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Sample records for ptxa1 prn2 genotype

  1. Changes in genetic diversity of the Bordetella pertussis population in Serbia between 1953 and 2011

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    Plješa Tatjana

    2014-01-01

    Full Text Available Mass vaccination has significantly reduced the incidence of pertussis, however, the disease is re-emerging, even in some countries with high vaccination coverage. In Serbia, whole cell pertussis vaccine was introduced in 1957. To monitor changes in bacterial population, 77 isolates collected from 1953 to 2011 were studied. The methods included serotyping of fimbriae (Fim, genotyping of pertactin (prn and pertussis toxin S1 subunit (ptxA. A shift from ptxA2 to ptxA1 has been observed in isolates since the late of 1960s. In the period 1961-1979, the genotype ptxA1 became as common as genotype ptxA2. After that, during the period 1980-1989, the predominant ptx genotype was ptxA1. The reappearance of the ptxA2 allele followed an addition of the two strains harboring ptxA1 in the vaccine in 1985. The allele prn1 was predominant among the Serbian isolates, though prn3 and prn11 have been detected since 1981. The prn2 allele was only found in one strain isolated in 1984, two of the four strains isolated in 2000 and in three isolated strains from 2011. Serotype Fim2.3 disappeared before 1980 and serotype Fim2 became predominant thereafter. The results of this study indicate that the B. pertussis population in Serbia is different from other vaccinated populations and that this difference may be related to the vaccine used.

  2. Sequence variation in virulence-related genes of Bordetella pertussis isolates from Poland in the period 1959-2013.

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    Mosiej, E; Zawadka, M; Krysztopa-Grzybowska, K; Polak, M; Augustynowicz, E; Piekarska, K; Lutyńska, A

    2015-01-01

    This study aimed to characterise Bordetella pertussis isolates circulating in Poland since 1959. Sequence analysis of ptxA, ptxC, prn, tcfA, fim2, fim3 and ptxP for 175 clinical isolates and currently and previously used vaccine strains was performed. Clinical isolates from the period 1995-2013 were found to be different to three currently used vaccine strains harbouring the allelic combination ptxA2-ptxC1-ptxP1-prn1-tcfA2-fim2-1-fim3-1, seen frequently in Poland in the early pertussis vaccination period but not found after 1995. Generally, among B. pertussis isolates from the period 2000-2013, two genotypes predominated, ptxA1-ptxC1-ptxP1-prn1-tcfA2-fim2-2-fim3-1 and ptxA1-ptxC1-ptxP1-prn2-tcfA2-fim2-1-fim3-1, with frequencies of 45% and 32.5%, respectively. The isolates harbouring ptxA1-ptxC2-ptxP3-prn2-tcfA2-fim2-1-fim3-2 and ptxA1-ptxC2-ptxP3-prn2-tcfA2-fim2-1-fim3-1 profiles, currently highly prevalent within other European Union (EU) countries, were rarely found in Poland, as they circulated in the period 2000-2013 with frequencies of 10% and 5%, respectively. We hypothesise that several previous changes of strain composition in whole-cell pertussis vaccine produced locally and used since 1960 in Poland resulted in a more diverse immune pressure in the population, resulting in different prevalence of alleles compared to elsewhere.

  3. Desmanthus GENOTYPES

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    JOSÉ HENRIQUE DE ALBUQUERQUE RANGEL

    2015-01-01

    Full Text Available Desmanthus is a genus of forage legumes with potential to improve pastures and livestock produc-tion on clay soils of dry tropical and subtropical regions such as the existing in Brazil and Australia. Despite this patterns of natural or enforced after-ripening of Desmanthus seeds have not been well established. Four year old seed banks of nine Desmanthus genotypes at James Cook University were accessed for their patterns of seed softe-ning in response to a range of temperatures. Persistent seed banks were found to exist under all of the studied ge-notypes. The largest seeds banks were found in the genotypes CPI 78373 and CPI 78382 and the smallest in the genotypes CPI’s 37143, 67643, and 83563. An increase in the percentage of softened seeds was correlated with higher temperatures, in two patterns of response: in some accessions seeds were not significantly affected by tempe-ratures below 80º C; and in others, seeds become soft when temperature rose to as little as 60 ºC. At 80 °C the heat started to depress germination. High seed production of Desmanthus associated with dependence of seeds on eleva-ted temperatures to softening can be a very important strategy for plants to survive in dry tropical regions.

  4. Genotype adaptability and stability

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    Dimitrijević Miodrag

    2000-01-01

    Full Text Available One of the primary concerns in breeding programs is a small genotype reaction to environmental factor variation for better usage of yield genetic potential. Particularly if one takes in consideration that yield could van greatly because of more and more variable meteorological conditions. Studies conducted to observe genotype and environmental relations relay on numerous mathematical models, but genotype behavior in various ecological conditions is not, still, precisely defined Major sources of variation influencing genotype behavior in different environments are genotype/environment interaction, genetic background and environmental conditions. These factors could play an important role in establishing growth regions for maximal realization of genotype genetic potential, as well as in selection of genotypes having better response to complex requirements of particular growth region. Stability, the genotype ability to perform high, uniform yield no meter of different environmental conditions, and adaptability, genotype ability to give uniform yield in a different environmental conditions, are two common terms used to define genotype reaction in a consequence of environmental changes. Most of the models dealing with stability and adaptability are based on variation sources appearing under the influence of treatment, multivariate effects and residue. No meter which statistical model is used for GE interaction estimation, there is an opinion that no solid proof for the existence of stable genotypes obtained in breeding programs, which make some space for further investigations. There are still questions to answer dealing with definitions, sources of variation, usage value of existent models and interpretation of the results. .

  5. APOE Genotyping, Cardiovascular Disease

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    ... Home Visit Global Sites Search Help? APOE Genotyping, Cardiovascular Disease Share this page: Was this page helpful? Also ... of choice to decrease the risk of developing cardiovascular disease (CVD) . However, there is a wide variability in ...

  6. Rapid increase in pertactin-deficient Bordetella pertussis isolates, Australia.

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    Lam, Connie; Octavia, Sophie; Ricafort, Lawrence; Sintchenko, Vitali; Gilbert, Gwendolyn L; Wood, Nicholas; McIntyre, Peter; Marshall, Helen; Guiso, Nicole; Keil, Anthony D; Lawrence, Andrew; Robson, Jenny; Hogg, Geoff; Lan, Ruiting

    2014-04-01

    Acellular vaccines against Bordetella pertussis were introduced in Australia in 1997. By 2000, these vaccines had replaced whole-cell vaccines. During 2008-2012, a large outbreak of pertussis occurred. During this period, 30% (96/320) of B. pertussis isolates did not express the vaccine antigen pertactin (Prn). Multiple mechanisms of Prn inactivation were documented, including IS481 and IS1002 disruptions, a variation within a homopolymeric tract, and deletion of the prn gene. The mechanism of lack of expression of Prn in 16 (17%) isolates could not be determined at the sequence level. These findings suggest that B. pertussis not expressing Prn arose independently multiple times since 2008, rather than by expansion of a single Prn-negative clone. All but 1 isolate had ptxA1, prn2, and ptxP3, the alleles representative of currently circulating strains in Australia. This pattern is consistent with continuing evolution of B. pertussis in response to vaccine selection pressure.

  7. Axiom turkey genotyping array

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    The Axiom®Turkey Genotyping Array interrogates 643,845 probesets on the array, covering 643,845 SNPs. The array development was led by Dr. Julie Long of the USDA-ARS Beltsville Agricultural Research Center under a public-private partnership with Hendrix Genetics, Aviagen, and Affymetrix. The Turk...

  8. (Brassica napus L.) genotypes

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-05

    Oct 5, 2009 ... The genetic diversity and relationships among rapeseed genotypes were ... dent of environment and plant growth stage, unlimited ..... interactions that lead to the expression of particular traits .... thesis, Faculty of Agriculture, University of Novi Sad. ... in the U.S. hard red winter wheat cultivars as reveled by.

  9. Hepatitis C Virus Genotypes

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    Kayhan Azadmanesh

    2005-09-01

    the ultimate source of the virus's genetic diversity. HCV circulates as a heterogeneous population of genetically different but closely related genomes known as the quasispecies(15.As only 30-35% of nucleotides actually differ, there is obviously considerable heterogeneity in evolutionary rates among nucleotide sites in the genome. This heterogeneity is the result of variable evolutionary constraints. The 5'-UTR contains extensive secondary RNA structure and is correspondingly the slowest evolving genomic region(16. The next slowest region is the C (Core gene, which evolves three times faster than the 5'- UTR. The envelope genes E1 and E2 constitute the most diverse genome region and evolve about nine times faster than the 5'-UTR(16, probably as a result of their presumed role in evading the host immune response. Genomic Heterogeneity and ClassificationSystemsShortly after its discovery in 1989, it became clear that HCV had substantial nucleotide sequence diversity, with only 66 to 80% overall sequencesimilarity among strains belonging to different genotypes or subtypes(17. HCV isolates show four levels of genomic variations: types, subtypes, isolates, andquasispecies. The overall sequence similarities over complete genomic sequences are at least 91% within quasispecies, approximately 79% (range, 77 to 80% between subtypes, and about 68% (range, 66 to 69% between different types. This quasispecies is composed of a group of heterogeneous RNA sequences centered around a dominant nucleotide sequence that changes, throughout the course of the infection, under the selective pressure of the host immune system(18. More than one genotype can be found in the circulations of some HCV-infected patients, particularly in individuals who have received multiple transfusions and intravenous drug users. These are referred to as mixed-genotype infections(19, 20.The lack of a routinely available cell culture system and an easily available animal model has rendered classification of HCV

  10. SNP genotyping technologies

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland

    2013-01-01

    for this is the availability of high-throughput platforms for multiplexed SNP genotyping. Advancements in these technologies have enabled increased flexibility and throughput, allowing for the generation of adequate SNP marker data at very competitive cost per data point.......In the recent years, single nucleotide polymorphism (SNP) markers have emerged as the marker technology of choice for plant genetics and breeding applications. Besides the efficient technologies available for SNP discovery even in complex genomes, one of the main reasons...

  11. SNP genotyping technologies

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland

    2013-01-01

    In the recent years, single nucleotide polymorphism (SNP) markers have emerged as the marker technology of choice for plant genetics and breeding applications. Besides the efficient technologies available for SNP discovery even in complex genomes, one of the main reasons...... for this is the availability of high-throughput platforms for multiplexed SNP genotyping. Advancements in these technologies have enabled increased flexibility and throughput, allowing for the generation of adequate SNP marker data at very competitive cost per data point....

  12. Susceptibility of biallelic haplotype and genotype frequencies to genotyping error.

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    Moskvina, Valentina; Schmidt, Karl Michael

    2006-12-01

    With the availability of fast genotyping methods and genomic databases, the search for statistical association of single nucleotide polymorphisms with a complex trait has become an important methodology in medical genetics. However, even fairly rare errors occurring during the genotyping process can lead to spurious association results and decrease in statistical power. We develop a systematic approach to study how genotyping errors change the genotype distribution in a sample. The general M-marker case is reduced to that of a single-marker locus by recognizing the underlying tensor-product structure of the error matrix. Both method and general conclusions apply to the general error model; we give detailed results for allele-based errors of size depending both on the marker locus and the allele present. Multiple errors are treated in terms of the associated diffusion process on the space of genotype distributions. We find that certain genotype and haplotype distributions remain unchanged under genotyping errors, and that genotyping errors generally render the distribution more similar to the stable one. In case-control association studies, this will lead to loss of statistical power for nondifferential genotyping errors and increase in type I error for differential genotyping errors. Moreover, we show that allele-based genotyping errors do not disturb Hardy-Weinberg equilibrium in the genotype distribution. In this setting we also identify maximally affected distributions. As they correspond to situations with rare alleles and marker loci in high linkage disequilibrium, careful checking for genotyping errors is advisable when significant association based on such alleles/haplotypes is observed in association studies.

  13. Visible Genotype Sensor Array

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    Takashi Imai

    2008-04-01

    Full Text Available A visible sensor array system for simultaneous multiple SNP genotyping has been developed using a new plastic base with specific surface chemistry. Discrimination of SNP alleles is carried out by an allele-specific extension reaction using immobilized oligonucleotide primers. The 3’-ends of oligonucleotide primers are modified with a locked nucleic acid to enhance their efficiency in allelic discrimination. Biotin-dUTPs included in the reaction mixture are selectively incorporated into extending primer sequences and are utilized as tags for alkaline phosphatase-mediated precipitation of colored chemical substrates onto the surface of the plastic base. The visible precipitates allow immediate inspection of typing results by the naked eye and easy recording by a digital camera equipped on a commercial mobile phone. Up to four individuals can be analyzed on a single sensor array and multiple sensor arrays can be handled in a single operation. All of the reactions can be performed within one hour using conventional laboratory instruments. This visible genotype sensor array is suitable for “focused genomics” that follows “comprehensive genomics”.

  14. STR MARKERS. GENOTYPING APPLICATIONS

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    I. O. Sirbu

    2001-01-01

    Full Text Available STR (short tandem repeats loci consist of short, repetitive sequence elements of 2-8 bp in length. These abundant repeats are well distributed throughout the human genome and are rich source of highly polymorphic markers. There are literally hundreds of STR systems which have been mapped throughout the human genome. Several dozen have been investigated for application to human identity testing. These STR loci are found on almost every chromosome in the genome. They may be amplified using a variety of PCR primers. Tetranucleotide repeats have been most popular among forensic scientists due to their fidelity in PCR amplification although some tri- and pentanucleotide repeats are also in use. In this paper we intend (far from being exhaustive to present a synthesis of the characteristics of these genetic markers and their applications in genotyping, giving as an example the use of the STRs in a paternity testing case.

  15. HBV genotypic variability in Cuba.

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    Loureiro, Carmen L; Aguilar, Julio C; Aguiar, Jorge; Muzio, Verena; Pentón, Eduardo; Garcia, Daymir; Guillen, Gerardo; Pujol, Flor H

    2015-01-01

    The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions.

  16. HBV Genotypic Variability in Cuba

    Science.gov (United States)

    Loureiro, Carmen L.; Aguilar, Julio C.; Aguiar, Jorge; Muzio, Verena; Pentón, Eduardo; Garcia, Daymir; Guillen, Gerardo; Pujol, Flor H.

    2015-01-01

    The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions. PMID:25742179

  17. Genotype transposer: automated genotype manipulation for linkage disequilibrium analysis.

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    Cox, D G; Canzian, F

    2001-08-01

    The purpose of this work is to provide the modern molecular geneticist with tools to perform more efficient and more accurate analysis of the genotype data they produce. By using Microsoft Excel macros written in Visual Basic, we can translate genotype data into a form readable by the versatile software 'Arlequin', read the Arlequin output, calculate statistics of linkage disequilibrium, and put the results in a format for viewing with the software 'GOLD'. The software is available by FTP at: ftp://xcsg.iarc.fr/cox/Genotype_Transposer/. Detailed instruction and examples are available at: ftp://xcsg.iarc.fr/cox/Genotype&_Transposer/. Arlequin is available at: http://lgb.unige.ch/arlequin/. GOLD is available at: http://www.well.ox.ac.uk/asthma/GOLD/.

  18. Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

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    Brian O'Farrell

    Full Text Available Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of 200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

  19. Haplotypes versus genotypes on pedigrees

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    Kirkpatrick Bonnie B

    2011-04-01

    Full Text Available Abstract Background Genome sequencing will soon produce haplotype data for individuals. For pedigrees of related individuals, sequencing appears to be an attractive alternative to genotyping. However, methods for pedigree analysis with haplotype data have not yet been developed, and the computational complexity of such problems has been an open question. Furthermore, it is not clear in which scenarios haplotype data would provide better estimates than genotype data for quantities such as recombination rates. Results To answer these questions, a reduction is given from genotype problem instances to haplotype problem instances, and it is shown that solving the haplotype problem yields the solution to the genotype problem, up to constant factors or coefficients. The pedigree analysis problems we will consider are the likelihood, maximum probability haplotype, and minimum recombination haplotype problems. Conclusions Two algorithms are introduced: an exponential-time hidden Markov model (HMM for haplotype data where some individuals are untyped, and a linear-time algorithm for pedigrees having haplotype data for all individuals. Recombination estimates from the general haplotype HMM algorithm are compared to recombination estimates produced by a genotype HMM. Having haplotype data on all individuals produces better estimates. However, having several untyped individuals can drastically reduce the utility of haplotype data.

  20. Population samples and genotyping technology.

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    Mack, S J; Sanchez-Mazas, A; Single, R M; Meyer, D; Hill, J; Dron, H A; Jani, A J; Thomson, G; Erlich, H A

    2007-04-01

    The 14th International HLA (human leukocyte antigen) Immunogenetics Workshop (14th-IHIWS) Biostatistics and Anthropology/Human Genetic Diversity project continues the population sampling, genotype data generation, and biostatistic analyses of the 13th International Histocompatibility Workshop Anthropology/Human Genetic Diversity Component, with the overall goal of further characterizing global HLA allele and haplotype diversity and better describing the relationships between major histocompatibility complex diversity, geography, linguistics, and population history. Since the 13th Workshop, new investigators have and continue to be recruited to the project and new high-resolution class I and class II genotype data are being generated for 112 population samples from around the world.

  1. Pooled DNA genotyping on Affymetrix SNP genotyping arrays

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    Owen Michael J

    2006-02-01

    Full Text Available Abstract Background Genotyping technology has advanced such that genome-wide association studies of complex diseases based upon dense marker maps are now technically feasible. However, the cost of such projects remains high. Pooled DNA genotyping offers the possibility of applying the same technologies at a fraction of the cost, and there is some evidence that certain ultra-high throughput platforms also perform with an acceptable accuracy. However, thus far, this conclusion is based upon published data concerning only a small number of SNPs. Results In the current study we prepared DNA pools from the parents and from the offspring of 30 parent-child trios that have been extensively genotyped by the HapMap project. We analysed the two pools with Affymetrix 10 K Xba 142 2.0 Arrays. The availability of the HapMap data allowed us to validate the performance of 6843 SNPs for which we had both complete individual and pooled genotyping data. Pooled analyses averaged over 5–6 microarrays resulted in highly reproducible results. Moreover, the accuracy of estimating differences in allele frequency between pools using this ultra-high throughput system was comparable with previous reports of pooling based upon lower throughput platforms, with an average error for the predicted allelic frequencies differences between the two pools of 1.37% and with 95% of SNPs showing an error of Conclusion Genotyping thousands of SNPs with DNA pooling using Affymetrix microarrays produces highly accurate results and can be used for genome-wide association studies.

  2. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D

    2016-01-01

    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURC...

  3. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D;

    2016-01-01

    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURC...

  4. Microsatellite genotyping of carnation varieties

    NARCIS (Netherlands)

    Smulders, M.J.M.; Noordijk, Y.; Rus-Kortekaas, W.; Bredemeijer, G.M.M.; Vosman, B.

    2003-01-01

    A set of 11 sequence-tagged microsatellite markers for carnation (Dianthus caryophyllus) was developed using a DNA library enriched for microsatellites. Supplemented with three markers derived from sequence database entries, these were used to genotype carnation varieties using a semi-automated fluo

  5. Genotyping with TaqMAMA.

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    Li, Baohui; Kadura, Ibrahim; Fu, Dong-Jing; Watson, David E

    2004-02-01

    TaqMAMA combines the quantitative strengths of TaqMan with the allele-specific PCR of MAMA. In this article we develop TaqMAMA as a technique for screening human DNA samples for known genetic polymorphisms. In the first set of experiments, plasmids that model all types of genetic polymorphisms were used to understand the relationship between TaqMAMA primer/template mismatches and their strength of allelic discrimination. These data can be used to improve allelic discrimination of other primer extension genotyping methodologies through directed use of nucleotide mismatches. We used the data to derive a guide for TaqMAMA primer design and DNA strand selection for TaqMAMA genotyping assays. The guide was then used to develop assays for 11 known and novel human genetic polymorphisms. Genotypes were assigned quickly and accurately in all cases. TaqMAMA genotyping assays require minimal development time, have a high probability of success, produce reliable data that are straightforward to analyze, and are very cost-competitive.

  6. Colonization of Bordetella pertussis clinical isolates that differ by pulsed field gel electrophoresis types in the lungs of naïve mice or mice immunized with the whole-cell pertussis vaccine used in Poland.

    Science.gov (United States)

    Polak, Maciej; Zawadka, Monika; Mosiej, Ewa; Rabczenko, Daniel; Augustynowicz, Ewa; Guiso, Nicole; Lutyńska, Anna

    2015-04-01

    The goal of our study was to compare the elimination of Bordetella pertussis clinical isolates that differ according to pulsed field gel electrophoresis (PFGE), serotypes and genes encoding virulence factors from the lungs of naïve mice or mice immunized with commercial diphtheria-tetanus-whole-cell pertussis vaccine used in Poland. When a mixture of four isolates, given in equal proportions and harboring different PFGE profiles, serotypes, and alleles encoding virulence factors, was used to infect non-immunized mice, a single isolate, characterized by PFGE type IVγ, Fim2 phenotype and ptxA1-prn2-tcfA2-fim2-1-ptxP1-ptxC1-fim3-1 alleles, was found to be significantly predominant compared to the others. This PFGE profile is commonly found in B. pertussis isolates circulating in some European countries since the late 1990s, confirming its high fitness. The Polish commercial whole-cell pertussis vaccine induced an immunity effective at eliminating the B. pertussis isolates from the lungs. However, the elimination of the isolate harboring PFGE type C profile, Fim2,3 phenotype and ptxA1-prn1-tcfA2-fim2-1-ptxP1-ptxC1-fim3-1 alleles was delayed as compared to the others, suggesting phenotypic differences with the other isolates and vaccine strains. Nevertheless, the same isolate, when challenged into mice in the defined mixture of strains, lost the competition with the others, as measured by lung colonization efficiency. This PFGE profile represents 15 % of the isolates circulating in Poland between 2001 and 2012.

  7. Genotype × genotype interactions between the toxic cyanobacterium Microcystis and its grazer, the waterflea Daphnia

    Science.gov (United States)

    Lemaire, Veerle; Brusciotti, Silvia; van Gremberghe, Ineke; Vyverman, Wim; Vanoverbeke, Joost; De Meester, Luc

    2012-01-01

    Toxic algal blooms are an important problem worldwide. The literature on toxic cyanobacteria blooms in inland waters reports widely divergent results on whether zooplankton can control cyanobacteria blooms or cyanobacteria suppress zooplankton by their toxins. Here we test whether this may be due to genotype × genotype interactions, in which interactions between the large-bodied and efficient grazer Daphnia and the widespread cyanobacterium Microcystis are not only dependent on Microcystis strain or Daphnia genotype but are specific to genotype × genotype combinations. We show that genotype × genotype interactions are important in explaining mortality in short-time exposures of Daphnia to Microcystis. These genotype × genotype interactions may result in local coadaptation and a geographic mosaic of coevolution. Genotype × genotype interactions can explain why the literature on zooplankton–cyanobacteria interactions is seemingly inconsistent, and provide hope that zooplankton can contribute to the suppression of cyanobacteria blooms in restoration projects. PMID:25568039

  8. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D;

    2016-01-01

    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURCES...... well to dietary, physical activity, or drug based weight loss interventions and thus genetic predisposition to obesity associated with the FTO minor allele can be at least partly counteracted through such interventions. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42015015969.......: Ovid Medline, Scopus, Embase, and Cochrane from inception to November 2015. ELIGIBILITY CRITERIA FOR STUDY SELECTION: Randomised controlled trials in overweight or obese adults reporting reduction in body mass index, body weight, or waist circumference by FTO genotype (rs9939609 or a proxy) after...

  9. Two-mode clustering of genotype by trait and genotype by environment data

    NARCIS (Netherlands)

    Hageman, J.A.; Malosetti, M.; Eeuwijk, van F.A.

    2012-01-01

    In this paper, we demonstrate the use of two-mode clustering for genotype by trait and genotype by environment data. In contrast to two separate (one mode) clusterings on genotypes or traits/environments, two-mode clustering simultaneously produces homogeneous groups of genotypes and traits/environm

  10. Selection of common bean (Phaseolus vulgaris L.) genotypes using a genotype plus genotype x environment interaction biplot.

    Science.gov (United States)

    Corrêa, A M; Teodoro, P E; Gonçalves, M C; Santos, A; Torres, F E

    2016-08-05

    Recently, the genotype plus genotype x environment interaction (GGE) biplot methodology has been used to investigate genotype x environment interactions in several crop species, but has not been applied to the common bean (Phaseolus vulgaris L.) crop in Brazil. The aim of this study was to identify common bean genotypes that exhibit high grain yield and stability in the State of Mato Grosso do Sul, Brazil. We conducted 12 trials from 2000 to 2006 in the municipalities of Aquidauana and Dourados, and evaluated 13 genotypes in a randomized block design with three replications. Grain yield data were subjected to individual and joint analyses of variance. After analyzing the GE interaction, the adaptability and phenotypic stability of the common bean genotypes were analyzed using GGE biplot methodology. The genotypes EMGOPA-201, Xamego, and Aporé are recommended for growing in Mato Grosso do Sul, because they exhibited high grain yield and phenotypic stability.

  11. Progress in genotyping of Chlamydia trachomatis

    Institute of Scientific and Technical Information of China (English)

    Xia Yong; Xiong Likuan

    2014-01-01

    Objective To review the common genotyping techniques of Chlamydia trachomatis in terms of their principles,characteristics,applications and limitations.Data sources Data used in this review were mainly from English literatures of PubMed database.The search terms were "Chlamydia trachomatis" and "genotyping".Meanwhile,data from World Health Organization were also cited.Study selection Original articles and reviews relevant to present review's theme were selected.Results Different genotyping techniques were applied on different occasions according to their characteristics,especially in epidemiological studies worldwide,which pushed the study of Chlamydia trachomatis forward greatly.In addition,summaries of some epidemiological studies by genotyping were also included in this work for reference and comparison.Conclusions A clear understanding of common genotyping techniques could be helpful to genotype C.trachomatis more appropriately and effectively.Furthermore,more studies on the association of genotypes of Ch/amydia trachomatis with clinical manifestations should be performed.

  12. Rotavirus genotypes in Belarus, 2008-2012.

    Science.gov (United States)

    Semeiko, Galina V; Yermalovich, Marina A; Poliakova, Nadezhda; Mijatovic-Rustempasic, Slavica; Kerin, Tara K; Wasley, Annemarie; Videbaek, Dovile; Gentsch, Jon R; Bowen, Michael D; Samoilovich, Elena O

    2014-12-01

    This study describes group A rotavirus (RVA) genotype prevalence in Belarus from 2008 to 2012. In 2008, data from 3 sites in Belarus (Brest, Mogilev, Minsk) indicated that G4P[8] was the predominant genotype. Data from Minsk (2008-2012) showed that G4P[8] was the predominant RVA genotype in all years except in 2011 when G3P[8] was most frequently detected. Other RVA genotypes common in Europe (G1P[8], G2P[4]) were detected each year of the study. This study reveals the dominance of genotype G4P[8] in Belarus and helps to establish the baseline genotype prevalence prior to RVA vaccine introduction in the country.

  13. Grain yield stability of early maize genotypes

    Directory of Open Access Journals (Sweden)

    Chitra Bahadur Kunwar

    2016-12-01

    Full Text Available The objective of this study was to estimate grain yield stability of early maize genotypes. Five early maize genotypes namely Pool-17, Arun1EV, Arun-4, Arun-2 and Farmer’s variety were evaluated using Randomized Complete Block Design along with three replications at four different locations namely Rampur, Rajahar, Pakhribas and Kabre districts of Nepal during summer seasons of three consecutive years from 2010 to 2012 under farmer’s fields. Genotype and genotype × environment (GGE biplot was used to identify superior genotype for grain yield and stability pattern. The genotypes Arun-1 EV and Arun-4 were better adapted for Kabre and Pakhribas where as pool-17 for Rajahar environments. The overall findings showed that Arun-1EV was more stable followed by Arun-2 therefore these two varieties can be recommended to farmers for cultivation in both environments.

  14. Hepatitis C virus genotypes in Myanmar.

    Science.gov (United States)

    Win, Nan Nwe; Kanda, Tatsuo; Nakamoto, Shingo; Yokosuka, Osamu; Shirasawa, Hiroshi

    2016-07-21

    Myanmar is adjacent to India, Bangladesh, Thailand, Laos and China. In Myanmar, the prevalence of hepatitis C virus (HCV) infection is 2%, and HCV infection accounts for 25% of hepatocellular carcinoma. In this study, we reviewed the prevalence of HCV genotypes in Myanmar. HCV genotypes 1, 3 and 6 were observed in volunteer blood donors in and around the Myanmar city of Yangon. Although there are several reports of HCV genotype 6 and its variants in Myanmar, the distribution of the HCV genotypes has not been well documented in areas other than Yangon. Previous studies showed that treatment with peginterferon and a weight-based dose of ribavirin for 24 or 48 wk could lead to an 80%-100% sustained virological response (SVR) rates in Myanmar. Current interferon-free treatments could lead to higher SVR rates (90%-95%) in patients infected with almost all HCV genotypes other than HCV genotype 3. In an era of heavy reliance on direct-acting antivirals against HCV, there is an increasing need to measure HCV genotypes, and this need will also increase specifically in Myanmar. Current available information of HCV genotypes were mostly from Yangon and other countries than Myanmar. The prevalence of HCV genotypes in Myanmar should be determined.

  15. Hepatitis B virus genotypes:an overview

    Institute of Scientific and Technical Information of China (English)

    Mamun-Al Mahtab; Salimur Rahman; Mobin Khan; Fazal Karim

    2008-01-01

    BACKGROUND: Hepatitis B virus (HBV) infection is a major cause of mortality and morbidity globally. The quest continues to identify viral factors that inlfuence disease progression and severity as well as responses to treatment of HBV infection. Based on variations in HBV, the virus has been divided into a number of genotypes. DATA SOURCES: Review of published literature on HBV genotypes. RESULTS: HBV genotypes are likely to be important in determining the severity and progression of HBV-induced liver disease as well as responses to different anti-viral agents. CONCLUSION: Although HBV genotyping is not yet recommended for routine use in treating HBV infection, available data suggest that, as in hepatitis C virus infection, HBV genotyping is also likely to become a routine investigation for HBV treatment, perhaps in the not too distant future.

  16. Toward fully automated genotyping: Genotyping microsatellite markers by deconvolution

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Lancia, G.; See-Kiong, Ng [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    1995-11-01

    Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA){sub n} repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements. 32 refs., 5 figs., 3 tabs.

  17. Identification of Mislabeled Samples and Sample Mix-ups in Genotype Data using Barcode Genotypes

    DEFF Research Database (Denmark)

    Have, Christian Theil; Appel, Emil Vincent Rosenbaum; Grarup, Niels

    2014-01-01

    barcode genotypes. To detect mislabeled samples we calculate the probability that the discordance between genotypes in the data and in the independent genotypes can be attributed to random (non-mislabeling) genotyping errors. To identify mix-ups we calculate the probability of identifying the set...... of identical genotypes between sample x and sample y by chance. Based on this we calculate a mix-up confidence score with penalization for introducing mismatches in the proposed new label and adjustment for independency among the genotypes. This confidence score is used to identify probable mix-ups.......Abstract—Undetected mislabeled samples may affect the results of genotype studies, particular when rare genetic variants are investigated. Mislabeled samples are often not detected during quality control and if they are detected, they are normally discarded due to a lack of a reliable method...

  18. Genomic evaluations with many more genotypes

    Directory of Open Access Journals (Sweden)

    Wiggans George R

    2011-03-01

    Full Text Available Abstract Background Genomic evaluations in Holstein dairy cattle have quickly become more reliable over the last two years in many countries as more animals have been genotyped for 50,000 markers. Evaluations can also include animals genotyped with more or fewer markers using new tools such as the 777,000 or 2,900 marker chips recently introduced for cattle. Gains from more markers can be predicted using simulation, whereas strategies to use fewer markers have been compared using subsets of actual genotypes. The overall cost of selection is reduced by genotyping most animals at less than the highest density and imputing their missing genotypes using haplotypes. Algorithms to combine different densities need to be efficient because numbers of genotyped animals and markers may continue to grow quickly. Methods Genotypes for 500,000 markers were simulated for the 33,414 Holsteins that had 50,000 marker genotypes in the North American database. Another 86,465 non-genotyped ancestors were included in the pedigree file, and linkage disequilibrium was generated directly in the base population. Mixed density datasets were created by keeping 50,000 (every tenth of the markers for most animals. Missing genotypes were imputed using a combination of population haplotyping and pedigree haplotyping. Reliabilities of genomic evaluations using linear and nonlinear methods were compared. Results Differing marker sets for a large population were combined with just a few hours of computation. About 95% of paternal alleles were determined correctly, and > 95% of missing genotypes were called correctly. Reliability of breeding values was already high (84.4% with 50,000 simulated markers. The gain in reliability from increasing the number of markers to 500,000 was only 1.6%, but more than half of that gain resulted from genotyping just 1,406 young bulls at higher density. Linear genomic evaluations had reliabilities 1.5% lower than the nonlinear evaluations with 50

  19. Flavonoid profile of green asparagus genotypes.

    Science.gov (United States)

    Fuentes-Alventosa, J M; Jaramillo, S; Rodríguez-Gutiérrez, G; Cermeño, P; Espejo, J A; Jiménez-Araujo, A; Guillén-Bejarano, R; Fernández-Bolaños, J; Rodríguez-Arcos, R

    2008-08-27

    The determination of flavonoid profiles from different genotypes of triguero asparagus and their comparison to those from green asparagus commercial hybrids was the main goal of this study. The samples consisted of 32 commercial hybrids and 65 genotypes from the Huetor-Tajar population variety (triguero). The analysis of individual flavonoids by HPLC-DAD-MS has allowed the determination of eight naturally occurring flavonol derivatives in several genotypes of triguero asparagus. Those compounds included mono-, di-, and triglycosides of three flavonols, that is, quercetin, isorhamnetin, and kaempferol. The detailed analysis of the flavonoid profiles revealed significant differences among the distinct genotypes. These have been classified in three distinct groups as the result of a k-means clustering analysis, two of them containing both commercial hybrids and triguero asparagus and another cluster constituted by 21 genotypes of triguero asparagus, which contain several key flavonol derivatives able to differentiate them. Hence, the triglycosides tentatively identified as quercetin-3-rhamnosyl-rutinoside, isorhamnetin-3-rhamnosyl-rutinoside, and isorhamnetin-3-O-glucoside have been detected only in the genotypes grouped in the above-mentioned cluster. On the other hand, the compound tentatively identified as isorhamnetin-3-glucosyl-rutinoside was present in most genotypes of triguero asparagus, whereas it has not been detected in any of the commercial hybrids.

  20. HPV Genotyping 9G Membrane Test

    Directory of Open Access Journals (Sweden)

    Danishmalik Rafiq Sayyed

    2013-11-01

    Full Text Available The results of the genital human papillomavirus (HPV detection in 439 cervical samples by cervical cytology were compared with sequencing analysis and a newly developed HPV genotyping 9G membrane test. The excellent sensitivity and specificity of the HPV genotyping 9G membrane test was assured by a signal to noise ratio of more than 300 and a target hybridization to non-target hybridization ratio of 300 ~ 400 at 25 °C. The final results can be obtained in 29 min by simple loading of the hybridization and washing solutions and scanning the membranes without any drying steps or special handling. The 100% identical results of the HPV genotyping 9G membrane test with sequencing results in 439 clinical samples demonstrate significant clinical application for this test. HPV genotyping 9G membrane tests can identify and discriminate five HR-HPV genotypes which are prevalent in almost 87% of cervical cancer cases. Its simple handling makes the HPV genotyping 9G membrane test a very convenient platform for accurate HPV genotyping.

  1. HCV genotype-specific correlation with serum markers: Higher predictability for genotype 4a

    Directory of Open Access Journals (Sweden)

    Asad Sultan

    2011-06-01

    Full Text Available Abstract Background Several factors have been proposed to assess the clinical outcome of HCV infection. The correlation of HCV genotypes to possible serum markers in clinical prediction is still controversial. The main objective of this study was to determine the existence of any correlation between HCV genotypes to viral load and different clinical serum markers. Methods We performed a prospective cross-sectional and observational study. About 3160 serum HCV RNA positive patients were chosen from 4020 randomly selected anti-HCV positive patients. Statistical analysis was performed using the SPSS 16 software package. ROC (receiver operating characteristics curves were used to compare diagnostic values of serum markers to predict genotypes. Results The most prevalent genotype was 3a (73.9% followed by 1a (10.7%, 4a (6.4% and 3b (6.1% in Pakistani population. No correlation was found between viral load and serum markers for genotype 3a in a large no. of sample (n = 2336. While significant correlation was observed between viral load and AST in genotype 3b, ALP with viral load and ALT for genotype 1a. Patients with genotype 4a showed a significant inverse correlation with viral load and Hb level and AST with ALP. For genotype 4a, AUC (area under the curve of ALT, ALP, AST, bilirubin, Hb level and viral load was 0.790, 0.763, 0.454, 0.664, 0.458 and 0.872 respectively. Conclusions In conclusion, there was a significant variable response of HCV genotypes with serum markers. Severity of disease is independent of serum marker level in genotype 3a, while the liver damage in genotype 4a may associate with viral cytopathic effect as well as the immune-mediated process. An index using six serum markers may correctly predict genotype 4a in patients with ≥75% accuracy.

  2. Hepatitis C virus genotypes in Pakistan: a systemic review

    Directory of Open Access Journals (Sweden)

    Ali Ijaz

    2011-09-01

    Full Text Available Abstract Background and aim Phylogenetic analysis has led to the classification of hepatitis C virus (HCV into 1-6 major genotypes. HCV genotypes have different biological properties, clinical outcome and response to antiviral treatment and provide important clues for studying the epidemiology, transmission and pathogenesis. This article deepens the current molecular information about the geographical distribution of HCV genotypes and subgenotypes in population of four provinces of Pakistan. 34 published papers (1996-2011 related to prevalence of HCV genotypes/serotypes and subgenotypes in Pakistan were searched. Result HCV genotype/s distribution from all 34 studies was observed in 28,400 HCV infected individuals in the following pattern: 1,999 (7.03% cases of genotype 1; 1,085 (3.81% cases of genotype 2; 22,429 (78.96% cases of genotype 3; 453 (1.59% cases of genotype 4; 29 (0.10% cases of genotype 5; 37 (0.13% cases of genotype 6; 1,429 (5.03% cases of mixed genotypes, and 939 (3.30% cases of untypeable genotypes. Overall, genotype 3a was the predominant genotype with a rate of 55.10%, followed by genotype 1a, 3b and mixed genotype with a rate of 10.25%, 8.20%, and 5.08%, respectively; and genotypes 4, 5 and 6 were rare. Genotype 3 occurred predominately in all the provinces of Pakistan. Second more frequently genotype was genotype 1 in Punjab province and untypeable genotypes in Sindh, Khyber Pakhtunkhwa and Balochistan provinces.

  3. Hepatitis B virus genotypes circulating in Brazil: molecular characterization of genotype F isolates

    Directory of Open Access Journals (Sweden)

    Virgolino Helaine A

    2007-11-01

    Full Text Available Abstract Background Hepatitis B virus (HBV isolates have been classified in eight genotypes, A to H, which exhibit distinct geographical distributions. Genotypes A, D and F are predominant in Brazil, a country formed by a miscegenated population, where the proportion of individuals from Caucasian, Amerindian and African origins varies by region. Genotype F, which is the most divergent, is considered indigenous to the Americas. A systematic molecular characterization of HBV isolates from different parts of the world would be invaluable in establishing HBV evolutionary origins and dispersion patterns. A large-scale study is needed to map the region-by-region distribution of the HBV genotypes in Brazil. Results Genotyping by PCR-RFLP of 303 HBV isolates from HBsAg-positive blood donors showed that at least two of the three genotypes, A, D, and F, co-circulate in each of the five geographic regions of Brazil. No other genotypes were identified. Overall, genotype A was most prevalent (48.5%, and most of these isolates were classified as subgenotype A1 (138/153; 90.2%. Genotype D was the most common genotype in the South (84.2% and Central (47.6% regions. The prevalence of genotype F was low (13% countrywide. Nucleotide sequencing of the S gene and a phylogenetic analysis of 32 HBV genotype F isolates showed that a great majority (28/32; 87.5% belonged to subgenotype F2, cluster II. The deduced serotype of 31 of 32 F isolates was adw4. The remaining isolate showed a leucine-to-isoleucine substitution at position 127. Conclusion The presence of genotypes A, D and F, and the absence of other genotypes in a large cohort of HBV infected individuals may reflect the ethnic origins of the Brazilian population. The high prevalence of isolates from subgenotype A1 (of African origin indicates that the African influx during the colonial slavery period had a major impact on the circulation of HBV genotype A currently found in Brazil. Although most genotype F

  4. Counsel the genotype, treat the phenotype

    NARCIS (Netherlands)

    van der Zwaag, Paul A.; van Tintelen, J. Peter

    2011-01-01

    This editorial refers to 'Novel correlations between the genotype and the phenotype of hypertrophic and dilated cardiomyopathy: results from the German Competence Network Heart Failure' by S. Waldmuller et al., published in this issue on pages 1185-1192.

  5. Global distribution of novel rhinovirus genotype

    DEFF Research Database (Denmark)

    Briese, Thomas; Renwick, Neil; Venter, Marietjie

    2008-01-01

    Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America. Molecular dating indicates that these viruses have been circulating for at least 250 years Udgivelsesdato...

  6. Global distribution of novel rhinovirus genotype

    DEFF Research Database (Denmark)

    Briese, Thomas; Renwick, Neil; Venter, Marietjie

    2008-01-01

    Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America. Molecular dating indicates that these viruses have been circulating for at least 250 years....

  7. HPV genotypes concordance between sex partners.

    Science.gov (United States)

    Benevolo, M; Mottolese, M; Marandino, F; Carosi, M; Diodoro, M G; Sentinelli, S; Visca, P; Rollo, F; Mariani, L; Vocaturo, G; Sindico, R; Di Giannuario, D; Perrone Donnorso, R; Pellicciotta, M; Vocaturo, A

    2007-12-01

    The HPV genotype concordance in the sexual couples could support the sexual viral transmission of HPV infection. The present study contains a case-report of a stable Italian sex couple harbouring the same five HPV genotypes in their genital samples. The female partner, affected by vulvar condilomatosis, evidenced positivity in her cervicovaginal scraping with high risk HPV DNA Hybrid Capture 2 test and was negative at liquid-based performed Pap Test and at colposcopic examination. The male partner was clinically healthy regarding his external genitalia. In both male and female genital scrapings, the following HPV genotypes were detected by means of a PCR-based assay: 6, 16, 53, 73 and 84. This considerably high genotype concordance does not appear to be casual and supports, in our opinion, the hypothesis that genital HPV types are sexually transmitted agents

  8. ApoE (Apolipoprotein E) Genotyping

    Science.gov (United States)

    ... Home Visit Global Sites Search Help? APOE Genotyping, Alzheimer Disease Share this page: Was this page helpful? Formal ... help in the diagnosis of probable late onset Alzheimer disease (AD) in symptomatic adults. It is called susceptibility ...

  9. Forensic SNP genotyping with SNaPshot

    DEFF Research Database (Denmark)

    Fondevila, M; Børsting, C; Phillips, C

    2017-01-01

    This review explores the key factors that influence the optimization, routine use, and profile interpretation of the SNaPshot single-base extension (SBE) system applied to forensic single-nucleotide polymorphism (SNP) genotyping. Despite being a mainly complimentary DNA genotyping technique...... to routine STR profiling, use of SNaPshot is an important part of the development of SNP sets for a wide range of forensic applications with these markers, from genotyping highly degraded DNA with very short amplicons to the introduction of SNPs to ascertain the ancestry and physical characteristics...... of an unidentified contact trace donor. However, this technology, as resourceful as it is, displays several features that depart from the usual STR genotyping far enough to demand a certain degree of expertise from the forensic analyst before tackling the complex casework on which SNaPshot application provides...

  10. Can Clustering in Genotype Space Reveal "Niches"?

    Science.gov (United States)

    D'Andrea, Rafael; Ostling, Annette

    2016-01-01

    Community ecology lacks the success enjoyed by population genetics to quantify the relative roles played by deterministic and stochastic processes. It has been proposed that clustered patterns of abundance in genotype space provide evidence of selection in microbial communities, since no such clustering would arise in the absence of selection. We critique this test for its unrealistic null hypothesis. We show mathematically and with simulations that point mutations alone lead to clustering in genotype space by causing correlations between abundances of similar genotypes. We also show potential deviations from the mutation-only pattern caused by immigration from a source pool. Clustered patterns in genotype space may still be revealing of selection if analyzed quantitatively but only if neutral and selective regimes can be distinguished once mutation and immigration are included in the null model.

  11. AFLP analysis among Ethiopian arabica coffee genotypes

    African Journals Online (AJOL)

    STORAGESEVER

    2008-09-17

    Sep 17, 2008 ... sequence information, produces a large number of infor- mative polymorphic markers per primer, requires a small amount of ..... and 53 were monomorphic across all coffee genotypes collected from .... molecular markers.

  12. Early seedling development of Medicago truncatula genotypes ...

    African Journals Online (AJOL)

    adel

    2014-01-08

    Jan 8, 2014 ... germinated on filter papers imbibed in distilled water or in sodium .... Wards minimum variance method as a clustering algorithm. ... Mean values of plumule: radicle ratio of M. truncatula genotypes under different salt stress ...

  13. HMSRP Hawaiian Monk Seal Microsatellite Genotypes

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Currently ~2,400 Hawaiian monk seal specimens have been analyzed genetically, providing genotypes at 18 microsatellite loci. These data are organized by individual,...

  14. Genotypic Variation for Salinity Tolerance in Sorghum (Sorghum bicolor (L. Moench Genotypes at Early Growth Stages

    Directory of Open Access Journals (Sweden)

    Tigabu, Endalew

    2013-04-01

    Full Text Available Sorghum (Sorghum bicolor L. Moench is the fifth most economically important crop among cereals in the world. Salinity is an abiotic factor which reduces productivity of sorghum. Exploiting genetic variability to identify salt tolerant genotype is one of the strategies used to overcome salinity. Pot experiment was carried out to evaluate the genetic variation of eleven sorghum genotypes for NaCl salinity response at germination and early seedling stages. The experimental treatments were five NaCl salinity levels (0, 2, 4, 8, and 16 dS m-1 and eleven sorghum genotypes (Gambella1107, Melkam, S-35, ESH-2, Gobye, 97MW6130, Meko, 76T1#23, ICSV-111, Abshir and Teshale. The experimental design was completely randomized design with three replicates.Data was analyzed using SAS (version 9.0 statistical software and means were separated by LSD. Germination rate, final germination percentage, seedling shoot length and seedling root length were measured. The ANOVA for treatments, genotypes and their interaction was found to be highly significant (p<0.001 with regard to all parameters. Genotypes Meko, Gambella1107, ICSV-111 and Melkam were found salt tolerant during germination and seedling growth stages. However, genotypes ESH-2 and Gobye were salt sensitive during both stages. The rest sorghum genotypes were intermediate in their salt tolerance. The study affirmed the presence of wide genotypic variation among the sorghum genotypes for NaCl salt tolerance.

  15. Blood Group ABO Genotyping in Paternity Testing.

    Science.gov (United States)

    Bugert, Peter; Rink, Gabriele; Kemp, Katharina; Klüter, Harald

    2012-06-01

    BACKGROUND: The ABO blood groups result from DNA sequence variations, predominantly single nucleotide and insertion/deletion polymorphisms (SNPs and indels), in the ABO gene encoding a glycosyltransferase. The ABO blood groups A(1), A(2), B and O predominantly result from the wild type allele A1 and the major gene variants that are characterized by four diallelic markers (261G>del, 802G>A, 803G>C, 1061C>del). Here, we were interested to evaluate the impact of ABO genotyping compared to ABO phenotyping in paternity testing. METHODS: The major ABO alleles were determined by PCR amplification with sequence-specific primers (PCR-SSP) in a representative sample of 1,335 blood donors. The genotypes were compared to the ABO blood groups registered in the blood donor files. Then, the ABO phenotypes and genotypes were determined in 95 paternity trio cases that have been investigated by 12 short tandem repeat (STR) markers before. We compared statistical parameters (PL, paternity likelihood; PE, power of exclusion) of both blood grouping approaches. RESULTS: The prevalence of the major ABO alleles and genotypes corresponded to the expected occurrence of ABO blood groups in a Caucasian population. The low resolution genotyping of 4 diallelic markers revealed a correct genotype-phenotype correlation in 1,331 of 1,335 samples (99.7%). In 60 paternity trios with confirmed paternity of the alleged father based on STR analysis both PL and PE of the ABO genotype was significantly higher than of the ABO phenotype. In 12 of 35 exclusion cases (34.3%) the ABO genotype also excluded the alleged father, whereas the ABO phenotype excluded the alleged father only in 7 cases (20%). CONCLUSION: In paternity testing ABO genotyping is superior to ABO phenotyping with regard to PL and PE, however, ABO genotyping is not sufficient for valid paternity testing. Due to the much lower mutation rate compared to STR markers, blood group SNPs in addition to anonymous SNPs could be considered for

  16. Blood Group ABO Genotyping in Paternity Testing

    Science.gov (United States)

    Bugert, Peter; Rink, Gabriele; Kemp, Katharina; Klüter, Harald

    2012-01-01

    Background The ABO blood groups result from DNA sequence variations, predominantly single nucleotide and insertion/deletion polymorphisms (SNPs and indels), in the ABO gene encoding a glycosyltransferase. The ABO blood groups A1, A2, B and O predominantly result from the wild type allele A1 and the major gene variants that are characterized by four diallelic markers (261G>del, 802G>A, 803G>C, 1061C>del). Here, we were interested to evaluate the impact of ABO genotyping compared to ABO phenotyping in paternity testing. Methods The major ABO alleles were determined by PCR amplification with sequence-specific primers (PCR-SSP) in a representative sample of 1,335 blood donors. The genotypes were compared to the ABO blood groups registered in the blood donor files. Then, the ABO phenotypes and genotypes were determined in 95 paternity trio cases that have been investigated by 12 short tandem repeat (STR) markers before. We compared statistical parameters (PL, paternity likelihood; PE, power of exclusion) of both blood grouping approaches. Results The prevalence of the major ABO alleles and genotypes corresponded to the expected occurrence of ABO blood groups in a Caucasian population. The low resolution genotyping of 4 diallelic markers revealed a correct genotype-phenotype correlation in 1,331 of 1,335 samples (99.7%). In 60 paternity trios with confirmed paternity of the alleged father based on STR analysis both PL and PE of the ABO genotype was significantly higher than of the ABO phenotype. In 12 of 35 exclusion cases (34.3%) the ABO genotype also excluded the alleged father, whereas the ABO phenotype excluded the alleged father only in 7 cases (20%). Conclusion In paternity testing ABO genotyping is superior to ABO phenotyping with regard to PL and PE, however, ABO genotyping is not sufficient for valid paternity testing. Due to the much lower mutation rate compared to STR markers, blood group SNPs in addition to anonymous SNPs could be considered for future

  17. Cotton genotypes selection through artificial neural networks.

    Science.gov (United States)

    Júnior, E G Silva; Cardoso, D B O; Reis, M C; Nascimento, A F O; Bortolin, D I; Martins, M R; Sousa, L B

    2017-09-27

    Breeding programs currently use statistical analysis to assist in the identification of superior genotypes at various stages of a cultivar's development. Differently from these analyses, the computational intelligence approach has been little explored in genetic improvement of cotton. Thus, this study was carried out with the objective of presenting the use of artificial neural networks as auxiliary tools in the improvement of the cotton to improve fiber quality. To demonstrate the applicability of this approach, this research was carried out using the evaluation data of 40 genotypes. In order to classify the genotypes for fiber quality, the artificial neural networks were trained with replicate data of 20 genotypes of cotton evaluated in the harvests of 2013/14 and 2014/15, regarding fiber length, uniformity of length, fiber strength, micronaire index, elongation, short fiber index, maturity index, reflectance degree, and fiber quality index. This quality index was estimated by means of a weighted average on the determined score (1 to 5) of each characteristic of the HVI evaluated, according to its industry standards. The artificial neural networks presented a high capacity of correct classification of the 20 selected genotypes based on the fiber quality index, so that when using fiber length associated with the short fiber index, fiber maturation, and micronaire index, the artificial neural networks presented better results than using only fiber length and previous associations. It was also observed that to submit data of means of new genotypes to the neural networks trained with data of repetition, provides better results of classification of the genotypes. When observing the results obtained in the present study, it was verified that the artificial neural networks present great potential to be used in the different stages of a genetic improvement program of the cotton, aiming at the improvement of the fiber quality of the future cultivars.

  18. Phenotypic and genotypic variation in Iranian Pistachios

    Directory of Open Access Journals (Sweden)

    Somayeh Tayefeh Aliakbarkhani

    2015-12-01

    Full Text Available As Iran is one of the richest pistachio germplasms a few studies have been conducted on different sexes of pistachio trees, in areas where this crop emerged. To this end, 40 male and female Iranian pistachio genotypes from Feizabad region, Khorasan, Iran; were evaluated using morphological characters and randomly amplified polymorphic DNA (RAPD markers. For morphological assessments, 54 variables were considered to investigate similarities between and among the studied genotypes. Morphological data indicated relative superiority in some female genotypes (such as Sefid 1, Sefid Sabuni 2, Garmesiah, and Ghermezdorosht Z regarding characters such as halfcrackedness, the percentages of protein and fat content. 115 polymorphic bands were recorded with 92.83% average polymorphism among all primers. The total resolving power (Rp of the primers was 74.54. The range of genetic similarity varied from about 0.31 to about 0.70. Genotypes were segregated into eight groups at the similarity limit of 0.41. Results of present investigation could be helpful for strategic decisions for maintaining Iranian pistachio genotypes.

  19. Automated SNP Genotype Clustering Algorithm to Improve Data Completeness in High-Throughput SNP Genotyping Datasets from Custom Arrays

    Institute of Scientific and Technical Information of China (English)

    Edward; M.; Smith; Jack; Littrell; Michael; Olivier

    2007-01-01

    High-throughput SNP genotyping platforms use automated genotype calling algo- rithms to assign genotypes. While these algorithms work efficiently for individual platforms, they are not compatible with other platforms, and have individual biases that result in missed genotype calls. Here we present data on the use of a second complementary SNP genotype clustering algorithm. The algorithm was originally designed for individual fluorescent SNP genotyping assays, and has been opti- mized to permit the clustering of large datasets generated from custom-designed Affymetrix SNP panels. In an analysis of data from a 3K array genotyped on 1,560 samples, the additional analysis increased the overall number of genotypes by over 45,000, significantly improving the completeness of the experimental data. This analysis suggests that the use of multiple genotype calling algorithms may be ad- visable in high-throughput SNP genotyping experiments. The software is written in Perl and is available from the corresponding author.

  20. Identification of Some Walnut Genotypes in Lorestan Province of Iran and Selection of 54 Superior Genotypes

    Directory of Open Access Journals (Sweden)

    A. Mohammadi

    2015-06-01

    Full Text Available Identification and selection of superior genotypes is the first step in walnut breeding programs. For identifying superior genotypes in Lorestan province, Iran, 35000 seedling genotypes were evaluated during 2008-2009. 29 Phenological traits were evaluated using IPGIRI descriptors in 288 selected seedling genotypes. Finally 54 promising genotypes with 10 major phenological traits were evaluated and classified to five groups. Based on the results, The first group included B17 alone as a late leafing genotype. The second group included A11, J14, K20, H19, M13, J1, B14, E14, E6, G17, M7, O9, B7, L6, L10, F12, D6, J15, J16, N5 and N15 genotypes with high kernel percentage, very bright kernel colors, less shell thickness and medium basal fruit pore. M9 with the highest kernel percent among all of the genotypes and 80% of lateral bearing, closed basal fruit pore, less shell thickness and high fruit and kernel weight was classified in another groupe. A7, C5, N3, N18, A17, D1, N14, D4, I4, J6, K17, N4, N19, C10, E13, N13 and N16 genotypes with medium to high fruit diameter, less shell thickness, medium fruit and kernel weight and kernel percentage were classified in the next group. The fifth group included 10 promising genotypes consisting A1, A2, C12, D10, D11, D13, F3, D17, A3, N7, I13, J7, K9 and N11 with quite late leafing and lateral fruit bearing of more than 90% .

  1. Saponin profile of green asparagus genotypes.

    Science.gov (United States)

    Vázquez-Castilla, Sara; Jaramillo-Carmona, Sara; Fuentes-Alventosa, Jose María; Jiménez-Araujo, Ana; Rodríguez-Arcos, Rocío; Cermeño-Sacristán, Pedro; Espejo-Calvo, Juan Antonio; Guillén-Bejarano, Rafael

    2013-11-20

    The main goal of this study was to determine the saponin profiles of different "triguero" asparagus genotypes and to compare them to green asparagus commercial hybrids. The samples consisted of 31 commercial hybrids and 58 genotypes from the Huétor-Tájar (HT) population variety ("triguero"). The saponin analysis by high-performance liquid chromatography-mass spectrometry allowed for the determination of 12 saponins derived from a furostan-type steroidal genin, 4 of which had never been described in the edible part of asparagus. The saponin profile of "triguero" asparagus was a combination of these new saponins and protodioscin. Although protodioscin was the major saponin found in commercial hybrids, some of these 12 saponins were detected as major components in some of the commercial hybrids. The total contents of saponins described in some of these HT genotypes reach values as high as 10-100 times higher than those found in commercial hybrids.

  2. ABO Genotyping of Complete Hydatidiform Moles

    Directory of Open Access Journals (Sweden)

    R. A. Fisher

    1993-01-01

    Full Text Available It has been suggested that the ABO blood group of a patient and her partner influence the clinical outcome for patients having a pregnancy with a complete hydatidiform mole (CHM. Since CHM lack red blood Cells, it has not previously been possible to type CHM serologically and investigate the relationship between the blood group of the CHM and that of the patient. In the present study we have demonstrated the feasibility of using molecular genotyping to determine the ABO genotype of CHM, the ABO genotype being consistent with the androgenetic origin of CHM in all cases. In the series of 48 cases of CHM, the requirement for chemotherapy was not significantly different in those patients with a CHM of like blood group compared with those with a CHM of unlike blood group.

  3. An Application of Molecular Genotyping in Mice

    Directory of Open Access Journals (Sweden)

    Underkoffler Lara A.

    2003-01-01

    Full Text Available Microsatellite markers are simple sequence repeats within the mammalian genome that can be used for identifying disease loci, mapping genes of interest as well as studying segregation patterns related to meiotic nondisjunction. Different strains of mice have variable CA repeat lengths and PCR based methods can be used to identify them, thus allowing for specific genotypes to be assigned. Molecular genotyping offers such identification at any developmental stage, which allows for a broad range of anomalies to be studied. We studied chromosomal segregation in relation to nondisjunction in early-gestation mouse embryos using molecular genotyping. Information on the parental origin as well as the number of chromosomes a given progeny carried was obtained in our analysis.

  4. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

    OpenAIRE

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-01-01

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicoch...

  5. Specificity of the Linear Array HPV Genotyping Test for detecting human papillomavirus genotype 52 (HPV-52)

    OpenAIRE

    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja

    2015-01-01

    Introduction: HPV-52 is one of the most frequent human papillomavirus (HPV) genotypes causing significant cervical pathology. The most widely used HPV genotyping assay, the Roche Linear Array HPV Genotyping Test (Linear Array), is unable to identify HPV- 52 status in samples containing HPV-33, HPV-35, and/or HPV-58. Methods: Linear Array HPV-52 analytical specificity was established by testing 100 specimens reactive with the Linear Array HPV- 33/35/52/58 cross-reactive probe, but not with the...

  6. Use of supplementary genotypes in AMMI analysis.

    Science.gov (United States)

    Pacheco, R M; Duarte, J B; Vencovsky, R; Pinheiro, J B; Oliveira, A B

    2005-03-01

    Improving stability of crop yield in a target production environment is an important breeding objective. It is well known that selection for better stability generally results in lower mean yields and, conversely, that selection for higher mean yields may lead to poorer stability. This paper explores the equivalence between the singular value decomposition used in AMMI analysis and the spectral decomposition used in principal components analysis. This equivalence enables scores of a "supplementary genotype" made up of the highest yield value within each environment to be obtained, and these may serve as the ideal check treatment for selection purposes. These scores are used to (1) display this check in a biplot graph, thereby providing a qualitative comparison with the real genotypes related to their interaction with environments; (2) obtain estimates of the squared distances from the projection of each real genotype to the projection of the "supplementary treatment", thereby allowing conclusions to be made on the yield stability of each real genotype. This procedure was effective in identifying the most stable soybean cultivars in an example shown for illustration.

  7. Polyembryony in non-apomictic citrus genotypes

    Science.gov (United States)

    Aleza, Pablo; Juárez, José; Ollitrault, Patrick; Navarro, Luis

    2010-01-01

    Background and Aims Adventitious embryony from nucellar cells is the mechanism leading to apomixis in Citrus sp. However, singular cases of polyembryony have been reported in non-apomictic genotypes as a consequence of 2x × 4x hybridizations and in vitro culture of isolated nucelli. The origin of the plants arising from the aforementioned processes remains unclear. Methods The genetic structure (ploidy and allelic constitution with microsatellite markers) of plants obtained from polyembryonic seeds arising from 2x × 4x sexual hybridizations and those regenerated from nucellus culture in vitro was systematically analysed in different non-apomictic citrus genotypes. Histological studies were also conducted to try to identify the initiation process underlying polyembryony. Key Results All plants obtained from the same undeveloped seed in 2x × 4x hybridizations resulted from cleavage of the original zygotic embryo. Also, the plants obtained from in vitro nucellus culture were recovered by somatic embryogenesis from cells that shared the same genotype as the zygotic embryos of the same seed. Conclusions It appears that in non-apomictic citrus genotypes, proembryos or embryogenic cells are formed by cleavage of the zygotic embryos and that the development of these adventitious embryos, normally hampered, can take place in vivo or in vitro as a result of two different mechanisms that prevent the dominance of the initial zygotic embryo. PMID:20675656

  8. Phenotyping peanut genotypes for drought tolerance

    Science.gov (United States)

    Drought and heat stress can result in aflatoxin contamination of peanuts especially when this occurs during the last three to six weeks of the growing season. Identifying drought-tolerant genotypes may aid in development of peanuts that are less susceptible to aflatoxin contamination. This study w...

  9. 6 HCV genotyping 9G test and its comparison with VERSANT HCV genotype 2.0 assay (LiPA) for the hepatitis C virus genotyping.

    Science.gov (United States)

    Chantratita, Wasun; Song, Keum-Soo; GunHo, Choi; Pongthanapisith, Viroj; Thongbaiphet, Nipa; Wongtabtim, Garanyuta; Pasomsub, Ekawat; Angkanavin, Kanokwan; Nimse, Satish Balasaheb; Sonawane, Mukesh Digambar; Warkad, Shrikant Dasharath; Kim, Taisun

    2017-01-01

    In this article, we describe the 6 HCV Genotyping 9G test and its evaluation by using clinical samples and plasmid DNA standards. In tests with 981 plasmid DNA standards, the 6 HCV Genotyping 9G test showed higher than 92.5% sensitivity and 99.4% specificity. The 6 HCV Genotyping 9G test was compared with the VERSANT HCV Genotype 2.0 assay (LiPA 2.0) for detection and discrimination of HCV genotypes in clinical samples. The results of both tests were verified by genomic sequencing. The 6 HCV Genotyping 9G test demonstrated a 100% agreement with the sequencing results, which was higher than LiPA 2.0. These results indicate that the 6 HCV Genotyping 9G test can be a reliable, sensitive, and accurate diagnostic tool for the correct identification of HCV genotypes in clinical specimens. 6 HCV Genotyping 9G test can genotype six HCV types in 1 PCR in 30min after PCR amplification. The 6 HCV Genotyping 9G test, thus provide critical information to physicians and assist them to apply accurate drug regimen for the effective hepatitis C treatment.

  10. Identification of zoonotic genotypes of Giardia duodenalis.

    Science.gov (United States)

    Sprong, Hein; Cacciò, Simone M; van der Giessen, Joke W B

    2009-12-01

    Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G) which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals in the epidemiology of human infection is still unclear, despite the fact that the zoonotic potential of Giardia was recognised by the WHO some 30 years ago. Here, we performed an extensive genetic characterization of 978 human and 1440 animal isolates, which together comprise 3886 sequences from 4 genetic loci. The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset). The zoonotic potential of both assemblages A and B is evident when studied at the level of assemblages, sub-assemblages, and even at each single locus. However, when genotypes are defined using a multi-locus sequence typing scheme, only 2 multi-locus genotypes (MLG) of assemblage A and none of assemblage B appear to have a zoonotic potential. Surprisingly, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the zoonotic

  11. Multivariate Analysis of Genotype-Phenotype Association.

    Science.gov (United States)

    Mitteroecker, Philipp; Cheverud, James M; Pavlicev, Mihaela

    2016-04-01

    With the advent of modern imaging and measurement technology, complex phenotypes are increasingly represented by large numbers of measurements, which may not bear biological meaning one by one. For such multivariate phenotypes, studying the pairwise associations between all measurements and all alleles is highly inefficient and prevents insight into the genetic pattern underlying the observed phenotypes. We present a new method for identifying patterns of allelic variation (genetic latent variables) that are maximally associated-in terms of effect size-with patterns of phenotypic variation (phenotypic latent variables). This multivariate genotype-phenotype mapping (MGP) separates phenotypic features under strong genetic control from less genetically determined features and thus permits an analysis of the multivariate structure of genotype-phenotype association, including its dimensionality and the clustering of genetic and phenotypic variables within this association. Different variants of MGP maximize different measures of genotype-phenotype association: genetic effect, genetic variance, or heritability. In an application to a mouse sample, scored for 353 SNPs and 11 phenotypic traits, the first dimension of genetic and phenotypic latent variables accounted for >70% of genetic variation present in all 11 measurements; 43% of variation in this phenotypic pattern was explained by the corresponding genetic latent variable. The first three dimensions together sufficed to account for almost 90% of genetic variation in the measurements and for all the interpretable genotype-phenotype association. Each dimension can be tested as a whole against the hypothesis of no association, thereby reducing the number of statistical tests from 7766 to 3-the maximal number of meaningful independent tests. Important alleles can be selected based on their effect size (additive or nonadditive effect on the phenotypic latent variable). This low dimensionality of the genotype-phenotype map

  12. The potential of plant viruses to promote genotypic diversity via genotype x environment interactions

    DEFF Research Database (Denmark)

    van Mölken, Tamara; Stuefer, Josef F.

    2011-01-01

    † Background and Aims Genotype by environment (G × E) interactions are important for the long-term persistence of plant species in heterogeneous environments. It has often been suggested that disease is a key factor for the maintenance of genotypic diversity in plant populations. However, empirical...... evidence for this contention is scarce. Here virus infection is proposed as a possible candidate for maintaining genotypic diversity in their host plants. † Methods The effects of White clover mosaic virus (WClMV) on the performance and development of different Trifolium repens genotypes were analysed...... and the G × E interactions were examined with respect to genotypespecific plant responses to WClMV infection. Thus, the environment is defined as the presence or absence of the virus. † Key Results WClMV had a negative effect on plant performance as shown by a decrease in biomass and number of ramets...

  13. HPV genotypes in invasive cervical cancer in Danish women

    DEFF Research Database (Denmark)

    Kirschner, Benny; Junge, Jette; Holl, Katsiaryna

    2013-01-01

    Human papillomavirus (HPV) genotype distribution in invasive cervical cancers may differ by geographic region. The primary objective of this study was to estimate HPV-genotype distribution in Danish women with a diagnosis of invasive cervical cancer....

  14. Agronomical and phytochemical evaluation of Stevia rebaudiana genotypes

    National Research Council Canada - National Science Library

    Vouillamoz, José F; Wolfram-Schilling, Evelyn; Carron, Claude-Alain; Baroffio, Catherine A

    2016-01-01

    The agronomical potential and the phytochemical variability of 18 genotypes of the Paraguayan plant Stevia rebaudiana have been investigated in Switzerland in order identify the best genotype for local cultivation...

  15. Resistance of corn genotypes to fall armyworm Spodoptera ...

    African Journals Online (AJOL)

    Tuoyo Aghomotsegin

    2016-08-31

    Aug 31, 2016 ... The objective of this study was to evaluate resistance mechanisms in 12 corn genotypes (transgenic hybrids: ..... FAW that fed on GM corn genotypes exhibited lower ... preference for other food types, particularly given the.

  16. Comparison and suitability of genotype by environment analysis ...

    African Journals Online (AJOL)

    ACSS

    showed that genotype by environment interactions were significant at p<0.05 for grain .... Genotype by environment analysis methods for yield-related traits of pearl millet ...... PhD Thesis, Louisiana State ... set of sweet potato clones evaluated.

  17. Genotype W environment interaction effects on some physiological ...

    African Journals Online (AJOL)

    Genotype W environment interaction effects on some physiological yield ... Ghana Journal of Agricultural Science ... study the yield basis and environmental effects on 31cowpea genotypes of early, medium and late maturities. ... Article Metrics.

  18. HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma.

    Science.gov (United States)

    Qiu, Ping; Stevens, Richard; Wei, Bo; Lahser, Fred; Howe, Anita Y M; Klappenbach, Joel A; Marton, Matthew J

    2015-01-01

    Genotyping of hepatitis C virus (HCV) plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS) allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B) in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection.

  19. HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma.

    Directory of Open Access Journals (Sweden)

    Ping Qiu

    Full Text Available Genotyping of hepatitis C virus (HCV plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection.

  20. Genotype 3 is the predominant hepatitis C genotype in a multi-ethnic Asian population in Malaysia.

    Science.gov (United States)

    Ho, Shiaw-Hooi; Ng, Kee-Peng; Kaur, Harvinder; Goh, Khean-Lee

    2015-06-01

    Genotypes of hepatitis C virus (HCV) are distributed differently across the world. There is a paucity of such data in a multi-ethnic Asian population like Malaysia. The objectives of this study were to determine the distribution of HCV genotypes between major ethnic groups and to ascertain their association with basic demographic variables like age and gender. This was a cross-sectional prospective study conducted from September 2007 to September 2013. Consecutive patients who were detected to have anti-HCV antibodies in the University of Malaya Medical Centre were included and tested for the presence of HCV RNA using Roche Cobas Amplicor Analyzer and HCV genotype using Roche single Linear Array HCV Genotyping strip. Five hundred and ninety-six subjects were found to have positive anti-HCV antibodies during this period of time. However, only 396 (66.4%) were HCV RNA positive and included in the final analysis. Our results showed that HCV genotype 3 was the predominant genotype with overall frequency of 61.9% followed by genotypes 1 (35.9%), 2 (1.8%) and 6 (0.5%). There was a slightly higher prevalence of HCV genotype 3 among the Malays when compared to the Chinese (P=0.043). No other statistical significant differences were observed in the distribution of HCV genotypes among the major ethnic groups. There was also no association between the predominant genotypes and basic demographic variables. In a multi-ethnic Asian society in Malaysia, genotype 3 is the predominant genotype among all the major ethnic groups with genotype 1 as the second commonest genotype. Both genotypes 2 and 6 are uncommon. Neither genotype 4 nor 5 was detected. There is no identification of HCV genotype according to ethnic origin, age and gender.

  1. Angiotensin converting enzyme genotype in cardiovascular disease

    Energy Technology Data Exchange (ETDEWEB)

    Summers, K.M.; Huggard, P.R.; West, M.J. [Univ. of Queensland, Brisbane (Australia)] [and others

    1994-09-01

    Angiotensin converting enzyme (ACE) catalyses formation of angiotensin II and degradation of bradykinin, vasoactive peptides with opposing properties. The result of ACE action is to promote vasoconstriction and cell growth. PCR is used to detect a common polymorphism due to the insertion of an Alu repeat element of 287 bp into intron 16. ACE genotype has been implicated in risk for myocardial infarction (MI) and hypertension in humans. We have studied a group of 640 patients (61% male aged 64 {plus_minus} 11 years) with myocardial ischaemic syndromes, followed for 12 months after initial hospital admission. In this group, the frequency of the insertion (I) allele was 0.47 (N=1170 chromosomes), not significantly higher than the frequency of 0.46 in 112 local blood donors (50% male aged 59 {plus_minus}5 years). In the 300 patients with diagnosed MI, I allele frequency was 0.48. This is significantly higher ({chi}{sup 2}=5.78, P=0.015) than the frequency of 0.42 reported in a multi-centre study of ACE genotype in 600 male European patients with MI . There was a non-significant increase in the frequency of a cardiac event within 6 months of hospital admission in those of II genotype (N=464, 47 events to date). These results suggest that in our population, the I allele and/or II genotype may be associated with risk of MI. This contrasts with the study cited above, where the D (deletion) allele and DD genotype frequency were raised in patients compared with controls. Hypertension is associated with the ACE D allele, and does not explain the heart disease risk, which may be associated with the I allele, in this group of survivors of myocardial ischaemic disease. The difference between our results and the previous study may be due to ascertainment or ethnic differences or to problems amplifying the I allele in some heterozygotes. Clearly, the role of ACE genotype in these diseases is complex.

  2. [Hepatitis B virus genotypes and the response to lamivudine therapy].

    Science.gov (United States)

    Zalewska, Małgorzata; Domagała, Małgorzata; Simon, Krzysztof; Gładysz, Andrzej

    2005-12-01

    Hepatitis B virus (HBV) can be classified into eight major genotypes (A-H) that have mainly a geographic distribution. The HBV genotype may influence disease progression, HBeAg seroconversion rates, response to antiviral treatment. The aim of study was to analyze the distribution and frequency of genotypes in patients with chronic hepatitis B. Response to lamivudine 100 mg daily therapy was examined in respect to genotype. Sixty six patients (45 (68,2%) male, 21 (31,8%) female) with chronic hepatits B were enrolled. HBV genotypes were assigned before treatment with INNO-LiPA HBV Genotyping, Innogenetics, N. V., Ghent assay, which is a line probe test based on the reverse hybridization principle. In baseline and after 12 months of treatment serological markers of HBV infection, alanine aminotransferase (ALT) activities and HBV DNA serum levels were tested. Patients with chronic hepatitis B were infected predominantly with genotype A. HBV genotype distribution was: 78,8% for genotype A, 13,6% for genotype D, 1,5% for mixed infection with genotypes A and D. Distribution of genotypes A and D was asymmetrically regardless of sex, HBeAg status, ALT and HBV DNA levels. Four (6,1%) specimens had indeterminate A results by LiPA. There were no significant differences between patients with genotypes A and D regarding age and sex. There were also no significant differences between these two groups regarding rates of HBeAg and anti-HBe positivity, ALT activity and viral load. Twenty months of lamivudine (100 mg daily) therapy resulted in significant decreases in serum HBV DNA and ALT activities in patients with genotype A as well as with genotype D. After 12 months of treatment there were no statistical differences in HBeAg seroconversion rates, ALT activities, viral loads, frequency of HBeAg and anti-HBe between genotypes A and D.

  3. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

    Directory of Open Access Journals (Sweden)

    Didion John P

    2012-01-01

    Full Text Available Abstract Background High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs. Results We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains. Conclusion The problems of ascertainment bias and missing

  4. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias.

    Science.gov (United States)

    Didion, John P; Yang, Hyuna; Sheppard, Keith; Fu, Chen-Ping; McMillan, Leonard; de Villena, Fernando Pardo-Manuel; Churchill, Gary A

    2012-01-19

    High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs) in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs. We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO) probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno) that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains. The problems of ascertainment bias and missing information due to genotyping errors are widely recognized as

  5. megasat: automated inference of microsatellite genotypes from sequence data.

    Science.gov (United States)

    Zhan, Luyao; Paterson, Ian G; Fraser, Bonnie A; Watson, Beth; Bradbury, Ian R; Nadukkalam Ravindran, Praveen; Reznick, David; Beiko, Robert G; Bentzen, Paul

    2017-03-01

    megasat is software that enables genotyping of microsatellite loci using next-generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. megasat reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification products, replication slippage during PCR (amplification stutter) and differential amplification of alleles. An important feature of megasat is the generation of histograms of the length-frequency distributions of amplification products for each locus and each individual. These histograms, analogous to electropherograms traditionally used to score microsatellite genotypes, enable rapid evaluation and editing of automatically scored genotypes. megasat is written in Perl, runs on Windows, Mac OS X and Linux systems, and includes a simple graphical user interface. We demonstrate megasat using data from guppy, Poecilia reticulata. We genotype 1024 guppies at 43 microsatellites per run on an Illumina MiSeq sequencer. We evaluated the accuracy of automatically called genotypes using two methods, based on pedigree and repeat genotyping data, and obtained estimates of mean genotyping error rates of 0.021 and 0.012. In both estimates, three loci accounted for a disproportionate fraction of genotyping errors; conversely, 26 loci were scored with 0-1 detected error (error rate ≤0.007). Our results show that with appropriate selection of loci, automated genotyping of microsatellite loci can be achieved with very high throughput, low genotyping error and very low genotyping costs.

  6. A genotype probability index for multiple alleles and haplotypes.

    Science.gov (United States)

    Percy, A; Kinghorn, B P

    2005-12-01

    We use linear algebra to calculate an index of information content in genotype probabilities which has previously been calculated using trigonometry. The new method can be generalized allowing the index to be calculated for loci with more than two alleles. Applications of this index include its use in genotyping strategies, strategies to manage genetic disorders and in estimation of genotype effects.

  7. 21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid...

  8. Strongyloides stercoralis genotypes in humans in Cambodia.

    Science.gov (United States)

    Schär, Fabian; Guo, Li; Streit, Adrian; Khieu, Virak; Muth, Sinuon; Marti, Hanspeter; Odermatt, Peter

    2014-06-01

    Little is known about the genetic variability of the soil-transmitted nematode, Strongyloides stercoralis, in humans. We sequenced portions of the small subunit rDNA (SSU), including the hyper variable regions (HVR) I and IV from S. stercoralis larvae derived from individuals living in a rural setting in Cambodia. We identified three polymorphic positions, including a previously reported one within the HVR I. HVR IV was invariable. Six different SSU alleles existed in our sample. Although different genotypes of S. stercoralis were found in the same individuals, no heterozygous larvae were found. This indicates that there is no or very little interbreeding between the different genotypes. Further studies are needed to examine if this is because sexual reproduction, which is facultative, is rare in our study area's S. stercoralis population or because what is considered to be S. stercoralis today is actually a complex of closely related species or subspecies.

  9. COMT genotype, gambling activity, and cognition

    DEFF Research Database (Denmark)

    Grant, Jon E; Leppink, Eric W; Redden, Sarah A

    2015-01-01

    gambling. This study examined adults with varying levels of gambling behavior to determine whether COMT genotype was associated with differences in gambling symptoms and cognitive functioning. 260 non-treatment-seeking adults aged 18-29 years with varying degrees of gambling behavior provided saliva...... significantly different from the Val/Met (13.2%) group (p = 0.001). The Val/Val COMT group was also associated with significantly more gambling disorder diagnostic criteria being met, greater frequency of gambling behavior, and significantly worse cognitive performance on the Cambridge Gamble Task (risk...... adjustment and delay aversion) and the Spatial Working Memory task (total errors). This study adds to the growing literature on the role of COMT in impulsive behaviors by showing that the Val/Val genotype was associated with specific clinical and cognitive elements among young adults who gamble...

  10. Huntington's Disease: Relationship Between Phenotype and Genotype.

    Science.gov (United States)

    Sun, Yi-Min; Zhang, Yan-Bin; Wu, Zhi-Ying

    2017-01-01

    Huntington's disease (HD) is an autosomal dominant inherited neurodegenerative disease with the typical manifestations of involuntary movements, psychiatric and behavior disorders, and cognitive impairment. It is caused by the dynamic mutation in CAG triplet repeat number in exon 1 of huntingtin (HTT) gene. The symptoms of HD especially the age at onset are related to the genetic characteristics, both the CAG triplet repeat and the modified factors. Here, we reviewed the recent advancement on the genotype-phenotype relationship of HD, mainly focus on the characteristics of different expanded CAG repeat number, genetic modifiers, and CCG repeat number in the 3' end of CAG triplet repeat and their effects on the phenotype. We also reviewed the special forms of HD (juvenile HD, atypical onset HD, and homozygous HD) and their phenotype-genotype correlations. The review will aid clinicians to predict the onset age and disease course of HD, give the genetic counseling, and accelerate research into the HD mechanism.

  11. Indexing Finite Language Representation of Population Genotypes

    CERN Document Server

    Sirén, Jouni; Mäkinen, Veli

    2010-01-01

    We propose a way to index population genotype information together with the complete genome sequence so that one can use the index to efficiently align a given sequence to the genome with all plausible genotype recombinations taken into account. This is achieved through converting the multiple alignment of individual genomes into a finite automaton recognizing the language of all substrings read from the alignment by switching the row at any time. The finite automaton is then indexed with an extension of Burrows-Wheeler transform to allow pattern search inside the plausible recombinant sequences generated in this way. The size of the finite automaton and the index created from it stay limited because of the high similarity of the individual genomes in the multiple alignment. In our experiments, the index took even less space than previous ones designed for indexing just the individual genomes. On a short-read alignment experiment, we found about 1% of matches to novel recombinants.

  12. BCL2 genotypes and prostate cancer survival

    Energy Technology Data Exchange (ETDEWEB)

    Renner, Wilfried [Medical University of Graz, Clinical Institute of Medical and Chemical Laboratory Diagnostics, Graz (Austria); Langsenlehner, Uwe [GKK Outpatient Department, Division of Internal Medicine, Graz (Austria); Krenn-Pilko, Sabine; Langsenlehner, Tanja [Medical University of Graz, Department of Therapeutic Radiology and Oncology, Graz (Austria); Eder, Petra [University Hospital Wuerzburg, Department of Internal Medicine I, Wuerzburg (Germany)

    2017-06-15

    The antiapoptotic B-cell lymphoma 2 (BCL2) gene is a key player in cancer development and progression. A functional single-nucleotide polymorphism (c.-938C>A, rs2279115) in the inhibitory P2 BCL2 gene promoter has been associated with clinical outcomes in various types of cancer. Aim of the present study was to analyze the role of BCL2-938C>A genotypes in prostate cancer mortality. The association between BCL2-938C>A (rs2279115) genotypes and prostate cancer outcome was studied within the prospective PROCAGENE study comprising 702 prostate cancer patients. During a median follow-up time of 92 months, 120 (17.1%) patients died. A univariate Cox regression model showed a significant association of the CC genotype with reduced cancer-specific survival (CSS; hazard ratio, HR, 2.13, 95% confidence interval, CI, 1.10-4.12; p = 0.024) and overall survival (OS; HR 2.34, 95% CI 1.58-3.47; p < 0.001). In a multivariate Cox regression model including age at diagnosis, risk group, and androgen deprivation therapy, the CC genotype remained a significant predictor of poor CSS (HR 2.05, 95% CI 1.05-3.99; p = 0.034) and OS (HR 2.25, 95% CI 1.51-3.36; p < 0.001). This study provides evidence that the homozygous BCL2-938 CC genotype is associated with OS and C in prostate cancer patients. (orig.) [German] Das antiapoptotische Gen B cell lymphoma 2 (BCL2) spielt eine Schluesselrolle in der Entstehung und Progression von Krebserkrankungen. Ein funktioneller Einzelnukleotid-Polymorphismus (c.-938C>A, rs2279115) im inhibitorischen P2-BCL2-Promotor wurde mit dem klinischen Outcome verschiedener Krebserkrankungen verknuepft. Ziel der vorliegenden Studie war die Untersuchung der Rolle von BCL2-938C>A-Genotypen fuer die Mortalitaet bei Patienten mit Prostatakarzinom. Der Zusammenhang zwischen BCL2-938C>A-Genotypen (rs2279115) und dem Outcome bei Prostatakrebs wurde in der prospektiven PROCAGENE-Studie, die 702 Patienten mit Prostatakarzinom umfasste, untersucht. Waehrend der medianen

  13. Identification of Zoonotic Genotypes of Giardia duodenalis

    DEFF Research Database (Denmark)

    Sprong, H.; Cacciò, S.M.; van der Giessen, J.W.B

    2009-01-01

    Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect....... The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset). The zoonotic potential of both assemblages A and B......, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other...

  14. Human papillomaviruses genotyping in plantar warts.

    Science.gov (United States)

    de Planell-Mas, Elena; Martínez-Garriga, Blanca; Zalacain, Antonio Jesús; Vinuesa, Teresa; Viñas, Miguel

    2017-05-01

    Plantar warts are caused by human papillomaviruses (HPVs) and have been associated with several HPV genotypes. However, there are few studies focused exclusively on plantar warts. In this work, we aim to identify the HPV genotypes of plantar warts and explore their relation to demographic and clinical characteristics of patients. A total of 72 patients diagnosed with plantar warts were recruited at the Laser unit at Podiatric Hospital, University of Barcelona, Spain. Inner hyperkeratosis laminar sections of warts were collected and DNA of samples were extracted. Amplification of a conserved region of the HPV L1 gene was performed with the SK-Polymerase chain reaction method. DNA amplicons were sequenced and HPV types identified. The most prevalent genotypes detected among the 105 analyzed plantar warts were HPV-57 (37.1%), HPV-27 (23.8%), HPV-1a (20.9%), HPV-2 (15.2%), and HPV-65 (2.8%). The majority of patients (78%) presented one single plantar wart, whereas multiple warts were detected in 22.2% of patients. One patient with multiple warts presented HPV types from two different genera, suggesting the spread of warts by self-inoculation as well as by de novo infection. No significant differences between the number of warts in toes, midfoot and heel were found. The most prevalent HPV types detected in all areas belonged to the alpha genus. This work provides new insight on plantar warts and their associated HPV genotypes, and evidences the usefulness and reliability of both the sample collection procedure and the PCR method used for HPV detection and typing. J. Med. Virol. 89:902-907, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  15. Hepatitis C virus genotyping in Greece: unexpected high prevalence of genotype 5a in a Greek island.

    Science.gov (United States)

    Karatapanis, Stylianos; Tsoplou, Panagiota; Papastergiou, Vasilios; Vasiageorgi, Aggeliki; Stampori, Maria; Saitis, Ioannis; Tsitsopoulos, Eustathios; Lisgos, Phillipos; Skorda, Lamprini; Ketikoglou, Ioannis; Goulis, Ioannis

    2012-02-01

    Hepatitis C virus (HCV) genotype 5 (G5) is a rare genotype reported mainly in South Africa. However, increasing data suggest the sporadic presence of this genotype in different European countries. To assess the epidemiology of HCV-G5 in Greece, genotyping was performed in 973 consecutive patients infected with HCV, referred to 7 hepatology centers throughout Greece, from January 2005 to December 2009. Genotype 5a (19 patients, 1.9%) was the fifth most prevalent genotype after genotype 1 (408 patients, 41.9%), genotype 3 (318 patients, 32.7%), genotype 4 (158 patients, 16.2%), and genotype 2 (70 patients, 7.2%). The majority of patients infected with G5 (16/19,84.2%) were referred to the General Hospital of Rhodes, an island in south-east Greece. The HCV genotype distribution in that particular island, indicates a particularly high G5 prevalence of 12.8%, after genotype 1 (40%), genotype 3 (28%), and genotype 4 (15%). Among the patients from Rhodes infected with G5 (n = 16), 13 (81.2%) were females. The mean age was 62.3 ± 6.5 years, significantly older than the patients infected with other HCV genotypes (mean age 40.6 ± 7.2, P < 0.0001). Nine out of the 16 cases (56.2%) presented features of high pre-treatment viral loads. Advanced liver fibrosis (Metavir F3-F4) was found in four out of five performed liver biopsies. Ten patients received treatment with pegylated interferon plus ribavirin and a sustained viral response were achieved in six cases. The source of infection is unknown but parenteral iatrogenic routes of transmission seem to have contributed significantly to the spread of genotype 5a in this region.

  16. Screening cotton genotypes for seedling drought tolerance

    Directory of Open Access Journals (Sweden)

    Penna Julio C. Viglioni

    1998-01-01

    Full Text Available The objectives of this study were to adapt a screening method previously used to assess seedling drought tolerance in cereals for use in cotton (Gossypium hirsutum L. and to identify tolerant accessions among a wide range of genotypes. Ninety genotypes were screened in seven growth chamber experiments. Fifteen-day-old seedlings were subjected to four 4-day drought cycles, and plant survival was evaluated after each cycle. Three cycles are probably the minimum required in cotton work. Significant differences (at the 0.05 level or lower among entries were obtained in four of the seven experiments. A "confirmation test" with entries previously evaluated as "tolerant" (high survival and "susceptible" (low survival was run. A number of entries duplicated their earlier performance, but others did not, which indicates the need to reevaluate selections. Germplasms considered tolerant included: `IAC-13-1', `IAC-RM4-SM5', `Minas Sertaneja', `Acala 1517E-1' and `4521'. In general, the technique is simple, though time-consuming, with practical value for screening a large number of genotypes. Results from the screening tests generally agreed with field information. The screening procedure is suitable to select tolerant accessions from among a large number of entries in germplasm collections as a preliminary step in breeding for drought tolerance. This research also demonstrated the need to characterize the internal lack of uniformity in growth chambers to allow for adequate designs of experiments.

  17. Hepatitis B virus genotypes and hepatocellular carcinoma in Thailand

    Institute of Scientific and Technical Information of China (English)

    Pisit Tangkijvanich; Varocha Mahachai; Piyawat Komolmit; Juthatip Fongsaru; Apiradee Theamboonlers; Yong Poovorawan

    2005-01-01

    AIM: The role of hepatitis B virus (HBV) genotypes on the clinical features and prognosis of patients with hepatocellular carcinoma (HCC) is currently unknown. The aim of the present study was to evaluate the distribution of HBV genotypes and their clinical relevance in Thai patients.METHODS: HBV genotypes were determined by PCR-RFLP in stored sera of 93 asymptomatic carriers, 103 patients with chronic hepatitis, 60 patients with cirrhosis and 76patients with HCC. The clinical data were analyzed in relation to the HBV genotype.RESULTS: HBV genotypes C and B were predominant in Thailand, accounting for 73% and 21%, respectively. The distributions of genotypes B and C were similar in HCC patients compared to the other groups. Genotype C was significantly more common in HCC patients who were under 40 years old than genotype B (18% vs 0%, P= 0.03), but was significantly less common in patients older than 60 years (26% vs 56.5%, P= 0.01). The positive rate of hepatitis B e antigen (HBeAg) in patients with genotype C was significantly higher than that in patients with genotype B (71.6% vs 44.4%, P = 0.03 in chronic hepatitis; 56.8% vs 11.1%,P = 0.01 in cirrhosis). There were no differences between HCC patients with genotypes B and C regarding tumor staging by CLIP criteria and the overall median survival. Multivariate analyses showed that HBV genotype was not an independent prognostic factor of survival in HCC patients.CONCLUSION: Patients with genotype C had a higher positive rate of HBeAg and exhibited earlier progression of cirrhosis and HCC than those with genotype B. However,there were no differences in the risk of developing HCC and its prognosis between patients with these genotypes.

  18. Genetic diversity in soybean genotypes with resistance to Heterodera glycines

    Directory of Open Access Journals (Sweden)

    Ana Paula Oliveira Nogueira

    2011-01-01

    Full Text Available The purpose of this study was to analyze the genetic diversity among soybean genotypes inoculated with Heteroderaglycines race 3. The experiments were conducted in a greenhouse. In two performance tests of morphological characteristics andresistance to the pathogen, 27 soybean genotypes were assessed. The coefficient of genotypic determination was estimated by themethod of analysis of variance and the genetic diversity analyzed based on dendrograms and optimization method. The estimatedcoefficients of determination indicated a predominantly genetic origin of the genotypic differences in the traits. The genetic variabilitywas maintained in the superior genotypes, which can be used in breeding programs for resistance to soybean cyst nematode

  19. Hepatitis B virus taxonomy and hepatitis B virus genotypes

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Hepatitis B virus (HBV) is a member of the hepadnavirus family. Hepadnaviruses can be found in both mammals (orthohepadnaviruses) and birds (avihepadnaviruses).The genetic variability of HBV is very high. There are eight genotypes of HBV and three clades of HBV isolates from apes that appear to be additional genotypes of HBV. Most genotypes are now divided into subgenotypes with distinct virological and epidemiological properties. In addition, recombination among HBV genotypes increases the variability of HBV. This review summarises current knowledge of the epidemiology of genetic variability in hepadnaviruses and, due to rapid progress in the field,updates several recent reviews on HBV genotypes and subgenotypes.

  20. Identification of polymorphic inversions from genotypes

    Directory of Open Access Journals (Sweden)

    Cáceres Alejandro

    2012-02-01

    Full Text Available Abstract Background Polymorphic inversions are a source of genetic variability with a direct impact on recombination frequencies. Given the difficulty of their experimental study, computational methods have been developed to infer their existence in a large number of individuals using genome-wide data of nucleotide variation. Methods based on haplotype tagging of known inversions attempt to classify individuals as having a normal or inverted allele. Other methods that measure differences between linkage disequilibrium attempt to identify regions with inversions but unable to classify subjects accurately, an essential requirement for association studies. Results We present a novel method to both identify polymorphic inversions from genome-wide genotype data and classify individuals as containing a normal or inverted allele. Our method, a generalization of a published method for haplotype data 1, utilizes linkage between groups of SNPs to partition a set of individuals into normal and inverted subpopulations. We employ a sliding window scan to identify regions likely to have an inversion, and accumulation of evidence from neighboring SNPs is used to accurately determine the inversion status of each subject. Further, our approach detects inversions directly from genotype data, thus increasing its usability to current genome-wide association studies (GWAS. Conclusions We demonstrate the accuracy of our method to detect inversions and classify individuals on principled-simulated genotypes, produced by the evolution of an inversion event within a coalescent model 2. We applied our method to real genotype data from HapMap Phase III to characterize the inversion status of two known inversions within the regions 17q21 and 8p23 across 1184 individuals. Finally, we scan the full genomes of the European Origin (CEU and Yoruba (YRI HapMap samples. We find population-based evidence for 9 out of 15 well-established autosomic inversions, and for 52 regions

  1. Identification of zoonotic genotypes of Giardia duodenalis.

    Directory of Open Access Journals (Sweden)

    Hein Sprong

    Full Text Available Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals in the epidemiology of human infection is still unclear, despite the fact that the zoonotic potential of Giardia was recognised by the WHO some 30 years ago. Here, we performed an extensive genetic characterization of 978 human and 1440 animal isolates, which together comprise 3886 sequences from 4 genetic loci. The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset. The zoonotic potential of both assemblages A and B is evident when studied at the level of assemblages, sub-assemblages, and even at each single locus. However, when genotypes are defined using a multi-locus sequence typing scheme, only 2 multi-locus genotypes (MLG of assemblage A and none of assemblage B appear to have a zoonotic potential. Surprisingly, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the

  2. Avian nephritis virus (ANV) on Brazilian chickens farms: circulating genotypes and intra-genotypic diversity.

    Science.gov (United States)

    Espinoza, Luis Luna; Beserra, Laila A R; Soares, Rodrigo M; Gregori, Fabio

    2016-12-01

    Avian nephritis virus (ANV), which belongs to the family Astroviridae, is associated with different clinical manifestations (including enteric disorders). Despite being frequently found in the avian industry worldwide, information regarding genetic features of these viruses in Brazil is scarce. Therefore, sixty fecal sample pools (5-6 birds of the same flock), representing 60 poultry farms from six Brazilian States, were screened using an astrovirus-specific hemi-nested-PCR assay targeting the conserved ORF1b gene, followed by nucleotide sequencing of amplified products. PCR and phylogenetic analysis confirmed the detection of 21 positive samples to ANV (35 %). In order to investigate the genetic diversity represented by these viruses, amplification, cloning and phylogenetic analysis of the deduced amino acid sequence of ORF2 gene were attempted. Eight samples were successfully cloned (generating 32 clones in total) and sequenced. Based on phylogenetic analysis of ORF2, sequences defined in this study were classified into three genotypes: genotype 5, which has already been described in birds, and two other novel genotypes, tentatively named genotype 8 and 9, all of which occurred in single or mixed infections. Moreover, high intra-genotypic diversity and co-circulation of distinct strains in a same host population were observed. This study revealed the presence of new strains of ANV in Brazilian poultry and their circulation in commercial chicken flocks.

  3. Entire genome sequence analysis of genotype IX Newcastle disease viruses reveals their early-genotype phylogenetic position and recent-genotype genome size

    Directory of Open Access Journals (Sweden)

    Hu Shunling

    2011-03-01

    Full Text Available Abstract Background Six nucleotide (nt insertion in the 5'-noncoding region (NCR of the nucleoprotein (NP gene of Newcaslte disease virus (NDV is considered to be a genetic marker for recent genotypes of NDV, which emerged after 1960. However, F48-like NDVs from China, identified a 6-nt insert in the NP gene, have been previously classified into genotype III or genotype IX. Results In order to clarify their phylogenetic position and explore the origin of NDVs with the 6-nt insert and its significance in NDV evolution, we determined the entire genome sequences of five F48-like viruses isolated in China between 1946 and 2002 by RT-PCR amplification of overlapping fragments of full-length genome and rapid amplification of cDNA ends. All the five NDV isolates shared the same genome size of 15,192-nt with the recent genotype V-VIII viruses whereas they had the highest homology with early genotype III and IV isolates. Conclusions The unique characteristic of the genome size and phylogenetic position of F48-like viruses warrants placing them in a separate geno-group, genotype IX. Results in this study also suggest that genotype IX viruses most likely originate from a genotype III virus by insertion of a 6-nt motif in the 5'-NCR of the NP gene which had occurred as early as in 1940 s, and might be the common origin of genotype V-VIII viruses.

  4. Citrus tristeza virus: Evolution of Complex and Varied Genotypic Groups

    Science.gov (United States)

    Harper, S. J.

    2013-01-01

    Amongst the Closteroviridae, Citrus tristeza virus (CTV) is almost unique in possessing a number of distinct and characterized strains, isolates of which produce a wide range of phenotype combinations among its different hosts. There is little understanding to connect genotypes to phenotypes, and to complicate matters more, these genotypes are found throughout the world as members of mixed populations within a single host plant. There is essentially no understanding of how combinations of genotypes affect symptom expression and disease severity. We know little about the evolution of the genotypes that have been characterized to date, little about the biological role of their diversity and particularly, about the effects of recombination. Additionally, genotype grouping has not been standardized. In this study we utilized an extensive array of CTV genomic information to classify the major genotypes, and to determine the major evolutionary processes that led to their formation and subsequent retention. Our analyses suggest that three major processes act on these genotypes: (1) ancestral diversification of the major CTV lineages, followed by (2) conservation and co-evolution of the major functional domains within, though not between CTV genotypes, and (3) extensive recombination between lineages that have given rise to new genotypes that have subsequently been retained within the global population. The effects of genotype diversity and host-interaction are discussed, as is a proposal for standardizing the classification of existing and novel CTV genotypes. PMID:23630519

  5. Genotypic diversity of root and shoot characteristics of

    Directory of Open Access Journals (Sweden)

    ali ganjali

    2009-06-01

    Full Text Available Root and shoot characteristics of chickpea (Cicer arietinum L. genotypes are believed to be important in drought tolerance. There is a little information about the response of genotypes root growth in hydroponics and greenhouse culture, also the relationships between root size and drought tolerance. This study was conducted to observe whether genotypes differ in root size, and to see that root size is associated with drought tolerance during early vegetative growth. We found significant differences (p0.01 in root dry weight, total root length, tap root length, root area, leaf dry weight, leaf area and shoot biomass per plant among 30 genotypes of chickpea grown in hydroponics culture for three weeks. Each of these parameters correlated with all others, positively. Among 30 genotypes, 10 genotypes with different root sizes were selected and were grown in a greenhouse in sand culture experiment under drought stress (FC %30 for three weeks. There were not linear or non-linear significant correlations between root characters in hydroponics and greenhouse environments. It seems that environmental factors are dominant on genetic factors in seedling stage and so, the expression of genotypics potential for root growth characteristics of genotypes are different in hydroponic and greenhouse conditions. In this study, the selection of genotypes with vigorous roots system in hydroponic condition did not lead to genotypes with the same root characters in greenhouse environment. The genotype×drought interactions for root characters of chickpea seedlings in 30 days were not significant (p

  6. Epidemiology and Treatment of Hepatitis C Genotypes 5 and 6

    Directory of Open Access Journals (Sweden)

    Khalid Al Naamani

    2013-01-01

    Full Text Available Chronic hepatitis C infection is a major global health problem. The WHO estimates the number of infected people worldwide to be approximately 170 million. The estimated number of hepatitis C virus (HCV-infected people in Canada is approximately 250,000, with approximately 5000 Canadians newly infected each year. Based on the identification of genomic differences, HCV has been classified into six genotypes; genotype may influence the outcome of antiviral therapy. HCV genotypes 1, 2 and 3 are widely distributed throughout the world and have been the focus of the majority of epidemiological, natural course and treatment studies. Although HCV genotypes 5 and 6 are prevalent in certain geographical areas, they are studied less extensively. HCV genotypes 5 and 6 are uncommon in Canada and account for less than 5% of HCV-infected Canadians. However, immigration and travel can alter the epidemiology of these uncommon genotypes. The present article reviews and summarizes the available data regarding the epidemiology and treatment of HCV genotypes 5 and 6. Genotype 5 is endemic in the northern part of South Africa while genotype 6 is reported primarily in Asia. Available data show that 48 weeks of treatment with a combination of pegylated interferon and ribavirin lead to a higher sustained virological response compared with HCV genotypes 1 and 4. None of the approved direct-acting antiviral agents is currently recommended for the treatment of HCV genotypes 5 or 6.

  7. Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping

    Directory of Open Access Journals (Sweden)

    Prasanth VP

    2006-08-01

    Full Text Available Abstract Background With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. Results A laboratory information management system (LIMS has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat genotyping data from the legume (chickpea, groundnut and pigeonpea and cereal (sorghum and millets crops of importance in the semi-arid tropics. Conclusion A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping

  8. Phylogenetic Analysis of Human Parvovirus B19 Sequences from Eleven Different Countries Confirms the Predominance of Genotype 1 and Suggests the Spread of Genotype 3b▿

    Science.gov (United States)

    Hübschen, Judith M.; Mihneva, Zefira; Mentis, Andreas F.; Schneider, François; Aboudy, Yair; Grossman, Zehava; Rudich, Hagit; Kasymbekova, Kalia; Sarv, Inna; Nedeljkovic, Jasminka; Tahita, Marc C.; Tarnagda, Zekiba; Ouedraogo, Jean-Bosco; Gerasimova, A. G.; Moskaleva, T. N.; Tikhonova, Nina T.; Chitadze, Nazibrola; Forbi, J. C.; Faneye, Adedayo O.; Otegbayo, Jesse A.; Charpentier, Emilie; Muller, Claude P.

    2009-01-01

    Phylogenetic analysis of 166 human parvovirus B19 sequences from 11 different countries attributed 91.57% to genotype 1, 5.42% to genotype 3b, and 3.01% to genotype 3a. Very similar viruses of genotype 1 circulated widely in Europe and Israel. Genotype 3b seems to show an increasing spread outside of Africa. PMID:19741071

  9. SBE primer : multiplexing minisequencing-based genotyping

    Energy Technology Data Exchange (ETDEWEB)

    Kaderali, L. (Lars); Deshpande, A. (Alina); Uribe-Romeo, F. J. (Francisco J.); Schliep, A.; Torney, D. C. (David C.)

    2002-01-01

    Single-nucleotide polymorphism (SNP) analysis is a powerful tool for mapping and diagnosing disease-related alleles. Most of the known genetic diseases are caused by point mutations, and a growing number of SNPs will be routinely analyzed to diagnose genetic disorders. Mutation analysis by polymerase mediated single-base primer extension (minisequencing) can be massively parallelized using for example DNA microchips or flow cytometry with microspheres as solid support. By adding a unique oligonucleotide tag to the 5-inch end of the minisequencing primer and attaching the complementary anti-tag to the array or bead surface, the assay can be 'demultiplexed'. However, such high-throughput scoring of SNPs requires a high level of primer multiplexing in order to analyze multiple loci in one assay, thus enabling inexpensive and fast polymorphism scoring. Primers can be chosen from either the plus or the minus strand, and primers used in the same experiment must not bind to one another. To genotype a given number of polymorphic sites, the question is which primer to use for each SNP, and which primers to group into the same experiment. Furthermore, a crosshybridization-free tag/anti-tag code is required in order to sort the extended primers to the corresponding microspheres or chip spots. These problems pose challenging algorithmic questions. We present a computer program lo automate the design process for the assay. Oligonucleotide primers for the reaction are automatically selected by the software, a unique DNA tag/anti-tag system is generated, and the pairing of primers and DNA-Tags is automatically done in a way to avoid any crossreactivity. We report first results on a 45-plex genotyping assay, indicating that minisequencing can be adapted to be a powerful tool for high-throughput, massively parallel genotyping.

  10. Genotyping of Coxiella burnetii from domestic ruminants in northern Spain

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    Astobiza Ianire

    2012-12-01

    Full Text Available Abstract Background Information on the genotypic diversity of Coxiella burnetii isolates from infected domestic ruminants in Spain is limited. The aim of this study was to identify the C. burnetii genotypes infecting livestock in Northern Spain and compare them to other European genotypes. A commercial real-time PCR targeting the IS1111a insertion element was used to detect the presence of C. burnetii DNA in domestic ruminants from Spain. Genotypes were determined by a 6-loci Multiple Locus Variable number tandem repeat analysis (MLVA panel and Multispacer Sequence Typing (MST. Results A total of 45 samples from 4 goat herds (placentas, N = 4, 12 dairy cattle herds (vaginal mucus, individual milk, bulk tank milk, aerosols, N = 20 and 5 sheep flocks (placenta, vaginal swabs, faeces, air samples, dust, N = 21 were included in the study. Samples from goats and sheep were obtained from herds which had suffered abortions suspected to be caused by C. burnetii, whereas cattle samples were obtained from animals with reproductive problems compatible with C. burnetii infection, or consisted of bulk tank milk (BTM samples from a Q fever surveillance programme. C. burnetii genotypes identified in ruminants from Spain were compared to those detected in other countries. Three MLVA genotypes were found in 4 goat farms, 7 MLVA genotypes were identified in 12 cattle herds and 4 MLVA genotypes were identified in 5 sheep flocks. Clustering of the MLVA genotypes using the minimum spanning tree method showed a high degree of genetic similarity between most MLVA genotypes. Overall 11 different MLVA genotypes were obtained corresponding to 4 different MST genotypes: MST genotype 13, identified in goat, sheep and cattle from Spain; MST genotype 18, only identified in goats; and, MST genotypes 8 and 20, identified in small ruminants and cattle, respectively. All these genotypes had been previously identified in animal and human clinical samples from several

  11. Development and application of genotyping technologies

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    With the completion of Human Genome Project,International HapMap Project and the publication of copy number variation in human genome,a great number of accurate,rapid,and cost-effective technologies for SNP analysis have been developed,promoting the research of the complex diseases.This article presents a review of widely used genotyping techniques,and the progress and prospect in the study of complex diseases in terms of the projects and achievements of Chinese National Human Genome Center at Shanghai(CHGCs).

  12. Development and application of genotyping technologies

    Institute of Scientific and Technical Information of China (English)

    SHI JinXiu; WANG Ying; HUANG Wei

    2009-01-01

    With the completion of Human Genome Project, International HapMap Project and the publication of copy number variation in human genome, a great number of accurate, rapid, and cost-effective tech-nologies for SNP analysis have been developed, promoting the research of the complex diseases. This article presents a review of widely used genotyping techniques, and the progress and prospect in the study of complex diseases in terms of the projects and achievements of Chinese National Human Genome Center at Shanghai (CHGCs).

  13. Celer: an Efficient Program for Genotype Elimination

    Directory of Open Access Journals (Sweden)

    Nicoletta De Francesco

    2010-08-01

    Full Text Available This paper presents an efficient program for checking Mendelian consistency in a pedigree. Since pedigrees may contain incomplete and/or erroneous information, geneticists need to pre-process them before performing linkage analysis. Removing superfluous genotypes that do not respect the Mendelian inheritance laws can speed up the linkage analysis. We have described in a formal way the Mendelian consistency problem and algorithms known in literature. The formalization helped to polish the algorithms and to find efficient data structures. The performance of the tool has been tested on a wide range of benchmarks. The results are promising if compared to other programs that treat Mendelian consistency.

  14. Celer: an Efficient Program for Genotype Elimination

    CERN Document Server

    De Francesco, Nicoletta; Martini, Luca; 10.4204/EPTCS.33.4

    2010-01-01

    This paper presents an efficient program for checking Mendelian consistency in a pedigree. Since pedigrees may contain incomplete and/or erroneous information, geneticists need to pre-process them before performing linkage analysis. Removing superfluous genotypes that do not respect the Mendelian inheritance laws can speed up the linkage analysis. We have described in a formal way the Mendelian consistency problem and algorithms known in literature. The formalization helped to polish the algorithms and to find efficient data structures. The performance of the tool has been tested on a wide range of benchmarks. The results are promising if compared to other programs that treat Mendelian consistency.

  15. Prevalence of hepatitis C virus (HCV) genotypes in Balochistan.

    Science.gov (United States)

    Afridi, Sarwat; Naeem, Muhammad; Hussain, Abid; Kakar, Naseebullah; Babar, Masroor Ellahi; Ahmad, Jamil

    2009-07-01

    A molecular study was conducted to investigate the prevalence of Hepatitis C virus genotypes in HCV infected population of Balochistan. Forty HCV seropositive samples belonging to seven different locations of Balochistan were collected from different health care centres. Qualitative analysis of these samples using PCR resulted in 28 positive samples. The PCR positive samples were subjected to genotyping using the method described by Ohno et al (J Clin Microbiol 35:201-202, 1997) with minor modifications. Genotyping of 28 samples revealed three different genotypes including 3a, 3b and 1a. The most prevalent genotype was 3a with rate of 50% followed by genotype 3b and 1a, respectively. Nine samples remained untyped, suggesting the need of further investigation of genotypes in this region. It has been proposed that sequencing of these samples may be helpful to unreveal these genotypes and further epidemiology of HCV genotypes. Further more, extensive and large scale studies are needed to understand the epidemiology of HCV genotypes, as no such study has been carried in this province.

  16. The distribution of hepatitis B virus genotypes in Thailand.

    Science.gov (United States)

    Louisirirotchanakul, Suda; Olinger, Christophe M; Arunkaewchaemsri, Panida; Poovorawan, Yong; Kanoksinsombat, Chinda; Thongme, Chittima; Sa-Nguanmoo, Pattaratida; Krasae, Sasithorn; Theamboonlert, Apiradee; Oota, Sineenart; Fongsatitkul, Ladda; Puapairoj, Chintana; Promwong, Charuporn; Weber, Bernard

    2012-10-01

    Phylogenetic analysis was performed on hepatitis B virus (HBV) strains obtained from 86 hepatitis B surface antigen (HBsAg) positive donors from Thailand originating throughout the country. Based on the S gene, 87.5% of strains were of genotype C while 10.5% were of genotype B, with all genotype B strains obtained from patients originating from the central or the south Thailand. No genotype B strains were found in the north of Thailand. Surprisingly, one patient was infected with a genotype H strain while another patient was infected with a genotype G strain. Complete genome sequencing and recombination analysis identified the latter as being a genotype G and C2 recombinant with the breakpoint around nucleotide position 700. The origin of the genotype G fragment was not identifiable while the genotype C2 fragment most likely came from strains circulating in Laos or Malaysia. The performance of different HBsAg diagnostic kits and HBV nucleic acid amplification technology (NAT) was evaluated. The genotype H and G/C2 recombination did not interfere with HBV detection.

  17. Geographic distribution of hepatitis C virus genotypes in Brazil

    Directory of Open Access Journals (Sweden)

    Campiotto S.

    2005-01-01

    Full Text Available Brazil is a country of continental dimension with a population of different ethnic backgrounds. Thus, a wide variation in the frequencies of hepatitis C virus (HCV genotypes is expected to occur. To address this point, 1,688 sequential samples from chronic HCV patients were analyzed. HCV-RNA was amplified by the RT-PCR from blood samples collected from 1995 to 2000 at different laboratories located in different cities from all Brazilian States. Samples were collected in tubes containing a gel separator, centrifuged in the site of collection and sent by express mail in a refrigerated container to Laboratório Bioquímico Jardim Paulista, São Paulo, SP, Brazil. HCV- RNA was extracted from serum and submitted to RT and nested PCR using standard procedures. Nested PCR products were submitted to cycle sequencing reactions without prior purification. Sequences were analyzed for genotype determination and the following frequencies were found: 64.9% (1,095 for genotype 1, 4.6% (78 for genotype 2, 30.2% (510 for genotype 3, 0.2% (3 for genotype 4, and 0.1% (2 for genotype 5. The frequencies of HCV genotypes were statistically different among Brazilian regions (P = 0.00017. In all regions, genotype 1 was the most frequent (51.7 to 74.1%, reaching the highest value in the North; genotype 2 was more prevalent in the Center-West region (11.4%, especially in Mato Grosso State (25.8%, while genotype 3 was more common in the South (43.2%. Genotypes 4 and 5 were rarely found and only in the Southeast, in São Paulo State. The present data indicate the need for careful epidemiological surveys throughout Brazil since knowing the frequency and distribution of the genotypes would provide key information for understanding the spread of HCV.

  18. Effect of reference population size and available ancestor genotypes on imputation of Mexican Holstein genotypes

    Science.gov (United States)

    The effects of reference population size and the availability of information from genotyped ancestors on the accuracy of imputation of single nucleotide polymorphisms (SNPs) were investigated for Mexican Holstein cattle. Three scenarios for reference population size were examined: (1) a local popula...

  19. The potential of plant viruses to promote genotypic diversity via genotype x environment interactions

    DEFF Research Database (Denmark)

    van Mölken, Tamara; Stuefer, Josef F.

    2011-01-01

    for WClMV to provoke differential selection on T. repens genotypes, which may lead to negative frequency-dependent selection in host populations. †Conclusions The apparent G × E interaction and evident repercussions for relative fitness reported in this study stress the importance of viruses...

  20. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

    Science.gov (United States)

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-11-01

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest.

  1. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

    Science.gov (United States)

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-01-01

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest. PMID:27857198

  2. Molecular genotyping of HCV infection in seropositive blood donor

    Science.gov (United States)

    Zarin, Siti Noraziah Abu; Ibrahim, Nazlina

    2013-11-01

    This study is to investigate the prevalence of hepatitis C virus infection in seropositive blood donor. RNA was extracted from 32 positive samples in National Blood Centre and Melaka Hospital. The core and NS5B sequences were obtained from 23 samples. Genotype 3a is most prevalent in this study followed by genotype 1a. Evidence of mixed-genotypes (3a and 1b) infections was found in 5 subjects.

  3. Deep sequencing analysis of HBV genotype shift and correlation with antiviral efficiency during adefovir dipivoxil therapy.

    Directory of Open Access Journals (Sweden)

    Yuwei Wang

    Full Text Available Viral genotype shift in chronic hepatitis B (CHB patients during antiviral therapy has been reported, but the underlying mechanism remains elusive.38 CHB patients treated with ADV for one year were selected for studying genotype shift by both deep sequencing and Sanger sequencing method.Sanger sequencing method found that 7.9% patients showed mixed genotype before ADV therapy. In contrast, all 38 patients showed mixed genotype before ADV treatment by deep sequencing. 95.5% mixed genotype rate was also obtained from additional 200 treatment-naïve CHB patients. Of the 13 patients with genotype shift, the fraction of the minor genotype in 5 patients (38% increased gradually during the course of ADV treatment. Furthermore, responses to ADV and HBeAg seroconversion were associated with the high rate of genotype shift, suggesting drug and immune pressure may be key factors to induce genotype shift. Interestingly, patients with genotype C had a significantly higher rate of genotype shift than genotype B. In genotype shift group, ADV treatment induced a marked enhancement of genotype B ratio accompanied by a reduction of genotype C ratio, suggesting genotype C may be more sensitive to ADV than genotype B. Moreover, patients with dominant genotype C may have a better therapeutic effect. Finally, genotype shifts was correlated with clinical improvement in terms of ALT.Our findings provided a rational explanation for genotype shift among ADV-treated CHB patients. The genotype and genotype shift might be associated with antiviral efficiency.

  4. Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

    Directory of Open Access Journals (Sweden)

    Joaquim Manoel da Silva

    Full Text Available High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

  5. Genotype X environment interactions. II. Some genetical considerations.

    Science.gov (United States)

    Mather, K

    1975-08-01

    An algebraic formulation, alternative to that of Mather and Jones (1958) and hierarchial rather than factorial in nauture, is presented for describing the differences among the phenotypes produced by a number of genotypes each grown in each of a number of environments. This formuationdoes not include terms representing statistical interactions between genotypes and environments: it depends instead on comparisons between the different genotypes in their variation over the relevant ranges of environemnts. The two-line case is considered ant eht condition established for linearity of the regress ion of genotype X enviroment interaction (g in Mather and Jones' formulation) on overall effect of the envirronment (e in Mather and Jones' formulation)...

  6. Trichothecene genotypes of Fusarium graminearum from wheat in Uruguay.

    Science.gov (United States)

    Pan, Dinorah; Calero, Natalia; Mionetto, Ana; Bettucci, Lina

    2013-03-01

    Gibberella zeae (Schwein.) Petch (anamorph F. graminearum Schwabe) is the primary causal agent of FHB of wheat in Uruguay. In the last decade, F. graminearum has produced destructive epidemics on wheat in Uruguay, causing yield losses and price discounts due to reduced seed quality. Strains of F. graminearum clade usually express one of three strain-specific profiles of trichothecene metabolites: nivalenol and its acetylated derivatives (NIV chemotype), deoxynivalenol and 3-acetyldeoxynivalenol (3-AcDON chemotype), or deoxynivalenol and 15-acetyldeoxynivalenol (15-AcDON chemotype). A multiplex PCR assay of Tri3, Tri5, and Tri7 was used to determine the trichothecene genotype of 111 strains of F. graminearum collected during 2003 and 2009 growing seasons from fields located in the major wheat production area of Uruguay. The result showed that all except one of the isolates were of DON genotype, with the remainder of NIV genotype in years 2003 and 2009. All strains with the DON genotype were also of the 15-AcDON genotype in 2003 and nearly all (45/50) in 2009. No DON/3-AcDON genotypes were found in either growing season. No potential shifts in the populations were found in the trichothecene genotypes between 2003 and the 2009 epidemic FHB harvest seasons. This study provides the first data on trichothecene genotypes of F. graminearum strains isolated from wheat in Uruguay and add to the current regional knowledge of trichothecene genotypes.

  7. Variability of acorn anatomical characteristics in Quercus robur L. genotypes

    Directory of Open Access Journals (Sweden)

    Nikolić Nataša P.

    2010-01-01

    Full Text Available The aim of this study was to examine variability of acorn anatomical characteristics in seventeen Quercus robur L. genotypes. Acorns were collected in clonal seed orchard Banov Brod (Srem, Vojvodina, Serbia. Microscopic measurements were done for pericarp (total thickness, thickness of exocarp and mesocarp, seed coat (total thickness, thickness of outer epidermis, parenchyma, and inner epidermis, and embryo axis (diameter, thickness of cortical region, and diameter of stellar zone. Obtained results revealed certain divergence between genotypes. The thickness of pericarp varied from 418 to 559 mm (genotypes 20 and 22, respectively. On average, the participation of exocarp in the total thickness of pericarp was 36.3%, of mesocarp 61.0%, while of endocarp 2.6%. The thickness of seed coat for individual genotypes ranged from 71 mm (genotype 28 to 157 mm (genotype 38. In addition, anatomic parameters of embryo axis varied among studied genotypes. The lowest cortical zone thickness and stellar zone diameter were measured in genotype 40, while the highest values in genotype 33.

  8. Plant genotype, microbial recruitment and nutritional security.

    Science.gov (United States)

    Patel, Jai S; Singh, Akanksha; Singh, Harikesh B; Sarma, Birinchi K

    2015-01-01

    Agricultural food products with high nutritional value should always be preferred over food products with low nutritional value. Efforts are being made to increase nutritional value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritional value of food is increased under natural environmental conditions especially in agricultural farms. Fragmented researches have demonstrated possibilities in achieving the same. The rhizosphere is vital in this regard for not only health and nutritional status of plants but also for the microorganisms colonizing the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of a plant host in discriminating its colonizers (Zancarini et al., 2012). A large number of biotic and abiotic factors are believed to manipulate the microbial communities in the rhizosphere. However, plant genotype has proven to be the key in giving the final shape of the rhizosphere microbiome (Berendsen et al., 2012; Marques et al., 2014).

  9. Apolipoprotein-E genotypes and myasthenia gravis.

    Science.gov (United States)

    Suhail, Hamid; Soundararajan, Christhunesa C; Vivekanandhan, Subbiah; Singh, Sumit; Behari, Madhuri

    2010-01-01

    Autoimmune myasthenia gravis (MG) is a disorder of neuromuscular junction. Possible role of multiple genes in the development of the MG has been documented. This case-control study, studied the association of apolipoprotein E (Apo-E) alleles with MG. Anti-AChR antibody was measured using radio receptor immunoassay. Apo-E genotypes were analyzed in 120 MG patients and 120 healthy subjects. Comparison between patients with MG and controls showed no significant association with Apo-E allelic variants. However, a significant association of Apo-E4 allele with AChR-antibody positive patients was observed (P = 0.007). Also, among seropositive patients, a significant association was seen between female gender and Apo-E4 allele (P = 0.023). Our results suggest that the presence of Apo-E4 allele might influence seropositive status in patients with MG and seems an associated susceptible factor in female patients.

  10. Probabilistic Transcriptome Assembly and Variant Graph Genotyping

    DEFF Research Database (Denmark)

    Sibbesen, Jonas Andreas

    the resulting sequencing data should be interpreted. This has over the years spurred the development of many probabilistic methods that are capable of modelling dierent aspects of the sequencing process. Here, I present two of such methods that were developed to each tackle a dierent problem in bioinformatics......, together with an application of the latter method to a large Danish sequencing project. The rst is a probabilistic method for transcriptome assembly that is based on a novel generative model of the RNA sequencing process and provides condence estimates on the assembled transcripts. We show...... that this approach outperforms existing state-of-the-art methods measured using sensitivity and precision on both simulated and real data. The second is a novel probabilistic method that uses exact alignment of k-mers to a set of variants graphs to provide unbiased estimates of genotypes in a population...

  11. Automated genotyping of dinucleotide repeat markers

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  12. Hepatitis C virus genotypes in Cordoba, Argentina unexpected high prevalence of genotype 2

    Directory of Open Access Journals (Sweden)

    V. Re

    2003-06-01

    Full Text Available To determine hepatitis C virus (HCV genotypes circulating in the central region of Argentina, 96 consecutive anti-HCV positive subjects were studied. The presence of HCV RNA was detected in 60 samples by RT-nested PCR of the 5' noncoding region (5' NCR. Genotyping was performed by restriction fragment length polymorphism analysis of 5' NCR region combined with PCR using type-specific primers of the core region. The groups of individuals in this study included hemophilia and hemodialysis patients, injecting drug users, screened blood donors, and patients with acute or chronic liver disease, all from Córdoba, Argentina. Overall, genotype 2 was the most prevalent (55.0%, followed by genotypes 1 (38.3 %, and 3 (5.0%. Within genotype 1, subtype 1b was the most prevalent. An unexpected high prevalence of genotype 2 (61.9% was found among patients with acute or chronic HCV infection (without known risk factors. These figures differ from other cohorts from East-Argentina where genotype 1 has been found as the most prevalent. This indicates that regional differences of genotype distribution might exist between Central and East Argentina.A fin de determinar los genotipos del virus de la hepatitis C (HCV circulantes en la región central de Argentina, se estudiaron 96 individuos anti-HCV positivos. La presencia del ARN de HCV se detectó en 60 muestras mediante RT-nested PCR de la región 5' no codificante (5' NCR. La genotipificación se realizó mediante restricción enzimática y el análisis del polimorfismo de los fragmentos largos de la región 5' NCR combinada con PCR usando primers tipo específico de la región del core. El grupo de individuos estudiados incluyó pacientes hemofílicos y hemodializados, drogadictos intravenosos, donantes de sangre y pacientes con enfermedad hepática aguda y crónica, todos provenientes de Córdoba, Argentina. El genotipo 2 fue el más prevalente (55.0%, seguido por los genotipos 1 (38.3 %, con mayor prevalencia

  13. Genotypic and phenotypic characterization of Chikungunya virus of different genotypes from Malaysia.

    Directory of Open Access Journals (Sweden)

    I-Ching Sam

    Full Text Available BACKGROUND: Mosquito-borne Chikungunya virus (CHIKV has recently re-emerged globally. The epidemic East/Central/South African (ECSA strains have spread for the first time to Asia, which previously only had endemic Asian strains. In Malaysia, the ECSA strain caused an extensive nationwide outbreak in 2008, while the Asian strains only caused limited outbreaks prior to this. To gain insight into these observed epidemiological differences, we compared genotypic and phenotypic characteristics of CHIKV of Asian and ECSA genotypes isolated in Malaysia. METHODS AND FINDINGS: CHIKV of Asian and ECSA genotypes were isolated from patients during outbreaks in Bagan Panchor in 2006, and Johor in 2008. Sequencing of the CHIKV strains revealed 96.8% amino acid similarity, including an unusual 7 residue deletion in the nsP3 protein of the Asian strain. CHIKV replication in cells and Aedes mosquitoes was measured by virus titration. There were no differences in mammalian cell lines. The ECSA strain reached significantly higher titres in Ae. albopictus cells (C6/36. Both CHIKV strains infected Ae. albopictus mosquitoes at a higher rate than Ae. aegypti, but when compared to each other, the ECSA strain had much higher midgut infection and replication, and salivary gland dissemination, while the Asian strain infected Ae. aegypti at higher rates. CONCLUSIONS: The greater ability of the ECSA strain to replicate in Ae. albopictus may explain why it spread far more quickly and extensively in humans in Malaysia than the Asian strain ever did, particularly in rural areas where Ae. albopictus predominates. Intergenotypic genetic differences were found at E1, E2, and nsP3 sites previously reported to be determinants of host adaptability in alphaviruses. Transmission of CHIKV in humans is influenced by virus strain and vector species, which has implications for regions with more than one circulating CHIKV genotype and Aedes species.

  14. Genotypic character relationship and phenotypic path coefficient analysis in chili pepper genotypes grown under tropical condition.

    Science.gov (United States)

    Usman, Magaji G; Rafii, Mohd Y; Martini, Mohammad Y; Oladosu, Yusuff; Kashiani, Pedram

    2017-03-01

    Studies on genotypic and phenotypic correlations among characters of crop plants are useful in planning, evaluating and setting selection criteria for the desired characters in a breeding program. The present study aimed to estimate the phenotypic correlation coefficients among yield and yield attributed characters and to work out the direct and indirect effects of yield-related characters on yield per plant using path coefficient analysis. Twenty-six genotypes of chili pepper were laid out in a randomized complete block design with three replications. Yield per plant showed positive and highly significant (P ≤ 0.01) correlations with most of the characters studied at both the phenotypic and genotypic levels. By contrast, disease incidence and days to flowering showed a significant negative association with yield. Fruit weight and number of fruits exerted positive direct effect on yield and also had a positive and significant (P ≤ 0.01) correlation with yield per plant. However, fruit length showed a low negative direct effect with a strong and positive indirect effect through fruit weight on yield and had a positive and significant association with yield. Longer fruits, heavy fruits and a high number of fruits are variables that are related to higher yields of chili pepper under tropical conditions and hence could be used as a reliable indicator in indirect selection for yield. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  15. Distribution of HCV genotypes in the metropolitan area of Naples

    Directory of Open Access Journals (Sweden)

    Giuseppe Sodano

    2013-08-01

    Full Text Available The Hepatitis C virus is characterized by high genomic variability that leads to the identification of six different genotypes and many subtypes. In this work, we show the prevalence of genotypes in patients living in the metropolitan area of Naples collected in one year, analyzing differences in the distribution depending on sex and age groups.

  16. The influence of temperature on photosynthesis of different tomato genotypes

    NARCIS (Netherlands)

    Gosiewski, W.; Nilwik, H.J.M.; Bierhuizen, J.F.

    1982-01-01

    Net photosynthesis and dark respiration from whole plants of various tomato genotypes were measured in a closed system. At low irradiance (27 W m−2) and low external CO2 concentration (550 mg m−3), net photosynthesis of 10 genotypes was found to vary between 0.122 and 0.209 mg CO2 m−2 s−1. Correlati

  17. Breeding of a Tomato Genotype Readily Accessible to Genetic Manipulation

    NARCIS (Netherlands)

    Koornneef, Maarten; Hanhart, Corrie; Jongsma, Maarten; Toma, Ingrid; Weide, Rob; Zabel, Pim; Hille, Jacques

    1986-01-01

    A tomato genotype, superior in regenerating plants from cell cultures, was obtained by transferring regeneration capacity from Lycopersicon peruvianum into L. esculentum by classical breeding. This genotype, MsK93, greatly facilitates genetic manipulation of tomato, as was demonstrated by successful

  18. Reaction of Drought Tolerant Soybean Genotypes to Macrophomina phaseolina

    Science.gov (United States)

    Charcoal rot caused by Macrophomina phaseolina is a common disease of soybean, and resistant genotypes are not available. Level of soybean genotype resistance and susceptibility to M. phaseolina is most frequently measured by determining colony forming units of M. phaseolina/g root, but using this ...

  19. Paternity testing and delivering trait-predictive genotypic data

    Science.gov (United States)

    In the RosBREED project, the Genotyping Team (Team Leader: Nahla Bassil) leads the effort to obtain DNA data needed to enable marker-assisted breeding for critical fruit quality traits. These data are obtained from reference genotypes of apple, peach, cherry and strawberry carefully chosen to repres...

  20. Genotyping of FCN and MBL2 polymorphisms using pyrosequencing

    DEFF Research Database (Denmark)

    Munthe-Fog, Lea; Madsen, Hans O.; Garred, Peter

    2014-01-01

    Pyrosequencing represents one of the most thorough methods used to analyze polymorphisms. One advantage of using pyrosequencing for genotyping is the ability to identify not only single-nucleotide polymorphisms (SNPs) but also tri-allelic variations, insertions and deletions (InDels). In contrast...... to most other genotyping assays the sequence surrounding the polymorphism provides an internal control making this method highly reliable....

  1. Clusters of incompatible genotypes evolve with limited dispersal

    Science.gov (United States)

    Erin L. Landguth; Norman A. Johnson; Samuel A. Cushman

    2015-01-01

    Theoretical and empirical studies have shown heterogeneous selection to be the primary driver for the evolution of reproductively isolated genotypes in the absence of geographic barriers. Here, we ask whether limited dispersal alone can lead to the evolution of reproductively isolated genotypes despite the absence of any geographic barriers or heterogeneous...

  2. Protein profiles and immunoreactivities of Acanthamoeba morphological groups and genotypes.

    Science.gov (United States)

    Pumidonming, Wilawan; Koehsler, Martina; Leitsch, David; Walochnik, Julia

    2014-11-01

    Acanthamoeba is a free-living protozoan found in a wide variety of habitats. A classification of Acanthamoeba into currently eighteen genotypes (T1-T18) has been established, however, data on differences between genotypes on the protein level are scarce. The aim of this study was to compare protein and immunoreactivity profiles of Acanthamoeba genotypes. Thirteen strains, both clinical and non-clinical, from genotypes T4, T5, T6, T7, T9, T11 and T12, representing three morphological groups, were investigated for their protein profiles and IgG, IgM and IgA immunoreactivities. It was shown that protein and immunoreactivity profiles of Acanthamoeba genotypes T4, T5, T6, T7, T9, T11 and T12 are clearly distinct from each other, but the banding patterns correlate to the morphological groups. Normal human sera revealed anti-Acanthamoeba antibodies against isolates of all investigated genotypes, interestingly, however only very weak IgM and virtually no IgA immunoreactivity with T7 and T9, both representing morphological group I. The strongest IgG, IgM and IgA immunoreactivities were observed for genotypes T4, T5 and T6. Differences of both, protein and immunological patterns, between cytopathic and non-cytopathic strains, particularly within genotype T4, were not at the level of banding patterns, but rather in expression levels.

  3. compensatory and susceptive responses of cowpea genotypes to ...

    African Journals Online (AJOL)

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    ABSTRACT. The aim of the study was to estimate yield loss to10 selected genotypes of cowpea as a result of ... Aphid's infestation period for studies in susceptive response in medium to .... The dry grain and biomass loss/gain due to ... Mean Grain weight (±SE) and Dry biomass (±SE) of cowpea genotypes on no infesta-.

  4. Characterization of cassava starch attributes of different genotypes

    NARCIS (Netherlands)

    Anggraini, V.; Sudarmonowati, E.; Hartati, N.Sri.; Suurs, L.C.J.M.; Visser, R.G.F.

    2009-01-01

    The genetic variation of starch of Indonesian cassava genotypes with various morphological characteristics of roots and eco-geographical origin was characterized and compared. The morphological characteristics of the roots of 71 collected cassava genotypes were classified into yellow and white for

  5. Breeding of a Tomato Genotype Readily Accessible to Genetic Manipulation

    NARCIS (Netherlands)

    Koornneef, Maarten; Hanhart, Corrie; Jongsma, Maarten; Toma, Ingrid; Weide, Rob; Zabel, Pim; Hille, Jacques

    1986-01-01

    A tomato genotype, superior in regenerating plants from cell cultures, was obtained by transferring regeneration capacity from Lycopersicon peruvianum into L. esculentum by classical breeding. This genotype, MsK93, greatly facilitates genetic manipulation of tomato, as was demonstrated by successful

  6. Caffeoylquinic Acids in Storage Roots of Sixteen Sweetpotato Genotypes

    Science.gov (United States)

    The contents of chlorogenic acid and the 3,4-, 3,5- and 4,5- isomers of dicaffeoylquinic acid (DCQA) in the storage root tissues of sixteen sweetpotato genotypes were determined. Averaged over genotypes, the contents of the four compounds were highest in the cortex, intermediate in the stele and lo...

  7. MLVA genotyping of human Brucella isolates from Peru

    NARCIS (Netherlands)

    H.L. Smits; B. Espinosa; R. Castillo; E. Hall; A. Guillen; M. Zevaleta; R.H. Gilman; P. Melendez; C. Guerra; A. Draeger; A. Broglia; K. Nöckler

    2009-01-01

    Recent human Brucella melitensis isolates from Peru were genotyped by multiple locus variable number repeat analysis. All 24 isolates originated from hospitalized patients living in the central part of Peru and consisted of six genomic groups comprising two to four isolates and nine unique genotypes

  8. Regional selection of hybrid Nacional cacao genotypes in Coastal Ecuador

    Science.gov (United States)

    Recent international demand for “nacional” flavour cacao has increased the need for local cacao producers in Ecuador to use high-yielding “nacional” hybrid genotypes. The relative potential of cacao genotypes over various environments needs to be assessed prior to final selection of potential candid...

  9. Apolipoprotein E genotype, cardiovascular biomarkers and risk of stroke

    DEFF Research Database (Denmark)

    Khan, Tauseef A; Shah, Tina; Prieto, David;

    2013-01-01

    At the APOE gene, encoding apolipoprotein E, genotypes of the ε2/ε3/ε4 alleles associated with higher LDL-cholesterol (LDL-C) levels are also associated with higher coronary risk. However, the association of APOE genotype with other cardiovascular biomarkers and risk of ischaemic stroke is less...

  10. Hepatitis B virus genotypes and resistance mutations in patients under long term lamivudine therapy: characterization of genotype G in Brazil

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    Brandão Carlos E

    2008-01-01

    Full Text Available Abstract Background Lamivudine is an oral nucleoside analogue widely used for the treatment of chronic hepatitis B. The main limitation of lamivudine use is the selection of resistant mutations that increases with time of utilization. Hepatitis B virus (HBV isolates have been classified into eight genotypes (A to H with distinct geographical distributions. HBV genotypes may also influence pathogenic properties and therapeutic features. Here, we analyzed the HBV genotype distribution and the nature and frequency of lamivudine resistant mutations among 36 patients submitted to lamivudine treatment for 12 to 84 months. Results Half of the patients were homosexual men. Only 4/36 (11% patients were HBV DNA negative. As expected for a Brazilian group, genotypes A (24/32 positive individuals, 75%, D (3/32, 9.3% and F (1/32, 3% were present. One sample was from genotype C, which is a genotype rarely found in Brazil. Three samples were from genotype G, which had not been previously detected in Brazil. Lamivudine resistance mutations were identified in 20/32 (62% HBV DNA positive samples. Mean HBV loads of patients with and without lamivudine resistance mutations were not very different (2.7 × 107 and 6.9 × 107 copies/mL, respectively. Fifteen patients showed the L180M/M204V lamivudine resistant double mutation. The triple mutant rt173V/180M/204V, which acts as a vaccine escape mutant, was found in two individuals. The three isolates of genotype G were entirely sequenced. All three showed the double mutation L180M/M204V and displayed a large genetic divergence when compared with other full-length genotype G isolates. Conclusion A high (55% proportion of patients submitted to long term lamivudine therapy displayed resistant mutations, with elevated viral load. The potential of transmission of such HBV mutants should be monitored. The identification of genotypes C and G, rarely detected in South America, seems to indicate a genotype distribution different

  11. The Association of Il28b Genotype with the Histological Features of Chronic Hepatitis C Is HCV Genotype Dependent

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    Roberta D'Ambrosio

    2014-04-01

    Full Text Available The interleukin 28B (IL28B rs12979860 polymorphism is associated with treatment outcome in hepatitis C virus (HCV genotype 1 and 4 patients. Its association with the histological features of chronic hepatitis C and disease severity needs further clarifications. To assess the correlation between IL28B genotype, HCV genotype and liver biopsy findings in untreated patients. Materials and Methods: Pre-treatment liver biopsies from 335 HCV Caucasian patients (59% males, age 50 years enrolled in the MIST study were staged for fibrosis and inflammation according to the METAVIR and the Ishak scoring systems; steatosis was dichotomized as <5% or ≥5%. IL28B was typed by Taqman Single Nucleotide Polymorphism (SNP genotyping assay. HCV genotype was 1 in 151 (45%, 2 in 99 (30%, 3 in 50 (15% and 4 in 35 (10% patients. IL28B genotype was CC in 117 (34%, CT in 166 (49% and TT in 52 (15%. At univariate analysis, the IL28B CC genotype was associated with severe portal inflammation in HCV-1 patients (CC vs. CT/TT: 86% vs. 63%, p = 0.005, severe lobular inflammation in HCV-2 patients (CC vs. CT/TT: 44% vs. 23%, p = 0.03, and less fatty infiltration in HCV-1 patients (CC vs. CT/TT: 72% vs. 51%, p = 0.02. Despite the lack of any association between IL28B and fibrosis stage, in HCV-3 patients IL28B CC correlated with METAVIR F3-F4 (CC vs. CT/TT: 74% vs. 26%, p = 0.05. At multivariate analysis, the genotype CC remained associated with severe portal inflammation in HCV-1, only (Odds Ratio (OR: 95% Confidence Interval (CI: 3.24 (1.23–8.51. IL28B genotype is associated with the histological features of chronic hepatitis C in a HCV genotype dependent manner, with CC genotype being independently associated with severe portal inflammation.

  12. Distribution study of Chlamydia trachomatis genotypes in symptomatic patients in Buenos Aires, Argentina: association between genotype E and neonatal conjunctivitis

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    Corominas Ana I

    2010-02-01

    Full Text Available Abstract Background Chlamydia trachomatis infections are the most prevalent sexually transmitted bacterial infections in the world. There is scarce data available referring to the distribution of C. trachomatis genotypes in Argentina. The aim of this study was to identify the genotypes of C. trachomatis circulating in the metropolitan area of Buenos Aires (Argentina associated with ophthalmia neonatorum and genital infections. Findings From 2001 to 2006, 199 positive samples for C. trachomatis infection from symptomatic adult patients and neonates with ophthalmia neonatorum from two public hospitals were studied. C. trachomatis genotypes were determined by PCR-RFLP of an ompA fragment. Genotype E was the most prevalent regardless of the sample origin (46.3% 57/123 in adults and 72.4% 55/76 in neonates, followed by genotype D (19.5% 24/123 and F (14.6% 18/123 in adults, and G (9.2% 7/76 and D (7.9% 6/76 in neonates. We detected a significantly higher frequency of genotype E (p ophthalmia neonatorum than in genital specimens. Genotype D was associated with genital localization (p Conclusion We found a particularly increased frequency of C. trachomatis genotype E in neonatal conjunctivitis, which may indicate an epidemiological association between this genotype and the newborn population. The present study also contributed to increase the knowledge on genotype distribution of Chlamydia trachomatis in symptomatic adult patients in Buenos Aires, Argentina, in which genotypes E, D and F were the predominant ones.

  13. Silhouette scores for assessment of SNP genotype clusters

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    Jonsson Mats

    2005-03-01

    Full Text Available Abstract Background High-throughput genotyping of single nucleotide polymorphisms (SNPs generates large amounts of data. In many SNP genotyping assays, the genotype assignment is based on scatter plots of signals corresponding to the two SNP alleles. In a robust assay the three clusters that define the genotypes are well separated and the distances between the data points within a cluster are short. "Silhouettes" is a graphical aid for interpretation and validation of data clusters that provides a measure of how well a data point was classified when it was assigned to a cluster. Thus "Silhouettes" can potentially be used as a quality measure for SNP genotyping results and for objective comparison of the performance of SNP assays at different circumstances. Results We created a program (ClusterA for calculating "Silhouette scores", and applied it to assess the quality of SNP genotype clusters obtained by single nucleotide primer extension ("minisequencing" in the Tag-microarray format. A Silhouette score condenses the quality of the genotype assignment for each SNP assay into a single numeric value, which ranges from 1.0, when the genotype assignment is unequivocal, down to -1.0, when the genotype assignment has been arbitrary. In the present study we applied Silhouette scores to compare the performance of four DNA polymerases in our minisequencing system by analyzing 26 SNPs in both DNA polarities in 16 DNA samples. We found Silhouettes to provide a relevant measure for the quality of SNP assays at different reaction conditions, illustrated by the four DNA polymerases here. According to our result, the genotypes can be unequivocally assigned without manual inspection when the Silhouette score for a SNP assay is > 0.65. All four DNA polymerases performed satisfactorily in our Tag-array minisequencing system. Conclusion "Silhouette scores" for assessing the quality of SNP genotyping clusters is convenient for evaluating the quality of SNP genotype

  14. SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays

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    Stephen W. Erickson

    2016-07-01

    Full Text Available SNPMClust is an R package for genotype clustering and calling with Illumina microarrays. It was originally developed for studies using the GoldenGate custom genotyping platform but can be used with other Illumina platforms, including Infinium BeadChip. The algorithm first rescales the fluorescent signal intensity data, adds empirically derived pseudo-data to minor allele genotype clusters, then uses the package mclust for bivariate Gaussian model fitting. We compared the accuracy and sensitivity of SNPMClust to that of GenCall, Illumina's proprietary algorithm, on a data set of 94 whole-genome amplified buccal (cheek swab DNA samples. These samples were genotyped on a custom panel which included 1064 SNPs for which the true genotype was known with high confidence. SNPMClust produced uniformly lower false call rates over a wide range of overall call rates.

  15. Effect of genotype on sugar beet yield and quality

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    Nenadić N.

    2003-01-01

    Full Text Available The effect of a considerable number of both domestic and foreign sugar beet genotypes on root yield and quality was investigated. The data demonstrated the most favorable results of some genotypes for root yield and sugar content. Trials were conducted on rhizomania infested soil, thus tolerant genotypes were used. Susceptible cultivars represented the control. In the trial root yield was high and sugar content low. On average, in the genotypes tested, root yield varied from 73.98 to 93.30 t/ha and sugar content from 11.90 to 13.36%, depending on weather conditions. Root yield of the genotypes investigated varied from 30.61 to 112.64 t/ha and sugar content from 10.60 to 14.20%. The Swedish cultivar Dorotea (tolerant to both rhizomania and cercospora was the most yielding. The least yielding (susceptible to both rhizomania and cercospora was the domestic cultivar Dana.

  16. Genetic relationships among some hawthorn (Crataegus spp.) species and genotypes.

    Science.gov (United States)

    Yilmaz, Kadir Ugurtan; Yanar, Makbule; Ercisli, Sezai; Sahiner, Hatice; Taskin, Tuncer; Zengin, Yasar

    2010-10-01

    The genus Crataegus is well distributed in Turkey as a wild plant, with numerous, inherently variable species and genotypes. RAPD markers were used to study 17 hawthorn genotypes belonging to Crataegus monogyna ssp. monogyna Jacq (2 genotypes), C. monogyna ssp. azarella Jacq (1), Crataegus pontica K.Koch (3), Crataegus orientalis var. orientalis Pallas Ex Bieb (3), Crataegus pseudoheterophylla Pojark (1), Crataegus aronia var. dentata Browicz (1), C. aronia var. aronia Browicz (4), and Crateagus x bornmuelleri Zabel (2). The 10 RAPD primers produced 72 polymorphic bands (88% polymorphism). A dendrogram based on Jaccard's index included four major groups and one outgroup according to taxa. The lowest genetic variability was observed within C. aronia var. aronia genotypes. The study demonstrated that RAPD analysis is efficient for genotyping wild-grown hawthorns.

  17. HCV prevalence and predominant genotype in IV drug users

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    Asad Andalibalshohada

    2014-07-01

    Full Text Available Hepatitis C virus (HCV causes 308000 deaths due to liver cancer and 758000 deaths due to cirrhosis every year. Almost 170 million people have HCV infection around the world. Information regarding this virus helps us to determine the prevalence of other hepatitis C genotypes in population, especially in intravenous drug users. It is assumed that some genotypes are more common in certain areas or groups of people. A recent study strongly confirms the central role of injecting network traits, not only as a transmission factor but also as a predictor of HCV genotype and phylogenetic determination in different communities. Hepatitis C genotypes and subtypes have different prevalence considering the country. Risk factors such as transfusion, hemodialysis, root of acquisition and etc, are detected in intravenous drug users. Several conducted studies have investigated the prevalence, risk factors, and predominance of HCV genotypes infection in different parts of Iran.

  18. Micropropagation of six Paulownia genotypes through tissue culture

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    Lydia Shtereva

    2014-12-01

    Full Text Available We investigated the effect of genotype and culture medium on the in vitro germination and development of plantlets from seeds of 6 different Paulownia genotypes (P. tomentosa, hybrid lines P. tomentosa P. fortunei (Mega, Ganter and Caroline, P. elongata and hybrid line P. elongata P. fortunei. Nodal and shoot tip explants were used for micropropagation of Paulownia genotypes by manipulating plant growth regulators. The highest germination percentage for all genotypes was obtained for seeds inoculated on medium supplemented with 50 mg*L GA3 (MSG2. On Thidiazuron containing media, the explants of hybrid line P. elongata P. fortunei exhibited the highest frequency of axillary shoot proliferation following by P. tomentosa P. fortunei. The results are discussed with the perspective of applying an improved protocol for in vitro seed germination and plantlet formation in several economically valuable Paulownia genotypes.

  19. Comparison of methods for analysis of selective genotyping survival data

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    Dekkers Jack CM

    2006-11-01

    Full Text Available Abstract Survival traits and selective genotyping datasets are typically not normally distributed, thus common models used to identify QTL may not be statistically appropriate for their analysis. The objective of the present study was to compare models for identification of QTL associated with survival traits, in particular when combined with selective genotyping. Data were simulated to model the survival distribution of a population of chickens challenged with Marek disease virus. Cox proportional hazards (CPH, linear regression (LR, and Weibull models were compared for their appropriateness to analyze the data, ability to identify associations of marker alleles with survival, and estimation of effects when all individuals were genotyped (full genotyping and when selective genotyping was used. Little difference in power was found between the CPH and the LR model for low censoring cases for both full and selective genotyping. The simulated data were not transformed to follow a Weibull distribution and, as a result, the Weibull model generally resulted in less power than the other two models and overestimated effects. Effect estimates from LR and CPH were unbiased when all individuals were genotyped, but overestimated when selective genotyping was used. Thus, LR is preferred for analyzing survival data when the amount of censoring is low because of ease of implementation and interpretation. Including phenotypic data of non-genotyped individuals in selective genotyping analysis increased power, but resulted in LR having an inflated false positive rate, and therefore the CPH model is preferred for this scenario, although transformation of the data may also make the Weibull model appropriate for this case. The results from the research presented herein are directly applicable to interval mapping analyses.

  20. Genetic diversity of the genotype VII Newcastle disease virus: identification of a novel VIIj sub-genotype.

    Science.gov (United States)

    Xue, Cong; Cong, Yanlong; Yin, Renfu; Sun, Yixue; Ding, Chan; Yu, Shengqing; Liu, Xiufan; Hu, Shunlin; Qian, Jing; Yuan, Qianliang; Yang, Mingxi; Wang, Chunfeng; Ding, Zhuang

    2017-02-01

    Newcastle disease (ND) is a highly contagious disease of poultry caused by Newcastle disease virus (NDV). Multiple genotypes of NDV have been circulating worldwide and NDV is continuously evolving, resulting into more diversity. Of multiple viral genotypes, VII is particularly important given that it had been associated with most recent ND outbreaks worldwide. In this study, an epidemiological investigation performed in northeastern China during 2014-2015 showed that 11 genotype VII isolates amounted to 55 percent in a total number of NDV isolates. Therefore, to evaluate the genetic diversity worldwide and epidemiological distribution in China of genotype VII NDV, a phylogenetic analysis based on the 1255 complete F gene sequences showed that VII is the most predominant genotype worldwide. A further detailed characterization on genotype VII was conducted based on the 477 complete F gene sequences from 11 isolates and 466 reference viruses available in GenBank. The results demonstrated that VII can be further divided into 8 sub-genotypes (VIIb, VIId-VIIj), indicating its complex genetic diversity. It is worthy of note that the isolation rate of VIIj is increasing recently. It emphasizes the necessity to pay close attention to the epidemiological dynamic of genotype VII NDV and highlights the importance of vaccination program.

  1. Pepino mosaic virus genotype shift in North America and rapid genotype identification using loop-mediated isothermal amplification

    Science.gov (United States)

    Pepino mosaic, once an emerging disease a decade ago, has become endemic on greenhouse tomatoes worldwide in recent years. Three distinct genotypes of Pepino mosaic virus (PepMV), including EU, US1 and CH2 have been recognized. Our earlier study in 2006-2007 demonstrated a predominant EU genotype ...

  2. Changing genotypes of cholera toxin (CT) of Vibrio cholerae O139 in Bangladesh and description of three new CT genotypes.

    Science.gov (United States)

    Bhuiyan, Nurul A; Nusrin, Suraia; Alam, Munirul; Morita, Masatomo; Watanabe, Haruo; Ramamurthy, Thandavarayan; Cravioto, Alejandro; Nair, Gopinath Balakrish

    2009-11-01

    We determined the genotype of cholera toxin by amplifying and sequencing the B-subunit in a sequential collection of 90 strains of Vibrio cholerae O139 isolated over the past 13 years since its first description in 1992. Representative strains isolated during 1993-1997 harboured ctxB of El Tor type (genotype 3). Twenty-six strains isolated during 1999, 2001, 2005 and three strains isolated in 1998, 2000 and 2002 were identified to belong to new ctxB genotypes 4 and 5, respectively. Genotype 5 was similar to genotype 1 except at position 28 (D-->A). The genotype 6 was similar to genotype 4 except at position 34 (H-->P). The implication of switch in terms of function of the toxin and its impact on human disease is unclear. How this change has influenced their prevalence relative to that of V. cholerae O1 in human infection is also not clear. The other common virulence gene clusters including the Vibrio pathogenicity island-1, Vibrio seventh pandemic island (VSP)-I and VSP-II of V. cholerae O139 did not show any remarkable difference from that of the O1 El Tor strains. Overall, the majority of the O139 strains tested in this study were similar to the El Tor strains but had altered ctxB genotype. This change and the impact that it causes to the epidemiology of cholera caused by O139 should be closely monitored.

  3. Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data

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    Nettelblad Carl

    2012-10-01

    Full Text Available Abstract Background In many contexts, pedigrees for individuals are known even though not all individuals have been fully genotyped. In one extreme case, the genotypes for a set of full siblings are known, with no knowledge of parental genotypes. We propose a method for inferring phased haplotypes and genotypes for all individuals, even those with missing data, in such pedigrees, allowing a multitude of classic and recent methods for linkage and genome analysis to be used more efficiently. Results By artificially removing the founder generation genotype data from a well-studied simulated dataset, the quality of reconstructed genotypes in that generation can be verified. For the full structure of repeated matings with 15 offspring per mating, 10 dams per sire, 99.89%of all founder markers were phased correctly, given only the unphased genotypes for offspring. The accuracy was reduced only slightly, to 99.51%, when introducing a 2% error rate in offspring genotypes. When reduced to only 5 full-sib offspring in a single sire-dam mating, the corresponding percentage is 92.62%, which compares favorably with 89.28%from the leading Merlin package. Furthermore, Merlin is unable to handle more than approximately 10 sibs, as the number of states tracked rises exponentially with family size, while our approach has no such limit and handles 150 half-sibs with ease in our experiments. Conclusions Our method is able to reconstruct genotypes for parents when genotype data is only available for offspring individuals, as well as haplotypes for all individuals. Compared to the Merlin package, we can handle larger pedigrees and produce superior results, mainly due to the fact that Merlin uses the Viterbi algorithm on the state space to infer the genotype sequence. Tracking of haplotype and allele origin can be used in any application where the marker set does not directly influence genotype variation influencing traits. Inference of genotypes can also reduce the

  4. Combined use of phenotypic and genotypic information in sampling animalsfor genotyping in detection of quantitative trait loci

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P

    2008-01-01

    Conventional selective genotyping which is using the extreme phenotypes (EP) was compared with alternative criteria to find the most informative animals for genotyping with respects to mapping quantitative trait loci (QTL). Alternative sampling strategies were based on minimizing the sampling error...... of the estimated QTL effect (MinERR) and maximizing likelihood ratio test (MaxLRT) using both phenotypic and genotypic information. In comparison, animals were randomly genotyped either within or across families. One hundred data sets were simulated each with 30 half-sib families and 120 daughters per family....... The strategies were compared in these datasets with respect to estimated effect and position of a QTL within a previously defined genomic region at genotyping 10, 20 or 30% of the animals. Combined linkage disequilibrium linkage analysis (LDLA) was applied in a variance component approach. Power to detect QTL...

  5. Comparison of two PCR-based human papillomavirus genotyping methods.

    Science.gov (United States)

    Castle, Philip E; Porras, Carolina; Quint, Wim G; Rodriguez, Ana Cecilia; Schiffman, Mark; Gravitt, Patti E; González, Paula; Katki, Hormuzd A; Silva, Sandra; Freer, Enrique; Van Doorn, Leen-Jan; Jiménez, Silvia; Herrero, Rolando; Hildesheim, Allan

    2008-10-01

    We compared two consensus primer PCR human papillomavirus (HPV) genotyping methods for the detection of individual HPV genotypes and carcinogenic HPV genotypes as a group, using a stratified sample of enrollment cervical specimens from sexually active women participating in the NCI/Costa Rica HPV16/18 Vaccine Efficacy Trial. For the SPF(10) method, DNA was extracted from 0.1% of the cervical specimen by using a MagNA Pure LC instrument, a 65-bp region of the HPV L1 gene was targeted for PCR amplification by using SPF(10) primers, and 25 genotypes were detected by reverse-line blot hybridization of the amplicons. For the Linear Array (LA) method, DNA was extracted from 0.5% of the cervical specimen by using an MDx robot, a 450-bp region of the HPV L1 gene was targeted for PCR amplification by using PGMY09/11 L1 primers, and 37 genotypes were detected by reverse-line blot hybridization of the amplicons. Specimens (n = 1,427) for testing by the LA method were randomly selected from strata defined on the basis of enrollment test results from the SPF(10) method, cytology, and Hybrid Capture 2. LA results were extrapolated to the trial cohort (n = 5,659). The LA and SPF(10) methods detected 21 genotypes in common; HPV16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -66, -68, and -73 were considered the carcinogenic HPV genotypes. There was no difference in the overall results for grouped detection of carcinogenic HPV by the SPF(10) and LA methods (35.3% versus 35.9%, respectively; P = 0.5), with a 91.8% overall agreement and a kappa value of 0.82. In comparisons of individual HPV genotypes, the LA method detected significantly more HPV16, HPV18, HPV39, HPV58, HPV59, HPV66, and HPV68/73 and less HPV31 and HPV52 than the SPF(10) method; inclusion of genotype-specific testing for HPV16 and HPV18 for those specimens testing positive for HPV by the SPF(10) method but for which no individual HPV genotype was detected abrogated any differences between the LA and SPF

  6. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing.

    Science.gov (United States)

    Campbell, Nathan R; Harmon, Stephanie A; Narum, Shawn R

    2015-07-01

    Genotyping-in-Thousands by sequencing (GT-seq) is a method that uses next-generation sequencing of multiplexed PCR products to generate genotypes from relatively small panels (50-500) of targeted single-nucleotide polymorphisms (SNPs) for thousands of individuals in a single Illumina HiSeq lane. This method uses only unlabelled oligos and PCR master mix in two thermal cycling steps for amplification of targeted SNP loci. During this process, sequencing adapters and dual barcode sequence tags are incorporated into the amplicons enabling thousands of individuals to be pooled into a single sequencing library. Post sequencing, reads from individual samples are split into individual files using their unique combination of barcode sequences. Genotyping is performed with a simple perl script which counts amplicon-specific sequences for each allele, and allele ratios are used to determine the genotypes. We demonstrate this technique by genotyping 2068 individual steelhead trout (Oncorhynchus mykiss) samples with a set of 192 SNP markers in a single library sequenced in a single Illumina HiSeq lane. Genotype data were 99.9% concordant to previously collected TaqMan(™) genotypes at the same 192 loci, but call rates were slightly lower with GT-seq (96.4%) relative to Taqman (99.0%). Of the 192 SNPs, 187 were genotyped in ≥90% of the individual samples and only 3 SNPs were genotyped in <70% of samples. This study demonstrates amplicon sequencing with GT-seq greatly reduces the cost of genotyping hundreds of targeted SNPs relative to existing methods by utilizing a simple library preparation method and massive efficiency of scale.

  7. Molecular characterization of the Hepatitis B virus genotypes in Colombia: a Bayesian inference on the genotype F.

    Science.gov (United States)

    Alvarado Mora, Mónica Viviana; Romano, Camila Malta; Gomes-Gouvêa, Michele Soares; Gutierrez, Maria Fernanda; Botelho, Livia; Carrilho, Flair José; Pinho, João Renato Rebello

    2011-01-01

    Hepatitis B is a worldwide health problem affecting about 2 billion people and more than 350 million are chronic carriers of the virus. Nine HBV genotypes (A to I) have been described. The geographical distribution of HBV genotypes is not completely understood due to the limited number of samples from some parts of the world. One such example is Colombia, in which few studies have described the HBV genotypes. In this study, we characterized HBV genotypes in 143 HBsAg-positive volunteer blood donors from Colombia. A fragment of 1306 bp partially comprising HBsAg and the DNA polymerase coding regions (S/POL) was amplified and sequenced. Bayesian phylogenetic analyses were conducted using the Markov Chain Monte Carlo (MCMC) approach to obtain the maximum clade credibility (MCC) tree using BEAST v.1.5.3. Of all samples, 68 were positive and 52 were successfully sequenced. Genotype F was the most prevalent in this population (77%) - subgenotypes F3 (75%) and F1b (2%). Genotype G (7.7%) and subgenotype A2 (15.3%) were also found. Genotype G sequence analysis suggests distinct introductions of this genotype in the country. Furthermore, we estimated the time of the most recent common ancestor (TMRCA) for each HBV/F subgenotype and also for Colombian F3 sequences using two different datasets: (i) 77 sequences comprising 1306 bp of S/POL region and (ii) 283 sequences comprising 681 bp of S/POL region. We also used two other previously estimated evolutionary rates: (i) 2.60 × 10(-4)s/s/y and (ii) 1.5 × 10(-5)s/s/y. Here we report the HBV genotypes circulating in Colombia and estimated the TMRCA for the four different subgenotypes of genotype F.

  8. Plant genotype, microbial recruitment and nutritional security

    Directory of Open Access Journals (Sweden)

    Jai Singh Patel

    2015-08-01

    Full Text Available Agricultural food products with high nutritive value are always preferred over food products with low nutritive value. Efforts are being made to increase the nutritive value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritive value of food is increased under natural conditions in the food products especially in the agricultural produces. Fragmented researches have led to the conclusion that it is possible to increase nutritive value of the agricultural products naturally in agricultural fields. The rhizosphere is of vital importance in this regard for not only health and nutritional status of plants but also for the microorganisms colonising the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of plant host in discriminating its colonisers. A large amount of biotic and abiotic factors are believed to manipulate the microbial communities in the rhizosphere. However, plant genotype has proven to be the key in giving the final shape of the rhizosphere microbiome.

  9. Probabilistic Transcriptome Assembly and Variant Graph Genotyping

    DEFF Research Database (Denmark)

    Sibbesen, Jonas Andreas

    The introduction of second-generation sequencing, has in recent years allowed the biological community to determine the genomes and transcriptomes of organisms and individuals at an unprecedented rate. However, almost every step in the sequencing protocol introduces uncertainties in how the resul......The introduction of second-generation sequencing, has in recent years allowed the biological community to determine the genomes and transcriptomes of organisms and individuals at an unprecedented rate. However, almost every step in the sequencing protocol introduces uncertainties in how...... the resulting sequencing data should be interpreted. This has over the years spurred the development of many probabilistic methods that are capable of modelling dierent aspects of the sequencing process. Here, I present two of such methods that were developed to each tackle a dierent problem in bioinformatics...... that this approach outperforms existing state-of-the-art methods measured using sensitivity and precision on both simulated and real data. The second is a novel probabilistic method that uses exact alignment of k-mers to a set of variants graphs to provide unbiased estimates of genotypes in a population...

  10. A SNP Genotyping Array for Hexaploid Oat

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    Nicholas A. Tinker

    2014-11-01

    Full Text Available Recognizing a need in cultivated hexaploid oat ( L. for a reliable set of reference single nucleotide polymorphisms (SNPs, we have developed a 6000 (6K BeadChip design containing 257 Infinium I and 5486 Infinium II designs corresponding to 5743 SNPs. Of those, 4975 SNPs yielded successful assays after array manufacturing. These SNPs were discovered based on a variety of bioinformatics pipelines in complementary DNA (cDNA and genomic DNA originating from 20 or more diverse oat cultivars. The array was validated in 1100 samples from six recombinant inbred line (RIL mapping populations and sets of diverse oat cultivars and breeding lines, and provided approximately 3500 discernible Mendelian polymorphisms. Here, we present an annotation of these SNPs, including methods of discovery, gene identification and orthology, population-genetic characteristics, and tentative positions on an oat consensus map. We also evaluate a new cluster-based method of calling SNPs. The SNP design sequences are made publicly available, and the full SNP genotyping platform is available for commercial purchase from an independent third party.

  11. Genotyping of Canine parvovirus in western Mexico.

    Science.gov (United States)

    Pedroza-Roldán, César; Páez-Magallan, Varinia; Charles-Niño, Claudia; Elizondo-Quiroga, Darwin; De Cervantes-Mireles, Raúl Leonel; López-Amezcua, Mario Alberto

    2015-01-01

    Canine parvovirus (CPV) is one of the most common infectious agents related to high morbidity rates in dogs. In addition, the virus is associated with severe gastroenteritis, diarrhea, and vomiting, resulting in high death rates, especially in puppies and nonvaccinated dogs. To date, there are 3 variants of the virus (CPV-2a, CPV-2b, and CPV-2c) circulating worldwide. In Mexico, reports describing the viral variants circulating in dog populations are lacking. In response to this deficiency, a total of 41 fecal samples of suspected dogs were collected from October 2013 through April 2014 in the Veterinary Hospital of the University of Guadalajara in western Mexico. From these, 24 samples resulted positive by polymerase chain reaction, and the viral variant was determined by restriction fragment length polymorphism. Five positive diagnosed samples were selected for partial sequencing of the vp2 gene and codon analysis. The results demonstrated that the current dominant viral variant in Mexico is CPV-2c. The current study describes the genotyping of CPV strains, providing valuable evidence of the dominant frequency of this virus in a dog population from western Mexico.

  12. Genotype phenotype classification of hepatocellular adenoma

    Institute of Scientific and Technical Information of China (English)

    Paulette Bioulac-Sage; Jean Frédéric Blanc; Sandra Rebouissou; Charles Balabaud; Jessica Zucman-Rossi

    2007-01-01

    Studies that compare tumor genotype with phenotype have provided the basis of a new histological/molecular classification of hepatocellular adenomas. Based on two molecular criteria (presence of a TCF1/HNF1α or β-catenin mutation), and an additional histological criterion (presence or absence of an inflammatory infiltrate), subgroups of hepatocellular adenoma can be defined and distinguished from focal nodular hyperplasia. Analysis of 96 hepatocellular adenomas performed by a French collaborative network showed that they can be divided into four broad subgroups: the first one is defined by the presence of mutations in TCF1 gene inactivating the hepatocyte nuclear factor 1 (HNF1α); the second by the presence of β-catenin activating mutations; the category without mutations of HNF1α or β-catenin is further divided into 2 subgroups depending on the presence or absence of inflammation. Therefore, the approach to the diagnosis of problematic benign hepatocytic nodules may be entering a new era directed by new molecular information. It is hoped that immunohistological tools will improve significantly diagnosis of liver biopsy in our ability to distinguish hepatocellular adenoma from focal nodular hyperplasia (FNH), and to delineate clinically meaningful entities within each group to define the best clinical management. The optimal care of patients with a liver nodule will benefit from the recent knowledge coming from molecular biology and the combined expertise of hepatologists, pathologists, radiologists, and surgeons.

  13. Hepatitis B virus genotypes and lamivudine resistance mutations in Jordan

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    AIM: To investigate and identify prevalent hepatitis B virus (HBV) genotypes and to explore lamivudine-resistant mutations among treated and untreated patients in Jordan.METHODS: A total of 107 cases with chronic hepatitis B were recruited from different medical centers in Jordan. Serological tests were preformed for all cases using a microparticle enzyme immunoassay. HBV Genotyping was performed for 70 cases using Line probe genotyping assay, The YMDD mutations were explored for 20 cases (4 were lamivudine naive) using the INNO-LiPA HBV DR assay.RESULTS: Genotype D was the only detected genotype. A total of 6 YMDD mutations were detected in 5 treated patients (31%) while one mutation was detected in the naive patients. Seventeen percent of cases were positive for HBeAg and had statistically significant higher levels of serum aminotransferases.CONCLUSION: HBV genotype D appears to be the only circulating type in Jordanian patients. The YMDD mutations were detected in 31% of lamivudine-treated cases with similar patterns to those found in the lit-erature. We also found a relatively low prevalence of HBeAg expression among examined cases (17%). Awareness of these serologic, genotypic and resistance patterns might help in the formulation of management plans and for predicting clinical outcomes. Further larger scale studies are needed to confirm our results and to examine possible associations among clinical, serologic, and genetic patterns of HBV infections in Jordan.

  14. Preliminary report of hepatitis B virus genotype prevalence in Iran

    Institute of Scientific and Technical Information of China (English)

    Seyed-Moayed Alavian; Hossein Keyvani; Mahdi Rezai; Neda Ashayeri; Homa Mohammad Sadeghi

    2006-01-01

    AIM: To determine the prevalence of hepatitis B virus (HBV) genotypes in Iranian hepatitis B surface antigen (HBsAg) carriers, chronic hepatitis B and cirrhotic patients.METIHODS: A total of 109 HBsAg-positive patients were included in this study. HBV genotypes were determined by using INNO-LiPA methodology which is based on the reverse hybridization principle.RESULTS: The distribution of patients with different stages of liver disease was as follows: 95 (86.4%) chronic hepatitis, 11 (10%) liver cirrhosis, and 3 (2.7%)inactive carrier. Of the chronic hepatitis and liver cirrhosis patients, 26.4% were HBeAg-positive while 70% were HBeAg-negative. Genotype D was the only detected type found in all patients. CONCLUSION: Classifying HBV into genotypes has to be cost-effective and clinically relevant. Our study indicates that HBV genotype D prevails in the Mediterranean area, Near and Middle East, and South Asia. Continued efforts for understanding HBV genotype through international co-operation will reveal further virological differences of the genotypes and their clinical relevance.

  15. Antixenosis of bean genotypes to Chrysodeixis includens (Lepidoptera: Noctuidae

    Directory of Open Access Journals (Sweden)

    Rafaela Morando

    2015-06-01

    Full Text Available The objective of this work was to evaluate bean genotypes for resistance to soybean looper (Chrysodeixis includens. Initially, free-choice tests were carried out with 59 genotypes, divided into three groups according to leaf color intensity (dark green, light green, and medium green, in order to evaluate oviposition preference. Subsequently, 12 genotypes with high potential for resistance were selected, as well as two susceptible commercial standards. With these genotypes, new tests were performed for oviposition in a greenhouse, besides tests for attractiveness and consumption under laboratory conditions (26±2ºC, 65±10% RH, and 14 h light: 10 h dark photophase. In the no-choice test with adults, in the greenhouse, the 'IAC Jabola', Arcelina 1, 'IAC Boreal', 'Flor de Mayo', and 'IAC Formoso' genotypes were the least oviposited, showing antixenosis-type resistance for oviposition. In the free-choice test with larvae, Arcelina 4, 'BRS Horizonte', 'Pérola', H96A102-1-1-1-52, 'IAC Boreal', 'IAC Harmonia', and 'IAC Formoso' were the less consumed genotypes, which indicates antixenosis to feeding. In the no-choice test, all genotypes (except for 'IAPAR 57' expressed moderate levels of antixenosis to feeding against C. includens larvae.

  16. Static and Evolving Norovirus Genotypes: Implications for Epidemiology and Immunity

    Science.gov (United States)

    Karangwa, Consolee K.; Sosnovtsev, Stanislav V.

    2017-01-01

    Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII.4. The non-GII.4 genotypes were comprised of one or more intra-genotypic variants, with each variant containing strains that differed by only a few residues over several decades (remaining “static”) and that have co-circulated with no clear epidemiologic pattern. In contrast, the GII.4 genotype presented the largest number of variants (>10) that have evolved over time with a clear pattern of periodic variant replacement. To expand our understanding of these two patterns of diversification (“static” versus “evolving”), we analyzed using NGS the nearly full-length norovirus genome in healthy individuals infected with GII.4, GII.6 or GII.17 viruses in different outbreak settings. The GII.4 viruses accumulated mutations rapidly within and between hosts, while the GII.6 and GII.17 viruses remained relatively stable, consistent with their diversification patterns. Further analysis of genetic relationships and natural history patterns identified groupings of certain genotypes into larger related clusters designated here as “immunotypes”. We propose that “immunotypes” and their evolutionary patterns influence the prevalence of a particular norovirus genotype in the human population. PMID:28103318

  17. Imputation of missing genotypes: an empirical evaluation of IMPUTE

    Directory of Open Access Journals (Sweden)

    Steinberg Martin H

    2008-12-01

    Full Text Available Abstract Background Imputation of missing genotypes is becoming a very popular solution for synchronizing genotype data collected with different microarray platforms but the effect of ethnic background, subject ascertainment, and amount of missing data on the accuracy of imputation are not well understood. Results We evaluated the accuracy of the program IMPUTE to generate the genotype data of partially or fully untyped single nucleotide polymorphisms (SNPs. The program uses a model-based approach to imputation that reconstructs the genotype distribution given a set of referent haplotypes and the observed data, and uses this distribution to compute the marginal probability of each missing genotype for each individual subject that is used to impute the missing data. We assembled genome-wide data from five different studies and three different ethnic groups comprising Caucasians, African Americans and Asians. We randomly removed genotype data and then compared the observed genotypes with those generated by IMPUTE. Our analysis shows 97% median accuracy in Caucasian subjects when less than 10% of the SNPs are untyped and missing genotypes are accepted regardless of their posterior probability. The median accuracy increases to 99% when we require 0.95 minimum posterior probability for an imputed genotype to be acceptable. The accuracy decreases to 86% or 94% when subjects are African Americans or Asians. We propose a strategy to improve the accuracy by leveraging the level of admixture in African Americans. Conclusion Our analysis suggests that IMPUTE is very accurate in samples of Caucasians origin, it is slightly less accurate in samples of Asians background, but substantially less accurate in samples of admixed background such as African Americans. Sample size and ascertainment do not seem to affect the accuracy of imputation.

  18. Genotype by sex and genotype by age interactions with sedentary behavior: the Portuguese Healthy Family Study.

    Directory of Open Access Journals (Sweden)

    Daniel M V Santos

    Full Text Available Sedentary behavior (SB expression and its underlying causal factors have been progressively studied, as it is a major determinant of decreased health quality. In the present study we applied Genotype x Age (GxAge and Genotype x Sex (GxSex interaction methods to determine if the phenotypic expression of different SB traits is influenced by an interaction between genetic architecture and both age and sex. A total of 1345 subjects, comprising 249 fathers, 327 mothers, 334 sons and 325 daughters, from 339 families of The Portuguese Healthy Family Study were included in the analysis. SB traits were assessed by means of a 3-d physical activity recall, the Baecke and IPAQ questionnaires. GxAge and GxSex interactions were analyzed using SOLAR 4.0 software. Sedentary behaviour heritability estimates were not always statistically significant (p>0.05 and ranged from 3% to 27%. The GxSex and GxAge interaction models were significantly better than the single polygenic models for TV (min/day, EEsed (kcal/day, personal computer (PC usage and physical activty (PA tertiles. The GxAge model is also significantly better than the polygenic model for Sed (min/day. For EEsed, PA tertiles, PC and Sed, the GxAge interaction was significant because the genetic correlation between SB environments was significantly different from 1. Further, PC and Sed variance heterogeneity among distinct ages were observed. The GxSex interaction was significant for EEsed due to genetic variance heterogeneity between genders and for PC due to a genetic correlation less than 1 across both sexes. Our results suggest that SB expression may be influenced by the interactions between genotype with both sex and age. Further, different sedentary behaviors seem to have distinct genetic architectures and are differentially affected by age and sex.

  19. Genotype networks, innovation, and robustness in sulfur metabolism

    Science.gov (United States)

    2011-01-01

    Background A metabolism is a complex network of chemical reactions. This network synthesizes multiple small precursor molecules of biomass from chemicals that occur in the environment. The metabolic network of any one organism is encoded by a metabolic genotype, defined as the set of enzyme-coding genes whose products catalyze the network's reactions. Each metabolic genotype has a metabolic phenotype. We define this metabolic phenotype as the spectrum of different sources of a chemical element that a metabolism can use to synthesize biomass. We here focus on the element sulfur. We study properties of the space of all possible metabolic genotypes in sulfur metabolism by analyzing random metabolic genotypes that are viable on different numbers of sulfur sources. Results We show that metabolic genotypes with the same phenotype form large connected genotype networks - networks of metabolic networks - that extend far through metabolic genotype space. How far they reach through this space depends linearly on the number of super-essential reactions. A super-essential reaction is an essential reaction that occurs in all networks viable in a given environment. Metabolic networks can differ in how robust their phenotype is to the removal of individual reactions. We find that this robustness depends on metabolic network size, and on other variables, such as the size of minimal metabolic networks whose reactions are all essential in a specific environment. We show that different neighborhoods of any genotype network harbor very different novel phenotypes, metabolic innovations that can sustain life on novel sulfur sources. We also analyze the ability of evolving populations of metabolic networks to explore novel metabolic phenotypes. This ability is facilitated by the existence of genotype networks, because different neighborhoods of these networks contain very different novel phenotypes. Conclusions We show that the space of metabolic genotypes involved in sulfur metabolism

  20. Phasing of many thousands of genotyped samples.

    Science.gov (United States)

    Williams, Amy L; Patterson, Nick; Glessner, Joseph; Hakonarson, Hakon; Reich, David

    2012-08-10

    Haplotypes are an important resource for a large number of applications in human genetics, but computationally inferred haplotypes are subject to switch errors that decrease their utility. The accuracy of computationally inferred haplotypes increases with sample size, and although ever larger genotypic data sets are being generated, the fact that existing methods require substantial computational resources limits their applicability to data sets containing tens or hundreds of thousands of samples. Here, we present HAPI-UR (haplotype inference for unrelated samples), an algorithm that is designed to handle unrelated and/or trio and duo family data, that has accuracy comparable to or greater than existing methods, and that is computationally efficient and can be applied to 100,000 samples or more. We use HAPI-UR to phase a data set with 58,207 samples and show that it achieves practical runtime and that switch errors decrease with sample size even with the use of samples from multiple ethnicities. Using a data set with 16,353 samples, we compare HAPI-UR to Beagle, MaCH, IMPUTE2, and SHAPEIT and show that HAPI-UR runs 18× faster than all methods and has a lower switch-error rate than do other methods except for Beagle; with the use of consensus phasing, running HAPI-UR three times gives a slightly lower switch-error rate than Beagle does and is more than six times faster. We demonstrate results similar to those from Beagle on another data set with a higher marker density. Lastly, we show that HAPI-UR has better runtime scaling properties than does Beagle so that for larger data sets, HAPI-UR will be practical and will have an even larger runtime advantage. HAPI-UR is available online (see Web Resources).

  1. PAX6 mutations: genotype-phenotype correlations

    Directory of Open Access Journals (Sweden)

    Hanson Isabel M

    2005-05-01

    Full Text Available Abstract Background The PAX6 protein is a highly conserved transcriptional regulator that is important for normal ocular and neural development. In humans, heterozygous mutations of the PAX6 gene cause aniridia (absence of the iris and related developmental eye diseases. PAX6 mutations are archived in the Human PAX6 Allelic Variant Database, which currently contains 309 records, 286 of which are mutations in patients with eye malformations. Results We examined the records in the Human PAX6 Allelic Variant Database and documented the frequency of different mutation types, the phenotypes associated with different mutation types, the contribution of CpG transitions to the PAX6 mutation spectrum, and the distribution of chain-terminating mutations in the open reading frame. Mutations that introduce a premature termination codon into the open reading frame are predominantly associated with aniridia; in contrast, non-aniridia phenotypes are typically associated with missense mutations. Four CpG dinucleotides in exons 8, 9, 10 and 11 are major mutation hotspots, and transitions at these CpG's account for over half of all nonsense mutations in the database. Truncating mutations are distributed throughout the PAX6 coding region, except for the last half of exon 12 and the coding part of exon 13, where they are completely absent. The absence of truncating mutations in the 3' part of the coding region is statistically significant and is consistent with the idea that nonsense-mediated decay acts on PAX6 mutant alleles. Conclusion The PAX6 Allelic Variant Database is a valuable resource for studying genotype-phenotype correlations. The consistent association of truncating mutations with the aniridia phenotype, and the distribution of truncating mutations in the PAX6 open reading frame, suggests that nonsense-mediated decay acts on PAX6 mutant alleles.

  2. Reduced Uptake of Family Screening in Genotype-Negative Versus Genotype-Positive Long QT Syndrome.

    Science.gov (United States)

    Hanninen, Mikael; Klein, George J; Laksman, Zachary; Conacher, Susan S; Skanes, Allan C; Yee, Raymond; Gula, Lorne J; Leong-Sit, Peter; Manlucu, Jaimie; Krahn, Andrew D

    2015-08-01

    The acceptance and yield of family screening in genotype-negative long QT syndrome (LQTS) remains incompletely characterized. In this study of family screening for phenotype-definite Long QT Syndrome (LQTS, Schwartz score ≥3.5), probands at a regional Inherited Cardiac Arrhythmia clinic were reviewed. All LQTS patients were offered education by a qualified genetic counselor, along with materials for family screening including electronic and paper correspondence to provide to family members. Thirty-eight qualifying probands were identified and 20 of these had family members who participated in cascade screening. The acceptance of screening was found to be lower among families without a known pathogenic mutation (33 vs. 77 %, p = 0.02). A total of 52 relatives were screened; fewer relatives were screened per index case when the proband was genotype-negative (1.7 vs. 3.1, p = 0.02). The clinical yield of screening appeared to be similar irrespective of gene testing results (38 vs. 33 %, p = 0.69). Additional efforts to promote family screening among gene-negative long QT families may be warranted.

  3. Connecting functional and statistical definitions of genotype by genotype interactions in coevolutionary studies

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    Katy Denise Heath

    2014-04-01

    Full Text Available Predicting how species interactions evolve requires that we understand the mechanistic basis of coevolution, and thus the functional genotype-by-genotype interactions (G × G that drive reciprocal natural selection. Theory on host-parasite coevolution provides testable hypotheses for empiricists, but depends upon models of functional G × G that remain loosely tethered to the molecular details of any particular system. In practice, reciprocal cross-infection studies are often used to partition the variation in infection or fitness in a population that is attributable to G × G (statistical G × G. Here we use simulations to demonstrate that within-population statistical G × G likely tells us little about the existence of coevolution, its strength, or the genetic basis of functional G × G. Combined with studies of multiple populations or points in time, mapping and molecular techniques can bridge the gap between natural variation and mechanistic models of coevolution, while model-based statistics can formally confront coevolutionary models with cross-infection data. Together these approaches provide a robust framework for inferring the infection genetics underlying statistical G × G, helping unravel the genetic basis of coevolution.

  4. In Vitro screening of tomato genotypes for drought resistance using ...

    African Journals Online (AJOL)

    ... crop and area under production is limited by irrigation water scarcity. ... conditions indicating there ability to fight with sever water stress situation. ... and hybrids performed better than cultivated genotypes under all levels of water stress.

  5. Identification of blast resistance expression in rice genotypes using ...

    African Journals Online (AJOL)

    USER

    2010-06-14

    Jun 14, 2010 ... genotypes were evaluated for resistance to blast disease under induced epiphytotic conditions obtained in the ..... desirable changes in the population through selection ..... that resistance sources are non-allelic for resistance.

  6. genotype by environment interaction and grain yield stability ...

    African Journals Online (AJOL)

    Preferred Customer

    ABSTRACT: Genotypes by environment (GXE) interactions are almost unanimously considered to be ... important tool in plant breeding and this has to be ..... Pakistan Journal of Biological Sci- ... mosome Engineering and Crop Improvement.

  7. Large SNP arrays for genotyping in crop plants

    Indian Academy of Sciences (India)

    Martin W Ganal; Andreas Polley; Eva-Maria Graner; Joerg Plieske; Ralf Wieseke; Hartmut Luerssen; Gregor Durstewitz

    2012-11-01

    Genotyping with large numbers of molecular markers is now an indispensable tool within plant genetics and breeding. Especially through the identification of large numbers of single nucleotide polymorphism (SNP) markers using the novel high-throughput sequencing technologies, it is now possible to reliably identify many thousands of SNPs at many different loci in a given plant genome. For a number of important crop plants, SNP markers are now being used to design genotyping arrays containing thousands of markers spread over the entire genome and to analyse large numbers of samples. In this article, we discuss aspects that should be considered during the design of such large genotyping arrays and the analysis of individuals. The fact that crop plants are also often autopolyploid or allopolyploid is given due consideration. Furthermore, we outline some potential applications of large genotyping arrays including high-density genetic mapping, characterization (fingerprinting) of genetic material and breeding-related aspects such as association studies and genomic selection.

  8. Multiple centroid method to evaluate the adaptability of alfalfa genotypes

    Directory of Open Access Journals (Sweden)

    Moysés Nascimento

    2015-02-01

    Full Text Available This study aimed to evaluate the efficiency of multiple centroids to study the adaptability of alfalfa genotypes (Medicago sativa L.. In this method, the genotypes are compared with ideotypes defined by the bissegmented regression model, according to the researcher's interest. Thus, genotype classification is carried out as determined by the objective of the researcher and the proposed recommendation strategy. Despite the great potential of the method, it needs to be evaluated under the biological context (with real data. In this context, we used data on the evaluation of dry matter production of 92 alfalfa cultivars, with 20 cuttings, from an experiment in randomized blocks with two repetitions carried out from November 2004 to June 2006. The multiple centroid method proved efficient for classifying alfalfa genotypes. Moreover, it showed no unambiguous indications and provided that ideotypes were defined according to the researcher's interest, facilitating data interpretation.

  9. Genotype by Environment Interaction (G x E) and Grain Yield ...

    African Journals Online (AJOL)

    SARAH

    2014-08-31

    Aug 31, 2014 ... Genotype by Environment Interaction and Grain yield stability analysis of Ethiopian ..... common bean (Abeya et al., 2008); for durum wheat. (Alamnie et al. .... A thesis presented in accordance with the requirements for the ...

  10. Molecular methods for bacterial genotyping and analyzed gene regions

    Directory of Open Access Journals (Sweden)

    İbrahim Halil Yıldırım1, Seval Cing Yıldırım2, Nadir Koçak3

    2011-06-01

    Full Text Available Bacterial strain typing is an important process for diagnosis, treatment and epidemiological investigations. Current bacterial strain typing methods may be classified into two main categories: phenotyping and genotyping. Phenotypic characters are the reflection of genetic contents. Genotyping, which refers discrimination of bacterial strains based on their genetic content, has recently become widely used for bacterial strain typing. The methods already used in genotypingof bacteria are quite different from each other. In this review we tried to summarize the basic principles of DNA-based methods used in genotyping of bacteria and describe some important DNA regions that are used in genotyping of bacteria. J Microbiol Infect Dis 2011;1(1:42-46.

  11. Superoxide Dismutase and Catalase Genotypes in Pediatric Migraine Patients.

    Science.gov (United States)

    Saygi, Semra; Erol, İlknur; Alehan, Füsun; Yalçın, Yaprak Yılmaz; Kubat, Gözde; Ataç, Fatma Belgin

    2015-10-01

    This study compared superoxide dismutase (SOD) and catalase (CAT) alleles in 97 consecutive children and adolescents with migraine to 96 healthy children and adolescents. Isolated genomic DNA was used as a template for SOD1 (35 A/C), SOD2 16 C/T, and CAT2 [(-262 C/T) and (-21 A/T)] allele genotyping. The SOD2 16 C/T genotype and C allele frequency differed significantly between controls and migraine (P = .047; P = .038). CAT -21 AA genotype and A allele frequency were significantly higher in both migraine with aura patients (P = .013; P = .004) and migraine without aura patients (P = .003; P = .001) compared to controls. To our knowledge, this is the first demonstration of differences in SOD and CAT genotypes between pediatric migraine patients and age-matched controls. Further studies on the functional implications of these genetic variants on neural antioxidant capacity and the use of antioxidant modulators for migraine treatment are warranted.

  12. Molecular methods for genotyping complex copy number polymorphisms.

    Science.gov (United States)

    Cantsilieris, Stuart; Baird, Paul N; White, Stefan J

    2013-02-01

    Genome structural variation shows remarkable complexity with respect to copy number, sequence content and distribution. While the discovery of copy number polymorphisms (CNP) has increased exponentially in recent years, the transition from discovery to genotyping has proved challenging, particularly for CNPs embedded in complex regions of the genome. CNPs that are collectively common in the population and possess a dynamic range of copy numbers have proved the most difficult to genotype in association studies. This is in some part due to technical limitations of genotyping assays and the sequence properties of the genomic region being analyzed. Here we describe in detail the basis of a number of molecular techniques used to genotype complex CNPs, compare and contrast these approaches for determination of multi-allelic copy number, and discuss the potential application of these techniques in genetic studies.

  13. Genotype versus phenotype in families with androgen insensitivity syndrome

    NARCIS (Netherlands)

    Boehmer, ALM; Bruggenwirth, H; Van Assendelft, C; Otten, BJ; Verleun-Mooijman, MCT; Niermeijer, MF; Brunner, HG; Rouwe, CW; Waelkens, JJ; Oostdijk, W; Kleijer, WJ; Van der Kwast, TH; De Vroede, MA; Drop, SLS

    2001-01-01

    Androgen insensitivity syndrome encompasses a wide range of phenotypes, which are caused by numerous different mutations in the AR gene. Detailed information on the genotype/ phenotype relationship in androgen insensitivity syndrome is important for sex assignment, treatment of androgen insensitivit

  14. relationship of status of polymorphic rapd bands with genotypic ...

    African Journals Online (AJOL)

    jen

    The nine primers produced 60 amplification products, of which 9 were monomorphic and 51 were polymorphic. The ... Key Words: Eleusine coracana, genotypic adaptation, molecular markers .... Table 2 presents detailed information about the.

  15. Characterization of cowpea genotype resistance to Callosobruchus maculatus

    Directory of Open Access Journals (Sweden)

    Maria de Jesus Passos de Castro

    2013-09-01

    Full Text Available The objective of this work was to characterize the resistance of 50 cowpea (Vigna unguiculata genotypes to Callosobruchus maculatus. A completely randomized design with five replicates per treatment (genotype was used. No-choice tests were performed using the 50 cowpea genotypes to evaluate the preference for oviposition and the development of the weevil. The genotypes IT85 F-2687, MN05-841 B-49, MNC99-508-1, MNC99-510-8, TVu 1593, Canapuzinho-1-2, and Sanzi Sambili show non-preference-type resistance (oviposition and feeding. IT81 D-1045 Ereto and IT81 D-1045 Enramador exhibit antibiosis against C. maculatus and descend from resistant genitors, which grants them potential to be used in future crossings to obtain cowpea varieties with higher levels of resistance.

  16. Forensic SNP Genotyping using Nanopore MinION Sequencing

    Science.gov (United States)

    Cornelis, Senne; Gansemans, Yannick; Deleye, Lieselot; Deforce, Dieter; Van Nieuwerburgh, Filip

    2017-01-01

    One of the latest developments in next generation sequencing is the Oxford Nanopore Technologies’ (ONT) MinION nanopore sequencer. We studied the applicability of this system to perform forensic genotyping of the forensic female DNA standard 9947 A using the 52 SNP-plex assay developed by the SNPforID consortium. All but one of the loci were correctly genotyped. Several SNP loci were identified as problematic for correct and robust genotyping using nanopore sequencing. All these loci contained homopolymers in the sequence flanking the forensic SNP and most of them were already reported as problematic in studies using other sequencing technologies. When these problematic loci are avoided, correct forensic genotyping using nanopore sequencing is technically feasible. PMID:28155888

  17. Effect of Genotypes and Seed Production Environments on Seed ...

    African Journals Online (AJOL)

    Key words: Genotypes. plant popUlation, seed production. seed quality. sesame. ..... (68%). Greater standard gennination and EWSG occurred in seed produced in 2001 .... Table 7: Heritability (H2B) and genetic advance (GA) of seed quality ...

  18. Circulation of genotype-I hepatitis B virus in the primitive tribes of Arunachal Pradesh in early sixties and molecular evolution of genotype-I.

    Science.gov (United States)

    Haldipur, Bangari P; Walimbe, Atul M; Arankalle, Vidya A

    2014-10-01

    Retrospective serologic screening of 1077 serum samples collected from the primitive tribe from north-eastern India in 1963 revealed high prevalence of HBV (15% HBsAg carrier rate) and HCV (7% anti-HCV positivity) and co-circulation of multiple HBV genotypes-A, C, D and G. Full genome sequencing classified all the G-genotype samples as genotype-I. Comparison of genotype-I-HBV full-genome sequences representing 1963 (n=5, this study) and 2005 (reported earlier) showed identical recombination break-points of genotypes-A/G/C. Genotype-C and genotype-C-fragment of I-genotype circulating in 1963 were distinctly different. The data demonstrates that the recombination events were not recent. Molecular clock analysis predicted existence of genotype-I in this tribe during 1920s.

  19. Robust SNP genotyping by multiplex PCR and arrayed primer extension

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    Podder Mohua

    2008-01-01

    Full Text Available Abstract Background Arrayed primer extension (APEX is a microarray-based rapid minisequencing methodology that may have utility in 'personalized medicine' applications that involve genetic diagnostics of single nucleotide polymorphisms (SNPs. However, to date there have been few reports that objectively evaluate the assay completion rate, call rate and accuracy of APEX. We have further developed robust assay design, chemistry and analysis methodologies, and have sought to determine how effective APEX is in comparison to leading 'gold-standard' genotyping platforms. Our methods have been tested against industry-leading technologies in two blinded experiments based on Coriell DNA samples and SNP genotype data from the International HapMap Project. Results In the first experiment, we genotyped 50 SNPs across the entire 270 HapMap Coriell DNA sample set. For each Coriell sample, DNA template was amplified in a total of 7 multiplex PCRs prior to genotyping. We obtained good results for 41 of the SNPs, with 99.8% genotype concordance with HapMap data, at an automated call rate of 94.9% (not including the 9 failed SNPs. In the second experiment, involving modifications to the initial DNA amplification so that a single 50-plex PCR could be achieved, genotyping of the same 50 SNPs across each of 49 randomly chosen Coriell DNA samples allowed extremely robust 50-plex genotyping from as little as 5 ng of DNA, with 100% assay completion rate, 100% call rate and >99.9% accuracy. Conclusion We have shown our methods to be effective for robust multiplex SNP genotyping using APEX, with 100% call rate and >99.9% accuracy. We believe that such methodology may be useful in future point-of-care clinical diagnostic applications where accuracy and call rate are both paramount.

  20. Antioxidant Defense Mechanisms of Salinity Tolerance in Rice Genotypes

    Directory of Open Access Journals (Sweden)

    Mohammad Golam Kibria

    2017-05-01

    Full Text Available In order to elucidate the role of antioxidant responses in salinity tolerance in rice genotypes under salt stress, experiments were conducted using four rice varieties, including salt-sensitive BRRI dhan 28 and three salt-tolerant varieties BRRI dhan 47, BINA dhan 8 and BINA dhan 10. Thirty-day-old rice seedlings were transplanted into pots. At the active tillering stage (35 d after transplanting, plants were exposed to different salinity levels (0, 20, 40 and 60 mmol/L NaCl. Salt stress caused a significant reduction in growth for all the rice genotypes. Growth reduction was higher in the salt-sensitive genotype than in the salt-tolerant ones, and BINA dhan 10 showed higher salt tolerance in all measured physiological parameters. The reduction in shoot and root biomass was found to be minimal in BINA dhan 10. Chlorophyll content significantly decreased under salt stress except for BINA dhan 10. Proline content significantly increased in salt-tolerant rice genotypes with increased salt concentration, and the highest proline content was obtained from BINA dhan 10 under salt stress. Catalase and ascorbate peroxidase activities significantly decreased in salt-sensitive genotype whereas significantly increased in salt-tolerant ones with increasing salt concentration. However, salt stress significantly decreased guaiacol peroxidase activity in all the rice genotypes irrespective of salt tolerance. K+/Na+ ratio also significantly decreased in shoots and roots of all the rice genotypes. The salt-tolerant genotype BINA dhan 10 maintained higher levels of chlorophyll and proline contents as well as catalase and ascorbate peroxidase activities under salt stress, thus, this might be the underlying mechanism for salt tolerance.

  1. ABO genotyping in leukemia patients reveals new ABO variant alleles

    OpenAIRE

    Novaretti,M.C.Z.; DOMINGUES, A. E.; MANHANI, R.; Pinto, E M; Dorlhiac-Llacer, P.E.; Chamone, D.A.F.

    2008-01-01

    The ABO blood group is the most important blood group system in transfusion medicine and organ transplantation. To date, more than 160 ABO alleles have been identified by molecular investigation. Almost all ABO genotyping studies have been performed in blood donors and families and for investigation of ABO subgroups detected serologically. The aim of the present study was to perform ABO genotyping in patients with leukemia. Blood samples were collected from 108 Brazilian patients with chronic...

  2. Campylobacter concisus: an evaluation of certain phenotypic and genotypic characteristics

    DEFF Research Database (Denmark)

    Engberg, J.; Bang, D. D.; Aabenhus, R.

    2005-01-01

    The clinical relevance of Campylobacter concisus in gastrointestinal disease has not been determined definitively. This study investigated the phenotypic and genotypic characteristics of 39 C. concisus isolates from Danish patients with diarrhoea, three isolates from healthy individuals and the t......The clinical relevance of Campylobacter concisus in gastrointestinal disease has not been determined definitively. This study investigated the phenotypic and genotypic characteristics of 39 C. concisus isolates from Danish patients with diarrhoea, three isolates from healthy individuals...

  3. Sex and PRNP genotype determination in preimplantation caprine embryos.

    Science.gov (United States)

    Guignot, F; Perreau, C; Cavarroc, C; Touzé, J-L; Pougnard, J-L; Dupont, F; Beckers, J-F; Rémy, B; Babilliot, J-M; Bed'Hom, B; Lamorinière, J M; Mermillod, P; Baril, G

    2011-08-01

    The objective of this study was to test the accuracy of genotype diagnosis after whole amplification of DNA extracted from biopsies obtained by trimming goat embryos and to evaluate the viability of biopsied embryos after vitrification/warming and transfer. Whole genome amplification (WGA) was performed using Multiple Displacement Amplification (MDA). Sex and prion protein (PRNP) genotypes were determined. Sex diagnosis was carried out by PCR amplification of ZFX/ZFY and Y chromosome-specific sequences. Prion protein genotype determination was performed on codons 142, 154, 211, 222 and 240. Embryos were collected at day 7 after oestrus and biopsied either immediately after collection (blastocysts and expanded blastocysts) or after 24 h of in vitro culture (compacted morulae). Biopsied embryos were frozen by vitrification. Vitrified whole embryos were kept as control. DNA of biopsies was extracted and amplified using MDA. Sex diagnosis was efficient for 97.4% of biopsies and PRNP genotyping was determined in 78.7% of biopsies. After embryo transfer, no significant difference was observed in kidding rate between biopsied and vitrified control embryos, whereas embryo survival rate was different between biopsied and whole vitrified embryos (p = 0.032). At birth, 100% of diagnosed sex and 98.2% of predetermined codons were correct. Offspring PRNP profiles were in agreement with parental genotype. Whole genome amplification with MDA kit coupled with sex diagnosis and PRNP genotype predetermination are very accurate techniques to genotype goat embryos before transfer. These novel results allow us to plan selection of scrapie-resistant genotypes and kid sex before transfer of cryopreserved embryo.

  4. Variability of traits quinoa introduced genotypes (Chenopodium quinoa Willd.)

    OpenAIRE

    Dražić, Slobodan; ŽIVANOVIĆ, Tomislav; Maletić, Radojka; Glamočlija, Đorđe; Žarković, Branka; Dražić, Milena

    2013-01-01

    We analyzed variability and influence of investigated factors on grain yield of quinoa during three year period (2009, 2010, 2011). The experiment was conducted at two locations (Nova Pazova and Surduk), using two introduced genotypes of quinoa: KVL 37 and KVL 52. We detected that location and genotype had important impact. Grain yield varied according to years of study (1224 kg/ha to 1671 kg/ha). Results of regression and correlation analysis indicate on variation of the impact of plant heig...

  5. Evaluation of allelopathic potential of safflower genotypes (Carthamus tinctorius L.

    Directory of Open Access Journals (Sweden)

    Motamedi Marzieh

    2016-12-01

    Full Text Available Forty safflower genotypes were grown under normal irrigation and drought stress. In the first experiment, the allelopathic potential of shoot residues was evaluated using the sandwich method. Each genotype residue (0.4 g was placed in a sterile Petri dish and two layers of agar were poured on that. Radish seeds were placed on agar medium. The radish seeds were cultivated without safflower residues as the controls. The length of the radicle, hypocotyl, and fresh biomass weight and seed germination percentages were measured. A pot experiment was also done on two genotypes with the highest and two with the lowest allelopathic activity selected after screening genotypes in the first experiment. Before entering the reproductive phase, irrigation treatments (normal irrigation and drought stress were applied. Shoots were harvested, dried, milled and mixed with the topsoil of new pots and then radish seeds were sown. The pots with safflower genotypes were used to evaluate the effect of root residue allelopathy. The shoot length, fresh biomass weight, and germination percentage were measured. Different safflower genotypes showed varied allelopathic potential. The results of the first experiment showed that Egypt and Iran-Khorasan genotypes caused maximum inhibitory responses and Australia and Iran-Kerman genotypes resulted in minimum inhibitory responses on radish seedling growth. Fresh biomass weight had the most sensitivity to safflower residues. The results of the pot experiment were consistent with the results of in vitro experiments. Residues produced under drought stress had more inhibitory effects on the measured traits. Safflower root residue may have a higher level of allelochemicals or different allelochemicals than shoot residue.

  6. Genotype and SNP calling from next-generation sequencing data

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Paul, Joshua S.; Albrechtsen, Anders

    2011-01-01

    Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated w...... with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data. We review these methods and provide a guide for their use in NGS studies....

  7. Performance of genotype-MTBDR test directly on clinical specimens

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    Gülden Yılmaz

    2012-12-01

    Full Text Available Objectives: Most important point for the control and effective treatment of multidrug resistant tuberculosis (MDR-TBis early diagnosis and rapid determination of the resistance. The aim of this study is to assess the performance of theGenotype-MTBDR assay applied directly on sputum samples and compare the results with those obtained by DNA sequencingand phenotypic susceptibility testing.Materials and methods: Between November 2005 and February 2006, 93 smear and culture positive sputum sampleswere included in the study. Drug susceptibility results for rifampin (RIF and isoniazid (INH, obtained by proportionmethod on L-J medium, Genotype-MTBDR and DNA sequencing were compared.Results: The rate of concordance between the results of the Genotype-MTBDR and DNA sequencing was 93.5% and96.7% for RIF and INH, respectively. Moreover, Genotype-MTBDR detected all the RIF (24 and INH (18 resistant strainsobtained by sequencing (100%. Compared to the DNA sequencing method; the sensitivity, specificity, positive predictiveand negative predictive value for RIF and INH were 100%, 91.3%, 80%, 100% and 100%, 96%, 85.7%, 100% respectively.Conclusion: Genotype-MTBDR, one of molecular assays, distinctly shortens the time for diagnosis and detection of resistanceto INH and RIF, essential for management of MDR-TB. The test appears to have good sensitivity and specificitywhen also used directly on sputum specimens. J Microbiol Infect Dis 2012; 2(4: 135-141Key words: Mycobacterium tuberculosis; drug resistance; genotype-MTBDR.

  8. Genetic diversity of some chili (Capsicum annuum L. genotypes

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    M.J. Hasan

    2014-06-01

    Full Text Available A study on genetic diversity was conducted with 54 Chili (Capsicum annuum L. genotypes through Mohalanobis’s D2 and principal component analysis for twelve quantitative characters viz. plant height, number of secondary branch/plant, canopy breadth , days to first flowering, days to 50% flowering, fruits/plant, 5 fruits weight, fruit length, fruit diameter, seeds/fruit, 1000 seed weight and yield/plant were taken into consideration. Cluster analysis was used for grouping of 54 chili genotypes and the genotypes were fallen into seven clusters. Cluster II had maximum (13 and cluster III had the minimum number (1 of genotypes. The highest inter-cluster distance was observed between cluster I and III and the lowest between cluster II and VII. The characters yield/plant, canopy breadth, secondary branches/plant, plant height and seeds/fruit contributed most for divergence in the studied genotypes. Considering group distance, mean performance and variability the inter genotypic crosses between cluster I and cluster III, cluster III and cluster VI, cluster II and cluster III and cluster III and cluster VII may be suggested to use for future hybridization program.

  9. Genotyping panel for assessing response to cancer chemotherapy

    Directory of Open Access Journals (Sweden)

    Hampel Heather

    2008-06-01

    Full Text Available Abstract Background Variants in numerous genes are thought to affect the success or failure of cancer chemotherapy. Interindividual variability can result from genes involved in drug metabolism and transport, drug targets (receptors, enzymes, etc, and proteins relevant to cell survival (e.g., cell cycle, DNA repair, and apoptosis. The purpose of the current study is to establish a flexible, cost-effective, high-throughput genotyping platform for candidate genes involved in chemoresistance and -sensitivity, and treatment outcomes. Methods We have adopted SNPlex for genotyping 432 single nucleotide polymorphisms (SNPs in 160 candidate genes implicated in response to anticancer chemotherapy. Results The genotyping panels were applied to 39 patients with chronic lymphocytic leukemia undergoing flavopiridol chemotherapy, and 90 patients with colorectal cancer. 408 SNPs (94% produced successful genotyping results. Additional genotyping methods were established for polymorphisms undetectable by SNPlex, including multiplexed SNaPshot for CYP2D6 SNPs, and PCR amplification with fluorescently labeled primers for the UGT1A1 promoter (TAnTAA repeat polymorphism. Conclusion This genotyping panel is useful for supporting clinical anticancer drug trials to identify polymorphisms that contribute to interindividual variability in drug response. Availability of population genetic data across multiple studies has the potential to yield genetic biomarkers for optimizing anticancer therapy.

  10. Genotyping of Rotavirus by Using RT-PCR Methods

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    Hera Nirwati

    2015-11-01

    Full Text Available There is a great diversity of rotavirus genotypes circulating worldwide, with dominant genotypes changing from year to year. Rotavirus genotyping was performed by using reverse transcription PCR with type-specifi c-primers. Since rotavirus is a RNA virus that has high mutation rate, there was a possibility of technical diffi culty in genotyping due to mutation in the primer binding sites. During Indonesian rotavirus surveillance study 2006-2009, it was reported that 17% of samples subjected for G type and 21% of samplessubjected for P type were untypeable. The objective of this study was to identify genotypes of the samples that were untypeable previously using RT-PCR based on the method described by Das et al. (1994 and Gentsch et al. (1992. There were 30 samples subjected to G type and 61 samples subjected to P type to be re-typed using method described by Gouvea et al. (1990 and Simmond et al. (2008 for G and P typing, respectively. By using another set of primer, the genotype of all samples was identifi ed. This study highlights the importance of a constant reconsideration of primer sequences employed for the molecular typing of rotaviruses.Key words: rotavirus, G typing, P typing

  11. Analyzing genotype-by-environment interaction using curvilinear regression

    Directory of Open Access Journals (Sweden)

    Dulce Gamito Santinhos Pereira

    2012-12-01

    Full Text Available In the context of multi-environment trials, where a series of experiments is conducted across different environmental conditions, the analysis of the structure of genotype-by-environment interaction is an important topic. This paper presents a generalization of the joint regression analysis for the cases where the response (e.g. yield is not linear across environments and can be written as a second (or higher order polynomial or another non-linear function. After identifying the common form regression function for all genotypes, we propose a selection procedure based on the adaptation of two tests: (i a test for parallelism of regression curves; and (ii a test of coincidence for those regressions. When the hypothesis of parallelism is rejected, subgroups of genotypes where the responses are parallel (or coincident should be identified. The use of the Scheffé multiple comparison method for regression coefficients in second-order polynomials allows to group the genotypes in two types of groups: one with upward-facing concavity (i.e. potential yield growth, and the other with downward-facing concavity (i.e. the yield approaches saturation. Theoretical results for genotype comparison and genotype selection are illustrated with an example of yield from a non-orthogonal series of experiments with winter rye (Secalecereale L.. We have deleted 10 % of that data at random to show that our meteorology is fully applicable to incomplete data sets, often observed in multi-environment trials.

  12. Methylenetetrahydrofolate Reductase Genotypes, Dietary Habits and Susceptibility to Stomach Cancer

    Institute of Scientific and Technical Information of China (English)

    ChangmingGao; TakezakiToshiro; JianzhongWu; JianhuoDing; YantingLiu; SupingLi; PingSu; XuHu; TianliongXu; HamajimaNobuyuki; TajimaKazuo

    2004-01-01

    OBJECTIVE To study the relation among methylenetetrahydrofolate reductase (MTHFR) C677T genotypes, dietary habits and the risk of stomach cancer (SC).METHODS A case-control study was conducted with 107 cases of SC and 200 population-based controls in Chuzhou district, Huaian, Jiangsu province, China. The epidemiological data were collected, and DNA of peripheral blood leukocytes was obtained from all of the subjects..MTHFR genotypes were detected by PCR-RFLP. RESULTS (1) The prevalence of the MTHFR C/T or T/T genotypes was found to be significantly different between controls (68.5%) and SC cases (79.4%,P=0.0416), the increased risk had an adjusted OR of 1.79 (95%C1:1.01-3.19). (2) Among subjects who had a low intake of garlic or Chinese onion, MTHFR C/T or T/T genotypes significantly increased the risk of developing SC. Among non-tea drinkers or among subjects who had a frequent intakeof meat, the carriers of the MTHFR C/T or T/T genotypes had a higher risk of SC than individuals with the C/C type MTHFR. CONCLUSION The polymorphism of MTHFR C677T was associated with increased risk of developing SC, and that individuals with differing genotypes may have different susceptibilities to SC, based on their exposure level to environmental factors.

  13. Differential activation of dendritic cells by Mycobacterium tuberculosis Beijing genotype.

    Science.gov (United States)

    Reyes-Martínez, Juana Elizabeth; Nieto-Patlán, Erik; Nieto-Patlán, Alejandro; Gonzaga-Bernachi, Job; Santos-Mendoza, Teresa; Serafín-López, Jeanet; Chávez-Blanco, Alma; Sandoval-Montes, Claudia; Flores-Romo, Leopoldo; Estrada-Parra, Sergio; Estrada-García, Iris; Chacón-Salinas, Rommel

    2014-01-01

    Mycobacterium tuberculosis (Mtb) inhibits dendritric cells (DC) function in order to delay T cell response. Furthermore, there is increasing evidence that genetic diversity of Mtb strains can affect their interaction with the immune system. Beijing genotype has attracted attention because of its high prevalence and multi-drug resistance. Although it is known that this genotype is hypervirulent and differentially activates macrophages when compared to other genotypes, little is known about its interaction with DC. In order to address this issue, murine bone marrow derived DC (BMDC) were stimulated with soluble extracts (SE) from BCG, H37Rv, Canetti and Beijing genotypes. We observed that unlike other mycobacteria strains, SE-Beijing was unable to induce maturation of DC as assessed by cell surface MHC-II expression. DC stimulated with SE-Beijing failed to produce IL-12 and TNF-α, but did secrete IL-10. Interestingly, SE-Beijing induced CCR7 and PDL-1 on BMDC, but did not induce the expression of CD86. When BMDC stimulated with SE-Beijing were used to activate CD4+ cells they were unable to induce a Th1 response when compared with less virulent genotypes. These results indicate that Beijing is able to modulate DC activation and function, which may be related to the pathogenesis induced by this genotype.

  14. In vitro screening of potato genotypes for osmotic stress tolerance

    Directory of Open Access Journals (Sweden)

    Gelmesa Dandena

    2017-02-01

    Full Text Available Potato (Solanum tuberosum L. is a cool season crop which is susceptible to both drought and heat stresses. Lack of suitable varieties of the crop adapted to drought-prone areas of the lowland tropics deprives farmers living in such areas the opportunity to produce and use the crop as a source of food and income. As a step towards developing such varieties, the present research was conducted to evaluate different potato genotypes for osmotic stress tolerance under in vitro conditions and identify drought tolerant genotypes for future field evaluation. The experiment was carried out at the Leibniz University of Hannover, Germany, by inducing osmotic stress using sorbitol at two concentrations (0.1 and 0.2 M in the culture medium. A total of 43 genotypes collected from different sources (27 advanced clones from CIP, nine improved varieties, and seven farmers’ cultivars were used in a completely randomized design with four replications in two rounds. Data were collected on root and shoot growth. The results revealed that the main effects of genotype, sorbitol treatment, and their interactions significantly (P < 0.01 influenced root and shoot growthrelated traits. Under osmotic stress, all the measured root and shoot growth traits were significantly correlated. The dendrogram obtained from the unweighted pair group method with arithmetic mean allowed grouping of the genotypes into tolerant, moderately tolerant, and susceptible ones to a sorbitol concentration of 0.2 M in the culture medium. Five advanced clones (CIP304350.100, CIP304405.47, CIP392745.7, CIP388676.1, and CIP388615.22 produced shoots and rooted earlier than all other genotypes, with higher root numbers, root length, shoot and root mass under osmotic stress conditions induced by sorbitol. Some of these genotypes had been previously identified as drought-tolerant under field conditions, suggesting the capacity of the in vitro evaluation method to predict drought stress tolerant

  15. Hepatitis C virus genotypes: A plausible association with viral loads

    Directory of Open Access Journals (Sweden)

    Salma Ghulam Nabi

    2013-01-01

    Full Text Available Background and Aim: The basic aim of this study was to find out the association of genotypes with host age, gender and viral load. Material and Methods: The present study was conducted at Social Security Hospital, Pakistan. This study included 320 patients with chronic hepatitis C virus (HCV infection who were referred to the hospital between November 2011 and July 2012. HCV viral detection and genotyping was performed and the association was seen between genotypes and host age, gender and viral load. Results : The analysis revealed the presence of genotypes 1 and 3 with further subtypes 1a, 1b, 3a, 3b and mixed genotypes 1b + 3a, 1b + 3b and 3a + 3b. Viral load quantification was carried out in all 151 HCV ribonucleic acid (RNA positive patients. The genotype 3a was observed in 124 (82.12% patients, 3b was found in 21 (13.91%, 1a was seen in 2 (1.32%, 1b in 1 (0.66%, mixed infection with 1b + 3a in 1 (0.66%, 1b + 3b in 1 (0.66% and 3a + 3b was also found in 1 (0.66% patient. Viral load quantification was carried out in all 151 HCV RNA positive patients and was compared between the various genotypes. The mean viral load in patients infected with genotype 1a was 2.75 × 10 6 , 1b 3.9 × 10 6 , 3a 2.65 × 10 6 , 3b 2.51 × 10 6 , 1b + 3a 3.4 × 106, 1b + 3b 2.7 × 106 and 3a + 3b 3.5 × 10 6 . An association between different types of genotypes and viral load was observed. Conclusion : Further studies should be carried out to determine the association of viral load with different genotypes so that sufficient data is available and can be used to determine the type and duration of therapy needed and predict disease outcome.

  16. Rapid typing of Mannheimia haemolytica major genotypes 1 and 2 using MALDI-TOF mass spectrometry.

    Science.gov (United States)

    Loy, John Dustin; Clawson, Michael L

    2017-05-01

    Genotype 2M. haemolytica predominantly associate over genotype 1 with the lungs of cattle with respiratory disease and ICEs containing antimicrobial resistance genes. Distinct protein masses were detected by MALDI-TOF MS between genotype 1 and 2 strains. MALDI-TOF MS could rapidly differentiate genotype 2 strains in veterinary diagnostic laboratories.

  17. Research on Hepatitis B virus Genotypes and Subgenotypes among Bai Nationality in Dali, Yunnan Province

    Institute of Scientific and Technical Information of China (English)

    Wei LI; Yuan-ying SHEN; Xuan-rong ZHANG; Lai-feng REN; Qiang LI; Ru SHEN; Hai-ping ZHAO

    2008-01-01

    To investigate the distribution of hepatitis B virus (HBV) genotypes and subgenotypes among the Bai nationality in Dali, a total of 100 serum samples from patients with chronic HBV-infection were collected for the detection of HBV genotypes and subgenotypes by genotype-specific primers and restriction fragment length polymorphism (RLFP), respectively. Among the 100 samples, the proportions of genotype B, C and mixed genotype (B+C) were 41%, 25% and 34%, respectively. All the genotype B strains belonged to subgenotype Ba. In genotype C, 84% were Subgenotype Cs and 12% were subgenotype Ce. The distribution of genotypes B, C and B+C showed no significant difference between male and female patients (P=0.182) and among the age groups of patients (P=0.812). The rates of HBeAg/HBeAg positivity were no significantly different among genotypes B, genotype C and mixed genotype (B+C) (P=0.077/P=0.663). In Dali, genotypes B, B+C and C existed among Bai nationality with chronic HBV-infection, and genotype B was the major genotype. Subgenotypes Ba and Cs were the predominant strains in patients with HBV genotype B/C infection. The most prominent characteristic was the higher prevalent rate of mixed genotype (B+C) in patients.

  18. Epidemiology and genetic characterization of hepatitis A virus genotype IIA.

    Science.gov (United States)

    Desbois, Delphine; Couturier, Elisabeth; Mackiewicz, Vincent; Graube, Arielle; Letort, Marie-José; Dussaix, Elisabeth; Roque-Afonso, Anne-Marie

    2010-09-01

    Three hepatitis A virus (HAV) genotypes, I, II, and III, divided into subtypes A and B, infect humans. Genotype I is the most frequently reported, while genotype II is hardly ever isolated, and its genetic diversity is unknown. From 2002 to 2007, a French epidemiological survey of HAV identified 6 IIA isolates, mostly from patients who did not travel abroad. The possible African origin of IIA strains was investigated by screening the 2008 mandatory notification records of HAV infection: 171 HAV strains from travelers to West Africa and Morocco were identified. Genotyping was performed by sequencing of the VP1/2A junction in 68 available sera. Entire P1 and 5' untranslated regions of IIA strains were compared to reference sequences of other genotypes. The screening retrieved 5 imported IIA isolates. An additional autochthonous case and 2 more African cases were identified in 2008 and 2009, respectively. A total of 14 IIA isolates (8 African and 6 autochthonous) were analyzed. IIA sequences presented lower nucleotide and amino acid variability than other genotypes. The highest variability was observed in the N-terminal region of VP1, while for other genotypes the highest variability was observed at the VP1/2A junction. Phylogenetic analysis identified 2 clusters, one gathering all African and two autochthonous cases and a second including only autochthonous isolates. In conclusion, most IIA strains isolated in France are imported by travelers returning from West Africa. However, the unexplained contamination mode of autochthonous cases suggests another, still to be discovered geographical origin or a French reservoir to be explored.

  19. Assessment of HCV genotypes in Yunnan Province of Southwest China.

    Science.gov (United States)

    Li, Qiongfen; Yao, Yufeng; Shen, Yunsong; Cao, Danfeng; Li, Yalin; Zhang, Shuqiong; Cun, Wei; Sun, Mingbo; Yu, Jiankun; Shi, Li; Dong, Shaozhong

    2016-12-23

    Recently, we reported that the frequency of hepatitis C virus (HCV) genotypes and subtypes has rapidly changed among intravenous drug users (IDUs) in Yunnan Province over the last 5 years; this is especially true for subtype 6a which has increased in frequency from 5 to 15%. Here, we assessed 120 HCV-positive plasma samples from the general population (GP). HCV NS5B fragments were amplified and sequenced by PCR. We identified four HCV genotypes (1, 2, 3 and 6) and seven HCV subtypes (1b, 2a, 3a, 3b, 6a, 6n, and 6k) in this population. Genotype 3 was predominant, with a distribution frequency of 0.484, followed by genotype 1 (0.283), genotype 6 (0.133) and genotype 2 (0.100). HCV subtypes 3b (frequency 0.292) and 1b (frequency 0.283) were the most common subtypes. A comparison of the current data with previous results reported for IDUs showed that the distribution frequencies of genotypes 1, 2 and 6 were significantly different between patients in the GP and IDUs (P HCV subtypes, the distribution frequencies of 1b, 2a, 6a, and 6n were significantly different between patients in the GP and IDU groups (P HCV subtype 6a strains isolated from IDUs and the GP were intermixed and not separately clustered. HCV subtype 6a was predominant not only among IDUs but also among those in the GP in the Guangdong Province and Vietnam. However, HCV subtype 6a was predominant only among IDUs and not among those in the GP in the Yunnan and Guangxi Provinces. Our results indicate that the HCV subtype 6a could rapidly spread across China.

  20. Is incidence of multiple HPV genotypes rising in genital infections?

    Science.gov (United States)

    Sohrabi, Amir; Hajia, Masoud; Jamali, Firouzeh; Kharazi, Faranak

    2017-02-16

    Frequency of cervical cancer related to Human Papilloma Virus (HPV) has increased remarkably in less-developed countries. Hence, applying capable diagnostic methods is urgently needed, as is having a therapeutic strategy as an effective step for cervical cancer prevention. The aim of this study was to investigate the prevalence of various multi-type HPV infection patterns and their possible rising incidence in women with genital infections. This descriptive study was conducted on women who attended referral clinical laboratories in Tehran for genital infections from January 2012 until December 2013. A total of 1387 archival cervical scraping and lesion specimens were collected from referred women. HPV genotyping was performed using approved HPV commercial diagnostic technologies with either INNO-LiPA HPV or Geno Array Test kits. HPV was positive in 563 cases (40.59%) with mean age of 32.35±9.96. Single, multiple HPV genotypes and untypable cases were detected in 398 (70.69%), 160 (28.42%) and 5 (0.89%) cases, respectively. Multiple HPV infections were detected in 92 (57.5%), 42 (26.2%), 17 (10.6%) and 9 (5.7%) cases as two, three, four and five or more genotypes, respectively. The prevalence of 32 HPV genotypes was determined one by one. Seventeen HPV genotypes were identified in 95.78% of all positive infections. Five dominant genotypes, HPV6, 16, 53, 11 and 31, were identified in a total of 52.35%of the HPV positive cases. In the present study, we were able to evaluate the rate of multiple HPV types in genital infections. Nevertheless, it is necessary to evaluate the role of the dominant HPV low-risk types and the new probably high-risk genotypes, such as HPV53, in the increasing incidences of genital infections.

  1. Influence of Acanthamoeba genotype on clinical course and outcomes for patients with Acanthamoeba keratitis in Spain.

    Science.gov (United States)

    Arnalich-Montiel, Francisco; Lumbreras-Fernández, Blanca; Martín-Navarro, Carmen M; Valladares, Basilio; Lopez-Velez, Rogelio; Morcillo-Laiz, Rafael; Lorenzo-Morales, Jacob

    2014-04-01

    Genotype T4 is by far the most frequent genotype of Acanthamoeba keratitis (AK) and therefore has been considered the most virulent. This study included 14 cases of AK of genotype T4 and three cases of non-T4 genotype. We found that cases of non-T4 genotype had a worse response to medical therapy, greater need for surgical intervention, greater risk of extracorneal involvement, and remarkably poorer final visual outcome than those of T4 genotype, suggesting an association between Acanthamoeba virulence and genotype that requires additional case investigation.

  2. HBV genotypes prevalence, precore and basal core mutants in Morocco.

    Science.gov (United States)

    Baha, Warda; Ennaji, My Mustapha; Lazar, Fatiha; Melloul, Marouane; El Fahime, Elmostafa; El Malki, Abdelouahad; Bennani, Abdelouaheb

    2012-08-01

    The study of hepatitis B virus (HBV) genomic heterogeneity has become a major issue in investigations aimed at understanding the relationship between HBV mutants and the wide spectrum of clinical and pathological conditions associated with HBV infection. The objective of the current study was to find out the pattern of HBV genotypes circulating in Morocco and to investigate the precore (PC) and basal core promoter (BCP) mutants' status in Moroccan chronic hepatitis B patients. Viral genotypes were determined in 221 chronic carriers using INNO-LiPA HBV assay and hemi-nested PCR. Phylogenetic analysis was performed in 70 samples, and multiplex PCR method was used to confirm some genotyping results. PC and CP mutants were determined using Inno-Lipa. All isolates were successfully genotyped. The genotype distribution was D in 90.45% of cases, A (5.9%), E (1 case), and mixed genotypes (5 A/D and 2 D/F) in 3.17% patients. HBV carried in the HBV/D samples could be assigned to D7 (63.3%), D1 (32.7%) and 2% of strains to each D4 and D5, all HBV/A belonged to A2 subgenotype and HBV/E strain could not be sub-genotyped. In 70 studied strains, HBV mutants were detected in 88.6% of cases; PC mutants were detected in (40%) of patients and 21.5% present a mixture of wild type and G1896A mutation. BCP mutants were observed in 65.7% of cases, 22.9% were found to have the T1762/1764A double mutation, 18.6% had A1762/1764T mutation and 22.9% of patients showed the A1762T/G1764A double mutation with either A1762T/G1764T mutation. Co-infection by PC and BCP mutants was detected in 52.9% of cases. Movement from place to place most likely shapes the observed genotype distribution and consequent prevalence of genotypes other than A2 or D7 in this population. High circulation of PC and BCP mutants is common in chronic hepatitis B infection in Morocco.

  3. Physiological and Molecular Analysis of Applied Nitrogen in Rice Genotypes

    Institute of Scientific and Technical Information of China (English)

    Khalid Rehman HAKEEM; Ruby CHANDNA; Altaf AHMAD; Muhammad IQBAL

    2012-01-01

    Ten genotypes of rice (Oryza sativa L.) were grown for 30 d in complete nutrient solution with 1 mmol/L (N-insufficient),4 mmol/L (N-moderate) and 10 mmol/L (N-high) nitrogen levels,and nitrogen efficiency (NE) was analyzed.Growth performance,measured in terms of fresh weight,dry weight and lengths of root and shoot,was higher in N-efficient than in N-inefficient rice genotypes at low N level.Of these 10 genotypes,Suraksha was identified as the most N-efficient,while Vivek Dhan the most N-inefficient.To find out the physiological basis of this difference,the nitrate uptake rate of root and the activities of nitrate assimilatory enzymes in leaves of N-efficient and N-inefficient rice genotypes were studied.Uptake experiments revealed the presence of two separate nitrate transporter systems mediating high- and low-affinity nitrate uptake.Interestingly,the nitrate uptake by the roots of Suraksha is mediated by both high- and low-affinity nitrate transporter systems,while that of Vivek Dhan by only low-affinity nitrate transporter system.Study of the activities and expression levels of nitrate assimilatory enzymes in N-efficient and N-inefficient rice genotypes showed that nitrate reductase (NR) and glutamine svnthetase (GS) play important roles in N assimilation under low-nitrogen conditions.

  4. The quality of silage of different sorghum genotypes

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    Daniella Cangussú Tolentino

    2016-05-01

    Full Text Available The objective was to select from among 24 sorghum genotypes the superior ones for silage production. The study was conducted in the experimental field of Embrapa Maize & Sorghum, in the municipality of Sete Lagoas, Minas Gerais State. It used 24 forage sorghum genotypes, 21 being hybrids from the crossing of grain sorghum females and forage males (12F38019, 12F38006, 12F40006, 12F40005, 12F40019, 12F37016, 12F37005, 12F37043, 12F39006, 12F39005, 12F39019, 12F38005, 12F38007, 12F37007, 12F39007, 12F40007, 12F38014, 12F37014, 12F39014, 12F40014 e 12F38009 and three witnesses: BRS 610, BRS 655 and Volumax. It estimated productivity per area, in vitro dry matter digestibility, and assessed the bromatological and fermentation characteristics of sorghum silage. In vitro dry matter digestibility, unavailable protein in neutral detergent, neutral detergent fiber corrected for ashes and protein, acid detergent fiber, hemicellulose and lignin differed as to the genotypes tested. The pH and the ammoniacal nitrogen of the silage also showed differences between genotypes. Most of the genotypes tested are favorable for silage production, except the hybrid with higher lignin content 12F370014, and the hybrids 12F37007 and 12F370014, which showed the highest NDFap values.

  5. Physiological responses of genotypes soybean to simulated drought stress

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    Eleonóra Krivosudská

    2016-12-01

    Full Text Available The objective of this research was to investigate possible genetic variation in the sensitivity of soybean cultivars for nitrogen fixation rates in response to soil drying. The work confirmed that the selected physiological characteristics (RWC, osmotic potential, stress index and created nodules on roots are good evaluating parameters for the determination of water stress in plant. In the floricultural year 2014 an experiment with four genetic resources of soybean was launched. Sowing of Maverick (USA, Drina (HRV, Nigra (SVK and Polanka (CZK genotypes was carried out in the containers of 15 l capacity. This stress had a negative impact on the physiological parameters. By comparing the RWC values, the decrease was more significant at the end of dehydration, which was monitored in Maverick and Drina genotypes using the Nitrazon inoculants and water stress effect. Inoculated stressed Nigra and Polanka genotypes have kept higher water content till the end of dehydration period. Also the proline accumulation was monitored during the water stress, whilst higher content of free proline reached of Maverick. More remarkable decrease of osmotic potential was again registered in a foreign Drina and Maverick genotypes in the inoculated variations. Nigra and Polanka genotypes responses not so significant in the given conditions.

  6. Does sex trade with violence among genotypes in Drosophila melanogaster?

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    Larry G Cabral

    Full Text Available The evolutionary forces shaping the ability to win competitive interactions, such as aggressive encounters, are still poorly understood. Given a fitness advantage for competitive success, variance in aggressive and sexual display traits should be depleted, but a great deal of variation in these traits is consistently found. While life history tradeoffs have been commonly cited as a mechanism for the maintenance of variation, the variability of competing strategies of conspecifics may mean there is no single optimum strategy. We measured the genetically determined outcomes of aggressive interactions, and the resulting effects on mating success, in a panel of diverse inbred lines representing both natural variation and artificially selected genotypes. Males of one genotype which consistently lost territorial encounters with other genotypes were nonetheless successful against males that were artificially selected for supernormal aggression and dominated all other lines. Intransitive patterns of territorial success could maintain variation in aggressive strategies if there is a preference for territorial males. Territorial success was not always associated with male mating success however and females preferred 'winners' among some male genotypes, and 'losers' among other male genotypes. This suggests that studying behaviour from the perspective of population means may provide limited evolutionary and genetic insight. Overall patterns of competitive success among males and mating transactions between the sexes are consistent with mechanisms proposed for the maintenance of genetic variation due to nonlinear outcomes of competitive interactions.

  7. Analysis of pomological traits in new promising sweet cherry genotypes

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    Fotirić-Akšić Milica

    2013-01-01

    Full Text Available Sweet cherry breeding programs are interested in developing new cultivars that are very early or very late in ripening, high yielding, with excellent fruit size and quality. The aim of this study was to evaluate new, promising, sweet cherry genotypes (G-1 and G-2 for ripening time, fruit morphology and fruit chemical content, and compare it with the standard sweet cherry cultivars (Bigarreau Jaboulay, B. H. Burlat, Seneca, Hedelfiger Riesenkirsche, Germersdorfer Grosse Kirsche, Emperor Francis and Bing. Experiment was done during four consecutive years (2006-2009 in Grocka, near Belgrade. The earliest fruit ripening was recorded in G-2 (22nd April while the latest in `Bing` (2nd June. Fruit weight varied from 5.83 g (G-2 up to 8.93 g (G-1. Soluble solid content and total sugar content were the lowest in genotype G-2 (10.48%; 8.45%, respectively but the highest in Emperor Francis (18.28%; 15.98%, respectively. No matter the fact that some standard cultivars showed better results for some traits, genotypes G-1 and G-2 are considered very promising. So, genotype G-1 could be intended for table consumption since it ripens 2-3 days after cv. B. H. Burlat, but have much higher fruit weight. Also, genotype G-2, the earliest in this trial, showed satisfactory fruit weight for this ripening time, which makes it very interesting for fresh market production. [Projekat Ministarstva nauke Republike Srbije, br. 31063 i br. 31038

  8. New technologies for ultra-high throughput genotyping in plants.

    Science.gov (United States)

    Appleby, Nikki; Edwards, David; Batley, Jacqueline

    2009-01-01

    Molecular genetic markers represent one of the most powerful tools for the analysis of plant genomes and the association of heritable traits with underlying genetic variation. Molecular marker technology has developed rapidly over the last decade, with the development of high-throughput genotyping methods. Two forms of sequence-based marker, simple sequence repeats (SSRs), also known as microsatellites and single nucleotide polymorphisms (SNPs) now predominate applications in modern plant genetic analysis, along the anonymous marker systems such as amplified fragment length polymorphisms (AFLPs) and diversity array technology (DArT). The reducing cost of DNA sequencing and increasing availability of large sequence data sets permits the mining of this data for large numbers of SSRs and SNPs. These may then be used in applications such as genetic linkage analysis and trait mapping, diversity analysis, association studies and marker-assisted selection. Here, we describe automated methods for the discovery of molecular markers and new technologies for high-throughput, low-cost molecular marker genotyping. Genotyping examples include multiplexing of SSRs using Multiplex-Ready marker technology (MRT); DArT genotyping; SNP genotyping using the Invader assay, the single base extension (SBE), oligonucleotide ligation assay (OLA) SNPlex system, and Illumina GoldenGate and Infinium methods.

  9. Phenotypic characterization of papaya genotypes to determine powdery mildew resistance

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    Marcelo Vivas

    2017-06-01

    Full Text Available In support of breeding of papaya (Carica papaya, the disease incidence and severity of powdery mildew (Ovulariopsis caricicola were evaluated in papaya genotypes. Two experiments in complete randomized blocks were carried out, one in the field and the other in a greenhouse. In field experiments, the lowest mean disease incidence was observed on the genotypes ‘Costa Rica’ and ‘Baixinho Super’, and the lowest mean disease severity on ‘Caliman M5’, ‘GTF’, ‘SH 11-08’, and ‘JS 11’. In the greenhouse experiment, the genotypes ‘Caliman M5’, ‘Golden’, ‘Kapoho Solo’, ‘Waimanalo’, ‘Mamão Bené’, ‘SH 12-07’, ‘JS 12’, and ‘GTF’ had the lowest mean incidence in at least one evaluation. On the other hand, for severity, the genotypes ‘Diva’, ‘Sunrise Solo 72/12’, ‘Kapoho Solo PA’, ‘Waimanalo’, ‘Maradol’, ‘Maradol GL’, ‘SH 15-04’, ‘FMV, ‘JS 12-4’, ‘SH 12-07’ and ‘Sekati FLM’ had the lowest means. These results indicate these genotypes for a possible use in breeding for reduction of powdery mildew intensity

  10. Research Status Quo and Future of Low Temperature Wheat Genotypes

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Low temperature wheat genotypes are a group of wheat with a slightly low canopy (plant) temperature, and the research on their biological characters and utilization in wheat breeding has been done at home and abroad for more than 20 years, and has made great progress. The research contents and advances include the following respects: Wheat genotypes with slightly low canopy temperature have been verified to exist in nature; these wheat genotypes, which present cold temperature, are superior to conventional wheat materials in some important biological characters and particularly prominently in metabolic function and cellular structure; when they suffer stresses such as drought, high temperature and overcast and rainy weather, they still retain their superiority in some of their important biological characters and therefore have a wide range of ecological adaptability; slightly low canopy temperatures of these genotypes are closely correlated with low temperatures of their second heat sources and their vigorous plants; since their low canopy temperatures can be inherited, they can exert favorable influence on the temperatures of their offspring while crossing with other wheat materials, and in particular, the discovery of cold-source wheat as a contributor to low temperature, has further formed good conditions for breeding high and stable quality low temperature wheat varieties with a high and stable yield. Thus, low temperature wheat genotypes are of great research importance and have great prospects.

  11. Repeated measurement sampling in genetic association analysis with genotyping errors.

    Science.gov (United States)

    Lai, Renzhen; Zhang, Hong; Yang, Yaning

    2007-02-01

    Genotype misclassification occurs frequently in human genetic association studies. When cases and controls are subject to the same misclassification model, Pearson's chi-square test has the correct type I error but may lose power. Most current methods adjusting for genotyping errors assume that the misclassification model is known a priori or can be assessed by a gold standard instrument. But in practical applications, the misclassification probabilities may not be completely known or the gold standard method can be too costly to be available. The repeated measurement design provides an alternative approach for identifying misclassification probabilities. With this design, a proportion of the subjects are measured repeatedly (five or more repeats) for the genotypes when the error model is completely unknown. We investigate the applications of the repeated measurement method in genetic association analysis. Cost-effectiveness study shows that if the phenotyping-to-genotyping cost ratio or the misclassification rates are relatively large, the repeat sampling can gain power over the regular case-control design. We also show that the power gain is not sensitive to the genetic model, genetic relative risk and the population high-risk allele frequency, all of which are typically important ingredients in association studies. An important implication of this result is that whatever the genetic factors are, the repeated measurement method can be applied if the genotyping errors must be accounted for or the phenotyping cost is high.

  12. Evaluation of Drought Tolerance in Grain Sorghum Genotypes ( Sorghum

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    A.R Beheshti

    2012-06-01

    Full Text Available Evaluation of drought stress tolerance in sorghum genotypes at different growth stages and severity of stress and their reaction is very important in breeding programs. This study was conducted with the 13 grain sorghum genotypes in 3 different environmental conditions including normal condition and two water deficit conditions at vegetative and reproductive stages using randomized complete block design with 3 replications. Genotypes grouping were performed based on tolerance and sensitivity indices by cluster analysis. There was a positive and significant correlation between grain yield with tolerance indices (MP, GMP and STI and sensitivity indices (SSI and TOL in both normal and two water deficit conditions. The results showed that STI, GMP and MP indices were the best indices for evaluation of genotypes response in drought stress conditions. Cluster analysis showed that B26 genotype and M2 promising line had the most grain yield and higher values of STI ،GMP and MP indices in both normal and stress conditions and they grouped in the same cluster.

  13. Genotyping of Mycobacterium leprae in Myanmar and possible transmission modes.

    Science.gov (United States)

    Aye, Khin Saw; Oo, Yin Thet Nu; Kyaw, Kyaw; Win, Aye Aye; Matsuoka, Masanori

    2012-09-01

    The polymorphism of TTC repeats in Mycobacterium leprae was examined using bacilli from slit skin samples of leprosy patients attending at Central Special Skin Clinic, Yangon General Hospital and nasal swabs of their contacts to elucidate the possible mode of leprosy transmission. It was found that bacilli with different TTC genotypes were distributed among same household contacts and also harbored bacilli in patients were different TTC genotype from that harbored on the nasal mucus of the healthy contacts. Genotypes of TTC repeats were found to differ between husband under treatment and his wife and also mother under treatment and her sons living in same house. This study revealed that TTC genotype of bacilli harbored by household contacts was different with the TTC genotype by index cases. These results indicate that the family members get transmission from outside the dwellings rather than from commonly supposed their MB index cases. There might have been some infectious sources to which the populace had been commonly exposed outside the dwellings.

  14. Sorghum Seedling Drought Response: in Search of Tolerant Genotypes

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    Irawati Chanaigo

    2017-06-01

    Full Text Available Drought stress is a major factor contributing disease susceptibility and yield loss in agricultural crops. The experiment reported here was aimed at studying the germination and early growth of ten sorghum (Sorghum bicolor L. Moench genotypes in 0 or 20% (w/v polyethylene glycol (PEG 6000 solution as a model to mimic drought stress. The experiment was carried out at the Laboratory of Seed Technology and a glass house of Faculty of Agriculture, Andalas University Padang from March to April 2015. A two-way factorial experiment in a completely randomised design with three replicates was assigned. Data were analysed with analysis of variance and mean comparisons of Duncan’s New Multiple Range Test at 5% level. When only PEG was found to be significant then mean comparisons was calculated according to t-Dunnet test. Sorghum seeds were germinated on two layers of Whatmann paper in Petri dishs either in 0% or 20% PEG for seven days prior to transfer into Hoagland solution containing 0 or 20% PEG with layer of paraffin wax for 21 days in a glass house. Results indicated that 20% PEG solution reduced seedling dry weight and the length or roots protruding from the paraffin wax layer in some genotypes. Sorghum genotype No. 5 was more tolerant to drought stress in their early growth followed by genotypes Samurai 2, Samurai Batan, and Pahat Batan. In contrast, genotypes Advanta and No. 44 were found to be the most susceptible.

  15. Super-genotype: global monoclonality defies the odds of nature.

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    Johannes J Le Roux

    Full Text Available The ability to respond to natural selection under novel conditions is critical for the establishment and persistence of introduced alien species and their ability to become invasive. Here we correlated neutral and quantitative genetic diversity of the weed Pennisetum setaceum Forsk. Chiov. (Poaceae with differing global (North American and African patterns of invasiveness and compared this diversity to native range populations. Numerous molecular markers indicate complete monoclonality within and among all of these areas (F(ST = 0.0 and is supported by extreme low quantitative trait variance (Q(ST = 0.00065-0.00952. The results support the general-purpose-genotype hypothesis that can tolerate all environmental variation. However, a single global genotype and widespread invasiveness under numerous environmental conditions suggests a super-genotype. The super-genotype described here likely evolved high levels of plasticity in response to fluctuating environmental conditions during the Early to Mid Holocene. During the Late Holocene, when environmental conditions were predominantly constant but extremely inclement, strong selection resulted in only a few surviving genotypes.

  16. Super-genotype: global monoclonality defies the odds of nature.

    Science.gov (United States)

    Le Roux, Johannes J; Wieczorek, Ania M; Wright, Mark G; Tran, Carol T

    2007-07-04

    The ability to respond to natural selection under novel conditions is critical for the establishment and persistence of introduced alien species and their ability to become invasive. Here we correlated neutral and quantitative genetic diversity of the weed Pennisetum setaceum Forsk. Chiov. (Poaceae) with differing global (North American and African) patterns of invasiveness and compared this diversity to native range populations. Numerous molecular markers indicate complete monoclonality within and among all of these areas (F(ST) = 0.0) and is supported by extreme low quantitative trait variance (Q(ST) = 0.00065-0.00952). The results support the general-purpose-genotype hypothesis that can tolerate all environmental variation. However, a single global genotype and widespread invasiveness under numerous environmental conditions suggests a super-genotype. The super-genotype described here likely evolved high levels of plasticity in response to fluctuating environmental conditions during the Early to Mid Holocene. During the Late Holocene, when environmental conditions were predominantly constant but extremely inclement, strong selection resulted in only a few surviving genotypes.

  17. STUDY ON CROSSING ABILITY OF ANNUAL CHRYSANTHEMUM GENOTYPES

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    Suneetha Kattera

    2014-03-01

    Full Text Available The experiment comprised of six genotypes viz., NAC-01-10, NAC-02-10, NAC-03-10, NAC-04-10, NAC-05-10, NAC-06-10 selected for petal colour and number of layers of petals to estimate pollen viability, in-vitro pollen germination, stigma receptivity and crossed seed set percentage to find out the crossing ability of genotypes. The present experiment was laid out at the experimental field of Horticulture Section, College of Agriculture, Nagpur, during 2010-11. Pollen viability of six genotypes of annual chrysanthemum showed a range of 69.69% to 86.66% viability, Percentage of germination on the day of anthesis ranged from 22.72% (NAC-06-10 to 66.66% (NAC-01-10. First day pollen pollinated on first day stigma showed 100% stigma receptivity in all six genotypes and the crossed seed set ranged from 61.60% (NAC-04-10 × NAC-05-10 to 92.00% (NAC-01-10 × NAC-04-10 among direct crosses whereas, the percentage ranged from 42.00% (NAC-04-10 × NAC-02-10 to 90.00% (NAC-05-10 × NAC-01-10 among the reciprocal crosses. All the six genotypes are highly suitable for their use as parents in crossing program.

  18. Serotonin transporter genotype (5-HTTLPR predicts utilitarian moral judgments.

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    Abigail A Marsh

    Full Text Available BACKGROUND: The psychological and neurobiological processes underlying moral judgment have been the focus of extensive recent research. Here we show that serotonin transporter (5-HTTLPR genotype predicts responses to moral dilemmas featuring foreseen harm to an innocent. METHODOLOGY/PRINCIPAL FINDINGS: Participants in this study judged the acceptability of actions that would unintentionally or intentionally harm an innocent victim in order to save others' lives. An analysis of variance revealed a genotype × scenario interaction, F(2, 63 = 4.52, p = .02. Results showed that, relative to long allele homozygotes (LL, carriers of the short (S allele showed particular reluctance to endorse utilitarian actions resulting in foreseen harm to an innocent individual. LL genotype participants rated perpetrating unintentional harm as more acceptable (M = 4.98, SEM = 0.20 than did SL genotype participants (M = 4.65, SEM = 0.20 or SS genotype participants (M = 4.29, SEM = 0.30. No group differences in moral judgments were observed in response to scenarios featuring intentional harm. CONCLUSIONS/SIGNIFICANCE: The results indicate that inherited variants in a genetic polymorphism that influences serotonin neurotransmission influence utilitarian moral judgments as well. This finding is interpreted in light of evidence that the S allele is associated with elevated emotional responsiveness.

  19. Characteristics of general distribution of hepatitis B virus genotypes in China

    Institute of Scientific and Technical Information of China (English)

    Chang-Tai Zhu; Chun-Lei Dong

    2009-01-01

    BACKGROUND:Based on differences in the virus nucleotide sequence, hepatitis B virus (HBV) genotypes are presently divided into genotypes A-H. The geographic distributions of HBV genotypes differ in countries and regions. To determine the general characteristics of their distributions in the mainland of China, we reviewed articles on HBV genotypes published in China. METHODS:The Wanfang Database and the CNKI Database were searched for original articles involving HBV in China, and then the data from the articles were classiifed according to genotype and latitude and analyzed using SPSS 11.0. RESULTS:The main HBV genotypes were C, B and BC, and their rates were 50.99%, 35.58%, 6.07%, respectively;other genotypes were rare. There was a negative correlation between latitude and the rate of genotype B (r=-0.782,P0.05). CONCLUSIONS:In China, HBV genotype C predominates, followed by genotype C and mixed genotype BC; genotypes A, D and others are rare. With an increasing latitude, the distribution of genotype B decreases gradually, while that of genotype C tends to increase. The other genotypes do not show any changes.

  20. Comparative analysis of minor histocompatibility antigens genotyping methods

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    A. S. Vdovin

    2016-01-01

    Full Text Available The wide range of techniques could be employed to find mismatches in minor histocompatibility antigens between transplant recipients and their donors. In the current study we compared three genotyping methods based on polymerase chain reaction (PCR for four minor antigens. Three of the tested methods: allele-specific PCR, restriction fragment length polymorphism and real-time PCR with TaqMan probes demonstrated 100% reliability when compared to Sanger sequencing for all of the studied polymorphisms. High resolution melting analysis was unsuitable for genotyping of one of the tested minor antigens (HA-1 as it has linked synonymous polymorphism. Obtained data could be used to select the strategy for large-scale clinical genotyping.

  1. Agronomical and phytochemical evaluation of Stevia rebaudiana genotypes

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    Vouillamoz, José F.

    2016-07-01

    Full Text Available The agronomical potential and the phytochemical variability of 18 genotypes of the Paraguayan plant Stevia rebaudiana have been investigated in Switzerland in order identify the best genotype for local cultivation. Over a two years period, yields in dry leaves ranged from 10 to 170 g m-2, with a percentage of leaves ranging from 53 to 75 %. HPLC analyses showed a notable variability in phytochemical composition, with stevioside content ranging from 0.3 to 7.9 % w/w and rebaudioside A from 0.3 to 6.5 % w/w. Cultivation of S. rebaudiana in Switzerland is feasible. With a density of 10 plants per m2, the potential yields of dry matter are approximately 1-2 t ha-1. The most productive genotypes (Pharmasaat, Hem Zaden, Stepa and Mediplant 3 and 11 will be submitted to the industry for organoleptic evaluation.

  2. The metabolomic profile of red non-V. vinifera genotypes

    DEFF Research Database (Denmark)

    Ruocco, Silvia; Stefanini, Marco; Stanstrup, Jan

    2017-01-01

    composition of their grapes has not been widely investigated. This study aimed to explore in detail the metabolomic profile in terms of simple phenolic, proanthocyanidin, anthocyanin and lipid compounds in two hybrids and five American genotypes. The results were compared with those of two V. vinifera...... cultivars. A multi-targeted metabolomics approach using a combination of LC-MS and LC-DAD methods was used to identify and quantify 124 selected metabolites. The genotypes studied showed considerable variability in the metabolomic profile according to the grape composition of V. vinifera and other Vitis......-chain polymers. The analysis of lipids in wild Vitis genotypes, here reported for the first time, showed the existence of a certain diversity in their composition suggesting a strong influence of the environmental conditions on the general lipid pattern....

  3. Equine cryptosporidial infection associated with Cryptosporidium hedgehog genotype in Algeria.

    Science.gov (United States)

    Laatamna, Abd Elkarim; Wagnerová, Pavla; Sak, Bohumil; Květoňová, Dana; Aissi, Miriem; Rost, Michael; Kváč, Martin

    2013-10-18

    Faecal samples from two horse farms in Algeria keeping Arabian, Thoroughbred, and Barb horses were examined for the presence of Cryptosporidium in 2010-2011. A total of 138 faecal samples (16 from a farm keeping 50 animals and 122 from a farm with 267 horses) were screened for Cryptosporidium spp. infection using molecular tools. DNA was extracted from all samples. Nested PCR was performed to amplify fragments of the SSU rDNA and gp60 genes to determine the presence of Cryptosporidium species and genotypes. Sequence analyses of SSU and gp60 genes revealed four animals positive for the presence of subtype XIIIa A22R9 of the Cryptosporidium hedgehog genotype. The infections were not associated with diarrhoea. This study reports, for the first time, the occurrence of Cryptosporidium in Algeria and the first occurrence of the hedgehog genotype in horses. These findings support the potential role of infected horses in sylvatic-domestic transmission of Cryptosporidium.

  4. Noninvasive genotyping of common marmoset (Callithrix jacchus) by fingernail PCR.

    Science.gov (United States)

    Takabayashi, Shuji; Katoh, Hideki

    2015-07-01

    The common marmoset (Callithrix jacchus) is a New World primate that is a useful model for medical studies. In this study, we report a convenient, reliable, and noninvasive procedure to genotype a living common marmoset by using fingernails. This method was used to successfully genotype DNA by restriction fragment length polymorphism (RFLP) PCR without prior purification, by using the KOD FX PCR enzyme kit. Additionally, there is no sample contamination from hematopoietic chimera derived from fused placenta in utero. We compared chimeric levels between various tissues in females with male littermates using quantitative fluorescent (QF)-PCR to prepare a reliable DNA source for genetic analyses, such as genotyping, gene mapping, or genomic sequencing. The chimerism detected appeared to be restricted to lymphatic tissues, such as bone marrow, thymus, spleen, lymph nodes and blood cells. As a result, DNA from fingernails with the quick is the best DNA source for genetic research in living marmosets.

  5. Phenotypic and genotypic characterization of Italian Phytophthora infestans isolates

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    Federica SAVAZZINI

    2015-12-01

    Full Text Available Phytophthora infestans (Mont. de Bary causes late blight of potato. After the 1970s, several changes have occurred in the European P. infestans population, frequently associated with an increased virulence. While the genotypic and phenotypic diversity of P. infestans has been studied in-depth in northern and central Europe, only a few reports are available regarding Italian isolates, mainly based on phenotypic traits. We report data of phenotypic and genotypic characteristics of isolates collected from infected potato and tomato plants in different Italian regions in 2006‒2008. A prevalence of the A1 mating type and a majority of metalaxyl-resistant isolates were found. Tomato-derived isolates showed fungicide sensitivity, confirming previous reports. One of the isolates showed the rare IIb mitochondrial DNA haplotype. Genetic analyses of the single-sequence repeats (SSRs and of the internal transcribed spacers gave similar results, although SSRs gave the best discrimination of genotypes.

  6. Cytological Effects of Space Environment on Different Genotype of Rice

    Institute of Scientific and Technical Information of China (English)

    WEI Li-jun; QIAN Yu; YANG Qian; XU Jian-long; WANG Jun-min; SUN Ye-qing

    2007-01-01

    For exploring the biological effect of space environment on different genotype of rice seeds, the cytological effects of M1 generation after space flight were studied.Twelve different genotypes of rice seeds which belong to different climate ecotype (early, medium and late) of indica and japonica were onboard "Shenzhou 4" spaceship for 162 h.After recovered the total number of mitosis cells and chromosomal aberration were observed.In all the lines the mitotic index (MIs) of space flight are much higher than control, which indicates the stimulate effect of space environment.The cell rate of chromosomal aberration (CRCA) of space flight is also much higher than control, but varies from line to line.It indicates that biological effect of space environment on rice seed dependents not only on flight duration but also on rice genotype.The radiosensitivities of different lines were also discussed according to CRCAs.

  7. Acanthamoeba T4 genotype associated with keratitis infections in Tunisia.

    Science.gov (United States)

    Dendana, F; Sellami, H; Trabelsi, H; Neji, S; Cheikhrouhou, F; Makni, F; Ayadi, A

    2013-01-01

    Acanthamoeba keratitis (AK) is a sight-threatening infection. We report five cases of AK diagnosed from 2005 to 2009 in the Laboratory of Parasitology-Mycology at Habib Bourguiba Sfax Hospital, Tunisia. All were associated with improper care of contact lenses (rinsing of contact lenses with tap water and inappropriate cleaning) and lens storage. The patients displayed different clinical presentations: corneal inflammation, corneal ulceration, and corneal abscess. The diagnosis was made after direct examination, culture, and polymerase chain reaction amplification with specific primers. The genotype classification was based on the highly variable DF3 region in the 18S rRNA gene. This is the first study characterizing Acanthamoeba genotype in Tunisia and North Africa. All Acanthamoeba isolates were associated to the T4 genotype. Three different DF3 sequence types were related to AK infections T4/10, T4/15, and T4/16.

  8. ENVIRONMENTAL AND SOCIO-ECONOMIC ASPECT OF GROWING MISCANTHUS GENOTYPES

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    Marián KOTRLA

    2013-01-01

    Full Text Available Deliberate cultivation of plants for energy biomass is becoming increasingly important. Biomass should significantly contribute to increase the share of renewable energy in the European Union. On the research locality of Slovak University of Agriculture in Nitra localized in the village Kolíňany (Slovak Republic is implemented basic research focused on the growth and production of the two genotypes energy grass Miscanthus. Research is carried out since 2010. In the third year after planting (the year 2012 were confirmed biomass production depending on the genotype of 35.45 and 36.67 t ha-1. Based on the analysis of growth and production performance of Miscanthus genotypes can be evaluated the high environmental and socio-economic aspects of growing energy crops, depending on the specific agro-ecological conditions.

  9. Carcass traits and meat quality of two different rabbit genotypes

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    Maria D'Agata

    2012-07-01

    Full Text Available To evaluate the effect of genotype on carcass traits and meat quality, thirty-two rabbits for two genotypes (local population – LP; commercial hybrids – HY were used. Rabbits were weaned at 35 days old and slaughtered at 103 days of age for LP and 87 days of age for HY. Comparing the slaughtering traits of two genotypes, LP provided higher dressing out (59.4% vs 56.2%, Pvs 14.2%, Pvs 22.3, Pvs 8,9%, Pvs 0.86%, Pvs 1.12%; Pvs 19.2%; Pvs 31.6%; Pvs 3.8%; P*, higher redness (a*, yellowness (b* and C* value than HY (P

  10. Clinical utility of thiopurine S-methyltransferase genotyping.

    Science.gov (United States)

    Corominas, Hèctor; Baiget, Montserrat

    2004-01-01

    Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme that plays a major role in the metabolism of thiopurine drugs such as mercaptopurine and azathioprine. The interindividual differences in response to thiopurine administration is in part due to the presence of genetic polymorphisms in the gene that regulates TPMT activity. TPMT genotype correlates well with the in vivo enzyme activity within erythrocytes. Patients with genetically determined decreased TPMT activity develop severe myelosuppression when treated with standard doses of thiopurine drugs because an excess of thioguanine nucleotides accumulates in hematopoietic tissues. TPMT genotyping provides clinicians with a reliable method for identifying TPMT-deficient patients who can benefit from low doses of thiopurine drugs in order to reduce the risk of developing adverse effects. Moreover, the administration of higher doses of the drug could improve therapeutic response in patients in whom the TPMT genotyping demonstrates the absence of mutated alleles.

  11. Investigation of the genotype III to genotype I shift in Japanese encephalitis virus and the impact on human cases.

    Science.gov (United States)

    Han, Na; Adams, James; Fang, Wei; Liu, Si-Qing; Rayner, Simon

    2015-08-01

    Japanese encephalitis is a mosquito borne disease and is the leading cause of viral encephalitis in the Asia-Pacific area. The causative agent, Japanese encephalitis virus (JEV) can be phylogenetically classified into five genotypes based on nucleotide sequence. In recent years, genotype I (GI) has displaced genotype III (GIII) as the dominant lineage, but the mechanisms behind this displacement event requires elucidation. In an earlier study, we compared host variation over time between the two genotypes and observed that GI appears to have evolved to achieve more efficient infection in hosts in the replication cycle, with the tradeoff of reduced infectivity in secondary hosts such as humans. To further investigate this phenomenon, we collected JEV surveillance data on human cases and, together with sequence data, and generated genotype/case profiles from seven Asia-Pacific countries and regions to characterize the GI/GIII displacement event. We found that, when comprehensive and consistent vaccination and surveillance data was available, and the GIII to GI shift occurred within a well-defined time period, there was a statistically significant drop in JEV human cases. Our findings provide further support for the argument that GI is less effective in infecting humans, who represent a dead end host. However, experimental investigation is necessary to confirm this hypothesis. The study highlights the value of alternative approaches to investigation of epidemics, as well as the importance of effective data collection for disease surveillance and control.

  12. Relation between hepatitis B virus genotypes and gene mutation of basic core promoter in Li nationality

    Institute of Scientific and Technical Information of China (English)

    Juntao Zeng; Zhengwen Liu; Shiping Zeng; Jing Chen

    2009-01-01

    Objective:To investigate the relation between hepatitis B virus(HBV) genotypes and the double mutation of A-to-T nucleotide(nt) 1762 and G-to-A nt 1764 in basic core promotev(BCP T1762/A1764) in patients of the Li nationality. Methods:Subjects were 125 HBV DNA positive patients that belong to the Li nationality on Hainan Island. HBV DNA genotype was determined by real time fluorimetrypolymerase chain reaction. BCP T1762/A1764 mutation was performed using the direct sequencing method. Results:The prevalence rates of genotype B, genotype C, genotype D, genotype C and D mixed infection(genotype C+D) and genotype B and D mixed infection (genotype B+C) were 31.20%, 53.60%, 12.00%, 2.40% and 0.80% respectively. Mutation frequencies in patients infected with HBV genotype C(58.21%) were significantly higher than in those infected with other genotypes (P <0.01). The serum viral load of the patients with genotype C(5.74±1.21) was also higher than that of those with genotype B(P <0.01). Conclusion:The major genotypes in the Li nationality were genotype C and genotype B. The infection of genotype D and mixed infection also occurred in the Li nationality. Genotype C HBV has a higher replication rate, and the different degrees of pathogenecity among HBV genotypes may be related to BCP T1762/ A1764 mutation frequency.

  13. Measles virus genotypes circulating in India, 2011-2015.

    Science.gov (United States)

    Vaidya, Sunil R; Chowdhury, Deepika T

    2017-05-01

    The Government of India is accepted to participate in the measles elimination and rubella control goal 2020, hence genetic characterization of measles viruses (MeV) becomes essential. At National Reference Laboratory (National Institute of Virology, Pune), the throat swabs/urine specimens (n = 380) or PCR products (n = 219) obtained from the suspected measles cases were referred for the molecular testing and subsequently, MeV nucleoprotein (N) gene sequencing/genotyping. In addition, 2,449 suspected measles cases, mainly from the Maharashtra state were referred for the laboratory diagnosis. A detailed study was performed on N gene sequences obtained during last two decades. Indian MeV sequences obtained during 2011-2015 were compared with 1996-2010 sequences and genetic divergence was studied. Circulation of measles genotypes B3 (n = 3), D4 (n = 49), and D8 (n = 351) strains were observed in 19 States and three Union Territories of India. In addition, 64 measles viruses were isolated from 253 throat swab or urine specimens obtained from the suspected measles cases. During 2011-2015, 67.9% (1,663/2,449) suspected measles cases were laboratory confirmed. Molecular studies showed circulation of measles genotype B3 in India along with prominently circulating genotypes D4 and D8 except D7 strains. The genetic diversion within Indian B3, D4, and D8 genotypes was 0.3%, 1.1%, and 2.1%, respectively. The genetic divergence of Indian B3, D4, and D8 measles strains with the WHO reference sequences was 2.5%, 2.6%, and 1.8%, respectively. It is crucial data for national immunization program. More measles/rubella genotyping studies are necessary to track transmission and to support measles elimination and rubella control. J. Med. Virol. 89:753-758, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  14. Direct maximum parsimony phylogeny reconstruction from genotype data

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    Ravi R

    2007-12-01

    Full Text Available Abstract Background Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. Results In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Conclusion Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.

  15. Genotyping of Brucella species using clade specific SNPs

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    Foster Jeffrey T

    2012-06-01

    Full Text Available Abstract Background Brucellosis is a worldwide disease of mammals caused by Alphaproteobacteria in the genus Brucella. The genus is genetically monomorphic, requiring extensive genotyping to differentiate isolates. We utilized two different genotyping strategies to characterize isolates. First, we developed a microarray-based assay based on 1000 single nucleotide polymorphisms (SNPs that were identified from whole genome comparisons of two B. abortus isolates , one B. melitensis, and one B. suis. We then genotyped a diverse collection of 85 Brucella strains at these SNP loci and generated a phylogenetic tree of relationships. Second, we developed a selective primer-extension assay system using capillary electrophoresis that targeted 17 high value SNPs across 8 major branches of the phylogeny and determined their genotypes in a large collection ( n = 340 of diverse isolates. Results Our 1000 SNP microarray readily distinguished B. abortus, B. melitensis, and B. suis, differentiating B. melitensis and B. suis into two clades each. Brucella abortus was divided into four major clades. Our capillary-based SNP genotyping confirmed all major branches from the microarray assay and assigned all samples to defined lineages. Isolates from these lineages and closely related isolates, among the most commonly encountered lineages worldwide, can now be quickly and easily identified and genetically characterized. Conclusions We have identified clade-specific SNPs in Brucella that can be used for rapid assignment into major groups below the species level in the three main Brucella species. Our assays represent SNP genotyping approaches that can reliably determine the evolutionary relationships of bacterial isolates without the need for whole genome sequencing of all isolates.

  16. Whole genome amplification of DNA for genotyping pharmacogenetics candidate genes.

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    Santosh ePhilips

    2012-03-01

    Full Text Available Whole genome amplification (WGA technologies can be used to amplify genomic DNA when only small amounts of DNA are available. The Multiple Displacement Amplification Phi polymerase based amplification has been shown to accurately amplify DNA for a variety of genotyping assays; however, it has not been tested for genotyping many of the clinically relevant genes important for pharmacogenetic studies, such as the cytochrome P450 genes, that are typically difficult to genotype due to multiple pseudogenes, copy number variations, and high similarity to other related genes. We evaluated whole genome amplified samples for Taqman™ genotyping of SNPs in a variety of pharmacogenetic genes. In 24 DNA samples from the Coriell human diversity panel, the call rates and concordance between amplified (~200-fold amplification and unamplified samples was 100% for two SNPs in CYP2D6 and one in ESR1. In samples from a breast cancer clinical trial (Trial 1, we compared the genotyping results in samples before and after WGA for four SNPs in CYP2D6, one SNP in CYP2C19, one SNP in CYP19A1, two SNPs in ESR1, and two SNPs in ESR2. The concordance rates were all >97%. Finally, we compared the allele frequencies of 143 SNPs determined in Trial 1 (whole genome amplified DNA to the allele frequencies determined in unamplified DNA samples from a separate trial (Trial 2 that enrolled a similar population. The call rates and allele frequencies between the two trials were 98% and 99.7%, respectively. We conclude that the whole genome amplified DNA is suitable for Taqman™ genotyping for a wide variety of pharmacogenetically relevant SNPs.

  17. Chimpanzee Personality and the Arginine Vasopressin Receptor 1A Genotype.

    Science.gov (United States)

    Wilson, V A D; Weiss, A; Humle, T; Morimura, N; Udono, T; Idani, G; Matsuzawa, T; Hirata, S; Inoue-Murayama, M

    2017-03-01

    Polymorphisms of the arginine vasopressin receptor 1a (AVPR1a) gene have been linked to various measures related to human social behavior, including sibling conflict and agreeableness. In chimpanzees, AVPR1a polymorphisms have been associated with traits important for social interactions, including sociability, joint attention, dominance, conscientiousness, and hierarchical personality dimensions named low alpha/stability, disinhibition, and negative emotionality/low dominance. We examined associations between AVPR1a and six personality domains and hierarchical personality dimensions in 129 chimpanzees (Pan troglodytes) living in Japan or in a sanctuary in Guinea. We fit three linear and three animal models. The first model included genotype, the second included sex and genotype, and the third included genotype, sex, and sex × genotype. All personality phenotypes were heritable. Chimpanzees possessing the long form of the allele were higher in conscientiousness, but only in models that did not include the other predictors; however, additional analyses suggested that this may have been a consequence of study design. In animal models that included sex and sex × genotype, chimpanzees homozygous for the short form of the allele were higher in extraversion. Taken with the findings of previous studies of chimpanzees and humans, the findings related to conscientiousness suggest that AVPR1a may be related to lower levels of impulsive aggression. The direction of the association between AVPR1a genotype and extraversion ran counter to what one would expect if AVPR1a was related to social behaviors. These results help us further understand the genetic basis of personality in chimpanzees.

  18. Photosynthesis, photorespiration and productivity of wheat and soybean genotypes.

    Science.gov (United States)

    Aliyev, Jalal A

    2012-07-01

    The results of the numerous measurements obtained during the last 40 years on gas exchange rate, photosynthetic carbon metabolism by exposition in ¹⁴CO₂ and activities of primary carbon fixation enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPC/O), in various wheat and soybean genotypes grown over a wide area in the field and contrasting in photosynthetic traits and productivity are presented in this article. It was established that high productive wheat genotypes (7-9 t ha⁻¹) with the optimal architectonics possess higher rate of CO₂ assimilation during the leaf ontogenesis. Along with the high rate of photosynthesis, high values of photorespiration are characteristic for the high productive genotypes. Genotypes with moderate (4-5 t ha⁻¹) and low (3 t ha⁻¹) grain yield are characterized by relatively low rates of both CO₂ assimilation and photorespiration. A value of photorespiration constitutes 28-35% of photosynthetic rate in contrasting genotypes. The activities of RuBPC and RuBPO were changing in a similar way in the course of the flag leaf and ear elements development. High productive genotypes are also characterized by a higher rate of biosynthesis and total value of glycine-serine and a higher photosynthetic rate. Therefore, contrary to conception arisen during many years on the wastefulness of photorespiration, taking into account the versatile investigations on different aspects of photorespiration, it was proved that photorespiration is one of the evolutionarily developed vital metabolic processes in plants and the attempts to reduce this process with the purpose of increasing the crop productivity are inconsistent.

  19. Differentiation in quinolone resistance by virulence genotype in Pseudomonas aeruginosa.

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    Melissa Agnello

    Full Text Available Pseudomonas aeruginosa is a leading pathogen that has become increasingly resistant to the fluoroquinolone antibiotics due to widespread prescribing. Adverse outcomes have been shown for patients infected with fluoroquinolone-resistant strains. The type III secretion system (TTSS is a major virulence determinant during acute infections through the injection of effector toxins into host cells. Most strains exhibit a unique TTSS virulence genotype defined by the presence of either exoS or exoU gene encoding two of the effector toxins, ExoS and ExoU, respectively. Specific TTSS effector genotype has been shown previously to differentially impact virulence in pneumonia. In this study, we examined the relationship between TTSS effector genotype and fluoroquinolone resistance mechanisms in a collection of 270 respiratory isolates. We found that a higher proportion of exoU+ strains were fluoroquinolone-resistant compared to exoS+ strains (63% vs 49%, p = 0.03 despite its lower overall prevalence (38% exoU+ vs 56% exoS+. Results from sequencing the quinolone resistance determining regions (QRDRs of the 4 target genes (gyrA, gyrB, parC, parE indicated that strains containing the exoU gene were more likely to acquire ≥ 2 mutations than exoS+ strains at MICs ≤ 8 µg/ml (13% vs none and twice as likely to have mutations in both gyrA and parC than exoS+ strains (48% vs 24% p = 0.0439. Our findings indicate that P. aeruginosa strains differentially develop resistance-conferring mutations that correlate with TTSS effector genotype and the more virulent exoU+ subpopulation. Differences in mutational processes by virulence genotype that were observed suggest co-evolution of resistance and virulence traits favoring a more virulent genotype in the quinolone-rich clinical environment.

  20. Neuregulin-1 genotypes and eye movements in schizophrenia

    DEFF Research Database (Denmark)

    Haraldsson, H.M.; Ettinger, U.; Magnusdottir, B.B.;

    2010-01-01

    Neuregulin-1 (NRG-1) is a putative susceptibility gene for schizophrenia but the neurocognitive processes that may involve NRG-1 in schizophrenia are unknown. Deficits in antisaccade (AS) and smooth pursuit eye movements (SPEM) are promising endophenotypes, which may be associated with brain...... dysfunctions underlying the pathophysiology of schizophrenia. The aim of this study was to investigate the associations of NRG-1 genotypes with AS and SPEM in schizophrenia patients and healthy controls. Patients (N = 113) and controls (N = 106) were genotyped for two NRG-1 single nucleotide polymorphisms...... findings of impaired AS and SPEM performance in schizophrenia patients (all P

  1. [Present and future of genotype-based personalized nutrition].

    Science.gov (United States)

    Sarkadi Nagy, Eszter; Martos, Éva

    2014-05-18

    After the completion of the Human Genome Project, the era of providing personalized dietary advice based on an individual's genetic profile seemed near. Since then more than a decade has passed and the pace of development has been slower than expected. Genotyping single nucleotide polymorphisms which may determine susceptibility to multifactorial diseases is cheaper and more accessible than it was ten years ago. However, few of them are supported by such solid scientific evidence which would justify their use for personalized dietary advice. The future of genotype-based personalized nutrition depends on whether a sufficient amount of gene-diet-disease interactions are identified and scientifically confirmed.

  2. Chlorophyll a fluorescence to phenotype wheat genotypes for heat tolerance

    DEFF Research Database (Denmark)

    Sharma, Dew Kumari; Andersen, Sven Bode; Ottosen, Carl-Otto

    . Chlorophyll a fluorescence has been a versatile tool in photosynthesis research to measure plant responses to various abiotic stresses that affect PSII. We aim to establish a reproducible protocol to measure response of wheat genotypes to high temperature, based on the physiological marker, maximum quantum......%. Our protocol seems to be stable over environments since interaction between genotypes and the three repeated experiments separated in time was not statistically significant. The chlorophyll a fluorescence protocol may enable identification of wheat lines reliably more or less tolerant to heat stress...

  3. Nephele: genotyping via complete composition vectors and MapReduce

    Directory of Open Access Journals (Sweden)

    Mardis Scott

    2011-08-01

    Full Text Available Abstract Background Current sequencing technology makes it practical to sequence many samples of a given organism, raising new challenges for the processing and interpretation of large genomics data sets with associated metadata. Traditional computational phylogenetic methods are ideal for studying the evolution of gene/protein families and using those to infer the evolution of an organism, but are less than ideal for the study of the whole organism mainly due to the presence of insertions/deletions/rearrangements. These methods provide the researcher with the ability to group a set of samples into distinct genotypic groups based on sequence similarity, which can then be associated with metadata, such as host information, pathogenicity, and time or location of occurrence. Genotyping is critical to understanding, at a genomic level, the origin and spread of infectious diseases. Increasingly, genotyping is coming into use for disease surveillance activities, as well as for microbial forensics. The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, these traditional single-processor methods are suboptimal for rapidly growing sequence datasets being generated by next-generation DNA sequencing machines, because they increase in computational complexity quickly with the number of sequences. Results Nephele is a suite of tools that uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers by passing the need for multiple sequence alignment, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods run on

  4. Two-temperature LATE-PCR endpoint genotyping

    Directory of Open Access Journals (Sweden)

    Reis Arthur H

    2006-12-01

    Full Text Available Abstract Background In conventional PCR, total amplicon yield becomes independent of starting template number as amplification reaches plateau and varies significantly among replicate reactions. This paper describes a strategy for reconfiguring PCR so that the signal intensity of a single fluorescent detection probe after PCR thermal cycling reflects genomic composition. The resulting method corrects for product yield variations among replicate amplification reactions, permits resolution of homozygous and heterozygous genotypes based on endpoint fluorescence signal intensities, and readily identifies imbalanced allele ratios equivalent to those arising from gene/chromosomal duplications. Furthermore, the use of only a single colored probe for genotyping enhances the multiplex detection capacity of the assay. Results Two-Temperature LATE-PCR endpoint genotyping combines Linear-After-The-Exponential (LATE-PCR (an advanced form of asymmetric PCR that efficiently generates single-stranded DNA and mismatch-tolerant probes capable of detecting allele-specific targets at high temperature and total single-stranded amplicons at a lower temperature in the same reaction. The method is demonstrated here for genotyping single-nucleotide alleles of the human HEXA gene responsible for Tay-Sachs disease and for genotyping SNP alleles near the human p53 tumor suppressor gene. In each case, the final probe signals were normalized against total single-stranded DNA generated in the same reaction. Normalization reduces the coefficient of variation among replicates from 17.22% to as little as 2.78% and permits endpoint genotyping with >99.7% accuracy. These assays are robust because they are consistent over a wide range of input DNA concentrations and give the same results regardless of how many cycles of linear amplification have elapsed. The method is also sufficiently powerful to distinguish between samples with a 1:1 ratio of two alleles from samples comprised of

  5. Two-temperature LATE-PCR endpoint genotyping

    Science.gov (United States)

    Sanchez, J Aquiles; Abramowitz, Jessica D; Salk, Jesse J; Reis, Arthur H; Rice, John E; Pierce, Kenneth E; Wangh, Lawrence J

    2006-01-01

    Background In conventional PCR, total amplicon yield becomes independent of starting template number as amplification reaches plateau and varies significantly among replicate reactions. This paper describes a strategy for reconfiguring PCR so that the signal intensity of a single fluorescent detection probe after PCR thermal cycling reflects genomic composition. The resulting method corrects for product yield variations among replicate amplification reactions, permits resolution of homozygous and heterozygous genotypes based on endpoint fluorescence signal intensities, and readily identifies imbalanced allele ratios equivalent to those arising from gene/chromosomal duplications. Furthermore, the use of only a single colored probe for genotyping enhances the multiplex detection capacity of the assay. Results Two-Temperature LATE-PCR endpoint genotyping combines Linear-After-The-Exponential (LATE)-PCR (an advanced form of asymmetric PCR that efficiently generates single-stranded DNA) and mismatch-tolerant probes capable of detecting allele-specific targets at high temperature and total single-stranded amplicons at a lower temperature in the same reaction. The method is demonstrated here for genotyping single-nucleotide alleles of the human HEXA gene responsible for Tay-Sachs disease and for genotyping SNP alleles near the human p53 tumor suppressor gene. In each case, the final probe signals were normalized against total single-stranded DNA generated in the same reaction. Normalization reduces the coefficient of variation among replicates from 17.22% to as little as 2.78% and permits endpoint genotyping with >99.7% accuracy. These assays are robust because they are consistent over a wide range of input DNA concentrations and give the same results regardless of how many cycles of linear amplification have elapsed. The method is also sufficiently powerful to distinguish between samples with a 1:1 ratio of two alleles from samples comprised of 2:1 and 1:2 ratios of the

  6. Evaluation of some Phenological and Pomological Characteristics of Selected Walnut Genotypes from Shahroud-Iran

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    Sara Akhiani

    2017-05-01

    Full Text Available The first step in walnut breeding programs is to identify and evaluate superior genotypes of fruit trees. Hence, there are various walnut breeding programs in various areas of Iran. A study aimed to evaluate the morphological and chemical characteristics of selected superior genotypes of walnut was conducted in the Shahroud region in 2011-2012.  The following genotypes were selected in this study as the best walnut genotypes:  X-18 homogamous genotypes due to desirable late leafing;   genotype X-11 for its high percentage of kernel production, easily removal of shell, thin shell; genotype X-52 due to its kernel plumpness compared to other genotypes, thin shell and high percentage of kernel and genotype X-70 for its kernel brightness, easily kernel extracting and high percentage of kernels. The X-49 and X-5 genotypes had the highest amount of linoleic and linolenic fatty acids and higher nutritional quality compared to other genotypes. Three genotypes, X-3, X-11 and X-22, had the highest amount of oil. Genotypes X-9 and X-45 had the highest amount of protein. The difference between oil content and fatty acid compositions was presumably due to genetic diversity and ecological conditions of the studied genotypes cultivation.

  7. Experimental evidence for competitive growth advantage of genotype VII over VI: implications for foot-and-mouth disease virus serotype A genotype turnover in nature.

    Science.gov (United States)

    Mohapatra, J K; Subramaniam, S; Singh, N K; Sanyal, A; Pattnaik, B

    2012-04-01

    In India, systematic genotype replacement has been observed for serotype A foot-and-mouth disease virus. After a decade of co-circulation of genotypes VI and VII, genotype VII emerged as the single dominant genotype since 2001. To derive possible explanations for such epochal evolution dynamics, in vitro intergenotype growth competition experiments involving both co- and superinfection regimes were conducted. Coinfection of BHK-21 cells demonstrated abrupt loss in the genotype VI viral load with commensurate increase in the load of genotype VII as measured by the genotype differentiating ELISA, RT-PCR and real-time RT-PCR. The superinfection dynamics was shaped by temporal spacing of infection, where the invading genotype VII took more number of passages than coinfection to eventually overtake the resident genotype VI. It was speculated that such superior replicative fitness of genotype VII could have been a possible factor for the ultimate dominance of genotype VII in nature. Copyright © 2011 Elsevier Ltd. All rights reserved.

  8. Differences in ovarian aging patterns between races are associated with ovarian genotypes and sub-genotypes of the FMR1 gene

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    Gleicher Norbert

    2012-09-01

    Full Text Available Abstract Background Ovarian aging patterns differ between races, and appear to affect fertility treatment outcomes. What causes these differences is, however, unknown. Variations in ovarian aging patterns have recently been associated with specific ovarian genotypes and sub-genotypes of the FMR1 gene. We, therefore, attempted to determine differences in how functional ovarian reserve (FOR changes with advancing age between races, and whether changes are associated with differences in distribution of ovarian genotypes and sub-genotypes of the FMR1 gene. Methods We determined in association with in vitro fertilization (IVF FOR in 62 young Caucasian, African and Asian oocyte donors and 536 older infertility patients of all three races, based on follicle stimulating hormone (FSH, anti-Müllerian hormone (AMH and oocyte yields, and investigated whether differences between races are associated with differences in distribution of FMR1 genotypes and sub-genotypes. Results Changes in distribution of mean FSH, AMH and oocyte yields between young donors and older infertility patients were significant (all P FMR1 genotypes and sub-genotypes in patients varied significantly between races, with Asians demonstrating fewer het-norm/low sub-genotypes than Caucasians and Africans (P = 0.012. Conclusion FOR changes in different races at different rates, and appears to parallel ovarian FMR1 genotypes and sub-genotype distributions. Differences in ovarian aging between races may, therefore, be FMR1-associated.

  9. Pattern and molecular epidemiology of Hepatitis B virus genotypes circulating in Pakistan.

    Science.gov (United States)

    Awan, Zunaira; Idrees, Muhammad; Amin, Irum; Butt, Sadia; Afzal, Samia; Akbar, Haji; Rehman, Irshad-ur; Younas, Saima; Shahid, Muhammad; Lal, Amreek; Saleem, Sana; Rauff, Bisma

    2010-12-01

    The continuously mutating nature of Hepatitis B virus (HBV) is responsible for the emergence of varying genotypes in different regions of the world affecting the disease outcome. The objective of the current study was to find out the pattern of HBV genotypes circulating in Pakistan. HBV genotypes were determined in HBV chronic patients of different age and gender from all the four different geographical regions (provinces) of Pakistan for a period of 2 years (2007-2009). Out of the total 3137 consecutive patients, 300 (175; 58.3% males and 125; 41.7% females) were randomly selected for HBV genotype A through H determination using molecular genotyping methods. Total 269 (89.6%) isolates were successfully genotyped where as 31 (10.3%) samples failed to generate a type-specific PCR band and were found untypable. Out of the successfully genotyped samples, 43 (14.3%) were with type A, 54 (18%) were with type B, 83 (27.6%) were with type C, 39 (13%) were with type D, 2 (0.6%) were with type E, 4 (1.3%) were with genotype F and total 44 (14.6%) were with mixed HBV infections. Of the mixed genotype infection cases, 16 were with genotypes A/D, 9 were B/C, six were A/D/F, five were with genotypes A/F, two were with A/B/D and B/E and one each for A/C as well as A/E genotypes. Four common genotypes of HBV found worldwide (A, B, C & D) were isolated from Pakistan along with uncommon genotypes E and F for the first time in Pakistan. Overall Genotype C is the most prevalent genotype. Genotypes B and C are predominant in Punjab & Balochistan and Khyber Pakhtoonkhwa, respectively whereas genotype A in Sindh.

  10. Comparison of potentials between genotype-based selection and genotypic value-based selection of quantitative traits

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    According to the difference of selection criteria, methods of marker-assisted selection (MAS) of quantitative traits can be divided into genotype-based selection (GS) and genotypic value-based selection (GVS). By means of computer simulation, potentials of the two methods were compared. Results showed that the two methods had similar basic laws and their efficiencies were not significantly different except that GS behaved better in the case where the number of QTLs was large and QTL effects were equal. From the application point of view, combination of GS and GVS should be the development direction of MAS research in the future.

  11. Prior infection of pigs with a genotype 3 swine hepatitis E virus (HEV) protects against subsequent challenges with homologous and heterologous genotypes 3 and 4 human HEV.

    Science.gov (United States)

    Sanford, Brenton J; Dryman, Barbara A; Huang, Yao-Wei; Feagins, Alicia R; Leroith, Tanya; Meng, Xiang-Jin

    2011-07-01

    Hepatitis E virus (HEV) is an important human pathogen. At least four recognized and two putative genotypes of mammalian HEV have been reported: genotypes 1 and 2 are restricted to humans whereas genotypes 3 and 4 are zoonotic. The current experimental vaccines are all based on a single strain of HEV, even though multiple genotypes of HEV are co-circulating in some countries and thus an individual may be exposed to more than one genotype. Genotypes 3 and 4 swine HEV is widespread in pigs and known to infect humans. Therefore, it is important to know if prior infection with a genotype 3 swine HEV will confer protective immunity against subsequent exposure to genotypes 3 and 4 human and swine HEV. In this study, specific-pathogen-free pigs were divided into 4 groups of 6 each. Pigs in the three treatment groups were each inoculated with a genotype 3 swine HEV, and 12 weeks later, challenged with the same genotype 3 swine HEV, a genotype 3 human HEV, and a genotype 4 human HEV, respectively. The control group was inoculated and challenged with PBS buffer. Weekly sera from all pigs were tested for HEV RNA and IgG anti-HEV, and weekly fecal samples were also tested for HEV RNA. The pigs inoculated with swine HEV became infected as evidenced by fecal virus shedding and viremia, and the majority of pigs also developed IgG anti-HEV prior to challenge at 12 weeks post-inoculation. After challenge, viremia was not detected and only two pigs challenged with swine HEV had 1-week fecal virus shedding, suggesting that prior infection with a genotype 3 swine HEV prevented pigs from developing viremia and fecal virus shedding after challenges with homologous and heterologous genotypes 3 and 4 HEV. The results from this study have important implications for future development of an effective HEV vaccine.

  12. Nuclear DNA content and chromosome number in Brachiaria spp. genotypes

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    Ana Luiza de Oliveira Timbó

    Full Text Available Breeding programs for Brachiaria spp. use both intraspecies and interspecies crosses between sexual and apomictic plants in order to obtain new cultivars with the desired characteristics. As there are different ploidy levels both within and between species of this genus, it becomes necessary to evaluate the genotypes used in breeding programs, as a guide to breeders when adopting crossing strategies. In this work, DNA content and chromosome number were determined in order to characterise ploidy levels in Brachiaria spp. genotypes. In the analysis of 15 genotypes, DNA content varied with the ploidy levels (2x, 3x and 4x, and between species and/or taxon. The average DNA content was 1.74 pg (2x in B. ruziziensis, 3.74 pg (4x in B. decumbens and 3.52 pg (4x for B. brizantha. For the genotype 86, 2.57 pg of DNA was obtained and 2n = 3x = 27, indicating a triploid accession, probably a natural hybrid. The variation in the total DNA content allowed the differentiation of Brachiaria ruziziensis (2n = 2x = 18 from the tetraploid species Brachiaria Brizantha and Brachiaria decumbens (2n = 4x = 36, as well as the probable hybrid triploid (2n = 3x = 18 of these species.

  13. Diagnostic multiplex PCR for toxin genotyping of Clostridium perfringens isolates.

    Science.gov (United States)

    Baums, Christoph G; Schotte, Ulrich; Amtsberg, Gunter; Goethe, Ralph

    2004-05-20

    In this study we provide a protocol for genotyping Clostridium perfringens with a new multiplex PCR. This PCR enables reliable and specific detection of the toxin genes cpa, cpb, etx, iap, cpe and cpb2 from heat lysed bacterial suspensions. The efficiency of the protocol was demonstrated by typing C. perfringens reference strains and isolates from veterinary bacteriological routine diagnostic specimens.

  14. Response of cowpea genotypes to Alectra vogelii parasitism in Kenya

    African Journals Online (AJOL)

    jakakah

    2013-11-20

    Nov 20, 2013 ... Significant differences were observed amongst cowpea genotypes in days to first .... crop production, have to cope in an environment charac- ..... plant resistance to striga hermonthica in maize. ... Host plant interactions throughout the striga ... Doctor of Philosophy Thesis, Department of Agronomy, Ahmadu.

  15. Comparing performance of modern genotype imputation methods in different ethnicities

    Science.gov (United States)

    Roshyara, Nab Raj; Horn, Katrin; Kirsten, Holger; Ahnert, Peter; Scholz, Markus

    2016-10-01

    A variety of modern software packages are available for genotype imputation relying on advanced concepts such as pre-phasing of the target dataset or utilization of admixed reference panels. In this study, we performed a comprehensive evaluation of the accuracy of modern imputation methods on the basis of the publicly available POPRES samples. Good quality genotypes were masked and re-imputed by different imputation frameworks: namely MaCH, IMPUTE2, MaCH-Minimac, SHAPEIT-IMPUTE2 and MaCH-Admix. Results were compared to evaluate the relative merit of pre-phasing and the usage of admixed references. We showed that the pre-phasing framework SHAPEIT-IMPUTE2 can overestimate the certainty of genotype distributions resulting in the lowest percentage of correctly imputed genotypes in our case. MaCH-Minimac performed better than SHAPEIT-IMPUTE2. Pre-phasing always reduced imputation accuracy. IMPUTE2 and MaCH-Admix, both relying on admixed-reference panels, showed comparable results. MaCH showed superior results if well-matched references were available (Nei’s GST ≤ 0.010). For small to medium datasets, frameworks using genetically closest reference panel are recommended if the genetic distance between target and reference data set is small. Our results are valid for small to medium data sets. As shown on a larger data set of population based German samples, the disadvantage of pre-phasing decreases for larger sample sizes.

  16. LHRH and LHR genotypes and prostate cancer incidence and survival.

    Science.gov (United States)

    Ingles, Sue Ann; Liu, Stephen V; Pinski, Jacek

    2013-01-01

    Despite their crucial role in initiating steroid-hormone synthesis, the hypothalamic and pituitary hormones (LH, LHRH) and their receptors have received scant attention in genetic studies of hormone-related diseases. This study included 1,170 men diagnosed with prostate cancer (PC) in Los Angeles County between 1999 and 2003. LHRH and LH receptor genotypes were examined for association with PC survival. Additionally, associations with PC incidence were examined by comparing PC cases to control men of similar age and race/ethnicity. The LHR 312 G allele was found to be associated with increased PC mortality (p=0.01). Ten years after diagnosis, 16% of men carrying two copies of the G allele (genotype GG) had died of PC, compared to 11% of those with genotype AG and 9% of those with AA. In a case-control comparison, this same allele was significantly associated with decreased PC risk: OR=0.68 (95% CI: 0.49, 0.93) for genotype GG vs. AA. These results suggest that androgens may play opposing roles in PC initiation and progression, and highlight the need to include these important but overlooked genes in future studies of PC etiology, prognosis, and treatment.

  17. Microsatellite analysis of selected Lablab purpureus genotypes in ...

    African Journals Online (AJOL)

    cntaganda

    Information on genetic worth and diversity of lablab genotypes in Kenya is scanty and ... Due to advances in molecular biology techniques, large numbers of highly ..... program for effective and efficient management/utilization of plant genetic ... response to selection pressures to suit particular environments (Maass and.

  18. Genotype x environment interaction, environmental heterogeneity, and the lek paradox

    Science.gov (United States)

    Substantial additive genetic variance (VA) often exists for male signaling traits in spite of the directional selection that female choice imposes. One solution to this problem, generally termed the ‘lek paradox’, is that genotype x environment interaction (GEI) occurs and generates a ‘crossover’ of...

  19. Effects of genotype x bradyrhizobium inoculation or x fertilizer n ...

    African Journals Online (AJOL)

    Genotype x inoculation interaction was significant only for protein and oil content in one year. ... seed composition, or other agronoi:nic traits including plant .... used to compare expected genetic of inoculation on maturity, p;ant height, a;:d yick!

  20. effect of phosphorus nutrition on growth of potato genotypes with ...

    African Journals Online (AJOL)

    Administrator

    were grown under two P levels [100 mg P kg-1 soil (low P) and 700 mg P kg-1 of soil (high P)]. Treatments were .... was sieved through 5 mm mesh and pH was adjusted to 6.7 by ... Potato genotypes with contrasting phosphorus efficiency. 201.

  1. Evaluation of soybean genotypes for resistance to charcoal rot

    Science.gov (United States)

    Charcoal rot caused by Macrophomina phaseolina causes more yield loss in soybean than most other diseases in the southern U.S.A. There are no commercial genotypes marketed as resistant to charcoal rot of soybean. Reactions of 27 maturity group (MG) III, 29 Early MG IV, 34 Late MG IV, and 59 MG V gen...

  2. [National Database of Genotypes--ethical and legal issues].

    Science.gov (United States)

    Franková, Vera; Tesínová, Jolana; Brdicka, Radim

    2011-01-01

    National Database of Genotypes--ethical and legal issues The aim of the project National Database of Genotypes is to outline structure and rules for the database operation collecting information about genotypes of individual persons. The database should be used entirely for health care. Its purpose is to enable physicians to gain quick and easy access to the information about persons requiring specialized care due to their genetic constitution. In the future, another introduction of new genetic tests into the clinical practice can be expected thus the database of genotypes facilitates substantial financial savings by exclusion of duplicates of the expensive genetic testing. Ethical questions connected with the creating and functioning of such database concern mainly privacy protection, confidentiality of personal sensitive data, protection of database from misuse, consent with participation and public interests. Due to necessity of correct interpretation by qualified professional (= clinical geneticist), particular categorization of genetic data within the database is discussed. The function of proposed database has to be governed in concordance with the Czech legislation together with solving ethical problems.

  3. Competitive ability of black common bean genotypes with weeds

    Directory of Open Access Journals (Sweden)

    Gilcimar Adriano Vogt

    2013-10-01

    Full Text Available The morpho-physiologic characteristics of common bean plants can affect their competitive ability with weeds. The objective of this work was to evaluate the competitive ability of black bean genotypes with weeds. An experiment was carried out in the 2010/11 cropping season in Papanduva, SC, southern Brazil, in order to verify the variability of some plant characteristics among genotypes of common bean. The randomized block design was used, with four replications. Seven cultivars underwent the treatments: BRS Campeiro, CHP 01-238, CHP 01-239, Diamante Negro, BRS Supremo, BRS Valente, IPR Uirapuru, FTS Soberano, IPR Graúna, IPR Tiziu e IAC Diplomata. At 6, 14, 18, 25 and 32 days after emergence (DAE were evaluated plant height, ground cover by common bean plants, dry biomass of stems and leaves, and grain yield. In the 2011/12 cropping season the same cultivars were grown in the presence or absence of weeds, adopting similar methodology to the 2010/11. The losses of grain yield in black common bean genotypes due to weed interference ranged from 30.8% to 54.9%. There was a positive correlation between yield reduction promoted by the weed infestation and dry biomass produced by the weeds. In addition, there was a positive correlation between percentage of yield reduction due to the weed infestation and grain yield without weed interference. The characteristics evaluated did not estimate the competitive ability of black common bean genotypes with weeds.

  4. Coral host transcriptomic states are correlated with Symbiodinium genotypes

    KAUST Repository

    DeSalvo, Michael K.

    2010-03-01

    A mutualistic relationship between reef-building corals and endosymbiotic dinoflagellates (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. In this study, we monitored Symbiodinium physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered fragments of the coral Montastraea faveolata using a custom cDNA gene expression microarray. Interestingly, gene expression was more similar among samples with the same Symbiodinium content rather than the same experimental condition. In order to discount for host-genotypic effects, we sampled fragments from a single colony of M. faveolata containing different symbiont types, and found that the host transcriptomic states grouped according to Symbiodinium genotype rather than thermal stress. As the first study that links coral host transcriptomic patterns to the clade content of their Symbiodinium community, our results provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-Symbiodinium partnerships. © 2010 Blackwell Publishing Ltd.

  5. Peptostreptococcus micros smooth and rough genotypes in periodontitis and gingivitis

    NARCIS (Netherlands)

    Kremer, BHA; Loos, BG; van der Velden, U; van Winkelhoff, AJ; Craandijk, J; Bulthuis, HM; Hutter, J; Varoufaki, AS; van Steenbergen, TJM

    2000-01-01

    Background: Two genotypes can be distinguished within the species Peptostreptococcus micros: a smooth (Sm) and a rough (Rg) type. To date no systematic study has been performed on the prevalence and proportion of both types in untreated periodontitis patients and subjects without destructive periodo

  6. Speech Characteristics Associated with Three Genotypes of Ataxia

    Science.gov (United States)

    Sidtis, John J.; Ahn, Ji Sook; Gomez, Christopher; Sidtis, Diana

    2011-01-01

    Purpose: Advances in neurobiology are providing new opportunities to investigate the neurological systems underlying motor speech control. This study explores the perceptual characteristics of the speech of three genotypes of spino-cerebellar ataxia (SCA) as manifest in four different speech tasks. Methods: Speech samples from 26 speakers with SCA…

  7. Genotype-phenotype associations in children with congenital hyperinsulinism

    DEFF Research Database (Denmark)

    Melikyan, Maria; Brusgaard, Klaus; Petraykina, Elena

    Congenital hyperinsulinism (CHI) is a heterogeneous disease in terms of clinical presentation, genetics and histology. Mutations in eight genes are known to be a cause of CHI, of which ABCC8, KCNJ11 and GCK are among the most common. We investigated genotype-phenotype associations in a cohort of ...

  8. Hepatitis E Virus Genotype 3 in Humans and Swine, Bolivia

    Science.gov (United States)

    Cavallo, Annalisa; Gonzales, José Luis; Bonelli, Sara Irene; Valda, Ybar; Pieri, Angela; Segundo, Higinio; Ibañez, Ramón; Mantella, Antonia; Bartalesi, Filippo; Tolari, Francesco; Bartoloni, Alessandro

    2011-01-01

    We determined the seroprevalence of hepatitis E virus (HEV) in persons in 2 rural communities in southeastern Bolivia and the presence of HEV in human and swine fecal samples. HEV seroprevalence was 6.3%, and HEV genotype 3 strains with high sequence homology were detected. PMID:21801630

  9. Genotypic characterization of amoeba isolated from Acanthamoeba keratitis in Poland.

    Science.gov (United States)

    Derda, Monika; Solarczyk, Piotr; Cholewiński, Marcin; Hadaś, Edward

    2015-03-01

    Free-living amoebae belonging to the genus Acanthamoeba are the causative factor of many diseases. Among others, they cause Acanthamoeba keratitis (AK), a condition that usually occurs in contact lens wearers, though it is also observed in non-wearers. The number of diagnosed cases of AK increased more than eightfold during 8 years in the USA, and a proportional increase in frequency also occurred in Poland and Europe. Cases of AK are usually diagnosed late, and their therapy is difficult and rarely successful. AK is an uncommon diagnosis in Poland. The increased number of positive cases observed in our laboratory may reflect the growing at-risk population of contact lens wearers. Acanthamoeba as a genus of facultative human parasites is currently classified into 17 genotypes. Isolates belonging to seven genotypes were found to be associated with AK. One genotype in particular, T4, was found to be overrepresented in human disease. The main finding of our study is that in Poland, AK is almost always associated with the T4 genotype.

  10. Behavior of durum wheat genotypes under normal irrigation and ...

    African Journals Online (AJOL)

    AJL

    2012-01-26

    Jan 26, 2012 ... suggested the use of deviations from the linear regression of SSI on ... indices favors genotypes with low yield under non-stress conditions and high ... Ramirez and Kelly (1998) reported that selection based on combination of ...

  11. Genotype-phenotype associations in children with congenital hyperinsulinism

    DEFF Research Database (Denmark)

    Melikyan, Maria; Brusgaard, Klaus; Petraykina, Elena

    Congenital hyperinsulinism (CHI) is a heterogeneous disease in terms of clinical presentation, genetics and histology. Mutations in eight genes are known to be a cause of CHI, of which ABCC8, KCNJ11 and GCK are among the most common. We investigated genotype-phenotype associations in a cohort of ...

  12. Surveillance for Echinococcus canadensis genotypes in Canadian ungulates.

    Science.gov (United States)

    Schurer, Janna; Shury, Todd; Leighton, Frederick; Jenkins, Emily

    2013-12-01

    The geographic and host distribution, prevalence and genotypes of Echinococcus canadensis in wild ungulates in Canada are described to better understand the significance for wildlife and public health. We observed E. canadensis in 10.5% (11/105) of wild elk (wapiti; Cervus canadensis) in Riding Mountain National Park, Manitoba, examined at necropsy, over two consecutive years (2010-2011). Molecular characterization of hydatid cyst material from these elk, as well as three other intermediate wildlife host species, was based on sequence of a 470 bp region of the NADH dehydrogenase subunit 1 (NAD1) mitochondrial gene. In moose [Alces alces], elk, and caribou [Rangifer tarandus] from northwestern Canada, the G10 genotype was the only one present, and the G8 genotype was detected in a muskox (Ovibos moschatus) from northeastern Canada. On a search of the national wildlife health database (1992-2010), cervids with hydatid cysts were reported in all provinces and territories except the Atlantic provinces, from which wolves [Canis lupis] are historically absent. Of the 93 cervids with records of hydatid cysts, 42% were elk, 37% were moose, 14% were caribou, and 6% were white-tailed and mule deer [Odocoileus virginianus and Odocoileus hemonius]. In these animals, 83% of cysts were detected in lungs alone, 8% in both lungs and liver, 3% in liver alone, and 6% in other organs. These observations can help target surveillance programs and contribute to a better understanding of ecology, genetic diversity, and genotype pathogenicity in the Echinococcus granulosus species complex.

  13. The genotype-phenotype correlation in Pompe disease.

    Science.gov (United States)

    Kroos, Marian; Hoogeveen-Westerveld, Marianne; van der Ploeg, Ans; Reuser, Arnold J J

    2012-02-15

    Pompe disease is an autosomal recessive lysosomal glycogen storage disorder that is caused by acid α-glucosidase (GAA) deficiency and is due to pathogenic sequence variations in the corresponding GAA gene. The correlation between genotypes and phenotypes is strict, in that patients with the most severe phenotype, classic infantile Pompe disease, have two pathogenic mutations, one in each GAA allele, that prevent the formation of GAA or totally obliterates its function. All patients with less progressive phenotypes have at least one sequence variation that allows normal or low level synthesis of GAA leading to the formation of analytically measurable, low level GAA activity in most cases. There is an overall trend of finding higher GAA enzyme levels in patients with onset of symptoms in adulthood when compared to patients who show clinical manifestations in early childhood, aged 0-5 years, with a rapidly progressive course, but who lack the severe characteristics of classic infantile Pompe disease. However, several cases have been reported of adult-onset disease with very low GAA activity, which in all those cases corresponds with the GAA genotype. The clinical diversity observed within a large group of patients with functionally the same GAA genotype and the same c.-32-13C > T haplotype demonstrates that modifying factors can have a substantial effect on the clinical course of Pompe disease, disturbing the GAA genotype-phenotype correlation. The present day challenge is to identify these factors and explore them as therapeutic targets.

  14. Nutrient composition of strawberry genotypes cultivated in a horticulture farm.

    Science.gov (United States)

    Hossain, Ashrafi; Begum, Parveen; Salma Zannat, M; Hafizur Rahman, Md; Ahsan, Monira; Islam, Sheikh Nazrul

    2016-05-15

    This article decribes the nutrient composition of four strawberry genotypes cultivated at the Sher-e-Bangla Agriculture University horticulture farm in Dhaka (Bangladesh). AOAC and standard validated methods were employed to analyse the nutrient composition. Protein, fat and ash contents were found to be vary significantly (LSD<0.05), while the variation in moisture (LSD<1.33), dietary fibre (LSD<0.15) and total sugar (LSD<0.09) were found to be insignificant among the genotypes. Vitamin C content ranged from 26.46 mg to 37.77 mg per 100g edible strawberries (LSD<0.060). Amount of carotenoids were found to be very low being in a range of 0.99-3.30 μg per 100g edible fruit. Analysis of mineral revealed that strawberry genotypes contained a wide array of minerals including Ca, Mg, Na, K, P, Mn, Zn, Cu and Fe; most of which varied significantly (LSD<0.05) among the genotypes. Strawberries could be a potential dietary supplement for vitamin C along with minerals, particularly for the children who do not like local fruits, but love to eat the colourful strawberries.

  15. Physiological response of soybean genotypes to plant density

    NARCIS (Netherlands)

    Gan, Y.; Stulen, H.; Keulen, van H.; Kuiper, P.J.C.

    2002-01-01

    Response of soybean (Glycine max (L.) Merr.) to plant density has occupied a segment of agronomic research for most of the century. Genotype differences have been noted especially in response to planting date, lodging problems and water limitation. There is limited information on the physiological g

  16. Root response of Jerusalem artichoke genotypes to different water regimes

    Science.gov (United States)

    The objective of this study was to determine effects of drought on selected root growth parameters and develop relationships between root parameters and tuber yield for selected Jerusalem artichoke (JA) genotypes. Three water regimes (Field capacity, 50% available water (AW) and 25% AW) and five JA...

  17. Protein landmarks for diversity assessment in wheat genotypes

    African Journals Online (AJOL)

    jai ganesha

    1Department of Molecular Biology and Biotechnology, MPUAT Udaipur, Rajasthan, India. ... attributes exhibited the importance of seed storage as a marker system. .... were monomorphic for all genotypes. ..... bands, percent polymorphism Nei's gene diversity (h), Shannon's Information index (I), total genetic diversity.

  18. Selecting additional tag SNPs for tolerating missing data in genotyping

    Directory of Open Access Journals (Sweden)

    Chen Ting

    2005-11-01

    Full Text Available Abstract Background Recent studies have shown that the patterns of linkage disequilibrium observed in human populations have a block-like structure, and a small subset of SNPs (called tag SNPs is sufficient to distinguish each pair of haplotype patterns in the block. In reality, some tag SNPs may be missing, and we may fail to distinguish two distinct haplotypes due to the ambiguity caused by missing data. Results We show there exists a subset of SNPs (referred to as robust tag SNPs which can still distinguish all distinct haplotypes even when some SNPs are missing. The problem of finding minimum robust tag SNPs is shown to be NP-hard. To find robust tag SNPs efficiently, we propose two greedy algorithms and one linear programming relaxation algorithm. The experimental results indicate that (1 the solutions found by these algorithms are quite close to the optimal solution; (2 the genotyping cost saved by using tag SNPs can be as high as 80%; and (3 genotyping additional tag SNPs for tolerating missing data is still cost-effective. Conclusion Genotyping robust tag SNPs is more practical than just genotyping the minimum tag SNPs if we can not avoid the occurrence of missing data. Our theoretical analysis and experimental results show that the performance of our algorithms is not only efficient but the solution found is also close to the optimal solution.

  19. Phenotypic and genotypic characterization of Rhodococcus equi isolated from sputum

    Directory of Open Access Journals (Sweden)

    Paulo da Silva

    Full Text Available INTRODUCTION: Rhodococcus equi is an opportunistic pathogen, causing rhodococcosis, a condition that can be confused with tuberculosis. Often, without identifying M. tuberculosis, physicians initiate empiric treatment for tuberculosis. R. equi and M. tuberculosis have different susceptibility to drugs. Identification of R. equi is based on a variety of phenotypic, chromatographic, and genotypic characteristics. OBJECTIVE: This study aimed to characterize bacterial isolates from sputum samples suggestive of R. equi. METHODS: The phenotypic identification included biochemical assays; thin-layer chromatography (TLC and polymerase chain reaction (PCR were used for genotypic identification. RESULTS: Among 78 Gram-positive and partially acid-fast bacilli isolated from the sputum of tuberculosis-suspected patients, 51 were phenotypically and genotypically characterized as R. equi based on literature data. Mycolic acid analysis showed that all suspected R. equi had compounds with a retention factor (Rf between 0.4-0.5. Genotypic characterization indicated the presence of the choE gene 959 bp fragments in 51 isolates CAMP test positive. Twenty-two CAMP test negative isolates were negative for the choE gene. Five isolates presumptively identified as R. equi, CAMP test positive, were choE gene negative, and probably belonged to other bacterial species. CONCLUSIONS: The phenotypic and molecular techniques used constitute a good methodological tool to identify R. equi.

  20. Phenotypic and genotypic characterization of Rhodococcus equi isolated from sputum.

    Science.gov (United States)

    Silva, Paulo da; Santos, Adolfo Carlos Barreto; Sato, Daisy Nakamura; Silva, Jaqueline Otero; Medeiros, Marta Inês Cazentini; Carneiro, Ana Maria Machado; Leite, Sergio Roberto de Andrade; Leite, Clarice Queico Fujimura

    2012-01-01

    Rhodococcus equi is an opportunistic pathogen, causing rhodococcosis, a condition that can be confused with tuberculosis. Often, without identifying M. tuberculosis, physicians initiate empiric treatment for tuberculosis. R. equi and M. tuberculosis have different susceptibility to drugs. Identification of R. equi is based on a variety of phenotypic, chromatographic, and genotypic characteristics. This study aimed to characterize bacterial isolates from sputum samples suggestive of R. equi. The phenotypic identification included biochemical assays; thin-layer chromatography (TLC) and polymerase chain reaction (PCR) were used for genotypic identification. Among 78 Gram-positive and partially acid-fast bacilli isolated from the sputum of tuberculosis-suspected patients, 51 were phenotypically and genotypically characterized as R. equi based on literature data. Mycolic acid analysis showed that all suspected R. equi had compounds with a retention factor (R(f)) between 0.4-0.5. Genotypic characterization indicated the presence of the choE gene 959bp fragments in 51 isolates CAMP test positive. Twenty-two CAMP test negative isolates were negative for the choE gene. Five isolates presumptively identified as R. equi, CAMP test positive, were choE gene negative, and probably belonged to other bacterial species. The phenotypic and molecular techniques used constitute a good methodological tool to identify R. equi. Copyright © 2012 Elsevier Editora Ltda. All rights reserved.

  1. Comparative analysis of African swine fever virus genotypes and serogroups.

    Science.gov (United States)

    Malogolovkin, Alexander; Burmakina, Galina; Titov, Ilya; Sereda, Alexey; Gogin, Andrey; Baryshnikova, Elena; Kolbasov, Denis

    2015-02-01

    African swine fever virus (ASFV) causes highly lethal hemorrhagic disease among pigs, and ASFV's extreme antigenic diversity hinders vaccine development. We show that p72 ASFV phylogenetic analysis does not accurately define ASFV hemadsorption inhibition assay serogroups. Thus, conventional ASFV genotyping cannot discriminate between viruses of different virulence or predict efficacy of a specific ASFV vaccine.

  2. Genotype and ancestry modulate brain's DAT availability in healthy humans.

    Directory of Open Access Journals (Sweden)

    Elena Shumay

    Full Text Available The dopamine transporter (DAT is a principal regulator of dopaminergic neurotransmission and its gene (the SLC6A3 is a strong biological candidate gene for various behavioral- and neurological disorders. Intense investigation of the link between the SLC6A3 polymorphisms and behavioral phenotypes yielded inconsistent and even contradictory results. Reliance on objective brain phenotype measures, for example, those afforded by brain imaging, might critically improve detection of DAT genotype-phenotype association. Here, we tested the relationship between the DAT brain availability and the SLC6A3 genotypes using an aggregate sample of 95 healthy participants of several imaging studies. These studies employed positron emission tomography (PET with [¹¹C]cocaine wherein the DAT availability was estimated as Bmax/Kd; while the genotype values were obtained on two repeat polymorphisms--3-UTR- and intron 8--VNTRs. The main findings are the following: 1 both polymorphisms analyzed as single genetic markers and in combination (haplotype modulate DAT density in midbrain; 2 ethnic background and age influence the strength of these associations; and 3 age-related changes in DAT availability differ in the 3-UTR and intron 8--genotype groups.

  3. High-Throughput, Large-Scale SNP Genotyping: Bioinformatics Considerations

    OpenAIRE

    Margetic, Nino

    2004-01-01

    In order to provide a high-throughput, large-scale genotyping facility at the national level we have developed a set of inter-dependent information systems. A combination of commercial, publicly-available and in-house developed tools links a series of data repositories based both on flat files and relational databases providing an almost complete semi-automated pipeline.

  4. Potential antioxidant response to coffee — A matter of genotype?

    Directory of Open Access Journals (Sweden)

    Ute Hassmann

    2014-12-01

    Full Text Available In a human intervention study, coffee combining natural green coffee bean constituents and dark roast products was identified as a genotype-dependent inducer of the Nrf2/ARE pathway, significantly affecting Nrf2 gene expression and downstream GST1A1 and UGT1A1 gene transcription. The observed transcriptional changes correlated with the presence of specific Nrf2 genotypes suggesting their influence on both Nrf2 and subsequent ARE-dependent GST1A1 and UGT1A1 transcription. While the presence of the −653 SNP seems to be advantageous, resulting in higher Nrf2, GST1A1 and UGT1A1 gene transcription following coffee consumption, in contrast, the presence of the −651 SNP significantly down-regulated the response to the study coffee. Furthermore, the presence of the B/B genotype in GST1A1 along with the frequency of the [TA]6/6 and [TA]7/7 polymorphisms in UGT1A1 appeared to significantly increase sensitivity toward coffee-induced gene transcription. This data suggests that when examining the role of the Nrf2/ARE pathway in the regulation of antioxidative and chemopreventive phase II efficacy, individual genotypes should be included when considering the potency of bioactive food/food constituents and their therapeutic potential.

  5. Detection of genotype recycling fraud in U.S. immigrants.

    Science.gov (United States)

    Wenk, Robert E

    2011-01-01

    Relationship testing laboratories provide genetic evidence to support or refute claims of kinship between U.S. citizen petitioners and potential immigrant beneficiaries. One female beneficiary presented a male amelogenin type and alleles at 15 autosomal loci that were identical to an alleged brother's. Laboratory records showed that her alleged father had petitioned to have 15 children emigrate from Ghana. The petitioner's 15 paternity indices exceeded 10⁵, but the children shared only four short tandem repeat (STR) profiles, suggesting fraudulent reuse of genotypes in this alleged pedigree (AP). To determine the extent of this "genotype recycling," I examined the laboratory's 555 APs from Ghana and 532 control APs from Nigeria. Seventeen Ghanaian APs (3.1%) but no Nigerian APs showed genotype recycling. Of 90 tested people in the 17 APs, 56 shared identical STR profiles with others in their AP. Of these 56 people, 10 were petitioners with unexpectedly high parentage indices. Seven of 56 had amelogenin types that disagreed with their declared genders. Database searches for identical multilocus genotypes in allegedly different people would best detect this fraud.

  6. Childhood Pompe disease: clinical spectrum and genotype in 31 patients

    NARCIS (Netherlands)

    Capelle, C.I. van; Meijden, J.C. van der; Hout, J.M. van den; Jaeken, J.; Baethmann, M.; Voit, T.; Kroos, M.A.; Derks, T.G.; Rubio-Gozalbo, M.E.; Willemsen, M.A.A.P.; Lachmann, R.H.; Mengel, E.; Michelakakis, H.; Jongste, J.C. de; Reuser, A.J.; Ploeg, A.T. van der

    2016-01-01

    BACKGROUND: As little information is available on children with non-classic presentations of Pompe disease, we wished to gain knowledge of specific clinical characteristics and genotypes. We included all patients younger than 18 years, who had been evaluated at the Pompe Center in Rotterdam, the Net

  7. Childhood Pompe disease: Clinical spectrum and genotype in 31 patients

    NARCIS (Netherlands)

    C.I. van Capelle (Carine); J.C. van der Meijden (J.); J.M.P. van den Hout (Johanna); J. Jaeken; M. Baethmann; T. Voit; M.A. Kroos (Marian); T.G.J. Derks (Terry G J); M.E. Rubio-Gozalbo (Estela); M.A. Willemsen (Michél); R. Lachmann (Robin); E. Mengel; H. Michelakakis (Helen); J.C. de Jongste (Johan); A.J.J. Reuser (Arnold); A.T. van der Ploeg (Ans)

    2016-01-01

    textabstractBackground: As little information is available on children with non-classic presentations of Pompe disease, we wished to gain knowledge of specific clinical characteristics and genotypes. We included all patients younger than 18 years, who had been evaluated at the Pompe Center in Rotter

  8. Childhood Pompe disease : clinical spectrum and genotype in 31 patients

    NARCIS (Netherlands)

    van Capelle, C I; van der Meijden, J C; van den Hout, J M P; Jaeken, J; Baethmann, M; Voit, T; Kroos, M A; Derks, T G J; Rubio-Gozalbo, M E; Willemsen, M A; Lachmann, R H; Mengel, E; Michelakakis, H; de Jongste, J C; Reuser, A J J; van der Ploeg, A T

    2016-01-01

    BACKGROUND: As little information is available on children with non-classic presentations of Pompe disease, we wished to gain knowledge of specific clinical characteristics and genotypes. We included all patients younger than 18 years, who had been evaluated at the Pompe Center in Rotterdam, the Net

  9. Antimicrobial susceptibility and tetracycline resistance determinant genotyping of Gallibacterium anatis

    DEFF Research Database (Denmark)

    Bojesen, Anders M.; Vazquez, Maria E.; Bager, Ragnhild J.;

    2011-01-01

    these figures were 67% and 42%, respectively, for the reference strains.Genotyping of tetracycline resistance determinants was performed with primers specific for tet(A–E, H, K–M, O). Strains positive for tet(B), tet(H) and tet(L) were identified, however, in 20 out of 49 tetracycline resistant strains...

  10. Temperature alters host genotype-specific susceptibility to chytrid infection

    NARCIS (Netherlands)

    Gsell, A.S.; De Senerpont Domis, L.N.; Van Donk, E.; Ibelings, B.W.

    2013-01-01

    The cost of parasitism often depends on environmental conditions and host identity. Therefore, variation in the biotic and abiotic environment can have repercussions on both, species-level host-parasite interaction patterns but also on host genotype-specific susceptibility to disease. We exposed sev

  11. KIR genotype distribution among Lebanese patients with Hodgkin's lymphoma

    Directory of Open Access Journals (Sweden)

    Rouba Hoteit

    2015-06-01

    Conclusion: In this first study from the Mediterranean region, KIR genotype does not seem to be associated with Hodgkin's lymphoma. Further clinical and translational research is needed to rule out the protective or predisposing role of KIR genes in this important clinical entity.

  12. Genotyping of FCN and MBL2 Polymorphisms Using Pyrosequencing

    DEFF Research Database (Denmark)

    Munthe-Fog, Lea; Madsen, Hans Ole; Garred, Peter

    2014-01-01

    Pyrosequencing represents one of the most thorough methods used to analyze polymorphisms. One advantage of using pyrosequencing for genotyping is the ability to identify not only single-nucleotide polymorphisms (SNPs) but also tri-allelic variations, insertions and deletions (InDels). In contrast...

  13. Estimation of partial resistance in potato genotypes against Meloidogyne chitwoodi

    NARCIS (Netherlands)

    Norshie, P.M.; Been, T.H.; Schomaker, C.H.

    2011-01-01

    Three new potato genotypes, designated AR 04-4107, AR 04-4096 and AR 04-4098, with resistance towards Meloidogyne chitwoodi, and the susceptible cv. Désirée were grown at a range of population densities of M. chitwoodi in a climate-controlled glasshouse in order to establish the presence and degree

  14. Human platelet antigen genotyping of platelet donors in southern Brazil.

    Science.gov (United States)

    Merzoni, J; Fagundes, I S; Lunardi, L W; Lindenau, J D-R; Gil, B C; Jobim, M; Dias, V G; Merzoni, L; Sekine, L; Onsten, T G H; Jobim, L F

    2015-10-01

    Human platelet antigens (HPA) are immunogenic structures that result from single nucleotide polymorphisms (SNPs) leading to single amino acid substitutions. This study sought to determine the allele and genotype frequencies of HPA-1, HPA-2, HPA-3, HPA-4, HPA-5 and HPA-15 in platelet donors from the state of Rio Grande do Sul (RS), Brazil, and compare their allele frequencies to those observed in other populations. HPA genotyping was performed by PCR-SSP method. The study sample comprised 201 platelet donors (167 Caucasians and 34 non-Caucasians). Allele 'a' was that most commonly found for HPA-1 to 5 in both groups. The HPA-15ab genotype predominated over homozygous genotypes of this system. Fisher's exact test revealed statistically significant differences for the HPA-5 system, with a greater prevalence of the HPA-5b allele in non-Caucasians. The neighbour-joining method and principal components analysis revealed genetic proximity between our Caucasian group and European populations. We conclude that the allele frequencies of HPA-1 to 5 and HPA-15 found in our Caucasian sample are similar to those reported for European populations. These findings corroborate the ethnic makeup of the population of RS. The higher frequency of the HPA-5b allele found in the non-Caucasian group of our sample suggests the possibility of allosensitization in patients who receive platelet transfusions from genetically incompatible donors.

  15. Speech Characteristics Associated with Three Genotypes of Ataxia

    Science.gov (United States)

    Sidtis, John J.; Ahn, Ji Sook; Gomez, Christopher; Sidtis, Diana

    2011-01-01

    Purpose: Advances in neurobiology are providing new opportunities to investigate the neurological systems underlying motor speech control. This study explores the perceptual characteristics of the speech of three genotypes of spino-cerebellar ataxia (SCA) as manifest in four different speech tasks. Methods: Speech samples from 26 speakers with SCA…

  16. Childhood Pompe disease: Clinical spectrum and genotype in 31 patients

    NARCIS (Netherlands)

    C.I. van Capelle (Carine); J.C. van der Meijden (J.); J.M.P. van den Hout (Johanna); J. Jaeken; M. Baethmann; T. Voit; M.A. Kroos (Marian); T.G.J. Derks (Terry G J); M.E. Rubio-Gozalbo (Estela); M.A. Willemsen (Michél); R. Lachmann (Robin); E. Mengel; H. Michelakakis (Helen); J.C. de Jongste (Johan); A.J.J. Reuser (Arnold); A.T. van der Ploeg (Ans)

    2016-01-01

    textabstractBackground: As little information is available on children with non-classic presentations of Pompe disease, we wished to gain knowledge of specific clinical characteristics and genotypes. We included all patients younger than 18 years, who had been evaluated at the Pompe Center in

  17. Childhood Pompe disease: clinical spectrum and genotype in 31 patients

    NARCIS (Netherlands)

    Capelle, C.I. van; Meijden, J.C. van der; Hout, J.M. van den; Jaeken, J.; Baethmann, M.; Voit, T.; Kroos, M.A.; Derks, T.G.; Rubio-Gozalbo, M.E.; Willemsen, M.A.A.P.; Lachmann, R.H.; Mengel, E.; Michelakakis, H.; Jongste, J.C. de; Reuser, A.J.; Ploeg, A.T. van der

    2016-01-01

    BACKGROUND: As little information is available on children with non-classic presentations of Pompe disease, we wished to gain knowledge of specific clinical characteristics and genotypes. We included all patients younger than 18 years, who had been evaluated at the Pompe Center in Rotterdam, the

  18. Childhood Pompe disease : clinical spectrum and genotype in 31 patients

    NARCIS (Netherlands)

    van Capelle, C I; van der Meijden, J C; van den Hout, J M P; Jaeken, J; Baethmann, M; Voit, T; Kroos, M A; Derks, T G J; Rubio-Gozalbo, M E; Willemsen, M A; Lachmann, R H; Mengel, E; Michelakakis, H; de Jongste, J C; Reuser, A J J; van der Ploeg, A T

    2016-01-01

    Background: As little information is available on children with non-classic presentations of Pompe disease, we wished to gain knowledge of specific clinical characteristics and genotypes. We included all patients younger than 18 years, who had been evaluated at the Pompe Center in Rotterdam, the

  19. Tamarix (Tamaricaceae) hybrids: most dominant invasive genotype in southern Africa

    Science.gov (United States)

    Hybridization can potentially enhance invasiveness. Tamarix (Tamaricaceae) hybrids appear to be the dominant genotypes in their invasions. Exotic Tamarix are declared invasive in South Africa and the exotic T. chinensis and T. ramosissima are known to hybridize between themselves, and with the nativ...

  20. Coral host transcriptomic states are correlated with Symbiodinium genotypes.

    Science.gov (United States)

    DeSalvo, M K; Sunagawa, S; Fisher, P L; Voolstra, C R; Iglesias-Prieto, R; Medina, M

    2010-03-01

    A mutualistic relationship between reef-building corals and endosymbiotic dinoflagellates (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. In this study, we monitored Symbiodinium physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered fragments of the coral Montastraea faveolata using a custom cDNA gene expression microarray. Interestingly, gene expression was more similar among samples with the same Symbiodinium content rather than the same experimental condition. In order to discount for host-genotypic effects, we sampled fragments from a single colony of M. faveolata containing different symbiont types, and found that the host transcriptomic states grouped according to Symbiodinium genotype rather than thermal stress. As the first study that links coral host transcriptomic patterns to the clade content of their Symbiodinium community, our results provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-Symbiodinium partnerships.

  1. Molecular characterization of Bartonella vinsonii subsp. berkhoffii genotype III.

    Science.gov (United States)

    Cadenas, Maria B; Bradley, Julie; Maggi, Ricardo G; Takara, Matt; Hegarty, Barbara C; Breitschwerdt, Edward B

    2008-05-01

    The molecular characterization of a Bartonella vinsonii subsp. berkhoffii genotype III strain (NCSU strain 06-CO1) isolated from the blood of a military working dog diagnosed with endocarditis is reported in this study. Several genes were amplified and sequenced for comparative sequence similarity with other strains.

  2. Distribution of Candida albicans genotypes among family members

    Science.gov (United States)

    Mehta, S. K.; Stevens, D. A.; Mishra, S. K.; Feroze, F.; Pierson, D. L.

    1999-01-01

    Thirty-three families (71 subjects) were screened for the presence of Candida albicans in mouthwash or stool specimens; 12 families (28 subjects) were culture-positive for this yeast. An enrichment procedure provided a twofold increase in the recovery of C. albicans from mouthwash specimens. Nine of the twelve culture-positive families had two positive members each, two families had three positive members each, and one family had four positive members. Genetic profiles were obtained by three methods: pulsed-field gel electrophoresis; restriction endonuclease analysis, and random amplification of polymorphic DNA analysis. DNA fingerprinting of C. albicans isolated from one body site three consecutive times revealed that each of the 12 families carried a distinct genotype. No two families shared the same strain, and two or more members of a family commonly shared the same strain. Intrafamily genotypic identity (i.e., each member within the family harbored the same strain) was demonstrated in six families. Genotypes of isolates from husband and wife differed from one another in five families. All three methods were satisfactory in determining genotypes; however, we concluded that restriction endonuclease analysis provided adequate resolving power.

  3. ACE Gene DD Genotype Association with Obesity in Pakistani Population

    Directory of Open Access Journals (Sweden)

    Amara Javaid

    2011-05-01

    Full Text Available The renin-angiotensin system (RAS has an established role in pathogenesis of metabolic etiologies. Angiotensin converting enzyme (ACE is an important component of RAS that may influence metabolic outcomes in adipose tissue. The deletion “D allele”, of ACE gene I/D (insertion/deletion polymorphism has been shown to be associated with rise in the serum level of ACE. This study is designed to correlate the association between ACE gene I/D polymorphism and obesity in adult population of Pakistan. Our study included 535 individuals; 147 normal with body mass index (BMI 19-24.9, 183 overweight (BMI 26-29.9 and 205 obese (BMI > 30. The individuals were genotyped for ACE gene I/D polymorphism. The ratio of ACE gene II and ID genotypes were not significantly different among normal, overweight and obese individuals. However, the DD genotype in normal, overweight and obese individuals was 12.9%, 18.0% and 28.8% respectively. DD genotype is significantly high (P = 0.002 in obese than in overweight and normal individuals. Thus the results of this study may suggest a possible association of the D allele in adipogenesis and adipocyte metabolism by affecting the ACE plasma level.

  4. SHOOT AND ROOT EVALUATIONS ON SEEDLINGS FROM Coffea GENOTYPES

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    RAMOS LUIS CARLOS DA SILVA

    1997-01-01

    Full Text Available Roots and shoots from seedlings of 29 coffee genotypes were studied to better characterize the entries from the Coffea germplasm bank of the Instituto Agronômico (IAC, Campinas, State of São Paulo, Brasil. The varieties were seeded in a randomized complete block design with 6 replications and 10 plants per plot. The characters evaluated were: plant (PL, shoot (SL and root (RL length; total plant (PDM, shoot (SDM, root (RDM and lateral root (LRDM dry matter. A lateral root index (LRI and shoot root dry matter (SRDM = SDM/RDM and length ratios; (SRL = SL/RL were calculated. The dwarf varieties (Catuaí, Icatu-caturra, Vila Sarchi, San Ramon, Vila Lobos, São Bernardo presented higher LRDM and lower SDM than the normal size varieties such as Mundo Novo, Bourbon Vermelho, Arábica, Amarelo de Botucatu, Glaucia, etc. The varieties Macrodiscus, Icatu-caturra, Bourbon Amarelo, Vila Lobos and C. congensis showed higher root development related to shoot. The Arábica coffee standard variety showed intermediary root and shoot development. Genotypes of high yield background were higher in SL and SDM, while the dwarf types had only lower SL than the normal ones, but higher RL and dry matters. Seedlings from genotypes of known higher field drought tolerance had lower SL and RL, but higher RDM. Significant phenotypic and genotypic correlation coefficients were obtained, such the genotypes for PL and PDM (r = 0.64; P = 0.01, SL and SDM (r = 0.40; P = 0.05, SDM and LRDM (r = 0.52; P = 0.05, RDM and LRI (r = 0.68; P = 0.01, LRI and SRDM (r = 0.85; P = 0.01 and LRI and LRDM (r = 0.84; P = 0.01. High genotypic correlations suggest that selection directed to one character will directly affect the other. Conversely, low or non-significant correlations suggest independence of association, an indication that it would be possible to select two characteristics to diverse directions. Selection could be done towards different goals to change root and shoot measures

  5. Lactase persistence genotypes and malaria susceptibility in Fulani of Mali

    Directory of Open Access Journals (Sweden)

    Dolo Amagana

    2011-01-01

    Full Text Available Abstract Background Fulani are a widely spread African ethnic group characterized by lower susceptibility to Plasmodium falciparum, clinical malaria morbidity and higher rate of lactase persistence compared to sympatric tribes. Lactase non-persistence, often called lactose intolerance, is the normal condition where lactase activity in the intestinal wall declines after weaning. Lactase persistence, common in Europe, and in certain African people with traditions of raising cattle, is caused by polymorphisms in the enhancer region approximately 14 kb upstream of the lactase gene. Methods To evaluate the relationship between malaria and lactase persistence genotypes, a 400 bp region surrounding the main European C/T-13910 polymorphism upstream of the lactase gene was sequenced. DNA samples used in the study originated from 162 Fulani and 79 Dogon individuals from Mali. Results Among 79 Dogon only one heterozygote of the lactase enhancer polymorphism was detected, whereas all others were homozygous for the ancestral C allele. Among the Fulani, the main European polymorphism at locus C/T-13910 was by far the most common polymorphism, with an allele frequency of 37%. Three other single-nucleotide polymorphisms were found with allele frequencies of 3.7%, 1.9% and 0.6% each. The novel DNA polymorphism T/C-13906 was seen in six heterozygous Fulani. Among the Fulani with lactase non-persistence CC genotypes at the C/T-13910 locus, 24% had malaria parasites detectable by microscopy compared to 18% for lactase persistent genotypes (P = 0.29. Pooling the lactase enhancer polymorphisms to a common presumptive genotype gave 28% microscopy positives for non-persistent and 17% for others (P = 0.11. Conclusions Plasmodium falciparum parasitaemia in asymptomatic Fulani is more common in individuals with lactase non-persistence genotypes, but this difference is not statistically significant. The potential immunoprotective properties of dietary cow milk as a reason

  6. "GenotypeColour™": colour visualisation of SNPs and CNVs

    Directory of Open Access Journals (Sweden)

    Magri Chiara

    2009-02-01

    Full Text Available Abstract Background The volume of data available on genetic variations has increased considerably with the recent development of high-density, single-nucleotide polymorphism (SNP arrays. Several software programs have been developed to assist researchers in the analysis of this huge amount of data, but few can rely upon a whole genome variability visualisation system that could help data interpretation. Results We have developed GenotypeColour™ as a rapid user-friendly tool able to upload, visualise and compare the huge amounts of data produced by Affymetrix Human Mapping GeneChips without losing the overall view of the data. Some features of GenotypeColour™ include visualising the entire genome variability in a single screenshot for one or more samples, the simultaneous display of the genotype and Copy Number state for thousands of SNPs, and the comparison of large amounts of samples by producing "consensus" images displaying regions of complete or partial identity. The software is also useful for genotype analysis of trios and to show regions of potential uniparental disomy (UPD. All information can then be exported in a tabular format for analysis with dedicated software. At present, the software can handle data from 10 K, 100 K, 250 K, 5.0 and 6.0 Affymetrix chips. Conclusion We have created a software that offers a new way of displaying and comparing SNP and CNV genomic data. The software is available free at http://www.med.unibs.it/~barlati/GenotypeColour and is especially useful for the analysis of multiple samples.

  7. Identification of novel Coxiella burnetii genotypes from Ethiopian ticks.

    Directory of Open Access Journals (Sweden)

    Kinga M Sulyok

    Full Text Available BACKGROUND: Coxiella burnetii, the etiologic agent of Q fever, is a highly infectious zoonotic bacterium. Genetic information about the strains of this worldwide distributed agent circulating on the African continent is limited. The aim of the present study was the genetic characterization of C. burnetii DNA samples detected in ticks collected from Ethiopian cattle and their comparison with other genotypes found previously in other parts of the world. METHODOLOGY/PRINCIPAL FINDINGS: A total of 296 tick samples were screened by real-time PCR targeting the IS1111 region of C. burnetii genome and from the 32 positive samples, 8 cases with sufficient C. burnetii DNA load (Amblyomma cohaerens, n = 6; A. variegatum, n = 2 were characterized by multispacer sequence typing (MST and multiple-locus variable-number tandem repeat analysis (MLVA. One novel sequence type (ST, the proposed ST52, was identified by MST. The MLVA-6 discriminated the proposed ST52 into two newly identified MLVA genotypes: type 24 or AH was detected in both Amblyomma species while type 26 or AI was found only in A. cohaerens. CONCLUSIONS/SIGNIFICANCE: Both the MST and MLVA genotypes of the present work are closely related to previously described genotypes found primarily in cattle samples from different parts of the globe. This finding is congruent with the source hosts of the analyzed Ethiopian ticks, as these were also collected from cattle. The present study provides genotype information of C. burnetii from this seldom studied East-African region as well as further evidence for the presumed host-specific adaptation of this agent.

  8. Genotypes and antibiotic resistance of canine Campylobacter jejuni isolates.

    Science.gov (United States)

    Amar, Chantal; Kittl, Sonja; Spreng, David; Thomann, Andreas; Korczak, Bożena M; Burnens, André P; Kuhnert, Peter

    2014-01-10

    Campylobacter jejuni is the most important cause of bacterial gastroenteritis in humans. It is a commensal in many wild and domestic animals, including dogs. Whereas genotypes of human and chicken C. jejuni isolates have been described in some detail, only little information on canine C. jejuni genotypes is available. To gain more information on genotypes of canine C. jejuni and their zoonotic potential, isolates from routine diagnostics of diarrheic dogs as well as isolates of a prevalence study in non-diarrheic dogs were analyzed. Prevalence of thermophilic Campylobacter among non-diarrheic dogs was 6.3% for C. jejuni, 5.9% for Campylobacter upsaliensis and 0.7% for Campylobacter coli. The C. jejuni isolates were genotyped by multi locus sequence typing (MLST) and flaB typing. Resistance to macrolides and quinolones was genetically determined in parallel. Within the 134 genotyped C. jejuni isolates 57 different sequence types (ST) were found. Five STs were previously unrecognized. The most common STs were ST-48 (11.2%), ST-45 (10.5%) and ST-21 (6.0%). Whereas no macrolide resistance was found, 28 isolates (20.9%) were resistant to quinolones. ST-45 was significantly more prevalent in diarrheic than in non-diarrheic dogs. Within the common time frame of isolation 94% of the canine isolates had a ST that was also found in human clinical isolates. In conclusion, prevalence of C. jejuni in Swiss dogs is low but there is a large genetic overlap between dog and human isolates. Given the close contact between human and dogs, the latter should not be ignored as a potential source of human campylobacteriosis. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. Epigenomics and bolting tolerance in sugar beet genotypes

    Science.gov (United States)

    Hébrard, Claire; Peterson, Daniel G.; Willems, Glenda; Delaunay, Alain; Jesson, Béline; Lefèbvre, Marc; Barnes, Steve; Maury, Stéphane

    2016-01-01

    In sugar beet (Beta vulgaris altissima), bolting tolerance is an essential agronomic trait reflecting the bolting response of genotypes after vernalization. Genes involved in induction of sugar beet bolting have now been identified, and evidence suggests that epigenetic factors are involved in their control. Indeed, the time course and amplitude of DNA methylation variations in the shoot apical meristem have been shown to be critical in inducing sugar beet bolting, and a few functional targets of DNA methylation during vernalization have been identified. However, molecular mechanisms controlling bolting tolerance levels among genotypes are still poorly understood. Here, gene expression and DNA methylation profiles were compared in shoot apical meristems of three bolting-resistant and three bolting-sensitive genotypes after vernalization. Using Cot fractionation followed by 454 sequencing of the isolated low-copy DNA, 6231 contigs were obtained that were used along with public sugar beet DNA sequences to design custom Agilent microarrays for expression (56k) and methylation (244k) analyses. A total of 169 differentially expressed genes and 111 differentially methylated regions were identified between resistant and sensitive vernalized genotypes. Fourteen sequences were both differentially expressed and differentially methylated, with a negative correlation between their methylation and expression levels. Genes involved in cold perception, phytohormone signalling, and flowering induction were over-represented and collectively represent an integrative gene network from environmental perception to bolting induction. Altogether, the data suggest that the genotype-dependent control of DNA methylation and expression of an integrative gene network participate in bolting tolerance in sugar beet, opening up perspectives for crop improvement. PMID:26463996

  10. Lactase persistence genotypes and malaria susceptibility in Fulani of Mali.

    Science.gov (United States)

    Lokki, A Inkeri; Järvelä, Irma; Israelsson, Elisabeth; Maiga, Bakary; Troye-Blomberg, Marita; Dolo, Amagana; Doumbo, Ogobara K; Meri, Seppo; Holmberg, Ville

    2011-01-14

    Fulani are a widely spread African ethnic group characterized by lower susceptibility to Plasmodium falciparum, clinical malaria morbidity and higher rate of lactase persistence compared to sympatric tribes. Lactase non-persistence, often called lactose intolerance, is the normal condition where lactase activity in the intestinal wall declines after weaning. Lactase persistence, common in Europe, and in certain African people with traditions of raising cattle, is caused by polymorphisms in the enhancer region approximately 14 kb upstream of the lactase gene. To evaluate the relationship between malaria and lactase persistence genotypes, a 400 bp region surrounding the main European C/T-13910 polymorphism upstream of the lactase gene was sequenced. DNA samples used in the study originated from 162 Fulani and 79 Dogon individuals from Mali. Among 79 Dogon only one heterozygote of the lactase enhancer polymorphism was detected, whereas all others were homozygous for the ancestral C allele. Among the Fulani, the main European polymorphism at locus C/T-13910 was by far the most common polymorphism, with an allele frequency of 37%. Three other single-nucleotide polymorphisms were found with allele frequencies of 3.7%, 1.9% and 0.6% each. The novel DNA polymorphism T/C-13906 was seen in six heterozygous Fulani. Among the Fulani with lactase non-persistence CC genotypes at the C/T-13910 locus, 24% had malaria parasites detectable by microscopy compared to 18% for lactase persistent genotypes (P = 0.29). Pooling the lactase enhancer polymorphisms to a common presumptive genotype gave 28% microscopy positives for non-persistent and 17% for others (P = 0.11). Plasmodium falciparum parasitaemia in asymptomatic Fulani is more common in individuals with lactase non-persistence genotypes, but this difference is not statistically significant. The potential immunoprotective properties of dietary cow milk as a reason for the partial malaria resistance of Fulani warrant further

  11. Molecular Characterization of Prunus angustifolia Genotypes from Turkey.

    Science.gov (United States)

    Akbulut, Mustafa; Polat, Mehmet; Ercisli, Sezai; Sorkheh, Karim

    2016-08-25

    Prunus angustifolia var. angustifolia is a deciduous shrub with 1.5-3.0 m plant height and mostly found in rural areas between 1400 and 1600 m in northeastern Turkey including Bayburt, Gumushane, and Kars provinces. The plant has multistems and well known to adapt severe winter and dry-hot summer conditions. In this study, we aimed to explore the genetic diversity within this specie and also to investigate its phylogenetic relationship with economically important the other cherry species; Prunus avium, Prunus cerasus, Prunus laurocerasus, and Prunus mahaleb. A total of 50 simple sequence repeats (SSRs) markers used to elucidate the genetic variation among 32 P. angustifolia var. angustifolia genotypes selected from three locations (Bayburt, Gumushane, and Kars) in northeastern Turkey. The cross-species transportability of used 50 SSRs was 80 % indicating a high degree of homology between P. angustifolia and the other Prunus species. The genetic distance between P. angustifolia var. angustifolia genotypes belonging to a particular geographic site was lower than that between genotypes of different geographic origins. Cluster analysis in general differentiated P. angustifolia var. angustifolia genotypes according to their geographic sites and separated them from the other Prunus species. P. angustifolia found more closer to P. mahaleb and P. cerasus, in the subgenus Cerasus, The analysis of molecular variance revealed that genetic variation among individuals within populations was much higher than among Prunus groups and among P. angustifolia var. angustifolia populations of different geographic sites. The results indicate a substantial genetic diversity in P. angustifolia var. angustifolia and the need of exploring a wider area to increase the chance of finding a particular genotype.

  12. Genotyping and surveillance for scrapie in Finnish sheep

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    Hautaniemi Maria

    2012-07-01

    Full Text Available Abstract Background The progression of scrapie is known to be influenced by the amino acid polymorphisms of the host prion protein (PrP gene. There is no breeding programme for TSE resistance in sheep in Finland, but a scrapie control programme has been in place since 1995. In this study we have analysed PrP genotypes of total of 928 purebred and crossbred sheep together with the data of scrapie survey carried out in Finland during 2002–2008 in order to gain knowledge of the genotype distribution and scrapie prevalence in Finnish sheep. Results The ARQ/ARQ genotype was the most common genotype in all breeds studied. ARR allele frequency was less than 12% in purebred Finnish sheep and in most genotypes heterozygous for ARR, the second allele was ARQ. The VRQ allele was not detected in the Grey race sheep of Kainuu or in the Aland sheep, and it was present in less than 6% of the Finnish Landrace sheep. Leucine was the most prominent amino acid found in codon 141. In addition, one novel prion dimorphisms of Q220L was detected. During the scrapie survey of over 15 000 sheep in 2002–2008, no classical scrapie cases and only five atypical scrapie cases were detected. Conclusions The results indicate that the Finnish sheep populations have genetically little resistance to classical scrapie, but no classical scrapie was detected during an extensive survey in 2002–2008. However, five atypical scrapie cases emerged; thus, the disease is present in the Finnish sheep population at a low level.

  13. Genotype and phylogenetic characterization of hepatitis B virus among multi-ethnic cohort in Hawaii

    Institute of Scientific and Technical Information of China (English)

    Mayumi Sakurai; Fuminaka Sugauchi; Naoky Tsai; Seiji Suzuki; Izumi Hasegawa; Kei Fujiwara; Etsuro Orito; Ryuzo Ueda; Masashi Mizokami

    2004-01-01

    AIM: Hepatitis B virus (HBV) genomes in carriers from Hawaii have not been evaluated previously. The aim of the present study was to evaluate the distribution of HBV genotypes and their clinical relevance in Hawaii.METHODS: Genotyping of HBV among 61 multi-ethnic carriers in Hawaii was performed by genetic methods.Three complete genomes and 61 core promoter/precore regions of HBV were sequenced directly.RESULTS: HBV genotype distribution among the 61 carriers was 23.0% for genotype A, 14.7% for genotype B and 62.3% for genotype C. Genotypes A, B and C were obtained from the carriers whose ethnicities were Filipino and Caucasian,Southeast Asian, and various Asian and Micronesian,respectively. All cases of genotype B were composed of recombinant strains with genotype C in the precore plus core region named genotype Ba. HBeAg was detected more frequently in genotype C than in genotype B (68.4% vs 33.3%, P<0.05) and basal core promoter (BCP) mutation (T1762/A1764) was more frequently found in genotype C than in genotype B. Twelve of the 38 genotype C strains possessed C at nucleotide (nt) position 1858 (C-1858).However there was no significant difference in clinical characteristics between C-1858 and T-1858 variants. Based on complete genome sequences, phylogenetic analysis revealed one patient of Micronesian ethnicity as having C-1858 clustered with two isolates from Polynesia with T-1858.In addition, two strains from Asian ethnicities were clustered with known isolates in carriers from Southeast Asia.CONCLUSION: Genotypes A, B and C are predominant types among multi-ethnic HBV carriers in Hawaii, and distribution of HBV genotypes is dependent on the ethnic background of the carriers in Hawaii.

  14. Distribution of Hepatitis C Virus Genotypes in the South Marmara Region

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    Harun Agca

    2014-03-01

    Full Text Available Aim: Hepatitis C virus (HCV is an important caustive agent of hepatitis, cirrhosis and hepatocellular carcinoma both in our country and the world. Prognosis and response to treatment is related with the genotype of HCV which has six genotypes and over a hundred quasispecies. Knowing the HCV genotype is also important for epidemiological data. In this study we aimed to investigate the HCV genotypes of samples sent to Uludag University Hospital Microbiology Laboratory which is the reference centre in the South Marmara Region. Material and Method: This study was done retrospectively to analyse the HCV patients%u2019 sera sent to our laboratory between July 2010and December 2012 for HCV genotyping. Artus HCV QS-RGQ PCR kit (Qiagene,Hilden, Germany was used in Rotor-Gene Q (Qiagene, Hilden Germany for detection of HCV RNA. HCV RNA positive samples of patients%u2019 sera were were used for genotyping by the Linear Array HCV genotyping test (Roche, NJ, USA.Results: 214 (92.6 % of total 231 patients included in the study were genotype 1, one (0.4 % was genotype 2, nine (3.9 % were genotype 3 and, seven (3.4 % were found genotype 4. Three of genotype 3 patients were of foreign nationality, two were born abroad and one of the genotype 4 patients were born abroad. Discussion: Concordant with our country data the most frequent genotype was 1, genotype 2 was seen in patients especially related with foreign countries and genotype 4 was seen rare. The importance of genotype 1, which is seen more frequent in our country and region is; resistance to antiviral treatment and prolonged treatment duration in chronic hepatitis C patients.

  15. A novel hepatitis C virus genotyping method based on liquid microarray.

    Directory of Open Access Journals (Sweden)

    Cesar A B Duarte

    Full Text Available The strategy used to treat HCV infection depends on the genotype involved. An accurate and reliable genotyping method is therefore of paramount importance. We describe here, for the first time, the use of a liquid microarray for HCV genotyping. This liquid microarray is based on the 5'UTR - the most highly conserved region of HCV - and the variable region NS5B sequence. The simultaneous genotyping of two regions can be used to confirm findings and should detect inter-genotypic recombination. Plasma samples from 78 patients infected with viruses with genotypes and subtypes determined in the Versant™ HCV Genotype Assay LiPA (version I; Siemens Medical Solutions, Diagnostics Division, Fernwald, Germany were tested with our new liquid microarray method. This method successfully determined the genotypes of 74 of the 78 samples previously genotyped in the Versant™ HCV Genotype Assay LiPA (74/78, 95%. The concordance between the two methods was 100% for genotype determination (74/74. At the subtype level, all 3a and 2b samples gave identical results with both methods (17/17 and 7/7, respectively. Two 2c samples were correctly identified by microarray, but could only be determined to the genotype level with the Versant™ HCV assay. Genotype "1" subtypes (1a and 1b were correctly identified by the Versant™ HCV assay and the microarray in 68% and 40% of cases, respectively. No genotype discordance was found for any sample. HCV was successfully genotyped with both methods, and this is of prime importance for treatment planning. Liquid microarray assays may therefore be added to the list of methods suitable for HCV genotyping. It provides comparable results and may readily be adapted for the detection of other viruses frequently co-infecting HCV patients. Liquid array technology is thus a reliable and promising platform for HCV genotyping.

  16. Further evidence of hepatitis B virus genotype I circulation in Northeast India.

    Science.gov (United States)

    Ismail, Ashrafali Mohamed; Goel, Ashish; Kannangai, Rajesh; Abraham, Priya

    2013-08-01

    Hepatitis B virus (HBV) genotypes have known to show a geographical pattern in their distribution and have been used to trace the migration of populations from geographically distant regions. Novel recombinants between HBV genotypes A, G and C referred as genotype I has been recently reported from Eastern India. In our investigation to characterise antiviral resistance mutations, we identified a rare case of HBV genotype I infection in chronic hepatitis B subject. We encountered confounding results of this emerging genotype 'designated as genotype G' in three widely used HBV sequence database for genotype determination. The recombinant fragment of genotype G largely occupies the surface gene sequence of the newly identified genotype I and could hence lead to misclassification of genotype I. Additionally, recombination analysis of the generated sequences in Simplot and jpHMM model showed two different patterns of recombination events. In conclusion, the increasing recognition of genotype I in this population suggests that further studies may reveal uncommon genotypes from other geographically distant regions. Our observation of potential genotype I misclassification despite the use of public HBV sequence database and other recombination analysis tools highlights the need for updating and validating public sequence domains of diagnostic importance.

  17. Prevalence of hepatitis C genotypes in patients with hepatitis C in Lorestan province (2009-2013

    Directory of Open Access Journals (Sweden)

    Mohammad Reza Nazer

    2014-05-01

    Full Text Available Background: Determining hepatitis C genotypes is important to detect the various aspects of this infection, including its epidemiology, pathogenesis and response to anti-viral treatments. The aim of this study was to investigate the prevalence of hepatitis C genotypes in patients admitted to the Infectious Diseases Clinic in Khorramabad. Methods: Out of all the patients admitted to the Infectious Disease Clinic in Khorramabad in a four-year period (April 2009 to March 2013, 120 patients who met the inclusion criteria of the study were evaluated. The PCR method was used to examine the serums of the patients with hepatitis C in terms of the type of genotype. Results: Out of 120 patients, 101 (84.2% were male and 19 (15.8% were female. The most prevalent genotypes were 3a (65%, 1a (24.2%, 1a/1b (5%, and 2 (1.7%, respectively. The genotypes of 5 patients (4.2% could not be determined. No significant relationships were found between gender and genotype, and age group and genotype. Moreover, 18.3% of the patients were HIV-positive. Conclusion: In this study, genotype 3a, the most prevalent genotype, was not consistent with the prevalent genotypes in Arab, European, American, and African countries. Furthermore, genotype 1a was the second most prevalent genotype, while it has been reported as the most prevalent genotype by numerous studies conducted in Iran.

  18. Exploring genotype concordance in epidemiologically linked cases of tuberculosis in New York City.

    Science.gov (United States)

    Robbins, R S; Perri, B R; Ahuja, S D; Anger, H A; Sullivan Meissner, J; Shashkina, E; Kreiswirth, B N; Proops, D C

    2017-02-01

    Comparing genotype results of tuberculosis (TB) isolates from individuals diagnosed with TB can support or refute transmission; however, these conclusions are based upon the criteria used to define a genotype match. We used a genotype-match definition which allowed for variation in IS6110 restriction fragment length polymorphism (RFLP) to support transmission between epidemiologically linked persons. Contacts of individuals with infectious TB (index cases) diagnosed in New York City from 1997 to 2003 who subsequently developed TB (contact cases) from 1997 to 2007 were identified. For each contact case and index case (case-pair), isolate genotypes (spoligotype and RFLP results) were evaluated. Isolates from case-pairs were classified as exact or non-exact genotype match. Genotypes from non-exact match case-pairs were reviewed at the genotyping laboratory to determine if the isolates met the near-genotype-match criteria (exactly matching spoligotype and similar RFLP banding patterns). Of 118 case-pairs identified, isolates from 83 (70%) had exactly matching genotypes and 14 (12%) had nearly matching genotypes (supporting transmission), while the remaining 21 (18%) case-pairs had discordant genotypes (refuting transmission). Using identical genotype-match criteria for isolates from case-pairs epidemiologically linked through contact investigation may lead to underestimation of transmission. TB programmes should consider the value of expanding genotype-match criteria to more accurately assess transmission between such cases.

  19. NS4A protein as a marker of HCV history suggests that different HCV genotypes originally evolved from genotype 1b.

    Science.gov (United States)

    Sarwar, Muhammad T; Kausar, Humera; Ijaz, Bushra; Ahmad, Waqar; Ansar, Muhammad; Sumrin, Aleena; Ashfaq, Usman A; Asad, Sultan; Gull, Sana; Shahid, Imran; Hassan, Sajida

    2011-06-23

    The 9.6 kb long RNA genome of Hepatitis C virus (HCV) is under the control of RNA dependent RNA polymerase, an error-prone enzyme, for its transcription and replication. A high rate of mutation has been found to be associated with RNA viruses like HCV. Based on genetic variability, HCV has been classified into 6 different major genotypes and 11 different subtypes. However this classification system does not provide significant information about the origin of the virus, primarily due to high mutation rate at nucleotide level. HCV genome codes for a single polyprotein of about 3011 amino acids which is processed into structural and non-structural proteins inside host cell by viral and cellular proteases. We have identified a conserved NS4A protein sequence for HCV genotype 3a reported from four different continents of the world i.e. Europe, America, Australia and Asia. We investigated 346 sequences and compared amino acid composition of NS4A protein of different HCV genotypes through Multiple Sequence Alignment and observed amino acid substitutions C22, V29, V30, V38, Q46 and Q47 in NS4A protein of genotype 1b. Furthermore, we observed C22 and V30 as more consistent members of NS4A protein of genotype 1a. Similarly Q46 and Q47 in genotype 5, V29, V30, Q46 and Q47 in genotype 4, C22, Q46 and Q47 in genotype 6, C22, V38, Q46 and Q47 in genotype 3 and C22 in genotype 2 as more consistent members of NS4A protein of these genotypes. So the different amino acids that were introduced as substitutions in NS4A protein of genotype 1 subtype 1b have been retained as consistent members of the NS4A protein of other known genotypes. These observations indicate that NS4A protein of different HCV genotypes originally evolved from NS4A protein of genotype 1 subtype 1b, which in turn indicate that HCV genotype 1 subtype 1b established itself earlier in human population and all other known genotypes evolved later as a result of mutations in HCV genotype 1b. These results were further

  20. NS4A protein as a marker of HCV history suggests that different HCV genotypes originally evolved from genotype 1b

    Directory of Open Access Journals (Sweden)

    Asad Sultan

    2011-06-01

    Full Text Available Abstract Background The 9.6 kb long RNA genome of Hepatitis C virus (HCV is under the control of RNA dependent RNA polymerase, an error-prone enzyme, for its transcription and replication. A high rate of mutation has been found to be associated with RNA viruses like HCV. Based on genetic variability, HCV has been classified into 6 different major genotypes and 11 different subtypes. However this classification system does not provide significant information about the origin of the virus, primarily due to high mutation rate at nucleotide level. HCV genome codes for a single polyprotein of about 3011 amino acids which is processed into structural and non-structural proteins inside host cell by viral and cellular proteases. Results We have identified a conserved NS4A protein sequence for HCV genotype 3a reported from four different continents of the world i.e. Europe, America, Australia and Asia. We investigated 346 sequences and compared amino acid composition of NS4A protein of different HCV genotypes through Multiple Sequence Alignment and observed amino acid substitutions C22, V29, V30, V38, Q46 and Q47 in NS4A protein of genotype 1b. Furthermore, we observed C22 and V30 as more consistent members of NS4A protein of genotype 1a. Similarly Q46 and Q47 in genotype 5, V29, V30, Q46 and Q47 in genotype 4, C22, Q46 and Q47 in genotype 6, C22, V38, Q46 and Q47 in genotype 3 and C22 in genotype 2 as more consistent members of NS4A protein of these genotypes. So the different amino acids that were introduced as substitutions in NS4A protein of genotype 1 subtype 1b have been retained as consistent members of the NS4A protein of other known genotypes. Conclusion These observations indicate that NS4A protein of different HCV genotypes originally evolved from NS4A protein of genotype 1 subtype 1b, which in turn indicate that HCV genotype 1 subtype 1b established itself earlier in human population and all other known genotypes evolved later as a result of

  1. The impact in older women of ovarian FMR1 genotypes and sub-genotypes on ovarian reserve.

    Directory of Open Access Journals (Sweden)

    Norbert Gleicher

    Full Text Available We recently associated ovarian FMR1genotypes and sub-genotypes with distinct ovarian aging patterns. How they impact older females is, however, unknown. We, therefore, investigated 217 consecutive first in vitro fertilization (IVF cycles in women >40 assessing oocyte yields, stratified for better (anti-Müllerian hormone, AMH >1.05 ng/mL or poorer (AMH ≤ 1.05 ng/mL functional reserve (FOR. Mean age was 42.4 ± 2.0 years, mean AMH 0.76 ± 0.92 ng/mL and mean oocyte yield 5.3 ± 5.4. Overall, and in women with better FOR, FMR1 did not affect oocyte yields. With poorer FOR (AMH ≤ 1.05 ng/mL women with het-norm/high, however, demonstrated higher oocyte yields (5.0 ± 3.8 than those with het-norm/low sub-genotype 3.1 ± 2.5; P = 0.03, confirmed after log conversion. Known associated with low FOR at young age, het-norm/high, thus, appears to preserve FOR into older age, and both het sub-genotypes appear to expand female reproductive lifespan into opposite directions.

  2. Genotyping of human rhinovirus in adult patients with acute respiratory infections identified predominant infections of genotype A21

    Science.gov (United States)

    Ren, Lili; Yang, Donghong; Ren, Xianwen; Li, Mingkun; Mu, Xinlin; Wang, Qi; Cao, Jie; Hu, Ke; Yan, Chunliang; Fan, Hongwei; Li, Xiangxin; Chen, Yusheng; Wang, Ruiqin; An, Fucheng; An, Shuchang; Luo, Ming; Wang, Ying; Xiao, Yan; Xiang, Zichun; Xiao, Yan; Li, Li; Huang, Fang; Jin, Qi; Gao, Zhancheng; Wang, Jianwei

    2017-01-01

    Human rhinovirus (HRV) is an important causative agent of acute respiratory tract infections (ARTIs). The roles of specific HRV genotypes in patients suffering from ARTIs have not been well established. We recruited 147 adult inpatients with community-acquired pneumonia (CAP) and 291 adult outpatients with upper ARTIs (URTIs). Respiratory pathogens were screened via PCR assays. HRV was detected in 42 patients, with 35 species A, five B and two C. Seventeen genotypes were identified, and HRV-A21 ranked the highest (9/42, 21.4%). The HRV-A21-positive infections were detected in four patients with CAP and in five with URTIs, all without co-infections. The HRV-A21 genome sequenced in this study contained 12 novel coding polymorphisms in viral protein (VP) 1, VP2 EF loop, VP3 knob and 3D regions. The infections of HRV-A21 virus obtained in this study could not be neutralized by antiserum of HRV-A21 prototype strain (VR-1131), indicating remarkable antigenic variation. Metagenomic analysis showed the HRV-A21 reads were dominant in bronchoalveolar lavage fluid of the three HRV-A21-positive patients with severe CAP, in which two dead. Our results highlight an unexpected infection of genotype HRV-A21 in the clinic, indicating the necessity of precise genotyping and surveillance of HRVs to improve the clinical management of ARTIs. PMID:28128353

  3. Proteome Differences between Hepatitis B Virus Genotype-B- and Genotype-C-Induced Hepatocellular Carcinoma Revealed by iTRAQ-Based Quantitative Proteomics.

    Science.gov (United States)

    Wei, Dahai; Zeng, Yongyi; Xing, Xiaohua; Liu, Hongzhi; Lin, Minjie; Han, Xiao; Liu, Xiaolong; Liu, Jingfeng

    2016-02-05

    Hepatitis B virus (HBV) is the main cause of hepatocellular carcinoma (HCC) in southeast Asia where HBV genotype B and genotype C are the most prevalent. Viral genotypes have been reported to significantly affect the clinical outcomes of HCC. However, the underlying molecular differences among different genotypes of HBV virus infected HCC have not been revealed. Here, we applied isobaric tags for relative and absolute quantitation (iTRAQ) technology integrated with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify the proteome differences between the HBV genotypes B- and C-induced HCC. In brief, a total of 83 proteins in the surrounding noncancerous tissues and 136 proteins in the cancerous tissues between HBV genotype-B- and genotype-C-induced HCC were identified, respectively. This information revealed that there might be different molecular mechanisms of the tumorigenesis and development of HBV genotypes B- and C-induced HCC. Furthermore, our results indicate that the two proteins ARFIP2 and ANXA1 might be potential biomarkers for distinguishing the HBV genotypes B- and C-induced HCC. Thus, the quantitative proteomic analysis revealed molecular differences between the HBV genotypes B- and C-induced HCC, and might provide fundamental information for further deep study.

  4. Distribution of HBV genotypes among HBV carriers in Benin:phylogenetic analysis and virological characteristics of HBV genotype E

    Institute of Scientific and Technical Information of China (English)

    Kei Fujiwara; Atsushi Ozasa; Yuko Sakamoto; Isao Arita; Ahmed El-Gohary; Agossou Benoit; Sophie I Ogoundele-Akplogan; Namiko Yoshihara; Ryuzo Ueda; Masashi Mizokami; Yasuhito Tanaka; Etsuro Orito; Tomoyoshi Ohno; Takanobu Kato; Kanji Sugihara; Izumi Hasegawa; Mayumi Sakurai; Kiyoaki Ito

    2005-01-01

    AIM: To determine the distribution of Hepatitis B virus (HBV) genotypes in Benin, and to clarify the virological characteristics of the dominant genotype.METHODS: Among 500 blood donors in Benin, 21 HBsAg-positive donors were enrolled in the study. HBV genotypes were determined by enzyme immunoassay and restriction fragment length polymorphism. Complete genome sequences were determined by PCR and direct sequencing.RESULTS: HBV genotype E (HBV/E) was detected in 20/21 (95.2%), and HBV/A in 1/21 (4.8%). From the age-specific prevalence of HBeAg to anti-HBe seroconversion (SC) in 19 HBV/E subjects, SC was estimated to occur frequently in late teens in HBV/E.The comparison of four complete HBV/E genomes from HBeAg-positive subjects in this study and five HBV/E sequences recruited from the database revealed that HBV/E was distributed throughout West Africa with very low genetic divers ity (nucleotide homology 96.7-99.2%).Based on the sequences in the basic core promoter (BCP)to precore region of the nine HBV/E isolates compared to those of the other genotypes, a nucleotide substitution in the BCP, G1757A, was observed in HBV/E.CONCLUSION: HBV/E is predominant in the Republic of Benin, and SC is estimated to occur in late teens in HBV/E. The specific nucleotide substitution G1757A in BCP, which might influence the virological characteristics,is observed in HBV/E.

  5. Likelihood-Based Association Analysis for Nuclear Families and Unrelated Subjects with Missing Genotype Data

    National Research Council Canada - National Science Library

    Dudbridge, Frank

    2008-01-01

    ... by population stratification. Here a novel likelihood for nuclear families is proposed, in which distinct sets of association parameters are used to model the parental genotypes and the offspring genotypes...

  6. Rapid Spread and Diversification of Respiratory Syncytial Virus Genotype ON1, Kenya

    Science.gov (United States)

    Otieno, James R.; Gitahi, Caroline W.; Cane, Patricia A.; Nokes, D. James

    2014-01-01

    Respiratory syncytial virus genotype ON1, which is characterized by a 72-nt duplication in the attachment protein gene, has been detected in >10 countries since first identified in Ontario, Canada, in 2010. We describe 2 waves of genotype ON1 infections among children admitted to a rural hospital in Kenya during 2012. Phylogenetic analysis of attachment protein gene sequences showed multiple introductions of genotype ON1; variants distinct from the original Canadian viruses predominated in both infection waves. The genotype ON1 dominated over the other group A genotypes during the second wave, and some first wave ON1 variants reappeared in the second wave. An analysis of global genotype ON1 sequences determined that this genotype has become considerably diversified and has acquired signature coding mutations within immunogenic regions, and its most recent common ancestor dates to ≈2008–2009. Surveillance of genotype ON1 contributes to an understanding of the mechanisms of rapid emergence of respiratory viruses. PMID:24856417

  7. Sugarcane Genotype Performance in Three Environments (Based on Crop Cycle) at Mardan, Pakistan

    Science.gov (United States)

    Sugarcane breeders often face significant genotype x environment interactions in their trials grown under multiple environments. Hence, genotypes need to be tested for their stability across different environments keeping in view the significant interactions. An experiment comprising 28 sugarcane ge...

  8. Chlamydia trachomatis Genotypes and the Swedish New Variant among Urogenital Chlamydia trachomatis Strains in Finland

    Directory of Open Access Journals (Sweden)

    Suvi Niemi

    2011-01-01

    Full Text Available Our aims were to genotype Chlamydia trachomatis strains present in urogenital samples and to investigate the occurrence of the Swedish new variant of C. trachomatis in Finland. We genotyped 160 C. trachomatis positive samples with ompA real-time PCR and analyzed 495 samples for the new variant. The three most prevalent genotypes were E (40%, F (28%, and G (13%. Only two specimens containing bacteria with the variant plasmid were detected. It seems that in Finland the percentage of infections due to genotypes F and G has slightly increased during the last 20 years. Genotypes E and G appear to be more common, and genotypes J/Ja and I/Ia appear to be less common in Europe than in the USA. Although the genotype E was the most common genotype among C. trachomatis strains, the new variant was rarely found in Finland.

  9. Microbe-ID: An open source toolbox for microbial genotyping and species identification

    Science.gov (United States)

    Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user...

  10. Genotype × Environment Interaction for Iron Concentration of Rice in Central Java of Indonesia

    Institute of Scientific and Technical Information of China (English)

    Suwarto; Nasrullah

    2011-01-01

    To explore the effect of genotype and genotype × environment interaction on Fe concentration in rice grains,Fe concentrations of 10 genotypes were analyzed across eight paddy field environments during 2007-2008 using the AMMI-biplot method.Experiments were conducted using a randomized completely block design with three replications in eight environments.Results indicated that environment (E),genotype (G) and genotype × environment interaction (GE) significantly affected Fe concentration in rice grains.Environment explained 74.43 % of total (G+E+GE) variation,whereas G and GE captured 5.60% and 19.67%,respectively.Rice genotype Barumun was desirable in terms of the highest ability and stability for Fe concentration in rice grains.Environment in genotype Cilongok was the best representative of the overall environments and the most powerful to discriminate rice genotypes.

  11. Prevalence of Helicobacter pylori virulence genotypes among children in Eastern Turkey

    National Research Council Canada - National Science Library

    Ozbey, Gokben; Dogan, Yasar; Demiroren, Kaan

    2013-01-01

    To identify the virulence genotypes of Helicobacter pylori (H. pylori) if present in children in Eastern Turkey and if those genotypes are mostly associated with severe clinical presentations. A total of 49 H...

  12. Drug susceptibility of Mycobacterium tuberculosis Beijing genotype and association with MDR TB

    NARCIS (Netherlands)

    Steenwinkel, J.E. de; Kate, M.T. Ten; Knegt, G.J. de; Kremer, K.; Aarnoutse, R.E.; Boeree, M.J.; Verbrugh, H.A.; Soolingen, D. van; Bakker-Woudenberg, I.A.

    2012-01-01

    To determine differences in the ability of Mycobacterium tuberculosis strains to withstand antituberculosis drug treatment, we compared the activity of antituberculosis drugs against susceptible Beijing and East-African/Indian genotype M. tuberculosis strains. Beijing genotype strains showed high ra

  13. Drug susceptibility of mycobacterium tuberculosis Beijing genotype and association with MDR TB

    NARCIS (Netherlands)

    J.E.M. de Steenwinkel (Jurriaan); M.T. ten Kate (Marian); G.J. de Knegt (Gerjo); K. Kremer (Kristin); E.J. Aarnoutse (E. J.); M. Boeree (Martin); H.A. Verbrugh (Henri); D. van Soolingen (Dick); I.A.J.M. Bakker-Woudenberg (Irma)

    2012-01-01

    textabstractTo determine differences in the ability of Mycobacterium tuberculosis strains to withstand antituberculosis drug treatment, we compared the activity of antituberculosis drugs against susceptible Beijing and East-African/Indian genotype M. tuberculosis strains. Beijing genotype strains sh

  14. Biological and phylogenetic characterization of a genotype VII Newcastle disease virus from Venezuela: Efficacy of vaccination

    Science.gov (United States)

    Here we describe the characterization a virulent genotype VII Newcastle disease virus (NDV) from Venezuela and evaluate the efficacy of heterologous genotype commercial vaccination under field and controlled rearing conditions. Biological pathotyping and molecular analysis were applied. Results sh...

  15. Biotyping and genotyping (MLVA16 of Brucella abortus isolated from cattle in Brazil, 1977 to 2008.

    Directory of Open Access Journals (Sweden)

    Sílvia Minharro

    Full Text Available Brucellosis is a worldwide distributed zoonosis that causes important economic losses to animal production. In Brazil, information on the distribution of biovars and genotypes of Brucella spp. is scarce or unavailable. This study aimed (i to biotype and genotype 137 Brazilian cattle isolates (from 1977 to 2008 of B. abortus and (ii to analyze their distribution. B. abortus biovars 1, 2 and 3 (subgroup 3b were confirmed and biovars 4 and 6 were first described in Brazil. Genotyping by the panel 1 revealed two groups, one clustering around genotype 40 and another around genotype 28. Panels 2A and 2B disclosed a high diversity among Brazilian B. abortus strains. Eighty-nine genotypes were found by MLVA16. MLVA16 panel 1 and 2 showed geographic clustering of some genotypes. Biotyping and MLVA16 genotyping of Brazilian B. abortus isolates were useful to better understand the epidemiology of bovine brucellosis in the region.

  16. Standardized ileal digestibility of amino acids in eight genotypes of barley fed to growing pigs

    DEFF Research Database (Denmark)

    Spindler, H K; Mosenthin, R; Rosenfelder, Pia

    2016-01-01

    To determine chemical composition, physical characteristics and standardized ileal digestibility (SID) of CP and amino acids (AA) in eight current hulled barley genotypes, an experiment with growing pigs has been conducted. These genotypes included Yool, Campanile, Lomerit, Travira, Anisette...

  17. A novel hepatitis B virus genotyping system by using restriction fragment length polymorphism patterns of S gene amplicons

    Institute of Scientific and Technical Information of China (English)

    Guo-Bing Zeng; Shu-Juan Wen; Zhan-Hui Wang; Li Yan; Jian Sun; Jin-Lin Hou

    2004-01-01

    AIM: Traditional hepatitis B virus (HBV) genotyping methods using restriction fragment length polymorphism (RFLP) can reliably identify genotypes A to F. As HBV genotypes G and H have been recently identified, this study was to establish an accurate and simple genotyping method for all eight HBV genotypes (A to H).METHODS: Two hundred and forty HBV small S sequences obtained from GeneBank were analysed for restriction enzyme sites that would be genotype-specific. Restriction patterns following digestion with restriction enzymes BsrⅠ,StyⅠ, DpnⅠ, HpaⅡ, and EaeⅠ, were determined to identify all eight HBV genotypes. Mixed genotype infections were confirmed by cloning and further RFLP analysis.RESULTS: The new genotyping method could identify HBV genotypes A to H. Genotypes B and C could be determined by a single step digestion with BsrⅠ and StyⅠ in parallel. This was particularly useful in the Far East where genotypes B and C are predominant. Serum samples from 187 Chinese HBV carriers were analysed with this genotyping system, and the genotype distribution was 1.1% (2), 51.9% (97), 40.6% (76) and 4.8%(9) for genotypes A, B, C, and D, respectively. Mixed genotypes were found in only 3 patients (1.6%). Sequence data analysis confirmed the validity of this new method.CONCLUSION: This HBV genotyping system can identify all eight HBV genotypes. It is accurate and simple, and can be widely used for studies on HBV genotyping.

  18. Distribution of Hepatitis B Virus Genotypes and Its Clinical Significance in Hubei Province, China

    Institute of Scientific and Technical Information of China (English)

    TONG Qiaoxia; WU Yanyan; LUO Duande

    2007-01-01

    The distribution of hepatitis B virus genotype in Hubei province and its clinical significance were investigated. HBV genotypes of 276 patients were detected by PCR-microplate sandwich hybrization-ELISA technique. The level of HBV DNA was detected by using PCR-fluorescence quantification test. Among 276 patients, there were 78 cases of HBV asymptomatic carriers, 110 cases of chronic hepatitis B (CHB), 62 cases of severe hepatitis (SH) or liver cirrhosis (LC) and 26 cases of hepatocellular carcinoma (HCC). The genotypes of HBV included C, B, mixtures (B+C, B+D, C+D) and D, accounting for 55.8%, 25.4%, 16.7% and 2.1% respectively. The average level of HBV DNA in genotypes C, B, mixtures and D was 1.20×106, 7.81×104, 3.26×105 and 5.01×104 copies/mL respectively. The ratio of SH, LC and HCC in genotype B, C and mixtures was 20%, 30% and 48% respectively. Statistical analysis revealed the percentage of genotype mixtures infection was significantly higher than that of genotype B infection. There was no significant difference in the percentage between genotype B and genotype C or between genotype C and mixtures. The distribution of genotype B, C and mixtures in SH, LC and HCC was significantly different. The frequency of HCC was zero in patients with co-infection. Genotype D was only related with SH and LC. The increased ALT could be converted to categorical grades of severity. From mild, moderate to severity,the prevalence of genotype C showed an opposite trend, although no statistically significant difference was observed. The HBeAg positive rate was higher in patients with genotype C infection than in those with genotype B, especially in the patients whose ages were from 31 to 40 years old. Compared with genotype B, genotype C showed a higher HBeAg positive rate in patients with SH and LC. The percentage of SH, LC and HCC was higher in patients with genotype C and mixtures infection. On the contrary, the percentage of genotype B was lower. The HBeAg positive rate

  19. Hepatitis B virus genotypes in chronic liver disease patients from New Delhi, India

    Institute of Scientific and Technical Information of China (English)

    Saket Chattopadhyay; Bhudev Chandra Das; Premashis Kar

    2006-01-01

    AIM: To study the Hepatitis B virus (HBV) genotypes and their effect on the progression and outcome in patients with chronic liver diseases from New Delhi, India.METHODS: Sera from 100 HBV-related chronic liver disease (CLDB) cases were tested for HBV genotype using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and Type-specific primers-based PCR (TSP-PCR) targeting to the surface (S)gene encoding hepatitis B surface antigen.RESULTS: Only genotypes A and D were present and genotype D was dominant. Genotype D was present in all CLDB patient categories. The genotype distribution for the 100 patients with CLDB was as follows: genotype A, 16/100 (16%) (7/40- 17% chronic hepatitis B (CHB);8/47, 17%, HBV-related cirrhosis (CRB); 1/13, 7.6%,HBV-related hepatocellular carcinoma (HCCB); genotype D- 84/100 (84%) (32/40- 80% CHB; 38/47- 81%, CRB;11/13, 85%, HCCB); genotype A + D, 3/100 (3%) (1/40-3% CHB; 1/47- 2%, CRB; 1/13, 7.6%, HCCB); C, 0; B, 0;E, 0; F, 0; G 0, H 0; (P < 0.01, genotype D vs A).CONCLUSION: Only HBV genotypes A and D were present in patients with CLDB from New Delhi, India.Compared with genotype D, genotype A patients had no significant clinical or biochemical differences (P > 0.05).Mixed infection with genotype A and D were seen in 3%of the cases. Genotype D was the dominant genotype prevalent in all patient categories.

  20. The HBV E Genotype Discover in Dai Nationality in Xishuangbanna, Yunnan Province

    Institute of Scientific and Technical Information of China (English)

    Hai-ping ZHAO; Yuan-ying SHEN; Ru SHEN; Yuan-yi WANG; Mei-ya FU

    2009-01-01

    To investigate the distribution of Hepatitis B virus (HBV) genotypes among the population of Dai nationality in Xishuangbanna, Yurman Province HBV genotypes of the Serum samples were tested by PCR-RFLP. This is the first time to discover the B+E genotypes in China. This finding provides new information for understanding the distribution of HBV genotype in China and a provides a basis for establishing a Chinese gene bank.

  1. Prevalence of mixed hepatitis C virus (HCV genotypes among recently diagnosed dialysis patients with HCV infection

    Directory of Open Access Journals (Sweden)

    Mohammed A Al Balwi

    2011-01-01

    Full Text Available Hepatitis C virus (HCV infection is considered a major health problem recognized globally. HCV is a major cause of chronic liver disease that may lead to cirrhosis and hepatocellular carcinoma. The aim of this study was to investigate the prevalence of multiple (mixed HCV genotypes in Saudi patients recently diagnosed with HCV infection and their association with various clinical risk factors. We examined a total of 1,292 newly diagnosed HCV-positive cases between January 2006 and July 2009 at the Molecular Pathology Laboratory, King Abdulaziz Medical City, Riyadh. The clinical and laboratory data of the study patients were collected. The HCV-RNA viral load and its genotyping were carried out with RT-PCR technology to assist in the follow-up and management of HCV-infected patients undergoing antiviral therapy. Twenty-two patients (1.7% were found to have mixed HCV genotypes; of them, mixed genotypes associated with genotype-4 were seen in 19 patients (86%, mixed genotypes associated with genotype-1 were found in 68.4%, with genotype-3 in 26.3% and with genotype-2 in 5.3%. Additionally, mixed genotypes associated with genotype-1 were seen in three cases (13.6%; they were associated with genotype-2 in two (66.7% and with genotype-5 in one patient (33.3%. In conclusion, the prevalence rate of mixed HCV genotypes in the cohort of the newly infected Saudi patients was 1.7%, with genotype-4 being the most frequent genotype encountered.

  2. Evaluation of Mungbean Genotypes Based on Yield Stability and Reaction to Mungbean Yellow Mosaic Virus Disease

    OpenAIRE

    AKM Mahbubul Alam; Prakit Somta; Choosak Jompuk; Prasert Chatwachirawong; Peerasak Srinives

    2014-01-01

    This work was conducted to identify mungbean genotypes showing yield stability and resistance to mungbean yellow mosaic virus (MYMV) disease. Sixteen genotypes were evaluated in a randomized complete block design with two replications for two years (2011 and 2012) at three locations (Gazipur, Ishurdi and Madaripur) of the Bangladesh Agricultural Research Institute. An analysis of variance exhibited significant effects of genotype (G), environment (E), and genotype × environment (G×E) on grain...

  3. Comparison of reverse hybridization, microarray, and sequence analysis for genotyping hepatitis B virus

    NARCIS (Netherlands)

    Pas, Suzan D; Tran, Nathalie; de Man, Robert A; Burghoorn-Maas, C; Vernet, Guy; Niesters, Hubert G M

    2008-01-01

    Hepatitis B virus (HBV) genotyping has become important in epidemiological and clinical diagnoses, given the relationship between the viral genotype and the progression of disease or the appearance of antiviral resistance. Since genotyping by sequence and phylogenetic analyses is not convenient in t

  4. Hepatitis B virus with a proposed genotype I was found in Sichuan Province, China.

    Science.gov (United States)

    Tong, Wenbin; He, Jilan; Sun, Li; He, Shusen; Qi, Qi

    2012-06-01

    To date, eight hepatitis B virus (HBV) genotypes, A-H, have been designated, and two additional genotypes, I and J, have also been proposed. A serological survey targeting children in difficult-to-reach vaccination areas was carried out in remote counties of Sichuan Province, China. HBV genotypes and serotypes were also determined from HBsAg-positive serum samples by direct sequencing. Phylogenetic analysis showed two strains isolated from the Yi ethnic children clustered with the proposed genotype I. The pairwise genome genetic distance was 7.5% between genotypes I and C, and ranged from 8.4% to 15.2% between genotype I and other genotypes, except genotype C. Grouping Scan analyses of the two strains revealed apparent recombination events between an unknown genotype and genotype C. Two out of four HBV strains isolated from the Yi ethnic children were confirmed to be genotype I, suggesting widespread circulation and common infection with genotype I HBV in the local Yi population. High prevalence of HBsAg and low hepatitis B vaccination coverage indicated that additional efforts are needed to control HBV infection in those areas.

  5. MICA/B genotyping of Tujias from Zhangjiajie, Hunan Province, China.

    Science.gov (United States)

    Wang, Y J; Zhang, N J; Chen, E; Chen, C J; Bu, Y H; Yu, P

    2016-04-01

    One hundred eighty-seven Tujia individuals from Zhangjiajie, Hunan Province, China were genotyped at the MICA and MICB loci using polymerase chain reaction-sequence specific priming and sequencing-based typing methods. MICA and MCB genotypes are consistent with expected HW proportions. These genotype data are available in the Allele Frequencies Net Database.

  6. Pathogenesis of new sub-genotypes of Newcastle disease virus strains from Israel and Pakistan

    Science.gov (United States)

    Newcastle disease (ND) is a devastating disease of poultry worldwide caused by virulent strains of Newcastle disease virus (NDV). New genotypes and sub-genotypes of NDV frequently emerge. In the past few years, NDV strains belonging to sub-genotype VIIi and XIIIb emerged in the Middle East and Asi...

  7. Selective genotyping to detect QTL for multiple traits in outbred populations

    NARCIS (Netherlands)

    Bovenhuis, H.; Spelman, R.J.

    2000-01-01

    Selective genotyping (i.e., genotyping of individuals that are extreme for a quantitative trait) has been undertaken in many studies but has usually been limited to one trait of interest. This paper outlines the implications of selective genotyping when applied to a daughter design. Formulas are pre

  8. Choosing tree genotypes for phytoremediation of landfill leachate using phyto-recurrent selection

    Science.gov (United States)

    Jill A. Zalesny; Ronald S., Jr. Zalesny; Adam H. Wiese; Richard B. Hall

    2007-01-01

    Information about the response of poplar (Populus spp.) genotypes to landfill leachate irrigation is needed, along with efficient methods for choosing genotypes based on leachate composition. Poplar clones were irrigated during three cycles of phyto-recurrent selection to test whether genotypes responded differently to leachate and water, and to test...

  9. Rapid typing of Mannheimia haemolytica major genotypes 1 and 2 using MALDI-TOF mass spectrometry

    Science.gov (United States)

    Genotype 2 M. haemolytica predominantly associate over genotype 1 with the lungs of cattle with respiratory disease and ICEs containing antimicrobial resistance genes. Distinct protein masses were detected by MALDI-TOF MS between genotype 1 and 2 strains. MALDI-TOF MS could rapidly differentiate ge...

  10. The prevalence of mixed genotype infections in Polish patients with hepatitis C

    Directory of Open Access Journals (Sweden)

    Ewelina Gowin

    2016-02-01

    Conclusions: The results obtained showed that infection with mixed HCV genotypes in Polish patients with hepatitis C is uncommon. The selective elimination of genotypes 3a and 4a after therapy confirms the greater resistance to treatment of genotype 1b. In the context of new anti-HCV drug development, further investigations are needed to determine the clinical importance of mixed HCV infection.

  11. AMMI AND GGE BIPLOT ANALYSIS OF BREAD WHEAT GENOTYPES IN THE NORTHERN PART OF ETHIOPIA

    Directory of Open Access Journals (Sweden)

    Fetien Abay

    2013-04-01

    Full Text Available The genotype environment interaction manipulates the selection criteria in a multipurpose crop like wheat. Ten bread wheat genotypes were evaluated at five wheat growing locations of Tigray region in the year 2011. Yield data was analyzed using the additive main effect and multiplication interaction model (AMMI and GGE biplot. The AMMI analysis of variance for grain yield detected significant effects for genotype, location and genotype by location interaction. Location effect was responsible for the greatest part of the variation, followed by genotype and genotype by location interaction effects. Based on AMMI stability value, G4, G10, G8 and G9 were the most stable genotypes, while G1, G2, and G3 were the most responsive genotypes. The GGE biplot also showed G1, G2, G3, and G4 have long vectors and located far away from the biplot origin and hence are considered to have larger contribution to GEI (specifically adapted genotypes. G10 however is widely adapted genotype. The ‘which won where’ feature of the GGE biplot identified G4 as the winning genotype at Samre, Hagereselam, and Atsbi, while G1 winning at Quiha and Wukro. The GGE biplot also identified two bread wheat mega-environments. This indicates that analysis of multi-location trail data using GGE and AMMI model is important for determining visual comparisons, adaptability/stability focusing on overall performance to identify superior genotypes

  12. Helicobacter Genotyping and Detection in Peroperative Lavage Fluid in Patients with Perforated Peptic Ulcer

    NARCIS (Netherlands)

    N.A.P. Komen (Niels); M.J.O.E. Bertleff (Marietta); J.F. Lange (Johan); P.W. de Graaf

    2008-01-01

    textabstractIntroduction and Objectives Certain Helicobacter pylori genotypes are associated with peptic ulcer disease; however, little is known about associations between the H. pylori genotype and perforated peptic ulcer (PPU). The primary aim of this study was to evaluate which genotypes are pre

  13. AMMI AND GGE BIPLOT ANALYSIS OF BREAD WHEAT GENOTYPES IN THE NORTHERN PART OF ETHIOPIA

    Directory of Open Access Journals (Sweden)

    Hintsa G. Hagos

    2013-04-01

    Full Text Available The genotype environment interaction manipulates the selection criteria in a multipurpose crop like wheat. Ten bread wheat genotypes were evaluated at five wheat growing locations of Tigray region in the year 2011. Yield data was analyzed using the additive main effect and multiplication interaction model (AMMI and GGE biplot. The AMMI analysis of variance for grain yield detected significant effects for genotype, location and genotype by location interaction. Location effect was responsible for the greatest part of the variation, followed by genotype and genotype by location interaction effects. Based on AMMI stability value, G4, G10, G8 and G9 were the most stable genotypes, while G1, G2, and G3 were the most responsive genotypes. The GGE biplot also showed G1, G2, G3, and G4 have long vectors and located far away from the biplot origin and hence are considered to have larger contribution to GEI (specifically adapted genotypes. G10 however is widely adapted genotype. The ‘which won where’ feature of the GGE biplot identified G4 as the winning genotype at Samre, Hagereselam, and Atsbi, while G1 winning at Quiha and Wukro. The GGE biplot also identified two bread wheat mega-environments. This indicates that analysis of multi-location trail data using GGE and AMMI model is important for determining visual comparisons, adaptability/stability focusing on overall performance to identify superior genotypes.

  14. Drug Susceptibility of Mycobacterium tuberculosis Beijing Genotype and Association with MDR TB

    OpenAIRE

    2012-01-01

    To determine differences in the ability of Mycobacterium tuberculosis strains to withstand antituberculosis drug treatment, we compared the activity of antituberculosis drugs against susceptible Beijing and East-African/Indian genotype M. tuberculosis strains. Beijing genotype strains showed high rates of mutation within a wide range of drug concentrations, possibly explaining this genotype's association with multidrug-resistant tuberculosis.

  15. Drug susceptibility of Mycobacterium tuberculosis Beijing genotype and association with MDR TB.

    Science.gov (United States)

    de Steenwinkel, Jurriaan E M; ten Kate, Marian T; de Knegt, Gerjo J; Kremer, Kristin; Aarnoutse, Rob E; Boeree, Martin J; Verbrugh, Henri A; van Soolingen, Dick; Bakker-Woudenberg, Irma A J M

    2012-04-01

    To determine differences in the ability of Mycobacterium tuberculosis strains to withstand antituberculosis drug treatment, we compared the activity of antituberculosis drugs against susceptible Beijing and East-African/Indian genotype M. tuberculosis strains. Beijing genotype strains showed high rates of mutation within a wide range of drug concentrations, possibly explaining this genotype's association with multidrug-resistant tuberculosis.

  16. Population structure of mixed Mycobacterium tuberculosis infection is strain genotype and culture medium dependent.

    NARCIS (Netherlands)

    Hanekom, M.; Streicher, E.M.; Berg, D. Van den; Cox, H.; McDermid, C.; Bosman, M.; Pittius, N.C. Gey van; Victor, T.C.; Kidd, M.; Soolingen, D. van; Helden, P.D. van; Warren, R.M.

    2013-01-01

    BACKGROUND: Molecular genotyping methods have shown infection with more than one Mycobacterium tuberculosis strain genotype in a single sputum culture, indicating mixed infection. AIM: This study aimed to develop a PCR-based genotyping tool to determine the population structure of M. tuberculosis st

  17. Mixed genotype transmission bodies and virions contribute to the maintenance of diversity in an insect virus

    Science.gov (United States)

    Clavijo, Gabriel; Williams, Trevor; Muñoz, Delia; Caballero, Primitivo; López-Ferber, Miguel

    2010-01-01

    An insect nucleopolyhedrovirus naturally survives as a mixture of at least nine genotypes. Infection by multiple genotypes results in the production of virus occlusion bodies (OBs) with greater pathogenicity than those of any genotype alone. We tested the hypothesis that each OB contains a genotypically diverse population of virions. Few insects died following inoculation with an experimental two-genotype mixture at a dose of one OB per insect, but a high proportion of multiple infections were observed (50%), which differed significantly from the frequencies predicted by a non-associated transmission model in which genotypes are segregated into distinct OBs. By contrast, insects that consumed multiple OBs experienced higher mortality and infection frequencies did not differ significantly from those of the non-associated model. Inoculation with genotypically complex wild-type OBs indicated that genotypes tend to be transmitted in association, rather than as independent entities, irrespective of dose. To examine the hypothesis that virions may themselves be genotypically heterogeneous, cell culture plaques derived from individual virions were analysed to reveal that one-third of virions was of mixed genotype, irrespective of the genotypic composition of the OBs. We conclude that co-occlusion of genotypically distinct virions in each OB is an adaptive mechanism that favours the maintenance of virus diversity during insect-to-insect transmission. PMID:19939845

  18. Liquid biopsy genotyping in lung cancer: ready for clinical utility?

    Science.gov (United States)

    Huang, Wei-Lun; Chen, Yi-Lin; Yang, Szu-Chun; Ho, Chung-Liang; Wei, Fang; Wong, David T; Su, Wu-Chou; Lin, Chien-Chung

    2017-03-14

    Liquid biopsy is a blood test that detects evidence of cancer cells or tumor DNA in the circulation. Despite complicated collection methods and the requirement for technique-dependent platforms, it has generated substantial interest due, in part, to its potential to detect driver oncogenes such as epidermal growth factor receptor (EGFR) mutants in lung cancer. This technology is advancing rapidly and is being incorporated into numerous EGFR tyrosine kinase inhibitor (EGFR-TKI) development programs. It appears ready for integration into clinical care. Recent studies have demonstrated that biological fluids such as saliva and urine can also be used for detecting EGFR mutant DNA through application other user-friendly techniques. This review focuses on the clinical application of liquid biopsies to lung cancer genotyping, including EGFR and other targets of genotype-directed therapy and compares multiple platforms used for liquid biopsy.

  19. Rationality and emotionality: serotonin transporter genotype influences reasoning bias

    Science.gov (United States)

    Bean, Stephanie E.; Anderson, Lindsay M.; Devaney, Joseph M.; Vaidya, Chandan J.

    2013-01-01

    Reasoning often occurs under emotionally charged, opinion-laden circumstances. The belief-bias effect indexes the extent to which reasoning is based upon beliefs rather than logical structure. We examined whether emotional content increases this effect, particularly for adults genetically predisposed to be more emotionally reactive. SS/SLG carriers of the serotonin transporter genotype (5-HTTLPR) were less accurate selectively for evaluating emotional relational reasoning problems with belief-logic conflict relative to LALA carriers. Trait anxiety was positively associated with emotional belief-bias, and the 5-HTTLPR genotype significantly accounted for the variance in this association. Thus, deductive reasoning, a higher cognitive ability, is sensitive to differences in emotionality rooted in serotonin neurotransmitter function. PMID:22275169

  20. Genotyping, evolution and epidemiological findings of Rickettsia species.

    Science.gov (United States)

    Merhej, Vicky; Angelakis, Emmanouil; Socolovschi, Cristina; Raoult, Didier

    2014-07-01

    Rickettsiae are obligate intracellular bacteria that can cause mild to life-threatening diseases, including epidemic typhus, one of the oldest pernicious diseases of mankind. Clinical awareness of rickettsial diseases and molecular diagnosis have shown that rickettsioses should be viewed as new emerging and reemerging diseases. Rickettsia has been shown to be a large genus with a worldwide distribution, a very diverse host range, including hosts that have no relationship with vertebrate. Genomic studies have demonstrated genome reduction due to gene loss associated with increased pathogenicity and horizontal DNA acquisition according to a sympatric mode of evolution in hosts that contain several organisms. This article presents a review of genotyping techniques and examines the principle of genotype determination in terms of taxonomic strategies and detection methods. This article summarizes the epidemiological and pathological features of Rickettsia and discusses the genomic findings that help the understanding of the evolution of pathogenicity including the deleterious mutations of repair systems and the toxin-antitoxin systems.

  1. Galaxy High Throughput Genotyping Pipeline for GeneTitan.

    Science.gov (United States)

    Karpenko, Oleksiy; Bahroos, Neil; Chukhman, Morris; Dong, Xiao; Kanabar, Pinal; Arbieva, Zarema; Jackson, Tommie; Hendrickson, William

    2013-01-01

    Latest genotyping solutions allow for rapid testing of more than two million markers in one experiment. Fully automated instruments such as Affymetrix GeneTitan enable processing of large numbers of samples in a truly high-throughput manner. In concert with solutions like Axiom, fully customizable array plates can now utilize automated workflows that can leverage multi-channel instrumentation like the GeneTitan. With the growing size of raw data output, the serial computational architecture of the software, typically distributed by the vendors on turnkey desktop solutions for quality control and genotype calling, becomes legacy rather than an advantage. Advanced software techniques provide power, flexibility, and can be deployed in an HPC environment, but become technically inconvenient for biologists to use. Here we present a pipeline that uses Galaxy as a mechanism to lower the barrier for complex analysis, and increase efficiency by leveraging high-throughput computing.

  2. Physiological sex predicts hybrid sterility regardless of genotype.

    Science.gov (United States)

    Malone, John H; Michalak, P

    2008-01-01

    Reproductive isolation between biological species is characterized by Haldane's rule, which states that the heterogametic sex (XY or ZW) suffers the most dysfunctional effects of hybridization. It has been hypothesized that, in addition to X-linked recessive genes, Haldane's rule also reflects the faster evolution of genes related to male reproduction (faster-male evolution). We used sex-reversed hybrid Xenopus to test faster-male evolution by examining the fertility of sex-reversed individuals with the genotype of the inverse phenotypic sex. Hybrid males are sterile and hybrid females are fertile irrespective of their genotypic sex. Gene expression profiles match these adult phenotypes, and our results demonstrate that faster-male evolution is the most likely mechanism producing hybrid male sterility.

  3. Comprehensive Annotation of Mature Peptides and Genotypes for Zika Virus

    Science.gov (United States)

    Sun, Guangyu; Baumgarth, Nicole; Klem, Edward B.; Scheuermann, Richard H.

    2017-01-01

    The rapid spread of Zika virus (ZIKV) has caused much concern in the global health community, due in part to a link to fetal microcephaly and other neurological illnesses. While an increasing amount of ZIKV genomic sequence data is being generated, an understanding of the virus molecular biology is still greatly lacking. A significant step towards establishing ZIKV proteomics would be the compilation of all proteins produced by the virus, and the resultant virus genotypes. Here we report for the first time such data, using new computational methods for the annotation of mature peptide proteins, genotypes, and recombination events for all ZIKV genomes. The data is made publicly available through the Virus Pathogen Resource at www.viprbrc.org. PMID:28125631

  4. Cloning of Omp1 Gene from Chlamydia trachomatis F Genotype

    Institute of Scientific and Technical Information of China (English)

    QI Manli(齐蔓莉); LIU Quanzhong(刘全中); JIAO Wenling(缴稳苓); TIAN Jingqun(田敬群); CHEN Jinying(陈锦英)

    2002-01-01

    Objectives: To directionally clone the omp1 gene fromChlamydia trachomatis (Ct) F genotype onto a plasmid vectorfor constructing a rudimentary DNA vaccine.Methods: The complete omp1 gene from genomic DNA of CtF genotype wild species was amplified with primers designedby computer. The recombinant gene was obtained byrestriction enzyme cutting, linking the gene with the plasmidvector in vitro, transforming the recombinant gene intobacteria, and extracting the DNA from the bacteria.Results: DNA extracted from the bacteria was composed ofthe omp1 gene and plasmid, which is identified by threemethods of singular restrictive enzyme cutting, doublerestrictive enzyme cutting and PCR.Conclusion: Cloning of the omp1 gene from the Ct Fgenotype means that a rudimentary DNA vaccine wassuccessfully constructed.

  5. Genotyping of Bacillus cereus strains by microarray-based resequencing.

    Directory of Open Access Journals (Sweden)

    Michael E Zwick

    Full Text Available The ability to distinguish microbial pathogens from closely related but nonpathogenic strains is key to understanding the population biology of these organisms. In this regard, Bacillus anthracis, the bacterium that causes inhalational anthrax, is of interest because it is closely related and often difficult to distinguish from other members of the B. cereus group that can cause diverse diseases. We employed custom-designed resequencing arrays (RAs based on the genome sequence of Bacillus anthracis to generate 422 kb of genomic sequence from a panel of 41 Bacillus cereus sensu lato strains. Here we show that RAs represent a "one reaction" genotyping technology with the ability to discriminate between highly similar B. anthracis isolates and more divergent strains of the B. cereus s.l. Clade 1. Our data show that RAs can be an efficient genotyping technology for pre-screening the genetic diversity of large strain collections to selected the best candidates for whole genome sequencing.

  6. Genotyping of Bacillus cereus strains by microarray-based resequencing.

    Science.gov (United States)

    Zwick, Michael E; Kiley, Maureen P; Stewart, Andrew C; Mateczun, Alfred; Read, Timothy D

    2008-07-02

    The ability to distinguish microbial pathogens from closely related but nonpathogenic strains is key to understanding the population biology of these organisms. In this regard, Bacillus anthracis, the bacterium that causes inhalational anthrax, is of interest because it is closely related and often difficult to distinguish from other members of the B. cereus group that can cause diverse diseases. We employed custom-designed resequencing arrays (RAs) based on the genome sequence of Bacillus anthracis to generate 422 kb of genomic sequence from a panel of 41 Bacillus cereus sensu lato strains. Here we show that RAs represent a "one reaction" genotyping technology with the ability to discriminate between highly similar B. anthracis isolates and more divergent strains of the B. cereus s.l. Clade 1. Our data show that RAs can be an efficient genotyping technology for pre-screening the genetic diversity of large strain collections to selected the best candidates for whole genome sequencing.

  7. Improving the precision of genotype selection in wheat performance trials

    Directory of Open Access Journals (Sweden)

    Giovani Benin

    2013-12-01

    Full Text Available The aim of this study was to verify whether using the Papadakis method improves model assumptions and experimental accuracy in field trials used to determine grain yield for wheat lineages indifferent Value for Cultivation and Use (VCU regions. Grain yield data from 572 field trials at 31 locations in the VCU Regions 1, 2, 3 and 4 in 2007-2011 were used. Each trial was run with and without the use of the Papadakis method. The Papadakis method improved the indices of experimental precision measures and reduced the number of experimental repetitions required to predict grain yield performance among the wheat genotypes. There were differences among the wheat adaptation regions in terms of the efficiency of the Papadakis method, the adjustment coefficient of the genotype averages and the increases in the selective accuracy of grain yield.

  8. Rationality and emotionality: serotonin transporter genotype influences reasoning bias.

    Science.gov (United States)

    Stollstorff, Melanie; Bean, Stephanie E; Anderson, Lindsay M; Devaney, Joseph M; Vaidya, Chandan J

    2013-04-01

    Reasoning often occurs under emotionally charged, opinion-laden circumstances. The belief-bias effect indexes the extent to which reasoning is based upon beliefs rather than logical structure. We examined whether emotional content increases this effect, particularly for adults genetically predisposed to be more emotionally reactive. SS/SL(G) carriers of the serotonin transporter genotype (5-HTTLPR) were less accurate selectively for evaluating emotional relational reasoning problems with belief-logic conflict relative to L(A)L(A) carriers. Trait anxiety was positively associated with emotional belief-bias, and the 5-HTTLPR genotype significantly accounted for the variance in this association. Thus, deductive reasoning, a higher cognitive ability, is sensitive to differences in emotionality rooted in serotonin neurotransmitter function.

  9. Identification of new sub-genotypes of virulent Newcastle disease virus with potential panzootic features.

    Science.gov (United States)

    Miller, Patti J; Haddas, Ruth; Simanov, Luba; Lublin, Avishay; Rehmani, Shafqat Fatima; Wajid, Abdul; Bibi, Tasra; Khan, Taseer Ahmad; Yaqub, Tahir; Setiyaningsih, Surachmi; Afonso, Claudio L

    2015-01-01

    Virulent Newcastle disease virus (NDV) isolates from new sub-genotypes within genotype VII are rapidly spreading through Asia and the Middle East causing outbreaks of Newcastle disease (ND) characterized by significant illness and mortality in poultry, suggesting the existence of a fifth panzootic. These viruses, which belong to the new sub-genotypes VIIh and VIIi, have epizootic characteristics and do not appear to have originated directly from other genotype VII NDV isolates that are currently circulating elsewhere, but are related to the present and past Indonesian NDV viruses isolated from wild birds since the 80s. Viruses from sub-genotype VIIh were isolated in Indonesia (2009-2010), Malaysia (2011), China (2011), and Cambodia (2011-2012) and are closely related to the Indonesian NDV isolated in 2007, APMV1/Chicken/Karangasem, Indonesia (Bali-01)/2007. Since 2011 and during 2012 highly related NDV isolates from sub-genotype VIIi have been isolated from poultry production facilities and occasionally from pet birds, throughout Indonesia, Pakistan and Israel. In Pakistan, the viruses of sub-genotype VIIi have replaced NDV isolates of genotype XIII, which were commonly isolated in 2009-2011, and they have become the predominant sub-genotype causing ND outbreaks since 2012. In a similar fashion, the numbers of viruses of sub-genotype VIIi isolated in Israel increased in 2012, and isolates from this sub-genotype are now found more frequently than viruses from the previously predominant sub-genotypes VIId and VIIb, from 2009 to 2012. All NDV isolates of sub-genotype VIIi are approximately 99% identical to each other and are more closely related to Indonesian viruses isolated from 1983 through 1990 than to those of genotype VII, still circulating in the region. Similarly, in addition to the Pakistani NDV isolates of the original genotype XIII (now called sub-genotype XIIIa), there is an additional sub-genotype (XIIIb) that was initially detected in India and Iran

  10. Hepatitis B virus genotype C isolates with wild-type core promoter sequence replicate less efficiently than genotype B isolates but possess higher virion secretion capacity.

    Science.gov (United States)

    Qin, Yanli; Tang, Xiaoli; Garcia, Tamako; Hussain, Munira; Zhang, Jiming; Lok, Anna; Wands, Jack; Li, Jisu; Tong, Shuping

    2011-10-01

    Infection by hepatitis B virus (HBV) genotype C is associated with a prolonged viremic phase, delayed hepatitis B e antigen (HBeAg) seroconversion, and an increased incidence of liver cirrhosis and hepatocellular carcinoma compared with genotype B infection. Genotype C is also associated with the more frequent emergence of core promoter mutations, which increase genome replication and are independently associated with poor clinical outcomes. We amplified full-length HBV genomes from serum samples from Chinese and U. S. patients with chronic HBV infection and transfected circularized genome pools or dimeric constructs of individual clones into Huh7 cells. The two genotypes could be differentiated by Western blot analysis due to the reactivities of M and L proteins toward a monoclonal pre-S2 antibody and slightly different S-protein mobilities. Great variability in replication capacity was observed for both genotypes. The A1762T/G1764A core promoter mutations were prevalent in genotype C isolates and correlated with increased replication capacity, while the A1752G/T mutation frequently found in genotype B isolates correlated with a low replication capacity. Importantly, most genotype C isolates with wild-type core promoter sequence replicated less efficiently than the corresponding genotype B isolates due to less efficient transcription of the 3.5-kb RNA. However, genotype C isolates often displayed more efficient virion secretion. We propose that the low intracellular levels of viral DNA and core protein of wild-type genotype C delay immune clearance and trigger the subsequent emergence of A1762T/G1764A core promoter mutations to upregulate replication; efficient virion secretion compensates for the low replication capacity to ensure the establishment of persistent infection by genotype C.

  11. Myeloperoxidase genotype, fruit and vegetable consumption, and breast cancer risk.

    Science.gov (United States)

    Ahn, Jiyoung; Gammon, Marilie D; Santella, Regina M; Gaudet, Mia M; Britton, Julie A; Teitelbaum, Susan L; Terry, Mary Beth; Neugut, Alfred I; Josephy, P David; Ambrosone, Christine B

    2004-10-15

    Myeloperoxidase (MPO), an antimicrobial enzyme in the breast, generates reactive oxygen species (ROS) endogenously. An MPO G463A polymorphism exists in the promoter region, with the variant A allele conferring lower transcription activity than the common G allele. Because oxidative stress may play a role in breast carcinogenesis, we evaluated MPO genotypes in relation to breast cancer risk among 1,011 cases and 1,067 controls from the Long Island Breast Cancer Study Project (1996-1997). We also assessed the potential modifying effects of dietary antioxidants and hormonally related risk factors on these relationships. Women over 20 years with incident breast cancer who were residents of Nassau and Suffolk Counties, NY, were identified as potential cases. Population-based controls were frequency matched by 5-year age groups. Genotyping was performed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) technology, and suspected breast cancer risk factors and usual dietary intake were assessed during an in-person interview. Unconditional logistic regression was used to estimate odds ratios and 95% confidence intervals. Having at least one A allele was associated with an overall 13% reduction in breast cancer risk. When consumption of fruits and vegetables and specific dietary antioxidants were dichotomized at the median, inverse associations with either GA or AA genotypes were most pronounced among women who consumed higher amounts of total fruits and vegetables (odds ratio, 0.75; 95% confidence interval, 0.58-0.97); this association was not noted among the low-consumption group (P for interaction = 0.04). Relationships were strongest among premenopausal women. Results from this first study of MPO genotypes and breast cancer risk indicate that MPO variants, related to reduced generation of ROS, are associated with decreased breast cancer risk, and emphasize the importance of fruit and vegetable consumption in reduction of breast

  12. Morphology and viability of castor bean genotypes pollen grains

    OpenAIRE

    Maria Selma Alves Silva Diamantino; Maria Angélica Pereira de Carvalho Costa; Taliane Leila Soares; Daniel Vieira Morais; Simone Alves Silva; Everton Hilo Souza

    2016-01-01

    The objective of this work was to characterize the morphology and viability of the pollen of 15 genotypes of castor bean (Ricinus communis L.) and to generate information that can assist in the selection of highly promising male parents for future use in genetic improvement programs aimed at producing seeds for oil extraction. Acetolysis and scanning electron microscopy was used to characterize the morphology of the pollen. The viability of the pollen grains was estimated by in vitro germinat...

  13. Morphology and viability of castor bean genotypes pollen grains

    OpenAIRE

    Diamantino,Maria Selma Alves Silva; Costa,Maria Angélica Pereira de Carvalho; Soares,Taliane Leila; Morais,Daniel Vieira; Silva,Simone Alves; Souza,Everton Hilo de

    2016-01-01

    ABSTRACT. The objective of this work was to characterize the morphology and viability of the pollen of 15 genotypes of castor bean (Ricinus communis L.) and to generate information that can assist in the selection of highly promising male parents for future use in genetic improvement programs aimed at producing seeds for oil extraction. Acetolysis and scanning electron microscopy was used to characterize the morphology of the pollen. The viability of the pollen grains was estimated by in vitr...

  14. Genetic diversity in palmyrah genotypes using morphological and molecular markers

    Directory of Open Access Journals (Sweden)

    V.Ponnuswami

    2010-07-01

    Full Text Available Palms are woody monocotyledons in the family Arecaceae which is placed in the order Arecales. Slow and tall growing,hardy and non branching, dioecious and perennial in nature, palmyrah palm has no distinguishing features to identify sex,stature and high neera yielding types until flowering age of about 12 to 15 years. Under these circumstances molecularmarkers can be effectively utilized to diagnose and select a genotype. Twenty palmyrah accessions were analysed usingRAPD and ISSR markers. In RAPD analysis, a total of 57 bands were obtained, among them 43 were polymorphic and restof them were monomorphic. Amplification size ranged between 250 and 3200 bp. UPGMA based cluster diagram showedthat all 20 different genotypes were grouped into four different clusters based on the stature, sex and high neera yieldingtypes. The distance matrix between genotypes showed an average distance range from 0.54 to 0.91 with a mean of 0.70. Atotal of 130 ISSR markers were scored, of which 65 were polymorphic, equivalent to 47.94% polymorphism. These markerswere used to estimate the genetic similarity among accessions using Jaccard’s similarity coefficient, with similarity valuesranging from 71.6 to 95.7%. The average number of markers produced per primer was 6.11. For each of the 21 ISSRprimers PIC value ranged between 0 and 0.46. Cluster analysis based on ISSR data grouped the 20 palmyrah accessions intotwo major clusters. PCA based on ISSR data clearly distinguished genotypes similar to the results of cluster analysis.

  15. Analysis of linear and nonlinear genotype × environment interaction

    Directory of Open Access Journals (Sweden)

    Rong-Cai eYang

    2014-07-01

    Full Text Available The usual analysis of genotype × environment interaction (GxE is based on the linear regression of genotypic performance on environmental changes (e.g., classic stability analysis. This linear model may often lead to lumping together of the nonlinear responses to the whole range of environmental changes from suboptimal and superoptimal conditions, thereby lowering the power of detecting GxE variation. On the other hand, the GxE is present when the magnitude of the genetic effect differs across the range of environmental conditions regardless of whether the response to environmental changes is linear or nonlinear. The objectives of this study are: (i explore the use of four commonly used nonlinear functions (logistic, parabola, normal and Cauchy functions for modeling nonlinear genotypic responses to environmental changes and (ii to investigate the difference in the magnitude of estimated genetic effects under different environmental conditions. The use of nonlinear functions was illustrated through the analysis of one data set taken from barley cultivar trials in Alberta, Canada (Data A and the examination of change in effect sizes is through the analysis another data set taken from the North America Barley Genome Mapping Project (Data B. The analysis of Data A showed that the Cauchy function captured an average of >40% of total GxE variation whereas the logistic function captured less GxE variation than the linear function. The analysis of Data B showed that genotypic responses were largely linear and that strong QTL × environment interaction existed as the positions, sizes and directions of QTL detected differed in poor vs. good environments. We conclude that (i the nonlinear functions should be considered when analyzing multi-environmental trials with a wide range of environmental variation and (ii QTL × environment interaction can arise from the difference in effect sizes across environments.

  16. Phylogeography of Japanese encephalitis virus: genotype is associated with climate.

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    Amy J Schuh

    Full Text Available The circulation of vector-borne zoonotic viruses is largely determined by the overlap in the geographical distributions of virus-competent vectors and reservoir hosts. What is less clear are the factors influencing the distribution of virus-specific lineages. Japanese encephalitis virus (JEV is the most important etiologic agent of epidemic encephalitis worldwide, and is primarily maintained between vertebrate reservoir hosts (avian and swine and culicine mosquitoes. There are five genotypes of JEV: GI-V. In recent years, GI has displaced GIII as the dominant JEV genotype and GV has re-emerged after almost 60 years of undetected virus circulation. JEV is found throughout most of Asia, extending from maritime Siberia in the north to Australia in the south, and as far as Pakistan to the west and Saipan to the east. Transmission of JEV in temperate zones is epidemic with the majority of cases occurring in summer months, while transmission in tropical zones is endemic and occurs year-round at lower rates. To test the hypothesis that viruses circulating in these two geographical zones are genetically distinct, we applied Bayesian phylogeographic, categorical data analysis and phylogeny-trait association test techniques to the largest JEV dataset compiled to date, representing the envelope (E gene of 487 isolates collected from 12 countries over 75 years. We demonstrated that GIII and the recently emerged GI-b are temperate genotypes likely maintained year-round in northern latitudes, while GI-a and GII are tropical genotypes likely maintained primarily through mosquito-avian and mosquito-swine transmission cycles. This study represents a new paradigm directly linking viral molecular evolution and climate.

  17. Surveillance for Echinococcus canadensis genotypes in Canadian ungulates☆

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    Schurer, Janna; Shury, Todd; Leighton, Frederick; Jenkins, Emily

    2013-01-01

    The geographic and host distribution, prevalence and genotypes of Echinococcus canadensis in wild ungulates in Canada are described to better understand the significance for wildlife and public health. We observed E. canadensis in 10.5% (11/105) of wild elk (wapiti; Cervus canadensis) in Riding Mountain National Park, Manitoba, examined at necropsy, over two consecutive years (2010–2011). Molecular characterization of hydatid cyst material from these elk, as well as three other intermediate wildlife host species, was based on sequence of a 470 bp region of the NADH dehydrogenase subunit 1 (NAD1) mitochondrial gene. In moose [Alces alces], elk, and caribou [Rangifer tarandus] from northwestern Canada, the G10 genotype was the only one present, and the G8 genotype was detected in a muskox (Ovibos moschatus) from northeastern Canada. On a search of the national wildlife health database (1992–2010), cervids with hydatid cysts were reported in all provinces and territories except the Atlantic provinces, from which wolves [Canis lupis] are historically absent. Of the 93 cervids with records of hydatid cysts, 42% were elk, 37% were moose, 14% were caribou, and 6% were white-tailed and mule deer [Odocoileus virginianus and Odocoileus hemonius]. In these animals, 83% of cysts were detected in lungs alone, 8% in both lungs and liver, 3% in liver alone, and 6% in other organs. These observations can help target surveillance programs and contribute to a better understanding of ecology, genetic diversity, and genotype pathogenicity in the Echinococcus granulosus species complex. PMID:24533321

  18. Rhizosphere properties of maize genotypes with contrasting phosphorus efficiency

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    Edilson Carvalho Brasil

    2011-02-01

    Full Text Available An experiment was conducted in a growth chamber to evaluate characteristics of the rhizosphere of maize genotypes contrasting in P-use efficiency, by determining length and density of root hairs, the rhizosphere pH and the functional diversity of rhizosphere bacteria. A sample of a Red Oxisol was limed and fertilized with N, K and micronutrients. In the treatment with the highest P level, 174 mg kg-1 P was added. Each experimental unit corresponded to a PVC rhizobox filled with 2.2 dm-3 soil. The experiment was completely randomized with three replications in a 5 x 2 factorial design, corresponding to five genotypes (H1, H2 and H3 = P-efficient hybrids, H4 and H5 = P-inefficient hybrids and two P levels (low = 3 mg dm-3, high = 29 mg dm-3. It was found that 18 days after transplanting, the nodal roots of the hybrids H3 and H2 had the longest root hairs. In general, the pH in the rhizosphere of the different genotypes was higher than in non-rhizosphere soil, irrespective of the P level. The pH was higher in the rhizosphere of lateral than of nodal roots. At low P levels, the pH variation of the hybrids H2, H4 and H5 was greater in rhizospheric than in non-rhizospheric soil. The functional microbial activity in the rhizosphere of the hybrids H3 and H5 was highest. At low soil P levels, the indices of microbial functional diversity were also higher. The microbial metabolic profile in the rhizosphere of hybrids H1, H2, H3, and H5 remained unaltered when the plants were grown at low P. The variations in the rhizosphere properties could not be related to patterns of P-use efficiency in the tested genotypes.

  19. Clinical presentation and genotype of hepatitis delta in Karachi

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    Tariq Moatter; Zaigham Abbas; Sabhita Shabir; Wasim Jafri

    2007-01-01

    AIM: To assess the clinical presentation and genotypes of delta hepatitis in local population.METHODS: In this prospective study, 39 consecutive patients who were positive for HBsAg and hepatitis D virus (HDV) antibody were included. The patients were divided in two groups on the basis of presence or absence of HDV RNA and a comparative study was done. Genotype of HDV was determined in PCR positive patients.RESULTS: Overall there is male dominance, in which 34 patients out of 39 (87.2%) were male. Twenty (51%) patients were from the adjacent areas of three provinces; Sindh, Punjab and Balochistan indicating the higher prevalence of delta hepatitis in this mid region of Pakistan. Patients of all age groups were affected with delta hepatitis (median 31.5 years, range 12-75).HDV RNA was detectable in 23 patients (59%). All the HDV strains belonged to genotype Ⅰ. HBV DNA was detectable only in 3 cases who were also HBeAg and HDV RNA positive. Patients with detectable HDV RNA were younger than patients with undetectable RNA; mean age 29.7 ± 12.8 years vs 36.8 ± 15.2.There were no statistically significant differences in the clinical presentation and routine biochemical profile of patients with detectable or undetectable HDV RNA.Clinical cirrhosis was present in 19 (49%) patients; 12 with detectable RNA and 7 with undetectable HDV RNA (P = 0.748). Decompensated disease was seen in eight patients; five and three respectively from each group.Four patients with undetectable RNA and two patients with detectable RNA had normal ALT and ultrasound abdomen.CONCLUSION: HDV may infect at any age, usually young adult males. Genotype Ⅰ is prevalent. With time some of the patients become HDV RNA negative or asymptomatic carrier. Most of the patients have suppressed HBV DNA replication. Significant numbers of patients have cirrhosis.

  20. HCV genotype distribution and possible transmission risks in Lahore, Pakistan

    Institute of Scientific and Technical Information of China (English)

    Waqar; Ahmad; Bushra; Ijaz; Fouzia; Tahir; Javed; Shah; Jahan; Imran; Shahid; Fawad; Mumtaz; Khan; Sajida; Hassan

    2010-01-01

    AIM: To investigate the prevalence of hepatitis C virus (HCV) genotypes and their association with possible transmission routes in the general population of Lahore, as the data exclusively related to this city is limited. METHODS: Complete data regarding patient's history, possible route of infection and biochemical tests was collected from the public hospital for 1364 patients. SPSS version 16 windows software was used for data analysis by univariate and multivariate techniques. RESULTS: Age range ≤ 40 yea...

  1. Genotype and environment shape the fitness of Drosophila melanogaster

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    Wesam S. Meshrif

    2015-01-01

    Full Text Available Fitness traits of Drosophila are believed to be expressed under genetic control and the environment. This study focuses on the interaction between the genotype (expressing high and low fitness level of Drosophila melanogaster and the environment (diet and infection. The environmental factors are supposed to modify traits such as the survival rate, development time, adult dry weight and response to microbial infection. The results indicated that yeast species (nutrients, bacterial infection and the genotype of Drosophila affected the survival rates and the development time of Drosophila. The fit Drosophila produces more survivors and develops faster than the unfit one. The yeast, Pichia toletana induced the highest survival and the fastest development of Drosophila, while Metschnikowia pulcherrima induced the opposite. The origin also had an effect on the development time; the African lines developed faster than the European ones. The yeast species and its concentration appeared to affect the dry weight of Drosophila too. Following infection with Pseudomonas stutzeri, several antimicrobial peptides, such as drosomycin and metchnikowin have been activated in Drosophila adults when they feed on less nutritive yeast (M. pulcherrima. The above mentioned results support the capacity of genotype-by-environment interactions to shape the fitness of D. melanogaster, where the contribution of each factor may differ according to the trait observed and the population under investigation.

  2. Genotyping of circulating measles strains in Italy in 2010

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    Melissa Baggieri

    2014-12-01

    Full Text Available INTRODUCTION: The European Regional Office of the World Health Organization developed a strategic approach to stop the indigenous transmission of measles in its 53 Member States by 2015. In Italy, laboratory surveillance activity is implemented by the National Reference Laboratory for Measles and Rubella at the Italian National Institute of Health (Istituto Superiore di Sanità, Rome. The role of the National Reference Laboratory is to strengthen surveillance systems through rigorous case investigation and laboratory confirmation of suspected sporadic cases and outbreaks. Genetic characterization of wild-type measles virus is an essential component of the laboratory-based surveillance. This study describes the molecular characterization of measles virus strains isolated during 2010. METHODS: Dried blood spots, urine and oral fluid samples were collected from patients with a suspected measles infection. Serological tests were performed on capillary blood, and viral detection was performed on urine and oral fluid samples through molecular assay. Positive samples were sequenced and phylogenetically analysed. RESULTS AND DISCUSSION: The phylogenetic analysis showed a co-circulation of genotypes D4 and D8, and sporadic cases associated to genotypes D9 and B3. Then, molecular epidemiology of measles cases permitted to establish that D4 and D8 were the endemic genotypes in Italy during 2010.

  3. Identification of Cryptosporidiumspecies and genotypes in dairy cattle in Brazil

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    Flavio Medeiros Paz e Silva

    Full Text Available In this study, we identified Cryptosporidium species and genotypes present in dairy cattle in the central region of São Paulo state, Brazil. Fecal specimens were collected from 200 animals (100 calves and 100 cows in ten dairy farms. Fecal samples were examined using microscopic examination (ME, enzyme immunoassay (EIA and polymerase chain reaction (PCR. Cryptosporidiumspecies and genotypes were determined by restriction fragment length polymorphism (RFLP or DNA sequencing analysis of the SSU-rRNA and GP60 genes. The occurrence of Cryptosporidium spp. infection was 14% (28/200. The occurrence in calves (26% was significantly higher than in cows (2%. Of the 27 Cryptosporidium-positive specimens submitted to genotyping, C. andersoni was identified in 23 (85.1%, C. bovis in three (11.1%, and the zoonotic C. parvum subtype IIaA15G2R1 in one (3.7%. The study demonstrates thatCryptosporidium spp. infection was common and widespread in dairy cattle in this region and that calves have a high prevalence of C. andersoni. Furthermore, the presence of C. parvumsubtype IIaA15G2R1 indicates that dairy calves from this region should be considered a potential source of zoonotic Cryptosporidiumoocysts.

  4. Reaction of Cauliflower Genotypes to Black Rot of Crucifers

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    da Silva, Lincon Rafael; da Silva, Renan César Dias; Cardoso, Atalita Francis; de Mello Pelá, Gláucia; Carvalho, Daniel Diego Costa

    2015-01-01

    This study aimed to evaluate six cauliflower genotypes regarding their resistance to black rot and their production performance. To do so, it was conducted two field experiments in Ipameri, Goiás, Brazil, in 2012 and 2013. It was used a randomized block design, with four replications (total of 24 plots). Each plot consisted of three planting lines 2.5 m long (six plants/line), spaced 1.0 m apart, for a total area of 7.5 m2. Evaluations of black rot severity were performed at 45 days after transplanting, this is, 75 days after sowing (DAS), and yield evaluations at 90 to 105 DAS. The Verona 184 genotype was the most resistant to black rot, showing 1.87 and 2.25% of leaf area covered by black rot symptom (LACBRS) in 2012 and 2013. However, it was not among the most productive materials. The yield of the genotypes varied between 15.14 and 25.83 t/ha in both years, Lisvera F1 (21.78 and 24.60 t/ha) and Cindy (19.95 and 23.56 t/ha) being the most productive. However, Lisvera F1 showed 6.37 and 9.37% of LACBRS and Cindy showed 14.25 and 14.87% of LACBRS in 2012 and 2013, being both considered as tolerant to black rot. PMID:26060437

  5. Reaction of Cauliflower Genotypes to Black Rot of Crucifers

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    Lincon Rafael da Silva

    2015-06-01

    Full Text Available This study aimed to evaluate six cauliflower genotypes regarding their resistance to black rot and their production performance. To do so, it was conducted two field experiments in Ipameri, Goiás, Brazil, in 2012 and 2013. It was used a randomized block design, with four replications (total of 24 plots. Each plot consisted of three planting lines 2.5 m long (six plants/line, spaced 1.0 m apart, for a total area of 7.5 m². Evaluations of black rot severity were performed at 45 days after transplanting, this is, 75 days after sowing (DAS, and yield evaluations at 90 to 105 DAS. The Verona 184 genotype was the most resistant to black rot, showing 1.87 and 2.25% of leaf area covered by black rot symptom (LACBRS in 2012 and 2013. However, it was not among the most productive materials. The yield of the genotypes varied between 15.14 and 25.83 t/ha in both years, Lisvera F1 (21.78 and 24.60 t/ha and Cindy (19.95 and 23.56 t/ha being the most productive. However, Lisvera F1 showed 6.37 and 9.37% of LACBRS and Cindy showed 14.25 and 14.87% of LACBRS in 2012 and 2013, being both considered as tolerant to black rot.

  6. Targeted SNP genotyping using the TaqMan® assay.

    Science.gov (United States)

    Schleinitz, Dorit; Distefano, Johanna K; Kovacs, Peter

    2011-01-01

    More than 99% of genomic DNA sequence is identical among humans, and not surprisingly, slight variations in sequence can often produce a major effect on phenotype. Sequence variants may also mediate the manner in which humans are susceptible to disease or respond to environmental factors such as bacteria, viruses, toxins, chemicals, drugs, and therapeutic interventions. Single-nucleotide polymorphisms (SNPs) are DNA sequence variations that occur when a single base in the genome sequence can be represented by at least two different nucleotides. In the last decade, numerous SNPs have been identified that explain, at least partially, the genetic architecture of complex diseases such as cancer, diabetes, vascular complications, some forms of mental illness, and a multitude of other disorders. Disease-related SNPs are commonly identified through candidate gene approaches, or more recently, through genome-wide association studies. In either case, findings of association require verification in independent, population-based, study samples, usually consisting of several hundreds/thousands of individuals. A convenient technique to genotype a moderate number of markers in this kind of study is available with the TaqMan® platform (Applied Biosystems; Foster City, CA), which utilizes polymerase chain reaction amplification and allelic discrimination to easily and efficiently generate genotype data in a cost-effective way. Here, we introduce and describe this commonly used technique and include protocols that can be directly used in laboratories aiming to perform moderate- to large-scale genotyping studies.

  7. Inverse association between obesity predisposing FTO genotype and completed suicide.

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    Izabela Chojnicka

    Full Text Available The A allele of rs9939609 in the FTO gene predisposes to increased body mass index (BMI and obesity. Recently we showed an inverse association between the obesity related A allele of rs9939609 and alcohol dependence which was replicated by others. Since this finding raises a possibility that FTO may be associated with other psychiatric phenotypes, we aimed to examine association of rs9939609 with completed suicide. We genotyped rs9939609 in 912 suicide victims and 733 controls using TaqMan approach. We observed an inverse association between suicide and the rs9939609 A allele (OR = 0.80, P = 0.002, Pcor = 0.006 with genotype distribution suggesting a co-dominant effect. Given the link between alcoholism and suicide under influence of alcohol reported in Polish population, confounding by alcohol addiction was unlikely due to apparently similar effect size among cases who were under influence of ethanol at the time of death (OR = 0.76, P = 0.003, N = 361 and those who were not (OR = 0.80, P = 0.007, N = 469. The search for genotype-phenotype correlations did not show significant results. In conclusion, our study proves that there is an inverse association between rs9939609 polymorphism in FTO gene and completed suicide which is independent from association between FTO and alcohol addiction.

  8. Seroprevalence and genotype of Chlamydia in pet parrots in China.

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    Zhang, N-Z; Zhang, X-X; Zhou, D-H; Huang, S-Y; Tian, W-P; Yang, Y-C; Zhao, Q; Zhu, X-Q

    2015-01-01

    Parrots are one of the most popular pet birds in China, and can harbour Chlamydia which has significance for human and animal health. We investigated, by indirect haemagglutination assay, the seroprevalence of Chlamydia infection in four species of parrots, namely budgerigars (Melopsittacus undulatus), lovebirds (Agapornis sp.), cockatiels (Nymphicus hollandicus) and Alexandrine parakeets (Psittacula eupatria) that were collected from Weifang and Beijing cities, North China and explored the association between potential risk factors and chlamydial seropositivity. We further determined the genotype of Chlamydia in 21 fresh faecal samples based on the ompA sequence by reconstruction of phylogenetic relationships. Of the 311 parrots examined, 35·37% (95% confidence interval 30·06-40·68) were seropositive, and species, gender, age, season and geographical location were identified as risk factors. Two PCR-positive samples represented Chlamydia psittaci genotype A. The occurrence of C. psittaci genotype A in the droppings of two pet parrots in China suggests potential environmental contamination with Chlamydiaceae and may raise a public health concern.

  9. Angiogenin levels and ANG genotypes: dysregulation in amyotrophic lateral sclerosis.

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    Russell Lewis McLaughlin

    Full Text Available OBJECTIVE: To determine whether 5 single nucleotide polymorphisms (SNPs associate with ALS in 3 different populations. We also assessed the contribution of genotype to angiogenin levels in plasma and CSF. METHODS: Allelic association statistics were calculated for polymorphisms in the ANG gene in 859 patients and 1047 controls from Sweden, Ireland and Poland. Plasma, serum and CSF angiogenin levels were quantified and stratified according to genotypes across the ANG gene. The contribution of SNP genotypes to variance in circulating angiogenin levels was estimated in patients and controls. RESULTS: All SNPs showed association with ALS in the Irish group. The SNP rs17114699 replicated in the Swedish cohort. No SNP associated in the Polish cohort. Age- and sex-corrected circulating angiogenin levels were significantly lower in patients than in controls (p<0.001. An allele dose-dependent regulation of angiogenin levels was observed in controls. This regulation was attenuated in the ALS cohort. A significant positive correlation between CSF plasma angiogenin levels was present in controls and abolished in ALS. CONCLUSIONS: ANG variants associate with ALS in the Irish and Swedish populations, but not in the Polish. There is evidence of dysregulation of angiogenin expression in plasma and CSF in sporadic ALS. Angiogenin expression is likely to be important in the pathogenesis of ALS.

  10. Global genotype-phenotype correlations in Pseudomonas aeruginosa.

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    Claudia Pommerenke

    Full Text Available Once the genome sequence of an organism is obtained, attention turns from identifying genes to understanding their function, their organization and control of metabolic pathways and networks that determine its physiology. Recent technical advances in acquiring genome-wide data have led to substantial progress in identifying gene functions. However, we still do not know the function of a large number of genes and, even when a gene product has been assigned to a functional class, we cannot normally predict its contribution to the phenotypic behaviour of the cell or organism--the phenome. In this study, we assessed bacterial growth parameters of 4030 non-redundant PA14 transposon mutants in the pathogenic bacterium Pseudomonas aeruginosa. The genome-wide simultaneous analysis of 119 distinct growth-related phenotypes uncovered a comprehensive phenome and provided evidence that most genotypes are not phenotypically isolated but rather define specific complex phenotypic clusters of genotypes. Since phenotypic overlap was demonstrated to reflect the relatedness of genotypes on a global scale, knowledge of an organism's phenome might significantly contribute to the advancement of functional genomics.

  11. Genotype Reconstruction of Paternity in European Lobsters (Homarus gammarus.

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    Charlie D Ellis

    Full Text Available Decapod crustaceans exhibit considerable variation in fertilisation strategies, ranging from pervasive single paternity to the near-ubiquitous presence of multiple paternity, and such knowledge of mating systems and behaviour are required for the informed management of commercially-exploited marine fisheries. We used genetic markers to assess the paternity of individual broods in the European lobster, Homarus gammarus, a species for which paternity structure is unknown. Using 13 multiplexed microsatellite loci, three of which are newly described in this study, we genotyped 10 eggs from each of 34 females collected from an Atlantic peninsula in the south-western United Kingdom. Single reconstructed paternal genotypes explained all observed progeny genotypes in each of the 34 egg clutches, and each clutch was fertilised by a different male. Simulations indicated that the probability of detecting multiple paternity was in excess of 95% if secondary sires account for at least a quarter of the brood, and in excess of 99% where additional sire success was approximately equal. Our results show that multiple paternal fertilisations are either absent, unusual, or highly skewed in favour of a single male among H. gammarus in this area. Potential mechanisms upholding single paternal fertilisation are discussed, along with the prospective utility of parentage assignments in evaluations of hatchery stocking and other fishery conservation approaches in light of this finding.

  12. Cyclooxygenase 2 genotypes influence prostate cancer susceptibility in Japanese Men.

    Science.gov (United States)

    Sugie, Satoru; Tsukino, Hiromasa; Mukai, Shoichiro; Akioka, Takahiro; Shibata, Norihiko; Nagano, Masafumi; Kamoto, Toshiyuki

    2014-03-01

    This study aims to evaluate the relationship between the cyclooxygenase 2 (COX2) G1195A (rs689465) polymorphism and the risk of prostate cancer in a Japanese population and the associations between COX2 polymorphisms and clinicopathological characteristics, including Gleason grade and prostate-specific antigen (PSA) grade. We recruited 134 patients with prostate cancer and 86 healthy controls matched for age and smoking status. The COX2 G1195A polymorphism status was determined by polymerase chain reaction and restriction fragment length polymorphism analysis. Genotype distributions (p = 0.028) and allelic frequencies (p = 0.014) differed significantly between prostate cancer and control groups in terms of the COX2 G1195A polymorphism (Pearson's χ (2) test). Logistic regression analysis of case and control outcomes showed an odds ratio between the GG and AA genotypes of 3.15 (95% confidence interval = 1.27-8.08, p = 0.014), indicating an increased risk of prostate cancer associated with the AA genotype. Subset analysis revealed no significant associations between this polymorphism and clinicopathological characteristics of prostate cancer. This study demonstrated a relationship between the COX2 G1195A variant and prostate cancer risk. This polymorphism may merit further investigation as a potential genomic marker for the early detection of prostate cancer. Our results support the hypothesis that rs689465 influences susceptibility to prostate cancer; however, prostate cancer progression was not associated with rs689465 in a Japanese population.

  13. S-Genotype Profiles of Turkish Apricot Germplasm

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    Kadir Ugurtan YILMAZ

    2016-06-01

    Full Text Available In flowering plants, gametophytic self-incompatibility, controlled by a single locus with several allelic variants, is one of the major problems preventing self-fertilization. Among fruit trees, apricots show to a high degree self-incompatibility, especially in Middle-Asian and Iranian-Caucasian eco-geographical groups. In the present study, self-(incompatibility characteristics of a total of 236 apricot genotypes (218 Turkish and 18 foreign found within the National Apricot Germplasms of Apricot Research Institute in Malatya, Turkey was studied. Analyses were carried out by using four primer pairs (SRc-F and SRc-R, EM-PC2consFD and EM-PC3consRD, AprSC8-R and PaConsI-F, AprFBC8-F and AprFBC8-R. A total of 11 S-RNase alleles (S2, S3, S6, S7, S8, S9, S11, S12, S13, S20 and Sc were determined in the 236 apricot genotypes. As Turkish and foreign apricot genotypes are determined mostly self-incompatible, the data obtained hereby might be of good use for apricot breeding programs and more practically, for apricot new plantations; thus pollinator cultivars should be considered when self-incompatible apricot cultivars are being used.

  14. Geographical Distribution of Trypanosoma cruzi Genotypes in Venezuela

    Science.gov (United States)

    Carrasco, Hernán J.; Segovia, Maikell; Llewellyn, Martin S.; Morocoima, Antonio; Urdaneta-Morales, Servio; Martínez, Cinda; Martínez, Clara E.; Garcia, Carlos; Rodríguez, Marlenes; Espinosa, Raul; de Noya, Belkisyolé A.; Díaz-Bello, Zoraida; Herrera, Leidi; Fitzpatrick, Sinead; Yeo, Matthew; Miles, Michael A.; Feliciangeli, M. Dora

    2012-01-01

    Chagas disease is an endemic zoonosis native to the Americas and is caused by the kinetoplastid protozoan parasite Trypanosoma cruzi. The parasite is also highly genetically diverse, with six discrete typing units (DTUs) reported TcI – TcVI. These DTUs broadly correlate with several epidemiogical, ecological and pathological features of Chagas disease. In this manuscript we report the most comprehensive evaluation to date of the genetic diversity of T. cruzi in Venezuela. The dataset includes 778 samples collected and genotyped over the last twelve years from multiple hosts and vectors, including nine wild and domestic mammalian host species, and seven species of triatomine bug, as well as from human sources. Most isolates (732) can be assigned to the TcI clade (94.1%); 24 to the TcIV group (3.1%) and 22 to TcIII (2.8%). Importantly, among the 95 isolates genotyped from human disease cases, 79% belonged to TcI - a DTU common in the Americas, however, 21% belonged to TcIV- a little known genotype previously thought to be rare in humans. Furthermore, were able to assign multiple oral Chagas diseases cases to TcI in the area around the capital, Caracas. We discuss our findings in the context of T. cruzi DTU distributions elsewhere in the Americas, and evaluate the impact they have on the future of Chagas disease control in Venezuela. PMID:22745843

  15. Different genotypes of alternative small grains in organic farming

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    Kovačević Dušan Đ.

    2014-01-01

    Full Text Available The main objectives were to examine different genotypes of alternative small grains important for food technology in organic farming conditions on morphological and productive characteristics. Four genotypes of different alternative small grains were included in the trial. Three of them were chosen for specific usage in food technology compact wheat Bambi -Triticum aestivum L. ssp. compactum, spelt Nirvana (Triticum aestivum L. ssp. spelta, durum wheat Durumko-(Triticum durum L., and one which leads as a genotype for intensive conventional common wheat production in Serbia -NS 40S (Triticum aestivum L. ssp. vulgare. Plots were fertilized with biohumus "Royal ofert" (30 t ha-1 applied in autumn with basic tillage and microbial fertilizer "Slavol" ad as in spring foliar treatment in full tillering (5 l ha-1. Alternative small grains durum wheat and compact wheat except splet gives lower grain yield in organic condition compared with comercial cultivar for high-input NS-40S. [Projekat Ministarstva nauke Republike Srbije, br. TR-31066

  16. Does copper reduce cadmium uptake by different rice genotypes?

    Institute of Scientific and Technical Information of China (English)

    CUI Yujing; ZHANG Xuhong; ZHU Yongguan

    2008-01-01

    A hydroponics experiment was conducted to investigate the effect of copper (Cu) on cadmium (Cd),calcium (Ca),iron (Fe),and zinc (Zn) uptake by several rice genotypes.The experiment was carried out as a 2×2×4 factorial with four rice genotypes and two levels of Cu and Cd in nutrient solution.Plants were grown in a growth chamber with controlled environment.The results showed a significant difference between the biomass of different rice genotypes (P<0.001).The Cd and Cu concentration in the solution had no significant effect on the biomass.The addition of Cu significantly decreased Cd uptake by shoots and roots of rice (P<0.001).The Cd concentration did not significantly influence Ca uptake by plants,whereas the Cu concentration did (P=0.034).There was a significant influence of Cd on Fe uptake by shoots and roots (P<0.001,P=0.003,respectively).Zn uptake decreased significantly as the addition of Cd and Cu increased in shoots.We concluded that Cu had significant influence on Cd uptake.The possible mechanisms were discussed.

  17. Human papillomavirus genotypes and cervical cancer in northeast Thailand.

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    Natphopsuk, Sitakan; Settheetham-Ishida, Wannapa; Pientong, Chamsai; Sinawat, Supat; Yuenyao, Pissamai; Ishida, Takafumi; Settheetham, Dariwan

    2013-01-01

    Human papillomavirus (HPV) is a major cause of cervical cancer. More than 100 HPV genotypes have been identified; however the distribution varies geographically and according to ethnicity. The purpose of this study was to investigate the prevalence and distribution of HPV subtypes among Northeast Thai women. Subjects included 198 cases of SCCA and 198 age-matched, healthy controls. HPV-DNA was amplified by PCR using the consensus primers GP5+/6+ system followed by reverse line blot hybridization genotyping. The prevalence of high-risk HPV infection was 21 (10.1%) and 152 (76.8%) in the controls and in the cases, respectively. High-risk HPV significantly increased the risk for cervical cancer with an OR of 42.4 (95%CI: 22.4-81.4, p<0.001) and an adjusted OR of 40.7-fold (95%CI: 21.5-76.8, p <0.001). HPV-16 was the most prevalent HPV type in the SCCA (56.2%) followed by HPV-58 (17.8%) and HPV-18 (13.6%); whereas HPV-58 (46.4%) was a prominent genotype in the controls followed by HPV-16 (39.3%) and unidentified HPV types (25.0%). These findings indicate that HPV infection remains a critical risk factor for SCCA; particularly, HPV-16, HPV-58 and HPV-18. In order to eradicate cervical cancer, sustained health education, promoted use of prophylactics and a HPV-58 vaccine should be introduced in this region.

  18. Archaeology of NIDDM. Excavation of the "thrifty" genotype.

    Science.gov (United States)

    Wendorf, M; Goldfine, I D

    1991-02-01

    Since the 1940s, numerous cases of non-insulin-dependent diabetes mellitus (NIDDM) have been observed in certain American Indian populations. Extremely high prevalence rates of NIDDM occur most strikingly in several tribes of Paleo-Indians, whose ancestors migrated to North America greater than 11,000 yr ago. Archaeological evidence from that period indicates that certain groups of Paleo-Indians maintained an arctic-like hunter-gatherer life-style in an area in temperate North America ranging from Wyoming to Arizona. This life-style featured a reliance on unpredictable big game species as a major food source. However, at this time, big game species were becoming extinct. It is hypothesized that those Paleo-Indians who relied on big game as a food source developed a "thrifty" genotype that allowed a selective advantage during the periods of fasting that occurred between big game kills. It also is hypothesized that this thrifty genotype in these Indians may contribute to NIDDM when a sedentary life-style is adopted and food sources are constant. Because insulin resistance in muscle is a major feature of NIDDM, it is possible that insulin resistance per se is the phenotypic expression of the thrifty genotype.

  19. Genotyping of clinical isolates of Acanthamoeba genus in Venezuela.

    Science.gov (United States)

    Wagner, Carolina; Reyes-Batlle, María; Ysea, María Alejandra Vethencourt; Pérez, Mónica V Galindo; de Rondón, Carmen Guzmán; Paduani, Anaibeth J Nessi; Pérez, Angelyseb Dorta; López-Arencibia, Atteneri; Sifaoui, Ines; de Galindo, María Virginia Pérez; de Suárez, Eva Pérez; Martínez-Carretero, Enrique; Valladares, Basilio; Piñero, José E; Lorenzo-Morales, Jacob

    2016-12-01

    Free-living amoebae of Acanthamoeba genus are opportunistic pathogens distributed worldwide. Strains included in this genus are causative agents of a fatal encephalitis and a sight-threating keratitis in humans and other animals. In this study, 550 clinical samples which were collected between 1984 and 2014 from different patients with suspected infections due to Acanthamoeba were initially screened for the presence of this amoebic genus at the Laboratorio de Amibiasis-Escuela de Bioanálisis at the Universidad Central de Venezuela. Samples were cultured in 2% Non-Nutrient agar plates seeded with a layer of heat killed Escherichia coli. From the 550 clinical samples included in this study, 18 of them were positive for Acanthamoeba genus after culture identification. Moreover, positive samples were confirmed after amplification of the Diagnostic Fragment 3 (DF3) of the Acanthamoeba18S rDNA genus and sequencing was carried out in order to genotype the isolated strains of Acanthamoeba. Furthermore, the pathogenic potential of the strains was checked by performing thermotolerance and osmotolerance assays. Sequencing of the DF3 region resulted in the identification of genotype T4 in all the isolated strains. Moreover, most isolates were thermotolerant or both thermotolerant and osmotolerant and thus were classified as potentially pathogenic strains. To the best of our knowledge, this is the first report on the molecular characterization at the genotype level of Acanthamoeba strains in Venezuela.

  20. Pros and cons of direct genotyping on tuberculosis clinical samples.

    Science.gov (United States)

    Sadegh, Hamidreza; Kargarpour Kamakoli, Mansour; Farmanfarmaei, Ghazaleh; Masoumi, Morteza; Abdolrahimi, Farid; Fateh, Abolfazl; Ebrahimzadeh, Nayereh; Rahimi Jamnani, Fatemeh; Vaziri, Farzam; Siadat, Seyed Davar

    2017-02-01

    Prompt genotyping of Mycobacterium tuberculosis (M. tuberculosis) is crucial for improving molecular epidemiological investigation of tuberculosis (TB). We performed a retrospective study to evaluate the use of 24 loci MIRU-VNTR (mycobacterial interspersed repetitive unit-variable number of tandem-repeat) directly on 135 clinical samples from 84 TB patients. There was a direct correlation between genotyping on clinical samples by MIRU-VNTR and bacterial load (P = 0.001). VNTR loci were amplified successfully for 41.5% of the clinical samples (19-24 loci), 32.6% (13-18 loci), 23.7% (7-12 loci) and 2.2% (1-6 loci). Loci of 2401, 577, 2996 and 154 had the highest power to show the mixed strains infection in clinical samples. Direct MIRU-VNTR is partially successful in complete genotyping of M. tuberculosis strains. On the other hand, detection of polyclonal infection is undoubtedly reliable based on the direct MIRU-VNTR. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. The Role of Haptoglobin Genotypes in Chagas Disease

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    Ninomar Mundaray Fernández

    2014-01-01

    Full Text Available Although the number of people infected with T. cruzi is on the rise, host genetic and immune components that are crucial in the development of the Chagas disease have been discovered. We investigated the frequency of polymorphisms in the gene encoding haptoglobin of patients with chronic Chagas disease. The results suggest that while the HP1-1 genotype may confer protection against infection and the development of chronic Chagas disease due to the rapid metabolism of the Hp1-1-Hb complex and its anti-inflammatory activity, the presence of HP2-2 genotype may increase susceptibility towards a chronic condition of the disease due to a slow metabolism of the Hp2-2-Hb complex, lower antioxidant activity, and increased inflammatory reactivity, which lead to cell damage and a deterioration of the cardiac function. Finally, correlations between HP genotypes in different age groups and cardiac manifestations suggest that HP polymorphism could influence the prognosis of this infectious disease. This study shows some of the relevant aspects of the haptoglobin gene polymorphism and its implications in the T. cruzi infection.

  2. The Role of Haptoglobin Genotypes in Chagas Disease

    Science.gov (United States)

    Mundaray Fernández, Ninomar; Fernández-Mestre, Mercedes

    2014-01-01

    Although the number of people infected with T. cruzi is on the rise, host genetic and immune components that are crucial in the development of the Chagas disease have been discovered. We investigated the frequency of polymorphisms in the gene encoding haptoglobin of patients with chronic Chagas disease. The results suggest that while the HP1-1 genotype may confer protection against infection and the development of chronic Chagas disease due to the rapid metabolism of the Hp1-1-Hb complex and its anti-inflammatory activity, the presence of HP2-2 genotype may increase susceptibility towards a chronic condition of the disease due to a slow metabolism of the Hp2-2-Hb complex, lower antioxidant activity, and increased inflammatory reactivity, which lead to cell damage and a deterioration of the cardiac function. Finally, correlations between HP genotypes in different age groups and cardiac manifestations suggest that HP polymorphism could influence the prognosis of this infectious disease. This study shows some of the relevant aspects of the haptoglobin gene polymorphism and its implications in the T. cruzi infection. PMID:25147423

  3. Distribution of Hepatitis B virus genotypes among healthy blood donors in eastern part of North India

    Directory of Open Access Journals (Sweden)

    Kumar Kailash

    2011-01-01

    Full Text Available Aim: We evaluated the distribution HBV genotypes among non-remunerated healthy blood donors in eastern North India. Materials and Methods: During screening of donated blood, 176 consecutive HBsAg positive, samples comprised the study. HBV-DNA was quantitative detected in 150 samples by PCR. HBV genotype was determined by identifying genotype-specific DNA band using nested PCR. Results: Majorities were of age group 31-40 yrs (65.3%. Males (92.7% outnumbered females (7.3% and were HbeAg-negative HBsAg carriers. Over all, genotype-A was the most prevalent (54% followed by D (21.3%. We did not find genotype-G and H. Districts under study, divided into four zones: Zone-I genotype-A was most common (62.3% followed by D (18.8%; Zone-II genotype-C (41.2% was more frequent followed by D (20.6% and A (17.7%. Zone-III in adjoining Bihar state close to Zone-I, A was more prevalent (81.8% followed by B and C (9.1%. In Zone-IV adjoining Zone- II had genotype-A (100% only. Genotype-D had more sporadic distribution. Genotype-E and F were prevalent in Zone I and II (3/150, 2%. Conclusions: Among blood donors HBV genotype-A followed by D was the most prevalent in eastern North India. Genotype-A had pattern of distribution signifying common focus, while D was more sporadic and C had single large pocket (Zone-II probably common focus but restricting to particular area. Evidences are suggestive of association of HBV genotype in liver dysfunction. An effective treatment and preventive strategies based of genotypes will reduce the disease burden and increase the blood safety.

  4. Temporal dynamics and subpopulation analysis of Theileria orientalis genotypes in cattle.

    Science.gov (United States)

    Jenkins, C; Micallef, M; Alex, S M; Collins, D; Djordjevic, S P; Bogema, D R

    2015-06-01

    In Australia, outbreaks of clinical theileriosis caused by Theileria orientalis have been largely associated with the Ikeda genotype which can occur as a sole infection, or more commonly, as a mixture of genotypes. The most prevalent genotype, Chitose, frequently co-occurs with type Ikeda, however the role of this genotype in clinical disease has not been clearly established. Furthermore, the dynamics of individual genotypes in field infection of cattle have not been examined. In this study we developed quantitative PCR (qPCR) and genotyping methods to examine the role of the Chitose genotype in clinical disease and to investigate the temporal dynamics of T. orientalis Ikeda, Chitose and Buffeli genotypes in naïve animals introduced to a T. orientalis-endemic area. Analysis of the major piroplasm surface protein (MPSP) genes of Chitose isolates revealed the presence of two distinct phylogenetic clusters, Chitose A and Chitose B. A genotyping assay aimed at determining Chitose A/B allele frequency revealed that the Chitose A phylogenetic cluster is strongly associated with clinical disease but nearly always co-occurs with the Ikeda genotype. qPCR revealed that the Chitose genotype (particularly Chitose A), undergoes temporal switching in conjunction with the Ikeda genotype and contributes substantially to the overall parasite burden. The benign Buffeli genotype can also undergo temporal switching but levels of this genotype appear to remain low relative to the Ikeda and Chitose types. Interplay between vector and host immunological factors is presumed to be critical to the population dynamics observed in this study. Genotypic switching likely contributes to the persistence of T. orientalis in the host.

  5. Population structure of mixed Mycobacterium tuberculosis infection is strain genotype and culture medium dependent.

    Directory of Open Access Journals (Sweden)

    Madeleine Hanekom

    Full Text Available BACKGROUND: Molecular genotyping methods have shown infection with more than one Mycobacterium tuberculosis strain genotype in a single sputum culture, indicating mixed infection. AIM: This study aimed to develop a PCR-based genotyping tool to determine the population structure of M. tuberculosis strain genotypes in primary Mycobacterial Growth Indicator Tubes (MGIT and Löwenstein-Jensen (LJ cultures to identify mixed infections and to establish whether the growth media influenced the recovery of certain strain genotypes. METHOD: A convenience sample of 206 paired MGIT and LJ M. tuberculosis cultures from pulmonary tuberculosis patients resident in Khayelitsha, South Africa were genotyped using an in-house PCR-based method to detect defined M. tuberculosis strain genotypes. RESULTS: The sensitivity and specificity of the PCR-based method for detecting Beijing, Haarlem, S-family, and LAM genotypes was 100%, and 75% and 50% for detecting the Low Copy Clade, respectively. Thirty-one (15% of the 206 cases showed the presence of more than one M. tuberculosis strain genotype. Strains of the Beijing and Haarlem genotypes were significantly more associated with a mixed infection (on both media when compared to infections with a single strain (Beijing MGIT p = 0.02; LJ, p<0.01 and (Haarlem: MGIT p<0.01; LJ, p = 0.01. Strains with the Beijing genotype were less likely to be with "other genotype" strains (p<0.01 while LAM, Haarlem, S-family and LCC occurred independently with the Beijing genotype. CONCLUSION: The PCR-based method was able to identify mixed infection in at least 15% of the cases. LJ media was more sensitive in detecting mixed infections than MGIT media, implying that the growth characteristics of M. tuberculosis on different media may influence our ability to detect mixed infections. The Beijing and Haarlem genotypes were more likely to occur in a mixed infection than any of the other genotypes tested suggesting pathogen

  6. Neutralizing antibodies in patients with chronic hepatitis C, genotype 1, against a panel of genotype 1 culture viruses

    DEFF Research Database (Denmark)

    Pedersen, Jannie; Jensen, Tanja B; Carlsen, Thomas H R;

    2013-01-01

    patients with chronic HCV infection with and without sustained virologic response when tested against any of the included culture viruses. However, NAb50-titers varied significantly with a mean reciprocal NAb50-titer of 800 (range: 100-6400) against DH6/JFH1 compared to a mean NAb50-titer of 50 (range:......The correlation of neutralizing antibodies to treatment outcome in patients with chronic hepatitis C virus (HCV) infection has not been established. The aim of this study was to determine whether neutralizing antibodies could be used as an outcome predictor in patients with chronic HCV, genotype 1......, infection treated with pegylated interferon-α and ribavirin. Thirty-nine patients with chronic hepatitis C, genotype 1a or 1b, with either sustained virologic response (n = 23) or non-sustained virologic response (n = 16) were enrolled. Samples taken prior to treatment were tested for their ability...

  7. Correlation between Thymidylate Synthase Genotype and Susceptibility to Gastric Carcinoma

    Institute of Scientific and Technical Information of China (English)

    Lei Yang; Mingbing Xiao; Runzhou Ni; Qinghe Tan; Jinzhi Wei; Jianhong Wang; Bojian Ge

    2008-01-01

    OBTECTIVE TO investigate the COrrelation betweenpolymorphism of the 5'-untranslated region(5'-UTR)ofthymidylate synthase genes,as well as the lifestyle,and thesusceptibility of gastric carcinoma.METHoDS A case-control study,with 60 cases of gastriccarcinoma and 170 cases of general risk population-based controlsfrom Nantong,Jiangsu province,China,was conducted.Theepidemiological data,such as living habits of the cancer patients,were collected.DNA of peripheral blood leukocytes was obtainedfrom all of the subjects.The TS 5-UTR tandem repeat genotypewas detected using polymerase chain reaction(PCR).RESULTS There were three TS 5'-UTR genotypes in the groupof gastric cancer cases(2R/2R,2R/3R and 3R/3R)and six TS5'-UTR genotypes in the group of the controls(2R/2R,2R/3R,3R/3R,2R/4R,2R/5R and 3R/4R).The genotypic frequencies wererespectively 5.0%,43.3%and 51.7%in the gastric cancer group.Compared with the parameters in the control group,i,e., 4.7%,31.7%,60.6%,1.2%,1.2%and 0.6%.There were no significantdifferences between the two groups.Compared with the 3R/3R-genotvpe individuals who Where non.smokers,drank alcoholtwice or less each week,drank tea and did not intake pickled food(PF),the risk of gastric cancer significantly went up in the 2R/2Ror 2R/3R-genotype people who had habits of smoking,drinkingalcohol more than twice each week,no tea drinking but withfrequent intake of PF.The adjusted ORs were as follows,3.79 (95%CI:2.45-8.64),3.41(95%CI:1.21-8.47),5.99(95%CI:3.01-14_7),and 3.61(95%CI:1.81-8.78).CoNCLUSIoN There iS an obvious correlation between thepolymorphisms of TS 5'-UTR genotypes and the lifestyle ofindividuals in the development of gastric carcinoma.smoking,alcohol drinking,tea drinking,pickled food.Hospital and Springer

  8. Distribution of Hepatitis B Virus Genotypes among Patients with Chronic Infection in Japan Shifting toward an Increase of Genotype A▿

    Science.gov (United States)

    Matsuura, Kentaro; Tanaka, Yasuhito; Hige, Shuhei; Yamada, Gotaro; Murawaki, Yoshikazu; Komatsu, Masafumi; Kuramitsu, Tomoyuki; Kawata, Sumio; Tanaka, Eiji; Izumi, Namiki; Okuse, Chiaki; Kakumu, Shinichi; Okanoue, Takeshi; Hino, Keisuke; Hiasa, Yoichi; Sata, Michio; Maeshiro, Tatsuji; Sugauchi, Fuminaka; Nojiri, Shunsuke; Joh, Takashi; Miyakawa, Yuzo; Mizokami, Masashi

    2009-01-01

    Acute hepatitis B virus (HBV) infection has been increasing through promiscuous sexual contacts, and HBV genotype A (HBV/A) is frequent in patients with acute hepatitis B (AHB) in Japan. To compare the geographic distribution of HBV genotypes in patients with chronic hepatitis B (CHB) in Japan between 2005 and 2006 and between 2000 and 2001, with special attention to changes in the proportion of HBV/A, a cohort study was performed to survey changes in genotypes of CHB patients at 16 hospitals throughout Japan. Furthermore, we investigated the clinical characteristics of each genotype and examined the genomic characteristics of HBV/A isolates by molecular evolutionary analyses. Of the 1,271 patients, 3.5%, 14.1%, and 82.3% were infected with HBV/A, -B, and -C, respectively. In comparison with our previous survey during 2000 and 2001, HBV/A was twice as frequent (3.5% versus 1.7%; P = 0.02). The mean age was lower in the patients with HBV/A than in those with HBV/B or -C. Based on phylogenetic analyses of 11 full-length genomes and 29 pre-S2/S region sequences from patients, HBV/A isolates were imported from Europe and the United States, as well as the Philippines and India. They clustered with HBV/A from AHB patients and have spread throughout Japan. HBV/A has been increasing in CHB patients in Japan as a consequence of AHB spreading in the younger generation through promiscuous sexual contacts, aided by a tendency of HBV/A to induce chronic hepatitis. The spread of HBV/A infection in Japan should be prevented by universal vaccination programs. PMID:19297602

  9. Phenylalanine hydroxylase deficiency in the Slovak population: genotype-phenotype correlations and genotype-based predictions of BH4-responsiveness.

    Science.gov (United States)

    Polak, Emil; Ficek, Andrej; Radvanszky, Jan; Soltysova, Andrea; Urge, Otto; Cmelova, Eleonora; Kantarska, Dana; Kadasi, Ludevit

    2013-09-10

    We investigated the mutation spectrum of the phenylalanine hydroxylase gene (PAH) in a cohort of patients from 135 Slovak PKU families. Mutational screening of the known coding region, including conventional intron splice sites, was performed using high-resolution melting analysis, with subsequent sequencing analysis of the samples showing deviated melting profiles compared to control samples. The PAH gene was also screened for deletions and duplications using MLPA analysis. Forty-eight different disease causing mutations were identified in our patient group, including 30 missense, 8 splicing, 7 nonsense, 2 large deletions and 1 small deletion with frameshift; giving a detection rate of 97.6%. The most prevalent mutation was the p.R408W, occurring in 47% of all alleles, which concurs with results from neighboring and other Slavic countries. Other frequent mutations were: p.R158Q (5.3%), IVS12+1G>A (5.3%), p.R252W (5.1%), p.R261Q (3.9%) and p.A403V (3.6%). We also identified three novel missense mutations: p.F233I, p.R270I, p.F331S and one novel variant: c.-30A>T in the proximal part of the PAH gene promoter. A spectrum of 84 different genotypes was observed and a genotype based predictions of BH4-responsiveness were assessed. Among all genotypes, 36 were predicted to be BH4-responsive represented by 51 PKU families. In addition, genotype-phenotype correlations were performed.

  10. A latent modeling approach to genotype-phenotype relationships: maternal problem behavior clusters, prenatal smoking, and MAOA genotype.

    Science.gov (United States)

    McGrath, L M; Mustanski, B; Metzger, A; Pine, D S; Kistner-Griffin, E; Cook, E; Wakschlag, L S

    2012-08-01

    This study illustrates the application of a latent modeling approach to genotype-phenotype relationships and gene × environment interactions, using a novel, multidimensional model of adult female problem behavior, including maternal prenatal smoking. The gene of interest is the monoamine oxidase A (MAOA) gene which has been well studied in relation to antisocial behavior. Participants were adult women (N = 192) who were sampled from a prospective pregnancy cohort of non-Hispanic, white individuals recruited from a neighborhood health clinic. Structural equation modeling was used to model a female problem behavior phenotype, which included conduct problems, substance use, impulsive-sensation seeking, interpersonal aggression, and prenatal smoking. All of the female problem behavior dimensions clustered together strongly, with the exception of prenatal smoking. A main effect of MAOA genotype and a MAOA × physical maltreatment interaction were detected with the Conduct Problems factor. Our phenotypic model showed that prenatal smoking is not simply a marker of other maternal problem behaviors. The risk variant in the MAOA main effect and interaction analyses was the high activity MAOA genotype, which is discrepant from consensus findings in male samples. This result contributes to an emerging literature on sex-specific interaction effects for MAOA.

  11. Genotyping of Echinococcus granulosus from goats and sheep indicating G7 genotype in goats in the Northeast of Iran.

    Science.gov (United States)

    Fadakar, Bahman; Tabatabaei, Nasim; Borji, Hassan; Naghibi, Abolghasem

    2015-11-30

    Although cystic echinococcosis (CE) has been a human public health problem in the Northeast of Iran, molecular data regarding the genotypes of Echinococcus granulosus in goats and sheep in these regions are still scarce. In the present study, we determined the genotypes of E. granulosus infecting sheep and goats in northeast of Iran. During April 2013-June 2014, 50 and 30 hydatid cysts were recovered from liver tissue of sheep and goats, respectively,. Protoscoleces or germinal layers were collected from individual cysts, DNA was extracted, and the ribosomal DNA internal transcribed spacer 1 (ITS1) gene was amplified by PCR. The results of PCR-RFLP and the sequence analysis showed that all the samples isolated from sheep (n=50) and most of samples in goats (n=24) were G1 strain, the most prevalent strain in livestock ruminants of Iran. Furthermore, six parasites isolated from goats were found to correspond to E. intermedius (G7 genotype), here reported for the first time from Iran. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. The potential of different lime tree (Tilia spp genotypes for phytoextraction of heavy metals

    Directory of Open Access Journals (Sweden)

    Šijačić-Nikolić Mirjana

    2012-01-01

    Full Text Available The research of heavy metals contents (Pb, Mn, Zn, Ni, Fe in soil in the area of the National Park „Fruška gora”, along the highway M21 shows lower values for manganese, zinc and iron than the maximum allowed quantity prescribed by law. For nickel and lead it shows higher values than maximum allowed quantity. The heavy metals contents in leaves of lime tree in 12 analyzed genotypes are far below average values in accordance with ECCE with all genotypes except genotype 7 for lead and genotypes 7 and 8 for iron. The results of analysis of variance components show that out of four components (locality, genotype, locality x genotype and error only the interaction between locality and genotype does not contribute to variance. The contents of Pb, Mn, Fe and Zn in leaves is primarily influenced by genotype while Ni contents may be considered a consequence of locality. The selection of genotypes which is able to uptake greater quantities of heavy metals than other genotypes may serve as a solid basis for phytoextraction of heavy metals as a technology by which heavy metals, metalloids and radionuclides are extracted from environment through usage of suitable species and plant genotypes able to uptake and accumulate the given pollutants in parts of plant tissue. [Projekat Ministarstva nauke Republike Srbije, br. 43007: Studying climate change and its influence on the environment: Impacts, adaptation and mitigation

  13. Novel hepatitis C virus reporter replicon cell lines enable efficient antiviral screening against genotype 1a.

    Science.gov (United States)

    Robinson, Margaret; Yang, Huiling; Sun, Siu-Chi; Peng, Betty; Tian, Yang; Pagratis, Nikos; Greenstein, Andrew E; Delaney, William E

    2010-08-01

    The hepatitis C virus (HCV) subgenomic replicon is the primary tool for evaluating the activity of anti-HCV compounds in drug discovery research. Despite the prevalence of HCV genotype 1a (approximately 70% of U.S. HCV patients), few genotype 1a reporter replicon cell lines have been described; this is presumably due to the low replication capacity of such constructs in available Huh-7 cells. In this report, we describe the selection of highly permissive Huh-7 cell lines that support robust replication of genotype 1a subgenomic replicons harboring luciferase reporter genes. These novel cell lines support the replication of multiple genotype 1a replicons (including the H77 and SF9 strains), are significantly more permissive to genotype 1a HCV replication than parental Huh7-Lunet cells, and maintain stable genotype 1a replication levels suitable for antiviral screening. We found that the sensitivity of genotype 1a luciferase replicons to known antivirals was highly consistent between individual genotype 1a clonal cell lines but could vary significantly between genotypes 1a and 1b. Sequencing of the nonstructural region of 12 stable replicon cell clones suggested that the enhanced permissivity is likely due to cellular component(s) in these new cell lines rather than the evolution of novel adaptive mutations in the replicons. These new reagents will enhance drug discovery efforts targeting genotype 1a and facilitate the profiling of compound activity among different HCV genotypes and subtypes.

  14. Evidence of occult HCV genotypes in haemophilic individuals with unapparent HCV mixed infections.

    Science.gov (United States)

    Parodi, C; Culasso, A; Aloisi, N; García, G; Bastón, M; Corti, M; Bianco, R P; Campos, R; Ares, B R; Baré, P

    2008-07-01

    Individuals with haemophilia who received non heat-treated factor concentrates were likely to undergo multiple exposures to the hepatitis C virus (HCV). Therefore, HCV mixed-genotype infections might be more frequent in these patients than in the general population. Their prevalence is extremely variable in similar groups of patients tested by different assays due to the fact that currently available genotyping techniques are not suitable to detect multiple HCV genotypes in a viral population. As an HCV viral reservoir, the peripheral blood mononuclear cell (PBMC) might harbor viral variants distinct from the genotypes detected in plasma. We investigated the presence of HCV genotypes in a group of chronically infected haemophilic patients in the PBMC compartment using a non-stimulated cell culture system that allows the detection of the HCV genome in culture supernatants. We compared them to the HCV genotypes found in plasma samples. Cell culture experiments performed with PBMC demonstrated the presence of additional HCV genotypes that were undetected in the corresponding plasma samples with the same genotyping technique. Although mixed infections at HCV genotype level became evident in 5.6% of the patients (16/288), the culture methodology increased the number of HCV infections with multiple genotypes to 62.5% (10/16) (P HCV viral reservoirs is emphasized. Considering minor strains could influence the outcome of treatment, detection of covert HCV mixed-genotype infections might be essential for choosing the adequate therapeutic regimen.

  15. VO2 max is associated with ACE genotype in postmenopausal women.

    Science.gov (United States)

    Hagberg, J M; Ferrell, R E; McCole, S D; Wilund, K R; Moore, G E

    1998-11-01

    Relationships have frequently been found between angiotensin-converting enzyme (ACE) genotype and various pathological and physiological cardiovascular outcomes and functions. Thus we sought to determine whether ACE genotype affected maximal O2 consumption (VO2 max) and maximal exercise hemodynamics in postmenopausal women with different habitual physical activity levels. Age, body composition, and habitual physical activity levels did not differ among ACE genotype groups. However, ACE insertion/insertion (II) genotype carriers had a 6.3 ml . kg-1 . min-1 higher VO2 max (P VO2 max (P VO2 max than the DD genotype group, but the difference was not significant. ACE genotype accounted for 12% of the variation in VO2 max among women after accounting for the effect of habitual physical activity levels. The entire difference in VO2 max among ACE genotype groups was the result of differences in maximal arteriovenous O2 difference (a-vDO2). ACE genotype accounted for 17% of the variation in maximal a-vDO2 in these women. Maximal cardiac output index did not differ whatsoever among ACE genotype groups. Thus it appears that ACE genotype accounts for a significant portion of the interindividual differences in VO2 max among these women. However, this difference is the result of genotype-dependent differences in maximal a-vDO2 and not of maximal stroke volume and maximal cardiac output.

  16. Detecting small-scale genotype-environment interactions in apomictic dandelion (Taraxacum officinale) populations.

    Science.gov (United States)

    McLeod, K A; Scascitelli, M; Vellend, M

    2012-08-01

    Studies of genotype × environment interactions (G × E) and local adaptation provide critical tests of natural selection's ability to counter opposing forces such as gene flow. Such studies may be greatly facilitated in asexual species, given the possibility for experimental replication at the level of true genotypes (rather than populations) and the possibility of using molecular markers to assess genotype-environment associations in the field (neither of which is possible for most sexual species). Here, we tested for G × E in asexual dandelions (Taraxacum officinale) by subjecting six genotypes to experimental drought, mown and benign (control) conditions and subsequently using microsatellites to assess genotype-environment associations in the field. We found strong G × E, with genotypes that performed poorly under benign conditions showing the highest performance under stressful conditions (drought or mown). Our six focal genotypes comprise > 80% of plants in local populations. The most common genotype in the field showed its highest relative performance under mown conditions (the most common habitat in our study area), and almost all plants of this genotype in the field were found growing in mowed lawns. Genotypes performing best under benign experimental conditions were found most frequently in unmown conditions in the field. These results are strongly indicative of local adaptation at a very small scale, with unmown microsites of only a few square metres typically embedded within larger mown lawns. By studying an asexual species, we were able to map genotypes with known ecological characteristics to environments with high spatial precision.

  17. Biplot analysis of phenotypic stability in upland cotton genotypes in Mato Grosso.

    Science.gov (United States)

    Farias, F J C; Carvalho, L P; Silva Filho, J L; Teodoro, P E

    2016-05-20

    Seed cotton yield is a trait governed by multiple genes that cause changes in the performance of genotypes depending on the cultivation environment. Breeding programs examine the genotype x environment interaction (GE) using precise statistical methods, such as AMMI (additive main effects and multiplicative interaction) and GGE biplot (genotype main effects + genotype x environment interaction). The AMMI method combines the analysis of variance and principal components, to adjust the main effects (genotypes and environments) and the effects of GE interaction, respectively. The GGE biplot groups the genotype additive effect together with the multiplicative effect of the GE interaction, and submits both of these to the principal components analysis. The aim of this study was to investigate the association between the AMMI and GGE biplot methods and select cotton genotypes that simultaneously showed high productivity of seed cotton and stability in Mato Grosso environments. Trials were conducted with cotton cultivars in eight environments across Mato Grosso State in the 2008/2009 crop season. The experiment used a randomized block design with 16 genotypes and four replicates per genotype x environment combination. Data for seeds cotton productivity were analyzed by AMMI and GGE biplot methods. Both methods were concordant in the discrimination of environments and genotypes for phenotypic stability. The genotypes BRS ARAÇÁ and LD 05 CV had high seed cotton productivity and phenotypic stability, and could be grown in all environments across Mato Grosso State.

  18. Variation in toxicity of a current-use insecticide among resurrected Daphnia pulicaria genotypes.

    Science.gov (United States)

    Simpson, Adam M; Jeyasingh, Punidan D; Belden, Jason B

    2015-04-01

    This study examined how genotypes of Daphnia pulicaria from a single population, separated by thousands of generations of evolution in the wild, differ in their sensitivity to a novel anthropogenic stressor. These genotypes were resurrected from preserved resting eggs isolated from sediments belonging to three time periods: 2002-2008, 1967-1977, and 1301-1646 A.D. Toxicity of the organophosphate insecticide chlorpyrifos was determined through a series of acute toxicity tests. There was a significant dose-response effect in all genotypes studied. Moreover, significant variation in toxicity among genotypes within each time period was detected. Importantly, a significant effect of time period on sensitivity to chlorpyrifos was found. Analysis of the median effect concentrations (EC50s) for genotypes within each time period indicated that the 1301-1646 genotypes were 2.7 times more sensitive than the 1967-1977 genotypes. This trend may be partially explained by microevolutionary shifts in response to cultural eutrophication.

  19. Mineral content of sorghum genotypes and the influence of water stress.

    Science.gov (United States)

    Paiva, Caroline Liboreiro; Queiroz, Valéria Aparecida Vieira; Simeone, Maria Lúcia Ferreira; Schaffert, Robert Eugene; de Oliveira, Antônio Carlos; da Silva, Camila Santana

    2017-01-01

    Sorghum is a source of several minerals whose content may vary depending on the genotype and the production environment. The objective of this study was to screen sorghum genotypes for mineral content and to investigate the effect of water stress on it. A large variability was observed in the mineral content of 100 sorghum genotypes grown in environments without (WoWS) and with water stress (WthWS). The water stress decreased Mn, P, Mg and S contents in 100, 96, 93 and 56% of genotypes, respectively. The genotypes and other factors seemed to have more impact than water stress on K, Ca, Cu, Fe and Zn levels. In 100 sorghum genotypes, 2 were classified as excellent sources of Fe and 25 of Zn, in both environments. The best two genotypes to Fe content were SC21 and SC655 and to Zn were SC320 and SHAN-QUI-RED which showed great potential for use in biofortification.

  20. Occupational Tuberculosis in Denmark through 21 Years Analysed by Nationwide Genotyping

    DEFF Research Database (Denmark)

    Pedersen, Mathias Klok; Andersen, Aase Bengaard; Andersen, Peter Henrik;

    2016-01-01

    Tuberculosis (TB) is a well-known occupational hazard. Based on more than two decades (1992-2012) of centralized nationwide genotyping of all Mycobacterium tuberculosis culture-positive TB patients in Denmark, we compared M. tuberculosis genotypes from all cases notified as presumed occupational (N...... = 130) with M. tuberculosis genotypes from all TB cases present in the country (N = 7,127). From 1992 through 2006, the IS6110 Restriction Fragment Length Polymorphism (RFLP) method was used for genotyping, whereas from 2005 to present, the 24-locus-based Mycobacterial Interspersed Repetitive Unit......-Variable Number of Tandem Repeat (MIRU-VNTR) was used. An occupational TB case was classified as clustered if the genotype was 100% identical to at least one other genotype. Subsequently, based on genotype, time period, smear positivity, geography, susceptibility pattern, and any reported epidemiological links...

  1. Association between histological findings, aminotransferase levels and viral genotype in chronic hepatitis C infection

    Directory of Open Access Journals (Sweden)

    Amanda Alves Fecury

    2014-02-01

    Full Text Available Introduction: The genomic heterogeneity of hepatitis C virus (HCV influences liver disorders. This study aimed to determine the prevalence of HCV genotypes and to investigate the influence of these genotypes on disease progression. Methods: Blood samples and liver biopsies were collected from HCV-seropositive patients for serological analysis, biochemical marker measurements, HCV genotyping and histopathological evaluation. Results: Hepatitis C virus-ribonucleic acid (HCV-RNA was detected in 107 patients (90.6% with genotype 1 and 9.4% with genotype 3. Patients infected with genotype 1 exhibited higher mean necroinflammatory activity and fibrosis. Conclusions: HCV genotype 1 was the most prevalent and was associated with greater liver dysfunction.

  2. Genotypes of Candida albicans isolated from healthy individuals and their distribution in patients with oral candidiasis.

    Science.gov (United States)

    Takagi, Yuki; Fukano, Hideo; Shimozato, Kazuo; Tanaka, Reiko; Horii, Toshinobu; Kawamoto, Fumihiko; Kanbe, Toshio

    2013-12-01

    For the study of Candida albicans genotypes involved in development of candidiasis, Candida albicans isolates were collected from healthy volunteers and patients with oral candidiasis and genotyped on the basis of 25S rDNA and microsatellite polymorphisms. In the microsatellite analysis using two microsatellite markers (CDC3 and CAI), 63 healthy volunteer isolates were classified into 35 genotypes (allelic relations to CDC3 alleles 1:2/CAI alleles 1:2), among which genotypes II (115:119/23:23), III (115:123/18:27), and V (123:127/32:41) were found at frequencies of 12.7%, 7.9%, and 7.9%, respectively. In 68 oral candidiasis isolates classified into 39 genotypes, genotypes II and III were identified in 4.4% and 20.6% of the isolates, respectively. The frequency of genotype III was higher in the candidiasis isolates than in the healthy isolates (p oral candidiasis.

  3. Genetic diversity for grain Zn concentration in finger millet genotypes: Potential for improving human Zn nutrition

    Directory of Open Access Journals (Sweden)

    Ramegowda Yamunarani

    2016-06-01

    Full Text Available Nearly half of the world population suffers from micronutrient malnutrition, particularly Zn deficiency. It is important to understand genetic variation for uptake and translocation behaviors of Zn in relevant crop species to increase Zn concentration in edible parts. In the present study, genetic variation in grain Zn concentration of 319 finger millet genotypes was assessed. Large genetic variation was found among the genotypes, with concentrations ranging from 10 to 86 μg g− 1 grain. Uptake and translocation studies with Zn/65Zn application in 12 selected low-Zn genotypes showed wide variation in root uptake and shoot translocation, with genotypes GEC331 and GEC164 showing greater uptake and translocation. Genotypes GEC164 and GEC543 showed increased grain Zn concentration. Genotypes GEC331 and GEC164 also showed improved yield under Zn treatment. Appreciable variation in grain Zn concentration among finger millet genotypes found in this study offers opportunities to improve Zn nutrition through breeding.

  4. Detection and genotyping of enteroviruses in cerebrospinal fluid in patients in Victoria, Australia, 2007-2013.

    Science.gov (United States)

    Papadakis, Georgina; Chibo, Doris; Druce, Julian; Catton, Michael; Birch, Chris

    2014-09-01

    Genotyping by VP1 fragment polymerase chain reaction (PCR) and nucleic acid sequencing to detect enterovirus (EV) genotypes was performed directly on 729 EV PCR positive cerebrospinal fluid (CSF) samples collected between 2007 and 2012 from Victorian hospital inpatients. The overall genotype identification rate from CSF-positive material was 43%. The four most common genotypes identified were Echovirus 6 (24%), Echovirus 30 (17%), Echovirus 25 (10%), and Coxsackievirus A9 (10%), together comprising 61% of all EVs typed. The seasonal distribution of all EVs identified followed the recognized pattern of mainly summer epidemics. Three of the four predominant genotypes were present in each of the 6 years in which the study was conducted, with 20 other EV genotypes also detected, often in only a single year. Genotyping of EVs directly in CSF is faster, simpler and more sensitive than traditional virus neutralization assays performed on EV positive samples. © 2014 Wiley Periodicals, Inc.

  5. Development of a monoclonal antibody against viral haemorrhagic septicaemia virus (VHSV) genotype IVa

    DEFF Research Database (Denmark)

    Ito, T.; Olesen, Niels Jørgen; Skall, Helle Frank

    2010-01-01

    of the spread of genotypes to new geographical areas. A monoclonal antibody (MAb) against VHSV genotype IVa was produced, with the aim of providing a simple method of discriminating this genotype from the other VHSV genotypes (I, II, III and IVb). Balb/c mice were injected with purified VHSV-JF00Ehil (genotype...... IVa) from diseased farmed Japanese flounder. Ten hybridoma clones secreting monoclonal antibodies (MAbs) against VHSV were established. One of these, MAb VHS-10, reacted only with genotype IVa in indirect fluorescent antibody technique (IFAT) and ELISA. Using cell cultures that were transfected...... with each of the viral protein genes, it was shown that the MAb VHS-10 recognizes a nonlinear genotype IVa-specific epitope on the VHSV N-protein....

  6. Molecular and phylogenetic analyses suggest an additional hepatitis B virus genotype "I".

    Directory of Open Access Journals (Sweden)

    Hai Yu

    Full Text Available A novel hepatitis B virus (HBV strain (W29 was isolated from serum samples in the northwest of China. Phylogenetic and distance analyses indicate that this strain is grouped with a series of distinct strains discovered in Vietnam and Laos that have been proposed to be a new genotype I. TreeOrderScan and GroupScan methods were used to study the intergenotype recombination of this special group. Recombination plots and tree maps of W29 and these putative genotype I strains exhibit distinct characteristics that are unexpected in typical genotype C strains of HBV. The amino acids of P gene, S gene, X gene, and C gene of all genotypes (including subtypes were compared, and eight unique sites were found in genotype I. In vitro and in vivo experiments were also conducted to determine phenotypic characteristics between W29 and other representative strains of different genotypes obtained from China. Secretion of HBsAg in Huh7 cells is uniformly abundant among genotypes A, B, C, and I (W29, but not genotype D. HBeAg secretion is low in genotype I (W29, whose level is close to genotype A and much lower than genotypes B, C, and D. Results from the acute hydrodynamic injection mouse model also exhibit a similar pattern. From an overview of the results, the viral markers of W29 (I1 in Huh7 cells and mice had a more similar level to genotype A than genotype C, although the latter was closer to W29 in distance analysis. All evidence suggests that W29, together with other related strains found in Vietnam and Laos, should be classified into a new genotype.

  7. Hepatitis C viral load, genotype 3 and interleukin-28B CC genotype predict mortality in HIV and hepatitis C-coinfected individuals

    DEFF Research Database (Denmark)

    Clausen Nygaard, Louise; Astvad, Karen; Ladelund, Steen;

    2012-01-01

    : We hypothesized that hepatitis C virus (HCV) load and genotype may influence all-cause mortality in HIV-HCV-coinfected individuals.......: We hypothesized that hepatitis C virus (HCV) load and genotype may influence all-cause mortality in HIV-HCV-coinfected individuals....

  8. Distribution and molecular evolution of bacillus anthracis genotypes in Namibia.

    Directory of Open Access Journals (Sweden)

    Wolfgang Beyer

    Full Text Available The recent development of genetic markers for Bacillus anthracis has made it possible to monitor the spread and distribution of this pathogen during and between anthrax outbreaks. In Namibia, anthrax outbreaks occur annually in the Etosha National Park (ENP and on private game and livestock farms. We genotyped 384 B. anthracis isolates collected between 1983-2010 to identify the possible epidemiological correlations of anthrax outbreaks within and outside the ENP and to analyze genetic relationships between isolates from domestic and wild animals. The isolates came from 20 animal species and from the environment and were genotyped using a 31-marker multi-locus-VNTR-analysis (MLVA and, in part, by twelve single nucleotide polymorphism (SNP markers and four single nucleotide repeat (SNR markers. A total of 37 genotypes (GT were identified by MLVA, belonging to four SNP-groups. All GTs belonged to the A-branch in the cluster- and SNP-analyses. Thirteen GTs were found only outside the ENP, 18 only within the ENP and 6 both inside and outside. Genetic distances between isolates increased with increasing time between isolations. However, genetic distance between isolates at the beginning and end of the study period was relatively small, indicating that while the majority of GTs were only found sporadically, three genetically close GTs, accounting for more than four fifths of all the ENP isolates, appeared dominant throughout the study period. Genetic distances among isolates were significantly greater for isolates from different host species, but this effect was small, suggesting that while species-specific ecological factors may affect exposure processes, transmission cycles in different host species are still highly interrelated. The MLVA data were further used to establish a model of the probable evolution of GTs within the endemic region of the ENP. SNR-analysis was helpful in correlating an isolate with its source but did not elucidate

  9. Scanning fluorescence detector for high-throughput DNA genotyping

    Science.gov (United States)

    Rusch, Terry L.; Petsinger, Jeremy; Christensen, Carl; Vaske, David A.; Brumley, Robert L., Jr.; Luckey, John A.; Weber, James L.

    1996-04-01

    A new scanning fluorescence detector (SCAFUD) was developed for high-throughput genotyping of short tandem repeat polymorphisms (STRPs). Fluorescent dyes are incorporated into relatively short DNA fragments via polymerase chain reaction (PCR) and are separated by electrophoresis in short, wide polyacrylamide gels (144 lanes with well to read distances of 14 cm). Excitation light from an argon laser with primary lines at 488 and 514 nm is introduced into the gel through a fiber optic cable, dichroic mirror, and 40X microscope objective. Emitted fluorescent light is collected confocally through a second fiber. The confocal head is translated across the bottom of the gel at 0.5 Hz. The detection unit utilizes dichroic mirrors and band pass filters to direct light with 10 - 20 nm bandwidths to four photomultiplier tubes (PMTs). PMT signals are independently amplified with variable gain and then sampled at a rate of 2500 points per scan using a computer based A/D board. LabView software (National Instruments) is used for instrument operation. Currently, three fluorescent dyes (Fam, Hex and Rox) are simultaneously detected with peak detection wavelengths of 543, 567, and 613 nm, respectively. The detection limit for fluorescein-labeled primers is about 100 attomoles. Planned SCAFUD upgrades include rearrangement of laser head geometry, use of additional excitation lasers for simultaneous detection of more dyes, and the use of detector arrays instead of individual PMTs. Extensive software has been written for automatic analysis of SCAFUD images. The software enables background subtraction, band identification, multiple- dye signal resolution, lane finding, band sizing and allele calling. Whole genome screens are currently underway to search for loci influencing such complex diseases as diabetes, asthma, and hypertension. Seven production SCAFUDs are currently in operation. Genotyping output for the coming year is projected to be about one million total genotypes (DNA

  10. Bison PRNP genotyping and potential association with Brucella spp. seroprevalence

    Science.gov (United States)

    Seabury, C.M.; Halbert, N.D.; Gogan, P.J.P.; Templeton, J.W.; Derr, J.N.

    2005-01-01

    The implication that host cellular prion protein (PrPC) may function as a cell surface receptor and/or portal protein for Brucella abortus in mice prompted an evaluation of nucleotide and amino acid variation within exon 3 of the prion protein gene (PRNP) for six US bison populations. A non-synonymous single nucleotide polymorphism (T50C), resulting in the predicted amino acid replacement M17T (Met ??? Thr), was identified in each population. To date, no variation (T50: Met) has been detected at the corresponding exon 3 nucleotide and/or amino acid position for domestic cattle. Notably, 80% (20 of 25) of the Yellowstone National Park bison possessing the C/C genotype were Brucella spp. seropositive, representing a significant (P = 0.021) association between seropositivity and the C/C genotypic class. Moreover, significant differences in the distribution of PRNP exon 3 alleles and genotypes were detected between Yellowstone National Park bison and three bison populations that were either founded from seronegative stock or previously subjected to test-and-slaughter management to eradicate brucellosis. Unlike domestic cattle, no indel polymorphisms were detected within the corresponding regions of the putative bison PRNP promoter, intron 1, octapeptide repeat region or 3???-untranslated region for any population examined. This study provides the first evidence of a potential association between nucleotide variation within PRNP exon 3 and the presence of Brucella spp. antibodies in bison, implicating PrPC in the natural resistance of bison to brucellosis infection. ?? 2005 International Society for Animal Genetics.

  11. Survival of North American genotypes of Trichinella in frozen pork.

    Science.gov (United States)

    Hill, D E; Forbes, L; Zarlenga, D S; Urban, J F; Gajadhar, A A; Gamble, H R

    2009-12-01

    North American genotypes of Trichinella spiralis (T-1), Trichinella nativa (T-2), Trichinella pseudospiralis (T-4), Trichinella murrelli (T-5), and Trichinella T-6 were examined for susceptibility to freezing in pork using time-temperature combinations that have been proven to inactivate T. spiralis. Infections were established in 3-month-old pigs of mixed sex and breed by oral inoculation of 10,000 muscle larvae (ML) (all genotypes, rodent-derived ML), 20,000 ML (T-1, T-4, and T-5; cat-derived ML), or 30,000 ML (T-2 and T-6; cat-derived ML). Pigs were euthanized 60 days postinoculation. Muscles from the tongue, masseter muscles, diaphragm, triceps, hams, neck, rump, and loins were ground, pooled, and mixed to ensure even distribution of larvae. Samples (20 g) containing each Trichinella species, genotype, and source combination were placed in heat-sealable pouches, transferred to a constant temperature refrigerant bath, and maintained according to defined time and temperature combinations. Larvae recovered from cold-treated pork samples were inoculated into mice to determine infectivity. Results indicated that the time-temperature combinations known to render pork safe for T. spiralis are sufficient to inactivate T. nativa and T-6 (the freeze-resistant isolates), T. murrelli (the most common sylvatic species in the United States excluding Alaska), and T. pseudospiralis (a species that lacks a muscle nurse cell). These data close a gap in knowledge about the effectiveness of freezing for inactivating these parasites in pork and should alleviate concern about the safety of frozen pork products from the United States.

  12. Male Gametophytic Screening of Citrus Genotypes for Salt Stress Tolerance

    Directory of Open Access Journals (Sweden)

    A. Barandan

    2016-07-01

    Full Text Available Citrus species are classified as a sensitive group of trees to salt stress, but the levels of their sensitivity or tolerance to salt are different among cultivars. In order to evaluate the effects of salinity stress on pollen germination of some citrus cultivars, an experiment was performed in factorial, based on completely randomized design in three replications with Cleopatra mandarin (Citrus reshni and Poncirus trifoliata as tolerant and sensitive controls along with 13 genotypes. Pollen grains of these genotypes were cultured in media containing different levels of sodium chloride (0, 0.87, 1.6, 2.4, 3.1 dS/m along with 15% sucrose, 0.7% agar and 100 mg/L boric acid. In order to understand the biochemical responses of pollen grains to salt stress, they were cultured in liquid media with three levels of salinity (i.e. 0, 0.87 and 1.6 dS/m and then the amounts of total protein and enzyme activities of superoxide dismutase (SOD and ascorbate peroxidase (APX were evaluated. Significant differences of pollen germination (P ≤ 0.01 were observed in different salinity levels, but there were no significant differences in pollen tube growth. Pollen germination in Cleopatra was greater in comparison to Poncirus trifoliate, indicating that Cleopatra is a tolerant cultivar. The amounts of total protein and enzyme activities of SOD and APX were influenced by genotypes, salinity levels and their interactions (P ≤ 0.01. Considering the fastness and accuracy of this type of experiment, the evaluation of citrus pollen responses may, potentially, be hired as an initial screening criteria for detecting salt-sensitive varieties from the tolerant citrus ones.

  13. Genotype Analysis of Bacillus anthracis Strains Circulating in Bangladesh.

    Science.gov (United States)

    Rume, Farzana Islam; Affuso, Alessia; Serrecchia, Luigina; Rondinone, Valeria; Manzulli, Viviana; Campese, Emanuele; Di Taranto, Pietro; Biswas, Paritosh Kumar; Ahsan, Chowdhury Rafiqul; Yasmin, Mahmuda; Fasanella, Antonio; Hugh-Jones, Martin

    2016-01-01

    In Bangladesh, anthrax, caused by the bacterium Bacillus anthracis, is considered an endemic disease affecting ruminants with sporadic zoonotic occurrences in humans. Due to the lack of knowledge about risks from an incorrect removal of infected carcasses, the disease is not properly monitored, and because of the socio-economic conditions, the situation is under-reported and under-diagnosed. For sensitive species, anthrax represents a fatal outcome with sudden death and sometimes bleeding from natural orifices. The most common source of infection for ruminants is ingestion of spores during grazing in contaminated pastures or through grass and water contaminated with anthrax spores. Domestic cattle, sheep and goats can also become infected through contaminated bone meal (used as feed) originating from anthrax-infected carcasses. The present investigation was conducted to isolate B. anthracis organisms from 169 samples (73 soil, 1 tissue, 4 bone and 91 bone meal samples) collected from 12 different districts of Bangladesh. The sampling was carried out from 2012 to 2015. Twelve samples resulted positive for B. anthracis. Biomolecular analyses were conducted starting from the Canonical Single Nucleotide Polymorphism (CanSNP) to analyze the phylogenetic origin of strains. The analysis of genotype, obtained through the Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) with the analysis of 15 Variable Number Tandem Repeats (VNTR), demonstrated four different genotypes: two of them were previously identified in the district of Sirajganj. The sub-genotyping, conducted with Single Nucleotide Repeats analysis, revealed the presence of eight subgenotypes. The data of the present study concluded that there was no observed correlation between imported cattle feed and anthrax occurrence in Bangladesh and that the remarkable genetic variations of B. anthracis were found in the soil of numerous outbreaks in this country.

  14. Microcytic hypochromic anemia patients with thalassemia : Genotyping approach

    Directory of Open Access Journals (Sweden)

    Rahim Fakher

    2009-03-01

    Full Text Available Background: Microcytic hypochromic anemia is a common condition in clinical practice, and alpha-thalassemia has to be considered as a differential diagnosis. Aims: This study was conducted to evaluate the frequency of α-gene, β-gene and hemoglobin variant numbers in subjects with microcytic hypochromic anemia. Setting And Designs: Population-based case-control study in the Iranian population. Materials And Methods: A total of 340 subjects from southwest part of Iran were studied in the Research Center of Thalassemia and Hemoglobinopathies (RCTH, Iran. Genotyping for known a- and b-gene mutations was done with gap-PCR and ARMS. In cases of some rare mutations, the genotyping was done with the help of other techniques such as RFLP and ARMS-PCR. Statistical Analysis: Statistical analysis was carried out by SPSS 11.5 and an independent-sample t test. Results: Out of the total 340 individuals, 325 individuals were evaluated to have microcytic hypochromic anemia based on initial hematological parameters such as MCV< 80 fl; MCH < 27 pg; the remaining 15 patients were diagnosed with no definite etiology. The overall frequency of -α3.7 deletion in 325 individuals was 20.3%. The most frequent mutations were IVS II-I, CD 36/37 and IVS I-110 with frequencies of 6.31%, 5.27% and 1.64%, respectively. Only, there was a significant difference between beta-thalassemia trait and beta-thalassemia major with regard to MCV (P < 0.05 and MCH (P < 0.05 indices, and also MCH index between beta-thalassemia trait and Hb variants (P < 0.05. Conclusion: Molecular genotyping provides a rapid and reliable method for identification of common, rare and unknown a- and b-gene mutations, which help to diagnose unexplained microcytosis and thus prevent unnecessary iron supplementation.

  15. Interleukin-6 genotypes and serum levels in Chinese Hui population.

    Science.gov (United States)

    Gao, Shu-Ping; Liang, Shu; Pan, Min; Sun, Rong-Liang; Chen, Chu; Luan, Hong; Jiang, Min-Hui

    2014-01-01

    Interleukin-6 (IL-6) is a key pro-inflammatory cytokine involved in different physiologic and pathophysiologic processes, and circulating levels of IL-6 differ greatly between individuals. The Chinese Hui is one of the largest ethnic minorities, little is known about the distribution of IL-6 genetic variations and their effects on serum levels in Hui population. The aim of the present study is to determine the prevalence of -174G/C (rs1800795), -597G/A (rs1800797), and -634C/G (rs1800796) polymorphisms in the IL-6 gene promoter region and their association with IL-6 serum levels in the Ningxia Hui population. A total of 96 Hui subjects, (57 men and 39 women; mean age 49.65 ± 19.73 years) unrelated nationality residents in Ningxia Hui Autonomous Region were enrolled. Genotyping of the three polymorphisms were performed by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) combined with gel electrophoresis and then confirmed by direct sequencing. The -174G/C (97.92% GG, 2.08% GC, and 0% CC) and -597G/A (98.96% GG, 1.04% GA, and 0% AA) polymorphisms were rare. The frequencies of -634C/G genotypes CC, CG, and GG were found to be 54.17%, 40.62%, and 5.21%, respectively in total studied subjects, the derived allele frequencies for the C and G alleles were 74.48% and 25.52%. Increased IL-6 levels were correlated with the IL-6 -634G allele carriers (CG+GG genotypes). The results suggest that IL-6 -174G/C and -597G/A are rare but -634C/G is common in the Ningxia Hui population, and the -634G allele is associated with circulating levels of IL-6.

  16. Orodental phenotype and genotype findings in all subtypes of hypophosphatasia

    Directory of Open Access Journals (Sweden)

    Clauss François

    2009-02-01

    Full Text Available Abstract Background Hypophosphatasia (HP is a rare inherited disorder characterized by a wide spectrum of defects in mineralized tissues and caused by deficiency in the tissue non-specific alkaline phosphatase gene (ALPL. The symptoms are highly variable in their clinical expression, and relate to numerous mutations in this gene. The first clinical sign of the disease is often a premature loss of deciduous teeth, mostly in the moderate forms. Aim The purpose of this study was to document the oral features of HP patients and to relate theses features to the six recognized forms of HP in 5 patients with known genotype and to investigate the genotype-phenotype correlations. Methods Clinical and radiographic examinations were carried out. We collected medical and dental history in the kindred and biochemical data. Finally, mutations in the ALPL gene were tested by DNA sequencing in SESEP laboratory. Results We have for the first time related the known dental anomalies which occur as integral features of HP to the recognized clinical forms of HP. We also pointed out striking dental abnormalities which were never described in association with this rare disease. Accurate genotype-phenotype severity correlations were observed. Conclusion This work allowed us to compare orodental manifestations in all the clinical forms of HP within the patient's sample. According to the severity of the disorder, some dental defects were infrequent, while other were always present. The long term prognosis of the permanent teeth varies from a patient to another. As premature loss of primary teeth is often the first, and sometimes the only visible symptom of the milder forms, the paediatric dentist plays a critical role in the detection and diagnosis of the disease.

  17. Phenotypic and Genotypic Diversity of Salmonella in Finishing Swine.

    Science.gov (United States)

    Pires, Alda F A; Funk, Julie A; Habing, Greg G; Bolin, Carole

    2016-04-01

    Salmonella enterica (nontyphoidal) is one of the major causes of foodborne diseases in the United States and worldwide. Molecular typing methods are significant tools used to better understand the transmission and ecology of Salmonella in order to implement pre-harvest control measures. The objectives of this study were to describe the Salmonella genotypes, the distribution of isolate subtypes from different ecological niches (i.e., barn environment, nursery, and individual pigs) and their evolution over time in a longitudinal study conducted in three finishing sites (housing pigs from 10 weeks of age until slaughter at 24-26 weeks of age). Among the 107 Salmonella isolates submitted for pulsed-field gel electrophoresis (PFGE) analysis, there were 25 distinct subtypes. PFGE genotyping results were consistent with the serotype findings. A large number of distinguishable PFGE patterns (i.e., within the same serovar) were observed and different combinations of subtypes were identified within and across sites and cohorts. New subtypes may result of the introduction of new strains, genetic changes, or ongoing transmission of evolved strains within the production system. The same subtypes were detected intermittently during the study period, which suggests the persistence of indistinguishable subtypes in this production system. In addition, this study suggests persistence of the same subtype over several cohorts of pigs and potential residual contamination from the barn. Factors affecting adaptation and transmission of Salmonella within and among ecological systems (e.g., finishing pigs, nursery, and environment) should be further investigated. Understanding genotypic diversity of Salmonella in different ecological niches during pre-harvest may contribute to the development of more targeted and cost effective control programs during nursery and finishing phases.

  18. Development of a genotyping microarray for Usher syndrome

    Science.gov (United States)

    Cremers, Frans P M; Kimberling, William J; Külm, Maigi; de Brouwer, Arjan P; van Wijk, Erwin; te Brinke, Heleen; Cremers, Cor W R J; Hoefsloot, Lies H; Banfi, Sandro; Simonelli, Francesca; Fleischhauer, Johannes C; Berger, Wolfgang; Kelley, Phil M; Haralambous, Elene; Bitner‐Glindzicz, Maria; Webster, Andrew R; Saihan, Zubin; De Baere, Elfride; Leroy, Bart P; Silvestri, Giuliana; McKay, Gareth J; Koenekoop, Robert K; Millan, Jose M; Rosenberg, Thomas; Joensuu, Tarja; Sankila, Eeva‐Marja; Weil, Dominique; Weston, Mike D; Wissinger, Bernd; Kremer, Hannie

    2007-01-01

    Background Usher syndrome, a combination of retinitis pigmentosa (RP) and sensorineural hearing loss with or without vestibular dysfunction, displays a high degree of clinical and genetic heterogeneity. Three clinical subtypes can be distinguished, based on the age of onset and severity of the hearing impairment, and the presence or absence of vestibular abnormalities. Thus far, eight genes have been implicated in the syndrome, together comprising 347 protein‐coding exons. Methods: To improve DNA diagnostics for patients with Usher syndrome, we developed a genotyping microarray based on the arrayed primer extension (APEX) method. Allele‐specific oligonucleotides corresponding to all 298 Usher syndrome‐associated sequence variants known to date, 76 of which are novel, were arrayed. Results Approximately half of these variants were validated using original patient DNAs, which yielded an accuracy of >98%. The efficiency of the Usher genotyping microarray was tested using DNAs from 370 unrelated European and American patients with Usher syndrome. Sequence variants were identified in 64/140 (46%) patients with Usher syndrome type I, 45/189 (24%) patients with Usher syndrome type II, 6/21 (29%) patients with Usher syndrome type III and 6/20 (30%) patients with atypical Usher syndrome. The chip also identified two novel sequence variants, c.400C>T (p.R134X) in PCDH15 and c.1606T>C (p.C536S) in USH2A. Conclusion The Usher genotyping microarray is a versatile and affordable screening tool for Usher syndrome. Its efficiency will improve with the addition of novel sequence variants with minimal extra costs, making it a very useful first‐pass screening tool. PMID:16963483

  19. Clinical characteristics and distribution of hepatitis B virus genotypes in Guangxi Zhuang population

    Institute of Scientific and Technical Information of China (English)

    Zhong-Min Huang; Qi-Wen Huang; Ya-Qin Qin; Chun-He Huang; Hou-Ji Qin; Yiao-Nan Zhou; Xiang Xu; Chun-Lei Lu

    2005-01-01

    AIM: To investigate the distribution of HBV genotypes and their YMDD mutations in Guangxi Zhuang population, China, and to study the relationship between HBV genotypes and clinical types of HB, ALT, HBV DNA, HBe system as well as the curative effect of Lamivudine (LAM) on hepatitis B.METHODS: A total of 156 cases were randomly chosen as study subjects from 317 patients with chronic hepatitis B (CHB). HBV genotypes were determined by PCR-microcosmic nucleic acid cross-ELISA. YMDD mutations were detected by microcosmic nucleic acid cross-nucleic acid quantitative determination. HBV DNA was detected by fluorescence ratio PCR analysis.LAM was given to 81 cases and its curative effect was observed by measuring ALT, HBV DNA load, HBeAg, and HBeAg/HBeAb conversion rate.RESULTS: HBV genotypes B, C, D, and non-classified genotypes were found in Guangxi Zhuang population.accounting for 25.6%, 47.4%, 58.3%, and 16.0%,respectively. Seventy-four cases were CD-, CB-, BD-mixed genotypes (47.7%). Forty-six (29.5%) cases had YMDD mutations. Genotype B was mostly found in mild and moderate CHB patients. Genotypes C, D and mixed genotype mostly occurred in severe CHB cases.Genotypes D and CD HBV-infected patients had higher ALT and HBV DNA than patients with other types of HBV infection. There was no significant difference among the genotypes in YMDD mutations, clinical types, ALT and HBV DNA level. Non-classified types geno had a significantly lower positive rate of HBeAg than other genotypes (x2= 12.841, P<0.05). There was no significant difference in ALT recovery rate, HBV DNA load, HBeAg,and HBeAg/HBeAb conversion rate, 48 wk after LAM treatment between groups of genotypes D, CD, and nonclassified type.CONCLUSION: Genotypes B, C, and D, non-classified and mixed genotype of HBV are identified in the Guangxi Zhuang population. Variations in genotypes are associated with clinical severity and serum ALT levels, but not with YMDD mutation or HBV DNA load.Therapeutic effects of LAM

  20. Study of Various HCV Genotypes in Patients Managing by Referral Clinic in Yazd Province

    Directory of Open Access Journals (Sweden)

    M Pedarzadeh

    2012-02-01

    Full Text Available Introduction: Determining virus genotype is a major factor for initiation of treatment because various kinds of genotypes need different antiviral drugs. Distribution of hepatitis C genotype in the word is variable in each country or even in each province. So we need to determine distribution pattern of hepatitis C genotype in our region. This study was performed in referral clinic of Yazd province. Methods: This was a descriptive study conducted between 2007 and 2010 on patients who were observed by Yazd referral clinic (the clinic for evaluating and management of patients with high risk behaviors. Ninety two patients who had positive RIBA test for hepatitis C infection were randomly selected and entered the study. Genotyping was performed using RT-PCR method. The primer was "universal primer HCV". Prevalence of various genotypes was analyzed according to gender, addiction and co- existence of HCV-HIV infection. Personal information and laboratory results were analyzed using SPSS. Results: The most common genotype in our study was genotype 3a (65% of cases, followed by 1a (35%. Globally 83% of patients were IV drug addict. Genotype distribution in these patients was similar to others. Fifteen patients had co-infection of HCV-HIV, and 47% of them were contaminated by genotype 1a and 53% with 3a. We could not find any patient contaminated with genotypes 2 or 4. No other genotypes except 1 & 3 or mixed genotype infection could be determined in our patients. Twenty three percent of patients had negative PCR despite positive RIBA test. This indicates that self improvement from acute hepatitis C infection in IV drug addict patients is similar to other people. Conclusion: According to the results of our study, about 2/3 of patients were infected by genotype 3a. This kind of chronic hepatitis C shows a better response to treatment comparing genotype 1a (or 1b with shorter duration and lower cost drugs. But despite higher incidence of genotype 3a, we

  1. Asian genotypes of dengue virus 4 in Brazil.

    Science.gov (United States)

    Pinho, A C O; Sardi, S I; Paula, F L; Peixoto, I B; Brandão, C J; Fernandez, F M C; Campos, G S

    2015-10-01

    Dengue virus, commonly transmitted by mosquitoes, causes a human disease of significant social impact and presents a serious public health problem in Brazil. This report describes the unusual emergence of DENV-4 in northern Brazil after a nearly 30-year-long absence. DENV-4 genotype I is of Asian origin and was identified in the serum of patients receiving treatment at a hospital serving the Salvador area (Brazilian state of Bahia). The identification of dengue virus serotypes through molecular and phylogenetic analysis is essential for predicting disease severity or fatal illness, principally in endemic countries such as Brazil.

  2. The nickel dose–response relationship by filaggrin genotype (FLG)

    DEFF Research Database (Denmark)

    Ross-Hansen, Katrine; Johansen, Jeanne D; Vølund, Aage;

    2014-01-01

    for differences between the two groups. RESULTS: No difference was found in the dose-response relationship between FLG mutation and non-mutation carriers. CONCLUSIONS: On the basis of this small patient study, it appears that the elicitation threshold level for nickel is independent of FLG null mutation single......-sensitized female patients, seven heterozygous mutation carriers and six non-mutation carriers (genotyped for R501X, 2282del4, or R2447X), were patch tested and performed a repeated open application test (ROAT) with a nickel sulfate dilution series. Logistic threshold dose-response analyses were used to test...

  3. Precision medicine of frontotemporal dementia: from genotype to phenotype.

    Science.gov (United States)

    Che, Xiang-Qian; Song, Ning; Gao, Ying; Ren, Ru-Jing; Wang, Gang

    2018-01-01

    Frontotemporal dementia (FTD) is the second most common neurodegenerative  cause of early-onset dementia. FTD has an important genetic component contributing to its pathogenic mechanisms. Currently, extensive research on neuroimaging biomarkers and neurochemical biomarkers in FTD is being conducted to address the clinical need for a sensitive and specific diagnostic marker. Here, we review the advances in genetics, biomarkers and treatment of FTD and how this may represent a shift towards precision medicine. To advance the clinical use of precision medicine, big data cohort for genotype/phenotype research and multidisciplinary team approaches are necessary.

  4. Human papillomavirus testing and genotyping in cervical screening

    DEFF Research Database (Denmark)

    Rebolj, Matejka; Lynge, Elsebeth; Bonde, Jesper

    2011-01-01

    the incidence of cervical cancer, but has a low sensitivity for high-grade cervical intraepithelial neoplasia (CIN) and requires frequent testing. Several HPV tests have become available commercially. They appear to be more sensitive for high-grade CIN, and may further reduce the incidence of cervical cancer......Mass vaccination against human papillomavirus (HPV) genotypes 16 and 18 will, in the long term, reduce the incidence of cervical cancer, but screening will remain an important cancer control measure in both vaccinated and unvaccinated women. Since the 1960s, cytology screening has helped to reduce...

  5. Mechanistic modeling of turkey growth response to genotype and nutrition.

    Science.gov (United States)

    Rivera-Torres, V; Ferket, P R; Sauvant, D

    2011-10-01

    Along with the fast genetic improvement, nutritional and environmental effects on poultry growth performance have made it necessary to develop growth models that have the flexibility to adapt to different genotypes and growing conditions. A mechanistic simulation model of energy and nutrient utilization in growing turkeys is presented herein. The model consists of simulating the average homeorhetic and homeostatic regulations associated with the utilization of circulating glucose, fatty acid, AA, and acetyl-CoA for protein and lipid retention in carcass, viscera, and feathers in a turkey population. Homeorhesis plays a major role in the control of protein and lipid turnover for the definition of genetic potential and feed intake, whereas homeostasis adjusts growth rate through protein and lipid turnover rates and, therefore, BW gain and feed intake to the growing conditions. Also, homeostasis enables the maintenance of a dynamic balance state during all the growing period through the control of circulating nutrient concentration. The model was developed and calibrated with experimental data that described energy utilization in male and female growing turkeys. Then, the ability of the model to adapt to genotypes and to predict the average response of a turkey population to dietary energy was evaluated. Model calibration showed simulations of energy and nutrient utilization that fitted well with the experimental data because ME was satisfyingly partitioned into heat production and energy retention as protein and lipid, and nutrient intake accurately partitioned BW gain into carcass, viscera, and feathers. The evaluation of the model was also satisfactory because BW gain and feed-to-gain ratio were globally in accordance with the observations in different male and female genotypes, in spite of an overestimation of the feed-to-gain ratio during the first weeks of age. Model evaluation showed that the BW gain and feed intake response of growing turkeys to dietary energy

  6. Rapid genotyping using pyrene-perylene locked nucleic acid complexes

    DEFF Research Database (Denmark)

    Kumar, Santhosh T.; Myznikova, Anna; Samokhina, Evgeniya

    2013-01-01

    We have developed an assay for single strand DNA and RNA detection which is based on novel pyrene-perylene FRET pairs attached to short LNA/DNA probes. The assay is based on ratiometric emission upon binding of target DNA/RNA by three combinations of fluorescent LNA/DNA reporter strands. Specific...... is achieved with advantages of large Stokes shift (115 nm), high fluorescence quantum yields and low limit of target detection values (Rapid and accurate genotyping of highly polymorphic HIV Pol cDNA and RNA fragments performed herein proves the possibility for broad application of the novel pyrene...

  7. Fattening and slaughter traits of four rabbit genotypes

    OpenAIRE

    Silvester Zgur; Ajda Kermauner

    2010-01-01

    Growth rate of 4 genotypes, two lines of Slovene SIKA meat rabbit (maternal line A and sire line C, both 50 rabbits), hybrid AxC (50 rabbits) and crossbred AxCal (A and Californian, 38 rabbits) was recorded from weaning (35 days of age) to slaughter (93 days). Growth performance and slaughter traits of AxC were different from line A (live weight at 91st day: A 2720, C 3158, AxC 3043 g (P£0.05), heterosis effect (H) +3.38%; carcass weight: A 1490, C 1787, AxC 1716 g (P£0.05), H +5....

  8. MOLECULAR IDENTIFICATION AND GENOTYPING OF CIAUSCOLO AUTOCHTHONOUS MICROFLORA: PRELIMINARY STUDY

    Directory of Open Access Journals (Sweden)

    A. Petruzzelli

    2011-01-01

    Full Text Available The present study reports the results of a preliminary characterization of the bacterial population of Ciauscolo, a typical Italian fermented sausage, traditionally manufactured in Marche region. The bacterial community involved in Ciauscolo fermentation was investigated using both molecular and culturebased methods. The estimation of genotypic intra-species variation of the autochthonous bacteria isolated was also evaluated by using randomly amplified polymorphic DNA (RAPD analysis and unweighted pairgroup method with arithmetic averages (UPGMA cluster analysis. Our findings revealed an high diversity of the autochthonous bacterial population investigated, both at species and strain level.

  9. Apolipoprotein E genotype in patients with Alzheimer's disease

    Institute of Scientific and Technical Information of China (English)

    罗本燕; 陈智; 张艳艳; 潘小平; 李霞; 陈峰

    2003-01-01

    Objective To explore the frequency and significance of ApoE gene polymorphisms in patients with sporadic Alzheimer's disease (AD).Methods Single nucleotide polymorphisms of the ApoE gene were analyzed in 32 cases of AD and 26 controls, using PCR and gene sequencing.Results The single nucleotide polymorphism of ApoE gene 462C/G was significantly associated with AD (P<0.05).Conclusions The 462C/G polymorphism might be a specific genotype in Chinese patients with sporadic AD.

  10. DORMANCY RELEASING MECHANISMS IN SOIL SEED BANKS OF Desmanthus GENOTYPES

    OpenAIRE

    JOSÉ HENRIQUE DE ALBUQUERQUE RANGEL; CHRISTOPHER PETER GARDINER; ROBERT LEWIS BURT

    2015-01-01

    Desmanthus is a genus of forage legumes with potential to improve pastures and livestock produc-tion on clay soils of dry tropical and subtropical regions such as the existing in Brazil and Australia. Despite this patterns of natural or enforced after-ripening of Desmanthus seeds have not been well established. Four year old seed banks of nine Desmanthus genotypes at James Cook University were accessed for their patterns of seed softe-ning in response to a range of temperatures. Persistent se...

  11. Genotyping of Chlamydophila abortus strains by multilocus VNTR analysis.

    Science.gov (United States)

    Laroucau, Karine; Vorimore, Fabien; Bertin, Claire; Mohamad, Khalil Yousef; Thierry, Simon; Hermann, Willems; Maingourd, Cyril; Pourcel, Christine; Longbottom, David; Magnino, Simone; Sachse, Konrad; Vretou, Evangelia; Rodolakis, Annie

    2009-06-12

    Chlamydophila (C.) abortus is the causative agent of ovine enzootic abortion with zoonotic potential whose epidemiology has been held back because of the obligate intracellular habitat of the bacterium. In the present study, we report on a molecular typing method termed multiple loci variable number of tandem repeats (VNTR) Analysis (MLVA) for exploring the diversity of C. abortus. An initial analysis performed with 34 selected genetic loci on 34 ruminant strains including the variant Greek strains LLG and POS resulted in the identification of five polymorphic loci, confirming the widely held notion that C. abortus is a very homogeneous species. Analysis of additional 111 samples with the selected five loci resulted in the classification of all strains into six genotypes with distinct molecular patterns termed genotypes [1] through [6]. Interestingly, the classification of the isolates in the six genotypes was partly related to their geographical origin. Direct examination of clinical samples proved the MLVA to be suitable for direct typing. Analysis of the genomic sequences in six C. abortus prototypes of amplicons generated with each of the five selected VNTR primers revealed that variation between genotypes was caused by the presence or absence of coding tandem repeats in three loci. Amplification of Chlamydophila psittaci reference strains with the five selected VNTR primers and of the six C. abortus prototype strains with the eight VNTR primers established for the typing of C. psittaci [Laroucau, K., Thierry, S., Vorimore, F., Blanco, K., Kaleta, E., Hoop, R., Magnino, S., Vanrompay, D., Sachse, K., Myers, G.S., Bavoil, P.M., Vergnaud, G., Pourcel, C., 2008. High resolution typing of Chlamydophila psittaci by multilocus VNTR analysis (MLVA). Infect. Genet. Evol. 8(2), 171-181] showed that both MLVA typing systems were species-specific when all respective VNTR primer sets were used. In conclusion, the newly developed MLVA system provides a highly sensitive

  12. A condition for the genotype-phenotype mapping Causality

    CERN Document Server

    Sendhoff, B; Von Seelen, W; Sendhoff, Bernhard; Kreutz, Martin; Seelen, Werner von

    1997-01-01

    The appropriate choice of the genotype-phenotype mapping in combination with the mutation operator is important for a successful evolutionary search process. We suggest a measure to quantify the quality of this combination by addressing the question whether the relation among distances is carried over from one space to the other. Search processes which do not destroy the neighbourhood structure are termed strongly causal. We apply the proposed measure to parameter and structure optimisation problems in order to assess the combination (mapping, mutation operator) and at the same time to be able to propose improved settings.

  13. Towards standardization of microarray-based genotyping of Salmonella

    DEFF Research Database (Denmark)

    Löfström, Charlotta; Grønlund, Hugo Ahlm; Riber, Leise

    2010-01-01

    Genotyping is becoming an increasingly important tool to improve risk assessments of Salmonella. DNA microarray technology is a promising diagnostic tool that can provide high resolution genomic profile of many genes simultaneously. However, standardization of DNA microarray analysis is needed...... of Salmonella at two different laboratories. The low-density array contained 281 of 57-60-mer oligonucleotide probes for detecting a wide range of specific genomic markers associated with antibiotic resistance, cell envelope structures, mobile genetic elements and pathogenicity. Several test parameters...... for a decentralized and simple-to-implement DNA microarray as part of a pan-European source-attribution model for risk assessment of Salmonella....

  14. Biochemical Screening for Osmotic Adjustement of Wheat Genotypes under Drought Stress

    Directory of Open Access Journals (Sweden)

    Chorfi, A.

    2011-01-01

    Full Text Available The aim of this work is to study the effect of water scarcity on some physiological and biochemical markers of durum wheat genotypes. Two genotypes differing in their origin were tested. Measurements of drought effects were carried out after ten days of exposure to gradual levels, and allowed us to examine if there exists a differential response of synthesis, accumulation and transport between leaves and roots regarding total proteins, proline and soluble sugars, with respect of membrane stability and water content, to reveal any patterns of discrimination between genotypes. It seems that the two genotypes develop the same strategies under drought conditions with a significant difference in the rate of osmoticums synthesis and accumulation. This difference concerns mainly proline accumulation which appears to be strongly correlated with genotypic variability. Indeed, there is a large accumulation of proline in the local genotype Oued Zenati compared to the genotype Acsad 289 although both genotypes showed an ability to synthesize them leading to adapt drought conditions. The parameters studied in the present investigation could be very useful for screening of wheat genotypes resistant to drought. Considering our results, the exploitation of local genotype Oued Zenati could constitute a basis of selection for agriculture in arid and semiarid regions.

  15. Morphological and Physiological Characteristics of Shading Tolerant and Sensitive Mungbean Genotypes

    Directory of Open Access Journals (Sweden)

    TITIK SUNDARI

    2009-12-01

    Full Text Available Study of morphological and physiological characteristics of the tolerant and sensitive mungbean genotypes to shading was carried out in the Station Research of the Indonesian Legume and Tuber Crops Research Institute (ILETRI from September to December 2004. Nine tolerant genotypes (MMC 87 D-KP-2, MLG 369, MLG 310, MLG 424, MLG 336, MLG 428, MLG 237, MLG 429, and VC2768B and three sensitive genotypes to shading (Nuri, MLG 460, and MLG 330 were tested in two shading levels, that were without shading and shading of 52%. The randomized complete block design with three replications analysis. The results showed that leaf characters of shading tolerant and sensitive genotypes were different. The shading tolerant mungbean genotypes had good response to light stress so that the growth and development of the leaves were better than that of sensitive genotypes. The shading tolerant mungbean genotypes had bigger and thicker leaves than that of sensitive genotypes. The shading treatments caused reducing rate of PAR absorption, transpiration, photosynthesis, and CO2 stomata conductance. The reduction of all parameters in tolerant genotype was smaller than that of sensitive genotype. The specific leaf area at four weeks after planting could be used as shading tolerant indicator of mungbeans.

  16. Effects of elevated CO2 and plant genotype on interactions among cotton, aphids and parasitoids

    Institute of Scientific and Technical Information of China (English)

    Yu-Cheng Sun; Li Feng; Feng Gao; Feng Ge

    2011-01-01

    Effects of CO2 level (ambient vs.elevated) on the interactions among three cotton (Gossypium hirsutum) genotypes,the cotton aphid (Aphis gossypii Glover),and its hymenoptera parasitoid (Lysiphlebiajaponica Ashrnead) were quantified.It was hypothesized that aphid-parasitoid interactions in crop systems may be altered by elevated CO2,and that the degree of change is influenced by plant genotype.The cotton genotypes had high (M9101),medium (HZ401) and low (ZMS 13) gossypol contents,and the response to elevated CO2 was genotype-specific.Elevated CO2 increased the ratio of total non-structural carbohydrates to nitrogen (TNC:N) in the high-gossypol genotype and the mediumgossypol genotype.For all three genotypes,elevated CO2 had no effect on concentrations of gossypol and condensed tannins.A.gossypii fitness declined when aphids were reared on the high-gossypol genotype versus the low-gossypol genotype under elevated CO2.Furthermore,elevated CO2 decreased the developmental time of L.japonica associated with the high-gossypol genotype and the low-gossypol genotype,but did not affect parasitism or emergence rates.Our study suggests that the abundance of A.gossypii on cotton will not be directly affected by increases in atmospheric CO2.We speculate that A.gossypii may diminish in pest status in elevated CO2 and high-gossypol genotype environments because of reduced fitness to the high-gossypol genotype and shorter developmental time of L.japonica.

  17. [Hepatitis c virus genotype research by ABC programs of 5'-NCR restriction endonuclease digestion].

    Science.gov (United States)

    Qiu, Guo-hua; Du, Shao-cai; Sun, Nan-xiong; You, Peng; Fan, Xiao-feng; Zhang, Yong-xiang; Wei, Lai

    2004-04-01

    In order to fully understand hepatitis c virus (HCV) genotype 3b, 1a, 2b and 6a infection in China, We built HCV 5'-noncoding region (5'-NCR) of different genotypes and subtypes. The classification HCV into variable genotypes (subtypes) was carried on by programs A, B and C A. Using a combination of three restriction endonuclease BHH' (BsrB I, Hae II, Hinf I) digestions at the same time. The distinct genotypes were classified into 5 groups: genotype 1 (1a, 1b), 6a, 2 (2a, 2b), genotype 3 (3a, 3b), genotype4 (4a). B. With regard to genotype 1, we could distinguish subtype 1a from 1b using BstU I digestion. C. Using restriction endonuclease Hae III, genotype 2a, 2b, 3b, 4a, 6a are differentiated respectively. (1) HCV genotype 1a, 1b, 2a, 2b, 3a, 3b, 4a, 6a are fully discriminated by comparison with the genotypes regular samples. (2) Of the 93 patients, HCV genotype distribution in China was 66.67% for 1b, 18.28% for 2a, 3.23% for 1b/2b, 3b, 2b respectively. 2.15% for 2a/2b, 1b/2a respectively. 1.08% for 1a. This research indicated that adoption of HCV 5'-NCR A B C restriction endonuclease digestions techniques, might be sensitive and efficient to detect HCV and discriminate HCV genotype (subtypes) 1a to 6a.

  18. Genetic diversity analysis of highly incomplete SNP genotype data with imputations: an empirical assessment.

    Science.gov (United States)

    Fu, Yong-Bi

    2014-03-13

    Genotyping by sequencing (GBS) recently has emerged as a promising genomic approach for assessing genetic diversity on a genome-wide scale. However, concerns are not lacking about the uniquely large unbalance in GBS genotype data. Although some genotype imputation has been proposed to infer missing observations, little is known about the reliability of a genetic diversity analysis of GBS data, with up to 90% of observations missing. Here we performed an empirical assessment of accuracy in genetic diversity analysis of highly incomplete single nucleotide polymorphism genotypes with imputations. Three large single-nucleotide polymorphism genotype data sets for corn, wheat, and rice were acquired, and missing data with up to 90% of missing observations were randomly generated and then imputed for missing genotypes with three map-independent imputation methods. Estimating heterozygosity and inbreeding coefficient from original, missing, and imputed data revealed variable patterns of bias from assessed levels of missingness and genotype imputation, but the estimation biases were smaller for missing data without genotype imputation. The estimates of genetic differentiation were rather robust up to 90% of missing observations but became substantially biased when missing genotypes were imputed. The estimates of topology accuracy for four representative samples of interested groups generally were reduced with increased levels of missing genotypes. Probabilistic principal component analysis based imputation performed better in terms of topology accuracy than those analyses of missing data without genotype imputation. These findings are not only significant for understanding the reliability of the genetic diversity analysis with respect to large missing data and genotype imputation but also are instructive for performing a proper genetic diversity analysis of highly incomplete GBS or other genotype data.

  19. Differences between soybean genotypes in physiological response to sequential soil drying and rewetting

    Institute of Scientific and Technical Information of China (English)

    Md; Mokter; Hossain; Xueyi; Liu; Xusheng; Qi; Hon-Ming; Lam; Jianhua; Zhang

    2014-01-01

    Soybean genotypes show diverse physiological responses to drought, but specific physiological traits that can be used to evaluate drought tolerance have not been identified. In the present study we investigated physiological traits of soybean genotypes under progressive soil drying and rewetting, using a treatment mimicking field conditions.After a preliminary study with eight soybean genotypes, two drought-tolerant genotypes and one susceptible genotype were grown in the greenhouse and subjected to water restriction. Leaf expansion rate, gas exchange, water relation parameters, total chlorophyll(Chl), proline contents of leaves, and root xylem p H were monitored in a time course, and plant growth and root traits were measured at the end of the stress cycle. Drought-tolerant genotypes maintained higher leaf expansion rate, net photosynthetic rate(Pn), Chl content,instantaneous water use efficiency(WUEi), % relative water content(RWC), water potential(ψw), and turgor potential(ψp) during progressive soil drying and subsequent rewetting than the susceptible genotypes. By contrast, stomatal conductance(gs) and transpiration rate(Tr)of tolerant genotypes declined faster owing to dehydration and recovered more sharply after rehydration than the same parameters in susceptible ones. Water stress caused a significant increase in leaf proline level and root xylem sap p H of both genotypes but tolerant genotypes recovered to pre-stress levels more quickly after rehydration. Tolerant genotypes also produced longer roots with higher dry mass than susceptible genotypes. We conclude that rapid perception and adjustment in response to soil drying and rewetting as well as the maintenance of relatively high Pn, %RWC, and root growth constitute the mechanisms by which drought-tolerant soybean genotypes cope with water stress.

  20. Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes.

    Science.gov (United States)

    Fu, Yong-Bi; Peterson, Gregory W; Dong, Yibo

    2016-04-07

    Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for exploring genome-wide genetic variation. However, GBS commonly samples a genome unevenly and can generate a substantial amount of missing data. These technical features would limit the power of various GBS-based genetic and genomic analyses. Here we present software called IgCoverage for in silico evaluation of genomic coverage through GBS with an individual or pair of restriction enzymes on one sequenced genome, and report a new set of 21 restriction enzyme combinations that can be applied to enhance GBS applications. These enzyme combinations were developed through an application of IgCoverage on 22 plant, animal, and fungus species with sequenced genomes, and some of them were empirically evaluated with different runs of Illumina MiSeq sequencing in 12 plant species. The in silico analysis of 22 organisms revealed up to eight times more genome coverage for the new combinations consisted of pairing four- or five-cutter restriction enzymes than the commonly used enzyme combination PstI + MspI. The empirical evaluation of the new enzyme combination (HinfI + HpyCH4IV) in 12 plant species showed 1.7-6 times more genome coverage than PstI + MspI, and 2.3 times more genome coverage in dicots than monocots. Also, the SNP genotyping in 12 Arabidopsis and 12 rice plants revealed that HinfI + HpyCH4IV generated 7 and 1.3 times more SNPs (with 0-16.7% missing observations) than PstI + MspI, respectively. These findings demonstrate that these novel enzyme combinations can be utilized to increase genome sampling and improve SNP genotyping in various GBS applications.

  1. Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes

    Directory of Open Access Journals (Sweden)

    Yong-Bi Fu

    2016-04-01

    Full Text Available Genotyping-by-sequencing (GBS has emerged as a useful genomic approach for exploring genome-wide genetic variation. However, GBS commonly samples a genome unevenly and can generate a substantial amount of missing data. These technical features would limit the power of various GBS-based genetic and genomic analyses. Here we present software called IgCoverage for in silico evaluation of genomic coverage through GBS with an individual or pair of restriction enzymes on one sequenced genome, and report a new set of 21 restriction enzyme combinations that can be applied to enhance GBS applications. These enzyme combinations were developed through an application of IgCoverage on 22 plant, animal, and fungus species with sequenced genomes, and some of them were empirically evaluated with different runs of Illumina MiSeq sequencing in 12 plant species. The in silico analysis of 22 organisms revealed up to eight times more genome coverage for the new combinations consisted of pairing four- or five-cutter restriction enzymes than the commonly used enzyme combination PstI + MspI. The empirical evaluation of the new enzyme combination (HinfI + HpyCH4IV in 12 plant species showed 1.7–6 times more genome coverage than PstI + MspI, and 2.3 times more genome coverage in dicots than monocots. Also, the SNP genotyping in 12 Arabidopsis and 12 rice plants revealed that HinfI + HpyCH4IV generated 7 and 1.3 times more SNPs (with 0–16.7% missing observations than PstI + MspI, respectively. These findings demonstrate that these novel enzyme combinations can be utilized to increase genome sampling and improve SNP genotyping in various GBS applications.

  2. [25S intron analysis followed by restriction enzyme digestion performed for genotyping Candida albicans isolates].

    Science.gov (United States)

    Karahan, Zeynep Ceren; Saran, Begüm; Yenice, Sevinç; Ağırbaşlı, Handan; Arıkan Akan, Ozay; Tekeli, Alper

    2012-04-01

    Candida albicans is the most frequently encountered fungal pathogen especially in the immunocompromised hosts. Genotyping clinical microbial isolates is important for obtaining epidemiological data and for establishing appropriate infection control strategies in the hospital setting. 25S intron analysis is an easy and reliable method used for genotyping C.albicans strains. As it has a low discriminatory power, its use is limited in epidemiological studies. In this study, our aim was to genotype clinical C.albicans isolates by using 25S intron analysis followed by restriction enzyme digestion in order to develop a more discriminative genotyping system for C.albicans. A total of 260 clinical C.albicans strains isolated from various infection sites (121 blood, 69 sputum, 36 vaginal discharge, 26 wound, 8 urine samples) were genotyped by 25S intron analysis, and all the products obtained by polymerase chain reaction (PCR) were digested with HaeIII restriction enzyme. Discriminatory power of each method was calculated. Among the isolates 184 (70.8%) were classified as genotype A, 42 (16.2%) as genotype B, and 34 (13%) as genotype C by 25S intron analysis. Discriminatory power of the method was calculated as 0.46. HaeIII restriction of genotype A, B and C isolates produced ten, one, and five restriction patterns (genotypes), respectively. By the addition of restriction enzyme analysis, the number of genotypes obtained was increased to 16, and the discriminatory power of the method to 0.79. Combining different genotyping methods increases the discriminatory power by increasing the number of genotypes obtained. However, there is also a risk to split certain strains in different genotypes by the different methods used and this makes the genotypic evaluation more difficult. On the other hand, combining 25S intron analysis with restriction enzyme analysis increases the discriminatory power without introducing a totally different method, and makes the method more suitable for

  3. Subgenotype reclassification of genotype B hepatitis B virus

    Directory of Open Access Journals (Sweden)

    Shi Weifeng

    2012-08-01

    Full Text Available Abstract Background Nine subgenotypes from genotype B have been identified for hepatitis B virus (HBV. However, these subgenotypes were less conclusive as they were often designated based on a few representative strains. In addition, subgenotype B6 was designated twice for viruses of different origin. Methods All complete genome sequences of genotype B HBV were phylogenetically analyzed. Sequence divergences between different potential subgenotypes were also assessed. Results Both phylogenetic and sequence divergence analyses supported the designation of subgenotypes B1, B2, B4, and B6 (from Arctic. However, sequence divergences between previously designated B3, B5, B7, B8, B9 and another B6 (from China were mostly less than 4%. In addition, subgenotype B3 did not form a monophyly. Conclusion Current evidence failed to classify original B5, B7, B8, B9, and B6 (from China as subgenotypes. Instead, they could be considered as a quasi-subgenotype B3 of Southeast Asian and Chinese origin. In addition, previously designated B6 (from Arctic should be renamed as B5 for continuous numbering. This novel classification is well supported by both the phylogeny and sequence divergence of > 4%.

  4. Bioaccumulation and degradation of atrazine in several Chinese ryegrass genotypes.

    Science.gov (United States)

    Sui, Ying; Yang, Hong

    2013-12-01

    Soil pollution with herbicides is a global problem. Before phytoremediation technology is developed for the plant-based clean-up of polluted soils, investigation of potential plants that can be used to accumulate and degrade herbicides is a critical step. In this study, three selected genotypes of ryegrass were comprehensively analyzed with regard to the atrazine accumulation, degradation and toxicological response. Under the conditions of soil with 0.8 mg kg(-1) atrazine, the maximum value for atrazine accumulation was 2.70 mg kg(-1) in shoots and 0.58 mg kg(-1) in roots. The residue of atrazine in soil with ryegrass cultivation was much lower than that in soil without ryegrass cultivation. Also, the content of atrazine residues in the rhizosphere was significantly lower than that in the non-rhizosphere soil. Activities of several enzymes (urease, invertase, polyphenol oxidase, acid phosphatase and alkaline phosphatase) in soil were assayed. These enzymes were depressed by atrazine but activated by ryegrass cultivation, even in the presence of atrazine. Finally, comparative studies have been conducted on the ryegrass genotypes in response to atrazine. They showed different capacities of degradation and bioaccumulation of atrazine. One of the grass cultivars Changjiang II (CJ) had better growth and higher levels of chlorophyll, but displayed less oxidative injury than two others, Abode (AB) and Jiewei (JW), under atrazine exposure.

  5. Genotyping and Bio-Sensing Chemosensory Proteins in Insects

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    Guoxia Liu

    2017-08-01

    Full Text Available Genotyping is the process of determining differences in the genetic make-up of an individual and comparing it to that of another individual. Focus on the family of chemosensory proteins (CSPs in insects reveals differences at the genomic level across various strains and biotypes, but none at the level of individuals, which could be extremely useful in the biotyping of insect pest species necessary for the agricultural, medical and veterinary industries. Proposed methods of genotyping CSPs include not only restriction enzymatic cleavage and amplification of cleaved polymorphic sequences, but also detection of retroposons in some specific regions of the insect chromosome. Design of biosensors using CSPs addresses tissue-specific RNA mutations in a particular subtype of the protein, which could be used as a marker of specific physiological conditions. Additionally, we refer to the binding properties of CSP proteins tuned to lipids and xenobiotic insecticides for the development of a new generation of biosensor chips, monitoring lipid blood concentration and chemical environmental pollution.

  6. Selection of ectomycorrhizal willow genotype in phytoextraction of heavy metals.

    Science.gov (United States)

    Hrynkiewicz, Katarzyna; Baum, Christel

    2013-01-01

    Willow clones are used for the phytoextraction of heavy metals from contaminated soils and are usually mycorrhizal. The receptiveness of willow clones for mycorrhizal inoculum varies specific to genotype; however, it is unknown if this might have a significant impact on their efficiency in phytoextraction of heavy metals. Therefore, a model system with mycorrhizal and non-mycorrhizal willows of two different genotypes--one with usually stronger natural mycorrhizal colonization (Salix dasyclados), and one with lower natural mycorrhizal colonization (S. viminalis)--was investigated for its efficiency of phytoextraction of heavy metals (Cd, Pb, Cu, Zn) from contaminated soil. Inoculation with the ectomycorrhizal fungus Amanita muscaria significantly decreased the biomass of leaves of both inoculated willow clones, and increased or had no effect on the biomass of trunks and roots of S. dasyclados and S. viminalis, respectively. The concentrations of heavy metals in the biomass of S. dasyclados were in general higher than in S. viminalis irrespective of inoculation with the ectomycorrhizal fungus. Inoculation with A. muscaria significantly decreased the concentration of Cu in the trunks of both Salix taxa, but did not affected the concentrations of other heavy metals in the biomass. In conclusion, stronger receptiveness of willow clones for mycorrhizal inoculum was correlated with an increased total extraction of heavy metals from contaminated soils. Therefore, this seems to be a suitable criterion for effective willow clone selection for phytoremediation. Increased biomass production with relatively constant metal concentrations seems to be a major advantage of mycorrhizal formation of willows in phytoremediation of contaminated soils.

  7. Heterogeneity of Helicobacter pylori cag genotypes in experimentally infected mice.

    Science.gov (United States)

    Sozzi, M; Crosatti, M; Kim, S K; Romero, J; Blaser, M J

    2001-09-11

    Our aim was to assess whether the Helicobacter pylori population recovered from experimentally infected mice show heterogeneity in cag genotypes. Wild-type FVB/N mice were challenged with strain Hp1 and sacrificed 8 weeks later. Direct PCR on gastric tissue was performed using primers for glmM and cagA, and for these two genes and for cagE and virB11 using DNA from the infecting and the emerging strains. The gastric tissues of two of five mice were PCR+ for glmM but not cagA. For the infecting strain, the PCRs for all four genes studied were strongly positive, but the sweeps from the emerging strains from both mice gave weaker signals for cagA and cagE. Examination of single colonies showed reduced or absent signals for cagA and cagE in relation to glmM and virB11. Serial dilution PCR of sweep isolates from the mice showed a 10- to 100-fold decrease in cagA signal compared to the infecting strain. The decrease of cagA and cagE, but not virB11, amplification and lack of cagA hybridization in Southern blots indicates a selective loss of the right half of the cag island during murine infection. This phenomenon is consistent with host-induced adaptive changes of cag genotype in the population of colonizing H. pylori cells.

  8. An overview on hepatitis C virus genotypes and its control

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    Faisal Nouroz

    2015-10-01

    Full Text Available Hepatitis C virus (HCV is a blood borne, circular and positive single stranded virus with high spread rates. With the passage of time the frequency of HCV is increasing in different parts of the world. HCV is a major cause, which may end in liver cirrhosis and hepatocellular carcinoma. HCV has six main genotypes with many subtypes, which have variable sequence homology with each other. Symptoms can appear anytime from 2 weeks to 6 months, which include jaundice, fatigue, gray-colored stool, joint pain, belly pain, weakness, anorexia, itchy skin and dark urine. Genotyping is more significant for planning of HCV treatment period and helps to cure HCV infections. For the quantification and identification of hepatitis C virus-ribonucleic acid, many molecular techniques are performed; the most significant are HCV ELISA, quantitative HCV-RNA PCR and recombinant immunoblot assay. PCR is the major technique targeting 5′ untranslated region (UTR. HCV can be transmitted by contaminated blood, ear and nose piercing and contaminated medical instruments. To overcome the rate of HCV, guidance should be provided to make aware the persons about risk factors, transmission and prevention. Discovery and designing of new therapies and vaccines to overcome this disease are the necessity of the present era. Four types of vaccines such as vector vaccines, peptide vaccines, DNA vaccines and recombinant protein vaccines are available in clinical trials.

  9. Genotypic characterization of psittacid herpesvirus isolates from Brazil

    Science.gov (United States)

    Luppi, Marcela Miranda; Luiz, Ana Paula Moreira Franco; Coelho, Fabiana Magalhães; Ecco, Roselene; da Fonseca, Flávio Guimarães; Resende, Mauricio

    2016-01-01

    Thirty-six isolates of psittacid herpesvirus (PsHV), obtained from 12 different species of psittacids in Brazil, were genotypically characterized by restriction fragment length polymorphism (RFLP) analysis and PCR amplification. RFLP analysis with the PstI enzyme revealed four distinct restriction patterns (A1, X, W and Y), of which only A1 (corresponding to PsHV-1) had previously been described. To study PCR amplification patterns, six pairs of primers were used. Using this method, six variants were identified, of which, variants 10, 8, and 9 (in this order) were most prevalent, followed by variants 1, 4, and 5. It was not possible to correlate the PCR and RFLP patterns. Twenty-nine of the 36 isolates were shown to contain a 419 bp fragment of the UL16 gene, displaying high similarity to the PsHV-1 sequences available in GenBank. Comparison of the results with the literature data suggests that the 36 Brazilian isolates from this study belong to genotype 1 and serotype 1. PMID:26887248

  10. War exposure, 5-HTTLPR genotype and lifetime risk of depression

    Science.gov (United States)

    Artero, Sylvaine; Touchon, Jacques; Dupuy, Anne-Marie; Malafosse, Alain; Ritchie, Karen

    2011-01-01

    Background in 1962, during the Algerian war, approximately one and a half million French people living in Algeria were repatriated to France in very poor and often life-threatening conditions. These subjects constitute a cohort for the study of the long term impact of gene-environment interaction on depression. Aims To examine the interaction between a highly stressful life event and subsequent depression, and its modulation by the serotonin transporter gene (5-HTTLPR). Method A community sample of elderly persons aged 65 years and over residing in the Montpellier region of the South of France was randomly recruited from electoral rolls. Genotyping was performed on 248 repatriated persons and 632 controls. Current and lifetime major and minor depressions were assessed according to DSM-IV criteria. Results A significant relationship was observed between exposure to repatriation and subsequent depression (pwar repatriation is significantly modulated by 5-HTTLPR genotype but this appears to occur only in persons who were younger at the time of exposure. PMID:21593514

  11. Analysis of Helicobacter pylori genotypes in clinical gastric wash samples.

    Science.gov (United States)

    Miyamoto, Shuichi; Watanabe, Yoshiyuki; Oikawa, Ritsuko; Ono, Shoko; Mabe, Katsuhiro; Kudo, Takahiko; Yamamoto, Hiroyuki; Itoh, Fumio; Kato, Mototsugu; Sakamoto, Naoya

    2016-08-01

    Helicobacter pylori is a key factor in the development of gastric cancer; indeed, clearance of H. pylori helps prevent gastric cancer. However, the relationship between gastric cancer and the abundance and diversity of H. pylori genotypes in the stomach remains unknown. Here, we present, for the first time, a quantitative analysis of H. pylori genotypes in gastric washes. A method was first developed to assess diversity and abundance by pyrosequencing and analysis of single nucleotide polymorphisms in 23S ribosomal RNA (rRNA), a gene associated with clarithromycin resistance. This method was then validated using arbitrarily mixed plasmids carrying 23S rRNA with single nucleotide polymorphisms. Multiple strains were detected in many of 34 clinical samples, with frequency 24.3 ± 24.2 and 26.3 ± 33.8 % for the A2143G and A2144G strains, respectively. Importantly, results obtained from gastric washes were similar to those obtained from biopsy samples. The method provides opportunities to investigate drug resistance in H. pylori and assess potential biomarkers of gastric cancer risk, and should thus be validated in large-scale clinical trials.

  12. Neuregulin-1 genotypes and eye movements in schizophrenia

    DEFF Research Database (Denmark)

    Haraldsson, H.M.; Ettinger, U.; Magnusdottir, B.B.;

    2010-01-01

    Neuregulin-1 (NRG-1) is a putative susceptibility gene for schizophrenia but the neurocognitive processes that may involve NRG-1 in schizophrenia are unknown. Deficits in antisaccade (AS) and smooth pursuit eye movements (SPEM) are promising endophenotypes, which may be associated with brain dysf...... performance. However, the power of the sample to identify small effects is limited and the possibility of a type II error must be kept in mind. Larger samples may be needed to reliably investigate such gene effects on oculomotor endophenotypes...... dysfunctions underlying the pathophysiology of schizophrenia. The aim of this study was to investigate the associations of NRG-1 genotypes with AS and SPEM in schizophrenia patients and healthy controls. Patients (N = 113) and controls (N = 106) were genotyped for two NRG-1 single nucleotide polymorphisms...... (SNPs); SNP8NRG222662, a surrogate marker for the originally described Icelandic NRG-1 risk haplotype, and SNP8NRG243177, which has recently been associated with individual differences in brain function. Subjects underwent infrared oculographic assessment of AS and SPEM. The study replicates previous...

  13. Chromatic, Phenolic and Antioxidant Properties of Sorghum bicolor Genotypes

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    José Juan LÓPEZ-CONTRERAS

    2015-12-01

    Full Text Available Chromatic, phenolic and antioxidant properties were evaluated in ten sorghum genotypes grown in Nuevo León, México. Lightness, Chroma and hue angle ranged from 64 to 83, 12 to 20 and 61 to 82 respectively, indicating that colour of the samples were located in the gray orange-yellow zone of the hue circle. Based on these results, samples were classified in three colour groups being Very Soft Orange, Slightly Desaturated Orange and Grayish Orange. Results in phenolics ranged from 796 to 15,949, 175 to 12,674 and 193 to 25,780 µgCE g-1 in total phenolics by Folin-Ciocalteu, total flavonoids by Aluminum Chloride and condensed tannins by Vanillin-HCl respectively. On the other hand, antioxidant capacity ranged from 1.20 to 93.83, 30.25 to 156.08 and 2.62 to 98.50 μmolTE g-1 in 2,2-diphenyl-1-picrylhydrazyl, 3-ethyl-benzothiazoline-6-sulfonic acid and Ferric Reducing Antioxidant Power respectively. Significant differences (p≤0.05 were observed in statistical analysis for both individual and group colour samples in chromatic, phenolics and antioxidant activity evaluations, showing ‘Rox Orange’ genotype and Grayish Orange colour group the highest levels.

  14. NEW GENOTYPES AND TECHNOLOGICAL INDICATORS OF WINTER TRITICALE

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    T. Z.

    2016-02-01

    Full Text Available The aim of the research was to conduct basic screening of new lines and cultivars of winter hexaploid triticale by the technological and molecular genetics indicators. Molecular and genetic research conducted by polymerase chain reaction allelic variants of gene loci Wx-A1, Wx-B1, and quality parameters of grain, flour and bread – on technological markers. The new cultivars and lines of winter hexaploid triticale of Nosivka Breeding and Research Station of Remeslo Myronivka Institute of Wheat by technological indicators of grain, flour and bread quality were studied. According to representative criteria’s the most promising genotypes, which are the main products in terms Forest-Steppe ecotypes’ and a high-quality raw materials for bakeries and bioethanol were identified. Molecular and genetic identifications of allelic variants of genes loci Wx-A1, Wx-B1 triticale, which in the early stages of ontogenesis to predict targeted uses genotypes were conducted. The first among a series of triticale cultivars and lines Forest-Steppe ecotypes and biotypes with nonfunctional b gene allele WxA1, which defines a high content of amylopectin of starch, an important release for more ethanol was identified. It was found that technological characteristics of grain, flour and bread of new cultivars and lines of winter triticale meet the modern requirements production dietetic food and bioenergy products is important and relevant in the context of food security of Ukraine.

  15. The APOE Genotype in Idiopathic Normal Pressure Hydrocephalus.

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    Yi Yang

    Full Text Available Amyloid plaque has been reported in brain biopsies from patients with idiopathic normal-pressure hydrocephalus (iNPH and proposed as a significant feature of the pathophysiology. Presence of the apolipoprotein E ε4 (APOE ε4 allele is associated with increased risk of Alzheimer's disease (AD.To compare the distribution of APOE genotype in iNPH patients with an age-matched population-based control group and with Alzheimer's disease (AD patients.APOE genotype frequencies were determined in 77 iNPH patients (50 men and 27 women, mean age 71.7 years diagnosed with iNPH, a sample of 691 AD patients and 638 age-matched population controls (299 men and 339 women from the INTERGENE cohort.The APOE distribution did not differ significantly between the iNPH patients and the control population. The per e4-allele odds-ratio (OR of iNPH was given by OR = 0.90, 95% confidence interval (CI = (0.50, 1.60 that was considerably smaller than the per-allele OR of AD, OR = 5.34 (4.10, 7.00.The results suggest that the APOE-related risk of AD in patients with iNPH is not higher than in the general population.

  16. Biosurveillance of emerging biothreats using scalable genotype clustering.

    Science.gov (United States)

    Gallego, Blanca; Sintchenko, Vitali; Wang, Qinning; Hiley, Lester; Gilbert, Gwendolyn L; Coiera, Enrico

    2009-02-01

    Developments in molecular fingerprinting of pathogens with epidemic potential have offered new opportunities for improving detection and monitoring of biothreats. However, the lack of scalable definitions for infectious disease clustering presents a barrier for effective use and evaluation of new data types for early warning systems. A novel working definition of an outbreak based on temporal and spatial clustering of molecular genotypes is introduced in this paper. It provides an unambiguous way of clustering of causative pathogens and is adjustable to local disease prevalence and availability of public health resources. The performance of this definition in prospective surveillance is assessed in the context of community outbreaks of food-borne salmonellosis. Molecular fingerprinting augmented with the scalable clustering allows the detection of more than 50% of the potential outbreaks before they reach the midpoint of the cluster duration. Clustering in time by imposing restrictions on intervals between collection dates results in a smaller number of outbreaks but does not significantly affect the timeliness of detection. Clustering in space and time by imposing restrictions on the spatial and temporal distance between cases results in a further reduction in the number of outbreaks and decreases the overall efficiency of prospective detection. Innovative bacterial genotyping technologies can enhance early warning systems for public health by aiding the detection of moderate and small epidemics.

  17. Implications of Genotype by Environment Interactions in Dairy Sheep Welfare

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    Dinu Gavojdian

    2014-05-01

    Full Text Available Small ruminants are the most extensively farmed livestock species in Europe, as a result being extremely exposed to natural hazards which leads to strong interactions between genotype and environment. Aim of the current review was to outline and discuss the main welfare issues and economic implications with regards to the genotype by environment interactions in dairy sheep. Researches concerning the additive genetic effect on milk yield, shown that this accounts only for 10%, while the milk production is 90% influenced by environmental factors, highlighting the major role that management and nutrition play in the dairy production of sheep. Nowadays, dairy sheep breeds (e.g. Eastern Friesian and Lacaune, are being introduced and reared in various countries under an extremely wide range of rearing conditions, without adequate knowledge on their acclimatization to the new specific conditions. It was concluded that a welfare assessment protocol for dairy sheep does not exist up today, moreover, there is a serious lack of data concerning the genetic and environmental factors affecting the welfare status of dairy sheep at farm level under different production systems.

  18. Microfluidic hydrogel arrays for direct genotyping of clinical samples.

    Science.gov (United States)

    Jung, Yun Kyung; Kim, Jungkyu; Mathies, Richard A

    2016-05-15

    A microfluidic hydrogel DNA microarray is developed to overcome the limitations of conventional planar microarrays such as low sensitivity, long overnight hybridization time, lack of a melting verification of proper hybrid, and complicated sample preparation process for genotyping of clinical samples. Unlike our previous prototype hydrogel array which can analyze only single-stranded DNA (ssDNA) targets, the device is the first of its type to allow direct multiplexed single nucleotide polymorphism (SNP) detection of human clinical samples comprising double-stranded DNA (dsDNA). This advance is made possible by incorporating a streptavidin (SA) hydrogel capture/purification element in a double T-junction at the start of the linear hydrogel array structure and fabricating ten different probe DNAs-entrapped hydrogels in microfluidic channels. The purified or unpurified polymerase chain reaction (PCR) products labeled with a fluorophore and a biotin are electrophoresed through the SA hydrogel for binding and purification. After electrophoretic washing, the fluorophore-labeled DNA strand is then thermally released for hybridization capture by its complementary probe gel element. We demonstrate the precise and rapid discrimination of the genotypes of five different clinical targets by melting curve analysis based on temperature-gradient electrophoresis within 3h, which is at least 3-fold decrease in incubation time compared to conventional microarrays. In addition, a 1.7 pg (0.024 femtomoles) limit of detection for clinical samples is achieved which is ~100-fold better sensitivity than planar microarrays.

  19. Different norovirus genotypes in patients with gastroenteritis in Kuwait.

    Science.gov (United States)

    Al-Rashidi, Amirah; Chehadeh, Wassim; Szücs, György G; Albert, M John

    2013-09-01

    Norovirus is a leading cause of acute gastroenteritis worldwide. The importance of this virus infection in Kuwait is not known. Eight out of 100 stool samples (8.0%) from children up to 5 years of age with gastroenteritis studied during 2006-2007 from one hospital, and 6 out of 70 stool samples (8.5%) from similar children studied from another hospital during 2010-2011 were positive for norovirus by RT-PCR. Out of these 170 samples studied from both hospitals, 10 samples were positive for norovirus when tested by ELISA. Phylogenetic tree analysis of norovirus strains showed that 50% of the norovirus strains belonged to genotype GII.4, and the predominant strain was GII.4 2006b. Other detected genotypes were GII.12, GII.b, GII.3, GII.8, and GII.7. This study highlights the importance of screening for norovirus infection in acute gastroenteritis and having a reporting system to understand better the epidemiology of norovirus infection in Kuwait.

  20. Morphology and viability of castor bean genotypes pollen grains

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    Maria Selma Alves Silva Diamantino

    2016-01-01

    Full Text Available The objective of this work was to characterize the morphology and viability of the pollen of 15 genotypes of castor bean (Ricinus communis L. and to generate information that can assist in the selection of highly promising male parents for future use in genetic improvement programs aimed at producing seeds for oil extraction. Acetolysis and scanning electron microscopy was used to characterize the morphology of the pollen. The viability of the pollen grains was estimated by in vitro germination and colorimetric analysis (acetocarmine 2% and 2, 3, 5-triphenyltetrazolium chloride 1%. For the in vitro germination, pollen grains were grown in 10 types of solidified culture medium consisting of different concentrations of sucrose, boric acid, calcium nitrate, magnesium sulfate and potassium nitrate. The pollen grains had the following characteristics: medium size, isopolar and subspheroidal shape, radial symmetry, circular ambit, 3-colporate, elongated endoapertures, tectate exine and granulated sexine. The acetocarmine dye overestimated pollen viability. The media M5 and M8 were the most efficient at promoting the germination of pollen grains. The studied genotypes had high levels of viability and can therefore be used as male parents in genetic improvement programs.