horizontal gene transfer through a 2-step approach, by first comparing a genomic sequence to itself and, subsequently, comparing it to the genomic sequence of a closely related taxon. Moreover, by comparing these suspect sequences to one another, we can estimate a minimum number of sources for these putative xenologous sequences. We illustrate the uses of S-plot in a comparison involving Escherichia coli K12 and E. coli O157:H7. In O157:H7, we found 145 regions that have most probably originated through horizontal gene transfer. By using S-plot to compare each of these regions with 277 completely sequenced prokaryotic genomes, 1 sequence was found to have similar compositional properties to the Yersinia pseudotuberculosis genome, indicating a transfer from a Yersinia or Yersinia relative. Based upon our analysis of RUCPs in O157:H7, we infer that there were at least 53 sources of horizontally transferred sequences.

  13. Horizontal Transfer of a Subtilisin Gene from Plants into an Ancestor of the Plant Pathogenic Fungal Genus Colletotrichum

    PubMed Central

    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. PMID:23554975

  14. Experimental examination of EFL and MATX eukaryotic horizontal gene transfers: coexistence of mutually exclusive transcripts predates functional rescue.

    PubMed

    Szabová, Jana; Ruzicka, Petr; Verner, Zdenek; Hampl, Vladimír; Lukes, Julius

    2011-08-01

    Many eukaryotic genes do not follow simple vertical inheritance. Elongation factor 1α (EF-1α) and methionine adenosyl transferase (MAT) are enzymes with complicated evolutionary histories and, interestingly, the two cases have several features in common. These essential enzymes occur as two relatively divergent paralogs (EF-1α/EFL, MAT/MATX) that have patchy distributions in eukaryotic lineages that are nearly mutually exclusive. To explain such distributions, we must invoke either multiple eukaryote-to-eukaryote horizontal gene transfers (HGTs) followed by functional replacement or presence of both paralogs in the common ancestor followed by long-term coexistence and differential losses in various eukaryotic lineages. To understand the evolution of these paralogs, we have performed in vivo experiments in Trypanosoma brucei addressing the consequences of long-term coexpression and functional replacement. In the first experiment of its kind, we have demonstrated that EF-1α and MAT can be simultaneously expressed with EFL and MATX, respectively, without affecting the growth of the flagellates. After the endogenous MAT or EF-1α was downregulated by RNA interference, MATX immediately substituted for its paralog, whereas EFL was not able to substitute for EF-1α, leading to mortality. We conclude that MATX is naturally capable of evolving patchy paralog distribution via HGTs and/or long- term coexpression and differential losses. The capability of EFL to spread by HGT is lower and so the patchy distribution of EF-1α/EFL paralogs was probably shaped mainly by deep paralogy followed by long-term coexistence and differential losses.

  15. Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea.

    PubMed

    Brochier-Armanet, Céline; Deschamps, Philippe; López-García, Purificación; Zivanovic, Yvan; Rodríguez-Valera, Francisco; Moreira, David

    2011-08-01

    The extent of horizontal gene transfer (HGT) among marine pelagic prokaryotes and the role that HGT may have played in their adaptation to this particular environment remain open questions. This is partly due to the paucity of cultured species and genomic information for many widespread groups of marine bacteria and archaea. Molecular studies have revealed a large diversity and relative abundance of marine planktonic archaea, in particular of Thaumarchaeota (also known as group I Crenarchaeota) and Euryarchaeota of groups II and III, but only one species (the thaumarchaeote Candidatus Nitrosopumilus maritimus) has been isolated in pure culture so far. Therefore, metagenomics remains the most powerful approach to study these environmental groups. To investigate the impact of HGT in marine archaea, we carried out detailed phylogenetic analyses of all open reading frames of 21 archaeal 16S rRNA gene-containing fosmids and, to extend our analysis to other genomic regions, also of fosmid-end sequences of 12 774 fosmids from three different deep-sea locations (South Atlantic and Adriatic Sea at 1000 m depth, and Ionian Sea at 3000 m depth). We found high HGT rates in both marine planktonic Thaumarchaeota and Euryarchaeota, with remarkable converging values estimated from complete-fosmid and fosmid-end sequence analysis (25 and 21% of the genes, respectively). Most HGTs came from bacterial donors (mainly from Proteobacteria, Firmicutes and Chloroflexi) but also from other archaea and eukaryotes. Phylogenetic analyses showed that in most cases HGTs are shared by several representatives of the studied groups, implying that they are ancient and have been conserved over relatively long evolutionary periods. This, together with the functions carried out by these acquired genes (mostly related to energy metabolism and transport of metabolites across membranes), suggests that HGT has played an important role in the adaptation of these archaea to the cold and nutrient

  16. Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile “Ferrovum”

    PubMed Central

    Ullrich, Sophie R.; González, Carolina; Poehlein, Anja; Tischler, Judith S.; Daniel, Rolf; Schlömann, Michael; Holmes, David S.; Mühling, Martin

    2016-01-01

    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

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

    PubMed

    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.

  18. Multiple horizontal gene transfer events and domain fusions have created novel regulatory and metabolic networks in the oomycete genome.

    PubMed

    Morris, Paul Francis; Schlosser, Laura Rose; Onasch, Katherine Diane; Wittenschlaeger, Tom; Austin, Ryan; Provart, Nicholas

    2009-07-02

    Complex enzymes with multiple catalytic activities are hypothesized to have evolved from more primitive precursors. Global analysis of the Phytophthora sojae genome using conservative criteria for evaluation of complex proteins identified 273 novel multifunctional proteins that were also conserved in P. ramorum. Each of these proteins contains combinations of protein motifs that are not present in bacterial, plant, animal, or fungal genomes. A subset of these proteins were also identified in the two diatom genomes, but the majority of these proteins have formed after the split between diatoms and oomycetes. Documentation of multiple cases of domain fusions that are common to both oomycetes and diatom genomes lends additional support for the hypothesis that oomycetes and diatoms are monophyletic. Bifunctional proteins that catalyze two steps in a metabolic pathway can be used to infer the interaction of orthologous proteins that exist as separate entities in other genomes. We postulated that the novel multifunctional proteins of oomycetes could function as potential Rosetta Stones to identify interacting proteins of conserved metabolic and regulatory networks in other eukaryotic genomes. However ortholog analysis of each domain within our set of 273 multifunctional proteins against 39 sequenced bacterial and eukaryotic genomes, identified only 18 candidate Rosetta Stone proteins. Thus the majority of multifunctional proteins are not Rosetta Stones, but they may nonetheless be useful in identifying novel metabolic and regulatory networks in oomycetes. Phylogenetic analysis of all the enzymes in three pathways with one or more novel multifunctional proteins was conducted to determine the probable origins of individual enzymes. These analyses revealed multiple examples of horizontal transfer from both bacterial genomes and the photosynthetic endosymbiont in the ancestral genome of Stramenopiles. The complexity of the phylogenetic origins of these metabolic pathways and

  19. Identification of Bari Transposons in 23 Sequenced Drosophila Genomes Reveals Novel Structural Variants, MITEs and Horizontal Transfer.

    PubMed

    Palazzo, Antonio; Lovero, Domenica; D'Addabbo, Pietro; Caizzi, Ruggiero; Marsano, René Massimiliano

    2016-01-01

    Bari elements are members of the Tc1-mariner superfamily of DNA transposons, originally discovered in Drosophila melanogaster, and subsequently identified in silico in 11 sequenced Drosophila genomes and as experimentally isolated in four non-sequenced Drosophila species. Bari-like elements have been also studied for their mobility both in vivo and in vitro. We analyzed 23 Drosophila genomes and carried out a detailed characterization of the Bari elements identified, including those from the heterochromatic Bari1 cluster in D. melanogaster. We have annotated 401 copies of Bari elements classified either as putatively autonomous or inactive according to the structure of the terminal sequences and the presence of a complete transposase-coding region. Analyses of the integration sites revealed that Bari transposase prefers AT-rich sequences in which the TA target is cleaved and duplicated. Furthermore evaluation of transposon's co-occurrence near the integration sites of Bari elements showed a non-random distribution of other transposable elements. We also unveil the existence of a putatively autonomous Bari1 variant characterized by two identical long Terminal Inverted Repeats, in D. rhopaloa. In addition, we detected MITEs related to Bari transposons in 9 species. Phylogenetic analyses based on transposase gene and the terminal sequences confirmed that Bari-like elements are distributed into three subfamilies. A few inconsistencies in Bari phylogenetic tree with respect to the Drosophila species tree could be explained by the occurrence of horizontal transfer events as also suggested by the results of dS analyses. This study further clarifies the Bari transposon's evolutionary dynamics and increases our understanding on the Tc1-mariner elements' biology.

  20. Multiple Horizontal Gene Transfer Events and Domain Fusions Have Created Novel Regulatory and Metabolic Networks in the Oomycete Genome

    PubMed Central

    Morris, Paul Francis; Schlosser, Laura Rose; Onasch, Katherine Diane; Wittenschlaeger, Tom; Austin, Ryan; Provart, Nicholas

    2009-01-01

    Complex enzymes with multiple catalytic activities are hypothesized to have evolved from more primitive precursors. Global analysis of the Phytophthora sojae genome using conservative criteria for evaluation of complex proteins identified 273 novel multifunctional proteins that were also conserved in P. ramorum. Each of these proteins contains combinations of protein motifs that are not present in bacterial, plant, animal, or fungal genomes. A subset of these proteins were also identified in the two diatom genomes, but the majority of these proteins have formed after the split between diatoms and oomycetes. Documentation of multiple cases of domain fusions that are common to both oomycetes and diatom genomes lends additional support for the hypothesis that oomycetes and diatoms are monophyletic. Bifunctional proteins that catalyze two steps in a metabolic pathway can be used to infer the interaction of orthologous proteins that exist as separate entities in other genomes. We postulated that the novel multifunctional proteins of oomycetes could function as potential Rosetta Stones to identify interacting proteins of conserved metabolic and regulatory networks in other eukaryotic genomes. However ortholog analysis of each domain within our set of 273 multifunctional proteins against 39 sequenced bacterial and eukaryotic genomes, identified only 18 candidate Rosetta Stone proteins. Thus the majority of multifunctional proteins are not Rosetta Stones, but they may nonetheless be useful in identifying novel metabolic and regulatory networks in oomycetes. Phylogenetic analysis of all the enzymes in three pathways with one or more novel multifunctional proteins was conducted to determine the probable origins of individual enzymes. These analyses revealed multiple examples of horizontal transfer from both bacterial genomes and the photosynthetic endosymbiont in the ancestral genome of Stramenopiles. The complexity of the phylogenetic origins of these metabolic pathways and

  1. Identification of Bari Transposons in 23 Sequenced Drosophila Genomes Reveals Novel Structural Variants, MITEs and Horizontal Transfer

    PubMed Central

    D’Addabbo, Pietro; Caizzi, Ruggiero

    2016-01-01

    Bari elements are members of the Tc1-mariner superfamily of DNA transposons, originally discovered in Drosophila melanogaster, and subsequently identified in silico in 11 sequenced Drosophila genomes and as experimentally isolated in four non-sequenced Drosophila species. Bari-like elements have been also studied for their mobility both in vivo and in vitro. We analyzed 23 Drosophila genomes and carried out a detailed characterization of the Bari elements identified, including those from the heterochromatic Bari1 cluster in D. melanogaster. We have annotated 401 copies of Bari elements classified either as putatively autonomous or inactive according to the structure of the terminal sequences and the presence of a complete transposase-coding region. Analyses of the integration sites revealed that Bari transposase prefers AT-rich sequences in which the TA target is cleaved and duplicated. Furthermore evaluation of transposon’s co-occurrence near the integration sites of Bari elements showed a non-random distribution of other transposable elements. We also unveil the existence of a putatively autonomous Bari1 variant characterized by two identical long Terminal Inverted Repeats, in D. rhopaloa. In addition, we detected MITEs related to Bari transposons in 9 species. Phylogenetic analyses based on transposase gene and the terminal sequences confirmed that Bari-like elements are distributed into three subfamilies. A few inconsistencies in Bari phylogenetic tree with respect to the Drosophila species tree could be explained by the occurrence of horizontal transfer events as also suggested by the results of dS analyses. This study further clarifies the Bari transposon’s evolutionary dynamics and increases our understanding on the Tc1-mariner elements’ biology. PMID:27213270

  2. Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case of horizontal gene transfer.

    PubMed Central

    Lamour, V; Quevillon, S; Diriong, S; N'Guyen, V C; Lipinski, M; Mirande, M

    1994-01-01

    An important step ensuring the fidelity in protein biosynthesis is the aminoacylation of tRNAs by aminoacyl-tRNA synthetases. The accuracy of this process rests on a family of 20 enzymes, one for each amino acid. One exception is the formation of Gln-tRNA(Gln) that can be accomplished by two different pathways: aminoacylation of tRNA(Gln) with Gln by glutaminyl-tRNA synthetase (GlnRS; EC 6.1.1.18) or transamidation of Glu from Glu-tRNA(Gln) mischarged by glutamyl-tRNA synthetase (GluRS; EC 6.1.1.17). The latter pathway is widespread among bacteria and organelles that, accordingly, lack GlnRS. However, some bacterial species, such as Escherichia coli, do possess a GlnRS activity, which is responsible for Gln-tRNA(Gln) formation. In the cytoplasm of eukaryotic cells, both GluRS and GlnRS activities can be detected. To gain more insight into the evolutionary relationship between GluRS and GlnRS enzyme species, we have now isolated and characterized a human cDNA encoding GlnRS. The deduced amino acid sequence shows a strong similarity with other known GlnRSs and with eukaryotic GluRSs. A molecular phylogenetic analysis was conducted on the 14 GlxRS (GluRS or GlnRS) sequences available to date. Our data suggest that bacterial GlnRS has a eukaryotic origin and was acquired by a mechanism of horizontal gene transfer. Images PMID:8078941

  3. The advantages of complementing MT profiles in 3-D environments with geomagnetic transfer function and interstation horizontal magnetic transfer function data: results from a synthetic case study

    NASA Astrophysics Data System (ADS)

    Campanyà, Joan; Ogaya, Xènia; Jones, Alan G.; Rath, Volker; Vozar, Jan; Meqbel, Naser

    2016-12-01

    As a consequence of measuring time variations of the electric and the magnetic field, which are related to current flow and charge distribution, magnetotelluric (MT) data in 2-D and 3-D environments are not only sensitive to the geoelectrical structures below the measuring points but also to any lateral anomalies surrounding the acquisition site. This behaviour complicates the characterization of the electrical resistivity distribution of the subsurface, particularly in complex areas. In this manuscript we assess the main advantages of complementing the standard MT impedance tensor (Z) data with interstation horizontal magnetic tensor (H) and geomagnetic transfer function (T) data in constraining the subsurface in a 3-D environment beneath a MT profile. Our analysis was performed using synthetic responses with added normally distributed and scattered random noise. The sensitivity of each type of data to different resistivity anomalies was evaluated, showing that the degree to which each site and each period is affected by the same anomaly depends on the type of data. A dimensionality analysis, using Z, H and T data, identified the presence of the 3-D anomalies close to the profile, suggesting a 3-D approach for recovering the electrical resistivity values of the subsurface. Finally, the capacity for recovering the geoelectrical structures of the subsurface was evaluated by performing joint inversion using different data combinations, quantifying the differences between the true synthetic model and the models from inversion process. Four main improvements were observed when performing joint inversion of Z, H and T data: (1) superior precision and accuracy at characterizing the electrical resistivity values of the anomalies below and outside the profile; (2) the potential to recover high electrical resistivity anomalies that are poorly recovered using Z data alone; (3) improvement in the characterization of the bottom and lateral boundaries of the anomalies with low

  4. Regulation control and energy management scheme for wireless power transfer

    SciTech Connect

    Miller, John M.

    2015-12-29

    Power transfer rate at a charging facility can be maximized by employing a feedback scheme. The state of charge (SOC) and temperature of the regenerative energy storage system (RESS) pack of a vehicle is monitored to determine the load due to the RESS pack. An optimal frequency that cancels the imaginary component of the input impedance for the output signal from a grid converter is calculated from the load of the RESS pack, and a frequency offset f* is made to the nominal frequency f.sub.0 of the grid converter output based on the resonance frequency of a magnetically coupled circuit. The optimal frequency can maximize the efficiency of the power transfer. Further, an optimal grid converter duty ratio d* can be derived from the charge rate of the RESS pack. The grid converter duty ratio d* regulates wireless power transfer (WPT) power level.

  5. Regulation of Lipid and Glucose Metabolism by Phosphatidylcholine Transfer Protein

    PubMed Central

    Kang, Hye Won; Wei, Jie; Cohen, David E.

    2010-01-01

    Phosphatidylcholine transfer protein (PC-TP, a.k.a. StARD2) binds phosphatidylcholines and catalyzes their intermembrane transfer and exchange in vitro. The structure of PC-TP comprises a hydrophobic pocket and a well-defined head-group binding site, and its gene expression is regulated by peroxisome proliferator activated receptor α. Recent studies have revealed key regulatory roles for PC-TP in lipid and glucose metabolism. Notably, Pctp−/− mice are sensitized to insulin action and exhibit more efficient brown fat-mediated thermogenesis. PC-TP appears to limit access of fatty acids to mitochondria by stimulating the activity of thioesterase superfamily member 2, a newly characterized long-chain fatty acyl-CoA thioesterase. Because PC-TP discriminates among phosphatidylcholines within lipid bilayers, it may function as a sensor that links metabolic regulation to membrane composition. PMID:20338778

  6. Natural convection heat transfer from horizontal concentric and eccentric cylinder systems cooling in the ambient air and determination of inner cylinder location

    NASA Astrophysics Data System (ADS)

    Atayılmaz, Ş. Özgür; Demir, Hakan; Sevindir, Mustafa Kemal; Ağra, Özden; Teke, İsmail; Dalkılıç, Ahmet Selim

    2017-03-01

    Heat transfer characteristics of horizontal copper concentric cylinders in the case of natural convection was investigated numerically and experimentally. While the inner cylinder had an electric heater to keep it at a constant temperature, annulus was filled with water. There were two different test sections as bare and concentric cylinder systems located in different ambient temperatures in a conditioned room for the comparison of the results. Comparison of average Nusselt numbers for the air side of the concentric cylinder system and the effective thermal conductivity of the annulus were calculated with both experimental data, numerical results and a well-known correlation. Annulus and the air side isotherms and streamlines are shown for RaL = 9 × 105-5 × 106 and Ra = 2 × 105-7 × 105 respectively. Additionally, a numerical study was conducted by forming eccentric cylinder systems to determine the optimum location of inner cylinder to maximize the heat transfer rate. Comparison of heat transfer rates from bare and concentric horizontal cylinders were done under steady state conditions. Heat transfer enhancement, the effect of the decrease in condensing temperature of the inner cylinder surface on COP of an ideal Carnot refrigeration cycle and rise in COP were determined in the study. Also the optimum location of inner cylinder to maximize the heat transfer rate was determined as at the bottom quadrant of outer cylinder.

  7. Modulation of cone horizontal cell activity in the teleost fish retina. II. Role of interplexiform cells and dopamine in regulating light responsiveness.

    PubMed

    Yang, X L; Tornqvist, K; Dowling, J E

    1988-07-01

    Following the destruction of the terminals of the dopaminergic interplexiform cells by intraocular injections of 6-hydroxydopamine (6-OHDA), cone horizontal cells exhibited high light responsiveness in prolonged darkness and their responses to moderate and bright full-field flashes were as large as 60 mV. Furthermore, the light responsiveness of these cells in the 6-OHDA-treated retinas was not enhanced by background illumination. The application of dopamine (50 microM) by superfusion to 6-OHDA-treated retinas resulted in a decrease in light responsiveness and changes in response waveform of the cone horizontal cells. Twenty minutes following dopamine application the responses of the cone horizontal cells closely resembled the response of cells recorded in prolonged dark-adapted retinas. Dopamine caused similar changes in cone horizontal cells recorded in light-exposed retinas, but had no obvious effects on rod horizontal cells. The selective dopamine D1 receptor antagonist, Sch 23390, enhanced cone horizontal cell responsiveness when applied to prolonged dark-adapted retinas, mimicking background illumination. The light responsiveness of cone horizontal cells recorded after application of Sch 23390 was less than that for cells in retinas that had been exposed to background lights, but light responsiveness could not be further enhanced by background illumination. Another dopamine antagonist, (+)-butaclamol, was found to have effects similar to Sch 23390 on cone horizontal cells, but (-)-butaclamol, the inactive enantiomer, did not enhance the light responsiveness of these cells. The results suggest that the dopaminergic interplexiform cells play a crucial role in the regulation of cone horizontal cell responsiveness by prolonged darkness and background illumination. These cells may release dopamine tonically in the dark, which suppresses cone horizontal cell responsiveness. Background illumination may decrease dopamine release and liberate cone horizontal cells

  8. Evidence for Horizontal Transfer of SsuDAT1I Restriction-Modification Genes to the Streptococcus suis Genome

    PubMed Central

    Sekizaki, Tsutomu; Otani, Yoshiko; Osaki, Makoto; Takamatsu, Daisuke; Shimoji, Yoshihiro

    2001-01-01

    Different strains of Streptococcus suis serotypes 1 and 2 isolated from pigs either contained a restriction-modification (R-M) system or lacked it. The R-M system was an isoschizomer of Streptococcus pneumoniae DpnII, which recognizes nucleotide sequence 5′-GATC-3′. The nucleotide sequencing of the genes encoding the R-M system in S. suis DAT1, designated SsuDAT1I, showed that the SsuDAT1I gene region contained two methyltransferase genes, designated ssuMA and ssuMB, as does the DpnII system. The deduced amino acid sequences of M.SsuMA and M.SsuMB showed 70 and 90% identity to M.DpnII and M.DpnA, respectively. However, the SsuDAT1I system contained two isoschizomeric restriction endonuclease genes, designated ssuRA and ssuRB. The deduced amino acid sequence of R.SsuRA was 49% identical to that of R.DpnII, and R.SsuRB was 72% identical to R.LlaDCHI of Lactococcus lactis subsp. cremoris DCH-4. The four SsuDAT1I genes overlapped and were bounded by purine biosynthetic gene clusters in the following gene order: purF-purM-purN-purH-ssuMA-ssuMB-ssuRA-ssuRB-purD-purE. The G+C content of the SsuDAT1I gene region (34.1%) was lower than that of the pur region (48.9%), suggesting horizontal transfer of the SsuDAT1I system. No transposable element or long-repeat sequence was found in the flanking regions. The SsuDAT1I genes were functional by themselves, as they were individually expressed in Escherichia coli. Comparison of the sequences between strains with and without the R-M system showed that only the region from 53 bp upstream of ssuMA to 5 bp downstream of ssuRB was inserted in the intergenic sequence between purH and purD and that the insertion target site was not the recognition site of SsuDAT1I. No notable substitutions or insertions could be found, and the structures were conserved among all the strains. These results suggest that the SsuDAT1I system could have been integrated into the S. suis chromosome by an illegitimate recombination mechanism. PMID:11133943

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

    PubMed

    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.

  10. Wolbachia co-infection in a hybrid zone: discovery of horizontal gene transfers from two Wolbachia supergroups into an animal genome.

    PubMed

    Funkhouser-Jones, Lisa J; Sehnert, Stephanie R; Martínez-Rodríguez, Paloma; Toribio-Fernández, Raquel; Pita, Miguel; Bella, José L; Bordenstein, Seth R

    2015-01-01

    Hybrid zones and the consequences of hybridization have contributed greatly to our understanding of evolutionary processes. Hybrid zones also provide valuable insight into the dynamics of symbiosis since each subspecies or species brings its unique microbial symbionts, including germline bacteria such as Wolbachia, to the hybrid zone. Here, we investigate a natural hybrid zone of two subspecies of the meadow grasshopper Chorthippus parallelus in the Pyrenees Mountains. We set out to test whether co-infections of B and F Wolbachia in hybrid grasshoppers enabled horizontal transfer of phage WO, similar to the numerous examples of phage WO transfer between A and B Wolbachia co-infections. While we found no evidence for transfer between the divergent co-infections, we discovered horizontal transfer of at least three phage WO haplotypes to the grasshopper genome. Subsequent genome sequencing of uninfected grasshoppers uncovered the first evidence for two discrete Wolbachia supergroups (B and F) contributing at least 448 kb and 144 kb of DNA, respectively, into the host nuclear genome. Fluorescent in situ hybridization verified the presence of Wolbachia DNA in C. parallelus chromosomes and revealed that some inserts are subspecies-specific while others are present in both subspecies. We discuss our findings in light of symbiont dynamics in an animal hybrid zone.

  11. Wolbachia co-infection in a hybrid zone: discovery of horizontal gene transfers from two Wolbachia supergroups into an animal genome

    PubMed Central

    Sehnert, Stephanie R.; Martínez-Rodríguez, Paloma; Toribio-Fernández, Raquel; Pita, Miguel; Bella, José L.; Bordenstein, Seth R.

    2015-01-01

    Hybrid zones and the consequences of hybridization have contributed greatly to our understanding of evolutionary processes. Hybrid zones also provide valuable insight into the dynamics of symbiosis since each subspecies or species brings its unique microbial symbionts, including germline bacteria such as Wolbachia, to the hybrid zone. Here, we investigate a natural hybrid zone of two subspecies of the meadow grasshopper Chorthippus parallelus in the Pyrenees Mountains. We set out to test whether co-infections of B and F Wolbachia in hybrid grasshoppers enabled horizontal transfer of phage WO, similar to the numerous examples of phage WO transfer between A and B Wolbachia co-infections. While we found no evidence for transfer between the divergent co-infections, we discovered horizontal transfer of at least three phage WO haplotypes to the grasshopper genome. Subsequent genome sequencing of uninfected grasshoppers uncovered the first evidence for two discrete Wolbachia supergroups (B and F) contributing at least 448 kb and 144 kb of DNA, respectively, into the host nuclear genome. Fluorescent in situ hybridization verified the presence of Wolbachia DNA in C. parallelus chromosomes and revealed that some inserts are subspecies-specific while others are present in both subspecies. We discuss our findings in light of symbiont dynamics in an animal hybrid zone. PMID:26664808

  12. Senstitivity analysis of horizontal heat and vapor transfer coefficients for a cloud-topped marine boundary layer during cold-air outbreaks. M.S. Thesis

    NASA Technical Reports Server (NTRS)

    Chang, Y. V.

    1986-01-01

    The effects of external parameters on the surface heat and vapor fluxes into the marine atmospheric boundary layer (MABL) during cold-air outbreaks are investigated using the numerical model of Stage and Businger (1981a). These fluxes are nondimensionalized using the horizontal heat (g1) and vapor (g2) transfer coefficient method first suggested by Chou and Atlas (1982) and further formulated by Stage (1983a). In order to simplify the problem, the boundary layer is assumed to be well mixed and horizontally homogeneous, and to have linear shoreline soundings of equivalent potential temperature and mixing ratio. Modifications of initial surface flux estimates, time step limitation, and termination conditions are made to the MABL model to obtain accurate computations. The dependence of g1 and g2 in the cloud topped boundary layer on the external parameters (wind speed, divergence, sea surface temperature, radiative sky temperature, cloud top radiation cooling, and initial shoreline soundings of temperature, and mixing ratio) is studied by a sensitivity analysis, which shows that the uncertainties of horizontal transfer coefficients caused by changes in the parameters are reasonably small.

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

    NASA Astrophysics Data System (ADS)

    Sheikhnejad, Yahya; Hosseini, Reza; Saffar Avval, Majid

    2017-02-01

    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.

  14. Naturally mosaic operons for secondary metabolite biosynthesis: variability and putative horizontal transfer of discrete catalytic domains of the epothilone polyketide synthase locus.

    PubMed

    Lopez, J V

    2003-12-01

    A putative instance of horizontal gene transfer (HGT) involving adjacent, discrete beta-ketoacyl synthase (KS), acyl carrier protein (ACP) and nonribosomal peptide synthase (NRPS) domains of the epothilone Type I polyketide biosynthetic gene cluster from the myxobacterium Sorangium cellulosom was identified using molecular phylogenetics and sequence analyses. The specific KS domain of the module EPO B fails to cluster phylogenetically with other epothilone KS sequences present at this locus, in contrast to what is typically observed in many other Type I polyketide synthase (PKS) biosynthetic loci. Furthermore, the GC content of the epoB KS, epoA ACP and NRPS domains differs significantly from the base composition of other epothilone domain sequences. In addition, the putatively transferred epothilone loci are located near previously identified transposon-like sequences. Lastly, comparison with other KS loci revealed another possible case of horizontal transfer of secondary metabolite genes in the genus Pseudomonas. This study emphasizes the use of several lines of concordant evidence (phylogenetics, base composition, transposon sequences) to infer the evolutionary history of particular gene and enzyme sequences, and the results support the idea that genes coding for adaptive traits, e.g. defensive natural products, may be prone to transposition between divergent prokaryotic taxa and genomes.

  15. The horizontally-acquired response regulator SsrB drives a Salmonella lifestyle switch by relieving biofilm silencing

    PubMed Central

    Desai, Stuti K; Winardhi, Ricksen S; Periasamy, Saravanan; Dykas, Michal M; Jie, Yan; Kenney, Linda J

    2016-01-01

    A common strategy by which bacterial pathogens reside in humans is by shifting from a virulent lifestyle, (systemic infection), to a dormant carrier state. Two major serovars of Salmonella enterica, Typhi and Typhimurium, have evolved a two-component regulatory system to exist inside Salmonella-containing vacuoles in the macrophage, as well as to persist as asymptomatic biofilms in the gallbladder. Here we present evidence that SsrB, a transcriptional regulator encoded on the SPI-2 pathogenicity-island, determines the switch between these two lifestyles by controlling ancestral and horizontally-acquired genes. In the acidic macrophage vacuole, the kinase SsrA phosphorylates SsrB, and SsrB~P relieves silencing of virulence genes and activates their transcription. In the absence of SsrA, unphosphorylated SsrB directs transcription of factors required for biofilm formation specifically by activating csgD (agfD), the master biofilm regulator by disrupting the silenced, H-NS-bound promoter. Anti-silencing mechanisms thus control the switch between opposing lifestyles. DOI: http://dx.doi.org/10.7554/eLife.10747.001 PMID:26880544

  16. Investigation of the effect of wall materials and tube diameter by heat transfer from horizontal tubes to boiling liquids

    NASA Astrophysics Data System (ADS)

    Siebert, Matthias

    1987-09-01

    Heating surface materials like copper, brass, and stainless steel are studied for their heat transfer coefficient through tubes of 8 mm diameter. Refrigerants considered are R12, R113, R114, methane, and pentane. Heat transfer measurements are carried out in dependence on boiling pressure, liquid properties, bubble formation, and size and bubble deposit thickness on heat surfaces. Nucleate boiling is visualized and observed.

  17. Monitoring of possible horizontal gene transfer from transgenic potatoes to soil microorganisms in the potato fields and the emergence of variants in Phytophthora infestans.

    PubMed

    Kim, Sung Eun; Moon, Jae Sun; Kim, Jung Kyu; Yoo, Ran Hee; Choi, Won Sik; Lee, Eun Na; Lee, Sang Han; Kim, Sung Uk

    2010-06-01

    To examine the possibility of horizontal gene transfer between transgenic potatoes and microorganisms in potato fields, the gene flow from transgenic potatoes containing nucleoside diphosphate kinase 2 (NDPK2) gene to microorganisms in soils was investigated. The soil samples collected from the potato fields from March to October in 2007 were examined by PCR, Southern hybridization, and AFLP fingerprinting. The NDPK2 gene from soil genomic DNAs was not detected by both PCR and Southern hybridization, indicating that gene-transfer did not occur in the potato fields. In addition, no discrepancy was found in pathogenicity and noticeable changes for the appearance of variants of Phytophthora infestans in each generation when serial inoculations and the analysis of genomic DNAs by AFLP was conducted. Thus, these data suggest that transgenic potatoes do not give significant impacts on the communities of soil microorganisms and the emergence of variants although continued research efforts may be necessary to make a decisive conclusion.

  18. Horizontal gene transfer as adaptive response to heavy metal stress in subsurface microbial communities. Final report for period October 15, 1997 - October 15, 2000

    SciTech Connect

    Smets, B. F.

    2001-12-21

    Horizontal gene transfer as adaptive response to heavy metal stress in the presence of heavy metal stress was evaluated in oligotrophic subsurface soil laboratory scale microcosms. Increasing levels of cadmium (10, 100 and 1000 mM) were applied and an E. coli donor was used to deliver the target plasmids, pMOL187 and pMOL222, which contained the czc and ncc operons, and the helper plasmid RP4. Plasmid transfer was evaluated through monitoring of the heavy metal resistance and presence of the genes. The interactive, clearly revealed, effect of biological and chemical external factors on the extent of plasmid-DNA propagation in microbial communities in contaminated soil environments was observed in this study. Additionally, P.putida LBJ 415 carrying a suicide construct was used to evaluate selective elimination of a plasmid donor.

  19. Transfer of the horizontal patient: the effect of a friction reducing assistive device on low back mechanics.

    PubMed

    McGill, S M; Kavcic, N S

    2005-06-22

    Recognizing that the transfer of bedridden patients is associated with a high rate of low back injuries, various devices have been developed to assist with sparing the patient handlers. The purpose of this study was to quantify the friction-reducing ability of three different 'sliding' patient transfer devices together with the subsequent consequences on the low back loads of people performing the transfers. Coefficients of friction of the devices were determined by 'transferring' a standard object and a 'patient' over several surfaces common to a hospital setting. Then three participants performed controlled transfers with the various devices. Electromyography to measure muscle activation levels together with external forces and kinematic positional data were collected during push, pull and twist transfers. Spine loads were estimated with a three-dimensional biomechanical static link-segment model of the human body. Simply sliding a patient on a cotton sheet (control condition) produced a coefficient of friction of 0.45. The assistive devices substantially reduced friction by well over one-half (coefficients of 0.18 - 0.21). However, when using the devices the subjects adopted a variety of postures and techniques, such that there were no consistent influences on trunk inclination, low back compression or muscle activation profiles. Direct measurement of reduced friction between the bed and the patient with a friction-reducing device together with measurement of the back loads when actually transferring a patient formed a proof of principle. Specifically, while the device lowers friction, the transfer technique adopted by the lifter must be proper to reduce low back loading and any subsequent risks of back troubles associated with patient transfers. The direction of hand forces and torso position remains important.

  20. Horizontal gene transfer and the rock record: comparative genomics of phylogenetically distant bacteria that induce wrinkle structure formation in modern sediments.

    PubMed

    Flood, B E; Bailey, J V; Biddle, J F

    2014-03-01

    Wrinkle structures are sedimentary features that are produced primarily through the trapping and binding of siliciclastic sediments by mat-forming micro-organisms. Wrinkle structures and related sedimentary structures in the rock record are commonly interpreted to represent the stabilizing influence of cyanobacteria on sediments because cyanobacteria are known to produce similar textures and structures in modern tidal flat settings. However, other extant bacteria such as filamentous representatives of the family Beggiatoaceae can also interact with sediments to produce sedimentary features that morphologically resemble many of those associated with cyanobacteria-dominated mats. While Beggiatoa spp. and cyanobacteria are metabolically and phylogenetically distant, genomic analyses show that the two groups share hundreds of homologous genes, likely as the result of horizontal gene transfer. The comparative genomics results described here suggest that some horizontally transferred genes may code for phenotypic traits such as filament formation, chemotaxis, and the production of extracellular polymeric substances that potentially underlie the similar biostabilizing influences of these organisms on sediments. We suggest that the ecological utility of certain basic life modes such as the construction of mats and biofilms, coupled with the lateral mobility of genes in the microbial world, introduces an element of uncertainty into the inference of specific phylogenetic origins from gross morphological features preserved in the ancient rock record.

  1. Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers

    PubMed Central

    2013-01-01

    Background Trypanosomatids of the genera Angomonas and Strigomonas live in a mutualistic association characterized by extensive metabolic cooperation with obligate endosymbiotic Betaproteobacteria. However, the role played by the symbiont has been more guessed by indirect means than evidenced. Symbiont-harboring trypanosomatids, in contrast to their counterparts lacking symbionts, exhibit lower nutritional requirements and are autotrophic for essential amino acids. To evidence the symbiont’s contributions to this autotrophy, entire genomes of symbionts and trypanosomatids with and without symbionts were sequenced here. Results Analyses of the essential amino acid pathways revealed that most biosynthetic routes are in the symbiont genome. By contrast, the host trypanosomatid genome contains fewer genes, about half of which originated from different bacterial groups, perhaps only one of which (ornithine cyclodeaminase, EC:4.3.1.12) derived from the symbiont. Nutritional, enzymatic, and genomic data were jointly analyzed to construct an integrated view of essential amino acid metabolism in symbiont-harboring trypanosomatids. This comprehensive analysis showed perfect concordance among all these data, and revealed that the symbiont contains genes for enzymes that complete essential biosynthetic routes for the host amino acid production, thus explaining the low requirement for these elements in symbiont-harboring trypanosomatids. Phylogenetic analyses show that the cooperation between symbionts and their hosts is complemented by multiple horizontal gene transfers, from bacterial lineages to trypanosomatids, that occurred several times in the course of their evolution. Transfers occur preferentially in parts of the pathways that are missing from other eukaryotes. Conclusion We have herein uncovered the genetic and evolutionary bases of essential amino acid biosynthesis in several trypanosomatids with and without endosymbionts, explaining and complementing decades of

  2. Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella

    PubMed Central

    Papenfort, Kai; Espinosa, Elena; Casadesús, Josep; Vogel, Jörg

    2015-01-01

    Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution but constitutes a complex process that requires synchronization with the physiological state of the host bacteria. Although several host transcription factors are known to regulate plasmid-borne transfer genes, RNA-based regulatory circuits for host–plasmid communication remain unknown. We describe a posttranscriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two separate seed-pairing domains to activate the mRNAs of both the sigma-factor σS and the RicI protein, a previously uncharacterized membrane protein here shown to inhibit conjugation. Transcription of ricI requires σS and, together, RprA and σS orchestrate a coherent feedforward loop with AND-gate logic to tightly control the activation of RicI synthesis. RicI interacts with the conjugation apparatus protein TraV and limits plasmid transfer under membrane-damaging conditions. To our knowledge, this study reports the first small RNA-controlled feedforward loop relying on posttranscriptional activation of two independent targets and an unexpected role of the conserved RprA small RNA in controlling extrachromosomal DNA transfer. PMID:26307765

  3. Demonstrating plasmid-based horizontal gene transfer in complex environmental matrices: a practical approach for a critical review.

    PubMed

    Bellanger, Xavier; Guilloteau, Hélène; Bonot, Sébastien; Merlin, Christophe

    2014-09-15

    Plasmid-based dissemination of antibiotic resistance genes in environmental microbial communities is a matter of concern for public health, but it remains difficult to study for methodological reasons. In this study, we used the broad host range plasmid pB10 to compare and to point out the main drawbacks of the three different approaches currently used to evaluate plasmid transfer in natural communities. Culture-based selection of transconjugants appeared to be compromised by high prevalence of antibiotic resistances among natural communities, unless high loads of initial pB10-donor inocula were used. Fluorescence-based detection of transconjugants reached a dead-end consequently to the narrow host range of bacteria expressing fluorescent proteins from a genetically modified pB10 plasmid, in addition to the relatively high background level of fluorescence exhibited by some environmental matrices. The molecular-based approach was the only one to provide a mean to detect rare plasmid transfer events following a low but realistic initial pB10-donor inoculation. Whatever the method, culture-based or molecular-based, the detection of successful transfer events in a given environmental matrix seemed to be linked to the initial stability of the donor inoculum. Depending on the matrix considered, eukaryotic predation plays a significant role in either limiting or promoting the plasmid transfer events.

  4. Influence of temperature on rate of uptake and subsequent horizontal transfer of [14C]fipronil by eastern subterranean termites (Isoptera: Rhinotermitidae).

    PubMed

    Spomer, Neil A; Kamble, Shripat T; Warriner, Richard A; Davis, Robert W

    2008-06-01

    The effect of temperature on [14C]fipronil uptake and transfer from donor (D) to recipient (R) Reticulitermes flavipes (Kollar) (Isoptera: Rhinotermitidae) workers was evaluated. Test chambers used in the fipronil uptake study were constructed from petri dishes containing autoclaved soil treated with 1 ppm [14C]fipronil (1.14 microCi of total radioactivity per petri dish), distilled water, and R. flavipes workers. Test chambers were held in environmental growth chambers preset at 12, 17, 22, 27, and 32 degrees C. For the fipronil transfer study, donor termites stained with Nile blue-A were exposed to soil treated with 1 ppm [14C]fipronil for 2 h. Donors were then combined with unexposed recipient termite workers at either 1D:5R, 1D:10R, or 1D:20R ratios. Test chambers consisted of a nest and feeding chamber connected by a piece of polyethylene tube and held in growth chambers at 12, 17, 22, 27, and 32 degrees C. Worker termites were sampled over time and the amount of [14C]fipronil present was measured by scintillation counting. Some degree of uptake and transfer occurred at all temperatures and ratios in this study. The highest level of uptake occurred by termites held at 22-32 degrees C, followed decreasingly by 17 and 12 degrees C. Maximum transfer of [14C]fipronil occurred at the higher ratios (1:5 > 1:10 > 1:20) of donors to recipients. Data presented in this study suggest that temperature is one of the key factors affecting the rate of uptake and subsequent horizontal transfer of [14C]fipronil in subterranean termites.

  5. Field study results on the probability and risk of a horizontal gene transfer from transgenic herbicide-resistant oilseed rape pollen to gut bacteria of bees.

    PubMed

    Mohr, Kathrin I; Tebbe, Christoph C

    2007-06-01

    Bees are specifically subjected to intimate contacts with transgenic plants due to their feeding activities on pollen. In this study, the probability and ecological risk of a gene transfer from pollen to gut bacteria of bees was investigated with larvae of Apis mellifera (honeybee), Bombus terrestris (bumblebee), and Osmia bicornis (red mason bee), all collected at a flowering transgenic oilseed rape field. The plants were genetically engineered with the pat-gene, conferring resistance against glufosinate (syn. phosphinothricin), a glutamine-synthetase inhibitor in plants and microorganisms. Ninety-six bacterial strains were isolated and characterized by 16S rRNA gene sequencing, revealing that Firmicutes represented 58% of the isolates, Actinobacteria 31%, and Proteobacteria 11%, respectively. Of all isolates, 40% were resistant to 1 mM glufosinate, and 11% even to 10 mM. Resistant phenotypes were found in all phylogenetic groups. None of the resistant phenotypes carried the recombinant pat-gene in its genome. The threshold of detecting gene transfer in this field study was relatively insensitive due to the high background of natural glufosinate resistance. However, the broad occurrence of glufosinate-resistant bacteria from different phylogenetic groups suggests that rare events of horizontal gene transfer will not add significantly to natural bacterial glufosinate resistance.

  6. Loss of two introns from the Magnolia tripetala mitochondrial cox2 gene implicates horizontal gene transfer and gene conversion as a novel mechanism of intron loss.

    PubMed

    Hepburn, Nancy J; Schmidt, Derek W; Mower, Jeffrey P

    2012-10-01

    Intron loss is often thought to occur through retroprocessing, which is the reverse transcription and genomic integration of a spliced transcript. In plant mitochondria, several unambiguous examples of retroprocessing are supported by the parallel loss of an intron and numerous adjacent RNA edit sites, but in most cases, the evidence for intron loss via retroprocessing is weak or lacking entirely. To evaluate mechanisms of intron loss, we designed a polymerase chain reaction (PCR)-based assay to detect recent intron losses from the mitochondrial cox2 gene within genus Magnolia, which was previously suggested to have variability in cox2 intron content. Our assay showed that all 22 examined species have a cox2 gene with two introns. However, one species, Magnolia tripetala, contains an additional cox2 gene that lacks both introns. Quantitative PCR showed that both M. tripetala cox2 genes are present in the mitochondrial genome. Although the intronless gene has lost several ancestral RNA edit sites, their distribution is inconsistent with retroprocessing models. Instead, phylogenetic and gene conversion analyses indicate that the intronless gene was horizontally acquired from a eudicot and then underwent gene conversion with the native intron-containing gene. The models are presented to summarize the roles of horizontal gene transfer and gene conversion as a novel mechanism of intron loss.

  7. CFD analysis of heat transfer and friction factor charaterstics in a circular tube fitted with horizontal baffles twisted tape inserts

    NASA Astrophysics Data System (ADS)

    Salman, Sami D.; Kadhum, Abdul Amir H.; Takriff, Mohd S.; Bakar Mohamad, Abu

    2013-12-01

    Swirl/vortex flow generator is an important form of passive augmentation techniques. Twisted-tape is one of the most important members of this form which is used extensively in different type heat exchangers. This paper reports the effect of twisted tape inserts on heat transfer and friction factor characteristics in circular tube under constant heat flux and laminar flow conditions using CFD simulation. Plain twisted tape inserts with twist ratios (y = 2.93, 3.91) and baffled twisted tape inserts with twist ratio (y = 2.93) have been used for the simulation using Fluent version 6.3.26. The results obtained by simulation matched with the literature correlations for plain tube with the discrepancy of less than ± 8% for Nusselt number and ± 6.25% for friction factor. The results have also revealed that the heat transfer in term of the Nusselt number enhanced with increases of Reynolds number, decreases of twist ratio and baffle insert. Among the various twist ratios, the twisted tape with twist ratio of y=2.93 and baffle is offered a maximum heat transfer enhancement.

  8. Nematode-derived drosomycin-type antifungal peptides provide evidence for plant-to-ecdysozoan horizontal transfer of a disease resistance gene.

    PubMed

    Zhu, Shunyi; Gao, Bin

    2014-01-01

    Drosomycin-type antifungal peptides (DTAFPs) are key innate immunity components of Drosophila and plants and confer resistance to fungal infection. Here we report the discovery of a multigene family of DTAFPs, comprising of 15 members (termed cremycin-1 to crymycin-15), in the fruit nematode Caenorhabditis remanei. Cremycins share highly similar amino-acid sequences and identical precursor organization to drosomycins. Of the 15 cremycin genes, 10 are found to be transcriptionally active and 6 are upregulated after fungal challenge. Synthetic cremycin-5 is active on filamentous fungi and a series of clinical isolates of human pathogenic yeasts and exhibits low haemolysis and high serum stability. The specific distribution of DTAFPs in a clade of moulting animals (Ecdysozoa), including Arthropoda, Nematoda and Tardigrada, together with the widespread presence in plants but the absence in fungi and protozoans, provides evidence for horizontal transfer of a disease resistance gene between plants and ecdysozoans.

  9. Occurrence of horizontal gene transfer of P(IB)-type ATPase genes among bacteria isolated from the uranium rich deposit of Domiasiat in North East India.

    PubMed

    Nongkhlaw, Macmillan; Kumar, Rakshak; Acharya, Celin; Joshi, Santa Ram

    2012-01-01

    Uranium (U) tolerant aerobic heterotrophs were isolated from the subsurface soils of one of the pre-mined U-rich deposits at Domiasiat located in the north-eastern part of India. On screening of genomic DNA from 62 isolates exhibiting superior U and heavy metal tolerance, 32 isolates were found to be positive for P(IB)-type ATPase genes. Phylogenetic incongruence and anomalous DNA base compositions revealed the acquisition of P(IB)-type ATPase genes by six isolates through horizontal gene transfer (HGT). Three of these instances of HGT appeared to have occurred at inter-phylum level and the other three instances indicated to have taken place at intra-phylum level. This study provides an insight into one of the possible survival strategies that bacteria might employ to adapt to environments rich in uranium and heavy metals.

  10. Occurrence of Horizontal Gene Transfer of PIB-type ATPase Genes among Bacteria Isolated from the Uranium Rich Deposit of Domiasiat in North East India

    PubMed Central

    Acharya, Celin; Joshi, Santa Ram

    2012-01-01

    Uranium (U) tolerant aerobic heterotrophs were isolated from the subsurface soils of one of the pre-mined U-rich deposits at Domiasiat located in the north-eastern part of India. On screening of genomic DNA from 62 isolates exhibiting superior U and heavy metal tolerance, 32 isolates were found to be positive for PIB-type ATPase genes. Phylogenetic incongruence and anomalous DNA base compositions revealed the acquisition of PIB-type ATPase genes by six isolates through horizontal gene transfer (HGT). Three of these instances of HGT appeared to have occurred at inter-phylum level and the other three instances indicated to have taken place at intra-phylum level. This study provides an insight into one of the possible survival strategies that bacteria might employ to adapt to environments rich in uranium and heavy metals. PMID:23133569

  11. The protease inhibitor chagasin of Trypanosoma cruzi adopts an immunoglobulin-type fold and may have arisen by horizontal gene transfer.

    PubMed

    Rigden, D J; Monteiro, A C; Grossi de Sá, M F

    2001-08-24

    Chagasin, a protein from Trypanosoma cruzi, is the first member of a new family of tight binding cysteine protease inhibitors [Monteiro, A.C.S., Abrahamson, M., Lima, A.P.C., Vannier-Santos, M.A. and Scharfstein, J. (2001) J. Cell Sci., in press] [corrected]. Despite its lack of significant sequence identity with known proteins, convincing structural models, using variable light chain templates, could be constructed on the basis of threading results. Experimental support for the final structure came from inhibition data for overlapping oligopeptides spanning the chagasin sequence. Chagasin therefore exemplifies a new protease inhibitor structural class and a new natural use for an immunoglobulin-like domain. Limited sequence resemblance suggests that chagasin may represent the result of a rare horizontal gene transfer from host to parasite.

  12. GTOs and HGT: genes are older than expected and can be installed by horizontal gene transfer, especially with help from viruses

    NASA Astrophysics Data System (ADS)

    Klyce, Brig

    2012-10-01

    The origin of life on Earth took a puzzlingly short time. Panspermia is appealing because it means that the origin of life need not be confined to a few million years on one planet. Similar puzzles arise in the evolution of higher life forms. Punctuated equilibrium, for example, seems to violate the darwinian account of gradual evolution by trial-and-error, a few DNA nucleotides at a time. The strong version of panspermia alleviates this puzzle as well. If all of life comes ultimately from space, genes may appear to be older than necessary, evolution by the acquisition of whole genes or suites of genes, by horizontal gene transfer (HGT), becomes much more important, and punctuated equilibrium is not surprising. Does evidence support this supposition? How common are old genes? How important is HGT versus the gradual composition of genetic programs? We will look at these questions.

  13. Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea.

    PubMed

    Caro-Quintero, Alejandro; Deng, Jie; Auchtung, Jennifer; Brettar, Ingrid; Höfle, Manfred G; Klappenbach, Joel; Konstantinidis, Konstantinos T

    2011-01-01

    High-throughput sequencing studies during the last decade have uncovered that bacterial genomes are very diverse and dynamic, resulting primarily from the frequent and promiscuous horizontal gene exchange that characterizes the bacterial domain of life. However, a robust understanding of the rates of genetic exchange for most bacterial species under natural conditions and the influence of the ecological settings on the rates remain elusive, severely limiting our view of the microbial world. Here, we analyzed the complete genomic sequences and expressed transcriptomes of several Shewanella baltica isolates recovered from different depths in the Baltic Sea and found that isolates from more similar depths had exchanged a larger fraction of their core and auxiliary genome, up to 20% of the total, compared with isolates from more different depths. The exchanged genes seem to be ecologically important and contribute to the successful adaptation of the isolates to the unique physicochemical conditions of the depth. Importantly, the latter genes were exchanged in very recent past, presumably as an effect of isolate's seasonal migration across the water column, and reflected sexual speciation within the same depth. Therefore, our findings reveal that genetic exchange in response to environmental settings may be surprisingly rapid, which has important broader impacts for understanding bacterial speciation and evolution and for modeling bacterial responses to human-induced environmental impacts.

  14. Pyriproxyfen for mosquito control: female sterilization or horizontal transfer to oviposition substrates by Anopheles gambiae sensu stricto and Culex quinquefasciatus

    PubMed Central

    2014-01-01

    Background The use of gravid mosquitoes as vehicles to auto-disseminate larvicides was recently demonstrated for the transfer of pyriproxyfen (PPF) by container-breeding Aedes mosquitoes and presents an appealing idea to explore for other disease vectors. The success of this approach depends on the female’s behaviour, the time of exposure and the amount of PPF that can be carried by an individual. We explore the effect of PPF exposure at seven time points around blood feeding on individual Anopheles gambiae sensu stricto and Culex quinquefasciatus fecundity and ability to transfer in laboratory assays. Method Mosquitoes were exposed to 2.6 mg PPF per m2 at 48, 24 and 0.5 hours before and after a blood meal and on the day of egg-laying. The proportion of exposed females (N = 80-100) laying eggs, the number of eggs laid and hatched was studied. Transfer of PPF to oviposition cups was assessed by introducing 10 late instar insectary-reared An. gambiae s.s. larvae into all the cups and monitored for adult emergence inhibition. Results Exposure to PPF between 24 hours before and after a blood meal had significant sterilizing effects: females of both species were 6 times less likely (Odds ratio (OR) 0.16, 95% confidence interval (CI) 0.10-0.26) to lay eggs than unexposed females. Of the few eggs laid, the odds of an egg hatching was reduced 17 times (OR 0.06, 95% CI 0.04-0.08) in Anopheles but only 1.2 times (OR 0.82, 95% CI 0.73-0.93) in Culex. Adult emergence inhibition from larvae introduced in the oviposition cups was observed only from cups in which eggs were laid. When females were exposed to PPF close to egg laying they transferred enough PPF to reduce emergence by 65-71% (95% CI 62-74%). Conclusion PPF exposure within a day before and after blood feeding affects egg-development in An. gambiae s.s. and Cx. quinquefasciatus and presents a promising opportunity for integrated control of vectors and nuisance mosquitoes. However, sterilized females are

  15. EARE-1, a Transcriptionally Active Ty1/Copia-Like Retrotransposon Has Colonized the Genome of Excoecaria agallocha through Horizontal Transfer

    PubMed Central

    Huang, Jianhua; Wang, Yushuai; Liu, Wenwen; Shen, Xu; Fan, Qiang; Jian, Shuguang; Tang, Tian

    2017-01-01

    Long terminal repeat (LTR) retrotransposons constitute the majority of the content of angiosperm genomes, but their evolutionary dynamics remain poorly understood. Here, we report the isolation and characterization of a putative full-length (~9550 bp) Ty1/copia-like retrotransposon in Excoecaria agallocha and its evolution in Euphorbiaceae. The so-called EARE-1 is phylogenetically closely related to RIRE-1 from Oryza australiensis, and has proliferated recently (~7.19 Mya) in the E. agallocha genome. An RT-PCR analysis revealed substantial transcription of EARE-1 in all examined organs (leaves, staminate flowers, pistillate flowers, seeds, and roots) in unstressed E. agallocha plants and indications of elevated expression under stress. We conducted sequence analyses of 256 RT-RH fragments (~860 bp) of EARE-1 from 34 species representing four subfamilies of Euphorbiaceae that exist in China. EARE-1 copies from two Excoecaria species and Phyllanthus urinaria showed incongruent phylogeny with the host species and exhibited high sequence similarity to the host genes, suggesting a horizontal transfer from P. urinaria to the common ancestor of Excoecaria. However, SSAP analysis detected no new insertions of EARE-1 among full-sibling progeny plants of E. agallocha, despite considerable SSAP polymorphisms among half-siblings. EARE-1 is the first transcriptionally active Ty1/copia-like retrotransposon isolated from E. agallocha. Our results provide empirical evidence of the horizontal transfer of LTR retrotransposons in plants, and may suggest a significant role of post-transcriptional host control in the life cycles of transposable elements. PMID:28174588

  16. A comparison of natural convection heat transfer for a staggered versus an aligned array of horizontal spent nuclear fuel rods within a rectangular enclosure

    SciTech Connect

    Triplett, C.E.; Canaan, R.E.; Klein, D.E.

    2000-04-01

    Natural convection heat transfer was experimentally investigated in a staggered array of heated cylinders, oriented horizontally within a rectangular isothermal enclosure. The test conditions were characteristic of a spent-fuel assembly during transport or horizontal dry storage. The assembly was configured with a pitch-to-diameter ratio of 1.33 and backfilled with pressurized helium or nitrogen. The backfill pressure was varied between 1 and 5 atm, while the assembly power was varied between 1 and 5 W per heater rod. The resulting data are presented in the form of Nusselt-Rayleigh number correlations, where the Nusselt number has been corrected for thermal radiation using a numerical technique. The staggered-array data are compared to previous data for a similar-pitch aligned rod array (a simulated boiling water reactor fuel assembly) to determine if convective heat transfer is enhanced or hindered in a staggered configuration. For the overall array, both the staggered and aligned configurations yield Nusselt-Rayleigh curves with a three-regime trend, which suggests distinct conduction and convection regimes separated by a transition regime. For lower Rayleigh numbers (10{sup 6}), representative of the conduction regime, the aligned-array Nusselt number is 10 to 12% higher than the corresponding staggered-array value. However, in the convection regime at higher Rayleigh numbers, the staggered-array Nusselt number slightly exceeds the aligned-array Nusselt number. This is attributed to the fact that the staggered array begins to transition into the convection regime at lower Rayleigh number than the aligned array. For both configurations, the slope of the Nusselt-Rayleigh curve in the convection regime suggests turbulent flow conditions.

  17. 77 FR 6193 - Electronic Fund Transfers (Regulation E)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-07

    ... instance through wire transfers or automated clearing house (ACH) transactions. Furthermore, consumers in... Dodd-Frank Amendments, Congress had specifically structured the EFTA to exclude wire transfers,\\13\\ and... of certain methods, particularly consumer wire transfers, is very limited, but the Bureau...

  18. Transstadial and horizontal transfer of bacteria within a colony of Anopheles gambiae (Diptera: Culicidae) and oviposition response to bacteria-containing water.

    PubMed

    Lindh, J M; Borg-Karlson, A-K; Faye, I

    2008-09-01

    In a paratransgenic approach, genetically modified bacteria are utilized to kill the parasite in the vector gut. A critical component for paratransgenics against malaria is how transgenic bacteria can be introduced and then kept in a mosquito population. Here, we investigated transstadial and horizontal transfer of bacteria within an Anopheles gambiae mosquito colony with the focus on spiked breeding sites as a possible means of introducing bacteria to mosquitoes. A Pantoea stewartii strain, previously isolated from An. gambiae, marked with a green fluorescent protein (GFP), was introduced to mosquitoes in different life stages. The following life stages or older mosquitoes in the case of adults were screened for bacteria in their guts. In addition to P. stewartii other bacteria were isolated from the guts: these were identified by 16S rRNA sequence analysis and temporal temperature gradient gel electrophoresis (TTGE). Bacteria were transferred from larvae to pupae but not from pupae to adults. The mosquitoes were able to take up bacteria from the water they emerged from and transfer the same bacteria to the water they laid eggs in. Elizabethkingia meningoseptica was more often isolated from adult mosquitoes than P. stewartii. A bioassay was used to examine An. gambiae oviposition responses towards bacteria-containing solutions. The volatiles emitted from the solutions were sampled by headspace-solid phase microextraction (SPME) and identified by gas chromatography and mass spectrometry (GC-MS) analysis. P. stewartii but not E. meningoseptica mediated a positive oviposition response. The volatiles emitted by P. stewartii include indole and 3-methyl-1-butanol, which previously have been shown to affect An. gambiae mosquito behaviour. E. meningoseptica emitted indole but not 3-methyl-1-butanol, when suspended in saline. Taken together, this indicates that it may be possible to create attractive breeding sites for distribution of genetically modified bacteria in the

  19. Effect of adiabatic wall on the natural convection heat transfer from a wavy surface created by attached horizontal cylinders

    SciTech Connect

    Harsini, I.; Ashjaee, M.

    2010-09-15

    The effect of a vertical adiabatic wall on the natural convection heat transfer from vertical array of attached cylinders, which can be considered as wavy surface, was investigated experimentally and numerically. The experiments were carried out using Mach-Zehnder interferometer and the commercial FLUENT code was used for numerical study. This paper focuses on the effect of wall-wavy surface spacing and Rayleigh number variation on the local and average free convection heat transfer coefficients from the each cylinder and the wavy surface. Rayleigh number ranges from 2400 to 10,000 and from 300,000 to 1,250,000 based on cylinder diameter and wavy surface height respectively. The local and average Nusselt numbers were determined for the different Rayleigh numbers, and the ratio of wall- wavy surface spacing to cylinder diameter 0.75, 1, 1.5, 2, 3, 4, 5, and {infinity}. Results are indicated with a single correlation which gives the average Nusselt number as a function of the ratio of the wall-wavy surface spacing to cylinder diameter and the Rayleigh numbers. There is an optimum distance between the wall and wavy surface in which the Nusselt number attain its maximum value. This optimum distance depends on the Rayleigh number. (author)

  20. Horizontal Transfer of a Novel Soil Agarase Gene from Marine Bacteria to Soil Bacteria via Human Microbiota

    PubMed Central

    Song, Tao; Xu, Hui; Wei, Congchong; Jiang, Tengfei; Qin, Shishang; Zhang, Weijia; Cao, Yu; Hu, Chao; Zhang, Fan; Qiao, Dairong; Cao, Yi

    2016-01-01

    Seaweed is receiving an increasing amount of attention as a “sea vegetable”. The microbiota of coastal populations may acquire seaweed associated enzymes through marine food. Several agarases have been found in non-marine environments; however, their origin is unknown. In this study, a hypothetical protein, Aga1, was identified as an agarase from an inland soil agar-degrading bacterium, Paenibacillus sp. SSG-1.Having low similarity to known glycoside hydrolases, Aga1 may be a distant member of the glycoside hydrolase family 86. Aga1 has good pH stability (pH 3–11) and is stable in the presence of various metal ions. Aga1 is an exo-type β-agarase that produces NA 4 (neoagarotetraose) and NA 6 (neoagarohexaose) as its main products. In addition, Aga1 may be a cell-surface-binding protein. The bioinformatic analysis showed aga1 may have been transfered together with its surrounding genes, from marine bacteria to soil bacteria via human microbiota. The use of seaweed as food and the disposal of human faeces or saliva were the most likely reasons for this gene transfer pathway. Notably, the results also indicated that microbes from inland humans may degrade agar and that these microbes may have acquired seaweed associated genes because of increased seaweed in diets. PMID:27756908

  1. The Histidine Decarboxylase Gene Cluster of Lactobacillus parabuchneri Was Gained by Horizontal Gene Transfer and Is Mobile within the Species

    PubMed Central

    Wüthrich, Daniel; Berthoud, Hélène; Wechsler, Daniel; Eugster, Elisabeth; Irmler, Stefan; Bruggmann, Rémy

    2017-01-01

    Histamine in food can cause intolerance reactions in consumers. Lactobacillus parabuchneri (L. parabuchneri) is one of the major causes of elevated histamine levels in cheese. Despite its significant economic impact and negative influence on human health, no genomic study has been published so far. We sequenced and analyzed 18 L. parabuchneri strains of which 12 were histamine positive and 6 were histamine negative. We determined the complete genome of the histamine positive strain FAM21731 with PacBio as well as Illumina and the genomes of the remaining 17 strains using the Illumina technology. We developed the synteny aware ortholog finding algorithm SynOrf to compare the genomes and we show that the histidine decarboxylase (HDC) gene cluster is located in a genomic island. It is very likely that the HDC gene cluster was transferred from other lactobacilli, as it is highly conserved within several lactobacilli species. Furthermore, we have evidence that the HDC gene cluster was transferred within the L. parabuchneri species. PMID:28261177

  2. Buoyancy and blockage effects on transient laminar opposing mixed convection heat transfer from two horizontal confined isothermal cylinder in tandem

    NASA Astrophysics Data System (ADS)

    Martínez-Suástegui, Lorenzo; Salcedo, Erick; Cajas, Juan; Treviño, César

    2015-11-01

    Transient mixed convection in a laminar cross-flow from two isothermal cylinders in tandem arrangement confined inside a vertical channel is studied numerically using the vorticity-stream function formulation of the unsteady two-dimensional Navier-Stokes and energy equations. Numerical experiments are performed for a Reynolds number based on cylinder diameter of Re = 200, Prandtl number of Pr = 7, blockage ratio of D/H = 0.2, a pitch-to-diameter ratio of L/D = 2, and several values of buoyancy strength or Richardson number Ri = Gr/Re2. The results reported herein demonstrate how the wall confinement, interference effects and opposing buoyancy affect the flow structure and heat transfer characteristics of the cylinder array. This research was supported by the Consejo Nacional de Ciencia y Tecnología (CONACYT), Grant number 167474 and by the Secretaría de Investigación y Posgrado del IPN, Grant number SIP 20141309.

  3. Mixed convection heat transfer to and from a horizontal cylinder in cross-flow with heating from below.

    SciTech Connect

    Greif, Ralph; Evans, Gregory Herbert; Kearney, Sean Patrick; Laskowski, Gregory Michael

    2006-02-01

    Heat transfer to and from a circular cylinder in a cross-flow of water at low Reynolds number was studied both experimentally and numerically. The experiments were carried out in a high aspect ratio water channel. The test section inflow temperature and velocity, channel lower surface temperature and cylinder surface temperature were controlled to yield either laminar or turbulent flow for a desired Richardson number. When the lower surface was unheated, the temperatures of the lower surface and water upstream of the cylinder were maintained approximately equal and the flow was laminar. When the lower surface was heated, turbulence intensities as high as 20% were measured several cylinder diameters upstream of the cylinder due to turbulent thermal plumes produced by heating the lower surface. Variable property, two-dimensional simulations were undertaken using a variant of the u{sup 2}-f turbulence model with buoyancy production of turbulence accounted for by a simple gradient diffusion model. Predicted and measured heat flux distributions around the cylinder are compared for values of the Richardson number, Gr{sub d}/Re{sub d}{sup 2} from 0.3 to 9.3. For laminar flow, the predicted and measured heat flux results agreed to within the experimental uncertainty. When the lower surface was heated, and the flow was turbulent, there was qualitative agreement between predicted and measured heat flux distributions around the cylinder. However the predicted spatially averaged Nusselt number was from 37% to 53% larger than the measured spatially averaged Nusselt number. Additionally, spatially averaged Nusselt numbers are compared to correlations in the literature for mixed convection heat transfer to/from cylinders in cross-flow. The results presented here are larger than the correlation values. This is believed to be due to the effects of buoyancy-induced turbulence resulting from heating the lower surface and the proximity of the cylinder to that surface.

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

    PubMed

    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.

  5. Study of hydrodynamics and heat transfer in non-Newtonian liquid-gas two-phase flow in horizontal pipes

    SciTech Connect

    Deshpande, S.D.

    1985-01-01

    Non-Newtonian liquid-gas stratified flow data in 0.026- and 0.052-m-diameter pipes were obtained. Interfacial level gradients between the two phases were observed. The Heywood-Charles model is found to be valid for pseudoplastic liquid-gas uniform stratified flow. Two-phase drag reduction in non-Newtonian systems was not achieved as the transition to semi-slug flow occurred before the model criteria were reached. Interfacial liquid and gas shear stresses were compared. A new parameter ..sigma../sup 2/ is introduced which is a numerical indication of the interfacial level gradient. Two-phase drag reduction was experimentally observed in polymer solution-air plug-slug flow in 0.026- and 0.052-m-diameter pipes. The Hubbard-Dukler pressure drop model was extended to non-Newtonian systems. Reasonable agreement between the experiment and the model predictions is obtained. However, more work needs to be done in order to better understand the two-phase drag reduction phenomena. Liquid holdup correlations were developed for both Newtonian and non-Newtonian systems which successfully correlate the holdup over a wide range of parameters. The Petukhov correlation is found to be better than the Dittus-Boelter correlation in predicting the single-phase water heat-transfer coefficients.

  6. A new subclass of intrinsic aminoglycoside nucleotidyltransferases, ANT(3")-II, is horizontally transferred among Acinetobacter spp. by homologous recombination

    PubMed Central

    Zhang, Gang; Leclercq, Sébastien Olivier; Tian, Jingjing; Wang, Chao; Ai, Guomin; Liu, Shuangjiang

    2017-01-01

    The emergence and spread of antibiotic resistance among Acinetobacter spp. have been investigated extensively. Most studies focused on the multiple antibiotic resistance genes located on plasmids or genomic resistance islands. On the other hand, the mechanisms controlling intrinsic resistance are still not well understood. In this study, we identified the novel subclass of aminoglycoside nucleotidyltransferase ANT(3")-II in Acinetobacter spp., which comprised numerous variants distributed among three main clades. All members of this subclass can inactivate streptomycin and spectinomycin. The three ant(3")-II genes, encoding for the three ANT(3")-II clades, are widely distributed in the genus Acinetobacter and always located in the same conserved genomic region. According to their prevalence, these genes are intrinsic in Acinetobacter baumannii, Acinetobacter pittii, and Acinetobacter gyllenbergii. We also demonstrated that the ant(3")-II genes are located in a homologous recombination hotspot and were recurrently transferred among Acinetobacter species. In conclusion, our findings demonstrated a novel mechanism of natural resistance in Acinetobacter spp., identified a novel subclass of aminoglycoside nucleotidyltransferase and provided new insight into the evolutionary history of intrinsic resistance genes. PMID:28152054

  7. pAO1 of Arthrobacter nicotinovorans and the spread of catabolic traits by horizontal gene transfer in gram-positive soil bacteria.

    PubMed

    Mihasan, Marius; Brandsch, Roderich

    2013-08-01

    The 165-kb megaplasmid pAO1 of Arthrobacter nicotinovorans carries two large gene clusters, one involved in nicotine catabolism (nic-gene cluster) and one in carbohydrate utilization (ch-gene cluster). Here, we propose that both gene clusters were acquired by A. nicotinovorans by horizontal gene transfer mediated by pAO1. Protein-protein blast search showed that none of the published Arthrobacter genomes contains nic-genes, but Rhodococcus opacus carries on its chromosome a nic-gene cluster highly similar to that of pAO1. Analysis of the nic-genes in the two species suggested a recombination event between their nic-gene clusters. Apparently, there was a gene exchange between pAO1, or a precursor plasmid, and a nic-gene cluster of an as yet unidentified Arthrobacter specie or other soil bacterium, possibly related to Rhodococcus, leading to the transfer by pAO1 of this catabolic trait to A. nicotinovorans. Analysis of the pAO1 ch-gene cluster revealed a virtually identical counterpart on the chromosome of Arthrobacter phenanthrenivorans. Moreover, the sequence analysis of the genes flanking the ch-gene cluster suggested that it was acquired by pAO1 by Xer-related site directed recombination and transferred via the plasmid to A. nicotinovorans. The G+C content, the level of sequence identity, gene co-linearity of nic- and ch-gene clusters as well as the signs of recombination events clearly supports the notion of pAO1 and its precursor plasmids as vehicles in HGT among Gram + soil bacteria.

  8. Interspecies Dissemination of a Mobilizable Plasmid Harboring blaIMP-19 and the Possibility of Horizontal Gene Transfer in a Single Patient

    PubMed Central

    Gomi, Ryota; Matsuda, Tomonari; Tanaka, Michio; Nagao, Miki; Takakura, Shunji; Uemoto, Shinji; Ichiyama, Satoshi

    2016-01-01

    Carbapenemase-producing Gram-negative bacilli have been a global concern over the past 2 decades because these organisms can cause severe infections with high mortality rates. Carbapenemase genes are often carried by mobile genetic elements, and resistance plasmids can be transferred through conjugation. We conducted whole-genome sequencing (WGS) to demonstrate that the same plasmid harboring a metallo-β-lactamase gene was detected in two different species isolated from a single patient. Metallo-β-lactamase-producing Achromobacter xylosoxidans (KUN4507), non-metallo-β-lactamase-producing Klebsiella pneumoniae (KUN4843), and metallo-β-lactamase-producing K. pneumoniae (KUN5033) were sequentially isolated from a single patient and then analyzed in this study. Antimicrobial susceptibility testing, molecular typing (pulsed-field gel electrophoresis and multilocus sequence typing), and conjugation analyses were performed by conventional methods. Phylogenetic and molecular clock analysis of K. pneumoniae isolates were performed with WGS, and the nucleotide sequences of plasmids detected from these isolates were determined using WGS. Conventional molecular typing revealed that KUN4843 and KUN5033 were identical, whereas the phylogenetic tree analysis revealed a slight difference. These two isolates were separated from the most recent common ancestor 0.74 years before they were isolated. The same resistance plasmid harboring blaIMP-19 was detected in metallo-β-lactamase-producing A. xylosoxidans and K. pneumoniae. Although this plasmid was not self-transferable, the conjugation of this plasmid from A. xylosoxidans to non-metallo-β-lactamase-producing K. pneumoniae was successfully performed. The susceptibility patterns for metallo-β-lactamase-producing K. pneumoniae and the transconjugant were similar. These findings supported the possibility of the horizontal transfer of plasmid-borne blaIMP-19 from A. xylosoxidans to K. pneumoniae in a single patient. PMID

  9. 77 FR 50243 - Electronic Fund Transfers (Regulation E)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-20

    ... course of business'' in the definition of ``remittance transfer provider,'' which determines whether a... in the United States to individuals and businesses in foreign countries. For covered transactions... providing remittance transfers in the ``normal course of business,'' and thus is a ``remittance...

  10. 77 FR 6310 - Electronic Fund Transfers (Regulation E)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-07

    ... discontinue providing a small number of transfers per year to accommodate customers of its regular business... phrase ``normal course of business'' in the definition of ``remittance transfer provider.'' This... 1700 G Street, NW., Washington, DC 20006, on official business days between the hours of 10 a.m. and...

  11. Vertical evolution and horizontal transfer of CR1 non-LTR retrotransposons and Tc1/mariner DNA transposons in Lepidoptera species.

    PubMed

    Sormacheva, Irina; Smyshlyaev, Georgiy; Mayorov, Vladimir; Blinov, Alexander; Novikov, Anton; Novikova, Olga

    2012-12-01

    Horizontal transfer (HT) is a complex phenomenon usually used as an explanation of phylogenetic inconsistence, which cannot be interpreted in terms of vertical evolution. Most examples of HT of eukaryotic genes involve transposable elements. An intriguing feature of HT is that its frequency differs among transposable elements classes. Although HT is well known for DNA transposons and long terminal repeat (LTR) retrotransposons, non-LTR retrotransposons rarely undergo HT, and their phylogenies are largely congruent to those of their hosts. Previously, we described HT of CR1-like non-LTR retrotransposons between butterflies (Maculinea) and moths (Bombyx), which occurred less than 5 million years ago (Novikova O, Sliwinska E, Fet V, Settele J, Blinov A, Woyciechowski M. 2007. CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae): evidence for recent horizontal transmission. BMC Evol Biol. 7:93). In this study, we continued to explore the diversity of CR1 non-LTR retrotransposons among lepidopterans providing additional evidences to support HT hypothesis. We also hypothesized that DNA transposons could be involved in HT of non-LTR retrotransposons. Thus, we performed analysis of one of the groups of DNA transposons, mariner-like DNA elements, as potential vectors for HT of non-LTR retrotransposons. Our results demonstrate multiple HTs between Maculinea and Bombyx genera. Although we did not find strong evidence for our hypothesis of the involvement of DNA transposons in HT of non-LTR retrotransposons, we demonstrated that recurrent and/or simultaneous flow of TEs took place between distantly related moths and butterflies.

  12. Presence and potential for horizontal transfer of antibiotic resistance in oxidase-positive bacteria populating raw salad vegetables.

    PubMed

    Bezanson, G S; MacInnis, R; Potter, G; Hughes, T

    2008-09-30

    To assess whether domestically grown fresh salad vegetables constitute a possible reservoir of antibiotic resistance for Canadian consumers, aerobic bacteria capable of forming colonies at 30 degrees C on nutrient-limited media were recovered from a single sampling of Romaine lettuce, Savoy spinach and alfalfa sprouts, then examined for their susceptibility to ten antibiotics and the carriage of potentially mobile R-plasmids and integrons. Of the 140 isolates resistant to one or more antibiotic, 93.5 and 90.0% were resistant to ampicillin and cephalothin; 35.7% to chloramphenicol, 10.0% to streptomycin, 4.2% to nalidixic acid, 4.2% to kanamycin, and 2.8% to gentamicin. Gram-positive isolates accounted for less than 4% of the antibiotic resistant strains. A small portion (23.1%) of the predominant oxidase-positive, gram-negative isolates was resistant to two or more antimicrobials. Members of the Pseudomonas fluorescens/putida complex were most prevalent among the 34 resistant strains identified. Sphingobacterium spp. and Acinetobacter baumanni also were detected. Ten of 52 resistant strains carried plasmids, 3 of which were self-transmissible and bore resistance to ampicillin and kanamycin. Eighteen of 48 gave PCR evidence for integron DNA. Class 2 type integrons were the most prevalent, followed by class 1. We conclude that the foods examined here carry antibiotic resistant bacteria at the retail level. Further, our determination that resistant strains contain integron-specific DNA sequences and self-transmissible R-plasmids indicates their potential to influence the pool of antibiotic resistance in humans via lateral gene transfer subsequent to ingestion.

  13. Reevaluation of the cox1 group I intron in Araceae and angiosperms indicates a history dominated by loss rather than horizontal transfer.

    PubMed

    Cusimano, Natalie; Zhang, Li-Bing; Renner, Susanne S

    2008-02-01

    The origin and modes of transmission of introns remain matters of much debate. Previous studies of the group I intron in the angiosperm cox1 gene inferred frequent angiosperm-to-angiosperm horizontal transmission of the intron from apparent incongruence between intron phylogenies and angiosperm phylogenies, patchy distribution of the intron among angiosperms, and differences between cox1 exonic coconversion tracts (the first 22 nt downstream of where the intron inserted). We analyzed the cox1 gene in 179 angiosperms, 110 of them containing the intron (intron(+)) and 69 lacking it (intron(-)). Our taxon sampling in Araceae is especially dense to test hypotheses about vertical and horizontal intron transmission put forward by Cho and Palmer (1999. Multiple acquisitions via horizontal transfer of a group I intron in the mitochondrial coxl gene during evolution of the Araceae family. Mol Biol Evol. 16:1155-1165). Maximum likelihood trees of Araceae cox1 introns, and also of all angiosperm cox1 introns, are largely congruent with known phylogenetic relationships in these taxa. The exceptions can be explained by low signal in the intron and long-branch attraction among a few taxa with high mitochondrial substitution rates. Analysis of the 179 coconversion tracts reveals 20 types of tracts (11 of them only found in single species, all involving silent substitutions). The distribution of these tracts on the angiosperm phylogeny shows a common ancestral type, characterizing most intron(+) and some intron(-) angiosperms, and several derivative tract types arising from gradual back mutation of the coconverted nucleotides. Molecular clock dating of small intron(+) and intron(-) sister clades suggests that coconversion tracts have persisted for 70 Myr in Araceae, whose cox1 sequences evolve comparatively slowly. Sequence similarity among the 110 introns ranges from 91% to identical, whereas putative homologs from fungi are highly different, but sampling in fungi is still sparse

  14. Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer

    PubMed Central

    2017-01-01

    ABSTRACT Bacteria use a variety of DNA-mobilizing enzymes to facilitate environmental niche adaptation via horizontal gene transfer. This has led to real-world problems, like the spread of antibiotic resistance, yet many mobilization proteins remain undefined. In the study described here, we investigated the uncharacterized family of YhgA-like transposase_31 (Pfam PF04754) proteins. Our primary focus was the genetic and biochemical properties of the five Escherichia coli K-12 members of this family, which we designate RpnA to RpnE, where Rpn represents recombination-promoting nuclease. We employed a conjugal system developed by our lab that demanded RecA-independent recombination following transfer of chromosomal DNA. Overexpression of RpnA (YhgA), RpnB (YfcI), RpnC (YadD), and RpnD (YjiP) increased RecA-independent recombination, reduced cell viability, and induced the expression of reporter of DNA damage. For the exemplar of the family, RpnA, mutational changes in proposed catalytic residues reduced or abolished all three phenotypes in concert. In vitro, RpnA displayed magnesium-dependent, calcium-stimulated DNA endonuclease activity with little, if any, sequence specificity and a preference for double-strand cleavage. We propose that Rpn/YhgA-like family nucleases can participate in gene acquisition processes. IMPORTANCE Bacteria adapt to new environments by obtaining new genes from other bacteria. Here, we characterize a set of genes that can promote the acquisition process by a novel mechanism. Genome comparisons had suggested the horizontal spread of the genes for the YhgA-like family of proteins through bacteria. Although annotated as transposase_31, no member of the family has previously been characterized experimentally. We show that four Escherichia coli K-12 paralogs contribute to a novel RecA-independent recombination mechanism in vivo. For RpnA, we demonstrate in vitro action as a magnesium-dependent, calcium-stimulated nonspecific DNA endonuclease

  15. 78 FR 76768 - Removal of Transferred OTS Regulations Regarding Disclosure and Reporting of CRA-Related...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-19

    ...In this notice of proposed rulemaking, the Federal Deposit Insurance Corporation (``FDIC'') proposes to rescind and remove a regulation entitled ``Disclosure and Reporting of CRA-Related Agreements.'' This regulation was included in the regulations that were transferred to the FDIC from the Office of Thrift Supervision (``OTS'') on July 21, 2011, in connection with the implementation of......

  16. Genomic Sequence and Transcriptional Analysis of a 23-Kilobase Mycobacterial Linear Plasmid: Evidence for Horizontal Transfer and Identification of Plasmid Maintenance Systems

    PubMed Central

    Le Dantec, Corinne; Winter, Nathalie; Gicquel, Brigitte; Vincent, Véronique; Picardeau, Mathieu

    2001-01-01

    Linear plasmids were unknown in mycobacteria until recently. Here, we report the complete nucleotide sequence of 23-kb linear plasmid pCLP from Mycobacterium celatum, an opportunistic pathogen. The sequence of pCLP revealed at least 19 putative open reading frames (ORFs). Expression of pCLP genes in exponential-phase cultures was determined by reverse transcriptase PCR (RT-PCR). Twelve ORFs were expressed, whereas no transcription of the 7 other ORFs of pCLP was detected. Five of the 12 transcribed ORFs detected by RT-PCR are of unknown function. Sequence analysis revealed similar loci in both M. celatum pCLP and the Mycobacterium tuberculosis chromosome, including transposase-related sequences. This result suggests horizontal transfer between these two organisms. pCLP also contains ORFs that are similar to genes of bacterial circular plasmids involved in partition (par operon) and postsegregational (pem operon) mechanisms. Functional analysis of these ORFs suggests that they probably carry out similar maintenance roles in pCLP. PMID:11244052

  17. Horizontal transfer of the OXA-24 carbapenemase gene via outer membrane vesicles: a new mechanism of dissemination of carbapenem resistance genes in Acinetobacter baumannii.

    PubMed

    Rumbo, Carlos; Fernández-Moreira, Esteban; Merino, María; Poza, Margarita; Mendez, Jose Antonio; Soares, Nelson C; Mosquera, Alejandro; Chaves, Fernando; Bou, Germán

    2011-07-01

    The resistance of Acinetobacter baumannii strains to carbapenems is a worrying problem in hospital settings. The main mechanism of carbapenem resistance is the expression of β-lactamases (metalloenzymes or class D enzymes). The mechanisms of the dissemination of these genes among A. baumannii strains are not fully understood. In this study we used two carbapenem-resistant clinical strains of A. baumannii (AbH12O-A2 and AbH12O-CU3) expressing the plasmid-borne bla(OXA-24) gene (plasmids pMMA2 and pMMCU3, respectively) to demonstrate that A. baumannii releases outer membrane vesicles (OMVs) during in vitro growth. The use of hybridization studies enabled us to show that these OMVs harbored the bla(OXA-24) gene. The incubation of these OMVs with the carbapenem-susceptible A. baumannii ATCC 17978 host strain yielded full resistance to carbapenems. The presence of the original plasmids harboring the bla(OXA-24) gene was detected in strain ATCC 17978 after the transformation of OMVs. New OMVs harboring bla(OXA-24) were released by A. baumannii ATCC 17978 after it was transformed with the original OMV-mediated plasmids, indicating the universality of the process. We present the first experimental evidence that clinical isolates of A. baumannii may release OMVs as a mechanism of horizontal gene transfer whereby carbapenem resistance genes are delivered to surrounding A. baumannii bacterial isolates.

  18. Horizontal Gene Transfer of a ColV Plasmid Has Resulted in a Dominant Avian Clonal Type of Salmonella enterica Serovar Kentucky

    PubMed Central

    Johnson, Timothy J.; Thorsness, Jessica L.; Anderson, Cole P.; Lynne, Aaron M.; Foley, Steven L.; Han, Jing; Fricke, W. Florian; McDermott, Patrick F.; White, David G.; Khatri, Mahesh; Stell, Adam L.; Flores, Cristian; Singer, Randall S.

    2010-01-01

    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. PMID:21203520

  19. Cloning of the organophosphorus pesticide hydrolase gene clusters of seven degradative bacteria isolated from a methyl parathion contaminated site and evidence of their horizontal gene transfer.

    PubMed

    Zhang, Ruifu; Cui, Zhongli; Zhang, Xiaozhou; Jiang, Jiandong; Gu, Ji-Dong; Li, Shunpeng

    2006-10-01

    Seven organophosphorus pesticide-degrading bacteria harboring the methyl parathion degrading (mpd) gene were isolated from a methyl parathion contaminated site. In this study, the 4.7 kb mpd gene cluster, conserved in all seven bacteria capable of degrading methyl parathion, was cloned and further analysis revealed that this cluster contained five ORFs and the mpd gene was associated with a mobile element, IS6100. In addition to mpd gene ORF and tnpA ORF, three other ORFs showed high homology to the permease component of ABC-type transport system, the general secretion pathway protein B, and the RNA polymerase sigma 70 factor, respectively. The mpd genes of these 7 strains were subcloned and expressed in E. coli, SDS-PAGE and zymogram analysis showed that two expression products of mpd genes in E. coli were found, but the one without signal peptide showed the hydrolytic activities. Our evidences collectively suggest that mpd gene cluster may be disseminated through horizontal gene transfer based on phylogenetic analysis of the cluster and their host bacterial strains, and comparisons of GC content of the cluster and respective host's chromosome.

  20. Edible Safety Assessment of Genetically Modified Rice T1C-1 for Sprague Dawley Rats through Horizontal Gene Transfer, Allergenicity and Intestinal Microbiota

    PubMed Central

    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. PMID:27706188

  1. Acquisition of the capsule locus by horizontal gene transfer in Neisseria meningitidis is often accompanied by the loss of UDP-GalNAc synthesis

    PubMed Central

    Bartley, Stephanie N.; Mowlaboccus, Shakeel; Mullally, Christopher A.; Stubbs, Keith A.; Vrielink, Alice; Maiden, Martin C. J.; Harrison, Odile B.; Perkins, Timothy T.; Kahler, Charlene M.

    2017-01-01

    Pathogenic meningococci have acquired a 24 kb capsule synthesis island (cps) by horizontal gene transfer which consists of a synthetic locus and associated capsule transport genes flanked by repetitive Regions D and D’. Regions D and D’ contain an intact gene encoding a UDP-galactose epimerase (galE1) and a truncated remnant (galE2), respectively. In this study, GalE protein alleles were shown to be either mono-functional, synthesising UDP-galactose (UDP-Gal), or bi-functional, synthesising UDP-Gal and UDP-galactosamine (UDP-GalNAc). Meningococci possessing a capsule null locus (cnl) typically possessed a single bi-functional galE. Separation of functionality between galE1 and galE2 alleles in meningococcal isolates was retained for all serogroups except serogroup E which has a synthetic requirement for UDP-GalNAc. The truncated galE2 remnant in Region D’ was also phylogenetically related to the bi-functional galE of the cnl locus suggesting common ancestry. A model is proposed in which the illegitimate recombination of the cps island into the galE allele of the cnl locus results in the formation of Region D’ containing the truncated galE2 locus and the capture of the cps island en bloc. The retention of the duplicated Regions D and D’ enables inversion of the synthetic locus within the cps island during bacterial growth. PMID:28290510

  2. Evidence for the Role of Horizontal Transfer in Generating pVT1, a Large Mosaic Conjugative Plasmid from the Clam Pathogen, Vibrio tapetis

    PubMed Central

    Bidault-Toffin, Adeline; Le Chevalier, Patrick; Bouloc, Philippe; Paillard, Christine; Jacq, Annick

    2011-01-01

    The marine bacterium Vibrio tapetis is the causative agent of the brown ring disease, which affects the clam Ruditapes philippinarum and causes heavy economic losses in North of Europe and in Eastern Asia. Further characterization of V. tapetis isolates showed that all the investigated strains harbored at least one large plasmid. We determined the sequence of the 82,266 bp plasmid pVT1 from the CECT4600T reference strain and analyzed its genetic content. pVT1 is a mosaic plasmid closely related to several conjugative plasmids isolated from Vibrio vulnificus strains and was shown to be itself conjugative in Vibrios. In addition, it contains DNA regions that have similarity with several other plasmids from marine bacteria (Vibrio sp., Shewanella sp., Listonella anguillarum and Photobacterium profundum). pVT1 contains a number of mobile elements, including twelve Insertion Sequences or inactivated IS genes and an RS1 phage element related to the CTXphi phage of V. cholerae. The genetic organization of pVT1 underscores an important role of horizontal gene transfer through conjugative plasmid shuffling and transposition events in the acquisition of new genetic resources and in generating the pVT1 modular organization. In addition, pVT1 presents a copy number of 9, relatively high for a conjugative plasmid, and appears to belong to a new type of replicon, which may be specific to Vibrionaceae and Shewanelleacae. PMID:21326607

  3. BuT2 Is a Member of the Third Major Group of hAT Transposons and Is Involved in Horizontal Transfer Events in the Genus Drosophila

    PubMed Central

    Rossato, Dirleane Ottonelli; Ludwig, Adriana; Deprá, Maríndia; Loreto, Elgion L. S.; Ruiz, Alfredo; Valente, Vera L. S.

    2014-01-01

    The hAT superfamily comprises a large and diverse array of DNA transposons found in all supergroups of eukaryotes. Here we characterized the Drosophila buzzatii BuT2 element and found that it harbors a five-exon gene encoding a 643-aa putatively functional transposase. A phylogeny built with 85 hAT transposases yielded, in addition to the two major groups already described, Ac and Buster, a third one comprising 20 sequences that includes BuT2, Tip100, hAT-4_BM, and RP-hAT1. This third group is here named Tip. In addition, we studied the phylogenetic distribution and evolution of BuT2 by in silico searches and molecular approaches. Our data revealed BuT2 was, most often, vertically transmitted during the evolution of genus Drosophila being lost independently in several species. Nevertheless, we propose the occurrence of three horizontal transfer events to explain its distribution and conservation among species. Another aspect of BuT2 evolution and life cycle is the presence of short related sequences, which contain similar 5′ and 3′ regions, including the terminal inverted repeats. These sequences that can be considered as miniature inverted repeat transposable elements probably originated by internal deletion of complete copies and show evidences of recent mobilization. PMID:24459285

  4. Deep sequencing revealed molecular signature of horizontal gene transfer of plant like transcripts in the mosquito Anopheles culicifacies: an evolutionary puzzle

    PubMed Central

    Sharma, Punita; Das De, Tanwee; Sharma, Swati; Kumar Mishra, Ashwani; Thomas, Tina; Verma, Sonia; Kumari, Vandana; Lata, Suman; Singh, Namita; Valecha, Neena; Chand Pandey, Kailash; Dixit, Rajnikant

    2015-01-01

    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. PMID:26998230

  5. BuT2 is a member of the third major group of hAT transposons and is involved in horizontal transfer events in the genus Drosophila.

    PubMed

    Rossato, Dirleane Ottonelli; Ludwig, Adriana; Deprá, Maríndia; Loreto, Elgion L S; Ruiz, Alfredo; Valente, Vera L S

    2014-02-01

    The hAT superfamily comprises a large and diverse array of DNA transposons found in all supergroups of eukaryotes. Here we characterized the Drosophila buzzatii BuT2 element and found that it harbors a five-exon gene encoding a 643-aa putatively functional transposase. A phylogeny built with 85 hAT transposases yielded, in addition to the two major groups already described, Ac and Buster, a third one comprising 20 sequences that includes BuT2, Tip100, hAT-4_BM, and RP-hAT1. This third group is here named Tip. In addition, we studied the phylogenetic distribution and evolution of BuT2 by in silico searches and molecular approaches. Our data revealed BuT2 was, most often, vertically transmitted during the evolution of genus Drosophila being lost independently in several species. Nevertheless, we propose the occurrence of three horizontal transfer events to explain its distribution and conservation among species. Another aspect of BuT2 evolution and life cycle is the presence of short related sequences, which contain similar 5' and 3' regions, including the terminal inverted repeats. These sequences that can be considered as miniature inverted repeat transposable elements probably originated by internal deletion of complete copies and show evidences of recent mobilization.

  6. Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly.

    PubMed

    Llorens-Marès, Tomàs; Liu, Zhenfeng; Allen, Lisa Zeigler; Rusch, Douglas B; Craig, Matthew T; Dupont, Chris L; Bryant, Donald A; Casamayor, Emilio O

    2017-01-01

    A natural planktonic bloom of a brown-pigmented photosynthetic green sulfur bacteria (GSB) from the disphotic zone of karstic Lake Banyoles (NE Spain) was studied as a natural enrichment culture from which a nearly complete genome was obtained after metagenomic assembly. We showed in situ a case where horizontal gene transfer (HGT) explained the ecological success of a natural population unveiling ecosystem-specific adaptations. The uncultured brown-pigmented GSB was 99.7% identical in the 16S rRNA gene sequence to its green-pigmented cultured counterpart Chlorobium luteolum DSM 273(T). Several differences were detected for ferrous iron acquisition potential, ATP synthesis and gas vesicle formation, although the most striking trait was related to pigment biosynthesis strategy. Chl. luteolum DSM 273(T) synthesizes bacteriochlorophyll (BChl) c, whereas Chl. luteolum CIII incorporated by HGT a 18-kbp cluster with the genes needed for BChl e and specific carotenoids biosynthesis that provided ecophysiological advantages to successfully colonize the dimly lit waters. We also genomically characterized what we believe to be the first described GSB phage, which based on the metagenomic coverage was likely in an active state of lytic infection. Overall, we observed spread HGT and we unveiled clear evidence for virus-mediated HGT in a natural population of photosynthetic GSB.

  7. The role of horizontal gene transfer in the dissemination of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae isolates in an endemic setting

    PubMed Central

    Doi, Yohei; Adams-Haduch, Jennifer M.; Peleg, Anton Y.; D’Agata, Erika MC

    2012-01-01

    The contribution of horizontal gene transmission (HGT) in the emergence and spread of extended-spectrum beta-lactamase (ESBL)-producing gram-negative bacteria during periods of endemicity is unclear. Over a 12-month period, rectal colonization with SHV-5 and SHV-12 producing-Escherichia coli and Klebsiella pneumoniae was quantified among a cohort of residents in a long-term care facility. Demographic and clinical data were collected on colonized residents. Transferability of SHV-encoding plasmids and pulsed-field gel electrophoresis was performed to quantify the contribution of HGT and cross-transmission, respectively. A total of 25 (12%) of 214 enrolled patients were colonized with 11 SHV-5- and 17 SVH-12-producing E. coli and K. pneumoniae. Clonally-related isolates were detected among multiple residents residing on the same and different wards. Among 12 clonally-distinct isolates, HGT of SHV-5- and SHV-12-encoding plasmids was identified among 6 (50%) isolates. HGT among clonally-distinct strains contributes to the transmission dynamics of these ESBL-producing gram-negative bacteria and should be considered when evaluating the spread of these pathogens. PMID:22722012

  8. Horizontal Transfer of the OXA-24 Carbapenemase Gene via Outer Membrane Vesicles: a New Mechanism of Dissemination of Carbapenem Resistance Genes in Acinetobacter baumannii ▿

    PubMed Central

    Rumbo, Carlos; Fernández-Moreira, Esteban; Merino, María; Poza, Margarita; Mendez, Jose Antonio; Soares, Nelson C.; Mosquera, Alejandro; Chaves, Fernando; Bou, Germán

    2011-01-01

    The resistance of Acinetobacter baumannii strains to carbapenems is a worrying problem in hospital settings. The main mechanism of carbapenem resistance is the expression of β-lactamases (metalloenzymes or class D enzymes). The mechanisms of the dissemination of these genes among A. baumannii strains are not fully understood. In this study we used two carbapenem-resistant clinical strains of A. baumannii (AbH12O-A2 and AbH12O-CU3) expressing the plasmid-borne blaOXA-24 gene (plasmids pMMA2 and pMMCU3, respectively) to demonstrate that A. baumannii releases outer membrane vesicles (OMVs) during in vitro growth. The use of hybridization studies enabled us to show that these OMVs harbored the blaOXA-24 gene. The incubation of these OMVs with the carbapenem-susceptible A. baumannii ATCC 17978 host strain yielded full resistance to carbapenems. The presence of the original plasmids harboring the blaOXA-24 gene was detected in strain ATCC 17978 after the transformation of OMVs. New OMVs harboring blaOXA-24 were released by A. baumannii ATCC 17978 after it was transformed with the original OMV-mediated plasmids, indicating the universality of the process. We present the first experimental evidence that clinical isolates of A. baumannii may release OMVs as a mechanism of horizontal gene transfer whereby carbapenem resistance genes are delivered to surrounding A. baumannii bacterial isolates. PMID:21518847

  9. Horizontally Transferred Genetic Elements in the Tsetse Fly Genome: An Alignment-Free Clustering Approach Using Batch Learning Self-Organising Map (BLSOM)

    PubMed Central

    Nakao, Ryo; Funayama, Shunsuke

    2016-01-01

    Tsetse flies (Glossina spp.) are the primary vectors of trypanosomes, which can cause human and animal African trypanosomiasis in Sub-Saharan African countries. The objective of this study was to explore the genome of Glossina morsitans morsitans for evidence of horizontal gene transfer (HGT) from microorganisms. We employed an alignment-free clustering method, that is, batch learning self-organising map (BLSOM), in which sequence fragments are clustered based on the similarity of oligonucleotide frequencies independently of sequence homology. After an initial scan of HGT events using BLSOM, we identified 3.8% of the tsetse fly genome as HGT candidates. The predicted donors of these HGT candidates included known symbionts, such as Wolbachia, as well as bacteria that have not previously been associated with the tsetse fly. We detected HGT candidates from diverse bacteria such as Bacillus and Flavobacteria, suggesting a past association between these taxa. Functional annotation revealed that the HGT candidates encoded loci in various functional pathways, such as metabolic and antibiotic biosynthesis pathways. These findings provide a basis for understanding the coevolutionary history of the tsetse fly and its microbes and establish the effectiveness of BLSOM for the detection of HGT events. PMID:28074180

  10. The Secreted Proteins of Achlya hypogyna and Thraustotheca clavata Identify the Ancestral Oomycete Secretome and Reveal Gene Acquisitions by Horizontal Gene Transfer

    PubMed Central

    Misner, Ian; Blouin, Nic; Leonard, Guy; Richards, Thomas A.; Lane, Christopher E.

    2015-01-01

    Saprotrophic and parasitic microorganisms secrete proteins into the environment to breakdown macromolecules and obtain nutrients. The molecules secreted are collectively termed the “secretome” and the composition and function of this set of proteins varies depending on the ecology, life cycle, and environment of an organism. Beyond the function of nutrient acquisition, parasitic lineages must also secrete molecules to manipulate their host. Here, we use a combination of de novo genome and transcriptome sequencing and bioinformatic identification of signal peptides to identify the putative secreted proteome of two oomycetes, the facultative parasite Achlya hypogyna and free-living Thraustotheca clavata. By comparing the secretomes of these saprolegnialean oomycetes with that of eight other oomycetes, we were able to characterize the evolution of this protein set across the oomycete clade. These species span the last common ancestor of the two major oomycete families allowing us to identify the ancestral secretome. This putative ancestral secretome consists of at least 84 gene families. Only 11 of these gene families are conserved across all 10 secretomes analyzed and the two major branches in the oomycete radiation. Notably, we have identified expressed elicitin-like effector genes in the saprotrophic decomposer, T. clavata. Phylogenetic analyses show six novel horizontal gene transfers to the oomycete secretome from bacterial and fungal donor lineages, four of which are specific to the Saprolegnialeans. Comparisons between free-living and pathogenic taxa highlight the functional changes of oomycete secretomes associated with shifts in lifestyle. PMID:25527045

  11. 78 FR 30661 - Electronic Fund Transfers (Regulation E)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-22

    ... involved in open network transfers may learn about each other's practices regarding fees or other matters..., even a large correspondent bank, attempting to learn and accurately disclose these fees. Relatedly... introductory language in Sec. 1005.30 states that ``for purposes of this subpart, the following...

  12. Geometric phase and quantum interference in photosynthetic reaction center: Regulation of electron transfer

    NASA Astrophysics Data System (ADS)

    Sun, Yuming; Su, Yuehua; Dai, Zhenhong; Wang, WeiTian

    2016-10-01

    Photosynthesis is driven by electron transfer in reaction centers in which the functional unit is composed of several simple molecules C2-symmetrically arranged into two branches. In view of quantum mechanism, both branches are possible pathways traversed by the transferred electron. Due to different evolution of spin state along two pathways in transmembrane electric potential (TEP), quantum state of the transferred electron at the bridged site acquires a geometric phase difference dependent on TEP, the most efficient electron transport takes place in a specific range of TEP beyond which electron transfer is dramatically suppressed. What's more, reaction center acts like elaborately designed quantum device preparing polarized spin dependent on TEP for the transferred electron to regulate the reduction potential at bridged site. In brief, electron transfer generates the TEP, reversely, TEP modulates the efficiency of electron transfer. This may be an important approach to maintaining an appreciable pH environment in photosynthesis.

  13. Characterization of a Novel Megabirnavirus from Sclerotinia sclerotiorum Reveals Horizontal Gene Transfer from Single-Stranded RNA Virus to Double-Stranded RNA Virus

    PubMed Central

    Wang, Minghong; Wang, Yong; Sun, Xiangzhong; Cheng, Jiasen; Fu, Yanping; Liu, Huiquan; Jiang, Daohong; Ghabrial, Said A.

    2015-01-01

    ABSTRACT Mycoviruses have been detected in all major groups of filamentous fungi, and their study represents an important branch of virology. Here, we characterized a novel double-stranded RNA (dsRNA) mycovirus, Sclerotinia sclerotiorum megabirnavirus 1 (SsMBV1), in an apparently hypovirulent strain (SX466) of Sclerotinia sclerotiorum. Two similarly sized dsRNA segments (L1- and L2-dsRNA), the genome of SsMBV1, are packaged in rigid spherical particles purified from strain SX466. The full-length cDNA sequence of L1-dsRNA/SsMBV1 comprises two large open reading frames (ORF1 and ORF2), which encode a putative coat protein and an RNA-dependent RNA polymerase (RdRp), respectively. Phylogenetic analysis of the RdRp domain clearly indicates that SsMBV1 is related to Rosellinia necatrix megabirnavirus 1 (RnMBV1). L2-dsRNA/SsMBV1 comprises two nonoverlapping ORFs (ORFA and ORFB) encoding two hypothetical proteins with unknown functions. The 5′-terminal regions of L1- and L2-dsRNA/SsMBV1 share strictly conserved sequences and form stable stem-loop structures. Although L2-dsRNA/SsMBV1 is dispensable for replication, genome packaging, and pathogenicity of SsMBV1, it enhances transcript accumulation of L1-dsRNA/SsMBV1 and stability of virus-like particles (VLPs). Interestingly, a conserved papain-like protease domain similar to a multifunctional protein (p29) of Cryphonectria hypovirus 1 was detected in the ORFA-encoded protein of L2-dsRNA/SsMBV1. Phylogenetic analysis based on the protease domain suggests that horizontal gene transfer may have occurred from a single-stranded RNA (ssRNA) virus (hypovirus) to a dsRNA virus, SsMBV1. Our results reveal that SsMBV1 has a slight impact on the fundamental biological characteristics of its host regardless of the presence or absence of L2-dsRNA/SsMBV1. IMPORTANCE Mycoviruses are widespread in all major fungal groups, and they possess diverse genomes of mostly ssRNA and dsRNA and, recently, circular ssDNA. Here, we have characterized

  14. 77 FR 22516 - Certain Transfers of Property to Regulated Investment Companies [RICs] and Real Estate Investment...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-16

    ... Companies and Real Estate Investment Trusts AGENCY: Internal Revenue Service (IRS), Treasury. ACTION: Notice... transfers of property from a C corporation to a Regulated Investment Company (RIC) or a Real Estate... may not be circumvented * * * through the use of a regulated investment company, a real...

  15. A horizontally transferred tRNA(Cys) gene in the sugar beet mitochondrial genome: evidence that the gene is present in diverse angiosperms and its transcript is aminoacylated.

    PubMed

    Kitazaki, Kazuyoshi; Kubo, Tomohiko; Kagami, Hiroyo; Matsumoto, Takuma; Fujita, Asami; Matsuhira, Hiroaki; Matsunaga, Muneyuki; Mikami, Tetsuo

    2011-10-01

    Of the two tRNA(Cys) (GCA) genes, trnC1-GCA and trnC2-GCA, previously identified in mitochondrial genome of sugar beet, the former is a native gene and probably a pseudo-copy, whereas the latter, of unknown origin, is transcribed into a tRNA [tRNA(Cys2) (GCA)]. In this study, the trnC2-GCA sequence was mined from various public databases. To evaluate whether or not the trnC2-GCA sequence is located in the mitochondrial genome, the relative copy number of its sequence to nuclear gene was assessed in a number of angiosperm species, using a quantitative real-time PCR assay. The trnC2-GCA sequence was found to exist sporadically in the mitochondrial genomes of a wide range of angiosperms. The mitochondrial tRNA(Cys2) (GCA) species from sugar beet (Beta vulgaris), spinach (Spinacea oleracea) and cucumber (Cucumis sativus) were found to be aminoacylated, indicating that they may participate in translation. We also identified a sugar beet nuclear gene that encodes cysteinyl-tRNA synthetase, which is dual-targeted to mitochondria and plastids, and may aminoacylate tRNA(Cys2) (GCA). What is of particular interest is that trnC1-GCA and trnC2-GCA co-exist in the mitochondrial genomes of eight diverse angiosperms, including spinach, and that the spinach tRNA(Cys1) (GCA) is also aminoacylated. Taken together, our observations lead us to surmise that trnC2-GCA may have been horizontally transferred to a common ancestor of eudicots, followed by co-existence and dual expression of trnC1-GCA and trnC2-GCA in mitochondria with occasional loss or inactivation of either trnC-GCA gene during evolution.

  16. Genome analysis of Elysia chlorotica Egg DNA provides no evidence for horizontal gene transfer into the germ line of this Kleptoplastic Mollusc.

    PubMed

    Bhattacharya, Debashish; Pelletreau, Karen N; Price, Dana C; Sarver, Kara E; Rumpho, Mary E

    2013-08-01

    The sea slug Elysia chlorotica offers a unique opportunity to study the evolution of a novel function (photosynthesis) in a complex multicellular host. Elysia chlorotica harvests plastids (absent of nuclei) from its heterokont algal prey, Vaucheria litorea. The "stolen" plastids are maintained for several months in cells of the digestive tract and are essential for animal development. The basis of long-term maintenance of photosynthesis in this sea slug was thought to be explained by extensive horizontal gene transfer (HGT) from the nucleus of the alga to the animal nucleus, followed by expression of algal genes in the gut to provide essential plastid-destined proteins. Early studies of target genes and proteins supported the HGT hypothesis, but more recent genome-wide data provide conflicting results. Here, we generated significant genome data from the E. chlorotica germ line (egg DNA) and from V. litorea to test the HGT hypothesis. Our comprehensive analyses fail to provide evidence for alga-derived HGT into the germ line of the sea slug. Polymerase chain reaction analyses of genomic DNA and cDNA from different individual E. chlorotica suggest, however, that algal nuclear genes (or gene fragments) are present in the adult slug. We suggest that these nucleic acids may derive from and/or reside in extrachromosomal DNAs that are made available to the animal through contact with the alga. These data resolve a long-standing issue and suggest that HGT is not the primary reason underlying long-term maintenance of photosynthesis in E. chlorotica. Therefore, sea slug photosynthesis is sustained in as yet unexplained ways that do not appear to endanger the animal germ line through the introduction of dozens of foreign genes.

  17. In vivo Acquisition of Carbapenemase Gene blaKPC-2 in Multiple Species of Enterobacteriaceae through Horizontal Transfer of Insertion Sequence or Plasmid

    PubMed Central

    Ding, Baixing; Shen, Zhen; Hu, Fupin; Ye, Meiping; Xu, Xiaogang; Guo, Qinglan; Wang, Minggui

    2016-01-01

    Objectives: Current worldwide spread of carbapenem resistance in Enterobacteriaceae constitutes a critical public health threat. This study aims to investigate how carbapenem resistance is acquired in Enterobacteriaceae in patients during antimicrobial therapy. Methods: Clinical strains from the same anatomical site of the same patients that converted from carbapenem-susceptible to resistant during antimicrobial therapy and showed identical or similar PFGE patterns were identified. The similarly sized plasmids carried by the susceptible and resistant strains, the latter containing the carbapenemase genes, were sequenced and analyzed. Results: Paired strains were identified from four patients: three had neurosurgical conditions while the other had acute exacerbation of COPD. Two pairs of Klebsiella pneumoniae (KP1-S/R and KP2-S/R, S and R indicating susceptible and resistant strains, respectively), one pair of Morganella morganii (MM-S/R) and one pair of Enterobacter aerogenes (EA-S/R) were collected. All four carbapenem-resistant strains carried plasmids harboring blaKPC−2. Compared with the similarly sized plasmids in KP1-S and KP2-S, an insertion sequence that includes ISKpn6-like, blaKPC−2 and ISKpn8 was noted in pKP1-R and pKP2-R. Strains MM-R and EA-R had blaKPC−2-carrying plasmids not resembling plasmids in strains MM-S and EA-S suggesting their new acquisition while on therapy. Conclusions: Enterobacteriaceae can acquire carbapenem resistance during antimicrobial therapy through horizontal transfer of an insertion sequence or plasmid. PMID:27818649

  18. Complete Chloroplast Genome Sequence of Holoparasite Cistanche deserticola (Orobanchaceae) Reveals Gene Loss and Horizontal Gene Transfer from Its Host Haloxylon ammodendron (Chenopodiaceae)

    PubMed Central

    Qiao, Qin; Ren, Zhumei; Zhao, Jiayuan; Yonezawa, Takahiro; Hasegawa, Masami; Crabbe, M. James C; Li, Jianqiang; Zhong, Yang

    2013-01-01

    Background The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. Principal Findings/Significance Here we report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae. The cp genome of C. deserticola is greatly reduced both in size (102,657 bp) and in gene content, indicating that all genes required for photosynthesis suffer from gene loss and pseudogenization, except for psbM. The striking difference from other holoparasitic plants is that it retains almost a full set of tRNA genes, and it has lower dN/dS for most genes than another close holoparasitic plant, E. virginiana, suggesting that Cistanche deserticola has undergone fewer losses, either due to a reduced level of holoparasitism, or to a recent switch to this life history. We also found that the rpoC2 gene was present in two copies within C. deserticola. Its own copy has much shortened and turned out to be a pseudogene. Another copy, which was not located in its cp genome, was a homolog of the host plant, Haloxylon ammodendron (Chenopodiaceae), suggesting that it was acquired from its host via a horizontal gene transfer. PMID:23554920

  19. In vivo Acquisition of Carbapenemase Gene blaKPC-2 in Multiple Species of Enterobacteriaceae through Horizontal Transfer of Insertion Sequence or Plasmid.

    PubMed

    Ding, Baixing; Shen, Zhen; Hu, Fupin; Ye, Meiping; Xu, Xiaogang; Guo, Qinglan; Wang, Minggui

    2016-01-01

    Objectives: Current worldwide spread of carbapenem resistance in Enterobacteriaceae constitutes a critical public health threat. This study aims to investigate how carbapenem resistance is acquired in Enterobacteriaceae in patients during antimicrobial therapy. Methods: Clinical strains from the same anatomical site of the same patients that converted from carbapenem-susceptible to resistant during antimicrobial therapy and showed identical or similar PFGE patterns were identified. The similarly sized plasmids carried by the susceptible and resistant strains, the latter containing the carbapenemase genes, were sequenced and analyzed. Results: Paired strains were identified from four patients: three had neurosurgical conditions while the other had acute exacerbation of COPD. Two pairs of Klebsiella pneumoniae (KP1-S/R and KP2-S/R, S and R indicating susceptible and resistant strains, respectively), one pair of Morganella morganii (MM-S/R) and one pair of Enterobacter aerogenes (EA-S/R) were collected. All four carbapenem-resistant strains carried plasmids harboring blaKPC-2. Compared with the similarly sized plasmids in KP1-S and KP2-S, an insertion sequence that includes ISKpn6-like, blaKPC-2 and ISKpn8 was noted in pKP1-R and pKP2-R. Strains MM-R and EA-R had blaKPC-2-carrying plasmids not resembling plasmids in strains MM-S and EA-S suggesting their new acquisition while on therapy. Conclusions: Enterobacteriaceae can acquire carbapenem resistance during antimicrobial therapy through horizontal transfer of an insertion sequence or plasmid.

  20. The Complete Genome Sequence of Plodia Interpunctella Granulovirus: Evidence for Horizontal Gene Transfer and Discovery of an Unusual Inhibitor-of-Apoptosis Gene

    PubMed Central

    Harrison, Robert L.; Rowley, Daniel L.; Funk, C. Joel

    2016-01-01

    The Indianmeal moth, Plodia interpunctella (Lepidoptera: Pyralidae), is a common pest of stored goods with a worldwide distribution. The complete genome sequence for a larval pathogen of this moth, the baculovirus Plodia interpunctella granulovirus (PiGV), was determined by next-generation sequencing. The PiGV genome was found to be 112, 536 bp in length with a 44.2% G+C nucleotide distribution. A total of 123 open reading frames (ORFs) and seven homologous regions (hrs) were identified and annotated. Phylogenetic inference using concatenated alignments of 36 baculovirus core genes placed PiGV in the “b” clade of viruses from genus Betabaculovirus with a branch length suggesting that PiGV represents a distinct betabaculovirus species. In addition to the baculovirus core genes and orthologues of other genes found in other betabaculovirus genomes, the PiGV genome sequence contained orthologues of the bidensovirus NS3 gene, as well as ORFs that occur in alphabaculoviruses but not betabaculoviruses. While PiGV contained an orthologue of inhibitor of apoptosis-5 (iap-5), an orthologue of inhibitor of apoptosis-3 (iap-3) was not present. Instead, the PiGV sequence contained an ORF (PiGV ORF81) encoding an IAP homologue with sequence similarity to insect cellular IAPs, but not to viral IAPs. Phylogenetic analysis of baculovirus and insect IAP amino acid sequences suggested that the baculovirus IAP-3 genes and the PiGV ORF81 IAP homologue represent different lineages arising from more than one acquisition event. The presence of genes from other sources in the PiGV genome highlights the extent to which baculovirus gene content is shaped by horizontal gene transfer. PMID:27472489

  1. Expression of the sub-pathways of the Chloroflexus aurantiacus 3-hydroxypropionate carbon fixation bicycle in E. coli: Toward horizontal transfer of autotrophic growth.

    PubMed

    Mattozzi, Matthew d; Ziesack, Marika; Voges, Mathias J; Silver, Pamela A; Way, Jeffrey C

    2013-03-01

    The 3-hydroxypropionate (3-HPA) bicycle is unique among CO2-fixing systems in that none of its enzymes appear to be affected by oxygen. Moreover, the bicycle includes a number of enzymes that produce novel intermediates of biotechnological interest, and the CO2-fixing steps in this pathway are relatively rapid. We expressed portions of the 3-HPA bicycle in a heterologous organism, E. coli K12. We subdivided the 3-HPA bicycle into four sub-pathways: (1) synthesis of propionyl-CoA from acetyl-CoA, (2) synthesis of succinate from propionyl-CoA, (3) glyoxylate production and regeneration of acetyl-CoA, and (4) assimilation of glyoxylate and propionyl-CoA to form pyruvate and regenerate acetyl-CoA. We expressed the novel enzymes of the 3-HPA bicycle in operon form and used phenotypic tests for activity. Sub-pathway 1 activated a propionate-specific biosensor. Sub-pathway 2, found in non-CO2-fixing bacteria, was reassembled in E. coli using genes from diverse sources. Sub-pathway 3, operating in reverse, generated succinyl-CoA sufficient to rescue a sucAD(-) double mutant of its diaminopimelic acid (DAP) auxotrophy. Sub-pathway 4 was able to reduce the toxicity of propionate and allow propionate to contribute to cell biomass in a prpC(-)(2 methylcitrate synthase) mutant strain. These results indicate that all of the sub-pathways of the 3-HPA bicycle can function to some extent in vivo in a heterologous organism, as indicated by growth tests. Overexpression of certain enzymes was deleterious to cell growth, and, in particular, expression of MMC-CoA lyase caused a mucoid phenotype. These results have implications for metabolic engineering and for bacterial evolution through horizontal gene transfer.

  2. Genome Analysis of Elysia chlorotica Egg DNA Provides No Evidence for Horizontal Gene Transfer into the Germ Line of This Kleptoplastic Mollusc

    PubMed Central

    Bhattacharya, Debashish; Pelletreau, Karen N.; Price, Dana C.; Sarver, Kara E.; Rumpho, Mary E.

    2013-01-01

    The sea slug Elysia chlorotica offers a unique opportunity to study the evolution of a novel function (photosynthesis) in a complex multicellular host. Elysia chlorotica harvests plastids (absent of nuclei) from its heterokont algal prey, Vaucheria litorea. The “stolen” plastids are maintained for several months in cells of the digestive tract and are essential for animal development. The basis of long-term maintenance of photosynthesis in this sea slug was thought to be explained by extensive horizontal gene transfer (HGT) from the nucleus of the alga to the animal nucleus, followed by expression of algal genes in the gut to provide essential plastid-destined proteins. Early studies of target genes and proteins supported the HGT hypothesis, but more recent genome-wide data provide conflicting results. Here, we generated significant genome data from the E. chlorotica germ line (egg DNA) and from V. litorea to test the HGT hypothesis. Our comprehensive analyses fail to provide evidence for alga-derived HGT into the germ line of the sea slug. Polymerase chain reaction analyses of genomic DNA and cDNA from different individual E. chlorotica suggest, however, that algal nuclear genes (or gene fragments) are present in the adult slug. We suggest that these nucleic acids may derive from and/or reside in extrachromosomal DNAs that are made available to the animal through contact with the alga. These data resolve a long-standing issue and suggest that HGT is not the primary reason underlying long-term maintenance of photosynthesis in E. chlorotica. Therefore, sea slug photosynthesis is sustained in as yet unexplained ways that do not appear to endanger the animal germ line through the introduction of dozens of foreign genes. PMID:23645554

  3. Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification.

    PubMed

    McDonald, Tami R; Dietrich, Fred S; Lutzoni, François

    2012-01-01

    The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane. Although it has been established that the Rh proteins are distantly related to the other members of the family, the evolutionary history of the AMT/MEP/Rh family remains unclear. Here, we use phylogenetic analysis to infer the evolutionary history of this family of proteins across 191 genomes representing all main lineages of life and to provide a new classification of the proteins in this family. Our phylogenetic analysis suggests that what has heretofore been conceived of as a protein family with two clades (AMT/MEP and Rh) is instead a protein family with three clades (AMT, MEP, and Rh). We show that the AMT/MEP/Rh family illustrates two contrasting modes of gene transmission: The AMT family as defined here exhibits vertical gene transfer (i.e., standard parent-to-offspring inheritance), whereas the MEP family as defined here is characterized by several ancient independent horizontal gene transfers (HGTs). These ancient HGT events include a gene replacement during the early evolution of the fungi, which could be a defining trait for the kingdom Fungi, a gene gain from hyperthermophilic chemoautolithotrophic prokaryotes during the early evolution of land plants (Embryophyta), and an independent gain of this same gene in the filamentous ascomycetes (Pezizomycotina) that was subsequently lost in most lineages but retained in even distantly related lichenized fungi. This recircumscription of the ammonium transporters/ammonia permeases family into MEP and AMT families informs the debate on the mechanism of transport in these proteins and on the nature of the transported molecule because published crystal structures of proteins from the MEP and Rh clades may not be representative of the AMT clade. The clades as depicted in this phylogenetic study appear to correspond to

  4. Experimental Horizontal Gene Transfer of Methylamine Dehydrogenase Mimics Prevalent Exchange in Nature and Overcomes the Methylamine Growth Constraints Posed by the Sub-Optimal N-Methylglutamate Pathway

    PubMed Central

    Nayak, Dipti D.; Marx, Christopher J.

    2015-01-01

    Methylamine plays an important role in the global carbon and nitrogen budget; microorganisms that grow on reduced single carbon compounds, methylotrophs, serve as a major biological sink for methylamine in aerobic environments. Two non-orthologous, functionally degenerate routes for methylamine oxidation have been studied in methylotrophic Proteobacteria: Methylamine dehydrogenase and the N-methylglutamate pathway. Recent work suggests the N-methylglutamate (NMG) pathway may be more common in nature than the well-studied methylamine dehydrogenase (MaDH, encoded by the mau gene cluster). However, the distribution of these pathways across methylotrophs has never been analyzed. Furthermore, even though horizontal gene transfer (HGT) is commonly invoked as a means to transfer these pathways between strains, the physiological barriers to doing so have not been investigated. We found that the NMG pathway is both more abundant and more universally distributed across methylotrophic Proteobacteria compared to MaDH, which displays a patchy distribution and has clearly been transmitted by HGT even amongst very closely related strains. This trend was especially prominent in well-characterized strains of the Methylobacterium extroquens species, which also display significant phenotypic variability during methylamine growth. Strains like Methylobacterium extorquens PA1 that only encode the NMG pathway grew on methylamine at least five-fold slower than strains like Methylobacterium extorquens AM1 that also possess the mau gene cluster. By mimicking a HGT event through the introduction of the M. extorquens AM1 mau gene cluster into the PA1 genome, the resulting strain instantaneously achieved a 4.5-fold increase in growth rate on methylamine and a 11-fold increase in fitness on methylamine, which even surpassed the fitness of M. extorquens AM1. In contrast, when three replicate populations of wild type M. extorquens PA1 were evolved on methylamine as the sole carbon and energy

  5. Multiple Horizontal Gene Transfers of Ammonium Transporters/Ammonia Permeases from Prokaryotes to Eukaryotes: Toward a New Functional and Evolutionary Classification

    PubMed Central

    McDonald, Tami R.; Dietrich, Fred S.; Lutzoni, François

    2012-01-01

    The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane. Although it has been established that the Rh proteins are distantly related to the other members of the family, the evolutionary history of the AMT/MEP/Rh family remains unclear. Here, we use phylogenetic analysis to infer the evolutionary history of this family of proteins across 191 genomes representing all main lineages of life and to provide a new classification of the proteins in this family. Our phylogenetic analysis suggests that what has heretofore been conceived of as a protein family with two clades (AMT/MEP and Rh) is instead a protein family with three clades (AMT, MEP, and Rh). We show that the AMT/MEP/Rh family illustrates two contrasting modes of gene transmission: The AMT family as defined here exhibits vertical gene transfer (i.e., standard parent-to-offspring inheritance), whereas the MEP family as defined here is characterized by several ancient independent horizontal gene transfers (HGTs). These ancient HGT events include a gene replacement during the early evolution of the fungi, which could be a defining trait for the kingdom Fungi, a gene gain from hyperthermophilic chemoautolithotrophic prokaryotes during the early evolution of land plants (Embryophyta), and an independent gain of this same gene in the filamentous ascomycetes (Pezizomycotina) that was subsequently lost in most lineages but retained in even distantly related lichenized fungi. This recircumscription of the ammonium transporters/ammonia permeases family into MEP and AMT families informs the debate on the mechanism of transport in these proteins and on the nature of the transported molecule because published crystal structures of proteins from the MEP and Rh clades may not be representative of the AMT clade. The clades as depicted in this phylogenetic study appear to correspond to

  6. The master regulator of IncA/C plasmids is recognized by the Salmonella Genomic island SGI1 as a signal for excision and conjugal transfer

    PubMed Central

    Kiss, János; Papp, Péter Pál; Szabó, Mónika; Farkas, Tibor; Murányi, Gábor; Szakállas, Erik; Olasz, Ferenc

    2015-01-01

    The genomic island SGI1 and its variants, the important vehicles of multi-resistance in Salmonella strains, are integrative elements mobilized exclusively by the conjugative IncA/C plasmids. Integration and excision of the island are carried out by the SGI1-encoded site-specific recombinase Int and the recombination directionality factor Xis. Chromosomal integration ensures the stable maintenance and vertical transmission of SGI1, while excision is the initial step of horizontal transfer, followed by conjugation and integration into the recipient. We report here that SGI1 not only exploits the conjugal apparatus of the IncA/C plasmids but also utilizes the regulatory mechanisms of the conjugation system for the exact timing and activation of excision to ensure efficient horizontal transfer. This study demonstrates that the FlhDC-family activator AcaCD, which regulates the conjugation machinery of the IncA/C plasmids, serves as a signal of helper entry through binding to SGI1 xis promoter and activating SGI1 excision. Promoters of int and xis genes have been identified and the binding site of the activator has been located by footprinting and deletion analyses. We prove that expression of xis is activator-dependent while int is constitutively expressed, and this regulatory mechanism is presumably responsible for the efficient transfer and stable maintenance of SGI1. PMID:26209134

  7. The master regulator of IncA/C plasmids is recognized by the Salmonella Genomic island SGI1 as a signal for excision and conjugal transfer.

    PubMed

    Kiss, János; Papp, Péter Pál; Szabó, Mónika; Farkas, Tibor; Murányi, Gábor; Szakállas, Erik; Olasz, Ferenc

    2015-10-15

    The genomic island SGI1 and its variants, the important vehicles of multi-resistance in Salmonella strains, are integrative elements mobilized exclusively by the conjugative IncA/C plasmids. Integration and excision of the island are carried out by the SGI1-encoded site-specific recombinase Int and the recombination directionality factor Xis. Chromosomal integration ensures the stable maintenance and vertical transmission of SGI1, while excision is the initial step of horizontal transfer, followed by conjugation and integration into the recipient. We report here that SGI1 not only exploits the conjugal apparatus of the IncA/C plasmids but also utilizes the regulatory mechanisms of the conjugation system for the exact timing and activation of excision to ensure efficient horizontal transfer. This study demonstrates that the FlhDC-family activator AcaCD, which regulates the conjugation machinery of the IncA/C plasmids, serves as a signal of helper entry through binding to SGI1 xis promoter and activating SGI1 excision. Promoters of int and xis genes have been identified and the binding site of the activator has been located by footprinting and deletion analyses. We prove that expression of xis is activator-dependent while int is constitutively expressed, and this regulatory mechanism is presumably responsible for the efficient transfer and stable maintenance of SGI1.

  8. The genome of Polaromonas naphthalenivorans strain CJ2, isolated from coal tar-contaminated sediment, reveals physiological and metabolic versatility and evolution through extensive horizontal gene transfer.

    PubMed

    Yagi, Jane M; Sims, David; Brettin, Thomas; Bruce, David; Madsen, Eugene L

    2009-09-01

    We analysed the genome of the aromatic hydrocarbon-degrading, facultatively chemolithotrophic betaproteobacterium, Polaromonas naphthalenivorans strain CJ2. Recent work has increasingly shown that Polaromonas species are prevalent in a variety of pristine oligotrophic environments, as well as polluted habitats. Besides a circular chromosome of 4.4 Mb, strain CJ2 carries eight plasmids ranging from 353 to 6.4 kb in size. Overall, the genome is predicted to encode 4929 proteins. Comparisons of DNA sequences at the individual gene, gene cluster and whole-genome scales revealed strong trends in shared heredity between strain CJ2 and other members of the Comamonadaceae and Burkholderiaceae. blastp analyses of protein coding sequences across strain CJ2's genome showed that genetic commonalities with other betaproteobacteria diminished significantly in strain CJ2's plasmids compared with the chromosome, especially for the smallest ones. Broad trends in nucleotide characteristics (GC content, GC skew, Karlin signature difference) showed at least six anomalous regions in the chromosome, indicating alteration of genome architecture via horizontal gene transfer. Detailed analysis of one of these anomalous regions (96 kb in size, containing the nag-like naphthalene catabolic operon) indicates that the fragment's insertion site was within a putative MiaB-like tRNA-modifying enzyme coding sequence. The mosaic nature of strain CJ2's genome was further emphasized by the presence of 309 mobile genetic elements scattered throughout the genome, including 131 predicted transposase genes, 178 phage-related genes, and representatives of 12 families of insertion elements. A total of three different terminal oxidase genes were found (putative cytochrome aa(3)-type oxidase, cytochrome cbb(3)-type oxidase and cytochrome bd-type quinol oxidase), suggesting adaptation by strain CJ2 to variable aerobic and microaerobic conditions. Sequence-suggested abilities of strain CJ2 to carry out

  9. 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

    PubMed Central

    Brouard, Jean-Simon; Otis, Christian; Lemieux, Claude; Turmel, Monique

    2008-01-01

    include the retention of psaM, rpl32 and trnL(caa), the loss of petA, the disruption of three ancestral clusters and the presence of five derived gene clusters. Conclusion The Oedogonium chloroplast genome disclosed additional characters that bolster the evidence for a close alliance between the Oedogoniales and Chaetophorales. Our unprecedented finding of int and dpoB in this cpDNA provides a clear example that novel genes were acquired by the chloroplast genome through horizontal transfers, possibly from a mitochondrial genome donor. PMID:18558012

  10. The ancestor of the Paulinella chromatophore obtained a carboxysomal operon by horizontal gene transfer from a Nitrococcus-like γ-proteobacterium

    PubMed Central

    Marin, Birger; Nowack, Eva CM; Glöckner, Gernot; Melkonian, Michael

    2007-01-01

    Background Paulinella chromatophora is a freshwater filose amoeba with photosynthetic endosymbionts (chromatophores) of cyanobacterial origin that are closely related to free-living Prochlorococcus and Synechococcus species (PS-clade). Members of the PS-clade of cyanobacteria contain a proteobacterial form 1A RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) that was acquired by horizontal gene transfer (HGT) of a carboxysomal operon. In rDNA-phylogenies, the Paulinella chromatophore diverged basal to the PS-clade, raising the question whether the HGT occurred before or after the split of the chromatophore ancestor. Results Phylogenetic analyses of the almost complete rDNA operon with an improved taxon sampling containing most known cyanobacterial lineages recovered the Paulinella chromatophore as sister to the complete PS-clade. The sequence of the complete carboxysomal operon of Paulinella was determined. Analysis of RubisCO large subunit (rbcL) sequences revealed that Paulinella shares the proteobacterial form 1A RubisCO with the PS-clade. The γ-proteobacterium Nitrococcus mobilis was identified as sister of the Paulinella chromatophore and the PS-clade in the RubisCO phylogeny. Gene content and order in the carboxysomal operon correlates well with the RubisCO phylogeny demonstrating that the complete carboxysomal operon was acquired by the common ancestor of the Paulinella chromatophore and the PS-clade through HGT. The carboxysomal operon shows a significantly elevated AT content in Paulinella, which in the rbcL gene is confined to third codon positions. Combined phylogenies using rbcL and the rDNA-operon resulted in a nearly fully resolved tree of the PS-clade. Conclusion The HGT of the carboxysomal operon predated the divergence of the chromatophore ancestor from the PS-clade. Following HGT and divergence of the chromatophore ancestor, diversification of the PS-clade into at least three subclades occurred. The γ-proteobacterium Nitrococcus mobilis

  11. ARCHITECTURE OF A CHARGE-TRANSFER STATE REGULATING LIGHT HARVESTING IN A PLANT ANTENNA PROTEIN

    SciTech Connect

    Fleming, Graham; Ahn, Tae Kyu; Avenson, Thomas J.; Ballottari, Matteo; Cheng, Yuan-Chung; Niyogi, Krishna K.; Bassi, Roberto; Fleming, Graham R.

    2008-04-02

    Energy-dependent quenching of excess absorbed light energy (qE) is a vital mechanism for regulating photosynthetic light harvesting in higher plants. All of the physiological characteristics of qE have been positively correlated with charge-transfer between coupled chlorophyll and zeaxanthin molecules in the light-harvesting antenna of photosystem II (PSII). In this work, we present evidence for charge-transfer quenching in all three of the individual minor antenna complexes of PSII (CP29, CP26, and CP24), and we conclude that charge-transfer quenching in CP29 involves a de-localized state of an excitonically coupled chlorophyll dimer. We propose that reversible conformational changes in CP29 can `tune? the electronic coupling between the chlorophylls in this dimer, thereby modulating the energy of the chlorophylls-zeaxanthin charge-transfer state and switching on and off the charge-transfer quenching during qE.

  12. Sensitivity control through attenuation of signal transfer efficiency by negative regulation of cellular signalling.

    PubMed

    Toyoshima, Yu; Kakuda, Hiroaki; Fujita, Kazuhiro A; Uda, Shinsuke; Kuroda, Shinya

    2012-03-13

    Sensitivity is one of the hallmarks of biological and pharmacological responses. However, the principle of controlling sensitivity remains unclear. Here we theoretically analyse a simple biochemical reaction and find that the signal transfer efficiency of the transient peak amplitude attenuates depending on the strength of negative regulation. We experimentally find that many signalling pathways in various cell lines, including the Akt and ERK pathways, can be approximated by simple biochemical reactions and that the same property of the attenuation of signal transfer efficiency was observed for such pathways. Because of this property, a downstream molecule should show higher sensitivity to an activator and lower sensitivity to an inhibitor than an upstream molecule. Indeed, we experimentally verify that S6, which lies downstream of Akt, shows lower sensitivity to an epidermal growth factor receptor inhibitor than Akt. Thus, cells can control downstream sensitivity through the attenuation of signal transfer efficiency by changing the expression level of negative regulators.

  13. TE-domestication and horizontal transfer in a putative Nef-AP1mu mimic of HLA-A cytoplasmic domain re-trafficking.

    PubMed

    Murray, Joseph S; Murray, Elaina H

    2016-01-01

    Loc-103275158 provisional protein conserved the nominal MHC-I CD tyrosine phosphorylation site, and it has an N-terminal SH3 domain that we docked in one conformation to its internal Nef-like domain. Here, we suggest that phosphorylation of the protein's CD-loop signals an exchange between the internal Nef-like domain and a lentiviral-Nef for binding the N-terminal SH3 domain - freeing the Nef-like domain to bind MHC-I CD. Since the 5'-tigger sequence encodes part of the pseudo α1/α2 MHC-I domain, and the 3'-tigger part of the Nef-like domain, we speculate that transposition proceeded phylogenetically disparate horizontal transfers, involving adjacent 5'- and 3'- parasitic footprints, which we also found in the Loc-103275158 orf.

  14. Evidence for 5S rDNA Horizontal Transfer in the toadfish Halobatrachus didactylus (Schneider, 1801) based on the analysis of three multigene families

    PubMed Central

    2012-01-01

    and Clupeiformes orders. Two hypotheses have been outlined: one is the possible vertical permanence of the shared type in some fish lineages, and the other is the possibility of a horizontal transference event between ancient species of the Perciformes and Batrachoidiformes orders. This finding opens a new perspective in fish evolution and in the knowledge of the dynamism of the 5S rDNA. Cytogenetic analysis allowed some evolutionary trends to be roughed out, such as the progressive change in the U2 snDNA and the organization of (GATA)n repeats, from dispersed to localized in one locus. The accumulation of (GATA)n repeats in one chromosome pair could be implicated in the evolution of a pair of proto-sex chromosomes. This possibility could situate H. didactylus as the most highly evolved of the Batrachoididae family in terms of sex chromosome biology. PMID:23039906

  15. Regulation of Transfer Functions by the imp Locus of the Streptomyces coelicolor Plasmidogenic Element SLP1

    PubMed Central

    Hagege, Juliette M.; Brasch, Michael A.; Cohen, Stanley N.

    1999-01-01

    SLP1int is a 17.2-kb genetic element that normally is integrated site specifically into the chromosome of Streptomyces coelicolor A3(2). The imp operon within SLP1int represses replication of both chromosomally integrated and extrachromosomal SLP1. During mating with S. lividans, SLP1int can excise, delete part of imp, and form a family of autonomously replicating conjugative plasmids. Earlier work has shown that impA and impC gene products act in concert to control plasmid maintenance and regulate their own transcription. Here we report that these imp genes act also on a second promoter, Popimp (promoter opposite imp), located adjacent to, and initiating transcription divergent from, imp to regulate loci involved in the intramycelial transfer of SLP1 plasmids. spdB1 and spdB2, two overlapping genes immediately 3′ to Popimp and directly regulated by imp, are shown by Tn5 mutagenesis to control transfer-associated growth inhibition (i.e., pocking). Additional genes resembling transfer genes of other Streptomyces spp. plasmids and required for SLP1 transfer an