WorldWideScience

Sample records for genetically remote pathogenic

  1. The Genetically Remote Pathogenic Strain NVH391-98 of the Bacillus cereus Group Represents the Cluster of Thermophilic Strains

    Energy Technology Data Exchange (ETDEWEB)

    Auger, Sandrine; Galleron, Nathalie; Bidnenko, Elena; Ehrlich, S. Dusko; Lapidus, Alla; Sorokin, Alexei

    2007-10-02

    Bacteria of the Bacillus cereus group are known to cause food poisoning. A rare phylogenetically remote strain, NVH391-98, was recently characterized to encode a particularly efficient cytotoxin K presumably responsible for food poisoning. This pathogenic strain and its close relatives can be phenotypically distinguished from other strains of the B. cereus group by the inability to grow at temperatures below 17 degrees C and by the ability to grow at temperatures from 48 to 53 degrees C. A temperate phage, phBC391A2, residing in the genome of NVH391-98 allows us to distinguish the three known members of this thermophilic strain cluster.

  2. The Genetic and Molecular Basis of Plant Resistance to Pathogens

    Institute of Scientific and Technical Information of China (English)

    Yan Zhang; Thomas Lubberstedt; Mingliang Xu

    2013-01-01

    Plant pathogens have evolved numerous strategies to obtain nutritive materials from their host,and plants in turn have evolved the preformed physical and chemical barriers as well as sophisticated two-tiered immune system to combat pathogen attacks.Genetically,plant resistance to pathogens can be divided into qualitative and quantitative disease resistance,conditioned by major gene(s) and multiple genes with minor effects,respectively.Qualitative disease resistance has been mostly detected in plant defense against biotrophic pathogens,whereas quantitative disease resistance is involved in defense response to all plant pathogens,from biotrophs,hemibiotrophs to necrotrophs.Plant resistance is achieved through interception of pathogen-derived effectors and elicitation of defense response.In recent years,great progress has been made related to the molecular basis underlying host-pathogen interactions.In this review,we would like to provide an update on genetic and molecular aspects of plant resistance to pathogens.

  3. Reverse genetics approaches to combat pathogenic arenaviruses.

    Science.gov (United States)

    de la Torre, Juan C

    2008-12-01

    Several arenaviruses cause hemorrhagic fever (HF) in humans, and evidence indicates that the worldwide-distributed prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) is a neglected human pathogen of clinical significance. Moreover, arenaviruses pose a biodefense threat. No licensed anti-arenavirus vaccines are available, and current anti-arenavirus therapy is limited to the use of ribavirin, which is only partially effective and is associated with anemia and other side effects. Therefore, it is important to develop effective vaccines and better antiviral drugs to combat the dual threats of naturally occurring and intentionally introduced arenavirus infections. The development of arenavirus reverse genetic systems is allowing investigators to conduct a detailed molecular characterization of the viral cis-acting signals and trans-acting factors that control each of the steps of the arenavirus life cycle, including RNA synthesis, packaging and budding. Knowledge derived from these studies is uncovering potential novel targets for therapeutic intervention, as well as facilitating the establishment of assays to identify and characterize candidate antiviral drugs capable of interfering with specific steps of the virus life cycle. Likewise, the ability to generate predetermined specific mutations within the arenavirus genome and analyze their phenotypic expression would significantly contribute to the elucidation of arenavirus-host interactions, including the basis of their ability to cause severe HF. This, in turn, could lead to the development of novel, potent and safe arenavirus vaccines.

  4. Genetic variation and pathogenicity of Botrytis cinerea.

    NARCIS (Netherlands)

    Vlugt-Bergmans, van der C.J.B.

    1996-01-01

    Botrytis cinerea is a fungal pathogen of more than 200 hosts including a wide variety of economically important crops. Although many ecological and physiological studies on this destructive pathogen have been reported, not much is known about the molecular basis of the interaction of this pathogen w

  5. Determining the pathogenicity of genetic variants associated with cardiac channelopathies.

    Science.gov (United States)

    Campuzano, Oscar; Allegue, Catarina; Fernandez, Anna; Iglesias, Anna; Brugada, Ramon

    2015-01-22

    Advancements in genetic screening have generated massive amounts of data on genetic variation; however, a lack of clear pathogenic stratification has left most variants classified as being of unknown significance. This is a critical limitation for translating genetic data into clinical practice. Genetic screening is currently recommended in the guidelines for diagnosis and treatment of cardiac channelopathies, which are major contributors to sudden cardiac death in young people. We propose to characterize the pathogenicity of genetic variants associated with cardiac channelopathies using a stratified scoring system. The development of this system was considered by using all of the tools currently available to define pathogenicity. The use of this scoring system could help clinicians to understand the limitations of genetic associations with a disease, and help them better define the role that genetics can have in their clinical routine.

  6. Genetic characterization of mango anthracnose pathogen ...

    African Journals Online (AJOL)

    USER

    2010-06-28

    Jun 28, 2010 ... African Journal of Biotechnology Vol. 9(26), pp. ... 2Molecular Plant Pathology Laboratory, CISH, Lucknow-227 017, India. ... Fruit anthracnose pathogens, C. gloeosporioides, Colletotrichum .... On leaves, lesions, brown to.

  7. Pathogenicity of three genetically diverse strains of PRRSV Type 1 in specific pathogen free pigs

    DEFF Research Database (Denmark)

    Stadejek, Tomasz; Larsen, Lars E; Podgórska, Katarzyna

    2017-01-01

    Studies from Eastern European countries proved that porcine reproductive and respiratory syndrome virus Type 1 (PRRSV-1) harbours high genetic diversity and that genetically divergent subtypes 2-4 circulate in this area. In the present study, we compared the pathogenicity of two different PRRSV-1...

  8. Genetic diversity in the SIR model of pathogen evolution.

    Science.gov (United States)

    Gordo, Isabel; Gomes, M Gabriela M; Reis, Daniel G; Campos, Paulo R A

    2009-01-01

    We introduce a model for assessing the levels and patterns of genetic diversity in pathogen populations, whose epidemiology follows a susceptible-infected-recovered model (SIR). We model the population of pathogens as a metapopulation composed of subpopulations (infected hosts), where pathogens replicate and mutate. Hosts transmit pathogens to uninfected hosts. We show that the level of pathogen variation is well predicted by analytical expressions, such that pathogen neutral molecular variation is bounded by the level of infection and increases with the duration of infection. We then introduce selection in the model and study the invasion probability of a new pathogenic strain whose fitness (R(0)(1+s)) is higher than the fitness of the resident strain (R(0)). We show that this invasion probability is given by the relative increment in R(0) of the new pathogen (s). By analyzing the patterns of genetic diversity in this framework, we identify the molecular signatures during the replacement and compare these with those observed in sequences of influenza A.

  9. Genetic diversity in the SIR model of pathogen evolution.

    Directory of Open Access Journals (Sweden)

    Isabel Gordo

    Full Text Available We introduce a model for assessing the levels and patterns of genetic diversity in pathogen populations, whose epidemiology follows a susceptible-infected-recovered model (SIR. We model the population of pathogens as a metapopulation composed of subpopulations (infected hosts, where pathogens replicate and mutate. Hosts transmit pathogens to uninfected hosts. We show that the level of pathogen variation is well predicted by analytical expressions, such that pathogen neutral molecular variation is bounded by the level of infection and increases with the duration of infection. We then introduce selection in the model and study the invasion probability of a new pathogenic strain whose fitness (R(0(1+s is higher than the fitness of the resident strain (R(0. We show that this invasion probability is given by the relative increment in R(0 of the new pathogen (s. By analyzing the patterns of genetic diversity in this framework, we identify the molecular signatures during the replacement and compare these with those observed in sequences of influenza A.

  10. Genetic islands in pome fruit pathogenic and non-pathogenic Erwinia species and related plasmids.

    Science.gov (United States)

    Llop, Pablo

    2015-01-01

    New pathogenic bacteria belonging to the genus Erwinia associated with pome fruit trees (Erwinia, E. piriflorinigrans, E. uzenensis) have been increasingly described in the last years, and comparative analyses have found that all these species share several genetic characteristics. Studies at different level (whole genome comparison, virulence genes, plasmid content, etc.) show a high intraspecies homogeneity (i.e., among E. amylovora strains) and also abundant similarities appear between the different Erwinia species: presence of plasmids of similar size in the pathogenic species; high similarity in several genes associated with exopolysaccharide production and hence, with virulence, as well as in some other genes, in the chromosomes. Many genetic similarities have been observed also among some of the plasmids (and genomes) from the pathogenic species and E. tasmaniensis or E. billingiae, two epiphytic species on the same hosts. The amount of genetic material shared in this genus varies from individual genes to clusters, genomic islands and genetic material that even may constitute a whole plasmid. Recent research on evolution of erwinias point out the horizontal transfer acquisition of some genomic islands that were subsequently lost in some species and several pathogenic traits that are still present. How this common material has been obtained and is efficiently maintained in different species belonging to the same genus sharing a common ecological niche provides an idea of the origin and evolution of the pathogenic Erwinia and the interaction with non-pathogenic species present in the same niche, and the role of the genes that are conserved in all of them.

  11. Advances in genetic manipulation of obligate intracellular bacterial pathogens

    Directory of Open Access Journals (Sweden)

    Paul eBeare

    2011-05-01

    Full Text Available Infections by obligate intracellular bacterial pathogens result in significant morbidity and mortality worldwide. These bacteria include Chlamydia spp., which causes millions of cases of sexually transmitted disease and blinding trachoma annually, and members of the α-proteobacterial genera Anaplasma, Ehrlichia, Orientia and Rickettsia, agents of serious human illnesses including epidemic typhus. Coxiella burnetii, the agent of human Q fever, has also been considered a prototypical obligate intracellular bacterium, but recent host cell-free (axenic growth has rescued it from obligatism. The historic genetic intractability of obligate intracellular bacteria has severely limited molecular dissection of their unique lifestyles and virulence factors involved in pathogenesis. Host cell restricted growth is a significant barrier to genetic transformation that can make simple procedures for free-living bacteria, such as cloning, exceedingly difficult. Low transformation efficiency requiring long term culture in host cells to expand small transformant populations is another obstacle. Despite numerous technical limitations, the last decade has witnessed significant gains in genetic manipulation of obligate intracellular bacteria including allelic exchange. Continued development of genetic tools should soon enable routine mutation and complementation strategies for virulence factor discovery and stimulate renewed interest in these refractory pathogens. In this review, we discuss the technical challenges associated with genetic transformation of obligate intracellular bacteria and highlight advances made with individual genera.

  12. The Quantitative Basis of the Arabidopsis Innate Immune System to Endemic Pathogens Depends on Pathogen Genetics.

    Directory of Open Access Journals (Sweden)

    Jason A Corwin

    2016-02-01

    Full Text Available The most established model of the eukaryotic innate immune system is derived from examples of large effect monogenic quantitative resistance to pathogens. However, many host-pathogen interactions involve many genes of small to medium effect and exhibit quantitative resistance. We used the Arabidopsis-Botrytis pathosystem to explore the quantitative genetic architecture underlying host innate immune system in a population of Arabidopsis thaliana. By infecting a diverse panel of Arabidopsis accessions with four phenotypically and genotypically distinct isolates of the fungal necrotroph B. cinerea, we identified a total of 2,982 genes associated with quantitative resistance using lesion area and 3,354 genes associated with camalexin production as measures of the interaction. Most genes were associated with resistance to a specific Botrytis isolate, which demonstrates the influence of pathogen genetic variation in analyzing host quantitative resistance. While known resistance genes, such as receptor-like kinases (RLKs and nucleotide-binding site leucine-rich repeat proteins (NLRs, were found to be enriched among associated genes, they only account for a small fraction of the total genes associated with quantitative resistance. Using publically available co-expression data, we condensed the quantitative resistance associated genes into co-expressed gene networks. GO analysis of these networks implicated several biological processes commonly connected to disease resistance, including defense hormone signaling and ROS production, as well as novel processes, such as leaf development. Validation of single gene T-DNA knockouts in a Col-0 background demonstrate a high success rate (60% when accounting for differences in environmental and Botrytis genetic variation. This study shows that the genetic architecture underlying host innate immune system is extremely complex and is likely able to sense and respond to differential virulence among pathogen

  13. The quantitative basis of the Arabidopsis innate immune system to endemic pathogens depends on pathogen genetics

    DEFF Research Database (Denmark)

    Corwin, Jason A; Copeland, Daniel; Feusier, Julie

    2016-01-01

    the Arabidopsis-Botrytis pathosystem to explore the quantitative genetic architecture underlying host innate immune system in a population of Arabidopsis thaliana. By infecting a diverse panel of Arabidopsis accessions with four phenotypically and genotypically distinct isolates of the fungal necrotroph B...... of pathogen genetic variation in analyzing host quantitative resistance. While known resistance genes, such as receptor-like kinases (RLKs) and nucleotide-binding site leucine-rich repeat proteins (NLRs), were found to be enriched among associated genes, they only account for a small fraction of the total......, including defense hormone signaling and ROS production, as well as novel processes, such as leaf development. Validation of single gene T-DNA knockouts in a Col-0 background demonstrate a high success rate (60%) when accounting for differences in environmental and Botrytis genetic variation. This study...

  14. Pathogenicity of three genetically diverse strains of PRRSV Type 1 in specific pathogen free pigs.

    Science.gov (United States)

    Stadejek, Tomasz; Larsen, Lars E; Podgórska, Katarzyna; Bøtner, Anette; Botti, Sara; Dolka, Izabella; Fabisiak, Michał; Heegaard, Peter M H; Hjulsager, Charlotte K; Huć, Tomasz; Kvisgaard, Lise K; Sapierzyński, Rafał; Nielsen, Jens

    2017-05-16

    Studies from Eastern European countries proved that porcine reproductive and respiratory syndrome virus Type 1 (PRRSV-1) harbours high genetic diversity and that genetically divergent subtypes 2-4 circulate in this area. In the present study, we compared the pathogenicity of two different PRRSV-1 subtype 2 strains and a strain representing PRRSV-1 subtype 1. Four groups of 8-week-old specific pathogen free pigs were either infected with subtype 2 strain ILI6, subtype 2 strain or BOR59, subtype 1 strain 18794, or mock inoculated. The most pronounced clinical signs were observed in pigs infected with BOR59. Pigs from both subtype 2 strain infected groups exhibited significantly elevated mean body temperatures on DPI 2 compared to the other two groups, the difference remaining significant up to DPI 13 for the BOR59 group, only. The pigs in the latter group also displayed significantly highest levels of early viremia together with the most rapid APP response. Overall, the results indicated that BOR59 strain can be considered a highly pathogenic strain, similarly to subtype 3 strains Lena and SU1-bel, while the virulence of the other subtype 2 strain ILI6 was intermediate between BOR59 and subtype 1 strain. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. The quantitative basis of the Arabidopsis innate immune system to endemic pathogens depends on pathogen genetics

    DEFF Research Database (Denmark)

    Corwin, Jason A; Copeland, Daniel; Feusier, Julie;

    2016-01-01

    The most established model of the eukaryotic innate immune system is derived from examples of large effect monogenic quantitative resistance to pathogens. However, many host-pathogen interactions involve many genes of small to medium effect and exhibit quantitative resistance. We used...... the Arabidopsis-Botrytis pathosystem to explore the quantitative genetic architecture underlying host innate immune system in a population of Arabidopsis thaliana. By infecting a diverse panel of Arabidopsis accessions with four phenotypically and genotypically distinct isolates of the fungal necrotroph B....... cinerea, we identified a total of 2,982 genes associated with quantitative resistance using lesion area and 3,354 genes associated with camalexin production as measures of the interaction. Most genes were associated with resistance to a specific Botrytis isolate, which demonstrates the influence...

  16. Pathogenic Ischemic Stroke Phenotypes in the NINDS-Stroke Genetics Network

    National Research Council Canada - National Science Library

    Ay, Hakan; Arsava, Ethem Murat; Andsberg, Gunnar; Benner, Thomas; Brown, Jr, Robert D; Chapman, Sherita N; Cole, John W; Delavaran, Hossein; Dichgans, Martin; Engström, Gunnar; Giralt-Steinhauer, Eva; Grewal, Raji P; Gwinn, Katrina; Jern, Christina; Jimenez-Conde, Jordi; Jood, Katarina; Katsnelson, Michael; Kissela, Brett; Kittner, Steven J; Kleindorfer, Dawn O; Labovitz, Daniel L; Lanfranconi, Silvia; Lee, Jin-Moo; Lehm, Manuel; Lemmens, Robin; Levi, Chris; Li, Linxin; Lindgren, Arne; Markus, Hugh S; McArdle, Patrick F; Melander, Olle; Norrving, Bo; Peddareddygari, Leema Reddy; Pedersén, Annie; Pera, Joanna; Rannikmäe, Kristiina; Rexrode, Kathryn M; Rhodes, David; Rich, Stephen S; Roquer, Jaume; Rosand, Jonathan; Rothwell, Peter M; Rundek, Tatjana; Sacco, Ralph L; Schmidt, Reinhold; Schürks, Markus; Seiler, Stephan; Sharma, Pankaj; Slowik, Agnieszka; Sudlow, Cathie; Thijs, Vincent; Woodfield, Rebecca; Worrall, Bradford B; Meschia, James F

    2014-01-01

    ...)-SiGN (Stroke Genetics Network) is an international consortium of ischemic stroke studies that aims to generate high-quality phenotype data to identify the genetic basis of pathogenic stroke subtypes...

  17. Genetic Manipulation of Pathogenicity Loci in Non-Typhimurium Salmonella

    Science.gov (United States)

    Butela, Kristen; Lawrence, Jeffrey G.

    2012-01-01

    The traditional genetic tools used in Salmonella enterica serovar Typhimurium rely heavily on a high-transducing mutant of bacteriophage P22. P22 recognizes its hosts by the structure of their O-antigens, which vary among serovars of Salmonella; therefore, it cannot be used in most non-Typhimurium Salmonella, including the majority of those causing food-borne illnesses in both humans and livestock. Bacteriophage P1 infects a variety of enteric bacteria, including galE mutants of serovar Typhimurium; however, the degree to which the presence of coimmune prophages, the lack of required attachment sites or the lack of host factors act as barriers to using phage P1 in natural isolates of Salmonella is unknown. Here, we show that recombineering can be used to make virtually any serovar of Salmonella susceptible to P1 infection; as a result, P1 can be utilized for facile genetic manipulation of non-Typhimurium Salmonella, including movement of very large pathogenicity islands. A toolkit for easy manipulation of non-Typhimurium serovars of Salmonella is described. PMID:23041268

  18. Horizontal transfer generates genetic variation in an asexual pathogen

    Directory of Open Access Journals (Sweden)

    Xiaoqiu Huang

    2014-10-01

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

  19. Genetics and Genomics of Pathogens: Fighting Infections with Genome-Sequencing Technology.

    Science.gov (United States)

    Plavskin, Alexandra

    2016-01-01

    Discussions of clinical genetics and genomics often focus on screening for disease-causing genes in humans and the promise of targeted therapies. Another important area of research is analysis of pathogen genomes. Genetics and genomics-based approaches, such as population genomics and phylogenetics, provide insight into mechanisms of resistance, sources of infections, and pathogen transmission routes.

  20. Genetic parameters for pathogen-specific mastitis resistance in Danish Holstein cattle

    DEFF Research Database (Denmark)

    Sørensen, Lars Peter; Madsen, P.; Mark, Thomas;

    2009-01-01

    . uberis, respectively. The heritabilities of groups of pathogen ranged from 0.053 to 0.087. Genetic correlations among the pathogen-specific mastitis traits ranged from 0.45 to 0.77. These estimates tended to be lowest for bacteria eliciting very different immune responses, which can be considered...... as the overall pleiotropic effect of genes affecting resistance to a specific pathogen, and highest for bacteria sharing characteritics regarding immune response. The genetic correlations between the groups of pathogens were high, 0.73 and 0.83. Results showed that the pathogen-specific traits used in this study......The objective of this study was to estimate heritabilities for and genetic correlations among different pathogen-specific mastitis traits. The traits were unspecific mastitis, which is all mastitis treatments regardless of the causative pathogen as well as mastitis caused by Streptococcus...

  1. A RBF classification method of remote sensing image based on genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The remote sensing image classification has stimulated considerable interest as an effective method for better retrieving information from the rapidly increasing large volume, complex and distributed satellite remote imaging data of large scale and cross-time, due to the increase of remote image quantities and image resolutions. In the paper, the genetic algorithms were employed to solve the weighting of the radial basis faction networks in order to improve the precision of remote sensing image classification. The remote sensing image classification was also introduced for the GIS spatial analysis and the spatial online analytical processing (OLAP) ,and the resulted effectiveness was demonstrated in the analysis of land utilization variation of Daqing city.

  2. The genetics of non-host resistance to the lettuce pathogen Bremia lactucae in Lactuca saligna

    NARCIS (Netherlands)

    Jeuken, M.J.W.

    2002-01-01

    Plants are continuously exposed to a wide variety of pathogens. However, all plant species are non-hosts for the majority of the potential plant pathogens. The genetic dissection of non-host resistance is hampered by the lack of segregating population from crosses between host and non-host species,

  3. Evolution and population genetics of exotic and reemerging pathogens: traditional and novel tools and approaches

    Science.gov (United States)

    N.J. Grünwald; E.M. Goss

    2011-01-01

    Given human population growth and accelerated global trade, the rate of emergence of exotic plant pathogens is bound to increase. Understanding the processes that lead to the emergence of new pathogens can help manage emerging epidemics. Novel tools for analyzing population genetic variation can be used to infer the evolutionary history of populations or species,...

  4. Genetic parameters of pathogen-specific incidence of clinical mastitis in dairy cows

    NARCIS (Netherlands)

    Haas, de Y.; Barkema, H.W.; Veerkamp, R.F.

    2002-01-01

    The objective of this study was to estimate heritabilities for and genetic correlations among different pathogen-specific mastitis traits. The traits were unspecific mastitis, which is all mastitis treatments regardless of the causative pathogen as well as mastitis caused by Streptococcus

  5. Genetic versus antigenic differences among highly pathogenic H5N1 avian influenza A viruses

    NARCIS (Netherlands)

    Peeters, Ben; Reemers, Sylvia; Dortmans, Jos; Vries, de Erik; Jong, de Mart; Zande, van de Saskia; Rottier, Peter J.M.; Haan, de Cornelis A.M.

    2017-01-01

    Highly pathogenic H5N1 avian influenza A viruses display a remarkable genetic and antigenic diversity. We examined to what extent genetic distances between several H5N1 viruses from different clades correlate with antigenic differences and vaccine performance. H5-specific antisera were generated, an

  6. Genetic parameters for pathogen-specific mastitis resistance in Danish Holstein Cattle

    DEFF Research Database (Denmark)

    Sørensen, L P; Madsen, P; Mark, T

    2009-01-01

    The objective of this study was to estimate heritabilities for and genetic correlations among different pathogen-specific mastitis traits. The traits were unspecific mastitis, which is all mastitis treatments regardless of the causative pathogen as well as mastitis caused by Streptococcus...... and 2006 were used in the analyses. Variances and covariances were estimated using uni- and bivariate threshold models via Gibbs sampling. Posterior means of heritabilities of pathogen-specific mastitis were lower than the heritability of unspecific mastitis, ranging from 0.035 to 0.076 for S. aureus and S....... uberis, respectively. The heritabilities of groups of pathogen ranged from 0.053 to 0.087. Genetic correlations among the pathogen-specific mastitis traits ranged from 0.45 to 0.77. These estimates tended to be lowest for bacteria eliciting very different immune responses, which can be considered...

  7. Assessment of genetic variation for pathogen-specific mastitis resistance in Valle del Belice dairy sheep.

    Science.gov (United States)

    Tolone, Marco; Larrondo, Cristian; Yáñez, José M; Newman, Scott; Sardina, Maria Teresa; Portolano, Baldassare

    2016-07-28

    Mastitis resistance is a complex and multifactorial trait, and its expression depends on both genetic and environmental factors, including infection pressure. The objective of this research was to determine the genetic basis of mastitis resistance to specific pathogens using a repeatability threshold probit animal model. The most prevalent isolated pathogens were coagulase-negative staphylococci (CNS); 39 % of records and 77 % of the animals infected at least one time in the whole period of study. There was significant genetic variation only for Streptococci (STR). In addition, there was a positive genetic correlation between STR and all pathogens together (ALL) (0.36 ± 0.22), and CNS and ALL (0.92 ± 0.04). The results of our study support the presence of significant genetic variation for mastitis caused by Streptococci and suggest the importance of discriminating between different pathogens causing mastitis due to the fact that they most likely influence different genetic traits. Low heritabilities for pathogen specific-mastitis resistance may be considered when including bacteriological status as a measure of mastitis presence to implement breeding strategies for improving udder health in dairy ewes.

  8. Emancipating Chlamydia: Advances in the Genetic Manipulation of a Recalcitrant Intracellular Pathogen.

    Science.gov (United States)

    Bastidas, Robert J; Valdivia, Raphael H

    2016-06-01

    Chlamydia species infect millions of individuals worldwide and are important etiological agents of sexually transmitted disease, infertility, and blinding trachoma. Historically, the genetic intractability of this intracellular pathogen has hindered the molecular dissection of virulence factors contributing to its pathogenesis. The obligate intracellular life cycle of Chlamydia and restrictions on the use of antibiotics as selectable markers have impeded the development of molecular tools to genetically manipulate these pathogens. However, recent developments in the field have resulted in significant gains in our ability to alter the genome of Chlamydia, which will expedite the elucidation of virulence mechanisms. In this review, we discuss the challenges affecting the development of molecular genetic tools for Chlamydia and the work that laid the foundation for recent advancements in the genetic analysis of this recalcitrant pathogen.

  9. Wildlife translocation: the conservation implications of pathogen exposure and genetic heterozygosity

    Science.gov (United States)

    2011-01-01

    Background A key challenge for conservation biologists is to determine the most appropriate demographic and genetic management strategies for wildlife populations threatened by disease. We explored this topic by examining whether genetic background and previous pathogen exposure influenced survival of translocated animals when captive-bred and free-ranging bighorn sheep (Ovis canadensis) were used to re-establish a population that had been extirpated in the San Andres Mountains in New Mexico, USA. Results Although the free-ranging source population had significantly higher multi-locus heterozygosity at 30 microsatellite loci than the captive bred animals, neither source population nor genetic background significantly influenced survival or cause of death. The presence of antibodies to a respiratory virus known to cause pneumonia was associated with increased survival, but there was no correlation between genetic heterozygosity and the presence of antibodies to this virus. Conclusions Although genetic theory predicts otherwise, increased heterozygosity was not associated with increased fitness (survival) among translocated animals. While heterosis or genetic rescue effects may occur in F1 and later generations as the two source populations interbreed, we conclude that previous pathogen exposure was a more important marker than genetic heterozygosity for predicting survival of translocated animals. Every wildlife translocation is an experiment, and whenever possible, translocations should be designed and evaluated to test hypotheses that will further improve our understanding of how pathogen exposure and genetic variability influence fitness. PMID:21284886

  10. Wildlife translocation: the conservation implications of pathogen exposure and genetic heterozygosity

    Directory of Open Access Journals (Sweden)

    Penedo M Cecilia T

    2011-02-01

    Full Text Available Abstract Background A key challenge for conservation biologists is to determine the most appropriate demographic and genetic management strategies for wildlife populations threatened by disease. We explored this topic by examining whether genetic background and previous pathogen exposure influenced survival of translocated animals when captive-bred and free-ranging bighorn sheep (Ovis canadensis were used to re-establish a population that had been extirpated in the San Andres Mountains in New Mexico, USA. Results Although the free-ranging source population had significantly higher multi-locus heterozygosity at 30 microsatellite loci than the captive bred animals, neither source population nor genetic background significantly influenced survival or cause of death. The presence of antibodies to a respiratory virus known to cause pneumonia was associated with increased survival, but there was no correlation between genetic heterozygosity and the presence of antibodies to this virus. Conclusions Although genetic theory predicts otherwise, increased heterozygosity was not associated with increased fitness (survival among translocated animals. While heterosis or genetic rescue effects may occur in F1 and later generations as the two source populations interbreed, we conclude that previous pathogen exposure was a more important marker than genetic heterozygosity for predicting survival of translocated animals. Every wildlife translocation is an experiment, and whenever possible, translocations should be designed and evaluated to test hypotheses that will further improve our understanding of how pathogen exposure and genetic variability influence fitness.

  11. Coherent spectroscopic methods for monitoring pathogens, genetically modified products and nanostructured materials in colloidal solution

    Science.gov (United States)

    Moguilnaya, T.; Suminov, Y.; Botikov, A.; Ignatov, S.; Kononenko, A.; Agibalov, A.

    2016-12-01

    We developed the new automatic method that combines the method of forced luminescence and stimulated Brillouin scattering. This method is used for monitoring pathogens, genetically modified products and nanostructured materials in colloidal solution. We carried out the statistical spectral analysis of pathogens, genetically modified soy and nano-particles of silver in water from different regions in order to determine the statistical errors of the method. We studied spectral characteristics of these objects in water to perform the initial identification with 95% probability. These results were used for creation of the model of the device for monitor of pathogenic organisms and working model of the device to determine the genetically modified soy in meat.

  12. Coherent spectroscopic methods for monitoring pathogens, genetically modified products and nanostructured materials in colloidal solution

    Directory of Open Access Journals (Sweden)

    Moguilnaya T.

    2017-01-01

    Full Text Available We developed the new automatic method that combines the method of forced luminescence and stimulated Brillouin scattering. This method is used for monitoring pathogens, genetically modified products and nanostructured materials in colloidal solution. We carried out the statistical spectral analysis of pathogens, genetically modified soy and nano-particles of silver in water from different regions in order to determine the statistical errors of the method. We studied spectral characteristics of these objects in water to perform the initial identification with 95% probability. These results were used for creation of the model of the device for monitor of pathogenic organisms and working model of the device to determine the genetically modified soy in meat.

  13. Coherent spectroscopic methods for monitoring pathogens, genetically modified products and nanostructured materials in colloidal solution

    Science.gov (United States)

    Moguilnaya, T.; Suminov, Y.; Botikov, A.; Ignatov, S.; Kononenko, A.; Agibalov, A.

    2017-01-01

    We developed the new automatic method that combines the method of forced luminescence and stimulated Brillouin scattering. This method is used for monitoring pathogens, genetically modified products and nanostructured materials in colloidal solution. We carried out the statistical spectral analysis of pathogens, genetically modified soy and nano-particles of silver in water from different regions in order to determine the statistical errors of the method. We studied spectral characteristics of these objects in water to perform the initial identification with 95% probability. These results were used for creation of the model of the device for monitor of pathogenic organisms and working model of the device to determine the genetically modified soy in meat.

  14. Genetics of Dothistromin Biosynthesis in the Peanut Pathogen Passalora arachidicola

    Directory of Open Access Journals (Sweden)

    Rosie E. Bradshaw

    2010-11-01

    Full Text Available The peanut leaf spot pathogen Passalora arachidicola (Mycosphaerella arachidis is known to produce dothistromin, a mycotoxin related to aflatoxin. This is a feature shared with the pine needle pathogen Dothistroma septosporum (Mycosphaerella pini. Dothistromin biosynthesis in D. septosporum commences at an unusually early stage of growth in culture compared to most other fungal secondary metabolites, and the biosynthetic genes are arranged in fragmented groups, in contrast to aflatoxin gene clusters. Dothistromin biosynthetic genes were identified and studied in P. arachidicola to determine if the attributes described in D. septosporum are shared by another dothistromin-producing species within the Class Dothideomycetes. It was shown that dothistromin biosynthesis is very similar in the two species with regard to gene sequence and gene synteny. Functional complementation of D. septosporum mutants with P. arachidicola dothistromin genes was also possible. These similarities support a vertical mode of dothistromin gene transmission. P. arachidicola also produced dothistromin at an early growth stage in culture, suggesting that this type of regulation pattern may be relevant to the biological role of dothistromin.

  15. Drosophila as a genetic model for studying pathogenic human viruses.

    Science.gov (United States)

    Hughes, Tamara T; Allen, Amanda L; Bardin, Joseph E; Christian, Megan N; Daimon, Kansei; Dozier, Kelsey D; Hansen, Caom L; Holcomb, Lisa M; Ahlander, Joseph

    2012-02-05

    Viruses are infectious particles whose viability is dependent on the cells of living organisms, such as bacteria, plants, and animals. It is of great interest to discover how viruses function inside host cells in order to develop therapies to treat virally infected organisms. The fruit fly Drosophila melanogaster is an excellent model system for studying the molecular mechanisms of replication, amplification, and cellular consequences of human viruses. In this review, we describe the advantages of using Drosophila as a model system to study human viruses, and highlight how Drosophila has been used to provide unique insight into the gene function of several pathogenic viruses. We also propose possible directions for future research in this area.

  16. Wildlife translocation: the conservation implications of pathogen exposure and genetic heterozygosity

    OpenAIRE

    Penedo M Cecilia T; Weisenberger Mara E; Boyce Walter M; Johnson Christine K

    2011-01-01

    Abstract Background A key challenge for conservation biologists is to determine the most appropriate demographic and genetic management strategies for wildlife populations threatened by disease. We explored this topic by examining whether genetic background and previous pathogen exposure influenced survival of translocated animals when captive-bred and free-ranging bighorn sheep (Ovis canadensis) were used to re-establish a population that had been extirpated in the San Andres Mountains in Ne...

  17. Elevated Genetic Diversity in the Emerging Blueberry Pathogen Exobasidium maculosum.

    Directory of Open Access Journals (Sweden)

    Jane E Stewart

    Full Text Available Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus Exobasidium maculosum, is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of E. maculosum in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of E. maculosum are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry (Vaccinium virgatum, highbush blueberry (V. corymbosum, and southern highbush blueberry (V. corymbosum hybrids from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (V. angustifolium from Maine, USA, and Nova Scotia, Canada. Populations of E. maculosum from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall, E. maculosum showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of E. maculosum, but more likely as a result of an increasing

  18. Stable genetic diversity despite parasite and pathogen spread in honey bee colonies

    Science.gov (United States)

    Jara, Laura; Muñoz, Irene; Cepero, Almudena; Martín-Hernández, Raquel; Serrano, José; Higes, Mariano; De la Rúa, Pilar

    2015-10-01

    In the last decades, the rapid spread of diseases, such as varroosis and nosemosis, associated with massive honey bee colonies mortality around the world has significantly decreased the number and size of honey bee populations and possibly their genetic diversity. Here, we compare the genetic diversity of Iberian honey bee colonies in two samplings performed in 2006 and 2010 in relation to the presence of the pathogenic agents Nosema apis, Nosema ceranae, and Varroa destructor in order to determine whether parasite and pathogen spread in honey bee colonies reflects changes in genetic diversity. We found that the genetic diversity remained similar, while the incidence of N. ceranae increased and the incidence of N. apis and V. destructor decreased slightly. These results indicate that the genetic diversity was not affected by the presence of these pathogenic agents in the analyzed period. However, the two groups of colonies with and without Nosema/Varroa detected showed significant genetic differentiation (G test). A detailed analysis of the allelic segregation of microsatellite loci in Nosema/Varroa-negative colonies and parasitized ones revealed two outlier loci related to genes involved in immune response.

  19. Simulating population genetics of pathogen vectors in changing landscapes: guidelines and application with Triatoma brasiliensis.

    Directory of Open Access Journals (Sweden)

    Francois Rebaudo

    2014-08-01

    Full Text Available Understanding the mechanisms that influence the population dynamics and spatial genetic structure of the vectors of pathogens infecting humans is a central issue in tropical epidemiology. In view of the rapid changes in the features of landscape pathogen vectors live in, this issue requires new methods that consider both natural and human systems and their interactions. In this context, individual-based model (IBM simulations represent powerful yet poorly developed approaches to explore the response of pathogen vectors in heterogeneous social-ecological systems, especially when field experiments cannot be performed.We first present guidelines for the use of a spatially explicit IBM, to simulate population genetics of pathogen vectors in changing landscapes. We then applied our model with Triatoma brasiliensis, originally restricted to sylvatic habitats and now found in peridomestic and domestic habitats, posing as the most important Trypanosoma cruzi vector in Northeastern Brazil. We focused on the effects of vector migration rate, maximum dispersal distance and attraction by domestic habitat on T. brasiliensis population dynamics and spatial genetic structure. Optimized for T. brasiliensis using field data pairwise fixation index (FST from microsatellite loci, our simulations confirmed the importance of these three variables to understand vector genetic structure at the landscape level. We then ran prospective scenarios accounting for land-use change (deforestation and urbanization, which revealed that human-induced land-use change favored higher genetic diversity among sampling points.Our work shows that mechanistic models may be useful tools to link observed patterns with processes involved in the population genetics of tropical pathogen vectors in heterogeneous social-ecological landscapes. Our hope is that our study may provide a testable and applicable modeling framework to a broad community of epidemiologists for formulating scenarios of

  20. Stream Flow Prediction by Remote Sensing and Genetic Programming

    Science.gov (United States)

    Chang, Ni-Bin

    2009-01-01

    A genetic programming (GP)-based, nonlinear modeling structure relates soil moisture with synthetic-aperture-radar (SAR) images to present representative soil moisture estimates at the watershed scale. Surface soil moisture measurement is difficult to obtain over a large area due to a variety of soil permeability values and soil textures. Point measurements can be used on a small-scale area, but it is impossible to acquire such information effectively in large-scale watersheds. This model exhibits the capacity to assimilate SAR images and relevant geoenvironmental parameters to measure soil moisture.

  1. Genetic Transformation System for the Fungal Soybean Pathogen Cercospora kikuchii.

    Science.gov (United States)

    Upchurch, R G; Ehrenshaft, M; Walker, D C; Sanders, L A

    1991-10-01

    An altered beta-tubulin gene that confers resistance to the fungicide benomyl was isolated from a genomic library of a UV-induced mutant of Cercospora kikuchii and used as a selectable marker for transformation. The level of benomyl resistance conferred to the transformants was at least 150-fold greater than the intrinsic resistance of the C. kikuchii recipient protoplasts. In the majority of cases, the tubulin fragment was integrated at the native beta-tubulin locus, apparently by gene replacement or gene conversion. The frequency of transformation ranged from 0.2 to 6 transformants per mug of DNA, depending on the recipient strain. Transformation with linearized plasmid resulted in a higher frequency, without changing the type of integration event. Transformants were phenotypically stable after eight consecutive transfers on medium without benomyl. This is the first report of a genetic transformation system for a Cercospora species.

  2. Population genetic structure of the seed pathogen Pyrenophora semeniperda on Bromus tectorum in western North America

    Science.gov (United States)

    David Boose; Steven Harrison; Suzette Clement; Susan E. Meyer

    2011-01-01

    We examined genetic variation in the ascomycete pathogen Pyrenophora semeniperda cultured from seeds of the invasive grass Bromus tectorum in the Intermountain West of North America. We sequenced the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA genome in 417 monoconidial cultures collected from 20 sites in Washington, Idaho, Utah and Colorado,...

  3. Characterizing the Pyrenophora teres f. maculata – barley interaction using pathogen genetics

    Science.gov (United States)

    Pyrenophora teres f. maculata is the cause of the foliar disease spot form net blotch (SFNB) on barley. To evaluate pathogen genetics underlying the P. teres f. maculata- barley interaction, we developed a 105-progeny population by crossing two globally diverse isolates, one from North Dakota, USA a...

  4. Genetic and genomic dissection of resistance genes to the rice sheath blight pathogen

    Science.gov (United States)

    Rice sheath blight disease caused by the anastomosis group AG1-IA of the fungal pathogen Rhizoctonia solani is one of the most serious rice diseases in the southern US and the world. The use of fungicides is a popular but costly method to control this disease worldwide. Genetic analysis of host re...

  5. [Genetic determinants of pathogenicity of opportunistic enterobacteria isolated from children with acute intestinal infections].

    Science.gov (United States)

    Anganova, E V; Dukhanina, A V; Savilov, E D

    2012-01-01

    Detection of nucleotide sequences of genes controlling synthesis of pathogenicity factors in clinical strains of opportunistic enterobacteria isolated from children with acute intestinal infections (AII), as well as their association with resistance to antibiotics and the course of the infectious process. 175 clinical strains obtained from children with AII undergoing treatment in Irkutsk state infectious diseases hospital (2007-2010) were studied. Primers to a number of genes detected in Escherichia coli pathogenicity islands, controlling type S and type 1 adhesion; formation of hemolysins; iron-regulatory protein synthesis; capsule formation were used in the study. PCR products analysis was performed by agar gel electrophoresis. Genetic determinants of pathogenicity were detected in bacteria genera Klebsiella, Citrobacter, Enterobacter, Proteus, Kluyvera, Morganella, Pantoea, Serratia. Fragments of hlyA and hlyB genes (hemolysin production) were detected more frequently; less frequently--sfaA, sfaG, fimA (adhesion), as well as irp-2 gene (synthesis of iron-regulatory protein). The largest set of genetic determinants of pathogenicity was noted in clinical strains of Klebsiella spp. Cultures with DNA fragments specific to genes of E. coli pathogenicity clusters were obtained predominately from children aged up to 3 years, had multiple antibiotic resistance and were isolated significantly more frequently in severe forms of AII when compared with strains in which these determinants were not detected. The studies performed showed that clinical strains of opportunistic bacteria isolated from patients with AII have a certain pathogenic potential, as evidenced by the presence of genetic pathogenicity markers in them.

  6. The mammalian complement system as an epitome of host-pathogen genetic conflicts.

    Science.gov (United States)

    Cagliani, Rachele; Forni, Diego; Filippi, Giulia; Mozzi, Alessandra; De Gioia, Luca; Pontremoli, Chiara; Pozzoli, Uberto; Bresolin, Nereo; Clerici, Mario; Sironi, Manuela

    2016-03-01

    The complement system is an innate immunity effector mechanism; its action is antagonized by a wide array of pathogens and complement evasion determines the virulence of several infections. We investigated the evolutionary history of the complement system and of bacterial-encoded complement-interacting proteins. Complement components targeted by several pathogens evolved under strong selective pressure in primates, with selection acting on residues at the contact interface with microbial/viral proteins. Positively selected sites in CFH and C4BPA account for the human specificity of gonococcal infection. Bacterial interactors, evolved adaptively as well, with selected sites located at interaction surfaces with primate complement proteins. These results epitomize the expectation under a genetic conflict scenario whereby the host's and the pathogen's genes evolve within binding avoidance-binding seeking dynamics. In silico mutagenesis and protein-protein docking analyses supported this by showing that positively selected sites, both in the host's and in the pathogen's interacting partner, modulate binding.

  7. Genetic islands in pome fruit pathogenic and nonpathogenic Erwinia species and related plasmids

    Directory of Open Access Journals (Sweden)

    Pablo eLlop

    2015-08-01

    Full Text Available New pathogenic bacteria species belonging to the genus Erwinia associated with pome fruit trees (Erwinia pyrifoliae, E. piriflorinigrans, E. uzenensis have been increasingly described in the last years, and comparative analyses have found that all these species share several genetic characteristics. Studies at different level (whole genome comparison, virulence genes, plasmid content, etc. show a high intraspecies homogeneity (i.e. among E. amylovora strains and also abundant similarities appear between the different Erwinia species: presence of plasmids of similar size in the pathogenic species; high similarity in several genes associated with exopolysaccharide production and hence, with virulence, as well as in some other genes, in the chromosomes. Many genetic similarities have been observed also among some of the plasmids (and genomes from the pathogenic species and E. tasmaniensis or E. billingiae, two epiphytic species on the same hosts. The amount of genetic material shared in this genus varies from individual genes to clusters, genomic islands and genetic material that even may constitute a whole plasmid. Recent research on evolution of erwinias point out the horizontal transfer acquisition of some genomic islands that were subsequently lost in some species and several pathogenic traits that are still present. How this common material has been obtained and is efficiently maintained in different species belonging to the same genus sharing a common ecological niche provides an idea of the origin and evolution of the pathogenic Erwinia and the interaction with nonpathogenic species present in the same niche, and the role of the genes that are conserved in all of them.

  8. Pseudomonas viridiflava, a multi host plant pathogen with significant genetic variation at the molecular level.

    Directory of Open Access Journals (Sweden)

    Panagiotis F Sarris

    Full Text Available The pectinolytic species Pseudomonas viridiflava has a wide host range among plants, causing foliar and stem necrotic lesions and basal stem and root rots. However, little is known about the molecular evolution of this species. In this study we investigated the intraspecies genetic variation of P. viridiflava amongst local (Cretan, as well as international isolates of the pathogen. The genetic and phenotypic variability were investigated by molecular fingerprinting (rep-PCR and partial sequencing of three housekeeping genes (gyrB, rpoD and rpoB, and by biochemical and pathogenicity profiling. The biochemical tests and pathogenicity profiling did not reveal any variability among the isolates studied. However, the molecular fingerprinting patterns and housekeeping gene sequences clearly differentiated them. In a broader phylogenetic comparison of housekeeping gene sequences deposited in GenBank, significant genetic variability at the molecular level was found between isolates of P. viridiflava originated from different host species as well as among isolates from the same host. Our results provide a basis for more comprehensive understanding of the biology, sources and shifts in genetic diversity and evolution of P. viridiflava populations and should support the development of molecular identification tools and epidemiological studies in diseases caused by this species.

  9. Genetic analysis of pathogen-specific clinical mastitis in Norwegian Red cows.

    Science.gov (United States)

    Haugaard, K; Heringstad, B; Whist, A C

    2012-03-01

    The objective of this study was to estimate heritabilities and genetic correlations for pathogen-specific clinical mastitis (CM) in Norwegian Red cows. In Norway, breeding values for mastitis are predicted based on records of veterinary treatments of clinical mastitis. Bacteriological milk sample results from the mastitis laboratories have been recorded routinely into the Norwegian Dairy Herd Recording System since 2000, but have so far not been used in genetic analyses. This additional source of data may provide valuable information on pathogen-specific CM. Records from 234,088 first-lactation Norwegian Red cows, daughters of 1,656 sires, were used for genetic analyses of unspecific, Staphylococcus aureus, Streptococcus dysgalactiae, and Escherichia coli CM. The 4 CM traits were defined as binary and scored as 1 if the cow had at least 1 case of the CM in question and 0 otherwise. A Bayesian approach using Gibbs sampling was applied, and a multivariate threshold liability model was used for the analyses. The posterior mean (SD ≤ 0.01) of the heritabilities were 0.06 for liability of unspecific CM, 0.04 for Staph. aureus CM, 0.02 for Strep. dysgalactiae CM, and 0.03 for E. coli CM. The posterior mean (SD) of the genetic correlations were all high, ranging from 0.75 (0.14) to 0.87 (0.07). The highest genetic correlation was found between unspecific CM and Strep. dysgalactiae CM, whereas the lowest was found for E. coli CM and Staph. aureus CM. Genetic correlations lower than 1 indicate that mastitis caused by different pathogens can be considered as partly different traits. In spite of high rank correlations (0.95-0.98), some re-ranking of sires was observed. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  10. Genetic correlations between pathogen-specific mastitis and somatic cell count in Danish Holsteins

    DEFF Research Database (Denmark)

    Sørensen, Lars Peter; Mark, Thomas; Madsen, P.;

    2009-01-01

    _170) or 300 d (LASCC_300) after calving, and the mastitis traits were unspecific mastitis (all mastitis treatments, both clinical and subclinical, regardless of the causative pathogen) and mastitis caused by either Streptococcus dysgalactiae, Escherichia coli, coagulase-negative staphylococci (CNS......, especially for Strep. uberis, Strep. dysgalactiae, and CNS and, to a lesser extent, for Staph. aureus and E. coli. Data recording should preferably be improved, and economic weights for the pathogen-specific mastitis traits should be estimated before implementing an udder health index that includes pathogen....... uberis, and E. coli (r(a) = 0.54 to 0.69) and were lowest for Staph. aureus mastitis (r(a) = 0.44). The genetic correlation between LASCC_300 and the mastitis traits were generally smaller (r(a) = 0.47 to 0.69). Caution should be taken when interpreting the results, however, because some posterior...

  11. Genetics of Resistance and Pathogenicity in the Maize/Setosphaeria turcica Pathosystem and Implications for Breeding

    Directory of Open Access Journals (Sweden)

    Ana L. Galiano-Carneiro

    2017-08-01

    Full Text Available Northern corn leaf blight (NCLB, the most devastating leaf pathogen in maize (Zea mays L., is caused by the heterothallic ascomycete Setosphaeria turcica. The pathogen population shows an extremely high genetic diversity in tropical and subtropical regions. Varietal resistance is the most efficient technique to control NCLB. Host resistance can be qualitative based on race-specific Ht genes or quantitative controlled by many genes with small effects. Quantitative resistance is moderately to highly effective and should be more durable combatting all races of the pathogen. Quantitative resistance must, however, be analyzed in many environments (= location × year combinations to select stable resistances. In the tropical and subtropical environments, quantitative resistance is the preferred option to manage NCLB epidemics. Resistance level can be increased in practical breeding programs by several recurrent selection cycles based on disease severity rating and/or by genomic selection. This review aims to address two important aspects of the NCLB pathosystem: the genetics of the fungus S. turcica and the modes of inheritance of the host plant maize, including successful breeding strategies regarding NCLB resistance. Both drivers of this pathosystem, pathogen, and host, must be taken into account to result in more durable resistance.

  12. Molecular Identification and Genetic Characterization of Macrophomina phaseolina Strains Causing Pathogenicity on Sunflower and Chickpea

    Directory of Open Access Journals (Sweden)

    Ali N. Khan

    2017-07-01

    Full Text Available Macrophomina phaseolina is the most devastating pathogen which causes charcoal rot and root rot diseases in various economically important crops. Three strains M. phaseolina 1156, M. phaseolina 1160, and M. phaseolina PCMC/F1 were tested for their virulence on sunflower (Helianthus annuus L. and chickpea (Cicer arietinum L.. The strains showed high virulence on both hosts with a disease score of 2 on chickpea and sunflower. The strains also increased the hydrogen per oxide (H2O2 content by 1.4- to 1.6-fold in root as well as shoot of chickpea and sunflower. A significant increase in antioxidant enzymes was observed in fungal infected plants which indicated prevalence of oxidative stress during pathogen propagation. The M. phaseolina strains also produced hydrolytic enzymes such as lipase, amylase, and protease with solubilization zone of 5–43 mm, 5–45 mm, and 12–35 mm, respectively. The M. phaseolina strains were identified by 18S rRNA and analyzed for genetic diversity by using random amplified polymorphic DNA (RAPD markers. The findings based on RAPD markers and 18S rRNA sequence analysis clearly indicate genetic variation among the strains collected from different hosts. The genetically diverse strains were found to be pathogenic to sunflower and chickpea.

  13. Molecular Identification and Genetic Characterization of Macrophomina phaseolina Strains Causing Pathogenicity on Sunflower and Chickpea.

    Science.gov (United States)

    Khan, Ali N; Shair, Faluk; Malik, Kamran; Hayat, Zafar; Khan, Muhammad Ayub; Hafeez, Fauzia Yusuf; Hassan, Muhammad Nadeem

    2017-01-01

    Macrophomina phaseolina is the most devastating pathogen which causes charcoal rot and root rot diseases in various economically important crops. Three strains M. phaseolina 1156, M. phaseolina 1160, and M. phaseolina PCMC/F1 were tested for their virulence on sunflower (Helianthus annuus L.) and chickpea (Cicer arietinum L.). The strains showed high virulence on both hosts with a disease score of 2 on chickpea and sunflower. The strains also increased the hydrogen per oxide (H2O2) content by 1.4- to 1.6-fold in root as well as shoot of chickpea and sunflower. A significant increase in antioxidant enzymes was observed in fungal infected plants which indicated prevalence of oxidative stress during pathogen propagation. The M. phaseolina strains also produced hydrolytic enzymes such as lipase, amylase, and protease with solubilization zone of 5-43 mm, 5-45 mm, and 12-35 mm, respectively. The M. phaseolina strains were identified by 18S rRNA and analyzed for genetic diversity by using random amplified polymorphic DNA (RAPD) markers. The findings based on RAPD markers and 18S rRNA sequence analysis clearly indicate genetic variation among the strains collected from different hosts. The genetically diverse strains were found to be pathogenic to sunflower and chickpea.

  14. Coping with genetic diversity: the contribution of pathogen and human genomics to modern vaccinology

    Energy Technology Data Exchange (ETDEWEB)

    Lemaire, D. [Universidade Federal da Bahia and Universidade Estadual da Bahia, Salvador, BA (Brazil); Barbosa, T. [Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, BA (Brazil); Rihet, P. [TAGC-INSERM U928, Aix-Marseille Université, Marseille (France)

    2011-10-28

    Vaccine development faces major difficulties partly because of genetic variation in both infectious organisms and humans. This causes antigenic variation in infectious agents and a high interindividual variability in the human response to the vaccine. The exponential growth of genome sequence information has induced a shift from conventional culture-based to genome-based vaccinology, and allows the tackling of challenges in vaccine development due to pathogen genetic variability. Additionally, recent advances in immunogenetics and genomics should help in the understanding of the influence of genetic factors on the interindividual and interpopulation variations in immune responses to vaccines, and could be useful for developing new vaccine strategies. Accumulating results provide evidence for the existence of a number of genes involved in protective immune responses that are induced either by natural infections or vaccines. Variation in immune responses could be viewed as the result of a perturbation of gene networks; this should help in understanding how a particular polymorphism or a combination thereof could affect protective immune responses. Here we will present: i) the first genome-based vaccines that served as proof of concept, and that provided new critical insights into vaccine development strategies; ii) an overview of genetic predisposition in infectious diseases and genetic control in responses to vaccines; iii) population genetic differences that are a rationale behind group-targeted vaccines; iv) an outlook for genetic control in infectious diseases, with special emphasis on the concept of molecular networks that will provide a structure to the huge amount of genomic data.

  15. Alternative Fuzzy Cluster Segmentation of Remote Sensing Images Based on Adaptive Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    WANG Jing; TANG Jilong; LIU Jibin; REN Chunying; LIU Xiangnan; FENG Jiang

    2009-01-01

    Remote sensing image segmentation is the basis of image understanding and analysis. However, the precision and the speed of segmentation can not meet the need of image analysis, due to strong uncertainty and rich texture details of remote sensing images. We proposed a new segmentation method based on Adaptive Genetic Algorithm (AGA) and Alternative Fuzzy C-Means (AFCM). Segmentation thresholds were identified by AGA. Then the image was segmented by AFCM. The results indicate that the precision and the speed of segmentation have been greatly increased, and the accuracy of threshold selection is much higher compared with traditional Otsu and Fuzzy C-Means (FCM) segmentation methods. The segmentation results also show that multi-thresholds segmentation has been achieved by combining AGA with AFCM.

  16. Genetic Evidence for Elevated Pathogenicity of Mitochondrial DNA Heteroplasmy in Autism Spectrum Disorder.

    Directory of Open Access Journals (Sweden)

    Yiqin Wang

    2016-10-01

    Full Text Available Increasing clinical and biochemical evidence implicate mitochondrial dysfunction in the pathophysiology of Autism Spectrum Disorder (ASD, but little is known about the biological basis for this connection. A possible cause of ASD is the genetic variation in the mitochondrial DNA (mtDNA sequence, which has yet to be thoroughly investigated in large genomic studies of ASD. Here we evaluated mtDNA variation, including the mixture of different mtDNA molecules in the same individual (i.e., heteroplasmy, using whole-exome sequencing data from mother-proband-sibling trios from simplex families (n = 903 where only one child is affected by ASD. We found that heteroplasmic mutations in autistic probands were enriched at non-polymorphic mtDNA sites (P = 0.0015, which were more likely to confer deleterious effects than heteroplasmies at polymorphic mtDNA sites. Accordingly, we observed a ~1.5-fold enrichment of nonsynonymous mutations (P = 0.0028 as well as a ~2.2-fold enrichment of predicted pathogenic mutations (P = 0.0016 in autistic probands compared to their non-autistic siblings. Both nonsynonymous and predicted pathogenic mutations private to probands conferred increased risk of ASD (Odds Ratio, OR[95% CI] = 1.87[1.14-3.11] and 2.55[1.26-5.51], respectively, and their influence on ASD was most pronounced in families with probands showing diminished IQ and/or impaired social behavior compared to their non-autistic siblings. We also showed that the genetic transmission pattern of mtDNA heteroplasmies with high pathogenic potential differed between mother-autistic proband pairs and mother-sibling pairs, implicating developmental and possibly in utero contributions. Taken together, our genetic findings substantiate pathogenic mtDNA mutations as a potential cause for ASD and synergize with recent work calling attention to their unique metabolic phenotypes for diagnosis and treatment of children with ASD.

  17. Genetic Evidence for Elevated Pathogenicity of Mitochondrial DNA Heteroplasmy in Autism Spectrum Disorder

    Science.gov (United States)

    Wang, Yiqin; Picard, Martin; Gu, Zhenglong

    2016-01-01

    Increasing clinical and biochemical evidence implicate mitochondrial dysfunction in the pathophysiology of Autism Spectrum Disorder (ASD), but little is known about the biological basis for this connection. A possible cause of ASD is the genetic variation in the mitochondrial DNA (mtDNA) sequence, which has yet to be thoroughly investigated in large genomic studies of ASD. Here we evaluated mtDNA variation, including the mixture of different mtDNA molecules in the same individual (i.e., heteroplasmy), using whole-exome sequencing data from mother-proband-sibling trios from simplex families (n = 903) where only one child is affected by ASD. We found that heteroplasmic mutations in autistic probands were enriched at non-polymorphic mtDNA sites (P = 0.0015), which were more likely to confer deleterious effects than heteroplasmies at polymorphic mtDNA sites. Accordingly, we observed a ~1.5-fold enrichment of nonsynonymous mutations (P = 0.0028) as well as a ~2.2-fold enrichment of predicted pathogenic mutations (P = 0.0016) in autistic probands compared to their non-autistic siblings. Both nonsynonymous and predicted pathogenic mutations private to probands conferred increased risk of ASD (Odds Ratio, OR[95% CI] = 1.87[1.14–3.11] and 2.55[1.26–5.51], respectively), and their influence on ASD was most pronounced in families with probands showing diminished IQ and/or impaired social behavior compared to their non-autistic siblings. We also showed that the genetic transmission pattern of mtDNA heteroplasmies with high pathogenic potential differed between mother-autistic proband pairs and mother-sibling pairs, implicating developmental and possibly in utero contributions. Taken together, our genetic findings substantiate pathogenic mtDNA mutations as a potential cause for ASD and synergize with recent work calling attention to their unique metabolic phenotypes for diagnosis and treatment of children with ASD. PMID:27792786

  18. Genetic Diversity of Tick-Borne Rickettsial Pathogens; Insights Gained from Distant Strains

    Directory of Open Access Journals (Sweden)

    Sebastián Aguilar Pierlé

    2014-01-01

    Full Text Available The ability to capture genetic variation with unprecedented resolution improves our understanding of bacterial populations and their ability to cause disease. The goal of the pathogenomics era is to define genetic diversity that results in disease. Despite the economic losses caused by vector-borne bacteria in the Order Rickettsiales, little is known about the genetic variants responsible for observed phenotypes. The tick-transmitted rickettsial pathogen Anaplasma marginale infects cattle in tropical and subtropical regions worldwide, including Australia. Genomic analysis of North American A. marginale strains reveals a closed core genome defined by high levels of Single Nucleotide Polymorphisms (SNPs. Here we report the first genome sequences and comparative analysis for Australian strains that differ in virulence and transmissibility. A list of genetic differences that segregate with phenotype was evaluated for the ability to distinguish the attenuated strain from virulent field strains. Phylogenetic analyses of the Australian strains revealed a marked evolutionary distance from all previously sequenced strains. SNP analysis showed a strikingly reduced genetic diversity between these strains, with the smallest number of SNPs detected between any two A. marginale strains. The low diversity between these phenotypically distinct bacteria presents a unique opportunity to identify the genetic determinants of virulence and transmission.

  19. SSR-based detection of genetic variability in the charcoal root rot pathogen Macrophomina phaseolina.

    Science.gov (United States)

    Jana, Tarakanta; Sharma, Tilak R; Singh, Nagendra K

    2005-01-01

    Macrophomina phaseolina, the causal agent of charcoal root or collar rot, is an important plant pathogen especially in soybean and cotton. Single primers of simple sequence repeats (SSR) or microsatellite markers have been used for the characterization of genetic variability of different populations of M. phaseolina obtained from soybean and cotton grown in India and the USA. Genetic similarity between isolates was calculated, and cluster analysis was used to generate a dendrogram showing relationships between isolates collected from the two hosts. Forty isolates could be clustered into three major groups corresponding to their hosts and geographical region. The wide distribution of microsatellites in M. phaseolina genome was assessed by agarose gel electrophoresis of the PCR products generated by direct amplification of inter SSR regions DNA. This is the first report of the use of microsatellite markers to characterize the charcoal root rot pathogen. The SSR fingerprints (0.25-3.5 kb) generated using DNA from different populations of M. phaseolina of two hosts indicated that these repeats are interspersed within the genome of this pathogen. The variability found within closely related isolates of M. phaseolina indicated that such microsatellites are useful in population studies and represents a step towards identification of potential isolate diagnostic markers specific to soybean and cotton.

  20. Characterization of Fusarium verticillioides strains isolated from maize in Italy: fumonisin production, pathogenicity and genetic variability.

    Science.gov (United States)

    Covarelli, Lorenzo; Stifano, Simonetta; Beccari, Giovanni; Raggi, Lorenzo; Lattanzio, Veronica Maria Teresa; Albertini, Emidio

    2012-08-01

    Fusarium verticillioides (teleomorph Gibberella moniliformis) is the main fungal agent of ear and kernel rot of maize (Zea mays L.) worldwide, including Italy. F.verticillioides is a highly toxigenic species since it is able to produce the carcinogenic mycotoxins fumonisins. In this study, 25 F. verticillioides strains, isolated from maize in different regions of Italy were analyzed for their ability to produce fumonisins, their pathogenicity and their genetic variability. A further referenced strain of G. moniliformis isolated from maize in USA was also used as outgroup. The fumonisins B₁, B₂, and B₃ were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Pathogenicity tests were carried out by symptom observation and determination of growth parameters after inoculation of maize seeds, seedlings and wounded detached leaves. Total genomic DNA was used for Amplified Fragment Length Polymorphism (AFLP) analysis. About 20% of the analyzed strains were unable to produce fumonisins in in vitro experiments on inoculated maize flour, while, among fumonisin producers, a great variability was observed, with values ranging from 1 to 115 mg kg⁻¹. The different analyzed strains showed a wide range of pathogenicity in terms of effect on seed germination, seedling development and of symptoms produced on detached leaves, which were not correlated with the different in vitro fumonisin production. AFLP analysis indicated the presence of genetic diversity not only between the Italian strains and the American reference but also among the Italian isolates. Copyright © 2012 Elsevier Ltd. All rights reserved.

  1. Pathogenic ischemic stroke phenotypes in the NINDS-stroke genetics network.

    Science.gov (United States)

    Ay, Hakan; Arsava, Ethem Murat; Andsberg, Gunnar; Benner, Thomas; Brown, Robert D; Chapman, Sherita N; Cole, John W; Delavaran, Hossein; Dichgans, Martin; Engström, Gunnar; Giralt-Steinhauer, Eva; Grewal, Raji P; Gwinn, Katrina; Jern, Christina; Jimenez-Conde, Jordi; Jood, Katarina; Katsnelson, Michael; Kissela, Brett; Kittner, Steven J; Kleindorfer, Dawn O; Labovitz, Daniel L; Lanfranconi, Silvia; Lee, Jin-Moo; Lehm, Manuel; Lemmens, Robin; Levi, Chris; Li, Linxin; Lindgren, Arne; Markus, Hugh S; McArdle, Patrick F; Melander, Olle; Norrving, Bo; Peddareddygari, Leema Reddy; Pedersén, Annie; Pera, Joanna; Rannikmäe, Kristiina; Rexrode, Kathryn M; Rhodes, David; Rich, Stephen S; Roquer, Jaume; Rosand, Jonathan; Rothwell, Peter M; Rundek, Tatjana; Sacco, Ralph L; Schmidt, Reinhold; Schürks, Markus; Seiler, Stephan; Sharma, Pankaj; Slowik, Agnieszka; Sudlow, Cathie; Thijs, Vincent; Woodfield, Rebecca; Worrall, Bradford B; Meschia, James F

    2014-12-01

    NINDS (National Institute of Neurological Disorders and Stroke)-SiGN (Stroke Genetics Network) is an international consortium of ischemic stroke studies that aims to generate high-quality phenotype data to identify the genetic basis of pathogenic stroke subtypes. This analysis characterizes the etiopathogenetic basis of ischemic stroke and reliability of stroke classification in the consortium. Fifty-two trained and certified adjudicators determined both phenotypic (abnormal test findings categorized in major pathogenic groups without weighting toward the most likely cause) and causative ischemic stroke subtypes in 16 954 subjects with imaging-confirmed ischemic stroke from 12 US studies and 11 studies from 8 European countries using the web-based Causative Classification of Stroke System. Classification reliability was assessed with blinded readjudication of 1509 randomly selected cases. The distribution of pathogenic categories varied by study, age, sex, and race (Pstroke pathogenesis (phenotypic subtype) were classified into the same final causative category with high confidence. There was good agreement for both causative (κ 0.72; 95% confidence interval, 0.69-0.75) and phenotypic classifications (κ 0.73; 95% confidence interval, 0.70-0.75). This study demonstrates that pathogenic subtypes can be determined with good reliability in studies that include investigators with different expertise and background, institutions with different stroke evaluation protocols and geographic location, and patient populations with different epidemiological characteristics. The discordance between phenotypic and causative stroke subtypes highlights the fact that the presence of an abnormality in a patient with stroke does not necessarily mean that it is the cause of stroke. © 2014 American Heart Association, Inc.

  2. Advances in Human Mitochondrial Diseases Molecular Genetic Analysis of Pathogenic mtDNA Mutations.

    Science.gov (United States)

    Davidson, E; King, M P

    1997-01-01

    The mitochondrial diseases are a heterogeneous group of disorders that have been defined by specific morphological alterations in muscle and by deficits of the mitochondrial respiratory chain. The morphological hallmarks of these diseases include ragged-red fibers (an extensive proliferation of mitochondria in muscle fibers) and abnormal paracrystalline inclusions and membrane structures in mitochondria. The identification of pathogenic mutations in mitochondrial DNA (mtDNA) has resulted in a genetic classification of mitochondrial diseases. Investigations are being conducted to understand the molecular basis for the biochemical and morphological alterations of mitochondria associated with mtDNA mutations. © 1997, Elsevier Science Inc. (Trends Cardiovasc Med 1997;7:16-24).

  3. Coping with genetic diversity: the contribution of pathogen and human genomics to modern vaccinology

    Directory of Open Access Journals (Sweden)

    D. Lemaire

    2012-05-01

    Full Text Available Vaccine development faces major difficulties partly because of genetic variation in both infectious organisms and humans. This causes antigenic variation in infectious agents and a high interindividual variability in the human response to the vaccine. The exponential growth of genome sequence information has induced a shift from conventional culture-based to genome-based vaccinology, and allows the tackling of challenges in vaccine development due to pathogen genetic variability. Additionally, recent advances in immunogenetics and genomics should help in the understanding of the influence of genetic factors on the interindividual and interpopulation variations in immune responses to vaccines, and could be useful for developing new vaccine strategies. Accumulating results provide evidence for the existence of a number of genes involved in protective immune responses that are induced either by natural infections or vaccines. Variation in immune responses could be viewed as the result of a perturbation of gene networks; this should help in understanding how a particular polymorphism or a combination thereof could affect protective immune responses. Here we will present: i the first genome-based vaccines that served as proof of concept, and that provided new critical insights into vaccine development strategies; ii an overview of genetic predisposition in infectious diseases and genetic control in responses to vaccines; iii population genetic differences that are a rationale behind group-targeted vaccines; iv an outlook for genetic control in infectious diseases, with special emphasis on the concept of molecular networks that will provide a structure to the huge amount of genomic data.

  4. Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution.

    Science.gov (United States)

    Fumagalli, Matteo; Sironi, Manuela; Pozzoli, Uberto; Ferrer-Admetlla, Anna; Ferrer-Admettla, Anna; Pattini, Linda; Nielsen, Rasmus

    2011-11-01

    Previous genome-wide scans of positive natural selection in humans have identified a number of non-neutrally evolving genes that play important roles in skin pigmentation, metabolism, or immune function. Recent studies have also shown that a genome-wide pattern of local adaptation can be detected by identifying correlations between patterns of allele frequencies and environmental variables. Despite these observations, the degree to which natural selection is primarily driven by adaptation to local environments, and the role of pathogens or other ecological factors as selective agents, is still under debate. To address this issue, we correlated the spatial allele frequency distribution of a large sample of SNPs from 55 distinct human populations to a set of environmental factors that describe local geographical features such as climate, diet regimes, and pathogen loads. In concordance with previous studies, we detected a significant enrichment of genic SNPs, and particularly non-synonymous SNPs associated with local adaptation. Furthermore, we show that the diversity of the local pathogenic environment is the predominant driver of local adaptation, and that climate, at least as measured here, only plays a relatively minor role. While background demography by far makes the strongest contribution in explaining the genetic variance among populations, we detected about 100 genes which show an unexpectedly strong correlation between allele frequencies and pathogenic environment, after correcting for demography. Conversely, for diet regimes and climatic conditions, no genes show a similar correlation between the environmental factor and allele frequencies. This result is validated using low-coverage sequencing data for multiple populations. Among the loci targeted by pathogen-driven selection, we found an enrichment of genes associated to autoimmune diseases, such as celiac disease, type 1 diabetes, and multiples sclerosis, which lends credence to the hypothesis that some

  5. Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution.

    Directory of Open Access Journals (Sweden)

    Matteo Fumagalli

    2011-11-01

    Full Text Available Previous genome-wide scans of positive natural selection in humans have identified a number of non-neutrally evolving genes that play important roles in skin pigmentation, metabolism, or immune function. Recent studies have also shown that a genome-wide pattern of local adaptation can be detected by identifying correlations between patterns of allele frequencies and environmental variables. Despite these observations, the degree to which natural selection is primarily driven by adaptation to local environments, and the role of pathogens or other ecological factors as selective agents, is still under debate. To address this issue, we correlated the spatial allele frequency distribution of a large sample of SNPs from 55 distinct human populations to a set of environmental factors that describe local geographical features such as climate, diet regimes, and pathogen loads. In concordance with previous studies, we detected a significant enrichment of genic SNPs, and particularly non-synonymous SNPs associated with local adaptation. Furthermore, we show that the diversity of the local pathogenic environment is the predominant driver of local adaptation, and that climate, at least as measured here, only plays a relatively minor role. While background demography by far makes the strongest contribution in explaining the genetic variance among populations, we detected about 100 genes which show an unexpectedly strong correlation between allele frequencies and pathogenic environment, after correcting for demography. Conversely, for diet regimes and climatic conditions, no genes show a similar correlation between the environmental factor and allele frequencies. This result is validated using low-coverage sequencing data for multiple populations. Among the loci targeted by pathogen-driven selection, we found an enrichment of genes associated to autoimmune diseases, such as celiac disease, type 1 diabetes, and multiples sclerosis, which lends credence to the

  6. Potential applications of cryogenic technologies to plant genetic improvement and pathogen eradication.

    Science.gov (United States)

    Wang, Biao; Wang, Ren-Rui; Cui, Zhen-Hua; Bi, Wen-Lu; Li, Jing-Wei; Li, Bai-Quan; Ozudogru, Elif Aylin; Volk, Gayle M; Wang, Qiao-Chun

    2014-01-01

    Rapid increases in human populations provide a great challenge to ensure that adequate quantities of food are available. Sustainable development of agricultural production by breeding more productive cultivars and by increasing the productive potential of existing cultivars can help meet this demand. The present paper provides information on the potential uses of cryogenic techniques in ensuring food security, including: (1) long-term conservation of a diverse germplasm and successful establishment of cryo-banks; (2) maintenance of the regenerative ability of embryogenic tissues that are frequently the target for genetic transformation; (3) enhancement of genetic transformation and plant regeneration of transformed cells, and safe, long-term conservation for transgenic materials; (4) production and maintenance of viable protoplasts for transformation and somatic hybridization; and (5) efficient production of pathogen-free plants. These roles demonstrate that cryogenic technologies offer opportunities to ensure food security. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Application of reverse genetics for producing attenuated vaccine strains against highly pathogenic avian influenza viruses.

    Science.gov (United States)

    Uchida, Yuko; Takemae, Nobuhiro; Saito, Takehiko

    2014-08-01

    In this study, reverse genetics was applied to produce vaccine candidate strains against highly pathogenic avian influenza viruses (HPAIVs) of the H5N1 subtype. The H5 subtype vaccine strains were generated by a reverse genetics method in a biosafety level 2 facility. The strain contained the HA gene from the H5N1 subtype HPAIV attenuated by genetic modification at the cleavage site, the NA gene derived from the H5N1 subtype HPAI or the H5N3 subtype of avian influenza virus and internal genes from A/Puerto Rico/8/34. Vaccination with an inactivated recombinant virus with oil-emulsion completely protected chickens from a homologous viral challenge with a 640 HAU or 3,200 HAU/vaccination dose. Vaccination with a higher dose of antigen, 3,200 HAU, was effective at increasing survival and efficiently reduced viral shedding even when challenged by a virus of a different HA clade. The feasibility of differentiation of infected from vaccinated animals (DIVA) was demonstrated against a challenge with H5N1 HPAIVs when the recombinant H5N3 subtype viruses were used as the antigens of the vaccine. Our study demonstrated that the use of reverse genetics would be an option to promptly produce an inactivated vaccine with better matching of antigenicity to a circulating strain.

  8. Genetic Predisposition To Acquire a Polybasic Cleavage Site for Highly Pathogenic Avian Influenza Virus Hemagglutinin

    Science.gov (United States)

    Nao, Naganori; Yamagishi, Junya; Miyamoto, Hiroko; Igarashi, Manabu; Manzoor, Rashid; Ohnuma, Aiko; Tsuda, Yoshimi; Furuyama, Wakako; Shigeno, Asako; Kajihara, Masahiro; Kishida, Noriko; Yoshida, Reiko

    2017-01-01

    ABSTRACT Highly pathogenic avian influenza viruses with H5 and H7 hemagglutinin (HA) subtypes evolve from low-pathogenic precursors through the acquisition of multiple basic amino acid residues at the HA cleavage site. Although this mechanism has been observed to occur naturally only in these HA subtypes, little is known about the genetic basis for the acquisition of the polybasic HA cleavage site. Here we show that consecutive adenine residues and a stem-loop structure, which are frequently found in the viral RNA region encoding amino acids around the cleavage site of low-pathogenic H5 and H7 viruses isolated from waterfowl reservoirs, are important for nucleotide insertions into this RNA region. A reporter assay to detect nontemplated nucleotide insertions and deep-sequencing analysis of viral RNAs revealed that an increased number of adenine residues and enlarged stem-loop structure in the RNA region accelerated the multiple adenine and/or guanine insertions required to create codons for basic amino acids. Interestingly, nucleotide insertions associated with the HA cleavage site motif were not observed principally in the viral RNA of other subtypes tested (H1, H2, H3, and H4). Our findings suggest that the RNA editing-like activity is the key mechanism for nucleotide insertions, providing a clue as to why the acquisition of the polybasic HA cleavage site is restricted to the particular HA subtypes. PMID:28196963

  9. GENETIC VARIABILITY ASSESSMENT OF FUSARIUM WILT PATHOGEN RACES AFFECTING CHICKPEA USING MOLECULAR MARKERS

    Directory of Open Access Journals (Sweden)

    Jhuma Datta

    2013-06-01

    Full Text Available Genetic diversity in Chickpea wilt pathogen has been characterized using 14 isolates of Fusarium oxysporum f. sp. ciceri (foc collected from major pulse growing regions of India. Out of 247 bands produced by 24 Random Amplified Polymorphic DNA (RAPD primers in Foc isolates, 210 (85% were polymorphic. A maximum of 14 amplicons were generated by primer OPF 05 whereas minimum 7 amplicons were generated by primer K7. A total of 24 alleles were produced by twelve simple sequence repeat (SSR primers with an average of two alleles per marker in foc isolates. The maximum number of 4 alleles was obtained with primer SSR 12. SSR amplicon size ranged from 100 to 400 bp. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA cluster analysis based on RAPD and SSR profiles grouped the fourteen foc isolates into four major clusters. The universal Inter Transcribed Spacer (ITS primer pair amplified 630 bp bands in all fourteen foc isolates while significant length polymorphism was obtained only when analysed by restriction digestion with EcoRI and MspI enzymes. The cluster analysis of ITS-RFLP grouped all 14 Foc isolates into three major clusters. The cluster analysis using RAPD, SSR and ITS-RFLP markers show the grouping of Fusarium isolates strictly according to their cultural characteristics and degree of pathogenicity and not the geographical origin. This information will be helpful for pathologists and plant breeders to design effective resistance breeding programs in chickpea taking into account the diversity in wilt pathogen.

  10. Are all the previously reported genetic variants in limb girdle muscular dystrophy genes pathogenic?

    Science.gov (United States)

    Di Fruscio, Giuseppina; Garofalo, Arcomaria; Mutarelli, Margherita; Savarese, Marco; Nigro, Vincenzo

    2016-01-01

    Hundreds of variants in autosomal genes associated with the limb girdle muscular dystrophies (LGMDs) have been reported as being causative. However, in most cases the proof of pathogenicity derives from their non-occurrence in hundreds of healthy controls and/or from segregation studies in small families. The limited statistics of the genetic variations in the general population may hamper a correct interpretation of the effect of variants on the protein. To clarify the meaning of low-frequency variants in LGMD genes, we have selected all variants described as causative in the Leiden Open Variation Database and the Human Gene Mutation Database. We have systematically searched for their frequency in the NHLBI GO Exome Sequencing Project (ESP) and in our internal database. Surprisingly, the ESP contains about 4% of the variants previously associated with a dominant inheritance and about 9% of those associated with a recessive inheritance. The putative disease alleles are much more frequent than those estimated considering the disease prevalence. In conclusion, we hypothesize that a number of disease-associated variants are non-pathogenic and that other variations are not fully penetrant, even if they affect the protein function, suggesting a more complex genetic mechanisms for such heterogeneous disorders.

  11. Genetic differentiation of charcoal rot pathogen, Macrophomina phaseolina, into specific groups using URP-PCR.

    Science.gov (United States)

    Jana, T K; Singh, N K; Koundal, K R; Sharma, T R

    2005-02-01

    Forty isolates of Macrophomina phaseolina, a pathogen causing charcoal dry root rot of soybean, cotton, and chickpea, were genetically characterized with universal rice primers (URP; primers derived from DNA repeat sequences in the rice genome) using polymerase chain reaction (URP-PCR). Out of 12 URPs used in this study, 5 primers were effective in producing polymorphic fingerprint patterns from the DNA of M. phaseolina isolates. Three primers (URP-2F, URP-6R, and URP-30F) were quite informative and produced high levels of polymorphism among the isolates of M. phaseolina. Analysis of the entire fingerprint profiles using unweighted pair-group method with arithmetic averages (UPGMA) clearly differentiated M. phaseolina isolates obtained from soybean, cotton, and chickpea hosts into specific groups. In this study, we found for the first time transferability and use of PCR primers derived from plant genomes to generate host-specific fingerprint profiles of M. phaseolina, a broad host range plant pathogenic fungus. These results demonstrate that URPs are sensitive and technically simple to use for assaying genetic variability in M. phaseolina populations.

  12. Genetic Predisposition To Acquire a Polybasic Cleavage Site for Highly Pathogenic Avian Influenza Virus Hemagglutinin.

    Science.gov (United States)

    Nao, Naganori; Yamagishi, Junya; Miyamoto, Hiroko; Igarashi, Manabu; Manzoor, Rashid; Ohnuma, Aiko; Tsuda, Yoshimi; Furuyama, Wakako; Shigeno, Asako; Kajihara, Masahiro; Kishida, Noriko; Yoshida, Reiko; Takada, Ayato

    2017-02-14

    Highly pathogenic avian influenza viruses with H5 and H7 hemagglutinin (HA) subtypes evolve from low-pathogenic precursors through the acquisition of multiple basic amino acid residues at the HA cleavage site. Although this mechanism has been observed to occur naturally only in these HA subtypes, little is known about the genetic basis for the acquisition of the polybasic HA cleavage site. Here we show that consecutive adenine residues and a stem-loop structure, which are frequently found in the viral RNA region encoding amino acids around the cleavage site of low-pathogenic H5 and H7 viruses isolated from waterfowl reservoirs, are important for nucleotide insertions into this RNA region. A reporter assay to detect nontemplated nucleotide insertions and deep-sequencing analysis of viral RNAs revealed that an increased number of adenine residues and enlarged stem-loop structure in the RNA region accelerated the multiple adenine and/or guanine insertions required to create codons for basic amino acids. Interestingly, nucleotide insertions associated with the HA cleavage site motif were not observed principally in the viral RNA of other subtypes tested (H1, H2, H3, and H4). Our findings suggest that the RNA editing-like activity is the key mechanism for nucleotide insertions, providing a clue as to why the acquisition of the polybasic HA cleavage site is restricted to the particular HA subtypes.IMPORTANCE Influenza A viruses are divided into subtypes based on the antigenicity of the viral surface glycoproteins hemagglutinin (HA) and neuraminidase. Of the 16 HA subtypes (H1 to -16) maintained in waterfowl reservoirs of influenza A viruses, H5 and H7 viruses often become highly pathogenic through the acquisition of multiple basic amino acid residues at the HA cleavage site. Although this mechanism has been known since the 1980s, the genetic basis for nucleotide insertions has remained unclear. This study shows the potential role of the viral RNA secondary structure for

  13. Genetic diversity of Salmonella pathogenicity islands SPI-5 and SPI-6 in Salmonella Newport.

    Science.gov (United States)

    Cao, Guojie; Allard, Marc; Strain, Errol; Stones, Robert; Zhao, Shaohua; Brown, Eric; Meng, Jianghong

    2014-10-01

    Salmonella enterica subspecies enterica serotype Newport is one of the common serotypes causing foodborne salmonellosis outbreaks in the United States. Salmonella Newport consists of three lineages exhibiting extensive genetic diversity. Due to the importance of Salmonella pathogenicity islands 5 and 6 (SPI-5 and SPI-6) in virulence of pathogenic Salmonella, the genetic diversity of these two SPIs may relate to different potentials of Salmonella Newport pathogenicity. Most Salmonella Newport strains from North America belong to Salmonella Newport lineages II and III. A total 28 Salmonella Newport strains of lineages II and III from diverse sources and geographic locations were analyzed, and 11 additional Salmonella genomes were used as outgroup in phylogenetic analyses. SPI-5 was identified in all Salmonella Newport strains and 146 single nucleotide polymorphisms (SNPs) were detected. Thirty-nine lineage-defining SNPs were identified, including 18 nonsynonymous SNPs. Two 40-kb genomic islands (SPI5-GI1 and SPI5-GI2) encoding bacteriophage genes were found between tRNA-ser and pipA. SPI5-GI1 was only present in Salmonella Newport multidrug-resistant strains of lineage II. SPI-6 was found in all strains but three Asian strains in Salmonella Newport lineage II, whereas the three Asian strains carried genomic island SPI6-GI1 at the same locus as SPI-6 in other Salmonella. SPI-6 exhibited 937 SNPs, and phylogenetic analysis demonstrated that clustering of Salmonella Newport isolates was a reflection of their geographic origins. The sequence diversity within SPI-5 and SPI-6 suggests possible recombination events and different virulence potentials of Salmonella Newport. The SNPs could be used as biomarkers during epidemiological investigations.

  14. Morphotype transition and sexual reproduction are genetically associated in a ubiquitous environmental pathogen.

    Science.gov (United States)

    Wang, Linqi; Tian, Xiuyun; Gyawali, Rachana; Upadhyay, Srijana; Foyle, Dylan; Wang, Gang; Cai, James J; Lin, Xiaorong

    2014-06-01

    Sexual reproduction in an environmental pathogen helps maximize its lineage fitness to changing environment and the host. For the fungal pathogen Cryptococcus neoformans, sexual reproduction is proposed to have yielded hyper virulent and drug resistant variants. The life cycle of this pathogen commences with mating, followed by the yeast-hypha transition and hyphal growth, and it concludes with fruiting body differentiation and sporulation. How these sequential differentiation events are orchestrated to ensure developmental continuality is enigmatic. Here we revealed the genetic network of the yeast-to-hypha transition in Cryptococcus by analyzing transcriptomes of populations with a homogeneous morphotype generated by an engineered strain. Among this network, we found that a Pumilio-family protein Pum1 and the matricellular signal Cfl1 represent two major parallel circuits directing the yeast-hypha transition. Interestingly, only Pum1 coordinates the sequential morphogenesis events during a-α bisexual and α unisexual reproduction. Pum1 initiates the yeast-to-hypha transition, partially through a novel filament-specific secretory protein Fas1; Pum1 is also required to sustain hyphal growth after the morphological switch. Furthermore, Pum1 directs subsequent differentiation of aerial hyphae into fruiting bodies in both laboratory and clinical isolates. Pum1 exerts its control on sexual reproduction partly through regulating the temporal expression of Dmc1, the meiosis-specific recombinase. Therefore, Pum1 serves a pivotal role in bridging post-mating morphological differentiation events with sexual reproduction in Cryptococcus. Our findings in Cryptococcus illustrate how an environmental pathogen can ensure the completion of its life cycle to safeguard its long-term lineage success.

  15. Morphotype transition and sexual reproduction are genetically associated in a ubiquitous environmental pathogen.

    Directory of Open Access Journals (Sweden)

    Linqi Wang

    2014-06-01

    Full Text Available Sexual reproduction in an environmental pathogen helps maximize its lineage fitness to changing environment and the host. For the fungal pathogen Cryptococcus neoformans, sexual reproduction is proposed to have yielded hyper virulent and drug resistant variants. The life cycle of this pathogen commences with mating, followed by the yeast-hypha transition and hyphal growth, and it concludes with fruiting body differentiation and sporulation. How these sequential differentiation events are orchestrated to ensure developmental continuality is enigmatic. Here we revealed the genetic network of the yeast-to-hypha transition in Cryptococcus by analyzing transcriptomes of populations with a homogeneous morphotype generated by an engineered strain. Among this network, we found that a Pumilio-family protein Pum1 and the matricellular signal Cfl1 represent two major parallel circuits directing the yeast-hypha transition. Interestingly, only Pum1 coordinates the sequential morphogenesis events during a-α bisexual and α unisexual reproduction. Pum1 initiates the yeast-to-hypha transition, partially through a novel filament-specific secretory protein Fas1; Pum1 is also required to sustain hyphal growth after the morphological switch. Furthermore, Pum1 directs subsequent differentiation of aerial hyphae into fruiting bodies in both laboratory and clinical isolates. Pum1 exerts its control on sexual reproduction partly through regulating the temporal expression of Dmc1, the meiosis-specific recombinase. Therefore, Pum1 serves a pivotal role in bridging post-mating morphological differentiation events with sexual reproduction in Cryptococcus. Our findings in Cryptococcus illustrate how an environmental pathogen can ensure the completion of its life cycle to safeguard its long-term lineage success.

  16. Co-infection and genetic diversity of tick-borne pathogens in roe deer from Poland.

    Science.gov (United States)

    Welc-Falęciak, Renata; Werszko, Joanna; Cydzik, Krystian; Bajer, Anna; Michalik, Jerzy; Behnke, Jerzy M

    2013-05-01

    Wild species are essential hosts for maintaining Ixodes ticks and the tick-borne diseases. The aim of our study was to estimate the prevalence, the rate of co-infection with Babesia, Bartonella, and Anaplasma phagocytophilum, and the molecular diversity of tick-borne pathogens in roe deer in Poland. Almost half of the tested samples provided evidence of infection with at least 1 species. A. phagocytophilum (37.3%) was the most common and Bartonella (13.4%) the rarest infection. A total of 18.3% of all positive samples from roe deer were infected with at least 2 pathogens, and one-third of those were co-infected with A. phagocytophilum, Bartonella, and Babesia species. On the basis of multilocus molecular studies we conclude that: (1) Two different genetic variants of A. phagocytophilum, zoonotic and nonzoonotic, are widely distributed in Polish roe deer population; (2) the roe deer is the host for zoonotic Babesia (Bab. venatorum, Bab. divergens), closely related or identical with strains/species found in humans; (3) our Bab. capreoli and Bab. divergens isolates differed from reported genotypes at 2 conserved base positions, i.e., positions 631 and 663; and (4) this is the first description of Bart. schoenbuchensis infections in roe deer in Poland. We present 1 of the first complex epidemiological studies on the prevalence of Babesia, Bartonella, and A. phagocytophilum in naturally infected populations of roe deer. These game animals clearly have an important role as reservoir hosts of tick-borne pathogens, but the pathogenicity and zoonotic potential of the parasite genotypes hosted by roe deer requires further detailed investigation.

  17. Two Genetically Similar H9N2 Influenza A Viruses Show Different Pathogenicity in Mice

    Directory of Open Access Journals (Sweden)

    Qingtao Liu

    2016-11-01

    Full Text Available H9N2 Avian influenza virus has repeatedly infected humans and other mammals, which highlights the need to determine the pathogenicity and the corresponding mechanism of this virus for mammals. In this study, we found two H9N2 viruses with similar genetic background but with different pathogenicity in mice. The A/duck/Nanjing/06/2003 (NJ06 virus was highly pathogenic for mice, with a 50% mouse lethal dose of 102.83 50% egg infectious dose, whereas the A/duck/Nanjing/01/1999 (NJ01 virus was low pathogenic for mice, with a 50% mouse lethal dose of >106.81 50% egg infectious dose. Further studies showed that the NJ06 virus grew faster and reached significantly higher titers than NJ01 in vivo and in vitro. Moreover, the NJ06 virus induced more severe lung lesions, and higher levels of inflammatory cellular infiltration and cytokine response in lungs than NJ01 did. However, only twelve different amino acid residues (HA-K157E, NA-A9T, NA-R435K, PB2-T149P, PB2-K627E, PB1-R187K, PA-L548M, PA-M550L, NP-G127E, NP-P277H, NP-D340N, NS1-D171N were found between the two viruses, and all these residues except for NA-R435K were located in the known functional regions involved in interaction of viral proteins or between the virus and host factors. Summary, our results suggest that multiple amino acid differences may be responsible for the higher pathogenicity of the NJ06 virus for mice, resulting in lethal infection, enhanced viral replication, severe lung lesions, and excessive inflammatory cellular infiltration and cytokine response in lungs. These observations will be helpful for better understanding the pathogenic potential and the corresponding molecular basis of H9N2 viruses that might pose threats to human health in the future.

  18. Linking social and pathogen transmission networks using microbial genetics in giraffe (Giraffa camelopardalis).

    Science.gov (United States)

    VanderWaal, Kimberly L; Atwill, Edward R; Isbell, Lynne A; McCowan, Brenda

    2014-03-01

    Although network analysis has drawn considerable attention as a promising tool for disease ecology, empirical research has been hindered by limitations in detecting the occurrence of pathogen transmission (who transmitted to whom) within social networks. Using a novel approach, we utilize the genetics of a diverse microbe, Escherichia coli, to infer where direct or indirect transmission has occurred and use these data to construct transmission networks for a wild giraffe population (Giraffe camelopardalis). Individuals were considered to be a part of the same transmission chain and were interlinked in the transmission network if they shared genetic subtypes of E. coli. By using microbial genetics to quantify who transmits to whom independently from the behavioural data on who is in contact with whom, we were able to directly investigate how the structure of contact networks influences the structure of the transmission network. To distinguish between the effects of social and environmental contact on transmission dynamics, the transmission network was compared with two separate contact networks defined from the behavioural data: a social network based on association patterns, and a spatial network based on patterns of home-range overlap among individuals. We found that links in the transmission network were more likely to occur between individuals that were strongly linked in the social network. Furthermore, individuals that had more numerous connections or that occupied 'bottleneck' positions in the social network tended to occupy similar positions in the transmission network. No similar correlations were observed between the spatial and transmission networks. This indicates that an individual's social network position is predictive of transmission network position, which has implications for identifying individuals that function as super-spreaders or transmission bottlenecks in the population. These results emphasize the importance of association patterns in

  19. Population genetic structure of the seed pathogen Pyrenophora semeniperda on Bromus tectorum in western North America.

    Science.gov (United States)

    Boose, David; Harrison, Steven; Clement, Suzette; Meyer, Susan

    2011-01-01

    We examined genetic variation in the ascomycete pathogen Pyrenophora semeniperda cultured from seeds of the invasive grass Bromus tectorum in the Intermountain West of North America. We sequenced the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA genome in 417 monoconidial cultures collected from 20 sites in Washington, Idaho, Utah and Colorado, USA. ITS sequence diversity was surprisingly high; 12 unique haplotypes were identified, averaging 1.3% pairwise sequence divergence. All sites had at least two haplotypes present, and three sites had seven or more. One haplotype composed 60% of the isolates and occurred at all 20 locations; the remaining haplotypes generally occurred at low frequencies within sites but at multiple sites throughout the region. Sites in Washington and Idaho were more diverse than those in Utah and Colorado, averaging two more haplotypes and 67% more pairwise differences among haplotypes at a site. Analysis of molecular variance (AMOVA) indicated that more than 80% of the genetic variation was found within sampling locations, while 7-11% of the variation can be attributed to differences between northern (Washington and Idaho) and southern (Utah and Colorado) populations. The wide distribution of even uncommon haplotypes among sampling sites and weak correlations between genetic and geographic distances among populations (grass from its native Eurasian range.

  20. The Optimazation of Multi Resolution Segmentation of Remotely Sensed Data Using Genetic Alghorithm

    Science.gov (United States)

    Saba, F.; Valadanzouj, M. J.; Mokhtarzade, M.

    2013-09-01

    Object oriented analysis is widely used in interpretation of remote sensing images in comparison with pixel based approaches. A key step for achieving an acceptable classification result is meaningful image segmentation. Multi resolution segmentation is known as one of the most popular approaches in image segmentation that have been implemented in commercial software on the market, eCognition. However, this algorithm needs a set of optimum parameters which usually obtained by trial and error task. This technique not only is tedious and time consuming, also rely on the user's experience. So In this study in order to alleviate this problem, genetic algorithm is proposed to find the optimal parameters for multi resolution segmentation by focusing on road feature. This method is implemented on a pan-sharpened IKONOS image covering a part of Shiraz city, Iran. The results show that, with parameters found by GA, multi resolution segmentation accuracy is higher than obtained accuracy with parameters found by user. The evaluation of results confirms the importance of genetic algorithm to get optimal parameters.

  1. Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

    Directory of Open Access Journals (Sweden)

    Félix Marie-Anne

    2013-01-01

    Full Text Available Abstract Background In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. Methods Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. Results Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. Conclusions The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and

  2. Adaptation of the genetically tractable malaria pathogen Plasmodium knowlesi to continuous culture in human erythrocytes

    KAUST Repository

    Moon, Robert

    2012-12-24

    Research into the aetiological agent of the most widespread form of severe malaria, Plasmodium falciparum, has benefitted enormously from the ability to culture and genetically manipulate blood-stage forms of the parasite in vitro. However, most malaria outside Africa is caused by a distinct Plasmodium species, Plasmodium vivax, and it has become increasingly apparent that zoonotic infection by the closely related simian parasite Plasmodium knowlesi is a frequent cause of life-threatening malaria in regions of southeast Asia. Neither of these important malarial species can be cultured in human cells in vitro, requiring access to primates with the associated ethical and practical constraints. We report the successful adaptation of P. knowlesi to continuous culture in human erythrocytes. Human-adapted P. knowlesi clones maintain their capacity to replicate in monkey erythrocytes and can be genetically modified with unprecedented efficiency, providing an important and unique model for studying conserved aspects of malarial biology as well as species-specific features of an emerging pathogen.

  3. Genetic Factors and Host Traits Predict Spore Morphology for a Butterfly Pathogen

    Directory of Open Access Journals (Sweden)

    Jacobus C. de Roode

    2013-08-01

    Full Text Available Monarch butterflies (Danaus plexippus throughout the world are commonly infected by the specialist pathogen Ophryocystis elektroscirrha (OE. This protozoan is transmitted when larvae ingest infectious stages (spores scattered onto host plant leaves by infected adults. Parasites replicate internally during larval and pupal stages, and adult monarchs emerge covered with millions of dormant spores on the outsides of their bodies. Across multiple monarch populations, OE varies in prevalence and virulence. Here, we examined geographic and genetic variation in OE spore morphology using clonal parasite lineages derived from each of four host populations (eastern and western North America, South Florida and Hawaii. Spores were harvested from experimentally inoculated, captive-reared adult monarchs. Using light microscopy and digital image analysis, we measured the size, shape and color of 30 replicate spores per host. Analyses examined predictors of spore morphology, including parasite source population and clone, parasite load, and the following host traits: family line, sex, wing area, and wing color (orange and black pigmentation. Results showed significant differences in spore size and shape among parasite clones, suggesting genetic determinants of morphological variation. Spore size also increased with monarch wing size, and monarchs with larger and darker orange wings tended to have darker colored spores, consistent with the idea that parasite development depends on variation in host quality and resources. We found no evidence for effects of source population on variation in spore morphology. Collectively, these results provide support for heritable variation in spore morphology and a role for host traits in affecting parasite development.

  4. Ecological genetic divergence of the fungal pathogen Didymella rabiei on sympatric wild and domesticated Cicer spp. (Chickpea).

    Science.gov (United States)

    Frenkel, Omer; Peever, Tobin L; Chilvers, Martin I; Ozkilinc, Hilal; Can, Canan; Abbo, Shahal; Shtienberg, Dani; Sherman, Amir

    2010-01-01

    For millennia, chickpea (Cicer arietinum) has been grown in the Levant sympatrically with wild Cicer species. Chickpea is traditionally spring-sown, while its wild relatives germinate in the autumn and develop in the winter. It has been hypothesized that the human-directed shift of domesticated chickpea to summer production was an attempt to escape the devastating Ascochyta disease caused by Didymella rabiei. We estimated genetic divergence between D. rabiei isolates sampled from wild Cicer judaicum and domesticated C. arietinum and the potential role of temperature adaptation in this divergence. Neutral genetic markers showed strong differentiation between pathogen samples from the two hosts. Isolates from domesticated chickpea demonstrated increased adaptation to higher temperatures when grown in vitro compared with isolates from the wild host. The distribution of temperature responses among progeny from crosses of isolates from C. judaicum with isolates from C. arietinum was continuous, suggesting polygenic control of this trait. In vivo inoculations of host plants indicated that pathogenic fitness of the native isolates was higher than that of their hybrid progeny. The results indicate that there is a potential for adaptation to higher temperatures; however, the chances for formation of hybrids which are capable of parasitizing both hosts over a broad temperature range are low. We hypothesize that this pathogenic fitness cost is due to breakdown of coadapted gene complexes controlling pathogenic fitness on each host and may be responsible for maintenance of genetic differentiation between the pathogen demes.

  5. Population Genetic Analyses of the Fungal Pathogen Colletotrichum fructicola on Tea-Oil Trees in China

    Science.gov (United States)

    Li, He; Zhou, Guo-Ying; Liu, Jun-Ang; Xu, Jianping

    2016-01-01

    The filamentous fungus Colletotrichum fructicola is found in all five continents and is capable of causing severe diseases in a number of economically important plants such as avocado, fig, cocoa, pear, and tea-oil trees. However, almost nothing is known about its patterns of genetic variation and epidemiology on any of its host plant species. Here we analyzed 167 isolates of C. fructicola obtained from the leaves of tea-oil tree Camellia oleifera at 15 plantations in seven Chinese provinces. Multilocus sequence typing was conducted for all isolates based on DNA sequences at fragments of four genes: the internal transcribed spacers of the nuclear ribosomal RNA gene cluster (539 bp), calmodulin (633 bp), glutamine synthetase (711 bp), and glyceraldehyde-3-phosphate dehydrogenase (190 bp), yielding 3.52%, 0.63%, 8.44%, and 7.89% of single nucleotide polymorphic sites and resulting in 15, 5, 12 and 11 alleles respectively at the four gene fragments in the total sample. The combined allelic information from all four loci identified 53 multilocus genotypes with the most frequent represented by 21 isolates distributed in eight tea-oil plantations in three provinces, consistent with long-distance clonal dispersal. However, despite evidence for clonal dispersal, statistically significant genetic differentiation among geographic populations was detected. In addition, while no evidence of recombination was found within any of the four gene fragments, signatures of recombination were found among the four gene fragments in most geographic populations, consistent with sexual mating of this species in nature. Our study provides the first insights into the population genetics and epidemiology of the important plant fungal pathogen C. fructicola. PMID:27299731

  6. Population Genetic Analyses of the Fungal Pathogen Colletotrichum fructicola on Tea-Oil Trees in China.

    Directory of Open Access Journals (Sweden)

    He Li

    Full Text Available The filamentous fungus Colletotrichum fructicola is found in all five continents and is capable of causing severe diseases in a number of economically important plants such as avocado, fig, cocoa, pear, and tea-oil trees. However, almost nothing is known about its patterns of genetic variation and epidemiology on any of its host plant species. Here we analyzed 167 isolates of C. fructicola obtained from the leaves of tea-oil tree Camellia oleifera at 15 plantations in seven Chinese provinces. Multilocus sequence typing was conducted for all isolates based on DNA sequences at fragments of four genes: the internal transcribed spacers of the nuclear ribosomal RNA gene cluster (539 bp, calmodulin (633 bp, glutamine synthetase (711 bp, and glyceraldehyde-3-phosphate dehydrogenase (190 bp, yielding 3.52%, 0.63%, 8.44%, and 7.89% of single nucleotide polymorphic sites and resulting in 15, 5, 12 and 11 alleles respectively at the four gene fragments in the total sample. The combined allelic information from all four loci identified 53 multilocus genotypes with the most frequent represented by 21 isolates distributed in eight tea-oil plantations in three provinces, consistent with long-distance clonal dispersal. However, despite evidence for clonal dispersal, statistically significant genetic differentiation among geographic populations was detected. In addition, while no evidence of recombination was found within any of the four gene fragments, signatures of recombination were found among the four gene fragments in most geographic populations, consistent with sexual mating of this species in nature. Our study provides the first insights into the population genetics and epidemiology of the important plant fungal pathogen C. fructicola.

  7. Population Genetic Analyses of the Fungal Pathogen Colletotrichum fructicola on Tea-Oil Trees in China.

    Science.gov (United States)

    Li, He; Zhou, Guo-Ying; Liu, Jun-Ang; Xu, Jianping

    2016-01-01

    The filamentous fungus Colletotrichum fructicola is found in all five continents and is capable of causing severe diseases in a number of economically important plants such as avocado, fig, cocoa, pear, and tea-oil trees. However, almost nothing is known about its patterns of genetic variation and epidemiology on any of its host plant species. Here we analyzed 167 isolates of C. fructicola obtained from the leaves of tea-oil tree Camellia oleifera at 15 plantations in seven Chinese provinces. Multilocus sequence typing was conducted for all isolates based on DNA sequences at fragments of four genes: the internal transcribed spacers of the nuclear ribosomal RNA gene cluster (539 bp), calmodulin (633 bp), glutamine synthetase (711 bp), and glyceraldehyde-3-phosphate dehydrogenase (190 bp), yielding 3.52%, 0.63%, 8.44%, and 7.89% of single nucleotide polymorphic sites and resulting in 15, 5, 12 and 11 alleles respectively at the four gene fragments in the total sample. The combined allelic information from all four loci identified 53 multilocus genotypes with the most frequent represented by 21 isolates distributed in eight tea-oil plantations in three provinces, consistent with long-distance clonal dispersal. However, despite evidence for clonal dispersal, statistically significant genetic differentiation among geographic populations was detected. In addition, while no evidence of recombination was found within any of the four gene fragments, signatures of recombination were found among the four gene fragments in most geographic populations, consistent with sexual mating of this species in nature. Our study provides the first insights into the population genetics and epidemiology of the important plant fungal pathogen C. fructicola.

  8. Exploring the landscape of pathogenic genetic variation in the ExAC population database: insights of relevance to variant classification.

    Science.gov (United States)

    Song, Wei; Gardner, Sabrina A; Hovhannisyan, Hayk; Natalizio, Amanda; Weymouth, Katelyn S; Chen, Wenjie; Thibodeau, Ildiko; Bogdanova, Ekaterina; Letovsky, Stanley; Willis, Alecia; Nagan, Narasimhan

    2016-08-01

    We evaluated the Exome Aggregation Consortium (ExAC) database as a control cohort to classify variants across a diverse set of genes spanning dominant and recessively inherited disorders. The frequency of pathogenic variants in ExAC was compared with the estimated maximal pathogenic allele frequency (MPAF), based on the disease prevalence, penetrance, inheritance, allelic and locus heterogeneity of each gene. Additionally, the observed carrier frequency and the ethnicity-specific variant distribution were compared between ExAC and the published literature. The carrier frequency and ethnic distribution of pathogenic variants in ExAC were concordant with reported estimates. Of 871 pathogenic/likely pathogenic variants across 19 genes, only 3 exceeded the estimated MPAF. Eighty-four percent of variants with ExAC frequencies above the estimated MPAF were classified as "benign." Additionally, 20% of the cardiac and 19% of the Lynch syndrome gene variants originally classified as "VUS" occurred with ExAC frequencies above the estimated MPAF, making these suitable for reassessment. The ExAC database is a useful source for variant classification and is not overrepresented for pathogenic variants in the genes evaluated. However, the mutational spectrum, pseudogenes, genetic heterogeneity, and paucity of literature should be considered in deriving meaningful classifications using ExAC.Genet Med 18 8, 850-854.

  9. In vitro biofilm formation of commensal and pathogenic Escherichia coli strains: impact of environmental and genetic factors

    DEFF Research Database (Denmark)

    Reisner, A.; Krogfelt, Karen; Klein, B.M.

    2006-01-01

    Our understanding of Escherichia coli biofilm formation in vitro is based on studies of laboratory K-12 strains grown in standard media. However, pathogenic E. coli isolates differ substantially in their genetic repertoire from E. coli K-12 and are subject to heterogeneous environmental condition...

  10. Resequencing of the Phytophthora ramorum genome to characterize genetic variation and population dynamics of the invasive pathogen

    Science.gov (United States)

    Jennifer Yuzon; David M. Rizzo; Mathu Malar C; Sucheta Tripathy; Takao Kasuga

    2017-01-01

    Phytophthora ramorum has spread and diversified throughout California’s northwestern coast since its introduction in the 1990s. Tracking the spread of P. ramorum and the functional response of the pathogen to the environment is of particular interest to managing the epidemic. Using genetic tools such as microsatellite...

  11. Genetic diversity of Phytophthora infestans sensu lato in Ecuador provides new insight into the origin of this important plant pathogen

    NARCIS (Netherlands)

    Adler, N.E.; Erselius, L.J.; Chacón, G.M.; Flier, W.G.; Ordonez, M.E.; Kroon, L.P.N.M.; Forbes, G.A.

    2004-01-01

    The metapopulation structure of Phytophthora infestans sensu lato is genetically diverse in the highlands of Ecuador. Previous reports documented the diversity associated with four putative clonal lineages of the pathogen collected from various hosts in the genus Solanum. This paper simultaneously a

  12. Pathogenicity of Genetically Similar, H5N1 Highly Pathogenic Avian Influenza Virus Strains in Chicken and the Differences in Sensitivity among Different Chicken Breeds.

    Science.gov (United States)

    Matsuu, Aya; Kobayashi, Tomoko; Patchimasiri, Tuangthong; Shiina, Takashi; Suzuki, Shingo; Chaichoune, Kridsada; Ratanakorn, Parntep; Hiromoto, Yasuaki; Abe, Haruka; Parchariyanon, Sujira; Saito, Takehiko

    2016-01-01

    Differences in the pathogenicity of genetically closely related H5N1 highly pathogenic avian influenza viruses (HPAIVs) were evaluated in White Leghorn chickens. These viruses varied in the clinical symptoms they induced, including lethality, virus shedding, and replication in host tissues. A comparison of the host responses in the lung, brain, and spleen suggested that the differences in viral replication efficiency were related to the host cytokine response at the early phase of infection, especially variations in the proinflammatory cytokine IL-6. Based on these findings, we inoculated the virus that showed the mildest pathogenicity among the five tested, A/pigeon/Thailand/VSMU-7-NPT/2004, into four breeds of Thai indigenous chicken, Phadu-Hung-Dang (PHD), Chee, Dang, and Luang-Hung-Khao (LHK), to explore effects of genetic background on host response. Among these breeds, Chee, Dang, and LHK showed significantly longer survival times than White Leghorns. Virus shedding from dead Thai indigenous chickens was significantly lower than that from White Leghorns. Although polymorphisms were observed in the Mx and MHC class I genes, there was no significant association between the polymorphisms in these loci and resistance to HPAIV.

  13. Toxin production in a rare and genetically remote cluster of strains of the Bacillus cereus group

    Directory of Open Access Journals (Sweden)

    Granum Per

    2007-05-01

    Full Text Available Abstract Background Three enterotoxins are implicated in diarrhoeal food poisoning due to Bacillus cereus: Haemolysin BL (Hbl, Non-haemolytic enterotoxin (Nhe, and Cytotoxin K (CytK. Toxin gene profiling and assays for detection of toxin-producing stains have been used in attempts to evaluate the enterotoxic potential of B. cereus group strains. B. cereus strain NVH 391/98, isolated from a case of fatal enteritis, was genetically remote from other B. cereus group strains. This strain lacked the genes encoding Hbl and Nhe, but contains CytK-1. The high virulence of this strain is thought to be due to the greater cytotoxic activity of CytK-1 compared to CytK-2, and to a high level of cytK expression. To date, only three strains containing cytK-1 have been identified; B. cereus strains NVH 391/98, NVH 883/00, and INRA AF2. Results A novel gene variant encoding Nhe was identified in these three strains, which had an average of 80% identity in protein sequence with previously identified Nhe toxins. While culture supernatants containing CytK and Nhe from NVH 391/98 and INRA AF2 were highly cytotoxic, NVH 883/00 expressed little or no CytK and Nhe and was non-cytotoxic. Comparative sequence and expression studies indicated that neither the PlcR/PapR quorum sensing system, nor theYvrGH and YvfTU two-component systems, were responsible for the observed difference in toxin production. Additionally, phylogenetic analysis of 13 genes showed that NVH 391/98, NVH 883/00, and INRA AF2 comprise a novel cluster of strains genetically distant from other B. cereus group strains. Conclusion Due to its divergent sequence, the novel nhe operon had previously not been detected in NVH 391/98 using PCR and several monoclonal antibodies. Thus, toxigenic profiling based on the original nhe sequence will fail to detect the toxin in this group of strains. The observation that strain NVH 883/00 carries cytK-1 but is non-cytotoxic indicates that the detection of this gene

  14. Genetic inverse algorithm for retrieval of component temperature of mixed pixel by multi-angle thermal infrared remote sensing data

    Institute of Scientific and Technical Information of China (English)

    XU; Xiru; (徐希孺); CHEN; Liangfu; (陈良富); ZHUANG; Jiali; (庄家礼)

    2001-01-01

    After carefully studying the results of retrieval of land surface temperature(LST) by multi-channel thermal infrared remote sensing data, the authors of this paper point out that its accuracy and significance for applications are seriously damaged by the high correlation coefficient among multi-channel information and its disablement of direct retrieval of component temperature. Based on the model of directional radiation of non-isothermal mixed pixel, the authors point out that multi-angle thermal infrared remote sensing can offer the possibility to directly retrieve component temperature, but it is also a multi-parameter synchronous inverse problem. The results of digital simulation and field experiments show that the genetic inverse algorithm (GIA) is an effective method to fulfill multi-parameter synchronous retrieval. So it is possible to realize retrieval of component temperature with error less than 1K by multi-angle thermal infrared remote sensing data and GIA.

  15. Phenotypic and genetic diversity of rice seed-associated bacteria and their role in pathogenicity and biological control.

    Science.gov (United States)

    Cottyn, B; Debode, J; Regalado, E; Mew, T W; Swings, J

    2009-09-01

    To study the phenotypic and genetic diversity of culturable bacteria associated with rice seed and to asses the antagonistic and pathogenic potential of the isolated bacteria. Seed of rice cultivar PSBRc14 was collected from farmers' fields of irrigated lowland in southern Luzon, Philippines. Isolations of distinct colonies yielded 498 isolates. Classification of the isolates according to similarities in cellular characteristics, whole-cell fatty acid composition, and colony appearance differentiated 101 morphotype groups. Predominant bacteria were Coryneform spp., Pantoea spp. and Pseudomonas spp. Other bacteria regularly present were Actinomycetes spp., Bacillus pumilus, B. subtilis, Burkholderia glumae, Enterobacter cloacae, Paenibacillus polymyxa, Staphylococcus spp. and Xanthomonas spp. The genetic diversity among isolates was assessed by BOX-PCR fingerprinting of genomic DNA and represented 284 fingerprint types (FPTs). Most FPTs (78%) were not shared among samples, while eight FPTs occurred frequently in the samples. Seven of these FPTs also occurred frequently in a previous collection made from rainfed lowlands of Iloilo island, Philippines. Sixteen per cent of the isolates inhibited in vitro the mycelial growth of the rice pathogens Rhizoctonia solani and Pyricularia grisea, whereas 4% were pathogens identified as Burkholderia glumae, Burkholderia gladioli and Acidovorax avenae ssp. avenae. This study reveals a broad morphological and genetic diversity of bacteria present on seed of a single rice cultivar. This line of work contributes to a better understanding of the microbial diversity present on rice seed and stresses its importance as a carrier of antagonists and pathogens.

  16. Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici.

    Science.gov (United States)

    Stewart, Ethan L; Croll, Daniel; Lendenmann, Mark H; Sanchez-Vallet, Andrea; Hartmann, Fanny E; Palma-Guerrero, Javier; Ma, Xin; McDonald, Bruce A

    2016-11-21

    We conducted a comprehensive analysis of virulence in the fungal wheat pathogen Zymoseptoria tritici using quantitative trait locus (QTL) mapping. High-throughput phenotyping based on automated image analysis allowed the measurement of pathogen virulence on a scale and with a precision that was not previously possible. Across two mapping populations encompassing more than 520 progeny, 540 710 pycnidia were counted and their sizes and grey values were measured. A significant correlation was found between pycnidia size and both spore size and number. Precise measurements of percentage leaf area covered by lesions provided a quantitative measure of host damage. Combining these large and accurate phenotypic datasets with a dense panel of restriction site-associated DNA sequencing (RADseq) genetic markers enabled us to genetically dissect pathogen virulence into components related to host damage and those related to pathogen reproduction. We showed that different components of virulence can be under separate genetic control. Large- and small-effect QTLs were identified for all traits, with some QTLs specific to mapping populations, cultivars and traits and other QTLs shared among traits within the same mapping population. We associated the presence of four accessory chromosomes with small, but significant, increases in several virulence traits, providing the first evidence for a meaningful function associated with accessory chromosomes in this organism. A large-effect QTL involved in host specialization was identified on chromosome 7, leading to the identification of candidate genes having a large effect on virulence.

  17. A genetic screen reveals a periplasmic copper chaperone required for nitrite reductase activity in pathogenic Neisseria.

    Science.gov (United States)

    Jen, Freda E-C; Djoko, Karrera Y; Bent, Stephen J; Day, Christopher J; McEwan, Alastair G; Jennings, Michael P

    2015-09-01

    Under conditions of low oxygen availability, Neisseria meningitidis and Neisseria gonorrhoeae are able to respire via a partial denitrification pathway in which nitrite is converted to nitrous oxide. In this process, nitrite reductase (AniA), a copper (Cu)-containing protein converts nitrite to NO, and this product is converted to nitrous oxide by nitric oxide reductase (NorB). NorB also confers protection against toxic NO, and so we devised a conditional lethal screen, using a norB mutant, to identify mutants that were resistant to nitrite-dependent killing. After random-deletion mutagenesis of N. meningitidis, this genetic screen identified a gene encoding a Cu chaperone that is essential for AniA function, AccA. Purified AccA binds one Cu (I) ion and also possesses a second binding site for Cu (II). This novel periplasmic Cu chaperone (AccA) appears to be essential for provision of Cu ions to AniA of pathogenic Neisseria to generate an active nitrite reductase. Apart from the Neisseria genus, AccA is distributed across a wide range of environmental Proteobacteria species. © FASEB.

  18. Genetic characteristics and pathogenicity of human hepatitis E virus in Nanjing, China

    Institute of Scientific and Technical Information of China (English)

    Jia-Bao Geng; Mao-Rong Wang; Ling Wang; Jie Wang; Zhi-Guo Yang; Yan Cheng; Fei Qiao; Min Wang

    2012-01-01

    AIM:To investigate the genetic characteristics and pathogenicity of hepatitis E virus (HEV) and assess the potential risk factors for sporadic hepatitis E.METHODS:Sixty-two serum samples from the patients with acute hepatitis E were collected,including 23 cases coinfected with hepatitis B virus.Anti-HEV detection and partial HEV RNA amplification were performed by enzyme immunoassays and reverse transcriptionnested polymerase chain reaction (RT-nPCR) method,respectively,and PCR products were sequenced.The isolated human HEV sequences were analyzed phylogenetically.RESULTS:The positive rate of serum HEV RNA were 21.0% (13/62),including 5 cases of liver failure.All the 13 isolates shared a 82.1%-98.0% nucleotide homology with each other and had identities of 74.7%-81.0%,75.3%-78.6%,75.3%-80.0% and 82.1%-96.1% with the corresponding regions of HEV genotypes 1-4,respectively.The human HEV strain GS-NJ-12 shared a 100% nucleotide identity with the swine HEV strain swIM6-43 isolated from Inner Mongolia,China.CONCLUSION:Swine may be a principal risk factor for occurrence of sporadic hepatitis E in eastern China,and genotype 4 HEV can induce acute liver failure.

  19. Genetic engineering activates biosynthesis of aromatic fumaric acid amides in the human pathogen Aspergillus fumigatus.

    Science.gov (United States)

    Kalb, Daniel; Heinekamp, Thorsten; Lackner, Gerald; Scharf, Daniel H; Dahse, Hans-Martin; Brakhage, Axel A; Hoffmeister, Dirk

    2015-03-01

    The Aspergillus fumigatus nonribosomal peptide synthetase FtpA is among the few of this species whose natural product has remained unknown. Both FtpA adenylation domains were characterized in vitro. Fumaric acid was identified as preferred substrate of the first and both l-tyrosine and l-phenylalanine as preferred substrates of the second adenylation domain. Genetically engineered A. fumigatus strains expressed either ftpA or the regulator gene ftpR, encoded in the same cluster of genes, under the control of the doxycycline-inducible tetracycline-induced transcriptional activation (tet-on) cassette. These strains produced fumaryl-l-tyrosine and fumaryl-l-phenylalanine which were identified by liquid chromatography and high-resolution mass spectrometry. Modeling of the first adenylation domain in silico provided insight into the structural requirements to bind fumaric acid as peptide synthetase substrate. This work adds aromatic fumaric acid amides to the secondary metabolome of the important human pathogen A. fumigatus which was previously not known as a producer of these compounds.

  20. Genetic and phenotypic parameters estimated from Nebraska specific-pathogen-free swine field records.

    Science.gov (United States)

    David, P J; Johnson, R K; Socha, T E

    1983-11-01

    Records collected during 1971 through 1979 from 101,606 hogs raised in 18 Nebraska Specific Pathogen Free herds were analyzed. Traits considered were backfat at 100 kg (BF), weight at 140 d of age (WT) and, in some analyses, number of live pigs/litter at birth (NBA). The phenotypic correlation of BF and WT, averaged across herds, was -.07. The correlations between BF and NBA and between WT and NBA were .04 and -.05, respectively. Average phenotypic standard deviations for BF, WT and NBA were 2.6 mm, 8.8 kg and 2.0 pigs. Estimates of the heritability of BF and WT were lower than most estimates reported from university research herds. Within breed, herd and sex estimates of heritability ranged from -.22 and .51 (unweighted mean = .16 +/- .025) for BF and ranged from -.28 to .49 (mean = .16 +/- .016) for WT. Estimates of the genetic correlation between BF and WT were extremely variable (mean = -.62 +/- 14.3, range = -9.42 to 1.30) among breed-herd-sex subclasses.

  1. Genetic characterization and pathogenicity assessment of highly pathogenic H5N1 avian influenza viruses isolated from migratory wild birds in 2011, South Korea.

    Science.gov (United States)

    Kwon, Hyeok-Il; Song, Min-Suk; Pascua, Philippe Noriel Q; Baek, Yun Hee; Lee, Jun Han; Hong, Seung-Pyo; Rho, Jong-Bok; Kim, Jeong-Ki; Poo, Haryoung; Kim, Chul-Joong; Choi, Young Ki

    2011-09-01

    The continued spread of a highly pathogenic avian influenza (HPAI) H5N1 virus among wild birds and poultry has posed a potential threat to human public health. In the present study, we report the isolation of HPAI H5N1 viruses (A/Md/Korea/W401/11 and A/Md/Korea/W404/11) from fecal samples of migratory birds. Genetic and phlyogenetic analyses demonstrated that these viruses are genetically identical possessing gene segments from avian virus origin and showing highest sequence similarities (as high as 99.8%) to A/Ws/Hokkaido/4/11 and 2009-2010 Mongolian-like clade 2.3.2 isolates rather than previous Korean H5N1 viruses. Both viruses possess the polybasic motif (QRERRRK/R) in HA but other genes did not bear additional virulence markers. Pathogenicity of A/Md/Korea/W401/11 was assessed and compared with a 2006 clade 2.2 HPAI H5N1 migratory bird isolate (A/EM/Korea/W149/06) in chickens, ducks, mice and ferrets. Experimental infection in these hosts showed that both viruses have high pathogenic potential in chickens (2.3-3.0 LD(50)s) and mice (3.3-3.9 LD(50)s), but A/Md/Korea/W401/11 was less pathogenic in duck and ferret models. Despite recovery of both infection viruses in the upper respiratory tract, efficient ferret-to-ferret transmission was not observed. These data suggest that the 2011 Korean HPAI wild bird H5N1 virus could replicate in mammalian hosts without pre-adaptation but could not sustain subsequent infection. This study highlights the role of migratory birds in the perpetuation and spread of HPAI H5N1 viruses in Far-East Asia. With the changing pathobiology caused by H5N1 viruses among wild and poultry birds, continued surveillance of influenza viruses among migratory bird species remains crucial for effective monitoring of high-pathogenicity or pandemic influenza viruses.

  2. Pathogenicity for onion and genetic diversity of isolates of the pathogenic fungus Colletotrichum gloeosporioides (Phyllachoraceae) from the State of Pernambuco, Brazil.

    Science.gov (United States)

    Nova, M X Vila; Borges, L R; de Sousa, A C B; Brasileiro, B T R V; Lima, E A L A; da Costa, A F; de Oliveira, N T

    2011-02-22

    Onion anthracnose, caused by Colletotrichum gloeosporioides, is one of the main diseases of onions in the State of Pernambuco. We examined the pathogenicity of 15 C. gloeosporioides strains and analyzed their genetic variability using RAPDs and internal transcribed spacers (ITS) of the rDNA region. Ten of the strains were obtained from substrates and hosts other than onion, including chayote (Sechium edule), guava (Psidium guajava), pomegranate (Punica granatum), water from the Capibaribe River, maracock (Passiflora sp), coconut (Cocus nucifera), surinam cherry (Eugenia uniflora), and marine soil; five isolates came from onions collected from four different regions of the State of Pernambuco and one region of the State of Amazonas. Pathogenicity tests were carried out using onion leaves and bulbs. All strains were capable of causing disease in leaves, causing a variable degree of lesions on the leaves; four strains caused the most severe damage. In the onion bulb tests, only three of the above strains caused lesions. Seven primers of arbitrary sequences were used in the RAPD analysis, generating polymorphic bands that allowed the separation of the strains into three distinct groups. The amplification products generated with the primers ITS1 and ITS4 also showed polymorphism when digested with three restriction enzymes, DraI, HaeIII and MspI. Only the latter two demonstrated genetic variations among the strains. These two types of molecular markers were able to differentiate the strain from the State of Amazonas from those of the State of Pernambuco. However, there was no relationship between groups of strains, based on molecular markers, and degree of pathogenicity for onion leaves and bulbs.

  3. Within Host Evolution Selects for a Dominant Genotype of Mycobacterium tuberculosis while T Cells Increase Pathogen Genetic Diversity

    Science.gov (United States)

    Copin, Richard; Louie, Eddie; Escuyer, Vincent; Gagneux, Sebastien; Palmer, Guy H.

    2016-01-01

    Molecular epidemiological assessments, drug treatment optimization, and development of immunological interventions all depend on understanding pathogen adaptation and genetic variation, which differ for specific pathogens. Mycobacterium tuberculosis is an exceptionally successful human pathogen, yet beyond knowledge that this bacterium has low overall genomic variation but acquires drug resistance mutations, little is known of the factors that drive its population genomic characteristics. Here, we compared the genetic diversity of the bacteria that established infection to the bacterial populations obtained from infected tissues during murine M. tuberculosis pulmonary infection and human disseminated M. bovis BCG infection. We found that new mutations accumulate during in vitro culture, but that in vivo, purifying selection against new mutations dominates, indicating that M. tuberculosis follows a dominant lineage model of evolution. Comparing bacterial populations passaged in T cell-deficient and immunocompetent mice, we found that the presence of T cells is associated with an increase in the diversity of the M. tuberculosis genome. Together, our findings put M. tuberculosis genetic evolution in a new perspective and clarify the impact of T cells on sequence diversity of M. tuberculosis. PMID:27973588

  4. Genomic Analysis of Clavibacter michiganensis Reveals Insight Into Virulence Strategies and Genetic Diversity of a Gram-Positive Bacterial Pathogen.

    Science.gov (United States)

    Thapa, Shree P; Pattathil, Sivakumar; Hahn, Michael G; Jacques, Marie-Agnès; Gilbertson, Robert L; Coaker, Gitta

    2017-10-01

    Clavibacter michiganensis subsp. michiganensis is a gram-positive bacterial pathogen that proliferates in the xylem vessels of tomato, causing bacterial canker disease. In this study, we sequenced and assembled genomes of 11 C. michiganensis subsp. michiganensis strains isolated from infected tomato fields in California as well as five Clavibacter strains that colonize tomato endophytically but are not pathogenic in this host. The analysis of the C. michiganensis subsp. michiganensis genomes supported the monophyletic nature of this pathogen but revealed genetic diversity among strains, consistent with multiple introduction events. Two tomato endophytes that clustered phylogenetically with C. michiganensis strains capable of infecting wheat and pepper and were also able to cause disease in these plants. Plasmid profiles of the California strains were variable and supported the essential role of the pCM1-like plasmid and the CelA cellulase in virulence, whereas the absence of the pCM2-like plasmid in some pathogenic C. michiganensis subsp. michiganensis strains revealed it is not essential. A large number of secreted C. michiganensis subsp. michiganensis proteins were carbohydrate-active enzymes (CAZymes). Glycome profiling revealed that C. michiganensis subsp. michiganensis but not endophytic Clavibacter strains is able to extensively alter tomato cell-wall composition. Two secreted CAZymes found in all C. michiganensis subsp. michiganensis strains, CelA and PelA1, enhanced pathogenicity on tomato. Collectively, these results provide a deeper understanding of C. michiganensis subsp. michiganensis diversity and virulence strategies.

  5. Transfer of genetic material between pathogenic and food-borne yeasts

    DEFF Research Database (Denmark)

    Mentel, M.; Spirek, M.; Jorck-Ramberg, D.

    2006-01-01

    Many pathogenic yeast species are asexual and therefore not involved in intra- or interspecies mating. However, high-frequency transfer of plasmid DNA was observed when pathogenic and food-borne yeasts were grown together. This property could play a crucial role in the spread of virulence and drug...

  6. Unraveling the genetics of wheat-necrotrophic pathogen interactions reveals a conundrum

    Science.gov (United States)

    Interactions between wheat and the necrotrophic pathogens Parastagonospora nodorum (Pn) and Pyrenophora tritici-repentis (Ptr), which cause the foliar diseases Septoria nodorum blotch (SNB) and tan spot, respectively, involve host genes that recognize pathogen-produced necrotrophic effectors (NEs) i...

  7. Transfer of genetic material between pathogenic and food-borne yeasts

    DEFF Research Database (Denmark)

    Mentel, M.; Spirek, M.; Jorck-Ramberg, D.

    2006-01-01

    Many pathogenic yeast species are asexual and therefore not involved in intra- or interspecies mating. However, high-frequency transfer of plasmid DNA was observed when pathogenic and food-borne yeasts were grown together. This property could play a crucial role in the spread of virulence and drug...... resistance factors among yeasts....

  8. Three genetic groups of the Eucalyptus stem canker pathogen Teratosphaeria zuluensis introduced into Africa from an unknown source.

    Science.gov (United States)

    Jimu, Luke; Chen, ShuaiFei; Wingfield, Michael J; Mwenje, Eddie; Roux, Jolanda

    2016-01-01

    The Eucalyptus stem canker pathogen Teratosphaeria zuluensis was discovered in South Africa in 1988 and it has subsequently been found in several other African countries as well as globally. In this study, the population structure, genetic diversity and evolutionary history of T. z uluensis were analysed using microsatellite markers to gain an enhanced understanding of its movement in Africa. Isolates were collected from several sites in Malawi, Mozambique, Uganda and Zambia. Data obtained were compared with those previously published for a South African population. The data obtained from 334 isolates, amplified across eight microsatellite loci, were used for assignment, differentiation and genetic diversity tests. STRUCTURE analyses, θ st and genetic distances revealed the existence of two clusters, one dominated by isolates from South Africa and the other by isolates from the Zambezi basin including Malawi, Mozambique and Zambia. High levels of admixture were found within and among populations, dominated by the Mulanje population in Malawi. Moderate to low genetic diversity of the populations supports the previously held view that the pathogen was introduced into Africa. The clonal nature of the Ugandan population suggests a very recent introduction, most likely from southern Africa.

  9. Classification of ETM+ Remote Sensing Image Based on Hybrid Algorithm of Genetic Algorithm and Back Propagation Neural Network

    Directory of Open Access Journals (Sweden)

    Haisheng Song

    2013-01-01

    Full Text Available The back propagation neural network (BPNN algorithm can be used as a supervised classification in the processing of remote sensing image classification. But its defects are obvious: falling into the local minimum value easily, slow convergence speed, and being difficult to determine intermediate hidden layer nodes. Genetic algorithm (GA has the advantages of global optimization and being not easy to fall into local minimum value, but it has the disadvantage of poor local searching capability. This paper uses GA to generate the initial structure of BPNN. Then, the stable, efficient, and fast BP classification network is gotten through making fine adjustments on the improved BP algorithm. Finally, we use the hybrid algorithm to execute classification on remote sensing image and compare it with the improved BP algorithm and traditional maximum likelihood classification (MLC algorithm. Results of experiments show that the hybrid algorithm outperforms improved BP algorithm and MLC algorithm.

  10. Genetic and Epigenetic Effects of Plant-Pathogen Interactions: An Evolutionary Perspective

    Institute of Scientific and Technical Information of China (English)

    Alex Boyko; Igor Kovalchuk

    2011-01-01

    Recent reports suggest that exposure to stress is capable of influencing the frequency and pattern of inherited changes in various parts of the genome.In this review,we will discuss the influence of viral pathogens on somatic and meiotic genome stability of Nicotiana tabacum and Arabidopsis thaliana.Plants infected with a compatible pathogen generate a systemic recombination signal that precedes the spread of pathogens and results in changes in the somatic and meiotic recombination frequency.The progeny of infected plants exhibit changes in global and locusspecific DNA methylation patterns,genomic rearrangements at transgenic reporter loci and resistance gene-like-loci,and even tolerance to pathogen infection and abiotic stress.Here,we will discuss the contribution of environmental stresses to genome evolution and will focus on the role of heritable epigenetic changes in response to pathogen infection.

  11. 植物病原物的群体遗传学%Population genetics of plant pathogens

    Institute of Scientific and Technical Information of China (English)

    祝雯; 詹家绥

    2012-01-01

    Comparing to natural ecosystems, the evolution of plant pathogens in agricultural ecosystems is generally faster due to high-density monocultures, large-scale application of agrochemicals, and international trade in agricultural products. Knowledge of the population genetics and evolutionary biology of plant pathogens is necessary to understand disease epidemiology, effectively breed and use resistant cultivars, and control plant diseases. In this article, we outlined the aims of population genetic studies in plant pathogens, discuss contributions of five evolutionary forces (I.e., mutation, gene flow, recombination, random genetic drift, and natural selection) to origin, maintenance, and distribution of genetic variation in time and space, and gave an overview of current research status in this field.%品种单一化、生产密集型和一年多茬的现代农业特点导致病原物呈现出进化速度加快、致病力增强及流行风险增大趋势.深入研究病原物群体遗传学对认识病害的流行、有效选育和使用抗性品种乃至控制病害具有重要意义.文章阐述了植物病原物群体遗传学的研究目标和内容、突变、基因迁移、基因重组、随机遗传漂变和自然选择5大遗传机制在植物病原物进化过程中的作用,以及目前植物病原物群体遗传学研究的现状.

  12. High levels of genetic and genotypic diversity in field populations of the barley pathogen Ramularia collo-cygni

    DEFF Research Database (Denmark)

    Hjortshøj, Rasmus Lund; Ravnshøj, A.R.; Nyman, M.

    2013-01-01

    The ascomycete pathogen Ramularia collo-cygni causes Ramularia leaf spot (RLS) on barley. Although R. collo-cygni is considerd an emerging disease of barley, little is known about genetic diversity or population genetic structure of this pathogen. We applied a set of polymorphic AFLP (Amplified F...... result from considerable levels of gene flow between populations most likely mediated by seed borne dispersal of inoculum....

  13. Combination of RNAseq and SNP nanofluidic array reveals the center of genetic diversity of cacao pathogen Moniliophthora roreri in the upper Magdalena Valley of Colombia and its clonality

    Science.gov (United States)

    Moniliophthora roreri is the fungal pathogen that causes frosty pod rot (FPR) disease of Theobroma cacao L., the source of chocolate. FPR occurs in most of the cacao producing countries in the Western Hemisphere, causing yield losses up to 80%. Genetic diversity within the FPR pathogen population ma...

  14. Accelerating dynamic genetic conservation efforts: Use of FT-IR spectroscopy for the rapid identification of trees resistant to destructive pathogens

    Science.gov (United States)

    C. Villari; R.A. Sniezko; L.E. Rodriguez-Saona; P. Bonello

    2017-01-01

    A strong focus on tree germplasm that can resist threats such as non-native insects and pathogens, or a changing climate, is fundamental for successful genetic conservation efforts. However, the unavailability of tools for rapid screening of tree germplasm for resistance to critical pathogens and insect pests is becoming an increasingly serious bottleneck. Here we...

  15. Genetic and Pathogenic Variability of Fusarium oxysporum f. sp. cepae Isolated from Onion and Welsh Onion in Japan.

    Science.gov (United States)

    Sasaki, Kazunori; Nakahara, Katsuya; Tanaka, Shuhei; Shigyo, Masayoshi; Ito, Shin-ichi

    2015-04-01

    Fusarium oxysporum f. sp. cepae causes Fusarium basal rot in onion (common onion) and Fusarium wilt in Welsh onion. Although these diseases have been detected in various areas in Japan, knowledge about the genetic and pathogenic variability of F. oxysporum f. sp. cepae is very limited. In this study, F. oxysporum f. sp. cepae was isolated from onion and Welsh onion grown in 12 locations in Japan, and a total of 55 F. oxysporum f. sp. cepae isolates (27 from onion and 28 from Welsh onion) were characterized based on their rDNA intergenic spacer (IGS) and translation elongation factor-1α (EF-1α) nucleotide sequences, vegetative compatibility groups (VCGs), and the presence of the SIX (secreted in xylem) homologs. Phylogenetic analysis of IGS sequences showed that these isolates were grouped into eight clades (A to H), and 20 onion isolates belonging to clade H were monophyletic and assigned to the same VCG. All the IGS-clade H isolates possessed homologs of SIX3, SIX5, and SIX7. The SIX3 homolog was located on a 4 Mb-sized chromosome in the IGS-clade H isolates. Pathogenicity tests using onion seedlings showed that all the isolates with high virulence were in the IGS-clade H. These results suggest that F. oxysporum f. sp. cepae isolates belonging to the IGS-clade H are genetically and pathogenically different from those belonging to the other IGS clades.

  16. Structural and functional characterization of pathogenic non- synonymous genetic mutations of human insulin-degrading enzyme by in silico methods.

    Science.gov (United States)

    Shaik, Noor A; Kaleemuddin, Mohammed; Banaganapalli, Babajan; Khan, Fazal; Shaik, Nazia S; Ajabnoor, Ghada; Al-Harthi, Sameer E; Bondagji, Nabeel; Al-Aama, Jumana Y; Elango, Ramu

    2014-04-01

    Insulin-degrading enzyme (IDE) is a key protease involved in degrading insulin and amyloid peptides in human body. Several non-synonymous genetic mutations of IDE gene have been recently associated with susceptibility to both diabetes and Alzheimer's diseases. However, the consequence of these mutations on the structure of IDE protein and its substrate binding characteristics is not well elucidated. The computational investigation of genetic mutation consequences on structural level of protein is recently found to be an effective alternate to traditional in vivo and in vitro approaches. Hence, by using a combination of empirical rule and support vector machine based in silico algorithms, this study was able to identify that the pathogenic nonsynonymous genetic mutations corresponding to p.I54F, p.P122T, p.T533R, p.P581A and p.Y609A have more potential role in structural and functional deviations of IDE activity. Moreover, molecular modeling and secondary structure analysis have also confirmed their impact on the stability and secondary properties of IDE protein. The molecular docking analysis of IDE with combinational substrates has revealed that peptide inhibitors compared to small non-peptide inhibitor molecules possess good inhibitory activity towards mutant IDE. This finding may pave a way to design novel potential small peptide inhibitors for mutant IDE. Additionally by un-translated region (UTR) scanning analysis, two regulatory pathogenic genetic mutations i.e., rs5786997 (3' UTR) and rs4646954 (5' UTR), which can influence the translation pattern of IDE gene through sequence alteration of upstream-Open Reading Frame and Internal Ribosome Entry Site elements were identified. Our findings are expected to help in narrowing down the number of IDE genetic variants to be screened for disease association studies and also to select better competitive inhibitors for IDE related diseases.

  17. Genetic identification of Entamoeba polecki subtype 3 from pigs in Japan and characterisation of its pathogenic role in ulcerative colitis.

    Science.gov (United States)

    Matsubayashi, Makoto; Murakoshi, Naoko; Komatsu, Tetsuya; Tokoro, Masaharu; Haritani, Makoto; Shibahara, Tomoyuki

    2015-12-01

    To date, three Entamoeba spp. (E. suis, zoonotic E. polecki and E. histolytica) have been identified in pigs, but their pathogenicity and molecular classification have not been fully determined. Examination and pathological analysis of pigs (n=3) with diarrhoea was conducted and revealed the presence of Entamoeba organisms. We performed a genetic analysis of the isolate using the small-subunit ribosomal RNA (SSU rRNA) gene region to identify the species. A severe ulcerative colitis was observed histopathologically with inflammatory cells, including macrophages and neutrophils, infiltrating the mucous membranes of the cecum and colon. Many Entamoeba trophozoites were found at the erosion site or at ulcerative lesions. Pathogenic viruses or bacteria were not detected. The SSU rRNA sequence of the Entamoeba isolate was found to be completely homologous to that of E. polecki subtype 3.

  18. Genetic differentiation and recombination among geographic populations of the fungal pathogen Colletotrichum truncatum from chili peppers in China.

    Science.gov (United States)

    Diao, Yongzhao; Zhang, Can; Xu, Jianping; Lin, Dong; Liu, Li; Mtung'e, Olivo G; Liu, Xili

    2015-01-01

    Colletotrichum truncatum is an extremely important fungal pathogen. It can cause diseases both in humans and in over 460 plant species. However, little is known about its genetic diversity within and among populations. One of the major plant hosts of C. truncatum is pepper, and China is one of the main pepper-producing countries in the world. Here, we propose the hypotheses that geography has a major influence on the relationships among populations of C. truncatum in China and that infections in different populations need to be managed differently. To test these hypotheses, we obtained and analyzed 266 C. truncatum isolates from 13 regions representing the main pepper-growing areas throughout China. The analysis based on nine microsatellite markers identified high intrapopulation genetic diversity, evidence of sexual recombination, and geographic differentiation. The genetic differentiation was positively correlated with geographic distance, with the southern and northern China populations grouped in two distinct clusters. Interestingly, isolates collected from the pepper-breeding center harbored the most private alleles. The results suggest that the geographic populations of C. truncatum on peppers in China are genetically differentiated and should be managed accordingly. Our study also provides a solid foundation from which to further explore the global genetic epidemiology of C. truncatum in both plants and humans.

  19. Genetic differentiation and recombination among geographic populations of the fungal pathogen Colletotrichum truncatum from chili peppers in China

    OpenAIRE

    Diao, Yongzhao; Zhang, Can; Xu, Jianping; Lin, Dong; Liu, Li; Mtung'e, Olivo G; Liu, Xili

    2014-01-01

    Colletotrichum truncatum is an extremely important fungal pathogen. It can cause diseases both in humans and in over 460 plant species. However, little is known about its genetic diversity within and among populations. One of the major plant hosts of C. truncatum is pepper, and China is one of the main pepper-producing countries in the world. Here, we propose the hypotheses that geography has a major influence on the relationships among populations of C. truncatum in China and that infections...

  20. Systems biology and systems genetics - novel innovative approaches to study host-pathogen interactions during influenza infection.

    Science.gov (United States)

    Kollmus, Heike; Wilk, Esther; Schughart, Klaus

    2014-06-01

    Influenza represents a serious threat to public health with thousands of deaths each year. A deeper understanding of the host-pathogen interactions is urgently needed to evaluate individual and population risks for severe influenza disease and to identify new therapeutic targets. Here, we review recent progress in large scale omics technologies, systems genetics as well as new mathematical and computational developments that are now in place to apply a systems biology approach for a comprehensive description of the multidimensional host response to influenza infection. In addition, we describe how results from experimental animal models can be translated to humans, and we discuss some of the future challenges ahead.

  1. Genetic determinants of pathogenicity of Escherichia coli isolated from children with acute diarrhea in Maputo, Mozambique.

    Science.gov (United States)

    Sumbana, Jose; Taviani, Elisa; Manjate, Alice; Paglietti, Bianca; Santona, Antonella; Colombo, Mauro M

    2015-07-04

    Diarrheagenic Escherichia coli (DEC) represents one of the leading cause of diarrhoea in developing countries. In this study a molecular approach was applied for the detection of diarrheagenic Escherichia coli (DEC) circulating in Maputo, Mozambique. All isolates were PCR tested for species-specific genes and for 11 molecular markers: stx1, stx2, eae, bfpA, lt, st, ipaH, aap, aggR CVD432 and daaE. Of the 80 E. coli isolated, 74% were potential DEC: 21% EIEC, 19% EPEC, 15% EAEC, 13% ETEC, 5% DAEC and 1% hybrids. This study revealed the complexity of the etiology of diarrhea caused by pathogenic E. coli in Mozambique, and the risk of the emergence of new pathogenic variants due to the horizontal transmission of pathogenicity factors.

  2. Analysis of genetic and pathogenic variation among Alternaria solani in a potato production region

    Science.gov (United States)

    A two-year survey was conducted in a potato production region to investigate the genetic variability within naturally infecting populations of Alternaria solani, the cause of early blight in potato, and between species A. solani and A. dauci. Genetic diversity among 151 isolates was assessed using s...

  3. MOLECULAR-GENETIC BASIS OF PHYSIOLOGY AND PATHOGENICITY OF COXIELLA BURNETII

    Directory of Open Access Journals (Sweden)

    Yu. A. Panpherova

    2012-01-01

    Full Text Available Abstract. The agent of Q-fever Coxiella burnetii is unusual intracellular pathogen which is possessed of biggest transporting and metabolic abilities in compare with microorganisms with similar parasitic strategy. It is supposed that different strains of the pathogen exist in various stages of pathological adaption and have different potential of virulence. The structure of C. burnetii genome, characteristics of metabolic routes, mechanisms of interaction with host cells and possible virulence factors are discussed in the review. The special attention is paid to Coxiella genotyping methods and possible correlations between genomic polymorphism of different strains and their virulence potential.

  4. Genetic screens to identify pathogenic gene variants in the common cancer predisposition Lynch syndrome

    DEFF Research Database (Denmark)

    Drost, Mark; Lützen, Anne; van Hees, Sandrine

    2013-01-01

    In many individuals suspected of the common cancer predisposition Lynch syndrome, variants of unclear significance (VUS), rather than an obviously pathogenic mutations, are identified in one of the DNA mismatch repair (MMR) genes. The uncertainty of whether such VUS inactivate MMR, and therefore...... for the translation of personalized genomics into targeted healthcare....

  5. Genetics of mechanisms controlling responses to two major pathogens in broiler and layer chickens

    DEFF Research Database (Denmark)

    Hamzic, Edin

    The objective of this thesis was to improve the understanding of molecular mechanisms controlling the response to two major pathogens, Eimeria maxima (coccidiosis) and infectious bronchitis virus (IBV), in broiler and layer chickens, respectively. Breeding for the improved response to the two pat...

  6. Genetic aspects of ash dieback caused by the pathogenic fungus Chalara fraxinea on Fraxinus excelsior

    DEFF Research Database (Denmark)

    McKinney, Lea Vig

    ). This thesis comprises five papers that aim to contribute to the knowledge on the interaction between the pathogen and its host and the inherent natural resistance found within the host species. Paper I reviews the current literature on the aetiology of the fungus, the epidemic and its consequences...

  7. Molecular and biological analysis of eight genetic islands that distinguish Neisseria meningitidis from the closely related pathogen Neisseria gonorrhoeae.

    Science.gov (United States)

    Klee, S R; Nassif, X; Kusecek, B; Merker, P; Beretti, J L; Achtman, M; Tinsley, C R

    2000-04-01

    The pathogenic species Neisseria meningitidis and Neisseria gonorrhoeae cause dramatically different diseases despite strong relatedness at the genetic and biochemical levels. N. meningitidis can cross the blood-brain barrier to cause meningitis and has a propensity for toxic septicemia unlike N. gonorrhoeae. We previously used subtractive hybridization to identify DNA sequences which might encode functions specific to bacteremia and invasion of the meninges because they are specific to N. meningitidis and absent from N. gonorrhoeae. In this report we show that these sequences mark eight genetic islands that range in size from 1.8 to 40 kb and whose chromosomal location is constant. Five of these genetic islands were conserved within a representative set of strains and/or carried genes with homologies to known virulence factors in other species. These were deleted, and the mutants were tested for correlates of virulence in vitro and in vivo. This strategy identified one island, region 8, which is needed to induce bacteremia in an infant rat model of meningococcal infection. Region 8 encodes a putative siderophore receptor and a disulfide oxidoreductase. None of the deleted mutants was modified in its resistance to the bactericidal effect of serum. Neither were the mutant strains altered in their ability to interact with endothelial cells, suggesting that such interactions are not encoded by large genetic islands in N. meningitidis.

  8. Genetic diversity of non-pathogenic Clavibacter strains isolated from tomato seeds.

    Science.gov (United States)

    Zaluga, Joanna; Van Vaerenbergh, Johan; Stragier, Pieter; Maes, Martine; De Vos, Paul

    2013-09-01

    Clavibacter michiganensis subsp. michiganensis (Cmm) is a seed-transmitted, quarantine pathogen which causes bacterial wilt and canker of tomato. Despite efforts to prevent seed contamination, new introductions are regularly detected, associated with new regions of tomato seed production. It seems as if the expanding diversity of Cmm also challenges the limited host range. Clavibacter-like isolates from tomato seed are phenotypically similar to Cmm in the common diagnostic semi-selective media and are identified as Cmm in the customary tests but are not pathogenic to tomato. In our first study four representatives formed a separate cluster in gyrB sequence analysis and in MALDI-TOF MS. Their presence on seed prevents clear judgment on the health status of tomato seeds. As their nature and function are unclear we aimed to investigate and compare them to Cmm. Twenty strains described as Clavibacter-like isolated from tomato seed and not pathogenic to tomato plantlets were selected. Leaf spots, wilting or cankers were not induced after local or systemic inoculation. Tomato stems were not colonized nor was there evidence of survival in tomato stems. Total DNA-DNA hybridization and sequence analysis of gyrB and dnaA proved that they belong to the Cm species but can be unambiguously separated from Cmm. Some of the genes encoding virulence determinants in Cmm strains were also detected in some of the non-pathogenic isolates. Moreover, Cmm strains formed a coherent group, while non-pathogenic Cm strains were heterogenic. The latter was confirmed by BOX-PCR. We speculate that tomato seeds likely represent a larger reservoir of unexplored Clavibacter diversity. Copyright © 2013 Elsevier GmbH. All rights reserved.

  9. Optimal band selection for high dimensional remote sensing data using genetic algorithm

    Science.gov (United States)

    Zhang, Xianfeng; Sun, Quan; Li, Jonathan

    2009-06-01

    A 'fused' method may not be suitable for reducing the dimensionality of data and a band/feature selection method needs to be used for selecting an optimal subset of original data bands. This study examined the efficiency of GA in band selection for remote sensing classification. A GA-based algorithm for band selection was designed deliberately in which a Bhattacharyya distance index that indicates separability between classes of interest is used as fitness function. A binary string chromosome is designed in which each gene location has a value of 1 representing a feature being included or 0 representing a band being not included. The algorithm was implemented in MATLAB programming environment, and a band selection task for lithologic classification in the Chocolate Mountain area (California) was used to test the proposed algorithm. The proposed feature selection algorithm can be useful in multi-source remote sensing data preprocessing, especially in hyperspectral dimensionality reduction.

  10. Genetic structure of the fungal grapevine pathogen Eutypa lata from four continents

    Science.gov (United States)

    The generalist ascomycete fungus Eutypa lata causes Eutypa dieback of grapevine (Vitis vinifera) worldwide. To decipher the cosmopolitan distribution of this fungus, the population genetic structure of 17 geographic samples was investigated from four continental regions (Australia, California, Europ...

  11. Yellow Rust Epidemics Worldwide Were Caused by Pathogen Races from Divergent Genetic Lineages

    DEFF Research Database (Denmark)

    Ali, Sajid; Rodriguez Algaba, Julian; Thach, Tine

    2017-01-01

    We investigated whether the recent worldwide epidemics of wheat yellow rust were driven by races of few clonal lineage(s) or populations of divergent races. Race phenotyping of 887 genetically diverse Puccinia striiformis isolates sampled in 35 countries during 2009–2015 revealed that these epide......We investigated whether the recent worldwide epidemics of wheat yellow rust were driven by races of few clonal lineage(s) or populations of divergent races. Race phenotyping of 887 genetically diverse Puccinia striiformis isolates sampled in 35 countries during 2009–2015 revealed...

  12. New exome data question the pathogenicity of genetic variants previously associated with catecholaminergic polymorphic ventricular tachycardia

    DEFF Research Database (Denmark)

    Jabbari, Javad; Jabbari, Reza; Nielsen, Morten Wagner

    2013-01-01

    Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a lethal, rare hereditary disease with an estimated prevalence of 1:10 000. The genetic variants that cause CPVT are usually highly penetrant. To date, about 189 variants in 5 genes (RYR2, CASQ2, CALM1, TRND, and KCNJ2) have been...

  13. Classification, genetic variation and pathogenicity of Lymantria dispar nucleopolyhedrovirus isolates from Asia, Europe, and North America

    Science.gov (United States)

    Robert L. Harrison; Melody A. Keena; Daniel L. Rowley

    2014-01-01

    Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV) has been formulated and applied to control outbreaks of the gypsy moth, L. dispar. To classify and determine the degree of genetic variation among isolates of L. dispar NPVs from different parts of the range of the gypsy moth, partial sequences of the

  14. Maize Leaf Epiphytic Bacteria Diversity Patterns Are Genetically Correlated with Resistance to Fungal Pathogen Infection

    Science.gov (United States)

    Plant leaves host a specific set of microbial epiphytes. These phyllosphere organisms form a large community, with annual crops alone covering millions of hectares each year. Host plant genetic factors and abiotic stresses such as UV-B are key in shaping patterns of epiphyte diversity; we analyzed...

  15. Genetic Divergence and Chemotype Diversity in the Fusarium Head Blight Pathogen Fusarium poae

    Directory of Open Access Journals (Sweden)

    Adriaan Vanheule

    2017-08-01

    Full Text Available Fusarium head blight is a disease caused by a complex of Fusarium species. F. poae is omnipresent throughout Europe in spite of its low virulence. In this study, we assessed a geographically diverse collection of F. poae isolates for its genetic diversity using AFLP (Amplified Fragment Length Polymorphism. Furthermore, studying the mating type locus and chromosomal insertions, we identified hallmarks of both sexual recombination and clonal spread of successful genotypes in the population. Despite the large genetic variation found, all F. poae isolates possess the nivalenol chemotype based on Tri7 sequence analysis. Nevertheless, Tri gene clusters showed two layers of genetic variability. Firstly, the Tri1 locus was highly variable with mostly synonymous mutations and mutations in introns pointing to a strong purifying selection pressure. Secondly, in a subset of isolates, the main trichothecene gene cluster was invaded by a transposable element between Tri5 and Tri6. To investigate the impact of these variations on the phenotypic chemotype, mycotoxin production was assessed on artificial medium. Complex blends of type A and type B trichothecenes were produced but neither genetic variability in the Tri genes nor variability in the genome or geography accounted for the divergence in trichothecene production. In view of its complex chemotype, it will be of utmost interest to uncover the role of trichothecenes in virulence, spread and survival of F. poae.

  16. Fusarium spp. associated with rice Bakanae: ecology, genetic diversity, pathogenicity and toxigenicity

    DEFF Research Database (Denmark)

    Wulff, E.G.; Sørensen, Jens Laurids; Lubeck, M.;

    2010-01-01

    symptoms of Bakanae on rice, some species (i.e. F. fujikuroi) being more pathogenic than others. The ability to produce fumonisins (FB1 and FB2) and gibberellin A3 in vitro also differed according to the Fusarium species. While fumonisins were produced by most of the strains of F. verticillioides and F....... proliferatum, gibberellin A3 was only produced by F. fujikuroi. Neither fumonisin nor gibberellin was synthesized by most of the strains of F. andiyazi. These findings provide new information on the variation within the G. fujikuroi species complex associated with rice seed and Bakanae disease....

  17. Classification of hyperspectral remote sensing images based on simulated annealing genetic algorithm and multiple instance learning

    Institute of Scientific and Technical Information of China (English)

    高红民; 周惠; 徐立中; 石爱业

    2014-01-01

    A hybrid feature selection and classification strategy was proposed based on the simulated annealing genetic algorithm and multiple instance learning (MIL). The band selection method was proposed from subspace decomposition, which combines the simulated annealing algorithm with the genetic algorithm in choosing different cross-over and mutation probabilities, as well as mutation individuals. Then MIL was combined with image segmentation, clustering and support vector machine algorithms to classify hyperspectral image. The experimental results show that this proposed method can get high classification accuracy of 93.13%at small training samples and the weaknesses of the conventional methods are overcome.

  18. PECONPI: a novel software for uncovering pathogenic copy number variations in non-syndromic sensorineural hearing loss and other genetically heterogeneous disorders.

    Science.gov (United States)

    Tsai, Ellen A; Berman, Micah A; Conlin, Laura K; Rehm, Heidi L; Francey, Lauren J; Deardorff, Matthew A; Holst, Jenelle; Kaur, Maninder; Gallant, Emily; Clark, Dinah M; Glessner, Joseph T; Jensen, Shane T; Grant, Struan F A; Gruber, Peter J; Hakonarson, Hakon; Spinner, Nancy B; Krantz, Ian D

    2013-09-01

    This report describes an algorithm developed to predict the pathogenicity of copy number variants (CNVs) in large sample cohorts. CNVs (genomic deletions and duplications) are found in healthy individuals and in individuals with genetic diagnoses, and differentiation of these two classes of CNVs can be challenging and usually requires extensive manual curation. We have developed PECONPI, an algorithm to assess the pathogenicity of CNVs based on gene content and CNV frequency. This software was applied to a large cohort of patients with genetically heterogeneous non-syndromic hearing loss to score and rank each CNV based on its relative pathogenicity. Of 636 individuals tested, we identified the likely underlying etiology of the hearing loss in 14 (2%) of the patients (1 with a homozygous deletion, 7 with a deletion of a known hearing loss gene and a point mutation on the trans allele and 6 with a deletion larger than 1 Mb). We also identified two probands with smaller deletions encompassing genes that may be functionally related to their hearing loss. The ability of PECONPI to determine the pathogenicity of CNVs was tested on a second genetically heterogeneous cohort with congenital heart defects (CHDs). It successfully identified a likely etiology in 6 of 355 individuals (2%). We believe this tool is useful for researchers with large genetically heterogeneous cohorts to help identify known pathogenic causes and novel disease genes.

  19. Remediating Viking Origins: Genetic Code as Archival Memory of the Remote Past.

    Science.gov (United States)

    Scully, Marc; King, Turi; Brown, Steven D

    2013-10-01

    This article introduces some early data from the Leverhulme Trust-funded research programme, 'The Impact of the Diasporas on the Making of Britain: evidence, memories, inventions'. One of the interdisciplinary foci of the programme, which incorporates insights from genetics, history, archaeology, linguistics and social psychology, is to investigate how genetic evidence of ancestry is incorporated into identity narratives. In particular, we investigate how 'applied genetic history' shapes individual and familial narratives, which are then situated within macro-narratives of the nation and collective memories of immigration and indigenism. It is argued that the construction of genetic evidence as a 'gold standard' about 'where you really come from' involves a remediation of cultural and archival memory, in the construction of a 'usable past'. This article is based on initial questionnaire data from a preliminary study of those attending DNA collection sessions in northern England. It presents some early indicators of the perceived importance of being of Viking descent among participants, notes some emerging patterns and considers the implications for contemporary debates on migration, belonging and local and national identity.

  20. General surveillance of genetically modified crops : possibilities of GIS and remote sensing

    NARCIS (Netherlands)

    Roerink, G.J.; Danes, M.H.G.I.

    2010-01-01

    According EU legislation a General Surveillance is necessary to monitor for unanticipated adverse effects of genetically modified organisms on the environment. In this report a prototype of a monitoring system for such a Surveillance is introduced on the basis of time series analysis of satellite im

  1. Population Genetic Analyses of the Fungal Pathogen Colletotrichum fructicola on Tea-Oil Trees in China

    OpenAIRE

    He Li; Guo-Ying Zhou; Jun-Ang Liu; Jianping Xu

    2016-01-01

    The filamentous fungus Colletotrichum fructicola is found in all five continents and is capable of causing severe diseases in a number of economically important plants such as avocado, fig, cocoa, pear, and tea-oil trees. However, almost nothing is known about its patterns of genetic variation and epidemiology on any of its host plant species. Here we analyzed 167 isolates of C. fructicola obtained from the leaves of tea-oil tree Camellia oleifera at 15 plantations in seven Chinese provinces....

  2. On the remote interaction of biological objects with identical genetic structures

    CERN Document Server

    Berkovich, S Y

    2002-01-01

    The paper puts forward an unusual prediction that cultivating a clone can curtail the lifespan of the clone donor. Neither the arrangement of this suggested empirical study nor the analyses of the anticipated outcomes rely on the accompanying theoretical contemplations. This prediction has come from the interpretation of the genome as a "barcode". The genome is considered as an identification label rather than a repository of control information, so living beings are portrayed as a community of users on the "Internet of the physical Universe". Thus, biological objects with identical (or nearly identical) DNA structures can interfere, and the surmised remote impact appears tangible. The effect of clone-donor interaction leads to a decisive Experimentum Crucis that can reject the common view on the organization of biological information processing. Exploitation of this effect can be potentially dangerous.

  3. Molecular genetic analysis of consanguineous families with primary microcephaly identified pathogenic variants in the ASPM gene

    Indian Academy of Sciences (India)

    MUZAMMIL AHMAD KHAN; CHRISTIAN WINDPASSINGER; MUHAMMAD ZEESHAN ALI; MUHAMMAD ZUBAIR; HADIA GUL; SAFDAR ABBAS; SAADULLAH KHAN; MUHAMMAD BADAR; RAMZI M. MOHAMMAD; ZAFAR NAWAZ

    2017-06-01

    Autosomal recessive primary microcephaly is a rare genetic disorder that is characterized by reduced head circumference and a varying degree of intellectual disability. Genetic studies on consanguineous families with primary microcephaly have identified 15 (MCPH) causative genes that include MCPH1, WDR62, CDK5RAP2, CASC5, ASPM, CENPJ, STIL, CEP135,CEP152, ZNF335, PHC1, CDK6, CENPE, SASS6 MFSD2A ANKLE2 and CIT (Khan et al. 2014; Yamamoto et al. 2014; Alakbarzade et al. 2015;Morris-Rosendahl and Kaindl 2015; Basit et al. 2016). Physiologically, most of these MCPH proteins are involved in cell cycle and its regulation. In the present clinical genetic study, we have present two consanguineous Pakistanifamilies segregating primary microcephaly and intellectual disability. These families were ascertained from the Saraiki ethnic part of Khyber-Pakhtunkhwa province in Pakistan. Whole exome sequencing in one family revealed a novel 1-bp deletion NM_018136.4: c.10013delA (p.Asp3338Valfs*2), while the other family showed a previously reported nonsense mutation NM_018136.4: c.9730C>T (rs199422195 (p.Arg3244*)) in ASPM gene. The novel frame-shift mutation (p.Asp3338Valfs*2) in ASPM presumably truncates the protein synthesis that results in loss of armadillo-type fold domain.

  4. A practical guideline to remote biopsy darting of wildebeests for genetic sampling

    Directory of Open Access Journals (Sweden)

    Domnic Mijele

    2016-12-01

    Full Text Available The use of biopsy darts for remote collection of tissue samples from free-ranging terrestrial and aquatic animal species has gained popularity in the recent past. The success of darting is very important since scientists may not have many chances to re-dart the same animal, especially with the free-ranging elusive wildlife species. We used wildebeest (Connochaetes taurinus as a model to estimate the optimum shooting distance, pressure and the shot part of the body through which a researcher can optimize the success and amount of tissue collected from similar wild land mammalian species. Wildebeests were darted at six categories of distances ranging between 10 and 45 m and dart gun pressures of 5–14 millibar. The number of failed darts increased by increasing the darting distance: 0% (10 m, 0% (20 m, 6% (30 m, 20% (35 m, 71% (40 m, and 67% (45 m. There was a notable effect of the distances on the amount of tissue collected 20 m offered the best results. Dart gun pressure had no effect on the amount of tissue samples obtained. The amount of tissue obtained from successful darts was the same whether the animal was darted on the shoulder or thigh. In this paper, we present a practical guideline for remote biopsy darting of wildebeest to obtain optimum amount of tissue samples, which could be generalized for similar wild land mammalian species.

  5. Genetic and physiological activation of osmosensitive gene expression mimics transcriptional signatures of pathogen infection in C. elegans.

    Directory of Open Access Journals (Sweden)

    Anne-Katrin Rohlfing

    Full Text Available The soil-dwelling nematode C. elegans is a powerful system for comparative molecular analyses of environmental stress response mechanisms. Infection of worms with bacterial and fungal pathogens causes the activation of well-characterized innate immune transcriptional programs in pathogen-exposed hypodermal and intestinal tissues. However, the pathophysiological events that drive such transcriptional responses are not understood. Here, we show that infection-activated transcriptional responses are, in large part, recapitulated by either physiological or genetic activation of the osmotic stress response. Microarray profiling of wild type worms exposed to non-lethal hypertonicity identified a suite of genes that were also regulated by infection. Expression profiles of five different osmotic stress resistant (osr mutants under isotonic conditions reiterated the wild type transcriptional response to osmotic stress and also showed substantial similarity to infection-induced gene expression under isotonic conditions. Computational, transgenic, and functional approaches revealed that two GATA transcription factors previously implicated in infection-induced transcriptional responses, elt-2 and elt-3, are also essential for coordinated tissue-specific activation of osmosensitive gene expression and promote survival under osmotically stressful conditions. Together, our data suggest infection and osmotic adaptation share previously unappreciated transcriptional similarities which might be controlled via regulation of tissue-specific GATA transcription factors.

  6. Predicting the Pathogenic Potential of BRCA1 and BRCA2 Gene Variants Identified in Clinical Genetic Testing

    Directory of Open Access Journals (Sweden)

    Clare Brookes

    2015-05-01

    Full Text Available Objectives: Missense variants are very commonly detected when screening for mutations in the BRCA1 and BRCA2 genes. Pathogenic mutations in the BRCA1 and BRCA2 genes lead to an increased risk of developing breast, ovarian, prostate and/or pancreatic cancer. This study aimed to assess the predictive capability of in silico programmes and mutation databases in assisting diagnostic laboratories to determine the pathogenicity of sequence-detectable mutations. Methods: Between July 2011 and April 2013, an analysis was undertaken of 13 missense BRCA gene variants that had been detected in patients referred to the Genetic Health Services New Zealand (Northern Hub for BRCA gene analysis. The analysis involved the use of 13 in silico protein prediction programmes, two in silico transcript analysis programmes and the examination of three BRCA gene databases. Results: In most of the variants, the analysis showed different in silico interpretations. This illustrates the interpretation challenges faced by diagnostic laboratories. Conclusion: Unfortunately, when using online mutation databases and carrying out in silico analyses, there is significant discordance in the classification of some missense variants in the BRCA genes. This discordance leads to complexities in interpreting and reporting these variants in a clinical context. The authors have developed a simple procedure for analysing variants; however, those of unknown significance largely remain unknown. As a consequence, the clinical value of some reports may be negligible.

  7. The human genetic history of Oceania: near and remote views of dispersal.

    Science.gov (United States)

    Kayser, Manfred

    2010-02-23

    The human history of Oceania is unique in the way that it encompasses both the first out-of-Africa expansion of modern humans to New Guinea and Australia as well as the last regional human occupation of Polynesia. Other anthropological peculiarities of Oceania include features like the extraordinarily rich linguistic diversity especially of New Guinea with about 1,000 often very distinct languages, the independent and early development of agriculture in the highlands of New Guinea about 10,000 years ago, or the long-term isolation of the entire region from the outside world, which lasted as long as until the 1930s for most of the interior of New Guinea. This review will provide an overview on the genetic aspects of human population history of Oceania and how some of the anthropological peculiarities are reflected in human genetic data. Due to current data availability it will mostly focus on insights from sex-specifically inherited mitochondrial DNA and Y-chromosomal DNA, whereas more genome-wide autosomal DNA data are soon expected to add additional details or may correct views obtained from these two, albeit highly complex, genetic loci. Copyright 2010 Elsevier Ltd. All rights reserved.

  8. Biopreparedness in the Age of Genetically Engineered Pathogens and Open Access Science: An Urgent Need for a Paradigm Shift.

    Science.gov (United States)

    MacIntyre, C Raina

    2015-09-01

    Our systems, thinking, training, legislation, and policies are lagging far behind momentous changes in science, and leaving us vulnerable in biosecurity. Synthetic viruses and genetic engineering of pathogens are a reality, with a rapid acceleration of dual-use science. The public availability of methods for dual-use genetic engineering, coupled with the insider threat, poses an unprecedented risk for biosecurity. Case studies including the 1984 Rajneesh salmonella bioterrorism attack and the controversy over engineered transmissible H5N1 influenza are analyzed. Simple probability analysis shows that the risks of dual-use research are likely to outweigh potential benefits, yet this type of analysis has not been done to date. Many bioterrorism agents may also occur naturally. Distinguishing natural from unnatural epidemics is far more difficult than other types of terrorism. Public health systems do not have mechanisms for routinely considering bioterrorism, and an organizational culture that is reluctant to consider it. A collaborative model for flagging aberrant outbreak patterns and referral from the health to security sectors is proposed. Vulnerabilities in current approaches to biosecurity need to be reviewed and strengthened collaboratively by all stakeholders. New systems, legislation, collaborative operational models, and ways of thinking are required to effectively address the threat to global biosecurity.

  9. Genetic diversity and pathogenicity of Fusarium species associated with fruit rot disease in banana across Peninsular Malaysia.

    Science.gov (United States)

    Abd Murad, Nur Baiti; Nik Mohamed, Nik Mohd Izham; Shohaimi, Shamarina; Mohd Zainudin, Nur Ain Izzati

    2017-09-11

    The aims of this study are to identify the Fusarium isolates based on translation elongation factor (tef) 1α sequence, to determine the genetic diversity among isolates and species using selected microsatellite markers, and to examine the pathogenicity of Fusarium isolates causing fruit rot disease of banana. One-hundred thirteen microfungi isolates were obtained from fruit rot infected banana in Peninsular Malaysia. However, this study was focused on the dominant number of the discovered microfungi that belongs to the genus Fusarium. There were 48 isolates of the microfungi have been identified belonging to 11 species of Fusarium namely Fusarium incarnatum, Fusarium equiseti, Fusarium camptoceras, Fusarium solani, Fusarium concolor, Fusarium oxysporum, Fusarium proliferatum, Fusarium verticillioides, Fusarium sacchari, Fusarium concentricum, and Fusarium fujikuroi. All Fusarium isolates were grouped into their respective clades indicating their similarities and differences in genetic diversity among isolates. Out of 48 Fusarium isolates tested, 42 isolates causing the fruit rot symptom at different levels of severity based on Disease Severity Index (DSI). The most virulent isolate was F. proliferatum B2433B with DSI of 100%. All the isolated Fusarium species were successfully identified with some of them were confirmed as the causal agents of pre- and post-harvest fruit rot in banana across Peninsular Malaysia. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  10. Phylogenetic and population genetic divergence correspond with habitat for the pathogen Colletotrichum cereale and allied taxa across diverse grass communities.

    Science.gov (United States)

    Crouch, Jo Anne; Tredway, Lane P; Clarke, Bruce B; Hillman, Bradley I

    2009-01-01

    Over the past decade, the emergence of anthracnose disease has newly challenged the health of turfgrasses on North American golf courses, resulting in considerable economic loss. The fungus responsible for the outbreaks, Colletotrichum cereale, has also been identified from numerous natural grasses and cereal crops, although disease symptoms are generally absent. Here we utilize phylogenetic and population genetic analyses to determine the role of ecosystem in the advancement of turfgrass anthracnose and assess whether natural grass and/or cereal inhabitants are implicated in the epidemics. Using a four-gene nucleotide data set to diagnose the limits of phylogenetic species and population boundaries, we find that the graminicolous Colletotrichum diverged from a common ancestor into distinct lineages correspondent with host physiology (C3 or C4 photosynthetic pathways). In the C4 lineage, which includes the important cereal pathogens Colletotrichum graminicola, C. sublineolum, C. falcatum, C. eleusines, C. caudatum and several novel species, host specialization predominates, with host-associated lineages corresponding to isolated sibling species. Although the C3 lineage--C. cereale--is comprised of one wide host-range species, it is divided into 10 highly specialized populations corresponding to ecosystem and/or host plant, along with a single generalist population spread across multiple habitat types. Extreme differentiation between the specialized C. cereale populations suggests that asymptomatic nonturfgrass hosts are unlikely reservoirs of infectious disease propagules, but gene flow between the generalist population and the specialized genotypes provides an indirect mechanism for genetic exchange between otherwise isolated populations and ecosystems.

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

    Science.gov (United States)

    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.

  12. Evaluation and Genetic Analysis of Five Parental Varieties Resistant to Rice Blast Pathogen in Heilongjiang Province

    Institute of Scientific and Technical Information of China (English)

    Zhang Zhong-chen; Liu Hong-liang; Gao Hong-xiu; Liu Hai-ying; Jin Zheng-xun

    2012-01-01

    Five F2 segregation populations, derived from crosses between the susceptible japonica cultivars (cvs.) Kongyul31 and donor cvs. Aichi Asahi (AA), BL1, Digu, Pai-kan-tao (PKT) and Oryzica Llanos 5 (ORL5), were used to evaluate their natural resistance to blast in cold region. The field test of their blast resistance was conducted in 858 Farm, which showed that Aichi Asahi, BL 1 and Digu were highly resistant to either leaf blast or neck blast and could be used to develop molecular breeding by design, and genetic analysis indicated that the field resistance of Aichi Asahi, BLland Digu to leaf blast and neck blast was controlled by a single dominant gene, and the leaf blast and neck blast resistance in the donor cv. Pai-kan-tao was inherited as a single recessive gene, the neck blast resistance of the donor cv. Oryzica Llanos 5 was controlled by a single recessive gene while its leaf blast resistance was not controlled by this gene. These results suggested that five parental varieties positively contributed to resistance to either leaf blast or neck blast and could be used to expand the genetic germplasms resistant to blast in cold region using molecular assisted selection.

  13. Genetic characterization and pathogenicity assessment of Newcastle disease virus isolated from wild peacock.

    Science.gov (United States)

    Khulape, Sagar A; Gaikwad, Satish S; Chellappa, Madhan Mohan; Mishra, Bishnu Prasad; Dey, Sohini

    2014-12-01

    The continued spread and occurrence of Newcastle disease virus (NDV) has posed potential threat to domestic poultry industry around the globe. Mainly, wild avian species has always been implicated for the natural reservoir for virus and spread of the disease. In the present study, we report the isolation of Newcastle disease virus (NDV/Peacock/India/2012) in necropsy brain tissue sample of wild peacock from North India. Complete genome of the virus was found to be 15,186 nucleotides (nts) with six genes in order of 3'-N-P-M-F-HN-L-5', which was limited by 55-nts leader region at the 3' end and a 114-nts trailer sequence at 5' end. Sequence analysis of fusion protein revealed the dibasic amino acid cleavage site (112)R-R-Q-K-R-F(117), a characteristic motif of virulent virus. Phylogenetic analysis placed the isolate in genotype II of Newcastle disease virus showing the lowest mean percent divergence (6 %) with other genotype II counterparts. The isolate was characterized as mesogenic (intermediate pathotype) based on the mean death time (63 h) in embryonated chicken eggs and the intra-cerebral pathogenicity index (1.40) in day-old chicks. The report emphasizes the dynamic ecology of NDV strains circulating in a wild avian host during the outbreak of 2012 in North India. Further the genotypic and pathotypical characterizations of the isolate could help in development of homologous vaccine against NDV strain circulating in avian population.

  14. Genetic Analyses Suggest Separate Introductions of the Pine Pathogen Lecanosticta acicola Into Europe.

    Science.gov (United States)

    Janoušek, Josef; Wingfield, Michael J; Monsivais, José G Marmolejo; Jankovský, Libor; Stauffer, Christian; Konečný, Adam; Barnes, Irene

    2016-11-01

    Lecanosticta acicola is a heterothallic ascomycete that causes brown spot needle blight on native and nonnative Pinus spp. in many regions of the world. In this study we investigated the origin of European L. acicola populations and estimated the level of random mating of the pathogen in affected areas. Part of the elongation factor 1-α gene was sequenced, 11 microsatellite regions were screened, and the mating type idiomorphs were determined for 201 isolates of L. acicola collected from three continents and 17 host species. The isolates from Mexico and Guatemala were unique, highly diverse and could represent cryptic species of Lecanosticta. The isolates from East Asia formed a uniform and discrete group. Two distinct populations were identified in both North America and Europe. Approximate Bayesian computation analyses strongly suggest independent introductions of two populations from North America into Europe. Microsatellite data and mating type distributions indicated random recombination in the populations of North America and Europe. Its intercontinental introduction can most likely be explained as a consequence of the movement of infected plant material. In contrast, the spread of L. acicola within Europe appears to be primarily due to conidial dispersion and probably also ascospore dissemination.

  15. Genetics of biosynthesis and structure of the capsular exopolysaccharide from the Asian pear pathogen Erwinia pyrifoliae.

    Science.gov (United States)

    Kim, Won-Sik; Schollmeyer, Martin; Nimtz, Manfred; Wray, Victor; Geider, Klaus

    2002-12-01

    Erwinia pyrifoliae is a novel bacterial pathogen, which causes Asian pear blight and is related to Erwinia amylovora, the causative agent of fire blight. E. pyrifoliae produces exopolysaccharide (EPS) related to amylovoran in its sugar composition and sugar linkages. This was shown by degradation of the EPS with a viral depolymerase, and by methylation analysis and ESI/MS. The structure of the repeating units was confirmed by (1)H-NMR spectra. The EPS of E. pyrifoliae carried side chains, which were mainly terminated by acetyl and pyruvyl residues as found previously for amylovoran. On the other hand, a second side chain with glucose found for up to 65% of the repeating units of amylovoran was completely absent. The nucleotide sequences of five genes of the cps cluster of E. pyrifoliae encoding proteins for EPS synthesis were characterized and displayed a high homology with the corresponding ams genes. Similar functions of the gene products are assumed. As for ams mutants of E. amylovora, a cpsB mutant of E. pyrifoliae did not synthesize EPS and did not produce ooze on slices of immature pears or symptoms on pear seedlings. The cps mutant was complemented for EPS synthesis and virulence on pear slices with a gene cluster of E. amylovora that included amsB.

  16. Biological and genetic factors regulating natural competence in a bacterial plant pathogen.

    Science.gov (United States)

    Kung, Stephanie H; Almeida, Rodrigo P P

    2014-01-01

    For naturally competent bacteria, spatially structured growth can provide an environment for enhanced horizontal gene transfer through transformation and recombination. DNA is often present in the extracellular environment, such as in the extracellular matrix of biofilms, and the lysis of a single cell can result in high local DNA concentrations. Xylella fastidiosa is a naturally competent plant pathogen that typically lives in a surface-attached state, yet previous work characterizing the competence of this organism was conducted with planktonic cells in liquid environments. Here, we show that transformation and recombination efficiencies are two to three orders of magnitude higher for cells grown on solid compared with liquid media, with maximum recombination efficiencies of about 10(-3). Cells were highly competent throughout their exponential growth phase, with no significant change in recombination efficiencies until population growth rates began to slow. Mutations in type IV pili, competency-related, and cell-cell signalling genes significantly impacted the ability of X. fastidiosa to acquire and incorporate DNA. Because X. fastidiosa is highly competent when growing in a surface-attached state, as it does within its insect vectors and host plants, recombination of naturally transformed DNA could be a significant route by which horizontal gene transfer occurs in natural environments.

  17. Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome.

    Directory of Open Access Journals (Sweden)

    Tim van Opijnen

    2016-09-01

    Full Text Available The interaction between an antibiotic and bacterium is not merely restricted to the drug and its direct target, rather antibiotic induced stress seems to resonate through the bacterium, creating selective pressures that drive the emergence of adaptive mutations not only in the direct target, but in genes involved in many different fundamental processes as well. Surprisingly, it has been shown that adaptive mutations do not necessarily have the same effect in all species, indicating that the genetic background influences how phenotypes are manifested. However, to what extent the genetic background affects the manner in which a bacterium experiences antibiotic stress, and how this stress is processed is unclear. Here we employ the genome-wide tool Tn-Seq to construct daptomycin-sensitivity profiles for two strains of the bacterial pathogen Streptococcus pneumoniae. Remarkably, over half of the genes that are important for dealing with antibiotic-induced stress in one strain are dispensable in another. By confirming over 100 genotype-phenotype relationships, probing potassium-loss, employing genetic interaction mapping as well as temporal gene-expression experiments we reveal genome-wide conditionally important/essential genes, we discover roles for genes with unknown function, and uncover parts of the antibiotic's mode-of-action. Moreover, by mapping the underlying genomic network for two query genes we encounter little conservation in network connectivity between strains as well as profound differences in regulatory relationships. Our approach uniquely enables genome-wide fitness comparisons across strains, facilitating the discovery that antibiotic responses are complex events that can vary widely between strains, which suggests that in some cases the emergence of resistance could be strain specific and at least for species with a large pan-genome less predictable.

  18. Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome.

    Science.gov (United States)

    van Opijnen, Tim; Dedrick, Sandra; Bento, José

    2016-09-01

    The interaction between an antibiotic and bacterium is not merely restricted to the drug and its direct target, rather antibiotic induced stress seems to resonate through the bacterium, creating selective pressures that drive the emergence of adaptive mutations not only in the direct target, but in genes involved in many different fundamental processes as well. Surprisingly, it has been shown that adaptive mutations do not necessarily have the same effect in all species, indicating that the genetic background influences how phenotypes are manifested. However, to what extent the genetic background affects the manner in which a bacterium experiences antibiotic stress, and how this stress is processed is unclear. Here we employ the genome-wide tool Tn-Seq to construct daptomycin-sensitivity profiles for two strains of the bacterial pathogen Streptococcus pneumoniae. Remarkably, over half of the genes that are important for dealing with antibiotic-induced stress in one strain are dispensable in another. By confirming over 100 genotype-phenotype relationships, probing potassium-loss, employing genetic interaction mapping as well as temporal gene-expression experiments we reveal genome-wide conditionally important/essential genes, we discover roles for genes with unknown function, and uncover parts of the antibiotic's mode-of-action. Moreover, by mapping the underlying genomic network for two query genes we encounter little conservation in network connectivity between strains as well as profound differences in regulatory relationships. Our approach uniquely enables genome-wide fitness comparisons across strains, facilitating the discovery that antibiotic responses are complex events that can vary widely between strains, which suggests that in some cases the emergence of resistance could be strain specific and at least for species with a large pan-genome less predictable.

  19. The gonococcal genetic island and type IV secretion in the pathogenic Neisseria

    Directory of Open Access Journals (Sweden)

    Meghan E Ramsey

    2011-04-01

    Full Text Available Eighty percent of Neisseria gonorrhoeae strains and some Neisseria meningitidis strains encode a 57 kb gonococcal genetic island (GGI. The GGI was horizontally acquired and is inserted in the chromosome at the replication terminus. The GGI is flanked by direct repeats, and site-specific recombination at these sites results in excision of the GGI and may be responsible for its original acquisition. Although the role of the GGI in N. meningitidis is unclear, the GGI in N. gonorrhoeae encodes a type IV secretion system (T4SS. Type IV secretion systems are versatile multi-protein complexes and include both conjugation systems as well as effector systems that translocate either proteins or DNA-protein complexes. In N. gonorrhoeae, the T4SS secretes single-stranded chromosomal DNA into the extracellular milieu in a contact-independent manner. Importantly, the DNA secreted through the T4SS is effective in natural transformation and therefore contributes to the spread of genetic information through Neisseria populations. Mutagenesis experiments have identified genes for DNA secretion including those encoding putative structural components of the apparatus, peptidoglycanases which may act in assembly, and relaxosome components for processing the DNA and delivering it to the apparatus. The T4SS may also play a role in infection by N. gonorrhoeae. During intracellular infection, N. gonorrhoeae requires the Ton complex for iron acquisition and survival. However, N. gonorrhoeae strains that do not express the Ton complex can survive intracellularly if they express structural components of the T4SS. These data provide evidence that the T4SS is expressed during intracellular infection and suggest that the T4SS may provide an advantage for intracellular survival. Here we review our current understanding of how the GGI and type IV secretion affect natural transformation and pathogenesis in N. gonorrhoeae and N. meningitidis.

  20. Genetic signatures of variation in population size in a native fungal pathogen after the recent intensive plantation of its host tree

    NARCIS (Netherlands)

    Labbé, Frédéric; Fontaine, Michael Christophe; Robin, Cécile; Dutech, Cyril

    2017-01-01

    Historical fluctuations in forests’ distribution driven by past climate changes and anthropogenic activities can have large impacts on the demographic history of pathogens that have a long co-evolution history with these host trees. Using a population genetic approach, we investigated that

  1. Genetic structure and pathogenicity of populations of Phytophthora infestans from organic potato crops in France, Norway, Switzerland and the United Kingdom

    NARCIS (Netherlands)

    Flier, W.G.; Kroon, L.P.N.M.; Hermansen, A.; Raaij, van H.M.G.; Speiser, B.; Tamm, L.; Fuchs, J.G.; Lambion, J.; Razzaghian, J.; Andrivon, D.; Wilcockson, S.; Leifert, C.

    2007-01-01

    Genetic variation and pathogenicity of Pbytophthora infestans isolates collected from organic potato crops of the susceptible cv. Bintje and the moderately resistant cv. Sante were assessed in France, Norway, and the United Kingdom in 2001 and in Switzerland in 2001 and 2002. Population structures d

  2. Optimizing production of recombinant tissue plasminogen activator in non-pathogenic Leishmania by two genetic constructs

    Directory of Open Access Journals (Sweden)

    Hemayatkar M

    2011-02-01

    Full Text Available "nBackground: Recombinant tissue plasminogen activator (rt-PA is one of the most important thrombolytic agents used in patients with vascular occlusions such as acute ischemic stroke or myocardial infarction. A variety of recombinant protein expression systems have been developed for heterologous gene expression in prokaryotic and eukaryotic hosts. In recent years, Leishmania tarentolae (L. tarentolae, a non-pathogenic trypanosomatid protozoa, has come under consideration because of its safety and immunogenicity as a vaccine vector and special attributes in the expression of complex proteins. This study was done to improve rt-PA expression in this protozoon and create the opportunity for the replacement of rt-PA gene with other genes for the production of other complex proteins."n "n Methods: Two expression cassettes were used for the integration of two copies of t-PA cDNA, one copy in each cassette, into the parasite genome by electroporation. The transformed clones were selected by antibiotic resistancy. The expression of active secreted rt-PA was confirmed by Western blot analysis and Chromolize assay."n "n Results: Appearance of a 64 kD band in nitrocellulose membrane in the Western blot analysis confirmed the presence of full-length rt-PA in the culture media. Chromolize assay showed the expression levels of active recombinant t-PA in single and double transfected L. tarentolae clones- 375 IU/ml and 480 IU/ml of the culture media, respectively."n "n Conclusion: The produced rt-PA in the culture media containing the transfected cells was at least seven times higher than what has been reported in previous studies on L. tarentolae or on some other eukaryotic systems.

  3. Analysis of multi-strain Bartonella pathogens in natural host population--do they behave as species or minor genetic variants?

    Science.gov (United States)

    Chan, Kung-Sik; Kosoy, Michael

    2010-12-01

    Modern advances in genetic analysis have made it feasible to ascertain the variant type of a pathogen infecting a host. Classification of pathogen variants is commonly performed by clustering analysis of the observed genetic divergence among the variants. A natural question arises whether the genetically distinct variants are epidemiologically distinct. A broader question is whether the different variants constitute separate microbial species or represent minor variations of the same species. These important issues were addressed in the context of analyzing dynamics of genetically distinct variants of Bartonella bacteria in cotton rat hosts. Frequencies of acquiring a new variant were measured in relation to the genetic differences between variants successively infecting an individual rodent host. Two statistical techniques were introduced for performing such analysis, and the methodologies were illustrated with a set of data collected from a particular multi-strain Bartonella system. We carried out a frequency analysis of co-infection patterns, and a Markov chain analysis of panels of successive mixed infection time series for testing some particular gene-based grouping of the Bartonella variants with a panel of observed disease data from a rodent population. Our analysis suggests that the three genogroups A, B and C of Bartonella function as independent species but the variants within each genogroup enjoy some cross-immunity against each other. The newly developed methodologies are broadly applicable for analyzing other multi-strain pathogen data which are increasingly collected for diverse infectious diseases.

  4. Genetically Diverse Low Pathogenicity Avian Influenza A Virus Subtypes Co-Circulate among Poultry in Bangladesh.

    Science.gov (United States)

    Gerloff, Nancy A; Khan, Salah Uddin; Zanders, Natosha; Balish, Amanda; Haider, Najmul; Islam, Ausraful; Chowdhury, Sukanta; Rahman, Mahmudur Ziaur; Haque, Ainul; Hosseini, Parviez; Gurley, Emily S; Luby, Stephen P; Wentworth, David E; Donis, Ruben O; Sturm-Ramirez, Katharine; Davis, C Todd

    2016-01-01

    Influenza virus surveillance, poultry outbreak investigations and genomic sequencing were assessed to understand the ecology and evolution of low pathogenicity avian influenza (LPAI) A viruses in Bangladesh from 2007 to 2013. We analyzed 506 avian specimens collected from poultry in live bird markets and backyard flocks to identify influenza A viruses. Virus isolation-positive specimens (n = 50) were subtyped and their coding-complete genomes were sequenced. The most frequently identified subtypes among LPAI isolates were H9N2, H11N3, H4N6, and H1N1. Less frequently detected subtypes included H1N3, H2N4, H3N2, H3N6, H3N8, H4N2, H5N2, H6N1, H6N7, and H7N9. Gene sequences were compared to publicly available sequences using phylogenetic inference approaches. Among the 14 subtypes identified, the majority of viral gene segments were most closely related to poultry or wild bird viruses commonly found in Southeast Asia, Europe, and/or northern Africa. LPAI subtypes were distributed over several geographic locations in Bangladesh, and surface and internal protein gene segments clustered phylogenetically with a diverse number of viral subtypes suggesting extensive reassortment among these LPAI viruses. H9N2 subtype viruses differed from other LPAI subtypes because genes from these viruses consistently clustered together, indicating this subtype is enzootic in Bangladesh. The H9N2 strains identified in Bangladesh were phylogenetically and antigenically related to previous human-derived H9N2 viruses detected in Bangladesh representing a potential source for human infection. In contrast, the circulating LPAI H5N2 and H7N9 viruses were both phylogenetically and antigenically unrelated to H5 viruses identified previously in humans in Bangladesh and H7N9 strains isolated from humans in China. In Bangladesh, domestic poultry sold in live bird markets carried a wide range of LPAI virus subtypes and a high diversity of genotypes. These findings, combined with the seven year

  5. Genetically Diverse Low Pathogenicity Avian Influenza A Virus Subtypes Co-Circulate among Poultry in Bangladesh.

    Directory of Open Access Journals (Sweden)

    Nancy A Gerloff

    Full Text Available Influenza virus surveillance, poultry outbreak investigations and genomic sequencing were assessed to understand the ecology and evolution of low pathogenicity avian influenza (LPAI A viruses in Bangladesh from 2007 to 2013. We analyzed 506 avian specimens collected from poultry in live bird markets and backyard flocks to identify influenza A viruses. Virus isolation-positive specimens (n = 50 were subtyped and their coding-complete genomes were sequenced. The most frequently identified subtypes among LPAI isolates were H9N2, H11N3, H4N6, and H1N1. Less frequently detected subtypes included H1N3, H2N4, H3N2, H3N6, H3N8, H4N2, H5N2, H6N1, H6N7, and H7N9. Gene sequences were compared to publicly available sequences using phylogenetic inference approaches. Among the 14 subtypes identified, the majority of viral gene segments were most closely related to poultry or wild bird viruses commonly found in Southeast Asia, Europe, and/or northern Africa. LPAI subtypes were distributed over several geographic locations in Bangladesh, and surface and internal protein gene segments clustered phylogenetically with a diverse number of viral subtypes suggesting extensive reassortment among these LPAI viruses. H9N2 subtype viruses differed from other LPAI subtypes because genes from these viruses consistently clustered together, indicating this subtype is enzootic in Bangladesh. The H9N2 strains identified in Bangladesh were phylogenetically and antigenically related to previous human-derived H9N2 viruses detected in Bangladesh representing a potential source for human infection. In contrast, the circulating LPAI H5N2 and H7N9 viruses were both phylogenetically and antigenically unrelated to H5 viruses identified previously in humans in Bangladesh and H7N9 strains isolated from humans in China. In Bangladesh, domestic poultry sold in live bird markets carried a wide range of LPAI virus subtypes and a high diversity of genotypes. These findings, combined with the

  6. Genetic Particle Swarm Optimization-Based Feature Selection for Very-High-Resolution Remotely Sensed Imagery Object Change Detection.

    Science.gov (United States)

    Chen, Qiang; Chen, Yunhao; Jiang, Weiguo

    2016-07-30

    In the field of multiple features Object-Based Change Detection (OBCD) for very-high-resolution remotely sensed images, image objects have abundant features and feature selection affects the precision and efficiency of OBCD. Through object-based image analysis, this paper proposes a Genetic Particle Swarm Optimization (GPSO)-based feature selection algorithm to solve the optimization problem of feature selection in multiple features OBCD. We select the Ratio of Mean to Variance (RMV) as the fitness function of GPSO, and apply the proposed algorithm to the object-based hybrid multivariate alternative detection model. Two experiment cases on Worldview-2/3 images confirm that GPSO can significantly improve the speed of convergence, and effectively avoid the problem of premature convergence, relative to other feature selection algorithms. According to the accuracy evaluation of OBCD, GPSO is superior at overall accuracy (84.17% and 83.59%) and Kappa coefficient (0.6771 and 0.6314) than other algorithms. Moreover, the sensitivity analysis results show that the proposed algorithm is not easily influenced by the initial parameters, but the number of features to be selected and the size of the particle swarm would affect the algorithm. The comparison experiment results reveal that RMV is more suitable than other functions as the fitness function of GPSO-based feature selection algorithm.

  7. Associations of Leaf Spectra with Genetic and Phylogenetic Variation in Oaks: Prospects for Remote Detection of Biodiversity

    Directory of Open Access Journals (Sweden)

    Jeannine Cavender-Bares

    2016-03-01

    Full Text Available Species and phylogenetic lineages have evolved to differ in the way that they acquire and deploy resources, with consequences for their physiological, chemical and structural attributes, many of which can be detected using spectral reflectance form leaves. Recent technological advances for assessing optical properties of plants offer opportunities to detect functional traits of organisms and differentiate levels of biological organization across the tree of life. Here, we connect leaf-level full range spectral data (400–2400 nm of leaves to the hierarchical organization of plant diversity within the oak genus (Quercus using field and greenhouse experiments in which environmental factors and plant age are controlled. We show that spectral data significantly differentiate populations within a species and that spectral similarity is significantly associated with phylogenetic similarity among species. We further show that hyperspectral information allows more accurate classification of taxa than spectrally-derived traits, which by definition are of lower dimensionality. Finally, model accuracy increases at higher levels in the hierarchical organization of plant diversity, such that we are able to better distinguish clades than species or populations. This pattern supports an evolutionary explanation for the degree of optical differentiation among plants and demonstrates potential for remote detection of genetic and phylogenetic diversity.

  8. Genetic Diversity and Pathogenic Variation of Colletotrichum lindemuthianum in the Three Centers of Diversity of Its Host, Phaseolus vulgaris.

    Science.gov (United States)

    Sicard, D; Michalakis, Y; Dron, M; Neema, C

    1997-08-01

    ABSTRACT Population subdivision of Colletotrichum lindemuthianum, the causal agent of anthracnose, was studied in three regions located in three centers of diversity of its host, Phaseolus vulgaris. Random amplified polymorphic DNA (RAPD) markers, restriction endonuclease analysis of the amplified ribosomal internal transcribed spacer region, and virulence on a set of 12 cultivars were used to assess the genetic diversity of C. lindemuthianum strains isolated in Mexican, Ecuadorian, and Argentinean wild common bean populations. The three regions were significantly differentiated for molecular markers. For these markers, Mexico was the most polymorphic and the most distant from Ecuador and Argentina. The majority of the RAPD alleles present in Ecuador and Argentina were found in Mexico, suggesting that Andean populations have been derived from the Mesoamerican center. Pathogenicity tests on a set of 12 cultivars showed that all but one of the Mexican strains were virulent exclusively on Mesoamerican cultivars. Argentinean strains were virulent preferentially on southern Andes cultivars, and the Ecuadorian strains, except for one strain, were avirulent on all cultivars. These results suggest an adaptation of strains on cultivars of the same geographic origin. Thus, based on molecular and virulence markers, C. lindemuthianum strains isolated from wild common bean populations were divided into three groups corresponding to host gene pools.

  9. Amplification of the cap20 pathogenicity gene and genetic characterization using different markers molecular in Colletotrichum gloeosporioides isolates

    Directory of Open Access Journals (Sweden)

    Danielli Barreto Maciel

    2010-12-01

    Full Text Available Studies were performed to analyze the genetic characterization using RFLP-ITS and Intron (primer EI1 markers and the amplification of the cap20 pathogenicity gene by PCR in Colletotrichum gloeosporioides isolates of different hosts plant. The genetic variability was accessed using RFLP-ITS and Intron markers and grouping by UPGMA method. Primers to cap20 gene were constructed using selected sequences of the GenBank (National Center of Biotechnology Information, http://www.ncbi.nlm.nih.gov with the Primer 3 program. The dendrograms analysis showed that the RFLP-ITS marker was more informative to separate the Colletotrichum sp, and that primer EI1 demonstrated greater genetic diversity. The amplification of the DNA of the Colletotrichum isolates to the cap20 gene with primers P1 and P2 indicated that this gene could present variations into C. gloeosporioides related with the host, and also that it was present in other Colletotrichum sp.Estudos foram realizados para analisar a caracterização genética usando marcadores de RFLP-ITS e ISSP e a amplicação do gene de patogenicidade cap20 por PCR em isolados de Colletotrichum gloeosporioides de diferentes hospedeiros. Primers para o gene cap20 foram construídos a partir de seqüências selecionadas do GenBank (National Center of Biotechnology Information, http://www.ncbi.nlm.nih.gov com o programa Primer 3. A análise dos dendrogramas revelou que o marcador RFLP-ITS foi mais informativo em separar as espécies de Colletotrichum, e que o primer EI1 evidenciou maior diversidade genética. A amplificação do DNA dos isolados de Colletotrichum para o gene cap20 com os primers P1 e P2 indicou que este gene pode apresentar variações dentro de C. gloeosporioides relacionada ao hospedeiro, e que também está presente em outras espécies de Colletotrichum.

  10. The Pseudomonas viridiflava phylogroups in the P. syringae species complex are characterized by genetic variability and phenotypic plasticity of pathogenicity-related traits.

    Science.gov (United States)

    Bartoli, Claudia; Berge, Odile; Monteil, Caroline L; Guilbaud, Caroline; Balestra, Giorgio M; Varvaro, Leonardo; Jones, Corbin; Dangl, Jeffery L; Baltrus, David A; Sands, David C; Morris, Cindy E

    2014-07-01

    As a species complex, Pseudomonas syringae exists in both agriculture and natural aquatic habitats. P.viridiflava, a member of this complex, has been reported to be phenotypically largely homogenous. We characterized strains from different habitats, selected based on their genetic similarity to previously described P.viridiflava strains. We revealed two distinct phylogroups and two different kinds of variability in phenotypic traits and genomic content. The strains exhibited phase variation in phenotypes including pathogenicity and soft rot on potato. We showed that the presence of two configurations of the Type III Secretion System [single (S-PAI) and tripartite (T-PAI) pathogenicity islands] are not correlated with pathogenicity or with the capacity to induce soft rot in contrast to previous reports. The presence/absence of the avrE effector gene was the only trait we found to be correlated with pathogenicity of P.viridiflava. Other Type III secretion effector genes were not correlated with pathogenicity. A genomic region resembling an exchangeable effector locus (EEL) was found in S-PAI strains, and a probable recombination between the two PAIs is described. The ensemble of the variability observed in these phylogroups of P.syringae likely contributes to their adaptability to alternating opportunities for pathogenicity or saprophytic survival.

  11. MATLAB code to estimate landslide volume from single remote sensed image using genetic algorithm and imagery similarity measurement

    Science.gov (United States)

    Wang, Ting-Shiuan; Yu, Teng-To; Lee, Shing-Tsz; Peng, Wen-Fei; Lin, Wei-Ling; Li, Pei-Ling

    2014-09-01

    Information regarding the scale of a hazard is crucial for the evaluation of its associated impact. Quantitative analysis of landslide volume immediately following the event can offer better understanding and control of contributory factors and their relative importance. Such information cannot be gathered for each landslide event, owing to limitations in obtaining useable raw data and the necessary procedures of each applied technology. Empirical rules are often used to predict volume change, but the resulting accuracy is very low. Traditional methods use photogrammetry or light detection and ranging (LiDAR) to produce a post-event digital terrain model (DTM). These methods are both costly and time-intensive. This study presents a technique to estimate terrain change volumes quickly and easily, not only reducing waiting time but also offering results with less than 25% error. A genetic algorithm (GA) programmed MATLAB is used to intelligently predict the elevation change for each pixel of an image. This deviation from the pre-event DTM becomes a candidate for the post-event DTM. Thus, each changed DTM is converted into a shadow relief image and compared with a single post-event remotely sensed image for similarity ranking. The candidates ranked in the top two thirds are retained as parent chromosomes to produce offspring in the next generation according to the rules of GAs. When the highest similarity index reaches 0.75, the DTM corresponding to that hillshade image is taken as the calculated post-event DTM. As an example, a pit with known volume is removed from a flat, inclined plane to demonstrate the theoretical capability of the code. The method is able to rapidly estimate the volume of terrain change within an error of 25%, without the delays involved in obtaining stereo image pairs, or the need for ground control points (GCPs) or professional photogrammetry software.

  12. In vitro responses of chicken macrophage-like monocytes following exposure to pathogenic and non-pathogenic E. coli ghosts loaded with a rational design of conserved genetic materials of influenza and Newcastle disease viruses.

    Science.gov (United States)

    Lagzian, Milad; Bassami, Mohammad Reza; Dehghani, Hesam

    2016-08-01

    Avian influenza virus (AIV) and Newcastle disease virus (NDV) are two important viral diseases in the poultry industry. Therefore, new disease-fighting strategies, especially effective genetic vaccination, are in high demand. Bacterial Ghost (BG) is a promising platform for delivering genetic materials to macrophages, cells that are among the first to encounter these viruses. However, there is no investigation on the immune response of these macrophage-targeted treatments. Here, we investigated the effect of genetic materials of AIV and NDV on the gene expression profile of important pro-inflammatory cytokines, a chemokine, a transcription factor, major histocompatibility complexes, and the viability of the chicken macrophage-like monocyte cells (CMM). Our genetic construct contained the external domain of matrix protein 2 and nucleoprotein gene of AIV, and immunodominant epitopes of fusion and hemagglutinin-neuraminidase proteins of NDV (hereinafter referred to as pAIV-Vax), delivered via the pathogenic and non-pathogenic BGs (Escherichia coli O78K80 and E. coli TOP10 respectively). The results demonstrated that both types of BGs were able to efficiently deliver the construct to the CMM, although the pathogenic strain derived BG was a significantly better stimulant and delivery vehicle. Both BGs were safe regarding LPS toxicity and did not induce any cell death. Furthermore, the loaded BGs were more powerful in modulating the pro-inflammatory cytokines' responses and antigen presentation systems in comparison to the unloaded BGs. Nitric oxide production of the BG-stimulated cells was also comparable to those challenged by the live bacteria. According to the results, the combination of pAIV-Vax construct and E. coli O78K80 BG is promising in inducing a considerable innate and adaptive immune response against AIV-NDV and perhaps the pathogenic E. coli, provided that the current combination be a potential candidate for in vivo testing regarding the development of an

  13. Recent range expansion and agricultural landscape heterogeneity have only minimal effect on the spatial genetic structure of the plant pathogenic fungus Mycosphaerella fijiensis.

    Science.gov (United States)

    Rieux, A; De Lapeyre De Bellaire, L; Zapater, M-F; Ravigne, V; Carlier, J

    2013-01-01

    Understanding how geographical and environmental features affect genetic variation at both the population and individual levels is crucial in biology, especially in the case of pathogens. However, distinguishing between these factors and the effects of historical range expansion on spatial genetic structure remains challenging. In the present study, we investigated the case of Mycosphaerella fijiensis-a plant pathogenic fungus that has recently colonized an agricultural landscape characterized by the presence of potential barriers to gene flow, including several commercial plantations in which disease control practises such as the use of fungicides are applied frequently, and low host density areas. We first genotyped 300 isolates sampled at a global scale on untreated plants in two dimensions over a 50 × 80-km area. Using two different clustering algorithms, no genetic structure was detected in the studied area, suggesting expansion of large populations and/or no influence of potential barriers. Second, we investigated the potential effect of disease control practises on M. fijiensis diversity by comparing populations sampled in commercial vs food-crop plantations. At this local scale, we detected significantly higher allelic richness inside commercial plantations compared with the surrounding food-crop plantation populations. Analysis of molecular variance indicated that 99% of the total genetic variance occurred within populations. We discuss the suggestion that high population size and/or high migration rate between populations might be responsible for the absence of any effect of disease control practises on genetic diversity and differentiation.

  14. Genetic diversity of highly pathogenic H5N8 avian influenza viruses at a single overwintering site of migratory birds in Japan, 2014/15.

    Science.gov (United States)

    Ozawa, M; Matsuu, A; Tokorozaki, K; Horie, M; Masatani, T; Nakagawa, H; Okuya, K; Kawabata, T; Toda, S

    2015-05-21

    We isolated eight highly pathogenic H5N8 avian influenza viruses (H5N8 HPAIVs) in the 2014/15 winter season at an overwintering site of migratory birds in Japan. Genetic analyses revealed that these isolates were divided into three groups, indicating the co-circulation of three genetic groups of H5N8 HPAIV among these migratory birds. These results also imply the possibility of global redistribution of the H5N8 HPAIVs via the migration of these birds next winter.

  15. Physical and genetic interaction between ammonium transporters and the signaling protein Rho1 in the plant pathogen Ustilago maydis.

    Science.gov (United States)

    Paul, Jinny A; Barati, Michelle T; Cooper, Michael; Perlin, Michael H

    2014-10-01

    Dimorphic transitions between yeast-like and filamentous forms occur in many fungi and are often associated with pathogenesis. One of the cues for such a dimorphic switch is the availability of nutrients. Under conditions of nitrogen limitation, fungal cells (such as those of Saccharomyces cerevisiae and Ustilago maydis) switch from budding to pseudohyphal or filamentous growth. Ammonium transporters (AMTs) are responsible for uptake and, in some cases, for sensing the availability of ammonium, a preferred nitrogen source. Homodimer and/or heterodimer formation may be required for regulating the activity of the AMTs. To investigate the potential interactions of Ump1 and Ump2, the AMTs of the maize pathogen U. maydis, we first used the split-ubiquitin system, followed by a modified split-YFP (yellow fluorescent protein) system, to validate the interactions in vivo. This analysis showed the formation of homo- and hetero-oligomers by Ump1 and Ump2. We also demonstrated the interaction of the high-affinity ammonium transporter, Ump2, with the Rho1 GTPase, a central protein in signaling, with roles in controlling polarized growth. This is the first demonstration in eukaryotes of the physical interaction in vivo of an ammonium transporter with the signaling protein Rho1. Moreover, the Ump proteins interact with Rho1 during the growth of cells in low ammonium concentrations, a condition required for the expression of the Umps. Based on these results and the genetic evidence for the interaction of Ump2 with both Rho1 and Rac1, another small GTPase, we propose a model for the role of these interactions in controlling filamentation, a fundamental aspect of development and pathogenesis in U. maydis.

  16. Virulence on the fly: Drosophila melanogaster as a model genetic organism to decipher host-pathogen interactions.

    NARCIS (Netherlands)

    Limmer, S.; Quintin, J.; Hetru, C.; Ferrandon, D.

    2011-01-01

    To gain an in-depth grasp of infectious processes one has to know the specific interactions between the virulence factors of the pathogen and the host defense mechanisms. A thorough understanding is crucial for identifying potential new drug targets and designing drugs against which the pathogens mi

  17. Molecular genetic characterisation of the Asc locus of tomato conferring resistance to the fungal pathogen Alternaria alternata f. sp. lycopersici

    NARCIS (Netherlands)

    Biezen, E.A. van der; Overduin, B.; Kneppers, T.J.A.; Mesbah, L.A.; Nijkamp, H.J.J.; Hille, J.

    1994-01-01

    The Alternaria stem canker disease of tomato is caused by the fungal pathogen Alternaria alternata f. sp. lycopersici and its host-selective AAL-toxins. Resistance to the pathogen and insensitivity to the toxins are conferred by the Asc locus on chromosome 3L. Sensitivity to AAL-toxins is a relative

  18. An emerging avian influenza A virus H5N7 is a genetic reassortant of highly pathogenic genes

    DEFF Research Database (Denmark)

    Bragstad, K.; Jørgensen, Poul Henrik; Handberg, Kurt

    2006-01-01

    We full genome characterised the newly discovered avian influenza virus H5N7 subtype combination isolated from a stock of Danish game ducks to investigate the composition of the genome and possible features of high pathogenicity. It was found that the haemagglutinin and the acidic polymerase genes...... low pathogenic avian influenza A viruses. (c) 2006 Elsevier Ltd. All rights reserved....

  19. Combination of RNAseq and SNP nanofluidic array reveals the center of genetic diversity of cacao pathogen Moniliophthora roreri in the upper Magdalena Valley of Colombia and its clonality.

    Science.gov (United States)

    Ali, Shahin S; Shao, Jonathan; Strem, Mary D; Phillips-Mora, Wilberth; Zhang, Dapeng; Meinhardt, Lyndel W; Bailey, Bryan A

    2015-01-01

    Moniliophthora roreri is the fungal pathogen that causes frosty pod rot (FPR) disease of Theobroma cacao L., the source of chocolate. FPR occurs in most of the cacao producing countries in the Western Hemisphere, causing yield losses up to 80%. Genetic diversity within the FPR pathogen population may allow the population to adapt to changing environmental conditions and adapt to enhanced resistance in the host plant. The present study developed single nucleotide polymorphism (SNP) markers from RNASeq results for 13 M. roreri isolates and validated the markers for their ability to reveal genetic diversity in an international M. roreri collection. The SNP resources reported herein represent the first study of RNA sequencing (RNASeq)-derived SNP validation in M. roreri and demonstrates the utility of RNASeq as an approach for de novo SNP identification in M. roreri. A total of 88 polymorphic SNPs were used to evaluate the genetic diversity of 172 M. roreri cacao isolates resulting in 37 distinct genotypes (including 14 synonymous groups). Absence of heterozygosity for the 88 SNP markers indicates reproduction in M. roreri is clonal and likely due to a homothallic life style. The upper Magdalena Valley of Colombia showed the highest levels of genetic diversity with 20 distinct genotypes of which 13 were limited to this region, and indicates this region as the possible center of origin for M. roreri.

  20. Combination of RNAseq and SNP nanofluidic array reveals the center of genetic diversity of cacao pathogen Moniliophthora roreri in the upper Magdalena Valley of Colombia and its clonality

    Directory of Open Access Journals (Sweden)

    Shahin S Ali

    2015-08-01

    Full Text Available Moniliophthora roreri is the fungal pathogen that causes frosty pod rot (FPR disease of Theobroma cacao L., the source of chocolate. FPR occurs in most of the cacao producing countries in the Western Hemisphere, causing yield losses up to 80%. Genetic diversity within the FPR pathogen population may allow the population to adapt to changing environmental conditions and adapt to enhanced resistance in the host plant. The present study developed SNP markers from RNASeq results for 13 M. roreri isolates and validated the markers for their ability to reveal genetic diversity in an international M. roreri collection. The SNP resources reported herein represent the first study of RNASeq-derived SNP validation in M. roreri and demonstrates the utility of RNASeq as an approach for de novo SNP identification in M. roreri. A total of 88 polymorphic SNPs were used to evaluate the genetic diversity of 172 M. roreri cacao isolates resulting in 37 distinct genotypes (including 14 synonymous groups. Absence of heterozygosity for the 88 SNP markers indicates reproduction in M. roreri is clonal and likely due to a homothallic life style. The upper Magdalena Valley of Colombia showed the highest levels of genetic diversity with 20 distinct genotypes of which 13 were limited to this region, and indicates this region as the possible center of origin for M. roreri.

  1. Dynamic genetic conservation in the presence of invasive insect and pathogen threats to forest tree species of the United States

    Science.gov (United States)

    J.L. Koch; R.A. Sniezko

    2017-01-01

    Ex-situ genetic conservation focused on collection and storage of seed can play an important role in conserving the genetic diversity of species under grave threat by biotic organisms or a changing climate. However, ex-situ genetic conservation is primarily a static activity and does not allow for evolution of the species under a continuing,...

  2. Invasive blue mussels threaten regional scale genetic diversity in mainland and remote offshore locations: the need for baseline data and enhanced protection in the Southern Ocean.

    Science.gov (United States)

    Gardner, Jonathan P A; Zbawicka, Małgorzata; Westfall, Kristen M; Wenne, Roman

    2016-09-01

    Human-mediated biological transfers of species have substantially modified many ecosystems with profound environmental and economic consequences. However, in many cases, invasion events are very hard to identify because of the absence of an appropriate baseline of information for receiving sites/regions. In this study, use of high-resolution genetic markers (single nucleotide polymorphisms - SNPs) highlights the threat of introduced Northern Hemisphere blue mussels (Mytilus galloprovincialis) at a regional scale to Southern Hemisphere lineages of blue mussels via hybridization and introgression. Analysis of a multispecies SNP dataset reveals hotspots of invasive Northern Hemisphere blue mussels in some mainland New Zealand locations, as well as the existence of unique native lineages of blue mussels on remote oceanic islands in the Southern Ocean that are now threatened by invasive mussels. Samples collected from an oil rig that has moved between South Africa, Australia, and New Zealand were identified as invasive Northern Hemisphere mussels, revealing the relative ease with which such non-native species may be moved from region to region. In combination, our results highlight the existence of unique lineages of mussels (and by extension, presumably of other taxa) on remote offshore islands in the Southern Ocean, the need for more baseline data to help identify bioinvasion events, the ongoing threat of hybridization and introgression posed by invasive species, and the need for greater protection of some of the world's last great remote areas.

  3. SNP design from 454 sequencing of Podosphaera plantaginis transcriptome reveals a genetically diverse pathogen metapopulation with high levels of mixed-genotype infection.

    Directory of Open Access Journals (Sweden)

    Charlotte Tollenaere

    Full Text Available BACKGROUND: Molecular tools may greatly improve our understanding of pathogen evolution and epidemiology but technical constraints have hindered the development of genetic resources for parasites compared to free-living organisms. This study aims at developing molecular tools for Podosphaera plantaginis, an obligate fungal pathogen of Plantago lanceolata. This interaction has been intensively studied in the Åland archipelago of Finland with epidemiological data collected from over 4,000 host populations annually since year 2001. PRINCIPAL FINDINGS: A cDNA library of a pooled sample of fungal conidia was sequenced on the 454 GS-FLX platform. Over 549,411 reads were obtained and annotated into 45,245 contigs. Annotation data was acquired for 65.2% of the assembled sequences. The transcriptome assembly was screened for SNP loci, as well as for functionally important genes (mating-type genes and potential effector proteins. A genotyping assay of 27 SNP loci was designed and tested on 380 infected leaf samples from 80 populations within the Åland archipelago. With this panel we identified 85 multilocus genotypes (MLG with uneven frequencies across the pathogen metapopulation. Approximately half of the sampled populations contain polymorphism. Our genotyping protocol revealed mixed-genotype infection within a single host leaf to be common. Mixed infection has been proposed as one of the main drivers of pathogen evolution, and hence may be an important process in this pathosystem. SIGNIFICANCE: The developed SNP panel offers exciting research perspectives for future studies in this well-characterized pathosystem. Also, the transcriptome provides an invaluable novel genomic resource for powdery mildews, which cause significant yield losses on commercially important crops annually. Furthermore, the features that render genetic studies in this system a challenge are shared with the majority of obligate parasitic species, and hence our results provide

  4. Using Population and Comparative Genomics to Understand the Genetic Basis of Effector-Driven Fungal Pathogen Evolution

    Science.gov (United States)

    Plissonneau, Clémence; Benevenuto, Juliana; Mohd-Assaad, Norfarhan; Fouché, Simone; Hartmann, Fanny E.; Croll, Daniel

    2017-01-01

    Epidemics caused by fungal plant pathogens pose a major threat to agro-ecosystems and impact global food security. High-throughput sequencing enabled major advances in understanding how pathogens cause disease on crops. Hundreds of fungal genomes are now available and analyzing these genomes highlighted the key role of effector genes in disease. Effectors are small secreted proteins that enhance infection by manipulating host metabolism. Fungal genomes carry 100s of putative effector genes, but the lack of homology among effector genes, even for closely related species, challenges evolutionary and functional analyses. Furthermore, effector genes are often found in rapidly evolving chromosome compartments which are difficult to assemble. We review how population and comparative genomics toolsets can be combined to address these challenges. We highlight studies that associated genome-scale polymorphisms with pathogen lifestyles and adaptation to different environments. We show how genome-wide association studies can be used to identify effectors and other pathogenicity-related genes underlying rapid adaptation. We also discuss how the compartmentalization of fungal genomes into core and accessory regions shapes the evolution of effector genes. We argue that an understanding of genome evolution provides important insight into the trajectory of host-pathogen co-evolution. PMID:28217138

  5. An emerging avian influenza A virus H5N7 is a genetic reassortant of highly pathogenic genes.

    Science.gov (United States)

    Bragstad, K; Jørgensen, P H; Handberg, K J; Fomsgaard, A

    2006-11-10

    We full genome characterised the newly discovered avian influenza virus H5N7 subtype combination isolated from a stock of Danish game ducks to investigate the composition of the genome and possible features of high pathogenicity. It was found that the haemagglutinin and the acidic polymerase genes were closely related to a low pathogenic H5 strain (A/Duck/Denmark/65047/04 H5N2). The neuraminidase and the non-structural genes were closely related to the highly pathogenic H7N7 strains from The Netherlands 2003. The basic polymerase genes 1 and 2 were shared between the Danish H5N7 and H5N2 and the H7N7 from The Netherlands. The nucleoprotein and the matrix genes were closely related to H6 strains. Thus, the new H5N7 subtype share genes with H5, H7 and H6 subtypes and possesses internal genes originating from highly pathogenic strains. The findings emphasize the need for surveillance presumed low pathogenic avian influenza A viruses.

  6. Identification of genetic and environmental factors stimulating excision from Streptomyces scabiei chromosome of the toxicogenic region responsible for pathogenicity.

    Science.gov (United States)

    Chapleau, Mélanie; Guertin, Julien F; Farrokhi, Ali; Lerat, Sylvain; Burrus, Vincent; Beaulieu, Carole

    2016-05-01

    The genes conferring pathogenicity in Streptomyces turgidiscabies, a pathogen causing common scab of potato, are grouped together on a pathogenicity island (PAI), which has been found to be mobile and appears to transfer and disseminate like an integrative and conjugative element (ICE). However, in Streptomyces scabiei, another common scab-inducing species, the pathogenicity genes are clustered in two regions: the toxicogenic region (TR) and the colonization region. The S. scabiei 87.22 genome was analysed to investigate the potential mobility of the TR. Attachment sites (att), short homologous sequences that delineate ICEs, were identified at both extremities of the TR. An internal att site was also found, suggesting that the TR has a composite structure (TR1 and TR2). Thaxtomin biosynthetic genes, essential for pathogenicity, were found in TR1, whereas candidate genes with known functions in recombination, replication and conjugal transfer were found in TR2. Excision of the TR1 or TR2 subregions alone, or of the entire TR region, was observed, although the excision frequency of TR was low. However, the excision frequency was considerably increased in the presence of either mitomycin C or Streptomyces coelicolor cells. A composite TR structure was not observed in all S. scabiei and Streptomyces acidiscabies strains tested. Of the ten strains analysed, seven lacked TR2 and no TR excision event could be detected in these strains, thus suggesting the implication of TR2 in the mobilization of S. scabiei TR.

  7. Genetic diversity and pathogenicity of Metarhizium spp. associated with the white grub Phyllophaga capillata (Blanchard) (Coleoptera: Melolonthidae) in a soybean field.

    Science.gov (United States)

    Lopes, R B; Souza, D A; Oliveira, C M; Faria, M

    2013-08-01

    Phyllophaga capillata (Blanchard) was recently described as a soybean pest in Brazil. The occurrence of Metarhizium spp. associated with adults and their pathogenicity were investigated. Natural prevalence of Metarhizium anisopliae was 0.51% in adults collected by light trap. Most Metarhizium isolates were identified as Metarhizium robertsii, although M. anisopliae sensu stricto and a few unidentified isolates were also found. Bioassays with representative isolates selected from different genetic groups resulted in ≤5.6% confirmed mortality against larvae and adults, suggesting low potential of microbial control of this pest by use of indigenous Metarhizium isolates.

  8. Genetics

    Science.gov (United States)

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  9. Molecular genetic characterization of the koa-wilt pathogen (Fusarium oxysporum): Application of molecular genetic tools toward improving koa restoration in Hawai'i

    Science.gov (United States)

    Mee-Sook Kim; Jane E. Stewart; Nicklos Dudley; John Dobbs; Tyler Jones; Phil G. Cannon; Robert L. James; Kas Dumroese; Ned B. Klopfenstein

    2015-01-01

    Several forest diseases are causing serious threats to the native Hawaiian forest. Among them, koawilt disease (caused by Fusarium oxysporum) is damaging to native populations of koa (Acacia koa), and it also hinders koa restoration/reforestation. Because F. oxysporum likely represents a complex of species with distinct pathogenic activities, more detailed...

  10. Genetic diversity of the myrtle rust pathogen (Austropuccinia psidii) in the Americas and Hawaii: Global implications for invasive threat assessments

    Science.gov (United States)

    J. E. Stewart; A.L. Ross-Davis; R. N. Graҫa; A. C. Alfenas; T. L. Peever; J. W. Hanna; J. Y. Uchida; R. D. Hauff; C. Y. Kadooka; M.-S. Kim; P. G. Cannon; S. Namba; S. Simeto; C. A. Pérez; M. B. Rayamajhi; D.J. Lodge; M. Arguedas; R. Medel-Ortiz; M. A. López-Ramirez; P. Tennant; M. Glen; P. S. Machado; A. R. McTaggart; A. J. Carnegie; N. B. Klopfenstein; M. Cleary

    2017-01-01

    Since the myrtle rust pathogen (Austropuccinia psidii) was first reported (as Puccinia psidii) in Brazil on guava (Psidium guajava) in 1884, it has been found infecting diverse myrtaceous species. Because A. psidii has recently spread rapidly worldwide with an extensive host range,...

  11. Differences in pathogen colonization and mortality of genetically selected Japanese quail lines subjected to heat stress and Escherichia coli challenge

    Science.gov (United States)

    Japanese quail selected for divergent corticosterone response to restraint stress were evaluated for their resistance to heat stress and aerosol challenge with avian pathogenic Escherichia coli (APEC) to determine the impact of stress response on APEC pathogenesis and colonization with food-borne pa...

  12. The relevance of evolutionary genetics for identification of Trichinella sp. and other pathogens at the strain, subspecies and species levels

    Directory of Open Access Journals (Sweden)

    Tibayrenc M.

    2001-06-01

    Full Text Available In the specific field of Trichinella research, the impact of evolutionary methods has been until now limited. This is all the more distressing, since this group of parasites is characterized by hard taxonomical problems. Moreover, for the epidemiological tracking of Trichinella populations, high-discriminating genetic typing, conveniently analyzed by population genetic methods, could be of considerable help. With no additional efforts, many molecular data are already available and could be used for retrospective analyses able to solve many taxonomical problems. It is desirable that coming studies are specifically designed according to evolutionary genetics principles and the question under study (sample size, selection of the appropriate marker.

  13. Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli Using RNA Sequencing and Genotyping-By-Sequencing.

    Directory of Open Access Journals (Sweden)

    Carly F Summers

    Full Text Available RNA sequencing (RNA-seq and genotyping-by-sequencing (GBS were used for single nucleotide polymorphism (SNP identification from two economically important obligate plant pathogens, Pseudoperonospora cubensis and P. humuli. Twenty isolates of P. cubensis and 19 isolates of P. humuli were genotyped using RNA-seq and GBS. Principle components analysis (PCA of each data set showed genetic separation between the two species. Additionally, results supported previous findings that P. cubensis isolates from squash are genetically distinct from cucumber and cantaloupe isolates. A PCA-based procedure was used to identify SNPs correlated with the separation of the two species, with 994 and 4,231 PCA-correlated SNPs found within the RNA-seq and GBS data, respectively. The corresponding unigenes (n = 800 containing these potential species-specific SNPs were then annotated and 135 putative pathogenicity genes, including 3 effectors, were identified. The characterization of genes containing SNPs differentiating these two closely related downy mildew species may contribute to the development of improved detection and diagnosis strategies and improve our understanding of host specificity pathways.

  14. Targeted sequencing identifies a novel SH2D1A pathogenic variant in a Chinese family: Carrier screening and prenatal genetic testing

    Science.gov (United States)

    Chen, Yi-Yao; Li, Shu-Yuan; Zhang, Lan-Lan; Shen, Ying-Hua; Chang, Chun-Xin; Xiang, Yu-Qian; Huang, He-Feng; Xu, Chen-Ming

    2017-01-01

    X-linked lymphoproliferative disease type 1 (XLP1) is a rare primary immunodeficiency characterized by a clinical triad consisting of severe EBV-induced hemophagocytic lymphohistiocytosis, B-cell lymphoma, and dysgammaglobulinemia. Mutations in SH2D1A gene have been revealed as the cause of XLP1. In this study, a pregnant woman with recurrence history of birthing immunodeficiency was screened for pathogenic variant because the proband sample was unavailable. We aimed to clarify the genetic diagnosis and provide prenatal testing for the family. Next-generation sequencing (NGS)-based multigene panel was used in carrier screening of the pregnant woman. Variants of immunodeficiency related genes were analyzed and prioritized. Candidate variant was verified by using Sanger sequencing. The possible influence of the identified variant was evaluated through RNA assay. Amniocentesis, karyotyping, and Sanger sequencing were performed for prenatal testing. We identified a novel de novo frameshift SH2D1A pathogenic variant (c.251_255delTTTCA) in the pregnant carrier. Peripheral blood RNA assay indicated that the mutant transcript could escape nonsense-mediated mRNA decay (NMD) and might encode a C-terminal truncated protein. Information of the variant led to success prenatal diagnosis of the fetus. In conclusion, our study clarified the genetic diagnosis and altered disease prevention for a pregnant carrier of XLP1. PMID:28231257

  15. Pathogenicity and genetic characterization of a duck Tembusu virus associated with egg-dropping in Muscovy ducks.

    Science.gov (United States)

    Shen, Han-Qin; Lin, Wen-Cheng; Wang, Zhan-Xin; Zhang, Kai; Yan, Zhuan-Qiang; Zhou, Qing-Feng; Qin, Jian-Ping; Xie, Qing-Mei; Bi, Ying-Zuo; Chen, Feng

    2016-09-02

    Duck Tembusu virus (DTMUV) has spread to the major duck-farming region in China, causing acute egg-production drop in Chinese duck population. In this study, we characterized a DTMUV strain (named GD2014) isolated from an egg-production drop duck farm in Guangdong province, South China. The virus was pathogenic to Muscovy duck embryos and caused severe egg production drop for laying Muscovy ducks. The genome sequence of GD2014 shared 97-99% homologies with other waterfowl-origin Tembusu viruses, and shared 89% identities with MM1775 strain isolated from mosquito. Phylogenetic analysis of entire open reading frame (ORF), E gene and NS5 gene indicated that GD2014 belonged to Ntaya group. These results have implications for understanding the orgin, emergence and pathogenicity of DTMUV as well as for the development of vaccines and diagnostics based on epidemiological data. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Genetic Modulation of c-di-GMP Turnover Affects Multiple Virulence Traits and Bacterial Virulence in Rice Pathogen Dickeya zeae

    Science.gov (United States)

    Chen, Yufan; Lv, Mingfa; Liao, Lisheng; Gu, Yanfang; Liang, Zhibin; Shi, Zurong; Liu, Shiyin; Zhou, Jianuan; Zhang, Lianhui

    2016-01-01

    The frequent outbreaks of rice foot rot disease caused by Dickeya zeae have become a significant concern in rice planting regions and countries, but the regulatory mechanisms that govern the virulence of this important pathogen remain vague. Given that the second messenger cyclic di-GMP (c-di-GMP) is associated with modulation of various virulence-related traits in various microorganisms, here we set to investigate the role of the genes encoding c-di-GMP metabolism in the regulation of the bacterial physiology and virulence by construction all in-frame deletion mutants targeting the annotated c-di-GMP turnover genes in D. zeae strain EC1. Phenotype analyses identified individual mutants showing altered production of exoenzymes and phytotoxins, biofilm formation and bacterial motilities. The results provide useful clues and a valuable toolkit for further characterization and dissection of the regulatory complex that modulates the pathogenesis and persistence of this important bacterial pathogen. PMID:27855163

  17. Genetic structure and population dynamics of a heteroecious plant pathogen Melampsora larici-epitea in short-rotation coppice willow plantations.

    Science.gov (United States)

    Bayon, Carlos; Pei, Ming H; Ruiz, Carmen; Hunter, Tom; Karp, Angela; Tubby, Ian

    2009-07-01

    Complex life strategies are common among plant pathogens belonging to rust fungi (Uredinales). The heteroecious willow rust Melampsora larici-epitea produces five spore stages and alternates on larch (Larix). To shed light on the epidemiology of this pathogen, amplified fragment length polymorphisms (AFLPs) were used to determine the genetic diversity and genetic structure of rust samples collected from coppice willow (Salix) plantations at three UK sites (LA, CA and MC) over three sampling dates (September 2000, July 2001 and September 2001). Of the total of 819 isolates, 465 were unique AFLP phenotypes and there was a shift in genotype diversity between the two seasons (0.67 in 2000 and 0.87-0.89 in 2001). No phenotypes were common between the two seasons within a site, suggesting that the rust did not overwinter as an asexual stage within plantations. A temporal analysis detected large amounts of genetic drift (F(S) = 0.15-0.26) between the two seasons and very small effective population sizes (N(e) = 2-3) within sites. These results all point to a new colonization of the plantations by the rust in the second season (2001). The F(ST)-analogue values were Phi(CT) = 0.121, Weir and Cockerham's theta = 0.086 and the Bayesian estimate theta(B) = 0.087-0.096. The results suggest that the sources of inoculum were somewhat localized and the same sources were mainly responsible for disease epidemics in LA and CA over the two seasons. The relatively low F(ST)-values among sites (0.055-0.13) suggest the existence of significant gene flow among the three sampled sites.

  18. Do pathogens reduce genetic diversity of their hosts? Variable effects of sylvatic plague in black-tailed prairie dogs.

    Science.gov (United States)

    Sackett, Loren C; Collinge, Sharon K; Martin, Andrew P

    2013-05-01

    Introduced diseases can cause dramatic declines in-and even the loss of-natural populations. Extirpations may be followed by low recolonization rates, leading to inbreeding and a loss of genetic variation, with consequences on population viability. Conversely, extirpations may create vacant habitat patches that individuals from multiple source populations can colonize, potentially leading to an influx of variation. We tested these alternative hypotheses by sampling 15 colonies in a prairie dog metapopulation during 7 years that encompassed an outbreak of sylvatic plague, providing the opportunity to monitor genetic diversity before, during and after the outbreak. Analysis of nine microsatellite loci revealed that within the metapopulation, there was no change in diversity. However, within extirpated colonies, patterns varied: In half of the colonies, allelic richness after recovery was less than the preplague conditions, and in the other half, richness was greater than the preplague conditions. Finally, analysis of variation within individuals revealed that prairie dogs present in recolonized colonies had higher heterozygosity than those present before plague. We confirmed plague survivorship in six founders; these individuals had significantly higher heterozygosity than expected by chance. Collectively, our results suggest that high immigration rates can maintain genetic variation at a regional scale despite simultaneous extirpations in spatially proximate populations. Thus, virulent diseases may increase genetic diversity of host populations by creating vacant habitats that allow an influx of genetic diversity. Furthermore, even highly virulent diseases may not eliminate individuals randomly; rather, they may selectively remove the most inbred individuals. © 2013 Blackwell Publishing Ltd.

  19. [Researches of soil normalized difference water index (NDWI) of Yongding River based on multispectral remote sensing technology combined with genetic algorithm].

    Science.gov (United States)

    Mao, Hai-ying; Feng, Zhong-ke; Gong, Yin-xi; Yu, Jing-xin

    2014-06-01

    Basin soil type, moisture content and vegetation cover index are important factors affecting the basin water of Yongding River, using traditional sampling method to investigate soil moisture and the watershed soil type not only consuming a lot of manpower and material resources but also causing experimental error because of the instrument and other objective factors. This article selecting the Yongding River Basin-Beijing section as the study area, using total station instruments to survey field sampling and determination 34 plots, combined with 6 TM image data from 1978 to 2009 to extract soil information and the relationship between region's soil type, soil moisture and remote sensing factors. Using genetic algorithms normalization to select key factors which influenced NDWI, which is based on the green band and near-infrared bands normalized ratio index, usually used to extract water information in the image. In order to accurate screening and factors related to soil moisture, using genetic algorithms preferred characteristics, accelerate the convergence by controlling the number of iterations to filter key factor. Using multiple regression method to establish NDWI inversion model, which analysis the accuracy of model is 0.987, also use the species outside edges tree to meet accuracy test, which arrived that soil available nitrogen, phosphorus and potassium content and longitude correlation is not obvious, but a positive correlation with latitude and soil, inner precision researched 87.6% when the number of iterations to achieve optimal model calculation Maxgen. Models between NDWI and vegetation cover, topography, climate ect, through remote sensing and field survey methods could calculate the NDWI values compared with the traditional values, arrived the average relative error E is -0.021%, suits accord P reached 87.54%. The establishment of this model will be provide better practical and theoretical basis to the research and analysis of the watershed soil

  20. Multilocus ISSR markers reveal two major genetic groups in Spanish and South African populations of the grapevine fungal pathogen Cadophora luteo-olivacea.

    Directory of Open Access Journals (Sweden)

    David Gramaje

    Full Text Available Cadophora luteo-olivacea is a lesser-known fungal trunk pathogen of grapevine which has been recently isolated from vines showing decline symptoms in grape growing regions worldwide. In this study, 80 C. luteo-olivacea isolates (65 from Spain and 15 from South Africa were studied. Inter-simple-sequence repeat-polymerase chain reaction (ISSR-PCR generated 55 polymorphic loci from four ISSR primers selected from an initial screen of 13 ISSR primers. The ISSR markers revealed 40 multilocus genotypes (MLGs in the global population. Minimum spanning network analysis showed that the MLGs from South Africa clustered around the most frequent genotype, while the genotypes from Spain were distributed all across the network. Principal component analysis and dendrograms based on genetic distance and bootstrapping identified two highly differentiated genetic clusters in the Spanish and South African C. luteo-olivacea populations, with no intermediate genotypes between these clusters. Movement within the Spanish provinces may have occurred repeatedly given the frequent retrieval of the same genotype in distant locations. The results obtained in this study provide new insights into the population genetic structure of C. luteo-olivacea in Spain and highlights the need to produce healthy and quality planting material in grapevine nurseries to avoid the spread of this fungus throughout different grape growing regions.

  1. Exploration and conservation of bacterial genetic resources as bacteriocin producing inhibitory microorganisms to pathogen bacteria in livestock

    Directory of Open Access Journals (Sweden)

    Chotiah S

    2013-06-01

    Full Text Available Exploration and conservation of microorganisms producing bacteriocin was done as the primary study towards the collection of potential bacteria and its application in improving livestock health condition and inhibit food borne pathogens. Diferent kinds of samples such as beef cattle rectal swab, rumen fluids, cow’s milk, chicken gut content, goat’s milk were collected at Bogor cattle slaughter houses, poultry slaughter houses, dairy cattle and goat farms. A total of 452 bacterial isolates consisted of 73 Gram negative bacteria and 379 Gram positive bacteria were isolated from samples collected and screened for bacteriocin activity. Determination of bacteriocin activity with bioassay using agar spot tests were carried out on liquid and semisolid medium assessing 8 kins of indicators of pathogenic bacteria and food borne pathogens. A total of 51 bacteriocin producing strains were collected and some of the strains had high inhibitory zone such as Lactobacillus casei SS14C (26 mm, Enterobacter cloacae SRUT (24mm, Enterococcus faecalis SK39 (21mm and Bifidobacterium dentium SS14T (20mm respectively, to Salmonella typhimurium BCC B0046/ATCC 13311, E. coli O157 hemolytic BCC B2717, Listeria monocytogenes BCC B2767/ATCC 7764 and Escherichia coli VTEC O157 BCC B2687. Evaluation after conservation ex situ to all bacterocin producing strain at 5oC for 1 year in freeze drying ampoules in vacuum and dry condition revealed the decreasing viability starting from log 0.8 CFU/ml for Lactococcus and Leuconostoc to log 2.2. CFU/ml for Streptococcus. Result of the study showed that the bacteriocin producing strains obtained were offered a potential resource for preventing disease of livestock and food borne diseases.

  2. Variation in host and pathogen in the Neonectria/Malus interaction; towards an understanding of the genetic basis of resistance to European canker

    Directory of Open Access Journals (Sweden)

    Antonio Gomez-Cortecero

    2016-09-01

    Full Text Available Apple canker caused by the phytopathogenic fungus Neonectria ditissima is an economically important disease, which has spread in recent years to almost all pome-producing regions of the world. N. ditissima is able to cross-infect a wide range of apple varieties and causes branch and trunk lesions, known as cankers. Most modern apple varieties are susceptible and in extreme cases suffer from high mortality (up to 50% in the early phase of orchard establishment. There is no known race structure of the pathogen and the global level of genetic diversity of the pathogen population is unknown. Resistance breeding is underway in many global breeding programmes, but nevertheless, a total resistance to canker has not yet been demonstrated. Here we present preliminary data from a survey of the phylogenetic relationships between global isolates of N. ditissima which reveals only slight evidence for population structure. In addition we report the results of four rapid screening tests to assess the response to N. ditissima in different apple scion and rootstock varieties, which reveals abundant variation in resistance responses in both cultivar and rootstock material. Further seedling tests show that the segregation patterns of resistance and susceptibility vary widely between crosses. We discuss inconsistencies in test performance with field observations and discuss future research opportunities in this area.

  3. Genetic characterization of the HrpL regulon of the fire blight pathogen Erwinia amylovora reveals novel virulence factors.

    Science.gov (United States)

    McNally, R Ryan; Toth, Ian K; Cock, Peter J A; Pritchard, Leighton; Hedley, Pete E; Morris, Jenny A; Zhao, Youfu; Sundin, George W

    2012-02-01

    The bacterial pathogen Erwinia amylovora is the causal agent of fire blight, an economically significant disease of apple and pear. Disease initiation by E. amylovora requires the translocation of effector proteins into host cells via the hypersensitive response and pathogenicity (hrp) type III secretion system (T3SS). The alternative sigma factor HrpL positively regulates the transcription of structural and translocated components of the T3SS via hrp promoter elements. To characterize genome-wide HrpL-dependent gene expression in E. amylovora Ea1189, wild-type and Ea1189ΔhrpL strains were cultured in hrp-inducing minimal medium, and total RNA was compared using a custom microarray designed to represent the annotated genes of E. amylovora ATCC 49946. The results revealed 24 genes differentially regulated in Ea1189ΔhrpL relative to Ea1189 with fold-change expression ratios greater than 1.5; of these, 19 genes exhibited decreased transcript abundance and five genes showed increased transcript abundance relative to Ea1189. To expand our understanding of the HrpL regulon and to elucidate direct versus indirect HrpL-mediated effects on gene expression, the genome of E. amylovora ATCC 49946 was examined in silico using a hidden Markov model assembled from known Erwinia spp. hrp promoters. This technique identified 15 putative type III novel hrp promoters, seven of which were validated with quantitative polymerase chain reaction based on expression analyses. It was found that HrpL-regulated genes encode all known components of the hrp T3SS, as well as five putative type III effectors. Eight genes displayed apparent indirect HrpL regulation, suggesting that the HrpL regulon is connected to downstream signalling networks. The construction of deletion mutants of three novel HrpL-regulated genes resulted in the identification of additional virulence factors as well as mutants displaying abnormal motility and biofilm phenotypes.

  4. Radiation exposure in the remote period after the Chernobyl accident caused oxidative stress and genetic effects in Scots pine populations

    Science.gov (United States)

    Volkova, Polina Yu.; Geras'Kin, Stanislav A.; Kazakova, Elizaveta A.

    2017-02-01

    Even 30 years after the Chernobyl accident, biological effects of irradiation are observed in the chronically exposed Scots pine populations. Chronic radiation exposure at dose rates above 50 mGy•yr-1 caused oxidative stress and led to the increase of antioxidants concentrations in these populations. Genetic variability was examined for 6 enzymes and 14 enzymatic loci of 6 Scots pine populations. Dose rates over 10 mGy•yr-1 caused the increased frequency of mutations and changes in genetic structure of Scots pine populations. However, the same dose rates had no effect on enzymatic activities. The results indicate that even relatively low dose rates of radiation can be considered as an ecological factor which should be taken into account for ecological management and radiation protection of biota species.

  5. Assessing the intra-species genetic variability in the clonal pathogen Campylobacter fetus: CRISPRs are highly polymorphic DNA markers.

    Science.gov (United States)

    Calleros, Lucía; Betancor, Laura; Iraola, Gregorio; Méndez, Alejandra; Morsella, Claudia; Paolicchi, Fernando; Silveyra, Silvia; Velilla, Alejandra; Pérez, Ruben

    2017-01-01

    Campylobacter fetus is a Gram-negative, microaerophilic bacterium that infects animals and humans. The subspecies Campylobacter fetus subsp. fetus (Cff) affects a broad range of vertebrate hosts and induces abortion in cows and sheep. Campylobacter fetus subsp. venerealis (Cfv) is restricted to cattle and causes the endemic disease bovine genital campylobacteriosis, which triggers reproductive problems and is responsible for major economic losses. Campylobacter fetus subsp. testudinum (Cft) has been isolated mostly from apparently healthy reptiles belonging to different species but also from ill snakes and humans. Genotypic differentiation of Cff and Cfv is difficult, and epidemiological information is scarce because there are few methods to study the genetic diversity of the strains. We analyze the efficacy of MLST, ribosomal sequences (23S gene and internal spacer region), and CRISPRs to assess the genetic variability of C. fetus in bovine and human isolates. Sequences retrieved from complete genomes were included in the analysis for comparative purposes. MLST and ribosomal sequences had scarce or null variability, while the CRISPR-cas system structure and the sequence of CRISPR1 locus showed remarkable diversity. None of the sequences here analyzed provided evidence of a genetic differentiation of Cff and Cfv in bovine isolates. Comparison of bovine and human isolates with Cft strains showed a striking divergence. Inter-host differences raise the possibility of determining the original host of human infections using CRISPR sequences. CRISPRs are the most variable sequences analyzed in C. fetus so far, and constitute excellent representatives of a dynamic fraction of the genome. CRISPR typing is a promising tool to characterize isolates and to track the source and transmission route of C. fetus infections.

  6. Rapid Gene Turnover as a Significant Source of Genetic Variation in a Recently Seeded Population of a Healthcare-Associated Pathogen

    Directory of Open Access Journals (Sweden)

    Lucía Graña-Miraglia

    2017-09-01

    Full Text Available Genome sequencing has been useful to gain an understanding of bacterial evolution. It has been used for studying the phylogeography and/or the impact of mutation and recombination on bacterial populations. However, it has rarely been used to study gene turnover at microevolutionary scales. Here, we sequenced Mexican strains of the human pathogen Acinetobacter baumannii sampled from the same locale over a 3 year period to obtain insights into the microevolutionary dynamics of gene content variability. We found that the Mexican A. baumannii population was recently founded and has been emerging due to a rapid clonal expansion. Furthermore, we noticed that on average the Mexican strains differed from each other by over 300 genes and, notably, this gene content variation has accrued more frequently and faster than the accumulation of mutations. Moreover, due to its rapid pace, gene content variation reflects the phylogeny only at very short periods of time. Additionally, we found that the external branches of the phylogeny had almost 100 more genes than the internal branches. All in all, these results show that rapid gene turnover has been of paramount importance in producing genetic variation within this population and demonstrate the utility of genome sequencing to study alternative forms of genetic variation.

  7. Molecular genetics and pathogenic mechanisms for the severe ciliopathies: insights into neurodevelopment and pathogenesis of neural tube defects.

    Science.gov (United States)

    Logan, Clare V; Abdel-Hamed, Zakia; Johnson, Colin A

    2011-02-01

    Meckel-Gruber syndrome (MKS) is a severe autosomal recessively inherited disorder characterized by developmental defects of the central nervous system that comprise neural tube defects that most commonly present as occipital encephalocele. MKS is considered to be the most common syndromic form of neural tube defect. MKS is genetically heterogeneous with six known disease genes: MKS1, MKS2/TMEM216, MKS3/TMEM67, RPGRIP1L, CEP290, and CC2D2A with the encoded proteins all implicated in the correct function of primary cilia. Primary cilia are microtubule-based organelles that project from the apical surface of most epithelial cell types. Recent progress has implicated the involvement of cilia in the Wnt and Shh signaling pathways and has led to an understanding of their role in normal mammalian neurodevelopment. The aim of this review is to provide an overview of the molecular genetics of the human disorder, and to assess recent insights into the etiology and molecular cell biology of severe ciliopathies from mammalian animal models of MKS.

  8. Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats, Eidolon helvum.

    Science.gov (United States)

    Peel, Alison J; Baker, Kate S; Hayman, David T S; Suu-Ire, Richard; Breed, Andrew C; Gembu, Guy-Crispin; Lembo, Tiziana; Fernández-Loras, Andrés; Sargan, David R; Fooks, Anthony R; Cunningham, Andrew A; Wood, James L N

    2016-08-01

    Bats, including African straw-coloured fruit bats (Eidolon helvum), have been highlighted as reservoirs of many recently emerged zoonotic viruses. This common, widespread and ecologically important species was the focus of longitudinal and continent-wide studies of the epidemiological and ecology of Lagos bat virus, henipaviruses and Achimota viruses. Here we present a spatial, morphological, demographic, genetic and serological dataset encompassing 2827 bats from nine countries over an 8-year period. Genetic data comprises cytochrome b mitochondrial sequences (n=608) and microsatellite genotypes from 18 loci (n=544). Tooth-cementum analyses (n=316) allowed derivation of rare age-specific serologic data for a lyssavirus, a henipavirus and two rubulaviruses. This dataset contributes a substantial volume of data on the ecology of E. helvum and its viruses and will be valuable for a wide range of studies, including viral transmission dynamic modelling in age-structured populations, investigation of seasonal reproductive asynchrony in wide-ranging species, ecological niche modelling, inference of island colonisation history, exploration of relationships between island and body size, and various spatial analyses of demographic, morphometric or serological data.

  9. Genetic divergence of human pathogens Nanophyetus spp. (Trematoda: Troglotrematidae) on the opposite sides of the Pacific Rim.

    Science.gov (United States)

    Voronova, A N; Chelomina, G N; Besprozvannykh, V V; Tkach, V V

    2017-04-01

    Human and animal nanophyetiasis is caused by intestinal flukes belonging to the genus Nanophyetus distributed on both North American and Eurasian coasts of Northern Pacific. In spite of the wide geographical distribution and medical and veterinary importance of these flukes, the intra-generic taxonomy of Nanophyetus spp. remains unresolved. The two most widely distributed nominal species, Nanophyetus salmincola and Nanophyetus schikhobalowi, both parasitizing humans and carnivorous mammals, were described from North America and eastern Eurasia, respectively. However, due to their high morphological similarity their interrelationships remained unclear and taxonomic status unstable. In this study, we explored genetic diversity of Nanophyetus spp. from the Southern Russian Far East in comparison with that of samples from North America based on the sequence variation of the nuclear ribosomal gene family (18S, internal transcribed spacers, ITS1-5·8S-ITS2 and 28S). High levels of genetic divergence in each rDNA region (nucleotide substitutions, indels, alterations in the secondary structures of the ITS1 and ITS2 transcripts) as well as results of phylogenetic analysis provided strong support for the status of N. salmincola and N. schikhobalowi as independent species.

  10. Mating Type Alleles,Female Fertility and Genetic Diversity of Magnaporthe grisea Populations Pathogenic to Rice from Some Asian Countries

    Institute of Scientific and Technical Information of China (English)

    SHEN Ying; Joelle Milazzo; YUAN Xiao-ping; Henry Adreit; WANG Yan-li; Jean Loup Notteghem; Didier Tharreau

    2003-01-01

    Five hundred and twenty-two isolates of Magnaporthe grisea isolated from rice in 5 Asian countries were characterized for their mating type by crossing them with 4 hermaphroditic isolates (KA3 and TH2: MAT1.1; Guy11 and TH-16: MAT1.2). Among them, 41% were MAT1.1 and 25% were MAT1.2.The remaining 34% did not produce perithecia with any of the 4 hermaphroditic testers. In Bangladesh, India,Nepal, Vietnam and in most provinces of China, both mating types were present. Only one mating type was found in 3 provinces and 1 city of China. Almost all the isolates had very low fertility, as they were in general female sterile and sometimes also male sterile. Hermaphroditic isolates were recovered from the 5 countries. In these countries, they represented between 13% and 75% of the isolates. In Zhejiang, Guizhou, Guangdong,Hunan, Yunnan and H-ubei provinces of China, hermaphroditic isolates represented between 6% and 67%.The genetic diversity of 143 isolates from these countries and provinces, where hermaphroditic isolates had been collected, was analyzed using SCAR markers. Genetic diversity was high and population structure did not resemble classical clonal structure described in most rice growing regions. The existence of sexual reproduction in the field, localization of a center of diversity in China, and migration between countries were discussed in this paper.

  11. Genetic structure and parasitization-related ability divergence of a nematode fungal pathogen Hirsutella minnesotensis following founder effect in China.

    Science.gov (United States)

    Shu, Chi; Jiang, Xianzhi; Cheng, Xiaoli; Wang, Niuniu; Chen, Senyu; Xiang, Meichun; Liu, Xingzhong

    2015-08-01

    The fungal parasitoid, Hirsutella minnesotensis, is a dominant parasitoid of the soybean cyst nematode, which is a destruction pest of soybean crops. We investigated population structure and parasitism pattern in samples of H. minnesotensis in China to reveal the spreading pattern of this fungal species and the underlying mechanism generating the parasitization-related ability variability in Chinese population. In cross-inoculation experiments using different combinations of H. minnesotensis and soybean cyst nematode samples from China, most H. minnesotensis isolates fitted the criterion for "local versus foreign" parasitism profile, exhibiting local adaptation pattern to the SCN host. However, the genetic analysis of the single nucleotide polymorphisms with clone-corrected samples based on ten DNA fragments in 56 isolates of H. minnesotensis from China revealed that the Chinese H. minnesotensis population was a clonal lineage that underwent a founder event. The results demonstrated that the Chinese H. minnesotensis population had generated parasitization-related ability diversity after a founder event through individual variation or phenotypic plasticity other than local adaptation. The rapid divergence of parasitization-related abilities with simple genetic structure in Chinese H. minnesotensis population indicates a fundamental potential for the establishment of invasive fungal species, which is a prerequisite for biological control agents.

  12. Genetic affinities within a large global collection of pathogenic Leptospira: implications for strain identification and molecular epidemiology.

    Directory of Open Access Journals (Sweden)

    Kishore Nalam

    Full Text Available Leptospirosis is an important zoonosis with widespread human health implications. The non-availability of accurate identification methods for the individualization of different Leptospira for outbreak investigations poses bountiful problems in the disease control arena. We harnessed fluorescent amplified fragment length polymorphism analysis (FAFLP for Leptospira and investigated its utility in establishing genetic relationships among 271 isolates in the context of species level assignments of our global collection of isolates and strains obtained from a diverse array of hosts. In addition, this method was compared to an in-house multilocus sequence typing (MLST method based on polymorphisms in three housekeeping genes, the rrs locus and two envelope proteins. Phylogenetic relationships were deduced based on bifurcating Neighbor-joining trees as well as median joining network analyses integrating both the FAFLP data and MLST based haplotypes. The phylogenetic relationships were also reproduced through Bayesian analysis of the multilocus sequence polymorphisms. We found FAFLP to be an important method for outbreak investigation and for clustering of isolates based on their geographical descent rather than by genome species types. The FAFLP method was, however, not able to convey much taxonomical utility sufficient to replace the highly tedious serotyping procedures in vogue. MLST, on the other hand, was found to be highly robust and efficient in identifying ancestral relationships and segregating the outbreak associated strains or otherwise according to their genome species status and, therefore, could unambiguously be applied for investigating phylogenetics of Leptospira in the context of taxonomy as well as gene flow. For instance, MLST was more efficient, as compared to FAFLP method, in clustering strains from the Andaman island of India, with their counterparts from mainland India and Sri Lanka, implying that such strains share genetic

  13. Rivers and flooded areas identified by medium-resolution remote sensing improve risk prediction of the highly pathogenic avian influenza H5N1 in Thailand.

    Science.gov (United States)

    Thanapongtharm, Weerapong; Van Boeckel, Thomas P; Biradar, Chandrashekhar; Xiao, Xiang-Ming; Gilbert, Marius

    2013-11-01

    Thailand experienced several epidemic waves of the highly pathogenic avian influenza (HPAI) H5N1 between 2004 and 2005. This study investigated the role of water in the landscape, which has not been previously assessed because of a lack of high-resolution information on the distribution of flooded land at the time of the epidemic. Nine Landsat 7 - Enhanced Thematic Mapper Plus scenes covering 174,610 km(2) were processed using k-means unsupervised classification to map the distribution of flooded areas as well as permanent lakes and reservoirs at the time of the main epidemic HPAI H5N1 wave of October 2004. These variables, together with other factors previously identified as significantly associated with risk, were entered into an autologistic regression model in order to quantify the gain in risk explanation over previously published models. We found that, in addition to other factors previously identified as associated with risk, the proportion of land covered by flooding along with expansion of rivers and streams, derived from an existing, sub-district level (administrative level no. 3) geographical information system database, was a highly significant risk factor in this 2004 HPAI epidemic. These results suggest that water-borne transmission could have partly contributed to the spread of HPAI H5N1 during the epidemic. Future work stemming from these results should involve studies where the actual distribution of small canals, rivers, ponds, rice paddy fields and farms are mapped and tested against farm-level data with respect to HPAI H5N1.

  14. Rivers and flooded areas identified by medium-resolution remote sensing improve risk prediction of the highly pathogenic avian influenza H5N1 in Thailand

    Directory of Open Access Journals (Sweden)

    Weerapong Thanapongtharm

    2013-11-01

    Full Text Available Thailand experienced several epidemic waves of the highly pathogenic avian influenza (HPAI H5N1 between 2004 and 2005. This study investigated the role of water in the landscape, which has not been previously assessed because of a lack of high-resolution information on the distribution of flooded land at the time of the epidemic. Nine Landsat 7- Enhanced Thematic Mapper Plus scenes covering 174,610 km2 were processed using k-means unsupervised classification to map the distribution of flooded areas as well as permanent lakes and reservoirs at the time of the main epidemic HPAI H5N1 wave of October 2004. These variables, together with other factors previously identified as significantly associated with risk, were entered into an autologistic regression model in order to quantify the gain in risk explanation over previously published models. We found that, in addition to other factors previously identified as associated with risk, the proportion of land covered by flooding along with expansion of rivers and streams, derived from an existing, sub-district level (administrative level no. 3 geographical information system database, was a highly significant risk factor in this 2004 HPAI epidemic. These results suggest that water-borne transmission could have partly contributed to the spread of HPAI H5N1 during the epidemic. Future work stemming from these results should involve studies where the actual distribution of small canals, rivers, ponds, rice paddy fields and farms are mapped and tested against farm-level data with respect to HPAI H5N1.

  15. Photosynthesis-dependent physiological and genetic crosstalk between cold acclimation and cold-induced resistance to fungal pathogens in triticale (Triticosecale Wittm.).

    Science.gov (United States)

    Szechyńska-Hebda, Magdalena; Wąsek, Iwona; Gołębiowska-Pikania, Gabriela; Dubas, Ewa; Żur, Iwona; Wędzony, Maria

    2015-04-01

    The breeding for resistance against fungal pathogens in winter triticale (Triticosecale Wittm.) continues to be hindered by a complexity of the resistance mechanisms, strong interaction with environmental conditions, and dependence on the plant genotype. We showed, that temperature below 4 °C induced the plant genotype-dependent resistance against the fungal pathogen Microdochium nivale. The mechanism involved, at least, the adjustment of the reactions in the PSII proximity and photoprotection, followed by an improvement of the growth and development. The genotypes capable to develop the cold-induced resistance, showed a higher maximum quantum yield of PSII and a more efficient integration of the primary photochemistry of light reactions with the dark reactions. Moreover, induction of the photoprotective mechanism, involving at least the peroxidases scavenging hydrogen peroxide, was observed for such genotypes. Adjustment of the photosynthesis and stress acclimation has enabled fast plant growth and avoidance of the developmental stages sensitive to fungal infection. The same mechanisms allowed the quick regrow of plants during the post-disease period. In contrast, genotypes that were unable to develop resistance despite cold hardening had less flexible balancing of the photoprotection and photoinhibition processes. Traits related to: photosynthesis-dependent cold-acclimation and cold-induced resistance; biomass accumulation and growth; as well as protection system involving peroxidases; were integrated also at a genetic level. Analysing 95 lines of the mapping population SaKa3006×Modus we determined region on chromosomes 5B and 7R shared within all tested traits. Moreover, similar expression pattern of a set of the genes related to PSII was determined with the metaanalysis of the multiple microarray experiments. Comparable results for peroxidases, involving APXs and GPXs and followed by PRXs, indicated a similar function during cold acclimation and defense

  16. Genetic analysis of environmental strains of the plant pathogen Phytophthora capsici reveals heterogeneous repertoire of effectors and possible effector evolution via genomic island.

    Science.gov (United States)

    Iribarren, María Josefina; Pascuan, Cecilia; Soto, Gabriela; Ayub, Nicolás Daniel

    2015-11-01

    Phytophthora capsici is a virulent oomycete pathogen of many vegetable crops. Recently, it has been demonstrated that the recognition of the RXLR effector AVR3a1 of P. capsici (PcAVR3a1) triggers a hypersensitive response and plays a critical role in mediating non-host resistance. Here, we analyzed the occurrence of PcAVR3a1 in 57 isolates of P. capsici derived from globe squash, eggplant, tomato and bell pepper cocultivated in a small geographical area. The occurrence of PcAVR3a1 in environmental strains of P. capsici was confirmed by PCR in only 21 of these pathogen isolates. To understand the presence-absence pattern of PcAVR3a1 in environmental strains, the flanking region of this gene was sequenced. PcAVR3a1 was found within a genetic element that we named PcAVR3a1-GI (PcAVR3a1 genomic island). PcAVR3a1-GI was flanked by a 22-bp direct repeat, which is related to its site-specific recombination site. In addition to the PcAVR3a1 gene, PcAVR3a1-GI also encoded a phage integrase probably associated with the excision and integration of this mobile element. Exposure to plant induced the presence of an episomal circular intermediate of PcAVR3a1-GI, indicating that this mobile element is functional. Collectively, these findings provide evidence of PcAVR3a1 evolution via mobile elements in environmental strains of Phytophthora.

  17. Seasonal change detection of riparian zones with remote sensing images and genetic programming in a semi-arid watershed.

    Science.gov (United States)

    Makkeasorn, Ammarin; Chang, Ni-Bin; Li, Jiahong

    2009-02-01

    Riparian zones are deemed significant due to their interception capability of non-point source impacts and the maintenance of ecosystem integrity region wide. To improve classification and change detection of riparian buffers, this paper developed an evolutionary computational, supervised classification method--the RIparian Classification Algorithm (RICAL)--to conduct the seasonal change detection of riparian zones in a vast semi-arid watershed, South Texas. RICAL uniquely demonstrates an integrative effort to incorporate both vegetation indices and soil moisture images derived from LANDSAT 5 TM and RADARSAT-1 satellite images, respectively. First, an estimation of soil moisture based on RADARSAT-1 Synthetic Aperture Radar (SAR) images was conducted via the first-stage genetic programming (GP) practice. Second, for the statistical analyses and image classification, eight vegetation indices were prepared based on reflectance factors that were calculated as the response of the instrument on LANDSAT. These spectral vegetation indices were then independently used for discriminate analysis along with soil moisture images to classify the riparian zones via the second-stage GP practice. The practical implementation was assessed by a case study in the Choke Canyon Reservoir Watershed (CCRW), South Texas, which is mostly agricultural and range land in a semi-arid coastal environment. To enhance the application potential, a combination of Iterative Self-Organizing Data Analysis Techniques (ISODATA) and maximum likelihood supervised classification was also performed for spectral discrimination and classification of riparian varieties comparatively. Research findings show that the RICAL algorithm may yield around 90% accuracy based on the unseen ground data. But using different vegetation indices would not significantly improve the final quality of the spectral discrimination and classification. Such practices may lead to the formulation of more effective management strategies

  18. High pathogenicity and low genetic evolution of avian paramyxovirus type I (Newcastle disease virus) isolated from live bird markets in Uganda.

    Science.gov (United States)

    Byarugaba, Denis K; Mugimba, Kizito K; Omony, John B; Okitwi, Martin; Wanyana, Agnes; Otim, Maxwell O; Kirunda, Halid; Nakavuma, Jessica L; Teillaud, Angélique; Paul, Mathilde C; Ducatez, Mariette F

    2014-10-01

    Newcastle disease is still a serious disease of poultry especially in backyard free-range production systems despite the availability of cross protective vaccines. Healthy-looking poultry from live bird markets have been suspected as a major source of disease spread although limited studies have been conducted to ascertain the presence of the virulent strains in the markets and to understand how they are related to outbreak strains. This study evaluated the occurrence of Newcastle disease virus in samples collected from poultry in live bird markets across Uganda. The isolates were pathoyped using standard methods (mean death time (MDT), intracelebral pathogenicity index (ICPI), and sequencing of the fusion protein cleavage site motif) and also phylogenetically analysed after sequencing of the full fusion and hemagglutin-neuraminidase genes. The isolates were classified into genotypes and subgenotypes based on the full fusion protein gene classification system and compared with other strains in the region and world-wide. Virulent avian paramyxovirus type I (APMV-1) (Newcastle disease virus) was isolated in healthy-looking poultry in live bird markets. The viruses belonged to a new subgenotype, Vd, in genotype V, and clustered together with Tanzania and Kenya strains. They harbored low genetic diversity. The occurrence of virulent AMPV-1 strains in live bird markets may serve as sources of Newcastle disease outbreaks in non-commercial farms.

  19. Low genetic diversity among pathogenic strains of Erwinia psidii from Brazil Baixa diversidade genética entre estirpes patogênicas de Erwinia psidii no Brasil

    Directory of Open Access Journals (Sweden)

    Ana C. O. Teixeira

    2009-09-01

    Full Text Available Erwinia psidii causes bacterial disease of guava in Brazil. Phenotypic and molecular characterization through rep-PCR fingerprinting of 42 strains from different geographical regions showed that E. psidii populations in Brazil have a low level of genetic diversity and suggest that contaminated plant material is the main source for pathogen dissemination in the country.Erwinia psidii é o agente causal da seca-dos-ponteiros ou bacteriose da goiabeira no Brasil. A caracterização fenotípica e molecular através de rep-PCR de 42 estirpes patogênicas de diferentes regiões mostrou que as populações de E. psidii no Brasil têm um baixo nível de diversidade genética e sugere que material de propagação infectado é a principal fonte de disseminação do patógeno para novas áreas no país.

  20. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  1. Remote Research

    CERN Document Server

    Tulathimutte, Tony

    2011-01-01

    Remote studies allow you to recruit subjects quickly, cheaply, and immediately, and give you the opportunity to observe users as they behave naturally in their own environment. In Remote Research, Nate Bolt and Tony Tulathimutte teach you how to design and conduct remote research studies, top to bottom, with little more than a phone and a laptop.

  2. Remote Sensing

    CERN Document Server

    Khorram, Siamak; Koch, Frank H; van der Wiele, Cynthia F

    2012-01-01

    Remote Sensing provides information on how remote sensing relates to the natural resources inventory, management, and monitoring, as well as environmental concerns. It explains the role of this new technology in current global challenges. "Remote Sensing" will discuss remotely sensed data application payloads and platforms, along with the methodologies involving image processing techniques as applied to remotely sensed data. This title provides information on image classification techniques and image registration, data integration, and data fusion techniques. How this technology applies to natural resources and environmental concerns will also be discussed.

  3. A reverse genetics system for the Great Lakes strain of viral hemorrhagic septicemia virus: the NV gene is required for pathogenicity

    Science.gov (United States)

    Ammayappan, Arun; Kurath, Gael; Thompson, Tarin M.; Vakharia, Vikram N.

    2011-01-01

    Viral hemorrhagic septicemia virus (VHSV), belonging to the genus Novirhabdovirus in the family of Rhabdoviridae, causes a highly contagious disease of fresh and saltwater fish worldwide. Recently, a novel genotype of VHSV, designated IVb, has invaded the Great Lakes in North America, causing large-scale epidemics in wild fish. An efficient reverse genetics system was developed to generate a recombinant VHSV of genotype IVb from cloned cDNA. The recombinant VHSV (rVHSV) was comparable to the parental wild-type strain both in vitro and in vivo, causing high mortality in yellow perch (Perca flavescens). A modified recombinant VHSV was generated in which the NV gene was substituted with an enhanced green fluorescent protein gene (rVHSV-ΔNV-EGFP), and another recombinant was made by inserting the EGFP gene into the full-length viral clone between the P and M genes (rVHSV-EGFP). The in vitro replication kinetics of rVHSV-EGFP was similar to rVHSV; however, the rVHSV-ΔNV-EGFP grew 2 logs lower. In yellow perch challenges, wtVHSV and rVHSV induced 82-100% cumulative per cent mortality (CPM), respectively, whereas rVHSV-EGFP produced 62% CPM and rVHSV-ΔNV-EGFP caused only 15% CPM. No reversion of mutation was detected in the recovered viruses and the recombinant viruses stably maintained the foreign gene after several passages. These results indicate that the NV gene of VHSV is not essential for viral replication in vitro and in vivo, but it plays an important role in viral replication efficiency and pathogenicity. This system will facilitate studies of VHSV replication, virulence, and production of viral vectored vaccines.

  4. Genetic characterization by composite sequence analysis of a new pathogenic field strain of equine infectious anemia virus from the 2006 outbreak in Ireland.

    Science.gov (United States)

    Quinlivan, Michelle; Cook, Frank; Kenna, Rachel; Callinan, John J; Cullinane, Ann

    2013-03-01

    Equine infectious anemia virus (EIAV), the causative agent of equine infectious anaemia (EIA), possesses the least-complex genomic organization of any known extant lentivirus. Despite this relative genetic simplicity, all of the complete genomic sequences published to date are derived from just two viruses, namely the North American EIAV(WYOMING) (EIAV(WY)) and Chinese EIAV(LIAONING) (EIAV(LIA)) strains. In 2006, an outbreak of EIA occurred in Ireland, apparently as a result of the importation of contaminated horse plasma from Italy and subsequent iatrogenic transmission to foals. This EIA outbreak was characterized by cases of severe, sometimes fatal, disease. To begin to understand the molecular mechanisms underlying this pathogenic phenotype, complete proviral genomic sequences in the form of 12 overlapping PCR-generated fragments were obtained from four of the EIAV-infected animals, including two of the index cases. Sequence analysis of multiple molecular clones produced from each fragment demonstrated the extent of diversity within individual viral genes and permitted construction of consensus whole-genome sequences for each of the four viral isolates. In addition, complete env gene sequences were obtained from 11 animals with differing clinical profiles, despite exposure to a common EIAV source. Although the overall genomic organization of the Irish EIAV isolates was typical of that seen in all other strains, the European viruses possessed ≤80 % nucleotide sequence identity with either EIAV(WY) or EIAV(LIA). Furthermore, phylogenetic analysis suggested that the Irish EIAV isolates developed independently of the North American and Chinese viruses and that they constitute a separate monophyletic group.

  5. Genetic diversity and phylogenetic analysis of highly pathogenic avian influenza (HPAI) H5N1 viruses circulating in Bangladesh from 2007-2011.

    Science.gov (United States)

    Mondal, S P; Balasuriya, U B R; Yamage, M

    2013-12-01

    Highly pathogenic avian influenza (HPAI) H5N1 virus has been endemic in Bangladesh since its first isolation in February 2007. Phylogenetic analysis of the haemagglutinin (HA) gene of HPAI H5N1 viruses demonstrated that 25 Bangladeshi isolates including two human isolates from 2007-2011 along with some isolates from neighbouring Asian countries (India, Bhutan, Myanmar, Nepal, China and Vietnam) segregate into two distinct clades (2.2 and 2.3). There was clear evidence of introduction of clade 2.3.2 and 2.3.4 viruses in 2011 in addition to clade 2.2 viruses that had been in circulation in Bangladesh since 2007. The data clearly demonstrated the movement of H5N1 strains between Asian countries included in this study due to migration of wild birds and/or illegal movement of poultry across borders. Interestingly, the two human isolates were closely related to the clade 2.2 Bangladeshi chicken isolates indicating that they have originated from chickens. Furthermore, comparative amino acid sequence analysis revealed several substitutions (including 189R>K and 282I>V) in HA protein of some clade 2.2 Bangladeshi viruses including the human isolates, suggesting there was antigenic drift in clade 2.2.3 viruses that were circulating between 2008 and 2011. Overall, the data imply genetic diversity among circulating viruses and multiple introductions of H5N1 viruses with an increased risk of human infections in Bangladesh, and establishment of H5N1 virus in wild and domestic bird populations, which demands active surveillance. © 2013 Blackwell Verlag GmbH.

  6. Sequence and phylogenetic analysis of highly pathogenic avian influenza H5N1 viruses isolated during 2006–2008 outbreaks in Pakistan reveals genetic diversity

    Directory of Open Access Journals (Sweden)

    Siddique Naila

    2012-12-01

    Full Text Available Abstract Background Since the first outbreak recorded in northern areas of Pakistan in early 2006, highly pathogenic avian influenza H5N1 viruses were isolated from commercial poultry and wild/domestic birds from different areas of Pakistan up to July 2008. Different isolates of H5N1 were sequenced to explore the genetic diversity of these viruses. Results Phylogenetic analysis revealed close clustering and highest sequence identity in all 8 genes to HPAI H5N1 isolates belonging to unified H5 clade 2.2, sub-lineage EMA-3 recovered from Afghanistan during the same time period. Two subgroups within Pakistani H5N1 viruses, from domestic and wild birds, were observed on the basis of their sequence homology and mutations. HPAI motif, preferred receptor specificity for α-(2, 3 linkages, potential N-linked glycosylation sites and an additional glycosylation site at the globular head of HA protein of four Pakistani H5N1 isolates. While, the amino acids associated with sensitivities to various antiviral drugs (Oseltamivir, Zanamivir, Amantadine were found conserved for the Pakistani H5N1 isolates. Conspicuously, some important mutations observed at critical positions of antigenic sites (S141P, D155S, R162I & P181S and at receptor binding pocket (A185T, R189K & S217P of HA-1. A high sequence similarity between Pakistani HP H5N1 and LP H9N2 viruses was also observed. Avian like host specific markers with the exception of E627K in PB2, K356R in PA, V33I in NP, I28V in M2 and L107F in NS2 proteins were also observed. Conclusions Various point mutations in different genes of H5 viruses from Pakistan were observed during its circulation in the field. The outbreaks started in Khyber Pakhtoon Khawa (North West province in 2006 and spread to the Southern regions over a period of time. Though migratory birds may have a role for this continued endemicity of clade 2.2 H5N1 viruses during 2006–2008 in Pakistan, the possibility of their transmission through legal

  7. Remote Sensing.

    Science.gov (United States)

    Williams, Richard S., Jr.; Southworth, C. Scott

    1983-01-01

    The Landsat Program became the major event of 1982 in geological remote sensing with the successful launch of Landsat 4. Other 1982 remote sensing accomplishments, research, publications, (including a set of Landsat worldwide reference system index maps), and conferences are highlighted. (JN)

  8. Remote medicine

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-04-29

    The international oil industry, catalyzed by a surge in exploration and production projects in remote regions, is giving health care for its travelers and expatriates a high priority. L.R. Aalund, the Journal`s Managing Editor--Technology, reports on why and how this is happening now. He covers this in articles on: health care in Russia, air ambulance evacuations, and the deployment of remote paramedics. Aalund gathered the information during trips to Finland and Russia and interviews with oil industry personnel, physicians, and other medical professionals in North America, Europe, and Siberia. Titles of the four topics presented in this special section on remote medicine are as follows: Oil companies focus on emergency care for expats in Russia; Air ambulance plan can be critical; Remote paramedics have high level of training; and Other facets of remote medicine.

  9. 蟾蜍壶菌病病原遗传分化研究%Genetic Differentiation of the Pathogen of Batrachochytrium dendrobatidis in Toads

    Institute of Scientific and Technical Information of China (English)

    曾朝辉; 白世卓; 朱蕴绮; 王晓龙

    2011-01-01

    壶菌病为近年发现的两栖类动物重要传染病,对野生和养殖种群危害极大,为确定药用经济动物蟾蜍历史上壶菌病感染情况,提高养殖蟾蜍疾病防治水平,选取某博物馆馆藏采集于四川的蟾蜍标本32只,利用Taqman—MGB荧光探针定量PCR技术进行壶菌检测,并对定量PCR产物克隆、测序,通过序列比对和系统发育分析判定其来源。最终得到定量PCR标准曲线:Y=-3.0X+32.39;相关系数R0=0.9996;检测结果为阳性样本12只,检出率37.5%。同时系统发育分析表明,我国的壶菌存在一定程度的分化,一类与北美洲、南美洲、欧洲菌株呈现高度的亲缘关系;另一类则表现出与世界其他地区分布的壶菌有明显的不同,显示其独特性。这提示我国蟾蜍壶菌病的防制应更具针对性,不可盲目照搬国外经验。%The chytridiomycosis is a significant emerging disease of amphibians in recent years which seriuosly does harm to the wild and breeding population. To ascertain the condition of the Batrachochytrium dendrobatidis infection history in the population of toad, the medicinal economic animal, and enhance the prevention for this disease, 32 toad specimen collected from Sichwan keeping in a museum were assayed by Taqman-MGB fluorescence probe quantitative polymerase chain reaction to detect Batrachochytrium dendrobatidis. Besides, the products of QPCR were cloned and sequenced to identify the origin of the pathogen by sequence alignment and phylogenetie analysis. Finally we got the standard curve: Y = - 3.0X + 32.39 and the related coefficient: R2 = 0.999 6. Total 12 positive samples reported the detec- tion rate as 37.5 %. Meanwhile the phylogenetic analysis indicated that a certain extent differentiation of the chytrid fungi in our country exists. One kind of the tested strain showed highly genetic relationship with the strains from the North America, South America

  10. Genetic dissection of a TIR-NB-LRR locus from the wild North American grapevine species Muscadinia rotundifolia identifies paralogous genes conferring resistance to major fungal and oomycete pathogens in cultivated grapevine.

    Science.gov (United States)

    Feechan, Angela; Anderson, Claire; Torregrosa, Laurent; Jermakow, Angelica; Mestre, Pere; Wiedemann-Merdinoglu, Sabine; Merdinoglu, Didier; Walker, Amanda R; Cadle-Davidson, Lance; Reisch, Bruce; Aubourg, Sebastien; Bentahar, Nadia; Shrestha, Bipna; Bouquet, Alain; Adam-Blondon, Anne-Françoise; Thomas, Mark R; Dry, Ian B

    2013-11-01

    The most economically important diseases of grapevine cultivation worldwide are caused by the fungal pathogen powdery mildew (Erysiphe necator syn. Uncinula necator) and the oomycete pathogen downy mildew (Plasmopara viticola). Currently, grapegrowers rely heavily on the use of agrochemicals to minimize the potentially devastating impact of these pathogens on grape yield and quality. The wild North American grapevine species Muscadinia rotundifolia was recognized as early as 1889 to be resistant to both powdery and downy mildew. We have now mapped resistance to these two mildew pathogens in M. rotundifolia to a single locus on chromosome 12 that contains a family of seven TIR-NB-LRR genes. We further demonstrate that two highly homologous (86% amino acid identity) members of this gene family confer strong resistance to these unrelated pathogens following genetic transformation into susceptible Vitis vinifera winegrape cultivars. These two genes, designated resistance to Uncinula necator (MrRUN1) and resistance to Plasmopara viticola (MrRPV1) are the first resistance genes to be cloned from a grapevine species. Both MrRUN1 and MrRPV1 were found to confer resistance to multiple powdery and downy mildew isolates from France, North America and Australia; however, a single powdery mildew isolate collected from the south-eastern region of North America, to which M. rotundifolia is native, was capable of breaking MrRUN1-mediated resistance. Comparisons of gene organization and coding sequences between M. rotundifolia and the cultivated grapevine V. vinifera at the MrRUN1/MrRPV1 locus revealed a high level of synteny, suggesting that the TIR-NB-LRR genes at this locus share a common ancestor. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

  11. Genetic signature of a range expansion and leap-frog event after the recent invasion of Europe by the grapevine downy mildew pathogen Plasmopara viticola

    NARCIS (Netherlands)

    Fontaine, Michael C.; Austerlitz, Frederic; Giraud, Tatiana; Labbe, Frederic; Papura, Daciana; Richard-Cervera, Sylvie; Delmotte, Francois

    2013-01-01

    Biologic invasions can have important ecological, economic and social consequences, particularly when they involve the introduction and spread of plant invasive pathogens, as they can threaten natural ecosystems and jeopardize the production of human food. Examples include the grapevine downy mildew

  12. EFFECT OF DISINFECTANTS BASED ON POTASSIUM PERSULFATE, HYDROGEN PEROXIDE, GLUTARALDEHYDE AND QUATERNARY AMMONIUM COMPOUNDS ON THE GENETIC MATERIAL OF THE PATHOGEN BACTERIA SPECIFIC TO MEAT PROCESSING INDUSTRY

    Directory of Open Access Journals (Sweden)

    V. N. Afonyushkin

    2016-01-01

    Full Text Available Abstract The changes in bacterial genetic material under the action of different biocidal products have been investigated. It was confirmed by PCR and genetic engineering that biocidal product Ecocid was able to remove both chromosomal and plasmid DNA, either isolated or contained within the bacterial cells. Using a disinfectant that destroys DNA on the surfaces of meat production equipment is a promising measure to prevent horizontal transfer of unwanted genetic material, such as bacterial genes associated with the resistance to antibiotics, or genes of toxin production.

  13. Genetic characterization of clinical and environmental Vibrio parahaemolyticus from the Northeast USA reveals emerging resident and non-indigenous pathogen lineages

    Directory of Open Access Journals (Sweden)

    Feng eXu

    2015-04-01

    Full Text Available Gastric infections caused by the environmentally transmitted pathogen, Vibrio parahaemolyticus, have increased over the last two decades, including in many parts of the United States (US. However, until recently, infections linked to shellfish from the cool northeastern US waters were rare. Cases have risen in the Northeast, consistent with changes in local V. parahaemolyticus populations towards greater abundance or a shift in constituent pathogens. We examined 94 clinical isolates from a period of increasing disease in the region and compared them to 200 environmental counterparts to identify resident and non-indigenous lineages and to gain insight into the emergence of pathogenic types. Genotyping and multi-locus sequence analysis of clinical isolates collected from 2010-2013 in Massachusetts, New Hampshire and Maine revealed their polyphyletic nature. Although 80% of the clinical isolates harbored the trh hemolysin either alone or with tdh, and were urease positive, 14% harbored neither hemolysin exposing a limitation for these traits in pathogen detection. Resident sequence type (ST 631 strains caused seven infections, and show a relatively recent history of recombination with other clinical and environmental lineages present in the region. ST34 and ST674 strains were each linked to a single infection and these strain types were also identified from the environment as isolates harboring hemolysin genes. Forty-three ST36 isolates were identified from the clinical collection, consistent with reports that this strain type caused a rise in regional infections starting in 2012. Whole-genome phylogenies that included three ST36 outbreak isolates traced to at least two local sources demonstrated that the US Atlantic coastal population of this strain type was indeed derived from the Pacific population. This study lays the foundation for understanding dynamics within natural populations associated with emergence and invasion of pathogenic strain

  14. Remote viewing.

    Science.gov (United States)

    Scott, C

    1988-04-15

    Remote viewing is the supposed faculty which enables a percipient, sited in a closed room, to describe the perceptions of a remote agent visiting an unknown target site. To provide convincing demonstration of such a faculty poses a range of experimental and practical problems, especially if feedback to the percipient is allowed after each trial. The precautions needed are elaborate and troublesome; many potential loopholes have to be plugged and there will be strong temptations to relax standards, requiring exceptional discipline and dedication by the experimenters. Most reports of remote viewing experiments are rather superficial and do not permit assessment of the experimental procedures with confidence; in many cases there is clear evidence of particular loopholes left unclosed. Any serious appraisal of the evidence would have to go beyond the reports. Meanwhile the published evidence is far from compelling, and certainly insufficient to justify overthrow of well-established scientific principles.

  15. Genetic aspects of ash dieback caused by the pathogenic fungus Chalara fraxinea on Fraxinus excelsior

    DEFF Research Database (Denmark)

    McKinney, Lea Vig

    ). This thesis comprises five papers that aim to contribute to the knowledge on the interaction between the pathogen and its host and the inherent natural resistance found within the host species. Paper I reviews the current literature on the aetiology of the fungus, the epidemic and its consequences...... could be an effect of disease escape. The results suggest that a small fraction of the natural population may be able to resist the epidemic and proposes prospects for maintenance of the species through selection of highly resistant trees.......Ash dieback, caused by the invasive pathogen Chalara fraxinea T. Kowalski (teleomorph, Hymenoscyphus pseudoalbidus V. Queloz), has emerged and spread across Europe in the last two decades and currently affects most of the natural distribution of Fraxinus excelsior L. (common ash, European ash...

  16. The Clinical Next-Generation Sequencing Database: A Tool for the Unified Management of Clinical Information and Genetic Variants to Accelerate Variant Pathogenicity Classification.

    Science.gov (United States)

    Nishio, Shin-Ya; Usami, Shin-Ichi

    2017-03-01

    Recent advances in next-generation sequencing (NGS) have given rise to new challenges due to the difficulties in variant pathogenicity interpretation and large dataset management, including many kinds of public population databases as well as public or commercial disease-specific databases. Here, we report a new database development tool, named the "Clinical NGS Database," for improving clinical NGS workflow through the unified management of variant information and clinical information. This database software offers a two-feature approach to variant pathogenicity classification. The first of these approaches is a phenotype similarity-based approach. This database allows the easy comparison of the detailed phenotype of each patient with the average phenotype of the same gene mutation at the variant or gene level. It is also possible to browse patients with the same gene mutation quickly. The other approach is a statistical approach to variant pathogenicity classification based on the use of the odds ratio for comparisons between the case and the control for each inheritance mode (families with apparently autosomal dominant inheritance vs. control, and families with apparently autosomal recessive inheritance vs. control). A number of case studies are also presented to illustrate the utility of this database.

  17. Genetic mouse models for otitis media

    Institute of Scientific and Technical Information of China (English)

    Qingyin Zheng; Ken R Johnson

    2003-01-01

    @@ Genetics of Otitis Media (OM): OM is affected by multiple factors including eustachian tube (ET) structure and function, immune status, innate mucosal defense, genetic susceptibility, and pathogens.

  18. Pathogen intelligence

    Science.gov (United States)

    Steinert, Michael

    2014-01-01

    Different species inhabit different sensory worlds and thus have evolved diverse means of processing information, learning and memory. In the escalated arms race with host defense, each pathogenic bacterium not only has evolved its individual cellular sensing and behavior, but also collective sensing, interbacterial communication, distributed information processing, joint decision making, dissociative behavior, and the phenotypic and genotypic heterogeneity necessary for epidemiologic success. Moreover, pathogenic populations take advantage of dormancy strategies and rapid evolutionary speed, which allow them to save co-generated intelligent traits in a collective genomic memory. This review discusses how these mechanisms add further levels of complexity to bacterial pathogenicity and transmission, and how mining for these mechanisms could help to develop new anti-infective strategies. PMID:24551600

  19. Remote BCDGs

    Science.gov (United States)

    Erastova, L. K.

    2017-07-01

    The remote BCDGs with z>0.05 from the Second Byurakan Survey (SBS) are extracted. They are analogs of similar BCDGs in low-z Universe. The properties of these objects are discussed. Definitions of other physical types of active galaxies are considered and also clarified.

  20. A new genetic linkage map of tomato based on a Solanum lycopersicum x S. pimpinellifolium RIL population displaying locations of candidate pathogen response genes.

    Science.gov (United States)

    Ashrafi, Hamid; Kinkade, Matthew; Foolad, Majid R

    2009-11-01

    The narrow genetic base of the cultivated tomato, Solanum lycopersicum L., necessitates introgression of new variation from related species. Wild tomato species represent a rich source of useful genes and traits. Exploitation of genetic variation within wild species can be facilitated by the use of molecular markers and genetic maps. Recently we identified an accession (LA2093) within the red-fruited wild tomato species Solanum pimpinellifolium L. with exceptionally desirable characteristics, including disease resistance, abiotic stress tolerance, and high fruit lycopene content. To facilitate genetic characterization of such traits and their exploitation in tomato crop improvement, we developed a new recombinant inbred line (RIL) population from a cross between LA2093 and an advanced tomato breeding line (NCEBR-1). Furthermore, we constructed a medium-density molecular linkage map of this population using 294 polymorphic markers, including standard RFLPs, EST sequences (used as RFLP probes), CAPS, and SSRs. The map spanned 1091 cM of the tomato genome with an average marker spacing of 3.7 cM. A majority of the EST sequences, which were mainly chosen based on the putative role of their unigenes in disease resistance, defense-related response, or fruit quality, were mapped onto the tomato chromosomes for the first time. Co-localizations of relevant EST sequences with known disease resistance genes in tomato were also examined. This map will facilitate identification, genetic exploitation, and positional cloning of important genes or quantitative trait loci in LA2093. It also will allow the elucidation of the molecular mechanism(s) underlying important traits segregating in the RIL population. The map may further facilitate characterization and exploitation of genetic variation in other S. pimpinellifolium accessions as well as in modern cultivars of tomato.

  1. Transient virulence of emerging pathogens.

    Science.gov (United States)

    Bolker, Benjamin M; Nanda, Arjun; Shah, Dharmini

    2010-05-06

    Should emerging pathogens be unusually virulent? If so, why? Existing theories of virulence evolution based on a tradeoff between high transmission rates and long infectious periods imply that epidemic growth conditions will select for higher virulence, possibly leading to a transient peak in virulence near the beginning of an epidemic. This transient selection could lead to high virulence in emerging pathogens. Using a simple model of the epidemiological and evolutionary dynamics of emerging pathogens, along with rough estimates of parameters for pathogens such as severe acute respiratory syndrome, West Nile virus and myxomatosis, we estimated the potential magnitude and timing of such transient virulence peaks. Pathogens that are moderately evolvable, highly transmissible, and highly virulent at equilibrium could briefly double their virulence during an epidemic; thus, epidemic-phase selection could contribute significantly to the virulence of emerging pathogens. In order to further assess the potential significance of this mechanism, we bring together data from the literature for the shapes of tradeoff curves for several pathogens (myxomatosis, HIV, and a parasite of Daphnia) and the level of genetic variation for virulence for one (myxomatosis). We discuss the need for better data on tradeoff curves and genetic variance in order to evaluate the plausibility of various scenarios of virulence evolution.

  2. Molecular diagnostic and genetic characterization of highly pathogenic viruses: application during Crimean-Congo haemorrhagic fever virus outbreaks in Eastern Europe and the Middle East.

    Science.gov (United States)

    Filippone, C; Marianneau, P; Murri, S; Mollard, N; Avsic-Zupanc, T; Chinikar, S; Desprès, P; Caro, V; Gessain, A; Berthet, N; Tordo, N

    2013-02-01

    Several haemorrhagic fevers are caused by highly pathogenic viruses that must be handled in Biosafety level 4 (BSL-4) containment. These zoonotic infections have an important impact on public health and the development of a rapid and differential diagnosis in case of outbreak in risk areas represents a critical priority. We have demonstrated the potential of a DNA resequencing microarray (PathogenID v2.0) for this purpose. The microarray was first validated in vitro using supernatants of cells infected with prototype strains from five different families of BSL-4 viruses (e.g. families Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae and Paramyxoviridae). RNA was amplified based on isothermal amplification by Phi29 polymerase before hybridization. We were able to detect and characterize Nipah virus and Crimean-Congo haemorrhagic fever virus (CCHFV) in the brains of experimentally infected animals. CCHFV was finally used as a paradigm for epidemics because of recent outbreaks in Turkey, Kosovo and Iran. Viral variants present in human sera were characterized by BLASTN analysis. Sensitivity was estimated to be 10(5) -10(6) PFU/mL of hybridized cDNA. Detection specificity was limited to viral sequences having ~13-14% of global divergence with the tiled sequence, or stretches of ~20 identical nucleotides. These results highlight the benefits of using the PathogenID v2.0 resequencing microarray to characterize geographical variants in the follow-up of haemorrhagic fever epidemics; to manage patients and protect communities; and in cases of bioterrorism. © 2012 The Authors Clinical Microbiology and Infection © 2012 European Society of Clinical Microbiology and Infectious Diseases.

  3. Diversidad genética, patogénica y morfológica del hongo Colletotrichum gloeosporioides (Penz. de Michoacán, México Genetic, pathogenic and morphological diversity of fungi Colletotrichum gloeosporioides (Penz. from Michoacan, Mexico

    Directory of Open Access Journals (Sweden)

    Víctor Montero Tavera

    diversity of the population of this fungus has been studied in several parts of the world, yet in Mexico, its population structure, and especially the components of its diversity, are unknown. The genetic, pathogenic and morphological diversity was determined for 21 monoconidial strains of Colletotrichum gloeosporioides from Michoacán, Mexico. The genetic diversity was estimated by means of random amplified DNA polymorphism, and by determining the profiles of isoenzymes of each monoconidial strain. Pathogenic diversity was measured with the invasive capacity of avocado pulp and the growth rate in vitro was determined by comparing the characteristics of the mycelia of each monoconidial strain. Results showed a high diversity of Colletotrichum gloeosporioides with a genetic variability index of 0.3031, and the most accurate estimator was the random amplified DNA polymorphism (genetic variability index= 0.344 and isoenzyme profile (genetic variability index= 0.35. The typical characteristics were white mycelia, cotton-like consistency, white colony, random mycelia growth and short hyphae on the growth border. There was no relation between the pathogenicity measured as the invasive capacity of the pulp and this growth rate in vitro. The group analyses determined that the relations between the strains are established based mainly on the origin and, in a secondary manner, on the symptom in the fruit.

  4. Evidence of stable genetic structure across a remote island archipelago through self-recruitment in a widely dispersed coral reef fish

    KAUST Repository

    Priest, Mark

    2012-11-19

    We used microsatellite markers to assess the population genetic structure of the scribbled rabbitfish Siganus spinus in the western Pacific. This species is a culturally important food fish in the Mariana Archipelago and subject to high fishing pressure. Our primary hypothesis was to test whether the individuals resident in the southern Mariana Island chain were genetically distinct and hence should be managed as discrete stocks. In addition to spatial sampling of adults, newly-settled individuals were sampled on Guam over four recruitment events to assess the temporal stability of the observed spatial patterns, and evidence of self-recruitment. We found significant genetic structure in S. spinus across the western Pacific, with Bayesian analyses revealing three genetically distinct clusters: the southernMariana Islands, east Micronesia, and the west Pacific; with the southern Mariana Islands beingmore strongly differentiated fromthe rest of the region. Analyses of temporal samples from Guam indicated the southern Mariana cluster was stable over time, with no genetic differentiation between adults versus recruits, or between samples collected across four separate recruitment events spanning 11 months. Subsequent assignment tests indicated seven recruits had self-recruited from within the Southern Mariana Islands population. Our results confirm the relative isolation of the southern Mariana Islands population and highlight how local processes can act to isolate populations that, by virtue of their broad-scale distribution, have been subject to traditionally high gene flows. Our results add to a growing consensus that self-recruitment is a highly significant influence on the population dynamics of tropical reef fish. 2012 The Authors. Ecology and Evolution published by Blackwell Publishing Ltd.

  5. Evidence of stable genetic structure across a remote island archipelago through self-recruitment in a widely dispersed coral reef fish.

    Science.gov (United States)

    Priest, Mark A; Halford, Andrew R; McIlwain, Jennifer L

    2012-12-01

    We used microsatellite markers to assess the population genetic structure of the scribbled rabbitfish Siganus spinus in the western Pacific. This species is a culturally important food fish in the Mariana Archipelago and subject to high fishing pressure. Our primary hypothesis was to test whether the individuals resident in the southern Mariana Island chain were genetically distinct and hence should be managed as discrete stocks. In addition to spatial sampling of adults, newly-settled individuals were sampled on Guam over four recruitment events to assess the temporal stability of the observed spatial patterns, and evidence of self-recruitment. We found significant genetic structure in S. spinus across the western Pacific, with Bayesian analyses revealing three genetically distinct clusters: the southern Mariana Islands, east Micronesia, and the west Pacific; with the southern Mariana Islands being more strongly differentiated from the rest of the region. Analyses of temporal samples from Guam indicated the southern Mariana cluster was stable over time, with no genetic differentiation between adults versus recruits, or between samples collected across four separate recruitment events spanning 11 months. Subsequent assignment tests indicated seven recruits had self-recruited from within the Southern Mariana Islands population. Our results confirm the relative isolation of the southern Mariana Islands population and highlight how local processes can act to isolate populations that, by virtue of their broad-scale distribution, have been subject to traditionally high gene flows. Our results add to a growing consensus that self-recruitment is a highly significant influence on the population dynamics of tropical reef fish.

  6. High level of genetic compatibility between swine-origin H1N1 and highly pathogenic avian H5N1 influenza viruses.

    Science.gov (United States)

    Octaviani, Cássio Pontes; Ozawa, Makoto; Yamada, Shinya; Goto, Hideo; Kawaoka, Yoshihiro

    2010-10-01

    Reassortment is an important mechanism for the evolution of influenza viruses. Here, we coinfected cultured cells with the pandemic swine-origin influenza virus (S-OIV) and a contemporary H5N1 virus and found that these two viruses have high genetic compatibility. Studies of human lung cell lines indicated that some reassortants had better growth kinetics than their parental viruses. We conclude that reassortment between these two viruses can occur and could create pandemic H5N1 viruses.

  7. The Combined Deficiency of Immunoproteasome Subunits Affects Both the Magnitude and Quality of Pathogen- and Genetic Vaccination-Induced CD8+ T Cell Responses to the Human Protozoan Parasite Trypanosoma cruzi

    Science.gov (United States)

    Ersching, Jonatan; Vasconcelos, José R.; Ferreira, Camila P.; Caetano, Braulia C.; Machado, Alexandre V.; Bruna–Romero, Oscar; Baron, Monique A.; Ferreira, Ludmila R. P.; Cunha-Neto, Edécio; Rock, Kenneth L.

    2016-01-01

    The β1i, β2i and β5i immunoproteasome subunits have an important role in defining the repertoire of MHC class I-restricted epitopes. However, the impact of combined deficiency of the three immunoproteasome subunits in the development of protective immunity to intracellular pathogens has not been investigated. Here, we demonstrate that immunoproteasomes play a key role in host resistance and genetic vaccination-induced protection against the human pathogen Trypanosoma cruzi (the causative agent of Chagas disease), immunity to which is dependent on CD8+ T cells and IFN-γ (the classical immunoproteasome inducer). We observed that infection with T. cruzi triggers the transcription of immunoproteasome genes, both in mice and humans. Importantly, genetically vaccinated or T. cruzi-infected β1i, β2i and β5i triple knockout (TKO) mice presented significantly lower frequencies and numbers of splenic CD8+ effector T cells (CD8+CD44highCD62Llow) specific for the previously characterized immunodominant (VNHRFTLV) H-2Kb-restricted T. cruzi epitope. Not only the quantity, but also the quality of parasite-specific CD8+ T cell responses was altered in TKO mice. Hence, the frequency of double-positive (IFN-γ+/TNF+) or single-positive (IFN-γ+) cells specific for the H-2Kb-restricted immunodominant as well as subdominant T. cruzi epitopes were higher in WT mice, whereas TNF single-positive cells prevailed among CD8+ T cells from TKO mice. Contrasting with their WT counterparts, TKO animals were also lethally susceptible to T. cruzi challenge, even after an otherwise protective vaccination with DNA and adenoviral vectors. We conclude that the immunoproteasome subunits are key determinants in host resistance to T. cruzi infection by influencing both the magnitude and quality of CD8+ T cell responses. PMID:27128676

  8. Genetic transformation of cotton with a harpin-encoding gene hpaXoo confers an enhanced defense response against different pathogens through a priming mechanism

    Directory of Open Access Journals (Sweden)

    Song Congfeng

    2010-04-01

    Full Text Available Abstract Background The soil-borne fungal pathogen Verticillium dahliae Kleb causes Verticillium wilt in a wide range of crops including cotton (Gossypium hirsutum. To date, most upland cotton varieties are susceptible to V. dahliae and the breeding for cotton varieties with the resistance to Verticillium wilt has not been successful. Results Hpa1Xoo is a harpin protein from Xanthomonas oryzae pv. oryzae which induces the hypersensitive cell death in plants. When hpa1Xoo was transformed into the susceptible cotton line Z35 through Agrobacterium-mediated transformation, the transgenic cotton line (T-34 with an improved resistance to Verticillium dahliae was obtained. Cells of the transgenic T-34, when mixed with the conidia suspension of V. dahliae, had a higher tolerance to V. dahliae compared to cells of untransformed Z35. Cells of T-34 were more viable 12 h after mixing with V. dahliae conidia suspension. Immunocytological analysis showed that Hpa1Xoo, expressed in T-34, accumulated as clustered particles along the cell walls of T-34. In response to the infection caused by V. dahliae, the microscopic cell death and the generation of reactive oxygen intermediates were observed in leaves of T-34 and these responses were absent in leaves of Z35 inoculated with V. dahliae. Quantitative RT-PCR analysis indicated that five defense-related genes, ghAOX1, hin1, npr1, ghdhg-OMT, and hsr203J, were up-regulated in T-34 inoculated with V. dahliae. The up-regulations of these defense-relate genes were not observed or in a less extent in leaves of Z-35 after the inoculation. Conclusions Hpa1Xoo accumulates along the cell walls of the transgenic T-34, where it triggers the generation of H2O2 as an endogenous elicitor. T-34 is thus in a primed state, ready to protect the host from the pathogen. The results of this study suggest that the transformation of cotton with hpa1Xoo could be an effective approach for the development of cotton varieties with the

  9. Pathogen Sensors

    Directory of Open Access Journals (Sweden)

    Joseph Irudayaraj

    2009-10-01

    Full Text Available The development of sensors for detecting foodborne pathogens has been motivated by the need to produce safe foods and to provide better healthcare. However, in the more recent times, these needs have been expanded to encompass issues relating to biosecurity, detection of plant and soil pathogens, microbial communities, and the environment. The range of technologies that currently flood the sensor market encompass PCR and microarray-based methods, an assortment of optical sensors (including bioluminescence and fluorescence, in addition to biosensor-based approaches that include piezoelectric, potentiometric, amperometric, and conductometric sensors to name a few. More recently, nanosensors have come into limelight, as a more sensitive and portable alternative, with some commercial success. However, key issues affecting the sensor community is the lack of standardization of the testing protocols and portability, among other desirable elements, which include timeliness, cost-effectiveness, user-friendliness, sensitivity and specificity. [...

  10. Recommendations for reporting results of diagnostic genetic testing (biochemical, cytogenetic and molecular genetic)

    NARCIS (Netherlands)

    Claustres, Mireille; Kozich, Viktor; Dequeker, Els; Fowler, Brain; Hehir-Kwa, Jayne Y.; Miller, Konstantin; Oosterwijk, Cor; Peterlin, Borut; van Ravenswaaij-Arts, Conny; Zimmermann, Uwe; Zuffardi, Orsetta; Hastings, Ros J.; Barton, David E.

    Genetic test results can have considerable importance for patients, their parents and more remote family members. Clinical therapy and surveillance, reproductive decisions and genetic diagnostics in family members, including prenatal diagnosis, are based on these results. The genetic test report

  11. Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples.

    Science.gov (United States)

    Pettengill, James B; Pightling, Arthur W; Baugher, Joseph D; Rand, Hugh; Strain, Errol

    2016-01-01

    The adoption of whole-genome sequencing within the public health realm for molecular characterization of bacterial pathogens has been followed by an increased emphasis on real-time detection of emerging outbreaks (e.g., food-borne Salmonellosis). In turn, large databases of whole-genome sequence data are being populated. These databases currently contain tens of thousands of samples and are expected to grow to hundreds of thousands within a few years. For these databases to be of optimal use one must be able to quickly interrogate them to accurately determine the genetic distances among a set of samples. Being able to do so is challenging due to both biological (evolutionary diverse samples) and computational (petabytes of sequence data) issues. We evaluated seven measures of genetic distance, which were estimated from either k-mer profiles (Jaccard, Euclidean, Manhattan, Mash Jaccard, and Mash distances) or nucleotide sites (NUCmer and an extended multi-locus sequence typing (MLST) scheme). When analyzing empirical data (whole-genome sequence data from 18,997 Salmonella isolates) there are features (e.g., genomic, assembly, and contamination) that cause distances inferred from k-mer profiles, which treat absent data as informative, to fail to accurately capture the distance between samples when compared to distances inferred from differences in nucleotide sites. Thus, site-based distances, like NUCmer and extended MLST, are superior in performance, but accessing the computing resources necessary to perform them may be challenging when analyzing large databases.

  12. A genomic virulence reference map of Enterococcus faecalis reveals an important contribution of phage03-like elements in nosocomial genetic lineages to pathogenicity in a Caenorhabditis elegans infection model.

    Science.gov (United States)

    La Rosa, Sabina Leanti; Snipen, Lars-Gustav; Murray, Barbara E; Willems, Rob J L; Gilmore, Michael S; Diep, Dzung B; Nes, Ingolf F; Brede, Dag Anders

    2015-05-01

    virulence. Bioinformatics investigation indicated that, unlike other E. faecalis virulence traits, phage03-like elements were found at a higher frequency among nosocomial isolates. In conclusion, our report provides a valuable virulence map that explains enhancement in E. faecalis virulence and contributes to a deeper comprehension of the genetic mechanism leading to the transition from commensalism to a pathogenic lifestyle.

  13. Pathogen detection using engineered bacteriophages.

    Science.gov (United States)

    Smartt, Abby E; Xu, Tingting; Jegier, Patricia; Carswell, Jessica J; Blount, Samuel A; Sayler, Gary S; Ripp, Steven

    2012-04-01

    Bacteriophages, or phages, are bacterial viruses that can infect a broad or narrow range of host organisms. Knowing the host range of a phage allows it to be exploited in targeting various pathogens. Applying phages for the identification of microorganisms related to food and waterborne pathogens and pathogens of clinical significance to humans and animals has a long history, and there has to some extent been a recent revival in these applications as phages have become more extensively integrated into novel detection, identification, and monitoring technologies. Biotechnological and genetic engineering strategies applied to phages are responsible for some of these new methods, but even natural unmodified phages are widely applicable when paired with appropriate innovative detector platforms. This review highlights the use of phages as pathogen detector interfaces to provide the reader with an up-to-date inventory of phage-based biodetection strategies.

  14. Pathogenic monitoring and genetic diversity analysis of rabies virus in Yunnan Province%云南省狂犬病病原监测及病毒遗传多样性分析

    Institute of Scientific and Technical Information of China (English)

    杜传海; 张文东; 胡挺松; 赵焕云; 张应国; 范泉水; 张富强; 刘勇

    2013-01-01

    Objective To elucidate the pathogenic distribution and virus genetic diversity of rabies in Yunnan Province between 2006 and 2011. Methods Brain tissues or saliva swab samples were collected from suspected dogs with rabies in different areas in Yunnan Province for pathogenic monitoring between 2006 and 2011. The representative positive samples were selected for cloning and sequencing of the G genes and G-L intergenic regions. Comparison and phylogenic analysis were made between the sequence data of those samples and those of the reference strains. Results The positive samples had been found in 30 counties among 11 districts of Yunnan Province. The virus strains from these positive samples belonged to Serotype Ⅰ and Genotype Ⅰ . There were four different lineages or sub-lineages( China Ⅰ -1, China Ⅰ -2, China Ⅰ -3 , and Thailand )and seven types of genetic structures. Conclusion There is genetic diversity in G gene and G-L intergenic region of rabies virus in Yunnan Province. China Ⅰ -1 becomes the dominant epidemic strain.%目的 阐明2006~2011年期间云南省狂犬病病原分布状况和病毒基因结构特征.方法 2006~2011年期间,在云南省不同地点采集疑似狂犬病犬脑组织样品或唾液拭子样品,开展狂犬病病原监测;选择代表性阳性样品,对G基因、G-L间隔区进行克隆、测序,并与参考毒株序列进行比对及系统发育分析.结果 云南省11个地州30个县检出狂犬病病毒阳性样品,云南省狂犬病病毒均属于血清Ⅰ型和基因Ⅰ型毒株,至少存在4个不同遗传(亚)谱系(China Ⅰ-1、China Ⅰ-2、China Ⅰ-3、Thailand)、7种基因结构类型.结论 云南省狂犬病病毒G基因和G-L间隔区具有遗传多样性,China Ⅰ-1毒株已成为当前流行的优势毒株.

  15. Community composition and population genetics of insect pathogenic fungi in the genus Metarhizium from soils of a long-term agricultural research system.

    Science.gov (United States)

    Kepler, Ryan M; Ugine, Todd A; Maul, Jude E; Cavigelli, Michel A; Rehner, Stephen A

    2015-08-01

    Fungi in the genus Metarhizium are insect pathogens able to function in other niches, including soil and plant rhizosphere habitats. In agroecosystems, cropping and tillage practices influence soil fungal communities with unknown effects on the distribution of Metarhizium, whose presence can reduce populations of crop pests. We report results from a selective media survey of Metarhizium in soils sampled from a long-term experimental farming project in the mid-Atlantic region. Field plots under soybean cultivation produced higher numbers of Metarhizium colony-forming units (cfu) than corn or alfalfa. Plots managed organically and via chisel-till harboured higher numbers of Metarhizium cfu than no-till plots. Sequence typing of Metarhizium isolates revealed four species, with M. robertsii and M. brunneum predominating. The M. brunneum population was essentially fixed for a single clone as determined by multilocus microsatellite genotyping. In contrast, M. robertsii was found to contain significant diversity, with the majority of isolates distributed between two principal clades. Evidence for recombination was observed only in the most abundant clade. These findings illuminate multiple levels of Metarhizium diversity that can be used to inform strategies by which soil Metarhizium populations may be manipulated to exert downward pressure on pest insects and promote plant health. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle.

    Science.gov (United States)

    Załuga, Joanna; Stragier, Pieter; Baeyen, Steve; Haegeman, Annelies; Van Vaerenbergh, Johan; Maes, Martine; De Vos, Paul

    2014-05-22

    The genus Clavibacter harbors economically important plant pathogens infecting agricultural crops such as potato and tomato. Although the vast majority of Clavibacter strains are pathogenic, there is an increasing number of non-pathogenic isolates reported. Non-pathogenic Clavibacter strains isolated from tomato seeds are particularly problematic because they affect the current detection and identification tests for Clavibacter michiganensis subsp. michiganensis (Cmm), which is regulated with a zero tolerance in tomato seed. Their misidentification as pathogenic Cmm hampers a clear judgment on the seed quality and health. To get more insight in the genetic features linked to the lifestyle of these bacteria, a whole-genome sequence of the tomato seed-borne non-pathogenic Clavibacter LMG 26808 was determined. To gain a better understanding of the molecular determinants of pathogenicity, the genome sequence of LMG 26808 was compared with that of the pathogenic Cmm strain (NCPPB 382). The comparative analysis revealed that LMG 26808 does not contain plasmids pCM1 and pCM2 and also lacks the majority of important virulence factors described so far for pathogenic Cmm. This explains its apparent non-pathogenic nature in tomato plants. Moreover, the genome analysis of LMG 26808 detected sequences from a plasmid originating from a member of Enterobacteriaceae/Klebsiella relative. Genes received that way and coding for antibiotic resistance may provide a competitive advantage for survival of LMG 26808 in its ecological niche. Genetically, LMG 26808 was the most similar to the pathogenic Cmm NCPPB 382 but contained more mobile genetic elements. The genome of this non-pathogenic Clavibacter strain contained also a high number of transporters and regulatory genes. The genome sequence of the non-pathogenic Clavibacter strain LMG 26808 and the comparative analyses with other pathogenic Clavibacter strains provided a better understanding of the genetic bases of virulence and

  17. Genetic variation in Staphylococcus aureus surface and immune evasion genes is lineage associated: implications for vaccine design and host-pathogen interactions

    Directory of Open Access Journals (Sweden)

    Lindsay Jodi A

    2010-06-01

    Full Text Available Abstract Background S. aureus is a coloniser and pathogen of humans and mammals. Whole genome sequences of 58 strains of S. aureus in the public domain and data from multi-strain microarrays were compared to assess variation in the sequence of proteins known or putatively interacting with host. Results These included 24 surface proteins implicated in adhesion (ClfA, ClfB, Cna, Eap, Ebh, EbpS, FnBPA, FnBPB, IsaB, IsdA, IsdB, IsdH, SasB, SasC, SasD, SasF, SasG, SasH, SasK, SdrC, SdrD, SdrE, Spa and SraP and 13 secreted proteins implicated in immune response evasion (Coa, Ecb, Efb, Emp, EsaC, EsxA, EssC, FLIPr, FLIPr like, Sbi, SCIN-B, SCIN-C, VWbp located on the stable core genome. Many surface protein genes were missing or truncated, unlike immune evasion genes, and several distinct variants were identified. Domain variants were lineage specific. Unrelated lineages often possess the same sequence variant domains proving that horizontal transfer and recombination has contributed to their evolution. Surprisingly, sequenced strains from four animal S. aureus strains had surface and immune evasion proteins remarkably similar to those found in human strains, yet putative targets of these proteins vary substantially between different hosts. This suggests these proteins are not essential for virulence. However, the most variant protein domains were the putative functional regions and there is biological evidence that variants can be functional, arguing they do play a role. Conclusion Surface and immune evasion genes are candidates for S. aureus vaccines, and their distribution and functionality is key. Vaccines should contain cocktails of antigens representing all variants or they will not protect against naturally occurring S. aureus populations.

  18. Pathogenic potential, genetic diversity, and population structure of Escherichia coli strains isolated from a forest-dominated watershed (Comox Lake) in British Columbia, Canada.

    Science.gov (United States)

    Chandran, Abhirosh; Mazumder, Asit

    2015-03-01

    Escherichia coli isolates (n = 658) obtained from drinking water intakes of Comox Lake (2011 to 2013) were screened for the following virulence genes (VGs): stx1 and stx2 (Shiga toxin-producing E. coli [STEC]), eae and the adherence factor (EAF) gene (enteropathogenic E. coli [EPEC]), heat-stable (ST) enterotoxin (variants STh and STp) and heat-labile enterotoxin (LT) genes (enterotoxigenic E. coli [ETEC]), and ipaH (enteroinvasive E. coli [EIEC]). The only genes detected were eae and stx2, which were carried by 37.69% (n = 248) of the isolates. Only eae was harbored by 26.74% (n = 176) of the isolates, representing potential atypical EPEC strains, while only stx2 was detected in 10.33% (n = 68) of the isolates, indicating potential STEC strains. Moreover, four isolates were positive for both the stx2 and eae genes, representing potential EHEC strains. The prevalence of VGs (eae or stx2) was significantly (P < 0.0001) higher in the fall season, and multiple genes (eae plus stx2) were detected only in fall. Repetitive element palindromic PCR (rep-PCR) fingerprint analysis of 658 E. coli isolates identified 335 unique fingerprints, with an overall Shannon diversity (H') index of 3.653. Diversity varied among seasons over the years, with relatively higher diversity during fall. Multivariate analysis of variance (MANOVA) revealed that the majority of the fingerprints showed a tendency to cluster according to year, season, and month. Taken together, the results indicated that the diversity and population structure of E. coli fluctuate on a temporal scale, reflecting the presence of diverse host sources and their behavior over time in the watershed. Furthermore, the occurrence of potentially pathogenic E. coli strains in the drinking water intakes highlights the risk to human health associated with direct and indirect consumption of untreated surface water.

  19. The non-structural (NS) gene segment of H9N2 influenza virus isolated from backyard poultry in Pakistan reveals strong genetic and functional similarities to the NS gene of highly pathogenic H5N1.

    Science.gov (United States)

    Munir, Muhammad; Zohari, Siamak; Iqbal, Munir; Abbas, Muhammad; Perez, Daniel Roberto; Berg, Mikael

    2013-10-01

    Apart from natural reassortment, co-circulation of different avian influenza virus strains in poultry populations can lead to generation of novel variants and reassortant viruses. In this report, we studied the genetics and functions of a reassorted non-structural gene (NS) of H9N2 influenza virus collected from back yard poultry (BYP) flock. Phylogenetic reconstruction based on hemagglutinin and neuraminidase genes indicates that an isolate from BYP belongs to H9N2. However, the NS gene-segment of this isolate cluster into genotype Z, clade 2.2 of the highly pathogenic H5N1. The NS gene plays essential roles in the host-adaptation, cell-tropism, and virulence of influenza viruses. However, such interpretations have not been investigated in naturally recombinant H9N2 viruses. Therefore, we compared the NS1 protein of H9N2 (H9N2/NS1) and highly pathogenic H5N1 (H5N1/NS1) in parallel for their abilities to regulate different signaling pathways, and investigated the molecular mechanisms of IFN-β production in human, avian, and mink lung cells. We found that H9N2/NS1 and H5N1/NS1 are comparably similar in inhibiting TNF-α induced nuclear factor κB and double stranded RNA induced activator protein 1 and interferon regulatory factor 3 transcription factors. Thus, the production of IFN-β was inhibited equally by both NS1s as demonstrated by IFN stimulatory response element and IFN-β promoter activation. Moreover, both NS1s predominantly localized in the nucleus when transfected to human A549 cells. This study therefore suggests the possible increased virulence of natural reassortant viruses for their efficient invasion of host immune responses, and proposes that these should not be overlooked for their epizootic and zoonotic potential.

  20. Genetic evidence for a high diversity and wide distribution of endemic strains of the pathogenic chytrid fungus Batrachochytrium dendrobatidis in wild Asian amphibians.

    Science.gov (United States)

    Bataille, Arnaud; Fong, Jonathan J; Cha, Moonsuk; Wogan, Guinevere O U; Baek, Hae Jun; Lee, Hang; Min, Mi-Sook; Waldman, Bruce

    2013-08-01

    Population declines and extinctions of amphibians have been attributed to the chytrid fungus Batrachochytrium dendrobatidis (Bd), especially one globally emerging recombinant lineage ('Bd-GPL'). We used PCR assays that target the ribosomal internal transcribed spacer region (ITS) of Bd to determine the prevalence and genetic diversity of Bd in South Korea, where Bd is widely distributed but is not known to cause morbidity or mortality in wild populations. We isolated Korean Bd strains from native amphibians with low infection loads and compared them to known worldwide Bd strains using 19 polymorphic SNP and microsatellite loci. Bd prevalence ranged between 12.5 and 48.0%, in 11 of 17 native Korean species, and 24.7% in the introduced bullfrog Lithobates catesbeianus. Based on ITS sequence variation, 47 of the 50 identified Korean haplotypes formed a group closely associated with a native Brazilian Bd lineage, separated from the Bd-GPL lineage. However, multilocus genotyping of three Korean Bd isolates revealed strong divergence from both Bd-GPL and the native Brazilian Bd lineages. Thus, the ITS region resolves genotypes that diverge from Bd-GPL but otherwise generates ambiguous phylogenies. Our results point to the presence of highly diversified endemic strains of Bd across Asian amphibian species. The rarity of Bd-GPL-associated haplotypes suggests that either this lineage was introduced into Korea only recently or Bd-GPL has been outcompeted by native Bd strains. Our results highlight the need to consider possible complex interactions among native Bd lineages, Bd-GPL and their associated amphibian hosts when assessing the spread and impact of Bd-GPL on worldwide amphibian populations.

  1. Multiple node remote messaging

    Energy Technology Data Exchange (ETDEWEB)

    Blumrich, Matthias A. (Ridgefield, CT); Chen, Dong (Croton on Hudson, NY); Gara, Alan G. (Mount Kisco, NY); Giampapa, Mark E. (Irvington, NY); Heidelberger, Philip (Cortlandt Manor, NY); Ohmacht, Martin (Yorktown Heights, NY); Salapura, Valentina (Chappaqua, NY); Steinmacher-Burow, Burkhard (Esslingen, DE); Vranas, Pavlos (Danville, CA)

    2010-08-31

    A method for passing remote messages in a parallel computer system formed as a network of interconnected compute nodes includes that a first compute node (A) sends a single remote message to a remote second compute node (B) in order to control the remote second compute node (B) to send at least one remote message. The method includes various steps including controlling a DMA engine at first compute node (A) to prepare the single remote message to include a first message descriptor and at least one remote message descriptor for controlling the remote second compute node (B) to send at least one remote message, including putting the first message descriptor into an injection FIFO at the first compute node (A) and sending the single remote message and the at least one remote message descriptor to the second compute node (B).

  2. Plants versus pathogens: an evolutionary arms race.

    Science.gov (United States)

    Anderson, Jonathan P; Gleason, Cynthia A; Foley, Rhonda C; Thrall, Peter H; Burdon, Jeremy B; Singh, Karam B

    2010-05-20

    The analysis of plant-pathogen interactions is a rapidly moving research field and one that is very important for productive agricultural systems. The focus of this review is on the evolution of plant defence responses and the coevolution of their pathogens, primarily from a molecular-genetic perspective. It explores the evolution of the major types of plant defence responses including pathogen associated molecular patterns and effector triggered immunity as well as the forces driving pathogen evolution, such as the mechanisms by which pathogen lineages and species evolve. Advances in our understanding of plant defence signalling, stomatal regulation, R gene-effector interactions and host specific toxins are used to highlight recent insights into the coevolutionary arms race between pathogens and plants. Finally, the review considers the intriguing question of how plants have evolved the ability to distinguish friends such as rhizobia and mycorrhiza from their many foes.

  3. Pathogenic and Genetic Diversity among Iranian Isolates of Macrophomina phaseolina Diversidad Patogénica y Genética entre Aislamientos Iraníes de Macrophomina phaseolina

    Directory of Open Access Journals (Sweden)

    Siavosh Rayatpanah

    2012-03-01

    Full Text Available Charcoal rot, caused by Macrophomina phaseolina (Tassi Goid., is an economically important disease of oilseed plants in Northern Iran. Seventy isolates of M. phaseolina were obtained from different hosts, including soybean (Glycine max L., and sunflower (Helianthus annuus L. in the northern oilseed planting regions of Iran. RAPD-PCR amplification profiles, by using of six random OPA primers (kit A showed polymorphisms among the isolates. The primer OPA-13 (5'_ CAGCACCCAC_3' amplified the genomic DNA of all isolates of M.phaseolina producing 4-12 bands of sizes between 0.25 and 2.3 kb. Unweighted pair-group method with arithmetic mean (UPGMA analysis classified the isolates into the nine major groups with 64% similarity. Pathogenicity of isolates was evaluated at seedling stage of soybean, sunflower, and maize (Zea mays L. plants under in vitro conditions. None of the isolates were pathogenic on corn, while all of the isolates infected soybean and sunflower seedlings. Isolates were more virulent on soybean than sunflower. The disease index on sunflower and soybean varied between 19-24 and 27-30 respectively. These results indicated a significant pathogenic and genetic variability within the Iranian isolates of M. phaseolina. Cultivation with crop rotation was probably tended to induce less diversity of the pathogen isolates.Pudrición carbonosa, causada por Macrophomina phaseolina (Tassi Goid., es una enfermedad de importancia económica de las plantas de semillas oleaginosas en el norte de Irán. Setenta aislamientos de M. phaseolina se obtuvieron de diferentes hospederos, incluyendo soya (Glycine max L. y girasol (Helianthus annuus L. en las regiones de plantación de semillas oleaginosas del norte de Irán. Perfiles RAPD-PCR de amplificación, utilizando primers aleatorios de seis OPA (kit A mostraron polimorfismos entre los aislamientos. El primer OPA-13 (5'-CAGCACCCAC-3' amplificó el ADN genómico de todos los aislamientos de M. phaseolina

  4. The Venturia Apple Pathosystem: Pathogenicity Mechanisms and Plant Defense Responses

    Directory of Open Access Journals (Sweden)

    Gopaljee Jha

    2009-01-01

    Full Text Available Venturia inaequalis is the causal agent of apple scab, a devastating disease of apple. We outline several unique features of this pathogen which are useful for molecular genetics studies intended to understand plant-pathogen interactions. The pathogenicity mechanisms of the pathogen and overview of apple defense responses, monogenic and polygenic resistance, and their utilization in scab resistance breeding programs are also reviewed.

  5. Emerging Pathogens Initiative (EPI)

    Data.gov (United States)

    Department of Veterans Affairs — The Emerging Pathogens Initiative (EPI) database contains emerging pathogens information from the local Veterans Affairs Medical Centers (VAMCs). The EPI software...

  6. MARCADORES DE PATOGENICIDADE EM Yersinia enterocolitica O: 3 ISOLADAS DE SUÍNOS DO RIO DE JANEIRO Genetic markers of pathogenicity in Yersinia enterocolitica O: 3 isolated from healthy pigs from Rio de Janeiro

    Directory of Open Access Journals (Sweden)

    Tereza C. A. Leal

    1997-01-01

    Full Text Available Foi realizada a caracterização genotípica e fenotípica de fatores de patogenicidade em 16 amostras de Yersinia enterocolitica O:3 isoladas de suínos sadios do Rio de Janeiro. Foi observado que apenas 6 cepas possuíam o plasmídio de virulência, pYV (+ 70 kb e apresentavam dependência ao cálcio no meio MOX a 37C. Um plasmídio críptico de cerca de 8,6 kb foi encontrado em uma cepa. Doze cepas revelaram sensibilidade à pesticina enquanto que apenas três se revelaram capazes de hidrolisar a esculina. Através de PCR com "primers" específicos, foi constatada a presença dos genes ail em 14 cepas, irp2, em 1 cepa e a ausência de psaA em todas as cepas analisadas. Quanto aos quimioterápicos, a quase totalidade das cepas mostrou-se ao mesmo tempo resistente à ampicilina e carbenicilina e sensível ao sulfazotrin e à cefoxitina. As respostas foram variadas frente ao cloranfenicol, tetraciclina, kanamicina, gentamicina e ácido nalidíxo.Sixteen Yersinia enterocolitica serotype O:3 strains, isolated from pigs from Rio de Janeiro, have been analyzed for genetic and phenotypic markers of pathogenicity. It was observed that only 6 strains harbored the pYV (+70 kb plasmid and one strain harbored a small cryptic plasmid of about 8.6 kb. Accordingly only strains harboring pYV were calcium dependent in the MOX medium at 370C. Twelve strains showed pesticin sensitivity and the esculin reaction was negative in 13 strains. PCR analysis of pathogenicity genes using specific primers showed the presence of the ail gene in 14 strains, the irp2 gene in one and the psaA in none. Most of the strains were resistant to ampicillin and carbenicillin, although they were susceptible to sulfazotrin and cefoxitin. For chloramphenicol, tetracycline, kanamycin, gentamicin and nalidixic acid the results varied among the strains.

  7. A Glycine max homolog of NON-RACE SPECIFIC DISEASE RESISTANCE 1 (NDR1) alters defense gene expression while functioning during a resistance response to different root pathogens in different genetic backgrounds.

    Science.gov (United States)

    McNeece, Brant T; Pant, Shankar R; Sharma, Keshav; Niruala, Prakash; Lawrence, Gary W; Klink, Vincent P

    2017-05-01

    A Glycine max homolog of the Arabidopsis thaliana NON-RACE SPECIFIC DISEASE RESISTANCE 1 (NDR1) coiled-coil nucleotide binding leucine rich repeat (CC-NB-LRR) defense signaling gene (Gm-NDR1-1) is expressed in root cells undergoing a defense response to the root pathogenic nematode, Heterodera glycines. Gm-NDR1-1 overexpression in the H. glycines-susceptible genotype G. max[Williams 82/PI 518671] impairs parasitism. In contrast, Gm-NDR1-1 RNA interference (RNAi) in the H. glycines-resistant genotype G. max[Peking/PI 548402] facilitates parasitism. The broad effectiveness of Gm-NDR1-1 in impairing parasitism has then been examined by engineering its heterologous expression in Gossypium hirsutum which is susceptible to the root pathogenic nematode Meloidogyne incognita. The heterologous expression of Gm-NDR1-1 in G. hirsutum effectively impairs M. incognita parasitism, reducing gall, egg mass, egg and juvenile numbers. In contrast to our prior experiments examining the effectiveness of the heterologous expression of a G. max homolog of the A. thaliana salicyclic acid signaling (SA) gene NONEXPRESSOR OF PR1 (Gm-NPR1-2), no cumulative negative effect on M. incognita parasitism has been observed in G. hirsutum expressing Gm-NDR1-1. The results indicate a common genetic basis exists for plant resistance to parasitic nematodes that involves Gm-NDR1. However, the Gm-NDR1-1 functions in ways that are measurably dissimilar to Gm-NPR1-2. Notably, Gm-NDR1-1 overexpression leads to increased relative transcript levels of its homologs of A. thaliana genes functioning in SA signaling, including NPR1-2, TGA2-1 and LESION SIMULATING DISEASE1 (LSD1-2) that is lost in Gm-NDR1-1 RNAi lines. Similar observations have been made regarding the expression of other defense genes. Copyright © 2017 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

  8. The neuroscience of remote memory

    Science.gov (United States)

    Squire, Larry R; Bayley, Peter J

    2008-01-01

    Recently, there has been renewed interest in the organization and neurobiology of remote memory, and the pace of work in this area has accelerated. Yet the recent literature does not suggest that a consensus is developing, and there is disagreement about both facts and their interpretation. This article undertakes a comprehensive review of the three kinds of evidence that have been most prominent in recent discussion: studies of retrograde amnesia in memory-impaired patients who have well-characterized lesions, neuroimaging of healthy volunteers, and work with experimental animals including lesion studies, imaging and mouse genetics. The available evidence tells a coherent story and leads to some straightforward conclusions about the neuroscience of remote memory. PMID:17336513

  9. Weeds, as ancillary hosts, pose disproportionate risk for virulent pathogen transfer to crops.

    Science.gov (United States)

    Linde, Celeste C; Smith, Leon M; Peakall, Rod

    2016-05-12

    The outcome of the arms race between hosts and pathogens depends heavily on the interactions between their genetic diversity, population size and transmission ability. Theory predicts that genetically diverse hosts will select for higher virulence and more diverse pathogens than hosts with low genetic diversity. Cultivated hosts typically have lower genetic diversity and thus small effective population sizes, but can potentially harbour large pathogen population sizes. On the other hand, hosts, such as weeds, which are genetically more diverse and thus have larger effective population sizes, usually harbour smaller pathogen population sizes. Large pathogen population sizes may lead to more opportunities for mutation and hence more diverse pathogens. Here we test the predictions that pathogen neutral genetic diversity will increase with large pathogen population sizes and host diversity, whereas diversity under selection will increase with host diversity. We assessed and compared the diversity of a fungal pathogen, Rhynchosporium commune, on weedy barley grass (which have a large effective population size) and cultivated barley (low genetic diversity) using microsatellites, effector locus nip1 diversity and pathogen aggressiveness in order to assess the importance of weeds in the evolution of the neutral and selected diversity of pathogens. The findings indicated that the large barley acreage and low host diversity maintains higher pathogen neutral genetic diversity and lower linkage disequilibrium, while the weed maintains more pathotypes and higher virulence diversity at nip1. Strong evidence for more pathogen migration from barley grass to barley suggests transmission of virulence from barley grass to barley is common. Pathogen census population size is a better predictor for neutral genetic diversity than host diversity. Despite maintaining a smaller pathogen census population size, barley grass acts as an important ancillary host to R. commune, harbouring

  10. [Genetic virulence markers of opportunistic bacteria].

    Science.gov (United States)

    Bondarenko, V M

    2011-01-01

    The analysis of opportunistic bacteria phenotypic and genetic virulence markers indicates that pathogenicity formation is based on a structural modification of bacterial DNA which is linked with migration of interbacterial pathogenicity "islands" genetic determinants. Structural organization features of these mobile genetic elements determine high expression probability, and PCR detection of pathogenicity "islands" determinants that control adhesins, invasins, cytotoxic and cytolitic toxines synthesis may indicate etiopathogenetic significance of clinical isolates.

  11. Introduction to remote sensing

    CERN Document Server

    Cracknell, Arthur P

    2007-01-01

    Addressing the need for updated information in remote sensing, Introduction to Remote Sensing, Second Edition provides a full and authoritative introduction for scientists who need to know the scope, potential, and limitations in the field. The authors discuss the physical principles of common remote sensing systems and examine the processing, interpretation, and applications of data. This new edition features updated and expanded material, including greater coverage of applications from across earth, environmental, atmospheric, and oceanographic sciences. Illustrated with remotely sensed colo

  12. Lectins in human pathogenic fungi.

    Science.gov (United States)

    Gallegos, Belém; Martínez, Ruth; Pérez, Laura; Del Socorro Pina, María; Perez, Eduardo; Hernández, Pedro

    2014-01-01

    Lectins are carbohydrate-binding proteins widely distributed in nature. They constitute a highly diverse group of proteins consisting of many different protein families that are, in general, structurally unrelated. In the last few years, mushroom and other fungal lectins have attracted wide attention due to their antitumour, antiproliferative and immunomodulatory activities. The present mini-review provides concise information about recent developments in understanding lectins from human pathogenic fungi. A bibliographic search was performed in the Science Direct and PubMed databases, using the following keywords "lectin", "fungi", "human" and "pathogenic". Lectins present in fungi have been classified; however, the role played by lectins derived from human pathogenic fungi in infectious processes remains uncertain; thus, this is a scientific field requiring more research. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  13. Pathogenic mechanisms in centronuclear myopathies

    Directory of Open Access Journals (Sweden)

    Heinz eJungbluth

    2014-12-01

    Full Text Available Centronuclear myopathies (CNMs are a genetically heterogeneous group of inherited neuromuscular disorders characterized by clinical features of a congenital myopathy and abundant central nuclei as the most prominent histopathological feature. The most common forms of congenital myopathies with central nuclei have been attributed to X-linked recessive mutations in the MTM1 gene encoding myotubularin (X-linked myotubular myopathy, XLMTM, autosomal-dominant mutations in the DNM2 gene encoding dynamin-2 and the BIN1 gene encoding amphiphysin-2 (also named bridging integrator-1, BIN1, or SH3P9, and autosomal-recessive mutations in BIN1, the RYR1 gene encoding the skeletal muscle ryanodine receptor, and the TTN gene encoding titin. Models to study and rescue the affected cellular pathways are now available in yeast, C. elegans, drosophila, zebrafish, mouse and dog. Defects in membrane trafficking have emerged as a key pathogenic mechanisms, with aberrant T-tubule formation, abnormalities of triadic assembly and disturbance of the excitation-contraction machinery the main downstream effects studied to date. Abnormal autophagy has recently been recognized as another important collateral of defective membrane trafficking in different genetic forms of CNM, suggesting an intriguing link to primary disorders of defective autophagy with overlapping histopathological features.The following review will provide an overview of clinical, histopathological and genetic aspects of the CNMs in the context of the key pathogenic mechanism, outline unresolved questions and indicate promising future lines of enquiry.

  14. Deconstructing host-pathogen interactions in Drosophila

    Directory of Open Access Journals (Sweden)

    Ethan Bier

    2012-01-01

    Full Text Available Many of the cellular mechanisms underlying host responses to pathogens have been well conserved during evolution. As a result, Drosophila can be used to deconstruct many of the key events in host-pathogen interactions by using a wealth of well-developed molecular and genetic tools. In this review, we aim to emphasize the great leverage provided by the suite of genomic and classical genetic approaches available in flies for decoding details of host-pathogen interactions; these findings can then be applied to studies in higher organisms. We first briefly summarize the general strategies by which Drosophila resists and responds to pathogens. We then focus on how recently developed genome-wide RNA interference (RNAi screens conducted in cells and flies, combined with classical genetic methods, have provided molecular insight into host-pathogen interactions, covering examples of bacteria, fungi and viruses. Finally, we discuss novel strategies for how flies can be used as a tool to examine how specific isolated virulence factors act on an intact host.

  15. [Pathogenicity and pneumococcal capsular genes].

    Science.gov (United States)

    García, E; García, P; López, R

    1994-01-01

    Pneumococci remain to be one of the most prominent human pathogens. Increasing efforts are being dedicated to the development of improved vaccines with wider specificity. Since a clear understanding of the genetics of capsular types in Streptococcus pneumoniae is missing, our efforts are oriented to characterize, at the molecular level, the genes involved in capsular polysaccharide biosynthesis. We have cloned and sequenced a chromosomal DNA fragment of a clinical isolate of type 3 pneumococcus and showed that it contains a type 3 specific gene as well as genes common to other serotypes.

  16. Molecular Epidemiology of Foodborne Pathogens

    Science.gov (United States)

    Chen, Yi; Brown, Eric; Knabel, Stephen J.

    The purpose of this chapter is to describe the basic principles and advancements in the molecular epidemiology of foodborne pathogens. Epidemiology is the study of the distribution and determinants of infectious diseases and/or the dynamics of disease transmission. The goals of epidemiology include the identification of physical sources, routes of transmission of infectious agents, and distribution and relationships of different subgroups. Molecular epidemiology is the study of epidemiology at the molecular level. It has been defined as "a science that focuses on the contribution of potential genetic and environmental risk factors, identified at the molecular level, to the etiology, distribution and prevention of diseases within families and across populations".

  17. Sexual reproduction of human fungal pathogens.

    Science.gov (United States)

    Heitman, Joseph; Carter, Dee A; Dyer, Paul S; Soll, David R

    2014-08-01

    We review here recent advances in our understanding of sexual reproduction in fungal pathogens that commonly infect humans, including Candida albicans, Cryptococcus neoformans/gattii, and Aspergillus fumigatus. Where appropriate or relevant, we introduce findings on other species associated with human infections. In particular, we focus on rapid advances involving genetic, genomic, and population genetic approaches that have reshaped our view of how fungal pathogens evolve. Rather than being asexual, mitotic, and largely clonal, as was thought to be prevalent as recently as a decade ago, we now appreciate that the vast majority of pathogenic fungi have retained extant sexual, or parasexual, cycles. In some examples, sexual and parasexual unions of pathogenic fungi involve closely related individuals, generating diversity in the population but with more restricted recombination than expected from fertile, sexual, outcrossing and recombining populations. In other cases, species and isolates participate in global outcrossing populations with the capacity for considerable levels of gene flow. These findings illustrate general principles of eukaryotic pathogen emergence with relevance for other fungi, parasitic eukaryotic pathogens, and both unicellular and multicellular eukaryotic organisms.

  18. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis

    DEFF Research Database (Denmark)

    Carlton, Jane M.; Hirt, Robert P.; Silva, Joana C.

    2007-01-01

    We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion...

  19. Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis

    OpenAIRE

    Desjardins, Christopher A; Champion, Mia D.; Holder, Jason W.; Muszewska, Anna; Goldberg, Jonathan; Bailao, Alexandre M.; Brigido, Marcelo de Macedo; Silva Ferreira, Marcia Eliana da; Garcia, Ana Maria; Grynberg, Marcin; Gujja, Sharvari; Heiman, David I.; Henn, Matthew R.; Kodira, Chinnappa D.; Leon-Narvaez, Henry

    2011-01-01

    Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, is coupled with a thermally regulated transition from a soil-dwelling filamentous form to a yeast-like pathogenic form. To better understand the genetic basis of growth and pathogenicity in Paracoccidioides, we sequenced the genomes of two strains of Paracoccidioides brasi...

  20. Optical remote sensing

    CERN Document Server

    Prasad, Saurabh; Chanussot, Jocelyn

    2011-01-01

    Optical remote sensing relies on exploiting multispectral and hyper spectral imagery possessing high spatial and spectral resolutions respectively. These modalities, although useful for most remote sensing tasks, often present challenges that must be addressed for their effective exploitation. This book presents current state-of-the-art algorithms that address the following key challenges encountered in representation and analysis of such optical remotely sensed data: challenges in pre-processing images, storing and representing high dimensional data, fusing different sensor modalities, patter

  1. REMOTE SENSING IN OCEANOGRAPHY.

    Science.gov (United States)

    remote sensing from satellites. Sensing of oceanographic variables from aircraft began with the photographing of waves and ice. Since then remote measurement of sea surface temperatures and wave heights have become routine. Sensors tested for oceanographic applications include multi-band color cameras, radar scatterometers, infrared spectrometers and scanners, passive microwave radiometers, and radar imagers. Remote sensing has found its greatest application in providing rapid coverage of large oceanographic areas for synoptic and analysis and

  2. Pathogen Phytosensing: Plants to Report Plant Pathogens

    Directory of Open Access Journals (Sweden)

    C. Neal Stewart

    2008-04-01

    Full Text Available Real-time systems that provide evidence of pathogen contamination in crops can be an important new line of early defense in agricultural centers. Plants possess defense mechanisms to protect against pathogen attack. Inducible plant defense is controlled by signal transduction pathways, inducible promoters and cis-regulatory elements corresponding to key genes involved in defense, and pathogen-specific responses. Identified inducible promoters and cis-acting elements could be utilized in plant sentinels, or ‘phytosensors’, by fusing these to reporter genes to produce plants with altered phenotypes in response to the presence of pathogens. Here, we have employed cis-acting elements from promoter regions of pathogen inducible genes as well as those responsive to the plant defense signal molecules salicylic acid, jasmonic acid, and ethylene. Synthetic promoters were constructed by combining various regulatory elements supplemented with the enhancer elements from the Cauliflower mosaic virus (CaMV 35S promoter to increase basal level of the GUS expression. The inducibility of each synthetic promoter was first assessed in transient expression assays using Arabidopsis thaliana protoplasts and then examined for efficacy in stably transgenic Arabidopsis and tobacco plants. Histochemical and fluorometric GUS expression analyses showed that both transgenic Arabidopsis and tobacco plants responded to elicitor and phytohormone treatments with increased GUS expression when compared to untreated plants. Pathogen-inducible phytosensor studies were initiated by analyzing the sensitivity of the synthetic promoters against virus infection. Transgenic tobacco plants infected with Alfalfa mosaic virus showed an increase in GUS expression when compared to mock-inoculated control plants, whereas Tobacco mosaic virus infection caused no changes in GUS expression. Further research, using these transgenic plants against a range of different

  3. Finding all BRCA pathogenic mutation carriers : best practice models

    NARCIS (Netherlands)

    Hoogerbrugge, Nicoline; Jongmans, Marjolijn CJ

    2016-01-01

    Identifying germline BRCA pathogenic mutations in patients with ovarian or breast cancer is a crucial component in the medical management of affected patients. Furthermore, the relatives of affected patients can be offered genetic testing. Relatives who test positive for a germline BRCA pathogenic m

  4. Remote Maintenance Monitoring System -

    Data.gov (United States)

    Department of Transportation — The Remote Maintenance and Monitoring System (RMMS) is a collection of subsystems that includes telecommunication components, hardware, and software, which serve to...

  5. Remote Systems Design & Deployment

    Energy Technology Data Exchange (ETDEWEB)

    Bailey, Sharon A.; Baker, Carl P.; Valdez, Patrick LJ

    2009-08-28

    The Pacific Northwest National Laboratory (PNNL) was tasked by Washington River Protection Solutions, LLC (WRPS) to provide information and lessons learned relating to the design, development and deployment of remote systems, particularly remote arm/manipulator systems. This report reflects PNNL’s experience with remote systems and lays out the most important activities that need to be completed to successfully design, build, deploy and operate remote systems in radioactive and chemically contaminated environments. It also contains lessons learned from PNNL’s work experiences, and the work of others in the national laboratory complex.

  6. Optical Remote Sensing Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Optical Remote Sensing Laboratory deploys rugged, cutting-edge electro-optical instrumentation for the collection of various event signatures, with expertise in...

  7. Speciation in fungal and oomycete plant pathogens.

    Science.gov (United States)

    Restrepo, Silvia; Tabima, Javier F; Mideros, Maria F; Grünwald, Niklaus J; Matute, Daniel R

    2014-01-01

    The process of speciation, by definition, involves evolution of one or more reproductive isolating mechanisms that split a single species into two that can no longer interbreed. Determination of which processes are responsible for speciation is important yet challenging. Several studies have proposed that speciation in pathogens is heavily influenced by host-pathogen dynamics and that traits that mediate such interactions (e.g., host mobility, reproductive mode of the pathogen, complexity of the life cycle, and host specificity) must lead to reproductive isolation and ultimately affect speciation rates. In this review, we summarize the main evolutionary processes that lead to speciation of fungal and oomycete plant pathogens and provide an outline of how speciation can be studied rigorously, including novel genetic/genomic developments.

  8. Current concept on the pathogenesis of inflammatory bowel disease-crosstalk between genetic and microbial factors: Pathogenic bacteria and altered bacterial sensing or changes in mucosal integrity take "toll"?

    Institute of Scientific and Technical Information of China (English)

    Peter Laszlo Lakatos; Simon Fischer; Laszlo Lakatos; Istvan Gal; Janos Papp

    2006-01-01

    The pathogenesis of inflammatory bowel disease (IBD)is only partially understood. Various environmental and host (e.g. genetic-, epithelial-, immune and nonimmune) factors are involved. It is a multifactorial polygenic disease with probable genetic heterogeneity.Some genes are associated with IBD itself, while others increase the risk of ulcerative colitis (UC) or Crohn's disease (CD) or are associated with disease location and/or behaviour. This review addresses recent advances in the genetics of IBD. The article discusses the current information on the crosstalk between microbial and genetic factors (e.g. NOD2/CARD15, SLC22A46A5 and DLG5). The genetic data acquired in recent years help in understanding the pathogenesis of IBD and can identify a number of potential targets for therapeutic intervention.In the future, genetics may help more accurately diagnose and predict disease course in IBD.

  9. Molecular Mechanisms of Bacterial Pathogenicity

    Science.gov (United States)

    Fuchs, Thilo Martin

    Cautious optimism has arisen over recent decades with respect to the long struggle against bacteria, viruses, and parasites. This has been offset, however, by a fatal complacency stemming from previous successes such as the development of antimicrobial drugs, the eradication of smallpox, and global immunization programs. Infectious diseases nevertheless remain the world's leading cause of death, killing at least 17 million persons annually [61]. Diarrheal diseases caused by Vibrio cholerae or Shigella dysenteriae kill about 3 million persons every year, most of them young children: Another 4 million die of tuberculosis or tetanus. Outbreaks of diphtheria in Eastern Europe threatens the population with a disease that had previously seemed to be overcome. Efforts to control infectious diseases more comprehensively are undermined not only by socioeconomic conditions but also by the nature of the pathogenic organisms itself; some isolates of Staphylococcus aureus and Enterobacter have become so resistant to drugs by horizontal gene transfer that they are almost untreatable. In addition, the mechanism of genetic variability helps pathogens to evade the human immune system, thus compromising the development of powerful vaccines. Therefore detailed knowledge of the molecular mechanisms of microbial pathogenicity is absolutely necessary to develop new strategies against infectious diseases and thus to lower their impact on human health and social development.

  10. Hyperspectral remote sensing

    CERN Document Server

    Eismann, Michael

    2012-01-01

    Hyperspectral remote sensing is an emerging, multidisciplinary field with diverse applications that builds on the principles of material spectroscopy, radiative transfer, imaging spectrometry, and hyperspectral data processing. This book provides a holistic treatment that captures its multidisciplinary nature, emphasizing the physical principles of hyperspectral remote sensing.

  11. Remote actuated valve implant

    Energy Technology Data Exchange (ETDEWEB)

    McKnight, Timothy E.; Johnson, Anthony; Moise, Kenneth J.; Ericson, Milton Nance; Baba, Justin S.; Wilgen, John B.; Evans, Boyd Mccutchen

    2016-05-10

    Valve implant systems positionable within a flow passage, the systems having an inlet, an outlet, and a remotely activatable valve between the inlet and outlet, with the valves being operable to provide intermittent occlusion of the flow path. A remote field is applied to provide thermal or magnetic activation of the valves.

  12. Opening the psychological black box in genetic counseling. The psychological impact of DNA testing is predicted by the counselees' perception, the medical impact by the pathogenic or uninformative BRCA1/2-result

    NARCIS (Netherlands)

    Vos, Joel; Gomez-Garcia, Encarna; Oosterwijk, Jan C.; Menko, Fred H.; Stoel, Reinoud D.; van Asperen, Christi J.; Stiggelbout, Anne M.; Tibben, Aad; JANSEN, AM

    2012-01-01

    Background: It has been hypothesized that the Outcomes of DNA testing (O) are better predicted and/or mediated by the counselees' Perception P) than by the actually communicated genetic Information (I). In this study, we aimed at quantifying the effect that perception has in genetic counseling for h

  13. Pathogen pollution and the emergence of a deadly amphibian pathogen.

    Science.gov (United States)

    McKenzie, Valerie J; Peterson, Anna C

    2012-11-01

    ). In a new study published in this issue of Molecular Ecology, Schloegel et al. (2012) identify an additional unique Bd lineage that is endemic to the Atlantic Brazilian rainforests (Bd-Brazil) and provide striking evidence that the Bd-Brazil lineage has sexually recombined with the BdGPL lineage in an area where the two lineages likely came into contact as a result of classic anthropogenically mediated 'pathogen pollution'(see below). Fungal pathogens, including Bd, have the propensity to form recombinant lineages when allopatric populations that have not yet formed genetic reproductive barriers are provided with opportunities to intermingle, and virulent strains may be selected for because they tend to be highly transmissible (Fisher et al. 2012). As Schloegel et al. (2012) point out, the demonstrated ability for Bd to undergo meiosis may also mean that it has the capacity to form a resistant spore stage (as yet undiscovered), based on extrapolation from other sexually reproducing chytrids that all have spore stages.

  14. A genomic virulence reference map of Enterococcus faecalis reveals an important contribution of phage03-like elements in nosocomial genetic lineages to pathogenicity in a Caenorhabditis elegans infection model

    NARCIS (Netherlands)

    La Rosa, Sabina Leanti; Snipen, Lars Gustav; Murray, Barbara E.; Willems, Rob J L; Gilmore, Michael S.; Diep, Dzung B.; Nes, Ingolf F.; Brede, Dag Anders

    2015-01-01

    In the present study, the commensal and pathogenic host-microbe interaction of Enterococcus faecalis was explored using a Caenorhabditis elegans model system. The virulence of 28 E. faecalis isolates representing 24 multilocus sequence types (MLSTs), including human commensal and clinical isolates

  15. Genetic engineering of microbial pesticides

    Science.gov (United States)

    Bruce C. Carlton

    1985-01-01

    Recent advances in genetics and molecular biology make possible the cloning and genetic manipulation of genes for insecticidal activities from natural insect pathogens. Using recombinant DNA methods and site-directed mutagenesis of specific gene regions, production of new and improved biorationals should be possible.

  16. Antibody-mediated resistance against plant pathogens.

    Science.gov (United States)

    Safarnejad, Mohammad Reza; Jouzani, Gholamreza Salehi; Tabatabaei, Meisam; Tabatabaie, Meisam; Twyman, Richard M; Schillberg, Stefan

    2011-01-01

    Plant diseases have a significant impact on the yield and quality of crops. Many strategies have been developed to combat plant diseases, including the transfer of resistance genes to crops by conventional breeding. However, resistance genes can only be introgressed from sexually-compatible species, so breeders need alternative measures to introduce resistance traits from more distant sources. In this context, genetic engineering provides an opportunity to exploit diverse and novel forms of resistance, e.g. the use of recombinant antibodies targeting plant pathogens. Native antibodies, as a part of the vertebrate adaptive immune system, can bind to foreign antigens and eliminate them from the body. The ectopic expression of antibodies in plants can also interfere with pathogen activity to confer disease resistance. With sufficient knowledge of the pathogen life cycle, it is possible to counter any disease by designing expression constructs so that pathogen-specific antibodies accumulate at high levels in appropriate sub-cellular compartments. Although first developed to tackle plant viruses and still used predominantly for this purpose, antibodies have been targeted against a diverse range of pathogens as well as proteins involved in plant-pathogen interactions. Here we comprehensively review the development and implementation of antibody-mediated disease resistance in plants.

  17. Anaplasma marginale superinfection attributable to pathogen strains with distinct genomic backgrounds.

    Science.gov (United States)

    Microbial strain structure is dynamic over space and time; shifts in pathogen strain structure result in changing patterns of disease. The scale of change in space and time differs markedly among pathogens depending on multiple factors including pathogen-specific mechanisms of genetic change and the...

  18. Transcriptome sequencing of Mycosphaerella fijiensis during association with Musa acuminata reveals candidate pathogenicity genes

    OpenAIRE

    Noar, Roslyn D.; Daub, Margaret E.

    2016-01-01

    Background Mycosphaerella fijiensis, causative agent of the black Sigatoka disease of banana, is considered the most economically damaging banana disease. Despite its importance, the genetics of pathogenicity are poorly understood. Previous studies have characterized polyketide pathways with possible roles in pathogenicity. To identify additional candidate pathogenicity genes, we compared the transcriptome of this fungus during the necrotrophic phase of infection with that during saprophytic ...

  19. Potatoes, pathogens and pests

    NARCIS (Netherlands)

    Lazebnik, Jenny

    2017-01-01

    Currently, fungicides are necessary to protect potato crops against late blight, Phytophthora infestans, one of the world’s most damaging crop pathogens. The introgression of plant resistance genes from wild potato species targeted specifically to the late blight pathogen into susceptible

  20. Plant pathogen resistance

    Science.gov (United States)

    Greenberg, Jean T; Jung, Ho Won; Tschaplinski, Timothy

    2012-11-27

    Azelaic acid or its derivatives or analogs induce a robust and a speedier defense response against pathogens in plants. Azelaic acid treatment alone does not induce many of the known defense-related genes but activates a plant's defense signaling upon pathogen exposure.

  1. Plant pathogen resistance

    Energy Technology Data Exchange (ETDEWEB)

    Greenberg, Jean T.; Jung, Ho Won; Tschaplinski, Timothy

    2015-10-20

    Azelaic acid or its derivatives or analogs induce a robust and a speedier defense response against pathogens in plants. Azelaic acid treatment alone does not induce many of the known defense-related genes but activates a plant's defense signaling upon pathogen exposure.

  2. Genetic manipulation of Francisella tularensis

    Directory of Open Access Journals (Sweden)

    Xhavit eZogaj

    2011-01-01

    Full Text Available Francisella tularensis is a facultative intracellular pathogen that causes the disease tularemia. F. tularensis subsp. tularensis causes the most severe disease in humans and has been classified as a select A agent and potential bioweapon. There is currently no vaccine approved for human use, making genetic manipulation of this organism critical to unraveling the genetic basis of pathogenesis and developing countermeasures against tularemia. The development of genetic techniques applicable to F. tularensis have lagged behind those routinely used for other bacteria, primarily due to lack of research and the restricted nature of the biocontainment required for studying this pathogen. However, in recent years, genetic techniques, such as transposon mutagenesis and targeted gene disruption, have been developed, that have had a dramatic impact on our understanding of the genetic basis of F. tularensis virulence. In this review, we describe some of the methods developed for genetic manipulation of F. tularensis.

  3. Finding all BRCA pathogenic mutation carriers: best practice models.

    Science.gov (United States)

    Hoogerbrugge, Nicoline; Jongmans, Marjolijn Cj

    2016-09-01

    Identifying germline BRCA pathogenic mutations in patients with ovarian or breast cancer is a crucial component in the medical management of affected patients. Furthermore, the relatives of affected patients can be offered genetic testing. Relatives who test positive for a germline BRCA pathogenic mutation can take appropriate action to prevent cancer or have cancer diagnosed as early as possible for better treatment options. The recent discovery that BRCA pathogenic mutation status can inform treatment decisions in patients with ovarian cancer has led to an increased demand for BRCA testing, with testing taking place earlier in the patient care pathway. New approaches to genetic counselling may be required to meet this greater demand for BRCA testing. This review discusses the need for best practices for genetic counselling and BRCA testing; it examines the challenges facing current practice and looks at adapted models of genetic counselling.

  4. Remote Sensing Information Gateway

    Science.gov (United States)

    Remote Sensing Information Gateway, a tool that allows scientists, researchers and decision makers to access a variety of multi-terabyte, environmental datasets and to subset the data and obtain only needed variables, greatly improving the download time.

  5. Remote Control Reading.

    Science.gov (United States)

    Ervin, Helen

    1995-01-01

    Explains how students who have difficulty remembering what they have read may be taught how to reread sections of text by suggesting to them that reading is analogous to watching a video with the remote control in hand. (TB)

  6. Recommendations for reporting results of diagnostic genetic testing (biochemical, cytogenetic and molecular genetic)

    NARCIS (Netherlands)

    Claustres, Mireille; Kozich, Viktor; Dequeker, Els; Fowler, Brain; Hehir-Kwa, Jayne Y.; Miller, Konstantin; Oosterwijk, Cor; Peterlin, Borut; van Ravenswaaij-Arts, Conny; Zimmermann, Uwe; Zuffardi, Orsetta; Hastings, Ros J.; Barton, David E.

    2014-01-01

    Genetic test results can have considerable importance for patients, their parents and more remote family members. Clinical therapy and surveillance, reproductive decisions and genetic diagnostics in family members, including prenatal diagnosis, are based on these results. The genetic test report sho

  7. Innate immunity in Drosophila: Pathogens and pathways.

    Science.gov (United States)

    Govind, Shubha

    2008-02-01

    Following in the footsteps of traditional developmental genetics, research over the last 15 years has shown that innate immunity against bacteria and fungi is governed largely by two NF-kappaB signal transduction pathways, Toll and IMD. Antiviral immunity appears to stem from RNA interference, whereas resistance against parasitoids is conferred by Toll signaling. The identification of these post-transcriptional regulatory mechanisms and the annotation of most Drosophila immunity genes have derived from functional genomic studies using "model" pathogens, intact animals and cell lines. The D. melanogaster host has thus provided the core information that can be used to study responses to natural microbial and metazoan pathogens as they become identified, as well as to test ideas of selection and evolutionary change. These analyses are of general importance to understanding mechanisms of other insect host-pathogen interactions and determinants of variation in host resistance.

  8. Innate immunity in Drosophila: Pathogens and pathways

    Institute of Scientific and Technical Information of China (English)

    Shubha Govind

    2008-01-01

    Following in the footsteps of traditional developmental genetics, research over the last 15 years has shown that innate immunity against bacteria and fungi is governed largely by two NF-κB signal transduction pathways, Toll and IMD. Antiviral immunity appears to stem from RNA interference, whereas resistance against parasitoids is conferred by Toll signaling. The identification of these post-transcriptional regulatory mechanisms and the annotation of most Drosophila immunity genes have derived from functional genomic studies using "model" pathogens, intact animals and cell lines. The D. melanogaster host has thus provided the core information that can be used to study responses to natural microbial and metazoan pathogens as they become identified, as well as to test ideas of selection and evolutionary change. These analyses are of general importance to understanding mechanisms of other insect host-pathogen interactions and determinants of variation in host resistance.

  9. Genetic Discrimination

    Science.gov (United States)

    ... in Genetics Archive Regulation of Genetic Tests Genetic Discrimination Overview Many Americans fear that participating in research ... I) and employment (Title II). Read more Genetic Discrimination and Other Laws Genetic Discrimination and Other Laws ...

  10. LIDAR and atmosphere remote sensing

    CSIR Research Space (South Africa)

    Venkataraman, S

    2008-05-01

    Full Text Available and to consist of theory and practical exercises • Theory: Remote sensing process, Photogrammetry, introduction to multispectral, remote sensing systems, Thermal infra-red remote sensing, Active and passive remote sensing, LIDAR, Application of remotely... Aerosol measurements and cloud characteristics head2right Water vapour measurements in the lower troposphere region up to 8 km head2right Ozone measurements in the troposphere regions up to 18 km Slide 22 © CSIR 2008 www...

  11. Pathogenicity gene variations within the order Entomophthorales

    DEFF Research Database (Denmark)

    Grell, Morten Nedergaard; Jensen, Annette Bruun; Lange, Lene

    , conidia are produced and discharged when humidity gets high—usually during night. In an earlier secretome study of field-collected grain aphids (Sitobion avenae) infected with entomophthoralean fungi, a number of pathogenesis-related, secreted enzymes were discovered (Fungal Genetics and Biology 2011, vol...... pathogenicity genes within genera Entomophthora and Pandora, using fungal genomic DNA originating from field-collected, infected insect host species of dipteran (flies, mosquitoes) or hemipteran (aphid) origin....

  12. Quantitative Resistance: More Than Just Perception of a Pathogen.

    Science.gov (United States)

    Corwin, Jason A; Kliebenstein, Daniel J

    2017-04-01

    Molecular plant pathology has focused on studying large-effect qualitative resistance loci that predominantly function in detecting pathogens and/or transmitting signals resulting from pathogen detection. By contrast, less is known about quantitative resistance loci, particularly the molecular mechanisms controlling variation in quantitative resistance. Recent studies have provided insight into these mechanisms, showing that genetic variation at hundreds of causal genes may underpin quantitative resistance. Loci controlling quantitative resistance contain some of the same causal genes that mediate qualitative resistance, but the predominant mechanisms of quantitative resistance extend beyond pathogen recognition. Indeed, most causal genes for quantitative resistance encode specific defense-related outputs such as strengthening of the cell wall or defense compound biosynthesis. Extending previous work on qualitative resistance to focus on the mechanisms of quantitative resistance, such as the link between perception of microbe-associated molecular patterns and growth, has shown that the mechanisms underlying these defense outputs are also highly polygenic. Studies that include genetic variation in the pathogen have begun to highlight a potential need to rethink how the field considers broad-spectrum resistance and how it is affected by genetic variation within pathogen species and between pathogen species. These studies are broadening our understanding of quantitative resistance and highlighting the potentially vast scale of the genetic basis of quantitative resistance. © 2017 American Society of Plant Biologists. All rights reserved.

  13. Bacteriophage-Based Pathogen Detection

    Science.gov (United States)

    Ripp, Steven

    Considered the most abundant organism on Earth, at a population approaching 1031, bacteriophage, or phage for short, mediate interactions with myriad bacterial hosts that has for decades been exploited in phage typing schemes for signature identification of clinical, food-borne, and water-borne pathogens. With over 5,000 phage being morphologically characterized and grouped as to susceptible host, there exists an enormous cache of bacterial-specific sensors that has more recently been incorporated into novel bio-recognition assays with heightened sensitivity, specificity, and speed. These assays take many forms, ranging from straightforward visualization of labeled phage as they attach to their specific bacterial hosts to reporter phage that genetically deposit trackable signals within their bacterial hosts to the detection of progeny phage or other uniquely identifiable elements released from infected host cells. A comprehensive review of these and other phage-based detection assays, as directed towards the detection and monitoring of bacterial pathogens, will be provided in this chapter.

  14. An approach to pathogens flux simulation in a combined sewer system

    OpenAIRE

    Breil, P.; Petit, S.; Boukerb, A.; Namour, P.; McCarthy, D; Cournoyer, B

    2013-01-01

    International audience; Combined sewer systems convey organic matters and pathogens coming from human and animal faeces. They are mixed with rainfall runoff during storm event and can overflows to natural aquatic systems. Preliminary genetic analyses of pathogens were conducted in an experimental small water course and its lateral combined sewer system (OTHU site). Results indicate that natural system pathogens are an evolution of sewer system pathogens. However their presumed survival should...

  15. Least Wanted Foodborne Pathogens

    Science.gov (United States)

    Least Wanted Foodborne Pathogens The U.S. Public Health Service has identified the following microorganisms as being the biggest culprits of foodborne illness, either because of the severity of the ...

  16. T0 PATHOGENS

    African Journals Online (AJOL)

    African Crop Science Journal, Vol. ... Selection for durable resistance against such pathogens should consist ot' removing the ... major gene resistance has been overcome. .... a simple way. .... which causes either a change in the avirulence.

  17. Genetic mapping using the Diversity Arrays Technology (DArT) : application and validation using the whole-genome sequences of Arabidopsis thaliana and the fungal wheat pathogen Mycosphaerella graminicola

    NARCIS (Netherlands)

    Wittenberg, A.H.J.

    2007-01-01

    Diversity Arrays Technology (DArT) is a microarray-based DNA marker technique for genome-wide discovery and genotyping of genetic variation. DArT allows simultaneous scoring of hundreds- to thousands of restriction site based polymorphisms between genotypes and does not require DNA sequence informat

  18. Genetic mapping using the Diversity Arrays Technology (DArT) : application and validation using the whole-genome sequences of Arabidopsis thaliana and the fungal wheat pathogen Mycosphaerella graminicola

    NARCIS (Netherlands)

    Wittenberg, A.H.J.

    2007-01-01

    Diversity Arrays Technology (DArT) is a microarray-based DNA marker technique for genome-wide discovery and genotyping of genetic variation. DArT allows simultaneous scoring of hundreds- to thousands of restriction site based polymorphisms between genotypes and does not require DNA sequence informat

  19. Genetic mapping using the Diversity Arrays Technology (DArT) : application and validation using the whole-genome sequences of Arabidopsis thaliana and the fungal wheat pathogen Mycosphaerella graminicola

    NARCIS (Netherlands)

    Wittenberg, A.H.J.

    2007-01-01

    Diversity Arrays Technology (DArT) is a microarray-based DNA marker technique for genome-wide discovery and genotyping of genetic variation. DArT allows simultaneous scoring of hundreds- to thousands of restriction site based polymorphisms between genotypes and does not require DNA sequence

  20. Remote Nanodiamond Magnetometry

    CERN Document Server

    Ruan, Yinlan; Jeske, Jan; Ebendorff-Heidepriem, Heike; Lau, Desmond W M; Ji, Hong; Johnson, Brett C; Ohshima, Takeshi; V., Shahraam Afshar; Hollenberg, Lloyd; Greentree, Andrew D; Monro, Tanya M; Gibson, Brant C

    2016-01-01

    Optical fibres have transformed the way people interact with the world and now permeate many areas of science. Optical fibres are traditionally thought of as insensitive to magnetic fields, however many application areas from mining to biomedicine would benefit from fibre-based remote magnetometry devices. In this work, we realise such a device by embedding nanoscale magnetic sensors into tellurite glass fibres. Remote magnetometry is performed on magnetically active defect centres in nanodiamonds embedded into the glass matrix. Standard optical magnetometry techniques are applied to initialize and detect local magnetic field changes with a measured sensitivity of 26 micron Tesla/square root(Hz). Our approach utilizes straight-forward optical excitation, simple focusing elements, and low power components. We demonstrate remote magnetometry by direct reporting of the magnetic ground states of nitrogen-vacancy defect centres in the optical fibres. In addition, we present and describe theoretically an all-optica...

  1. Introduction to remote sensing

    CERN Document Server

    Campbell, James B

    2012-01-01

    A leading text for undergraduate- and graduate-level courses, this book introduces widely used forms of remote sensing imagery and their applications in plant sciences, hydrology, earth sciences, and land use analysis. The text provides comprehensive coverage of principal topics and serves as a framework for organizing the vast amount of remote sensing information available on the Web. Including case studies and review questions, the book's four sections and 21 chapters are carefully designed as independent units that instructors can select from as needed for their courses. Illustrations in

  2. Remote sensing image fusion

    CERN Document Server

    Alparone, Luciano; Baronti, Stefano; Garzelli, Andrea

    2015-01-01

    A synthesis of more than ten years of experience, Remote Sensing Image Fusion covers methods specifically designed for remote sensing imagery. The authors supply a comprehensive classification system and rigorous mathematical description of advanced and state-of-the-art methods for pansharpening of multispectral images, fusion of hyperspectral and panchromatic images, and fusion of data from heterogeneous sensors such as optical and synthetic aperture radar (SAR) images and integration of thermal and visible/near-infrared images. They also explore new trends of signal/image processing, such as

  3. New Genetics

    Science.gov (United States)

    ... Home > Science Education > The New Genetics The New Genetics Living Laboratories Classroom Poster Order a Free Copy ... Piece to a Century-Old Evolutionary Puzzle Computing Genetics Model Organisms RNA Interference The New Genetics is ...

  4. Remote RF Battery Charging

    NARCIS (Netherlands)

    Visser, H.J.; Pop, V.; Op het Veld, J.H.G.; Vullers, R.J.M.

    2011-01-01

    The design of a remote RF battery charger is discussed through the analysis and design of the subsystems of a rectenna (rectifying antenna): antenna, rectifying circuit and loaded DC-to-DC voltage (buck-boost) converter. Optimum system power generation performance is obtained by adopting a system in

  5. Remote Inspection Challenge

    Science.gov (United States)

    Roman, Harry T.

    2013-01-01

    The ability to remotely inspect equipment of an aging infrastructure is becoming of major interest to many industries. Often the ability to just get a look at a piece of critical equipment can yield very important information. With millions of miles of piping installed throughout the United States, this vast network is critical to oil, natural…

  6. EPA REMOTE SENSING RESEARCH

    Science.gov (United States)

    The 2006 transgenic corn imaging research campaign has been greatly assisted through a cooperative effort with several Illinois growers who provided planting area and crop composition. This research effort was designed to evaluate the effectiveness of remote sensed imagery of var...

  7. Section summary: Remote sensing

    Science.gov (United States)

    Belinda Arunarwati Margono

    2013-01-01

    Remote sensing is an important data source for monitoring the change of forest cover, in terms of both total removal of forest cover (deforestation), and change of canopy cover, structure and forest ecosystem services that result in forest degradation. In the context of Intergovernmental Panel on Climate Change (IPCC), forest degradation monitoring requires information...

  8. Remote sensing: best practice

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Gareth [Sgurr Energy (Canada)

    2011-07-01

    This paper presents remote sensing best practice in the wind industry. Remote sensing is a technique whereby measurements are obtained from the interaction of laser or acoustic pulses with the atmosphere. There is a vast diversity of tools and techniques available and they offer wide scope for reducing project uncertainty and risk but best practice must take into account versatility and flexibility. It should focus on the outcome in terms of results and data. However, traceability of accuracy requires comparison with conventional instruments. The framework for the Boulder protocol is given. Overviews of the guidelines for IEA SODAR and IEA LIDAR are also mentioned. The important elements of IEC 61400-12-1, an international standard for wind turbines, are given. Bankability is defined based on the Boulder protocol and a pie chart is presented that illustrates the uncertainty area covered by remote sensing. In conclusion it can be said that remote sensing is changing perceptions about how wind energy assessments can be made.

  9. Remote Agent Experiment

    Science.gov (United States)

    Benard, Doug; Dorais, Gregory A.; Gamble, Ed; Kanefsky, Bob; Kurien, James; Millar, William; Muscettola, Nicola; Nayak, Pandu; Rouquette, Nicolas; Rajan, Kanna; Norvig, Peter (Technical Monitor)

    2000-01-01

    Remote Agent (RA) is a model-based, reusable artificial intelligence (At) software system that enables goal-based spacecraft commanding and robust fault recovery. RA was flight validated during an experiment on board of DS1 between May 17th and May 21th, 1999.

  10. Bioterrorism: pathogens as weapons.

    Science.gov (United States)

    Anderson, Peter D; Bokor, Gyula

    2012-10-01

    Biowarfare has been used for centuries. The use of biological weapons in terrorism remains a threat. Biological weapons include infectious agents (pathogens) and toxins. The most devastating bioterrorism scenario would be the airborne dispersal of pathogens over a concentrated population area. Characteristics that make a specific pathogen a high-risk for bioterrorism include a low infective dose, ability to be aerosolized, high contagiousness, and survival in a variety of environmental conditions. The most dangerous potential bioterrorism agents include the microorganisms that produce anthrax, plague, tularemia, and smallpox. Other diseases of interest to bioterrorism include brucellosis, glanders, melioidosis, Q fever, and viral encephalitis. Food safety and water safety threats are another area of concern.

  11. Genetics Home Reference: Pelizaeus-Merzbacher disease

    Science.gov (United States)

    ... Garbern JY. Pelizaeus-Merzbacher disease: pathogenic mechanisms and insights into the roles of proteolipid protein 1 in ... healthcare professional . About Genetics Home Reference Site Map Customer Support Selection Criteria for Links USA.gov Copyright ...

  12. Remote implementation of quantum operations

    Energy Technology Data Exchange (ETDEWEB)

    Huelga, Susana F [Quantum Physics Group, STRI, Department of Physics, Astrophysics and Mathematics, University of Hertfordshire, Hatfield, Herts AL10 9AB (United Kingdom); Plenio, Martin B [QOLS, Blackett Laboratory, Imperial College London, London SW7 2BW (United Kingdom); Xiang Guoyong [Key Laboratory of Quantum Information and Department of Physics, University of Science and Technology of China, Hefei 230026 (China); Li Jian [Key Laboratory of Quantum Information and Department of Physics, University of Science and Technology of China, Hefei 230026 (China); Guo Guangcan [Key Laboratory of Quantum Information and Department of Physics, University of Science and Technology of China, Hefei 230026 (China)

    2005-10-01

    Shared entanglement allows, under certain conditions, the remote implementation of quantum operations. We revise and extend recent theoretical results on the remote control of quantum systems as well as experimental results on the remote manipulation of photonic qubits via linear optical elements.

  13. Remote Implementation of Quantum Operations

    CERN Document Server

    Huelga, S F; Xiang, G Y; Guo, J L G C; Huelga, Susana F.; Plenio, Martin B.; Xiang, Guo-Yong; Guo, Jian Li}and Guang-Can

    2005-01-01

    Shared entanglement allows, under certain conditions, the remote implementation of quantum operations. We revise and extend recent theoretical results on the remote control of quantum systems as well as experimental results on the remote manipulation of photonic qubits via linear optical elements.

  14. Remote Sensing and the Earth.

    Science.gov (United States)

    Brosius, Craig A.; And Others

    This document is designed to help senior high school students study remote sensing technology and techniques in relation to the environmental sciences. It discusses the acquisition, analysis, and use of ecological remote data. Material is divided into three sections and an appendix. Section One is an overview of the basics of remote sensing.…

  15. Remote Sensing and the Earth.

    Science.gov (United States)

    Brosius, Craig A.; And Others

    This document is designed to help senior high school students study remote sensing technology and techniques in relation to the environmental sciences. It discusses the acquisition, analysis, and use of ecological remote data. Material is divided into three sections and an appendix. Section One is an overview of the basics of remote sensing.…

  16. The pathogenic diversity and the genetic diversity of cotton Verticillium dahliae in the Yangtze River Basin%长江流域棉花黄萎病菌的致病力多样性和遗传多样性分析

    Institute of Scientific and Technical Information of China (English)

    金利容; 万鹏; 黄薇; 杨晓华

    2016-01-01

    Cotton Verticillium wilt is an important disease in the world, and a serious threat to cotton production.The four provinces, Hubei Province, Hunan Province, Jiangxi Province and Anhui Province, lie in the Yangtze River Basin.More than three hundreds isolates were collected and 67 isolates were selected from different cities and counties as the tested strains, then the cultural character, the pathogenic diversity and genetic diversity of the 67 strains were analyzed.The results showed that the high virulent types, the medium virulent types and the weak virulent types accounted for 35.82%, 43.28% and 17.91% respectively.The microsclerotia types, the intermediate types and the hyphae types acounted for 38.81%, 22.39% and 38.81%respectively.Further analysis showed that there was no correlation between the pathogenicity, the cultural character and the strain origin.However, there were some correlations between the pathogenicity and the cultural character.Most of high virulent strains belonged to microsclerotia types and the weak virulent strains dominate hyphae types.Fifteen pairs of RAPD primers were gained for DNA amplification, cluster analysis showed that the genetic diversity had no significant correlation with the strain origin.Furthermore, the genetic diversity of the strains had no significant correlation with the pathogenicity and the cultural character.%棉花黄萎病是棉花上的重要病害,严重威胁着棉花的产量.从长江流域4个省即湖北省、湖南省、江西省和安徽省采集300多个菌株,选择各省不同县市的67个菌株,对这67个供试菌株进行培养性状的鉴定、致病力的测定以及遗传多样性的分析,结果表明,在67个供试菌株中,就致病力类型而言,强致病力类型、中等致病力类型和弱致病力类型分别占35.82%、43.28%和17.91%.就培养性状类型而言,菌核型、中间型和菌丝型分别占38.81%、22.39%和38.81%.菌株的

  17. Actionable, pathogenic incidental findings in 1,000 participants' exomes.

    Science.gov (United States)

    Dorschner, Michael O; Amendola, Laura M; Turner, Emily H; Robertson, Peggy D; Shirts, Brian H; Gallego, Carlos J; Bennett, Robin L; Jones, Kelly L; Tokita, Mari J; Bennett, James T; Kim, Jerry H; Rosenthal, Elisabeth A; Kim, Daniel S; Tabor, Holly K; Bamshad, Michael J; Motulsky, Arno G; Scott, C Ronald; Pritchard, Colin C; Walsh, Tom; Burke, Wylie; Raskind, Wendy H; Byers, Peter; Hisama, Fuki M; Nickerson, Deborah A; Jarvik, Gail P

    2013-10-01

    The incorporation of genomics into medicine is stimulating interest on the return of incidental findings (IFs) from exome and genome sequencing. However, no large-scale study has yet estimated the number of expected actionable findings per individual; therefore, we classified actionable pathogenic single-nucleotide variants in 500 European- and 500 African-descent participants randomly selected from the National Heart, Lung, and Blood Institute Exome Sequencing Project. The 1,000 individuals were screened for variants in 114 genes selected by an expert panel for their association with medically actionable genetic conditions possibly undiagnosed in adults. Among the 1,000 participants, 585 instances of 239 unique variants were identified as disease causing in the Human Gene Mutation Database (HGMD). The primary literature supporting the variants' pathogenicity was reviewed. Of the identified IFs, only 16 unique autosomal-dominant variants in 17 individuals were assessed to be pathogenic or likely pathogenic, and one participant had two pathogenic variants for an autosomal-recessive disease. Furthermore, one pathogenic and four likely pathogenic variants not listed as disease causing in HGMD were identified. These data can provide an estimate of the frequency (∼3.4% for European descent and ∼1.2% for African descent) of the high-penetrance actionable pathogenic or likely pathogenic variants in adults. The 23 participants with pathogenic or likely pathogenic variants were disproportionately of European (17) versus African (6) descent. The process of classifying these variants underscores the need for a more comprehensive and diverse centralized resource to provide curated information on pathogenicity for clinical use to minimize health disparities in genomic medicine.

  18. Actionable, Pathogenic Incidental Findings in 1,000 Participants’ Exomes

    Science.gov (United States)

    Dorschner, Michael O.; Amendola, Laura M.; Turner, Emily H.; Robertson, Peggy D.; Shirts, Brian H.; Gallego, Carlos J.; Bennett, Robin L.; Jones, Kelly L.; Tokita, Mari J.; Bennett, James T.; Kim, Jerry H.; Rosenthal, Elisabeth A.; Kim, Daniel S.; Tabor, Holly K.; Bamshad, Michael J.; Motulsky, Arno G.; Scott, C. Ronald; Pritchard, Colin C.; Walsh, Tom; Burke, Wylie; Raskind, Wendy H.; Byers, Peter; Hisama, Fuki M.; Nickerson, Deborah A.; Jarvik, Gail P.

    2013-01-01

    The incorporation of genomics into medicine is stimulating interest on the return of incidental findings (IFs) from exome and genome sequencing. However, no large-scale study has yet estimated the number of expected actionable findings per individual; therefore, we classified actionable pathogenic single-nucleotide variants in 500 European- and 500 African-descent participants randomly selected from the National Heart, Lung, and Blood Institute Exome Sequencing Project. The 1,000 individuals were screened for variants in 114 genes selected by an expert panel for their association with medically actionable genetic conditions possibly undiagnosed in adults. Among the 1,000 participants, 585 instances of 239 unique variants were identified as disease causing in the Human Gene Mutation Database (HGMD). The primary literature supporting the variants’ pathogenicity was reviewed. Of the identified IFs, only 16 unique autosomal-dominant variants in 17 individuals were assessed to be pathogenic or likely pathogenic, and one participant had two pathogenic variants for an autosomal-recessive disease. Furthermore, one pathogenic and four likely pathogenic variants not listed as disease causing in HGMD were identified. These data can provide an estimate of the frequency (∼3.4% for European descent and ∼1.2% for African descent) of the high-penetrance actionable pathogenic or likely pathogenic variants in adults. The 23 participants with pathogenic or likely pathogenic variants were disproportionately of European (17) versus African (6) descent. The process of classifying these variants underscores the need for a more comprehensive and diverse centralized resource to provide curated information on pathogenicity for clinical use to minimize health disparities in genomic medicine. PMID:24055113

  19. Genetics of complex diseases.

    Science.gov (United States)

    Motulsky, Arno G

    2006-02-01

    Approaches to the study of the genetic basis of common complex diseases and their clinical applications are considered. Monogenic Mendelian inheritance in such conditions is infrequent but its elucidation may help to detect pathogenic mechanisms in the more common variety of complex diseases. Involvement by multiple genes in complex diseases usually occurs but the isolation and identification of specific genes so far has been exceptional. The role of common polymorphisms as indicators of disease risk in various studies is discussed.

  20. [Salmonella pathogenicity islands].

    Science.gov (United States)

    Sırıken, Belgin

    2013-01-01

    Salmonella species are facultative intracellular pathogenic bacteria. They can invade macrophages, dendritic and epithelial cells. The responsible virulence genes for invasion, survival, and extraintestinal spread are located in Salmonella pathogenicity islands (SPIs). SPIs are thought to be acquired by horizontal gene transfer. Some of the SPIs are conserved throughout the Salmonella genus, and some of them are specific for certain serovars. There are differences between Salmonella serotypes in terms of adaptation to host cell, virulence factors and the resulting infection according to SPA presence and characteristics. The most important Salmonella virulence gene clusters are located in 12 pathogenicity islands. Virulence genes that are involved in the intestinal phase of infection are located in SPI-1 and SPI-2 and the remaining SPIs are required for intracellular survival, fimbrial expression, magnesium and iron uptake, multiple antibiotic resistance and the development of systemic infections. In addition SPIs, Sigma ss (RpoS) factors and adaptive acid tolerance response (ATR) are the other two important virulence factors. RpoS and ATR found in virulent Salmonella strains help the bacteria to survive under inappropriate conditions such as gastric acidity, bile salts, inadequate oxygen concentration, lack of nutrients, antimicrobial peptides, mucus and natural microbiota and also to live in phagosomes or phagolysosomes. This review article summarizes the data related to pathogenicity islands in Salmonella serotypes and some factors which play role in the regulation of virulence genes.

  1. Fungal pathogens of Proteaceae

    NARCIS (Netherlands)

    Crous, P.W.; Summerell, B.A.; Swart, L.; Denman, S.; Taylor, J.E.; Bezuidenhout, C.M.; Palm, M.E.; Marincowitz, S.; Groenewald, J.Z.

    2011-01-01

    Species of Leucadendron, Leucospermum and Protea (Proteaceae) are in high demand for the international floriculture market due to their brightly coloured and textured flowers or bracts. Fungal pathogens, however, create a serious problem in cultivating flawless blooms. The aim of the present study

  2. Fungal pathogens of Proteaceae

    NARCIS (Netherlands)

    Crous, P.W.; Summerell, B.A.; Swart, L.; Denman, S.; Taylor, J.E.; Bezuidenhout, C.M.; Palm, M.E.; Marincowitz, S.; Groenewald, J.Z.

    2012-01-01

    Species of Leucadendron, Leucospermum and Protea (Proteaceae) are in high demand for the international floriculture market due to their brightly coloured and textured flowers or bracts. Fungal pathogens, however, create a serious problem in cultivating flawless blooms. The aim of the present study

  3. Remote maintenance development for ITER

    Energy Technology Data Exchange (ETDEWEB)

    Tada, Eisuke [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Shibanuma, Kiyoshi

    1998-04-01

    This paper describes the overall ITER remote maintenance design concept developed mainly for in-vessel components such as diverters and blankets, and outlines the ITER R and D program to develop remote handling equipment and radiation hard components. Reactor structures inside the ITER cryostat must be maintained remotely due to DT operation, making remote handling technology basic to reactor design. The overall maintenance scenario and design concepts have been developed, and maintenance design feasibility, including fabrication and testing of full-scale in-vessel remote maintenance handling equipment and tool, is being verified. (author)

  4. Accessing Remote Knowledge

    DEFF Research Database (Denmark)

    Maskell, Peter

    2014-01-01

    Work on clusters during the last few decades convincingly demonstrates enhanced opportunities for local growth and entrepreneurship, but external upstream knowledge linkages are often overlooked or taken for granted. This article is an attempt to remedy this situation by investigating why and how...... young, single-site firms search for distant sources of complementary competences. The discussion is positioned within a comprehensive framework that allows a systematic investigation of the approaches available to firms engaged in globally extended learning. By utilizing the distinction between problem...... awareness (what remote knowledge is needed?) and source awareness (where does this knowledge reside?) the article explores the relative merits and inherent limitations of pipelines, listening posts, crowdsourcing and trade fairs to acquire knowledge and solutions from geographically and relationally remote...

  5. Recruiting in remote locations

    Energy Technology Data Exchange (ETDEWEB)

    Ionel, C. [Enerflex Systems Ltd., Calgary, AB (Canada)

    2006-07-01

    This presentation provided details of Enerflex, a leading supplier of products and services to the oil and gas industry, and outlined their personnel hiring policies. Enerflex's core values include community involvement and divisional logo branding. The extensive training that is provided places an emphasis on employee empowerment. The company also places an emphasis on employee safety, diversity, and team building. Competitive salaries are offered along with generous equipment allowances and a flexible benefits program. Benefits include travel and overtime rates; health benefits; retirement savings; scholarship programs; career opportunities; and apprenticeship programs. External technical training is provided. An employee referral program has been developed, and the company's recruitment program also advertises in remote newspapers to develop career streams within remote communities. tabs., figs.

  6. REMOTELY CONTROLLED SEWERS

    OpenAIRE

    2014-01-01

    The basics of remotely controlled sewers [1] are presented focusing on Leipzig Municipality’s sewer control project [2] located in Germany. The consequences of sewer surcharge events are outlined considering possible counter measures. The required data basis, the controllable sewer objects and their relevant control units are pointed out. The presentation is finished exposing the types of control network, possible control algorithms as well as important aspects regarding the decision for / ag...

  7. Remote switch actuator

    Science.gov (United States)

    Haas, Edwin Gerard; Beauman, Ronald; Palo, Jr., Stefan

    2013-01-29

    The invention provides a device and method for actuating electrical switches remotely. The device is removably attached to the switch and is actuated through the transfer of a user's force. The user is able to remain physically removed from the switch site obviating need for protective equipment. The device and method allow rapid, safe actuation of high-voltage or high-current carrying electrical switches or circuit breakers.

  8. Advanced laser remote sensing

    Energy Technology Data Exchange (ETDEWEB)

    Schultz, J.; Czuchlewski, S.; Karl, R. [and others

    1996-11-01

    This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory. Remote measurement of wind velocities is critical to a wide variety of applications such as environmental studies, weather prediction, aircraft safety, the accuracy of projectiles, bombs, parachute drops, prediction of the dispersal of chemical and biological warfare agents, and the debris from nuclear explosions. Major programs to develop remote sensors for these applications currently exist in the DoD and NASA. At present, however, there are no real-time, three-dimensional wind measurement techniques that are practical for many of these applications and we report on two new promising techniques. The first new technique uses an elastic backscatter lidar to track aerosol patterns in the atmosphere and to calculate three dimensional wind velocities from changes in the positions of the aerosol patterns. This was first done by Professor Ed Eloranta of the University of Wisconsin using post processing techniques and we are adapting Professor Eloranta`s algorithms to a real-time data processor and installing it in an existing elastic backscatter lidar system at Los Alamos (the XM94 helicopter lidar), which has a compatible data processing and control system. The second novel wind sensing technique is based on radio-frequency (RF) modulation and spatial filtering of elastic backscatter lidars. Because of their compactness and reliability, solid state lasers are the lasers of choice for many remote sensing applications, including wind sensing.

  9. The THOSE remote interface

    Science.gov (United States)

    Klawon, Kevin; Gold, Josh; Bachman, Kristen

    2013-05-01

    The DIA, in conjunction with the Army Research Lab (ARL), wants to create an Unmanned Ground Sensor (UGS) controller that is (a) interoperable across all controller platforms, (b) capable of easily adding new sensors, radios, and processes and (c) backward compatible with existing UGS systems. To achieve this, a Terra Harvest controller was created that used Java JRE 1.6 and an Open Services Gateway initiative (OSGi) platform, named Terra Harvest Open Software Environment (THOSE). OSGi is an extensible framework that provides a modularized environment for deploying functionality in "bundles". These bundles can publish, discover, and share services available from other external bundles or bundles provided by the controller core. With the addition of a web GUI used for interacting with THOSE, a natural step was then to create a common remote interface that allows 3rd party real-time interaction with the controller. This paper provides an overview of the THOSE system and its components as well as a description of the architectural structure of the remote interface, highlighting the interactions occurring between the controller and the remote interface and its role in providing a positive user experience for managing UGSS functions.

  10. The floating (pathogenicity) island: a genomic dessert

    Science.gov (United States)

    Novick, Richard P.; Ram, Geeta

    2015-01-01

    Among the prokaryotic genomic islands (GIs) involved in horizontal gene transfer (HGT) are the classical pathogenicity islands, including the integrative and conjugative elements (ICEs), the gene-transfer agents (GTAs), and the staphylococcal pathogenicity islands (SaPIs), the primary focus of this review. While the ICEs and GTAs mediate HGT autonomously, the SaPIs are dependent on specific phages. The ICEs transfer primarily their own DNA the GTAs exclusively unlinked host DNA and the SaPIs combine the capabilities of both. Thus the SaPIs derive their importance from the genes they carry (their genetic cargo) and the genes they move. They act not only as versatile high frequency mobilizers, but also as mediators of phage interference, and consequently are major benefactors of their host bacteria. PMID:26744223

  11. Molecular techniques for characterisation of pathogens

    DEFF Research Database (Denmark)

    Kampmann, Marie-Louise

    Pathogens have always had a major interest to humans due to their central role in sickness and death. Influenza A annually kills at least 250,000 humans, and has been the cause of millions of further deaths during pandemic years in the past. Plague (Yersinia pestis) has been the cause of the Black...... Death that was leading to the desertion of whole cities, and as a result was for centuries one of the most feared events in human life. For both of these organisms we generally have situations with only very small amounts of pathogen nucleic acids available, usually because many interesting samples...... are degraded, as these samples are historic or generally patient samples. In this thesis we have principally explored methods to extract genetic information from such degraded samples, using the modern ‘high-throughput’ techniques of second generation sequencing (SGS) and mass spectrometry (MS), coupled...

  12. Phylogeographic Diversity of Pathogenic and Non-Pathogenic Hantaviruses in Slovenia

    Directory of Open Access Journals (Sweden)

    Miša Korva

    2013-12-01

    Full Text Available Slovenia is a very diverse country from a natural geography point of view, with many different habitats within a relatively small area, in addition to major geological and climatic differences. It is therefore not surprising that several small mammal species have been confirmed to harbour hantaviruses: A. flavicollis (Dobrava virus, A. agrarius (Dobrava virus–Kurkino, M. glareolus (Puumala virus, S. areanus (Seewis virus,M. agrestis, M. arvalis and M. subterraneus (Tula virus. Three of the viruses, namely the Dobrava, Dobrava–Kurkino and Puumala viruses, cause disease in humans, with significant differences in the severity of symptoms. Due to changes in haemorrhagic fever with renal syndrome cases (HFRS epidemiology, a detailed study on phylogenetic diversity and molecular epidemiology of pathogenic and non-pathogenic hantaviruses circulating in ecologically diverse endemic regions was performed. The study presents one of the largest collections of hantavirus L, M and S sequences obtained from hosts and patients within a single country. Several genetic lineages were determined for each hantavirus species, with higher diversity among non-pathogenic compared to pathogenic viruses. For pathogenic hantaviruses, a significant geographic clustering of human- and rodent-derived sequences was confirmed. Several geographic and ecological factors were recognized as influencing and limiting the formation of endemic areas.

  13. RELATIONSHIP BETWEEN PATHOGENICITY AND FUNGICIDE TOLERANCE IN THE WHEAT PATHOGEN MYCOSPHAERELLA GRAMINICOLA.

    Science.gov (United States)

    Siah, A; Deweer, C; Tisserant, B; Randoux, B; Halama, P; Reignault, Ph

    2015-01-01

    Septoria tritici blotch caused by Mycosphaerella graminicola (anamorph: Zymoseptoria tritici) is currently the most devastating disease on wheat crops worldwide, especially in regions with suitable climate conditions such as Western Europe. Pathogen control relies mainly on the use of fungicides and resistant cultivars. However, the durability of chemical and genetic control strategies is increasingly compromised in the field since the fungus frequently develops resistance to fungicides and overcomes host resistance. Here, we assessed the association between pathogenicity and fungicide tolerance in eighteen different M. graminicola strains isolated in 2009 from Northern France. These strains were chosen because they exhibited in preliminary experiments a wide range of in vitro tolerance levels against six demethylation inhibitors (epoxiconazole, cyproconazole, fluquinconazole, propiconazole, prothioconazole and pyrefenox). Inoculation of the Scorpion susceptible wheat cultivar in the greenhouse with these strains revealed a great variability in their pathogenicity levels (disease symptoms ranged from 0 to 66% of leaf area bearing pycnidia). Interestingly, strains with high fungicide tolerance levels caused overall the highest disease symptoms (45% of diseased leaf area on average) when compared to those with low fungicide tolerance levels (22% of diseased leaf area on average), thus confirming the association between pathogenicity level and fungicide tolerance in M. graminicola. The occurrence and selection in the field of fungal genotypes combining both pathogenicity and fungicide resistance should be taken into account in disease management strategies.

  14. Genetic algorithms

    Science.gov (United States)

    Wang, Lui; Bayer, Steven E.

    1991-01-01

    Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

  15. Genetic Mapping

    Science.gov (United States)

    ... Fact Sheets Fact Sheets En Español: Mapeo Genético Genetic Mapping What is genetic mapping? How do researchers create ... genetic map? What are genetic markers? What is genetic mapping? Among the main goals of the Human Genome ...

  16. PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens

    Directory of Open Access Journals (Sweden)

    Akhras Michael

    2006-11-01

    Full Text Available Abstract Background Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP oligonucleotides for use in pathogen identification and detection. The software designs unique and specific oligonucleotide probes targeting microbial or other genomes. The tool tailors all probe sequence components (including target-specific sequences, barcode sequences, universal primers and restriction sites and combines these components into ready-to-order probes for use in a MIP assay. The system can harness the genetic variability available in an entire genome in designing specific probes for the detection of multiple co-infections in a single tube using a MIP assay. Results PathogenMIPer can accept sequence data in FASTA file format, and other parameter inputs from the user through a graphical user interface. It can design MIPs not only for pathogens, but for any genome for use in parallel genomic analyses. The software was validated experimentally by applying it to the detection of human papilloma virus (HPV as a model system, which is associated with various human malignancies including cervical and skin cancers. Initial tests of laboratory samples using the MIPs developed by the PathogenMIPer to recognize 24 different types of HPVs gave very promising results, detecting even a small viral load of single as well as multiple infections (Akhras et al, personal communication. Conclusion PathogenMIPer is a software for designing molecular inversion probes for detection of multiple target DNAs in a sample using MIP assays. It enables broader use of MIP technology in the detection through genotyping of pathogens that are complex, difficult-to-amplify, or present in multiple subtypes in a sample.

  17. Machine learning in geosciences and remote sensing

    Institute of Scientific and Technical Information of China (English)

    David J. Lary; Amir H. Alavi; Amir H. Gandomi; Annette L. Walker

    2016-01-01

    Learning incorporates a broad range of complex procedures. Machine learning (ML) is a subdivision of artificial intelligence based on the biological learning process. The ML approach deals with the design of algorithms to learn from machine readable data. ML covers main domains such as data mining, difficult-to-program applications, and software applications. It is a collection of a variety of algorithms (e.g. neural networks, support vector machines, self-organizing map, decision trees, random forests, case-based reasoning, genetic programming, etc.) that can provide multivariate, nonlinear, nonparametric regres-sion or classification. The modeling capabilities of the ML-based methods have resulted in their extensive applications in science and engineering. Herein, the role of ML as an effective approach for solving problems in geosciences and remote sensing will be highlighted. The unique features of some of the ML techniques will be outlined with a specific attention to genetic programming paradigm. Furthermore, nonparametric regression and classification illustrative examples are presented to demonstrate the ef-ficiency of ML for tackling the geosciences and remote sensing problems.

  18. Machine learning in geosciences and remote sensing

    Directory of Open Access Journals (Sweden)

    David J. Lary

    2016-01-01

    Full Text Available Learning incorporates a broad range of complex procedures. Machine learning (ML is a subdivision of artificial intelligence based on the biological learning process. The ML approach deals with the design of algorithms to learn from machine readable data. ML covers main domains such as data mining, difficult-to-program applications, and software applications. It is a collection of a variety of algorithms (e.g. neural networks, support vector machines, self-organizing map, decision trees, random forests, case-based reasoning, genetic programming, etc. that can provide multivariate, nonlinear, nonparametric regression or classification. The modeling capabilities of the ML-based methods have resulted in their extensive applications in science and engineering. Herein, the role of ML as an effective approach for solving problems in geosciences and remote sensing will be highlighted. The unique features of some of the ML techniques will be outlined with a specific attention to genetic programming paradigm. Furthermore, nonparametric regression and classification illustrative examples are presented to demonstrate the efficiency of ML for tackling the geosciences and remote sensing problems.

  19. Genetically Engineering Entomopathogenic Fungi.

    Science.gov (United States)

    Zhao, H; Lovett, B; Fang, W

    2016-01-01

    Entomopathogenic fungi have been developed as environmentally friendly alternatives to chemical insecticides in biocontrol programs for agricultural pests and vectors of disease. However, mycoinsecticides currently have a small market share due to low virulence and inconsistencies in their performance. Genetic engineering has made it possible to significantly improve the virulence of fungi and their tolerance to adverse conditions. Virulence enhancement has been achieved by engineering fungi to express insect proteins and insecticidal proteins/peptides from insect predators and other insect pathogens, or by overexpressing the pathogen's own genes. Importantly, protein engineering can be used to mix and match functional domains from diverse genes sourced from entomopathogenic fungi and other organisms, producing insecticidal proteins with novel characteristics. Fungal tolerance to abiotic stresses, especially UV radiation, has been greatly improved by introducing into entomopathogens a photoreactivation system from an archaean and pigment synthesis pathways from nonentomopathogenic fungi. Conversely, gene knockout strategies have produced strains with reduced ecological fitness as recipients for genetic engineering to improve virulence; the resulting strains are hypervirulent, but will not persist in the environment. Coupled with their natural insect specificity, safety concerns can also be mitigated by using safe effector proteins with selection marker genes removed after transformation. With the increasing public concern over the continued use of synthetic chemical insecticides and growing public acceptance of genetically modified organisms, new types of biological insecticides produced by genetic engineering offer a range of environmentally friendly options for cost-effective control of insect pests. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Porphyromonas gingivalis: a clonal pathogen?

    Directory of Open Access Journals (Sweden)

    Morten Enersen

    2011-11-01

    Full Text Available The introduction of multilocus sequence typing (MLST in infectious disease research has allowed standardized typing of bacterial clones. Through multiple markers around the genome, it is possible to determine the sequence type (ST of bacterial isolates to establish the population structure of a species. For the periodontal pathogen, Porphyromonas gingivalis, the MLST scheme has been established at www.pubmlst.org/pgingivalis, and data from the database indicate a high degree of genetic diversity and a weakly clonal population structure comparable with Neisseria menigitidis. The major fimbriae (FimA have been held responsible for the adhesive properties of P. gingivalis and represent an important virulence factor. The fimA genotyping method (PCR based indicate that fimA genotype II, IV and Ib are associated with diseased sites in periodontitis and tissue specimens from cardiovascular disease. fimA genotyping of the isolates in the MLST database supports the association of genotypes II and IV with periodontitis. As a result of multiple positive PCR reactions in the fimA genotyping, sequencing of the fimA gene revealed only minor nucleotide variation between isolates of the same and different genotypes, suggesting that the method should be redesigned or re-evaluated. Results from several investigations indicate a higher intraindividual heterogeneity of P. gingivalis than found earlier. Detection of multiple STs from one site in several patients with “refractory” periodontitis, showed allelic variation in two housekeeping genes indicating recombination between different clones within the periodontal pocket.

  1. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Li Jun; van der Does, H. C.; Borkovich, Katherine A.; Coleman, Jeffrey J.; Daboussi, Marie-Jose; Di Pietro, Antonio; Dufresne, Marie; Freitag, Michael; Grabherr, Manfred; Henrissat, Bernard; Houterman, Petra M.; Kang, Seogchan; Shim, Won-Bo; Wolochuk, Charles; Xie, Xiaohui; Xu, Jin Rong; Antoniw, John; Baker, Scott E.; Bluhm, Burton H.; Breakspear, Andrew; Brown, Daren W.; Butchko, Robert A.; Chapman, Sinead; Coulson, Richard; Coutinho, Pedro M.; Danchin, Etienne G.; Diener, Andrew; Gale, Liane R.; Gardiner, Donald; Goff, Steven; Hammond-Kossack, Kim; Hilburn, Karen; Hua-Van, Aurelie; Jonkers, Wilfried; Kazan, Kemal; Kodira, Chinnappa D.; Koehrsen, Michael; Kumar, Lokesh; Lee, Yong Hwan; Li, Liande; Manners, John M.; Miranda-Saavedra, Diego; Mukherjee, Mala; Park, Gyungsoon; Park, Jongsun; Park, Sook Young; Proctor, Robert H.; Regev, Aviv; Ruiz-Roldan, M. C.; Sain, Divya; Sakthikumar, Sharadha; Sykes, Sean; Schwartz, David C.; Turgeon, Barbara G.; Wapinski, Ilan; Yoder, Olen; Young, Sarah; Zeng, Qiandong; Zhou, Shiguo; Galagan, James; Cuomo, Christina A.; Kistler, H. Corby; Rep, Martijn

    2010-03-18

    Fusarium species are among the most important phytopathogenic and toxigenic fungi, having significant impact on crop production and animal health. Distinctively, members of the F. oxysporum species complex exhibit wide host range but discontinuously distributed host specificity, reflecting remarkable genetic adaptability. To understand the molecular underpinnings of diverse phenotypic traits and their evolution in Fusarium, we compared the genomes of three economically important and phylogenetically related, yet phenotypically diverse plant-pathogenic species, F. graminearum, F. verticillioides and F. oxysporum f. sp. lycopersici. Our analysis revealed greatly expanded lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes, accounting for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity. Experimentally, we demonstrate for the first time the transfer of two LS chromosomes between strains of F. oxysporum, resulting in the conversion of a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in the F. oxysporum species complex, putting the evolution of fungal pathogenicity into a new perspective.

  2. Chapter VIII. Contributions of propagation techniques and genetic modification to breeding - genetic engineering for disease resistance

    Science.gov (United States)

    Genetic engineering offers an opportunity to develop flower bulb crops with resistance to fungal, viral, and bacterial pathogens. Several of the flower bulb crops, Lilium spp., Gladiolus, Zantedeschia, Muscari, Hyacinthus, Narcissus, Ornithogalum, Iris, and Alstroemeria, have been transformed with t...

  3. Genetic Counseling

    Science.gov (United States)

    Genetic counseling provides information and support to people who have, or may be at risk for, genetic disorders. A ... meets with you to discuss genetic risks. The counseling may be for yourself or a family member. ...

  4. Plant Pathogenic Fungi and Oomycetes

    NARCIS (Netherlands)

    Wit, de P.J.G.M.

    2015-01-01

    Fungi and Oomycetes are notorious plant pathogens and use similar strategies to infect plants. The majority of plants, however, is not infected by pathogens as they recognize pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors that mediate PAMP-triggered immunity (PTI) ,

  5. Plant Pathogenic Fungi and Oomycetes

    NARCIS (Netherlands)

    Wit, de P.J.G.M.

    2015-01-01

    Fungi and Oomycetes are notorious plant pathogens and use similar strategies to infect plants. The majority of plants, however, is not infected by pathogens as they recognize pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors that mediate PAMP-triggered immunity (PTI) ,

  6. Evolution of polyketide synthesis in a Dothidiomycete forest pathogen

    Science.gov (United States)

    Fungal secondary metabolites have many important biological roles and some, like the toxic polyketide aflatoxin, have been intensively studied at the genetic level. Complete sets of polyketide synthase (PKS) genes can now be identified in fungal pathogens by whole genome sequencing and studied in or...

  7. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis

    NARCIS (Netherlands)

    Carlton, Jane M.; Hirt, Robert P.; Silva, Joana C.; Delcher, Arthur L.; Schatz, Michael; Zhao, Qi; Wortman, Jennifer R.; Bidwell, Shelby L.; Alsmark, U. Cecilia M.; Besteiro, Sebastien; Sicheritz-Ponten, Thomas; Noel, Christophe J.; Dacks, Joel B.; Foster, Peter G.; Simillion, Cedric; Van de Peer, Yves; Miranda-Saavedra, Diego; Barton, Geoffrey J.; Westrop, Gareth D.; Mueller, Sylke; Dessi, Daniele; Fiori, Pier Luigi; Ren, Qinghu; Paulsen, Ian; Zhang, Hanbang; Bastida-Corcuera, Felix D.; Simoes-Barbosa, Augusto; Brown, Mark T.; Hayes, Richard D.; Mukherjee, Mandira; Okumura, Cheryl Y.; Schneider, Rachel; Smith, Alias J.; Vanacova, Stepanka; Villalvazo, Maria; Haas, Brian J.; Pertea, Mihaela; Feldblyum, Tamara V.; Utterback, Terry R.; Shu, Chung-Li; Osoegawa, Kazutoyo; de Jong, Pieter J.; Hrdy, Ivan; Horvathova, Lenka; Zubacova, Zuzana; Dolezal, Pavel; Malik, Shehre-Banoo; Logsdon, John M.; Henze, Katrin; Gupta, Arti; Wang, Ching C.; Dunne, Rebecca L.; Upcroft, Jacqueline A.; Upcroft, Peter; White, Owen; Salzberg, Steven L.; Tang, Petrus; Chiu, Cheng-Hsun; Lee, Ying-Shiung; Embley, T. Martin; Coombs, Graham H.; Mottram, Jeremy C.; Tachezy, Jan; Fraser-Liggett, Claire M.; Johnson, Patricia J.

    2007-01-01

    We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the similar to 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction wi

  8. 抗菌肽基因转化大白菜获得抗病转基因植株及稳定遗传%Pathogen-resistant Transgenic Plant of Brassica pekinensis by TransferingAntibacterial Peptide Gene and Its Genetic Stability

    Institute of Scientific and Technical Information of China (English)

    王关林; 方宏筠; 王火旭; 李洪艳; 魏毓堂

    2002-01-01

    软腐病是大白菜( Brassica pekinensis Rupr.)的三大病害之一.抗菌肽对软腐病菌有很强的杀伤作用.建立了根癌土壤杆菌( Agrobacterium tumefaciens ) EHA105(pMOG410)工程菌的高频转化载体系统,将抗菌肽基因导入目前推广种植的大白菜AB-81自交系,获得了转基因植株.PCR及 Southern blotting分子杂交鉴定表明抗菌肽基因已整合到白菜基因组.转基因植株提取液的体外抑菌实验、试管苗及盆栽转基因植株的病原菌接种抗病测试结果表明转基因植株具有明显的抗病特性,并且能稳定遗传,转基因植株R1自交分离比为3∶1,R5的转基因植株保持抗Km和抗病特性,可望以其为亲本选育出大白菜抗软腐病的新品种.%The soft rot infected by pathogenic bacterium Erwinia aroideae Holland is one of the three serious diseases of Chinese cabbage ( Brassica pekinensis Rupr.). By constructing vector system of high frequency transformation mediated by Agrobacterium tumefaciens EHA105, anti-bacterial peptide gene with strong bactericidal action to pathogenic bacteria was introduced into Chinese cabbage AB-81 self-bred line and the transgenic plants were obtained. PCR and Southern blotting detection showed that target gene was integrated into plant genome of Chinese cabbage. The tests of bacteriostasis action of the extract from transgenic plants in vitro, and the assay of disease-resistant of transgenic plantlets in the tube and the pot by perfusing inoculation with pathogenic bacteria showed obvious resistance to soft rot. This resistance can be a stable heredity by genetic analysis of generations of transgenic plants disease of soft rot was still kept in the R5. These results indicated the possibility of breeding new varieties of anti-soft rot Chinese cabbage by transgenic plants as parents.

  9. Pathogenicity of two seed-borne fungi commonly involved in maize ...

    African Journals Online (AJOL)

    Nazar Hussain

    2013-03-20

    Mar 20, 2013 ... deteriorate food grains by producing mycotoxins and aflotoxins during ... These species were tested to determine their pathogenicity to maize seed germination ..... genetically modified maize grown in France and Spain.

  10. Host-pathogen interactions in epidermolysis bullosa patients colonized with Staphylococcus aureus

    NARCIS (Netherlands)

    van der Kooi - Pol, Magdalena M.; Duipmans, Jose C.; Jonkman, Marcel F.; van Dijl, Jan Maarten

    Patients with the genetic blistering disease epidermolysis bullosa (EB) often have chronic wounds that can become colonized by different bacteria, especially the opportunistic pathogen Staphylococcus aureus. We therefore determined the S. aureus colonization rates in EB patients from the Netherlands

  11. Virulence genetic studies of pathogenic bacteria in Ningbo-Zhoushan port and channel waters%宁波-舟山港口航道水域致病性细菌的毒力基因型鉴定

    Institute of Scientific and Technical Information of China (English)

    管峰; 陈吉刚; 毛芝娟; 杨季芳

    2016-01-01

    Pathogenic bacteria from Ningbo-Zhoushan port and channel waters were isolated and identified with methods of molecular biology of 16S rDNA PCR and morphology.Besides,physicochemical properties,virulence gene types and the harm risk caused by these bacteria were studied.The results showed that,in 4 sampling areas, the identified bacteria were Escherichia coli,Salmonella sp.,Enterococcus faecalis,Listeria monocytogenes,Vibrio parahaemolyticus,Enterobacter cloacae,Vibrio alginolyticus,Edwardsiella tarda and Aeromonas hydrophila,among them Enterococcus faecalis had the highest isolate rate.Physicochemical properties of isolated bacteria were much similar to the reported terrestrial bacteria.There were many types of virulence genes in the isolated bacteria.The study by blast program on all 16S rDNA sequence found that the known sequences had similarities higher than 98%.The results can be taken for further studies of marine virulent gene diversity and for hazard risk evaluation.%根据标准对宁波-舟山港口航道致病性细菌进行分离,结合16S rDNA等方法鉴定分离菌株,研究其生理生化特征,通过PCR方法判断其毒力基因型,分析危害风险.结果表明,4个样品采集区的样品经分离鉴定,菌种分别为埃希氏大肠杆菌(Escherichia coli)、沙门氏菌(Salmonella sp.)、粪肠球菌(Enterococcus faecalis)、李斯特菌(Listeria monocytogenes)、副溶血弧菌(Vibrio parahaemolytic-us)、阴沟肠杆菌(Enterobacter cloacae)、溶藻弧菌(Vibrio alginolyticus)、迟缓爱德华菌(Edwardsiella tarda)、嗜水气单胞菌(Aeromonas hydrophila)等9种,其中粪肠球菌分离率最高.各种细菌的生理生化及形态特征与已报道陆源细菌相近,携带毒力基因型多样性丰富,提示具备致病力.运行Blast程序对所有分离株16S rDNA序列进行比对,发现与已知序列相似度均在98%以上.研究结果对海洋微生物的毒力

  12. Remotely controllable liquid marbles

    KAUST Repository

    Zhang, Lianbin

    2012-07-26

    Liquid droplets encapsulated by self-organized hydrophobic particles at the liquid/air interface - liquid marbles - are prepared by encapsulating water droplets with novel core/shell-structured responsive magnetic particles, consisting of a responsive block copolymer-grafted mesoporous silica shell and magnetite core (see figure; P2VP-b-PDMS: poly(2-vinylpyridine-b- dimethylsiloxane)). Desirable properties of the liquid marbles include that they rupture upon ultraviolet illumination and can be remotely manipulated by an external magnetic field. 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Remote robotic countermine systems

    Science.gov (United States)

    Wells, Peter

    2010-04-01

    QinetiQ North America (QNA) has approximately 27 years experience in the mine/countermine mission area. Our expertise covers mine development, detection, and neutralization and has always been intertwined with deployment of remote robotic systems. Our countermine payload systems have been used to detect limpet mines on ship hulls, antiassault mines in shallow water and littoral zones and currently for clearance and render safe of land-based routes. In our talk, we will address the challenges encountered in addressing the ongoing countermine mission over a diverse range of operational scenarios, environmental conditions and strategic priorities.

  14. PresenceRemote

    DEFF Research Database (Denmark)

    Sokoler, Tomas; Svensson, Marcus Sanchez

    2008-01-01

    This paper reports on our early experiences with the design of Social TV for senior citizens. Even though there seems to be a straight forward match between new interactive TV technologies on the rise and the notion of supporting social interaction amongst elderly TV viewers it is not at all clear...... how these technologies can accommodate the specific challenges related to the everyday life of elderly people. In particular, using an example concept – the PresenceRemote – we will discuss how the stigma associated with being lonely, an inherent part of senior living, can be addressed by leaving room...

  15. Remote Electro-Analytical Laboratory

    OpenAIRE

    Ratnanjali Gandhi; Rehan Mohd; Soami Satsangee

    2011-01-01

    Remote Laboratories are web based distance learning laboratories that have immense potential to disseminate technology in the area of practical science. These laboratories can be accessed through Internet. In the present paper, we will be discussing our experiences in setting up a remote analytical laboratory at our center. Further, we will discuss remote experiments in the area of electro-analytical chemistry & colorimetry and their role in strengthening the system of science educat...

  16. Remote Sensing and Imaging Physics

    Science.gov (United States)

    2012-03-07

    Program Manager AFOSR/RSE Air Force Research Laboratory Remote Sensing and Imaging Physics 7 March 2012 Report Documentation Page Form...00-00-2012 to 00-00-2012 4. TITLE AND SUBTITLE Remote Sensing And Imaging Physics 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT...Imaging of Space Objects •Information without Imaging •Predicting the Location of Space Objects • Remote Sensing in Extreme Conditions •Propagation

  17. Remote Electro-Analytical Laboratory

    Directory of Open Access Journals (Sweden)

    Ratnanjali Gandhi

    2011-02-01

    Full Text Available Remote Laboratories are web based distance learning laboratories that have immense potential to disseminate technology in the area of practical science. These laboratories can be accessed through Internet. In the present paper, we will be discussing our experiences in setting up a remote analytical laboratory at our center. Further, we will discuss remote experiments in the area of electro-analytical chemistry & colorimetry and their role in strengthening the system of science education.

  18. Experimental measures of pathogen competition and relative fitness.

    Science.gov (United States)

    Zhan, Jiasui; McDonald, Bruce A

    2013-01-01

    Competition among pathogen strains for limited host resources can have a profound effect on pathogen evolution. A better understanding of the principles and consequences of competition can be useful in designing more sustainable disease management strategies. The competitive ability and relative fitness of a pathogen strain are determined by its intrinsic biological properties, the resistance and heterogeneity of the corresponding host population, the population density and genetic relatedness of the competing strains, and the physical environment. Competitive ability can be inferred indirectly from fitness components, such as basic reproduction rate or transmission rate. However, pathogen strains that exhibit higher fitness components when they infect a host alone may not exhibit a competitive advantage when they co-infect the same host. The most comprehensive measures of competitive ability and relative fitness come from calculating selection coefficients in a mixed infection in a field setting. Mark-release-recapture experiments can be used to estimate fitness costs associated with unnecessary virulence and fungicide resistance.

  19. Chemoproteomic profiling of host and pathogen enzymes active in cholera.

    Science.gov (United States)

    Hatzios, Stavroula K; Abel, Sören; Martell, Julianne; Hubbard, Troy; Sasabe, Jumpei; Munera, Diana; Clark, Lars; Bachovchin, Daniel A; Qadri, Firdausi; Ryan, Edward T; Davis, Brigid M; Weerapana, Eranthie; Waldor, Matthew K

    2016-04-01

    Activity-based protein profiling (ABPP) is a chemoproteomic tool for detecting active enzymes in complex biological systems. We used ABPP to identify secreted bacterial and host serine hydrolases that are active in animals infected with the cholera pathogen Vibrio cholerae. Four V. cholerae proteases were consistently active in infected rabbits, and one, VC0157 (renamed IvaP), was also active in human choleric stool. Inactivation of IvaP influenced the activity of other secreted V. cholerae and rabbit enzymes in vivo, and genetic disruption of all four proteases increased the abundance of intelectin, an intestinal lectin, and its binding to V. cholerae in infected rabbits. Intelectin also bound to other enteric bacterial pathogens, suggesting that it may constitute a previously unrecognized mechanism of bacterial surveillance in the intestine that is inhibited by pathogen-secreted proteases. Our work demonstrates the power of activity-based proteomics to reveal host-pathogen enzymatic dialog in an animal model of infection.

  20. Chemoproteomic profiling of host and pathogen enzymes active in cholera

    Science.gov (United States)

    Hatzios, Stavroula K.; Hubbard, Troy; Sasabe, Jumpei; Munera, Diana; Clark, Lars; Bachovchin, Daniel A.; Qadri, Firdausi; Ryan, Edward T.; Davis, Brigid M.; Weerapana, Eranthie; Waldor, Matthew K.

    2016-01-01

    Activity-based protein profiling (ABPP) is a chemoproteomic tool for detecting active enzymes in complex biological systems. We used ABPP to identify secreted bacterial and host serine hydrolases that are active in animals infected with the cholera pathogen Vibrio cholerae. Four V. cholerae proteases were consistently active in infected rabbits, and one, VC0157 (renamed IvaP), was also active in human cholera stool. Inactivation of IvaP influenced the activity of other secreted V. cholerae and rabbit enzymes in vivo, while genetic disruption of all four proteases increased the abundance and binding of an intestinal lectin—intelectin—to V. cholerae in infected rabbits. Intelectin also bound to other enteric bacterial pathogens, suggesting it may constitute a previously unrecognized mechanism of bacterial surveillance in the intestine that is inhibited by pathogen-secreted proteases. Our work demonstrates the power of activity-based proteomics to reveal host-pathogen enzymatic dialogue in an animal model of infection. PMID:26900865

  1. Wireless Remote Control System

    Directory of Open Access Journals (Sweden)

    Adrian Tigauan

    2012-06-01

    Full Text Available This paper presents the design of a wireless remote control system based on the ZigBee communication protocol. Gathering data from sensors or performing control tasks through wireless communication is advantageous in situations in which the use of cables is impractical. An Atmega328 microcontroller (from slave device is used for gathering data from the sensors and transmitting it to a coordinator device with the help of the XBee modules. The ZigBee standard is suitable for low-cost, low-data-rate and low-power wireless networks implementations. The XBee-PRO module, designed to meet ZigBee standards, requires minimal power for reliable data exchange between devices over a distance of up to 1600m outdoors. A key component of the ZigBee protocol is the ability to support networking and this can be used in a wireless remote control system. This system may be employed e.g. to control temperature and humidity (SHT11 sensor and light intensity (TSL230 sensor levels inside a commercial greenhouse.

  2. Introduction to Pathogenic Protozoa

    Science.gov (United States)

    2011-06-01

    1 1 Introduction Mary K. Klassen-Fischer and Ronald C. Neafie Introduction Protozoa Protozoa are single-celled eukaryotic animals first dis...phylogeny of protozoa , see Table 1.1. A recent trend is to replace the term “ protozoa ” with “protista.” For these topics we retain “pro- tozoa” and...JUN 2011 2. REPORT TYPE 3. DATES COVERED 00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE Introduction to Pathogenic Protozoa 5a. CONTRACT

  3. Genomics, proteomics, and genetics of leptospira.

    Science.gov (United States)

    Picardeau, Mathieu

    2015-01-01

    Recent advances in molecular genetics, such as the ability to construct defined mutants, have allowed the study of virulence factors and more generally the biology in Leptospira. However, pathogenic leptospires remain much less easily transformable than the saprophyte L. biflexa and further development and improvement of genetic tools are required. Here, we review tools that have been used to genetically manipulate Leptospira. We also describe the major advances achieved in both genomics and postgenomics technologies, including transcriptomics and proteomics.

  4. Distribution of pathogenic Naegleria spp in Thailand.

    Science.gov (United States)

    Tiewcharoen, S; Junnu, V

    2001-01-01

    Research concerning the distribution, isolation, viability, ultrastructure, morphology and immunogenicity of Naegleria fowleri has been increasing in Thailand during 1988-2000. The distribution of the organism was carried out from 1985 to 1987 in Si Sa Ket and Ubon Rachathani Provinces, after the first fatal case was reported in Si Sa Ket. Since then in a 1998 survey of N. fowleri in stagnant water around industrial areas was carried out in Pathum Thani, Samut Prakan and Lopburi provinces. The results showed that 10% of pathogenic Naegleria belonged to species fowleri as characterized by morphology and the occurrence of pathogenesis in mice after nasal inoculation. In the same year, Nacapunchai et al (1999) determined the prevalence of amebae in aquatic habitat of human environments in five parts of Thailand during the summer. Fourteen percent of free living Naegleria spp were found in both soil and water resources. Recent studies of the ultrastructure, factors affecting the viability and SDS-PAGE electrophoretic patterns of 3 Thai strains of pathogenic Naegleria spp indicated their similarities in morphological characteristics of pathogenic reference control, Naegleria fowleri CDC VO 3081. Additional study using a genetic approach to species criteria using allozyme electrophoresis had been conducted.

  5. From cholera to corals: Viruses as drivers of virulence in a major coral bacterial pathogen

    KAUST Repository

    Weynberg, Karen D.

    2015-12-08

    Disease is an increasing threat to reef-building corals. One of the few identified pathogens of coral disease is the bacterium Vibrio coralliilyticus. In Vibrio cholerae, infection by a bacterial virus (bacteriophage) results in the conversion of non-pathogenic strains to pathogenic strains and this can lead to cholera pandemics. Pathogenicity islands encoded in the V. cholerae genome play an important role in pathogenesis. Here we analyse five whole genome sequences of V. coralliilyticus to examine whether virulence is similarly driven by horizontally acquired elements. We demonstrate that bacteriophage genomes encoding toxin genes with homology to those found in pathogenic V. cholerae are integrated in V. coralliilyticus genomes. Virulence factors located on chromosomal pathogenicity islands also exist in some strains of V. coralliilyticus. The presence of these genetic signatures indicates virulence in V. coralliilyticus is driven by prophages and other horizontally acquired elements. Screening for pathogens of coral disease should target conserved regions in these elements.

  6. From cholera to corals: Viruses as drivers of virulence in a major coral bacterial pathogen

    Science.gov (United States)

    Weynberg, Karen D.; Voolstra, Christian R.; Neave, Matthew J.; Buerger, Patrick; van Oppen, Madeleine J. H.

    2015-01-01

    Disease is an increasing threat to reef-building corals. One of the few identified pathogens of coral disease is the bacterium Vibrio coralliilyticus. In Vibrio cholerae, infection by a bacterial virus (bacteriophage) results in the conversion of non-pathogenic strains to pathogenic strains and this can lead to cholera pandemics. Pathogenicity islands encoded in the V. cholerae genome play an important role in pathogenesis. Here we analyse five whole genome sequences of V. coralliilyticus to examine whether virulence is similarly driven by horizontally acquired elements. We demonstrate that bacteriophage genomes encoding toxin genes with homology to those found in pathogenic V. cholerae are integrated in V. coralliilyticus genomes. Virulence factors located on chromosomal pathogenicity islands also exist in some strains of V. coralliilyticus. The presence of these genetic signatures indicates virulence in V. coralliilyticus is driven by prophages and other horizontally acquired elements. Screening for pathogens of coral disease should target conserved regions in these elements. PMID:26644037

  7. A Remote-Sensing Mission

    Science.gov (United States)

    Hotchkiss, Rose; Dickerson, Daniel

    2008-01-01

    Sponsored by NASA and the JASON Education Foundation, the remote Sensing Earth Science Teacher Education Program (RSESTeP) trains teachers to use state-of-the art remote-sensing technology with the idea that participants bring back what they learn and incorporate it into Earth science lessons using technology. The author's participation in the…

  8. A Remote-Sensing Mission

    Science.gov (United States)

    Hotchkiss, Rose; Dickerson, Daniel

    2008-01-01

    Sponsored by NASA and the JASON Education Foundation, the remote Sensing Earth Science Teacher Education Program (RSESTeP) trains teachers to use state-of-the art remote-sensing technology with the idea that participants bring back what they learn and incorporate it into Earth science lessons using technology. The author's participation in the…

  9. A Remote Quantum Adding Machine

    Institute of Scientific and Technical Information of China (English)

    张圣醒; 龙桂鲁; 刘晓曙

    2002-01-01

    We design a scheme to perform additions of N remote addends. This adder is useful for some quantum information processing purposes, such as statistics and multi-party quantum game. The quantum remote adder is constructed by using a multi-party superdense coding scheme.

  10. IbeR facilitates stress-resistance, invasion and pathogenicity of avian pathogenic Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Shaohui Wang

    Full Text Available Systemic infections by avian pathogenic Escherichia coli (APEC are economically devastating to poultry industries worldwide. IbeR, located on genomic island GimA, was shown to serve as an RpoS-like regulator in rpoS gene mutation neonatal meningitis E. coli (NMEC RS218. However, the role of IbeR in pathogenicity of APEC carrying active RpoS has not yet been investigated. We showed that the APEC IbeR could elicit antibodies in infected ducks, suggesting that IbeR might be involved in APEC pathogenicity. To investigate the function of IbeR in APEC pathogenesis, mutant and complementation strains were constructed and characterized. Inactivation of ibeR led to attenuated virulence and reduced invasion capacity towards DF-1 cells, brains and cerebrospinal fluid (CSF in vitro and in vivo. Bactericidal assays demonstrated that the mutant strain had impaired resistance to environmental stress and specific pathogen-free (SPF chicken serum. These virulence-related phenotypes were restored by genetic complementation. Quantitative real-time reverse transcription PCR revealed that IbeR controlled expression of stress-resistance genes and virulence genes, which might led to the associated virulence phenotype.

  11. Remote Microelectronics Fabrication Laboratory MEFLab

    Directory of Open Access Journals (Sweden)

    Jan Machotka

    2008-07-01

    Full Text Available Over the last decade, there has been a move towards using remote laboratories in engineering education. The majority of these laboratories are static, involving limited user-controlled mechanical movements. The University of South Australia has developed such a laboratory, called NetLab that has been successfully utilized for teaching both on-campus and transnational programs in electrical and electronics engineering. Following this success, we are now developing a remote laboratory for microelectronic fabrication, MEFLab. The first stage of the development is a remote laboratory for visual inspection and testing of electronic circuits directly on the silicon wafer under a microscope which is normally conducted in a cleanroom. The major challenge of this project is the accurate positioning of micro-probes remotely over the internet. This paper presents the details of the setup of this new remote laboratory, with a particular emphasis on the development of the hardware, software and graphical user interface.

  12. Remote control for motor vehicle

    Science.gov (United States)

    Johnson, Dale R. (Inventor); Ciciora, John A. (Inventor)

    1984-01-01

    A remote controller is disclosed for controlling the throttle, brake and steering mechanism of a conventional motor vehicle, with the remote controller being particularly advantageous for use by severely handicapped individuals. The controller includes a remote manipulator which controls a plurality of actuators through interfacing electronics. The remote manipulator is a two-axis joystick which controls a pair of linear actuators and a rotary actuator, with the actuators being powered by electric motors to effect throttle, brake and steering control of a motor vehicle adapted to include the controller. The controller enables the driver to control the adapted vehicle from anywhere in the vehicle with one hand with minimal control force and range of motion. In addition, even though a conventional vehicle is adapted for use with the remote controller, the vehicle may still be operated in the normal manner.

  13. Mobile Remote Control Architecture

    Directory of Open Access Journals (Sweden)

    George Stefan Bogdan

    2012-03-01

    Full Text Available When mobile device become more and more popular the need to have a software bridge between them and the old fashioned computers became evident. Many different solutions have appeared to fill the void but few offer more than file sinking or remote SSH (secure shell connections. For computer professionals and other alike a tool that can do more regarding this connectivity and control gap became necessary. With this paper it is described an architecture and an implementation for creating such a system, underlining the difficulties, challenges and the many choices regarding overall system design, security and implementation that need to be made in order to provide the user with a secure, reliable and professional solution.

  14. Pathogenic mycoflora on carrot seeds

    Directory of Open Access Journals (Sweden)

    Bogdan Nowicki

    2013-12-01

    Full Text Available Altogether 300 seed samples were collected during 9 years in 8 regions of Poland and the fungi Were isolated and their pathogenicity to carrot seedlings was examined. Alternaria rudicina provcd to be the most important pathogen although. A. alternata was more common. The other important pathogens were Fusarium spp., Phoma spp. and Botrytis cinerea. The infection of carrot seeds by A. radicina should be used as an important criterium in seed quality evaluation.

  15. Pathogenic mycoflora on carrot seeds

    OpenAIRE

    Bogdan Nowicki

    2013-01-01

    Altogether 300 seed samples were collected during 9 years in 8 regions of Poland and the fungi Were isolated and their pathogenicity to carrot seedlings was examined. Alternaria rudicina provcd to be the most important pathogen although. A. alternata was more common. The other important pathogens were Fusarium spp., Phoma spp. and Botrytis cinerea. The infection of carrot seeds by A. radicina should be used as an important criterium in seed quality evaluation.

  16. [Streptococcus pyogenes pathogenic factors].

    Science.gov (United States)

    Bidet, Ph; Bonacorsi, S

    2014-11-01

    The pathogenicity of ß-hemolytic group A streptococcus (GAS) is particularly diverse, ranging from mild infections, such as pharyngitis or impetigo, to potentially debilitating poststreptococcal diseases, and up to severe invasive infections such as necrotizing fasciitis or the dreaded streptococcal toxic shock syndrome. This variety of clinical expressions, often radically different in individuals infected with the same strain, results from a complex interaction between the bacterial virulence factors, the mode of infection and the immune system of the host. Advances in comparative genomics have led to a better understanding of how, following this confrontation, GAS adapts to the immune system's pressure, either peacefully by reducing the expression of certain virulence factors to achieve an asymptomatic carriage, or on the contrary, by overexpressing them disproportionately, resulting in the most severe forms of invasive infection.

  17. Rapid Detection of Pathogens

    Energy Technology Data Exchange (ETDEWEB)

    David Perlin

    2005-08-14

    Pathogen identification is a crucial first defense against bioterrorism. A major emphasis of our national biodefense strategy is to establish fast, accurate and sensitive assays for diagnosis of infectious diseases agents. Such assays will ensure early and appropriate treatment of infected patients. Rapid diagnostics can also support infection control measures, which monitor and limit the spread of infectious diseases agents. Many select agents are highly transmissible in the early stages of disease, and it is critical to identify infected patients and limit the risk to the remainder of the population and to stem potential panic in the general population. Nucleic acid-based molecular approaches for identification overcome many of the deficiencies associated with conventional culture methods by exploiting both large- and small-scale genomic differences between organisms. PCR-based amplification of highly conserved ribosomal RNA (rRNA) genes, intergenic sequences, and specific toxin genes is currently the most reliable approach for bacterial, fungal and many viral pathogenic agents. When combined with fluorescence-based oligonucleotide detection systems, this approach provides real-time, quantitative, high fidelity analysis capable of single nucleotide allelic discrimination (4). These probe systems offer rapid turn around time (<2 h) and are suitable for high throughput, automated multiplex operations that are critical for clinical diagnostic laboratories. In this pilot program, we have used molecular beacon technology invented at the Public health Research Institute to develop a new generation of molecular probes to rapidly detect important agents of infectious diseases. We have also developed protocols to rapidly extract nucleic acids from a variety of clinical specimen including and blood and tissue to for detection in the molecular assays. This work represented a cooperative research development program between the Kramer-Tyagi/Perlin labs on probe development

  18. Defining a multimodal signature of remote sports concussions.

    Science.gov (United States)

    Tremblay, Sébastien; Iturria-Medina, Yasser; Mateos-Pérez, José María; Evans, Alan C; De Beaumont, Louis

    2017-08-01

    Sports-related concussions lead to persistent anomalies of the brain structure and function that interact with the effects of normal ageing. Although post-mortem investigations have proposed a bio-signature of remote concussions, there is still no clear in vivo signature. In the current study, we characterized white matter integrity in retired athletes with a history of remote concussions by conducting a full-brain, diffusion-based connectivity analysis. Next, we combined MRI diffusion markers with MR spectroscopic, MRI volumetric, neurobehavioral and genetic markers to identify a multidimensional in vivo signature of remote concussions. Machine learning classifiers trained to detect remote concussions using this signature achieved detection accuracies up to 90% (sensitivity: 93%, specificity: 87%). These automated classifiers identified white matter integrity as the hallmark of remote concussions and could provide, following further validation, a preliminary unbiased detection tool to help medical and legal experts rule out concussion history in patients presenting or complaining about late-life abnormal cognitive decline. © 2017 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

  19. A distributed national network for label-free rapid identification of emerging pathogens

    Science.gov (United States)

    Robinson, J. Paul; Rajwa, Bartek P.; Dundar, M. Murat; Bae, Euiwon; Patsekin, Valery; Hirleman, E. Daniel; Roumani, Ali; Bhunia, Arun K.; Dietz, J. Eric; Davisson, V. Jo; Thomas, John G.

    2011-05-01

    Typical bioterrorism prevention scenarios assume well-known and well-characterized pathogens like anthrax or tularemia, which are serious public concerns if released into food and/or water supplies or distributed using other vectors. Common governmental contingencies include rapid response to these biological threats with predefined treatments and management operations. However, bioterrorist attacks may follow a far more sophisticated route. With the widely known and immense progress in genetics and the availability of molecular biology tools worldwide, the potential for malicious modification of pathogenic genomes is very high. Common non-pathogenic microorganisms could be transformed into dangerous, debilitating pathogens. Known pathogens could also be modified to avoid detection, because organisms are traditionally identified on the basis of their known physiological or genetic properties. In the absence of defined primers a laboratory using genetic biodetection methods such as PCR might be unable to quickly identify a modified microorganism. Our concept includes developing a nationwide database of signatures based on biophysical (such as elastic light scattering (ELS) properties and/or Raman spectra) rather than genetic properties of bacteria. When paired with a machine-learning system for emerging pathogen detection these data become an effective detection system. The approach emphasizes ease of implementation using a standardized collection of phenotypic information and extraction of biophysical features of pathogens. Owing to the label-free nature of the detection modalities ELS is significantly less costly than any genotypic or mass spectrometry approach.

  20. Genetic Architecture of Group A Streptococcal Necrotizing Soft Tissue Infections in the Mouse

    DEFF Research Database (Denmark)

    Chella Krishnan, Karthickeyan; Mukundan, Santhosh; Alagarsamy, Jeyashree;

    2016-01-01

    Host genetic variations play an important role in several pathogenic diseases, and we have previously provided strong evidences that these genetic variations contribute significantly to differences in susceptibility and clinical outcomes of invasive Group A Streptococcus (GAS) infections, includi...

  1. Investigating Transfer of Large Chromosomal Regions Containing the Pathogenicity Locus Between Clostridium difficile Strains

    NARCIS (Netherlands)

    Brouwer, Mike; Mullany, P.; Allan, E.; Roberts, P.

    2016-01-01

    The genomes of all sequenced Clostridium difficile isolates contain multiple mobile genetic elements. The chromosomally located pathogenicity locus (PaLoc), encoding the cytotoxins TcdA and TcdB, was previously hypothesized to be a mobile genetic element; however, mobility was not demonstrated. Here

  2. Investigating Transfer of Large Chromosomal Regions Containing the Pathogenicity Locus Between Clostridium difficile Strains

    NARCIS (Netherlands)

    Brouwer, Mike; Mullany, P.; Allan, E.; Roberts, P.

    2016-01-01

    The genomes of all sequenced Clostridium difficile isolates contain multiple mobile genetic elements. The chromosomally located pathogenicity locus (PaLoc), encoding the cytotoxins TcdA and TcdB, was previously hypothesized to be a mobile genetic element; however, mobility was not demonstrated. Here

  3. Host-Pathogen Coevolution: The Selective Advantage of Bacillus thuringiensis Virulence and Its Cry Toxin Genes.

    Directory of Open Access Journals (Sweden)

    Leila Masri

    2015-06-01

    Full Text Available Reciprocal coevolution between host and pathogen is widely seen as a major driver of evolution and biological innovation. Yet, to date, the underlying genetic mechanisms and associated trait functions that are unique to rapid coevolutionary change are generally unknown. We here combined experimental evolution of the bacterial biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans with large-scale phenotyping, whole genome analysis, and functional genetics to demonstrate the selective benefit of pathogen virulence and the underlying toxin genes during the adaptation process. We show that: (i high virulence was specifically favoured during pathogen-host coevolution rather than pathogen one-sided adaptation to a nonchanging host or to an environment without host; (ii the pathogen genotype BT-679 with known nematocidal toxin genes and high virulence specifically swept to fixation in all of the independent replicate populations under coevolution but only some under one-sided adaptation; (iii high virulence in the BT-679-dominated populations correlated with elevated copy numbers of the plasmid containing the nematocidal toxin genes; (iv loss of virulence in a toxin-plasmid lacking BT-679 isolate was reconstituted by genetic reintroduction or external addition of the toxins. We conclude that sustained coevolution is distinct from unidirectional selection in shaping the pathogen's genome and life history characteristics. To our knowledge, this study is the first to characterize the pathogen genes involved in coevolutionary adaptation in an animal host-pathogen interaction system.

  4. Pathogen-Driven Selection in the Human Genome

    Directory of Open Access Journals (Sweden)

    Rachele Cagliani

    2013-01-01

    Full Text Available Infectious diseases and epidemics have always accompanied and characterized human history, representing one of the main causes of death. Even today, despite progress in sanitation and medical research, infections are estimated to account for about 15% of deaths. The hypothesis whereby infectious diseases have been acting as a powerful selective pressure was formulated long ago, but it was not until the availability of large-scale genetic data and the development of novel methods to study molecular evolution that we could assess how pervasively infectious agents have shaped human genetic diversity. Indeed, recent evidences indicated that among the diverse environmental factors that acted as selective pressures during the evolution of our species, pathogen load had the strongest influence. Beside the textbook example of the major histocompatibility complex, selection signatures left by pathogen-exerted pressure can be identified at several human loci, including genes not directly involved in immune response. In the future, high-throughput technologies and the availability of genetic data from different populations are likely to provide novel insights into the evolutionary relationships between the human host and its pathogens. Hopefully, this will help identify the genetic determinants modulating the susceptibility to infectious diseases and will translate into new treatment strategies.

  5. Recommendations for reporting results of diagnostic genetic testing (biochemical, cytogenetic and molecular genetic).

    Science.gov (United States)

    Claustres, Mireille; Kožich, Viktor; Dequeker, Els; Fowler, Brain; Hehir-Kwa, Jayne Y; Miller, Konstantin; Oosterwijk, Cor; Peterlin, Borut; van Ravenswaaij-Arts, Conny; Zimmermann, Uwe; Zuffardi, Orsetta; Hastings, Ros J; Barton, David E

    2014-02-01

    Genetic test results can have considerable importance for patients, their parents and more remote family members. Clinical therapy and surveillance, reproductive decisions and genetic diagnostics in family members, including prenatal diagnosis, are based on these results. The genetic test report should therefore provide a clear, concise, accurate, fully interpretative and authoritative answer to the clinical question. The need for harmonizing reporting practice of genetic tests has been recognised by the External Quality Assessment (EQA), providers and laboratories. The ESHG Genetic Services Quality Committee has produced reporting guidelines for the genetic disciplines (biochemical, cytogenetic and molecular genetic). These guidelines give assistance on report content, including the interpretation of results. Selected examples of genetic test reports for all three disciplines are provided in an annexe.

  6. Pathogenic agents in freshwater resources

    Science.gov (United States)

    Geldreich, Edwin E.

    1996-02-01

    Numerous pathogenic agents have been found in freshwaters used as sources for water supplies, recreational bathing and irrigation. These agents include bacterial pathogens, enteric viruses, several protozoans and parasitic worms more common to tropical waters. Although infected humans are a major source of pathogens, farm animals (cattle, sheep, pigs), animal pets (dogs, cats) and wildlife serve as significant reservoirs and should not be ignored. The range of infected individuals within a given warm-blooded animal group (humans included) may range from 1 to 25%. Survival times for pathogens in the water environment may range from a few days to as much as a year (Ascaris, Taenia eggs), with infective dose levels varying from one viable cell for several primary pathogenic agents to many thousands of cells for a given opportunistic pathogen.As pathogen detection in water is complex and not readily incorporated into routine monitoring, a surrogate is necessary. In general, indicators of faecal contamination provide a positive correlation with intestinal pathogen occurrences only when appropriate sample volumes are examined by sensitive methodology.Pathways by which pathogens reach susceptible water users include ingestion of contaminated water, body contact with polluted recreational waters and consumption of salad crops irrigated by polluted freshwaters. Major contributors to the spread of various water-borne pathogens are sewage, polluted surface waters and stormwater runoff. All of these contributions are intensified during periods of major floods. Several water-borne case histories are cited as examples of breakdowns in public health protection related to water supply, recreational waters and the consumption of contaminated salad crops. In the long term, water resource management must focus on pollution prevention from point sources of waste discharges and the spread of pathogens in watershed stormwater runoff.

  7. Signal processing for remote sensing

    CERN Document Server

    Chen, CH

    2007-01-01

    Written by leaders in the field, Signal Processing for Remote Sensing explores the data acquisitions segment of remote sensing. Each chapter presents a major research result or the most up to date development of a topic. The book includes a chapter by Dr. Norden Huang, inventor of the Huang-Hilbert transform who, along with and Dr. Steven Long discusses the application of the transform to remote sensing problems. It also contains a chapter by Dr. Enders A. Robinson, who has made major contributions to seismic signal processing for over half a century, on the basic problem of constructing seism

  8. Practical lessons in remote connectivity.

    Science.gov (United States)

    Kouroubali, A.; Starren, J.; Barrows, R. C.; Clayton, P. D.

    1997-01-01

    Community Health Information Networks (CHINs) require the ability to provide computer network connections to many remote sites. During the implementation of the Washington Heights and Inwood Community Health Management Information System (WHICHIS) at the Columbia-Presbyterian Medical Center (CPMC), a number of remote connectivity issues have been encountered. Both technical and non-technical issues were significant during the installation. We developed a work-flow model for this process which may be helpful to any health care institution attempting to provide seamless remote connectivity. This model is presented and implementation lessons are discussed. PMID:9357643

  9. Classification of remotely sensed images

    CSIR Research Space (South Africa)

    Dudeni, N

    2008-10-01

    Full Text Available (s)) is the data vector for a pixel located at s θ(s) is an unknown ground class to which pixel s belongs Objective is to classify the pixel at location s to the one of the k clusters Classification of remotely sensed images N. Dudeni, P. Debba...(s) is an unknown ground class to which pixel s belongs Objective is to classify the pixel at location s to the one of the k clusters Classification of remotely sensed images N. Dudeni, P. Debba Introduction to Remote Sensing Introduction to Image...

  10. Genetic Disorders

    Science.gov (United States)

    ... This can cause a medical condition called a genetic disorder. You can inherit a gene mutation from ... during your lifetime. There are three types of genetic disorders: Single-gene disorders, where a mutation affects ...

  11. Deciphering Evolutionary Mechanisms Between Mutualistic and Pathogenic Symbioses.

    Science.gov (United States)

    Nishiguchi, M K; Hirsch, A M; Devinney, R; Vedantam, G; Riley, M A; Mansky, L M

    2008-01-01

    The continuum between mutualistic and pathogenic symbioses has been an underlying theme for understanding the evolution of infection and disease in a number of eukaryotic-microbe associations. The ability to monitor and then predict the spread of infectious diseases may depend upon our knowledge and capabilities of anticipating the behavior of virulent pathogens by studying related, benign symbioses. For instance, the ability of a symbiotic species to infect, colonize, and proliferate efficiently in a susceptible host will depend on a number of factors that influence both partners during the infection. Levels of virulence are not only affected by the genetic and phenotypic composite of the symbiont, but also the life history, mode(s) of transmission, and environmental factors that influence colonization, such as antibiotic treatment. Population dynamics of both host and symbiont, including densities, migration, as well as competition between symbionts will also affect infection rates of the pathogen as well as change the evolutionary dynamics between host and symbiont. It is therefore important to be able to compare the evolution of virulence between a wide range of mutualistic and pathogenic systems in order to determine when and where new infections might occur, and what conditions will render the pathogen ineffective. This perspective focuses on several symbiotic models that compare mutualistic associations to pathogenic forms and the questions posed regarding their evolution and radiation. A common theme among these systems is the prevailing concept of how heritable mutations can eventually lead to novel phenotypes and eventually new species.

  12. Genetic modification and genetic determinism.

    Science.gov (United States)

    Resnik, David B; Vorhaus, Daniel B

    2006-06-26

    In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions.

  13. USEPA PATHOGEN EQUIVALENCY COMMITTEE RETREAT

    Science.gov (United States)

    The Pathogen Equivalency Committee held its retreat from September 20-21, 2005 at Hueston Woods State Park in College Corner, Ohio. This presentation will update the PEC’s membership on emerging pathogens, analytical methods, disinfection techniques, risk analysis, preparat...

  14. Proteomics of Foodborne Bacterial Pathogens

    Science.gov (United States)

    Fagerquist, Clifton K.

    This chapter is intended to be a relatively brief overview of proteomic techniques currently in use for the identification and analysis of microorganisms with a special emphasis on foodborne pathogens. The chapter is organized as follows. First, proteomic techniques are introduced and discussed. Second, proteomic applications are presented specifically as they relate to the identification and qualitative/quantitative analysis of foodborne pathogens.

  15. Remote direct memory access

    Science.gov (United States)

    Archer, Charles J.; Blocksome, Michael A.

    2012-12-11

    Methods, parallel computers, and computer program products are disclosed for remote direct memory access. Embodiments include transmitting, from an origin DMA engine on an origin compute node to a plurality target DMA engines on target compute nodes, a request to send message, the request to send message specifying a data to be transferred from the origin DMA engine to data storage on each target compute node; receiving, by each target DMA engine on each target compute node, the request to send message; preparing, by each target DMA engine, to store data according to the data storage reference and the data length, including assigning a base storage address for the data storage reference; sending, by one or more of the target DMA engines, an acknowledgment message acknowledging that all the target DMA engines are prepared to receive a data transmission from the origin DMA engine; receiving, by the origin DMA engine, the acknowledgement message from the one or more of the target DMA engines; and transferring, by the origin DMA engine, data to data storage on each of the target compute nodes according to the data storage reference using a single direct put operation.

  16. remote sensor network

    Science.gov (United States)

    von Unold, Georg; Junker, Astrid; Altmann, Thomas

    2016-04-01

    High-throughput (HT) plant phenotyping systems enable the quantitative analysis of a variety of plant features in a fully automated fashion. The comprehensive phenomics infrastructure at IPK comprises three LemnaTec conveyor belt-based (plant-to-sensor) systems for the simultaneous analysis of large numbers of individual plants of different sizes. For monitoring of environmental conditions within the plant growth area and soil conditions in individual pots, highly modular and flexible remote sensing devices are required. We present the architecture of a wireless sensor network implemented in the HT plant phenotyping systems at IPK in the frame of the German Plant Phenotyping Network (DPPN). This system comprises 350 soil monitoring modules, each measuring water content, water matrix potential, temperature and electric conductivity. Furthermore small and large sensor platforms enable the continuous monitoring of environmental parameters such as incident photosynthetic active radiation, total radiation balance, relative humidity and CO2 concentration and more. Finally we present an introduction into data management and maintenance."

  17. REMOTE HANDLING ARRANGEMENTS

    Science.gov (United States)

    Ginns, D.W.

    1958-04-01

    A means for handling remotely a sample pellet to be irradiated in a nuclear reactor is proposed. It is comprised essentially of an inlet tube extending through the outer shield of the reactor and being inclined so that its outer end is at a higher elevation than its inner end, an outlet tube extending through the outer shield being inclined so that its inner end is at a higher elevation than its outer end, the inner ends of these two tubes being interconnected, and a straight tube extending through the outer shield and into the reactor core between the inlet and outlet tubes and passing through the juncture of said inner ends. A rod-like member is rotatably and slidely operated within the central straight tube and has a receptacle on its inner end for receiving a sample pellet from the inlet tube. The rod member is operated to pick up a sample pellet from the inlet tube, carry the sample pellet into the irradiating position within the core, and return to the receiving position where it is rotated to dump the irradiated pellet into the outlet tube by which it is conveyed by gravity to the outside of the reactor. Stop members are provided in the inlet tube, and electrical operating devices are provided to control the sequence of the operation automatically.

  18. Imaging Genetics

    Science.gov (United States)

    Munoz, Karen E.; Hyde, Luke W.; Hariri, Ahmad R.

    2009-01-01

    Imaging genetics is an experimental strategy that integrates molecular genetics and neuroimaging technology to examine biological mechanisms that mediate differences in behavior and the risks for psychiatric disorder. The basic principles in imaging genetics and the development of the field are discussed.

  19. Genetic principles.

    Science.gov (United States)

    Abuelo, D

    1987-01-01

    The author discusses the basic principles of genetics, including the classification of genetic disorders and a consideration of the rules and mechanisms of inheritance. The most common pitfalls in clinical genetic diagnosis are described, with emphasis on the problem of the negative or misleading family history.

  20. Imaging Genetics

    Science.gov (United States)

    Munoz, Karen E.; Hyde, Luke W.; Hariri, Ahmad R.

    2009-01-01

    Imaging genetics is an experimental strategy that integrates molecular genetics and neuroimaging technology to examine biological mechanisms that mediate differences in behavior and the risks for psychiatric disorder. The basic principles in imaging genetics and the development of the field are discussed.

  1. Rapid emergence of pathogens in agro-ecosystems: global threats to agricultural sustainability and food security.

    Science.gov (United States)

    McDonald, Bruce A; Stukenbrock, Eva H

    2016-12-05

    Agricultural ecosystems are composed of genetically depauperate populations of crop plants grown at a high density and over large spatial scales, with the regional composition of crop species changing little from year to year. These environments are highly conducive for the emergence and dissemination of pathogens. The uniform host populations facilitate the specialization of pathogens to particular crop cultivars and allow the build-up of large population sizes. Population genetic and genomic studies have shed light on the evolutionary mechanisms underlying speciation processes, adaptive evolution and long-distance dispersal of highly damaging pathogens in agro-ecosystems. These studies document the speed with which pathogens evolve to overcome crop resistance genes and pesticides. They also show that crop pathogens can be disseminated very quickly across and among continents through human activities. In this review, we discuss how the peculiar architecture of agro-ecosystems facilitates pathogen emergence, evolution and dispersal. We present four example pathosystems that illustrate both pathogen specialization and pathogen speciation, including different time frames for emergence and different mechanisms underlying the emergence process. Lastly, we argue for a re-design of agro-ecosystems that embraces the concept of dynamic diversity to improve their resilience to pathogens. This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

  2. Molecular pathogenicity of Streptococcus anginosus.

    Science.gov (United States)

    Asam, D; Spellerberg, B

    2014-08-01

    Streptococcus anginosus and the closely related species Streptococcus constellatus and Streptococcus intermedius, are primarily commensals of the mucosa. The true pathogenic potential of this group has been under-recognized for a long time because of difficulties in correct species identification as well as the commensal nature of these species. In recent years, streptococci of the S. anginosus group have been increasingly found as relevant microbial pathogens in abscesses and blood cultures and they play a pathogenic role in cystic fibrosis. Several international studies have shown a surprisingly high frequency of infections caused by the S. anginosus group. Recent studies and a genome-wide comparative analysis suggested the presence of multiple putative virulence factors that are well-known from other streptococcal species. However, very little is known about the molecular basis of pathogenicity in these bacteria. This review summarizes our current knowledge of pathogenicity factors and their regulation in S. anginosus.

  3. Persistent pollutants and the patchiness of urban green areas as drivers of genetic richness in the epiphytic moss Leptodon smithii

    Institute of Scientific and Technical Information of China (English)

    Valeria Spagnuolo; Flavia De Nicola; Stefano Terracciano; Roberto Bargagli; Daniela Baldantoni; Fabrizio Monaci; Anna Alfani

    2014-01-01

    We determined genetic variation and metal and polycyclic aromatic hydrocarbon concentrations in Leptodon smithii moss collected in holm oak stands at cities,outskirts and remote areas of Campania and Tuscany (Italy) to investigate if anthropogenic pressure (pollutant emissions and land use change) affects moss genetic richness.In both regions,metal and polycyclic aromatic hydrocarbon concentrations reflected the trend urban > outskirts > remote areas,excepting Tuscany remote site.In both regions,the moss gene diversity increased from urban to remote areas.The findings suggest the extent and the fragmentation of urban green areas,as drivers of moss genetic richness.

  4. Remote Sensing of Environmental Pollution

    Science.gov (United States)

    North, G. W.

    1971-01-01

    Environmental pollution is a problem of international scope and concern. It can be subdivided into problems relating to water, air, or land pollution. Many of the problems in these three categories lend themselves to study and possible solution by remote sensing. Through the use of remote sensing systems and techniques, it is possible to detect and monitor, and in some cases, identify, measure, and study the effects of various environmental pollutants. As a guide for making decisions regarding the use of remote sensors for pollution studies, a special five-dimensional sensor/applications matrix has been designed. The matrix defines an environmental goal, ranks the various remote sensing objectives in terms of their ability to assist in solving environmental problems, lists the environmental problems, ranks the sensors that can be used for collecting data on each problem, and finally ranks the sensor platform options that are currently available.

  5. Remote sensing of oil slicks

    Digital Repository Service at National Institute of Oceanography (India)

    Fondekar, S.P.; Rao, L.V.G.

    the drawback of expensive conventional surveying methods. An airborne remote sensing system used for monitoring and surveillance of oil comprises different sensors such as side-looking airborne radar, synthetic aperture radar, infrared/ultraviolet line scanner...

  6. Genetic blueprint of the zoonotic pathogen Toxocara canis

    DEFF Research Database (Denmark)

    Zhu, Xing-Quan; Korhonen, Pasi K.; Cai, Huimin;

    2015-01-01

    Toxocara canis is a zoonotic parasite of major socioeconomic importance worldwide. In humans, this nematode causes disease (toxocariasis) mainly in the under-privileged communities in developed and developing countries. Although relatively well studied from clinical and epidemiological perspectives...

  7. Genetics of morphogenesis and pathogenic development of Ustilago maydis.

    Science.gov (United States)

    Ustilago maydis has emerged as an important model system for the study of fungi. Like many fungi, U. maydis undergoes remarkable morphological transitions throughout its lifecycle. Fusion of compatible, budding, haploid cells leads to the production of a filamentous dikaryon that penetrates and colo...

  8. Genome Sequencing and Comparative Genomics Analysis Revealed Pathogenic Potential in Penicillium capsulatum as a Novel Fungal Pathogen Belonging to Eurotiales

    Science.gov (United States)

    Yang, Ying; Chen, Min; Li, Zongwei; Al-Hatmi, Abdullah M. S.; de Hoog, Sybren; Pan, Weihua; Ye, Qiang; Bo, Xiaochen; Li, Zhen; Wang, Shengqi; Wang, Junzhi; Chen, Huipeng; Liao, Wanqing

    2016-01-01

    Penicillium capsulatum is a rare Penicillium species used in paper manufacturing, but recently it has been reported to cause invasive infection. To research the pathogenicity of the clinical Penicillium strain, we sequenced the genomes and transcriptomes of the clinical and environmental strains of P. capsulatum. Comparative analyses of these two P. capsulatum strains and close related strains belonging to Eurotiales were performed. The assembled genome sizes of P. capsulatum are approximately 34.4 Mbp in length and encode 11,080 predicted genes. The different isolates of P. capsulatum are highly similar, with the exception of several unique genes, INDELs or SNPs in the genes coding for glycosyl hydrolases, amino acid transporters and circumsporozoite protein. A phylogenomic analysis was performed based on the whole genome data of 38 strains belonging to Eurotiales. By comparing the whole genome sequences and the virulence-related genes from 20 important related species, including fungal pathogens and non-human pathogens belonging to Eurotiales, we found meaningful pathogenicity characteristics between P. capsulatum and its closely related species. Our research indicated that P. capsulatum may be a neglected opportunistic pathogen. This study is beneficial for mycologists, geneticists and epidemiologists to achieve a deeper understanding of the genetic basis of the role of P. capsulatum as a newly reported fungal pathogen. PMID:27761131

  9. Scale issues in remote sensing

    CERN Document Server

    Weng, Qihao

    2014-01-01

    This book provides up-to-date developments, methods, and techniques in the field of GIS and remote sensing and features articles from internationally renowned authorities on three interrelated perspectives of scaling issues: scale in land surface properties, land surface patterns, and land surface processes. The book is ideal as a professional reference for practicing geographic information scientists and remote sensing engineers as well as a supplemental reading for graduate level students.

  10. Remote Atmospheric Nonlinear Optical Magnetometry

    Science.gov (United States)

    2014-04-28

    Boyd , Nonlinear Optics (Elsevier, Burlington, MA, 2008). [13] M. Scully and S. Zubairy, Quantum Optics (Cambridge U. Press, Cambridge, UK, 1997...Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6703--14-9548 Remote Atmospheric Nonlinear Optical Magnetometry PhilliP SPrangle...b. ABSTRACT c. THIS PAGE 18. NUMBER OF PAGES 17. LIMITATION OF ABSTRACT Remote Atmospheric Nonlinear Optical Magnetometry Phillip Sprangle, Luke

  11. Genomics of clostridial pathogens: implication of extrachromosomal elements in pathogenicity.

    Science.gov (United States)

    Brüggemann, Holger

    2005-10-01

    The recently decoded genomes of the major clostridial toxin-producing pathogens Clostridium perfringens, Clostridium tetani, Clostridium botulinum and Clostridium difficile have provided a huge amount of new sequence data. Recent studies have focused on the identification and investigation of pathogenic determinants and the regulatory events governing their expression. The sequence data revealed also the genomic background of virulence genes, as well as the contribution of extrachromosomal elements to a pathogenic phenotype. This has generated new insights in clostridial pathogenesis - and will continue to do so in the future - and has deepened our understanding of the anaerobic lifestyle of clostridial species.

  12. Genetic modification and genetic determinism

    OpenAIRE

    Vorhaus Daniel B; Resnik David B

    2006-01-01

    Abstract In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound....

  13. Vascular related pregnancy complications: genetics and remote cardiovascular risk

    NARCIS (Netherlands)

    A.L. Berends (Anne)

    2008-01-01

    textabstractPreeclampsia and intrauterine growth restriction (IUGR) are common vascular related pregnancy syndromes of unknown cause. Both preeclampsia and IUGR are responsible for a significant maternal and perinatal morbidity and mortality worldwide. Preeclampsia affects approximately 2.5-3.0% of

  14. Secondary metabolite arsenal of an opportunistic pathogenic fungus.

    Science.gov (United States)

    Bignell, Elaine; Cairns, Timothy C; Throckmorton, Kurt; Nierman, William C; Keller, Nancy P

    2016-12-05

    Aspergillus fumigatus is a versatile fungus able to successfully exploit diverse environments from mammalian lungs to agricultural waste products. Among its many fitness attributes are dozens of genetic loci containing biosynthetic gene clusters (BGCs) producing bioactive small molecules (often referred to as secondary metabolites or natural products) that provide growth advantages to the fungus dependent on environment. Here we summarize the current knowledge of these BGCs-18 of which can be named to product-their expression profiles in vivo, and which BGCs may enhance virulence of this opportunistic human pathogen. Furthermore, we find extensive evidence for the presence of many of these BGCs, or similar BGCs, in distantly related genera including the emerging pathogen Pseudogymnoascus destructans, the causative agent of white-nose syndrome in bats, and suggest such BGCs may be predictive of pathogenic potential in other fungi.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

  15. Multiple sclerosis: an example of pathogenic viral interaction?

    Science.gov (United States)

    Fierz, Walter

    2017-02-28

    A hypothesis is formulated on viral interaction between HHV-6A and EBV as a pathogenic mechanism in Multiple Sclerosis (MS). Evidence of molecular and genetic mechanisms suggests a link between HHV-6A infection and EBV activation in the brain of MS patients leading to intrathecal B-cell transformation. Consequent T-cell immune response against the EBV-infected cells is postulated as a pathogenic basis for inflammatory lesion formation in the brain of susceptible individuals. A further link between HHV-6A and EBV involves their induction of expression of the human endogenous retrovirus HERV-K18-encoded superantigen. Such virally induced T-cell responses might secondarily also lead to local autoimmune phenomena. Finally, research recommendations are formulated for substantiating the hypothesis on several levels: epidemiologically, genetically, and viral expression in the brain.

  16. analysis of genetic diversity in linseed using aflp markers

    African Journals Online (AJOL)

    ADMIN

    environments, enhanced resistance to pathogens, pests and other ... parental genotypes are often selected on the basis of phenotypic ..... M. Sc. Thesis, ... Genotype-environment interactions and ... genetic diversity assessment among wheat.

  17. Ecological niche of plant pathogens

    Directory of Open Access Journals (Sweden)

    Ecaterina Fodor

    2011-02-01

    Full Text Available Disease ecology is a new approach to the understanding of the spread and dynamics of pathogens in natural and man-made environments. Defining and describing the ecological niche of the pathogens is one of the major tasks for ecological theory, as well as for practitioners preoccupied with the control and forecasting of established and emerging diseases. Niche theory has been periodically revised, not including in an explicit way the pathogens. However, many progresses have been achieved in niche modeling of disease spread, but few attempts were made to construct a theoretical frame for the ecological niche of pathogens. The paper is a review of the knowledge accumulated during last decades in the niche theory of pathogens and proposes an ecological approach in research. It quest for new control methods in what concerns forest plant pathogens, with a special emphasis on fungi like organisms of the genus Phytophthora. Species of Phytophthora are the most successful plant pathogens of the moment, affecting forest and agricultural systems worldwide, many of them being invasive alien organisms in many ecosystems. The hyperspace of their ecological niche is defined by hosts, environment and human interference, as main axes. To select most important variables within the hyperspace, is important for the understanding of the complex role of pathogens in the ecosystems as well as for control programs. Biotic relationships within ecosystem of host-pathogen couple are depicted by ecological network and specific metrics attached to this. The star shaped network is characterized by few high degree nodes, by short path lengths and relatively low connectivity, premises for a rapid disturbance spread.

  18. Ecological niche of plant pathogens

    Directory of Open Access Journals (Sweden)

    Ecaterina Fodor

    2011-06-01

    Full Text Available Disease ecology is a new approach to the understanding of the spread and dynamics of pathogens in natural and man-made environments. Defining and describing the ecological niche of the pathogens is one of the major tasks for ecological theory, as well as for practitioners preoccupied with the control and forecasting of established and emerging diseases. Niche theory has been periodically revised, not including in an explicit way the pathogens. However, many progresses have been achieved in niche modeling of disease spread, but few attempts were made to construct a theoretical frame for the ecological niche of pathogens. The paper is a review of the knowledge accumulated during last decades in the niche theory of pathogens and proposes an ecological approach in research. It quest for new control methods in what concerns forest plant pathogens, with a special emphasis on fungi like organisms of the genus Phytophthora. Species of Phytophthora are the most successful plant pathogens of the moment, affecting forest and agricultural systems worldwide, many of them being invasive alien organisms in many ecosystems. The hyperspace of their ecological niche is defined by hosts, environment and human interference, as main axes. To select most important variables within the hyperspace, is important the understanding of the complex role of pathogens in the ecosystems as well as for control programs. Biotic relationships within ecosystem of host-pathogen couple are depicted by ecological network and specific metrics attached to this. The star shaped network is characterized by few high degree nodes, by short path lengths and relatively low connectivity, premises for a rapid disturbance spread. 

  19. Human metapneumovirus: a new respiratory pathogen

    Indian Academy of Sciences (India)

    S Broor; P Bharaj; H S Chahar

    2008-11-01

    Human metapneumovirus is a recently recognized pathogen of acute respiratory tract infection (ARI) in children as well as elderly and immunocompromised adults. The virus belongs to the family Paramyxoviridae, sub family Pneumovirinae and genus Metapneumovirus. Through genetic analysis it has been characterized into two groups A and B which are further divided into four sub-lineages. The virus is difficult to grow in tissue culture and hence reverse transcriptase-polymerase chain reaction (RT-PCR) for N and L gene is the method of choice for diagnosis. The virus has been seen in all countries with seasonal distribution in winter months for temperate and spring/summer for tropical countries. F gene is the most conserved among different lineages and efforts are underway to design recombination vaccine using F gene.

  20. Marburg Virus Reverse Genetics Systems.

    Science.gov (United States)

    Schmidt, Kristina Maria; Mühlberger, Elke

    2016-06-22

    The highly pathogenic Marburg virus (MARV) is a member of the Filoviridae family and belongs to the group of nonsegmented negative-strand RNA viruses. Reverse genetics systems established for MARV have been used to study various aspects of the viral replication cycle, analyze host responses, image viral infection, and screen for antivirals. This article provides an overview of the currently established MARV reverse genetic systems based on minigenomes, infectious virus-like particles and full-length clones, and the research that has been conducted using these systems.

  1. Marburg Virus Reverse Genetics Systems

    Directory of Open Access Journals (Sweden)

    Kristina Maria Schmidt

    2016-06-01

    Full Text Available The highly pathogenic Marburg virus (MARV is a member of the Filoviridae family and belongs to the group of nonsegmented negative-strand RNA viruses. Reverse genetics systems established for MARV have been used to study various aspects of the viral replication cycle, analyze host responses, image viral infection, and screen for antivirals. This article provides an overview of the currently established MARV reverse genetic systems based on minigenomes, infectious virus-like particles and full-length clones, and the research that has been conducted using these systems.

  2. Host Pathogen Relations: Exploring Animal Models for Fungal Pathogens

    Directory of Open Access Journals (Sweden)

    Catherine G. Harwood

    2014-06-01

    Full Text Available Pathogenic fungi cause superficial infections but pose a significant public health risk when infections spread to deeper tissues, such as the lung. Within the last three decades, fungi have been identified as the leading cause of nosocomial infections making them the focus of research. This review outlines the model systems such as the mouse, zebrafish larvae, flies, and nematodes, as well as ex vivo and in vitro systems available to study common fungal pathogens.

  3. Host pathogen relations: exploring animal models for fungal pathogens.

    Science.gov (United States)

    Harwood, Catherine G; Rao, Reeta P

    2014-06-30

    Pathogenic fungi cause superficial infections but pose a significant public health risk when infections spread to deeper tissues, such as the lung. Within the last three decades, fungi have been identified as the leading cause of nosocomial infections making them the focus of research. This review outlines the model systems such as the mouse, zebrafish larvae, flies, and nematodes, as well as ex vivo and in vitro systems available to study common fungal pathogens.

  4. Consideration of Cosegregation in the Pathogenicity Classification of Genomic Variants

    OpenAIRE

    Jarvik, Gail P.; Browning, Brian L.

    2016-01-01

    The American College of Medical Genetics and Genomics (ACMG) and Association of Molecular Pathology (AMP) recently published important new guidelines aiming to improve and standardize the pathogenicity classification of genomic variants. The Clinical Sequencing Exploratory Research (CSER) consortium evaluated the use of these guidelines across nine laboratories. One identified obstacle to consistent usage of the ACMG-AMP guidelines is the lack of a definition of cosegregation as criteria for ...

  5. Cryopreservation of sweetpotato (Ipomoea batatas) and its pathogen eradication by cryotherapy.

    Science.gov (United States)

    Feng, Chaohong; Yin, Zhenfang; Ma, Yanli; Zhang, Zhibo; Chen, Long; Wang, Biao; Li, Baiquan; Huang, Yushen; Wang, Qiaochun

    2011-01-01

    Sweetpotato (Ipomoea batatas) ranks as the seventh most important staple crop in the world and the fifth in developing countries after rice, wheat, maize and cassava. Sweetpotato is mainly grown in developing countries, which account for more than 95% of total production of the whole world. Genetic resources, including cultivated varieties and wild species, are a prerequisite for novel sweetpotato breeding in both conventional and genetic engineering programs. Various cryopreservation protocols have been developed for shoot tips and embryogenic tissues. The former explants are preferred for long-term conservation of sweetpotato genetic resources, while the latter are valuable for sweetpotato genetic improvement. This review provides update comprehensive information on cryopreservation of sweetpotato shoot tips and embryogenic tissues. Plant pathogens such as viruses and phytoplasma severely hamper high yield and high quality production of sweetpotato. Thus, usage of pathogen-free planting materials is pivotal for sustainable sweetpotato production. Cryotherapy of shoot tips can efficiently eradicate sweetpotato pathogens such as viruses and phytoplasma. The mechanism behind pathogen eradication by cryotherapy of shoot tips has been elucidated. Pathogen eradication by cryotherapy provides an alternative, efficient strategy for production of pathogen-free plants. In addition, cryopreserved tissues may also be considered to be safer for exchange of germplasm between countries and regions.

  6. Genomic Pathogen Typing Using Solid-State Nanopores.

    Directory of Open Access Journals (Sweden)

    Allison H Squires

    Full Text Available In clinical settings, rapid and accurate characterization of pathogens is essential for effective treatment of patients; however, subtle genetic changes in pathogens which elude traditional phenotypic typing may confer dangerous pathogenic properties such as toxicity, antibiotic resistance, or virulence. Existing options for molecular typing techniques characterize the critical genomic changes that distinguish harmful and benign strains, yet the well-established approaches, in particular those that rely on electrophoretic separation of nucleic acid fragments on a gel, have room for only incremental future improvements in speed, cost, and complexity. Solid-state nanopores are an emerging class of single-molecule sensors that can electrophoretically characterize charged biopolymers, and which offer significant advantages in terms of sample and reagent requirements, readout speed, parallelization, and automation. We present here the first application of nanopores for single-molecule molecular typing using length based "fingerprints" of critical sites in bacterial genomes. This technique is highly adaptable for detection of different types of genetic variation; as we illustrate using prototypical examples including Mycobacterium tuberculosis and methicillin-resistant Streptococcus aureus, the solid-state nanopore diagnostic platform may be used to detect large insertions or deletions, small insertions or deletions, and even single-nucleotide variations in bacterial DNA. We further show that Bayesian classification of test samples can provide highly confident pathogen typing results based on only a few tens of independent single-molecule events, making this method extremely sensitive and statistically robust.

  7. Novel disease susceptibility factors for fungal necrotrophic pathogens in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Albor Dobón

    2015-04-01

    Full Text Available Host cells use an intricate signaling system to respond to invasions by pathogenic microorganisms. Although several signaling components of disease resistance against necrotrophic fungal pathogens have been identified, our understanding for how molecular components and host processes contribute to plant disease susceptibility is rather sparse. Here, we identified four transcription factors (TFs from Arabidopsis that limit pathogen spread. Arabidopsis mutants defective in any of these TFs displayed increased disease susceptibility to Botrytis cinerea and Plectosphaerella cucumerina, and a general activation of non-immune host processes that contribute to plant disease susceptibility. Transcriptome analyses revealed that the mutants share a common transcriptional signature of 77 up-regulated genes. We characterized several of the up-regulated genes that encode peptides with a secretion signal, which we named PROVIR (for provirulence factors. Forward and reverse genetic analyses revealed that many of the PROVIRs are important for disease susceptibility of the host to fungal necrotrophs. The TFs and PROVIRs identified in our work thus represent novel genetic determinants for plant disease susceptibility to necrotrophic fungal pathogens.

  8. Linking questions to practices in the study of microbial pathogens: sampling bias and typing methods.

    Science.gov (United States)

    Gómez-Díaz, Elena

    2009-12-01

    The importance of understanding the population genetics and evolution of microbial pathogens is increasing as a result of the spread and re-emergence of many infectious diseases and their impact for public health. In the last few years, the development of high throughput multi-gene sequence methodologies has opened new opportunities for studying pathogen populations, providing reliable and robust means for both epidemiological and evolutionary investigations. For instance, for many pathogens, multilocus sequence typing has become the "gold standard" in molecular epidemiology, allowing strain identification and discovery. However, there is a huge gap between typing a clinical collection of isolates and making inferences about their evolutionary history and population genetics. Critical issues for studying microbial pathogens such as an adequate sampling design and the appropriate selection of the genetic technique are also required, and will rely on the scale of study and the characteristics of the biological system (e.g., multi- vs. single-host pathogens and vector vs. food or air-borne pathogens). My aim here is to discuss some of these issues in more detail and illustrate how these aspects are often overlooked and easily neglected in the field. Finally, given the rapid accumulation of complete genome sequences and the increasing effort on microbiology research, it is clear that now more than ever integrative approaches bringing together epidemiology and evolutionary biology are needed for understanding the diversity of microbial pathogens.

  9. Bacteriophage based probes for pathogen detection.

    Science.gov (United States)

    Singh, Amit; Arutyunov, Denis; Szymanski, Christine M; Evoy, Stephane

    2012-08-01

    Rapid and specific detection of pathogenic bacteria is important for the proper treatment, containment and prevention of human, animal and plant diseases. Identifying unique biological probes to achieve a high degree of specificity and minimize false positives has therefore garnered much interest in recent years. Bacteriophages are obligate intracellular parasites that subvert bacterial cell resources for their own multiplication and production of disseminative new virions, which repeat the cycle by binding specifically to the host surface receptors and injecting genetic material into the bacterial cells. The precision of host recognition in phages is imparted by the receptor binding proteins (RBPs) that are often located in the tail-spike or tail fiber protein assemblies of the virions. Phage host recognition specificity has been traditionally exploited for bacterial typing using laborious and time consuming bacterial growth assays. At the same time this feature makes phage virions or RBPs an excellent choice for the development of probes capable of selectively capturing bacteria on solid surfaces with subsequent quick and automatic detection of the binding event. This review focuses on the description of pathogen detection approaches based on immobilized phage virions as well as pure recombinant RBPs. Specific advantages of RBP-based molecular probes are also discussed.

  10. Future research needs involving pathogens in groundwater

    Science.gov (United States)

    Contamination of groundwater by enteric pathogens has commonly been associated with disease outbreaks. Proper management and treatment of pathogen sources are important barriers to preventing groundwater contamination. However, non-point sources of pathogen contamination are frequently difficult to ...

  11. Report: Genetics of complex diseases

    Institute of Scientific and Technical Information of China (English)

    MOTULSKY Arno G.

    2006-01-01

    Approaches to the study of the genetic basis of common complex diseases and their clinical applications are considered. Monogenic Mendelian inheritance in such conditions is infrequent but its elucidation may help to detect pathogenic mechanisms in the more common variety of complex diseases. Involvement by multiple genes in complex diseases usually occurs but the isolation and identification of specific genes so far has been exceptional. The role of common polymorphisms as indicators of disease risk in various studies is discussed.

  12. Mucin dynamics and enteric pathogens.

    Science.gov (United States)

    McGuckin, Michael A; Lindén, Sara K; Sutton, Philip; Florin, Timothy H

    2011-04-01

    The extracellular secreted mucus and the cell surface glycocalyx prevent infection by the vast numbers of microorganisms that live in the healthy gut. Mucin glycoproteins are the major component of these barriers. In this Review, we describe the components of the secreted and cell surface mucosal barriers and the evidence that they form an effective barricade against potential pathogens. However, successful enteric pathogens have evolved strategies to circumvent these barriers. We discuss the interactions between enteric pathogens and mucins, and the mechanisms that these pathogens use to disrupt and avoid mucosal barriers. In addition, we describe dynamic alterations in the mucin barrier that are driven by host innate and adaptive immune responses to infection.

  13. Evolution, global spread, and pathogenicity of highly pathogenic avian influenza H5Nx clade 2.3.4.4

    Science.gov (United States)

    Novel subtypes of Eurasian-origin (Goose/Guangdong lineage) H5 highly pathogenic avian influenza (HPAI) viruses belonging to clade 2.3.4 such as H5N2, H5N5, H5N6, and H5N8 have been identified in China since 2008 and subsequently evolved into four genetically distinct groups (A – D) of clade 2.3.4.4...

  14. Ecosystem Screening Approach for Pathogen-Associated Microorganisms Affecting Host Disease▿†

    Science.gov (United States)

    Galiana, Eric; Marais, Antoine; Mura, Catherine; Industri, Benoît; Arbiol, Gilles; Ponchet, Michel

    2011-01-01

    The microbial community in which a pathogen evolves is fundamental to disease outcome. Species interacting with a pathogen on the host surface shape the distribution, density, and genetic diversity of the inoculum, but the role of these species is rarely determined. The screening method developed here can be used to characterize pathogen-associated species affecting disease. This strategy involves three steps: (i) constitution of the microbial community, using the pathogen as a trap; (ii) community selection, using extracts from the pathogen as the sole nutrient source; and (iii) molecular identification and the screening of isolates focusing on their effects on the growth of the pathogen in vitro and host disease. This approach was applied to a soilborne plant pathogen, Phytophthora parasitica, structured in a biofilm, for screening the microbial community from the rhizosphere of Nicotiana tabacum (the host). Two of the characterized eukaryotes interfered with the oomycete cycle and may affect the host disease. A Vorticella species acted through a mutualistic interaction with P. parasitica, disseminating pathogenic material by leaving the biofilm. A Phoma species established an amensal interaction with P. parasitica, strongly suppressing disease by inhibiting P. parasitica germination. This screening method is appropriate for all nonobligate pathogens. It allows the definition of microbial species as promoters or suppressors of a disease for a given biotope. It should also help to identify important microbial relationships for ecology and evolution of pathogens. PMID:21742919

  15. Ecosystem screening approach for pathogen-associated microorganisms affecting host disease.

    Science.gov (United States)

    Galiana, Eric; Marais, Antoine; Mura, Catherine; Industri, Benoît; Arbiol, Gilles; Ponchet, Michel

    2011-09-01

    The microbial community in which a pathogen evolves is fundamental to disease outcome. Species interacting with a pathogen on the host surface shape the distribution, density, and genetic diversity of the inoculum, but the role of these species is rarely determined. The screening method developed here can be used to characterize pathogen-associated species affecting disease. This strategy involves three steps: (i) constitution of the microbial community, using the pathogen as a trap; (ii) community selection, using extracts from the pathogen as the sole nutrient source; and (iii) molecular identification and the screening of isolates focusing on their effects on the growth of the pathogen in vitro and host disease. This approach was applied to a soilborne plant pathogen, Phytophthora parasitica, structured in a biofilm, for screening the microbial community from the rhizosphere of Nicotiana tabacum (the host). Two of the characterized eukaryotes interfered with the oomycete cycle and may affect the host disease. A Vorticella species acted through a mutualistic interaction with P. parasitica, disseminating pathogenic material by leaving the biofilm. A Phoma species established an amensal interaction with P. parasitica, strongly suppressing disease by inhibiting P. parasitica germination. This screening method is appropriate for all nonobligate pathogens. It allows the definition of microbial species as promoters or suppressors of a disease for a given biotope. It should also help to identify important microbial relationships for ecology and evolution of pathogens.

  16. Magnetogenetics: Remote Control of Cellular Signaling with Magnetic Fields

    Science.gov (United States)

    Sauer, Jeremy P.

    Means for temporally regulating gene expression and cellular activity are invaluable for elucidating the underlying physiological processes and have therapeutic implications. Here we report the development of a system for remote regulation of gene expression by low frequency radiowaves (RF) or by a static magnetic field. We accomplished this by first adding iron oxide nanoparticles - either exogenously or as genetically encoded ferritin/ferric oxyhydroxide particle. These particles have been designed with affinity to the plasma membrane ion channel Transient Receptor Potential Vanilloid 1 (TRPV1) by a conjugated antibody. Application of a magnetic field stimulates the particle to gate the ion channel and this, in turn, initiates calcium-dependent transgene expression. We first demonstrated in vitro that TRPV1 can be actuated to cause calcium flux into the cell by directly applying a localized magnetic field. In mice expressing these genetically encoded components, application of external magnetic field caused remote stimulation of insulin transgene expression and significantly lowered blood glucose. In addition, we are investigating mechanisms by which iron oxide nanoparticles can absorb RF, and transduce this energy to cause channel opening. This robust, repeatable method for remote cellular regulation in vivo may ultimately have applications in basic science, as well as in technology and therapeutics.

  17. Genetic barcodes

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Heinz -Ulrich G

    2015-08-04

    Herein are described multicolor FISH probe sets termed "genetic barcodes" targeting several cancer or disease-related loci to assess gene rearrangements and copy number changes in tumor cells. Two, three or more different fluorophores are used to detect the genetic barcode sections thus permitting unique labeling and multilocus analysis in individual cell nuclei. Gene specific barcodes can be generated and combined to provide both numerical and structural genetic information for these and other pertinent disease associated genes.

  18. Remote Nodes Management Using RMI

    Directory of Open Access Journals (Sweden)

    Saurabh Malgaonkar

    2014-03-01

    Full Text Available We have focused upon the design and development of a remote desktop management system using Remote Method Invocation, since it has many advantages in terms of remote computation, software optimization, data access and storage services that do not require end-user knowledge of the physical location and configuration of the system. In this type of a system we have two types of users - clients and the server. The server can control all the activities of the clients and also impose certain restrictions on the clients. The clients can use the data or shared resources, software and information that are provided by the server to computers and other devices as a utility over a network. The major elements of desktop management are assets management, software deployment, patch management, remote desktop sharing, active directory reports and user logon reports. Remote desktop sharing enables users to access and use their own desktop from other machines or locations. This system is focused upon the real time events.

  19. Photogrammetry - Remote Sensing and Geoinformation

    Science.gov (United States)

    Lazaridou, M. A.; Patmio, E. N.

    2012-07-01

    Earth and its environment are studied by different scientific disciplines as geosciences, science of engineering, social sciences, geography, etc. The study of the above, beyond pure scientific interest, is useful for the practical needs of man. Photogrammetry and Remote Sensing (defined by Statute II of ISPRS) is the art, science, and technology of obtaining reliable information from non-contact imaging and other sensor systems about the Earth and its environment, and other physical objects and of processes through recording, measuring, analyzing and representation. Therefore, according to this definition, photogrammetry and remote sensing can support studies of the above disciplines for acquisition of geoinformation. This paper concerns basic concepts of geosciences (geomorphology, geology, hydrology etc), and the fundamentals of photogrammetry-remote sensing, in order to aid the understanding of the relationship between photogrammetry-remote sensing and geoinformation and also structure curriculum in a brief, concise and coherent way. This curriculum can represent an appropriate research and educational outline and help to disseminate knowledge in various directions and levels. It resulted from our research and educational experience in graduate and post-graduate level (post-graduate studies relative to the protection of environment and protection of monuments and historical centers) in the Lab. of Photogrammetry - Remote Sensing in Civil Engineering Faculty of Aristotle University of Thessaloniki.

  20. Association analysis of SP-SNPs and Avr genes in Puccinia striiformis f. sp. tritici, the wheat stripe rust pathogen

    Science.gov (United States)

    Puccinia striiformis f. sp. tritici (Pst) is one of the pathogenic fungi on wheat, caused stripe rust disease which is a great threat for wheat production all over the world. Intensive efforts have been made to study genetics of wheat resistance to this disease, but few on avirulence of the pathogen...

  1. Genetic screening of a pedigree with osteogenesis imperfecta type Ⅰand identification of a novel mutation in COL1A2 pathogenic gene%成骨不全Ⅰ型家系的基因检测和COL1A2基因新突变的致病性鉴定

    Institute of Scientific and Technical Information of China (English)

    李荣; 郭源平; 潘敬新; 郭奕斌

    2015-01-01

    To uncover the molecular pathogenic mechanism of congenital osteogenesis imperfecta (OI) type I, all the 103 exons of the COL1A1 (Collagen, type Ⅰ, alpha 1) and COL1A2 (Collagen, type Ⅰ, alpha 2) genes in a child with OI type Ⅰ were screened using PCR-DNA direct sequencing. The results showed no pathological mutation in COL1A1 gene, but a novel mutation c.946G>T/p.G316C in the exon 19 of COL1A2 gene, which was inherited from her father. This mutation was not found in her mother and other six phenotypically normal relatives. By denaturing high perfor-mance liquid chromatography (DHPLC) screening, the abnormal double-peak was visualized in PCR products of exon 19 of COL1A2 gene in the proband and her father, while the normal single-peak was shown in those of her mother and all the healthy controls. Using allele specific amplification (ASA) screening, a specific band of 391 bp in COL1A2 exon 19 was amplified only in the proband and her father, but not in other samples. The amino acid encoded by the mutation site is evolutionarily highly conserved, and this mutation was a“damaging”or“probably damaging”factor to OI type Ⅰ, based on the predicting results using SIFT and Polyphen-2 softwares. In conclusion, the novel c.946G>T/p.G316C mutation in COL1A2 gene is a pathogenic mutation that could result in OI type Ⅰ. If the couple wants to get pregnant again, it is necessary to screen the mutation site in COL1A2 gene through the prenatal genetic diagnosis in the first trimester or through preimplantation genetic diagnosis (PGD) in the progestation.%为了揭示成骨不全(Osteogenesis imperfecta, OI)Ⅰ型家系的分子遗传学发生机制,文章采用PCR-DNA直接测序法,对患儿 COL1A1和 COL1A2基因共103个外显子(E)进行突变检测。结果显示:患儿 COL1A1基因未发现任何病理性突变,而在 COL1A2基因 E19内发现一新的杂合错义突变(p.G316C),该突变来自其父,而其母正常,其他表型正常的6位

  2. 变异型PRRSV-FJ09A毒株ORF5和NSP2基因的遗传变异分析及致病性%Genetic Variations of ORF5, NSP2 of Variant PRRSV-FJ09A strain and It's Pathogenicity

    Institute of Scientific and Technical Information of China (English)

    王隆柏; 张志灯; 车勇良; 吴学敏; 陈如敬; 邵良平; 庄向生; 周伦江

    2012-01-01

    To fully understand the knowledge of variant porcine reproductive and respiratory syndrome virus (PRRSV) genetic variation and pathogenicity, the ORF5 and NSP2 genomes of PRRSV-FJ09A strain were amplified by RT-PCR and sequenced. Comparing with PRRSV-VR2332, ORF5 gene shared 87. 6% of nucleotide homologies and 88. 1 % of the deduced amino acid homologies, there were point mutations within deduced amino acids, focus on amino acids of associated with virulence, epitope and N-glycosylation sites; NSP2 gene shared 80. 9% of nucleotide homologies and 77. 0% of the deduced amino acid homologies, and it shared a common feature of 31 amino acids deletion in three places which one place more of a phenylalanine (F) than other local reports. Comparing these sequences with Chinese PRRSV strains published after 2006, ORF5 gene shared 98. 5 % - 99. 7% of nucleotide homologies and 97. 5% - 99. 5% of the deduced amino acid homologies, NSP2 gene shared 98. 4% - 99. 3% of nucleotide homologies and 97. 3% - 98. 9% of the deduced amino acid homologies. The phylogeneic tree revealed PRRSV-FJ09A strain isolated had closer relationship with PRRSV-FJ06A strain. According to the animal experiment PRRSV-FJ09A had a high pathogenicity to 30 d pigs.%采用RT-PCR方法及动物回归试验,对PRRSV-FJ09A毒株的ORF5与NSP2基因组进行遗传变异分析和致病性研究.结果表明:(1)与PRRSV-VR2332标准毒株比较,ORF5基因片段的核苷酸及推导的氨基酸的同源性分别为87.6%和88.1%,PRRSV-FJ09A毒株存在多个氨基酸发生突变,主要集中在抗原表位、毒力相关位点和糖基化位点;NSP2基因片段的核苷酸及推导的氨基酸的同源性分别为80.9%和77.0%,PRRSV-FJ09A毒株分3处共缺失31个氨基酸.(2)与国内2006年后流行的变异型PRRSV毒株比较,PRRSV-FJ09A毒株ORF5基因片段的核苷酸及推导的氨基酸的同源性分别为98.5%~99.7%和97.5%~99.5%,NSP2基因片段的核苷酸

  3. Fungi with multifunctional lifestyles: endophytic insect pathogenic fungi.

    Science.gov (United States)

    Barelli, Larissa; Moonjely, Soumya; Behie, Scott W; Bidochka, Michael J

    2016-04-01

    This review examines the symbiotic, evolutionary, proteomic and genetic basis for a group of fungi that occupy a specialized niche as insect pathogens as well as endophytes. We focus primarily on species in the genera Metarhizium and Beauveria, traditionally recognized as insect pathogenic fungi but are also found as plant symbionts. Phylogenetic evidence suggests that these fungi are more closely related to grass endophytes and diverged from that lineage ca. 100 MYA. We explore how the dual life cycles of these fungi as insect pathogens and endophytes are coupled. We discuss the evolution of insect pathogenesis while maintaining an endophytic lifestyle and provide examples of genes that may be involved in the transition toward insect pathogenicity. That is, some genes for insect pathogenesis may have been co-opted from genes involved in endophytic colonization. Other genes may be multifunctional and serve in both lifestyle capacities. We suggest that their evolution as insect pathogens allowed them to effectively barter a specialized nitrogen source (i.e. insects) with host plants for photosynthate. These ubiquitous fungi may play an important role as plant growth promoters and have a potential reservoir of secondary metabolites.

  4. Genetics of autoimmune diseases: insights from population genetics.

    Science.gov (United States)

    Ramos, Paula S; Shedlock, Andrew M; Langefeld, Carl D

    2015-11-01

    Human genetic diversity is the result of population genetic forces. This genetic variation influences disease risk and contributes to health disparities. Autoimmune diseases (ADs) are a family of complex heterogeneous disorders with similar underlying mechanisms characterized by immune responses against self. Collectively, ADs are common, exhibit gender and ethnic disparities, and increasing incidence. As natural selection is an important influence on human genetic variation, and immune function genes are enriched for signals of positive selection, it is thought that the prevalence of AD risk alleles seen in different population is partially the result of differing selective pressures (for example, due to pathogens). With the advent of high-throughput technologies, new analytical methodologies and large-scale projects, evidence for the role of natural selection in contributing to the heritable component of ADs keeps growing. This review summarizes the genetic regions associated with susceptibility to different ADs and concomitant evidence for selection, including known agents of selection exerting selective pressure in these regions. Examples of specific adaptive variants with phenotypic effects are included as an evidence of natural selection increasing AD susceptibility. Many of the complexities of gene effects in different ADs can be explained by population genetics phenomena. Integrating AD susceptibility studies with population genetics to investigate how natural selection has contributed to genetic variation that influences disease risk will help to identify functional variants and elucidate biological mechanisms. As such, the study of population genetics in human population holds untapped potential for elucidating the genetic causes of human disease and more rapidly focusing to personalized medicine.

  5. Remote sensing of natural phenomena

    Directory of Open Access Journals (Sweden)

    Miodrag D. Regodić

    2014-06-01

    Full Text Available There has always been a need to directly perceive and study the events whose extent is beyond people's possibilities. In order to get new data and to make observations and studying much more objective in comparison with past syntheses - a new method of examination called remote sensing has been adopted. The paper deals with the principles and elements of remote sensing, as well as with the basic aspects of using remote research in examining meteorological (weather parameters and the conditions of the atmosphere. The usage of satellite images is possible in all phases of the global and systematic research of different natural phenomena when airplane and satellite images of different characteristics are used and their analysis and interpretation is carried out by viewing and computer added procedures. Introduction Remote sensing of the Earth enables observing and studying global and local events that occur on it. Satellite images are nowadays used in geology, agriculture, forestry, geodesy, meteorology, spatial and urbanism planning, designing of infrastructure and other objects, protection from natural and technological catastrophes, etc. It it possible to use satellite images in all phases of global and systematic research of different natural phenomena. Basics of remote sensing Remote sensing is a method of the acquisition and interpretation of information about remote objects without making a physical contact with them. The term Daljinska detekcija is a literal translation of the English term Remote Sensing. In French it isTeledetection, in German - Fernerkundung, in Russian - дистанционие иследования. We also use terms such as: remote survailance, remote research, teledetection, remote methods, and distance research. The basic elements included in Remote Sensing are: object, electromagnetic energy, sensor, platform, image, analysis, interpretation and the information (data, fact. Usage of satellite remote research in

  6. Specialization for resistance in wild host-pathogen interaction networks

    Directory of Open Access Journals (Sweden)

    Luke eBarrett

    2015-09-01

    Full Text Available Properties encompassed by host-pathogen interaction networks have potential to give valuable insight into the evolution of specialization and coevolutionary dynamics in host-pathogen interactions. However, network approaches have been rarely utilized in previous studies of host and pathogen phenotypic variation. Here we applied quantitative analyses to eight networks derived from spatially and temporally segregated host (Linum marginale and pathogen (Melampsora lini populations. First, we found that resistance strategies are highly variable within and among networks, corresponding to a spectrum of specialist and generalist resistance types being maintained within all networks. At the individual level, specialization was strongly linked to partial resistance, such that partial resistance was effective against a greater number of pathogens compared to full resistance. Second, we found that all networks were significantly nested. There was little support for the hypothesis that temporal evolutionary dynamics may lead to the development of nestedness in host-pathogen infection networks. Rather, the common patterns observed in terms of nestedness suggests a universal driver (or multiple drivers that may be independent of spatial and temporal structure. Third, we found that resistance networks were significantly modular in two spatial networks, clearly reflecting spatial and ecological structure within one of the networks. We conclude that (1 overall patterns of specialization in the networks we studied mirror evolutionary trade-offs with the strength of resistance; (2 that specific network architecture can emerge under different evolutionary scenarios; and (3 network approaches offer great utility as a tool for probing the evolutionary and ecological genetics of host-pathogen interactions.

  7. Remote Sensing for Wind Energy

    DEFF Research Database (Denmark)

    The Remote Sensing in Wind Energy Compendium provides a description of several topics and it is our hope that students and others interested will learn from it. The idea behind this compendium began in year 2008 at Risø DTU during the first PhD Summer School: Remote Sensing in Wind Energy. Thus...... of the compendium, and we also acknowledge all our colleagues in the Meteorology and Test and Measurements Programs from the Wind Energy Division at Risø DTU in the PhD Summer Schools. We hope to continue adding more topics in future editions and to update and improve as necessary, to provide a truly state......-of-the-art compendium available for people involved in Remote Sensing in Wind Energy....

  8. Remote Sensing for Wind Energy

    DEFF Research Database (Denmark)

    The Remote Sensing in Wind Energy Compendium provides a description of several topics and it is our hope that students and others interested will learn from it. The idea behind this compendium began in year 2008 at Risø DTU during the first PhD Summer School: Remote Sensing in Wind Energy. Thus...... in the Meteorology and Test and Measurements Programs from the Wind Energy Division at Risø DTU in the PhD Summer Schools. We hope to add more topics in future editions and to update as necessary, to provide a truly state-of-the-art compendium available for people involved in Remote Sensing in Wind Energy....

  9. Remote Sensing for Wind Energy

    DEFF Research Database (Denmark)

    Peña, Alfredo; Hasager, Charlotte Bay; Badger, Merete

    The Remote Sensing in Wind Energy report provides a description of several topics and it is our hope that students and others interested will learn from it. The idea behind it began in year 2008 at DTU Wind Energy (formerly Risø) during the first PhD Summer School: Remote Sensing in Wind Energy...... colleagues in the Meteorology and Test and Measurements Sections from DTU Wind Energy in the PhD Summer Schools. We hope to continue adding more topics in future editions and to update and improve as necessary, to provide a truly state-of-the-art ‘guideline’ available for people involved in Remote Sensing...... in Wind Energy....

  10. Remote Sensing for Wind Energy

    DEFF Research Database (Denmark)

    Peña, Alfredo; Hasager, Charlotte Bay; Lange, Julia

    The Remote Sensing in Wind Energy report provides a description of several topics and it is our hope that students and others interested will learn from it. The idea behind it began in year 2008 at DTU Wind Energy (formerly Risø) during the first PhD Summer School: Remote Sensing in Wind Energy...... for their work in the writing of the chapters, and we also acknowledge all our colleagues in the Meteorology and Test and Measurements Sections from DTU Wind Energy in the PhD Summer Schools. We hope to continue adding more topics in future editions and to update and improve as necessary, to provide a truly...... state-of-the-art ‘guideline’ available for people involved in Remote Sensing in Wind Energy....

  11. Remote preparation of quantum states

    CERN Document Server

    Bennett, C H; Leung, D W; Shor, P W; Winter, A; Bennett, Charles H; Hayden, Patrick; Leung, Debbie W.; Shor, Peter W.; Winter, Andreas

    2003-01-01

    Remote state preparation is the variant of quantum state teleportation in which the sender knows the quantum state to be communicated. The original paper introducing teleportation established minimal requirements for classical communication and entanglement but the corresponding limits for remote state preparation have remained unknown until now: previous work has shown, however, that it not only requires less classical communication but also gives rise to a trade-off between these two resources in the appropriate setting. We discuss this problem from first principles, including the various choices one may follow in the definitions of the actual resources. Our main result is a general method of remote state preparation for arbitrary states of many qubits, at a cost of 1 bit of classical communication and 1 bit of entanglement per qubit sent. In this "universal" formulation, these ebit and cbit requirements are shown to be simultaneously optimal by exhibiting a dichotomy. This then yields the exact trade-off c...

  12. SMS BASED REMOTE CONTROL SYSTEM

    Directory of Open Access Journals (Sweden)

    Reecha Ranjan Singh , Sangeeta Agrawal , Saurabh Kapoor ,S. Sharma

    2011-08-01

    Full Text Available A modern world contains varieties of electronic equipment and systems like: TV, security system, Hi-fi equipment, central heating systems, fire alarm systems, security alarm systems, lighting systems, SET Top Box, AC (Air Conditioner etc., we need to handle, ON/OFF or monitor these electrical devices remotely or to communicate with these but, if you are not at the home or that place and you want to communicate with these device. So the new technology for handled these devices remotely and for communication to required the GSM, mobile technology, SMS (short message service and some hardware resources. SMS based remote control for home appliances is beneficial for the human generation, because mobile is most recently used technology nowadays.

  13. Remote sensing for urban planning

    Science.gov (United States)

    Davis, Bruce A.; Schmidt, Nicholas; Jensen, John R.; Cowen, Dave J.; Halls, Joanne; Narumalani, Sunil; Burgess, Bryan

    1994-01-01

    Utility companies are challenged to provide services to a highly dynamic customer base. With factory closures and shifts in employment becoming a routine occurrence, the utility industry must develop new techniques to maintain records and plan for expected growth. BellSouth Telecommunications, the largest of the Bell telephone companies, currently serves over 13 million residences and 2 million commercial customers. Tracking the movement of customers and scheduling the delivery of service are major tasks for BellSouth that require intensive manpower and sophisticated information management techniques. Through NASA's Commercial Remote Sensing Program Office, BellSouth is investigating the utility of remote sensing and geographic information system techniques to forecast residential development. This paper highlights the initial results of this project, which indicate a high correlation between the U.S. Bureau of Census block group statistics and statistics derived from remote sensing data.

  14. Remote field eddy current testing

    Energy Technology Data Exchange (ETDEWEB)

    Cheong, Y. M.; Jung, H. K.; Huh, H.; Lee, Y. S.; Shim, C. M

    2001-03-01

    The state-of-art technology of the remote field eddy current, which is actively developed as an electromagnetic non-destructive testing tool for ferromagnetic tubes, is described. The historical background and recent R and D activities of remote-field eddy current technology are explained including the theoretical development of remote field eddy current, such as analytical and numerical approach, and the results of finite element analysis. The influencing factors for actual applications, such as the effect of frequency, magnetic permeability, receiving sensitivity, and difficulties of detection and classification of defects are also described. Finally, two examples of actual application, 1) the gap measurement between pressure tubes and calandria tube in CANDU reactor and, 2) the detection of defects in the ferromagnetic heat exchanger tubes, are described. The future research efforts are also included.

  15. Genetic modification and genetic determinism

    Directory of Open Access Journals (Sweden)

    Vorhaus Daniel B

    2006-06-01

    Full Text Available Abstract In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions.

  16. KIR/HLA Interactions and Pathogen Immunity

    Directory of Open Access Journals (Sweden)

    Khaleel M. Jamil

    2011-01-01

    Full Text Available The innate immune system is the first line of defence in response to pathogen infection. Natural killer (NK cells perform a vital role in this response with the ability to directly kill infected cells, produce cytokines, and cross-talk with the adaptive immune system. These effector functions are dependent on activation of NK cells which is determined by surface receptor interactions with ligands on target cells. Of these receptors, the polymorphic killer immunoglobulin-like receptors (KIRs, which interact with MHC class 1 (also highly polymorphic, are largely inhibitory, and exhibit substantial genetic diversity. The result is a significant variation of NK cell repertoire between individuals and also between populations, with a multitude of possible KIR:HLA combinations. As each KIR:ligand interaction may have differential effects on NK cell activation and inhibition, this diversity has important potential influences on the host response to infections. Genetic studies have demonstrated associations between specific KIR:ligand combinations and the outcome of viral (and other infections, in particular hepatitis C and HIV infection. Detailed functional studies are not required to define the mechanisms underpinning these disease associations.

  17. Pathogenic Mechanisms of Pulmonary Arterial Hypertension

    Science.gov (United States)

    Chan, Stephen Y.; Loscalzo, Joseph

    2008-01-01

    Pulmonary arterial hypertension (PAH)1 is a complex disease that causes significant morbidity and mortality and is clinically characterized by an increase in pulmonary vascular resistance. The histopathology is marked by vascular proliferation/fibrosis, remodeling, and vessel obstruction. Development of PAH involves the complex interaction of multiple vascular effectors at all anatomic levels of the arterial wall. Subsequent vasoconstriction, thrombosis, and inflammation ensue, leading to vessel wall remodeling and cellular hyperproliferation as the hallmarks of severe disease. These processes are influenced by genetic predisposition as well as diverse endogenous and exogenous stimuli. Recent studies have provided a glimpse at certain molecular pathways that contribute to pathogenesis; these have led to the identification of attractive targets for therapeutic intervention. We will review our current understanding of the mechanistic underpinnings of the genetic and exogenous/acquired triggers of PAH. The resulting imbalance of vascular effectors provoking pathogenic vascular changes will also be discussed, with an emphasis on common and overarching regulatory pathways that may relate to the primary triggers of disease. The current conceptual framework should allow for future studies to refine our understanding of the molecular pathogenesis of PAH and improve the therapeutic regimen for this disease. PMID:17950310

  18. Fundamentals of polarimetric remote sensing

    CERN Document Server

    Schott, John R

    2009-01-01

    This text is for those who need an introduction to polarimetric signals to begin working in the field of polarimetric remote sensing, particularly where the contrast between manmade objects and natural backgrounds are the subjects of interest. The book takes a systems approach to the physical processes involved with formation, collection, and analysis of polarimetric remote sensing data in the visible through longwave infrared. Beginning with a brief review of the polarized nature of electromagnetic energy and radiometry, Dr. Schott then introduces ways to characterize a beam of polarized ene

  19. Lighting for remote viewing systems

    Energy Technology Data Exchange (ETDEWEB)

    Draper, J.V.

    1984-01-01

    Scenes viewed by television do not provide the same channels of information for judgement of distances as scenes viewed directly, since television eliminates or degrades several depth perception cues. However, it may be possible to improve depth perception of televised scenes by enhancing the information available through depth cues that are available from lighting. A literature survey and expert opinions were integrated to design a remote lighting arrangement which could enhance depth perception of operators performing remote handling operations. This paper describes the lighting arrangement and discusses some of its advantages and disadvantages. 10 references, 2 figures.

  20. Lighting for remote viewing systems

    Energy Technology Data Exchange (ETDEWEB)

    Draper, J.V.

    1984-01-01

    Scenes viewed by television do not provide the same channels of information for judgment of distances as scenes viewed directly, since television eliminates or degrades several depth perception cues. However, it may be possible to improve depth perception of televised scenes by enhancing the information available through depth cues that are available from lighting. A literature survey and expert opinions were integrated to design a remote lighting arrangement which could enhance depth perception of operators performing remote handling operations. This paper describes the lighting arrangement and discusses some of its advantages and disadvantages. 10 references, 2 figures.

  1. Remote Synchronization in Complex Networks

    CERN Document Server

    Gambuzza, Lucia Valentina; Fiasconaro, Alessandro; Fortuna, Luigi; Gómez-Gardeñes, Jesús; Frasca, Mattia

    2013-01-01

    We show the existence of a novel dynamical state called remote synchronization in general networks of coupled oscillators. This state is characterized by the synchronization of pairs of nodes that are not directly connected via a physical link or any sequence of synchronized nodes. This phenomenon cannot be observed in networks of phase oscillators as its underlying mechanism is the modulation of the amplitude of those intermediary nodes between the remotely synchronized units. Our findings thus show the ubiquity and robustness of these states and bridge the gap from their recent observation in simple toy graphs to complex networks.

  2. Emergency Medicine in Remote Regions.

    Science.gov (United States)

    Renouf, Tia; Pollard, Megan

    2016-09-09

    Rural and remote places like Sable Island (Nova Scotia) or François (Newfoundland) pose a challenge in delivering both health care and appropriate education that today's learners need to practice in a rural setting. This education can be difficult to deliver to students far from academic centers. This is especially true for learners and practitioners at offshore locations like ships, oil installations, or in the air when patients are transported via fixed wing aircraft or helicopter. The following editorial provides a snapshot of the setting and the challenges faced while working as a physician on a ship, in remote regions.

  3. Remote Testing of Timed Specifications

    DEFF Research Database (Denmark)

    David, Alexandre; Larsen, Kim Guldstrand; Mikucionis, Marius

    2013-01-01

    We present a study and a testing framework on black box remote testing of real-time systems using UPPAAL TIGA. One of the essential challenges of remote testing is the communication latency between the Tester and the System Under Test (IUT) that may lead to interleaving of inputs and outputs......-testability criterion for the requirement model where Delta describes the communication latency. The test case generation problem is then reduced into a controller synthesis problem. We use UPPAAL TIGA for this purpose to solve a timed game with partial observability between the tester and the communication media...

  4. Deterministic joint remote state preparation

    Energy Technology Data Exchange (ETDEWEB)

    An, Nguyen Ba, E-mail: nban@iop.vast.ac.vn [Center for Theoretical Physics, Institute of Physics, 10 Dao Tan, Ba Dinh, Hanoi (Viet Nam); Bich, Cao Thi [Center for Theoretical Physics, Institute of Physics, 10 Dao Tan, Ba Dinh, Hanoi (Viet Nam); Physics Department, University of Education No. 1, 136 Xuan Thuy, Cau Giay, Hanoi (Viet Nam); Don, Nung Van [Center for Theoretical Physics, Institute of Physics, 10 Dao Tan, Ba Dinh, Hanoi (Viet Nam); Physics Department, Hanoi National University, 334 Nguyen Trai, Thanh Xuan, Hanoi (Viet Nam)

    2011-09-26

    We put forward a new nontrivial three-step strategy to execute joint remote state preparation via Einstein-Podolsky-Rosen pairs deterministically. At variance with all existing protocols, in ours the receiver contributes actively in both preparation and reconstruction steps, although he knows nothing about the quantum state to be prepared. -- Highlights: → Deterministic joint remote state preparation via EPR pairs is proposed. → Both general single- and two-qubit states are studied. → Differently from all existing protocols, in ours the receiver participates actively. → This is for the first time such a strategy is adopted.

  5. A reservoir of drug-resistant pathogenic bacteria in asymptomatic hosts.

    Directory of Open Access Journals (Sweden)

    Gabriel G Perron

    Full Text Available The population genetics of pathogenic bacteria has been intensively studied in order to understand the spread of disease and the evolution of virulence and drug resistance. However, much less attention has been paid to bacterial carriage populations, which inhabit hosts without producing disease. Since new virulent strains that cause disease can be recruited from the carriage population of bacteria, our understanding of infectious disease is seriously incomplete without knowledge on the population structure of pathogenic bacteria living in an asymptomatic host. We report the first extensive survey of the abundance and diversity of a human pathogen in asymptomatic animal hosts. We have found that asymptomatic swine from livestock productions frequently carry populations of Salmonella enterica with a broad range of drug-resistant strains and genetic diversity greatly exceeding that previously described. This study shows how agricultural practice and human intervention may lead and influence the evolution of a hidden reservoir of pathogens, with important implications for human health.

  6. Method of inhibiting plant virus pathogen infections by crispr/cas9-mediated interference

    KAUST Repository

    Mahfouz, Magdy Mahmoud

    2016-11-24

    A genetically modified tobacco plant or tomato plant resistant to at least one pathogenic geminiviridae virus species is provided. The plant comprises a heterologous CRISPR/Cas9 system and at least one heterologous nucleotide sequence that is capable of hybridizing to a nucleotide sequence of the pathogenic virus and that directs inactivation of the pathogenic virus species or plurality of viral species by the CRISPR/Cas9 system. The heterologous nucleotide sequence can be complementary to, but not limited to an Intergenic Region (IR) of the Tomato Yellow Leaf Curl Virus (TYLCV), Further provided are methods of generating a genetically modified plant that is resistant to a virus pathogen by a heterologous CRISPR/Cas9 system and expression of a gRNA specifically targeting the virus.

  7. Genetic Engineering

    Science.gov (United States)

    Phillips, John

    1973-01-01

    Presents a review of genetic engineering, in which the genotypes of plants and animals (including human genotypes) may be manipulated for the benefit of the human species. Discusses associated problems and solutions and provides an extensive bibliography of literature relating to genetic engineering. (JR)

  8. Genetic Counseling

    Science.gov (United States)

    ... for certain types of genetic conditions (such as Down syndrome) in the baby if mother-to-be is 35 years of age or more, or is concerned at any age about her chances of having a child with a genetic condition To learn about the ...

  9. Physiologic and genetic characterization of Bacillus sphaericus native strains

    Directory of Open Access Journals (Sweden)

    Jenny Dussen Garzón

    2012-06-01

    Full Text Available Eighteen pathogenic native strains of Bacillus sphaericus that were pathogens to mosquito larvae were isolated from different Colombia regions. The objective of this study was to evaluate at physiological and molecular level pathogenic strains and to compare them with the reference 2362 one. Cellular growth, sporulation percentage, pathogenic activity against third instar larvae of Culex quinquejasciaius, the presence of toxigenic proteins, the size of native plasmids and the genetic polymorphism among pathogenic and non pathogenic isolations was evaluated. The evaluated strains of Bs presented a latency stage ranging from 2 to 3 h and one logarithmic phase of 7 h; the sporulation in BHI was lower than 1% to 40 h of incubation, in NYSM medium was obtained ten times more production of biomass and spores, 26% of the population showed sporulation percentage higher than 90%; the isolations were classified in three groups of pathogenicity with [Formula] and [Formula]. Punctual mutations on the genes which encoding for native toxins were detected and was found a exclusive protein of 30 kDa in pathogenic native strains. The isolations of Bs presented a plasmid of 118Kb that was not related to the toxicity; pathogenic strains are a homogenous group with a similarity between 90 to 100%, whereas non-pathogenic ones are genetically heterogeneous group and conform a cluster aside. The native strains have a great potential in biological control of mosquito larvae that transmitting diseases such as dengue, malaria, encephalitis and filariasis among others.

  10. Genetic Romanticism

    DEFF Research Database (Denmark)

    Tupasela, Aaro

    2016-01-01

    . This article compares and contrasts the work of two doctors in Finland, Elias Lönnrot and Reijo Norio, working over a century and a half apart, to examine the ways in which they have contributed to the formation of national identity and unity. The notion of genetic romanticism is introduced as a term...... to complement the notion of national romanticism that has been used to describe the ways in which nineteenth-century scholars sought to create and deploy common traditions for national-romantic purposes. Unlike national romanticism, however, strategies of genetic romanticism rely on the study of genetic...... inheritance as a way to unify populations within politically and geographically bounded areas. Thus, new genetics have contributed to the development of genetic romanticisms, whereby populations (human, plant, and animal) can be delineated and mobilized through scientific and medical practices to represent...

  11. Genomic diversity of bacteriophages infecting the fish pathogen Flavobacterium psychrophilum.

    Science.gov (United States)

    Castillo, Daniel; Middelboe, Mathias

    2016-12-01

    Bacteriophages infecting the fish pathogen Flavobacterium psychrophilum can potentially be used to prevent and control outbreaks of this bacterium in salmonid aquaculture. However, the application of bacteriophages in disease control requires detailed knowledge on their genetic composition. To explore the diversity of F. pyschrophilum bacteriophages, we have analyzed the complete genome sequences of 17 phages isolated from two distant geographic areas (Denmark and Chile), including the previously characterized temperate bacteriophage 6H. Phage genome size ranged from 39 302 to 89 010 bp with a G+C content of 27%-32%. None of the bacteriophages isolated in Denmark contained genes associated with lysogeny, whereas the Chilean isolates were all putative temperate phages and similar to bacteriophage 6H. Comparative genome analysis showed that phages grouped in three different genetic clusters based on genetic composition and gene content, indicating a limited genetic diversity of F. psychrophilum-specific bacteriophages. However, amino acid sequence dissimilarity (25%) was found in putative structural proteins, which could be related to the host specificity determinants. This study represents the first analysis of genomic diversity and composition among bacteriophages infecting the fish pathogen F. psychrophilum and discusses the implications for the application of phages in disease control. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Pathogen stress increases somatic recombination frequency in Arabidopsis.

    Science.gov (United States)

    Lucht, Jan M; Mauch-Mani, Brigitte; Steiner, Henry-York; Metraux, Jean-Pierre; Ryals, John; Hohn, Barbara

    2002-03-01

    Evolution is based on genetic variability and subsequent phenotypic selection. Mechanisms that modulate the rate of mutation according to environmental cues, and thus control the balance between genetic stability and flexibility, might provide a distinct evolutionary advantage. Stress-induced mutations stimulated by unfavorable environments, and possible mechanisms for their induction, have been described for several organisms, but research in this area has mainly focused on microorganisms. We have analyzed the influence of adverse environmental conditions on the genetic stability of the higher plant Arabidopsis thaliana. Here we show that a biotic stress factor-attack by the oomycete pathogen Peronospora parasitica-can stimulate somatic recombination in Arabidopsis. The same effect was observed when plant pathogen-defense mechanisms were activated by the chemicals 2,6-dichloroisonicotinic acid (INA) or benzothiadiazole (BTH), or by a mutation (cim3). Together with previous studies of recombination induced by abiotic factors, these findings suggest that increased somatic recombination is a general stress response in plants. The increased genetic flexibility might facilitate evolutionary adaptation of plant populations to stressful environments.

  13. Genomic Analysis of Pathogenicity Determinants in Mycobacterium kansasii Type I

    KAUST Repository

    Guan, Qingtian

    2016-05-01

    Mycobacteria, a genus within Actinobacteria Phylum, are well known for two pathogens that cause human diseases: leprosy and tuberculosis. Other than the obligate human mycobacteria, there is a group of bacteria that are present in the environment and occasionally cause diseases in immunocompromised persons: the non-tuberculosis mycobacteria (NTM). Mycobacterium kansasii, which was first discovered in the Kansas state, is the main etiologic agent responsible for lung infections caused by NTM and raises attention because of its co-infection with human immunodeficiency virus (HIV). Five subspecies of M. kansasii (Type I-V) were described and only M. kansasii Type I is pathogenic to humans. M. kansasii is a Gram-positive bacteria that has a unique cell wall and secretion system, which is essential for its pathogenicity. We undertook a comparative genomics and transcriptomic approach to identify components of M. kansasii Type I pathogenicity. Our previous study showed that espA (ESX-1 essential protein) operon, a major component of the secretion system, is exclusively present in M. kansasii Type I. The purpose of this study was to test the functional role of the espA operon in pathogenicity and identify other components that may also be involved in pathogenicity. This study provides a new molecular diagnostic method for M. kansasii Type I infection using PCR (Polymerase Chain Reaction) technique to target the espAoperon. With detailed manual curation of the comparative genomics datasets, we found several genes exclusively present in M. kansasii Type I including ppsA/ppsC and whiB6, that we believe are involved, or have an effect on ESX-mediated secretion system. We have also highlighted, in our study, the differences in genetic components coding for the cell membrane composition between the five subspecies of M. kansasii. These results shed light on genetic components that are responsible for pathogenicity determinants in Type I M. kansasii and may help to design better

  14. Genetic Manipulations in Dermatophytes.

    Science.gov (United States)

    Alshahni, Mohamed Mahdi; Yamada, Tsuyoshi

    2017-02-01

    Dermatophytes are a group of closely related fungi that nourish on keratinized materials for their survival. They infect stratum corneum, nails, and hair of human and animals, accounting the largest portion of fungi causing superficial mycoses. Huge populations are suffering from dermatophytoses, though the biology of these fungi is largely unknown yet. Reasons are partially attributed to the poor amenability of dermatophytes to genetic manipulation. However, advancements in this field over the last decade made it possible to conduct genetic studies to satisfying extents. These included genetic transformation methods, indispensable molecular tools, i.e., dominant selectable markers, inducible promoter, and marker recycling system, along with improving homologous recombination frequency and gene silencing. Furthermore, annotated genome sequences of several dermatophytic species have recently been available, ensuring an optimal recruitment of the molecular tools to expand our knowledge on these fungi. In conclusion, the establishment of basic molecular tools and the availability of genomic data will open a new era that might change our understanding on the biology and pathogenicity of this fungal group.

  15. Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

    Energy Technology Data Exchange (ETDEWEB)

    Manning, Viola A.; Pandelova, Iovanna; Dhillon, Braham; Wilhelm, Larry J.; Goodwin, Stephen B.; Berlin, Aaron M.; Figueroa, Melania; Freitag, Michael; Hane, James K.; Henrissat, Bernard; Holman, Wade H.; Kodira, Chinnappa D.; Martin, Joel; Oliver, Richard P.; Robbertse, Barbara; Schackwitz, Wendy; Schwartz, David C.; Spatafora, Joseph W.; Turgeon, B. Gillian; Yandava, Chandri; Young, Sarah; Zhou, Shiguo; Zeng, Qiandong; Grigoriev, Igor V.; Ma, Li-Jun; Ciuffetti, Lynda M.

    2012-08-16

    Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.

  16. Global Positioning Systems (GPS) Technology to Study Vector-Pathogen-Host Interactions

    Science.gov (United States)

    2016-12-01

    Award Number: W81XWH-11-2-0175 TITLE: Global Positioning Systems ( GPS ) Technology to Study Vector-Pathogen-Host Interactions PRINCIPAL...Positioning Systems ( GPS ) Technology to Study Vector-Pathogen-Host Interactions 5b. GRANT NUMBER W81XWH-11-2-0175 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S...sophisticated Global Positioning Systems ( GPS ) technology of isolated viruses and genetic characterization, spatial and temporal analysis are being

  17. Estimating the microbiological risks associated with inland flood events: Bridging theory and models of pathogen transport

    Science.gov (United States)

    Collender, Philip A.; Cooke, Olivia C.; Bryant, Lee D.; Kjeldsen, Thomas R.; Remais, Justin V.

    2017-01-01

    Flooding is known to facilitate infectious disease transmission, yet quantitative research on microbiological risks associated with floods has been limited. Pathogen fate and transport models provide a framework to examine interactions between landscape characteristics, hydrology, and waterborne disease risks, but have not been widely developed for flood conditions. We critically examine capabilities of current hydrological models to represent unusual flow paths, non-uniform flow depths, and unsteady flow velocities that accompany flooding. We investigate the theoretical linkages between hydrodynamic processes and spatio-temporally variable suspension and deposition of pathogens from soils and sediments; pathogen dispersion in flow; and concentrations of constituents influencing pathogen transport and persistence. Identifying gaps in knowledge and modeling practice, we propose a research agenda to strengthen microbial fate and transport modeling applied to inland floods: 1) development of models incorporating pathogen discharges from flooded sources (e.g., latrines), effects of transported constituents on pathogen persistence, and supply-limited pathogen transport; 2) studies assessing parameter identifiability and comparing model performance under varying degrees of process representation, in a range of settings; 3) development of remotely sensed datasets to support modeling of vulnerable, data-poor regions; and 4) collaboration between modelers and field-based researchers to expand the collection of useful data in situ. PMID:28757789

  18. Characterization of Pathogenicity, Virulence and Host-Pathogen Interractions

    Energy Technology Data Exchange (ETDEWEB)

    Krishnan, A; Folta, P

    2006-07-27

    The threats of bio-terrorism and newly emerging infectious diseases pose serious challenges to the national security infrastructure. Rapid detection and diagnosis of infectious disease in human populations, as well as characterizing pathogen biology, are critical for reducing the morbidity and mortality associated with such threats. One of the key challenges in managing an infectious disease outbreak, whether through natural causes or acts of overt terrorism, is detection early enough to initiate effective countermeasures. Much recent attention has been directed towards the utility of biomarkers or molecular signatures that result from the interaction of the pathogen with the host for improving our ability to diagnose and mitigate the impact of a developing infection during the time window when effective countermeasures can be instituted. Host responses may provide early signals in blood even from localized infections. Multiple innate and adaptive immune molecules, in combination with other biochemical markers, may provide disease-specific information and new targets for countermeasures. The presence of pathogen specific markers and an understanding of the molecular capabilities and adaptations of the pathogen when it interacts with its host may likewise assist in early detection and provide opportunities for targeting countermeasures. An important question that needs to be addressed is whether these molecular-based approaches will prove useful for early diagnosis, complement current methods of direct agent detection, and aid development and use of countermeasures. Lawrence Livermore National Laboratory (LLNL) will host a workshop to explore the utility of host- and pathogen-based molecular diagnostics, prioritize key research issues, and determine the critical steps needed to transition host-pathogen research to tools that can be applied towards a more effective national bio-defense strategy. The workshop will bring together leading researchers/scientists in the

  19. Variation in infectivity and aggressiveness in space and time in wild host-pathogen systems: causes and consequences.

    Science.gov (United States)

    Tack, A J M; Thrall, P H; Barrett, L G; Burdon, J J; Laine, A-L

    2012-10-01

    Variation in host resistance and in the ability of pathogens to infect and grow (i.e. pathogenicity) is important as it provides the raw material for antagonistic (co)evolution and therefore underlies risks of disease spread, disease evolution and host shifts. Moreover, the distribution of this variation in space and time may inform us about the mode of coevolutionary selection (arms race vs. fluctuating selection dynamics) and the relative roles of G × G interactions, gene flow, selection and genetic drift in shaping coevolutionary processes. Although variation in host resistance has recently been reviewed, little is known about overall patterns in the frequency and scale of variation in pathogenicity, particularly in natural systems. Using 48 studies from 30 distinct host-pathogen systems, this review demonstrates that variation in pathogenicity is ubiquitous across multiple spatial and temporal scales. Quantitative analysis of a subset of extensively studied plant-pathogen systems shows that the magnitude of within-population variation in pathogenicity is large relative to among-population variation and that the distribution of pathogenicity partly mirrors the distribution of host resistance. At least part of the variation in pathogenicity found at a given spatial scale is adaptive, as evidenced by studies that have examined local adaptation at scales ranging from single hosts through metapopulations to entire continents and - to a lesser extent - by comparisons of pathogenicity with neutral genetic variation. Together, these results support coevolutionary selection through fluctuating selection dynamics. We end by outlining several promising directions for future research.

  20. Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis

    Science.gov (United States)

    Desjardins, Christopher A.; Champion, Mia D.; Holder, Jason W.; Muszewska, Anna; Goldberg, Jonathan; Bailão, Alexandre M.; Brigido, Marcelo Macedo; Ferreira, Márcia Eliana da Silva; Garcia, Ana Maria; Grynberg, Marcin; Gujja, Sharvari; Heiman, David I.; Henn, Matthew R.; Kodira, Chinnappa D.; León-Narváez, Henry; Longo, Larissa V. G.; Ma, Li-Jun; Malavazi, Iran; Matsuo, Alisson L.; Morais, Flavia V.; Pereira, Maristela; Rodríguez-Brito, Sabrina; Sakthikumar, Sharadha; Salem-Izacc, Silvia M.; Sykes, Sean M.; Teixeira, Marcus Melo; Vallejo, Milene C.; Walter, Maria Emília Machado Telles; Yandava, Chandri; Young, Sarah; Zeng, Qiandong; Zucker, Jeremy; Felipe, Maria Sueli; Goldman, Gustavo H.; Haas, Brian J.; McEwen, Juan G.; Nino-Vega, Gustavo; Puccia, Rosana; San-Blas, Gioconda; Soares, Celia Maria de Almeida; Birren, Bruce W.; Cuomo, Christina A.

    2011-01-01

    Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, is coupled with a thermally regulated transition from a soil-dwelling filamentous form to a yeast-like pathogenic form. To better understand the genetic basis of growth and pathogenicity in Paracoccidioides, we sequenced the genomes of two strains of Paracoccidioides brasiliensis (Pb03 and Pb18) and one strain of Paracoccidioides lutzii (Pb01). These genomes range in size from 29.1 Mb to 32.9 Mb and encode 7,610 to 8,130 genes. To enable genetic studies, we mapped 94% of the P. brasiliensis Pb18 assembly onto five chromosomes. We characterized gene family content across Onygenales and related fungi, and within Paracoccidioides we found expansions of the fungal-specific kinase family FunK1. Additionally, the Onygenales have lost many genes involved in carbohydrate metabolism and fewer genes involved in protein metabolism, resulting in a higher ratio of proteases to carbohydrate active enzymes in the Onygenales than their relatives. To determine if gene content correlated with growth on different substrates, we screened the non-pathogenic onygenale Uncinocarpus reesii, which has orthologs for 91% of Paracoccidioides metabolic genes, for growth on 190 carbon sources. U. reesii showed growth on a limited range of carbohydrates, primarily basic plant sugars and cell wall components; this suggests that Onygenales, including dimorphic fungi, can degrade cellulosic plant material in the soil. In addition, U. reesii grew on gelatin and a wide range of dipeptides and amino acids, indicating a preference for proteinaceous growth substrates over carbohydrates, which may enable these fungi to also degrade animal biomass. These capabilities for degrading plant and animal substrates suggest a duality in lifestyle that could enable pathogenic species of