Evaluation of a highly discriminating multiplex multi-locus variable-number of tandem-repeats (MLVA) analysis for Vibrio cholerae.

Science.gov (United States)

Olsen, Jaran S; Aarskaug, Tone; Skogan, Gunnar; Fykse, Else Marie; Ellingsen, Anette Bauer; Blatny, Janet M

2009-09-01

Vibrio cholerae is the etiological agent of cholera and may be used in bioterror actions due to the easiness of its dissemination, and the public fear for acquiring the cholera disease. A simple and highly discriminating method for connecting clinical and environmental isolates of V. cholerae is needed in microbial forensics. Twelve different loci containing variable numbers of tandem-repeats (VNTRs) were evaluated in which six loci were polymorphic. Two multiplex reactions containing PCR primers targeting these six VNTRs resulted in successful DNA amplification of 142 various environmental and clinical V. cholerae isolates. The genetic distribution inside the V. cholerae strain collection was used to evaluate the discriminating power (Simpsons Diversity Index=0.99) of this new MLVA analysis, showing that the assay have a potential to differentiate between various strains, but also to identify those isolates which are collected from a common V. cholerae outbreak. This work has established a rapid and highly discriminating MLVA assay useful for track back analyses and/or forensic studies of V. cholerae infections.

Multi-locus variable-number tandem repeat analysis of Chinese Brucella strains isolated from 1953 to 2013.

Science.gov (United States)

Tian, Guo-Zhong; Cui, Bu-Yun; Piao, Dong-Ri; Zhao, Hong-Yan; Li, Lan-Yu; Liu, Xi; Xiao, Pei; Zhao, Zhong-Zhi; Xu, Li-Qing; Jiang, Hai; Li, Zhen-Jun

2017-05-02

Brucellosis was a common human and livestock disease caused by Brucella strains, the category B priority pathogens by the US Center for Disease Control (CDC). Identified as a priority disease in human and livestock populations, the increasing incidence in recent years in China needs urgent control measures for this disease but the molecular background important for monitoring the epidemiology of Brucella strains at the national level is still lacking. A total of 600 Brucella isolates collected during 60 years (from 1953 to 2013) in China were genotyped by multiple locus variable-number tandem repeat analysis (MLVA) and the variation degree of MLVA11 loci was calculated by the Hunter Gaston Diversity Index (HGDI) values. The charts and map were processed by Excel 2013, and cluster analysis and epidemiological distribution was performed using BioNumerics (version 5.1). The 600 representative Brucella isolates fell into 104 genotypes with 58 singleton genotypes by the MLVA11 assay, including B. melitensis biovars 2 and 3 (five main genotypes), B. abortus biovars 1 and 3 (two main genotypes), B. suis biovars 1 and 3 (three main genotypes), and B. canis (two main genotypes) respectively. While most B. suis biovar 1 and biovar 3 were respectively found in northern provinces and southern provinces, B. melitensis and B. abortus strains were dominant in China. Canine Brucellosis was only found in animals without any human cases reported. Eight Brucellosis epidemic peaks emerged during the 60 years between 1953 and 2013: 1955 - 1959, 1962 - 1969, 1971 - 1975, 1977 - 1983, 1985 - 1989, 1992 - 1997, 2000 - 2008 and 2010 - 2013 in China. Brucellosis has its unique molecular epidemiological patterns with specific spatial and temporal distribution according to MLVA. IDOP-D-16-00101.

Single-Locus versus Multilocus Patterns of Local Adaptation to Climate in Eastern White Pine (Pinus strobus, Pinaceae.

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Om P Rajora

Full Text Available Natural plant populations are often adapted to their local climate and environmental conditions, and populations of forest trees offer some of the best examples of this pattern. However, little empirical work has focused on the relative contribution of single-locus versus multilocus effects to the genetic architecture of local adaptation in plants/forest trees. Here, we employ eastern white pine (Pinus strobus to test the hypothesis that it is the inter-genic effects that primarily drive climate-induced local adaptation. The genetic structure of 29 range-wide natural populations of eastern white pine was determined in relation to local climatic factors using both a reference set of SSR markers, and SNPs located in candidate genes putatively involved in adaptive response to climate. Comparisons were made between marker sets using standard single-locus outlier analysis, single-locus and multilocus environment association analyses and a novel implementation of Population Graphs. Magnitudes of population structure were similar between the two marker sets. Outlier loci consistent with diversifying selection were rare for both SNPs and SSRs. However, genetic distances based on the multilocus among population covariances (cGD were significantly more correlated to climate, even after correcting for spatial effects, for SNPs as compared to SSRs. Coalescent simulations confirmed that the differences in mutation rates between SSRs and SNPs did not affect the topologies of the Population Graphs, and hence values of cGD and their correlations with associated climate variables. We conclude that the multilocus covariances among populations primarily reflect adaptation to local climate and environment in eastern white pine. This result highlights the complexity of the genetic architecture of adaptive traits, as well as the need to consider multilocus effects in studies of local adaptation.

Identification of Coxiella burnetii genotypes in Croatia using multi-locus VNTR analysis.

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Račić, Ivana; Spičić, Silvio; Galov, Ana; Duvnjak, Sanja; Zdelar-Tuk, Maja; Vujnović, Anja; Habrun, Boris; Cvetnić, Zeljko

2014-10-10

Although Q fever affects humans and animals in Croatia, we are unaware of genotyping studies of Croatian strains of the causative pathogen Coxiella burnetii, which would greatly assist monitoring and control efforts. Here 3261 human and animal samples were screened for C. burnetii DNA by conventional PCR, and 335 (10.3%) were positive. Of these positive samples, 82 were genotyped at 17 loci using the relatively new method of multi-locus variable number tandem repeat analysis (MLVA). We identified 13 C. burnetii genotypes not previously reported anywhere in the world. Two of these 13 genotypes are typical of the continental part of Croatia and share more similarity with genotypes outside Croatia than with genotypes within the country. The remaining 11 novel genotypes are typical of the coastal part of Croatia and show more similarity to one another than to genotypes outside the country. Our findings shed new light on the phylogeny of C. burnetii strains and may help establish MLVA as a standard technique for Coxiella genotyping. Copyright © 2014 Elsevier B.V. All rights reserved.

Visualization of pairwise and multilocus linkage disequilibrium structure using latent forests.

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Raphaël Mourad

Full Text Available Linkage disequilibrium study represents a major issue in statistical genetics as it plays a fundamental role in gene mapping and helps us to learn more about human history. The linkage disequilibrium complex structure makes its exploratory data analysis essential yet challenging. Visualization methods, such as the triangular heat map implemented in Haploview, provide simple and useful tools to help understand complex genetic patterns, but remain insufficient to fully describe them. Probabilistic graphical models have been widely recognized as a powerful formalism allowing a concise and accurate modeling of dependences between variables. In this paper, we propose a method for short-range, long-range and chromosome-wide linkage disequilibrium visualization using forests of hierarchical latent class models. Thanks to its hierarchical nature, our method is shown to provide a compact view of both pairwise and multilocus linkage disequilibrium spatial structures for the geneticist. Besides, a multilocus linkage disequilibrium measure has been designed to evaluate linkage disequilibrium in hierarchy clusters. To learn the proposed model, a new scalable algorithm is presented. It constrains the dependence scope, relying on physical positions, and is able to deal with more than one hundred thousand single nucleotide polymorphisms. The proposed algorithm is fast and does not require phase genotypic data.

Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme.

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Yanjun Li

Full Text Available Variable number of tandem repeats (VNTRs that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci.Capillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA in 956 Y. pestis strains. The general features and genetic diversities of 88 VNTR loci in Y. pestis were analyzed with BioNumerics, and a "14+12" loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established.Appropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized "14+12" loci are highly discriminative in genotyping and source-tracing Y. pestis for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of Y. pestis.

Molecular characterization of Giardia psittaci by multilocus sequence analysis.

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Abe, Niichiro; Makino, Ikuko; Kojima, Atsushi

2012-12-01

Multilocus sequence analyses targeting small subunit ribosomal DNA (SSU rDNA), elongation factor 1 alpha (ef1α), glutamate dehydrogenase (gdh), and beta giardin (β-giardin) were performed on Giardia psittaci isolates from three Budgerigars (Melopsittacus undulates) and four Barred parakeets (Bolborhynchus lineola) kept in individual households or imported from overseas. Nucleotide differences and phylogenetic analyses at four loci indicate the distinction of G. psittaci from the other known Giardia species: Giardia muris, Giardia microti, Giardia ardeae, and Giardia duodenalis assemblages. Furthermore, G. psittaci was related more closely to G. duodenalis than to the other known Giardia species, except for G. microti. Conflicting signals regarded as "double peaks" were found at the same nucleotide positions of the ef1α in all isolates. However, the sequences of the other three loci, including gdh and β-giardin, which are known to be highly variable, from all isolates were also mutually identical at every locus. They showed no double peaks. These results suggest that double peaks found in the ef1α sequences are caused not by mixed infection with genetically different G. psittaci isolates but by allelic sequence heterogeneity (ASH), which is observed in diplomonad lineages including G. duodenalis. No sequence difference was found in any G. psittaci isolates at the gdh and β-giardin, suggesting that G. psittaci is indeed not more diverse genetically than other Giardia species. This report is the first to provide evidence related to the genetic characteristics of G. psittaci obtained using multilocus sequence analysis. Copyright © 2012 Elsevier B.V. All rights reserved.

Multilocus inference of species trees and DNA barcoding.

Science.gov (United States)

Mallo, Diego; Posada, David

2016-09-05

The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree-gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

Evaluation of a Multilocus Sequence Typing (MLST) scheme for Leishmania (Viannia) braziliensis and Leishmania (Viannia) panamensis in Colombia.

Science.gov (United States)

Herrera, Giovanny; Hernández, Carolina; Ayala, Martha S; Flórez, Carolina; Teherán, Aníbal A; Ramírez, Juan David

2017-05-12

Leishmaniases are parasitic vector-borne diseases affecting more than 12 million people in 98 countries. In Colombia, leishmaniasis is widespread and the most common clinical manifestation is cutaneous, mainly caused by L. panamensis and L. braziliensis. Currently, the genetic diversity of these species in Colombia is unknown. To address this, we applied molecular techniques for their characterization, using multilocus sequence typing (MLST) to explore the genetic variability and phylodynamics of the disease. Seven previously described genetic markers were selected highlighting the implementation of a mitochondrial marker. Markers were applied to 163 samples from isolates obtained between 1980 and 2001. The identification of the samples showed an excellent correlation with typing tests previously applied (MLEE, monoclonal antibodies). Isolates of L. braziliensis showed greater genetic diversity than L. panamensis, and a greater number of diploid sequence types (DSTs). In addition, the geographical distribution of DSTs for each species were obtained through georeferencing maps. To our knowldge, this study represents the first description of the genetic variability of L. panamensis in Colombia and South America, and is the first to propose a scheme of MLST for epidemiological surveillance of leishmaniasis in the country.

Low Divergence of Clonorchis sinensis in China Based on Multilocus Analysis.

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Jiufeng Sun

Full Text Available Clonorchis sinensis, an ancient parasite that infects a number of piscivorous mammals, attracts significant public health interest due to zoonotic exposure risks in Asia. The available studies are insufficient to reflect the prevalence, geographic distribution, and intraspecific genetic diversity of C. sinensis in endemic areas. Here, a multilocus analysis based on eight genes (ITS1, act, tub, ef-1a, cox1, cox3, nad4 and nad5 [4.986 kb] was employed to explore the intra-species genetic construction of C. sinensis in China. Two hundred and fifty-six C. sinensis isolates were obtained from environmental reservoirs from 17 provinces of China. A total of 254 recognized Multilocus Types (MSTs showed high diversity among these isolates using multilocus analysis. The comparison analysis of nuclear and mitochondrial phylogeny supports separate clusters in a nuclear dendrogram. Genetic differentiation analysis of three clusters (A, B, and C showed low divergence within populations. Most isolates from clusters B and C are geographically limited to central China, while cluster A is extraordinarily genetically diverse. Further genetic analyses between different geographic distributions, water bodies and hosts support the low population divergence. The latter haplotype analyses were consistent with the phylogenetic and genetic differentiation results. A recombination network based on concatenated sequences showed a concentrated linkage recombination population in cox1, cox3, nad4 and nad5, with spatial structuring in ITS1. Coupled with the history record and archaeological evidence of C. sinensis infection in mummified desiccated feces, these data point to an ancient origin of C. sinensis in China. In conclusion, we present a likely phylogenetic structure of the C. sinensis population in mainland China, highlighting its possible tendency for biogeographic expansion. Meanwhile, ITS1 was found to be an effective marker for tracking C. sinensis infection

Low Divergence of Clonorchis sinensis in China Based on Multilocus Analysis

Science.gov (United States)

Sun, Jiufeng; Huang, Yan; Huang, Huaiqiu; Liang, Pei; Wang, Xiaoyun; Mao, Qiang; Men, Jingtao; Chen, Wenjun; Deng, Chuanhuan; Zhou, Chenhui; Lv, Xiaoli; Zhou, Juanjuan; Zhang, Fan; Li, Ran; Tian, Yanli; Lei, Huali; Liang, Chi; Hu, Xuchu; Xu, Jin; Li, Xuerong; XinbingYu

2013-01-01

Clonorchis sinensis, an ancient parasite that infects a number of piscivorous mammals, attracts significant public health interest due to zoonotic exposure risks in Asia. The available studies are insufficient to reflect the prevalence, geographic distribution, and intraspecific genetic diversity of C. sinensis in endemic areas. Here, a multilocus analysis based on eight genes (ITS1, act, tub, ef-1a, cox1, cox3, nad4 and nad5 [4.986 kb]) was employed to explore the intra-species genetic construction of C. sinensis in China. Two hundred and fifty-six C. sinensis isolates were obtained from environmental reservoirs from 17 provinces of China. A total of 254 recognized Multilocus Types (MSTs) showed high diversity among these isolates using multilocus analysis. The comparison analysis of nuclear and mitochondrial phylogeny supports separate clusters in a nuclear dendrogram. Genetic differentiation analysis of three clusters (A, B, and C) showed low divergence within populations. Most isolates from clusters B and C are geographically limited to central China, while cluster A is extraordinarily genetically diverse. Further genetic analyses between different geographic distributions, water bodies and hosts support the low population divergence. The latter haplotype analyses were consistent with the phylogenetic and genetic differentiation results. A recombination network based on concatenated sequences showed a concentrated linkage recombination population in cox1, cox3, nad4 and nad5, with spatial structuring in ITS1. Coupled with the history record and archaeological evidence of C. sinensis infection in mummified desiccated feces, these data point to an ancient origin of C. sinensis in China. In conclusion, we present a likely phylogenetic structure of the C. sinensis population in mainland China, highlighting its possible tendency for biogeographic expansion. Meanwhile, ITS1 was found to be an effective marker for tracking C. sinensis infection worldwide. Thus, the

Integration of least angle regression with empirical Bayes for multi-locus genome-wide association studies

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Multi-locus genome-wide association studies has become the state-of-the-art procedure to identify quantitative trait loci (QTL) associated with traits simultaneously. However, implementation of multi-locus model is still difficult. In this study, we integrated least angle regression with empirical B...

Genotyping analysis of Helicobacter pylori using multiple-locus variable-number tandem-repeats analysis in five regions of China and Japan

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Zhang Jinyong

2011-09-01

Full Text Available Abstract Background H. pylori (Helicobacter pylori is the major causative agent of chronic active gastritis. The population of H. pylori shows a high genomic variability among isolates. And the polymorphism of repeat-units of genomics had participated the important process of evolution. Its long term colonization of the stomach caused different clinical outcomes, which may relate to the high degree of genetic variation of H. pylori. A variety of molecular typing tools have been developed to access genetic relatedness in H. pylori isolates. However, there is still no standard genotyping system of this bacterium. The MLVA (Multi-locus of variable number of tandem repeat analysis method is useful for performing phylogenetic analysis and is widely used in bacteria genotyping; however, there's little application in H. pylori analysis. This article is the first application of the MLVA method to investigate H. pylori from different districts and ethnic groups of China. Results MLVA of 12 VNTR loci with high discrimination power based on 30 candidates were performed on a collection of 202 strains of H. pylori which originated from five regions of China and Japan. Phylogenetic tree was constructed using MLVA profiles. 12 VNTR loci presented with high various polymorphisms, and the results demonstrated very close relationships between genotypes and ethnic groups. Conclusions This study used MLVA methodology providing a new perspective on the ethnic groups and distribution characteristics of H. pylori.

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

DEFF Research Database (Denmark)

Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

2012-01-01

Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS...

A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis)

NARCIS (Netherlands)

Udayanga, D.; Liu, X.; Crous, P.W.; McKenzie, E.H.C.; Chukeatirote, E.; Hyde, K.D.

2012-01-01

The genus Diaporthe (Phomopsis) includes important plant pathogenic fungi with wide host ranges and geographic distributions. In the present study, phylogenetic species recognition in Diaporthe is re-evaluated using a multi-locus phylogeny based on a combined data matrix of rDNA ITS, and partial

Multilocus resolution of Mugilidae phylogeny (Teleostei: Mugiliformes): Implications for the family's taxonomy.

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Xia, Rong; Durand, Jean-Dominique; Fu, Cuizhang

2016-03-01

The interrelationships among mugilids (Mugiliformes: Mugilidae) remain highly debated. Using a mitochondrial gene-based phylogeny as criterion, a revised classification with 25 genera in the Mugilidae has recently been proposed. However, phylogenetic relationships of major mitochondrial lineages remain unresolved and to gain a general acceptance the classification requires confirmation based on multilocus evidence and diagnostic morphological characters. Here, we construct a species-tree using twelve nuclear and three mitochondrial loci and infer the evolution of 71 morphological characters. Our multilocus phylogeny does not agree with previous morphology-based hypotheses for the relationships within Mugilidae, confirms the revised classification with 25 genera and further resolves their phylogenetic relationships. Using the well-resolved multilocus phylogeny as the criterion, we reclassify Mugilidae genera into three new subfamilies (Myxinae, Rhinomugilinae, and Cheloninae) and one new, recombined, subfamily (Mugilinae). The Rhinomugilinae subfamily is further divided into four tribes. The revised classification of Mugilidae is supported by morpho-anatomical synapomorphies or a combination of characters. These characters are used to erect a key to the subfamilies and genera. Copyright © 2015 Elsevier Inc. All rights reserved.

A novel HURRAH protocol reveals high numbers of monomorphic MHC class II loci and two asymmetric multi-locus haplotypes in the Père David's deer.

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Qiu-Hong Wan

Full Text Available The Père David's deer is a highly inbred, but recovered, species, making it interesting to consider their adaptive molecular evolution from an immunological perspective. Prior to this study, genomic sequencing was the only method for isolating all functional MHC genes within a certain species. Here, we report a novel protocol for isolating MHC class II loci from a species, and its use to investigate the adaptive evolution of this endangered deer at the level of multi-locus haplotypes. This protocol was designated "HURRAH" based on its various steps and used to estimate the total number of MHC class II loci. We confirmed the validity of this novel protocol in the giant panda and then used it to examine the Père David's deer. Our results revealed that the Père David's deer possesses nine MHC class II loci and therefore has more functional MHC class II loci than the eight genome-sequenced mammals for which full MHC data are currently available. This could potentially account at least in part for the strong survival ability of this species in the face of severe bottlenecking. The results from the HURRAH protocol also revealed that: (1 All of the identified MHC class II loci were monomorphic at their antigen-binding regions, although DRA was dimorphic at its cytoplasmic tail; and (2 these genes constituted two asymmetric functional MHC class II multi-locus haplotypes: DRA1*01 ∼ DRB1 ∼ DRB3 ∼ DQA1 ∼ DQB2 (H1 and DRA1*02 ∼ DRB2 ∼ DRB4 ∼ DQA2 ∼ DQB1 (H2. The latter finding indicates that the current members of the deer species have lost the powerful ancestral MHC class II haplotypes of nine or more loci, and have instead fixed two relatively weak haplotypes containing five genes. As a result, the Père David's deer are currently at risk for increased susceptibility to infectious pathogens.

Evolution and polymorphism in the multilocus Levene model with no or weak epistasis.

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Bürger, Reinhard

2010-09-01

Evolution and the maintenance of polymorphism under the multilocus Levene model with soft selection are studied. The number of loci and alleles, the number of demes, the linkage map, and the degree of dominance are arbitrary, but epistasis is absent or weak. We prove that, without epistasis and under mild, generic conditions, every trajectory converges to a stationary point in linkage equilibrium. Consequently, the equilibrium and stability structure can be determined by investigating the much simpler gene-frequency dynamics on the linkage-equilibrium manifold. For a haploid species an analogous result is shown. For weak epistasis, global convergence to quasi-linkage equilibrium is established. As an application, the maintenance of multilocus polymorphism is explored if the degree of dominance is intermediate at every locus and epistasis is absent or weak. If there are at least two demes, then arbitrarily many multiallelic loci can be maintained polymorphic at a globally asymptotically stable equilibrium. Because this holds for an open set of parameters, such equilibria are structurally stable. If the degree of dominance is not only intermediate but also deme independent, and loci are diallelic, an open set of parameters yielding an internal equilibrium exists only if the number of loci is strictly less than the number of demes. Otherwise, a fully polymorphic equilibrium exists only nongenerically, and if it exists, it consists of a manifold of equilibria. Its dimension is determined. In the absence of genotype-by-environment interaction, however, a manifold of equilibria occurs for an open set of parameters. In this case, the equilibrium structure is not robust to small deviations from no genotype-by-environment interaction. In a quantitative-genetic setting, the assumptions of no epistasis and intermediate dominance are equivalent to assuming that in every deme directional selection acts on a trait that is determined additively, i.e., by nonepistatic loci with

Major clades of Agaricales: a multilocus phylogenetic overview.

Science.gov (United States)

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

2006-01-01

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

The number of subjects per variable required in linear regression analyses

NARCIS (Netherlands)

P.C. Austin (Peter); E.W. Steyerberg (Ewout)

2015-01-01

textabstractObjectives To determine the number of independent variables that can be included in a linear regression model. Study Design and Setting We used a series of Monte Carlo simulations to examine the impact of the number of subjects per variable (SPV) on the accuracy of estimated regression

Modeling Turbulent Combustion for Variable Prandtl and Schmidt Number

Science.gov (United States)

Hassan, H. A.

2004-01-01

This report consists of two abstracts submitted for possible presentation at the AIAA Aerospace Science Meeting to be held in January 2005. Since the submittal of these abstracts we are continuing refinement of the model coefficients derived for the case of a variable Turbulent Prandtl number. The test cases being investigated are a Mach 9.2 flow over a degree ramp and a Mach 8.2 3-D calculation of crossing shocks. We have developed an axisymmetric code for treating axisymmetric flows. In addition the variable Schmidt number formulation was incorporated in the code and we are in the process of determining the model constants.

Multilocus Sequence Analysis for Typing Leptospira interrogans and Leptospira kirschneri▿ †

OpenAIRE

Leon, Albertine; Pronost, Stéphane; Fortier, Guillaume; Andre-Fontaine, Geneviève; Leclercq, Roland

2009-01-01

Fifty-three strains belonging to the pathogenic species Leptospira interrogans and Leptospira kirschneri were analyzed by multilocus sequence analysis. The species formed two distinct branches. In the L. interrogans branch, the phylogenetic tree clustered the strains into three subgroups. Genogroups and serogroups were superimposed but not strictly.

DEVELOPMENT OF A MULTIPLE-LOCUS VARIABLE NUMBER OF TANDEM REPEAT ANALYSIS (MLVA FOR HELICOBACTER PYLORI AND ITS APPLICATION TO HELICOBACTER PYLORI ISOLATES FROM ROSTOV REGION,RUSSIA

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Sorokin VM

2012-09-01

Full Text Available Stomach infection with Helicobacter pylori (H. pylori is the second most common infectious disease of humans. The severe pathological consequences of this infection include gastric and duodenal ulcer disease, the development of gastric mucosal atrophy, gastric carcinoma, and, more rarely, malignant tumors of the lymphoma. H. pylori infections cause very high morbidity and mortality and are of particular concern in developing countries, where H. pylori prevalences as high as 90% have been reported. The population of H. pylori shows a high genomic variability among isolates. And the polymorphism of repeat-units of genomics had participated the important process of evolution. A variety of molecular typing tools have been developed to access genetic relatedness in H. pylori isolates. However, there is still no standard genotyping system of this bacterium. The MLVA (Multi-Locus of Variable number of tandem repeat Analysis method is useful for performing phylogenetic analysis and is widely used in bacteria genotyping; however, there's little application in H. pylori analysis. This article is the first application of the MLVA method to investigate H. pylori isolates in Russia. MLVA of 4 VNTR loci with high discrimination power based on 10 candidates were performed on a collection of 22 strains of H. pylori which originated from Rostov region of Russia. This method provides a starting point on which improvements to the method and comparisons to other techniques can be made.

Multilocus Sequence Analysis for Typing Leptospira interrogans and Leptospira kirschneri▿ †

Science.gov (United States)

Leon, Albertine; Pronost, Stéphane; Fortier, Guillaume; Andre-Fontaine, Geneviève; Leclercq, Roland

2010-01-01

Fifty-three strains belonging to the pathogenic species Leptospira interrogans and Leptospira kirschneri were analyzed by multilocus sequence analysis. The species formed two distinct branches. In the L. interrogans branch, the phylogenetic tree clustered the strains into three subgroups. Genogroups and serogroups were superimposed but not strictly. PMID:19955271

Modeling and designing of variable-period and variable-pole-number undulator

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I. Davidyuk

2016-02-01

Full Text Available The concept of permanent-magnet variable-period undulator (VPU was proposed several years ago and has found few implementations so far. The VPUs have some advantages as compared with conventional undulators, e.g., a wider range of radiation wavelength tuning and the option to increase the number of poles for shorter periods. Both these advantages will be realized in the VPU under development now at Budker INP. In this paper, we present the results of 2D and 3D magnetic field simulations and discuss some design features of this VPU.

Observer variability in estimating numbers: An experiment

Science.gov (United States)

Erwin, R.M.

1982-01-01

Census estimates of bird populations provide an essential framework for a host of research and management questions. However, with some exceptions, the reliability of numerical estimates and the factors influencing them have received insufficient attention. Independent of the problems associated with habitat type, weather conditions, cryptic coloration, ete., estimates may vary widely due only to intrinsic differences in observers? abilities to estimate numbers. Lessons learned in the field of perceptual psychology may be usefully applied to 'real world' problems in field ornithology. Based largely on dot discrimination tests in the laboratory, it was found that numerical abundance, density of objects, spatial configuration, color, background, and other variables influence individual accuracy in estimating numbers. The primary purpose of the present experiment was to assess the effects of observer, prior experience, and numerical range on accuracy in estimating numbers of waterfowl from black-and-white photographs. By using photographs of animals rather than black dots, I felt the results could be applied more meaningfully to field situations. Further, reinforcement was provided throughout some experiments to examine the influence of training on accuracy.

Role of updraft velocity in temporal variability of global cloud hydrometeor number

Science.gov (United States)

Sullivan, Sylvia C.; Lee, Dongmin; Oreopoulos, Lazaros; Nenes, Athanasios

2016-05-01

Understanding how dynamical and aerosol inputs affect the temporal variability of hydrometeor formation in climate models will help to explain sources of model diversity in cloud forcing, to provide robust comparisons with data, and, ultimately, to reduce the uncertainty in estimates of the aerosol indirect effect. This variability attribution can be done at various spatial and temporal resolutions with metrics derived from online adjoint sensitivities of droplet and crystal number to relevant inputs. Such metrics are defined and calculated from simulations using the NASA Goddard Earth Observing System Model, Version 5 (GEOS-5) and the National Center for Atmospheric Research Community Atmosphere Model Version 5.1 (CAM5.1). Input updraft velocity fluctuations can explain as much as 48% of temporal variability in output ice crystal number and 61% in droplet number in GEOS-5 and up to 89% of temporal variability in output ice crystal number in CAM5.1. In both models, this vertical velocity attribution depends strongly on altitude. Despite its importance for hydrometeor formation, simulated vertical velocity distributions are rarely evaluated against observations due to the sparsity of relevant data. Coordinated effort by the atmospheric community to develop more consistent, observationally based updraft treatments will help to close this knowledge gap.

Development and evaluation of a multi-locus sequence typing scheme for Mycoplasma synoviae.

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Dijkman, R; Feberwee, A; Landman, W J M

2016-08-01

Reproducible molecular Mycoplasma synoviae typing techniques with sufficient discriminatory power may help to expand knowledge on its epidemiology and contribute to the improvement of control and eradication programmes of this mycoplasma species. The present study describes the development and validation of a novel multi-locus sequence typing (MLST) scheme for M. synoviae. Thirteen M. synoviae isolates originating from different poultry categories, farms and lesions, were subjected to whole genome sequencing. Their sequences were compared to that of M. synoviae reference strain MS53. A high number of single nucleotide polymorphisms (SNPs) indicating considerable genetic diversity were identified. SNPs were present in over 40 putative target genes for MLST of which five target genes were selected (nanA, uvrA, lepA, ruvB and ugpA) for the MLST scheme. This scheme was evaluated analysing 209 M. synoviae samples from different countries, categories of poultry, farms and lesions. Eleven clonal clusters and 76 different sequence types (STs) were obtained. Clustering occurred following geographical origin, supporting the hypothesis of regional population evolution. M. synoviae samples obtained from epidemiologically linked outbreaks often harboured the same ST. In contrast, multiple M. synoviae lineages were found in samples originating from swollen joints or oviducts from hens that produce eggs with eggshell apex abnormalities indicating that further research is needed to identify the genetic factors of M. synoviae that may explain its variations in tissue tropism and disease inducing potential. Furthermore, MLST proved to have a higher discriminatory power compared to variable lipoprotein and haemagglutinin A typing, which generated 50 different genotypes on the same database.

Multi-locus estimates of population structure and migration in a fence lizard hybrid zone.

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Adam D Leaché

Full Text Available A hybrid zone between two species of lizards in the genus Sceloporus (S. cowlesi and S. tristichus on the Mogollon Rim in Arizona provides a unique opportunity to study the processes of lineage divergence and merging. This hybrid zone involves complex interactions between 2 morphologically and ecologically divergent subspecies, 3 chromosomal groups, and 4 mitochondrial DNA (mtDNA clades. The spatial patterns of divergence between morphology, chromosomes and mtDNA are discordant, and determining which of these character types (if any reflects the underlying population-level lineages that are of interest has remained impeded by character conflict. The focus of this study is to estimate the number of populations interacting in the hybrid zone using multi-locus nuclear data, and to then estimate the migration rates and divergence time between the inferred populations. Multi-locus estimates of population structure and gene flow were obtained from 12 anonymous nuclear loci sequenced for 93 specimens of Sceloporus. Population structure estimates support two populations, and this result is robust to changes to the prior probability distribution used in the Bayesian analysis and the use of spatially-explicit or non-spatial models. A coalescent analysis of population divergence suggests that gene flow is high between the two populations, and that the timing of divergence is restricted to the Pleistocene. The hybrid zone is more accurately described as involving two populations belonging to S. tristichus, and the presence of S. cowlesi mtDNA haplotypes in the hybrid zone is an anomaly resulting from mitochondrial introgression.

Rickettsia asembonensis Characterization by Multilocus Sequence Typing of Complete Genes, Peru.

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Loyola, Steev; Flores-Mendoza, Carmen; Torre, Armando; Kocher, Claudine; Melendrez, Melanie; Luce-Fedrow, Alison; Maina, Alice N; Richards, Allen L; Leguia, Mariana

2018-05-01

While studying rickettsial infections in Peru, we detected Rickettsia asembonensis in fleas from domestic animals. We characterized 5 complete genomic regions (17kDa, gltA, ompA, ompB, and sca4) and conducted multilocus sequence typing and phylogenetic analyses. The molecular isolate from Peru is distinct from the original R. asembonensis strain from Kenya.

Raw and Central Moments of Binomial Random Variables via Stirling Numbers

Science.gov (United States)

Griffiths, Martin

2013-01-01

We consider here the problem of calculating the moments of binomial random variables. It is shown how formulae for both the raw and the central moments of such random variables may be obtained in a recursive manner utilizing Stirling numbers of the first kind. Suggestions are also provided as to how students might be encouraged to explore this…

Genetic relationships between clinical and non-clinical strains of Yersinia enterocolitica biovar 1A as revealed by multilocus enzyme electrophoresis and multilocus restriction typing

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Virdi Jugsharan S

2010-05-01

Full Text Available Abstract Background Genetic relationships among 81 strains of Y. enterocolitica biovar 1A isolated from clinical and non-clinical sources were discerned by multilocus enzyme electrophoresis (MLEE and multilocus restriction typing (MLRT using six loci each. Such studies may reveal associations between the genotypes of the strains and their sources of isolation. Results All loci were polymorphic and generated 62 electrophoretic types (ETs and 12 restriction types (RTs. The mean genetic diversity (H of the strains by MLEE and MLRT was 0.566 and 0.441 respectively. MLEE (DI = 0.98 was more discriminatory and clustered Y. enterocolitica biovar 1A strains into four groups, while MLRT (DI = 0.77 identified two distinct groups. BURST (Based Upon Related Sequence Types analysis of the MLRT data suggested aquatic serotype O:6,30-6,31 isolates to be the ancestral strains from which, clinical O:6,30-6,31 strains might have originated by host adaptation and genetic change. Conclusion MLEE revealed greater genetic diversity among strains of Y. enterocolitica biovar 1A and clustered strains in four groups, while MLRT grouped the strains into two groups. BURST analysis of MLRT data nevertheless provided newer insights into the probable evolution of clinical strains from aquatic strains.

A single multilocus sequence typing (MLST) scheme for seven pathogenic Leptospira species

NARCIS (Netherlands)

Boonsilp, Siriphan; Thaipadungpanit, Janjira; Amornchai, Premjit; Wuthiekanun, Vanaporn; Bailey, Mark S.; Holden, Matthew T. G.; Zhang, Cuicai; Jiang, Xiugao; Koizumi, Nobuo; Taylor, Kyle; Galloway, Renee; Hoffmaster, Alex R.; Craig, Scott; Smythe, Lee D.; Hartskeerl, Rudy A.; Day, Nicholas P.; Chantratita, Narisara; Feil, Edward J.; Aanensen, David M.; Spratt, Brian G.; Peacock, Sharon J.

2013-01-01

The available Leptospira multilocus sequence typing (MLST) scheme supported by a MLST website is limited to L. interrogans and L. kirschneri. Our aim was to broaden the utility of this scheme to incorporate a total of seven pathogenic species. We modified the existing scheme by replacing one of the

Integrative taxonomy by molecular species delimitation: multi-locus data corroborate a new species of Balkan Drusinae micro-endemics.

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Vitecek, Simon; Kučinić, Mladen; Previšić, Ana; Živić, Ivana; Stojanović, Katarina; Keresztes, Lujza; Bálint, Miklós; Hoppeler, Felicitas; Waringer, Johann; Graf, Wolfram; Pauls, Steffen U

2017-06-06

Taxonomy offers precise species identification and delimitation and thus provides basic information for biological research, e.g. through assessment of species richness. The importance of molecular taxonomy, i.e., the identification and delimitation of taxa based on molecular markers, has increased in the past decade. Recently developed exploratory tools now allow estimating species-level diversity in multi-locus molecular datasets. Here we use molecular species delimitation tools that either quantify differences in intra- and interspecific variability of loci, or divergence times within and between species, or perform coalescent species tree inference to estimate species-level entities in molecular genetic datasets. We benchmark results from these methods against 14 morphologically readily differentiable species of a well-defined subgroup of the diverse Drusinae subfamily (Trichoptera, Limnephilidae). Using a 3798 bp (6 loci) molecular data set we aim to corroborate a geographically isolated new species by integrating comparative morphological studies and molecular taxonomy. Our results indicate that only multi-locus species delimitation provides taxonomically relevant information. The data further corroborate the new species Drusus zivici sp. nov. We provide differential diagnostic characters and describe the male, female and larva of this new species and discuss diversity patterns of Drusinae in the Balkans. We further discuss potential and significance of molecular species delimitation. Finally we argue that enhancing collaborative integrative taxonomy will accelerate assessment of global diversity and completion of reference libraries for applied fields, e.g., conservation and biomonitoring.

Multilocus Sequence Typing for Interpreting Blood Isolates of Staphylococcus epidermidis

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Prannda Sharma

2014-01-01

Full Text Available Staphylococcus epidermidis is an important cause of nosocomial infection and bacteremia. It is also a common contaminant of blood cultures and, as a result, there is frequently uncertainty as to its diagnostic significance when recovered in the clinical laboratory. One molecular strategy that might be of value in clarifying the interpretation of S. epidermidis identified in blood culture is multilocus sequence typing. Here, we examined 100 isolates of this species (50 blood isolates representing true bacteremia, 25 likely contaminant isolates, and 25 skin isolates and the ability of sequence typing to differentiate them. Three machine learning algorithms (classification regression tree, support vector machine, and nearest neighbor were employed. Genetic variability was substantial between isolates, with 44 sequence types found in 100 isolates. Sequence types 2 and 5 were most commonly identified. However, among the classification algorithms we employed, none were effective, with CART and SVM both yielding only 73% diagnostic accuracy and nearest neighbor analysis yielding only 53% accuracy. Our data mirror previous studies examining the presence or absence of pathogenic genes in that the overlap between truly significant organisms and contaminants appears to prevent the use of MLST in the clarification of blood cultures recovering S. epidermidis.

The role of updraft velocity in temporal variability of cloud hydrometeor number

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Sullivan, Sylvia; Nenes, Athanasios; Lee, Dong Min; Oreopoulos, Lazaros

2016-04-01

Significant effort has been dedicated to incorporating direct aerosol-cloud links, through parameterization of liquid droplet activation and ice crystal nucleation, within climate models. This significant accomplishment has generated the need for understanding which parameters affecting hydrometer formation drives its variability in coupled climate simulations, as it provides the basis for optimal parameter estimation as well as robust comparison with data, and other models. Sensitivity analysis alone does not address this issue, given that the importance of each parameter for hydrometer formation depends on its variance and sensitivity. To address the above issue, we develop and use a series of attribution metrics defined with adjoint sensitivities to attribute the temporal variability in droplet and crystal number to important aerosol and dynamical parameters. This attribution analysis is done both for the NASA Global Modeling and Assimilation Office Goddard Earth Observing System Model, Version 5 and the National Center for Atmospheric Research Community Atmosphere Model Version 5.1. Within the GEOS simulation, up to 48% of temporal variability in output ice crystal number and 61% in droplet number can be attributed to input updraft velocity fluctuations, while for the CAM simulation, they explain as much as 89% of the ice crystal number variability. This above results suggest that vertical velocity in both model frameworks is seen to be a very important (or dominant) driver of hydrometer variability. Yet, observations of vertical velocity are seldomly available (or used) to evaluate the vertical velocities in simulations; this strikingly contrasts the amount and quality of data available for aerosol-related parameters. Consequentially, there is a strong need for retrievals or measurements of vertical velocity for addressing this important knowledge gap that requires a significant investment and effort by the atmospheric community. The attribution metrics as a

Genetic Relationships among Reptilian and Mammalian Campylobacter fetus Strains Determined by Multilocus Sequence Typing

NARCIS (Netherlands)

Dingle, K.E.; Blaser, M.J.; Tu, Z.C.; Pruckler, J.; Fitzgerald, C.; Bergen, van M.A.P.; Lawson, A.J.; Owen, R.J.; Wagenaar, J.A.

2010-01-01

Reptile Campylobacter fetus isolates and closely related strains causing human disease were characterized by multilocus sequence typing. They shared similar to 90% nucleotide sequence identity with classical mammalian C. fetus, and there was evidence of recombination among members of these two

Application of multi-locus analytical methods to identify interacting loci in case-control studies.

NARCIS (Netherlands)

Vermeulen, S.; Heijer, M. den; Sham, P.; Knight, J.

2007-01-01

To identify interacting loci in genetic epidemiological studies the application of multi-locus methods of analysis is warranted. Several more advanced classification methods have been developed in the past years, including multiple logistic regression, sum statistics, logic regression, and the

The number of subjects per variable required in linear regression analyses.

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Austin, Peter C; Steyerberg, Ewout W

2015-06-01

To determine the number of independent variables that can be included in a linear regression model. We used a series of Monte Carlo simulations to examine the impact of the number of subjects per variable (SPV) on the accuracy of estimated regression coefficients and standard errors, on the empirical coverage of estimated confidence intervals, and on the accuracy of the estimated R(2) of the fitted model. A minimum of approximately two SPV tended to result in estimation of regression coefficients with relative bias of less than 10%. Furthermore, with this minimum number of SPV, the standard errors of the regression coefficients were accurately estimated and estimated confidence intervals had approximately the advertised coverage rates. A much higher number of SPV were necessary to minimize bias in estimating the model R(2), although adjusted R(2) estimates behaved well. The bias in estimating the model R(2) statistic was inversely proportional to the magnitude of the proportion of variation explained by the population regression model. Linear regression models require only two SPV for adequate estimation of regression coefficients, standard errors, and confidence intervals. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Core Genome Multilocus Sequence Typing Scheme for High-resolution Typing of Enterococcus faecium

DEFF Research Database (Denmark)

de Been, Mark; Pinholt, Mette; Top, Janetta

2015-01-01

Enterococcus faecium, a common inhabitant of the human gut, has emerged as an important multidrug-resistant nosocomial pathogen in the last two decades. Since the start of the 21(st) century, multi-locus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium. However...

Mycoplasma hyopneumoniae genetic variability within a swine operation.

Science.gov (United States)

Pantoja, Lucina Galina; Pettit, Kalie; Dos Santos, Lucas F; Tubbs, Rick; Pieters, Maria

2016-03-01

The objective of our study was to characterize the Mycoplasma hyopneumoniae genetic diversity within a swine operation comingling weaned pigs. Bronchial swabs and tracheal aspirates were collected from 3 nursery-to-finish farms. During the finishing production stages, samples were obtained from mortalities and from live coughing pigs in rooms where mortality was not observed. A total of 105 samples were examined by a M. hyopneumoniae real-time polymerase chain reaction and subjected to genetic typing using a multilocus variable number tandem repeat analysis (MLVA) assay. The MLVA was used to identify genetic variants based on the number of repeats in 2 variable number tandem repeats loci, namely P97 and P146, thought to mediate adherence of M. hyopneumoniae to swine cilia. Four distinguishable M. hyopneumoniae variants were identified: MVLA variants 9-15, 11-21, 9-21, and 7-15. Variant 9-15 was the most prevalent, observed in 79% of rooms, and detected on all 3 farms. Variant 11-21 was present in 37% of the rooms on 2 of the 3 farms. Only one 9-21 variant was identified in 1 farm, and all samples of variant 7-15 were recovered from another farm. Based on the low prevalence and limited geographic distribution of the last 2 variants, it is hypothesized that they might be the result of in-situ recombination. All variants detected in this investigation appeared to belong to 3 clusters. Overall, a limited number of variants and clusters were identified in a system that comingles pigs from different sources, suggesting limited M. hyopneumoniae genetic variation within commercial swine production environments. © 2016 The Author(s).

Development of new multilocus variable number of tandem repeat analysis (MLVA) for Listeria innocua and its application in a food processing plant.

Science.gov (United States)

Takahashi, Hajime; Ohshima, Chihiro; Nakagawa, Miku; Thanatsang, Krittaporn; Phraephaisarn, Chirapiphat; Chaturongkasumrit, Yuphakhun; Keeratipibul, Suwimon; Kuda, Takashi; Kimura, Bon

2014-01-01

Listeria innocua is an important hygiene indicator bacterium in food industries because it behaves similar to Listeria monocytogenes, which is pathogenic to humans. PFGE is often used to characterize bacterial strains and to track contamination source. However, because PFGE is an expensive, complicated, time-consuming protocol, and poses difficulty in data sharing, development of a new typing method is necessary. MLVA is a technique that identifies bacterial strains on the basis of the number of tandem repeats present in the genome varies depending on the strains. MLVA has gained attention due to its high reproducibility and ease of data sharing. In this study, we developed a MLVA protocol to assess L. innocua and evaluated it by tracking the contamination source of L. innocua in an actual food manufacturing factory by typing the bacterial strains isolated from the factory. Three VNTR regions of the L. innocua genome were chosen for use in the MLVA. The number of repeat units in each VNTR region was calculated based on the results of PCR product analysis using capillary electrophoresis (CE). The calculated number of repetitions was compared with the results of the gene sequence analysis to demonstrate the accuracy of the CE repeat number analysis. The developed technique was evaluated using 60 L. innocua strains isolated from a food factory. These 60 strains were classified into 11 patterns using MLVA. Many of the strains were classified into ST-6, revealing that this MLVA strain type can contaminate each manufacturing process in the factory. The MLVA protocol developed in this study for L. innocua allowed rapid and easy analysis through the use of CE. This technique was found to be very useful in hygiene control in factories because it allowed us to track contamination sources and provided information regarding whether the bacteria were present in the factories.

Development of new multilocus variable number of tandem repeat analysis (MLVA for Listeria innocua and its application in a food processing plant.

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Hajime Takahashi

Full Text Available Listeria innocua is an important hygiene indicator bacterium in food industries because it behaves similar to Listeria monocytogenes, which is pathogenic to humans. PFGE is often used to characterize bacterial strains and to track contamination source. However, because PFGE is an expensive, complicated, time-consuming protocol, and poses difficulty in data sharing, development of a new typing method is necessary. MLVA is a technique that identifies bacterial strains on the basis of the number of tandem repeats present in the genome varies depending on the strains. MLVA has gained attention due to its high reproducibility and ease of data sharing. In this study, we developed a MLVA protocol to assess L. innocua and evaluated it by tracking the contamination source of L. innocua in an actual food manufacturing factory by typing the bacterial strains isolated from the factory. Three VNTR regions of the L. innocua genome were chosen for use in the MLVA. The number of repeat units in each VNTR region was calculated based on the results of PCR product analysis using capillary electrophoresis (CE. The calculated number of repetitions was compared with the results of the gene sequence analysis to demonstrate the accuracy of the CE repeat number analysis. The developed technique was evaluated using 60 L. innocua strains isolated from a food factory. These 60 strains were classified into 11 patterns using MLVA. Many of the strains were classified into ST-6, revealing that this MLVA strain type can contaminate each manufacturing process in the factory. The MLVA protocol developed in this study for L. innocua allowed rapid and easy analysis through the use of CE. This technique was found to be very useful in hygiene control in factories because it allowed us to track contamination sources and provided information regarding whether the bacteria were present in the factories.

Multilocus sequence typing confirms synonymy but highlights differences between Candida albicans and Candida stellatoidea.

NARCIS (Netherlands)

Jacobsen, M.D.; Boekhout, T.; Odds, F.C.

2008-01-01

We used multi-locus sequence typing (MLST) to investigate 35 yeast isolates representing the two genome-sequenced strains plus the type strain of Candida albicans, four isolates originally identified as Candida stellatoidea type I and 28 representing type strains of other species now regarded as

Understanding Cirrus Ice Crystal Number Variability for Different Heterogeneous Ice Nucleation Spectra

Science.gov (United States)

Sullivan, Sylvia C.; Betancourt, Ricardo Morales; Barahona, Donifan; Nenes, Athanasios

2016-01-01

Along with minimizing parameter uncertainty, understanding the cause of temporal and spatial variability of the nucleated ice crystal number, Ni, is key to improving the representation of cirrus clouds in climate models. To this end, sensitivities of Ni to input variables like aerosol number and diameter provide valuable information about nucleation regime and efficiency for a given model formulation. Here we use the adjoint model of the adjoint of a cirrus formation parameterization (Barahona and Nenes, 2009b) to understand Ni variability for various ice-nucleating particle (INP) spectra. Inputs are generated with the Community Atmosphere Model version 5, and simulations are done with a theoretically derived spectrum, an empirical lab-based spectrum and two field-based empirical spectra that differ in the nucleation threshold for black carbon particles and in the active site density for dust. The magnitude and sign of Ni sensitivity to insoluble aerosol number can be directly linked to nucleation regime and efficiency of various INP. The lab-based spectrum calculates much higher INP efficiencies than field-based ones, which reveals a disparity in aerosol surface properties. Ni sensitivity to temperature tends to be low, due to the compensating effects of temperature on INP spectrum parameters; this low temperature sensitivity regime has been experimentally reported before but never deconstructed as done here.

Multilocus genotyping of Giardia duodenalis in captive non-human primates in Sichuan and Guizhou provinces, Southwestern China.

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Zhijun Zhong

Full Text Available Giardia duodenalis is a common human and animal pathogen. It has been increasingly reported in wild and captive non-human primates (NHPs in recent years. However, multilocus genotyping information for G. duodenalis infecting NHPs in southwestern China is limited. In the present study, the prevalence and multilocus genotypes (MLGs of G. duodenalis in captive NHPs in southwestern China were determined. We examined 207 fecal samples from NHPs in Sichuan and Guizhou provinces, and 16 specimens were positive for G. duodenalis. The overall infection rate was 7.7%, and only assemblage B was identified. G. duodenalis was detect positive in northern white-cheeked gibbon (14/36, 38.9%, crab-eating macaque (1/60, 1.7% and rhesus macaques (1/101, 0.9%. Multilocus sequence typing based on beta-giardin (bg, triose phosphate isomerase (tpi and glutamate dehydrogenase (gdh revealed nine different assemblage B MLGs (five known genotypes and four novel genotypes. Based on a phylogenetic analysis, one potentially zoonotic genotype of MLG SW7 was identified in a northern white-cheeked gibbon. A high degree of genetic diversity within assemblage B was observed in captive northern white-cheeked gibbons in Southwestern China, including a potentially zoonotic genotype, MLG SW7. To the best of our knowledge, this is the first report using a MLGs approach to identify G. duodenalis in captive NHPs in Southwestern China.

Equivalence of the spinning superparticle descriptions with Grassmann variables or with c-number spinors

International Nuclear Information System (INIS)

Barut, A.O.; Pavsic, M.

1988-05-01

A remarkable equivalence is established between the theories of spinning particles or superparticles using anticommuting Grassmann variables on the one hand and commuting c-number spinors on the other. We consider both real and complex Grassmann variables and map the equations of motion and the supersymmetry transformation from one theory to another. The more intuitive c-number theory allows us to generalize the notion of Zitterbewegung to strings and membranes. (A hidden supersymmetry exists in the classical model of the Dirac electron.) (author). 12 refs

Empirical Statistical Power for Testing Multilocus Genotypic Effects under Unbalanced Designs Using a Gibbs Sampler

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Chaeyoung Lee

2012-11-01

Full Text Available Epistasis that may explain a large portion of the phenotypic variation for complex economic traits of animals has been ignored in many genetic association studies. A Baysian method was introduced to draw inferences about multilocus genotypic effects based on their marginal posterior distributions by a Gibbs sampler. A simulation study was conducted to provide statistical powers under various unbalanced designs by using this method. Data were simulated by combined designs of number of loci, within genotype variance, and sample size in unbalanced designs with or without null combined genotype cells. Mean empirical statistical power was estimated for testing posterior mean estimate of combined genotype effect. A practical example for obtaining empirical statistical power estimates with a given sample size was provided under unbalanced designs. The empirical statistical powers would be useful for determining an optimal design when interactive associations of multiple loci with complex phenotypes were examined.

Exploring multilocus associations of inflammation genes and colorectal cancer risk using hapConstructor

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Abo Ryan

2010-12-01

Full Text Available Abstract Background In candidate-gene association studies of single nucleotide polymorphisms (SNPs, multilocus analyses are frequently of high dimensionality when considering haplotypes or haplotype pairs (diplotypes and differing modes of expression. Often, while candidate genes are selected based on their biological involvement in a given pathway, little is known about the functionality of SNPs to guide association studies. Investigators face the challenge of exploring multiple SNP models to elucidate which variants, independently or in combination, might be associated with a disease of interest. A data mining module, hapConstructor (freely-available in Genie software performs systematic construction and association testing of multilocus genotype data in a Monte Carlo framework. Our objective was to assess its utility to guide statistical analyses of haplotypes within a candidate region (or combined genotypes across candidate genes beyond that offered by a standard logistic regression approach. Methods We applied the hapConstructor method to a multilocus investigation of candidate genes involved in pro-inflammatory cytokine IL6 production, IKBKB, IL6, and NFKB1 (16 SNPs total hypothesized to operate together to alter colorectal cancer risk. Data come from two U.S. multicenter studies, one of colon cancer (1,556 cases and 1,956 matched controls and one of rectal cancer (754 cases and 959 matched controls. Results HapConstrcutor enabled us to identify important associations that were further analyzed in logistic regression models to simultaneously adjust for confounders. The most significant finding (nominal P = 0.0004; false discovery rate q = 0.037 was a combined genotype association across IKBKB SNP rs5029748 (1 or 2 variant alleles, IL6 rs1800797 (1 or 2 variant alleles, and NFKB1 rs4648110 (2 variant alleles which conferred an ~80% decreased risk of colon cancer. Conclusions Strengths of hapConstructor were: systematic identification of

All ternary permutation constraint satisfaction problems parameterized above average have kernels with quadratic numbers of variables

DEFF Research Database (Denmark)

Gutin, Gregory; Van Iersel, Leo; Mnich, Matthias

2010-01-01

A ternary Permutation-CSP is specified by a subset Π of the symmetric group S3. An instance of such a problem consists of a set of variables V and a multiset of constraints, which are ordered triples of distinct variables of V. The objective is to find a linear ordering α of V that maximizes...... the number of triples whose rearrangement (under α) follows a permutation in Π. We prove that all ternary Permutation-CSPs parameterized above average have kernels with quadratic numbers of variables....

Clostridium botulinum group I strain genotyping by 15-locus multilocus variable-number tandem-repeat analysis

NARCIS (Netherlands)

Fillo, S.; Giordani, F.; Anniballi, F.; Gorgé, O.; Ramisse, V.; Vergnaud, G.; Riehm, J.M.; Scholz, H.C.; Splettstoesser, W.D.; Kieboom, J.; Olsen, J.-S.; Fenicia, L.; Lista, F.

2011-01-01

Clostridium botulinum is a taxonomic designation that encompasses a broad variety of spore-forming, Gram-positive bacteria producing the botulinum neurotoxin (BoNT). C. botulinum is the etiologic agent of botulism, a rare but severe neuroparalytic disease. Fine-resolution genetic characterization of

A critical re-evaluation of multilocus sequence typing (MLST) efforts in Wolbachia.

Science.gov (United States)

Bleidorn, Christoph; Gerth, Michael

2018-01-01

Wolbachia (Alphaproteobacteria, Rickettsiales) is the most common, and arguably one of the most important inherited symbionts. Molecular differentiation of Wolbachia strains is routinely performed with a set of five multilocus sequence typing (MLST) markers. However, since its inception in 2006, the performance of MLST in Wolbachia strain typing has not been assessed objectively. Here, we evaluate the properties of Wolbachia MLST markers and compare it to 252 other single copy loci present in the genome of most Wolbachia strains. Specifically, we investigated how well MLST performs at strain differentiation, at reflecting genetic diversity of strains, and as phylogenetic marker. We find that MLST loci are outperformed by other loci at all tasks they are currently employed for, and thus that they do not reflect the properties of a Wolbachia strain very well. We argue that whole genome typing approaches should be used for Wolbachia typing in the future. Alternatively, if few loci approaches are necessary, we provide a characterisation of 252 single copy loci for a number a criteria, which may assist in designing specific typing systems or phylogenetic studies. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

[Standard algorithm of molecular typing of Yersinia pestis strains].

Science.gov (United States)

Eroshenko, G A; Odinokov, G N; Kukleva, L M; Pavlova, A I; Krasnov, Ia M; Shavina, N Iu; Guseva, N P; Vinogradova, N A; Kutyrev, V V

2012-01-01

Development of the standard algorithm of molecular typing of Yersinia pestis that ensures establishing of subspecies, biovar and focus membership of the studied isolate. Determination of the characteristic strain genotypes of plague infectious agent of main and nonmain subspecies from various natural foci of plague of the Russian Federation and the near abroad. Genotyping of 192 natural Y. pestis strains of main and nonmain subspecies was performed by using PCR methods, multilocus sequencing and multilocus analysis of variable tandem repeat number. A standard algorithm of molecular typing of plague infectious agent including several stages of Yersinia pestis differentiation by membership: in main and nonmain subspecies, various biovars of the main subspecies, specific subspecies; natural foci and geographic territories was developed. The algorithm is based on 3 typing methods--PCR, multilocus sequence typing and multilocus analysis of variable tandem repeat number using standard DNA targets--life support genes (terC, ilvN, inv, glpD, napA, rhaS and araC) and 7 loci of variable tandem repeats (ms01, ms04, ms06, ms07, ms46, ms62, ms70). The effectiveness of the developed algorithm is shown on the large number of natural Y. pestis strains. Characteristic sequence types of Y. pestis strains of various subspecies and biovars as well as MLVA7 genotypes of strains from natural foci of plague of the Russian Federation and the near abroad were established. The application of the developed algorithm will increase the effectiveness of epidemiologic monitoring of plague infectious agent, and analysis of epidemics and outbreaks of plague with establishing the source of origin of the strain and routes of introduction of the infection.

Strong Laws of Large Numbers for Arrays of Rowwise NA and LNQD Random Variables

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Jiangfeng Wang

2011-01-01

Full Text Available Some strong laws of large numbers and strong convergence properties for arrays of rowwise negatively associated and linearly negative quadrant dependent random variables are obtained. The results obtained not only generalize the result of Hu and Taylor to negatively associated and linearly negative quadrant dependent random variables, but also improve it.

Multilocus sequence typing of IncN plasmids

DEFF Research Database (Denmark)

García-Fernández, Aurora; Villa, Laura; Moodley, Arshnee

2011-01-01

that spread and persistence of this particular IncN-carrying blaVIM-1 lineage in Greece. CONCLUSIONS: This study proposes the use of pMLST as a suitable and rapid method for identification of IncN epidemic plasmid lineages. The recent spread of blaCTX-M-1 among humans and animals seems to be associated......OBJECTIVES: Incompatibility group N (IncN) plasmids have been associated with the dissemination of antimicrobial resistance and are a major vehicle for the spread of blaVIM-1 in humans and blaCTX-M-1 in animals. A plasmid multilocus sequence typing (pMLST) scheme was developed for rapid...... in different countries from both animals and humans belonged to ST1, suggesting dissemination of an epidemic plasmid through the food chain. Fifteen of 17 plasmids carrying blaVIM-1 from Klebsiella pneumoniae and Escherichia coli, isolated during a 5year period in Greece were assigned to ST10, suggesting...

Differentiation of Xylella fastidiosa strains via multilocus sequence analysis of environmentally mediated genes (MLSA-E).

Science.gov (United States)

Parker, Jennifer K; Havird, Justin C; De La Fuente, Leonardo

2012-03-01

Isolates of the plant pathogen Xylella fastidiosa are genetically very similar, but studies on their biological traits have indicated differences in virulence and infection symptomatology. Taxonomic analyses have identified several subspecies, and phylogenetic analyses of housekeeping genes have shown broad host-based genetic differences; however, results are still inconclusive for genetic differentiation of isolates within subspecies. This study employs multilocus sequence analysis of environmentally mediated genes (MLSA-E; genes influenced by environmental factors) to investigate X. fastidiosa relationships and differentiate isolates with low genetic variability. Potential environmentally mediated genes, including host colonization and survival genes related to infection establishment, were identified a priori. The ratio of the rate of nonsynonymous substitutions to the rate of synonymous substitutions (dN/dS) was calculated to select genes that may be under increased positive selection compared to previously studied housekeeping genes. Nine genes were sequenced from 54 X. fastidiosa isolates infecting different host plants across the United States. Results of maximum likelihood (ML) and Bayesian phylogenetic (BP) analyses are in agreement with known X. fastidiosa subspecies clades but show novel within-subspecies differentiation, including geographic differentiation, and provide additional information regarding host-based isolate variation and specificity. dN/dS ratios of environmentally mediated genes, though gene dN/dS ratios and correlate with increased sequence variability. MLSA-E can more precisely resolve relationships between closely related bacterial strains with low genetic variability, such as X. fastidiosa isolates. Discovering the genetic relationships between X. fastidiosa isolates will provide new insights into the epidemiology of populations of X. fastidiosa, allowing improved disease management in economically important crops.

Population genetic and evolution analysis of controversial genus Edwardsiella by multilocus sequence typing.

Science.gov (United States)

Buján, Noemí; Balboa, Sabela; L Romalde, Jesús; E Toranzo, Alicia; Magariños, Beatriz

2018-05-08

At present, the genus Edwardsiella compiles five species: E. tarda, E. hoshinae, E. ictaluri, E. piscicida and E. anguillarum. Some species of this genus such us E. ictaluri and E. piscicida are important pathogens of numerous fish species. With the description of the two latter species, the phylogeny of Edwardsiella became more complicated. With the aim to clarify the relationships among all species in the genus, a multilocus sequence typing (MLST) approach was developed and applied to characterize 56 isolates and 6 reference strains belonging to the five Edwardsiella species. Moreover, several analyses based on the MLST scheme were performed to investigate the evolution within the genus, as well as the influence of recombination and mutation in the speciation. Edwardsiella isolates presented a high genetic variability reflected in the fourteen sequence types (ST) represented by a single isolates out of eighteen total ST. Mutation events were considerably more frequent than recombination, although both approximately equal influenced the genetic diversification. However, the speciation among species occurred mostly by recombination. Edwardsiella genus displays a non-clonal population structure with some degree of geographical isolation followed by a population expansion of E. piscicida. A database from this study was created and hosted on pubmlst.org (http://pubmlst.org/edwardsiella/). Copyright © 2018 Elsevier Inc. All rights reserved.

Genotypic characterization of Salmonella by multilocus sequence typing, pulsed-field gel electrophoresis and amplified fragment length polymorphism

DEFF Research Database (Denmark)

Torpdahl, Mia; Skov, Marianne N.; Sandvang, Dorthe

2005-01-01

subspecies enterica isolates. A total of 25 serotypes were investigated that had been isolated from humans or veterinary sources in Denmark between 1995 and 2001. All isolates were genotyped by multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and amplified fragment length...

Systematic characterization of Bacillus Genetic Stock Center Bacillus thuringiensis strains using Multi-Locus Sequence Typing.

Science.gov (United States)

Wang, Kui; Shu, Changlong; Soberón, Mario; Bravo, Alejandra; Zhang, Jie

2018-04-30

The goal of this work was to perform a systematic characterization of Bacillus thuringiensis (Bt) strains from the Bacillus Genetic Stock Center (BGSC) collection using Multi-Locus Sequence Typing (MLST). Different genetic markers of 158 Bacillus thuringiensis (Bt) strains from 73 different serovars stored in the BGSC, that represented 92% of the different Bt serovars of the BGSC were analyzed, the 8% that were not analyzed were not available. In addition, we analyzed 72 Bt strains from 18 serovars available at the pubMLST bcereus database, and Bt strains G03, HBF18 and Bt185, with no H serovars provided by our laboratory. We performed a systematic MLST analysis using seven housekeeping genes (glpF, gmK, ilvD, pta, pur, pycA and tpi) and analyzed correlation of the results of this analysis with strain serovars. The 233 Bt strains analyzed were assigned to 119 STs from which 19 STs were new. Genetic relationships were established by phylogenetic analysis and showed that STs could be grouped in two major Clusters containing 21 sub-groups. We found that a significant number of STs (101 in total) correlated with specific serovars, such as ST13 that corresponded to nine Bt isolates from B. thuringiensis serovar kenyae. However, other serovars showed high genetic variability and correlated with multiple STs; for example, B. thuringiensis serovar morrisoni correlated with 11 different STs. In addition, we found that 16 different STs correlated with multiple serovars (2-4 different serovars); for example, ST12 correlated with B. thuringiensis serovar alesti, dakota, palmanyolensis and sotto/dendrolimus. These data indicated that only partial correspondence between MLST and serotyping can be established. Copyright © 2018 Elsevier Inc. All rights reserved.

MCMC multilocus lod scores: application of a new approach.

Science.gov (United States)

George, Andrew W; Wijsman, Ellen M; Thompson, Elizabeth A

2005-01-01

On extended pedigrees with extensive missing data, the calculation of multilocus likelihoods for linkage analysis is often beyond the computational bounds of exact methods. Growing interest therefore surrounds the implementation of Monte Carlo estimation methods. In this paper, we demonstrate the speed and accuracy of a new Markov chain Monte Carlo method for the estimation of linkage likelihoods through an analysis of real data from a study of early-onset Alzheimer's disease. For those data sets where comparison with exact analysis is possible, we achieved up to a 100-fold increase in speed. Our approach is implemented in the program lm_bayes within the framework of the freely available MORGAN 2.6 package for Monte Carlo genetic analysis (http://www.stat.washington.edu/thompson/Genepi/MORGAN/Morgan.shtml).

Multilocus sequence typing of commensal and enteropathogenic Escherichia coli from domestic and wild lagomorphs in Italy

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Giorgia Dotto

2015-12-01

Full Text Available The aim of the study was to determine the multilocus sequence types of Escherichia coli from diseased farm rabbits and apparently healthy wild lagomorphs, and the genetic relatedness among them. Fifty-five enteropathogenic E. coli from reared rabbits and 32 from wild rabbits and hares were characterised by multilocus sequence typing (MLST according to the Michigan State University EcMLST scheme. Isolates were differentiated into 37 sequence types (STs, which were grouped into 8 clonal complexes (CCs. The most common ST was ST140 (CC31, followed by ST238 and ST119 (CC17. MLST analysis revealed 22 novel STs. Phylogenetic analyses showed a heterogeneous distribution of STs into 3 clusters of genetically related strains. The genetic relationship among STs of different origin and the detection of new, as well as previously described STs as human pathogens, indicate a widespread distribution and adaptability of particular lineages to different hosts. These findings highlight the need for further research to improve the knowledge about E. coli populations colonising the gut of lagomorphs and their zoonotic potential.

Evolution in Australasian mangrove forests: multilocus phylogenetic analysis of the Gerygone warblers (Aves: Acanthizidae.

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Árpád S Nyári

Full Text Available The mangrove forests of Australasia have many endemic bird species but their evolution and radiation in those habitats has been little studied. One genus with several mangrove specialist species is Gerygone (Passeriformes: Acanthizidae. The phylogeny of the Acanthizidae is reasonably well understood but limited taxon sampling for Gerygone has constrained understanding of its evolution and historical biogeography in mangroves. Here we report on a phylogenetic analysis of Gerygone based on comprehensive taxon sampling and a multilocus dataset of thirteen loci spread across the avian genome (eleven nuclear and two mitochondrial loci. Since Gerygone includes three species restricted to Australia's coastal mangrove forests, we particularly sought to understand the biogeography of their evolution in that ecosystem. Analyses of individual loci, as well as of a concatenated dataset drawn from previous molecular studies indicates that the genus as currently defined is not monophyletic, and that the Grey Gerygone (G. cinerea from New Guinea should be transferred to the genus Acanthiza. The multilocus approach has permitted the nuanced view of the group's evolution into mangrove ecosystems having occurred on multiple occasions, in three non-overlapping time frames, most likely first by the G. magnirostris lineage, and subsequently followed by those of G. tenebrosa and G. levigaster.

Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations.

Science.gov (United States)

Yang, Qi; Franco, Christopher M M; Sorokin, Shirley J; Zhang, Wei

2017-02-02

For sponges (phylum Porifera), there is no reliable molecular protocol available for species identification. To address this gap, we developed a multilocus-based Sponge Identification Protocol (SIP) validated by a sample of 37 sponge species belonging to 10 orders from South Australia. The universal barcode COI mtDNA, 28S rRNA gene (D3-D5), and the nuclear ITS1-5.8S-ITS2 region were evaluated for their suitability and capacity for sponge identification. The highest Bit Score was applied to infer the identity. The reliability of SIP was validated by phylogenetic analysis. The 28S rRNA gene and COI mtDNA performed better than the ITS region in classifying sponges at various taxonomic levels. A major limitation is that the databases are not well populated and possess low diversity, making it difficult to conduct the molecular identification protocol. The identification is also impacted by the accuracy of the morphological classification of the sponges whose sequences have been submitted to the database. Re-examination of the morphological identification further demonstrated and improved the reliability of sponge identification by SIP. Integrated with morphological identification, the multilocus-based SIP offers an improved protocol for more reliable and effective sponge identification, by coupling the accuracy of different DNA markers.

A Variable Turbulent Schmidt Number Formulation for Scramjet Application

Science.gov (United States)

Xiao, X.; Edwards, J. R.; Hassan, H. A.; Cutler, A. D.

2004-01-01

In high speed engines, thorough turbulent mixing of fuel and air is required to obtain high performance and high efficiency. Thus, the ability to predict turbulent mixing is crucial in obtaining accurate numerical simulation of an engine and its performance. Current state of the art in CFD simulation is to assume both turbulent Prandtl number and Schmidt numbers to be constants. However, since the mixing of fuel and air is inversely proportional to the Schmidt number, a value of 0.45 for the Schmidt number will produce twice as much diffusion as that with a value of 0.9. Because of this, current CFD tools and models have not been able to provide the needed guidance required for the efficient design of a scramjet engine. The goal of this investigation is to develop the framework needed to calculate turbulent Prandtl and Schmidt numbers as part of the solution. This requires four additional equations: two for the temperature variance and its dissipation rate and two for the concentration variance and its dissipation rate. In the current investigation emphasis will be placed on studying mixing without reactions. For such flows, variable Prandtl number does not play a major role in determining the flow. This, however, will have to be addressed when combustion is present. The approach to be used is similar to that used to develop the k-zeta model. In this approach, relevant equations are derived from the exact Navier-Stokes equations and each individual correlation is modeled. This ensures that relevant physics is incorporated into the model equations. This task has been accomplished. The final set of equations have no wall or damping functions. Moreover, they are tensorially consistent and Galilean invariant. The derivation of the model equations is rather lengthy and thus will not be incorporated into this abstract, but will be included in the final paper. As a preliminary to formulating the proposed model, the original k-zeta model with constant turbulent Prandtl and

Differentiation of Xylella fastidiosa Strains via Multilocus Sequence Analysis of Environmentally Mediated Genes (MLSA-E)

OpenAIRE

Parker, Jennifer K.; Havird, Justin C.; De La Fuente, Leonardo

2012-01-01

Isolates of the plant pathogen Xylella fastidiosa are genetically very similar, but studies on their biological traits have indicated differences in virulence and infection symptomatology. Taxonomic analyses have identified several subspecies, and phylogenetic analyses of housekeeping genes have shown broad host-based genetic differences; however, results are still inconclusive for genetic differentiation of isolates within subspecies. This study employs multilocus sequence analysis of enviro...

Typing Chlamydia trachomatis: from egg yolk to nanotechnology

DEFF Research Database (Denmark)

Pedersen, Lisbeth Nørum; Herrmann, Bjørn; Møller, Jens Kjølseth

2009-01-01

A historical review is provided of the various methods used for half a century to differentiate and type Chlamydia trachomatis strains. Typing of C. trachomatis is an important tool for revealing transmission patterns in sexual networks, and enabling association with clinical manifestations......, insufficient epidemiological resolution is achieved by characterization of both MOMP and omp1. This calls for new high-resolution genotyping methods applying for example a multilocus variable number tandem repeat assay (MLVA) or multilocus sequence typing (MLST). The futuristic nanotechnology already seems...

Deciphering the genomic architecture of the stickleback brain with a novel multilocus gene-mapping approach.

Science.gov (United States)

Li, Zitong; Guo, Baocheng; Yang, Jing; Herczeg, Gábor; Gonda, Abigél; Balázs, Gergely; Shikano, Takahito; Calboli, Federico C F; Merilä, Juha

2017-03-01

Quantitative traits important to organismal function and fitness, such as brain size, are presumably controlled by many small-effect loci. Deciphering the genetic architecture of such traits with traditional quantitative trait locus (QTL) mapping methods is challenging. Here, we investigated the genetic architecture of brain size (and the size of five different brain parts) in nine-spined sticklebacks (Pungitius pungitius) with the aid of novel multilocus QTL-mapping approaches based on a de-biased LASSO method. Apart from having more statistical power to detect QTL and reduced rate of false positives than conventional QTL-mapping approaches, the developed methods can handle large marker panels and provide estimates of genomic heritability. Single-locus analyses of an F 2 interpopulation cross with 239 individuals and 15 198, fully informative single nucleotide polymorphisms (SNPs) uncovered 79 QTL associated with variation in stickleback brain size traits. Many of these loci were in strong linkage disequilibrium (LD) with each other, and consequently, a multilocus mapping of individual SNPs, accounting for LD structure in the data, recovered only four significant QTL. However, a multilocus mapping of SNPs grouped by linkage group (LG) identified 14 LGs (1-6 depending on the trait) that influence variation in brain traits. For instance, 17.6% of the variation in relative brain size was explainable by cumulative effects of SNPs distributed over six LGs, whereas 42% of the variation was accounted for by all 21 LGs. Hence, the results suggest that variation in stickleback brain traits is influenced by many small-effect loci. Apart from suggesting moderately heritable (h 2  ≈ 0.15-0.42) multifactorial genetic architecture of brain traits, the results highlight the challenges in identifying the loci contributing to variation in quantitative traits. Nevertheless, the results demonstrate that the novel QTL-mapping approach developed here has distinctive advantages

The effect of the number of seed variables on the performance of Cooke′s classical model

International Nuclear Information System (INIS)

Eggstaff, Justin W.; Mazzuchi, Thomas A.; Sarkani, Shahram

2014-01-01

In risk analysis, Cooke′s classical model for aggregating expert judgment has been widely used for over 20 years. However, the validity of this model has been the subject of much debate. Critics assert that this model′s scoring rule may unintentionally reward experts who manipulate their quantile estimates in order to receive a greater weight. In addition, the question of the number of seed variables required to ensure adequate performance of Cooke′s classical model remains unanswered. In this study, we conduct a comprehensive examination of the model through an iterative, cross validation test to perform an out-of-sample comparison between Cooke′s classical model and the equal-weight linear opinion pool method on almost all of the expert judgment studies compiled by Cooke and colleagues to date. Our results indicate that Cooke′s classical model significantly outperforms equally weighting expert judgment, regardless of the number of seed variables used; however, there may, in fact, be a maximum number of seed variables beyond which Cooke′s model cannot outperform an equally-weighted panel. - Highlights: • We examine Cooke′s classical model through an iterative, cross validation test. • The performance-based and equally weighted decision makers are compared. • Results strengthen Cooke′s argument for a two-fold cross-validation approach. • Accuracy test results show strong support in favor of Cooke′s classical method. • There may be a maximum number of seed variables that ensures model performance

Short read sequence typing (SRST: multi-locus sequence types from short reads

Directory of Open Access Journals (Sweden)

Inouye Michael

2012-07-01

Full Text Available Abstract Background Multi-locus sequence typing (MLST has become the gold standard for population analyses of bacterial pathogens. This method focuses on the sequences of a small number of loci (usually seven to divide the population and is simple, robust and facilitates comparison of results between laboratories and over time. Over the last decade, researchers and population health specialists have invested substantial effort in building up public MLST databases for nearly 100 different bacterial species, and these databases contain a wealth of important information linked to MLST sequence types such as time and place of isolation, host or niche, serotype and even clinical or drug resistance profiles. Recent advances in sequencing technology mean it is increasingly feasible to perform bacterial population analysis at the whole genome level. This offers massive gains in resolving power and genetic profiling compared to MLST, and will eventually replace MLST for bacterial typing and population analysis. However given the wealth of data currently available in MLST databases, it is crucial to maintain backwards compatibility with MLST schemes so that new genome analyses can be understood in their proper historical context. Results We present a software tool, SRST, for quick and accurate retrieval of sequence types from short read sets, using inputs easily downloaded from public databases. SRST uses read mapping and an allele assignment score incorporating sequence coverage and variability, to determine the most likely allele at each MLST locus. Analysis of over 3,500 loci in more than 500 publicly accessible Illumina read sets showed SRST to be highly accurate at allele assignment. SRST output is compatible with common analysis tools such as eBURST, Clonal Frame or PhyloViz, allowing easy comparison between novel genome data and MLST data. Alignment, fastq and pileup files can also be generated for novel alleles. Conclusions SRST is a novel

Design of a propeller turbine with a variable revolution number; Entwicklung einer Propellerturbine mit variabler Drehzahl

Energy Technology Data Exchange (ETDEWEB)

Fella, G.; Wierer, C. [Fella GmbH Maschinen- und Apparatebau, Amorbach (Germany); Goede, E.; Batrekhy, S.; Ruprecht, A. [Stuttgart Univ. (Germany). Inst. fuer Stroemungsmechanik und Hydraulische Stroemungsmaschinen

1997-12-31

The small hydroelectric power station of Rupboden in the Oberfranken district was reactivated after having been decommissioned for 30 years. This new low pressure plant consists of an open-flume turbine with an adjustable diffusor and a firm rotor disk (propeller) with a vertical rod. A large range of operation at a constant height of fall is ensured by a variable revolution number. The profiles of the adjustable diffusor and rotor disk and the design of the draft tube were optimized using numerical flow calculation. First operating experience is very positive. The turbine runs extremely smoothly over the entire range. (orig.) [Deutsch] Das Kleinwasserkraftwerk Rupboden in Oberfanken wurde nach 30 Jahren Stillstand reaktiviert. Die neue Niederdruckanlage besteht aus einer Schachtturbine mit verstellbarem Leitapparat, feststehendem Laufrad (Propeller) mit senkrechter Welle. Zum Erzielen eines grossen Betriebsbereiches bei gleichbleibender Fallhoehe wurde eine variable Drehzahl vorgesehen. Die Profilierung von Leitapparat und Laufrad sowie die Formgebung fuer das Saugrohr wurden mit numerischer Stroemungsberechnung optimiert. Erste Betriebserfahrungen sind sehr positiv. Die Turbine laeuft im gesamten Leistungsbereich ausserordentlich ruhig. (orig.)

Outbreak of listeriosis caused by infected beef meat from a meals-on-wheels delivery in Denmark 2009

DEFF Research Database (Denmark)

Smith, B; Larsson, J T; Lisby, M

2011-01-01

An outbreak of listeriosis in Denmark occurred in May 2009. Multilocus variable number of tandem repeats analysis typing, later confirmed by pulsed-field gel electrophoresis typing, showed that isolates from eight patients had identical patterns and were distinguishable from Listeria monocytogene...

Diversification and Distribution of Ruminant Chlamydia abortus Clones Assessed by MLST and MLVA

NARCIS (Netherlands)

Siarkou, Victoria I.; Vorimore, Fabien; Vicari, Nadia; Magnino, Simone; Rodolakis, Annie; Pannekoek, Yvonne; Sachse, Konrad; Longbottom, David; Laroucau, Karine

2015-01-01

Chlamydia abortus, an obligate intracellular bacterium, is the most common infectious cause of abortion in small ruminants worldwide and has zoonotic potential. We applied multilocus sequence typing (MLST) together with multiple-locus variable-number tandem repeat analysis (MLVA) to genotype 94

Study of Variable Turbulent Prandtl Number Model for Heat Transfer to Supercritical Fluids in Vertical Tubes

Science.gov (United States)

Tian, Ran; Dai, Xiaoye; Wang, Dabiao; Shi, Lin

2018-06-01

In order to improve the prediction performance of the numerical simulations for heat transfer of supercritical pressure fluids, a variable turbulent Prandtl number (Prt) model for vertical upward flow at supercritical pressures was developed in this study. The effects of Prt on the numerical simulation were analyzed, especially for the heat transfer deterioration conditions. Based on the analyses, the turbulent Prandtl number was modeled as a function of the turbulent viscosity ratio and molecular Prandtl number. The model was evaluated using experimental heat transfer data of CO2, water and Freon. The wall temperatures, including the heat transfer deterioration cases, were more accurately predicted by this model than by traditional numerical calculations with a constant Prt. By analyzing the predicted results with and without the variable Prt model, it was found that the predicted velocity distribution and turbulent mixing characteristics with the variable Prt model are quite different from that predicted by a constant Prt. When heat transfer deterioration occurs, the radial velocity profile deviates from the log-law profile and the restrained turbulent mixing then leads to the deteriorated heat transfer.

Taxonomic evaluation of putative Streptomyces scabiei strains held in the ARS (NRRL) Culture Collection using multi-locus sequence analysis

Science.gov (United States)

Multi-locus sequence analysis has been demonstrated to be a useful tool for identification of Streptomyces species and was previously applied to phylogenetically differentiate the type strains of species pathogenic on potatoes (Solanum tuberosum L.). The ARS Culture Collection (NRRL) contains 43 str...

Evaluation of Leishmania (Leishmania chagasi strains isolated from dogs originating from two visceral leishmaniasis-endemic areas in Brazil using multilocus enzyme electrophoresis

Directory of Open Access Journals (Sweden)

Carlos Eduardo Ribeiro Coutinho

2011-10-01

Full Text Available INTRODUCTION: Domestic dogs are the most important reservoir in the peridomestic transmission cycle of Leishmania (Leishmania chagasi. The genetic variability of subpopulations of this parasite circulating in dogs has not been thoroughly analyzed in Brazil, even though this knowledge has important implications in the clinical-epidemiological context. METHODS: The objective of this study was to evaluate and compare the phenotypic variability of 153 L. chagasi strains isolated from dogs originating from the municipalities of Rio de Janeiro (n = 57 and Belo Horizonte (n = 96, where the disease is endemic. Strains isolated only from intact skin were selected and analyzed by multilocus enzyme electrophoresis using nine enzyme systems (6PG, GPI, NH1 and NH2, G6P, PGM, MDH, ME, and IDHNADP. RESULTS: The electrophoretic profile was identical for all isolates analyzed and was the same as that of the L. chagasi reference strain (MHOM/BR/74/PP75. Phenetic analysis showed a similarity index of one for all strains, with the isolates sharing 100% of the characteristics analyzed. CONCLUSIONS: The results demonstrate that the L. chagasi populations circulating in dogs from Rio de Janeiro and Belo Horizonte belong to a single zymodeme.

Variability of the nucleoli number in the progenies of intact and UV-irradiated clonogenic Hela cells

International Nuclear Information System (INIS)

Kucheryavaya, N.A.; Zavol'naya, E.S.; Vakhtin, Yu.B.

1981-01-01

The coefficient of the ''nucleoli number'' character heritability (h 2 ) in the population of intact Hela cells equals 0.21 to 0.33. UV-irradiation enhances almost equally both the intraclonic and population variability of the nucleoli number and, as a result, the coefficient of the ''nucleoli number'' character heritability does not change in the population of UV-irradiated Hela cells

Genetic diversity analysis of Leuconostoc mesenteroides from Korean vegetables and food products by multilocus sequence typing.

Science.gov (United States)

Sharma, Anshul; Kaur, Jasmine; Lee, Sulhee; Park, Young-Seo

2018-06-01

In the present study, 35 Leuconostoc mesenteroides strains isolated from vegetables and food products from South Korea were studied by multilocus sequence typing (MLST) of seven housekeeping genes (atpA, groEL, gyrB, pheS, pyrG, rpoA, and uvrC). The fragment sizes of the seven amplified housekeeping genes ranged in length from 366 to 1414 bp. Sequence analysis indicated 27 different sequence types (STs) with 25 of them being represented by a single strain indicating high genetic diversity, whereas the remaining 2 were characterized by five strains each. In total, 220 polymorphic nucleotide sites were detected among seven housekeeping genes. The phylogenetic analysis based on the STs of the seven loci indicated that the 35 strains belonged to two major groups, A (28 strains) and B (7 strains). Split decomposition analysis showed that intraspecies recombination played a role in generating diversity among strains. The minimum spanning tree showed that the evolution of the STs was not correlated with food source. This study signifies that the multilocus sequence typing is a valuable tool to access the genetic diversity among L. mesenteroides strains from South Korea and can be used further to monitor the evolutionary changes.

Criterion for the nuclearity of spaces of functions of infinite number of variables

International Nuclear Information System (INIS)

Gali, I.M.

1977-08-01

The paper formulates a new necessary and sufficient condition for the nuclearity of spaces of infinite number of variables, and defines new nuclear spaces which play an important role in the field of functional analysis and quantum field theory. Also the condition for nuclearity of the infinite weighted tensor product of nuclear spaces is given

Surveillance of circulatingstrains in Europe during 1998-2015

DEFF Research Database (Denmark)

Barkoff, Alex-Mikael; Mertsola, Jussi; Pierard, Denis

2018-01-01

EUpert I-III studies (1998-2009). The analyses included genotyping, serotyping and pulsed-field gel electrophoresis (PFGE) and multi-locus variable-number tandem repeat analysis (MLVA). Genotyping results showed only small variation among the common virulence genes ofB. pertussisFrequencies of serotypes...

Molecular Investigation of Tularemia Outbreaks, Spain, 1997–2008

Science.gov (United States)

Ariza-Miguel, Jaime; Johansson, Anders; Fernández-Natal, María Isabel; Martínez-Nistal, Carmen; Orduña, Antonio; Rodríguez-Ferri, Elías F.; Hernández, Marta

2014-01-01

Tularemia outbreaks occurred in northwestern Spain in 1997–1998 and 2007–2008 and affected >1,000 persons. We assessed isolates involved in these outbreaks by using pulsed-field gel electrophoresis with 2 restriction enzymes and multilocus variable number tandem repeat analysis of 16 genomic loci of Francisella tularensis, the cause of this disease. Isolates were divided into 3 pulsotypes by pulsed-field gel electrophoresis and 8 allelic profiles by multilocus variable number tandem repeat analysis. Isolates obtained from the second tularemia outbreak had the same genotypes as isolates obtained from the first outbreak. Both outbreaks were caused by genotypes of genetic subclade B.Br:FTNF002–00, which is widely distributed in countries in central and western Europe. Thus, reemergence of tularemia in Spain was not caused by the reintroduction of exotic strains, but probably by persistence of local reservoirs of infection. PMID:24750848

Multilocus microsatellite typing (MLMT of strains from Turkey and Cyprus reveals a novel monophyletic L. donovani sensu lato group.

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Evi Gouzelou

Full Text Available BACKGROUND: New foci of human CL caused by strains of the Leishmania donovani (L. donovani complex have been recently described in Cyprus and the Çukurova region in Turkey (L. infantum situated 150 km north of Cyprus. Cypriot strains were typed by Multilocus Enzyme Electrophoresis (MLEE using the Montpellier (MON system as L. donovani zymodeme MON-37. However, multilocus microsatellite typing (MLMT has shown that this zymodeme is paraphyletic; composed of distantly related genetic subgroups of different geographical origin. Consequently the origin of the Cypriot strains remained enigmatic. METHODOLOGY/PRINCIPAL FINDINGS: The Cypriot strains were compared with a set of Turkish isolates obtained from a CL patient and sand fly vectors in south-east Turkey (Çukurova region; CUK strains and from a VL patient in the south-west (Kuşadasi; EP59 strain. These Turkish strains were initially analyzed using the K26-PCR assay that discriminates MON-1 strains by their amplicon size. In line with previous DNA-based data, the strains were inferred to the L. donovani complex and characterized as non MON-1. For these strains MLEE typing revealed two novel zymodemes; L. donovani MON-309 (CUK strains and MON-308 (EP59. A population genetic analysis of the Turkish isolates was performed using 14 hyper-variable microsatellite loci. The genotypic profiles of 68 previously analyzed L. donovani complex strains from major endemic regions were included for comparison. Population structures were inferred by combination of bayesian model-based and distance-based approaches. MLMT placed the Turkish and Cypriot strains in a subclade of a newly discovered, genetically distinct L. infantum monophyletic group, suggesting that the Cypriot strains may originate from Turkey. CONCLUSION: The discovery of a genetically distinct L. infantum monophyletic group in the south-eastern Mediterranean stresses the importance of species genetic characterization towards better understanding

Variability of the nucleoli number in the progenies of intact and UV-irradiated clonogenic Hela cells

Energy Technology Data Exchange (ETDEWEB)

Kucheryavaya, N.A.; Zavol' naya, E.S.; Vakhtin, Yu.B. (AN SSSR, Leningrad. Inst. Tsitologii)

1981-01-01

The coefficient of the ''nucleoli number'' character heritability (h/sup 2/) in the population of intact Hela cells equals 0.21 to 0.33. UV-irradiation enhances almost equally both the intraclonic and population variability of the nucleoli number and, as a result, the coefficient of the ''nucleoli number'' character heritability does not change in the population of UV-irradiated Hela cells.

Development of Mycoplasma synoviae (MS) core genome multilocus sequence typing (cgMLST) scheme.

Science.gov (United States)

Ghanem, Mostafa; El-Gazzar, Mohamed

2018-05-01

Mycoplasma synoviae (MS) is a poultry pathogen with reported increased prevalence and virulence in recent years. MS strain identification is essential for prevention, control efforts and epidemiological outbreak investigations. Multiple multilocus based sequence typing schemes have been developed for MS, yet the resolution of these schemes could be limited for outbreak investigation. The cost of whole genome sequencing became close to that of sequencing the seven MLST targets; however, there is no standardized method for typing MS strains based on whole genome sequences. In this paper, we propose a core genome multilocus sequence typing (cgMLST) scheme as a standardized and reproducible method for typing MS based whole genome sequences. A diverse set of 25 MS whole genome sequences were used to identify 302 core genome genes as cgMLST targets (35.5% of MS genome) and 44 whole genome sequences of MS isolates from six countries in four continents were used for typing applying this scheme. cgMLST based phylogenetic trees displayed a high degree of agreement with core genome SNP based analysis and available epidemiological information. cgMLST allowed evaluation of two conventional MLST schemes of MS. The high discriminatory power of cgMLST allowed differentiation between samples of the same conventional MLST type. cgMLST represents a standardized, accurate, highly discriminatory, and reproducible method for differentiation between MS isolates. Like conventional MLST, it provides stable and expandable nomenclature, allowing for comparing and sharing the typing results between different laboratories worldwide. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Multilocus phylogeny and antifungal susceptibility of Aspergillus section Circumdati from clinical samples and description of A. pseudosclerotiorum sp. nov.

Science.gov (United States)

A multilocus phylogenetic study was carried out to assess the species distribution in a set of 34 clinical isolates of Aspergillus section Circumdati from the USA and their in vitro antifungal susceptibility were determined against eight antifungal drugs. The genetic markers used were ITS, BenA, CaM...

An Extended Multilocus Sequence Typing (MLST) Scheme for Rapid Direct Typing of Leptospira from Clinical Samples

OpenAIRE

Weiss, Sabrina; Menezes, Angela; Woods, Kate; Chanthongthip, Anisone; Dittrich, Sabine; Opoku-Boateng, Agatha; Kimuli, Maimuna; Chalker, Victoria

2016-01-01

Background Rapid typing of Leptospira is currently impaired by requiring time consuming culture of leptospires. The objective of this study was to develop an assay that provides multilocus sequence typing (MLST) data direct from patient specimens while minimising costs for subsequent sequencing. Methodology and Findings An existing PCR based MLST scheme was modified by designing nested primers including anchors for facilitated subsequent sequencing. The assay was applied to various specimen t...

Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST

NARCIS (Netherlands)

O'Donnell, K.; Humber, R.A.; Geiser, D.M.; Kang, S.; Robert, V.; Park, B.; Crous, P.W.; Johnston, P.; Aoki, T.; Rooney, A.P.; Rehner, S.A.

2012-01-01

We constructed several multilocus DNA sequence datasets to assess the phylogenetic diversity of insecticolous fusaria, especially focusing on those housed at the Agricultural Research Service Collection of Entomopathogenic Fungi (ARSEF), and to aid molecular identifications of unknowns via the

Characterization of Dutch Staphylococcus aureus from bovine mastitis using a Multiple Locus Variable Number Tandem Repeat Analysis

NARCIS (Netherlands)

Ikawaty, R.; Brouwer, E.C.; Jansen, M.D.; Duijkeren, van E.; Mevius, D.J.; Verhoef, J.; Fluit, A.C.

2009-01-01

Current typing methods for Staphylococcus aureus have important drawbacks. We evaluated a Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) scheme with 6 loci which lacks most drawbacks on 85 bovine mastitis isolates from The Netherlands. For each locus the number of repeat units (RU) was

First worldwide proficiency study on variable-number tandem-repeat typing of Mycobacterium tuberculosis complex strains.

NARCIS (Netherlands)

Beer, J.L. de; Kremer, K.; Kodmon, C.; Supply, P.; Soolingen, D. van

2012-01-01

Although variable-number tandem-repeat (VNTR) typing has gained recognition as the new standard for the DNA fingerprinting of Mycobacterium tuberculosis complex (MTBC) isolates, external quality control programs have not yet been developed. Therefore, we organized the first multicenter proficiency

Multilocus sequence analysis (MLSA) of Bradyrhizobium strains: revealing high diversity of tropical diazotrophic symbiotic bacteria.

Science.gov (United States)

Delamuta, Jakeline Renata Marçon; Ribeiro, Renan Augusto; Menna, Pâmela; Bangel, Eliane Villamil; Hungria, Mariangela

2012-04-01

Symbiotic association of several genera of bacteria collectively called as rhizobia and plants belonging to the family Leguminosae (=Fabaceae) results in the process of biological nitrogen fixation, playing a key role in global N cycling, and also bringing relevant contributions to the agriculture. Bradyrhizobium is considered as the ancestral of all nitrogen-fixing rhizobial species, probably originated in the tropics. The genus encompasses a variety of diverse bacteria, but the diversity captured in the analysis of the 16S rRNA is often low. In this study, we analyzed twelve Bradyrhizobium strains selected from previous studies performed by our group for showing high genetic diversity in relation to the described species. In addition to the 16S rRNA, five housekeeping genes (recA, atpD, glnII, gyrB and rpoB) were analyzed in the MLSA (multilocus sequence analysis) approach. Analysis of each gene and of the concatenated housekeeping genes captured a considerably higher level of genetic diversity, with indication of putative new species. The results highlight the high genetic variability associated with Bradyrhizobium microsymbionts of a variety of legumes. In addition, the MLSA approach has proved to represent a rapid and reliable method to be employed in phylogenetic and taxonomic studies, speeding the identification of the still poorly known diversity of nitrogen-fixing rhizobia in the tropics.

Multilocus and SSU rRNA gene phylogenetic analyses of available cyanobacterial genomes, and their relation to the current taxonomic system

Czech Academy of Sciences Publication Activity Database

Mareš, Jan

2018-01-01

Roč. 811, č. 1 (2018), s. 19-34 ISSN 0018-8158 R&D Projects: GA ČR(CZ) GA15-11912S Institutional support: RVO:67985939 Keywords : 16S rRNA * Cyanobacterial orders * Multilocus phylogeny Subject RIV: EH - Ecology, Behaviour OBOR OECD: Ecology Impact factor: 2.056, year: 2016

Multilocus sequence typing and virulence analysis of Haemophilus parasuis strains isolated in five provinces of China.

Science.gov (United States)

Wang, Liyan; Ma, Lina; Liu, Yongan; Gao, Pengcheng; Li, Youquan; Li, Xuerui; Liu, Yongsheng

2016-10-01

Haemophilus parasuis is the etiological agent of Glässers disease, which causes high morbidity and mortality in swine herds. Although H. parasuis strains can be classified into 15 serovars with the Kielstein-Rapp-Gabrielson serotyping scheme, a large number of isolates cannot be classified and have been designated 'nontypeable' strains. In this study, multilocus sequence typing (MLST) of H. parasuis was used to analyze 48 H. parasuis field strains isolated in China and two strains from Australia. Twenty-six new alleles and 29 new sequence types (STs) were detected, enriching the H. parasuis MLST databases. A BURST analysis indicated that H. parasuis lacks stable population structure and is highly heterogeneous, and that there is no association between STs and geographic area. When an UPGMA dendrogram was constructed, two major clades, clade A and clade B, were defined. Animal experiments, in which guinea pigs were challenged intraperitoneally with the bacterial isolates, supported the hypothesis that the H. parasuis STs in clade A are generally avirulent or weakly virulent, whereas the STs in clade B tend to be virulent. Copyright © 2016 Elsevier B.V. All rights reserved.

Variable-number tandem repeats as molecular markers for biotypes of Pasteuria ramosa in Daphnia spp.

Science.gov (United States)

Mouton, Laurence; Nong, Guang; Preston, James F; Ebert, Dieter

2007-06-01

Variable-number tandem repeats (VNTRs) have been identified in populations of Pasteuria ramosa, a castrating endobacterium of Daphnia species. The allelic polymorphisms at 14 loci in laboratory and geographically diverse soil samples showed that VNTRs may serve as biomarkers for the genetic characterization of P. ramosa isolates.

The transition matrix element Agq(N) of the variable flavor number scheme at O(α3s)

International Nuclear Information System (INIS)

Ablinger, J.; Hasselhuhn, A.; Schneider, C.; Manteuffel, A. von

2014-01-01

We calculate the massive operator matrix element A (3) gq (N) to 3-loop order in Quantum Chromodynamics at general values of the Mellin variable N. This is the first complete transition function needed in the variable flavor number scheme obtained at O(α 3 s ). A fist independent recalculation is performed for the contributions ∝ N F of the 3-loop anomalous dimension γ (2) gq (N).

The transition matrix element Agq(N) of the variable flavor number scheme at O(αs3)

International Nuclear Information System (INIS)

Ablinger, J.; Blümlein, J.; De Freitas, A.; Hasselhuhn, A.; Manteuffel, A. von; Round, M.; Schneider, C.; Wißbrock, F.

2014-01-01

We calculate the massive unpolarized operator matrix element A gq (3) (N) to 3-loop order in Quantum Chromodynamics at general values of the Mellin variable N. This is the first complete transition function needed in the variable flavor number scheme obtained at O(α s 3 ). A first independent recalculation is performed for the contributions ∝N F of the 3-loop anomalous dimension γ gq (2) (N)

On the strong law of large numbers for $\\varphi$-subgaussian random variables

OpenAIRE

Zajkowski, Krzysztof

2016-01-01

For $p\\ge 1$ let $\\varphi_p(x)=x^2/2$ if $|x|\\le 1$ and $\\varphi_p(x)=1/p|x|^p-1/p+1/2$ if $|x|>1$. For a random variable $\\xi$ let $\\tau_{\\varphi_p}(\\xi)$ denote $\\inf\\{a\\ge 0:\\;\\forall_{\\lambda\\in\\mathbb{R}}\\; \\ln\\mathbb{E}\\exp(\\lambda\\xi)\\le\\varphi_p(a\\lambda)\\}$; $\\tau_{\\varphi_p}$ is a norm in a space $Sub_{\\varphi_p}=\\{\\xi:\\;\\tau_{\\varphi_p}(\\xi)1$) there exist positive constants $c$ and $\\alpha$ such that for every natural number $n$ the following inequality $\\tau_{\\varphi_p}(\\sum_{i=1...

Inclusive B-meson hadroproduction in the general-mass variable-flavor-number scheme

Energy Technology Data Exchange (ETDEWEB)

Kniehl, B.A.; Kramer, G. [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik; Schienbein, I. [Universite Joseph Fourier, Grenoble (France). Lab. de Physique Subatomique et de Cosmologie]|[CNRS/IN2P3, Inst. National Polytechnique de Grenoble (France); Spiesberger, H. [Johannes Gutenberg Univ., Mainz (Germany). Inst. fuer Physik

2007-05-15

We calculate the cross section for the inclusive hadroproduction of B mesons as a function of transverse momentum p{sub T} at next-to-leading order (NLO) in the general- mass variable-flavor-number scheme using realistic non-perturbative fragmentation functions that are obtained through a global fit to e{sup +}e{sup -} data from CERN LEP1 and SLAC SLC exploiting their universality and scaling violations. We find good agreement with recent p anti p data taken by the CDF Collaboration in run II at the Fermilab Tevatron. We also present comparisons with NLO results obtained in two other schemes. (orig.)

Multilocus analyses of an Antarctic fish species flock (Teleostei, Notothenioidei, Trematominae): Phylogenetic approach and test of the early-radiation event

Czech Academy of Sciences Publication Activity Database

Janko, Karel; Marshall, C.; Musilová, Zuzana; Van Houdt, J.; Couloux, A.; Cruaud, C.; Lecointre, G.

2011-01-01

Roč. 60, č. 3 (2011), s. 305-316 ISSN 1055-7903 R&D Projects: GA AV ČR KJB600450903; GA MŠk LC06073 Institutional research plan: CEZ:AV0Z50450515 Keywords : Species tree versus gene tree * Multilocus phylogeny * Diversification rate Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.609, year: 2011

Drivers of Seasonal Variability in Marine Boundary Layer Aerosol Number Concentration Investigated Using a Steady State Approach

Science.gov (United States)

Mohrmann, Johannes; Wood, Robert; McGibbon, Jeremy; Eastman, Ryan; Luke, Edward

2018-01-01

Marine boundary layer (MBL) aerosol particles affect the climate through their interaction with MBL clouds. Although both MBL clouds and aerosol particles have pronounced seasonal cycles, the factors controlling seasonal variability of MBL aerosol particle concentration are not well constrained. In this paper an aerosol budget is constructed representing the effects of wet deposition, free-tropospheric entrainment, primary surface sources, and advection on the MBL accumulation mode aerosol number concentration (Na). These terms are then parameterized, and by assuming that on seasonal time scales Na is in steady state, the budget equation is rearranged to form a diagnostic equation for Na based on observable variables. Using data primarily collected in the subtropical northeast Pacific during the MAGIC campaign (Marine ARM (Atmospheric Radiation Measurement) GPCI (GCSS Pacific Cross-Section Intercomparison) Investigation of Clouds), estimates of both mean summer and winter Na concentrations are made using the simplified steady state model and seasonal mean observed variables. These are found to match well with the observed Na. To attribute the modeled difference between summer and winter aerosol concentrations to individual observed variables (e.g., precipitation rate and free-tropospheric aerosol number concentration), a local sensitivity analysis is combined with the seasonal difference in observed variables. This analysis shows that despite wintertime precipitation frequency being lower than summer, the higher winter precipitation rate accounted for approximately 60% of the modeled seasonal difference in Na, which emphasizes the importance of marine stratocumulus precipitation in determining MBL aerosol concentrations on longer time scales.

How variable is the number of triggered aftershocks?

Science.gov (United States)

Marsan, D.; Helmstetter, A.

2017-07-01

Aftershock activity depends at first order on the main shock magnitude but also shows important fluctuations between shocks of equal magnitude. We here investigate these fluctuations, by quantifying them and by relating them to the main shock stress drop and other variables, for southern California earthquakes. A method is proposed in order to only count directly triggered aftershocks, rather than secondary aftershocks (i.e., triggered by previous aftershocks), and to only quantify fluctuations going beyond the natural Poisson variability. Testing of the method subjected to various model errors allows to quantify its robustness. It is found that these fluctuations follow a distribution that is well fitted by a lognormal distribution, with a coefficient of variation of about 1.0 to 1.1. A simple model is proposed to relate this observed dependence to main shock stress drop variability.

Mediating Role of the Reward Network in the Relationship between the Dopamine Multilocus Genetic Profile and Depression

Directory of Open Access Journals (Sweden)

Liang Gong

2017-09-01

Full Text Available Multiple genetic loci in the dopamine (DA pathway have been associated with depression symptoms in patients with major depressive disorder (MDD. However, the neural mechanisms underlying the polygenic effects of the DA pathway on depression remain unclear. We used an imaging genetic approach to investigate the polygenic effects of the DA pathway on the reward network in MDD. Fifty-three patients and 37 cognitively normal (CN subjects were recruited and underwent resting-state functional magnetic resonance imaging (R-fMRI scans. Multivariate linear regression analysis was employed to measure the effects of disease and multilocus genetic profile scores (MGPS on the reward network, which was constructed using the nucleus accumbens (NAc functional connectivity (NAFC network. DA-MGPS was widely associated within the NAFC network, mainly in the inferior frontal cortex, insula, hypothalamus, superior temporal gyrus, and occipital cortex. The pattern of DA-MGPS effects on the fronto-striatal pathway differed in MDD patients compared with CN subjects. More importantly, NAc-putamen connectivity mediates the association between DA MGPS and anxious depression traits in MDD patients. Our findings suggest that the DA multilocus genetic profile makes a considerable contribution to the reward network and anxious depression in MDD patients. These results expand our understanding of the pathophysiology of polygenic effects underlying brain network abnormalities in MDD.

Three loop contributions to the matrix elements in the variable flavor number scheme

Energy Technology Data Exchange (ETDEWEB)

Bluemlein, Johannes; Hasselhuhn, Alexander [DESY (Germany); Schneider, Carsten [RISC, JKU Linz (Austria)

2012-07-01

The variable flavor number scheme may be used to describe parton distributions in the transition region in which one heavy quark gradually becomes a light flavor. We present first three-loop results to the massive operator matrix elements A{sub gg} and A{sub gq} for the contributions due to bubble topologies {proportional_to}T{sub F}{sup 2} n{sub f} at general values of the Mellin variable N. The calculation has been performed using higher transcendental functions and by applying modern summation technologies encoded in the package Sigma. These massive operator matrix elements describe the universal contributions in the matching of different flavor sectors, which are the logarithmic and constant contributions in the ratio of m{sup 2}{sub H}/Q{sup 2}, with Q{sup 2} the virtuality and m{sub H} the respective heavy quark mass. The framework allows to derive heavy quark parton distributions which are of relevance for calculating specific processes at hadron-hadron colliders.

Salmonella typhi

OpenAIRE

Mochammad, Hatta

2008-01-01

This manuscript could use as research on infectious diseases Multi-locus variable-number tandem repeat analysis differentiated 297 Salmonella enterica serovar Typhi blood culture isolates from Makassar in 76 genotypes and a single unique S. Typhi genotype was isolated from the cholecystectomy specimens of four patients with cholelithiasis. The high diversity in S. Typhi genotypes circulating in Makassar indicates that the number of carriers could be very large, which may complicat...

Correlation of Metabolic Variables with the Number of ORFs in Human Pathogenic and Phylogenetically Related Non- or Less-Pathogenic Bacteria.

Science.gov (United States)

Brambila-Tapia, Aniel Jessica Leticia; Poot-Hernández, Augusto Cesar; Garcia-Guevara, Jose Fernando; Rodríguez-Vázquez, Katya

2016-06-01

To date, a few works have performed a correlation of metabolic variables in bacteria; however specific correlations with these variables have not been reported. In this work, we included 36 human pathogenic bacteria and 18 non- or less-pathogenic-related bacteria and obtained all metabolic variables, including enzymes, metabolic pathways, enzymatic steps and specific metabolic pathways, and enzymatic steps of particular metabolic processes, from a reliable metabolic database (KEGG). Then, we correlated the number of the open reading frames (ORF) with these variables and with the proportions of these variables, and we observed a negative correlation with the proportion of enzymes (r = -0.506, p < 0.0001), metabolic pathways (r = -0.871, p < 00.0001), enzymatic reactions (r = -0.749, p < 00.0001), and with the proportions of central metabolism variables as well as a positive correlation with the proportions of multistep reactions (r = 0.650, p < 00.0001) and secondary metabolism variables. The proportion of multifunctional reactions (r: -0.114, p = 0.41) and the proportion of enzymatic steps (r: -0.205, p = 0.14) did not present a significant correlation. These correlations indicate that as the size of a genome (measured in the number of ORFs) increases, the proportion of genes that encode enzymes significantly diminishes (especially those related to central metabolism), suggesting that when essential metabolic pathways are complete, an increase in the number of ORFs does not require a similar increase in the metabolic pathways and enzymes, but only a slight increase is sufficient to cope with a large genome.

MULTIPLE-LOCUS VARIABLE-NUMBER TANDEM REPEAT ANALYSIS OF BRUCELLA ISOLATES FROM THAILAND.

Science.gov (United States)

Kumkrong, Khurawan; Chankate, Phanita; Tonyoung, Wittawat; Intarapuk, Apiradee; Kerdsin, Anusak; Kalambaheti, Thareerat

2017-01-01

Brucellosis-induced abortion can result in significant economic loss to farm animals. Brucellosis can be transmitted to humans during slaughter of infected animals or via consumption of contaminated food products. Strain identification of Brucella isolates can reveal the route of transmission. Brucella strains were isolated from vaginal swabs of farm animal, cow milk and from human blood cultures. Multiplex PCR was used to identify Brucella species, and owing to high DNA homology among Brucella isolates, multiple-locus variable-number tandem repeat analysis (MLVA) based on the number of tandem repeats at 16 different genomic loci was used for strain identification. Multiplex PCR categorized the isolates into B. abortus (n = 7), B. melitensis (n = 37), B. suis (n = 3), and 5 of unknown Brucella spp. MLVA-16 clustering analysis differentiated the strains into various genotypes, with Brucella isolates from the same geographic region being closely related, and revealed that the Thai isolates were phylogenetically distinct from those in other countries, including within the Southeast Asian region. Thus, MLVA-16 typing has utility in epidemiological studies.

Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates

Energy Technology Data Exchange (ETDEWEB)

Jackson, P.J.; Walthers, E.A.; Richmond, K.L. [Los Alamos National Lab., NM (United States)] [and others

1997-04-01

PCR analysis of 198 Bacillus anthracis isolates revealed a variable region of DNA sequence differing in length among the isolates. Five Polymorphisms differed by the presence Of two to six copies of the 12-bp tandem repeat 5{prime}-CAATATCAACAA-3{prime}. This variable-number tandem repeat (VNTR) region is located within a larger sequence containing one complete open reading frame that encodes a putative 30-kDa protein. Length variation did not change the reading frame of the encoded protein and only changed the copy number of a 4-amino-acid sequence (QYQQ) from 2 to 6. The structure of the VNTR region suggests that these multiple repeats are generated by recombination or polymerase slippage. Protein structures predicted from the reverse-translated DNA sequence suggest that any structural changes in the encoded protein are confined to the region encoded by the VNTR sequence. Copy number differences in the VNTR region were used to define five different B. anthracis alleles. Characterization of 198 isolates revealed allele frequencies of 6.1, 17.7, 59.6, 5.6, and 11.1% sequentially from shorter to longer alleles. The high degree of polymorphism in the VNTR region provides a criterion for assigning isolates to five allelic categories. There is a correlation between categories and geographic distribution. Such molecular markers can be used to monitor the epidemiology of anthrax outbreaks in domestic and native herbivore populations. 22 refs., 4 figs., 3 tabs.

The Applied Development of a Tiered Multilocus Sequence Typing (MLST) Scheme for Dichelobacter nodosus.

Science.gov (United States)

Blanchard, Adam M; Jolley, Keith A; Maiden, Martin C J; Coffey, Tracey J; Maboni, Grazieli; Staley, Ceri E; Bollard, Nicola J; Warry, Andrew; Emes, Richard D; Davies, Peers L; Tötemeyer, Sabine

2018-01-01

Dichelobacter nodosus ( D. nodosus ) is the causative pathogen of ovine footrot, a disease that has a significant welfare and financial impact on the global sheep industry. Previous studies into the phylogenetics of D. nodosus have focused on Australia and Scandinavia, meaning the current diversity in the United Kingdom (U.K.) population and its relationship globally, is poorly understood. Numerous epidemiological methods are available for bacterial typing; however, few account for whole genome diversity or provide the opportunity for future application of new computational techniques. Multilocus sequence typing (MLST) measures nucleotide variations within several loci with slow accumulation of variation to enable the designation of allele numbers to determine a sequence type. The usage of whole genome sequence data enables the application of MLST, but also core and whole genome MLST for higher levels of strain discrimination with a negligible increase in experimental cost. An MLST database was developed alongside a seven loci scheme using publically available whole genome data from the sequence read archive. Sequence type designation and strain discrimination was compared to previously published data to ensure reproducibility. Multiple D. nodosus isolates from U.K. farms were directly compared to populations from other countries. The U.K. isolates define new clades within the global population of D. nodosus and predominantly consist of serogroups A, B and H, however serogroups C, D, E, and I were also found. The scheme is publically available at https://pubmlst.org/dnodosus/.

Molecular characterization and multilocus genotypes of Enterocytozoon bieneusi among horses in southwestern China

Directory of Open Access Journals (Sweden)

Lei Deng

2016-10-01

Full Text Available Abstract Background Enterocytozoon bieneusi is one of the most prevalent causative species of diarrhea and enteric diseases in various hosts. E. bieneusi has been identified in humans, mammals, birds, rodents and reptiles in China, but few studies have reported E. bieneusi in horses. Therefore, the present study was conducted to assess the prevalence, molecular characteristics and zoonotic potential of E. bieneusi among horses in southwestern China. Findings Three hundred and thirty-three fecal specimens were collected from horses on five farms in the Sichuan and Yunnan provinces of southwestern China. The prevalence of E. bieneusi was 22.5 % (75/333, as determined by nested polymerase chain reaction and sequencing analysis of the internal transcribed spacer region of the ribosomal RNA gene of E. bieneusi. Altogether, 10 genotypes were identified among the 75 E. bieneusi-positive samples: four of these genotypes were known (horse1, horse2, SC02 and D and six were novel (SCH1-4 and YNH1-2. Multilocus sequence typing using three microsatellites (MS1, MS3 and MS7 and one minisatellite (MS4 revealed three, two, three and three genotypes at these four loci, respectively. In phylogenetic analysis, all the genotypes of E. bieneusi obtained in this study were clustered into three distinct groups: D, SC02 and SCH1-3 were clustered into group 1 (zoonotic potential; SCH4 was clustered into group 2 (cattle-hosted; whereas horse2, YNH1 and YNH2 were clustered into group 6 (unclear zoonotic potential. Conclusions This is the first report of E. bieneusi among horses in southwestern China. This is also the first multilocus genotyping analysis using microsatellite and minisatellite markers of E. bieneusi in horses. The presence of genotype D, which was previously identified in humans, and genotypes SC02 and SCH1-3, which belong to potential zoonotic group 1, these results indicate that horses are a potential source of human E. bieneusi infections in China.

Multilocus sequence analysis of Treponema denticola strains of diverse origin

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Mo Sisu

2013-02-01

Full Text Available Abstract Background The oral spirochete bacterium Treponema denticola is associated with both the incidence and severity of periodontal disease. Although the biological or phenotypic properties of a significant number of T. denticola isolates have been reported in the literature, their genetic diversity or phylogeny has never been systematically investigated. Here, we describe a multilocus sequence analysis (MLSA of 20 of the most highly studied reference strains and clinical isolates of T. denticola; which were originally isolated from subgingival plaque samples taken from subjects from China, Japan, the Netherlands, Canada and the USA. Results The sequences of the 16S ribosomal RNA gene, and 7 conserved protein-encoding genes (flaA, recA, pyrH, ppnK, dnaN, era and radC were successfully determined for each strain. Sequence data was analyzed using a variety of bioinformatic and phylogenetic software tools. We found no evidence of positive selection or DNA recombination within the protein-encoding genes, where levels of intraspecific sequence polymorphism varied from 18.8% (flaA to 8.9% (dnaN. Phylogenetic analysis of the concatenated protein-encoding gene sequence data (ca. 6,513 nucleotides for each strain using Bayesian and maximum likelihood approaches indicated that the T. denticola strains were monophyletic, and formed 6 well-defined clades. All analyzed T. denticola strains appeared to have a genetic origin distinct from that of ‘Treponema vincentii’ or Treponema pallidum. No specific geographical relationships could be established; but several strains isolated from different continents appear to be closely related at the genetic level. Conclusions Our analyses indicate that previous biological and biophysical investigations have predominantly focused on a subset of T. denticola strains with a relatively narrow range of genetic diversity. Our methodology and results establish a genetic framework for the discrimination and phylogenetic

Investigating the Variability in Cumulus Cloud Number as a Function of Subdomain Size and Organization using large-domain LES

Science.gov (United States)

Neggers, R.

2017-12-01

Recent advances in supercomputing have introduced a "grey zone" in the representation of cumulus convection in general circulation models, in which this process is partially resolved. Cumulus parameterizations need to be made scale-aware and scale-adaptive to be able to conceptually and practically deal with this situation. A potential way forward are schemes formulated in terms of discretized Cloud Size Densities, or CSDs. Advantages include i) the introduction of scale-awareness at the foundation of the scheme, and ii) the possibility to apply size-filtering of parameterized convective transport and clouds. The CSD is a new variable that requires closure; this concerns its shape, its range, but also variability in cloud number that can appear due to i) subsampling effects and ii) organization in a cloud field. The goal of this study is to gain insight by means of sub-domain analyses of various large-domain LES realizations of cumulus cloud populations. For a series of three-dimensional snapshots, each with a different degree of organization, the cloud size distribution is calculated in all subdomains, for a range of subdomain sizes. The standard deviation of the number of clouds of a certain size is found to decrease with the subdomain size, following a powerlaw scaling corresponding to an inverse-linear dependence. Cloud number variability also increases with cloud size; this reflects that subsampling affects the largest clouds first, due to their typically larger neighbor spacing. Rewriting this dependence in terms of two dimensionless groups, by dividing by cloud number and cloud size respectively, yields a data collapse. Organization in the cloud field is found to act on top of this primary dependence, by enhancing the cloud number variability at the smaller sizes. This behavior reflects that small clouds start to "live" on top of larger structures such as cold pools, favoring or inhibiting their formation (as illustrated by the attached figure of cloud mask

Variability of sub-micrometer particle number size distributions and concentrations in the Western Mediterranean regional background

Directory of Open Access Journals (Sweden)

Michael Cusack

2013-02-01

Full Text Available This study focuses on the daily and seasonal variability of particle number size distributions and concentrations, performed at the Montseny (MSY regional background station in the western Mediterranean from October 2010 to June 2011. Particle number concentrations at MSY were shown to be within range of various other sites across Europe reported in literature, but the seasonality of the particle number size distributions revealed significant differences. The Aitken mode is the dominant particle mode at MSY, with arithmetic mean concentrations of 1698 cm3, followed by the accumulation mode (877 cm−3 and the nucleation mode (246 cm−3. Concentrations showed a strong seasonal variability with large increases in particle number concentrations observed from the colder to warmer months. The modality of median size distributions was typically bimodal, except under polluted conditions when the size distribution was unimodal. During the colder months, the daily variation of particle number size distributions are strongly influenced by a diurnal breeze system, whereby the Aitken and accumulation modes vary similarly to PM1 and BC mass concentrations, with nocturnal minima and sharp day-time increases owing to the development of a diurnal mountain breeze. Under clean air conditions, high levels of nucleation and lower Aitken mode concentrations were measured, highlighting the importance of new particle formation as a source of particles in the absence of a significant condensation sink. During the warmer months, nucleation mode concentrations were observed to be relatively elevated both under polluted and clean conditions due to increased photochemical reactions, with enhanced subsequent growth owing to elevated concentrations of condensable organic vapours produced from biogenic volatile organic compounds, indicating that nucleation at MSY does not exclusively occur under clean air conditions. Finally, mixing of air masses between polluted and non

Prompt neutrinos from atmospheric charm in the general-mass variable-flavor-number scheme

International Nuclear Information System (INIS)

Benzke, M.; Garzelli, M.V.; Kniehl, B.A.; Kramer, G.; Moch, S.; Sigl, G.

2017-08-01

We present predictions for the prompt-neutrino flux arising from the decay of charmed mesons and baryons produced by the interactions of high-energy cosmic rays in the Earth's atmosphere, making use of a QCD approach on the basis of the general-mass variable-flavor-number scheme for the description of charm hadroproduction at NLO, complemented by a consistent set of fragmentation functions. We compare the theoretical results to those already obtained by our and other groups with different theoretical approaches. We provide comparisons with the experimental results obtained by the IceCube Collaboration in two different analyses and we discuss the implications for parton distribution functions.

Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes

OpenAIRE

Chen, Yi; Gonzalez-Escalona, Narjol; Hammack, Thomas S.; Allard, Marc W.; Strain, Errol A.; Brown, Eric W.

2016-01-01

ABSTRACT Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST...

Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples.

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Arulandhu, Alfred J; Staats, Martijn; Hagelaar, Rico; Voorhuijzen, Marleen M; Prins, Theo W; Scholtens, Ingrid; Costessi, Adalberto; Duijsings, Danny; Rechenmann, François; Gaspar, Frédéric B; Barreto Crespo, Maria Teresa; Holst-Jensen, Arne; Birck, Matthew; Burns, Malcolm; Haynes, Edward; Hochegger, Rupert; Klingl, Alexander; Lundberg, Lisa; Natale, Chiara; Niekamp, Hauke; Perri, Elena; Barbante, Alessandra; Rosec, Jean-Philippe; Seyfarth, Ralf; Sovová, Tereza; Van Moorleghem, Christoff; van Ruth, Saskia; Peelen, Tamara; Kok, Esther

2017-10-01

DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance. © The Authors 2017. Published by Oxford University Press.

Interleukin 6 variable number of tandem repeats (VNTR) gene polymorphism in centenarians.

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Capurso, C; Solfrizzi, V; D'Introno, A; Colacicco, A M; Capurso, S A; Semeraro, C; Capurso, A; Panza, F

2007-11-01

Recent population-based studies identified the magnitude of interleukin 6 (IL6) serum levels as a marker for functional disability, and a predictor of disability and mortality among the elderly. We investigated whether there was evidence in Southern Italy of an association between the IL6 gene variable number of tandem repeats (VNTR) polymorphism and extreme longevity, and tested for the possible interaction of apolipoprotein E (APOE) alleles with the IL6 VNTR alleles. Four alleles coding for variants of four different lengths have been identified: allele A [760 base pairs (bp)], allele B (680 bp), allele C (640 bp), and allele D (610 bp). IL6 VNTR and APOE allele and genotype frequencies were studied in a total of 61 centenarians and 94 middle-aged subjects from Southern Italy. The IL6 VNTR allele B was overrepresented in the younger control group compared with centenarians (odds ratio: 0.56, 95% confidence interval: 0.35-0.88, Bonferroni p-value VNTR alleles and APOE alleles on the odds ratios to reach extreme longevity were evaluated for the smallest number of subjects in centenarians and younger controls. Our findings suggested that the presence of the IL6 VNTR allele B could be detrimental for reaching extreme longevity.

Population Genetic Structure of Listeria monocytogenes Strains as Determined by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing

DEFF Research Database (Denmark)

Henri, Clémentine; Félix, Benjamin; Guillier, Laurent

2016-01-01

on the basis of different pulsed-field gel electrophoresis (PFGE) clusters, serotypes, and strain origins and typed by multilocus sequence typing (MLST), and the MLST results were supplemented with MLST data available from Institut Pasteur, representing human and additional food strains from France....... The distribution of sequence types (STs) was compared between food and clinical strains on a panel of 675 strains. High congruence between PFGE and MLST was found. Out of 73 PFGE clusters, the two most prevalent corresponded to ST9 and ST121. Using original statistical analysis, we demonstrated that (i...

A random number generator for continuous random variables

Science.gov (United States)

Guerra, V. M.; Tapia, R. A.; Thompson, J. R.

1972-01-01

A FORTRAN 4 routine is given which may be used to generate random observations of a continuous real valued random variable. Normal distribution of F(x), X, E(akimas), and E(linear) is presented in tabular form.

Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering.

Science.gov (United States)

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor; Essex, M

2015-05-01

To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice.

Multilocus dataset reveals demographic histories of two peat mosses in Europe

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Hock Zsófia

2007-08-01

Full Text Available Abstract Background Revealing the past and present demographic history of populations is of high importance to evaluate the conservation status of species. Demographic data can be obtained by direct monitoring or by analysing data of historical and recent collections. Although these methods provide the most detailed information they are very time consuming. Another alternative way is to make use of the information accumulated in the species' DNA over its history. Recent development of the coalescent theory makes it possible to reconstruct the demographic history of species using nucleotide polymorphism data. To separate the effect of natural selection and demography, multilocus analysis is needed because these two forces can produce similar patterns of polymorphisms. In this study we investigated the amount and pattern of sequence variability of a Europe wide sample set of two peat moss species (Sphagnum fimbriatum and S. squarrosum with similar distributions and mating systems but presumably contrasting historical demographies using 3 regions of the nuclear genome (appr. 3000 bps. We aimed to draw inferences concerning demographic, and phylogeographic histories of the species. Results All three nuclear regions supported the presence of an Atlantic and Non-Atlantic clade of S. fimbriatum suggesting glacial survival of the species along the Atlantic coast of Europe. Contrarily, S. squarrosum haplotypes showed three clades but no geographic structure at all. Maximum likelihood, mismatch and Bayesian analyses supported a severe historical bottleneck and a relatively recent demographic expansion of the Non-Atlantic clade of S. fimbriatum, whereas size of S. squarrosum populations has probably decreased in the past. Species wide molecular diversity of the two species was nearly the same with an excess of replacement mutations in S. fimbriatum. Similar levels of molecular diversity, contrasting phylogeographic patterns and excess of replacement

Molecular Epidemiologic Analysis of Enterococcus faecalis Isolates in Cuba by Multilocus Sequence Typing

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Kobayashi, Nobumichi; Nagashima, Shigeo

2009-01-01

We carried out the first study of Enterococcus faecalis clinical isolates in Cuba by multilocus sequence typing linking the molecular typing data with the presence of virulence determinants and the antibiotic resistance genes. A total of 23 E. faecalis isolates recovered from several clinic sources and geographic areas of Cuba during a period between 2000 and 2005 were typed by multilocus sequence typing. Thirteen sequence types (STs) including five novel STs were identified, and the ST 64 (clonal complex [CC] 8), ST 6 (CC2), ST 21(CC21), and ST 16 (CC58) were found in more than one strain. Sixty-seven percent of STs corresponded to STs reported previously in Spain, Poland, and The Netherlands, and other STs (ST115, ST64, ST6, and ST40) were genetically close to those detected in the United States. Prevalence of both antimicrobial resistance genes [aac(6′)-aph(2″), aph(3′), ant(6), ant(3″)(9), aph(2″)-Id, aph(2″)-Ic, erm(B), erm(A), erm(C), mef(A), tet(M), and tet(L)] and virulence genes (agg, gelE, cylA, esp, ccf, and efaAfs) were examined by polymerase chain reaction. Aminoglycoside resistance genes aac(6′)-Ie-aph(2″)-Ia, aph(3′), ant(6), ant(3″)(9) were more frequently detected in ST6, ST16, ST23, ST64, and ST115. The multidrug resistance was distributed to all STs detected, except for ST117 and singleton ST225. The presence of cyl gene was specifically linked to the ST64 and ST16. Presence of the esp, gel, and agg genes was not specific to any particular ST. This research provided the first insight into the population structure of E. faecalis in Cuba, that is, most Cuban strains were related to European strains, whereas others to U.S. strains. The CC2, CC21, and CC8, three of the biggest CCs in the world, were evidently circulating in Cuba, associated with multidrug resistance and virulence traits. PMID:19857135

Towards multilocus sequence typing of the Leishmania donovani complex: Resolving genotypes and haplotypes for five polymorphic metabolic enzymes (ASAT, GPI, NH1, NH2, PGD)

Czech Academy of Sciences Publication Activity Database

Mauricio, I. L.; Yeo, M.; Baghaei, M.; Doto, D.; Pratlong, F.; Zemanová, Eva; Dedet, J.-P.; Lukeš, Julius; Miles, M. A.

2006-01-01

Roč. 36, č. 7 (2006), s. 757-769 ISSN 0020-7519 Grant - others:European Comission(EU) QLK2-CT-2001-01810 Institutional research plan: CEZ:AV0Z60220518 Keywords : Leishmania donovani * Leishmania infantum * multilocus sequence typing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.337, year: 2006

Multiple-locus variable-number tandem-repeat analysis of pathogenic Yersinia enterocolitica in China.

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Xin Wang

Full Text Available The predominant bioserotypes of pathogenic Yersinia enterocolitica in China are 2/O: 9 and 3/O: 3; no pathogenic O: 8 strains have been found to date. Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA based on seven loci was able to distinguish 104 genotypes among 218 pathogenic Y. enterocolitica isolates in China and from abroad, showing a high resolution. The major pathogenic serogroups in China, O: 3 and O: 9, were divided into two clusters based on MLVA genotyping. The different distribution of Y. enterocolitica MLVA genotypes maybe due to the recent dissemination of specific clones of 2/O: 9 and 3/O: 3 strains in China. MLVA was a helpful tool for bacterial pathogen surveillance and investigation of pathogenic Y. enterocolitica outbreaks.

Clinical Trials With Large Numbers of Variables: Important Advantages of Canonical Analysis.

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Cleophas, Ton J

2016-01-01

Canonical analysis assesses the combined effects of a set of predictor variables on a set of outcome variables, but it is little used in clinical trials despite the omnipresence of multiple variables. The aim of this study was to assess the performance of canonical analysis as compared with traditional multivariate methods using multivariate analysis of covariance (MANCOVA). As an example, a simulated data file with 12 gene expression levels and 4 drug efficacy scores was used. The correlation coefficient between the 12 predictor and 4 outcome variables was 0.87 (P = 0.0001) meaning that 76% of the variability in the outcome variables was explained by the 12 covariates. Repeated testing after the removal of 5 unimportant predictor and 1 outcome variable produced virtually the same overall result. The MANCOVA identified identical unimportant variables, but it was unable to provide overall statistics. (1) Canonical analysis is remarkable, because it can handle many more variables than traditional multivariate methods such as MANCOVA can. (2) At the same time, it accounts for the relative importance of the separate variables, their interactions and differences in units. (3) Canonical analysis provides overall statistics of the effects of sets of variables, whereas traditional multivariate methods only provide the statistics of the separate variables. (4) Unlike other methods for combining the effects of multiple variables such as factor analysis/partial least squares, canonical analysis is scientifically entirely rigorous. (5) Limitations include that it is less flexible than factor analysis/partial least squares, because only 2 sets of variables are used and because multiple solutions instead of one is offered. We do hope that this article will stimulate clinical investigators to start using this remarkable method.

Characterization of European Yersinia enterocolitica 1A strains using restriction fragment length polymorphism and multilocus sequence analysis.

Science.gov (United States)

Murros, A; Säde, E; Johansson, P; Korkeala, H; Fredriksson-Ahomaa, M; Björkroth, J

2016-10-01

Yersinia enterocolitica is currently divided into two subspecies: subsp. enterocolitica including highly pathogenic strains of biotype 1B and subsp. palearctica including nonpathogenic strains of biotype 1A and moderately pathogenic strains of biotypes 2-5. In this work, we characterized 162 Y. enterocolitica strains of biotype 1A and 50 strains of biotypes 2-4 isolated from human, animal and food samples by restriction fragment length polymorphism using the HindIII restriction enzyme. Phylogenetic relatedness of 20 representative Y. enterocolitica strains including 15 biotype 1A strains was further studied by the multilocus sequence analysis of four housekeeping genes (glnA, gyrB, recA and HSP60). In all the analyses, biotype 1A strains formed a separate genomic group, which differed from Y. enterocolitica subsp. enterocolitica and from the strains of biotypes 2-4 of Y. enterocolitica subsp. palearctica. Based on these results, biotype 1A strains considered nonpathogenic should not be included in subspecies palearctica containing pathogenic strains of biotypes 2-5. Yersinia enterocolitica strains are currently divided into six biotypes and two subspecies. Strains of biotype 1A, which are phenotypically and genotypically very heterogeneous, are classified as subspecies palearctica. In this study, European Y. enterocolitica 1A strains isolated from both human and nonhuman sources were characterized using restriction fragment length polymorphism and multilocus sequence analysis. The European biotype 1A strains formed a separate group, which differed from strains belonging to subspecies enterocolitica and palearctica. This may indicate that the current division between the two subspecies is not sufficient considering the strain diversity within Y. enterocolitica. © 2016 The Society for Applied Microbiology.

Low numbers of repeat units in variable number of tandem repeats (VNTR) regions of white spot syndrome virus are correlated with disease outbreaks.

Science.gov (United States)

Hoa, T T T; Zwart, M P; Phuong, N T; de Jong, M C M; Vlak, J M

2012-11-01

White spot syndrome virus (WSSV) is the most important pathogen in shrimp farming systems worldwide including the Mekong Delta, Vietnam. The genome of WSSV is characterized by the presence of two major 'indel regions' found at ORF14/15 and ORF23/24 (WSSV-Thailand) and three regions with variable number tandem repeats (VNTR) located in ORF75, ORF94 and ORF125. In the current study, we investigated whether or not the number of repeat units in the VNTRs correlates with virus outbreak status and/or shrimp farming practice. We analysed 662 WSSV samples from individual WSSV-infected Penaeus monodon shrimp from 104 ponds collected from two important shrimp farming regions of the Mekong Delta: Ca Mau and Bac Lieu. Using this large data set and statistical analysis, we found that for ORF94 and ORF125, the mean number of repeat units (RUs) in VNTRs was significantly lower in disease outbreak ponds than in non-outbreak ponds. Although a higher mean RU number was observed in the improved-extensive system than in the rice-shrimp or semi-intensive systems, these differences were not significant. VNTR sequences are thus not only useful markers for studying WSSV genotypes and populations, but specific VNTR variants also correlate with disease outbreaks in shrimp farming systems. © 2012 Blackwell Publishing Ltd.

Changes in Variable Number of Tandem Repeats in 'Candidatus Liberibacter asiaticus' through Insect Transmission.

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Hiroshi Katoh

Full Text Available Citrus greening (huanglongbing is the most destructive citrus disease worldwide. The disease is associated with three species of 'Candidatus Liberibacter' among which 'Ca. Liberibacter asiaticus' has the widest distribution. 'Ca. L. asiaticus' is commonly transmitted by a phloem-feeding insect vector, the Asian citrus psyllid Diaphorina citri. A previous study showed that isolates of 'Ca. L. asiaticus' were clearly differentiated by variable number of tandem repeat (VNTR profiles at four loci in the genome. In this study, the VNTR analysis was further validated by assessing the stability of these repeats after multiplication of the pathogen upon host-to-host transmission using a 'Ca. L. asiaticus' strain from Japan. The results showed that some tandem repeats showed detectable changes after insect transmission. To our knowledge, this is the first report to demonstrate that the repeat numbers VNTR 002 and 077 of 'Ca. L. asiaticus' change through psyllid transmission. VNTRs in the recipient plant were apparently unrelated to the growing phase of the vector. In contrast, changes in the number of tandem repeats increased with longer acquisition and inoculation access periods, whereas changes were not observed through psyllid transmission after relatively short acquisition and inoculation access periods, up to 20 and 19 days, respectively.

Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of Campylobacter jejuni

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Nash John HE

2008-08-01

Full Text Available Abstract Background Multi-Locus Sequence Typing (MLST has emerged as a leading molecular typing method owing to its high ability to discriminate among bacterial isolates, the relative ease with which data acquisition and analysis can be standardized, and the high portability of the resulting sequence data. While MLST has been successfully applied to the study of the population structure for a number of different bacterial species, it has also provided compelling evidence for high rates of recombination in some species. We have analyzed a set of Campylobacter jejuni strains using MLST and Comparative Genomic Hybridization (CGH on a full-genome microarray in order to determine whether recombination and high levels of genomic mosaicism adversely affect the inference of strain relationships based on the analysis of a restricted number of genetic loci. Results Our results indicate that, in general, there is significant concordance between strain relationships established by MLST and those based on shared gene content as established by CGH. While MLST has significant predictive power with respect to overall genome similarity of isolates, we also found evidence for significant differences in genomic content among strains that would otherwise appear to be highly related based on their MLST profiles. Conclusion The extensive genomic mosaicism between closely related strains has important implications in the context of establishing strain to strain relationships because it suggests that the exact gene content of strains, and by extension their phenotype, is less likely to be "predicted" based on a small number of typing loci. This in turn suggests that a greater emphasis should be placed on analyzing genes of clinical interest as we forge ahead with the next generation of molecular typing methods.

Addictive behaviors and addiction-prone personality traits: associations with a dopamine multilocus genetic profile.

Science.gov (United States)

Davis, Caroline; Loxton, Natalie J

2013-07-01

The purpose of this study was to examine reward-related genetic risk for addictive behaviors in a healthy community sample (n=217) of men and women. We tested a mediation model predicting that a quantitative multilocus genetic profile score - reflecting the additive effects of alleles known to confer relatively increased dopamine signaling in the ventral striatum - would relate positively to a composite measure of addictive behaviors, and that this association would be mediated by personality traits consistently associated with addiction disorders. Our model was strongly supported by the data, and accounted for 24% of the variance in addictive behaviors. These data suggest that brain reward processes tend to exert their influence on addiction risk by their role in the development of relatively stable personality traits associated with addictive behaviors. Copyright © 2013 Elsevier Ltd. All rights reserved.

Use of multi-locus sequencing typing as identification method for the food-borne pathogen Listeria monocytogenes: a review

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Sonia Lamon

2015-01-01

Full Text Available Listeria monocytogenes is an ubiquitous, intracellular pathogen which has been implicated within the past decade as the causative organism in several outbreaks of foodborne diseases. In this review, a new approach to molecular typing primarily designed for global epidemiology has been described: multi-locus sequencing typing (MLST. This approach is novel, in that it uses data that allow the unambiguous characterization of bacterial strains via the Internet. Our aim is to present the currently available selection of references on L. monocytogenes MLST detection methods and to discuss its use as gold standard to L. monocytogenes subtyping method.

Accuracy, calibration and clinical performance of the EuroSCORE: can we reduce the number of variables?

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Ranucci, Marco; Castelvecchio, Serenella; Menicanti, Lorenzo; Frigiola, Alessandro; Pelissero, Gabriele

2010-03-01

The European system for cardiac operative risk evaluation (EuroSCORE) is currently used in many institutions and is considered a reference tool in many countries. We hypothesised that too many variables were included in the EuroSCORE using limited patient series. We tested different models using a limited number of variables. A total of 11150 adult patients undergoing cardiac operations at our institution (2001-2007) were retrospectively analysed. The 17 risk factors composing the EuroSCORE were separately analysed and ranked for accuracy of prediction of hospital mortality. Seventeen models were created by progressively including one factor at a time. The models were compared for accuracy with a receiver operating characteristics (ROC) analysis and area under the curve (AUC) evaluation. Calibration was tested with Hosmer-Lemeshow statistics. Clinical performance was assessed by comparing the predicted with the observed mortality rates. The best accuracy (AUC 0.76) was obtained using a model including only age, left ventricular ejection fraction, serum creatinine, emergency operation and non-isolated coronary operation. The EuroSCORE AUC (0.75) was not significantly different. Calibration and clinical performance were better in the five-factor model than in the EuroSCORE. Only in high-risk patients were 12 factors needed to achieve a good performance. Including many factors in multivariable logistic models increases the risk for overfitting, multicollinearity and human error. A five-factor model offers the same level of accuracy but demonstrated better calibration and clinical performance. Models with a limited number of factors may work better than complex models when applied to a limited number of patients. Copyright (c) 2009 European Association for Cardio-Thoracic Surgery. Published by Elsevier B.V. All rights reserved.

Multilocus phylogenetic reconstruction of the Clavariaceae (Agaricales) reveals polyphyly of agaricoid members.

Science.gov (United States)

Birkebak, Joshua M; Adamčík, Slavomír; Looney, Brian P; Matheny, P Brandon

2016-09-01

The genus Camarophyllopsis contains species with lamellate (agaricoid) basidiomes in the family Clavariaceae (Agaricales), a group otherwise dominated by club-like (clavarioid) or branched (coralloid) forms. Previous studies have suggested that species classified in Camarophyllopsis occur in two independent lineages. We reconstructed a multilocus phylogeny of the Clavaria-Camarophyllopsis-Clavicorona clade in the Clavariaceae using RNA polymerase II second largest subunit (rpb2), nuclear ribosomal 28S, and nuclear ribosomal ITS1-5.8S-ITS2 regions data and detected three independent groups of agaricoid fungi, including the genera Camarophyllopsis, Hodophilus, and Lamelloclavaria gen. nov, which distinctly differ in their pileipellis structure. In all, nine major lineages within the Clavaria-Camarophyllopsis-Clavicorona clade were recovered: Clavaria sensu stricto, Camarophyllopsis sensu stricto, Hodophilus, the Clavaria pullei clade, the Clavaria fumosa clade, Lamelloclavaria gen. nov., the Clavaria atrofusca clade, Holocoryne (= Clavaria sect. Holocoryne), and Clavicorona Clavaria is paraphyletic and represented by five clades. Additional gene sampling is necessary to determine and confirm relatedness of these lineages before splitting Clavaria into additional genera. © 2016 by The Mycological Society of America.

Multilocus sequence typing reveals two evolutionary lineages of Acidovorax avenae subsp. citrulli.

Science.gov (United States)

Feng, Jianjun; Schuenzel, Erin L; Li, Jianqiang; Schaad, Norman W

2009-08-01

Acidovorax avenae subsp. citrulli, causal agent of bacterial fruit blotch, has caused considerable damage to the watermelon and melon industry in China and the United States. Understanding the emergence and spread of this pathogen is important for controlling the disease. To build a fingerprinting database for reliable identification and tracking of strains of A. avenae subsp. citrulli, a multilocus sequence typing (MLST) scheme was developed using seven conserved loci. The study included 8 original strains from the 1978 description of A. avenae subsp. citrulli, 51 from China, and 34 from worldwide collections. Two major clonal complexes (CCs), CC1 and CC2, were identified within A. avenae subsp. citrulli; 48 strains typed as CC1 and 45 as CC2. All eight original 1978 strains isolated from watermelon and melon grouped in CC1. CC2 strains were predominant in the worldwide collection and all but five were isolated from watermelon. In China, a major seed producer for melon and watermelon, the predominant strains were CC1 and were found nearly equally on melon and watermelon.

In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

DEFF Research Database (Denmark)

Carattoli, Alessandra; Zankari, Ea; García-Fernández, Aurora

2014-01-01

In the work presented here, we designed and developed two easy-to-use Web tools for in silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data from members of the family Enterobacteriaceae. These tools will facilitate bacterial typing based on draft...... genomes of multidrug-resistant Enterobacteriaceae species by the rapid detection of known plasmid types. Replicon sequences from 559 fully sequenced plasmids associated with the family Enterobacteriaceae in the NCBI nucleotide database were collected to build a consensus database for integration...... sequences identified in the 559 fully sequenced plasmids. For plasmid multilocus sequence typing (pMLST) analysis, a database that is updated weekly was generated from www.pubmlst.org and integrated into a Web tool called pMLST. Both databases were evaluated using draft genomes from a collection...

Multilocus sequence typing scheme for the Mycobacterium abscessus complex.

Science.gov (United States)

Macheras, Edouard; Konjek, Julie; Roux, Anne-Laure; Thiberge, Jean-Michel; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby E; Bodmer, Thomas; Jarlier, Vincent; Cambau, Emmanuelle; Brisse, Sylvain; Caro, Valérie; Rastogi, Nalin; Gaillard, Jean-Louis; Heym, Beate

2014-01-01

We developed a multilocus sequence typing (MLST) scheme for Mycobacterium abscessus sensu lato, based on the partial sequencing of seven housekeeping genes: argH, cya, glpK, gnd, murC, pta and purH. This scheme was used to characterize a collection of 227 isolates recovered between 1994 and 2010 in France, Germany, Switzerland and Brazil. We identified 100 different sequence types (STs), which were distributed into three groups on the tree obtained by concatenating the sequences of the seven housekeeping gene fragments (3576bp): the M. abscessus sensu stricto group (44 STs), the "M. massiliense" group (31 STs) and the "M. bolletii" group (25 STs). SplitTree analysis showed a degree of intergroup lateral transfers. There was also evidence of lateral transfer events involving rpoB. The most prevalent STs in our collection were ST1 (CC5; 20 isolates) and ST23 (CC3; 31 isolates). Both STs were found in Europe and Brazil, and the latter was implicated in a large post-surgical procedure outbreak in Brazil. Respiratory isolates from patients with cystic fibrosis belonged to a large variety of STs; however, ST2 was predominant in this group of patients. Our MLST scheme, publicly available at www.pasteur.fr/mlst, offers investigators a valuable typing tool for M. abscessus sensu lato in future epidemiological studies throughout the world. Copyright © 2013 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Development of a multilocus sequence typing scheme for Ureaplasma.

Science.gov (United States)

Zhang, J; Kong, Y; Feng, Y; Huang, J; Song, T; Ruan, Z; Song, J; Jiang, Y; Yu, Y; Xie, X

2014-04-01

Ureaplasma is a commensal of the human urogenital tract but is always associated with invasive diseases such as non-gonococcal urethritis and infertility adverse pregnancy outcomes. To better understand the molecular epidemiology and population structure of Ureaplasma, a multilocus sequence typing (MLST) scheme based on four housekeeping genes (ftsH, rpL22, valS, thrS) was developed and validated using 283 isolates, including 14 serovars of reference strains and 269 strains obtained from clinical patients. A total of 99 sequence types (STs) were revealed: the 14 type strains of the Ureaplasma serovars were assigned to 12 STs, and 87 novel and special STs appeared among the clinical isolates. ST1 and ST22 were the predominant STs, which contained 68 and 70 isolates, respectively. Two clonal lineages (CC1 and CC2) were shown by eBURST analysis, and linkage disequilibrium was revealed through a standardized index of association (I A (S)). The neighbor-joining tree results of 14 Ureaplasma serovars showed two genetically significantly distant clusters, which was highly congruent with the species taxonomy of ureaplasmas [Ureaplasma parvum (UPA) and Ureaplasma urealyticum (UUR)]. Analysis of the biotypes of 269 clinical isolates revealed that all the isolates of CC1 were UPA and those of CC2 were UUR. Additionally, CC2 was found more often in symptomatic patients with vaginitis, tubal obstruction, and cervicitis. In conclusion, this MLST scheme is adequate for investigations of molecular epidemiology and population structure with highly discriminating capacity.

Human Campylobacteriosis in Luxembourg, 2010?2013: A Case-Control Study Combined with Multilocus Sequence Typing for Source Attribution and Risk Factor Analysis

OpenAIRE

Mossong, Jo?l; Mughini-Gras, Lapo; Penny, Christian; Devaux, Anthony; Olinger, Christophe; Losch, Serge; Cauchie, Henry-Michel; van Pelt, Wilfrid; Ragimbeau, Catherine

2016-01-01

Campylobacteriosis has increased markedly in Luxembourg during recent years. We sought to determine which Campylobacter genotypes infect humans, where they may originate from, and how they may infect humans. Multilocus sequence typing was performed on 1153 Campylobacter jejuni and 136 C. coli human strains to be attributed to three putative animal reservoirs (poultry, ruminants, pigs) and to environmental water using the asymmetric island model. A nationwide case-control study (2010?2013) for...

A simulation study of sample size demonstrated the importance of the number of events per variable to develop prediction models in clustered data

NARCIS (Netherlands)

Wynants, L.; Bouwmeester, W.; Moons, K. G. M.; Moerbeek, M.; Timmerman, D.; Van Huffel, S.; Van Calster, B.; Vergouwe, Y.

2015-01-01

Objectives: This study aims to investigate the influence of the amount of clustering [intraclass correlation (ICC) = 0%, 5%, or 20%], the number of events per variable (EPV) or candidate predictor (EPV = 5, 10, 20, or 50), and backward variable selection on the performance of prediction models.

The effects of variability on the number-flux-density relationship for radio sources

International Nuclear Information System (INIS)

Schuch, N.J.

1981-01-01

It has been known for some time that the number-flux-density relationship for radio sources requires a population of sources whose properties evolve with cosmological epoch, at least in models where the redshifts are all taken to be cosmological. In particular, the surveys made at metre wavelengths show, for bright sources, a slope of the log N -log S curve which is steeper than the value -1.5 expected in a static, non-evolving Euclidean universe. Here, N is the number of radio sources brighter than flux density S. Expansion without evolution in conventional geometrical models predicts slopes flatter than -1.5. If the radio survey is carried out at higher frequencies (typically 2.7 or 5 GHz - 11 or 6 cm wavelength), the slope of the log N -log S curve is steeper than -1.5 but not so steep as the slopes found for the low-frequency surveys. Many of the sources found in high-frequency surveys have radio spectra with relatively higher flux-densities in the centimetre range; these sources are frequently variable at high frequencies, with time-scales from a month or two upwards. Some possible effects of the variations on the observed counts of radio sources are considered. (author)

Basketball lay-up - foot loading characteristics and the number of trials necessary to obtain stable plantar pressure variables.

Science.gov (United States)

Chua, YaoHui K; Quek, Raymond K K; Kong, Pui W

2017-03-01

This study aimed (1) to profile the plantar loading characteristics when performing the basketball lay-up in a realistic setting and (2) to determine the number of trials necessary to establish a stable mean for plantar loading variables during the lay-up. Thirteen university male basketball players [age: 23.0 (1.4) years, height: 1.75 (0.05) m, mass: 68.4 (8.6) kg] performed ten successful basketball lay-ups from a stationary position. Plantar loading variables were recorded using the Novel Pedar-X in-shoe system. Loading variables including peak force, peak pressure, and pressure-time integral were extracted from eight foot regions. Performance stability of plantar loading variables during the take-off and landing steps were assessed using the sequential averaging technique and intra-class correlation coefficient (ICC). High plantar loadings were experienced at the heel during the take-off steps, and both the heel and forefoot regions upon landing. The sequential estimation technique revealed a five-eight trial range to achieve a stable mean across all plantar loading variables, whereas ICC analysis was insensitive to inter-trial differences of repeated lay-up performances. Future studies and performance evaluation protocols on plantar loading during basketball lay-ups should include at least eight trials to ensure that the measurements obtained are sufficiently stable.

MULTILOCUS SEQUENCE TYPING OF BRUCELLA ISOLATES FROM THAILAND.

Science.gov (United States)

Chawjiraphan, Wireeya; Sonthayanon, Piengchan; Chanket, Phanita; Benjathummarak, Surachet; Kerdsin, Anusak; Kalambhaheti, Thareerat

2016-11-01

Although brucellosis outbreaks in Thailand are rare, they cause abortions and infertility in animals, resulting in significant economic loss. Because Brucella spp display > 90% DNA homology, multilocus sequence typing (MLST) was employed to categorize local Brucella isolates into sequence types (STs) and to determine their genetic relatedness. Brucella samples were isolated from vaginal secretion of cows and goats, and from blood cultures of infected individuals. Brucella species were determined by multiplex PCR of eight loci, in addition to MLST based on partial DNA sequences of nine house-keeping genes. MLST analysis of 36 isolates revealed 78 distinct novel allele types and 34 novel STs, while two isolates possessed the known ST8. Sequence alignments identified polymorphic sites in each allele, ranging from 2-6%, while overall genetic diversity was 3.6%. MLST analysis of the 36 Brucella isolates classified them into three species, namely, B. melitensis, B. abortus and B. suis, in agreement with multiplex PCR results. Genetic relatedness among ST members of B. melitensis and B. abortus determined by eBURST program revealed ST2 as founder of B. abortus isolates and ST8 the founder of B. melitensis isolates. ST 36, 41 and 50 of Thai Brucella isolates were identified as single locus variants of clonal cluster (CC) 8, while the majority of STs were diverse. The genetic diversity and relatedness identified using MLST revealed hitherto unexpected diversity among Thai Brucella isolates. Genetic classification of isolates could reveal the route of brucellosis transmission among humans and farm animals and also reveal their relationship with other isolates in the region and other parts of the world.

Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes.

Science.gov (United States)

Chen, Yi; Gonzalez-Escalona, Narjol; Hammack, Thomas S; Allard, Marc W; Strain, Errol A; Brown, Eric W

2016-10-15

Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST clusters were congruent with MLST-defined clonal groups, which had various degrees of diversity at the whole-genome level. Notably, cgMLST could distinguish among outbreak strains and epidemiologically unrelated strains of the same clonal group, which could not be achieved using classic MLST schemes. The precise selection of cgMLST gene targets may not be critical for the general identification of clonal groups and outbreak strains. cgMLST analyses further identified outbreak strains, including those associated with recent outbreaks linked to contaminated French-style cheese, Hispanic-style cheese, stone fruit, caramel apple, ice cream, and packaged leafy green salad, as belonging to major clonal groups. We further developed lineage-specific cgMLST schemes, which can include accessory genes when core genomes do not possess sufficient diversity, and this provided additional resolution over species-specific cgMLST. Analyses of isolates from different common-source listeriosis outbreaks revealed various degrees of diversity, indicating that the numbers of allelic differences should always be combined with cgMLST clustering and epidemiological evidence to define a listeriosis outbreak. Classic multilocus sequence typing (MLST) schemes targeting internal fragments of 6 to 8 genes that define clonal complexes or epidemic clones have been widely employed to study L. monocytogenes biodiversity and its relation to pathogenicity potential and epidemiology. We demonstrated that core genome MLST

The Leishmania donovani complex: Genotypes of five metabolic enzymes (ICD, ME, MPI, G6PDH and FH), new targets for multilocus sequence typing

Czech Academy of Sciences Publication Activity Database

Zemanová, Eva; Jirků, Milan; Mauricio, I. L.; Horák, Aleš; Miles, M. A.; Lukeš, Julius

2007-01-01

Roč. 37, č. 2 (2007), s. 149-160 ISSN 0020-7519 R&D Projects: GA MŠk 2B06129 Grant - others:EU(EU) QLK2-CT-2001-01810 Institutional research plan: CEZ:AV0Z60220518 Source of funding: R - rámcový projekt EK Keywords : Leishmania donovani complex * zymodeme * multilocus sequence typing * Leishmania * phylogenetic network Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.392, year: 2007

Delineation of the species Haemophilus influenzae by phenotype, multilocus sequence phylogeny, and detection of marker genes

DEFF Research Database (Denmark)

Nørskov-Lauritsen, Niels; Overballe, MD; Kilian, Mogens

2009-01-01

To obtain more information on the much-debated definition of prokaryotic species, we investigated the borders of Haemophilus influenzae by comparative analysis of H. influenzae reference strains with closely related bacteria including strains assigned to Haemophilus haemolyticus, cryptic genospec......To obtain more information on the much-debated definition of prokaryotic species, we investigated the borders of Haemophilus influenzae by comparative analysis of H. influenzae reference strains with closely related bacteria including strains assigned to Haemophilus haemolyticus, cryptic...... genospecies biotype IV, and the never formally validated species "Haemophilus intermedius". Multilocus sequence phylogeny based on six housekeeping genes separated a cluster encompassing the type and the reference strains of H. influenzae from 31 more distantly related strains. Comparison of 16S rRNA gene...

Population structure of Lactobacillus helveticus isolates from naturally fermented dairy products based on multilocus sequence typing.

Science.gov (United States)

Sun, Zhihong; Liu, Wenjun; Song, Yuqin; Xu, Haiyan; Yu, Jie; Bilige, Menghe; Zhang, Heping; Chen, Yongfu

2015-05-01

Lactobacillus helveticus is an economically important lactic acid bacterium used in industrial dairy fermentation. In the present study, the population structure of 245 isolates of L. helveticus from different naturally fermented dairy products in China and Mongolia were investigated using an multilocus sequence typing scheme with 11 housekeeping genes. A total of 108 sequence types were detected, which formed 8 clonal complexes and 27 singletons. Results from Structure, SplitsTree, and ClonalFrame software analyses demonstrated the presence of 3 subpopulations in the L. helveticus isolates used in our study, namely koumiss, kurut-tarag, and panmictic lineages. Most L. helveticus isolates from particular ecological origins had specific population structures. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing

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Pruckler James M

2008-11-01

Full Text Available Abstract Background Bacillus cereus is most commonly associated with foodborne illness (diarrheal and emetic but is also an opportunistic pathogen that can cause severe and fatal infections. Several multilocus sequence typing (MLST schemes have recently been developed to genotype B. cereus and analysis has suggested a clonal or weakly clonal population structure for B. cereus and its close relatives B. anthracis and B. thuringiensis. In this study we used MLST to determine if B. cereus isolates associated with illnesses of varying severity (e.g., severe, systemic vs. gastrointestinal (GI illness were clonal or formed clonal complexes. Results A retrospective analysis of 55 clinical B. cereus isolates submitted to the Centers for Disease Control and Prevention between 1954 and 2004 was conducted. Clinical isolates from severe infections (n = 27, gastrointestinal (GI illness (n = 18, and associated isolates from food (n = 10 were selected for analysis using MLST. The 55 isolates were diverse and comprised 38 sequence types (ST in two distinct clades. Of the 27 isolates associated with serious illness, 13 clustered in clade 1 while 14 were in clade 2. Isolates associated with GI illness were also found throughout clades 1 and 2, while no isolates in this study belonged to clade 3. All the isolates from this study belonging to the clade 1/cereus III lineage were associated with severe disease while isolates belonging to clade1/cereus II contained isolates primarily associated with severe disease and emetic illness. Only three STs were observed more than once for epidemiologically distinct isolates. Conclusion STs of clinical B. cereus isolates were phylogenetically diverse and distributed among two of three previously described clades. Greater numbers of strains will need to be analyzed to confirm if specific lineages or clonal complexes are more likely to contain clinical isolates or be associated with specific illness, similar to B. anthracis and

Unravelling the Molecular Epidemiology and Genetic Diversity among Burkholderia pseudomallei Isolates from South India Using Multi-Locus Sequence Typing.

Science.gov (United States)

Tellapragada, Chaitanya; Kamthan, Aayushi; Shaw, Tushar; Ke, Vandana; Kumar, Subodh; Bhat, Vinod; Mukhopadhyay, Chiranjay

2016-01-01

There is a slow but steady rise in the case detection rates of melioidosis from various parts of the Indian sub-continent in the past two decades. However, the epidemiology of the disease in India and the surrounding South Asian countries remains far from well elucidated. Multi-locus sequence typing (MLST) is a useful epidemiological tool to study the genetic relatedness of bacterial isolates both with-in and across the countries. With this background, we studied the molecular epidemiology of 32 Burkholderia pseudomallei isolates (31 clinical and 1 soil isolate) obtained during 2006-2015 from various parts of south India using multi-locus sequencing typing and analysis. Of the 32 isolates included in the analysis, 30 (93.7%) had novel allelic profiles that were not reported previously. Sequence type (ST) 1368 (n = 15, 46.8%) with allelic profile (1, 4, 6, 4, 1, 1, 3) was the most common genotype observed. We did not observe a genotypic association of STs with geographical location, type of infection and year of isolation in the present study. Measure of genetic differentiation (FST) between Indian and the rest of world isolates was 0.14413. Occurrence of the same ST across three adjacent states of south India suggest the dispersion of B.pseudomallei across the south western coastal part of India with limited geographical clustering. However, majority of the STs reported from the present study remained as "outliers" on the eBURST "Population snapshot", suggesting the genetic diversity of Indian isolates from the Australasian and Southeast Asian isolates.

Unravelling the Molecular Epidemiology and Genetic Diversity among Burkholderia pseudomallei Isolates from South India Using Multi-Locus Sequence Typing.

Directory of Open Access Journals (Sweden)

Chaitanya Tellapragada

Full Text Available There is a slow but steady rise in the case detection rates of melioidosis from various parts of the Indian sub-continent in the past two decades. However, the epidemiology of the disease in India and the surrounding South Asian countries remains far from well elucidated. Multi-locus sequence typing (MLST is a useful epidemiological tool to study the genetic relatedness of bacterial isolates both with-in and across the countries. With this background, we studied the molecular epidemiology of 32 Burkholderia pseudomallei isolates (31 clinical and 1 soil isolate obtained during 2006-2015 from various parts of south India using multi-locus sequencing typing and analysis. Of the 32 isolates included in the analysis, 30 (93.7% had novel allelic profiles that were not reported previously. Sequence type (ST 1368 (n = 15, 46.8% with allelic profile (1, 4, 6, 4, 1, 1, 3 was the most common genotype observed. We did not observe a genotypic association of STs with geographical location, type of infection and year of isolation in the present study. Measure of genetic differentiation (FST between Indian and the rest of world isolates was 0.14413. Occurrence of the same ST across three adjacent states of south India suggest the dispersion of B.pseudomallei across the south western coastal part of India with limited geographical clustering. However, majority of the STs reported from the present study remained as "outliers" on the eBURST "Population snapshot", suggesting the genetic diversity of Indian isolates from the Australasian and Southeast Asian isolates.

The influence of climate variability on numbers of three waterbird species in Western Port, Victoria, 1973 2002

Science.gov (United States)

Chambers, Lynda E.; Loyn, Richard H.

2006-05-01

Seasonal and annual movements of Australian waterbirds are generally more complex than those of their Northern Hemisphere counterparts, and long-term data are needed to understand their relationships with climatic variables. This paper explores a long-term (1973 2002) set of waterbird counts from coastal Victoria and relates them to climatic data at local and continental scales. Three species (Black Swan Cygnus atratus, White-faced Heron Egretta novaehollandiae and Grey Teal Anas gracilis) were chosen for this analysis. Black Swans have large local breeding populations near the study region; White-faced Herons have smaller local breeding populations and Grey Teal breed extensively in ephemeral inland floodplains, such as those in the Murray-Darling Basin. All showed significant relationships with streamflow, regional rainfall and the Southern Oscillation Index (SOI) at appropriate scales and time-lags, with streamflow explaining the most variance. Black Swans showed a strong seasonal cycle in abundance and local climate variables had the greatest influence on the counts. Numbers were positively correlated with streamflow in southern Victoria three to six seasons before each count. Broader-scale climatic patterns were more important for the other two species. Numbers of White-faced Herons were positively correlated with streamflow or rainfall over various parts of Australia seven to nine seasons before each count. Numbers of Grey Teal showed weak seasonal cycles, and were negatively correlated with rainfall in Victoria or the Murray-Darling Basin in the seasons before or during each count, and positively with streamflow in the Murray-Darling Basin 15 18 months before each count.

Evolutionary history of the PER3 variable number of tandem repeats (VNTR): idiosyncratic aspect of primate molecular circadian clock.

Science.gov (United States)

Sabino, Flávia Cal; Ribeiro, Amanda Oliveira; Tufik, Sérgio; Torres, Laila Brito; Oliveira, José Américo; Mello, Luiz Eugênio Araújo Moraes; Cavalcante, Jeferson Souza; Pedrazzoli, Mario

2014-01-01

The PER3 gene is one of the clock genes, which function in the core mammalian molecular circadian system. A variable number of tandem repeats (VNTR) locus in the 18th exon of this gene has been strongly associated to circadian rhythm phenotypes and sleep organization in humans, but it has not been identified in other mammals except primates. To better understand the evolution and the placement of the PER3 VNTR in a phylogenetical context, the present study enlarges the investigation about the presence and the structure of this variable region in a large sample of primate species and other mammals. The analysis of the results has revealed that the PER3 VNTR occurs exclusively in simiiforme primates and that the number of copies of the primitive unit ranges from 2 to 11 across different primate species. Two transposable elements surrounding the 18th exon of PER3 were found in primates with published genome sequences, including the tarsiiforme Tarsius syrichta, which lacks the VNTR. These results suggest that this VNTR may have evolved in a common ancestor of the simiiforme branch and that the evolutionary copy number differentiation of this VNTR may be associated with primate simiiformes sleep and circadian phenotype patterns.

Evolutionary history of the PER3 variable number of tandem repeats (VNTR: idiosyncratic aspect of primate molecular circadian clock.

Directory of Open Access Journals (Sweden)

Flávia Cal Sabino

Full Text Available The PER3 gene is one of the clock genes, which function in the core mammalian molecular circadian system. A variable number of tandem repeats (VNTR locus in the 18th exon of this gene has been strongly associated to circadian rhythm phenotypes and sleep organization in humans, but it has not been identified in other mammals except primates. To better understand the evolution and the placement of the PER3 VNTR in a phylogenetical context, the present study enlarges the investigation about the presence and the structure of this variable region in a large sample of primate species and other mammals. The analysis of the results has revealed that the PER3 VNTR occurs exclusively in simiiforme primates and that the number of copies of the primitive unit ranges from 2 to 11 across different primate species. Two transposable elements surrounding the 18th exon of PER3 were found in primates with published genome sequences, including the tarsiiforme Tarsius syrichta, which lacks the VNTR. These results suggest that this VNTR may have evolved in a common ancestor of the simiiforme branch and that the evolutionary copy number differentiation of this VNTR may be associated with primate simiiformes sleep and circadian phenotype patterns.

Multilocus sequence typing reveals a novel subspeciation of Lactobacillus delbrueckii.

Science.gov (United States)

Tanigawa, Kana; Watanabe, Koichi

2011-03-01

Currently, the species Lactobacillus delbrueckii is divided into four subspecies, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. indicus and L. delbrueckii subsp. lactis. These classifications were based mainly on phenotypic identification methods and few studies have used genotypic identification methods. As a result, these subspecies have not yet been reliably delineated. In this study, the four subspecies of L. delbrueckii were discriminated by phenotype and by genotypic identification [amplified-fragment length polymorphism (AFLP) and multilocus sequence typing (MLST)] methods. The MLST method developed here was based on the analysis of seven housekeeping genes (fusA, gyrB, hsp60, ileS, pyrG, recA and recG). The MLST method had good discriminatory ability: the 41 strains of L. delbrueckii examined were divided into 34 sequence types, with 29 sequence types represented by only a single strain. The sequence types were divided into eight groups. These groups could be discriminated as representing different subspecies. The results of the AFLP and MLST analyses were consistent. The type strain of L. delbrueckii subsp. delbrueckii, YIT 0080(T), was clearly discriminated from the other strains currently classified as members of this subspecies, which were located close to strains of L. delbrueckii subsp. lactis. The MLST scheme developed in this study should be a useful tool for the identification of strains of L. delbrueckii to the subspecies level.

Imported brucellosis in Denmark: Molecular identification and multiple-locus variable number tandem repeat analysis (MLVA) genotyping of the bacteria

DEFF Research Database (Denmark)

Aftab, H.; Dargis, R.; Christensen, J. J.

2011-01-01

A polymerase chain reaction was used to identify Brucella species isolated from humans in Denmark. Consecutive analysis of referred bacteria and re-examination of historical isolates identified all as Brucella melitensis. Multiple-locus variable number tandem repeat analysis (MLVA) placed...... the isolates in the previously defined 'East Mediterranean' B. melitensis group....

Are Macro variables good predictors? A prediction based on the number of total medals acquired

Directory of Open Access Journals (Sweden)

Shahram Shafiee

2012-01-01

Full Text Available A large amount of effort is spent on forecasting the outcome of sporting events. Moreover, there are large quantities of data regarding the outcomes of sporting events and the factors which are assumed to contribute to those outcomes. In this paper we tried to predict the success of nations at the Asian Games through macro-economic, political, social and cultural variables. we used the information of variables include urban population, Education Expenditures, Age Structure, GDP Real Growth Rate, GDP Per Capita, Unemployment Rate, Population, Inflation Average, current account balance, life expectancy at birth and Merchandise Trade for all of the participating countries in Asian Games from 1970 to 2006 in order to build the model and then this model was tested by the information of variables in 2010. The prediction is based on the number of total medals acquired each country. In this research we used WEKA software that is a popular suite of machine learning software written in Java. The value of correlation coefficient between the predicted and original ranks is 90.42%. Neural Network Model, between 28 countries mentioned, predicts their ranks according to the maximum difference between predicted and original ranks of 19 countries (67.85% is 3, the maximum difference between predicted and original ranks of 8 countries (28.57% is between 4 to 6 and the difference between predicted and original ranks of 1 countries (3.57% is more than 6.

Characterization of Campylobacter jejuni applying flaA short variable region sequencing, multilocus sequencing and Fourier transform infrared spectroscopy

DEFF Research Database (Denmark)

Josefsen, Mathilde Hartmann; Bonnichsen, Lise; Larsson, Jonas

flaA short variable region sequencing and phenetic Fourier transform infrared (FTIR) spectroscopy was applied on a collection of 102 Campylobacter jejuni isolated from continuous sampling of organic, free range geese and chickens. FTIR has been shown to serve as a valuable tool in typing...

Multilocus Sequence Typing of Historical Burkholderia pseudomallei Isolates Collected in Southeast Asia from 1964 to 1967 Provides Insight into the Epidemiology of Melioidosis

OpenAIRE

McCombie, Roberta L.; Finkelstein, Richard A.; Woods, Donald E.

2006-01-01

A collection of 207 historically relevant Burkholderia pseudomallei isolates was analyzed by multilocus sequence typing (MLST). The strain collection contains environmental isolates obtained from a geographical distribution survey of B. pseudomallei isolates in Thailand (1964 to 1967), as well as stock cultures and colony variants from the U.S. Army Medical Research Unit (Malaysia), the Walter Reed Army Institute for Research, and the Pasteur Institute (Vietnam). The 207 isolates of the colle...

Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates.

Science.gov (United States)

Cody, Alison J; Bray, James E; Jolley, Keith A; McCarthy, Noel D; Maiden, Martin C J

2017-07-01

Human campylobacteriosis, caused by Campylobacter jejuni and C. coli , remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterization methods. Whole-genome sequencing (WGS) data enable the improvement of sequence-based typing approaches, such as multilocus sequence typing (MLST), by substantially increasing the number of loci examined. A core genome MLST (cgMLST) scheme defines a comprehensive set of those loci present in most members of a bacterial group, balancing very high resolution with comparability across the diversity of the group. Here we propose a set of 1,343 loci as a human campylobacteriosis cgMLST scheme (v1.0), the allelic profiles of which can be assigned to core genome sequence types. The 1,343 loci chosen were a subset of the 1,643 loci identified in the reannotation of the genome sequence of C. jejuni isolate NCTC 11168, chosen as being present in >95% of draft genomes of 2,472 representative United Kingdom campylobacteriosis isolates, comprising 2,207 (89.3%) C. jejuni isolates and 265 (10.7%) C. coli isolates. Validation of the cgMLST scheme was undertaken with 1,478 further high-quality draft genomes, containing 150 or fewer contiguous sequences, from disease isolate collections: 99.5% of these isolates contained ≥95% of the 1,343 cgMLST loci. In addition to the rapid and effective high-resolution analysis of large numbers of diverse isolates, the cgMLST scheme enabled the efficient identification of very closely related isolates from a well-defined single-source campylobacteriosis outbreak. Copyright © 2017 Cody et al.

DNA fingerprinting of Mycobacterium leprae strains using variable number tandem repeat (VNTR) - fragment length analysis (FLA).

Science.gov (United States)

Jensen, Ronald W; Rivest, Jason; Li, Wei; Vissa, Varalakshmi

2011-07-15

The study of the transmission of leprosy is particularly difficult since the causative agent, Mycobacterium leprae, cannot be cultured in the laboratory. The only sources of the bacteria are leprosy patients, and experimentally infected armadillos and nude mice. Thus, many of the methods used in modern epidemiology are not available for the study of leprosy. Despite an extensive global drug treatment program for leprosy implemented by the WHO, leprosy remains endemic in many countries with approximately 250,000 new cases each year. The entire M. leprae genome has been mapped and many loci have been identified that have repeated segments of 2 or more base pairs (called micro- and minisatellites). Clinical strains of M. leprae may vary in the number of tandem repeated segments (short tandem repeats, STR) at many of these loci. Variable number tandem repeat (VNTR) analysis has been used to distinguish different strains of the leprosy bacilli. Some of the loci appear to be more stable than others, showing less variation in repeat numbers, while others seem to change more rapidly, sometimes in the same patient. While the variability of certain VNTRs has brought up questions regarding their suitability for strain typing, the emerging data suggest that analyzing multiple loci, which are diverse in their stability, can be used as a valuable epidemiological tool. Multiple locus VNTR analysis (MLVA) has been used to study leprosy evolution and transmission in several countries including China, Malawi, the Philippines, and Brazil. MLVA involves multiple steps. First, bacterial DNA is extracted along with host tissue DNA from clinical biopsies or slit skin smears (SSS). The desired loci are then amplified from the extracted DNA via polymerase chain reaction (PCR). Fluorescently-labeled primers for 4-5 different loci are used per reaction, with 18 loci being amplified in a total of four reactions. The PCR products may be subjected to agarose gel electrophoresis to verify the

Genetic Dissection of Maize Embryonic Callus Regenerative Capacity Using Multi-Locus Genome-Wide Association Studies

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Langlang Ma

2018-04-01

Full Text Available The regenerative capacity of the embryonic callus, a complex quantitative trait, is one of the main limiting factors for maize transformation. This trait was decomposed into five traits, namely, green callus rate (GCR, callus differentiating rate (CDR, callus plantlet number (CPN, callus rooting rate (CRR, and callus browning rate (CBR. To dissect the genetic foundation of maize transformation, in this study multi-locus genome-wide association studies (GWAS for the five traits were performed in a population of 144 inbred lines genotyped with 43,427 SNPs. Using the phenotypic values in three environments and best linear unbiased prediction (BLUP values, as a result, a total of 127, 56, 160, and 130 significant quantitative trait nucleotides (QTNs were identified by mrMLM, FASTmrEMMA, ISIS EM-BLASSO, and pLARmEB, respectively. Of these QTNs, 63 QTNs were commonly detected, including 15 across multiple environments and 58 across multiple methods. Allele distribution analysis showed that the proportion of superior alleles for 36 QTNs was <50% in 31 elite inbred lines. Meanwhile, these superior alleles had obviously additive effect on the regenerative capacity. This indicates that the regenerative capacity-related traits can be improved by proper integration of the superior alleles using marker-assisted selection. Moreover, a total of 40 candidate genes were found based on these common QTNs. Some annotated genes were previously reported to relate with auxin transport, cell fate, seed germination, or embryo development, especially, GRMZM2G108933 (WOX2 was found to promote maize transgenic embryonic callus regeneration. These identified candidate genes will contribute to a further understanding of the genetic foundation of maize embryonic callus regeneration.

pKWmEB: integration of Kruskal-Wallis test with empirical Bayes under polygenic background control for multi-locus genome-wide association study.

Science.gov (United States)

Ren, Wen-Long; Wen, Yang-Jun; Dunwell, Jim M; Zhang, Yuan-Ming

2018-03-01

Although nonparametric methods in genome-wide association studies (GWAS) are robust in quantitative trait nucleotide (QTN) detection, the absence of polygenic background control in single-marker association in genome-wide scans results in a high false positive rate. To overcome this issue, we proposed an integrated nonparametric method for multi-locus GWAS. First, a new model transformation was used to whiten the covariance matrix of polygenic matrix K and environmental noise. Using the transferred model, Kruskal-Wallis test along with least angle regression was then used to select all the markers that were potentially associated with the trait. Finally, all the selected markers were placed into multi-locus model, these effects were estimated by empirical Bayes, and all the nonzero effects were further identified by a likelihood ratio test for true QTN detection. This method, named pKWmEB, was validated by a series of Monte Carlo simulation studies. As a result, pKWmEB effectively controlled false positive rate, although a less stringent significance criterion was adopted. More importantly, pKWmEB retained the high power of Kruskal-Wallis test, and provided QTN effect estimates. To further validate pKWmEB, we re-analyzed four flowering time related traits in Arabidopsis thaliana, and detected some previously reported genes that were not identified by the other methods.

The transition matrix element A{sub gq}(N) of the variable flavor number scheme at O(α{sub s}{sup 3})

Energy Technology Data Exchange (ETDEWEB)

Ablinger, J. [Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstraße 69, A-4040 Linz (Austria); Blümlein, J.; De Freitas, A. [Deutsches Elektronen-Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany); Hasselhuhn, A. [Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstraße 69, A-4040 Linz (Austria); Manteuffel, A. von [PRISMA Cluster of Excellence and Institute of Physics, J. Gutenberg University, D-55099 Mainz (Germany); Round, M. [Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstraße 69, A-4040 Linz (Austria); Deutsches Elektronen-Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany); Schneider, C. [Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstraße 69, A-4040 Linz (Austria); Wißbrock, F. [Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstraße 69, A-4040 Linz (Austria); Deutsches Elektronen-Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany)

2014-05-15

We calculate the massive unpolarized operator matrix element A{sub gq}{sup (3)}(N) to 3-loop order in Quantum Chromodynamics at general values of the Mellin variable N. This is the first complete transition function needed in the variable flavor number scheme obtained at O(α{sub s}{sup 3}). A first independent recalculation is performed for the contributions ∝N{sub F} of the 3-loop anomalous dimension γ{sub gq}{sup (2)}(N)

Variable-number-of-tandem-repeats analysis of genetic diversity in Pasteuria ramosa.

Science.gov (United States)

Mouton, L; Ebert, D

2008-05-01

Variable-number-of-tandem-repeats (VNTR) markers are increasingly being used in population genetic studies of bacteria. They were recently developed for Pasteuria ramosa, an endobacterium that infects Daphnia species. In the present study, we genotyped P. ramosa in 18 infected hosts from the United Kingdom, Belgium, and two lakes in the United States using seven VNTR markers. Two Daphnia species were collected: D. magna and D. dentifera. Six loci showed length polymorphism, with as many as five alleles identified for a single locus. Similarity coefficient calculations showed that the extent of genetic variation between pairs of isolates within populations differed according to the population, but it was always less than the genetic distances among populations. Analysis of the genetic distances performed using principal component analysis revealed strong clustering by location of origin, but not by host Daphnia species. Our study demonstrated that the VNTR markers available for P. ramosa are informative in revealing genetic differences within and among populations and may therefore become an important tool for providing detailed analysis of population genetics and epidemiology.

Multilocus Sequence Analysis of Cercospora spp. from Different Host Plant Families

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Floreta Fiska Yuliarni

2014-06-01

Full Text Available Identification of the genus Cercospora is still complicated due to the host preferences often being used as the main criteria to propose a new name. We determined the relationship between host plants and multilocus sequence variations (ITS rDNA including 5.8S rDNA, elongation factor 1-α, and calmodulin in Cercospora spp. to investigate the host specificity. We used 53 strains of Cercospora spp. infecting 12 plant families for phylogenetic analysis. The sequences of 23 strains of Cercospora spp. infecting the plant families of Asteraceae, Cucurbitaceae, and Solanaceae were determined in this study. The sequences of 30 strains of Cercospora spp. infecting the plant families of Fabaceae, Amaranthaceae, Apiaceae, Plumbaginaceae, Malvaceae, Cistaceae, Plantaginaceae, Lamiaceae, and Poaceae were obtained from GenBank. The molecular phylogenetic analysis revealed that the majority of Cercospora species lack host specificity, and only C. zinniicola, C. zeina, C. zeae-maydis, C. cocciniae, and C. mikaniicola were found to be host-specific. Closely related species of Cercospora could not be distinguished using molecular analyses of ITS, EF, and CAL gene regions. The topology of the phylogenetic tree based on the CAL gene showed a better topology and Cercospora species separation than the trees developed based on the ITS rDNA region or the EF gene.

Use of multiple-locus variable-number tandem-repeats analysis (MLVA) typing to characterize Salmonella Typhimurium DT41 broiler breeder infections

DEFF Research Database (Denmark)

Litrup, E.; Christensen, H.; Nordentoft, Steen

2010-01-01

To characterize isolates of Salmonella Typhimurium DT41 obtained from infected flocks of broiler breeders by multiple-locus variable-number tandem-repeats analysis (MLVA) and compare results with a diverse strain collection from Germany and United Kingdom and isolates from Danish patients. A total...

Integer linear models with a polynomial number of variables and constraints for some classical combinatorial optimization problems

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Nelson Maculan

2003-01-01

Full Text Available We present integer linear models with a polynomial number of variables and constraints for combinatorial optimization problems in graphs: optimum elementary cycles, optimum elementary paths and optimum tree problems.Apresentamos modelos lineares inteiros com um número polinomial de variáveis e restrições para problemas de otimização combinatória em grafos: ciclos elementares ótimos, caminhos elementares ótimos e problemas em árvores ótimas.

The Comparison of Streptococcus agalactiae Isolated from Fish and Bovine using Multilocus Sequence Typing

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ANGELA MARIANA LUSIASTUTI

2013-12-01

Full Text Available Multilocus sequence typing (MLST has greater utility for determining the recent ancestral lineage and the relatedness of individual strains. Group B streptococci (GBS is one of the major causes of subclinical mastitis of dairy cattle in several countries. GBS also sporadically causes epizootic infections in fish. The aim of this study was to compare the evolutionary lineage of fish and bovine isolates in relation to the S. agalactiae global population as a whole by comparing the MLST profiles. Twenty S. agalactiae isolates were obtained from dairy cattle and fish. PCR products were amplified with seven different oligonucleotide primer pairs designed from the NEM316 GBS genome sequence. Clone complexes demonstrated that bovine and fish isolates were separate populations. These findings lead us to conclude that fish S. agalactiae is not a zoonotic agent for bovine. MLST could help clarify the emergence of pathogenic clones and to decide whether the host acts as a reservoir for another pathogenic lineage.

Diversification and Distribution of Ruminant Chlamydia abortus Clones Assessed by MLST and MLVA

OpenAIRE

Siarkou, Victoria I.; Vorimore, Fabien; Vicari, Nadia; Magnino, Simone; Rodolakis, Annie; Pannekoek, Yvonne; Sachse, Konrad; Longbottom, David; Laroucau, Karine

2015-01-01

Chlamydia abortus, an obligate intracellular bacterium, is the most common infectious cause of abortion in small ruminants worldwide and has zoonotic potential. We applied multilocus sequence typing (MLST) together with multiple-locus variable-number tandem repeat analysis (MLVA) to genotype 94 ruminant C. abortus strains, field isolates and samples collected from 1950 to 2011 in diverse geographic locations, with the aim of delineating C. abortus lineages and clones. MLST revealed the previo...

Use of Whole-Genus Genome Sequence Data To Develop a Multilocus Sequence Typing Tool That Accurately Identifies Yersinia Isolates to the Species and Subspecies Levels

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Hall, Miquette; Chattaway, Marie A.; Reuter, Sandra; Savin, Cyril; Strauch, Eckhard; Carniel, Elisabeth; Connor, Thomas; Van Damme, Inge; Rajakaruna, Lakshani; Rajendram, Dunstan; Jenkins, Claire; Thomson, Nicholas R.

2014-01-01

The genus Yersinia is a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identify Yersinia strains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic species Yersinia enterocolitica to whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification of Yersinia isolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available for Y. enterocolitica. PMID:25339391

Variable Copy Number, Intra-Genomic Heterogeneities and Lateral Transfers of the 16S rRNA Gene in Pseudomonas

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Bodilis, Josselin; Nsigue-Meilo, Sandrine; Besaury, Ludovic; Quillet, Laurent

2012-01-01

Even though the 16S rRNA gene is the most commonly used taxonomic marker in microbial ecology, its poor resolution is still not fully understood at the intra-genus level. In this work, the number of rRNA gene operons, intra-genomic heterogeneities and lateral transfers were investigated at a fine-scale resolution, throughout the Pseudomonas genus. In addition to nineteen sequenced Pseudomonas strains, we determined the 16S rRNA copy number in four other Pseudomonas strains by Southern hybridization and Pulsed-Field Gel Electrophoresis, and studied the intra-genomic heterogeneities by Denaturing Gradient Gel Electrophoresis and sequencing. Although the variable copy number (from four to seven) seems to be correlated with the evolutionary distance, some close strains in the P. fluorescens lineage showed a different number of 16S rRNA genes, whereas all the strains in the P. aeruginosa lineage displayed the same number of genes (four copies). Further study of the intra-genomic heterogeneities revealed that most of the Pseudomonas strains (15 out of 19 strains) had at least two different 16S rRNA alleles. A great difference (5 or 19 nucleotides, essentially grouped near the V1 hypervariable region) was observed only in two sequenced strains. In one of our strains studied (MFY30 strain), we found a difference of 12 nucleotides (grouped in the V3 hypervariable region) between copies of the 16S rRNA gene. Finally, occurrence of partial lateral transfers of the 16S rRNA gene was further investigated in 1803 full-length sequences of Pseudomonas available in the databases. Remarkably, we found that the two most variable regions (the V1 and V3 hypervariable regions) had probably been laterally transferred from another evolutionary distant Pseudomonas strain for at least 48.3 and 41.6% of the 16S rRNA sequences, respectively. In conclusion, we strongly recommend removing these regions of the 16S rRNA gene during the intra-genus diversity studies. PMID:22545126

Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya.

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Ingasia, Luicer A; Cheruiyot, Jelagat; Okoth, Sheila Akinyi; Andagalu, Ben; Kamau, Edwin

2016-04-01

Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p=0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; pKenya after introduction of the artemether-lumefantrine is important in refining the spread of drug resistant strains and malaria transmission for more effective control and eventual elimination of malaria in Kenya. Copyright © 2015. Published by Elsevier B.V.

Novel Polymorphic Multilocus Microsatellite Markers to Distinguish Candida tropicalis Isolates.

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Xin Fan

Full Text Available Candida tropicalis is an important pathogen. Here we developed and evaluated a polymorphic multilocus microsatellite scheme employing novel genetic markers for genotyping of C. tropicalis. Using 10 isolates from 10 unique (separate patients to screen over 4000 tandem repeats from the C. tropicalis genome (strain MYA-3404, six new candidate microsatellite loci (ctm1, ctm3, ctm8, ctm18, ctm24 and ctm26 were selected according to amplification success, observed polymorphisms and stability of flanking regions by preliminary testing. Two known microsatellite loci CT14 and URA3 were also studied. The 6-locus scheme was then tested against a set of 82 different isolates from 32 patients. Microsatellite genotypes of isolates from the same patient (two to five isolates per patient were identical. The six loci produced eight to 17 allele types and identified 11 to 24 genotypes amongst 32 patients' isolates, achieving a discriminatory power (DP of 0.76 to 0.97 (versus 0.78 for both CT14 and URA3 loci, respectively. Testing of a combination of only three loci, ctm1, ctm3 and ctm24, also achieved maximum typing efficiency (DP = 0.99, 29 genotypes. The microsatellite typing scheme had good correlation compared with pulsed-field gel electrophoresis, although was slightly less discriminatory. The new six-locus microsatellite typing scheme is a potentially valuable tool for genotyping and investigating microevolution of C. tropicalis.

Hydroxyl layer: trend of number density and intra-annual variability

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Sonnemann, G. R.; Hartogh, P.; Berger, U.; Grygalashvyly, M.

2015-06-01

The layer of vibrationally excited hydroxyl (OH*) near the mesopause in Earth's atmosphere is widely used to derive the temperature at this height and to observe dynamical processes such as gravity waves. The concentration of OH* is controlled by the product of atomic hydrogen, with ozone creating a layer of enhanced concentration in the mesopause region. However, the basic influences on the OH* layer are atomic oxygen and temperature. The long-term monitoring of this layer provides information on a changing atmosphere. It is important to know which proportion of a trend results from anthropogenic impacts on the atmosphere and which proportion reflects natural variations. In a previous paper (Grygalashvyly et al., 2014), the trend of the height of the layer and the trend in temperature were investigated particularly in midlatitudes on the basis of our coupled dynamic and chemical transport model LIMA (Leibniz Institute Middle Atmosphere). In this paper we consider the trend for the number density between the years 1961 and 2009 and analyze the reason of the trends on a global scale. Further, we consider intra-annual variations. Temperature and wind have the strongest impacts on the trend. Surprisingly, the increase in greenhouse gases (GHGs) has no clear influence on the chemistry of OH*. The main reason for this lies in the fact that, in the production term of OH*, if atomic hydrogen increases due to increasing humidity of the middle atmosphere by methane oxidation, ozone decreases. The maximum of the OH* layer is found in the mesopause region and is very variable. The mesopause region is a very intricate domain marked by changeable dynamics and strong gradients of all chemically active minor constituents determining the OH* chemistry. The OH* concentration responds, in part, very sensitively to small changes in these parameters. The cause for this behavior is given by nonlinear reactions of the photochemical system being a nonlinear enforced chemical oscillator

Hydroxyl layer: trend of number density and intra-annual variability

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G. R. Sonnemann

2015-06-01

Full Text Available The layer of vibrationally excited hydroxyl (OH* near the mesopause in Earth's atmosphere is widely used to derive the temperature at this height and to observe dynamical processes such as gravity waves. The concentration of OH* is controlled by the product of atomic hydrogen, with ozone creating a layer of enhanced concentration in the mesopause region. However, the basic influences on the OH* layer are atomic oxygen and temperature. The long-term monitoring of this layer provides information on a changing atmosphere. It is important to know which proportion of a trend results from anthropogenic impacts on the atmosphere and which proportion reflects natural variations. In a previous paper (Grygalashvyly et al., 2014, the trend of the height of the layer and the trend in temperature were investigated particularly in midlatitudes on the basis of our coupled dynamic and chemical transport model LIMA (Leibniz Institute Middle Atmosphere. In this paper we consider the trend for the number density between the years 1961 and 2009 and analyze the reason of the trends on a global scale. Further, we consider intra-annual variations. Temperature and wind have the strongest impacts on the trend. Surprisingly, the increase in greenhouse gases (GHGs has no clear influence on the chemistry of OH*. The main reason for this lies in the fact that, in the production term of OH*, if atomic hydrogen increases due to increasing humidity of the middle atmosphere by methane oxidation, ozone decreases. The maximum of the OH* layer is found in the mesopause region and is very variable. The mesopause region is a very intricate domain marked by changeable dynamics and strong gradients of all chemically active minor constituents determining the OH* chemistry. The OH* concentration responds, in part, very sensitively to small changes in these parameters. The cause for this behavior is given by nonlinear reactions of the photochemical system being a nonlinear enforced

Multilocus Sequence Typing and Virulence Profiles in Uropathogenic Escherichia coli Isolated from Cats in the United States.

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Xiaoqiang Liu

Full Text Available The population structure, virulence, and antimicrobial resistance of uropathogenic E. coli (UPEC from cats are rarely characterized. The aim of this study was to compare and characterize the UPEC isolated from cats in four geographic regions of USA in terms of their multilocus sequence typing (MLST, virulence profiles, clinical signs, antimicrobial resistance and phylogenetic grouping. The results showed that a total of 74 E. coli isolates were typed to 40 sequence types with 10 being novel. The most frequent phylogenetic group was B2 (n = 57. The most frequent sequence types were ST73 (n = 12 and ST83 (n = 6, ST73 was represented by four multidrug resistant (MDR and eight non-multidrug resistant (SDR isolates, and ST83 were significantly more likely to exhibit no drug resistant (NDR isolates carrying the highest number of virulence genes. Additionally, MDR isolates were more diverse, and followed by SDR and NDR isolates in regards to the distribution of the STs. afa/draBC was the most prevalent among the 29 virulence-associated genes. Linking virulence profile and antimicrobial resistance, the majority of virulence-associated genes tested were more prevalent in NDR isolates, and followed by SDR and MDR isolates. Twenty (50% MLST types in this study have previously been associated with human isolates, suggesting that these STs are potentially zoonotic. Our data enhanced the understanding of E. coli population structure and virulence association from cats. The diverse and various combinations of virulence-associated genes implied that the infection control may be challenging.

Variable-flavor-number scheme in analysis of heavy-quark electro-production data

International Nuclear Information System (INIS)

Alekhin, S.; Bluemlein, J.; Klein, S.; Moch, S.

2009-08-01

We check the impact of the factorization scheme employed in the calculation of the heavy-quark deep-inelastic scattering (DIS) electro-production on the PDFs determined in the NNLO QCD analysis of the world inclusive neutral-current DIS data combined with the ones on the neutrino-nucleon DIS di-muon production and the fixed-target Drell-Yan process. The charm-quark DIS contribution is calculated in the general-mass variable-flavor-number (GMVFN) scheme: At asymptotically large values of the momentum transfer Q it is given by the zero-mass 4-flavor scheme and at the value of Q equal to the charm-quark mass it is smoothly matched with the 3-flavor scheme using the Buza-Matiounine-Smith-van Neerven prescription. The PDFs obtained in this variant of the fit are very similar to the ones obtained in the fit with a 3-flavor scheme employed. Our 5-flavor PDFs derived from the 3-flavor ones using the NNLO matching conditions are used to calculate the rates of W ± /Z and t anti t production at the Tevatron collider and the LHC at NNLO. (orig.)

Analytic number theory an introductory course

CERN Document Server

Bateman, Paul T

2004-01-01

This valuable book focuses on a collection of powerful methods ofanalysis that yield deep number-theoretical estimates. Particularattention is given to counting functions of prime numbers andmultiplicative arithmetic functions. Both real variable ("elementary")and complex variable ("analytic") methods are employed.

Coagulase-Negative Staphylococci in Human Milk From Mothers of Preterm Compared With Term Neonates.

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Soeorg, Hiie; Metsvaht, Tuuli; Eelmäe, Imbi; Metsvaht, Hanna Kadri; Treumuth, Sirli; Merila, Mirjam; Ilmoja, Mari-Liis; Lutsar, Irja

2017-05-01

Human milk is the preferred nutrition for neonates and a source of bacteria. Research aim: The authors aimed to characterize the molecular epidemiology and genetic content of staphylococci in the human milk of mothers of preterm and term neonates. Staphylococci were isolated once per week in the 1st month postpartum from the human milk of mothers of 20 healthy term and 49 preterm neonates hospitalized in the neonatal intensive care unit. Multilocus variable-number tandem-repeats analysis and multilocus sequence typing were used. The presence of the mecA gene, icaA gene of the ica-operon, IS 256, and ACME genetic elements was determined by PCR. The human milk of mothers of preterm compared with term neonates had higher counts of staphylococci but lower species diversity. The human milk of mothers of preterm compared with term neonates more often contained Staphylococcus epidermidis mecA (32.7% vs. 2.6%), icaA (18.8% vs. 6%), IS 256 (7.9% vs. 0.9%), and ACME (15.4% vs. 5.1%), as well as Staphylococcus haemolyticus mecA (90.5% vs. 10%) and IS 256 (61.9% vs. 10%). The overall distribution of multilocus variable-number tandem-repeats analysis (MLVA) types and sequence types was similar between the human milk of mothers of preterm and term neonates, but a few mecA-IS 256-positive MLVA types colonized only mothers of preterm neonates. Maternal hospitalization within 1 month postpartum and the use of an arterial catheter or antibacterial treatment in the neonate increased the odds of harboring mecA-positive staphylococci in human milk. Limiting exposure of mothers of preterm neonates to the hospital could prevent human milk colonization with more pathogenic staphylococci.

spa Typing and Multilocus Sequence Typing Show Comparable Performance in a Macroepidemiologic Study of Staphylococcus aureus in the United States.

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O'Hara, F Patrick; Suaya, Jose A; Ray, G Thomas; Baxter, Roger; Brown, Megan L; Mera, Robertino M; Close, Nicole M; Thomas, Elizabeth; Amrine-Madsen, Heather

2016-01-01

A number of molecular typing methods have been developed for characterization of Staphylococcus aureus isolates. The utility of these systems depends on the nature of the investigation for which they are used. We compared two commonly used methods of molecular typing, multilocus sequence typing (MLST) (and its clustering algorithm, Based Upon Related Sequence Type [BURST]) with the staphylococcal protein A (spa) typing (and its clustering algorithm, Based Upon Repeat Pattern [BURP]), to assess the utility of these methods for macroepidemiology and evolutionary studies of S. aureus in the United States. We typed a total of 366 clinical isolates of S. aureus by these methods and evaluated indices of diversity and concordance values. Our results show that, when combined with the BURP clustering algorithm to delineate clonal lineages, spa typing produces results that are highly comparable with those produced by MLST/BURST. Therefore, spa typing is appropriate for use in macroepidemiology and evolutionary studies and, given its lower implementation cost, this method appears to be more efficient. The findings are robust and are consistent across different settings, patient ages, and specimen sources. Our results also support a model in which the methicillin-resistant S. aureus (MRSA) population in the United States comprises two major lineages (USA300 and USA100), which each consist of closely related variants.

Antimicrobial susceptibility among clinical Nocardia species identified by multilocus sequence analysis.

Science.gov (United States)

McTaggart, Lisa R; Doucet, Jennifer; Witkowska, Maria; Richardson, Susan E

2015-01-01

Antimicrobial susceptibility patterns of 112 clinical isolates, 28 type strains, and 9 reference strains of Nocardia were determined using the Sensititre Rapmyco microdilution panel (Thermo Fisher, Inc.). Isolates were identified by highly discriminatory multilocus sequence analysis and were chosen to represent the diversity of species recovered from clinical specimens in Ontario, Canada. Susceptibility to the most commonly used drug, trimethoprim-sulfamethoxazole, was observed in 97% of isolates. Linezolid and amikacin were also highly effective; 100% and 99% of all isolates demonstrated a susceptible phenotype. For the remaining antimicrobials, resistance was species specific with isolates of Nocardia otitidiscaviarum, N. brasiliensis, N. abscessus complex, N. nova complex, N. transvalensis complex, N. farcinica, and N. cyriacigeorgica displaying the traditional characteristic drug pattern types. In addition, the antimicrobial susceptibility profiles of a variety of rarely encountered species isolated from clinical specimens are reported for the first time and were categorized into four additional drug pattern types. Finally, MICs for the control strains N. nova ATCC BAA-2227, N. asteroides ATCC 19247(T), and N. farcinica ATCC 23826 were robustly determined to demonstrate method reproducibility and suitability of the commercial Sensititre Rapmyco panel for antimicrobial susceptibility testing of Nocardia spp. isolated from clinical specimens. The reported values will facilitate quality control and standardization among laboratories. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Genetic diversity of the red-spotted tokay gecko (Gekko gecko Linnaeus, 1758 (Squamata: Gekkonidae in Southeast Asia determined with multilocus enzyme electrophoresis

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Watee Kongbuntad

2016-03-01

Full Text Available Red-spotted tokay geckos, Gekko gecko, are distributed mainly in Southeast Asia. They are a traditional Chinese medicine, with the massive hunting for exports dramatically decreasing their numbers. Information on the genetic diversity of these geckos in Southeast Asia is very limited. This study aims to explore intrapopulation and interpopulation genetic variation and the genetic structure of 16 populations collected from different localities in Thailand, Lao People's Democratic Republic, and Cambodia using multilocus enzyme electrophoresis. Relatively high genetic diversity occurred at both the intrapopulation and interpopulation levels. Genetic differentiation with FST values ranging between 0.006–0.892 was found. Five distinct genetic groups of the red-spotted tokay populations could be classified. A group of populations from northern Thailand showed the highest genetic differentiation from the other groups. Moreover, there was a substantial genetic subdivision depending on the genetic groups with FCT=0.664 and FSC=0.185. This genetic structure is related to geographical distribution and distance between populations, R2=0.5614, p<0.001. Our findings of pronounced genetic structuring and the concomitant conservation genetic consequences if further population loss occurs mean that management actions should therefore focus on the conservation of all of the main sites where tokay geckos still occur.

Dynamics of chromosome number and genome size variation in a cytogenetically variable sedge (Carex scoparia var. scoparia, Cyperaceae).

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Chung, Kyong-Sook; Weber, Jaime A; Hipp, Andrew L

2011-01-01

High intraspecific cytogenetic variation in the sedge genus Carex (Cyperaceae) is hypothesized to be due to the "diffuse" or non-localized centromeres, which facilitate chromosome fission and fusion. If chromosome number changes are dominated by fission and fusion, then chromosome evolution will result primarily in changes in the potential for recombination among populations. Chromosome duplications, on the other hand, entail consequent opportunities for divergent evolution of paralogs. In this study, we evaluate whether genome size and chromosome number covary within species. We used flow cytometry to estimate genome sizes in Carex scoparia var. scoparia, sampling 99 plants (23 populations) in the Chicago region, and we used meiotic chromosome observations to document chromosome numbers and chromosome pairing relations. Chromosome numbers range from 2n = 62 to 2n = 68, and nuclear DNA 1C content from 0.342 to 0.361 pg DNA. Regressions of DNA content on chromosome number are nonsignificant for data analyzed by individual or population, and a regression model that excludes slope is favored over a model in which chromosome number predicts genome size. Chromosome rearrangements within cytogenetically variable Carex species are more likely a consequence of fission and fusion than of duplication and deletion. Moreover, neither genome size nor chromosome number is spatially autocorrelated, which suggests the potential for rapid chromosome evolution by fission and fusion at a relatively fine geographic scale (<350 km). These findings have important implications for ecological restoration and speciation within the largest angiosperm genus of the temperate zone.

Large-scale studies of the HphI insulin gene variable-number-of-tandem-repeats polymorphism in relation to Type 2 diabetes mellitus and insulin release

DEFF Research Database (Denmark)

Hansen, S K; Gjesing, A P; Rasmussen, S K

2004-01-01

The class III allele of the variable-number-of-tandem-repeats polymorphism located 5' of the insulin gene (INS-VNTR) has been associated with Type 2 diabetes and altered birthweight. It has also been suggested, although inconsistently, that the class III allele plays a role in glucose-induced ins......The class III allele of the variable-number-of-tandem-repeats polymorphism located 5' of the insulin gene (INS-VNTR) has been associated with Type 2 diabetes and altered birthweight. It has also been suggested, although inconsistently, that the class III allele plays a role in glucose...

The Effect of Unequal Samples, Heterogeneity of Covariance Matrices, and Number of Variables on Discriminant Analysis Classification Tables and Related Statistics.

Science.gov (United States)

Spearing, Debra; Woehlke, Paula

To assess the effect on discriminant analysis in terms of correct classification into two groups, the following parameters were systematically altered using Monte Carlo techniques: sample sizes; proportions of one group to the other; number of independent variables; and covariance matrices. The pairing of the off diagonals (or covariances) with…

Estimating Composite Curve Number Using an Improved SCS-CN Method with Remotely Sensed Variables in Guangzhou, China

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Qihao Weng

2013-03-01

Full Text Available The rainfall and runoff relationship becomes an intriguing issue as urbanization continues to evolve worldwide. In this paper, we developed a simulation model based on the soil conservation service curve number (SCS-CN method to analyze the rainfall-runoff relationship in Guangzhou, a rapid growing metropolitan area in southern China. The SCS-CN method was initially developed by the Natural Resources Conservation Service (NRCS of the United States Department of Agriculture (USDA, and is one of the most enduring methods for estimating direct runoff volume in ungauged catchments. In this model, the curve number (CN is a key variable which is usually obtained by the look-up table of TR-55. Due to the limitations of TR-55 in characterizing complex urban environments and in classifying land use/cover types, the SCS-CN model cannot provide more detailed runoff information. Thus, this paper develops a method to calculate CN by using remote sensing variables, including vegetation, impervious surface, and soil (V-I-S. The specific objectives of this paper are: (1 To extract the V-I-S fraction images using Linear Spectral Mixture Analysis; (2 To obtain composite CN by incorporating vegetation types, soil types, and V-I-S fraction images; and (3 To simulate direct runoff under the scenarios with precipitation of 57mm (occurred once every five years by average and 81mm (occurred once every ten years. Our experiment shows that the proposed method is easy to use and can derive composite CN effectively.

IDENTIFICATION OF THOSE VARIABLES THAT HAVE A SIGNIFICANT INFLUENCE ON THE EXPECTED NUMBER OF DAYS OF STAYING IN THE CENTRE DEVELOPMENT REGION OF ROMANIA

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Erika KULCSÁR

2010-06-01

Full Text Available I started from the assumption that there are more variables that have a significant influence on the expected number of days of staying in the Centre Development Region. To identify those variables this paper includes the analysis of variance with two variables that are not interacting, in this case the dependent variable is the question "How many days did you plan to stay in Centre Development Region?" and the independent variables are: "What is the purpose of your stay?" "What is the highest level of education?". Given that there are cases when interactions occur between variables, I also analyzed the interaction effects between the two independent variables. The paper also includes an ANOVA analysis with three variables between which interactions relationships occur. After identifying the dependency relations between the variables I found that the inclusion of the third variable, namely the "Marital status" of respondents, adds value to the model. Following the results obtained by ANOVA analysis, I identified those socio-demographic characteristics that, in my opinion, companies that operate on tourist market in the Center Development Region should consider when fundamenting marketing strategies in tourism.

Life on the rocks: Multilocus phylogeography of rock hyrax (Procavia capensis) from southern Africa.

Science.gov (United States)

Maswanganye, K Amanda; Cunningham, Michael J; Bennett, Nigel C; Chimimba, Christian T; Bloomer, Paulette

2017-09-01

Understanding the role of geography and climatic cycles in determining patterns of biodiversity is important in comparative and evolutionary biology and conservation. We studied the phylogeographic pattern and historical demography of a rock-dwelling small mammal species from southern Africa, the rock hyrax Procavia capensis capensis. Using a multilocus coalescent approach, we assessed the influence of strong habitat dependence and fluctuating regional climates on genetic diversity. We sequenced a mitochondrial gene (cytochrome b) and two nuclear introns (AP5, PRKC1) supplemented with microsatellite genotyping, in order to assess evolutionary processes over multiple temporal scales. In addition, distribution modelling was used to investigate the current and predicted distribution of the species under different climatic scenarios. Collectively, the data reveal a complex history of isolation followed by secondary contact shaping the current intraspecific diversity. The cyt b sequences confirmed the presence of two previously proposed geographically and genetically distinct lineages distributed across the southern African Great Escarpment and north-western mountain ranges. Molecular dating suggests Miocene divergence of the lineages, yet there are no discernible extrinsic barriers to gene flow. The nuclear markers reveal incomplete lineage sorting or ongoing mixing of the two lineages. Although the microsatellite data lend some support to the presence of two subpopulations, there is weak structuring within and between lineages. These data indicate the presence of gene flow from the northern into the southern parts of the southern African sub-region likely following the secondary contact. The distribution modelling predictably reveal the species' preference for rocky areas, with stable refugia through time in the northern mountain ranges, the Great Escarpment, as well as restricted areas of the Northern Cape Province and the Cape Fold Mountains of South Africa

Detection of a variable number of ribosomal DNA loci by fluorescent in situ hybridization in Populus species.

Science.gov (United States)

Prado, E A; Faivre-Rampant, P; Schneider, C; Darmency, M A

1996-10-01

Fluorescent in situ hybridization (FISH) was applied to related Populus species (2n = 19) in order to detect rDNA loci. An interspecific variability in the number of hybridization sites was revealed using as probe an homologous 25S clone from Populus deltoides. The application of image analysis methods to measure fluorescence intensity of the hybridization signals has enabled us to characterize major and minor loci in the 18S-5.8S-25S rDNA. We identified one pair of such rDNA clusters in Populus alba; two pairs, one major and one minor, in both Populus nigra and P. deltoides; and three pairs in Populus balsamifera, (two major and one minor) and Populus euroamericana (one major and two minor). FISH results are in agreement with those based on RFLP analysis. The pBG13 probe containing 5S sequence from flax detected two separate clusters corresponding to the two size classes of units that coexist within 5S rDNA of most Populus species. Key words : Populus spp., fluorescent in situ hybridization, FISH, rDNA variability, image analysis.

Optimal defense with variable number of overarching and individual protections

International Nuclear Information System (INIS)

Levitin, Gregory; Hausken, Kjell; Dai, Yuanshun

2014-01-01

The article considers a system consisting of identical elements. Each element can be protected individually. The groups of elements can have overarching protection. To destroy an element having both types of protections the attacker must always penetrate/destroy the overarching protection and then destroy the individual protection of the element. Both the attacker and the defender have limited resources. The resources needed to defend and attack the overarching protection are fixed, as is also the number of elements that can be protected by single overarching protection. The defender chooses the number of overarching protections and the number of individual protections within each protected group to minimize the expected damage caused by the attack. The attacker chooses the number of attacked overarching protections and after attacking the overarching protections it chooses the number of attacked elements to maximize the expected damage. The three period minmax game is formulated and an enumerative procedure for its solving is suggested. The influence of the game parameters on the optimal defense and attack strategies is discussed

[Evaluation of variable number of tandem repeats (VNTR) isolates of Mycobacterium bovis in Algeria].

Science.gov (United States)

Sahraoui, Naima; Muller, Borna; Djamel, Yala; Fadéla, Boulahbal; Rachid, Ouzrout; Jakob, Zinsstag; Djamel, Guetarni

2010-01-01

The discriminatory potency of variable number of tandem repeats (VNTR), based on 7 loci (MIRU 26, 27 and 5 ETRs A, B, C, D, E) was assayed on Mycobacterium bovis strains obtained from samples due to tuberculosis in two slaughterhouses in Algeria. The technique of MIRU-VNTR has been evaluated on 88 strains of M. bovis and one strain of M. caprea and shows 41 different profiles. Results showed that the VNTR were highly discriminatory with an allelic diversity of 0.930 when four loci (ETR A, B, C and MIRU 27) were highly discriminatory (h>0.25) and three loci (ETR D and E MIRU 26) moderately discriminatory (0.11VNTR loci were highly discriminatory be adequate for the first proper differentiation of strains of M. bovis in Algeria. The VNTR technique has proved a valuable tool for further development and application of epidemiological research for the of tuberculosis transmission in Algeria.

Hookworm infection, anaemia and genetic variability of the New Zealand sea lion.

Science.gov (United States)

Acevedo-Whitehouse, Karina; Petetti, Laura; Duignan, Padraig; Castinel, Aurelie

2009-10-07

Hookworms are intestinal blood-feeding nematodes that parasitize and cause high levels of mortality in a wide range of mammals, including otariid pinnipeds. Recently, an empirical study showed that inbreeding (assessed by individual measures of multi-locus heterozygosity) is associated with hookworm-related mortality of California sea lions. If inbreeding increases susceptibility to hookworms, effects would expectedly be stronger in small, fragmented populations. We tested this assumption in the New Zealand sea lion, a threatened otariid that has low levels of genetic variability and high hookworm infection rates. Using a panel of 22 microsatellites, we found that average allelic diversity (5.9) and mean heterozygosity (0.72) were higher than expected for a small population with restricted breeding, and we found no evidence of an association between genetic variability and hookworm resistance. However, similar to what was observed for the California sea lion, homozygosity at a single locus explained the occurrence of anaemia and thrombocytopenia in hookworm-infected pups (generalized linear model, F = 11.81, p < 0.001) and the effect was apparently driven by a particular allele (odds ratio = 34.95%; CI: 7.12-162.41; p < 0.00001). Our study offers further evidence that these haematophagus parasites exert selective pressure on otariid blood-clotting processes.

Optimization of Standard In-House 24-Locus Variable-Number Tandem-Repeat Typing for Mycobacterium tuberculosis and Its Direct Application to Clinical Material

NARCIS (Netherlands)

de Beer, Jessica L.; Akkerman, Onno W.; Schurch, Anita C.; Mulder, Arnout; van der Werf, Tjip S.; van der Zanden, Adri G. M.; van Ingen, Jakko; van Soolingen, Dick

Variable-number tandem-repeat (VNTR) typing with a panel of 24 loci is the current gold standard in the molecular typing of Mycobacterium tuberculosis complex isolates. However, because of technical problems, a part of the loci often cannot be amplified by multiplex PCRs. Therefore, a considerable

Rank-based characterization of pollen assemblages collected by honey bees using a multi-locus metabarcoding approach.

Science.gov (United States)

Richardson, Rodney T; Lin, Chia-Hua; Quijia, Juan O; Riusech, Natalia S; Goodell, Karen; Johnson, Reed M

2015-11-01

Difficulties inherent in microscopic pollen identification have resulted in limited implementation for large-scale studies. Metabarcoding, a relatively novel approach, could make pollen analysis less onerous; however, improved understanding of the quantitative capacity of various plant metabarcode regions and primer sets is needed to ensure that such applications are accurate and precise. We applied metabarcoding, targeting the ITS2, matK, and rbcL loci, to characterize six samples of pollen collected by honey bees, Apis mellifera. Additionally, samples were analyzed by light microscopy. We found significant rank-based associations between the relative abundance of pollen types within our samples as inferred by the two methods. Our findings suggest metabarcoding data from plastid loci, as opposed to the ribosomal locus, are more reliable for quantitative characterization of pollen assemblages. Furthermore, multilocus metabarcoding of pollen may be more reliable than single-locus analyses, underscoring the need for discovering novel barcodes and barcode combinations optimized for molecular palynology.

A variable turbulent Prandtl and Schmidt number model study for scramjet applications

Science.gov (United States)

Keistler, Patrick

A turbulence model that allows for the calculation of the variable turbulent Prandtl (Prt) and Schmidt (Sct) numbers as part of the solution is presented. The model also accounts for the interactions between turbulence and chemistry by modeling the corresponding terms. Four equations are added to the baseline k-zeta turbulence model: two equations for enthalpy variance and its dissipation rate to calculate the turbulent diffusivity, and two equations for the concentrations variance and its dissipation rate to calculate the turbulent diffusion coefficient. The underlying turbulence model already accounts for compressibility effects. The variable Prt /Sct turbulence model is validated and tuned by simulating a wide variety of experiments. Included in the experiments are two-dimensional, axisymmetric, and three-dimensional mixing and combustion cases. The combustion cases involved either hydrogen and air, or hydrogen, ethylene, and air. Two chemical kinetic models are employed for each of these situations. For the hydrogen and air cases, a seven species/seven reaction model where the reaction rates are temperature dependent and a nine species/nineteen reaction model where the reaction rates are dependent on both pressure and temperature are used. For the cases involving ethylene, a 15 species/44 reaction reduced model that is both pressure and temperature dependent is used, along with a 22 species/18 global reaction reduced model that makes use of the quasi-steady-state approximation. In general, fair to good agreement is indicated for all simulated experiments. The turbulence/chemistry interaction terms are found to have a significant impact on flame location for the two-dimensional combustion case, with excellent experimental agreement when the terms are included. In most cases, the hydrogen chemical mechanisms behave nearly identically, but for one case, the pressure dependent model would not auto-ignite at the same conditions as the experiment and the other

Variability and decline in the number of severe tropical cyclones making land-fall over eastern Australia since the late nineteenth century

Energy Technology Data Exchange (ETDEWEB)

Callaghan, Jeff [Bureau of Meteorology, Brisbane (Australia); Power, Scott B. [Bureau of Meteorology, Centre for Australian Weather and Climate Research, GPO Box 1289, Melbourne (Australia)

2011-08-15

Recent studies have raised concerns that tropical cyclones (TCs), particularly severe TCs, have become more frequent in many places in response to global warming. Other studies discuss errors in TC data that can cause large inaccuracies in some of the observed trends. Additional studies conclude that TCs are likely to become more intense in the future in response to global warming, while regional modelling studies for the south-west Pacific near north-eastern Australia project an intensification of TCs and either a decrease or no change in TC numbers. Here we describe and use a new data base of severe land-falling TCs for eastern Australia derived from numerous historical sources, that has taken over a decade to develop. It provides one of the world's longest reliable records of tropical cyclone activity, and allows us to document changes over much longer periods than has been done previously for the Southern Hemisphere. Land-fall numbers are shown to vary a great deal on interannual, decadal and longer time-scales. The interannual variability is consistent with previous studies using much shorter data sets: land-fall numbers are well-simulated as a Poisson process and are modulated by the El Nino-Southern Oscillation (ENSO). Land-falls occurred almost twice as often in La Nina years as they did in El Nino years, and multiple land-falls only occurred during La Nina years. The statistical link between land-falls and pre-season values of the Southern Oscillation Index provides a modest predictive capability. Decadal variability in ENSO drives some of the decadal variability in land-fall numbers. The sign and magnitude of trends calculated over 30 years periods vary substantially, highlighting that caution needs to be taken in making inferences about trends based on e.g. satellite era data only. The linear trend in the number of severe TCs making land-fall over eastern Australia declined from about 0.45 TCs/year in the early 1870s to about 0.17 TCs/year in recent

A novel multiple locus variable number of tandem repeat (VNTR) analysis (MLVA) method for Propionibacterium acnes.

Science.gov (United States)

Hauck, Yolande; Soler, Charles; Gérôme, Patrick; Vong, Rithy; Macnab, Christine; Appere, Géraldine; Vergnaud, Gilles; Pourcel, Christine

2015-07-01

Propionibacterium acnes plays a central role in the pathogenesis of acne and is responsible for severe opportunistic infections. Numerous typing schemes have been developed that allow the identification of phylotypes, but they are often insufficient to differentiate subtypes. To better understand the genetic diversity of this species and to perform epidemiological analyses, high throughput discriminant genotyping techniques are needed. Here we describe the development of a multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) method. Thirteen VNTRs were identified in the genome of P. acnes and were used to genotype a collection of clinical isolates. In addition, publically available sequencing data for 102 genomes were analyzed in silico, providing an MLVA genotype. The clustering of MLVA data was in perfect congruence with whole genome based clustering. Analysis of the clustered regularly interspaced short palindromic repeat (CRISPR) element uncovered new spacers, a supplementary source of genotypic information. The present MLVA13 scheme and associated internet database represents a first line genotyping assay to investigate large number of isolates. Particular strains may then be submitted to full genome sequencing in order to better analyze their pathogenic potential. Copyright © 2015 Elsevier B.V. All rights reserved.

[Multilocus sequence-typing for characterization of Moscow strains of Haemophilus influenzae type b].

Science.gov (United States)

Platonov, A E; Mironov, K O; Iatsyshina, S B; Koroleva, I S; Platonova, O V; Gushchin, A E; Shipulin, G A

2003-01-01

Haemophilius influenzae, type b (Hib) bacteria, were genotyped by multilocus sequence typing (MLST) using 5 loci (adk, fucK, mdh, pgi, recA). 42 Moscow Hib strains (including 38 isolates form cerebrospinal fluid of children, who had purulent meningitis in 1999-2001, and 4 strains isolated from healthy carriers of Hib), as well as 2 strains from Yekaterinburg were studied. In MLST a strain is characterized, by alleles and their combinations (an allele profile) referred to also as sequence-type (ST). 9 Sts were identified within the Russian Hib bacteria: ST-1 was found in 25 strains (57%), ST-12 was found in 8 strains (18%), ST-11 was found in 4 strains (9%) and ST-15 was found in 2 strains (4.5%); all other STs strains (13, 14, 16, 17, 51) were found in isolated cases (2.3%). A comparison of allelic profiles and of nucleotide sequences showed that 93% of Russian isolates, i.e. strain with ST-1, 11, 12, 13, 15 and 17, belong to one and the same clonal complex. 2 isolates from Norway and Sweden from among 7 foreign Hib strains studied up to now can be described as belonging to the same clonal complex; 5 Hib strains were different from the Russian ones.

Efficient DoA Tracking of Variable Number of Moving Stochastic EM Sources in Far-Field Using PNN-MLP Model

Directory of Open Access Journals (Sweden)

Zoran Stanković

2015-01-01

Full Text Available An efficient neural network-based approach for tracking of variable number of moving electromagnetic (EM sources in far-field is proposed in the paper. Electromagnetic sources considered here are of stochastic radiation nature, mutually uncorrelated, and at arbitrary angular distance. The neural network model is based on combination of probabilistic neural network (PNN and the Multilayer Perceptron (MLP networks and it performs real-time calculations in two stages, determining at first the number of moving sources present in an observed space sector in specific moments in time and then calculating their angular positions in azimuth plane. Once successfully trained, the neural network model is capable of performing an accurate and efficient direction of arrival (DoA estimation within the training boundaries which is illustrated on the appropriate example.

Systematic cloning of human minisatellites from ordered array charomid libraries.

Science.gov (United States)

Armour, J A; Povey, S; Jeremiah, S; Jeffreys, A J

1990-11-01

We present a rapid and efficient method for the isolation of minisatellite loci from human DNA. The method combines cloning a size-selected fraction of human MboI DNA fragments in a charomid vector with hybridization screening of the library in ordered array. Size-selection of large MboI fragments enriches for the longer, more variable minisatellites and reduces the size of the library required. The library was screened with a series of multi-locus probes known to detect a large number of hypervariable loci in human DNA. The gridded library allowed both the rapid processing of positive clones and the comparative evaluation of the different multi-locus probes used, in terms of both the relative success in detecting hypervariable loci and the degree of overlap between the sets of loci detected. We report 23 new human minisatellite loci isolated by this method, which map to 14 autosomes and the sex chromosomes.

Multilocus analysis of divergence and introgression in sympatric and allopatric sibling species of the Lutzomyia longipalpis complex in Brazil.

Science.gov (United States)

Araki, Alejandra S; Ferreira, Gabriel E M; Mazzoni, Camila J; Souza, Nataly A; Machado, Ricardo C; Bruno, Rafaela V; Peixoto, Alexandre A

2013-01-01

Lutzomyia longipalpis, the main vector of visceral leishmaniasis in Latin America, is a complex of sibling species. In Brazil, a number of very closely related sibling species have been revealed by the analyses of copulation songs, sex pheromones and molecular markers. However, the level of divergence and gene flow between the sibling species remains unclear. Brazilian populations of this vector can be divided in two main groups: one producing Burst-type songs and the Cembrene-1 pheromone and a second more diverse group producing various Pulse song subtypes and different pheromones. We analyzed 21 nuclear loci in two pairs of Brazilian populations: two sympatric populations from the Sobral locality (1S and 2S) in northeastern Brazil and two allopatric populations from the Lapinha and Pancas localities in southeastern Brazil. Pancas and Sobral 2S are populations of the Burst/Cembrene-1 species while Lapinha and Sobral 1S are two putative incipient species producing the same pheromone and similar Pulse song subtypes. The multilocus analysis strongly suggests the occurrence of gene flow during the divergence between the sibling species, with different levels of introgression between loci. Moreover, this differential introgression is asymmetrical, with estimated gene flow being higher in the direction of the Burst/Cembrene-1 species. The results indicate that introgressive hybridization has been a crucial phenomenon in shaping the genome of the L. longipalpis complex. This has possible epidemiological implications and is particularly interesting considering the potential for increased introgression caused by man-made environmental changes and the current trend of leishmaniasis urbanization in Brazil.

A Predominant Variable-Number Tandem-Repeat Cluster of Mycobacterium tuberculosis Isolates among Asylum Seekers in the Netherlands and Denmark, Deciphered by Whole-Genome Sequencing.

NARCIS (Netherlands)

Jajou, Rana; de Neeling, Albert; Rasmussen, Erik Michael; Norman, Anders; Mulder, Arnout; van Hunen, Rianne; de Vries, Gerard; Haddad, Walid; Anthony, Richard; Lillebaek, Troels; van der Hoek, Wim; van Soolingen, Dick

In many countries,Mycobacterium tuberculosisisolates are routinely subjected to variable-number tandem-repeat (VNTR) typing to investigateM. tuberculosistransmission. Unexpectedly, cross-border clusters were identified among African refugees in the Netherlands and Denmark, although transmission in

Using variable combination population analysis for variable selection in multivariate calibration.

Science.gov (United States)

Yun, Yong-Huan; Wang, Wei-Ting; Deng, Bai-Chuan; Lai, Guang-Bi; Liu, Xin-bo; Ren, Da-Bing; Liang, Yi-Zeng; Fan, Wei; Xu, Qing-Song

2015-03-03

Variable (wavelength or feature) selection techniques have become a critical step for the analysis of datasets with high number of variables and relatively few samples. In this study, a novel variable selection strategy, variable combination population analysis (VCPA), was proposed. This strategy consists of two crucial procedures. First, the exponentially decreasing function (EDF), which is the simple and effective principle of 'survival of the fittest' from Darwin's natural evolution theory, is employed to determine the number of variables to keep and continuously shrink the variable space. Second, in each EDF run, binary matrix sampling (BMS) strategy that gives each variable the same chance to be selected and generates different variable combinations, is used to produce a population of subsets to construct a population of sub-models. Then, model population analysis (MPA) is employed to find the variable subsets with the lower root mean squares error of cross validation (RMSECV). The frequency of each variable appearing in the best 10% sub-models is computed. The higher the frequency is, the more important the variable is. The performance of the proposed procedure was investigated using three real NIR datasets. The results indicate that VCPA is a good variable selection strategy when compared with four high performing variable selection methods: genetic algorithm-partial least squares (GA-PLS), Monte Carlo uninformative variable elimination by PLS (MC-UVE-PLS), competitive adaptive reweighted sampling (CARS) and iteratively retains informative variables (IRIV). The MATLAB source code of VCPA is available for academic research on the website: http://www.mathworks.com/matlabcentral/fileexchange/authors/498750. Copyright © 2015 Elsevier B.V. All rights reserved.

The precision of mapping between number words and the approximate number system predicts children's formal math abilities.

Science.gov (United States)

Libertus, Melissa E; Odic, Darko; Feigenson, Lisa; Halberda, Justin

2016-10-01

Children can represent number in at least two ways: by using their non-verbal, intuitive approximate number system (ANS) and by using words and symbols to count and represent numbers exactly. Furthermore, by the time they are 5years old, children can map between the ANS and number words, as evidenced by their ability to verbally estimate numbers of items without counting. How does the quality of the mapping between approximate and exact numbers relate to children's math abilities? The role of the ANS-number word mapping in math competence remains controversial for at least two reasons. First, previous work has not examined the relation between verbal estimation and distinct subtypes of math abilities. Second, previous work has not addressed how distinct components of verbal estimation-mapping accuracy and variability-might each relate to math performance. Here, we addressed these gaps by measuring individual differences in ANS precision, verbal number estimation, and formal and informal math abilities in 5- to 7-year-old children. We found that verbal estimation variability, but not estimation accuracy, predicted formal math abilities, even when controlling for age, expressive vocabulary, and ANS precision, and that it mediated the link between ANS precision and overall math ability. These findings suggest that variability in the ANS-number word mapping may be especially important for formal math abilities. Copyright © 2016 Elsevier Inc. All rights reserved.

Variable number of tandem repeats of 9 Plasmodium vivax genes among Southeast Asian isolates.

Science.gov (United States)

Wang, Bo; Nyunt, Myat Htut; Yun, Seung-Gyu; Lu, Feng; Cheng, Yang; Han, Jin-Hee; Ha, Kwon-Soo; Park, Won Sun; Hong, Seok-Ho; Lim, Chae-Seung; Cao, Jun; Sattabongkot, Jetsumon; Kyaw, Myat Phone; Cui, Liwang; Han, Eun-Taek

2017-06-01

The variable number of tandem repeats (VNTRs) provides valuable information about both the functional and evolutionary aspects of genetic diversity. Comparative analysis of 3 Plasmodium falciparum genomes has shown that more than 9% of its open reading frames (ORFs) harbor VNTRs. Although microsatellites and VNTR genes of P. vivax were reported, the VNTR polymorphism of genes has not been examined widely. In this study, 230 P. vivax genes were analyzed for VNTRs by SERV, and 33 kinds of TR deletions or insertions from 29 P. vivax genes (12.6%) were found. Of these, 9 VNTR fragments from 8 P. vivax genes were used for PCR amplification and sequence analysis to examine the genetic diversity among 134 isolates from four Southeast Asian countries (China, Republic of Korea, Thailand, and Myanmar) with different malaria endemicity. We confirmed the existence of extensive polymorphism of VNTR fragments in field isolates. This detection provides several suitable markers for analysis of the molecular epidemiology of P. vivax field isolates. Copyright © 2017 Elsevier B.V. All rights reserved.

Multilocus sequence typing of Lactococcus lactis from naturally fermented milk foods in ethnic minority areas of China.

Science.gov (United States)

Xu, Haiyan; Sun, Zhihong; Liu, Wenjun; Yu, Jie; Song, Yuqin; Lv, Qiang; Zhang, Jiachao; Shao, Yuyu; Menghe, Bilige; Zhang, Heping

2014-05-01

To determine the genetic diversity and phylogenetic relationships among Lactococcus lactis isolates, 197 strains isolated from naturally homemade yogurt in 9 ethnic minority areas of 6 provinces of China were subjected to multilocus sequence typing (MLST). The MLST analysis was performed using internal fragment sequences of 12 housekeeping genes (carB, clpX, dnaA, groEL, murC, murE, pepN, pepX, pyrG, recA, rpoB, and pheS). Six (dnaA) to 8 (murC) different alleles were detected for these genes, which ranged from 33.62 (clpX) to 41.95% (recA) GC (guanine-cytosine) content. The nucleotide diversity (π) ranged from 0.00362 (murE) to 0.08439 (carB). Despite this limited allelic diversity, the allele combinations of each strain revealed 72 different sequence types, which denoted significant genotypic diversity. The dN/dS ratios (where dS is the number of synonymous substitutions per synonymous site, and dN is the number of nonsynonymous substitutions per nonsynonymous site) were lower than 1, suggesting potential negative selection for these genes. The standardized index of association of the alleles IA(S)=0.3038 supported the clonality of Lc. lactis, but the presence of network structure revealed by the split decomposition analysis of the concatenated sequence was strong evidence for intraspecies recombination. Therefore, this suggests that recombination contributed to the evolution of Lc. lactis. A minimum spanning tree analysis of the 197 isolates identified 14 clonal complexes and 23 singletons. Phylogenetic trees were constructed based on the sequence types, using the minimum evolution algorithm, and on the concatenated sequence (6,192 bp), using the unweighted pair-group method with arithmetic mean, and these trees indicated that the evolution of our Lc. lactis population was correlated with geographic origin. Taken together, our results demonstrated that MLST could provide a better understanding of Lc. lactis genome evolution, as well as useful information for

Inclusive photoproduction of D*± mesons at next-to-leading order in the general-mass variable-flavor-number scheme

International Nuclear Information System (INIS)

Kniehl, B.A.; Kramer, G.; Schienbein, I.; Spiesberger, H.

2009-02-01

We discuss the inclusive production of D *± mesons in γp collisions at DESY HERA, based on a calculation at next-to-leading order in the general-mass variable-flavor-number scheme. In this approach, MS subtraction is applied in such a way that large logarithmic corrections are resummed in universal parton distribution and fragmentation functions and finite mass terms are taken into account. We present detailed numerical results for a comparison with data obtained at HERA and discuss various sources of theoretical uncertainties. (orig.)

Inclusive photoproduction of D{sup *{+-}} mesons at next-to-leading order in the general-mass variable-flavor-number scheme

Energy Technology Data Exchange (ETDEWEB)

Kniehl, B.A.; Kramer, G. [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik; Schienbein, I. [Univ. Joseph Fourier/CNRS-IN2P3, INPG, Grenoble (France). Lab. de Physique Subatomique et de Cosmologie; Spiesberger, H. [Mainz Univ. (Germany). Inst. fuer Physik

2009-02-15

We discuss the inclusive production of D{sup *{+-}} mesons in {gamma}p collisions at DESY HERA, based on a calculation at next-to-leading order in the general-mass variable-flavor-number scheme. In this approach, MS subtraction is applied in such a way that large logarithmic corrections are resummed in universal parton distribution and fragmentation functions and finite mass terms are taken into account. We present detailed numerical results for a comparison with data obtained at HERA and discuss various sources of theoretical uncertainties. (orig.)

Multilocus Bayesian Estimates of Intra-Oceanic Genetic Differentiation, Connectivity, and Admixture in Atlantic Swordfish (Xiphias gladius L..

Directory of Open Access Journals (Sweden)

Brad L Smith

Full Text Available Previous genetic studies of Atlantic swordfish (Xiphias gladius L. revealed significant differentiation among Mediterranean, North Atlantic and South Atlantic populations using both mitochondrial and nuclear DNA data. However, limitations in geographic sampling coverage, and the use of single loci, precluded an accurate placement of boundaries and of estimates of admixture. In this study, we present multilocus analyses of 26 single nucleotide polymorphisms (SNPs within 10 nuclear genes to estimate population differentiation and admixture based on the characterization of 774 individuals representing North Atlantic, South Atlantic, and Mediterranean swordfish populations. Pairwise FST values, AMOVA, PCoA, and Bayesian individual assignments support the differentiation of swordfish inhabiting these three basins, but not the current placement of the boundaries that separate them. Specifically, the range of the South Atlantic population extends beyond 5°N management boundary to 20°N-25°N from 45°W. Likewise the Mediterranean population extends beyond the current management boundary at the Strait of Gibraltar to approximately 10°W. Further, admixture zones, characterized by asymmetric contributions of adjacent populations within samples, are confined to the Northeast Atlantic. While South Atlantic and Mediterranean migrants were identified within these Northeast Atlantic admixture zones no North Atlantic migrants were identified respectively in these two neighboring basins. Owing to both, the characterization of larger number of loci and a more ample spatial sampling coverage, it was possible to provide a finer resolution of the boundaries separating Atlantic swordfish populations than previous studies. Finally, the patterns of population structure and admixture are discussed in the light of the reproductive biology, the known patterns of dispersal, and oceanographic features that may act as barriers to gene flow to Atlantic swordfish.

Exploratory Spectroscopy of Magnetic Cataclysmic Variables Candidates and Other Variable Objects

Energy Technology Data Exchange (ETDEWEB)

Oliveira, A. S.; Palhares, M. S. [IP and D, Universidade do Vale do Paraíba, 12244-000, São José dos Campos, SP (Brazil); Rodrigues, C. V.; Cieslinski, D.; Jablonski, F. J. [Divisão de Astrofísica, Instituto Nacional de Pesquisas Espaciais, 12227-010, São José dos Campos, SP (Brazil); Silva, K. M. G. [Gemini Observatory, Casilla 603, La Serena (Chile); Almeida, L. A. [Instituto de Astronomia, Geofísica e Ciências Atmosféricas, Universidade de São Paulo, 05508-900, São Paulo, SP (Brazil); Rodríguez-Ardila, A., E-mail: alexandre@univap.br [Laboratório Nacional de Astrofísica LNA/MCTI, 37504-364, Itajubá MG (Brazil)

2017-04-01

The increasing number of synoptic surveys made by small robotic telescopes, such as the photometric Catalina Real-Time Transient Survey (CRTS), provides a unique opportunity to discover variable sources and improves the statistical samples of such classes of objects. Our goal is the discovery of magnetic Cataclysmic Variables (mCVs). These are rare objects that probe interesting accretion scenarios controlled by the white-dwarf magnetic field. In particular, improved statistics of mCVs would help to address open questions on their formation and evolution. We performed an optical spectroscopy survey to search for signatures of magnetic accretion in 45 variable objects selected mostly from the CRTS. In this sample, we found 32 CVs, 22 being mCV candidates, 13 of which were previously unreported as such. If the proposed classifications are confirmed, it would represent an increase of 4% in the number of known polars and 12% in the number of known IPs. A fraction of our initial sample was classified as extragalactic sources or other types of variable stars by the inspection of the identification spectra. Despite the inherent complexity in identifying a source as an mCV, variability-based selection, followed by spectroscopic snapshot observations, has proved to be an efficient strategy for their discoveries, being a relatively inexpensive approach in terms of telescope time.

On the functional form of particle number size distributions: influence of particle source and meteorological variables

Science.gov (United States)

Cugerone, Katia; De Michele, Carlo; Ghezzi, Antonio; Gianelle, Vorne; Gilardoni, Stefania

2018-04-01

Particle number size distributions (PNSDs) have been collected periodically in the urban area of Milan, Italy, during 2011 and 2012 in winter and summer months. Moreover, comparable PNSD measurements were carried out in the rural mountain site of Oga-San Colombano (2250 m a.s.l.), Italy, during February 2005 and August 2011. The aerosol data have been measured through the use of optical particle counters in the size range 0.3-25 µm, with a time resolution of 1 min. The comparison of the PNSDs collected in the two sites has been done in terms of total number concentration, showing higher numbers in Milan (often exceeding 103 cm-3 in winter season) compared to Oga-San Colombano (not greater than 2×102 cm-3), as expected. The skewness-kurtosis plane has been used in order to provide a synoptic view, and select the best distribution family describing the empirical PNSD pattern. The four-parameter Johnson system-bounded distribution (called Johnson SB or JSB) has been tested for this aim, due to its great flexibility and ability to assume different shapes. The PNSD pattern has been found to be generally invariant under site and season changes. Nevertheless, several PNSDs belonging to the Milan winter season (generally more than 30 %) clearly deviate from the standard empirical pattern. The seasonal increase in the concentration of primary aerosols due to combustion processes in winter and the influence of weather variables throughout the year, such as precipitation and wind speed, could be considered plausible explanations of PNSD dynamics.

Rank-based characterization of pollen assemblages collected by honey bees using a multi-locus metabarcoding approach1

Science.gov (United States)

Richardson, Rodney T.; Lin, Chia-Hua; Quijia, Juan O.; Riusech, Natalia S.; Goodell, Karen; Johnson, Reed M.

2015-01-01

Premise of the study: Difficulties inherent in microscopic pollen identification have resulted in limited implementation for large-scale studies. Metabarcoding, a relatively novel approach, could make pollen analysis less onerous; however, improved understanding of the quantitative capacity of various plant metabarcode regions and primer sets is needed to ensure that such applications are accurate and precise. Methods and Results: We applied metabarcoding, targeting the ITS2, matK, and rbcL loci, to characterize six samples of pollen collected by honey bees, Apis mellifera. Additionally, samples were analyzed by light microscopy. We found significant rank-based associations between the relative abundance of pollen types within our samples as inferred by the two methods. Conclusions: Our findings suggest metabarcoding data from plastid loci, as opposed to the ribosomal locus, are more reliable for quantitative characterization of pollen assemblages. Furthermore, multilocus metabarcoding of pollen may be more reliable than single-locus analyses, underscoring the need for discovering novel barcodes and barcode combinations optimized for molecular palynology. PMID:26649264

Comparison of a newly developed binary typing with ribotyping and multilocus sequence typing methods for Clostridium difficile.

Science.gov (United States)

Li, Zhirong; Liu, Xiaolei; Zhao, Jianhong; Xu, Kaiyue; Tian, Tiantian; Yang, Jing; Qiang, Cuixin; Shi, Dongyan; Wei, Honglian; Sun, Suju; Cui, Qingqing; Li, Ruxin; Niu, Yanan; Huang, Bixing

2018-04-01

Clostridium difficile is the causative pathogen for antibiotic-related nosocomial diarrhea. For epidemiological study and identification of virulent clones, a new binary typing method was developed for C. difficile in this study. The usefulness of this newly developed optimized 10-loci binary typing method was compared with two widely used methods ribotyping and multilocus sequence typing (MLST) in 189 C. difficile samples. The binary typing, ribotyping and MLST typed the samples into 53 binary types (BTs), 26 ribotypes (RTs), and 33 MLST sequence types (STs), respectively. The typing ability of the binary method was better than that of either ribotyping or MLST expressed in Simpson Index (SI) at 0.937, 0.892 and 0.859, respectively. The ease of testing, portability and cost-effectiveness of the new binary typing would make it a useful typing alternative for outbreak investigations within healthcare facilities and epidemiological research. Copyright © 2018 Elsevier B.V. All rights reserved.

Generalized Bernoulli-Hurwitz numbers and the universal Bernoulli numbers

International Nuclear Information System (INIS)

Ônishi, Yoshihiro

2011-01-01

The three fundamental properties of the Bernoulli numbers, namely, the von Staudt-Clausen theorem, von Staudt's second theorem, and Kummer's original congruence, are generalized to new numbers that we call generalized Bernoulli-Hurwitz numbers. These are coefficients in the power series expansion of a higher-genus algebraic function with respect to a suitable variable. Our generalization differs strongly from previous works. Indeed, the order of the power of the modulus prime in our Kummer-type congruences is exactly the same as in the trigonometric function case (namely, Kummer's own congruence for the original Bernoulli numbers), and as in the elliptic function case (namely, H. Lang's extension for the Hurwitz numbers). However, in other past results on higher-genus algebraic functions, the modulus was at most half of its value in these classical cases. This contrast is clarified by investigating the analogue of the three properties above for the universal Bernoulli numbers. Bibliography: 34 titles.

Generalized Bernoulli-Hurwitz numbers and the universal Bernoulli numbers

Energy Technology Data Exchange (ETDEWEB)

Onishi, Yoshihiro [Faculty of Education Human Sciences, University of Yamanashi, Takeda, Kofu (Japan)

2011-10-31

The three fundamental properties of the Bernoulli numbers, namely, the von Staudt-Clausen theorem, von Staudt's second theorem, and Kummer's original congruence, are generalized to new numbers that we call generalized Bernoulli-Hurwitz numbers. These are coefficients in the power series expansion of a higher-genus algebraic function with respect to a suitable variable. Our generalization differs strongly from previous works. Indeed, the order of the power of the modulus prime in our Kummer-type congruences is exactly the same as in the trigonometric function case (namely, Kummer's own congruence for the original Bernoulli numbers), and as in the elliptic function case (namely, H. Lang's extension for the Hurwitz numbers). However, in other past results on higher-genus algebraic functions, the modulus was at most half of its value in these classical cases. This contrast is clarified by investigating the analogue of the three properties above for the universal Bernoulli numbers. Bibliography: 34 titles.

The discovery, function and development of the variable number tandem repeats in different Mycobacterium species.

Science.gov (United States)

Sun, Zhaogang; Li, Weimin; Xu, Shaofa; Huang, Hairong

2016-09-01

The method of genotyping by variable number tandem repeats (VNTRs) facilitates the epidemiological studies of different Mycobacterium species worldwide. Until now, the VNTR method is not fully understood, for example, its discovery, function and classification. The inconsistent nomenclature and terminology of VNTR is especially confusing. In this review, we first describe in detail the VNTRs in Mycobacterium tuberculosis (M. tuberculosis), as this pathogen resulted in more deaths than any other microbial pathogen as well as for which extensive studies of VNTRs were carried out, and then we outline the recent progress of the VNTR-related epidemiological research in several other Mycobacterium species, such as M. abscessus, M. africanum, M. avium, M. bovis, M. canettii, M. caprae, M. intracellulare, M. leprae, M. marinum, M. microti, M. pinnipedii and M. ulcerans from different countries and regions. This article is aimed mainly at the practical notes of VNTR to help the scientists in better understanding and performing this method.

Relationships between functional genes in Lactobacillus delbrueckii ssp. bulgaricus isolates and phenotypic characteristics associated with fermentation time and flavor production in yogurt elucidated using multilocus sequence typing.

Science.gov (United States)

Liu, Wenjun; Yu, Jie; Sun, Zhihong; Song, Yuqin; Wang, Xueni; Wang, Hongmei; Wuren, Tuoya; Zha, Musu; Menghe, Bilige; Heping, Zhang

2016-01-01

Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is well known for its worldwide application in yogurt production. Flavor production and acid producing are considered as the most important characteristics for starter culture screening. To our knowledge this is the first study applying functional gene sequence multilocus sequence typing technology to predict the fermentation and flavor-producing characteristics of yogurt-producing bacteria. In the present study, phenotypic characteristics of 35 L. bulgaricus strains were quantified during the fermentation of milk to yogurt and during its subsequent storage; these included fermentation time, acidification rate, pH, titratable acidity, and flavor characteristics (acetaldehyde concentration). Furthermore, multilocus sequence typing analysis of 7 functional genes associated with fermentation time, acid production, and flavor formation was done to elucidate the phylogeny and genetic evolution of the same L. bulgaricus isolates. The results showed that strains significantly differed in fermentation time, acidification rate, and acetaldehyde production. Combining functional gene sequence analysis with phenotypic characteristics demonstrated that groups of strains established using genotype data were consistent with groups identified based on their phenotypic traits. This study has established an efficient and rapid molecular genotyping method to identify strains with good fermentation traits; this has the potential to replace time-consuming conventional methods based on direct measurement of phenotypic traits. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Epidemiological characterization of a nosocomial outbreak of extended spectrum β-lactamase Escherichia coli ST-131 confirms the clinical value of core genome multilocus sequence typing.

Science.gov (United States)

Woksepp, Hanna; Ryberg, Anna; Berglind, Linda; Schön, Thomas; Söderman, Jan

2017-12-01

Enhanced precision of epidemiological typing in clinically suspected nosocomial outbreaks is crucial. Our aim was to investigate whether single nucleotide polymorphism (SNP) analysis and core genome (cg) multilocus sequence typing (MLST) of whole genome sequencing (WGS) data would more reliably identify a nosocomial outbreak, compared to earlier molecular typing methods. Sixteen isolates from a nosocomial outbreak of ESBL E. coli ST-131 in southeastern Sweden and three control strains were subjected to WGS. Sequences were explored by SNP analysis and cgMLST. cgMLST clearly differentiated between the outbreak isolates and the control isolates (>1400 differences). All clinically identified outbreak isolates showed close clustering (≥2 allele differences), except for two isolates (>50 allele differences). These data confirmed that the isolates with >50 differing genes did not belong to the nosocomial outbreak. The number of SNPs within the outbreak was ≤7, whereas the two discrepant isolates had >700 SNPs. Two of the ESBL E. coli ST-131 isolates did not belong to the clinically identified outbreak. Our results illustrate the power of WGS in terms of resolution, which may avoid overestimation of patients belonging to outbreaks as judged from epidemiological data and previously employed molecular methods with lower discriminatory ability. © 2017 APMIS. Published by John Wiley & Sons Ltd.

Inclusive photoproduction of bottom quarks for low and medium pT in the general-mass variable-flavour-number scheme

International Nuclear Information System (INIS)

Kramer, G.; Spiesberger, H.; Cape Town Univ., Rondebosch

2015-09-01

We present predictions for b-quark production in photoproduction and compare with experimental data from HERA. Our theoretical predictions are obtained at next-to-leading-order in the general-mass variable-flavor-number scheme, an approach which takes into account the finite mass of the b quarks. We use realistic evolved nonperturbative fragmentation functions obtained from fits to e + e - data. We find in general good agreement of data with both the GM-VFNS and the FFNS calculations, while the more precise ZEUS data seem to prefer the GM-VFNS predictions.

First Worldwide Proficiency Study on Variable-Number Tandem-Repeat Typing of Mycobacterium tuberculosis Complex Strains

Science.gov (United States)

de Beer, Jessica L.; Kremer, Kristin; Ködmön, Csaba; Supply, Philip

2012-01-01

Although variable-number tandem-repeat (VNTR) typing has gained recognition as the new standard for the DNA fingerprinting of Mycobacterium tuberculosis complex (MTBC) isolates, external quality control programs have not yet been developed. Therefore, we organized the first multicenter proficiency study on 24-locus VNTR typing. Sets of 30 DNAs of MTBC strains, including 10 duplicate DNA samples, were distributed among 37 participating laboratories in 30 different countries worldwide. Twenty-four laboratories used an in-house-adapted method with fragment sizing by gel electrophoresis or an automated DNA analyzer, nine laboratories used a commercially available kit, and four laboratories used other methods. The intra- and interlaboratory reproducibilities of VNTR typing varied from 0% to 100%, with averages of 72% and 60%, respectively. Twenty of the 37 laboratories failed to amplify particular VNTR loci; if these missing results were ignored, the number of laboratories with 100% interlaboratory reproducibility increased from 1 to 5. The average interlaboratory reproducibility of VNTR typing using a commercial kit was better (88%) than that of in-house-adapted methods using a DNA analyzer (70%) or gel electrophoresis (50%). Eleven laboratories using in-house-adapted manual typing or automated typing scored inter- and intralaboratory reproducibilities of 80% or higher, which suggests that these approaches can be used in a reliable way. In conclusion, this first multicenter study has documented the worldwide quality of VNTR typing of MTBC strains and highlights the importance of international quality control to improve genotyping in the future. PMID:22170917

The Precision of Mapping Between Number Words and the Approximate Number System Predicts Children’s Formal Math Abilities

Science.gov (United States)

Libertus, Melissa E.; Odic, Darko; Feigenson, Lisa; Halberda, Justin

2016-01-01

Children can represent number in at least two ways: by using their non-verbal, intuitive Approximate Number System (ANS), and by using words and symbols to count and represent numbers exactly. Further, by the time they are five years old, children can map between the ANS and number words, as evidenced by their ability to verbally estimate numbers of items without counting. How does the quality of the mapping between approximate and exact numbers relate to children’s math abilities? The role of the ANS-number word mapping in math competence remains controversial for at least two reasons. First, previous work has not examined the relation between verbal estimation and distinct subtypes of math abilities. Second, previous work has not addressed how distinct components of verbal estimation – mapping accuracy and variability – might each relate to math performance. Here, we address these gaps by measuring individual differences in ANS precision, verbal number estimation, and formal and informal math abilities in 5- to 7-year-old children. We found that verbal estimation variability, but not estimation accuracy, predicted formal math abilities even when controlling for age, expressive vocabulary, and ANS precision, and that it mediated the link between ANS precision and overall math ability. These findings suggest that variability in the ANS-number word mapping may be especially important for formal math abilities. PMID:27348475

Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae.

Directory of Open Access Journals (Sweden)

Justin C Bagley

Full Text Available Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-lineages' diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the

Benchmarking Variable Selection in QSAR.

Science.gov (United States)

Eklund, Martin; Norinder, Ulf; Boyer, Scott; Carlsson, Lars

2012-02-01

Variable selection is important in QSAR modeling since it can improve model performance and transparency, as well as reduce the computational cost of model fitting and predictions. Which variable selection methods that perform well in QSAR settings is largely unknown. To address this question we, in a total of 1728 benchmarking experiments, rigorously investigated how eight variable selection methods affect the predictive performance and transparency of random forest models fitted to seven QSAR datasets covering different endpoints, descriptors sets, types of response variables, and number of chemical compounds. The results show that univariate variable selection methods are suboptimal and that the number of variables in the benchmarked datasets can be reduced with about 60 % without significant loss in model performance when using multivariate adaptive regression splines MARS and forward selection. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A novel high-resolution multilocus sequence typing of Giardia intestinalis Assemblage A isolates reveals zoonotic transmission, clonal outbreaks and recombination.

Science.gov (United States)

Ankarklev, Johan; Lebbad, Marianne; Einarsson, Elin; Franzén, Oscar; Ahola, Harri; Troell, Karin; Svärd, Staffan G

2018-06-01

Molecular epidemiology and genotyping studies of the parasitic protozoan Giardia intestinalis have proven difficult due to multiple factors, such as low discriminatory power in the commonly used genotyping loci, which has hampered molecular analyses of outbreak sources, zoonotic transmission and virulence types. Here we have focused on assemblage A Giardia and developed a high-resolution assemblage-specific multilocus sequence typing (MLST) method. Analyses of sequenced G. intestinalis assemblage A genomes from different sub-assemblages identified a set of six genetic loci with high genetic variability. DNA samples from both humans (n = 44) and animals (n = 18) that harbored Giardia assemblage A infections, were PCR amplified (557-700 bp products) and sequenced at the six novel genetic loci. Bioinformatic analyses showed five to ten-fold higher levels of polymorphic sites than what was previously found among assemblage A samples using the classic genotyping loci. Phylogenetically, a division of two major clusters in assemblage A became apparent, separating samples of human and animal origin. A subset of human samples (n = 9) from a documented Giardia outbreak in a Swedish day-care center, showed full complementarity at nine genetic loci (the six new and the standard BG, TPI and GDH loci), strongly suggesting one source of infection. Furthermore, three samples of human origin displayed MLST profiles that were phylogenetically more closely related to MLST profiles from animal derived samples, suggesting zoonotic transmission. These new genotyping loci enabled us to detect events of recombination between different assemblage A isolates but also between assemblage A and E isolates. In summary, we present a novel and expanded MLST strategy with significantly improved sensitivity for molecular analyses of virulence types, zoonotic potential and source tracking for assemblage A Giardia. Copyright © 2018. Published by Elsevier B.V.

Variable volume combustor

Science.gov (United States)

Ostebee, Heath Michael; Ziminsky, Willy Steve; Johnson, Thomas Edward; Keener, Christopher Paul

2017-01-17

The present application provides a variable volume combustor for use with a gas turbine engine. The variable volume combustor may include a liner, a number of micro-mixer fuel nozzles positioned within the liner, and a linear actuator so as to maneuver the micro-mixer fuel nozzles axially along the liner.

Usefulness of the DNA-fingerprinting pattern and the multilocus enzyme electrophoresis profile in the assessment of outbreaks of meningococcal disease

DEFF Research Database (Denmark)

Weis, N; Lind, I

1996-01-01

cases were identical to the outbreak strain. None of the local serogroup C carrier strains isolated during the outbreak of serogroup C disease were identical to the outbreak strain. Both DNA-fingerprinting and MEE improved the differentiation of meningococci when compared with phenotypic......The objective of the study was to assess whether genotypic characterization by means of DNA-fingerprinting pattern (DFP) and multilocus enzyme electrophoresis (MEE) profile as compared to phenotypic characterization would improve the differentiation of Neisseria meningitidis strains associated...... in each outbreak were designated the index strains. Among the remaining 55 outbreak strains 52 were either DFP-identical or DFP-indistinguishable when compared with the one relevant out of the 4 index strains. This was only the case for 17 of the 37 strains isolated from sporadic cases caused by the same...

Multilocus Analysis of Divergence and Introgression in Sympatric and Allopatric Sibling Species of the Lutzomyia longipalpis Complex in Brazil

Science.gov (United States)

Mazzoni, Camila J.; Souza, Nataly A.; Machado, Ricardo C.; Bruno, Rafaela V.

2013-01-01

Background Lutzomyia longipalpis, the main vector of visceral leishmaniasis in Latin America, is a complex of sibling species. In Brazil, a number of very closely related sibling species have been revealed by the analyses of copulation songs, sex pheromones and molecular markers. However, the level of divergence and gene flow between the sibling species remains unclear. Brazilian populations of this vector can be divided in two main groups: one producing Burst-type songs and the Cembrene-1 pheromone and a second more diverse group producing various Pulse song subtypes and different pheromones. Methodology/Principal Findings We analyzed 21 nuclear loci in two pairs of Brazilian populations: two sympatric populations from the Sobral locality (1S and 2S) in northeastern Brazil and two allopatric populations from the Lapinha and Pancas localities in southeastern Brazil. Pancas and Sobral 2S are populations of the Burst/Cembrene-1 species while Lapinha and Sobral 1S are two putative incipient species producing the same pheromone and similar Pulse song subtypes. The multilocus analysis strongly suggests the occurrence of gene flow during the divergence between the sibling species, with different levels of introgression between loci. Moreover, this differential introgression is asymmetrical, with estimated gene flow being higher in the direction of the Burst/Cembrene-1 species. Conclusions/Significance The results indicate that introgressive hybridization has been a crucial phenomenon in shaping the genome of the L. longipalpis complex. This has possible epidemiological implications and is particularly interesting considering the potential for increased introgression caused by man-made environmental changes and the current trend of leishmaniasis urbanization in Brazil. PMID:24147172

A multilocus phylogeny reveals deep lineages within African galagids (Primates: Galagidae)

Science.gov (United States)

2014-01-01

Background Bushbabies (Galagidae) are among the most morphologically cryptic of all primates and their diversity and relationships are some of the most longstanding problems in primatology. Our knowledge of galagid evolutionary history has been limited by a lack of appropriate molecular data and a paucity of fossils. Most phylogenetic studies have produced conflicting results for many clades, and even the relationships among genera remain uncertain. To clarify galagid evolutionary history, we assembled the largest molecular dataset for galagos to date by sequencing 27 independent loci. We inferred phylogenetic relationships using concatenated maximum-likelihood and Bayesian analyses, and also coalescent-based species tree methods to account for gene tree heterogeneity due to incomplete lineage sorting. Results The genus Euoticus was identified as sister taxon to the rest of the galagids and the genus Galagoides was not recovered as monophyletic, suggesting that a new generic name for the Zanzibar complex is required. Despite the amount of genetic data collected in this study, the monophyly of the family Lorisidae remained poorly supported, probably due to the short internode between the Lorisidae/Galagidae split and the origin of the African and Asian lorisid clades. One major result was the relatively old origin for the most recent common ancestor of all living galagids soon after the Eocene-Oligocene boundary. Conclusions Using a multilocus approach, our results suggest an early origin for the crown Galagidae, soon after the Eocene-Oligocene boundary, making Euoticus one of the oldest lineages within extant Primates. This result also implies that one – or possibly more – stem radiations diverged in the Late Eocene and persisted for several million years alongside members of the crown group. PMID:24694188

Class Evolution Tree: A Graphical Tool to Support Decisions on the Number of Classes in Exploratory Categorical Latent Variable Modeling for Rehabilitation Research

Science.gov (United States)

Kriston, Levente; Melchior, Hanne; Hergert, Anika; Bergelt, Corinna; Watzke, Birgit; Schulz, Holger; von Wolff, Alessa

2011-01-01

The aim of our study was to develop a graphical tool that can be used in addition to standard statistical criteria to support decisions on the number of classes in explorative categorical latent variable modeling for rehabilitation research. Data from two rehabilitation research projects were used. In the first study, a latent profile analysis was…

Investigating Factorial Invariance of Latent Variables Across Populations When Manifest Variables Are Missing Completely.

Science.gov (United States)

Widaman, Keith F; Grimm, Kevin J; Early, Dawnté R; Robins, Richard W; Conger, Rand D

2013-07-01

Difficulties arise in multiple-group evaluations of factorial invariance if particular manifest variables are missing completely in certain groups. Ad hoc analytic alternatives can be used in such situations (e.g., deleting manifest variables), but some common approaches, such as multiple imputation, are not viable. At least 3 solutions to this problem are viable: analyzing differing sets of variables across groups, using pattern mixture approaches, and a new method using random number generation. The latter solution, proposed in this article, is to generate pseudo-random normal deviates for all observations for manifest variables that are missing completely in a given sample and then to specify multiple-group models in a way that respects the random nature of these values. An empirical example is presented in detail comparing the 3 approaches. The proposed solution can enable quantitative comparisons at the latent variable level between groups using programs that require the same number of manifest variables in each group.

Retention and Curve Number Variability in a Small Agricultural Catchment: The Probabilistic Approach

Directory of Open Access Journals (Sweden)

Kazimierz Banasik

2014-04-01

Full Text Available The variability of the curve number (CN and the retention parameter (S of the Soil Conservation Service (SCS-CN method in a small agricultural, lowland watershed (23.4 km2 to the gauging station in central Poland has been assessed using the probabilistic approach: distribution fitting and confidence intervals (CIs. Empirical CNs and Ss were computed directly from recorded rainfall depths and direct runoff volumes. Two measures of the goodness of fit were used as selection criteria in the identification of the parent distribution function. The measures specified the generalized extreme value (GEV, normal and general logistic (GLO distributions for 100-CN and GLO, lognormal and GEV distributions for S. The characteristics estimated from theoretical distribution (median, quantiles were compared to the tabulated CN and to the antecedent runoff conditions of Hawkins and Hjelmfelt. The distribution fitting for the whole sample revealed a good agreement between the tabulated CN and the median and between the antecedent runoff conditions (ARCs of Hawkins and Hjelmfelt, which certified a good calibration of the model. However, the division of the CN sample due to heavy and moderate rainfall depths revealed a serious inconsistency between the parameters mentioned. This analysis proves that the application of the SCS-CN method should rely on deep insight into the probabilistic properties of CN and S.

Mechanisms of global diversification in the marine species Madeiran Storm-petrel Oceanodroma castro and Monteiro's Storm-petrel O. monteiroi: Insights from a multi-locus approach.

Science.gov (United States)

Silva, Mauro F; Smith, Andrea L; Friesen, Vicki L; Bried, Joël; Hasegawa, Osamu; Coelho, M Manuela; Silva, Mónica C

2016-05-01

The evolutionary mechanisms underlying the geographic distribution of gene lineages in the marine environment are not as well understood as those affecting terrestrial groups. The continuous nature of the pelagic marine environment may limit opportunities for divergence to occur and lineages to spatially segregate, particularly in highly mobile species. Here, we studied the phylogeography and historical demography of two tropically distributed, pelagic seabirds, the Madeiran Storm-petrel Oceanodroma castro, sampled in the Azores, Madeira, Galapagos and Japan, and its sister species Monteiro's Storm-petrel O. monteiroi (endemic to the Azores), using a multi-locus dataset consisting of 12 anonymous nuclear loci and the mitochondrial locus control region. Both marker types support the existence of four significantly differentiated genetic clusters, including the sampled O. monteiroi population and three populations within O. castro, although only the mitochondrial locus suggests complete lineage sorting. Multi-locus coalescent analyses suggest that most divergence events occurred within the last 200,000years. The proximity in divergence times precluded robust inferences of the species tree, in particular of the evolutionary relationships of the Pacific populations. Despite the great potential for dispersal, divergence among populations apparently proceeded in the absence of gene flow, emphasizing the effect of non-physical barriers, such as those driven by the paleo-oceanographical environments, philopatry and local adaptation, as important mechanisms of population divergence and speciation in highly mobile marine species. In view of the predicted climate change impacts, future changes in the demography and evolutionary dynamics of marine populations might be expected. Copyright © 2016 Elsevier Inc. All rights reserved.

Development of a Hierarchical Variable-Number Tandem Repeat Typing Scheme for Mycobacterium tuberculosis in China

Science.gov (United States)

Luo, Tao; Yang, Chongguang; Pang, Yu; Zhao, Yanlin; Mei, Jian; Gao, Qian

2014-01-01

Molecular typing based on variable-number tandem repeats (VNTR) analysis is a promising tool for identifying transmission of Mycobacterium tuberculosis. However, the currently proposed 15- and 24-locus VNTR sets (VNTR-15/24) only have limited resolution and contain too many loci for large-scale typing in high burden countries. To develop an optimal typing scheme in China, we evaluated the resolution and robustness of 25 VNTR loci, using population-based collections of 1362 clinical isolates from six provinces across the country. The resolution of most loci showed considerable variations among regions. By calculating the average resolution of all possible combinations of 20 robust loci, we identified an optimal locus set with a minimum of 9 loci (VNTR-9) that could achieve comparable resolution of the standard VNTR-15. The VNTR-9 had consistently high resolutions in all six regions, and it was highly concordant with VNTR-15 for defining both clustered and unique genotypes. Furthermore, VNTR-9 was phylogenetically informative for classifying lineages/sublineages of M. tuberculosis. Three hypervariable loci (HV-3), VNTR 3232, VNTR 3820 and VNTR 4120, were proved important for further differentiating unrelated clustered strains based on VNTR-9. We propose the optimized VNTR-9 as first-line method and the HV-3 as second-line method for molecular typing of M. tuberculosis in China and surrounding countries. The development of hierarchical VNTR typing methods that can achieve high resolution with a small number of loci could be suitable for molecular epidemiology study in other high burden countries. PMID:24586989

Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Legionella pneumophila and Development of an Optimized Multiple-Locus VNTR Analysis Typing Scheme▿

Science.gov (United States)

Pourcel, Christine; Visca, Paolo; Afshar, Baharak; D'Arezzo, Silvia; Vergnaud, Gilles; Fry, Norman K.

2007-01-01

The utility of a genotypic typing assay for Legionella pneumophila was investigated. A multiple-locus variable number of tandem repeats (VNTR) analysis (MLVA) scheme using PCR and agarose gel electrophoresis is proposed based on eight minisatellite markers. Panels of well-characterized strains were examined in a multicenter analysis to validate the assay and to compare its performance to that of other genotyping assays. Excellent typeability, reproducibility, stability, and epidemiological concordance were observed. The MLVA type or profile is composed of a string of allele numbers, corresponding to the number of repeats at each VNTR locus, separated by commas, in a predetermined order. A database containing information from 99 L. pneumophila serogroup 1 strains and four strains of other serogroups and their MLVA profiles, which can be queried online, is available from http://bacterial-genotyping.igmors.u-psud.fr/. PMID:17251393

Genetic variability, heritability and genetic advance of quantitative ...

African Journals Online (AJOL)

Genetic variation has led to an increase in the quantitative traits of crops. The variability on genome is induced by mutation, which enhances the productivity. We evaluated variability on quantitative characters such as, plant height, number of branches/plant, number of leaves/plant, number of fruit clusters/plant, number of ...

The massive 3-loop operator matrix elements with two masses and the generalized variable flavor number scheme

Energy Technology Data Exchange (ETDEWEB)

Ablinger, J.; Schneider, C. [Johannes Kepler Univ., Linz (Austria). Research Inst. for Symbolic Computation (RISC); Bluemlein, J.; Freitas, A. de; Schoenwald, K. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Goedicke, A. [Karlsruher Institut fuer Technologie (KIT), Karlsruhe (Germany). Inst. fuer Theoretische Teilchenphysik; Wissbrock, F. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Johannes Kepler Univ., Linz (Austria). Research Inst. for Symbolic Computation (RISC)

2017-12-15

We report on our latest results in the calculation of the two-mass contributions to 3-loop operator matrix elements (OMEs). These OMEs are needed to compute the corresponding contributions to the deep-inelastic scattering structure functions and to generalize the variable flavor number scheme by including both charm and bottom quarks. We present the results for the non-singlet and A{sub gq,Q} OMEs, and compare the size of their contribution relative to the single mass case. Results for the gluonic OME A{sub gg,Q} are given in the physical case, going beyond those presented in a previous publication where scalar diagrams were computed. We also discuss our recently published two-mass contribution to the pure singlet OME, and present an alternative method of calculating the corresponding diagrams.

GIS Based Distributed Runoff Predictions in Variable Source Area Watersheds Employing the SCS-Curve Number

Science.gov (United States)

Steenhuis, T. S.; Mendoza, G.; Lyon, S. W.; Gerard Marchant, P.; Walter, M. T.; Schneiderman, E.

2003-04-01

Because the traditional Soil Conservation Service Curve Number (SCS-CN) approach continues to be ubiquitously used in GIS-BASED water quality models, new application methods are needed that are consistent with variable source area (VSA) hydrological processes in the landscape. We developed within an integrated GIS modeling environment a distributed approach for applying the traditional SCS-CN equation to watersheds where VSA hydrology is a dominant process. Spatial representation of hydrologic processes is important for watershed planning because restricting potentially polluting activities from runoff source areas is fundamental to controlling non-point source pollution. The methodology presented here uses the traditional SCS-CN method to predict runoff volume and spatial extent of saturated areas and uses a topographic index to distribute runoff source areas through watersheds. The resulting distributed CN-VSA method was incorporated in an existing GWLF water quality model and applied to sub-watersheds of the Delaware basin in the Catskill Mountains region of New York State. We found that the distributed CN-VSA approach provided a physically-based method that gives realistic results for watersheds with VSA hydrology.

Variable screening and ranking using sampling-based sensitivity measures

International Nuclear Information System (INIS)

Wu, Y-T.; Mohanty, Sitakanta

2006-01-01

This paper presents a methodology for screening insignificant random variables and ranking significant important random variables using sensitivity measures including two cumulative distribution function (CDF)-based and two mean-response based measures. The methodology features (1) using random samples to compute sensitivities and (2) using acceptance limits, derived from the test-of-hypothesis, to classify significant and insignificant random variables. Because no approximation is needed in either the form of the performance functions or the type of continuous distribution functions representing input variables, the sampling-based approach can handle highly nonlinear functions with non-normal variables. The main characteristics and effectiveness of the sampling-based sensitivity measures are investigated using both simple and complex examples. Because the number of samples needed does not depend on the number of variables, the methodology appears to be particularly suitable for problems with large, complex models that have large numbers of random variables but relatively few numbers of significant random variables

Comparison of double-locus sequence typing (DLST) and multilocus sequence typing (MLST) for the investigation of Pseudomonas aeruginosa populations.

Science.gov (United States)

Cholley, Pascal; Stojanov, Milos; Hocquet, Didier; Thouverez, Michelle; Bertrand, Xavier; Blanc, Dominique S

2015-08-01

Reliable molecular typing methods are necessary to investigate the epidemiology of bacterial pathogens. Reference methods such as multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) are costly and time consuming. Here, we compared our newly developed double-locus sequence typing (DLST) method for Pseudomonas aeruginosa to MLST and PFGE on a collection of 281 isolates. DLST was as discriminatory as MLST and was able to recognize "high-risk" epidemic clones. Both methods were highly congruent. Not surprisingly, a higher discriminatory power was observed with PFGE. In conclusion, being a simple method (single-strand sequencing of only 2 loci), DLST is valuable as a first-line typing tool for epidemiological investigations of P. aeruginosa. Coupled to a more discriminant method like PFGE or whole genome sequencing, it might represent an efficient typing strategy to investigate or prevent outbreaks. Copyright © 2015 Elsevier Inc. All rights reserved.

Combination of Single Nucleotide Polymorphism and Variable-Number Tandem Repeats for Genotyping a Homogenous Population of Mycobacterium tuberculosis Beijing Strains in China

OpenAIRE

Luo, Tao; Yang, Chongguang; Gagneux, Sebastien; Gicquel, Brigitte; Mei, Jian; Gao, Qian

2012-01-01

The standard 15- and 24-locus variable-number tandem repeat (VNTR) genotyping methods have demonstrated adequate discriminatory power and a small homoplasy effect for tracing tuberculosis (TB) transmission and predicting Mycobacterium tuberculosis lineages in European and North American countries. However, its validity for the definition of transmission in homogenous M. tuberculosis populations in settings with high TB burdens has been questioned. Here, we genotyped a population-based collect...

Complete Deletion of the Fucose Operon in Haemophilus influenzae Is Associated with a Cluster in Multilocus Sequence Analysis-Based Phylogenetic Group II Related to Haemophilus haemolyticus: Implications for Identification and Typing.

Science.gov (United States)

de Gier, Camilla; Kirkham, Lea-Ann S; Nørskov-Lauritsen, Niels

2015-12-01

Nonhemolytic variants of Haemophilus haemolyticus are difficult to differentiate from Haemophilus influenzae despite a wide difference in pathogenic potential. A previous investigation characterized a challenging set of 60 clinical strains using multiple PCRs for marker genes and described strains that could not be unequivocally identified as either species. We have analyzed the same set of strains by multilocus sequence analysis (MLSA) and near-full-length 16S rRNA gene sequencing. MLSA unambiguously allocated all study strains to either of the two species, while identification by 16S rRNA sequence was inconclusive for three strains. Notably, the two methods yielded conflicting identifications for two strains. Most of the "fuzzy species" strains were identified as H. influenzae that had undergone complete deletion of the fucose operon. Such strains, which are untypeable by the H. influenzae multilocus sequence type (MLST) scheme, have sporadically been reported and predominantly belong to a single branch of H. influenzae MLSA phylogenetic group II. We also found evidence of interspecies recombination between H. influenzae and H. haemolyticus within the 16S rRNA genes. Establishing an accurate method for rapid and inexpensive identification of H. influenzae is important for disease surveillance and treatment. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Multilocus sequence typing as a replacement for serotyping in Salmonella enterica.

Directory of Open Access Journals (Sweden)

Mark Achtman

Full Text Available Salmonella enterica subspecies enterica is traditionally subdivided into serovars by serological and nutritional characteristics. We used Multilocus Sequence Typing (MLST to assign 4,257 isolates from 554 serovars to 1092 sequence types (STs. The majority of the isolates and many STs were grouped into 138 genetically closely related clusters called eBurstGroups (eBGs. Many eBGs correspond to a serovar, for example most Typhimurium are in eBG1 and most Enteritidis are in eBG4, but many eBGs contained more than one serovar. Furthermore, most serovars were polyphyletic and are distributed across multiple unrelated eBGs. Thus, serovar designations confounded genetically unrelated isolates and failed to recognize natural evolutionary groupings. An inability of serotyping to correctly group isolates was most apparent for Paratyphi B and its variant Java. Most Paratyphi B were included within a sub-cluster of STs belonging to eBG5, which also encompasses a separate sub-cluster of Java STs. However, diphasic Java variants were also found in two other eBGs and monophasic Java variants were in four other eBGs or STs, one of which is in subspecies salamae and a second of which includes isolates assigned to Enteritidis, Dublin and monophasic Paratyphi B. Similarly, Choleraesuis was found in eBG6 and is closely related to Paratyphi C, which is in eBG20. However, Choleraesuis var. Decatur consists of isolates from seven other, unrelated eBGs or STs. The serological assignment of these Decatur isolates to Choleraesuis likely reflects lateral gene transfer of flagellar genes between unrelated bacteria plus purifying selection. By confounding multiple evolutionary groups, serotyping can be misleading about the disease potential of S. enterica. Unlike serotyping, MLST recognizes evolutionary groupings and we recommend that Salmonella classification by serotyping should be replaced by MLST or its equivalents.

[Evaluation of different sets of variable number of tandem repeats ioci for genotyping Mycobacterium tuberculosis isolates in China].

Science.gov (United States)

Liu, Mei; Luo, Tao; Yang, Chongguang; Liu, Qingyun; Gao, Qian

2015-10-01

To identify a variable number of tandem repeats (VNTR) typing method that is suitable for molecular epidemiological study of tuberculosis in China. We systematically evaluated the commonly used VNTR typing methods, including 4 methods (MIRU-12, VNTR-15/VNTR-24 and VNTR "24+4") proposed by foreign colleagues and 2 methods (VNTR-L15 and VNTR"9+3") developed by domestic researchers using population-based collection of 891 clinical isolates from 5 provinces across the country. The order (from high to low) of discriminatory power for the 6 VNTR typing methods was VNTR"24+4", VNTR"9+3", VNTR-24, VNTR-15, VNTR-L15 and MIRU-12. The discriminatory power of VNTR"9+3" was comparable with VNTR"24+4" and higher than that of VNTR-15/24. The concordance for defining clustered and unique genotypes between VNTR"9+3" and VNTR"24+4" was 96.59%. Our results suggest that VNTR"9+3" is a suitable method for molecular typing of M. tuberculosis in China by considering its high discriminatory power, high consistency with VNTR"24+4" and relative small number of VNTR locus.

The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae.

Science.gov (United States)

Diaz, Maureen H; Winchell, Jonas M

2016-01-01

Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen.

Using molecular tools to identify the geographical origin of a case of human brucellosis.

Science.gov (United States)

Muchowski, J K; Koylass, M S; Dainty, A C; Stack, J A; Perrett, L; Whatmore, A M; Perrier, C; Chircop, S; Demicoli, N; Gatt, A B; Caruana, P A; Gopaul, K K

2015-10-01

Although Malta is historically linked with the zoonosis brucellosis, there had not been a case of the disease in either the human or livestock population for several years. However, in July 2013 a case of human brucellosis was identified on the island. To determine whether this recent case originated in Malta, four isolates from this case were subjected to molecular analysis. Molecular profiles generated using multilocus sequence analysis and multilocus variable number tandem repeat for the recent human case isolates and 11 Brucella melitensis strains of known Maltese origin were compared with others held on in-house and global databases. While the 11 isolates of Maltese origin formed a distinct cluster, the recent human isolation was not associated with these strains but instead clustered with isolates originating from the Horn of Africa. These data was congruent with epidemiological trace-back showed that the individual had travelled to Malta from Eritrea. This work highlights the potential of using molecular typing data to aid in epidemiological trace-back of Brucella isolations and assist in monitoring of the effectiveness of brucellosis control schemes.

cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate.

Science.gov (United States)

Clevert, Djork-Arné; Mitterecker, Andreas; Mayr, Andreas; Klambauer, Günter; Tuefferd, Marianne; De Bondt, An; Talloen, Willem; Göhlmann, Hinrich; Hochreiter, Sepp

2011-07-01

Cost-effective oligonucleotide genotyping arrays like the Affymetrix SNP 6.0 are still the predominant technique to measure DNA copy number variations (CNVs). However, CNV detection methods for microarrays overestimate both the number and the size of CNV regions and, consequently, suffer from a high false discovery rate (FDR). A high FDR means that many CNVs are wrongly detected and therefore not associated with a disease in a clinical study, though correction for multiple testing takes them into account and thereby decreases the study's discovery power. For controlling the FDR, we propose a probabilistic latent variable model, 'cn.FARMS', which is optimized by a Bayesian maximum a posteriori approach. cn.FARMS controls the FDR through the information gain of the posterior over the prior. The prior represents the null hypothesis of copy number 2 for all samples from which the posterior can only deviate by strong and consistent signals in the data. On HapMap data, cn.FARMS clearly outperformed the two most prevalent methods with respect to sensitivity and FDR. The software cn.FARMS is publicly available as a R package at http://www.bioinf.jku.at/software/cnfarms/cnfarms.html.

Petroleomics by electrospray ionization FT-ICR mass spectrometry coupled to partial least squares with variable selection methods: prediction of the total acid number of crude oils.

Science.gov (United States)

Terra, Luciana A; Filgueiras, Paulo R; Tose, Lílian V; Romão, Wanderson; de Souza, Douglas D; de Castro, Eustáquio V R; de Oliveira, Mirela S L; Dias, Júlio C M; Poppi, Ronei J

2014-10-07

Negative-ion mode electrospray ionization, ESI(-), with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was coupled to a Partial Least Squares (PLS) regression and variable selection methods to estimate the total acid number (TAN) of Brazilian crude oil samples. Generally, ESI(-)-FT-ICR mass spectra present a power of resolution of ca. 500,000 and a mass accuracy less than 1 ppm, producing a data matrix containing over 5700 variables per sample. These variables correspond to heteroatom-containing species detected as deprotonated molecules, [M - H](-) ions, which are identified primarily as naphthenic acids, phenols and carbazole analog species. The TAN values for all samples ranged from 0.06 to 3.61 mg of KOH g(-1). To facilitate the spectral interpretation, three methods of variable selection were studied: variable importance in the projection (VIP), interval partial least squares (iPLS) and elimination of uninformative variables (UVE). The UVE method seems to be more appropriate for selecting important variables, reducing the dimension of the variables to 183 and producing a root mean square error of prediction of 0.32 mg of KOH g(-1). By reducing the size of the data, it was possible to relate the selected variables with their corresponding molecular formulas, thus identifying the main chemical species responsible for the TAN values.

Multi-locus phylogeny reveals instances of mitochondrial introgression and unrecognized diversity in Kenyan barbs (Cyprininae: Smiliogastrini).

Science.gov (United States)

Schmidt, Ray C; Bart, Henry L; Nyingi, Wanja Dorothy

2017-06-01

The phylogenetics and taxonomic status of small African barbs (Cyprininae: Smiliogastrini) remains unresolved despite the recent decision to elevate the genus name Enteromius for the group. The main barrier to understanding the origin of African small barbs and evolutionary relationships within the group is the poor resolution of phylogenies published to date. These phylogenies usually rely on mitochondrial markers and have limited taxon sampling. Here we investigate the phylogenetic relationships of small barbs of Kenya utilizing cytochrome b, Growth Hormone (GH) intron 2, and RAG1 markers from multiple populations of many species in the region. This multi-locus study produced well-supported phylogenies and revealed additional issues that complicate understanding the relationships among East African barbs. We observed widespread mtDNA introgression within the Kenyan barbs, highlighting the need to include nuclear markers in phylogenetic studies of the group. The GH intron 2 resolved heterospecific individuals and aided in inferring the species level phylogeny. The study reveals unrecognized diversity within the group, including within species reported to occur throughout East Africa, and it provides the groundwork for future taxonomic work in the region and across Africa. Copyright © 2017 Elsevier Inc. All rights reserved.

Longitudinal survey of Staphylococcus aureus in cystic fibrosis patients using a multiple-locus variable-number of tandem-repeats analysis method

OpenAIRE

Vergnaud Gilles; Moissenet Didier; Corvol Harriet; Fauroux Brigitte; Corbineau Gaëlle; Hormigos Katia; Vu-Thien Hoang; Pourcel Christine

2010-01-01

Abstract Background Staphylococcus aureus infection in patients with cystic fibrosis (CF) is frequent and may be due to colonization by a few pathogenic lineages. Systematic genotyping of all isolates, methicillin-susceptible S. aureus (MSSA) as well as methicillin-resistant S. aureus (MRSA) is necessary to identify such lineages and follow their evolution in patients. Multiple-locus variable-number tandem repeat analysis (MLVA/VNTR) was used to survey S. aureus clinical isolates in a French ...

Multilocus Sequence Analysis of Nectar Pseudomonads Reveals High Genetic Diversity and Contrasting Recombination Patterns

Science.gov (United States)

Álvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M.

2013-01-01

The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas ‘sensu stricto’ isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria. PMID:24116076

Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns.

Science.gov (United States)

Alvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M

2013-01-01

The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas 'sensu stricto' isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria.

DNF Tautologies with a Limited Number of Occurrences of Every Variable

Czech Academy of Sciences Publication Activity Database

Savický, Petr; Sgall, Jiří

2000-01-01

Roč. 238, 1-2 (2000), s. 495-498 ISSN 0304-3975 R&D Projects: GA ČR GA201/98/0717; GA AV ČR IAA1019602; GA ČR GA201/97/P038; GA MŠk ME 103 Institutional research plan: AV0Z1030915 Keywords : disjunctive normal form * tautology * occurences of variable Subject RIV: BA - General Mathematics Impact factor: 0.417, year: 2000

Exploratory Spectroscopy of Magnetic Cataclysmic Variables Candidates and Other Variable Objects

Science.gov (United States)

Oliveira, A. S.; Rodrigues, C. V.; Cieslinski, D.; Jablonski, F. J.; Silva, K. M. G.; Almeida, L. A.; Rodríguez-Ardila, A.; Palhares, M. S.

2017-04-01

The increasing number of synoptic surveys made by small robotic telescopes, such as the photometric Catalina Real-Time Transient Survey (CRTS), provides a unique opportunity to discover variable sources and improves the statistical samples of such classes of objects. Our goal is the discovery of magnetic Cataclysmic Variables (mCVs). These are rare objects that probe interesting accretion scenarios controlled by the white-dwarf magnetic field. In particular, improved statistics of mCVs would help to address open questions on their formation and evolution. We performed an optical spectroscopy survey to search for signatures of magnetic accretion in 45 variable objects selected mostly from the CRTS. In this sample, we found 32 CVs, 22 being mCV candidates, 13 of which were previously unreported as such. If the proposed classifications are confirmed, it would represent an increase of 4% in the number of known polars and 12% in the number of known IPs. A fraction of our initial sample was classified as extragalactic sources or other types of variable stars by the inspection of the identification spectra. Despite the inherent complexity in identifying a source as an mCV, variability-based selection, followed by spectroscopic snapshot observations, has proved to be an efficient strategy for their discoveries, being a relatively inexpensive approach in terms of telescope time. Based on observations obtained at the Observatório do Pico dos Dias/LNA, and at the Southern Astrophysical Research (SOAR) telescope, which is a joint project of the Ministério da Ciência, Tecnologia, e Inovação (MCTI) da República Federativa do Brasil, the U.S. National Optical Astronomy Observatory (NOAO), the University of North Carolina at Chapel Hill (UNC), and Michigan State University (MSU).

Aerodynamic Effects of Turbulence Intensity on a Variable-Speed Power-Turbine Blade with Large Incidence and Reynolds Number Variations

Science.gov (United States)

Flegel, Ashlie Brynn; Giel, Paul W.; Welch, Gerard E.

2014-01-01

The effects of inlet turbulence intensity on the aerodynamic performance of a variable speed power turbine blade are examined over large incidence and Reynolds number ranges. Both high and low turbulence studies were conducted in the NASA Glenn Research Center Transonic Turbine Blade Cascade Facility. The purpose of the low inlet turbulence study was to examine the transitional flow effects that are anticipated at cruise Reynolds numbers. The high turbulence study extends this to LPT-relevant turbulence levels while perhaps sacrificing transitional flow effects. Downstream total pressure and exit angle data were acquired for ten incidence angles ranging from +15.8 to 51.0. For each incidence angle, data were obtained at five flow conditions with the exit Reynolds number ranging from 2.12105 to 2.12106 and at a design exit Mach number of 0.72. In order to achieve the lowest Reynolds number, the exit Mach number was reduced to 0.35 due to facility constraints. The inlet turbulence intensity, Tu, was measured using a single-wire hotwire located 0.415 axial-chord upstream of the blade row. The inlet turbulence levels ranged from 0.25 - 0.4 for the low Tu tests and 8- 15 for the high Tu study. Tu measurements were also made farther upstream so that turbulence decay rates could be calculated as needed for computational inlet boundary conditions. Downstream flow field measurements were obtained using a pneumatic five-hole pitchyaw probe located in a survey plane 7 axial chord aft of the blade trailing edge and covering three blade passages. Blade and endwall static pressures were acquired for each flow condition as well. The blade loading data show that the suction surface separation that was evident at many of the low Tu conditions has been eliminated. At the extreme positive and negative incidence angles, the data show substantial differences in the exit flow field. These differences are attributable to both the higher inlet Tu directly and to the thinner inlet endwall

Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme▿†

Science.gov (United States)

Pourcel, Christine; Minandri, Fabrizia; Hauck, Yolande; D'Arezzo, Silvia; Imperi, Francesco; Vergnaud, Gilles; Visca, Paolo

2011-01-01

Acinetobacter baumannii is an important opportunistic pathogen responsible for nosocomial outbreaks, mostly occurring in intensive care units. Due to the multiplicity of infection sources, reliable molecular fingerprinting techniques are needed to establish epidemiological correlations among A. baumannii isolates. Multiple-locus variable-number tandem-repeat analysis (MLVA) has proven to be a fast, reliable, and cost-effective typing method for several bacterial species. In this study, an MLVA assay compatible with simple PCR- and agarose gel-based electrophoresis steps as well as with high-throughput automated methods was developed for A. baumannii typing. Preliminarily, 10 potential polymorphic variable-number tandem repeats (VNTRs) were identified upon bioinformatic screening of six annotated genome sequences of A. baumannii. A collection of 7 reference strains plus 18 well-characterized isolates, including unique types and representatives of the three international A. baumannii lineages, was then evaluated in a two-center study aimed at validating the MLVA assay and comparing it with other genotyping assays, namely, macrorestriction analysis with pulsed-field gel electrophoresis (PFGE) and PCR-based sequence group (SG) profiling. The results showed that MLVA can discriminate between isolates with identical PFGE types and SG profiles. A panel of eight VNTR markers was selected, all showing the ability to be amplified and good amounts of polymorphism in the majority of strains. Independently generated MLVA profiles, composed of an ordered string of allele numbers corresponding to the number of repeats at each VNTR locus, were concordant between centers. Typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. A database containing information and MLVA profiles for several A. baumannii strains is available from http://mlva.u-psud.fr/. PMID:21147956

Genotyping of Indian antigenic, vaccine, and field Brucella spp. using multilocus sequence typing.

Science.gov (United States)

Shome, Rajeswari; Krithiga, Natesan; Shankaranarayana, Padmashree B; Jegadesan, Sankarasubramanian; Udayakumar S, Vishnu; Shome, Bibek Ranjan; Saikia, Girin Kumar; Sharma, Narendra Kumar; Chauhan, Harshad; Chandel, Bharat Singh; Jeyaprakash, Rajendhran; Rahman, Habibur

2016-03-31

Brucellosis is one of the most important zoonotic diseases that affects multiple livestock species and causes great economic losses. The highly conserved genomes of Brucella, with > 90% homology among species, makes it important to study the genetic diversity circulating in the country. A total of 26 Brucella spp. (4 reference strains and 22 field isolates) and 1 B. melitensis draft genome sequence from India (B. melitensis Bm IND1) were included for sequence typing. The field isolates were identified by biochemical tests and confirmed by both conventional and quantitative polymerase chain reaction (qPCR) targeting bcsp 31Brucella genus-specific marker. Brucella speciation and biotyping was done by Bruce ladder, probe qPCR, and AMOS PCRs, respectively, and genotyping was done by multilocus sequence typing (MLST). The MLST typing of 27 Brucella spp. revealed five distinct sequence types (STs); the B. abortus S99 reference strain and 21 B. abortus field isolates belonged to ST1. On the other hand, the vaccine strain B. abortus S19 was genotyped as ST5. Similarly, B. melitensis 16M reference strain and one B. melitensis field isolate were grouped into ST7. Another B. melitensis field isolate belonged to ST8 (draft genome sequence from India), and only B. suis 1330 reference strain was found to be ST14. The sequences revealed genetic similarity of the Indian strains to the global reference and field strains. The study highlights the usefulness of MLST for typing of field isolates and validation of reference strains used for diagnosis and vaccination against brucellosis.

Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity.

Science.gov (United States)

Alström, Per; Barnes, Keith N; Olsson, Urban; Barker, F Keith; Bloomer, Paulette; Khan, Aleem Ahmed; Qureshi, Masood Ahmed; Guillaumet, Alban; Crochet, Pierre-André; Ryan, Peter G

2013-12-01

The Alaudidae (larks) is a large family of songbirds in the superfamily Sylvioidea. Larks are cosmopolitan, although species-level diversity is by far largest in Africa, followed by Eurasia, whereas Australasia and the New World have only one species each. The present study is the first comprehensive phylogeny of the Alaudidae. It includes 83.5% of all species and representatives from all recognised genera, and was based on two mitochondrial and three nuclear loci (in total 6.4 kbp, although not all loci were available for all species). In addition, a larger sample, comprising several subspecies of some polytypic species was analysed for one of the mitochondrial loci. There was generally good agreement in trees inferred from different loci, although some strongly supported incongruences were noted. The tree based on the concatenated multilocus data was overall well resolved and well supported by the data. We stress the importance of performing single gene as well as combined data analyses, as the latter may obscure significant incongruence behind strong nodal support values. The multilocus tree revealed many unpredicted relationships, including some non-monophyletic genera (Calandrella, Mirafra, Melanocorypha, Spizocorys). The tree based on the extended mitochondrial data set revealed several unexpected deep divergences between taxa presently treated as conspecific (e.g. within Ammomanes cinctura, Ammomanes deserti, Calandrella brachydactyla, Eremophila alpestris), as well as some shallow splits between currently recognised species (e.g. Certhilauda brevirostris-C. semitorquata-C. curvirostris; Calendulauda barlowi-C. erythrochlamys; Mirafra cantillans-M. javanica). Based on our results, we propose a revised generic classification, and comment on some species limits. We also comment on the extraordinary morphological adaptability in larks, which has resulted in numerous examples of parallel evolution (e.g. in Melanocorypha mongolica and Alauda leucoptera [both

Genetic analysis of Phytophthora infestans populations in the Nordic European countries reveals high genetic variability

DEFF Research Database (Denmark)

Brurberg, May Bente; Elameen, Abdelhameed; Le, Ving Hong

2011-01-01

different fields using nine simple-sequence repeat (SSR) markers. Forty-nine alleles were detected among the nine SSR loci and isolates from all four Nordic countries shared the most common alleles across the loci. In total 169 multilocus genotypes (based on seven loci) were identified among 191 isolates...

Molecular epidemiology and multilocus sequence analysis of potentially zoonotic Giardia spp. from humans and dogs in Jamaica.

Science.gov (United States)

Lee, Mellesia F; Cadogan, Paul; Eytle, Sarah; Copeland, Sonia; Walochnik, Julia; Lindo, John F

2017-01-01

Giardia spp. are the causative agents of intestinal infections in a wide variety of mammals including humans and companion animals. Dogs may be reservoirs of zoonotic Giardia spp.; however, the potential for transmission between dogs and humans in Jamaica has not been studied. Conventional PCR was used to screen 285 human and 225 dog stool samples for Giardia targeting the SSU rDNA gene followed by multilocus sequencing of the triosephosphate isomerase (tpi), glutamate dehydrogenase (gdh), and β-giardin (bg) genes. Prevalence of human infections based on PCR was 6.7 % (19/285) and canine infections 19.6 % (44/225). Nested PCR conducted on all 63 positive samples revealed the exclusive presence of assemblage A in both humans and dogs. Sub-assemblage A-II was responsible for 79.0 % (15/19) and 70.5 % (31/44) of the infections in humans and dogs, respectively, while sub-assemblage A-I was identified at a rate of 15.8 % (3/19) and 29.5 % (13/44) in humans and dogs, respectively. The predominance of a single circulating assemblage among both humans and dogs in Jamaica suggests possible zoonotic transmission of Giardia infections.

Genotyping of B. licheniformis based on a novel multi-locus sequence typing (MLST scheme

Directory of Open Access Journals (Sweden)

Madslien Elisabeth H

2012-10-01

Full Text Available Abstract Background Bacillus licheniformis has for many years been used in the industrial production of enzymes, antibiotics and detergents. However, as a producer of dormant heat-resistant endospores B. licheniformis might contaminate semi-preserved foods. The aim of this study was to establish a robust and novel genotyping scheme for B. licheniformis in order to reveal the evolutionary history of 53 strains of this species. Furthermore, the genotyping scheme was also investigated for its use to detect food-contaminating strains. Results A multi-locus sequence typing (MLST scheme, based on the sequence of six house-keeping genes (adk, ccpA, recF, rpoB, spo0A and sucC of 53 B. licheniformis strains from different sources was established. The result of the MLST analysis supported previous findings of two different subgroups (lineages within this species, named “A” and “B” Statistical analysis of the MLST data indicated a higher rate of recombination within group “A”. Food isolates were widely dispersed in the MLST tree and could not be distinguished from the other strains. However, the food contaminating strain B. licheniformis NVH1032, represented by a unique sequence type (ST8, was distantly related to all other strains. Conclusions In this study, a novel and robust genotyping scheme for B. licheniformis was established, separating the species into two subgroups. This scheme could be used for further studies of evolution and population genetics in B. licheniformis.

Concurrent variable-interval variable-ratio schedules in a dynamic choice environment.

Science.gov (United States)

Bell, Matthew C; Baum, William M

2017-11-01

Most studies of operant choice have focused on presenting subjects with a fixed pair of schedules across many experimental sessions. Using these methods, studies of concurrent variable- interval variable-ratio schedules helped to evaluate theories of choice. More recently, a growing literature has focused on dynamic choice behavior. Those dynamic choice studies have analyzed behavior on a number of different time scales using concurrent variable-interval schedules. Following the dynamic choice approach, the present experiment examined performance on concurrent variable-interval variable-ratio schedules in a rapidly changing environment. Our objectives were to compare performance on concurrent variable-interval variable-ratio schedules with extant data on concurrent variable-interval variable-interval schedules using a dynamic choice procedure and to extend earlier work on concurrent variable-interval variable-ratio schedules. We analyzed performances at different time scales, finding strong similarities between concurrent variable-interval variable-interval and concurrent variable-interval variable- ratio performance within dynamic choice procedures. Time-based measures revealed almost identical performance in the two procedures compared with response-based measures, supporting the view that choice is best understood as time allocation. Performance at the smaller time scale of visits accorded with the tendency seen in earlier research toward developing a pattern of strong preference for and long visits to the richer alternative paired with brief "samples" at the leaner alternative ("fix and sample"). © 2017 Society for the Experimental Analysis of Behavior.

Global diversity of the Ganoderma lucidum complex (Ganodermataceae, Polyporales) inferred from morphology and multilocus phylogeny.

Science.gov (United States)

Zhou, Li-Wei; Cao, Yun; Wu, Sheng-Hua; Vlasák, Josef; Li, De-Wei; Li, Meng-Jie; Dai, Yu-Cheng

2015-06-01

Species of the Ganoderma lucidum complex are used in many types of health products. However, the taxonomy of this complex has long been chaotic, thus limiting its uses. In the present study, 32 collections of the complex from Asia, Europe and North America were analyzed from both morphological and molecular phylogenetic perspectives. The combined dataset, including an outgroup, comprised 33 ITS, 24 tef1α, 24 rpb1 and 21 rpb2 sequences, of which 19 ITS, 20 tef1α, 20 rpb1 and 17 rpb2 sequences were newly generated. A total of 13 species of the complex were recovered in the multilocus phylogeny. These 13 species were not strongly supported as a single monophyletic lineage, and were further grouped into three lineages that cannot be defined by their geographic distributions. Clade A comprised Ganoderma curtisii, Ganoderma flexipes, Ganoderma lingzhi, Ganoderma multipileum, Ganoderma resinaceum, Ganoderma sessile, Ganoderma sichuanense and Ganoderma tropicum, Clade B comprised G. lucidum, Ganoderma oregonense and Ganoderma tsugae, and Clade C comprised Ganoderma boninense and Ganoderma zonatum. A dichotomous key to the 13 species is provided, and their key morphological characters from context, pores, cuticle cells and basidiospores are presented in a table. The taxonomic positions of these species are briefly discussed. Noteworthy, the epitypification of G. sichuanense is rejected. Copyright © 2014 Elsevier Ltd. All rights reserved.

Zinc Resistance within Swine-Associated Methicillin-Resistant Staphylococcus aureus Isolates in the United States Is Associated with Multilocus Sequence Type Lineage.

Science.gov (United States)

Hau, Samantha J; Frana, Timothy; Sun, Jisun; Davies, Peter R; Nicholson, Tracy L

2017-08-01

Zinc resistance in livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) sequence type 398 (ST398) is primarily mediated by the czrC gene colocated with the mecA gene, encoding methicillin resistance, within the type V staphylococcal cassette chromosome mec (SCC mec ) element. Because czrC and mecA are located within the same mobile genetic element, it has been suggested that the use of zinc in feed as an antidiarrheal agent has the potential to contribute to the emergence and spread of methicillin-resistant S. aureus (MRSA) in swine, through increased selection pressure to maintain the SCC mec element in isolates obtained from pigs. In this study, we report the prevalence of the czrC gene and phenotypic zinc resistance in U.S. swine-associated LA-MRSA ST5 isolates, MRSA ST5 isolates from humans with no swine contact, and U.S. swine-associated LA-MRSA ST398 isolates. We demonstrated that the prevalence of zinc resistance in U.S. swine-associated LA-MRSA ST5 isolates was significantly lower than the prevalence of zinc resistance in MRSA ST5 isolates from humans with no swine contact and swine-associated LA-MRSA ST398 isolates, as well as prevalences from previous reports describing zinc resistance in other LA-MRSA ST398 isolates. Collectively, our data suggest that selection pressure associated with zinc supplementation in feed is unlikely to have played a significant role in the emergence of LA-MRSA ST5 in the U.S. swine population. Additionally, our data indicate that zinc resistance is associated with the multilocus sequence type lineage, suggesting a potential link between the genetic lineage and the carriage of resistance determinants. IMPORTANCE Our data suggest that coselection thought to be associated with the use of zinc in feed as an antimicrobial agent is not playing a role in the emergence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) ST5 in the U.S. swine population. Additionally, our data indicate

A Single Multilocus Sequence Typing (MLST) Scheme for Seven Pathogenic Leptospira Species

Science.gov (United States)

Amornchai, Premjit; Wuthiekanun, Vanaporn; Bailey, Mark S.; Holden, Matthew T. G.; Zhang, Cuicai; Jiang, Xiugao; Koizumi, Nobuo; Taylor, Kyle; Galloway, Renee; Hoffmaster, Alex R.; Craig, Scott; Smythe, Lee D.; Hartskeerl, Rudy A.; Day, Nicholas P.; Chantratita, Narisara; Feil, Edward J.; Aanensen, David M.; Spratt, Brian G.; Peacock, Sharon J.

2013-01-01

Background The available Leptospira multilocus sequence typing (MLST) scheme supported by a MLST website is limited to L. interrogans and L. kirschneri. Our aim was to broaden the utility of this scheme to incorporate a total of seven pathogenic species. Methodology and Findings We modified the existing scheme by replacing one of the seven MLST loci (fadD was changed to caiB), as the former gene did not appear to be present in some pathogenic species. Comparison of the original and modified schemes using data for L. interrogans and L. kirschneri demonstrated that the discriminatory power of the two schemes was not significantly different. The modified scheme was used to further characterize 325 isolates (L. alexanderi [n = 5], L. borgpetersenii [n = 34], L. interrogans [n = 222], L. kirschneri [n = 29], L. noguchii [n = 9], L. santarosai [n = 10], and L. weilii [n = 16]). Phylogenetic analysis using concatenated sequences of the 7 loci demonstrated that each species corresponded to a discrete clade, and that no strains were misclassified at the species level. Comparison between genotype and serovar was possible for 254 isolates. Of the 31 sequence types (STs) represented by at least two isolates, 18 STs included isolates assigned to two or three different serovars. Conversely, 14 serovars were identified that contained between 2 to 10 different STs. New observations were made on the global phylogeography of Leptospira spp., and the utility of MLST in making associations between human disease and specific maintenance hosts was demonstrated. Conclusion The new MLST scheme, supported by an updated MLST website, allows the characterization and species assignment of isolates of the seven major pathogenic species associated with leptospirosis. PMID:23359622

VNTR diversity in Yersinia pestis isolates from an animal challenge study reveals the potential for in vitro mutations during laboratory cultivation

Science.gov (United States)

Vogler, Amy J.; Nottingham, Roxanne; Busch, Joseph D.; Sahl, Jason W.; Shuey, Megan M.; Foster, Jeffrey T.; Schupp, James M.; Smith, Susan; Rocke, Tonie E.; Klein, Paul; Wagner, David M.

2016-01-01

Underlying mutation rates and other evolutionary forces shape the population structure of bacteria in nature. Although easily overlooked, similar forces are at work in the laboratory and may influence observed mutations. Here, we investigated tissue samples and Yersinia pestis isolates from a rodent laboratory challenge with strain CO92 using whole genome sequencing and multi-locus variable-number tandem repeat (VNTR) analysis (MLVA). We identified six VNTR mutations that were found to have occurred in vitro during laboratory cultivation rather than in vivo during the rodent challenge. In contrast, no single nucleotide polymorphism (SNP) mutations were observed, either in vivo or in vitro. These results were consistent with previously published mutation rates and the calculated number of Y. pestis generations that occurred during the in vitro versus the in vivo portions of the experiment. When genotyping disease outbreaks, the potential for in vitro mutations should be considered, particularly when highly variable genetic markers such as VNTRs are used.

Foundations of analysis over surreal number fields

CERN Document Server

Alling, NL

1987-01-01

In this volume, a tower of surreal number fields is defined, each being a real-closed field having a canonical formal power series structure and many other higher order properties. Formal versions of such theorems as the Implicit Function Theorem hold over such fields. The Main Theorem states that every formal power series in a finite number of variables over a surreal field has a positive radius of hyper-convergence within which it may be evaluated. Analytic functions of several surreal and surcomplex variables can then be defined and studied. Some first results in the one variable case are derived. A primer on Conway''s field of surreal numbers is also given. Throughout the manuscript, great efforts have been made to make the volume fairly self-contained. Much exposition is given. Many references are cited. While experts may want to turn quickly to new results, students should be able to find the explanation of many elementary points of interest. On the other hand, many new results are given, and much mathe...

An evaluation of FIA's stand age variable

Science.gov (United States)

John D. Shaw

2015-01-01

The Forest Inventory and Analysis Database (FIADB) includes a large number of measured and computed variables. The definitions of measured variables are usually well-documented in FIA field and database manuals. Some computed variables, such as live basal area of the condition, are equally straightforward. Other computed variables, such as individual tree volume,...

Prevalence of Chlamydia trachomatis Genotypes in Men Who Have Sex with Men and Men Who Have Sex with Women Using Multilocus VNTR Analysis-ompA Typing in Guangzhou, China.

Directory of Open Access Journals (Sweden)

Xiaolin Qin

Full Text Available Chlamydia trachomatis is one of the most prevalent bacterial sexually transmitted infection in China. Although C. trachomatis genotypes can be discriminated by outer membrane protein gene (ompA sequencing, currently available methods have limited resolutions. This study used a high-resolution genotyping method, namely, multilocus variable number tandem-repeat analysis with ompA sequencing (MLVA-ompA, to investigate the local epidemiology of C. trachomatis infections among men who have sex with men (MSM and men who have sex with women (MSW attending a sexually transmitted diseases (STD clinic in Guangzhou, China.Rectal specimens from MSM and urethral specimens from MSW were collected between January 2013 and July 2014 at the Guangdong Provincial Center STD clinic. The specimens were sent to the laboratory for analyses. All specimens that were tested positive for C. trachomatis by the commercial nucleic acid amplification tests were genotyped by MLVA-ompA.Fifty-one rectal specimens from MSM and 96 urethral specimens from MSW were identified with C. trachomatis. One hundred and forty-four of the 147 specimens were fully genotyped by MLVA-ompA. Rectal specimens from MSM were divided into four ompA genotypes and urethral specimens from MSW into nine genotypes. No mixed infections were found among all specimens. The most frequent genotypes were D, G, J, E and F. All specimens were further divided into 46 types after ompA genotyping was combined with MLVA. Genotypes D-8.7.1 and G-3.4a.3 were the most frequent among MSM, whereas genotypes D-3.4a.4, E-8.5.1, F-8.5.1, and J-3.4a.2 were the most frequent subtypes among MSW. The discriminatory index D was 0.90 for MLVA, 0.85 for ompA, and 0.95 for MLVA-ompA.The most prevalent MLVA-ompA genotypes were significantly different between MSM and MSW from Guangzhou, China. Moreover, MLVA-ompA represented a more favorable degree of discrimination than ompA and could be a reliable complement for ompA for the routine

Multilocus Genetic Characterization of Lactobacillus fermentum Isolated from Ready-to-Eat Canned Food.

Science.gov (United States)

Sulaiman, Irshad M; Jacobs, Emily; Simpson, Steven; Kerdahi, Khalil

2017-06-01

The primary mission of the U.S. Food and Drug Administration is to enforce the Food, Drug, and Cosmetic Act and regulate food, drug, and cosmetic products. Thus, this agency monitors the presence of pathogenic microorganisms in these products, including canned foods, as one of the regulatory action criteria and also ensures that these products are safe for human consumption. This study was carried out to investigate the effectiveness of pathogen control and integrity of ready-to-eat canned food containing Black Bean Corn Poblano Salsa. A total of nine unopened and recalled canned glass jars from the same lot were examined initially by conventional microbiologic protocols that involved a two-step enrichment, followed by streaking on selective agar plates, for the presence of gram-positive and gram-negative bacteria. Of the eight subsamples examined for each sample, all subsamples of one of the containers were found positive for the presence of slow-growing rod-shaped, gram-positive, facultative anaerobic bacteria. The recovered isolates were subsequently sequenced at rRNA and gyrB loci. Afterward, multilocus sequence typing (MLST) was performed characterizing 11 additional known MLST loci (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC). Analyses of the nucleotide sequences of rRNA, gyrB, and 11 MLST loci confirmed these gram-positive bacteria recovered from canned food to be Lactobacillus fermentum . Thus, the DNA sequencing of housekeeping MLST genes can provide species identification of L. fermentum and can be used in the canned food monitoring program of public health importance.

Variability of rRNA Operon Copy Number and Growth Rate Dynamics of Bacillus Isolated from an Extremely Oligotrophic Aquatic Ecosystem

Science.gov (United States)

Valdivia-Anistro, Jorge A.; Eguiarte-Fruns, Luis E.; Delgado-Sapién, Gabriela; Márquez-Zacarías, Pedro; Gasca-Pineda, Jaime; Learned, Jennifer; Elser, James J.; Olmedo-Alvarez, Gabriela; Souza, Valeria

2016-01-01

The ribosomal RNA (rrn) operon is a key suite of genes related to the production of protein synthesis machinery and thus to bacterial growth physiology. Experimental evidence has suggested an intrinsic relationship between the number of copies of this operon and environmental resource availability, especially the availability of phosphorus (P), because bacteria that live in oligotrophic ecosystems usually have few rrn operons and a slow growth rate. The Cuatro Ciénegas Basin (CCB) is a complex aquatic ecosystem that contains an unusually high microbial diversity that is able to persist under highly oligotrophic conditions. These environmental conditions impose a variety of strong selective pressures that shape the genome dynamics of their inhabitants. The genus Bacillus is one of the most abundant cultivable bacterial groups in the CCB and usually possesses a relatively large number of rrn operon copies (6–15 copies). The main goal of this study was to analyze the variation in the number of rrn operon copies of Bacillus in the CCB and to assess their growth-related properties as well as their stoichiometric balance (N and P content). We defined 18 phylogenetic groups within the Bacilli clade and documented a range of from six to 14 copies of the rrn operon. The growth dynamic of these Bacilli was heterogeneous and did not show a direct relation to the number of operon copies. Physiologically, our results were not consistent with the Growth Rate Hypothesis, since the copies of the rrn operon were decoupled from growth rate. However, we speculate that the diversity of the growth properties of these Bacilli as well as the low P content of their cells in an ample range of rrn copy number is an adaptive response to oligotrophy of the CCB and could represent an ecological mechanism that allows these taxa to coexist. These findings increase the knowledge of the variability in the number of copies of the rrn operon in the genus Bacillus and give insights about the

Optimal number of circulating water pumps in a nuclear power plant

International Nuclear Information System (INIS)

Xia, Lin; Liu, Deyou; Zhou, Ling; Wang, Feng; Wang, Pei

2015-01-01

Highlights: • We present a novel method to optimize the number of variable speed pumps. • The economic effect of variable speed pumps number optimization is presented. • We present a novel method to optimize the number of constant speed pumps. • The proposed pumps number optimization method is more accurate than the widely used method. - Abstract: A circulating cooling system that uses variable speed pumps (VSPs) or constant-speed pumps (CSPs) as circulating water pumps (CWPs) is optimized to improve the cycle efficiency of nuclear power plants. This study focused on the optimal number of VSPs and CSPs. A novel method is proposed to optimize the number of VSPs with varying dry-bulb temperature and relative humidity, which could help decrease operation costs by $243,310 per year. This method is also used to optimize the number of CSPs and is compared with another widely used method that optimizes the number of CSPs according to the varying condenser inlet water temperature. A comparison shows that the proposed method is more accurate than the widely used method

Optimal number of circulating water pumps in a nuclear power plant

Energy Technology Data Exchange (ETDEWEB)

Xia, Lin [College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing 210098, Jiangsu (China); Liu, Deyou, E-mail: liudyhhuc@163.com [College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing 210098, Jiangsu (China); Zhou, Ling, E-mail: zlhhu@163.com [College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing 210098, Jiangsu (China); Wang, Feng [School of Hydraulic, Energy and Power Engineering, Yangzhou University, Yangzhou 225009, Jiangsu (China); Wang, Pei [College of Energy and Electrical Engineering, Hohai University, Nanjing 210098, Jiangsu (China)

2015-07-15

Highlights: • We present a novel method to optimize the number of variable speed pumps. • The economic effect of variable speed pumps number optimization is presented. • We present a novel method to optimize the number of constant speed pumps. • The proposed pumps number optimization method is more accurate than the widely used method. - Abstract: A circulating cooling system that uses variable speed pumps (VSPs) or constant-speed pumps (CSPs) as circulating water pumps (CWPs) is optimized to improve the cycle efficiency of nuclear power plants. This study focused on the optimal number of VSPs and CSPs. A novel method is proposed to optimize the number of VSPs with varying dry-bulb temperature and relative humidity, which could help decrease operation costs by $243,310 per year. This method is also used to optimize the number of CSPs and is compared with another widely used method that optimizes the number of CSPs according to the varying condenser inlet water temperature. A comparison shows that the proposed method is more accurate than the widely used method.

Clustering of Beijing genotype Mycobacterium tuberculosis isolates from the Mekong delta in Vietnam on the basis of variable number of tandem repeat versus restriction fragment length polymorphism typing.

NARCIS (Netherlands)

Huyen, M.N.; Kremer, K.; Lan, N.T.; Buu, T.N.; Cobelens, F.G.; Tiemersma, E.W.; Haas, P. de; Soolingen, D. van

2013-01-01

BACKGROUND: In comparison to restriction fragment length polymorphism (RFLP) typing, variable number of tandem repeat (VNTR) typing is easier to perform, faster and yields results in a simple, numerical format. Therefore, this technique has gained recognition as the new international gold standard

Variable Saline Concentrations for Initial Resuscitation Following Polytrauma

Science.gov (United States)

2017-02-22

AFRL-SA-WP-TR-2017-0008 Variable Saline Concentrations for Initial Resuscitation Following Polytrauma Dr. Michael Goodman...Following Polytrauma 5a. CONTRACT NUMBER FA8650-10-2-6140 5b. GRANT NUMBER FA8650-14-2-6B29 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Dr. Michael...established. We investigated the utility of standard variable saline concentrations (0.9%, 3%, 23.4%) in a murine polytrauma model of traumatic brain injury

Long-term cloud condensation nuclei number concentration, particle number size distribution and chemical composition measurements at regionally representative observatories

Science.gov (United States)

Schmale, Julia; Henning, Silvia; Decesari, Stefano; Henzing, Bas; Keskinen, Helmi; Sellegri, Karine; Ovadnevaite, Jurgita; Pöhlker, Mira L.; Brito, Joel; Bougiatioti, Aikaterini; Kristensson, Adam; Kalivitis, Nikos; Stavroulas, Iasonas; Carbone, Samara; Jefferson, Anne; Park, Minsu; Schlag, Patrick; Iwamoto, Yoko; Aalto, Pasi; Äijälä, Mikko; Bukowiecki, Nicolas; Ehn, Mikael; Frank, Göran; Fröhlich, Roman; Frumau, Arnoud; Herrmann, Erik; Herrmann, Hartmut; Holzinger, Rupert; Kos, Gerard; Kulmala, Markku; Mihalopoulos, Nikolaos; Nenes, Athanasios; O'Dowd, Colin; Petäjä, Tuukka; Picard, David; Pöhlker, Christopher; Pöschl, Ulrich; Poulain, Laurent; Prévôt, André Stephan Henry; Swietlicki, Erik; Andreae, Meinrat O.; Artaxo, Paulo; Wiedensohler, Alfred; Ogren, John; Matsuki, Atsushi; Yum, Seong Soo; Stratmann, Frank; Baltensperger, Urs; Gysel, Martin

2018-02-01

Aerosol-cloud interactions (ACI) constitute the single largest uncertainty in anthropogenic radiative forcing. To reduce the uncertainties and gain more confidence in the simulation of ACI, models need to be evaluated against observations, in particular against measurements of cloud condensation nuclei (CCN). Here we present a data set - ready to be used for model validation - of long-term observations of CCN number concentrations, particle number size distributions and chemical composition from 12 sites on 3 continents. Studied environments include coastal background, rural background, alpine sites, remote forests and an urban surrounding. Expectedly, CCN characteristics are highly variable across site categories. However, they also vary within them, most strongly in the coastal background group, where CCN number concentrations can vary by up to a factor of 30 within one season. In terms of particle activation behaviour, most continental stations exhibit very similar activation ratios (relative to particles > 20 nm) across the range of 0.1 to 1.0 % supersaturation. At the coastal sites the transition from particles being CCN inactive to becoming CCN active occurs over a wider range of the supersaturation spectrum. Several stations show strong seasonal cycles of CCN number concentrations and particle number size distributions, e.g. at Barrow (Arctic haze in spring), at the alpine stations (stronger influence of polluted boundary layer air masses in summer), the rain forest (wet and dry season) or Finokalia (wildfire influence in autumn). The rural background and urban sites exhibit relatively little variability throughout the year, while short-term variability can be high especially at the urban site. The average hygroscopicity parameter, κ, calculated from the chemical composition of submicron particles was highest at the coastal site of Mace Head (0.6) and lowest at the rain forest station ATTO (0.2-0.3). We performed closure studies based on κ-Köhler theory

Multilocus sequence typing (MLST methods for the emerging Campylobacter species C. hyointestinalis, C. lanienae, C. sputorum, C. concisus and C. curvus

Directory of Open Access Journals (Sweden)

William G Miller

2012-04-01

Full Text Available Multilocus sequence typing (MLST systems have been reported previously for multiple food- and food animal-associated Campylobacter species (e.g. C. jejuni, C. coli, C. lari and C. fetus to both differentiate strains and identify clonal lineages. These MLST methods focused primarily on campylobacters of human clinical (e.g. C. jejuni or veterinary (e.g. C. fetus relevance. However, other, emerging, Campylobacter species have been isolated increasingly from environmental, food animal or human clinical samples. We describe herein MLST methods for five emerging Campylobacter species: C. hyointestinalis, C. lanienae, C. sputorum, C. concisus and C. curvus. The concisus/curvus method uses the loci aspA, atpA, glnA, gltA, glyA, ilvD and pgm, whereas the other methods use the seven loci defined for C. jejuni (i.e., aspA, atpA, glnA, gltA, glyA, pgm, and tkt. Multiple food animal and human clinical C. hyointestinalis (n=48, C. lanienae (n=34 and C. sputorum (n=24 isolates were typed, along with 86 human clinical C. concisus and C. curvus isolates. A large number of sequence types (STs were identified using all four MLST methods. Similar to Campylobacter MLST methods described previously, these novel MLST methods identified mixed isolates containing two or more strains of the same species. Additionally, these methods speciated unequivocally isolates that had been typed ambiguously using other molecular-based speciation methods, such as 16S rDNA sequencing. Finally, the design of degenerate primer pairs for some methods permitted the typing of related species; for example, the C. hyointestinalis primer pairs could be used to type C. fetus strains. Therefore, these novel Campylobacter MLST methods will prove useful in speciating and differentiating strains of multiple, emerging Campylobacter species.

Hookworm infection, anaemia and genetic variability of the New Zealand sea lion

OpenAIRE

Acevedo-Whitehouse, Karina; Petetti, Laura; Duignan, Padraig; Castinel, Aurelie

2009-01-01

Hookworms are intestinal blood-feeding nematodes that parasitize and cause high levels of mortality in a wide range of mammals, including otariid pinnipeds. Recently, an empirical study showed that inbreeding (assessed by individual measures of multi-locus heterozygosity) is associated with hookworm-related mortality of California sea lions. If inbreeding increases susceptibility to hookworms, effects would expectedly be stronger in small, fragmented populations. We tested this assumption in ...

Aerodynamic Effects of High Turbulence Intensity on a Variable-Speed Power-Turbine Blade With Large Incidence and Reynolds Number Variations

Science.gov (United States)

Flegel, Ashlie B.; Giel, Paul W.; Welch, Gerard E.

2014-01-01

The effects of high inlet turbulence intensity on the aerodynamic performance of a variable speed power turbine blade are examined over large incidence and Reynolds number ranges. These results are compared to previous measurements made in a low turbulence environment. Both high and low turbulence studies were conducted in the NASA Glenn Research Center Transonic Turbine Blade Cascade Facility. The purpose of the low inlet turbulence study was to examine the transitional flow effects that are anticipated at cruise Reynolds numbers. The current study extends this to LPT-relevant turbulence levels while perhaps sacrificing transitional flow effects. Assessing the effects of turbulence at these large incidence and Reynolds number variations complements the existing database. Downstream total pressure and exit angle data were acquired for 10 incidence angles ranging from +15.8deg to -51.0deg. For each incidence angle, data were obtained at five flow conditions with the exit Reynolds number ranging from 2.12×10(exp 5) to 2.12×10(exp 6) and at a design exit Mach number of 0.72. In order to achieve the lowest Reynolds number, the exit Mach number was reduced to 0.35 due to facility constraints. The inlet turbulence intensity, Tu, was measured using a single-wire hotwire located 0.415 axial-chord upstream of the blade row. The inlet turbulence levels ranged from 8 to 15 percent for the current study. Tu measurements were also made farther upstream so that turbulence decay rates could be calculated as needed for computational inlet boundary conditions. Downstream flow field measurements were obtained using a pneumatic five-hole pitch/yaw probe located in a survey plane 7 percent axial chord aft of the blade trailing edge and covering three blade passages. Blade and endwall static pressures were acquired for each flow condition as well. The blade loading data show that the suction surface separation that was evident at many of the low Tu conditions has been eliminated. At

Clustering of Beijing genotype Mycobacterium tuberculosis isolates from the Mekong delta in Vietnam on the basis of variable number of tandem repeat versus restriction fragment length polymorphism typing

NARCIS (Netherlands)

Huyen, Mai N. T.; Kremer, Kristin; Lan, Nguyen T. N.; Buu, Tran N.; Cobelens, Frank G. J.; Tiemersma, Edine W.; de Haas, Petra; van Soolingen, Dick

2013-01-01

In comparison to restriction fragment length polymorphism (RFLP) typing, variable number of tandem repeat (VNTR) typing is easier to perform, faster and yields results in a simple, numerical format. Therefore, this technique has gained recognition as the new international gold standard in typing of

NUMBER OF SUCCESSIVE CYCLES NECESSARY TO ACHIEVE STABILITY OF SELECTED GROUND REACTION FORCE VARIABLES DURING CONTINUOUS JUMPING

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Jasmes M.W. Brownjohn

2009-12-01

Full Text Available Because of inherent variability in all human cyclical movements, such as walking, running and jumping, data collected across a single cycle might be atypical and potentially unable to represent an individual's generalized performance. The study described here was designed to determine the number of successive cycles due to continuous, repetitive countermovement jumping which a test subject should perform in a single experimental session to achieve stability of the mean of the corresponding continuously measured ground reaction force (GRF variables. Seven vertical GRF variables (period of jumping cycle, duration of contact phase, peak force amplitude and its timing, average rate of force development, average rate of force relaxation and impulse were extracted on the cycle-by-cycle basis from vertical jumping force time histories generated by twelve participants who were jumping in response to regular electronic metronome beats in the range 2-2.8 Hz. Stability of the selected GRF variables across successive jumping cycles was examined for three jumping rates (2, 2.4 and 2.8 Hz using two statistical methods: intra-class correlation (ICC analysis and segmental averaging technique (SAT. Results of the ICC analysis indicated that an average of four successive cycles (mean 4.5 ± 2.7 for 2 Hz; 3.9 ± 2.6 for 2.4 Hz; 3.3 ± 2.7 for 2.8 Hz were necessary to achieve maximum ICC values. Except for jumping period, maximum ICC values took values from 0.592 to 0.991 and all were significantly (p < 0.05 different from zero. Results of the SAT revealed that an average of ten successive cycles (mean 10.5 ± 3.5 for 2 Hz; 9.2 ± 3.8 for 2.4 Hz; 9.0 ± 3.9 for 2.8 Hz were necessary to achieve stability of the selected parameters using criteria previously reported in the literature. Using 10 reference trials, the SAT required standard deviation criterion values of 0.49, 0.41 and 0.55 for 2 Hz, 2.4 Hz and 2.8 Hz jumping rates, respectively, in order to approximate

Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes

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McGregor Karen F

2008-04-01

Full Text Available Abstract Background The M type-specific surface protein antigens encoded by the 5' end of emm genes are targets of protective host immunity and attractive vaccine candidates against infection by Streptococcus pyogenes, a global human pathogen. A history of genetic change in emm was evaluated for a worldwide collection of > 500 S. pyogenes isolates that were defined for genetic background by multilocus sequence typing of housekeeping genes. Results Organisms were categorized by genotypes that roughly correspond to throat specialists, skin specialists, and generalists often recovered from infections at either tissue site. Recovery of distant clones sharing the same emm type was ~4-fold higher for skin specialists and generalists, as compared to throat specialists. Importantly, emm type was often a poor marker for clone. Recovery of clones that underwent recombinational replacement with a new emm type was most evident for the throat and skin specialists. The average ratio of nonsynonymous substitutions per nonsynonymous site (Ka and synonymous substitutions per synonymous site (Ks was 4.9, 1.5 and 1.3 for emm types of the throat specialist, skin specialist and generalist groups, respectively. Conclusion Data indicate that the relationships between emm type and genetic background differ among the three host tissue-related groups, and that the selection pressures acting on emm appear to be strongest for the throat specialists. Since positive selection is likely due in part to a protective host immune response, the findings may have important implications for vaccine design and vaccination strategies.

Software Testing Requires Variability

DEFF Research Database (Denmark)

Christensen, Henrik Bærbak

2003-01-01

Software variability is the ability of a software system or artefact to be changed, customized or configured for use in a particular context. Variability in software systems is important from a number of perspectives. Some perspectives rightly receive much attention due to their direct economic...... impact in software production. As is also apparent from the call for papers these perspectives focus on qualities such as reuse, adaptability, and maintainability....

Genetic diversity of Neisseria meningitidis serogroup C ST-4821 in China based on multiple-locus variable number tandem repeat analysis.

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Xiaoying Shan

Full Text Available Neisseria meningitidis sequence type (ST-4821 was first reported in China in 2003, and a new hyper-virulent lineage has been designated as the ST-4821 complex. A large number of N. meningitidis ST-4821 strains have been identified in China since 2003; however, the microevolution characteristics of this complex are unclear. Different combinations of variable number of tandem repeats (VNTR loci were used in multiple-locus VNTR analysis (MLVA to analyze 118 N. meningitidis serogroup C ST-4821 strains isolated from seventeen provinces between 2003 and 2012. Additionally, MLVA with five VNTR loci was performed due to its high discriminatory power. One hundred and eighteen isolates were found to comprise 112 subtypes based on MLVA, and 16 outbreak-associated strains were clustered into one group. These data indicate a high level of diversity for N. meningitidis ST-4821 due to microevolution in the last decade. In addition, the results revealed high similarity between isolates from the same geographic origins, which is helpful when monitoring the spread of N. meningitidis serogroup C ST-4821 and will provide valuable information for the control and prevention of bacterial meningitis in China.

Multilocus Sequence Typing of the Clinical Isolates of Salmonella Enterica Serovar Typhimurium in Tehran Hospitals

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Reza Ranjbar

2017-09-01

Full Text Available Background: Salmonella enterica serovar Typhimurium is one of the most important serovars of Salmonella enterica and is associated with human salmonellosis worldwide. Many epidemiological studies have focused on the characteristics of Salmonella Typhimurium in many countries as well as in Asia. This study was conducted to investigate the genetic characteristics of Salmonella Typhimurium using multilocus sequence typing (MLST. Methods: Clinical samples (urine, blood, and stool were collected from patients, who were admitted to 2 hospitals in Tehran between April and September, 2015. Salmonella Typhimurium strains were identified by conventional standard biochemical and serological testing. The antibiotic susceptibility patterns of the Salmonella Typhimurium isolates against 16 antibiotics was determined using the disk diffusion assay. The clonal relationship between the strains of Salmonella Typhimurium was analyzed using MLST. Results: Among the 68 Salmonella isolates, 31% (n=21 were Salmonella Typhimurium. Of the total 21 Salmonella Typhimurium isolates, 76% (n=16 were multidrug-resistant and showed resistance to 3 or more antibiotic families. The Salmonella Typhimurium isolates were assigned to 2 sequence types: ST19 and ST328. ST19 was more common (86%. Both sequence types were further assigned to 1 eBURST group. Conclusion: This is the first study of its kind in Iran to determine the sequence types of the clinical isolates of Salmonella Typhimurium in Tehran hospitals using MLST. ST19 was detected as the major sequence type of Salmonella Typhimurium.

Insights into the emergent bacterial pathogen Cronobacter spp., generated by multilocus sequence typing and analysis

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Susan eJoseph

2012-11-01

Full Text Available Cronobacter spp. (previously known as Enterobacter sakazakii is a bacterial pathogen affecting all age groups, with particularly severe clinical complications in neonates and infants. One recognised route of infection being the consumption of contaminated infant formula. As a recently recognised bacterial pathogen of considerable importance and regulatory control, appropriate detection and identification schemes are required. The application of multilocus sequence typing (MLST and analysis (MLSA of the seven alleles atpD, fusA, glnS, gltB, gyrB, infB and ppsA (concatenated length 3036 base pairs has led to considerable advances in our understanding of the genus. This approach is supported by both the reliability of DNA sequencing over subjective phenotyping and the establishment of a MLST database which has open access and is also curated; http://www.pubMLST.org/cronobacter. MLST has been used to describe the diversity of the newly recognised genus, instrumental in the formal recognition of new Cronobacter species (C. universalis and C. condimenti and revealed the high clonality of strains and the association of clonal complex 4 with neonatal meningitis cases. Clearly the MLST approach has considerable benefits over the use of non-DNA sequence based methods of analysis for newly emergent bacterial pathogens. The application of MLST and MLSA has dramatically enabled us to better understand this opportunistic bacterium which can cause irreparable damage to a newborn baby’s brain, and has contributed to improved control measures to protect neonatal health.

Diversification of the silverspot butterflies (Nymphalidae) in the Neotropics inferred from multi-locus DNA sequences.

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Massardo, Darli; Fornel, Rodrigo; Kronforst, Marcus; Gonçalves, Gislene Lopes; Moreira, Gilson Rudinei Pires

2015-01-01

The tribe Heliconiini (Lepidoptera: Nymphalidae) is a diverse group of butterflies distributed throughout the Neotropics, which has been studied extensively, in particular the genus Heliconius. However, most of the other lineages, such as Dione, which are less diverse and considered basal within the group, have received little attention. Basic information, such as species limits and geographical distributions remain uncertain for this genus. Here we used multilocus DNA sequence data and the geographical distribution analysis across the entire range of Dione in the Neotropical region in order to make inferences on the evolutionary history of this poorly explored lineage. Bayesian time-tree reconstruction allows inferring two major diversification events in this tribe around 25mya. Lineages thought to be ancient, such as Dione and Agraulis, are as recent as Heliconius. Dione formed a monophyletic clade, sister to the genus Agraulis. Dione juno, D. glycera and D. moneta were reciprocally monophyletic and formed genetic clusters, with the first two more close related than each other in relation to the third. Divergence time estimates support the hypothesis that speciation in Dione coincided with both the rise of Passifloraceae (the host plants) and the uplift of the Andes. Since the sister species D. glycera and D. moneta are specialized feeders on passion-vine lineages that are endemic to areas located either within or adjacent to the Andes, we inferred that they co-speciated with their host plants during this vicariant event. Copyright © 2014 Elsevier Inc. All rights reserved.

Multilocus analysis of introgression between two sympatric sister species of Drosophila: Drosophila yakuba and D. santomea.

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Llopart, Ana; Lachaise, Daniel; Coyne, Jerry A

2005-09-01

Drosophila yakuba is widely distributed in sub-Saharan Africa, while D. santomea is endemic to the volcanic island of São Tomé in the Atlantic Ocean, 280 km west of Gabon. On São Tomé, D. yakuba is found mainly in open lowland forests, and D. santomea is restricted to the wet misty forests at higher elevations. At intermediate elevations, the species form a hybrid zone where hybrids occur at a frequency of approximately 1%. To determine the extent of gene flow between these species we studied polymorphism and divergence patterns in 29 regions distributed throughout the genome, including mtDNA and three genes on the Y chromosome. This multilocus approach, together with the comparison to the two allopatric species D. mauritiana and D. sechellia, allowed us to distinguish between forces that should affect all genes and forces that should act on some genes (e.g., introgression). Our results show that D. yakuba mtDNA has replaced that of D. santomea and that there is also significant introgression for two nuclear genes, yellow and salr. The majority of genes, however, has remained distinct. These two species therefore do not form a "hybrid swarm" in which much of the genome shows substantial introgression while disruptive selection maintains distinctness for only a few traits (e.g., pigmentation and male genitalia).

The effect of normative context variability on recognition memory.

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Steyvers, Mark; Malmberg, Kenneth J

2003-09-01

According to some theories of recognition memory (e.g., S. Dennis & M. S. Humphreys, 2001), the number of different contexts in which words appear determines how memorable individual occurrences of words will be: A word that occurs in a small number of different contexts should be better recognized than a word that appears in a larger number of different contexts. To empirically test this prediction, a normative measure is developed, referred to here as context variability, that estimates the number of different contexts in which words appear in everyday life. These findings confirm the prediction that words low in context variability are better recognized (on average) than words that are high in context variability. (c) 2003 APA, all rights reserved

DATA COLLECTION METHOD FOR PEDESTRIAN MOVEMENT VARIABLES

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Hajime Inamura

2000-01-01

Full Text Available The need of tools for design and evaluation of pedestrian areas, subways stations, entrance hall, shopping mall, escape routes, stadium etc lead to the necessity of a pedestrian model. One approach pedestrian model is Microscopic Pedestrian Simulation Model. To be able to develop and calibrate a microscopic pedestrian simulation model, a number of variables need to be considered. As the first step of model development, some data was collected using video and the coordinate of the head path through image processing were also taken. Several numbers of variables can be gathered to describe the behavior of pedestrian from a different point of view. This paper describes how to obtain variables from video taking and simple image processing that can represent the movement of pedestrians and its variables

Effect of study design and setting on tuberculosis clustering estimates using Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR): a systematic review.

Science.gov (United States)

Mears, Jessica; Abubakar, Ibrahim; Cohen, Theodore; McHugh, Timothy D; Sonnenberg, Pam

2015-01-21

To systematically review the evidence for the impact of study design and setting on the interpretation of tuberculosis (TB) transmission using clustering derived from Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) strain typing. MEDLINE, EMBASE, CINHAL, Web of Science and Scopus were searched for articles published before 21st October 2014. Studies in humans that reported the proportion of clustering of TB isolates by MIRU-VNTR were included in the analysis. Univariable meta-regression analyses were conducted to assess the influence of study design and setting on the proportion of clustering. The search identified 27 eligible articles reporting clustering between 0% and 63%. The number of MIRU-VNTR loci typed, requiring consent to type patient isolates (as a proxy for sampling fraction), the TB incidence and the maximum cluster size explained 14%, 14%, 27% and 48% of between-study variation, respectively, and had a significant association with the proportion of clustering. Although MIRU-VNTR typing is being adopted worldwide there is a paucity of data on how study design and setting may influence estimates of clustering. We have highlighted study design variables for consideration in the design and interpretation of future studies. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Comparative study of IS6110 restriction fragment length polymorphism and variable-number tandem-repeat typing of Mycobacterium tuberculosis isolates in the Netherlands, based on a 5-year nationwide survey

NARCIS (Netherlands)

de Beer, Jessica L.; van Ingen, Jakko; de Vries, Gerard; Erkens, Connie; Sebek, Maruschka; Mulder, Arnout; Sloot, Rosa; van den Brandt, Anne-Marie; Enaimi, Mimount; Kremer, Kristin; Supply, Philip; van Soolingen, Dick

2013-01-01

In order to switch from IS6110 and polymorphic GC-rich repetitive sequence (PGRS) restriction fragment length polymorphism (RFLP) to 24-locus variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates in the national tuberculosis control program in The Netherlands, a

Comparative Study of IS6110 Restriction Fragment Length Polymorphism and Variable-Number Tandem-Repeat Typing of Mycobacterium tuberculosis Isolates in the Netherlands, Based on a 5-Year Nationwide Survey

NARCIS (Netherlands)

Beer, J.L. de; Ingen, J. van; Vries, G. de; Erkens, C.; Sebek, M.; Mulder, A.; Sloot, R.; Brandt, A.M. van den; Enaimi, M.; Kremer, K.; Supply, P.; Soolingen, D. van

2013-01-01

In order to switch from IS6110 and polymorphic GC-rich repetitive sequence (PGRS) restriction fragment length polymorphism (RFLP) to 24-locus variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates in the national tuberculosis control program in The Netherlands, a

Complex numbers in n dimensions

CERN Document Server

Olariu, Silviu

2002-01-01

Two distinct systems of hypercomplex numbers in n dimensions are introduced in this book, for which the multiplication is associative and commutative, and which are rich enough in properties such that exponential and trigonometric forms exist and the concepts of analytic n-complex function, contour integration and residue can be defined. The first type of hypercomplex numbers, called polar hypercomplex numbers, is characterized by the presence in an even number of dimensions greater or equal to 4 of two polar axes, and by the presence in an odd number of dimensions of one polar axis. The other type of hypercomplex numbers exists as a distinct entity only when the number of dimensions n of the space is even, and since the position of a point is specified with the aid of n/2-1 planar angles, these numbers have been called planar hypercomplex numbers. The development of the concept of analytic functions of hypercomplex variables was rendered possible by the existence of an exponential form of the n-complex numbe...

Sensori-motor synchronisation variability decreases as the number of metrical levels in the stimulus signal increases.

Science.gov (United States)

Madison, Guy

2014-03-01

Timing performance becomes less precise for longer intervals, which makes it difficult to achieve simultaneity in synchronisation with a rhythm. The metrical structure of music, characterised by hierarchical levels of binary or ternary subdivisions of time, may function to increase precision by providing additional timing information when the subdivisions are explicit. This hypothesis was tested by comparing synchronisation performance across different numbers of metrical levels conveyed by loudness of sounds, such that the slowest level was loudest and the fastest was softest. Fifteen participants moved their hand with one of 9 inter-beat intervals (IBIs) ranging from 524 to 3,125 ms in 4 metrical level (ML) conditions ranging from 1 (one movement for each sound) to 4 (one movement for every 8th sound). The lowest relative variability (SD/IBI<1.5%) was obtained for the 3 longest IBIs (1600-3,125 ms) and MLs 3-4, significantly less than the smallest value (4-5% at 524-1024 ms) for any ML 1 condition in which all sounds are identical. Asynchronies were also more negative with higher ML. In conclusion, metrical subdivision provides information that facilitates temporal performance, which suggests an underlying neural multi-level mechanism capable of integrating information across levels. © 2013.

On the Problem of Determining Aggregation Numbers from Surface Tension Measurements.

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Rusanov, Anatoly I

2017-11-07

In view of the recent discovery of variable aggregation numbers in the vicinity of the critical micelle concentration (CMC), the mass-action-law theory of the surface tension isotherm of a micellar solution with variable aggregation numbers is formulated both for nonionic and ionic surfactants. It is shown that the shape of the surface tension isotherm should be concave in the logarithmic scale above the CMC. Considering a change in the isotherm slope at the CMC apparent break point, the problems of determining the aggregation number for nonionic micelles and the degree of counterion binding for ionic micelles are discussed. In case of the aggregation number variability near the CMC, finding the aggregation number above the CMC apparent break point is considered and a computational scheme is elaborated, requiring a higher precision for experiment. Some experimental data from the literature are analyzed, and the method of estimating the degree of counterion binding is improved.

Long-term cloud condensation nuclei number concentration, particle number size distribution and chemical composition measurements at regionally representative observatories

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J. Schmale

2018-02-01

Full Text Available Aerosol–cloud interactions (ACI constitute the single largest uncertainty in anthropogenic radiative forcing. To reduce the uncertainties and gain more confidence in the simulation of ACI, models need to be evaluated against observations, in particular against measurements of cloud condensation nuclei (CCN. Here we present a data set – ready to be used for model validation – of long-term observations of CCN number concentrations, particle number size distributions and chemical composition from 12 sites on 3 continents. Studied environments include coastal background, rural background, alpine sites, remote forests and an urban surrounding. Expectedly, CCN characteristics are highly variable across site categories. However, they also vary within them, most strongly in the coastal background group, where CCN number concentrations can vary by up to a factor of 30 within one season. In terms of particle activation behaviour, most continental stations exhibit very similar activation ratios (relative to particles  > 20 nm across the range of 0.1 to 1.0 % supersaturation. At the coastal sites the transition from particles being CCN inactive to becoming CCN active occurs over a wider range of the supersaturation spectrum. Several stations show strong seasonal cycles of CCN number concentrations and particle number size distributions, e.g. at Barrow (Arctic haze in spring, at the alpine stations (stronger influence of polluted boundary layer air masses in summer, the rain forest (wet and dry season or Finokalia (wildfire influence in autumn. The rural background and urban sites exhibit relatively little variability throughout the year, while short-term variability can be high especially at the urban site. The average hygroscopicity parameter, κ, calculated from the chemical composition of submicron particles was highest at the coastal site of Mace Head (0.6 and lowest at the rain forest station ATTO (0.2–0.3. We performed closure

Comparison of multilocus sequence typing, RAPD, and MALDI-TOF mass spectrometry for typing of β-lactam-resistant Klebsiella pneumoniae strains.

Science.gov (United States)

Sachse, Svea; Bresan, Stephanie; Erhard, Marcel; Edel, Birgit; Pfister, Wolfgang; Saupe, Angela; Rödel, Jürgen

2014-12-01

Extended spectrum of β-lactam (ESBL) resistance of Klebsiella pneumoniae has become an increasing problem in hospital infections. Typing of isolates is important to establish the intrahospital surveillance of resistant clones. In this study, the discriminatory potential of randomly amplified polymorphic DNA and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analyses were compared with multilocus sequence typing (MLST) by using 17 β-lactam-resistant K. pneumoniae isolates of different genotypes. MLST alleles were distributed in 8 sequence types (STs). Among ESBL strains of the same ST, the presence of different β-lactamase genes was common. RAPD band patterns also revealed 8 types that corresponded to MLST-defined genotypes in 15 out of 17 cases. MALDI-TOF analysis could differentiate 5 clusters of strains. The results of this work show that RAPD may be usable as a rapid screening method for the intrahospital surveillance of K. pneumoniae, allowing a discrimination of clonally related strains. MALDI-TOF-based typing was not strongly corresponding to genotyping and warrants further investigation. Copyright © 2014 Elsevier Inc. All rights reserved.

Multilocus sequence data reveal dozens of putative cryptic species in a radiation of endemic Californian mygalomorph spiders (Araneae, Mygalomorphae, Nemesiidae).

Science.gov (United States)

Leavitt, Dean H; Starrett, James; Westphal, Michael F; Hedin, Marshal

2015-10-01

We use mitochondrial and multi-locus nuclear DNA sequence data to infer both species boundaries and species relationships within California nemesiid spiders. Higher-level phylogenetic data show that the California radiation is monophyletic and distantly related to European members of the genus Brachythele. As such, we consider all California nemesiid taxa to belong to the genus Calisoga Chamberlin, 1937. Rather than find support for one or two taxa as previously hypothesized, genetic data reveal Calisoga to be a species-rich radiation of spiders, including perhaps dozens of species. This conclusion is supported by multiple mitochondrial barcoding analyses, and also independent analyses of nuclear data that reveal general genealogical congruence. We discovered three instances of sympatry, and genetic data indicate reproductive isolation when in sympatry. An examination of female reproductive morphology does not reveal species-specific characters, and observed male morphological differences for a subset of putative species are subtle. Our coalescent species tree analysis of putative species lays the groundwork for future research on the taxonomy and biogeographic history of this remarkable endemic radiation. Copyright © 2015 Elsevier Inc. All rights reserved.

Use of number by fish.

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Christian Agrillo

Full Text Available BACKGROUND: Research on human infants, mammals, birds and fish has demonstrated that rudimentary numerical abilities pre-date the evolution of human language. Yet there is controversy as to whether animals represent numbers mentally or rather base their judgments on non-numerical perceptual variables that co-vary with numerosity. To date, mental representation of number has been convincingly documented only for a few mammals. METHODOLOGY/PRINCIPAL FINDINGS: Here we used a training procedure to investigate whether mosquitofish could learn to discriminate between two and three objects even when denied access to non-numerical information. In the first experiment, fish were trained to discriminate between two sets of geometric figures. These varied in shape, size, brightness and distance, but no control for non-numerical variables was made. Subjects were then re-tested while controlling for one non-numerical variable at a time. Total luminance of the stimuli and the sum of perimeter of figures appeared irrelevant, but performance dropped to chance level when stimuli were matched for the cumulative surface area or for the overall space occupied by the arrays, indicating that these latter cues had been spontaneously used by the fish during the learning process. In a second experiment, where the task consisted of discriminating 2 vs 3 elements with all non-numerical variables simultaneously controlled for, all subjects proved able to learn the discrimination, and interestingly they did not make more errors than the fish in Experiment 1 that could access non-numerical information in order to accomplish the task. CONCLUSIONS/SIGNIFICANCE: Mosquitofish can learn to discriminate small quantities, even when non-numerical indicators of quantity are unavailable, hence providing the first evidence that fish, like primates, can use numbers. As in humans and non-human primates, genuine counting appears to be a 'last resort' strategy in fish, when no other

Variability in human body size

Science.gov (United States)

Annis, J. F.

1978-01-01

The range of variability found among homogeneous groups is described and illustrated. Those trends that show significantly marked differences between sexes and among a number of racial/ethnic groups are also presented. Causes of human-body size variability discussed include genetic endowment, aging, nutrition, protective garments, and occupation. The information is presented to aid design engineers of space flight hardware and equipment.

Development of a Multilocus Sequence Typing (MLST) scheme for Treponema pallidum subsp. pertenue: Application to yaws in Lihir Island, Papua New Guinea.

Science.gov (United States)

Godornes, Charmie; Giacani, Lorenzo; Barry, Alyssa E; Mitja, Oriol; Lukehart, Sheila A

2017-12-01

Yaws is a neglected tropical disease, caused by Treponema pallidum subsp. pertenue. The disease causes chronic lesions, primarily in young children living in remote villages in tropical climates. As part of a global yaws eradication campaign initiated by the World Health Organization, we sought to develop and evaluate a molecular typing method to distinguish different strains of T. pallidum subsp. pertenue for disease control and epidemiological purposes. Published genome sequences of strains of T. pallidum subsp. pertenue and pallidum were compared to identify polymorphic genetic loci among the strains. DNA from a number of existing historical Treponema isolates, as well as a subset of samples from yaws patients collected in Lihir Island, Papua New Guinea, were analyzed using these targets. From these data, three genes (tp0548, tp0136 and tp0326) were ultimately selected to give a high discriminating capability among the T. pallidum subsp. pertenue samples tested. Intragenic regions of these three target genes were then selected to enhance the discriminating capability of the typing scheme using short readily amplifiable loci. This 3-gene multilocus sequence typing (MLST) method was applied to existing historical human yaws strains, the Fribourg-Blanc simian isolate, and DNA from 194 lesion swabs from yaws patients on Lihir Island, Papua New Guinea. Among all samples tested, fourteen molecular types were identified, seven of which were found in patient samples and seven among historical isolates or DNA. Three types (JG8, TD6, and SE7) were predominant on Lihir Island. This MLST approach allows molecular typing and differentiation of yaws strains. This method could be a useful tool to complement epidemiological studies in regions where T. pallidum subsp. pertenue is prevalent with the overall goals of improving our understanding of yaws transmission dynamics and helping the yaws eradication campaign to succeed.

Development of a Multilocus Sequence Typing (MLST) scheme for Treponema pallidum subsp. pertenue: Application to yaws in Lihir Island, Papua New Guinea

Science.gov (United States)

Godornes, Charmie; Giacani, Lorenzo; Barry, Alyssa E.; Mitja, Oriol

2017-01-01

Background Yaws is a neglected tropical disease, caused by Treponema pallidum subsp. pertenue. The disease causes chronic lesions, primarily in young children living in remote villages in tropical climates. As part of a global yaws eradication campaign initiated by the World Health Organization, we sought to develop and evaluate a molecular typing method to distinguish different strains of T. pallidum subsp. pertenue for disease control and epidemiological purposes. Methods and principal findings Published genome sequences of strains of T. pallidum subsp. pertenue and pallidum were compared to identify polymorphic genetic loci among the strains. DNA from a number of existing historical Treponema isolates, as well as a subset of samples from yaws patients collected in Lihir Island, Papua New Guinea, were analyzed using these targets. From these data, three genes (tp0548, tp0136 and tp0326) were ultimately selected to give a high discriminating capability among the T. pallidum subsp. pertenue samples tested. Intragenic regions of these three target genes were then selected to enhance the discriminating capability of the typing scheme using short readily amplifiable loci. This 3-gene multilocus sequence typing (MLST) method was applied to existing historical human yaws strains, the Fribourg-Blanc simian isolate, and DNA from 194 lesion swabs from yaws patients on Lihir Island, Papua New Guinea. Among all samples tested, fourteen molecular types were identified, seven of which were found in patient samples and seven among historical isolates or DNA. Three types (JG8, TD6, and SE7) were predominant on Lihir Island. Conclusions This MLST approach allows molecular typing and differentiation of yaws strains. This method could be a useful tool to complement epidemiological studies in regions where T. pallidum subsp. pertenue is prevalent with the overall goals of improving our understanding of yaws transmission dynamics and helping the yaws eradication campaign to succeed

Statistical Dependence of Pipe Breaks on Explanatory Variables

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Patricia Gómez-Martínez

2017-02-01

Full Text Available Aging infrastructure is the main challenge currently faced by water suppliers. Estimation of assets lifetime requires reliable criteria to plan assets repair and renewal strategies. To do so, pipe break prediction is one of the most important inputs. This paper analyzes the statistical dependence of pipe breaks on explanatory variables, determining their optimal combination and quantifying their influence on failure prediction accuracy. A large set of registered data from Madrid water supply network, managed by Canal de Isabel II, has been filtered, classified and studied. Several statistical Bayesian models have been built and validated from the available information with a technique that combines reference periods of time as well as geographical location. Statistical models of increasing complexity are built from zero up to five explanatory variables following two approaches: a set of independent variables or a combination of two joint variables plus an additional number of independent variables. With the aim of finding the variable combination that provides the most accurate prediction, models are compared following an objective validation procedure based on the model skill to predict the number of pipe breaks in a large set of geographical locations. As expected, model performance improves as the number of explanatory variables increases. However, the rate of improvement is not constant. Performance metrics improve significantly up to three variables, but the tendency is softened for higher order models, especially in trunk mains where performance is reduced. Slight differences are found between trunk mains and distribution lines when selecting the most influent variables and models.

Variability of HOMA and QUICKI insulin sensitivity indices.

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Žarković, Miloš; Ćirić, Jasmina; Beleslin, Biljana; Stojković, Mirjana; Savić, Slavica; Stojanović, Miloš; Lalić, Tijana

2017-07-01

Assessment of insulin sensitivity based on a single measurement of insulin and glucose, is both easy to understand and simple to perform. The tests most often used are HOMA and QUICKI. The aim of this study was to assess the biological variability of estimates of insulin sensitivity using HOMA and QUICKI indices. After a 12-h fast, blood was sampled for insulin and glucose determination. Sampling lasted for 90 min with an intersample interval of 2 min. A total of 56 subjects were included in the study, and in nine subjects sampling was done before and after weight reduction, so total number of analyzed series was 65. To compute the reference value of the insulin sensitivity index, averages of all 46 insulin and glucose samples were used. We also computed point estimates (single value estimates) of the insulin sensitivity index based on the different number of insulin/glucose samples (1-45 consecutive samples). To compute the variability of point estimates a bootstrapping procedure was used using 1000 resamples for each series and for each number of samples used to average insulin and glucose. Using a single insulin/glucose sample HOMA variability was 26.18 ± 4.31%, and QUICKI variability was 3.30 ± 0.54%. For 10 samples variability was 11.99 ± 2.22% and 1.62 ± 0.31% respectively. Biological variability of insulin sensitivity indices is significant, and it can be reduced by increasing the number of samples. Oscillations of insulin concentration in plasma are the major cause of variability of insulin sensitivity indices.

Impact analysis of flow variability in sizing kanbans

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Isaac Pergher

2014-02-01

Full Text Available The aim of this paper is to analyze the effects of variability flow, advocated by Factory Physics, in sizing Kanban production systems. The variability of flow presupposes that the variability of activities performed by a process is dissipated throughout the productive flow system, causing variations in the lead time, the work-in-process levels and the equipment availability, among others. To conduct the research, we created a didactic model of discrete event computer simulation. The proposed model aims to present the possible impacts caused by the variability flow in a production system regarding the sizing of the number of Kanbans cards, by using the results supplied by two different investigated scenarios. The main results of the research allow concluding that, by comparing the two scenarios developed in the model, the presence of variability in the production system caused an average increase of 32% in the number of Kanban cards (p=0,000. This implies that, in real productive systems, the study of Kanban sizing should consider the variability of individual operations, a fact often relegated as an assumption in the formulation from classical literature on the definition of the number of Kanbans, thus providing opportunities for the development of future research.

Spoligotyping and variable number tandem repeat analysis of Mycobacterium bovis isolates from cattle in Brazil

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Patrícia Martins Parreiras

2012-02-01

Full Text Available We performed spoligotyping and 12-mycobacterial interspersed repetitive unit-variable number tandem repeats (MIRU-VNTRs typing to characterise Mycobacterium bovis isolates collected from tissue samples of bovines with lesions suggestive for tuberculosis during slaughter inspection procedures in abattoirs in Brazil. High-quality genotypes were obtained with both procedures for 61 isolates that were obtained from 185 bovine tissue samples and all of these isolates were identified as M. bovis by conventional identification procedures. On the basis of the spoligotyping, 53 isolates were grouped into nine clusters and the remaining eight isolates were unique types, resulting in 17 spoligotypes. The majority of the Brazilian M. bovis isolates displayed spoligotype patterns that have been previously observed in strains isolated from cattle in other countries. MIRU-VNTR typing produced 16 distinct genotypes, with 53 isolates forming eight of the groups, and individual isolates with unique VNTR profiles forming the remaining eight groups. The allelic diversity of each VNTR locus was calculated and only two of the 12-MIRU-VNTR loci presented scores with either a moderate (0.4, MIRU16 or high (0.6, MIRU26 discriminatory index (h. Both typing methods produced similar discriminatory indexes (spoligotyping h = 0.85; MIRU-VNTR h = 0.86 and the combination of the two methods increased the h value to 0.94, resulting in 29 distinct patterns. These results confirm that spoligotyping and VNTR analysis are valuable tools for studying the molecular epidemiology of M. bovis infections in Brazil.

Determining Clostridium difficile intra-taxa diversity by mining multilocus sequence typing databases.

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Muñoz, Marina; Ríos-Chaparro, Dora Inés; Patarroyo, Manuel Alfonso; Ramírez, Juan David

2017-03-14

Multilocus sequence typing (MLST) is a highly discriminatory typing strategy; it is reproducible and scalable. There is a MLST scheme for Clostridium difficile (CD), a gram positive bacillus causing different pathologies of the gastrointestinal tract. This work was aimed at describing the frequency of sequence types (STs) and Clades (C) reported and evalute the intra-taxa diversity in the CD MLST database (CD-MLST-db) using an MLSA approach. Analysis of 1778 available isolates showed that clade 1 (C1) was the most frequent worldwide (57.7%), followed by C2 (29.1%). Regarding sequence types (STs), it was found that ST-1, belonging to C2, was the most frequent. The isolates analysed came from 17 countries, mostly from the United Kingdom (UK) (1541 STs, 87.0%). The diversity of the seven housekeeping genes in the MLST scheme was evaluated, and alleles from the profiles (STs), for identifying CD population structure. It was found that adk and atpA are conserved genes allowing a limited amount of clusters to be discriminated; however, different genes such as drx, glyA and particularly sodA showed high diversity indexes and grouped CD populations in many clusters, suggesting that these genes' contribution to CD typing should be revised. It was identified that CD STs reported to date have a mostly clonal population structure with foreseen events of recombination; however, one group of STs was not assigned to a clade being highly different containing at least nine well-supported clusters, suggesting a greater amount of clades for CD. This study shows the usefulness of CD-MLST-db as a tool for studying CD distribution and population structure, identifying the need for reviewing the usefulness of sodA as housekeeping gene within the MLST scheme and suggesting the existence of a greater amount of CD clades. The study also shows the plausible exchange of genetic material between STs, contributing towards intra-taxa genetic diversity.

Multilocus sequence typing of Trichomonas vaginalis clinical samples from Amsterdam, the Netherlands.

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van der Veer, C; Himschoot, M; Bruisten, S M

2016-10-13

In this cross-sectional epidemiological study we aimed to identify molecular profiles for Trichomonas vaginalis and to determine how these molecular profiles were related to patient demographic and clinical characteristics. Molecular typing methods previously identified two genetically distinct subpopulations for T. vaginalis; however, few molecular epidemiological studies have been performed. We now increased the sensitivity of a previously described multilocus sequence typing (MLST) tool for T. vaginalis by using nested PCR. This enabled the typing of direct patient samples. From January to December 2014, we collected all T. vaginalis positive samples as detected by routine laboratory testing. Samples from patients either came from general practitioners offices or from the sexually transmitted infections (STI) clinic in Amsterdam. Epidemiological data for the STI clinic patients were retrieved from electronic patient files. The primary outcome was the success rate of genotyping direct T. vaginalis positive samples. The secondary outcome was the relation between T. vaginalis genotypes and risk factors for STI. All 7 MLST loci were successfully typed for 71/87 clinical samples. The 71 typed samples came from 69 patients, the majority of whom were women (n=62; 90%) and half (n=34; 49%) were STI clinic patients. Samples segregated into a two population structure for T. vaginalis representing genotypes I and II. Genotype I was most common (n=40; 59.7%). STI clinic patients infected with genotype II reported more sexual partners in the preceding 6 months than patients infected with genotype I (p=0.028). No other associations for gender, age, ethnicity, urogenital discharge or co-occurring STIs with T. vaginalis genotype were found. MLST with nested PCR is a sensitive typing method that allows typing of direct (uncultured) patient material. Genotype II is possibly more prevalent in high-risk sexual networks. Published by the BMJ Publishing Group Limited. For

Modeling Scramjet Flows with Variable Turbulent Prandtl and Schmidt Numbers

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Xiao, X.; Hassan, H. A.; Baurle, R. A.

2006-01-01

A complete turbulence model, where the turbulent Prandtl and Schmidt numbers are calculated as part of the solution and where averages involving chemical source terms are modeled, is presented. The ability of avoiding the use of assumed or evolution Probability Distribution Functions (PDF's) results in a highly efficient algorithm for reacting flows. The predictions of the model are compared with two sets of experiments involving supersonic mixing and one involving supersonic combustion. The results demonstrate the need for consideration of turbulence/chemistry interactions in supersonic combustion. In general, good agreement with experiment is indicated.

Improved variable reduction in partial least squares modelling by Global-Minimum Error Uninformative-Variable Elimination.

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Andries, Jan P M; Vander Heyden, Yvan; Buydens, Lutgarde M C

2017-08-22

The calibration performance of Partial Least Squares regression (PLS) can be improved by eliminating uninformative variables. For PLS, many variable elimination methods have been developed. One is the Uninformative-Variable Elimination for PLS (UVE-PLS). However, the number of variables retained by UVE-PLS is usually still large. In UVE-PLS, variable elimination is repeated as long as the root mean squared error of cross validation (RMSECV) is decreasing. The set of variables in this first local minimum is retained. In this paper, a modification of UVE-PLS is proposed and investigated, in which UVE is repeated until no further reduction in variables is possible, followed by a search for the global RMSECV minimum. The method is called Global-Minimum Error Uninformative-Variable Elimination for PLS, denoted as GME-UVE-PLS or simply GME-UVE. After each iteration, the predictive ability of the PLS model, built with the remaining variable set, is assessed by RMSECV. The variable set with the global RMSECV minimum is then finally selected. The goal is to obtain smaller sets of variables with similar or improved predictability than those from the classical UVE-PLS method. The performance of the GME-UVE-PLS method is investigated using four data sets, i.e. a simulated set, NIR and NMR spectra, and a theoretical molecular descriptors set, resulting in twelve profile-response (X-y) calibrations. The selective and predictive performances of the models resulting from GME-UVE-PLS are statistically compared to those from UVE-PLS and 1-step UVE, one-sided paired t-tests. The results demonstrate that variable reduction with the proposed GME-UVE-PLS method, usually eliminates significantly more variables than the classical UVE-PLS, while the predictive abilities of the resulting models are better. With GME-UVE-PLS, a lower number of uninformative variables, without a chemical meaning for the response, may be retained than with UVE-PLS. The selectivity of the classical UVE method

Role of Turbulent Prandtl Number on Heat Flux at Hypersonic Mach Number

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Xiao, X.; Edwards, J. R.; Hassan, H. A.

2004-01-01

Present simulation of turbulent flows involving shock wave/boundary layer interaction invariably overestimates heat flux by almost a factor of two. One possible reason for such a performance is a result of the fact that the turbulence models employed make use of Morkovin's hypothesis. This hypothesis is valid for non-hypersonic Mach numbers and moderate rates of heat transfer. At hypersonic Mach numbers, high rates of heat transfer exist in regions where shock wave/boundary layer interactions are important. As a result, one should not expect traditional turbulence models to yield accurate results. The goal of this investigation is to explore the role of a variable Prandtl number formulation in predicting heat flux in flows dominated by strong shock wave/boundary layer interactions. The intended applications involve external flows in the absence of combustion such as those encountered in supersonic inlets. This can be achieved by adding equations for the temperature variance and its dissipation rate. Such equations can be derived from the exact Navier-Stokes equations. Traditionally, modeled equations are based on the low speed energy equation where the pressure gradient term and the term responsible for energy dissipation are ignored. It is clear that such assumptions are not valid for hypersonic flows. The approach used here is based on the procedure used in deriving the k-zeta model, in which the exact equations that governed k, the variance of velocity, and zeta, the variance of vorticity, were derived and modeled. For the variable turbulent Prandtl number, the exact equations that govern the temperature variance and its dissipation rate are derived and modeled term by term. The resulting set of equations are free of damping and wall functions and are coordinate-system independent. Moreover, modeled correlations are tensorially consistent and invariant under Galilean transformation. The final set of equations will be given in the paper.

Associations between dru Types and SCCmec Cassettes

DEFF Research Database (Denmark)

Bartels, Mette D; Boye, Kit; Oliveira, Duarte C

2013-01-01

SCCmec types I to VI. The isolates represented a broad genetic background based on Staphylococcal protein A (spa) typing and multilocus sequence typing (MLST) and included 68 isolates (68 patients) from an outbreak with t024-ST8-IVa and 26 isolates from the same patient. Sequencing identified 53 dru......Molecular typing is an important tool in the investigation of methicillin resistant Staphylococcus aureus (MRSA) outbreaks and in following the evolution of MRSA. The staphylococcal cassette chromosome mec (SCCmec) contains a hypervariable region with a variable number of 40 bp repeats named direct...... repeat units (dru). The dru region has been suggested as a supplementary typing method for MRSA and an international nomenclature exists. The purpose of this study was to investigate the diversity and variability of the dru region in a diverse collection of MRSA. We studied 302 MRSA isolates harbouring...

Multilocus genetic models of handedness closely resemble single-locus models in explaining family data and are compatible with genome-wide association studies.

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McManus, I C; Davison, Angus; Armour, John A L

2013-06-01

Right- and left-handedness run in families, show greater concordance in monozygotic than dizygotic twins, and are well described by single-locus Mendelian models. Here we summarize a large genome-wide association study (GWAS) that finds no significant associations with handedness and is consistent with a meta-analysis of GWASs. The GWAS had 99% power to detect a single locus using the conventional criterion of P < 5 × 10(-8) for the single locus models of McManus and Annett. The strong conclusion is that handedness is not controlled by a single genetic locus. A consideration of the genetic architecture of height, primary ciliary dyskinesia, and intelligence suggests that handedness inheritance can be explained by a multilocus variant of the McManus DC model, classical effects on family and twins being barely distinguishable from the single locus model. Based on the ENGAGE meta-analysis of GWASs, we estimate at least 40 loci are involved in determining handedness. © 2013 New York Academy of Sciences.

Multilocus Sequence Typing Scheme versus Pulsed-Field Gel Electrophoresis for Typing Mycobacterium abscessus Isolates

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Machado, Gabriel Esquitini; Matsumoto, Cristianne Kayoko; Chimara, Erica; Duarte, Rafael da Silva; de Freitas, Denise; Palaci, Moises; Hadad, David Jamil; Lima, Karla Valéria Batista; Lopes, Maria Luiza; Ramos, Jesus Pais; Campos, Carlos Eduardo; Caldas, Paulo César; Heym, Beate

2014-01-01

Outbreaks of infections by rapidly growing mycobacteria following invasive procedures, such as ophthalmological, laparoscopic, arthroscopic, plastic, and cardiac surgeries, mesotherapy, and vaccination, have been detected in Brazil since 1998. Members of the Mycobacterium chelonae-Mycobacterium abscessus group have caused most of these outbreaks. As part of an epidemiological investigation, the isolates were typed by pulsed-field gel electrophoresis (PFGE). In this project, we performed a large-scale comparison of PFGE profiles with the results of a recently developed multilocus sequence typing (MLST) scheme for M. abscessus. Ninety-three isolates were analyzed, with 40 M. abscessus subsp. abscessus isolates, 47 M. abscessus subsp. bolletii isolates, and six isolates with no assigned subspecies. Forty-five isolates were obtained during five outbreaks, and 48 were sporadic isolates that were not associated with outbreaks. For MLST, seven housekeeping genes (argH, cya, glpK, gnd, murC, pta, and purH) were sequenced, and each isolate was assigned a sequence type (ST) from the combination of obtained alleles. The PFGE patterns of DraI-digested DNA were compared with the MLST results. All isolates were analyzable by both methods. Isolates from monoclonal outbreaks showed unique STs and indistinguishable or very similar PFGE patterns. Thirty-three STs and 49 unique PFGE patterns were identified among the 93 isolates. The Simpson's index of diversity values for MLST and PFGE were 0.69 and 0.93, respectively, for M. abscessus subsp. abscessus and 0.96 and 0.97, respectively, for M. abscessus subsp. bolletii. In conclusion, the MLST scheme showed 100% typeability and grouped monoclonal outbreak isolates in agreement with PFGE, but it was less discriminative than PFGE for M. abscessus. PMID:24899019

Multiple-locus variable-number tandem repeat analysis for molecular typing of Aspergillus fumigatus

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Chermette René

2010-12-01

Full Text Available Abstract Background Multiple-locus variable-number tandem repeat (VNTR analysis (MLVA is a prominent subtyping method to resolve closely related microbial isolates to provide information for establishing genetic patterns among isolates and to investigate disease outbreaks. The usefulness of MLVA was recently demonstrated for the avian major pathogen Chlamydophila psittaci. In the present study, we developed a similar method for another pathogen of birds: the filamentous fungus Aspergillus fumigatus. Results We selected 10 VNTR markers located on 4 different chromosomes (1, 5, 6 and 8 of A. fumigatus. These markers were tested with 57 unrelated isolates from different hosts or their environment (53 isolates from avian species in France, China or Morocco, 3 isolates from humans collected at CHU Henri Mondor hospital in France and the reference strain CBS 144.89. The Simpson index for individual markers ranged from 0.5771 to 0.8530. A combined loci index calculated with all the markers yielded an index of 0.9994. In a second step, the panel of 10 markers was used in different epidemiological situations and tested on 277 isolates, including 62 isolates from birds in Guangxi province in China, 95 isolates collected in two duck farms in France and 120 environmental isolates from a turkey hatchery in France. A database was created with the results of the present study http://minisatellites.u-psud.fr/MLVAnet/. Three major clusters of isolates were defined by using the graphing algorithm termed Minimum Spanning Tree (MST. The first cluster comprised most of the avian isolates collected in the two duck farms in France, the second cluster comprised most of the avian isolates collected in poultry farms in China and the third one comprised most of the isolates collected in the turkey hatchery in France. Conclusions MLVA displayed excellent discriminatory power. The method showed a good reproducibility. MST analysis revealed an interesting clustering with a

Obstacles to Scientific Research in Light of a Number of Variables

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Algadheeb, Nourah A.; Almeqren, Monira A.

2014-01-01

The present study aimed to identify the scientific research obstacles facing faculty members in the College of Education at Princess Nora bint Abdul Rahman University (PNU) and to determine the differences in the obstacles according to age, academic rank, scientific specialty, marital status, number of completed studies, and time since the last…

Evidence for an association between post-fledging dispersal and microsatellite multilocus heterozygosity in a large population of greater flamingos.

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Mark A F Gillingham

Full Text Available Dispersal can be divided into three stages: departure, transience and settlement. Despite the fact that theoretical studies have emphasized the importance of heterozygosity on dispersal strategies, empirical evidence of its effect on different stages of dispersal is lacking. Here, using multi-event capture-mark-recapture models, we show a negative association between microsatellite multilocus heterozygosity (MLH; 10 loci; n = 1023 and post-fledging dispersal propensity for greater flamingos, Phoenicopterus roseus, born in southern France. We propose that the negative effects of inbreeding depression affects competitive ability and therefore more homozygous individuals are more likely to disperse because they are less able to compete within the highly saturated natal site. Finally, a model with the effect of MLH on propensity of post-fledgling dispersers to disperse to the long-distance sites of Africa was equivalent to the null model, suggesting that MLH had low to no effect on dispersal distance. Variations in individual genetic quality thus result in context-dependent heterogeneity in dispersal strategies at each stage of dispersal. Our results have important implications on fitness since sites visited early in life are known to influence site selection later on in life and future survival.

Life style factors and number of chronic diseases

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Mustehsan, Huma

2011-05-01

Full Text Available BACKGROUND: People all around the world are more concerned with living a long and healthy life, rather than just living longer. Many studies have examined the effects of lifestyle on the risk of developing chronic diseases, but typically, they focus on only one specific behavior. Individuals often follow a lifestyle pattern which combines more than one behavior. This paper examines the combined effect of several lifestyle factors on the number of chronic diseases.OBJECTIVE: The goal of this study was to determine how different lifestyle factors influence the number of chronic diseases a person can have.METHODS: Data from the survey “Health and Well-being in the Transitions” (2000 were used. Dependent variable was number of chronic diseases which ranged from zero to five. Independent variables included the level of physical activity, variables based on food frequency questions, and other behavioral activities, adjusted for age and gender. Generalized linear model with Poisson distribution was used for analysis.RESULTS: The analysis showed that males have more diseases than females if other factors are controlled (B=0.182, p=0.001. Diseases increase by age (B=0.021, p=0.000. Those who used dairy products daily had smaller number of diseases (B= -0.145, p=0.012. Those who used vegetable oil 3-7 days a week had smaller number of diseases than those who use it 0-2 days a week (B= -0.224, p=0.058. Other food frequencies and ever smoking had no clear association with number of diseases.CONCLUSION: Increasing age and male gender are two factors which are associated with larger number of chronic diseases. Regular use of vegetable oil and dairy products seems to be important towards the path of a healthier life.

Improved variable reduction in partial least squares modelling based on predictive-property-ranked variables and adaptation of partial least squares complexity.

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Andries, Jan P M; Vander Heyden, Yvan; Buydens, Lutgarde M C

2011-10-31

The calibration performance of partial least squares for one response variable (PLS1) can be improved by elimination of uninformative variables. Many methods are based on so-called predictive variable properties, which are functions of various PLS-model parameters, and which may change during the variable reduction process. In these methods variable reduction is made on the variables ranked in descending order for a given variable property. The methods start with full spectrum modelling. Iteratively, until a specified number of remaining variables is reached, the variable with the smallest property value is eliminated; a new PLS model is calculated, followed by a renewed ranking of the variables. The Stepwise Variable Reduction methods using Predictive-Property-Ranked Variables are denoted as SVR-PPRV. In the existing SVR-PPRV methods the PLS model complexity is kept constant during the variable reduction process. In this study, three new SVR-PPRV methods are proposed, in which a possibility for decreasing the PLS model complexity during the variable reduction process is build in. Therefore we denote our methods as PPRVR-CAM methods (Predictive-Property-Ranked Variable Reduction with Complexity Adapted Models). The selective and predictive abilities of the new methods are investigated and tested, using the absolute PLS regression coefficients as predictive property. They were compared with two modifications of existing SVR-PPRV methods (with constant PLS model complexity) and with two reference methods: uninformative variable elimination followed by either a genetic algorithm for PLS (UVE-GA-PLS) or an interval PLS (UVE-iPLS). The performance of the methods is investigated in conjunction with two data sets from near-infrared sources (NIR) and one simulated set. The selective and predictive performances of the variable reduction methods are compared statistically using the Wilcoxon signed rank test. The three newly developed PPRVR-CAM methods were able to retain

Investigating Reliabilities of Intraindividual Variability Indicators

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Wang, Lijuan; Grimm, Kevin J.

2012-01-01

Reliabilities of the two most widely used intraindividual variability indicators, "ISD[superscript 2]" and "ISD", are derived analytically. Both are functions of the sizes of the first and second moments of true intraindividual variability, the size of the measurement error variance, and the number of assessments within a burst. For comparison,…

Expression of Sme efflux pumps and multilocus sequence typing in clinical isolates of Stenotrophomonas maltophilia.

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Cho, Hye Hyun; Sung, Ji Youn; Kwon, Kye Chul; Koo, Sun Hoe

2012-01-01

Stenotrophomonas maltophilia has emerged as an important opportunistic pathogen, which causes infections that are often difficult to manage because of the inherent resistance of the pathogen to a variety of antimicrobial agents. In this study, we analyzed the expressions of smeABC and smeDEF and their correlation with antimicrobial susceptibility. We also evaluated the genetic relatedness and epidemiological links among 33 isolates of S. maltophilia. In total, 33 S. maltophilia strains were isolated from patients in a tertiary hospital in Daejeon. Minimum inhibitory concentrations (MICs) of 11 antimicrobial agents were determined by using agar dilution method and E-test (BioMérieux, France). Real-time PCR analysis was performed to evaluate the expression of the Sme efflux systems in the S. maltophilia isolates. Additionally, an epidemiological investigation was performed using multilocus sequence typing (MLST) assays. The findings of susceptibility testing showed that the majority of the S. maltophilia isolates were resistant to β-lactams and aminoglycosides. Twenty-one clinical isolates overexpressed smeABC and showed high resistance to ciprofloxacin. Moreover, a high degree of genetic diversity was observed among the S. maltophilia isolates; 3 sequence types (STs) and 23 allelic profiles were observed. The smeABC efflux pump was associated with multidrug resistance in clinical isolates of S. maltophilia. In particular, smeABC efflux pumps appear to perform an important role in ciprofloxacin resistance of S. maltophilia. The MLST scheme for S. maltophilia represents a discriminatory typing method with stable markers and is appropriate for studying population structures.

Use of multilocus sequence typing for the investigation of colonisation by Candida albicans in intensive care unit patients.

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Cliff, P R; Sandoe, J A T; Heritage, J; Barton, R C

2008-05-01

A prospective study was performed to determine the prevalence of candidal colonisation on the general intensive care unit at a large teaching hospital. Colonisation with Candida spp. was found to be common, occurring in 79% of patients on the unit. C. albicans was the commonest species, colonising 64% of patients, followed by C. glabrata (18%) and C. parapsilosis (14%). Most of the members of staff tested carried Candida spp. at some point, although carriage appeared to be transient. C. parapsilosis was the most commonly isolated species from staff hands, whereas C. albicans was the most commonly isolated species from the mouth. The molecular epidemiology of C. albicans was investigated using Ca3 typing and multilocus sequence typing (MLST). MLST proved to be a reproducible typing method and a useful tool for the investigation of the molecular epidemiology of C. albicans. The results of the molecular typing provided evidence for the presence of an endemic strain on the unit, which was isolated repeatedly from patients and staff. This finding suggests horizontal transmission of C. albicans on the unit though it may also reflect the relative frequency of C. albicans strain types colonising patients on admission. This study has important implications for the epidemiology of systemic candidal infections.

Area vs. density: influence of visual variables and cardinality knowledge in early number comparison.

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Abreu-Mendoza, Roberto A; Soto-Alba, Elia E; Arias-Trejo, Natalia

2013-01-01

Current research in the number development field has focused in individual differences regarding the acuity of children's approximate number system (ANS). The most common task to evaluate children's acuity is through non-symbolic numerical comparison. Efforts have been made to prevent children from using perceptual cues by controlling the visual properties of the stimuli (e.g., density, contour length, and area); nevertheless, researchers have used these visual controls interchangeably. Studies have also tried to understand the relation between children's cardinality knowledge and their performance in a number comparison task; divergent results may in fact be rooted in the use of different visual controls. The main goal of the present study is to explore how the usage of different visual controls (density, total filled area, and correlated and anti-correlated area) affects children's performance in a number comparison task, and its relationship to children's cardinality knowledge. For that purpose, 77 preschoolers participated in three tasks: (1) counting list elicitation to test whether children could recite the counting list up to ten, (2) give a number to evaluate children's cardinality knowledge, and (3) number comparison to evaluate their ability to compare two quantities. During this last task, children were asked to point at the set with more geometric figures when two sets were displayed on a screen. Children were exposed only to one of the three visual controls. Results showed that overall, children performed above chance in the number comparison task; nonetheless, density was the easiest control, while correlated and anti-correlated area was the most difficult in most cases. Only total filled area was sensitive to discriminate cardinal principal knowers from non-cardinal principal knowers. How this finding helps to explain conflicting evidence from previous research, and how the present outcome relates to children's number word knowledge is discussed.

Association between the dopamine D4 receptor gene exon III variable number of tandem repeats and political attitudes in female Han Chinese.

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Ebstein, Richard P; Monakhov, Mikhail V; Lu, Yunfeng; Jiang, Yushi; Lai, Poh San; Chew, Soo Hong

2015-08-22

Twin and family studies suggest that political attitudes are partially determined by an individual's genotype. The dopamine D4 receptor gene (DRD4) exon III repeat region that has been extensively studied in connection with human behaviour, is a plausible candidate to contribute to individual differences in political attitudes. A first United States study provisionally identified this gene with political attitude along a liberal-conservative axis albeit contingent upon number of friends. In a large sample of 1771 Han Chinese university students in Singapore, we observed a significant main effect of association between the DRD4 exon III variable number of tandem repeats and political attitude. Subjects with two copies of the 4-repeat allele (4R/4R) were significantly more conservative. Our results provided evidence for a role of the DRD4 gene variants in contributing to individual differences in political attitude particularly in females and more generally suggested that associations between individual genes, and neurochemical pathways, contributing to traits relevant to the social sciences can be provisionally identified. © 2015 The Author(s).

Association between the dopamine D4 receptor gene exon III variable number of tandem repeats and political attitudes in female Han Chinese

Science.gov (United States)

Ebstein, Richard P.; Monakhov, Mikhail V.; Lu, Yunfeng; Jiang, Yushi; Lai, Poh San; Chew, Soo Hong

2015-01-01

Twin and family studies suggest that political attitudes are partially determined by an individual's genotype. The dopamine D4 receptor gene (DRD4) exon III repeat region that has been extensively studied in connection with human behaviour, is a plausible candidate to contribute to individual differences in political attitudes. A first United States study provisionally identified this gene with political attitude along a liberal–conservative axis albeit contingent upon number of friends. In a large sample of 1771 Han Chinese university students in Singapore, we observed a significant main effect of association between the DRD4 exon III variable number of tandem repeats and political attitude. Subjects with two copies of the 4-repeat allele (4R/4R) were significantly more conservative. Our results provided evidence for a role of the DRD4 gene variants in contributing to individual differences in political attitude particularly in females and more generally suggested that associations between individual genes, and neurochemical pathways, contributing to traits relevant to the social sciences can be provisionally identified. PMID:26246555

The Evolution of the Number of Tourists accommodated in Arad

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Sergiu Rusu

2014-12-01

Full Text Available The paper analyses the evolution of the number of tourists accommodated in Arad between January 2006 and September 2009. For this purpose we have used the statistics data from the official sites. As variables we chose: X – independent variable - Total tourist arrival and accommodated in Arad, Y - dependent variable - Tourists staying in hotels.

Novel intron markers to study the phylogeny of closely related mammalian species

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Castresana Jose

2010-11-01

Full Text Available Abstract Background Multilocus phylogenies can be used to infer the species tree of a group of closely related species. In species trees, the nodes represent the actual separation between species, thus providing essential information about their evolutionary history. In addition, multilocus phylogenies can help in analyses of species delimitation, gene flow and genetic differentiation within species. However, few adequate markers are available for such studies. Results In order to develop nuclear markers that can be useful in multilocus studies of mammals, we analyzed the mammalian genomes of human, chimpanzee, macaque, dog and cow. Rodents were excluded due to their unusual genomic features. Introns were extracted from the mammalian genomes because of their greater genetic variability and ease of amplification from the flanking exons. To an initial set of more than 10,000 one-to-one orthologous introns we applied several filters to select introns that belong to single-copy genes, show neutral evolutionary rates and have an adequate length for their amplification. This analysis led to a final list of 224 intron markers randomly distributed along the genome. To experimentally test their validity, we amplified twelve of these introns in a panel of six mammalian species. The result was that seven of these introns gave rise to a PCR band of the expected size in all species. In addition, we sequenced these bands and analyzed the accumulation of substitutions in these introns in five pairs of closely related species. The results showed that the estimated genetic distances in the five species pairs was quite variable among introns and that this divergence cannot be directly predicted from the overall intron divergence in mammals. Conclusions We have designed a new set of 224 nuclear introns with optimal features for the phylogeny of closely related mammalian species. A large proportion of the introns tested experimentally showed a perfect amplification

New polymorphisms within the variable number tandem repeat (VNTR) 7 locus of Mycobacterium avium subsp. paratuberculosis.

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Fawzy, Ahmad; Zschöck, Michael; Ewers, Christa; Eisenberg, Tobias

2016-06-01

Variable number tandem repeat (VNTR) is a frequently employed typing method of Mycobacterium avium paratuberculosis (MAP) isolates. Based on whole genome sequencing in a previous study, allelic diversity at some VNTR loci seems to over- or under-estimate the actual phylogenetic variance among isolates. Interestingly, two closely related isolates on one farm showed polymorphism at the VNTR 7 locus, raising concerns about the misleading role that it might play in genotyping. We aimed to investigate the underlying basis of VNTR 7-polymorphism by analyzing sequence data for published genomes and field isolates of MAP and other M. avium complex (MAC) members. In contrast to MAP strains from cattle, strains from sheep displayed an "imperfect" repeat within VNTR 7, which was identical to respective allele types in other MAC genomes. Subspecies- and strain-specific single nucleotide polymorphisms (SNPs) and two novel (16 and 56 bp) repeats were detected. Given the combination of the three existing repeats, there are at least five different patterns for VNTR 7. The present findings highlight a higher polymorphism and probable instability of VNTR 7 locus that needs to be considered and challenged in future studies. Until then, sequencing of this locus in future studies is important to correctly assign the underlying allele types.(1). Copyright © 2016 Elsevier Ltd. All rights reserved.

High-resolution melting genotyping of Enterococcus faecium based on multilocus sequence typing derived single nucleotide polymorphisms.

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Steven Y C Tong

Full Text Available We have developed a single nucleotide polymorphism (SNP nucleated high-resolution melting (HRM technique to genotype Enterococcus faecium. Eight SNPs were derived from the E. faecium multilocus sequence typing (MLST database and amplified fragments containing these SNPs were interrogated by HRM. We tested the HRM genotyping scheme on 85 E. faecium bloodstream isolates and compared the results with MLST, pulsed-field gel electrophoresis (PFGE and an allele specific real-time PCR (AS kinetic PCR SNP typing method. In silico analysis based on predicted HRM curves according to the G+C content of each fragment for all 567 sequence types (STs in the MLST database together with empiric data from the 85 isolates demonstrated that HRM analysis resolves E. faecium into 231 "melting types" (MelTs and provides a Simpson's Index of Diversity (D of 0.991 with respect to MLST. This is a significant improvement on the AS kinetic PCR SNP typing scheme that resolves 61 SNP types with D of 0.95. The MelTs were concordant with the known ST of the isolates. For the 85 isolates, there were 13 PFGE patterns, 17 STs, 14 MelTs and eight SNP types. There was excellent concordance between PFGE, MLST and MelTs with Adjusted Rand Indices of PFGE to MelT 0.936 and ST to MelT 0.973. In conclusion, this HRM based method appears rapid and reproducible. The results are concordant with MLST and the MLST based population structure.

The effect of the number of consecutive night shifts on diurnal rhythms in cortisol, melatonin and heart rate variability (HRV)

DEFF Research Database (Denmark)

Jensen, Marie Aarrebo; Garde, Anne Helene; Kristiansen, Jesper

2016-01-01

PURPOSE: The purpose of this review is to summarize the current knowledge from field studies on how many consecutive night shifts are required for adaptation of diurnal rhythms in cortisol, melatonin and heart rate variability (HRV) to night work. METHODS: A systematic search of the databases Pub...... recordings for HRV. Most of the studies in the review were small studies with less than 30 participants, and most studies evaluated diurnal rhythms after only two consecutive night shifts whereas only six studies used seven or more consecutive night shifts. The majority of studies found that adaptation...... to night work had not occurred after two consecutive night shifts, whereas a small number found evidence for full adaptation after seven consecutive night shifts based on diurnal rhythms in cortisol and melatonin. CONCLUSION: There are methodological differences in the field studies analyzing diurnal...

Multilocus Microsatellite Typing reveals intra-focal genetic diversity among strains of Leishmania tropica in Chichaoua Province, Morocco.

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Krayter, Lena; Alam, Mohammad Zahangir; Rhajaoui, Mohamed; Schnur, Lionel F; Schönian, Gabriele

2014-12-01

In Morocco, cutaneous leishmaniasis (CL) caused by Leishmania (L.) tropica is a major public health threat. Strains of this species have been shown to display considerable serological, biochemical, molecular biological and genetic heterogeneity; and Multilocus Enzyme Electrophoresis (MLEE), has shown that in many countries including Morocco heterogenic variants of L. tropica can co-exist in single geographical foci. Here, the microsatellite profiles discerned by MLMT of nine Moroccan strains of L. tropica isolated in 2000 from human cases of CL from Chichaoua Province were compared to those of nine Moroccan strains of L. tropica isolated between 1988 and 1990 from human cases of CL from Marrakech Province, and also to those of 147 strains of L. tropica isolated at different times from different worldwide geographical locations within the range of distribution of the species. Several programs, each employing a different algorithm, were used for population genetic analysis. The strains from each of the two Moroccan foci separated into two phylogenetic clusters independent of their geographical origin. Genetic diversity and heterogeneity existed in both foci, which are geographically close to each other. This intra-focal distribution of genetic variants of L. tropica is not considered owing to in situ mutation. Rather, it is proposed to be explained by the importation of pre-existing variants of L. tropica into Morocco. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Serotypes, antibiotic susceptibilities, and multi-locus sequence type profiles of Streptococcus agalactiae isolates circulating in Beijing, China.

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Wang, Ping; Tong, Jing-jing; Ma, Xiu-hua; Song, Feng-li; Fan, Ling; Guo, Cui-mei; Shi, Wei; Yu, Sang-jie; Yao, Kai-hu; Yang, Yong-hong

2015-01-01

To investigate the serotypes, antibiotic susceptibilities, and multi-locus sequence type (MLST) profiles of Streptococcus agalactiae (S. agalactiae) in Beijing to provide references for the prevention and treatment of S. agalactiae infections. All isolates were identified using the CAMP test and the latex-agglutination assay and serotyped using a Strep-B-Latex kit, after which they were assessed for antibiotic susceptibility, macrolide-resistance genes, and MLST profiles. In total, 56 S. agalactiae isolates were identified in 863 pregnant women (6.5%). Serotypes Ia, Ib, II, III, and V were identified, among which types III (32.1%), Ia (17.9%), Ib (16.1%), and V (14.3%) were the predominant serotypes. All isolates were susceptible to penicillin and ceftriaxone. The nonsusceptiblity rates measured for erythromycin, clarithromycin, azithromycin, telithromycin, clindamycin, tetracycline, and levofloxacin were 85.7%, 92.9%, 98.2%, 30.4%, 73.2%, 91%, and 39.3%, respectively. We identified 14 sequence types (STs) for the 56 isolates, among which ST19 (30.4%) was predominant. The rate of fluoroquinolone resistance was higher in serotype III than in the other serotypes. Among the 44 erythromycin-resistant isolates, 32 (72.7%) carried ermB. S. agalactiae isolates of the serotypes Ia, Ib, III, and V are common in Beijing. Among the S. agalactiae isolates, the macrolide and clindamycin resistance rates are extremely high. Most of the erythromycin-resistant isolates carry ermB.

Multilocus enzyme electrophoresis on agarose gel as an aid to the identification of entomopathogenic Bacillus sphaericus strains.

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Zahner, V; Rabinovitch, L; Cavados, C F; Momen, H

1994-04-01

Sixty strains of Bacillus sphaericus, including 31 insect pathogens were studied by multilocus enzyme electrophoresis and were classified into 44 zymovars (electrophoretic types). Among the entomopathogenic strains, 11 belong to the same zymovar (Z59) indicating a widespread frequent genotype. Bands of enzyme activity were not detected among the strains for the loci GPI (E.C.5.3.1.9), G6P (E.C.1.1.1.49), 6PG (E.C.1.1.1.44) and ME (E.C.1.1.1.40). The enzymatic loci NP (E.C.2.4.2.1) and ACON (E.C.4.2.1.3) were monomorphic while the other enzymes, MDH (E.C.1.1.1.37), LeDH (E.C.1.4.1.9), ADH (E.C.1.4.1.1), EST (E.C.3.1.1.1), PEP-2 (E.C.3.4.11.1), PEP-3 (E.C.3.4.11) and PEP-D (E.C. 3.4.13.9) were polymorphic. The genetic variation in the non-insect pathogenic group seemed to be greater than in the entomopathogenic group. This latter group appears to be distinct from other strains of these species. All insect pathogens were recovered in the same phenetic cluster and a diagnostic allele is reported for the identification of entomopathogenic strains.

VARIABLE STARS IN THE GLOBULAR CLUSTER NGC 2808

International Nuclear Information System (INIS)

Kunder, Andrea; Walker, Alistair R.; Stetson, Peter B.; Catelan, Márcio; Amigo, Pía

2013-01-01

The first calibrated broadband BVI time-series photometry is presented for the variable stars in NGC 2808, with observations spanning a range of 28 years. We have also redetermined the variability types and periods for the variable stars identified previously by Corwin et al., revising the number of probable fundamental-mode RR Lyrae variables (RR0) to 11 and the number of first-overtone variables (RR1) to five. Our observations were insufficient to discern the nature of the previously identified RR1 star, V24, and the tentatively identified RR1 star, V13. These two variables are ∼0.8 mag brighter than the RR Lyrae variables, appear to have somewhat erratic period and/or luminosity changes, and lie inside the RR Lyrae instability strip. Curiously, all but one of the RR Lyrae stars studied in this relatively metal-rich cluster exhibit the Blazhko phenomenon, an effect thought to occur with higher frequency in metal-poor environments. The mean periods of the RR0 and RR1 variables are (P) RR0 = 0.56 ± 0.01 d and RR1 = 0.30 ± 0.02 d, respectively, supporting an Oosterhoff I classification of the cluster. On the other hand, the number ratio of RR1-to-RR0-type variables is high, though not unprecedented, for an Oosterhoff I cluster. The RR Lyrae variables have no period shifts at a given amplitude compared to the M3 variables, making it unlikely that these variables are He enhanced. Using the recent recalibration of the RR Lyrae luminosity scale by Catelan and Cortés, a mean distance modulus of (m – M) V = 15.57 ± 0.13 mag for NGC 2808 is obtained, in good agreement with that determined here from its type II Cepheid and SX Phoenicis population. Our data have also allowed the discovery of two new candidate SX Phoenicis stars and an eclipsing binary in the blue straggler region of the NGC 2808 color-magnitude diagram.

Combination of multilocus sequence typing and pulsed-field gel electrophoresis reveals an association of molecular clonality with the emergence of extensive-drug resistance (XDR) in Salmonella.

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Cao, Yongzhong; Shen, Yongxiu; Cheng, Lingling; Zhang, Xiaorong; Wang, Chao; Wang, Yan; Zhou, Xiaohui; Chao, Guoxiang; Wu, Yantao

2018-03-01

Salmonellae is one of the most important foodborne pathogens and becomes resistant to multiple antibiotics, which represents a significant challenge to food industry and public health. However, a molecular signature that can be used to distinguish antimicrobial resistance profile, particularly multi-drug resistance or extensive-drug resistance (XDR). In the current study, 168 isolates from the chicken and pork production chains and ill chickens were characterized by serotyping, antimicrobial susceptibility test, multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). The results showed that these isolates belonged to 13 serotypes, 14 multilocus sequence types (STs), 94 PFGE genotypes, and 70 antimicrobial resistant profiles. S. Enteritidis, S. Indiana, and S. Derby were the predominant serotypes, corresponding to the ST11, ST17, and ST40 clones, respectively and the PFGE Cluster A, Cluster E, and Cluster D, respectively. Among the ST11-S. Enteritidis (Cluster A) and the ST40-S. Derby (Cluster D) clones, the majority of isolates were resistant to 4-8 antimicrobial agents, whereas in the ST17S. Indiana (Cluster E) clone, isolates showed extensive-drug resistance (XDR) to 9-16 antimicrobial agents. The bla TEM-1-like gene was prevalent in the ST11 and ST17 clones corresponding to high ampicillin resistance. The bla TEM-1-like , bla CTX-M , bla OXA-1-like , sul1, aaC4, aac(6')-1b, dfrA17, and floR gene complex was highly prevalent among isolates of ST17, corresponding to an XDR phenotype. These results demonstrated the association of the resistant phenotypes and genotypes with ST clone and PFGE cluster. Our results also indicated that the newly identified gene complex comprising bla TEM-1-like , bla CTX-M , bla OXA-1-like , sul1, aaC4, aac(6')-1b, dfrA17, and floR, was responsible for the emergence of the ST17S. Indiana XDR clone. ST17 could be potentially used as a molecular signature to distinguish S. Indiana XDR clone. Copyright © 2017

Is the extremely rare Iberian endemic plant species Castrilanthemum debeauxii (Compositae, Anthemideae) a 'living fossil'? Evidence from a multi-locus species tree reconstruction.

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Tomasello, Salvatore; Álvarez, Inés; Vargas, Pablo; Oberprieler, Christoph

2015-01-01

The present study provides results of multi-species coalescent species tree analyses of DNA sequences sampled from multiple nuclear and plastid regions to infer the phylogenetic relationships among the members of the subtribe Leucanthemopsidinae (Compositae, Anthemideae), to which besides the annual Castrilanthemum debeauxii (Degen, Hervier & É.Rev.) Vogt & Oberp., one of the rarest flowering plant species of the Iberian Peninsula, two other unispecific genera (Hymenostemma, Prolongoa), and the polyploidy complex of the genus Leucanthemopsis belong. Based on sequence information from two single- to low-copy nuclear regions (C16, D35, characterised by Chapman et al. (2007)), the multi-copy region of the nrDNA internal transcribed spacer regions ITS1 and ITS2, and two intergenic spacer regions of the cpDNA gene trees were reconstructed using Bayesian inference methods. For the reconstruction of a multi-locus species tree we applied three different methods: (a) analysis of concatenated sequences using Bayesian inference (MrBayes), (b) a tree reconciliation approach by minimizing the number of deep coalescences (PhyloNet), and (c) a coalescent-based species-tree method in a Bayesian framework ((∗)BEAST). All three species tree reconstruction methods unequivocally support the close relationship of the subtribe with the hitherto unclassified genus Phalacrocarpum, the sister-group relationship of Castrilanthemum with the three remaining genera of the subtribe, and the further sister-group relationship of the clade of Hymenostemma+Prolongoa with a monophyletic genus Leucanthemopsis. Dating of the (∗)BEAST phylogeny supports the long-lasting (Early Miocene, 15-22Ma) taxonomical independence and the switch from the plesiomorphic perennial to the apomorphic annual life-form assumed for the Castrilanthemum lineage that may have occurred not earlier than in the Pliocene (3Ma) when the establishment of a Mediterranean climate with summer droughts triggered evolution towards

Development of a multi-locus sequence typing scheme for Laribacter hongkongensis, a novel bacterium associated with freshwater fish-borne gastroenteritis and traveler's diarrhea

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Lee Edwin KY

2009-01-01

Full Text Available Abstract Background Laribacter hongkongensis is a newly discovered, facultative anaerobic, Gram-negative, motile, sea gull-shaped rod associated with freshwater fish borne gastroenteritis and traveler's diarrhea. A highly reproducible and discriminative typing system is essential for better understanding of the epidemiology of L. hongkongensis. In this study, a multilocus sequence typing (MLST system was developed for L. hongkongensis. The system was used to characterize 146 L. hongkongensis isolates, including 39 from humans and 107 from fish. Results Fragments (362 to 504 bp of seven housekeeping genes were amplified and sequenced. Among the 3068 bp of the seven loci, 332 polymorphic sites were observed. The median number of alleles at each locus was 34 [range 22 (ilvC to 45 (thiC]. All seven genes showed very low dn/ds ratios of ISA measurement showed significant linkage disequilibrium in isolates from both humans and fish. The ISA for the isolates from humans and fish were 0.270 and 0.636, indicating the isolates from fish were more clonal than the isolates from humans. Only one interconnected network (acnB was detected in the split graphs. The P-value (P = 0 of sum of the squares of condensed fragments in Sawyer's test showed evidence of intragenic recombination in the rho, acnB and thiC loci, but the P-value (P = 1 of maximum condensed fragment in these gene loci did not show evidence of intragenic recombination. Congruence analysis showed that all the pairwise comparisons of the 7 MLST loci were incongruent, indicating that recombination played a substantial role in the evolution of L. hongkongensis. A website for L. hongkongensis MLST was set up and can be accessed at http://mlstdb.hku.hk:14206/MLST_index.html. Conclusion A highly reproducible and discriminative MLST system was developed for L. hongkongensis.

Forensic microbiology and the bioterrorism risk (Part I

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Maria Nasso

2007-02-01

Full Text Available The letters containing anthrax, sent in 2001 in USA, showed that pathogens and toxins can be effectively used for terrorist purposes. A new subfield of forensic science, called “microbial forensics”, has been developed. It is a new scientific discipline dedicated to collect and analyze microbiological evidence from a scene of crime. In addition to collecting and analyzing traditional forensic evidences, the microbial forensic investigation will attempt to determine the identity of the causal agent, as so as epidemiologic investigation, but with higher-resolution characterization. The tools for a successful attribution include genetically based-assays to determine the exact strain of isolate, aiming the individualization of the source of the pathogen used in a biological weapon. Following the 2001 anthrax attacks, genotyping of B. anthracis was done on 8 variable number tandem repeats loci (VNTR polymorphisms, with multilocus variable number tandem repeats (MLVA method. In recent years some research groups have increased the VNTR markers number to 25 loci, while other groups have identified single nucleotide repeat (SNR polymorphisms, which display very high mutation rates. SNR marker system allows the distinguishing of isolates with extremely low levels of genetic diversity within the same MLVA genotype.

Forensic microbiology and bioterrorism risk (Part II

Directory of Open Access Journals (Sweden)

Maria Nasso

2007-04-01

Full Text Available The letters containing anthrax, sent in 2001 in USA, showed that pathogens and toxins can be effectively used for terrorist purposes. A new subfield of forensic science, called “microbial forensics”, has been developed. It is a new scientific discipline dedicated to collect and analyze microbiological evidence from a scene of crime. In addition to collecting and analyzing traditional forensic evidences, the microbial forensic investigation will attempt to determine the identity of the causal agent, as so as epidemiologic investigation, but with higher-resolution characterization. The tools for a successful attribution include genetically based-assays to determine the exact strain of isolate, aiming the individualization of the source of the pathogen used in a biological weapon. Following the 2001 anthrax attacks, genotyping of B. anthracis was done on 8 variable number tandem repeats loci (VNTR polymorphisms, with multilocus variable number tandem repeats (MLVA method. In recent years some research groups have increased the VNTR markers number to 25 loci, while other groups have identified single nucleotide repeat (SNR polymorphisms, which display very high mutation rates. SNR marker system allows the distinguishing of isolates with extremely low levels of genetic diversity within the same MLVA genotype.

Sequence determinants of human microsatellite variability

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Jakobsson Mattias

2009-12-01

Full Text Available Abstract Background Microsatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their level of variability we have analyzed genotypes at 627 microsatellite loci in 1,048 worldwide individuals from the HGDP-CEPH cell line panel together with the DNA sequences of these microsatellites in the human RefSeq database. Results Calibrating PCR fragment lengths in individual genotypes by using the RefSeq sequence enabled us to infer repeat number in the HGDP-CEPH dataset and to calculate the mean number of repeats (as opposed to the mean PCR fragment length, under the assumption that differences in PCR fragment length reflect differences in the numbers of repeats in the embedded repeat sequences. We find the mean and maximum numbers of repeats across individuals to be positively correlated with heterozygosity. The size and composition of the repeat unit of a microsatellite are also important factors in predicting heterozygosity, with tetra-nucleotide repeat units high in G/C content leading to higher heterozygosity. Finally, we find that microsatellites containing more separate sets of repeated motifs generally have higher heterozygosity. Conclusions These results suggest that sequence properties of microsatellites have a significant impact in determining the features of human microsatellite variability.

VNTR diversity in Yersinia pestis isolates from an animal challenge study reveals the potential for in vitro mutations during laboratory cultivation.

Science.gov (United States)

Vogler, Amy J; Nottingham, Roxanne; Busch, Joseph D; Sahl, Jason W; Shuey, Megan M; Foster, Jeffrey T; Schupp, James M; Smith, Susan R; Rocke, Tonie E; Keim, Paul; Wagner, David M

2016-11-01

Underlying mutation rates and other evolutionary forces shape the population structure of bacteria in nature. Although easily overlooked, similar forces are at work in the laboratory and may influence observed mutations. Here, we investigated tissue samples and Yersinia pestis isolates from a rodent laboratory challenge with strain CO92 using whole genome sequencing and multi-locus variable-number tandem repeat (VNTR) analysis (MLVA). We identified six VNTR mutations that were found to have occurred in vitro during laboratory cultivation rather than in vivo during the rodent challenge. In contrast, no single nucleotide polymorphism (SNP) mutations were observed, either in vivo or in vitro. These results were consistent with previously published mutation rates and the calculated number of Y. pestis generations that occurred during the in vitro versus the in vivo portions of the experiment. When genotyping disease outbreaks, the potential for in vitro mutations should be considered, particularly when highly variable genetic markers such as VNTRs are used. Copyright © 2016 Elsevier B.V. All rights reserved.

Characterization of the Emerging Salmonella 4,[5],12:i:- in Danish Animal Production

DEFF Research Database (Denmark)

Argüello, Hector; Sørensen, Gitte; Carvajal, Ana

2014-01-01

Abstract The monophasic Salmonella variant with the antigenic formula Salmonella 4,[5],12:i:- has emerged in the last decade as one of the main serotypes related to human salmonellosis. In the present study, a collection of 94 isolates of the S. 4,12:i:- and S. 4,5,12:i:- coming from Danish farm ...... in Danish food animal production with well-characterized clones that are described by previous studies, demonstrating the emergence and spread of this serotype in Denmark....... animals, swine (86), cattle (7), and poultry (1), with well-defined identification was further typed by polymerase chain reaction serotyping, phage typing, and molecular typing (polymerase chain reaction and multilocus variable-number tandem-repeat analysis [MLVA]). Moreover, the determination...

Barn Owl Productivity Response to Variability of Vole Populations.

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Petr Pavluvčík

Full Text Available We studied the response of the barn owl annual productivity to the common vole population numbers and variability to test the effects of environmental stochasticity on their life histories. Current theory predicts that temporal environmental variability can affect long-term nonlinear responses (e.g., production of young both positively and negatively, depending on the shape of the relationship between the response and environmental variables. At the level of the Czech Republic, we examined the shape of the relationship between the annual sum of fledglings (annual productivity and vole numbers in both non-detrended and detrended data. At the districts' level, we explored whether the degree of synchrony (measured by the correlation coefficient and the strength of the productivity response increase (measured by the regression coefficient in areas with higher vole population variability measured by the s-index. We found that the owls' annual productivity increased linearly with vole numbers in the Czech Republic. Furthermore, based on district data, we also found that synchrony between dynamics in owls' reproductive output and vole numbers increased with vole population variability. However, the strength of the response was not affected by the vole population variability. Additionally, we have shown that detrending remarkably increases the Taylor's exponent b relating variance to mean in vole time series, thereby reversing the relationship between the coefficient of variation and the mean. This shift was not responsible for the increased synchrony with vole population variability. Instead, we suggest that higher synchrony could result from high food specialization of owls on the common vole in areas with highly fluctuating vole populations.

Einstein x-ray observations of cataclysmic variables

International Nuclear Information System (INIS)

Mason, K.O.; Cordova, F.A.

1982-01-01

Observations with the imaging x-ray detectors on the Einstein Observatory have led to a large increase in the number of low luminosity x-ray sources known to be associated with cataclysmic variable stars (CVs). The high sensitivity of the Einstein instrumentation has permitted study of their short timescale variability and spectra. The data are adding significantly to our knowledge of the accretion process in cataclysmic variables and forcing some revision in our ideas concerning the origin of the optical variability in these stars

In situ formation and spatial variability of particle number concentration in a European megacity

Science.gov (United States)

Pikridas, M.; Sciare, J.; Freutel, F.; Crumeyrolle, S.; von der Weiden-Reinmüller, S.-L.; Borbon, A.; Schwarzenboeck, A.; Merkel, M.; Crippa, M.; Kostenidou, E.; Psichoudaki, M.; Hildebrandt, L.; Engelhart, G. J.; Petäjä, T.; Prévôt, A. S. H.; Drewnick, F.; Baltensperger, U.; Wiedensohler, A.; Kulmala, M.; Beekmann, M.; Pandis, S. N.

2015-09-01

Ambient particle number size distributions were measured in Paris, France, during summer (1-31 July 2009) and winter (15 January to 15 February 2010) at three fixed ground sites and using two mobile laboratories and one airplane. The campaigns were part of the Megacities: Emissions, urban, regional and Global Atmospheric POLlution and climate effects, and Integrated tools for assessment and mitigation (MEGAPOLI) project. New particle formation (NPF) was observed only during summer on approximately 50 % of the campaign days, assisted by the low condensation sink (about 10.7 ± 5.9 × 10-3 s-1). NPF events inside the Paris plume were also observed at 600 m altitude onboard an aircraft simultaneously with regional events identified on the ground. Increased particle number concentrations were measured aloft also outside of the Paris plume at the same altitude, and were attributed to NPF. The Paris plume was identified, based on increased particle number and black carbon concentration, up to 200 km away from the Paris center during summer. The number concentration of particles with diameters exceeding 2.5 nm measured on the surface at the Paris center was on average 6.9 ± 8.7 × 104 and 12.1 ± 8.6 × 104 cm-3 during summer and winter, respectively, and was found to decrease exponentially with distance from Paris. However, further than 30 km from the city center, the particle number concentration at the surface was similar during both campaigns. During summer, one suburban site in the NE was not significantly affected by Paris emissions due to higher background number concentrations, while the particle number concentration at the second suburban site in the SW increased by a factor of 3 when it was downwind of Paris.

Performance of Savonius Blade Waterwheel with Variation of Blade Number

Science.gov (United States)

Sule, L.; Rompas, P. T. D.

2018-02-01

The utilization of water energy source is mainly used as a provider of electrical energy through hydroelectric power. The potential utilization of water flow energy is relatively small. The objective of this study is to know the best blade of Savonius waterwheel with various variables such as water discharge, blade number, and loading. The data used the efficiency of waterwheel, variation of blade number, variable water discharge, and loading in the shaft. The test results have shown that the performances of a top-water mill with the semicircular curve where the variation in the number of blades are 4, 6, and 8 at discharge and loading of 0.01587 m3/s and 1000 grams respectively were 9.945%, 13.929%, and 17.056% respectively. The blades number of 8 obtained the greatest performance. The more number of blades the greater the efficiency of the waterwheel Savonius.

Multilocus sequence analysis of Echinococcus granulosus strains isolated from humans and animals in Iran.

Science.gov (United States)

Nikmanesh, Bahram; Mirhendi, Hossein; Mahmoudi, Shahram; Rokni, Mohammad Bagher

2017-12-01

Echinococcus granulosus is now considered a complex consisting of at least four species and ten genotypes. Different molecular targets have been described for molecular characterization of E. granulosus; however, in almost all studies only one or two of the targets have been used, and only limited data is available on the utilization of multiple loci. Therefore, we investigated the genetic diversity among 64 strains isolated from 138 cyst specimens of human and animal isolates, using a set of nuclear and mitochondrial genes; i.e., cytochrome c oxidase subunit 1 (cox1), NADH dehydrogenase subunit 1 (nad1), ATPase subunit 6 (atp6), 12S rRNA (12S), and Actin II (act II). In comparison to the use of molecular reference targets (nad1 + cox1), using singular target (act II or 12S or atp6) yielded lower discriminatory power. Act II and 12S genes could accurately discriminate the G6 genotype, but they were not able to differentiate between G1 and G3 genotypes. As the G1 and G3 genotypes belong to the E. granulosus sensu stricto, low intra-species variation was observed for act II and 12S. The atp6 gene could identify the G3 genotype but could not differentiate G6 and G1 genotypes. Using concatenated sequence of five genes (cox1 + nad1 + atp6 + 12S + act II), genotypes were identified accurately, and markedly higher resolution was obtained in comparison with the use of reference markers (nad1 + cox1) only. Application of multilocus sequence analysis (MLSA) to large-scale studies could provide valuable epidemiological data to make efficient control and management measures for cystic echinococcosis. Copyright © 2017 Elsevier Inc. All rights reserved.

Multilocus sequence typing scheme versus pulsed-field gel electrophoresis for typing Mycobacterium abscessus isolates.

Science.gov (United States)

Machado, Gabriel Esquitini; Matsumoto, Cristianne Kayoko; Chimara, Erica; Duarte, Rafael da Silva; de Freitas, Denise; Palaci, Moises; Hadad, David Jamil; Lima, Karla Valéria Batista; Lopes, Maria Luiza; Ramos, Jesus Pais; Campos, Carlos Eduardo; Caldas, Paulo César; Heym, Beate; Leão, Sylvia Cardoso

2014-08-01

Outbreaks of infections by rapidly growing mycobacteria following invasive procedures, such as ophthalmological, laparoscopic, arthroscopic, plastic, and cardiac surgeries, mesotherapy, and vaccination, have been detected in Brazil since 1998. Members of the Mycobacterium chelonae-Mycobacterium abscessus group have caused most of these outbreaks. As part of an epidemiological investigation, the isolates were typed by pulsed-field gel electrophoresis (PFGE). In this project, we performed a large-scale comparison of PFGE profiles with the results of a recently developed multilocus sequence typing (MLST) scheme for M. abscessus. Ninety-three isolates were analyzed, with 40 M. abscessus subsp. abscessus isolates, 47 M. abscessus subsp. bolletii isolates, and six isolates with no assigned subspecies. Forty-five isolates were obtained during five outbreaks, and 48 were sporadic isolates that were not associated with outbreaks. For MLST, seven housekeeping genes (argH, cya, glpK, gnd, murC, pta, and purH) were sequenced, and each isolate was assigned a sequence type (ST) from the combination of obtained alleles. The PFGE patterns of DraI-digested DNA were compared with the MLST results. All isolates were analyzable by both methods. Isolates from monoclonal outbreaks showed unique STs and indistinguishable or very similar PFGE patterns. Thirty-three STs and 49 unique PFGE patterns were identified among the 93 isolates. The Simpson's index of diversity values for MLST and PFGE were 0.69 and 0.93, respectively, for M. abscessus subsp. abscessus and 0.96 and 0.97, respectively, for M. abscessus subsp. bolletii. In conclusion, the MLST scheme showed 100% typeability and grouped monoclonal outbreak isolates in agreement with PFGE, but it was less discriminative than PFGE for M. abscessus. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Compressing the hidden variable space of a qubit

OpenAIRE

Montina, Alberto

2010-01-01

In previously exhibited hidden variable models of quantum state preparation and measurement, the number of continuous hidden variables describing the actual state of a single realization is never smaller than the quantum state manifold dimension. We introduce a simple model for a qubit whose hidden variable space is one-dimensional, i.e., smaller than the two-dimensional Bloch sphere. The hidden variable probability distributions associated with the quantum states satisfy reasonable criteria ...

Control approach development for variable recruitment artificial muscles

Science.gov (United States)

Jenkins, Tyler E.; Chapman, Edward M.; Bryant, Matthew

2016-04-01

This study characterizes hybrid control approaches for the variable recruitment of fluidic artificial muscles with double acting (antagonistic) actuation. Fluidic artificial muscle actuators have been explored by researchers due to their natural compliance, high force-to-weight ratio, and low cost of fabrication. Previous studies have attempted to improve system efficiency of the actuators through variable recruitment, i.e. using discrete changes in the number of active actuators. While current variable recruitment research utilizes manual valve switching, this paper details the current development of an online variable recruitment control scheme. By continuously controlling applied pressure and discretely controlling the number of active actuators, operation in the lowest possible recruitment state is ensured and working fluid consumption is minimized. Results provide insight into switching control scheme effects on working fluids, fabrication material choices, actuator modeling, and controller development decisions.

Noise Reduction with Optimal Variable Span Linear Filters

DEFF Research Database (Denmark)

Jensen, Jesper Rindom; Benesty, Jacob; Christensen, Mads Græsbøll

2016-01-01

In this paper, the problem of noise reduction is addressed as a linear filtering problem in a novel way by using concepts from subspace-based enhancement methods, resulting in variable span linear filters. This is done by forming the filter coefficients as linear combinations of a number...... included in forming the filter. Using these concepts, a number of different filter designs are considered, like minimum distortion, Wiener, maximum SNR, and tradeoff filters. Interestingly, all these can be expressed as special cases of variable span filters. We also derive expressions for the speech...... demonstrate the advantages and properties of the variable span filter designs, and their potential performance gain compared to widely used speech enhancement methods....

Digital breast tomosynthesis: observer performance of clustered microcalcification detection on breast phantom images acquired with an experimental system using variable scan angles, angular increments, and number of projection views.

Science.gov (United States)

Chan, Heang-Ping; Goodsitt, Mitchell M; Helvie, Mark A; Zelakiewicz, Scott; Schmitz, Andrea; Noroozian, Mitra; Paramagul, Chintana; Roubidoux, Marilyn A; Nees, Alexis V; Neal, Colleen H; Carson, Paul; Lu, Yao; Hadjiiski, Lubomir; Wei, Jun

2014-12-01

To investigate the dependence of microcalcification cluster detectability on tomographic scan angle, angular increment, and number of projection views acquired at digital breast tomosynthesis ( DBT digital breast tomosynthesis ). A prototype DBT digital breast tomosynthesis system operated in step-and-shoot mode was used to image breast phantoms. Four 5-cm-thick phantoms embedded with 81 simulated microcalcification clusters of three speck sizes (subtle, medium, and obvious) were imaged by using a rhodium target and rhodium filter with 29 kV, 50 mAs, and seven acquisition protocols. Fixed angular increments were used in four protocols (denoted as scan angle, angular increment, and number of projection views, respectively: 16°, 1°, and 17; 24°, 3°, and nine; 30°, 3°, and 11; and 60°, 3°, and 21), and variable increments were used in three (40°, variable, and 13; 40°, variable, and 15; and 60°, variable, and 21). The reconstructed DBT digital breast tomosynthesis images were interpreted by six radiologists who located the microcalcification clusters and rated their conspicuity. The mean sensitivity for detection of subtle clusters ranged from 80% (22.5 of 28) to 96% (26.8 of 28) for the seven DBT digital breast tomosynthesis protocols; the highest sensitivity was achieved with the 16°, 1°, and 17 protocol (96%), but the difference was significant only for the 60°, 3°, and 21 protocol (80%, P .99). The conspicuity of subtle and medium clusters with the 16°, 1°, and 17 protocol was rated higher than those with other protocols; the differences were significant for subtle clusters with the 24°, 3°, and nine protocol and for medium clusters with 24°, 3°, and nine; 30°, 3°, and 11; 60°, 3° and 21; and 60°, variable, and 21 protocols (P tomosynthesis provided higher sensitivity and conspicuity than wide-angle DBT digital breast tomosynthesis for subtle microcalcification clusters. © RSNA, 2014.

Genotypic characterization by multi locus variable number of tandem repeats analysis international Bordetella pertussis vaccine strains

Directory of Open Access Journals (Sweden)

M. Fatah Moghadam

2017-10-01

Full Text Available Background: In 1930's first whole cell pertussis vaccines became available to the public heralding a dramatic success in overcoming the global burden of the disease. To date only a handful of B. pertussis strains have been used by international/local pertussis vaccine manufacturers. Inevitable well-documented genetic changes in the world population of this pathogen have prompted serious questions on suitability of traditional vaccine strains protect human against currently circulating wild isolates of Bordetella pertussis. Objective: Analyzing the genetic diversity within the most frequently-used vaccine strains of B. pertussis in the world Methods: A recently developed multi locus variable number of tandem repeats analysis (MLVA genotyping system along with a bioinforamtic piece of analysis was conducted on 11 strain / substrains of B137, B203 (10536, C393, Cs, E476, Tohama I, J445 (134, B202 and J446 (509 plus 2 sub-strains of 134 and 509 that are used at Razi institute for preparation of pertussis vaccine. In this study have used 6 individual loci of VNTR1, VNTR3a, VNTR3b, VNTR4, VNTR5 and VNTR6. Findings: Six distinct genotypes were recognized among the examined strains by comparing our data with the Dutch MLVA databank. These were all new and not reported before in the database. Conclusion: This observation reiterates on necessity for detection of predominant native strains to include in vaccine preparations suitable for different countries.

High-resolution typing of Chlamydia trachomatis: epidemiological and clinical uses.

Science.gov (United States)

de Vries, Henry J C; Schim van der Loeff, Maarten F; Bruisten, Sylvia M

2015-02-01

A state-of-the-art overview of molecular Chlamydia trachomatis typing methods that are used for routine diagnostics and scientific studies. Molecular epidemiology uses high-resolution typing techniques such as multilocus sequence typing, multilocus variable number of tandem repeats analysis, and whole-genome sequencing to identify strains based on their DNA sequence. These data can be used for cluster, network and phylogenetic analyses, and are used to unveil transmission networks, risk groups, and evolutionary pathways. High-resolution typing of C. trachomatis strains is applied to monitor treatment efficacy and re-infections, and to study the recent emergence of lymphogranuloma venereum (LGV) amongst men who have sex with men in high-income countries. Chlamydia strain typing has clinical relevance in disease management, as LGV needs longer treatment than non-LGV C. trachomatis. It has also led to the discovery of a new variant Chlamydia strain in Sweden, which was not detected by some commercial C. trachomatis diagnostic platforms. After a brief history and comparison of the various Chlamydia typing methods, the applications of the current techniques are described and future endeavors to extend scientific understanding are formulated. High-resolution typing will likely help to further unravel the pathophysiological mechanisms behind the wide clinical spectrum of chlamydial disease.

Genetic Relatedness of Staphylococcus haemolyticus in Gut and Skin of Preterm Neonates and Breast Milk of Their Mothers.

Science.gov (United States)

Soeorg, Hiie; Metsvaht, Hanna Kadri; Keränen, Evamaria Elisabet; Eelmäe, Imbi; Merila, Mirjam; Ilmoja, Mari-Liis; Metsvaht, Tuuli; Lutsar, Irja

2018-04-02

Staphylococcus haemolyticus is a common colonizer and cause of late-onset sepsis (LOS) in preterm neonates. By describing genetic relatedness, we aimed to determine whether mother's breast milk (BM) is a source of S. haemolyticus colonizing neonatal gut and skin and/or causing LOS. S. haemolyticus was isolated from stool and skin swabs of 49 BM-fed preterm neonates admitted to neonatal intensive care unit, 20 healthy BM-fed term neonates and BM of mothers once a week and typed by multilocus variable-number tandem-repeat analysis (MLVA) and multilocus sequence typing (MLST). Virulence-related genes were determined by PCR. Compared with term neonates S. haemolyticus colonized more commonly gut (35% vs 89.9%; pskin (50% vs 91.8%; pskin with MLVA-types indistinguishable from those in BM. Most frequent MLVA-types belonged to sequence type 3 or 42, comprised 71.1-78.4% of isolates from preterm neonates/mothers and caused all seven LOS episodes. LOS-causing strain colonized the gut of 4/7 and the skin of 5/7 neonates, but not BM, prior to onset of LOS. S. haemolyticus colonizing gut and skin or causing LOS in preterm neonates rarely originate from BM, but are mecA-positive strains adapted to hospital environment.

The influence of climate variables on dengue in Singapore.

Science.gov (United States)

Pinto, Edna; Coelho, Micheline; Oliver, Leuda; Massad, Eduardo

2011-12-01

In this work we correlated dengue cases with climatic variables for the city of Singapore. This was done through a Poisson Regression Model (PRM) that considers dengue cases as the dependent variable and the climatic variables (rainfall, maximum and minimum temperature and relative humidity) as independent variables. We also used Principal Components Analysis (PCA) to choose the variables that influence in the increase of the number of dengue cases in Singapore, where PC₁ (Principal component 1) is represented by temperature and rainfall and PC₂ (Principal component 2) is represented by relative humidity. We calculated the probability of occurrence of new cases of dengue and the relative risk of occurrence of dengue cases influenced by climatic variable. The months from July to September showed the highest probabilities of the occurrence of new cases of the disease throughout the year. This was based on an analysis of time series of maximum and minimum temperature. An interesting result was that for every 2-10°C of variation of the maximum temperature, there was an average increase of 22.2-184.6% in the number of dengue cases. For the minimum temperature, we observed that for the same variation, there was an average increase of 26.1-230.3% in the number of the dengue cases from April to August. The precipitation and the relative humidity, after analysis of correlation, were discarded in the use of Poisson Regression Model because they did not present good correlation with the dengue cases. Additionally, the relative risk of the occurrence of the cases of the disease under the influence of the variation of temperature was from 1.2-2.8 for maximum temperature and increased from 1.3-3.3 for minimum temperature. Therefore, the variable temperature (maximum and minimum) was the best predictor for the increased number of dengue cases in Singapore.

The WFCAM multiwavelength Variable Star Catalog

Science.gov (United States)

Ferreira Lopes, C. E.; Dékány, I.; Catelan, M.; Cross, N. J. G.; Angeloni, R.; Leão, I. C.; De Medeiros, J. R.

2015-01-01

Context. Stellar variability in the near-infrared (NIR) remains largely unexplored. The exploitation of public science archives with data-mining methods offers a perspective for a time-domain exploration of the NIR sky. Aims: We perform a comprehensive search for stellar variability using the optical-NIR multiband photometric data in the public Calibration Database of the WFCAM Science Archive (WSA), with the aim of contributing to the general census of variable stars and of extending the current scarce inventory of accurate NIR light curves for a number of variable star classes. Methods: Standard data-mining methods were applied to extract and fine-tune time-series data from the WSA. We introduced new variability indices designed for multiband data with correlated sampling, and applied them for preselecting variable star candidates, i.e., light curves that are dominated by correlated variations, from noise-dominated ones. Preselection criteria were established by robust numerical tests for evaluating the response of variability indices to the colored noise characteristic of the data. We performed a period search using the string-length minimization method on an initial catalog of 6551 variable star candidates preselected by variability indices. Further frequency analysis was performed on positive candidates using three additional methods in combination, in order to cope with aliasing. Results: We find 275 periodic variable stars and an additional 44 objects with suspected variability with uncertain periods or apparently aperiodic variation. Only 44 of these objects had been previously known, including 11 RR Lyrae stars on the outskirts of the globular cluster M 3 (NGC 5272). We provide a preliminary classification of the new variable stars that have well-measured light curves, but the variability types of a large number of objects remain ambiguous. We classify most of the new variables as contact binary stars, but we also find several pulsating stars, among which

Maximal Inequalities for Dependent Random Variables

DEFF Research Database (Denmark)

Hoffmann-Jorgensen, Jorgen

2016-01-01

Maximal inequalities play a crucial role in many probabilistic limit theorem; for instance, the law of large numbers, the law of the iterated logarithm, the martingale limit theorem and the central limit theorem. Let X-1, X-2,... be random variables with partial sums S-k = X-1 + ... + X-k. Then a......Maximal inequalities play a crucial role in many probabilistic limit theorem; for instance, the law of large numbers, the law of the iterated logarithm, the martingale limit theorem and the central limit theorem. Let X-1, X-2,... be random variables with partial sums S-k = X-1 + ... + X......-k. Then a maximal inequality gives conditions ensuring that the maximal partial sum M-n = max(1) (...

Variable volume combustor with a conical liner support

Science.gov (United States)

Johnson, Thomas Edward; McConnaughhay, Johnie Franklin; Keener, Chrisophter Paul; Ostebee, Heath Michael

2017-06-27

The present application provides a variable volume combustor for use with a gas turbine engine. The variable volume combustor may include a liner, a number of micro-mixer fuel nozzles positioned within the liner, and a conical liner support supporting the liner.

Association between Interleukin-1 Receptor Antagonist (IL1RN) Variable Number of Tandem Repeats (VNTR) Polymorphism and Pulmonary Tuberculosis.

Science.gov (United States)

Hashemi, Mohammad; Naderi, Mohammad; Ebrahimi, Mahboubeh; Amininia, Shadi; Bahari, Gholamreza; Taheri, Mohsen; Eskandari-Nasab, Ebrahim; Ghavami, Saeid

2015-02-01

Macrophages and T-lymphocytes are involved in immune response to Mycobacterium tuberculosis. Macrophage produces interleukin (IL)-1 as an inflammatory mediator. IL-1 receptor antagonist (IL1-Ra) is a natural antagonist of IL-1 receptors. In this study we aimed to examine the possible association between the variable number of tandem repeats (VNTR) of the IL-1 receptor antagonist (IL1RN) gene and pulmonary tuberculosis (TB) in a sample of Iranian population. Our study is a case-control study and we examined the VNTR of the IL1RN gene in 265 PTB and 250 healthy subjects by PCR. Neither the overall chi-square comparison of PTB and control subjects nor the logistic regression analysis indicated any association between VNTR IL1RN polymorphism and PTB. Our data suggest that VNTR IL1RN polymorphism may not be associated with the risk of PTB in a sample of Iranian population. Larger studies with different ethnicities are needed to find out the impact of IL1RN VNTR polymorphism on risk of developing TB.

Evaluation of two multi-locus sequence typing schemes for commensal Escherichia coli from dairy cattle in Washington State.

Science.gov (United States)

Ahmed, Sara; Besser, Thomas E; Call, Douglas R; Weissman, Scott J; Jones, Lisa P; Davis, Margaret A

2016-05-01

Multi-locus sequence typing (MLST) is a useful system for phylogenetic and epidemiological studies of multidrug-resistant Escherichiacoli. Most studies utilize a seven-locus MLST, but an alternate two-locus typing method (fumC and fimH; CH typing) has been proposed that may offer a similar degree of discrimination at lower cost. Herein, we compare CH typing to the standard seven-locus method for typing commensal E. coli isolates from dairy cattle. In addition, we evaluated alternative combinations of eight loci to identify combinations that maximize discrimination and congruence with standard seven-locus MLST among commensal E. coli while minimizing the cost. We also compared both methods when used for typing uropathogenic E. coli (UPEC). CH typing was less discriminatory for commensal E. coli than the standard seven-locus method (Simpson's Index of Diversity=0.933 [0.902-0.964] and 0.97 [0.96-0.979], respectively). Combining fimH with housekeeping gene loci improved discriminatory power for commensal E. coli from cattle but resulted in poor congruence with MLST. We found that a four-locus typing method including the housekeeping genes adk, purA, gyrB and recA could be used to minimize cost without sacrificing discriminatory power or congruence with Achtman seven-locus MLST when typing commensal E. coli. Copyright © 2016 Elsevier B.V. All rights reserved.

40 Variability Bugs in the Linux Kernel

DEFF Research Database (Denmark)

Abal Rivas, Iago; Brabrand, Claus; Wasowski, Andrzej

2014-01-01

Feature-sensitive verification is a recent field that pursues the effective analysis of the exponential number of variants of a program family. Today researchers lack examples of concrete bugs induced by variability, and occurring in real large-scale software. Such a collection of bugs is a requi......Feature-sensitive verification is a recent field that pursues the effective analysis of the exponential number of variants of a program family. Today researchers lack examples of concrete bugs induced by variability, and occurring in real large-scale software. Such a collection of bugs...... the outcome of our analysis into a database. In addition, we provide self-contained simplified C99 versions of the bugs, facilitating understanding and tool evaluation. Our study provides insights about the nature and occurrence of variability bugs in a large C software system, and shows in what ways...

Multi-locus sequence typing of Bartonella henselae isolates from three continents reveals hypervirulent and feline-associated clones.

Directory of Open Access Journals (Sweden)

Mardjan Arvand

Full Text Available Bartonella henselae is a zoonotic pathogen and the causative agent of cat scratch disease and a variety of other disease manifestations in humans. Previous investigations have suggested that a limited subset of B. henselae isolates may be associated with human disease. In the present study, 182 human and feline B. henselae isolates from Europe, North America and Australia were analysed by multi-locus sequence typing (MLST to detect any associations between sequence type (ST, host species and geographical distribution of the isolates. A total of 14 sequence types were detected, but over 66% (16/24 of the isolates recovered from human disease corresponded to a single genotype, ST1, and this type was detected in all three continents. In contrast, 27.2% (43/158 of the feline isolates corresponded to ST7, but this ST was not recovered from humans and was restricted to Europe. The difference in host association of STs 1 (human and 7 (feline was statistically significant (P< or =0.001. eBURST analysis assigned the 14 STs to three clonal lineages, which contained two or more STs, and a singleton comprising ST7. These groups were broadly consistent with a neighbour-joining tree, although splits decomposition analysis was indicative of a history of recombination. These data indicate that B. henselae lineages differ in their virulence properties for humans and contribute to a better understanding of the population structure of B. henselae.

Multilocus sequence typing of Xylella fastidiosa causing Pierce's disease and oleander leaf scorch in the United States.

Science.gov (United States)

Yuan, Xiaoli; Morano, Lisa; Bromley, Robin; Spring-Pearson, Senanu; Stouthamer, Richard; Nunney, Leonard

2010-06-01

Using a modified multilocus sequence typing (MLST) scheme for the bacterial plant pathogen Xylella fastidiosa based on the same seven housekeeping genes employed in a previously published MLST, we studied the genetic diversity of two subspecies, X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. sandyi, which cause Pierce's disease and oleander leaf scorch, respectively. Typing of 85 U.S. isolates (plus one from northern Mexico) of X. fastidiosa subsp. fastidiosa from 15 different plant hosts and 21 isolates of X. fastidiosa subsp. sandyi from 4 different hosts in California and Texas supported their subspecific status. Analysis using the MLST genes plus one cell-surface gene showed no significant genetic differentiation based on geography or host plant within either subspecies. Two cases of homologous recombination (with X. fastidiosa subsp. multiplex, the third U.S. subspecies) were detected in X. fastidiosa subsp. fastidiosa. Excluding recombination, MLST site polymorphism in X. fastidiosa subsp. fastidiosa (0.048%) and X. fastidiosa subsp. sandyi (0.000%) was substantially lower than in X. fastidiosa subsp. multiplex (0.240%), consistent with the hypothesis that X. fastidiosa subspp. fastidiosa and sandyi were introduced into the United States (probably just prior to 1880 and 1980, respectively). Using whole-genome analysis, we showed that MLST is more effective at genetic discrimination at the specific and subspecific level than other typing methods applied to X. fastidiosa. Moreover, MLST is the only technique effective in detecting recombination.

The bioinvasion of Guam: inferring geographic origin, pace, pattern and process of an invasive lizard (Carlia) in the Pacific using multi-locus genomic data

Science.gov (United States)

Austin, C.C.; Rittmeyer, E.N.; Oliver, L.A.; Andermann, J.O.; Zug, G.R.; Rodda, G.H.; Jackson, N.D.

2011-01-01

Invasive species often have dramatic negative effects that lead to the deterioration and loss of biodiversity frequently coupled with the burden of expensive biocontrol programs and subversion of socioeconomic stability. The fauna and flora of oceanic islands are particularly susceptible to invasive species and the increase of global movements of humans and their products since WW II has caused numerous anthropogenic translocations and increased the ills of human-mediated invasions. We use a multi-locus genomic dataset to identify geographic origin, pace, pattern and historical process of an invasive scincid lizard (Carlia) that has been inadvertently introduced to Guam, the Northern Marianas, and Palau. This lizard is of major importance as its introduction is thought to have assisted in the establishment of the invasive brown treesnake (Boiga irregularis) on Guam by providing a food resource. Our findings demonstrate multiple waves of introductions that appear to be concordant with movements of Allied and Imperial Japanese forces in the Pacific during World War II.

Effective Analysis of C Programs by Rewriting Variability

DEFF Research Database (Denmark)

Iosif-Lazar, Alexandru Florin; Melo, Jean; Dimovski, Aleksandar

2017-01-01

and effective analysis and verification of real-world C program families. Importance. We report some interesting variability-related bugs that we discovered using various state-of-the-art single-program C verification tools, such as Frama-C, Clang, LLBMC.......Context. Variability-intensive programs (program families) appear in many application areas and for many reasons today. Different family members, called variants, are derived by switching statically configurable options (features) on and off, while reuse of the common code is maximized. Inquiry....... Verification of program families is challenging since the number of variants is exponential in the number of features. Existing single-program analysis and verification tools cannot be applied directly to program families, and designing and implementing the corresponding variability-aware versions is tedious...

Microevolution and History of the Plague Bacillus, Yersinia pestis

National Research Council Canada - National Science Library

Achtman, Mark

2004-01-01

.... The microevolution of Y. pestis was therefore investigated by three different multilocus molecular methods, targeting genomewide synonymous SNPs, variation in number of tandem repeats, and insertion of IS100 insertion elements...

Latitudinal Clines of the Human Vitamin D Receptor and Skin Color Genes

Directory of Open Access Journals (Sweden)

Dov Tiosano

2016-05-01

Full Text Available The well-documented latitudinal clines of genes affecting human skin color presumably arise from the need for protection from intense ultraviolet radiation (UVR vs. the need to use UVR for vitamin D synthesis. Sampling 751 subjects from a broad range of latitudes and skin colors, we investigated possible multilocus correlated adaptation of skin color genes with the vitamin D receptor gene (VDR, using a vector correlation metric and network method called BlocBuster. We discovered two multilocus networks involving VDR promoter and skin color genes that display strong latitudinal clines as multilocus networks, even though many of their single gene components do not. Considered one by one, the VDR components of these networks show diverse patterns: no cline, a weak declining latitudinal cline outside of Africa, and a strong in- vs. out-of-Africa frequency pattern. We confirmed these results with independent data from HapMap. Standard linkage disequilibrium analyses did not detect these networks. We applied BlocBuster across the entire genome, showing that our networks are significant outliers for interchromosomal disequilibrium that overlap with environmental variation relevant to the genes’ functions. These results suggest that these multilocus correlations most likely arose from a combination of parallel selective responses to a common environmental variable and coadaptation, given the known Mendelian epistasis among VDR and the skin color genes.

Low numbers of repeat units in variable number of tandem repeats (VNTR) regions of white spot syndrome virus are correlated with disease outbreaks

NARCIS (Netherlands)

Tran Thi Tuyet, H.; Zwart, M.P.; Phuong, N.T.; Jong, de M.C.M.; Vlak, J.M.

2012-01-01

White spot syndrome virus (WSSV) is the most important pathogen in shrimp farming systems worldwide including the Mekong Delta, Vietnam. The genome of WSSV is characterized by the presence of two major 'indel regions' found at ORF14/15 and ORF23/24 (WSSV-Thailand) and three regions with variable

Large Diversity of Porcine Yersinia enterocolitica 4/O:3 in Eight European Countries Assessed by Multiple-Locus Variable-Number Tandem-Repeat Analysis.

Science.gov (United States)

Alakurtti, Sini; Keto-Timonen, Riikka; Virtanen, Sonja; Martínez, Pilar Ortiz; Laukkanen-Ninios, Riikka; Korkeala, Hannu

2016-06-01

A total of 253 multiple-locus variable-number tandem-repeat analysis (MLVA) types among 634 isolates were discovered while studying the genetic diversity of porcine Yersinia enterocolitica 4/O:3 isolates from eight different European countries. Six variable-number tandem-repeat (VNTR) loci V2A, V4, V5, V6, V7, and V9 were used to study the isolates from 82 farms in Belgium (n = 93, 7 farms), England (n = 41, 8 farms), Estonia (n = 106, 12 farms), Finland (n = 70, 13 farms), Italy (n = 111, 20 farms), Latvia (n = 66, 3 farms), Russia (n = 60, 10 farms), and Spain (n = 87, 9 farms). Cluster analysis revealed mainly country-specific clusters, and only one MLVA type consisting of two isolates was found from two countries: Russia and Italy. Also, farm-specific clusters were discovered, but same MLVA types could also be found from different farms. Analysis of multiple isolates originating either from the same tonsils (n = 4) or from the same farm, but 6 months apart, revealed both identical and different MLVA types. MLVA showed a very good discriminatory ability with a Simpson's discriminatory index (DI) of 0.989. DIs for VNTR loci V2A, V4, V5, V6, V7, and V9 were 0.916, 0.791, 0.901, 0.877, 0.912, and 0.785, respectively, when studying all isolates together, but variation was evident between isolates originating from different countries. Locus V4 in the Spanish isolates and locus V9 in the Latvian isolates did not differentiate (DI 0.000), and locus V9 in the English isolates showed very low discriminatory power (DI 0.049). The porcine Y. enterocolitica 4/O:3 isolates were diverse, but the variation in DI demonstrates that the well discriminating loci V2A, V5, V6, and V7 should be included in MLVA protocol when maximal discriminatory power is needed.

Multilocus lod scores in large pedigrees: combination of exact and approximate calculations.

Science.gov (United States)

Tong, Liping; Thompson, Elizabeth

2008-01-01

To detect the positions of disease loci, lod scores are calculated at multiple chromosomal positions given trait and marker data on members of pedigrees. Exact lod score calculations are often impossible when the size of the pedigree and the number of markers are both large. In this case, a Markov Chain Monte Carlo (MCMC) approach provides an approximation. However, to provide accurate results, mixing performance is always a key issue in these MCMC methods. In this paper, we propose two methods to improve MCMC sampling and hence obtain more accurate lod score estimates in shorter computation time. The first improvement generalizes the block-Gibbs meiosis (M) sampler to multiple meiosis (MM) sampler in which multiple meioses are updated jointly, across all loci. The second one divides the computations on a large pedigree into several parts by conditioning on the haplotypes of some 'key' individuals. We perform exact calculations for the descendant parts where more data are often available, and combine this information with sampling of the hidden variables in the ancestral parts. Our approaches are expected to be most useful for data on a large pedigree with a lot of missing data. (c) 2007 S. Karger AG, Basel

Optokinetic Stimulation Modulates Neglect for the Number Space: Evidence from Mental Number Interval Bisection

Science.gov (United States)

Priftis, Konstantinos; Pitteri, Marco; Meneghello, Francesca; Umiltà, Carlo; Zorzi, Marco

2012-01-01

Behavioral, neuropsychological, and neuroimaging data support the idea that numbers are represented along a mental number line (MNL), an analogical, visuospatial representation of number magnitude. The MNL is left-to-right oriented in Western cultures, with small numbers on the left and larger numbers on the right. Left neglect patients are impaired in the mental bisection of numerical intervals, with a bias toward larger numbers that are relatively to the right on the MNL. In the present study we investigated the effects of optokinetic stimulation (OKS) – a technique inducing visuospatial attention shifts by means of activation of the optokinetic nystagmus – on number interval bisection. One patient with left neglect following right-hemisphere stroke (BG) and four control patients with right-hemisphere damage, but without neglect, performed the number interval bisection task in three conditions of OKS: static, leftward, and rightward. In the static condition, BG misbisected to the right of the true midpoint. BG misbisected to the left following leftward OKS, and again to the right of the midpoint following rightward OKS. Moreover, the variability of BG’s performance was smaller following both leftward and rightward OKS, suggesting that the attentional bias induced by OKS reduced the “indifference zone” that is thought to underlie the length effect reported in bisection tasks. We argue that shifts of visuospatial attention, induced by OKS, may affect number interval bisection, thereby revealing an interaction between the processing of the perceptual space and the processing of the number space. PMID:22363280

Study of heavy meson production in p-Pb collisions at p√(S)=5.02 TeV in the general-mass variable-flavour-number scheme

Energy Technology Data Exchange (ETDEWEB)

Kramer, G. [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik; Spiesberger, H. [Mainz Univ. (Germany). PRISMA Cluster of Excellence, Inst. fuer Physik; Cape Town Univ., Rondebosch (South Africa). Centre for Theoretical and Mathematical Physics and Dept. of Physics

2017-03-16

We study inclusive charm and bottom production, for both D and B mesons, in p-Pb collisions at the LHC. Numerical results for p{sub T} -differential production cross sections are obtained at next-to-leading-order in the general-mass variable-flavor-number scheme. We compare our results with recent data from ALICE and CMS at a center-of-mass energy of 5 TeV and find good agreement. A comparison with p-p cross sections does not reveal the presence of nuclear initial-state interaction effects that could be expected to become visible as deviations of the ratio of p-Pb and p-p cross sections from one.

High mutation rates explain low population genetic divergence at copy-number-variable loci in Homo sapiens.

Science.gov (United States)

Hu, Xin-Sheng; Yeh, Francis C; Hu, Yang; Deng, Li-Ting; Ennos, Richard A; Chen, Xiaoyang

2017-02-22

Copy-number-variable (CNV) loci differ from single nucleotide polymorphic (SNP) sites in size, mutation rate, and mechanisms of maintenance in natural populations. It is therefore hypothesized that population genetic divergence at CNV loci will differ from that found at SNP sites. Here, we test this hypothesis by analysing 856 CNV loci from the genomes of 1184 healthy individuals from 11 HapMap populations with a wide range of ancestry. The results show that population genetic divergence at the CNV loci is generally more than three times lower than at genome-wide SNP sites. Populations generally exhibit very small genetic divergence (G st  = 0.05 ± 0.049). The smallest divergence is among African populations (G st  = 0.0081 ± 0.0025), with increased divergence among non-African populations (G st  = 0.0217 ± 0.0109) and then among African and non-African populations (G st  = 0.0324 ± 0.0064). Genetic diversity is high in African populations (~0.13), low in Asian populations (~0.11), and intermediate in the remaining 11 populations. Few significant linkage disequilibria (LDs) occur between the genome-wide CNV loci. Patterns of gametic and zygotic LDs indicate the absence of epistasis among CNV loci. Mutation rate is about twice as large as the migration rate in the non-African populations, suggesting that the high mutation rates play dominant roles in producing the low population genetic divergence at CNV loci.

[Discriminatory power of variable number on tandem repeats loci for genotyping Mycobacterium tuberculosis strains in China].

Science.gov (United States)

Chen, H X; Cai, C; Liu, J Y; Zhang, Z G; Yuan, M; Jia, J N; Sun, Z G; Huang, H R; Gao, J M; Li, W M

2017-06-10

Objective: Using the standard genotype method, variable number of tandem repeats (VNTR), we constructed a VNTR database to cover all provinces and proposed a set of optimized VNTR loci combinations for each province, in order to improve the preventive and control programs on tuberculosis, in China. Methods: A total of 15 loci VNTR was used to analyze 4 116 Mycobacterium tuberculosis strains, isolated from national survey of Drug Resistant Tuberculosis, in 2007. Hunter-Gaston Index (HGI) was also used to analyze the discriminatory power of each VNTR site. A set combination of 12-VNTR, 10-VNTR, 8-VNTR and 5-VNTR was respectively constructed for each province, based on 1) epidemic characteristics of M. tuberculosis lineages in China, with high discriminatory power and genetic stability. Results: Through the completed 15 loci VNTR patterns of 3 966 strains under 96.36 % (3 966/4 116) coverage, we found seven high HGI loci (including QUB11b and MIRU26) as well as low stable loci (including QUB26, MIRU16, Mtub21 and QUB11b) in several areas. In all the 31 provinces, we found an optimization VNTR combination as 10-VNTR loci in Inner Mongolia, Chongqing and Heilongjiang, but with 8-VNTR combination shared in other provinces. Conclusions: It is necessary to not only use the VNTR database for tracing the source of infection and cluster of M. tuberculosis in the nation but also using the set of optimized VNTR combinations in monitoring those local epidemics and M. tuberculosis (genetics in local) population.

Compressing the hidden variable space of a qubit

International Nuclear Information System (INIS)

Montina, Alberto

2011-01-01

In previously exhibited hidden variable models of quantum state preparation and measurement, the number of continuous hidden variables describing the actual state of single realizations is never smaller than the quantum state manifold dimension. We introduce a simple model for a qubit whose hidden variable space is one-dimensional, i.e., smaller than the two-dimensional Bloch sphere. The hidden variable probability distributions associated with quantum states satisfy reasonable criteria of regularity. Possible generalizations of this shrinking to an N-dimensional Hilbert space are discussed.

SU-E-T-230: Creating a Large Number of Focused Beams with Variable Patient Head Tilt to Improve Dose Fall-Off for Brain Radiosurgery

Energy Technology Data Exchange (ETDEWEB)

Chiu, J; Ma, L [Department of Radiation Oncology, University of California San Francisco School of Medicine, San Francisco, CA (United States)

2015-06-15

Purpose: To develop a treatment delivery and planning strategy by increasing the number of beams to minimize dose to brain tissue surrounding a target, while maximizing dose coverage to the target. Methods: We analyzed 14 different treatment plans via Leksell PFX and 4C. For standardization, single tumor cases were chosen. Original treatment plans were compared with two optimized plans. The number of beams was increased in treatment plans by varying tilt angles of the patient head, while maintaining original isocenter and the beam positions in the x-, y- and z-axes, collimator size, and beam blocking. PFX optimized plans increased beam numbers with three pre-set tilt angles, 70, 90, 110, and 4C optimized plans increased beam numbers with tilt angles increasing arbitrarily from range of 30 to 150 degrees. Optimized treatment plans were compared dosimetrically with original treatment plans. Results: Comparing total normal tissue isodose volumes between original and optimized plans, the low-level percentage isodose volumes decreased in all plans. Despite the addition of multiple beams up to a factor of 25, beam-on times for 1 tilt angle versus 3 or more tilt angles were comparable (<1 min.). In 64% (9/14) of the studied cases, the volume percentage decrease by >5%, with the highest value reaching 19%. The addition of more tilt angles correlates to a greater decrease in normal brain irradiated volume. Selectivity and coverage for original and optimized plans remained comparable. Conclusion: Adding large number of additional focused beams with variable patient head tilt shows improvement for dose fall-off for brain radiosurgery. The study demonstrates technical feasibility of adding beams to decrease target volume.

SU-E-T-230: Creating a Large Number of Focused Beams with Variable Patient Head Tilt to Improve Dose Fall-Off for Brain Radiosurgery

International Nuclear Information System (INIS)

Chiu, J; Ma, L

2015-01-01

Purpose: To develop a treatment delivery and planning strategy by increasing the number of beams to minimize dose to brain tissue surrounding a target, while maximizing dose coverage to the target. Methods: We analyzed 14 different treatment plans via Leksell PFX and 4C. For standardization, single tumor cases were chosen. Original treatment plans were compared with two optimized plans. The number of beams was increased in treatment plans by varying tilt angles of the patient head, while maintaining original isocenter and the beam positions in the x-, y- and z-axes, collimator size, and beam blocking. PFX optimized plans increased beam numbers with three pre-set tilt angles, 70, 90, 110, and 4C optimized plans increased beam numbers with tilt angles increasing arbitrarily from range of 30 to 150 degrees. Optimized treatment plans were compared dosimetrically with original treatment plans. Results: Comparing total normal tissue isodose volumes between original and optimized plans, the low-level percentage isodose volumes decreased in all plans. Despite the addition of multiple beams up to a factor of 25, beam-on times for 1 tilt angle versus 3 or more tilt angles were comparable (<1 min.). In 64% (9/14) of the studied cases, the volume percentage decrease by >5%, with the highest value reaching 19%. The addition of more tilt angles correlates to a greater decrease in normal brain irradiated volume. Selectivity and coverage for original and optimized plans remained comparable. Conclusion: Adding large number of additional focused beams with variable patient head tilt shows improvement for dose fall-off for brain radiosurgery. The study demonstrates technical feasibility of adding beams to decrease target volume

Fuzzy model for predicting the number of deformed wheels

Directory of Open Access Journals (Sweden)

Ž. Đorđević

2015-10-01

Full Text Available Deformation of the wheels damage cars and rails and affect on vehicle stability and safety. Repair and replacement cause high costs and lack of wagons. Planning of maintenance of wagons can not be done without estimates of the number of wheels that will be replaced due to wear and deformation in a given period of time. There are many influencing factors, the most important are: weather conditions, quality of materials, operating conditions, and distance between the two replacements. The fuzzy logic model uses the collected data as input variables to predict the output variable - number of deformed wheels for a certain type of vehicle in the defined period at a particular section of the railway.

Variable Dimension Trellis-Coded Quantization of Sinusoidal Parameters

DEFF Research Database (Denmark)

Larsen, Morten Holm; Christensen, Mads G.; Jensen, Søren Holdt

2008-01-01

In this letter, we propose joint quantization of the parameters of a set of sinusoids based on the theory of trellis-coded quantization. A particular advantage of this approach is that it allows for joint quantization of a variable number of sinusoids, which is particularly relevant in variable...

Comparison of the capillary and agarose electrophoresis based multiple locus VNTR (variable number of tandem repeats) analysis (MLVA) on Mycobacterium bovis isolates.

Science.gov (United States)

Jenkins, A O; Venter, E H; Hutamo, K; Godfroid, J

2010-09-28

Electrophoretic techniques that can be used for genotyping of bacterial pathogens ranges from manual, low-cost, agarose gels to high-throughput capillary electrophoresis sequencing machines. These two methods are currently employed in the electrophoresis of PCR products used in multiple locus VNTR (variable number of tandem repeats) analysis (MLVA), i.e. the agarose electrophoresis (AE) and the capillary electrophoresis (CE). Some authors have suggested that clusters generated by AE are less reliable than those generated by CE and that the latter is a more sensitive technique than the former when typing Mycobacterium tuberculosis complex (MTC) isolates. Because such a claim could have significant consequences for investigators in this field, a comparison was made on 19 Belgian Mycobacterium bovis strains which had previously been genotyped using CE VNTR analysis. The VNTR profiles of the CE VNTR analysis were compared with those obtained by AE VNTR analysis at 14 VNTR loci. Our results indicated that there were no differences in copy numbers at all loci tested when the copy numbers obtained by the AE VNTR analysis were compared with those obtained by CE VNTR analysis. The use of AE VNTR analysis in mycobacterial genotyping does not alter the sensitivity of the MLVA technique compared with the CE VNTR analysis. The AE VNTR can therefore be regarded as a viable alternative in moderately equipped laboratories that cannot afford the expensive equipment required for CE VNTR analysis and data obtained by AE VNTR analysis can be shared between laboratories which use the CE VNTR method. (c) 2010 Elsevier B.V. All rights reserved.

Biostatistics series module 4: Comparing groups - categorical variables

Directory of Open Access Journals (Sweden)

Avijit Hazra

2016-01-01

Full Text Available Categorical variables are commonly represented as counts or frequencies. For analysis, such data are conveniently arranged in contingency tables. Conventionally, such tables are designated as r × c tables, with r denoting number of rows and c denoting number of columns. The Chi-square (χ2 probability distribution is particularly useful in analyzing categorical variables. A number of tests yield test statistics that fit, at least approximately, a χ2 distribution and hence are referred to as χ2 tests. Examples include Pearson′s χ2 test (or simply the χ2 test, McNemar′s χ2 test, Mantel-Haenszel χ2 test and others. The Pearson′s χ2 test is the most commonly used test for assessing difference in distribution of a categorical variable between two or more independent groups. If the groups are ordered in some manner, the χ2 test for trend should be used. The Fisher′s exact probability test is a test of the independence between two dichotomous categorical variables. It provides a better alternative to the χ2 statistic to assess the difference between two independent proportions when numbers are small, but cannot be applied to a contingency table larger than a two-dimensional one. The McNemar′s χ2 test assesses the difference between paired proportions. It is used when the frequencies in a 2 × 2 table represent paired samples or observations. The Cochran′s Q test is a generalization of the McNemar′s test that compares more than two related proportions. The P value from the χ2 test or its counterparts does not indicate the strength of the difference or association between the categorical variables involved. This information can be obtained from the relative risk or the odds ratio statistic which is measures of dichotomous association obtained from 2 × 2 tables.

Classification and prediction of port variables

Energy Technology Data Exchange (ETDEWEB)

Molina Serrano, B.

2016-07-01

Many variables are included in planning and management of port terminals. They can beeconomic, social, environmental and institutional. Agent needs to know relationshipbetween these variables to modify planning conditions. Use of Bayesian Networks allowsfor classifying, predicting and diagnosing these variables. Bayesian Networks allow forestimating subsequent probability of unknown variables, basing on know variables.In planning level, it means that it is not necessary to know all variables because theirrelationships are known. Agent can know interesting information about how port variablesare connected. It can be interpreted as cause-effect relationship. Bayesian Networks can beused to make optimal decisions by introduction of possible actions and utility of theirresults.In proposed methodology, a data base has been generated with more than 40 port variables.They have been classified in economic, social, environmental and institutional variables, inthe same way that smart port studies in Spanish Port System make. From this data base, anetwork has been generated using a non-cyclic conducted grafo which allows for knowingport variable relationships - parents-children relationships-. Obtained network exhibits thateconomic variables are – in cause-effect terms- cause of rest of variable typologies.Economic variables represent parent role in the most of cases. Moreover, whenenvironmental variables are known, obtained network allows for estimating subsequentprobability of social variables.It has been concluded that Bayesian Networks allow for modeling uncertainty in aprobabilistic way, even when number of variables is high as occurs in planning andmanagement of port terminals. (Author)

Multilocus phylogeny and MALDI-TOF analysis of the plant pathogenic species Alternaria dauci and relatives.

Science.gov (United States)

Brun, Sophie; Madrid, Hugo; Gerrits Van Den Ende, Bert; Andersen, Birgitte; Marinach-Patrice, Carine; Mazier, Dominique; De Hoog, G Sybren

2013-01-01

The genus Alternaria includes numerous phytopathogenic species, many of which are economically relevant. Traditionally, identification has been based on morphology, but is often hampered by the tendency of some strains to become sterile in culture and by the existence of species-complexes of morphologically similar taxa. This study aimed to assess if strains of four closely-related plant pathogens, i.e., accurately Alternaria dauci (ten strains), Alternaria porri (six), Alternaria solani (ten), and Alternaria tomatophila (ten) could be identified using multilocus phylogenetic analysis and Matrix-Assisted Laser Desorption Ionisation Time of Flight (MALDI-TOF) profiling of proteins. Phylogenetic analyses were performed on three loci, i.e., the internal transcribed spacer (ITS) region of rRNA, and the glyceraldehyde-3-phosphate dehydrogenase (gpd) and Alternaria major antigen (Alt a 1) genes. Phylogenetic trees based on ITS sequences did not differentiate strains of A. solani, A. tomatophila, and A. porri, but these three species formed a clade separate from strains of A. dauci. The resolution improved in trees based on gpd and Alt a 1, which distinguished strains of the four species as separate clades. However, none provided significant bootstrap support for all four species, which could only be achieved when results for the three loci were combined. MALDI-TOF-based dendrograms showed three major clusters. The first comprised all A. dauci strains, the second included five strains of A. porri and one of A. solani, and the third included all strains of A. tomatophila, as well as all but one strain of A. solani, and one strain of A. porri. Thus, this study shows the usefulness of MALDI-TOF mass spectrometry as a promising tool for identification of these four species of Alternaria which are closely-related plant pathogens. Copyright © 2012 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Estimation of expected number of accidents and workforce unavailability through Bayesian population variability analysis and Markov-based model

International Nuclear Information System (INIS)

Chagas Moura, Márcio das; Azevedo, Rafael Valença; Droguett, Enrique López; Chaves, Leandro Rego; Lins, Isis Didier

2016-01-01

Occupational accidents pose several negative consequences to employees, employers, environment and people surrounding the locale where the accident takes place. Some types of accidents correspond to low frequency-high consequence (long sick leaves) events, and then classical statistical approaches are ineffective in these cases because the available dataset is generally sparse and contain censored recordings. In this context, we propose a Bayesian population variability method for the estimation of the distributions of the rates of accident and recovery. Given these distributions, a Markov-based model will be used to estimate the uncertainty over the expected number of accidents and the work time loss. Thus, the use of Bayesian analysis along with the Markov approach aims at investigating future trends regarding occupational accidents in a workplace as well as enabling a better management of the labor force and prevention efforts. One application example is presented in order to validate the proposed approach; this case uses available data gathered from a hydropower company in Brazil. - Highlights: • This paper proposes a Bayesian method to estimate rates of accident and recovery. • The model requires simple data likely to be available in the company database. • These results show the proposed model is not too sensitive to the prior estimates.

Clinical effect of fuzzy numbers based on center of gravity ...

African Journals Online (AJOL)

In this study, a model called “fuzzy reasoning model” was proposed for the case when the explanatory variables were crisp and the value of the binary response variable was reported as a number between zero and one. In this regard, the concept of possibilistic odds is also introduced. Then, the methodology and ...

The temporal variability of species densities

International Nuclear Information System (INIS)

Redfearn, A.; Pimm, S.L.

1993-01-01

Ecologists use the term 'stability' to mean to number of different things (Pimm 1984a). One use is to equate stability with low variability in population density over time (henceforth, temporal variability). Temporal variability varies greatly from species to species, so what effects it? There are at least three sets of factors: the variability of extrinsic abiotic factors, food web structure, and the intrinsic features of the species themselves. We can measure temporal variability using at least three statistics: the coefficient of variation of density (CV); the standard deviation of the logarithms of density (SDL); and the variance in the differences between logarithms of density for pairs of consecutive years (called annual variability, hence AV, b y Wolda 1978). There are advantages and disadvantages to each measure (Williamson 1984), though in our experience, the measures are strongly correlated across sets of taxonomically related species. The increasing availability of long-term data sets allows one to calculate these statistics for many species and so to begin to understand the various causes of species differences in temporal variability

Solar Variability and Planetary Climates

CERN Document Server

Calisesi, Y; Gray, L; Langen, J; Lockwood, M

2007-01-01

Variations in solar activity, as revealed by variations in the number of sunspots, have been observed since ancient times. To what extent changes in the solar output may affect planetary climates, though, remains today more than ever a subject of controversy. In 2000, the SSSI volume on Solar Variability and Climate reviewed the to-date understanding of the physics of solar variability and of the associated climate response. The present volume on Solar Variability and Planetary Climates provides an overview of recent advances in this field, with particular focus at the Earth's middle and lower atmosphere. The book structure mirrors that of the ISSI workshop held in Bern in June 2005, the collection of invited workshop contributions and of complementary introductory papers synthesizing the current understanding in key research areas such as middle atmospheric processes, stratosphere-troposphere dynamical coupling, tropospheric aerosols chemistry, solar storm influences, solar variability physics, and terrestri...

Gaia DR2 documentation Chapter 7: Variability

Science.gov (United States)

Eyer, L.; Guy, L.; Distefano, E.; Clementini, G.; Mowlavi, N.; Rimoldini, L.; Roelens, M.; Audard, M.; Holl, B.; Lanzafame, A.; Lebzelter, T.; Lecoeur-Taïbi, I.; Molnár, L.; Ripepi, V.; Sarro, L.; Jevardat de Fombelle, G.; Nienartowicz, K.; De Ridder, J.; Juhász, Á.; Molinaro, R.; Plachy, E.; Regibo, S.

2018-04-01

This chapter of the Gaia DR2 documentation describes the models and methods used on the 22 months of data to produce the Gaia variable star results for Gaia DR2. The variability processing and analysis was based mostly on the calibrated G and integrated BP and RP photometry. The variability analysis approach to the Gaia data has been described in Eyer et al. (2017), and the Gaia DR2 results are presented in Holl et al. (2018). Detailed methods on specific topics will be published in a number of separate articles. Variability behaviour in the colour magnitude diagram is presented in Gaia Collaboration et al. (2018c).

Comparison of a Variable-Number Tandem-Repeat (VNTR) Method for Typing Mycobacterium avium with Mycobacterial Interspersed Repetitive-Unit-VNTR and IS1245 Restriction Fragment Length Polymorphism Typing▿ †

OpenAIRE

Inagaki, Takayuki; Nishimori, Kei; Yagi, Tetsuya; Ichikawa, Kazuya; Moriyama, Makoto; Nakagawa, Taku; Shibayama, Takami; Uchiya, Kei-ichi; Nikai, Toshiaki; Ogawa, Kenji

2009-01-01

Mycobacterium avium complex (MAC) infections are increasing annually in various countries, including Japan, but the route of transmission and pathophysiology of the infection remain unclear. Currently, a variable-number tandem-repeat (VNTR) typing method using the Mycobacterium avium tandem repeat (MATR) loci (MATR-VNTR) is employed in Japan for epidemiological studies using clinical isolates of M. avium. In this study, the usefulness of this MATR-VNTR typing method was compared with that of ...

Violation of Bell's Inequality Using Continuous Variable Measurements

Science.gov (United States)

Thearle, Oliver; Janousek, Jiri; Armstrong, Seiji; Hosseini, Sara; Schünemann Mraz, Melanie; Assad, Syed; Symul, Thomas; James, Matthew R.; Huntington, Elanor; Ralph, Timothy C.; Lam, Ping Koy

2018-01-01

A Bell inequality is a fundamental test to rule out local hidden variable model descriptions of correlations between two physically separated systems. There have been a number of experiments in which a Bell inequality has been violated using discrete-variable systems. We demonstrate a violation of Bell's inequality using continuous variable quadrature measurements. By creating a four-mode entangled state with homodyne detection, we recorded a clear violation with a Bell value of B =2.31 ±0.02 . This opens new possibilities for using continuous variable states for device independent quantum protocols.

Dimensionless numbers in additive manufacturing

Science.gov (United States)

Mukherjee, T.; Manvatkar, V.; De, A.; DebRoy, T.

2017-02-01

The effects of many process variables and alloy properties on the structure and properties of additively manufactured parts are examined using four dimensionless numbers. The structure and properties of components made from 316 Stainless steel, Ti-6Al-4V, and Inconel 718 powders for various dimensionless heat inputs, Peclet numbers, Marangoni numbers, and Fourier numbers are studied. Temperature fields, cooling rates, solidification parameters, lack of fusion defects, and thermal strains are examined using a well-tested three-dimensional transient heat transfer and fluid flow model. The results show that lack of fusion defects in the fabricated parts can be minimized by strengthening interlayer bonding using high values of dimensionless heat input. The formation of harmful intermetallics such as laves phases in Inconel 718 can be suppressed using low heat input that results in a small molten pool, a steep temperature gradient, and a fast cooling rate. Improved interlayer bonding can be achieved at high Marangoni numbers, which results in vigorous circulation of liquid metal, larger pool dimensions, and greater depth of penetration. A high Fourier number ensures rapid cooling, low thermal distortion, and a high ratio of temperature gradient to the solidification growth rate with a greater tendency of plane front solidification.

Multilocus sequence typing and rtxA toxin gene sequencing analysis of Kingella kingae isolates demonstrates genetic diversity and international clones.

Directory of Open Access Journals (Sweden)

Romain Basmaci

Full Text Available BACKGROUND: Kingella kingae, a normal component of the upper respiratory flora, is being increasingly recognized as an important invasive pathogen in young children. Genetic diversity of this species has not been studied. METHODS: We analyzed 103 strains from different countries and clinical origins by a new multilocus sequence-typing (MLST schema. Putative virulence gene rtxA, encoding an RTX toxin, was also sequenced, and experimental virulence of representative strains was assessed in a juvenile-rat model. RESULTS: Thirty-six sequence-types (ST and nine ST-complexes (STc were detected. The main STc 6, 14 and 23 comprised 23, 17 and 20 strains respectively, and were internationally distributed. rtxA sequencing results were mostly congruent with MLST, and showed horizontal transfer events. Of interest, all members of the distantly related ST-6 (n = 22 and ST-5 (n = 4 harboured a 33 bp duplication or triplication in their rtxA sequence, suggesting that this genetic trait arose through selective advantage. The animal model revealed significant differences in virulence among strains of the species. CONCLUSION: MLST analysis reveals international spread of ST-complexes and will help to decipher acquisition and evolution of virulence traits and diversity of pathogenicity among K. kingae strains, for which an experimental animal model is now available.

The evolution and population structure of Lactobacillus fermentum from different naturally fermented products as determined by multilocus sequence typing (MLST).

Science.gov (United States)

Dan, Tong; Liu, Wenjun; Song, Yuqin; Xu, Haiyan; Menghe, Bilige; Zhang, Heping; Sun, Zhihong

2015-05-20

Lactobacillus fermentum is economically important in the production and preservation of fermented foods. A repeatable and discriminative typing method was devised to characterize L. fermentum at the molecular level. The multilocus sequence typing (MLST) scheme developed was based on analysis of the internal sequence of 11 housekeeping gene fragments (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC). MLST analysis of 203 isolates of L. fermentum from Mongolia and seven provinces/ autonomous regions in China identified 57 sequence types (ST), 27 of which were represented by only a single isolate, indicating high genetic diversity. Phylogenetic analyses based on the sequence of the 11 housekeeping gene fragments indicated that the L. fermentum isolates analyzed belonged to two major groups. A standardized index of association (I A (S)) indicated a weak clonal population structure in L. fermentum. Split decomposition analysis indicated that recombination played an important role in generating the genetic diversity observed in L. fermentum. The results from the minimum spanning tree strongly suggested that evolution of L. fermentum STs was not correlated with geography or food-type. The MLST scheme developed will be valuable for further studies on the evolution and population structure of L. fermentum isolates used in food products.

Tularemia in Alaska, 1938 - 2010

Directory of Open Access Journals (Sweden)

Hansen Cristina M

2011-11-01

Full Text Available Abstract Tularemia is a serious, potentially life threatening zoonotic disease. The causative agent, Francisella tularensis, is ubiquitous in the Northern hemisphere, including Alaska, where it was first isolated from a rabbit tick (Haemophysalis leporis-palustris in 1938. Since then, F. tularensis has been isolated from wildlife and humans throughout the state. Serologic surveys have found measurable antibodies with prevalence ranging from F. tularensis isolates from Alaska were analyzed using canonical SNPs and a multi-locus variable-number tandem repeats (VNTR analysis (MLVA system. The results show that both F. t. tularensis and F. t. holarctica are present in Alaska and that subtype A.I, the most virulent type, is responsible for most recently reported human clinical cases in the state.

Multi-locus phylogeny and taxonomy of Exserohilum

NARCIS (Netherlands)

Hernandez Restrepo, Margarita Ines; Madrid, H.; Tan, Y.P.; da Cunha, K.C.; Gene, Josepa; Guarro, Josep; Crous, P.W.

2018-01-01

Exserohilum includes a number of plant pathogenic, saprobic and clinically relevant fungi. Some of these species are of great importance in human activities, but the genus has never been revised in a phylogenetic framework. In this study, we revise Exserohilum based on available ex-type cultures

Particular Candida albicans strains in the digestive tract of dyspeptic patients, identified by multilocus sequence typing.

Directory of Open Access Journals (Sweden)

Yan-Bing Gong

Full Text Available BACKGROUND: Candida albicans is a human commensal that is also responsible for chronic gastritis and peptic ulcerous disease. Little is known about the genetic profiles of the C. albicans strains in the digestive tract of dyspeptic patients. The aim of this study was to evaluate the prevalence, diversity, and genetic profiles among C. albicans isolates recovered from natural colonization of the digestive tract in the dyspeptic patients. METHODS AND FINDINGS: Oral swab samples (n = 111 and gastric mucosa samples (n = 102 were obtained from a group of patients who presented dyspeptic symptoms or ulcer complaints. Oral swab samples (n = 162 were also obtained from healthy volunteers. C. albicans isolates were characterized and analyzed by multilocus sequence typing. The prevalence of Candida spp. in the oral samples was not significantly different between the dyspeptic group and the healthy group (36.0%, 40/111 vs. 29.6%, 48/162; P > 0.05. However, there were significant differences between the groups in the distribution of species isolated and the genotypes of the C. albicans isolates. C. albicans was isolated from 97.8% of the Candida-positive subjects in the dyspeptic group, but from only 56.3% in the healthy group (P < 0.001. DST1593 was the dominant C. albicans genotype from the digestive tract of the dyspeptic group (60%, 27/45, but not the healthy group (14.8%, 4/27 (P < 0.001. CONCLUSIONS: Our data suggest a possible link between particular C. albicans strain genotypes and the host microenvironment. Positivity for particular C. albicans genotypes could signify susceptibility to dyspepsia.

An Extended Multilocus Sequence Typing (MLST Scheme for Rapid Direct Typing of Leptospira from Clinical Samples.

Directory of Open Access Journals (Sweden)

Sabrina Weiss

2016-09-01

Full Text Available Rapid typing of Leptospira is currently impaired by requiring time consuming culture of leptospires. The objective of this study was to develop an assay that provides multilocus sequence typing (MLST data direct from patient specimens while minimising costs for subsequent sequencing.An existing PCR based MLST scheme was modified by designing nested primers including anchors for facilitated subsequent sequencing. The assay was applied to various specimen types from patients diagnosed with leptospirosis between 2014 and 2015 in the United Kingdom (UK and the Lao Peoples Democratic Republic (Lao PDR. Of 44 clinical samples (23 serum, 6 whole blood, 3 buffy coat, 12 urine PCR positive for pathogenic Leptospira spp. at least one allele was amplified in 22 samples (50% and used for phylogenetic inference. Full allelic profiles were obtained from ten specimens, representing all sample types (23%. No nonspecific amplicons were observed in any of the samples. Of twelve PCR positive urine specimens three gave full allelic profiles (25% and two a partial profile. Phylogenetic analysis allowed for species assignment. The predominant species detected was L. interrogans (10/14 and 7/8 from UK and Lao PDR, respectively. All other species were detected in samples from only one country (Lao PDR: L. borgpetersenii [1/8]; UK: L. kirschneri [1/14], L. santarosai [1/14], L. weilii [2/14].Typing information of pathogenic Leptospira spp. was obtained directly from a variety of clinical samples using a modified MLST assay. This assay negates the need for time-consuming culture of Leptospira prior to typing and will be of use both in surveillance, as single alleles enable species determination, and outbreaks for the rapid identification of clusters.

DETERMINING THE PREFERENCE OF GSM OPERATORS IN TURKEY WITH FUZZY TOPSIS AFTER MOBILE NUMBER PORTABILITY SYSTEM APPLICATION

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Nihal ERGİNEL

2010-12-01

Full Text Available Mobile number portability systems is a system that can allow portability of GSM (Global System for Mobile Communications number from another operator without changing GSM number. There are several criteria to select the GSM operators by customer after this system is legal in Turkey. The main purpose of this study is to determine the market sharing in the future of GSM operators by expressing the weighting grades of selection criteria and the relationship between criteria and alternatives that include uncertainty as fuzzy triangular numbers. In this study, the selection criteria of GSM operators are defined form literature and views of customer and weighted with linguistic variables by working group. Avea, Turkcell and Vodafone that active in Turkey are graded with linguistic variables to each criterion. Analyzing linguistic variables as qualitative variables and using graded linguistic variables in a specified interval are required fuzzy multi-criteria decision making methods. Expected market sharing of GSM operators is determined by using fuzzy TOPSIS method.

Integration of Multilocus Genetic Risk into the Default Mode Network Longitudinal Trajectory during the Alzheimer's Disease Process.

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Su, Fan; Shu, Hao; Ye, Qing; Xie, Chunming; Yuan, Baoyu; Zhang, Zhijun; Bai, Feng

2017-01-01

The aim of the study was to investigate the cognitive significance of the changes in default mode network (DMN) during the process of Alzheimer's disease (AD) and the genetic basis that drives the alteration. Eighty-seven subjects with mild cognitive impairment (MCI) and 131 healthy controls (HC) were employed at baseline, and they had the genetic risk scores (GRS) based on the GWAS-validated AD-related top loci. Eleven MCIs who converted to AD (c-MCIs), 32 subjects who remained stable (nc-MCIs), and 56 HCs participated in the follow-up analyses after an average of 35 months. Decreased functional connectivity (FC) within temporal cortex was identified for MCIs at baseline, which was partially determined by the GRS; moreover, compensations may occur within the frontal-parietal brain to maintain relatively intact cognition. During the follow-ups, c-MCIs exhibited more FC declines within the prefrontal-parietal lobes and parahippocampal gyrus/hippocampus than the HCs and nc-MCIs. The GRS did not significantly vary among the three groups, whereas associations were identified at risky alleles and FC declines in all AD spectra. Interestingly, the influence of APOEɛ4 varied as the disease progressed; APOEɛ4 was associated with longitudinal FC decreases only for HCs in the single variance-based analyses and deteriorated DMN integration in nc-MCIs by combining the effects of other loci. However, the GRS without APOEɛ4 predicted FC decline for converters. It is suggested that the integration of multilocus genetic risk predicted the longitudinal trajectory of DMN and may be used as a clinical strategy to track AD progression.

New variables for classical and quantum gravity

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Ashtekar, Abhay

1986-01-01

A Hamiltonian formulation of general relativity based on certain spinorial variables is introduced. These variables simplify the constraints of general relativity considerably and enable one to imbed the constraint surface in the phase space of Einstein's theory into that of Yang-Mills theory. The imbedding suggests new ways of attacking a number of problems in both classical and quantum gravity. Some illustrative applications are discussed.

Typing Candida albicans oral isolates from healthy Brazilian schoolchildren using multilocus enzyme electrophoresis reveals two highly polymorphic taxa

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Marcelo Fabiano Gomes Boriollo

2011-09-01

Full Text Available The genetic diversity of C. albicans oral isolates from 75 healthy schoolchildren from eight schools located in different geographic areas of Piracicaba city, São Paulo state, Brazil, was established using isoenzymes marker (Multilocus Enzyme Electrophoresis - MLEE and cluster analysis. Patterns of monoclonal and polyclonal oral colonization by C. albicans within and between groups of schoolchildren were identified. However, significant divergence between the observed and the expected genotypic frequencies (Hardy-Weinberg equilibrium test was not detected in the geographically adjacent groups, suggesting the hypothesis that populations of healthy schoolchildren do not correspond to the selection factor (differential survival of strains. Two highly polymorphic and distantly genetically related taxa (A and B were identified within the total population of yeasts, each contained subgroups (A1, A2, A3, A4, B1 and B2 and clusters of moderately related strains (from I to X, suggesting the existence of strains restricted or not to certain groups of geographically limited, healthy students. However, the coexistence of identical strains in healthy schoolchildren from the same school (geographically related reinforces the hypothesis of oral transmission, where the sources of propagation could be explored. Furthermore, this could also be used in current and retrospective analyses of C. albicans isolated from immunocompetent and immunocompromised people, in order to detect commensal or potentially pathogenic yeast groups, predominantly in candidiasis, and in the development of strategies to prevent transmission or human propagation.

Typing Candida albicans oral isolates from healthy brazilian schoolchildren using multilocus enzyme electrophoresis reveals two highly polymorphic taxa

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Boriollo, Marcelo Fabiano Gomes; Spolidorio, Denise Madalena Palomari; Barros, Letizia Monteiro; Bassi, Rodrigo Carlos; Garcia, José Antonio Dias; Costa, Ana Maria Duarte Dias; Rosa, Edvaldo Antonio Ribeiro; Höfling, José Francisco

2011-01-01

The genetic diversity of C. albicans oral isolates from 75 healthy schoolchildren from eight schools located in different geographic areas of Piracicaba city, São Paulo state, Brazil, was established using isoenzymes marker (Multilocus Enzyme Electrophoresis – MLEE) and cluster analysis. Patterns of monoclonal and polyclonal oral colonization by C. albicans within and between groups of schoolchildren were identified. However, significant divergence between the observed and the expected genotypic frequencies (Hardy-Weinberg equilibrium test) was not detected in the geographically adjacent groups, suggesting the hypothesis that populations of healthy schoolchildren do not correspond to the selection factor (differential survival) of strains. Two highly polymorphic and distantly genetically related taxa (A and B) were identified within the total population of yeasts, each contained subgroups (A1, A2, A3, A4, B1 and B2) and clusters of moderately related strains (from I to X), suggesting the existence of strains restricted or not to certain groups of geographically limited, healthy students. However, the coexistence of identical strains in healthy schoolchildren from the same school (geographically related) reinforces the hypothesis of oral transmission, where the sources of propagation could be explored. Furthermore, this could also be used in current and retrospective analyses of C. albicans isolated from immunocompetent and immunocompromised people, in order to detect commensal or potentially pathogenic yeast groups, predominantly in candidiasis, and in the development of strategies to prevent transmission or human propagation. PMID:24031720

KEELE, Minimization of Nonlinear Function with Linear Constraints, Variable Metric Method

International Nuclear Information System (INIS)

Westley, G.W.

1975-01-01

1 - Description of problem or function: KEELE is a linearly constrained nonlinear programming algorithm for locating a local minimum of a function of n variables with the variables subject to linear equality and/or inequality constraints. 2 - Method of solution: A variable metric procedure is used where the direction of search at each iteration is obtained by multiplying the negative of the gradient vector by a positive definite matrix which approximates the inverse of the matrix of second partial derivatives associated with the function. 3 - Restrictions on the complexity of the problem: Array dimensions limit the number of variables to 20 and the number of constraints to 50. These can be changed by the user

Charged Higgs production from polarized top-quark decay in the 2HDM considering the general-mass variable-flavor-number scheme

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Abbaspour, S.; Mohammad Moosavi Nejad, S.

2018-05-01

Charged Higgs bosons are predicted by some non-minimal Higgs scenarios, such as models containing Higgs triplets and two-Higgs-doublet models, so that the experimental observation of these bosons would indicate physics beyond the Standard Model. In the present work, we introduce a channel to indirect search for the charged Higgses through the hadronic decay of polarized top quarks where a top quark decays into a charged Higgs H+ and a bottom-flavored meson B via the hadronization process of the produced bottom quark, t (↑) →H+ + b (→ B + jet). To obtain the energy spectrum of produced B-mesons we present, for the first time, an analytical expression for the O (αs) corrections to the differential decay width of the process t →H+ b in presence of a massive b-quark in the General-Mass Variable-Flavor-Number (GM-VFN) scheme. We find that the most reliable predictions for the B-hadron energy spectrum are made in the GM-VFN scheme, specifically, when the Type-II 2HDM scenario is concerned.

Variability of rainfall over small areas

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Runnels, R. C.

1983-01-01

A preliminary investigation was made to determine estimates of the number of raingauges needed in order to measure the variability of rainfall in time and space over small areas (approximately 40 sq miles). The literature on rainfall variability was examined and the types of empirical relationships used to relate rainfall variations to meteorological and catchment-area characteristics were considered. Relations between the coefficient of variation and areal-mean rainfall and area have been used by several investigators. These parameters seemed reasonable ones to use in any future study of rainfall variations. From a knowledge of an appropriate coefficient of variation (determined by the above-mentioned relations) the number rain gauges needed for the precise determination of areal-mean rainfall may be calculated by statistical estimation theory. The number gauges needed to measure the coefficient of variation over a 40 sq miles area, with varying degrees of error, was found to range from 264 (10% error, mean precipitation = 0.1 in) to about 2 (100% error, mean precipitation = 0.1 in).

On the explaining-away phenomenon in multivariate latent variable models.

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van Rijn, Peter; Rijmen, Frank

2015-02-01

Many probabilistic models for psychological and educational measurements contain latent variables. Well-known examples are factor analysis, item response theory, and latent class model families. We discuss what is referred to as the 'explaining-away' phenomenon in the context of such latent variable models. This phenomenon can occur when multiple latent variables are related to the same observed variable, and can elicit seemingly counterintuitive conditional dependencies between latent variables given observed variables. We illustrate the implications of explaining away for a number of well-known latent variable models by using both theoretical and real data examples. © 2014 The British Psychological Society.

Diversity of Salmonella enterica serovar Typhi strains collected from india using variable number tandem repeat (VNTR)-PCR analysis.

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Sankar, Sathish; Kuppanan, Suresh; Nandagopal, Balaji; Sridharan, Gopalan

2013-08-01

Typhoid fever is endemic in India, and a seasonal increase of cases is observed annually. In spite of effective therapies and the availability of vaccines, morbidity is widespread owing to the circulation of multiple genetic variants, frequent migration of asymptomatic carriers, unhygienic food practices and the emergence of multidrug resistance and thus continues to be a major public health problem in developing countries, particularly in India. Classical methods of strain typing such as pulsed-field gel electrophoresis, ribotyping, random amplification of polymorphic DNA and amplified fragment length polymorphism are either laborious and technically complicated or less discriminatory. We investigated the molecular diversity of Indian strains of Salmonella enterica serovar Typhi (S. Typhi) isolated from humans from different parts of India to establish the molecular epidemiology of the organism using the variable number tandem repeat (VNTR)-PCR analysis. The electrophoretic band pattern was analysed using the GelCompar II software program. Of the 94 strains tested for three VNTRs loci, 75 VNTR genotypes were obtained. Of the three VNTRs tested in this study, VNTR1 was amplified in all the strains except one and found to be predominant. VNTR2 was amplified only in 57 strains with a Simpson diversity index of 0.93 indicating the high variability of this region within the strains. VNTR3 was amplified in 90 strains. The discriminatory power of this typing tool has been greatly enhanced by this VNTR2 region as the other two regions could not discriminate strains significantly. In our study, about 55 % of the strains amplified all three VNTR regions and 39 % of the strains lacked the VNTR2 region. Among the three VNTR regions tested, the majority of the strains produced similar banding pattern for any two regions grouped into a cluster. The strains grouped as a genotype were from the same geographical location. Strains collected from each geographical region were also

From grammatical number to exact numbers: early meanings of 'one', 'two', and 'three' in English, Russian, and Japanese.

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Sarnecka, Barbara W; Kamenskaya, Valentina G; Yamana, Yuko; Ogura, Tamiko; Yudovina, Yulia B

2007-09-01

This study examined whether singular/plural marking in a language helps children learn the meanings of the words 'one,' 'two,' and 'three.' First, CHILDES data in English, Russian (which marks singular/plural), and Japanese (which does not) were compared for frequency, variability, and contexts of number-word use. Then young children in the USA, Russia, and Japan were tested on Counting and Give-N tasks. More English and Russian learners knew the meaning of each number word than Japanese learners, regardless of whether singular/plural cues appeared in the task itself (e.g., "Give two apples" vs. "Give two"). These results suggest that the learning of "one," "two" and "three" is supported by the conceptual framework of grammatical number, rather than that of integers.

Variable Selection for Regression Models of Percentile Flows

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Fouad, G.

2017-12-01

Percentile flows describe the flow magnitude equaled or exceeded for a given percent of time, and are widely used in water resource management. However, these statistics are normally unavailable since most basins are ungauged. Percentile flows of ungauged basins are often predicted using regression models based on readily observable basin characteristics, such as mean elevation. The number of these independent variables is too large to evaluate all possible models. A subset of models is typically evaluated using automatic procedures, like stepwise regression. This ignores a large variety of methods from the field of feature (variable) selection and physical understanding of percentile flows. A study of 918 basins in the United States was conducted to compare an automatic regression procedure to the following variable selection methods: (1) principal component analysis, (2) correlation analysis, (3) random forests, (4) genetic programming, (5) Bayesian networks, and (6) physical understanding. The automatic regression procedure only performed better than principal component analysis. Poor performance of the regression procedure was due to a commonly used filter for multicollinearity, which rejected the strongest models because they had cross-correlated independent variables. Multicollinearity did not decrease model performance in validation because of a representative set of calibration basins. Variable selection methods based strictly on predictive power (numbers 2-5 from above) performed similarly, likely indicating a limit to the predictive power of the variables. Similar performance was also reached using variables selected based on physical understanding, a finding that substantiates recent calls to emphasize physical understanding in modeling for predictions in ungauged basins. The strongest variables highlighted the importance of geology and land cover, whereas widely used topographic variables were the weakest predictors. Variables suffered from a high

Multiple Locus Variable-Number Tandem-Repeat and Single-Nucleotide Polymorphism-Based Brucella Typing Reveals Multiple Lineages in Brucella melitensis Currently Endemic in China

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Mingjun Sun

2017-12-01

Full Text Available Brucellosis is a worldwide zoonotic disease caused by Brucella spp. In China, brucellosis is recognized as a reemerging disease mainly caused by Brucella melitensis specie. To better understand the currently endemic B. melitensis strains in China, three Brucella genotyping methods were applied to 110 B. melitensis strains obtained in past several years. By MLVA genotyping, five MLVA-8 genotypes were identified, among which genotypes 42 (1-5-3-13-2-2-3-2 was recognized as the predominant genotype, while genotype 63 (1-5-3-13-2-3-3-2 and a novel genotype of 1-5-3-13-2-4-3-2 were second frequently observed. MLVA-16 discerned a total of 57 MLVA-16 genotypes among these Brucella strains, with 41 genotypes being firstly detected and the other 16 genotypes being previously reported. By BruMLSA21 typing, six sequence types (STs were identified, among them ST8 is the most frequently seen in China while the other five STs were firstly detected and designated as ST137, ST138, ST139, ST140, and ST141 by international multilocus sequence typing database. Whole-genome sequence (WGS-single-nucleotide polymorphism (SNP-based typing and phylogenetic analysis resolved Chinese B. melitensis strains into five clusters, reflecting the existence of multiple lineages among these Chinese B. melitensis strains. In phylogeny, Chinese lineages are more closely related to strains collected from East Mediterranean and Middle East countries, such as Turkey, Kuwait, and Iraq. In the next few years, MLVA typing will certainly remain an important epidemiological tool for Brucella infection analysis, as it displays a high discriminatory ability and achieves result largely in agreement with WGS-SNP-based typing. However, WGS-SNP-based typing is found to be the most powerful and reliable method in discerning Brucella strains and will be popular used in the future.

Electric Motors Maintenance Planning From Its Operating Variables

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Rodrigues, Francisco; Fonseca, Inácio; Farinha, José Torres; Ferreira, Luís; Galar, Diego

2017-09-01

The maintenance planning corresponds to an approach that seeks to maximize the availability of equipment and, consequently, increase the levels of competitiveness of companies by increasing production times. This paper presents a maintenance planning based on operating variables (number of hours worked, duty cycles, number of revolutions) to maximizing the availability of operation of electrical motors. The reading of the operating variables and its sampling is done based on predetermined sampling cycles and subsequently is made the data analysis through time series algorithms aiming to launch work orders before reaching the variables limit values. This approach is supported by tools and technologies such as logical applications that enable a graphical user interface for access to relevant information about their Physical Asset HMI (Human Machine Interface), including the control and supervision by acquisition through SCADA (Supervisory Control And data acquisition) data, also including the communication protocols among different logical applications.

Molecular epidemiology of human oral Chagas disease outbreaks in Colombia.

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Juan David Ramírez

Full Text Available BACKGROUND: Trypanosoma cruzi, the causative agent of Chagas disease, displays significant genetic variability revealed by six Discrete Typing Units (TcI-TcVI. In this pathology, oral transmission represents an emerging epidemiological scenario where different outbreaks associated to food/beverages consumption have been reported in Argentina, Bolivia, Brazil, Ecuador and Venezuela. In Colombia, six human oral outbreaks have been reported corroborating the importance of this transmission route. Molecular epidemiology of oral outbreaks is barely known observing the incrimination of TcI, TcII, TcIV and TcV genotypes. METHODOLOGY AND PRINCIPAL FINDINGS: High-throughput molecular characterization was conducted performing MLMT (Multilocus Microsatellite Typing and mtMLST (mitochondrial Multilocus Sequence Typing strategies on 50 clones from ten isolates. Results allowed observing the occurrence of TcI, TcIV and mixed infection of distinct TcI genotypes. Thus, a majority of specific mitochondrial haplotypes and allelic multilocus genotypes associated to the sylvatic cycle of transmission were detected in the dataset with the foreseen presence of mitochondrial haplotypes and allelic multilocus genotypes associated to the domestic cycle of transmission. CONCLUSIONS: These findings suggest the incrimination of sylvatic genotypes in the oral outbreaks occurred in Colombia. We observed patterns of super-infection and/or co-infection with a tailored association with the severe forms of myocarditis in the acute phase of the disease. The transmission dynamics of this infection route based on molecular epidemiology evidence was unraveled and the clinical and biological implications are discussed.

Visualization of Variation and Variability

NARCIS (Netherlands)

Busking, S.

2014-01-01

As datasets grow in size and complexity, the importance of comparison as a tool for analysis is growing. We define comparison as the act of analyzing variation or variability based on two or more specific instances of the data. This thesis explores a number of cases spread across the range of

THE CLASSIFICATION OF KEPLER B-STAR VARIABLES

International Nuclear Information System (INIS)

McNamara, Bernard J.; Jackiewicz, Jason; McKeever, Jean

2012-01-01

The light curves of 252 B-star candidates in the Kepler database are analyzed in a similar fashion to that done by Balona et al. to further characterize B-star variability, increase the sample of variable B stars for future study, and to identify stars whose power spectra include particularly interesting features such as frequency groupings. Stars are classified as either constant light emitters, β Cep stars, slowly pulsating B stars (SPBs), hybrid pulsators, binaries or stars whose light curves are dominated by rotation (Bin/Rot), hot subdwarfs, or white dwarfs. One-hundred stars in our sample were found to be either light constants or to be variable at a level of less than 0.02 mmag. We increase the number of candidate B-star variables found in the Kepler database by Balona et al. in the following fashion: β Cep stars from 0 to 10, SPBs from eight to 54, hybrid pulsators from seven to 21, and Bin/Rot stars from 23 to 82. For comparison purposes, approximately 51 SPBs and six hybrids had been known prior to 2007. The number of β Cep stars known prior to 2004 was 93. A secondary result of this study is the identification of an additional 11 pulsating white dwarf candidates, four of which possess frequency groupings.

An overview of various typing methods for clinical epidemiology of the emerging pathogen Stenotrophomonas maltophilia.

Science.gov (United States)

Gherardi, Giovanni; Creti, Roberta; Pompilio, Arianna; Di Bonaventura, Giovanni

2015-03-01

Typing of bacterial isolates has been used for decades to study local outbreaks as well as in national and international surveillances for monitoring newly emerging resistant clones. Despite being recognized as a nosocomial pathogen, the precise modes of transmission of Stenotrophomonas maltophilia in health care settings are unknown. Due to the high genetic diversity observed among S. maltophilia clinical isolates, the typing results might be better interpreted if also environmental strains were included. This could help to identify preventative measures to be designed and implemented for decreasing the possibility of outbreaks and nosocomial infections. In this review, we attempt to provide an overview on the most common typing methods used for clinical epidemiology of S. maltophilia strains, such as PCR-based fingerprinting analyses, pulsed-field gel electrophoresis, multilocus variable number tandem repeat analysis, and multilocus sequence type. Application of the proteomic-based mass spectrometry by matrix-assisted laser desorption ionization-time of flight is also described. Improvements of typing methods already in use have to be achieved to facilitate S. maltophilia infection control at any level. In the near future, when novel Web-based platforms for rapid data processing and analysis will be available, whole genome sequencing technologies will likely become a highly powerful tool for outbreak investigations and surveillance studies in routine clinical practices. Copyright © 2015 Elsevier Inc. All rights reserved.

Bias in random forest variable importance measures: Illustrations, sources and a solution

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Hothorn Torsten

2007-01-01

Full Text Available Abstract Background Variable importance measures for random forests have been receiving increased attention as a means of variable selection in many classification tasks in bioinformatics and related scientific fields, for instance to select a subset of genetic markers relevant for the prediction of a certain disease. We show that random forest variable importance measures are a sensible means for variable selection in many applications, but are not reliable in situations where potential predictor variables vary in their scale of measurement or their number of categories. This is particularly important in genomics and computational biology, where predictors often include variables of different types, for example when predictors include both sequence data and continuous variables such as folding energy, or when amino acid sequence data show different numbers of categories. Results Simulation studies are presented illustrating that, when random forest variable importance measures are used with data of varying types, the results are misleading because suboptimal predictor variables may be artificially preferred in variable selection. The two mechanisms underlying this deficiency are biased variable selection in the individual classification trees used to build the random forest on one hand, and effects induced by bootstrap sampling with replacement on the other hand. Conclusion We propose to employ an alternative implementation of random forests, that provides unbiased variable selection in the individual classification trees. When this method is applied using subsampling without replacement, the resulting variable importance measures can be used reliably for variable selection even in situations where the potential predictor variables vary in their scale of measurement or their number of categories. The usage of both random forest algorithms and their variable importance measures in the R system for statistical computing is illustrated and

Using a topographic index to distribute variable source area runoff predicted with the SCS curve-number equation

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Lyon, Steve W.; Walter, M. Todd; Gérard-Marchant, Pierre; Steenhuis, Tammo S.

2004-10-01

Because the traditional Soil Conservation Service curve-number (SCS-CN) approach continues to be used ubiquitously in water quality models, new application methods are needed that are consistent with variable source area (VSA) hydrological processes in the landscape. We developed and tested a distributed approach for applying the traditional SCS-CN equation to watersheds where VSA hydrology is a dominant process. Predicting the location of source areas is important for watershed planning because restricting potentially polluting activities from runoff source areas is fundamental to controlling non-point-source pollution. The method presented here used the traditional SCS-CN approach to predict runoff volume and spatial extent of saturated areas and a topographic index, like that used in TOPMODEL, to distribute runoff source areas through watersheds. The resulting distributed CN-VSA method was applied to two subwatersheds of the Delaware basin in the Catskill Mountains region of New York State and one watershed in south-eastern Australia to produce runoff-probability maps. Observed saturated area locations in the watersheds agreed with the distributed CN-VSA method. Results showed good agreement with those obtained from the previously validated soil moisture routing (SMR) model. When compared with the traditional SCS-CN method, the distributed CN-VSA method predicted a similar total volume of runoff, but vastly different locations of runoff generation. Thus, the distributed CN-VSA approach provides a physically based method that is simple enough to be incorporated into water quality models, and other tools that currently use the traditional SCS-CN method, while still adhering to the principles of VSA hydrology.

Complex Variables throughout the Curriculum

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D'Angelo, John P.

2017-01-01

We offer many specific detailed examples, several of which are new, that instructors can use (in lecture or as student projects) to revitalize the role of complex variables throughout the curriculum. We conclude with three primary recommendations: revise the syllabus of Calculus II to allow early introductions of complex numbers and linear…

Bernoulli numbers and polynomials from a more general point of view

International Nuclear Information System (INIS)

Dattoli, G.; Cesarano, C.; Lorenzutta, S.

2000-01-01

In this work it is applied the method of generating function, to introduce new forms of Bernoulli numbers and polynomials, which are exploited to derive further classes of partial sums involving generalized many index many variable polynomials. Analogous considerations are developed for the Euler numbers and polynomials [it

The induction on a continuous variable

International Nuclear Information System (INIS)

Zhang Jingzhong.

1989-06-01

Mathematical induction is a useful tool. But it could be used to prove only the proposition with form P(n) for the natural number n. Could the natural number n be replaced by a continuous variable x? Yes, and then we have the continuous induction. The continuous induction is very easy to grasp by the students who have learned mathematical induction. And it can be used to prove many basic propositions in the elementary calculus. (author)

What is specific and what is shared between numbers and words?

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Júlia Beatriz Lopes-Silva

2016-02-01

Full Text Available Reading and spelling performance have a significant correlation with number transcoding, which is the ability to establish a relationship between the verbal and Arabic representations of numbers, when a conversion of numerical symbols from one notation to the other is necessary. The aim of the present study is to reveal shared and specific mechanisms involved in reading and writing words and Arabic numerals in Brazilian school-aged children. One hundred and seventy two children from 2nd to 4th grades were evaluated. All of them had normal intelligence. We conducted a series of hierarchical regression models using scores on word spelling and reading single words and Arabic numerals, as dependent variables. As predictor variables we investigated intelligence, the phonological and visuospatial components of working memory and phonemic awareness. All of the writing and reading tasks (single word spelling and reading as well as number reading and number writing were significantly correlated to each other. In the regressions models, phonological working memory was specifically associated to word reading. Phonemic awareness was the only cognitive variables that systematically predicted all of the school skills investigated, both numerical and word tasks. This suggests that phonemic awareness is a modular cognitive ability shared by several school tasks and might be an important factor associated to the comorbidity between dyslexia and dyscalculia.

Iterative Strain-Gage Balance Calibration Data Analysis for Extended Independent Variable Sets

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Ulbrich, Norbert Manfred

2011-01-01

A new method was developed that makes it possible to use an extended set of independent calibration variables for an iterative analysis of wind tunnel strain gage balance calibration data. The new method permits the application of the iterative analysis method whenever the total number of balance loads and other independent calibration variables is greater than the total number of measured strain gage outputs. Iteration equations used by the iterative analysis method have the limitation that the number of independent and dependent variables must match. The new method circumvents this limitation. It simply adds a missing dependent variable to the original data set by using an additional independent variable also as an additional dependent variable. Then, the desired solution of the regression analysis problem can be obtained that fits each gage output as a function of both the original and additional independent calibration variables. The final regression coefficients can be converted to data reduction matrix coefficients because the missing dependent variables were added to the data set without changing the regression analysis result for each gage output. Therefore, the new method still supports the application of the two load iteration equation choices that the iterative method traditionally uses for the prediction of balance loads during a wind tunnel test. An example is discussed in the paper that illustrates the application of the new method to a realistic simulation of temperature dependent calibration data set of a six component balance.

Multilocus Sequence Typing of Pathogenic Candida albicans Isolates Collected from a Teaching Hospital in Shanghai, China: A Molecular Epidemiology Study

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Li, Li; Zhang, Qiangqiang; Zhu, Junhao; Gao, Qian; Chen, Min; Zhu, Min

2015-01-01

Molecular typing of Candida albicans is important for studying the population structure and epidemiology of this opportunistic yeast, such as population dynamics, nosocomial infections, multiple infections and microevolution. The genetic diversity of C. albicans has been rarely studied in China. In the present study, multilocus sequence typing (MLST) was used to characterize the genetic diversity and population structure of 62 C. albicans isolates collected from 40 patients from Huashan Hospital in Shanghai, China. A total of 50 diploid sequence types (DSTs) were identified in the 62 C. albicans isolates, with 41 newly identified DSTs. Based on cluster analysis, the 62 isolates were classified into nine existing clades and two new clades (namely clades New 1 and New 2). The majority of the isolates were clustered into three clades, clade 6 (37.5%), clade 1 (15.0%) and clade 17 (15.0%). Isolates of clade New 2 were specifically identified in East Asia. We identified three cases of potential nosocomial transmission based on association analysis between patients’ clinical data and the genotypes of corresponding isolates. Finally, by analyzing the genotypes of serial isolates we further demonstrated that the microevolution of C. albicans was due to loss of heterozygosity. Our study represents the first molecular typing of C. albicans in eastern China, and we confirmed that MLST is a useful tool for studying the epidemiology and evolution of C. albicans. PMID:25919124

A novel multi-locus sequence typing (MLST) protocol for Leuconostoc lactis isolates from traditional dairy products in China and Mongolia.

Science.gov (United States)

Dan, Tong; Liu, Wenjun; Sun, Zhihong; Lv, Qiang; Xu, Haiyan; Song, Yuqin; Zhang, Heping

2014-06-09

Economically, Leuconostoc lactis is one of the most important species in the genus Leuconostoc. It plays an important role in the food industry including the production of dextrans and bacteriocins. Currently, traditional molecular typing approaches for characterisation of this species at the isolate level are either unavailable or are not sufficiently reliable for practical use. Multilocus sequence typing (MLST) is a robust and reliable method for characterising bacterial and fungal species at the molecular level. In this study, a novel MLST protocol was developed for 50 L. lactis isolates from Mongolia and China. Sequences from eight targeted genes (groEL, carB, recA, pheS, murC, pyrG, rpoB and uvrC) were obtained. Sequence analysis indicated 20 different sequence types (STs), with 13 of them being represented by a single isolate. Phylogenetic analysis based on the sequences of eight MLST loci indicated that the isolates belonged to two major groups, A (34 isolates) and B (16 isolates). Linkage disequilibrium analyses indicated that recombination occurred at a low frequency in L. lactis, indicating a clonal population structure. Split-decomposition analysis indicated that intraspecies recombination played a role in generating genotypic diversity amongst isolates. Our results indicated that MLST is a valuable tool for typing L. lactis isolates that can be used for further monitoring of evolutionary changes and population genetics.

Reduction of the Random Variables of the Turbulent Wind Field

DEFF Research Database (Denmark)

Sichani, Mahdi Teimouri; Nielsen, Søren R.K.

2012-01-01

.e. Importance Sampling (IS) or Subset Simulation (SS), will be deteriorated on problems with many random variables. The problem with PDEM is that a multidimensional integral has to be carried out over the space defined by the random variables of the system. The numerical procedure requires discretization......Applicability of the Probability Density Evolution Method (PDEM) for realizing evolution of the probability density for the wind turbines has rather strict bounds on the basic number of the random variables involved in the model. The efficiency of most of the Advanced Monte Carlo (AMC) methods, i...... of the integral domain; this becomes increasingly difficult as the dimensions of the integral domain increase. On the other hand efficiency of the AMC methods is closely dependent on the design points of the problem. Presence of many random variables may increase the number of the design points, hence affects...

Statistical identification of effective input variables

International Nuclear Information System (INIS)

Vaurio, J.K.

1982-09-01

A statistical sensitivity analysis procedure has been developed for ranking the input data of large computer codes in the order of sensitivity-importance. The method is economical for large codes with many input variables, since it uses a relatively small number of computer runs. No prior judgemental elimination of input variables is needed. The sceening method is based on stagewise correlation and extensive regression analysis of output values calculated with selected input value combinations. The regression process deals with multivariate nonlinear functions, and statistical tests are also available for identifying input variables that contribute to threshold effects, i.e., discontinuities in the output variables. A computer code SCREEN has been developed for implementing the screening techniques. The efficiency has been demonstrated by several examples and applied to a fast reactor safety analysis code (Venus-II). However, the methods and the coding are general and not limited to such applications

Escherichia coli O157:H7 Outbreak Associated with Restaurant Beef Grinding.

Science.gov (United States)

Torso, Lauren M; Voorhees, Ronald E; Forest, Stephen A; Gordon, Andrew Z; Silvestri, Sharon A; Kissler, Bonnie; Schlackman, Jessica; Sandt, Carol H; Toma, Paul; Bachert, Joel; Mertz, Kristen J; Harrison, Lee H

2015-07-01

Escherichia coli O157:H7 is a common cause of foodborne illness in the United States. Beef ground at establishments regulated by the U.S. Department of Agriculture, Food Safety and Inspection Service is routinely tested for E. coli O157:H7. Prior to December 2013, boxed beef product (wholesale cuts of beef, such as beef loin, packaged into bags and boxed for shipping) was not always tested for this pathogen. Downstream processors or retailers may grind the product; and, if the ground beef is not cooked to the recommended temperature, pathogens on the exterior of the beef introduced to the interior through grinding may survive. On 18 October 2013, the Allegheny County Health Department identified two E. coli O157:H7 cases, both of whom were food handlers at restaurant A, a restaurant that ground locally produced boxed beef for hamburgers on site. Case finding was conducted through public messaging, employee surveys, and disease surveillance. All potential cases were interviewed using a standard questionnaire. A confirmed case was defined as laboratory-confirmed E. coli O157:H7 with exposure to restaurant A. A probable case was defined as a patient with compatible symptoms and exposure to restaurant A but without laboratory confirmation. All human and food isolates were characterized by pulsed-field gel electrophoresis and multilocus variable-number tandem repeat analysis. The analysis identified 14 confirmed and 10 probable cases of E. coli; 18 nonintact ground beef samples tested positive for E. coli O157:H7. Nine confirmed cases were restaurant A employees. All confirmed cases recalled eating a restaurant A hamburger in the 10 days before illness onset; most cases reported consuming medium to rare hamburgers. Multiple pulsed-field gel electrophoresis and multilocus variable-number tandem repeat analysis patterns were identified among both the human and ground beef isolates, and the patient isolates matched those found in ground beef samples. Restaurant A

Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile.

Science.gov (United States)

Bletz, Stefan; Janezic, Sandra; Harmsen, Dag; Rupnik, Maja; Mellmann, Alexander

2018-06-01

Clostridium difficile , recently renamed Clostridioides difficile , is the most common cause of antibiotic-associated nosocomial gastrointestinal infections worldwide. To differentiate endogenous infections and transmission events, highly discriminatory subtyping is necessary. Today, methods based on whole-genome sequencing data are increasingly used to subtype bacterial pathogens; however, frequently a standardized methodology and typing nomenclature are missing. Here we report a core genome multilocus sequence typing (cgMLST) approach developed for C. difficile Initially, we determined the breadth of the C. difficile population based on all available MLST sequence types with Bayesian inference (BAPS). The resulting BAPS partitions were used in combination with C. difficile clade information to select representative isolates that were subsequently used to define cgMLST target genes. Finally, we evaluated the novel cgMLST scheme with genomes from 3,025 isolates. BAPS grouping ( n = 6 groups) together with the clade information led to a total of 11 representative isolates that were included for cgMLST definition and resulted in 2,270 cgMLST genes that were present in all isolates. Overall, 2,184 to 2,268 cgMLST targets were detected in the genome sequences of 70 outbreak-associated and reference strains, and on average 99.3% cgMLST targets (1,116 to 2,270 targets) were present in 2,954 genomes downloaded from the NCBI database, underlining the representativeness of the cgMLST scheme. Moreover, reanalyzing different cluster scenarios with cgMLST were concordant to published single nucleotide variant analyses. In conclusion, the novel cgMLST is representative for the whole C. difficile population, is highly discriminatory in outbreak situations, and provides a unique nomenclature facilitating interlaboratory exchange. Copyright © 2018 American Society for Microbiology.

Comparison of multilocus sequence typing and pulsed-field gel electrophoresis for Salmonella spp. identification in surface water

Science.gov (United States)

Kuo, Chun Wei; Hao Huang, Kuan; Hsu, Bing Mu; Tsai, Hsien Lung; Tseng, Shao Feng; Kao, Po Min; Shen, Shu Min; Chou Chiu, Yi; Chen, Jung Sheng

2013-04-01

Salmonella is one of the most important pathogens of waterborne diseases with outbreaks from contaminated water reported worldwide. In addition, Salmonella spp. can survive for long periods in aquatic environments. To realize genotypes and serovars of Salmonella in aquatic environments, we isolated the Salmonella strains by selective culture plates to identify the serovars of Salmonella by serological assay, and identify the genotypes by Multilocus sequence typing (MLST) based on the sequence data from University College Cork (UCC), respectively. The results show that 36 stream water samples (30.1%) and 18 drinking water samples (23.3%) were confirmed the existence of Salmonella using culture method combined PCR specific invA gene amplification. In this study, 24 cultured isolates of Salmonella from water samples were classified to fifteen Salmonella enterica serovars. In addition, we construct phylogenetic analysis using phylogenetic tree and Minimum spanning tree (MST) method to analyze the relationship of clinical, environmental, and geographical data. Phylogenetic tree showed that four main clusters and our strains can be distributed in all. The genotypes of isolates from stream water are more biodiversity while comparing the Salmonella strains genotypes from drinking water sources. According to MST data, we can found the positive correlation between serovars and genotypes of Salmonella. Previous studies revealed that the result of Pulsed field gel electrophoresis (PFGE) method can predict the serovars of Salmonella strain. Hence, we used the MLST data combined phylogenetic analysis to identify the serovars of Salmonella strain and achieved effectiveness. While using the geographical data combined phylogenetic analysis, the result showed that the dominant strains were existed in whole stream area in rainy season. Keywords: Salmonella spp., MLST, phylogenetic analysis, PFGE

Crossover from High to Low Reynolds Number Turbulence

NARCIS (Netherlands)

Lohse, Detlef

1994-01-01

The Taylor-Reynolds and Reynolds number (Re lambda and Re) dependence of the dimensionless energy dissipation rate c epsilon = epsilon L / u31,rms is derived for statistically stationary isotropic turbulence, employing the results of a variable range mean field theory. Here epsilon is the energy

ELECTRIC MOTORS MAINTENANCE PLANNING FROM ITS OPERATING VARIABLES

Directory of Open Access Journals (Sweden)

Francisco RODRIGUES

2017-07-01

Full Text Available The maintenance planning corresponds to an approach that seeks to maximize the availability of equipment and, conse-quently, increase the levels of competitiveness of companies by increasing production times. This paper presents a maintenance planning based on operating variables (number of hours worked, duty cycles, number of revolutions to maximizing the availability of operation of electrical motors. The reading of the operating variables and its sampling is done based on predetermined sampling cycles and subsequently is made the data analysis through time series algo-rithms aiming to launch work orders before reaching the variables limit values. This approach is supported by tools and technologies such as logical applications that enable a graphical user interface for access to relevant information about their Physical Asset HMI (Human Machine Interface, including the control and supervision by acquisition through SCADA (Supervisory Control And data acquisition data, also including the communication protocols among different logical applications.

The estimation of the catchment runoff using a small number of ...

African Journals Online (AJOL)

The estimation of the catchment runoff using a small number of rainfall stations in Burkina Faso. Youssouf Dembele, Jean Duchesne. Abstract. The objective of this study was to determine a suitable method to compute the runoff over a catchment with a few number of rainfall stations. Input hydrological variables were ...

Clonal structure in Ichthyobacterium seriolicida, the causative agent of bacterial haemolytic jaundice in yellowtail, Seriola quinqueradiata, inferred from molecular epidemiological analysis.

Science.gov (United States)

Matsuyama, T; Fukuda, Y; Sakai, T; Tanimoto, N; Nakanishi, M; Nakamura, Y; Takano, T; Nakayasu, C

2017-08-01

Bacterial haemolytic jaundice caused by Ichthyobacterium seriolicida has been responsible for mortality in farmed yellowtail, Seriola quinqueradiata, in western Japan since the 1980s. In this study, polymorphic analysis of I. seriolicida was performed using three molecular methods: amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST) and multiple-locus variable-number tandem repeat analysis (MLVA). Twenty-eight isolates were analysed using AFLP, while 31 isolates were examined by MLST and MLVA. No polymorphisms were identified by AFLP analysis using EcoRI and MseI, or by MLST of internal fragments of eight housekeeping genes. However, MLVA revealed variation in repeat numbers of three elements, allowing separation of the isolates into 16 sequence types. The unweighted pair group method using arithmetic averages cluster analysis of the MLVA data identified four major clusters, and all isolates belonged to clonal complexes. It is likely that I. seriolicida populations share a common ancestor, which may be a recently introduced strain. © 2016 John Wiley & Sons Ltd.

Multilocus Sequence Typing Reveals Relevant Genetic Variation and Different Evolutionary Dynamics among Strains of Xanthomonas arboricola pv. juglandis

Directory of Open Access Journals (Sweden)

Marco Scortichini

2010-11-01

Full Text Available Forty-five Xanthomonas arboricola pv. juglandis (Xaj strains originating from Juglans regia cultivation in different countries were molecularly typed by means of MultiLocus Sequence Typing (MLST, using acnB, gapA, gyrB and rpoD gene fragments. A total of 2.5 kilobases was used to infer the phylogenetic relationship among the strains and possible recombination events. Haplotype diversity, linkage disequilibrium analysis, selection tests, gene flow estimates and codon adaptation index were also assessed. The dendrograms built by maximum likelihood with concatenated nucleotide and amino acid sequences revealed two major and two minor phylotypes. The same haplotype was found in strains originating from different continents, and different haplotypes were found in strains isolated in the same year from the same location. A recombination breakpoint was detected within the rpoD gene fragment. At the pathovar level, the Xaj populations studied here are clonal and under neutral selection. However, four Xaj strains isolated from walnut fruits with apical necrosis are under diversifying selection, suggesting a possible new adaptation. Gene flow estimates do not support the hypothesis of geographic isolation of the strains, even though the genetic diversity between the strains increases as the geographic distance between them increases. A triplet deletion, causing the absence of valine, was found in the rpoD fragment of all 45 Xaj strains when compared with X. axonopodis pv. citri strain 306. The codon adaptation index was high in all four genes studied, indicating a relevant metabolic activity.

Assessing models of speciation under different biogeographic scenarios; An empirical study using multi-locus and RNA-seq analyses

Science.gov (United States)

Edwards, Taylor; Tollis, Marc; Hsieh, PingHsun; Gutenkunst, Ryan N.; Liu, Zhen; Kusumi, Kenro; Culver, Melanie; Murphy, Robert W.

2016-01-01

Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus. These lineages offer a powerful system to study speciation, because different biogeographic patterns (physical vs. ecological segregation) are observed at opposing ends of their distributions. We use 82 samples collected from 38 sites, representing the entire species' distribution and generate sequence data for mtDNA and four nuclear loci. A multilocus phylogenetic analysis in *BEAST estimates the species tree. RNA-seq data yield 20,126 synonymous variants from 7665 contigs from two individuals of each of the three lineages. Analyses of these data using the demographic inference package ∂a∂i serve to test the null hypothesis of no gene flow during divergence. The best-fit demographic model for the three taxa is concordant with the *BEAST species tree, and the ∂a∂i analysis does not indicate gene flow among any of the three lineages during their divergence. These analyses suggest that divergence among the lineages occurred in the absence of gene flow and in this scenario the genetic signature of ecological isolation (parapatric model) cannot be differentiated from geographic isolation (allopatric model).

A multilocus species delimitation reveals a striking number of species of coralline algae forming Maerl in the OSPAR maritime area.

Science.gov (United States)

Pardo, Cristina; Lopez, Lua; Peña, Viviana; Hernández-Kantún, Jazmin; Le Gall, Line; Bárbara, Ignacio; Barreiro, Rodolfo

2014-01-01

Maerl beds are sensitive biogenic habitats built by an accumulation of loose-lying, non-geniculate coralline algae. While these habitats are considered hot-spots of marine biodiversity, the number and distribution of maerl-forming species is uncertain because homoplasy and plasticity of morphological characters are common. As a result, species discrimination based on morphological features is notoriously challenging, making these coralline algae the ideal candidates for a DNA barcoding study. Here, mitochondrial (COI-5P DNA barcode fragment) and plastidial (psbA gene) sequence data were used in a two-step approach to delimit species in 224 collections of maerl sampled from Svalbard (78°96'N) to the Canary Islands (28°64'N) that represented 10 morphospecies from four genera and two families. First, the COI-5P dataset was analyzed with two methods based on distinct criteria (ABGD and GMYC) to delineate 16 primary species hypotheses (PSHs) arranged into four major lineages. Second, chloroplast (psbA) sequence data served to consolidate these PSHs into 13 secondary species hypotheses (SSHs) that showed biologically plausible ranges. Using several lines of evidence (e.g. morphological characters, known species distributions, sequences from type and topotype material), six SSHs were assigned to available species names that included the geographically widespread Phymatolithon calcareum, Lithothamnion corallioides, and L. glaciale; possible identities of other SSHs are discussed. Concordance between SSHs and morphospecies was minimal, highlighting the convenience of DNA barcoding for an accurate identification of maerl specimens. Our survey indicated that a majority of maerl forming species have small distribution ranges and revealed a gradual replacement of species with latitude.

A multilocus species delimitation reveals a striking number of species of coralline algae forming Maerl in the OSPAR maritime area.

Directory of Open Access Journals (Sweden)

Cristina Pardo

Full Text Available Maerl beds are sensitive biogenic habitats built by an accumulation of loose-lying, non-geniculate coralline algae. While these habitats are considered hot-spots of marine biodiversity, the number and distribution of maerl-forming species is uncertain because homoplasy and plasticity of morphological characters are common. As a result, species discrimination based on morphological features is notoriously challenging, making these coralline algae the ideal candidates for a DNA barcoding study. Here, mitochondrial (COI-5P DNA barcode fragment and plastidial (psbA gene sequence data were used in a two-step approach to delimit species in 224 collections of maerl sampled from Svalbard (78°96'N to the Canary Islands (28°64'N that represented 10 morphospecies from four genera and two families. First, the COI-5P dataset was analyzed with two methods based on distinct criteria (ABGD and GMYC to delineate 16 primary species hypotheses (PSHs arranged into four major lineages. Second, chloroplast (psbA sequence data served to consolidate these PSHs into 13 secondary species hypotheses (SSHs that showed biologically plausible ranges. Using several lines of evidence (e.g. morphological characters, known species distributions, sequences from type and topotype material, six SSHs were assigned to available species names that included the geographically widespread Phymatolithon calcareum, Lithothamnion corallioides, and L. glaciale; possible identities of other SSHs are discussed. Concordance between SSHs and morphospecies was minimal, highlighting the convenience of DNA barcoding for an accurate identification of maerl specimens. Our survey indicated that a majority of maerl forming species have small distribution ranges and revealed a gradual replacement of species with latitude.

Generating variable and random schedules of reinforcement using Microsoft Excel macros.

Science.gov (United States)

Bancroft, Stacie L; Bourret, Jason C

2008-01-01

Variable reinforcement schedules are used to arrange the availability of reinforcement following varying response ratios or intervals of time. Random reinforcement schedules are subtypes of variable reinforcement schedules that can be used to arrange the availability of reinforcement at a constant probability across number of responses or time. Generating schedule values for variable and random reinforcement schedules can be difficult. The present article describes the steps necessary to write macros in Microsoft Excel that will generate variable-ratio, variable-interval, variable-time, random-ratio, random-interval, and random-time reinforcement schedule values.

Induced variability for quantitative characters in Triticum aestivum L

International Nuclear Information System (INIS)

Khamankar, Y.G.

1989-01-01

Comparable doses of gamma rays, hydroxylamine, ethylmethane sulphonate and hydrazine have been compared for the magnitude of induced variability and their effects of mean. It was found that all the mutagenic treatments were effective in inducing variability for plant height, number of effective tillers/plant, 100-seed weight and single plant yield. Gamma rays were found to be most effective. While hydroxylamine and ethylmethane sulphonate were found to be equally effective, hydrazine was found to be least effective. Although, all the four characters showed increased variability, the mean for the characters of plant height and 100-grain weight remained unaltered. However, the mean for the characters number of effective tillers and single plant yield showed reduction. The greater effectiveness of gamma rays have been attributed to its characteristic mode of action and the polyploid nature of the wheat. (author). 9 refs., 2 tabs

HYPOTHETIC FIVE-DIMESION SPACE OF BASIC FACTORS EXTRACTED FROM THE FACTOR ANLYSIS OF CERTAIN NUMBERS OF MORPHOLOGIC, MOBILE AND MANIFEST MOBILE VARIABLES

Directory of Open Access Journals (Sweden)

Goran Šekeljić

2008-08-01

Full Text Available This research was made on sample of 183 schoolboys and school girls attending the fourth grade of the elementary school. It was conducted in order to examine the possibilities of the adoption of an alternative curriculum which contains the elemements of basket ball game. After an experimental treatament, the effects of the teaching were estmated in these segments of antropological space: antropometrical, mobile and manifest mobile space concerning the basic elements of basketball technique. It was applicated the method of canonic corelated analysis which means that there were determined statistically important coefficient of correlation based on certain number of prmal and basic vectors of morphological, mobile and manifest mobile variables. According to the results of the research we can expect that five-dimension hypothetic model should present some kind of base for an eventual progress: methods of Teaching Physical Education, cibernetic navigation of the training technology such as the selection of the pupils who are able to play basketball.

A multiple-locus variable-number tandem repeat analysis (MLVA) of Listeria monocytogenes isolated from Norwegian salmon-processing factories and from listeriosis patients.

Science.gov (United States)

Lunestad, B T; Truong, T T T; Lindstedt, B-A

2013-10-01

The objective of this study was to characterize Listeria monocytogenes isolated from farmed Atlantic salmon (Salmo salar) and the processing environment in three different Norwegian factories, and compare these to clinical isolates by multiple-locus variable-number tandem repeat analysis (MLVA). The 65 L. monocytogenes isolates obtained gave 15 distinct MLVA profiles. There was great heterogeneity in the distribution of MLVA profiles in factories and within each factory. Nine of the 15 MLVA profiles found in the fish-associated isolates were found to match human profiles. The MLVA profile 07-07-09-10-06 was the most common strain in Norwegian listeriosis patients. L. monocytogenes with this profile has previously been associated with at least two known listeriosis outbreaks in Norway, neither determined to be due to fish consumption. However, since this profile was also found in fish and in the processing environment, fish should be considered as a possible food vehicle during sporadic cases and outbreaks of listeriosis.

Staphylococcus aureus from 152 cases of bovine, ovine and caprine mastitis investigated by Multiple-locus variable number of tandem repeat analysis (MLVA).

Science.gov (United States)

Bergonier, Dominique; Sobral, Daniel; Feßler, Andrea T; Jacquet, Eric; Gilbert, Florence B; Schwarz, Stefan; Treilles, Michaël; Bouloc, Philippe; Pourcel, Christine; Vergnaud, Gilles

2014-10-02

Staphylococcus aureus is one of the main etiological agents of mastitis in ruminants. In the present retrospective study, we evaluated the potential interest of a previously described automated multiple loci Variable Number of Tandem Repeats (VNTR) Assay (MLVA) comprising 16 loci as a first line tool to investigate the population structure of S. aureus from mastitis. We determined the genetic diversity of S. aureus strains from cases of clinical and subclinical mastitis in dairy cattle (n = 118, of which 16 were methicillin-resistant), sheep (n = 18) and goats (n = 16). The 152 strains could be subdivided into 115 MLVA genotypes (including 14 genotypes for the ovine strains and 15 genotypes for the caprine strains). This corresponds to a discriminatory index (D) value of 0.9936. Comparison with published MLVA data obtained using the same protocol applied to strains from diverse human and animal origins revealed a low number (8.5%) of human-related MLVA genotypes among the present collection. Eighteen percent of the S. aureus mastitis collection belonged to clonal complexes apparently not associated with other pathological conditions. Some of them displayed a relatively low level of diversity in agreement with a restricted ecological niche. These findings provide arguments suggesting that specific S. aureus lineages particularly adapted to ruminant mammary glands have emerged and that MLVA is a convenient tool to provide a broad overview of the population, owing to the availability via internet of databases compiling published MLVA genotypes.

SRBreak: A read-depth and split-read framework to identify breakpoints of different events inside simple copy-number variable regions

Directory of Open Access Journals (Sweden)

HOANG T NGUYEN

2016-09-01

Full Text Available Copy-number variation (CNV has been associated with increased risk of complex diseases. High throughput sequencing (HTS technologies facilitate the detection of copy-number variable regions (CNVRs and their breakpoints. This helps in understanding genome structures of genomes as well as their evolution process. Various approaches have been proposed for detecting CNV breakpoints, but currently it is still challenging for tools based on a single analysis method to identify breakpoints of CNVs. It has been shown, however, that pipelines which integrate multiple approaches are able to report more reliable breakpoints. Here, based on HTS data, we have developed a pipeline to identify approximate breakpoints (±10 bp relating to different ancestral events within a specific CNVR. The pipeline combines read-depth and split-read information to infer breakpoints, using information from multiple samples to allow an imputation approach to be taken. The main steps involve using a normal mixture model to cluster samples into different groups, followed by simple kernel-based approaches to maximise information obtained from read-depth and split-read approaches, after which common breakpoints of groups are inferred. The pipeline uses split-read information directly from CIGAR strings of BAM files, without using a re-alignment step. On simulated data sets, it was able to report breakpoints for very low-coverage samples including those for which only single-end reads were available. When applied to three loci from existing human resequencing data sets (NEGR1, LCE3, IRGM the pipeline obtained good concordance with results from the 1000 Genomes Project (92%, 100% and 82%, respectively.The package is available at https://github.com/hoangtn/SRBreak, and also as a docker-based application at https://registry.hub.docker.com/u/hoangtn/srbreak/.

Genotyping of Bacillus anthracis strains based on automated capillary 25-loci Multiple Locus Variable-Number Tandem Repeats Analysis

Directory of Open Access Journals (Sweden)

Ciervo Alessandra

2006-04-01

Full Text Available Abstract Background The genome of Bacillus anthracis, the etiological agent of anthrax, is highly monomorphic which makes differentiation between strains difficult. A Multiple Locus Variable-number tandem repeats (VNTR Analysis (MLVA assay based on 20 markers was previously described. It has considerable discrimination power, reproducibility, and low cost, especially since the markers proposed can be typed by agarose-gel electrophoresis. However in an emergency situation, faster genotyping and access to representative databases is necessary. Results Genotyping of B. anthracis reference strains and isolates from France and Italy was done using a 25 loci MLVA assay combining 21 previously described loci and 4 new ones. DNA was amplified in 4 multiplex PCR reactions and the length of the resulting 25 amplicons was estimated by automated capillary electrophoresis. The results were reproducible and the data were consistent with other gel based methods once differences in mobility patterns were taken into account. Some alleles previously unresolved by agarose gel electrophoresis could be resolved by capillary electrophoresis, thus further increasing the assay resolution. One particular locus, Bams30, is the result of a recombination between a 27 bp tandem repeat and a 9 bp tandem repeat. The analysis of the array illustrates the evolution process of tandem repeats. Conclusion In a crisis situation of suspected bioterrorism, standardization, speed and accuracy, together with the availability of reference typing data are important issues, as illustrated by the 2001 anthrax letters event. In this report we describe an upgrade of the previously published MLVA method for genotyping of B. anthracis and apply the method to the typing of French and Italian B. anthracis strain collections. The increased number of markers studied compared to reports using only 8 loci greatly improves the discrimination power of the technique. An Italian strain belonging to the

Interleaved Buck Converter with Variable Number of Active Phases and a Predictive Current Sharing Scheme

DEFF Research Database (Denmark)

Jakobsen, Lars Tønnes; Garcia, O.; Oliver, J. A.

2008-01-01

The efficiency of an interleaved Buck converter is typically low at light load conditions because of the switching losses in each of the switching stages. Improvements in the converter efficiency can be achieved by dynamically changing the number of active phases depending on the load current....... This paper addresses the issues related to the transient response of the converter when the number of active phases is changed by a digital control scheme. The problem arises because the current in the individual phases of the interleaved Buck converter will not be equal immediately after the controller has...... changed the number of active phases. This paper proposes a current equalisation scheme that adjusts the duty cycle of each phase in a manner that ensures equal average inductor current in all active phases in one or two PWM periods. The current equalisation scheme relies on the measurement of the output...

Influence of IL-1RN intron 2 variable number of tandem repeats (VNTR) polymorphism on bipolar disorder.

Science.gov (United States)

Rafiei, A; Hosseini, S H; Taheri, M; Hosseni-khah, Z; Hajilooi, M; Mazaheri, Z

2013-01-01

Several lines of evidence point to the role of neurobiological mechanisms and genetic background in bipolar disorder (BD). The interleukin-1 receptor antagonist (IL-1Ra) is the principal regulator of IL-1α and IL-1β bioactivities. This study aimed to investigate the potential role of the variable number of tandem repeats (VNTR) polymorphisms of the IL-1Ra gene (IL1RN) in conferring susceptibility to BD. In total, 217 patients meeting DSM-IV-TR criteria for BD and 212 controls were recruited for the study. Genotyping of IL1RN was determined by polymerase chain reaction amplification of VNTR of 86 base pairs in intron 2 of IL1RN. The genotype distribution of IL1RN polymorphism was significantly different between BD patients and controls. The IL1RN*1/2 genotype was more prevalent in BD patients than in controls (44.2 vs. 30.2%, p = 0.003). Multiple logistic regression analysis demonstrated that IL1RN*1/2 heterozygotes had a significantly higher risk for BD (OR 1.83 and 95% CI 1.22-2.74, p = 0.003). Further stratification of the BD patients into IL1RN*2 allele carrier and noncarrier subgroups revealed a strong association between IL1RN*2 carriage and prolongation of the disease (p = 0.02). These findings suggest a positive association between VNTR polymorphism in IL1RN and BD. Additional studies, particularly with a prospective approach, are necessary to clarify the precise role of the VNTR polymorphism on the disease in different ethnic populations. Copyright © 2013 S. Karger AG, Basel.

Human Campylobacteriosis in Luxembourg, 2010-2013: A Case-Control Study Combined with Multilocus Sequence Typing for Source Attribution and Risk Factor Analysis.

Science.gov (United States)

Mossong, Joël; Mughini-Gras, Lapo; Penny, Christian; Devaux, Anthony; Olinger, Christophe; Losch, Serge; Cauchie, Henry-Michel; van Pelt, Wilfrid; Ragimbeau, Catherine

2016-02-10

Campylobacteriosis has increased markedly in Luxembourg during recent years. We sought to determine which Campylobacter genotypes infect humans, where they may originate from, and how they may infect humans. Multilocus sequence typing was performed on 1153 Campylobacter jejuni and 136 C. coli human strains to be attributed to three putative animal reservoirs (poultry, ruminants, pigs) and to environmental water using the asymmetric island model. A nationwide case-control study (2010-2013) for domestic campylobacteriosis was also conducted, including 367 C. jejuni and 48 C. coli cases, and 624 controls. Risk factors were investigated by Campylobacter species, and for strains attributed to different sources using a combined case-control and source attribution analysis. 282 sequence types (STs) were identified: ST-21, ST-48, ST-572, ST-50 and ST-257 were prevailing. Most cases were attributed to poultry (61.2%) and ruminants (33.3%). Consuming chicken outside the home was the dominant risk factor for both Campylobacter species. Newly identified risk factors included contact with garden soil for either species, and consuming beef specifically for C. coli. Poultry-associated campylobacteriosis was linked to poultry consumption in wintertime, and ruminant-associated campylobacteriosis to tap-water provider type. Besides confirming chicken as campylobacteriosis primary source, additional evidence was found for other reservoirs and transmission routes.

The Chandra Source Catalog: Source Variability

Science.gov (United States)

Nowak, Michael; Rots, A. H.; McCollough, M. L.; Primini, F. A.; Glotfelty, K. J.; Bonaventura, N. R.; Chen, J. C.; Davis, J. E.; Doe, S. M.; Evans, J. D.; Evans, I.; Fabbiano, G.; Galle, E. C.; Gibbs, D. G., II; Grier, J. D.; Hain, R.; Hall, D. M.; Harbo, P. N.; He, X.; Houck, J. C.; Karovska, M.; Lauer, J.; McDowell, J. C.; Miller, J. B.; Mitschang, A. W.; Morgan, D. L.; Nichols, J. S.; Plummer, D. A.; Refsdal, B. L.; Siemiginowska, A. L.; Sundheim, B. A.; Tibbetts, M. S.; van Stone, D. W.; Winkelman, S. L.; Zografou, P.

2009-09-01

The Chandra Source Catalog (CSC) contains fields of view that have been studied with individual, uninterrupted observations that span integration times ranging from 1 ksec to 160 ksec, and a large number of which have received (multiple) repeat observations days to years later. The CSC thus offers an unprecedented look at the variability of the X-ray sky over a broad range of time scales, and across a wide diversity of variable X-ray sources: stars in the local galactic neighborhood, galactic and extragalactic X-ray binaries, Active Galactic Nuclei, etc. Here we describe the methods used to identify and quantify source variability within a single observation, and the methods used to assess the variability of a source when detected in multiple, individual observations. Three tests are used to detect source variability within a single observation: the Kolmogorov-Smirnov test and its variant, the Kuiper test, and a Bayesian approach originally suggested by Gregory and Loredo. The latter test not only provides an indicator of variability, but is also used to create a best estimate of the variable lightcurve shape. We assess the performance of these tests via simulation of statistically stationary, variable processes with arbitrary input power spectral densities (here we concentrate on results of red noise simulations) at variety of mean count rates and fractional root mean square variabilities relevant to CSC sources. We also assess the false positive rate via simulations of constant sources whose sole source of fluctuation is Poisson noise. We compare these simulations to an assessment of the variability found in real CSC sources, and estimate the variability sensitivities of the CSC.

variability of in vitro and phenological behaviours of cocoa hybrids

African Journals Online (AJOL)

ACSS

analyse the variability of the in vitro and phenological behaviours of 6 cocoa ... The 4 aforementioned hybrids could be used to produce cocoa aroma, ... hybrids using a multivariate approach. .... 3 clusters and variables was assessed through ... function, and (iv) analysis of the representation quality. Thus, the number of ...

The gait standard deviation, a single measure of kinematic variability.

Science.gov (United States)

Sangeux, Morgan; Passmore, Elyse; Graham, H Kerr; Tirosh, Oren

2016-05-01

Measurement of gait kinematic variability provides relevant clinical information in certain conditions affecting the neuromotor control of movement. In this article, we present a measure of overall gait kinematic variability, GaitSD, based on combination of waveforms' standard deviation. The waveform standard deviation is the common numerator in established indices of variability such as Kadaba's coefficient of multiple correlation or Winter's waveform coefficient of variation. Gait data were collected on typically developing children aged 6-17 years. Large number of strides was captured for each child, average 45 (SD: 11) for kinematics and 19 (SD: 5) for kinetics. We used a bootstrap procedure to determine the precision of GaitSD as a function of the number of strides processed. We compared the within-subject, stride-to-stride, variability with the, between-subject, variability of the normative pattern. Finally, we investigated the correlation between age and gait kinematic, kinetic and spatio-temporal variability. In typically developing children, the relative precision of GaitSD was 10% as soon as 6 strides were captured. As a comparison, spatio-temporal parameters required 30 strides to reach the same relative precision. The ratio stride-to-stride divided by normative pattern variability was smaller in kinematic variables (the smallest for pelvic tilt, 28%) than in kinetic and spatio-temporal variables (the largest for normalised stride length, 95%). GaitSD had a strong, negative correlation with age. We show that gait consistency may stabilise only at, or after, skeletal maturity. Copyright © 2016 Elsevier B.V. All rights reserved.

Interleukin 6-174 G/C promoter and variable number of tandem repeats (VNTR) gene polymorphisms in sporadic Alzheimer's disease.

Science.gov (United States)

Capurso, Cristiano; Solfrizzi, Vincenzo; Colacicco, Anna Maria; D'Introno, Alessia; Frisardi, Vincenza; Imbimbo, Bruno P; Lorusso, Maria; Vendemiale, Gianluigi; Denitto, Marta; Santamato, Andrea; Seripa, Davide; Pilotto, Alberto; Fiore, Pietro; Capurso, Antonio; Panza, Francesco

2010-02-01

Previous studies examining the association between the interleukin 6 (IL-6)-174 C/G polymorphism and Alzheimer's disease (AD) have yielded conflicting results. Furthermore, the C allele of the IL-6 variable number of tandem repeats (VNTR) polymorphism was associated with a delayed onset and a decreased risk of AD. A total sample of 149 AD patients, and 298 age- and sex-matched unrelated caregivers from Apulia, southern Italy, were genotyped for the apolipoprotein E (APOE) polymorphism, the VNTR polymorphism in the 3' flanking region, and the -174G/C single-nucleotide polymorphism (SNP) in the promoter region of IL-6 gene on chromosome 7. Furthermore, we performed a haplotype analysis on these two polymorphisms on IL-6 locus. IL-6 VNTR and -174G/C allele and genotype frequencies were similar between AD patients and controls, also after stratification for late-onset (> or =65 years) and early-onset (VNTR and -174G/C polymorphisms, not supporting a previous reported additive effect of both IL-6 polymorphisms on AD risk. Our findings did not support a role of IL-6-174 G/C and IL-6 VNTR polymorphisms in the risk of sporadic AD in southern Italy, suggesting that these polymorphisms of IL-6 gene were at most weak genetic determinants of AD. Copyright 2009 Elsevier Inc. All rights reserved.

Persistent consequences of atypical early number concepts

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Michèle M. M. Mazzocco

2013-09-01

Full Text Available How does symbolic number knowledge performance help identify young children at risk for poor mathematics achievement outcomes? In research and practice, classification of mathematics learning disability (MLD, or dyscalculia is typically based on composite scores from broad measures of mathematics achievement. These scores do predict later math achievement levels, but do not specify the nature of math difficulties likely to emerge among students at greatest risk for long-term mathematics failure. Here we report that gaps in 2nd and 3rd graders’ number knowledge predict specific types of errors made on math assessments at Grade 8. Specifically, we show that early whole number misconceptions predict slower and less accurate performance, and atypical computational errors, on Grade 8 arithmetic tests. We demonstrate that basic number misconceptions can be detected by idiosyncratic responses to number knowledge items, and that when such misconceptions are evident during primary school they persist throughout the school age years, with variable manifestation throughout development. We conclude that including specific qualitative assessments of symbolic number knowledge in primary school may provide greater specificity of the types of difficulties likely to emerge among students at risk for poor mathematics outcomes.

Individual differences in nonverbal number skills predict math anxiety.

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Lindskog, Marcus; Winman, Anders; Poom, Leo

2017-02-01

Math anxiety (MA) involves negative affect and tension when solving mathematical problems, with potentially life-long consequences. MA has been hypothesized to be a consequence of negative learning experiences and cognitive predispositions. Recent research indicates genetic and neurophysiological links, suggesting that MA stems from a basic level deficiency in symbolic numerical processing. However, the contribution of evolutionary ancient purely nonverbal processes is not fully understood. Here we show that the roots of MA may go beyond symbolic numbers. We demonstrate that MA is correlated with precision of the Approximate Number System (ANS). Individuals high in MA have poorer ANS functioning than those low in MA. This correlation remains significant when controlling for other forms of anxiety and for cognitive variables. We show that MA mediates the documented correlation between ANS precision and math performance, both with ANS and with math performance as independent variable in the mediation model. In light of our results, we discuss the possibility that MA has deep roots, stemming from a non-verbal number processing deficiency. The findings provide new evidence advancing the theoretical understanding of the developmental etiology of MA. Copyright © 2016 Elsevier B.V. All rights reserved.

IMPROVED VARIABLE STAR SEARCH IN LARGE PHOTOMETRIC DATA SETS: NEW VARIABLES IN CoRoT FIELD LRa02 DETECTED BY BEST II

International Nuclear Information System (INIS)

Fruth, T.; Cabrera, J.; Csizmadia, Sz.; Eigmüller, P.; Erikson, A.; Kirste, S.; Pasternacki, T.; Rauer, H.; Titz-Weider, R.; Kabath, P.; Chini, R.; Lemke, R.; Murphy, M.

2012-01-01

The CoRoT field LRa02 has been observed with the Berlin Exoplanet Search Telescope II (BEST II) during the southern summer 2007/2008. A first analysis of stellar variability led to the publication of 345 newly discovered variable stars. Now, a deeper analysis of this data set was used to optimize the variability search procedure. Several methods and parameters have been tested in order to improve the selection process compared to the widely used J index for variability ranking. This paper describes an empirical approach to treat systematic trends in photometric data based upon the analysis of variance statistics that can significantly decrease the rate of false detections. Finally, the process of reanalysis and method improvement has virtually doubled the number of variable stars compared to the first analysis by Kabath et al. A supplementary catalog of 272 previously unknown periodic variables plus 52 stars with suspected variability is presented. Improved ephemerides are given for 19 known variables in the field. In addition, the BEST II results are compared with CoRoT data and its automatic variability classification.

Nationwide Macroeconomic Variables and the Growth Rate of Bariatric Surgeries in Brazil.

Science.gov (United States)

Cazzo, Everton; Ramos, Almino Cardoso; Pareja, José Carlos; Chaim, Elinton Adami

2018-06-06

The effect of nationwide economic issues on the necessary expansion in the number of bariatric procedures remains unclear. This study aims to determine whether there are correlations between the growth rate in the number of bariatric surgeries and the major macroeconomic variables over time in Brazil. It is a nationwide analysis regarding the number of bariatric surgeries in Brazil and the main national macroeconomic variables from 2003 through 2016: gross domestic product (GDP), inflation rate, and the unemployment rate, as well as the evolution in the number of registered bariatric surgeons. There were significant positive correlations of the growth rate of surgeries with the early variations of the GDP (R = 0.5558; p = 0.04863) and of the overall health expenditure per capita (R = 0.78322; p = 0.00259). The growth rate of the number of bariatric surgeries was not correlated with the unemployment and inflation rates, as well as with the growth rate of available bariatric surgeons. There were direct relationships between the growth rate of bariatric surgeries and the evolutions of the GDP and health care expenditure per capita. These variables appear to influence the nationwide offer of bariatric surgery.

Epidemiological analysis of Leishmania tropica strains and giemsa-stained smears from Syrian and Turkish leishmaniasis patients using multilocus microsatellite typing (MLMT.

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Mehmet Karakuş

2017-04-01

Full Text Available Turkey is located in an important geographical location, in terms of the epidemiology of vector-borne diseases, linking Asia and Europe. Cutaneous leishmaniasis (CL is one of the endemic diseases in a Turkey and according to the Ministry Health of Turkey, 45% of CL patients originate from Şanlıurfa province located in southeastern Turkey. Herein, the epidemiological status of CL, caused by L. tropica, in Turkey was examined using multilocus microsatellite typing (MLMT of strains obtained from Turkish and Syrian patients. A total of 38 cryopreserved strains and 20 Giemsa-stained smears were included in the present study. MLMT was performed using 12 highly specific microsatellite markers. Delta K (ΔK calculation and Bayesian statistics were used to determine the population structure. Three main populations (POP A, B and C were identified and further examination revealed the presence of three subpopulations for POP B and C. Combined analysis was performed using the data of previously typed L. tropica strains and Mediterranean and Şanlıurfa populations were identified. This finding suggests that the epidemiological status of L. tropica is more complicated than expected when compared to previous studies. A new population, comprised of Syrian L. tropica samples, was reported for the first time in Turkey, and the data presented here will provide new epidemiological information for further studies.

Multi-locus analyses of an Antarctic fish species flock (Teleostei, Notothenioidei, Trematominae): Phylogenetic approach and test of the early-radiation event

International Nuclear Information System (INIS)

Janko, K.; Musilova, Z.; Marshall, C.; Van Houdt, J.; Couloux, A.; Cruaud, C.; Lecointre, G.

2011-01-01

Clades that have undergone episodes of rapid cladogenesis are challenging from a phylogenetic point of view. They are generally characterised by short or missing internal branches in phylogenetic trees and by conflicting topologies among individual gene trees. This may be the case of the subfamily Trematominae, a group of marine teleosts of coastal Antarctic waters, which is considered to have passed through a period of rapid diversification. Despite much phylogenetic attention, the relationships among Trematominae species remain unclear. In contrast to previous studies that were mostly based on concatenated datasets of mitochondrial and/or single nuclear loci, we applied various single-locus and multi-locus phylogenetic approaches to sequences from 11 loci (eight nuclear) and we also used several methods to assess the hypothesis of a radiation event in Trematominae evolution. Diversification rate analyses support the hypothesis of a period of rapid diversification during Trematominae history and only a few nodes in the hypothetical species tree were consistently resolved with various phylogenetic methods. We detected significant discrepancies among trees from individual genes of these species, most probably resulting from incomplete lineage sorting, suggesting that concatenation of loci is not the most appropriate way to investigate Trematominae species interrelationships. These data also provide information about the possible effects of historic climate changes on the diversification rate of this group of fish. (authors)

Multilocus sequence typing, biochemical and antibiotic resistance characterizations reveal diversity of North American strains of the honey bee pathogen Paenibacillus larvae.

Science.gov (United States)

Krongdang, Sasiprapa; Evans, Jay D; Pettis, Jeffery S; Chantawannakul, Panuwan

2017-01-01

Paenibacillus larvae is a Gram positive bacterium and the causative agent of the most widespread fatal brood disease of honey bees, American foulbrood (AFB). A total of thirty-three independent Paenibacillus larvae isolates from various geographical origins in North America and five reference strains were investigated for genetic diversity using multilocus sequence typing (MLST). This technique is regarded to be a powerful tool for epidemiological studies of pathogenic bacteria and is widely used in genotyping assays. For MLST, seven housekeeping gene loci, ilvD (dihydroxy-acid dyhydrogenase), tri (triosephosphate isomerase), purH (phospharibosyl-aminoimidazolecarboxamide), recF (DNA replication and repair protein), pyrE (orotate phosphoribosyltransferase), sucC (succinyl coenzyme A synthetase β subunit) and glpF (glycerol uptake facilitator protein) were studied and applied for primer designs. Previously, ERIC type DNA fingerprinting was applied to these same isolates and the data showed that almost all represented the ERIC I type, whereas using BOX-PCR gave an indication of more diversity. All isolates were screened for resistance to four antibiotics used by U.S. beekeepers, showing extensive resistance to tetracycline and the first records of resistance to tylosin and lincomycin. Our data highlight the intraspecies relationships of P. larvae and the potential application of MLST methods in enhancing our understanding of epidemiological relationships among bacterial isolates of different origins.

Multilocus sequence typing, biochemical and antibiotic resistance characterizations reveal diversity of North American strains of the honey bee pathogen Paenibacillus larvae.

Directory of Open Access Journals (Sweden)

Sasiprapa Krongdang

Full Text Available Paenibacillus larvae is a Gram positive bacterium and the causative agent of the most widespread fatal brood disease of honey bees, American foulbrood (AFB. A total of thirty-three independent Paenibacillus larvae isolates from various geographical origins in North America and five reference strains were investigated for genetic diversity using multilocus sequence typing (MLST. This technique is regarded to be a powerful tool for epidemiological studies of pathogenic bacteria and is widely used in genotyping assays. For MLST, seven housekeeping gene loci, ilvD (dihydroxy-acid dyhydrogenase, tri (triosephosphate isomerase, purH (phospharibosyl-aminoimidazolecarboxamide, recF (DNA replication and repair protein, pyrE (orotate phosphoribosyltransferase, sucC (succinyl coenzyme A synthetase β subunit and glpF (glycerol uptake facilitator protein were studied and applied for primer designs. Previously, ERIC type DNA fingerprinting was applied to these same isolates and the data showed that almost all represented the ERIC I type, whereas using BOX-PCR gave an indication of more diversity. All isolates were screened for resistance to four antibiotics used by U.S. beekeepers, showing extensive resistance to tetracycline and the first records of resistance to tylosin and lincomycin. Our data highlight the intraspecies relationships of P. larvae and the potential application of MLST methods in enhancing our understanding of epidemiological relationships among bacterial isolates of different origins.

X-ray-induced specific-locus mutations in the ad-3 region of two-component heterokaryons of Neurospora crass

International Nuclear Information System (INIS)

De Serres, F.J.

1990-01-01

More extensive complementation tests than those performed initially on a series of 832 X-ray-induced specific-locus mutations in the adenine-4 (ad-3) region of a two-component heterokaryon (H-12) of Neurospora crassa showed that unexpectedly high frequencies of specific-locus mutations in the ad-3 region have additional, but separate, sites of recessive lethal damage in the immediately adjacent genetic regions. In the present paper, X-ray-induced irreparable ad-3 mutants of the folowing genotypes and numbers (ad-3A ad-3B, ad-3A ad-3B nic-2, and ad-3B nic-2) have also subjected to the same genetic fine structure analysis. These experiments, in the previous and present papers, were designed to determine the extent of the functional inactivation in the ad-3 and immediately adjacent genetic regions in individual mutants classified as presumptive multilocus deletions or multiplelocus mutations. The data in the present paper have shown that in Neurospora crassa most X-ray-induced irreparable mutants of genotype ad-3A ad-3B, ad-3A ad-3B nic-2, and ad-3 nic-2 map as a series of overlapping multilocus deletions. In addition, genetic fine structure analysis has shown that some of the mutants classified, initially, as multilocus deletions, are actually multiple-locus mutations: multilocus deletions with closely linked, and separate, sites of recessive lethal damage with a wide variety of genotyes. Combining data from the present experiments with previously published date, the frequency of multiple-locus mutations among X-ray-induced gene/point mutations and multilocus deletions in the ad-3 region is 6.2%. (author). 27 refs.; 4 figs.; 7 tab

Ratio index variables or ANCOVA? Fisher's cats revisited.

Science.gov (United States)

Tu, Yu-Kang; Law, Graham R; Ellison, George T H; Gilthorpe, Mark S

2010-01-01

Over 60 years ago Ronald Fisher demonstrated a number of potential pitfalls with statistical analyses using ratio variables. Nonetheless, these pitfalls are largely overlooked in contemporary clinical and epidemiological research, which routinely uses ratio variables in statistical analyses. This article aims to demonstrate how very different findings can be generated as a result of less than perfect correlations among the data used to generate ratio variables. These imperfect correlations result from measurement error and random biological variation. While the former can often be reduced by improvements in measurement, random biological variation is difficult to estimate and eliminate in observational studies. Moreover, wherever the underlying biological relationships among epidemiological variables are unclear, and hence the choice of statistical model is also unclear, the different findings generated by different analytical strategies can lead to contradictory conclusions. Caution is therefore required when interpreting analyses of ratio variables whenever the underlying biological relationships among the variables involved are unspecified or unclear. (c) 2009 John Wiley & Sons, Ltd.

Random numbers spring from alpha decay

International Nuclear Information System (INIS)

Frigerio, N.A.; Sanathanan, L.P.; Morley, M.; Clark, N.A.; Tyler, S.A.

1980-05-01

Congruential random number generators, which are widely used in Monte Carlo simulations, are deficient in that the number they generate are concentrated in a relatively small number of hyperplanes. While this deficiency may not be a limitation in small Monte Carlo studies involving a few variables, it introduces a significant bias in large simulations requiring high resolution. This bias was recognized and assessed during preparations for an accident analysis study of nuclear power plants. This report describes a random number device based on the radioactive decay of alpha particles from a 235 U source in a high-resolution gas proportional counter. The signals were fed to a 4096-channel analyzer and for each channel the frequency of signals registered in a 20,000-microsecond interval was recorded. The parity bits of these frequency counts (0 for an even count and 1 for an odd count) were then assembled in sequence to form 31-bit binary random numbers and transcribed to a magnetic tape. This cycle was repeated as many times as were necessary to create 3 million random numbers. The frequency distribution of counts from the present device conforms to the Brockwell-Moyal distribution, which takes into account the dead time of the counter (both the dead time and decay constant of the underlying Poisson process were estimated). Analysis of the count data and tests of randomness on a sample set of the 31-bit binary numbers indicate that this random number device is a highly reliable source of truly random numbers. Its use is, therefore, recommended in Monte Carlo simulations for which the congruential pseudorandom number generators are found to be inadequate. 6 figures, 5 tables

Advanced Daily Prediction Model for National Suicide Numbers with Social Media Data.

Science.gov (United States)

Lee, Kyung Sang; Lee, Hyewon; Myung, Woojae; Song, Gil-Young; Lee, Kihwang; Kim, Ho; Carroll, Bernard J; Kim, Doh Kwan

2018-04-01

Suicide is a significant public health concern worldwide. Social media data have a potential role in identifying high suicide risk individuals and also in predicting suicide rate at the population level. In this study, we report an advanced daily suicide prediction model using social media data combined with economic/meteorological variables along with observed suicide data lagged by 1 week. The social media data were drawn from weblog posts. We examined a total of 10,035 social media keywords for suicide prediction. We made predictions of national suicide numbers 7 days in advance daily for 2 years, based on a daily moving 5-year prediction modeling period. Our model predicted the likely range of daily national suicide numbers with 82.9% accuracy. Among the social media variables, words denoting economic issues and mood status showed high predictive strength. Observed number of suicides one week previously, recent celebrity suicide, and day of week followed by stock index, consumer price index, and sunlight duration 7 days before the target date were notable predictors along with the social media variables. These results strengthen the case for social media data to supplement classical social/economic/climatic data in forecasting national suicide events.

Variables associated with lung congestion as assessed by chest ultrasound in diabetics undergoing hemodialysis

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Paulo Roberto Santos

Full Text Available Abstract Introduction: Ultrasound is an emerging method for assessing lung congestion but is still seldom used. Lung congestion is an important risk of cardiac events and death in end-stage renal disease (ESRD patients on hemodialysis (HD. Objective: We investigated possible variables associated with lung congestion among diabetics with ESRD on HD, using chest ultrasound to detect extracellular lung water. Methods: We studied 73 patients with diabetes as the primary cause of ESRD, undergoing regular HD. Lung congestion was assessed by counting the number of B lines detected by chest ultrasound. Hydration status was assessed by bioimpedance analysis and cardiac function by echocardiography. The collapse index of the inferior vena cava (IVC was measured by ultrasonography. All patients were classified according to NYHA score. Correlations of the number of B lines with continuous variables and comparisons regarding the number of B lines according to categorical variables were performed. Multivariate linear regression was used to test the variables as independent predictors of the number of B lines. Results: None of the variables related to hydration status and cardiac function were associated with the number of B lines. In the multivariate analysis, only the IVC collapse index (b = 45.038; p < 0.001 and NYHA classes (b = 13.995; p = 0.006 were independent predictors of the number of B lines. Conclusion: Clinical evaluation based on NYHA score and measurement of the collapsed IVC index were found to be more reliable than bioimpedance analysis to predict lung congestion.

Enrichment of Multilocus Sequence Typing Clade 1 with Oral Candida albicans Isolates in Patients with Untreated Periodontitis

Science.gov (United States)

McManus, Brenda A.; Maguire, Rory; Cashin, Phillipa J.; Claffey, Noel; Flint, Stephen; Abdulrahim, Mohammed H.

2012-01-01

This study investigated the prevalence and cell density of Candida species in periodontal pockets, healthy subgingival sites, and oral rinse samples of patients with untreated periodontitis. Twenty-one periodontitis patients underwent sampling at two periodontitis sites, and 19/21 of these patients underwent sampling at one periodontally healthy site. Both paper point and curette sampling techniques were employed. The periodontitis patients and 50 healthy subjects were also sampled by oral rinse. Candida isolates were recovered on CHROMagar Candida medium, and representative isolates were identified. Candida spp. were recovered from 10/21 (46.7%) periodontitis patients and from 16/50 (32%) healthy subjects. C. albicans predominated in both groups and was recovered from all Candida-positive subjects. Candida-positive periodontitis patients yielded Candida from periodontal pockets with average densities of 3,528 and 3,910 CFU/sample from curette and paper point samples, respectively, and 1,536 CFU/ml from oral rinse samples. The majority (18/19) of the healthy sites sampled from periodontitis patients were Candida negative. The 16 Candida-positive healthy subjects yielded an average of 279 CFU/ml from oral rinse samples. C. albicans isolates were investigated by multilocus sequence typing (MLST) to determine if specific clonal groups were associated with periodontitis. MLST analysis of 31 C. albicans isolates from periodontitis patients yielded 19 sequence types (STs), 13 of which were novel. Eleven STs belonged to MLST clade 1. In contrast, 16 C. albicans isolates from separate healthy subjects belonged to 16 STs, with 4 isolates belonging to clade 1. The distributions of STs between both groups were significantly different (P = 0.04) and indicated an enrichment of C. albicans isolates in periodontal pockets, which warrants a larger study. PMID:22875886

Design of ideal cascades of gas centrifuges with variable separation factors

International Nuclear Information System (INIS)

Olander, D.R.

1976-01-01

A method of designing ideal cascades in which the separation factor varies with stage number is presented and applied to centrifuges as separating units. The centrifuge is characterized by a performance function, which gives the separative power, optimized with respect to all internal variables, as a function of cut and throughput. For centrifuges with certain types of performance functions, variable-α ideal cascades can provide a product at a lower cost than the conventional ideal cascade in which the separation factor is independent of stage number

Multi-locus sequence typing provides epidemiological insights for diseased sharks infected with fungi belonging to the Fusarium solani species complex.

Science.gov (United States)

Desoubeaux, Guillaume; Debourgogne, Anne; Wiederhold, Nathan P; Zaffino, Marie; Sutton, Deanna; Burns, Rachel E; Frasca, Salvatore; Hyatt, Michael W; Cray, Carolyn

2018-07-01

Fusarium spp. are saprobic moulds that are responsible for severe opportunistic infections in humans and animals. However, we need epidemiological tools to reliably trace the circulation of such fungal strains within medical or veterinary facilities, to recognize environmental contaminations that might lead to infection and to improve our understanding of factors responsible for the onset of outbreaks. In this study, we used molecular genotyping to investigate clustered cases of Fusarium solani species complex (FSSC) infection that occurred in eight Sphyrnidae sharks under managed care at a public aquarium. Genetic relationships between fungal strains were determined by multi-locus sequence typing (MLST) analysis based on DNA sequencing at five loci, followed by comparison with sequences of 50 epidemiologically unrelated FSSC strains. Our genotyping approach revealed that F. keratoplasticum and F. solani haplotype 9x were most commonly isolated. In one case, the infection proved to be with another Hypocrealian rare opportunistic pathogen Metarhizium robertsii. Twice, sharks proved to be infected with FSSC strains with the same MLST sequence type, supporting the hypothesis the hypothesis that common environmental populations of fungi existed for these sharks and would suggest the longtime persistence of the two clonal strains within the environment, perhaps in holding pools and life support systems of the aquarium. This study highlights how molecular tools like MLST can be used to investigate outbreaks of microbiological disease. This work reinforces the need for regular controls of water quality to reduce microbiological contamination due to waterborne microorganisms.

Spiroides shrubs on Qinghai-Tibetan Plateau: Multilocus phylogeography and palaeodistributional reconstruction of Spiraea alpina and S. Mongolica (Rosaceae).

Science.gov (United States)

Khan, Gulzar; Zhang, Faqi; Gao, Qingbo; Fu, Pengcheng; Zhang, Yu; Chen, Shilong

2018-06-01

A common hypothesis for the rich biodiversity found in mountains is uplift-driven diversification. Using a multilocus approach, here we assessed the influence of Qinghai-Tibetan Plateau (QTP) uplift and fluctuating regional climate on genetic diversity of two sister spiroides shrubs, Spiraea alpina and S. mongolica. Combined with palaeodistributional reconstruction modelling, we investigated the current and past-predicted distribution of these species under different climatic episodes. The study demonstrated that continuous pulses of retreat and expansion during last glacial-interglacial episodes, combined with the uplifting of QTP shaped the current distribution of these species. All the populations showed high level of genetic diversity based on both cpDNA and SSR markers. The average gene diversity within populations based on cpDNA markers was 0.383 ± 0.052 for S. alpina and 0.477 ± 0.048 for S. mongolica. The observed and expected heterozygosities based on SSR for both Spiraea alpina and S. mongolicawere H E (0.72-0.90)/H O (0.35-0.78) and H E (0.77-0.92)/H O (0.47-0.77) respectively. Palaeodistributional reconstruction indicated species' preferences at southeastern edge of the plateau during last glacial maximum, at higher altitude areas of QTP and range expansion to central plateau during the interglacial episodes. Assignment tests in STRUCTURE, discriminant analysis of principal coordinates and Immigrants analysis in GENECLASS based on nuclear SSR markers did not support the hypothesis of gene flow between both the species. However, maximum likelihood approach based on cpDNA showed sharing of haplotypes between both species. Copyright © 2018 Elsevier Inc. All rights reserved.

Use of multiple-locus variable-number of tandem repeats analysis (MLVA) to investigate genetic diversity of Salmonella enterica subsp. enterica serovar Typhimurium isolates from human, food, and veterinary sources

DEFF Research Database (Denmark)

Mateva, Gergana; Pedersen, Karl; Sørensen, Gitte

2017-01-01

-locus variable-number of tandem repeats analysis (MLVA) and compared results with antimicrobial resistance (AMR) determinations for 100 S. Typhimurium strains isolated in Bulgaria during 2008-2012 (50 veterinary/food and 50 human isolates). Results showed that isolates were divided into 80 and 34 groups using......). No clustering of isolates related to susceptibility/resistance to antimicrobials, source of isolation, or year of isolation was observed. Some MLVA types were found in both human and veterinary/food isolates, indicating a possible route of transmission. A majority (83%) of the isolates were found...

Recent speciation in three closely related sympatric specialists: inferences using multi-locus sequence, post-mating isolation and endosymbiont data.

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Huai-Jun Xue

Full Text Available Shifting between unrelated host plants is relatively rare for phytophagous insects, and distinct host specificity may play crucial roles in reproductive isolation. However, the isolation status and the relationship between parental divergence and post-mating isolation among closely related sympatric specialists are still poorly understood. Here, multi-locus sequence were used to estimate the relationship among three host plant-specific closely related flea beetles, Altica cirsicola, A. fragariae and A. viridicyanea (abbreviated as AC, AF and AV respectively. The tree topologies were inconsistent using different gene or different combinations of gene fragments. The relationship of AF+(AC+AV was supported, however, by both gene tree and species tree based on concatenated data. Post-mating reproductive data on the results of crossing these three species are best interpreted in the light of a well established phylogeny. Nuclear-induced but not Wolbachia-induced unidirectional cytoplasmic incompatibility, which was detected in AC-AF and AF-AV but not in AC-AV, may also suggest more close genetic affinity between AC and AV. Prevalence of Wolbachia in these three beetles, and the endosymbiont in most individuals of AV and AC sharing a same wsp haplotype may give another evidence of AF+(AC+AV. Our study also suggested that these three flea beetles diverged in a relative short time (0.94 My, which may be the result of shifting between unrelated host plants and distinct host specificity. Incomplete post-mating isolation while almost complete lineage sorting indicated that effective pre-mating isolation among these three species should have evolved.

The variable sky of deep synoptic surveys

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Ridgway, Stephen T.; Matheson, Thomas; Mighell, Kenneth J.; Olsen, Knut A. [National Optical Astronomy Observatory, Tucson, AZ 85725 (United States); Howell, Steve B., E-mail: ridgway@noao.edu [NASA Ames Research Center, P.O. Box 1, M/S 244-30, Moffett Field, CA 94035 (United States)

2014-11-20

The discovery of variable and transient sources is an essential product of synoptic surveys. The alert stream will require filtering for personalized criteria—a process managed by a functionality commonly described as a Broker. In order to understand quantitatively the magnitude of the alert generation and Broker tasks, we have undertaken an analysis of the most numerous types of variable targets in the sky—Galactic stars, quasi-stellar objects (QSOs), active galactic nuclei (AGNs), and asteroids. It is found that the Large Synoptic Survey Telescope (LSST) will be capable of discovering ∼10{sup 5} high latitude (|b| > 20°) variable stars per night at the beginning of the survey. (The corresponding number for |b| < 20° is orders of magnitude larger, but subject to caveats concerning extinction and crowding.) However, the number of new discoveries may well drop below 100 per night within less than one year. The same analysis applied to GAIA clarifies the complementarity of the GAIA and LSST surveys. Discovery of AGNs and QSOs are each predicted to begin at ∼3000 per night and decrease by 50 times over four years. Supernovae are expected at ∼1100 per night, and after several survey years will dominate the new variable discovery rate. LSST asteroid discoveries will start at >10{sup 5} per night, and if orbital determination has a 50% success rate per epoch, they will drop below 1000 per night within two years.

The variable sky of deep synoptic surveys

International Nuclear Information System (INIS)

Ridgway, Stephen T.; Matheson, Thomas; Mighell, Kenneth J.; Olsen, Knut A.; Howell, Steve B.

2014-01-01

The discovery of variable and transient sources is an essential product of synoptic surveys. The alert stream will require filtering for personalized criteria—a process managed by a functionality commonly described as a Broker. In order to understand quantitatively the magnitude of the alert generation and Broker tasks, we have undertaken an analysis of the most numerous types of variable targets in the sky—Galactic stars, quasi-stellar objects (QSOs), active galactic nuclei (AGNs), and asteroids. It is found that the Large Synoptic Survey Telescope (LSST) will be capable of discovering ∼10 5 high latitude (|b| > 20°) variable stars per night at the beginning of the survey. (The corresponding number for |b| < 20° is orders of magnitude larger, but subject to caveats concerning extinction and crowding.) However, the number of new discoveries may well drop below 100 per night within less than one year. The same analysis applied to GAIA clarifies the complementarity of the GAIA and LSST surveys. Discovery of AGNs and QSOs are each predicted to begin at ∼3000 per night and decrease by 50 times over four years. Supernovae are expected at ∼1100 per night, and after several survey years will dominate the new variable discovery rate. LSST asteroid discoveries will start at >10 5 per night, and if orbital determination has a 50% success rate per epoch, they will drop below 1000 per night within two years.

On the Interpretation of Instrumental Variables in the Presence of Specification Errors

Directory of Open Access Journals (Sweden)

P.A.V.B. Swamy

2015-01-01

Full Text Available The method of instrumental variables (IV and the generalized method of moments (GMM, and their applications to the estimation of errors-in-variables and simultaneous equations models in econometrics, require data on a sufficient number of instrumental variables that are both exogenous and relevant. We argue that, in general, such instruments (weak or strong cannot exist.

Evaluating two model reduction approaches for large scale hedonic models sensitive to omitted variables and multicollinearity

DEFF Research Database (Denmark)

Panduro, Toke Emil; Thorsen, Bo Jellesmark

2014-01-01

Hedonic models in environmental valuation studies have grown in terms of number of transactions and number of explanatory variables. We focus on the practical challenge of model reduction, when aiming for reliable parsimonious models, sensitive to omitted variable bias and multicollinearity. We...

Quantitative Tomography for Continuous Variable Quantum Systems.

Science.gov (United States)

Landon-Cardinal, Olivier; Govia, Luke C G; Clerk, Aashish A

2018-03-02

We present a continuous variable tomography scheme that reconstructs the Husimi Q function (Wigner function) by Lagrange interpolation, using measurements of the Q function (Wigner function) at the Padua points, conjectured to be optimal sampling points for two dimensional reconstruction. Our approach drastically reduces the number of measurements required compared to using equidistant points on a regular grid, although reanalysis of such experiments is possible. The reconstruction algorithm produces a reconstructed function with exponentially decreasing error and quasilinear runtime in the number of Padua points. Moreover, using the interpolating polynomial of the Q function, we present a technique to directly estimate the density matrix elements of the continuous variable state, with only a linear propagation of input measurement error. Furthermore, we derive a state-independent analytical bound on this error, such that our estimate of the density matrix is accompanied by a measure of its uncertainty.

Quantitative Tomography for Continuous Variable Quantum Systems

Science.gov (United States)

Landon-Cardinal, Olivier; Govia, Luke C. G.; Clerk, Aashish A.

2018-03-01

We present a continuous variable tomography scheme that reconstructs the Husimi Q function (Wigner function) by Lagrange interpolation, using measurements of the Q function (Wigner function) at the Padua points, conjectured to be optimal sampling points for two dimensional reconstruction. Our approach drastically reduces the number of measurements required compared to using equidistant points on a regular grid, although reanalysis of such experiments is possible. The reconstruction algorithm produces a reconstructed function with exponentially decreasing error and quasilinear runtime in the number of Padua points. Moreover, using the interpolating polynomial of the Q function, we present a technique to directly estimate the density matrix elements of the continuous variable state, with only a linear propagation of input measurement error. Furthermore, we derive a state-independent analytical bound on this error, such that our estimate of the density matrix is accompanied by a measure of its uncertainty.

Geodesics in hypercomplex number systems. Application to commutative quaternions

International Nuclear Information System (INIS)

Catoni, Francesco; Zampetti, Paolo; Cannata, Roberto; Bordoni, Luciana

1997-10-01

The functions of hypercomplex variable can be related to the physical fields. Following the Einstein's ideas, by which the Theory of General Relativity was developed, they want to verify if a generalisation is possible, in order to described the motion of a body in a gravitational field, by the geodesics in spaces ''deformed'' by functional transformations of hypercomplex variables. These number systems introduce new space symmetries. This paper is just a first step in the more extended study. As a first application they consider the ''commutative quaternions'' system that may be considered as a composition of complex and hyperbolic numbers. By using in this system the same functional transformations valid for the two dimensional case, elliptical geodesics are obtained, with the eccentricity related to the angle between the orbit plane and a reference plane. These geodesics do not describe the Kepler orbits, but they show a space anisotropy that might be related to planet orbits of the solar system

Seasonal Variability in European Radon Measurements

Science.gov (United States)

Groves-Kirkby, C. J.; Denman, A. R.; Phillips, P. S.; Crockett, R. G. M.; Sinclair, J. M.

2009-04-01

In temperate climates, domestic radon concentration levels are generally seasonally dependent, the level in the home reflecting the convolution of two time-dependent functions. These are the source soil-gas radon concentration itself, and the principal force driving radon into the building from the soil, namely the pressure-difference between interior and exterior environment. While the meteorological influence can be regarded as relatively uniform on a European scale, its variability being defined largely by the influence of North-Atlantic weather systems, soil-gas radon is generally more variable as it is essentially geologically dependent. Seasonal variability of domestic radon concentration can therefore be expected to exhibit geographical variability, as is indeed the case. To compensate for the variability of domestic radon levels when assessing the long term radon health risks, the results of individual short-term measurements are generally converted to equivalent mean annual levels by application of a Seasonal Correction Factor (SCF). This is a multiplying factor, typically derived from measurements of a large number of homes, applied to the measured short-term radon concentration to provide a meaningful annual mean concentration for dose-estimation purposes. Following concern as to the universal applicability of a single SCF set, detailed studies in both the UK and France have reported location-specific SCF sets for different regions of each country. Further results indicate that SCFs applicable to the UK differ significantly from those applicable elsewhere in Europe and North America in both amplitude and phase, supporting the thesis that seasonal variability in indoor radon concentration cannot realistically be compensated for by a single national or international SCF scheme. Published data characterising the seasonal variability of European national domestic radon concentrations, has been collated and analysed, with the objective of identifying

An AO-assisted Variability Study of Four Globular Clusters

Science.gov (United States)

Salinas, R.; Contreras Ramos, R.; Strader, J.; Hakala, P.; Catelan, M.; Peacock, M. B.; Simunovic, M.

2016-09-01

The image-subtraction technique applied to study variable stars in globular clusters represented a leap in the number of new detections, with the drawback that many of these new light curves could not be transformed to magnitudes due to severe crowding. In this paper, we present observations of four Galactic globular clusters, M 2 (NGC 7089), M 10 (NGC 6254), M 80 (NGC 6093), and NGC 1261, taken with the ground-layer adaptive optics module at the SOAR Telescope, SAM. We show that the higher image quality provided by SAM allows for the calibration of the light curves of the great majority of the variables near the cores of these clusters as well as the detection of new variables, even in clusters where image-subtraction searches were already conducted. We report the discovery of 15 new variables in M 2 (12 RR Lyrae stars and 3 SX Phe stars), 12 new variables in M 10 (11 SX Phe and 1 long-period variable), and 1 new W UMa-type variable in NGC 1261. No new detections are found in M 80, but previous uncertain detections are confirmed and the corresponding light curves are calibrated into magnitudes. Additionally, based on the number of detected variables and new Hubble Space Telescope/UVIS photometry, we revisit a previous suggestion that M 80 may be the globular cluster with the richest population of blue stragglers in our Galaxy. Based on observations obtained at the Southern Astrophysical Research (SOAR) telescope, which is a joint project of the Ministério da Ciência, Tecnologia, e Inovação (MCTI) da República Federativa do Brasil, the U.S. National Optical Astronomy Observatory (NOAO), the University of North Carolina at Chapel Hill (UNC), and Michigan State University (MSU).

Haplotype phasing and inheritance of copy number variants in nuclear families.

Science.gov (United States)

Palta, Priit; Kaplinski, Lauris; Nagirnaja, Liina; Veidenberg, Andres; Möls, Märt; Nelis, Mari; Esko, Tõnu; Metspalu, Andres; Laan, Maris; Remm, Maido

2015-01-01

DNA copy number variants (CNVs) that alter the copy number of a particular DNA segment in the genome play an important role in human phenotypic variability and disease susceptibility. A number of CNVs overlapping with genes have been shown to confer risk to a variety of human diseases thus highlighting the relevance of addressing the variability of CNVs at a higher resolution. So far, it has not been possible to deterministically infer the allelic composition of different haplotypes present within the CNV regions. We have developed a novel computational method, called PiCNV, which enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data. The algorithm allows to i) phase normal and CNV-carrying haplotypes in the copy number variable regions, ii) resolve the allelic copies of rearranged DNA sequence within the haplotypes and iii) infer the heritability of identified haplotypes in trios or larger nuclear families. To our knowledge this is the first program available that can deterministically phase null, mono-, di-, tri- and tetraploid genotypes in CNV loci. We applied our method to study the composition and inheritance of haplotypes in CNV regions of 30 HapMap Yoruban trios and 34 Estonian families. For 93.6% of the CNV loci, PiCNV enabled to unambiguously phase normal and CNV-carrying haplotypes and follow their transmission in the corresponding families. Furthermore, allelic composition analysis identified the co-occurrence of alternative allelic copies within 66.7% of haplotypes carrying copy number gains. We also observed less frequent transmission of CNV-carrying haplotypes from parents to children compared to normal haplotypes and identified an emergence of several de novo deletions and duplications in the offspring.

Haplotype phasing and inheritance of copy number variants in nuclear families.

Directory of Open Access Journals (Sweden)

Priit Palta

Full Text Available DNA copy number variants (CNVs that alter the copy number of a particular DNA segment in the genome play an important role in human phenotypic variability and disease susceptibility. A number of CNVs overlapping with genes have been shown to confer risk to a variety of human diseases thus highlighting the relevance of addressing the variability of CNVs at a higher resolution. So far, it has not been possible to deterministically infer the allelic composition of different haplotypes present within the CNV regions. We have developed a novel computational method, called PiCNV, which enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data. The algorithm allows to i phase normal and CNV-carrying haplotypes in the copy number variable regions, ii resolve the allelic copies of rearranged DNA sequence within the haplotypes and iii infer the heritability of identified haplotypes in trios or larger nuclear families. To our knowledge this is the first program available that can deterministically phase null, mono-, di-, tri- and tetraploid genotypes in CNV loci. We applied our method to study the composition and inheritance of haplotypes in CNV regions of 30 HapMap Yoruban trios and 34 Estonian families. For 93.6% of the CNV loci, PiCNV enabled to unambiguously phase normal and CNV-carrying haplotypes and follow their transmission in the corresponding families. Furthermore, allelic composition analysis identified the co-occurrence of alternative allelic copies within 66.7% of haplotypes carrying copy number gains. We also observed less frequent transmission of CNV-carrying haplotypes from parents to children compared to normal haplotypes and identified an emergence of several de novo deletions and duplications in the offspring.

Development and characterization of genomic microsatellite ...

Indian Academy of Sciences (India)

2016-10-18

Oct 18, 2016 ... Molecular Genetics Laboratory, Centre for Plant Sciences, Central ... containing SSRs were analyse using SSR Identification Tool ... The clusters of hidden population were distinguished on the basis of multi-locus. Bayesian analysis.For evaluation of optimum number of populations (K), a simulation was.

THE RR LYRAE VARIABLES AND HORIZONTAL BRANCH OF NGC 6656 (M22) {sup ,}

Energy Technology Data Exchange (ETDEWEB)

Kunder, Andrea; Walker, Alistair R.; Paredes Alvarez, Leonardo [Cerro Tololo Inter-American Observatory, Casilla 603, La Serena (Chile); Stetson, Peter B. [Dominion Astrophysical Observatory, NRC-Herzberg, National Research Council, Victoria BC, V9E 2E7 (Canada); Cassisi, Santi [INAF-Osservatorio Astronomico di Collurania, Via M. Maggini, I-64100 Teramo (Italy); Layden, Andrew [Bowling Green State University, Bowling Green, OH 43403 (United States); Bono, Giuseppe [Dipartimento di Fisica, Universita di Roma Tor Vergata, Rome (Italy); Catelan, Márcio [Pontificia Universidad Católica de Chile, Departamento de Astronomía y Astrofísica, Av. Vicuña Mackenna 4860, 782-0436 Macul, Santiago (Chile); Clem, James L. [Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA 70803-4001 (United States); Matsunaga, Noriyuki [Department of Astronomy, School of Science, The University of Tokyo (Japan); Salaris, Maurizio [Astrophysics Research Institute, Liverpool John Moores University, Twelve Quays House, Egerton Wharf, Birkenhead CH41 1LD (United Kingdom); Lee, Jae-Woo [Korea Astronomy and Space Science Institute, Daejeon 305-348 (Korea, Republic of); Chaboyer, Brian, E-mail: akunder@ctio.noao.edu, E-mail: mcatelan@astro.puc.cl [Department of Physics and Astronomy, Dartmouth College, Hanover, NH 03755 (United States)

2013-11-01

The first calibrated broadband UBVI time-series photometry is presented for the RR Lyrae variable stars in NGC 6656 (M22), with observations spanning a range of 22 years. We have also redetermined the variability types and periods for the RR Lyrae stars identified previously by photographic observations, revising the number of fundamental-mode RR Lyrae variables (RR0) to 10 and the number of first-overtone variables (RR1) to 16. The mean periods of the RR0 and RR1 variables are (P) {sub RR0} = 0.66 ± 0.02 days and (P) {sub RR1} = 0.33 ± 0.01 days, respectively, supporting an Oosterhoff II classification for the cluster. The number ratio of RR1-type to all RR-type variables is N {sub 1}/N{sub RR} = 0.61, also consistent with an Oosterhoff II designation. Both the RR Lyrae stars' minimum light colors and the blue edge of the RR Lyrae instability strip suggest E( B – – V) = 0.36 ± 0.02 mag toward M22. Regarding the HB morphology of M22, we find (B-R)/(B+V+R) = +0.97 ± 0.1 and at least one ''gap'' located in an unusual part of the blue HB, in the middle of the so-called hot HB stars.