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Sample records for vhsv genotype ii

  1. Viral haemorrhagic septicaemia virus (VHSV) genotype II isolated from European river lamprey Lampetra fluviatilis in Finland during surveillance from 1999 to 2008

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    Gadd, Tuija; Jakava-Viljanen, Miia; Einer-Jensen, Katja

    2010-01-01

    We examined the occurrence of viral haemorrhagic septicaemia virus (VHSV) in the main spawning stocks of wild European river lamprey Lampetra fluviatilis in the rivers of Finland from 1999 to 2008. Pooled samples of internal organs (kidney, liver and heart or brain) from 2621 lampreys were examined...... genotype II. The partial G gene sequences obtained (nt 1 to 672–1129) of all 5 lamprey VHSV isolates were identical, and so were the entire G genes (nt 1 to 1524) of 2 isolates sequenced. The virulence of one of the lamprey isolates was evaluated by an experimental infection trial in rainbow trout...... Oncorhynchus mykiss fry. No mortality was induced postinfection by waterborne and intraperitoneal challenge, respectively, while 2 genotype Id isolates originating from Finnish rainbow trout caused marked mortality under the same conditions. The infection in the European river lamprey is thought...

  2. Distinction of genotypes of viral haemorrhagic septicaemia virus (VHSV) by monoclonal antibodies

    DEFF Research Database (Denmark)

    Ito, Takafumi; Kurita, J.; Sano, M.

    outbreaks of VHS among susceptible fishes. According to the OIE Aquatic Animal Health Code, even if the same disease agent is present in both the import and the export country, the importing country can demand health certificate of the exporting country for imports when the pathogenicity or host range...... of the strain in the exporting country is significantly higher or larger than that in the importing country. In order to prevent introduction to or spreading in a country of new genotypes of VHSV and to facilitate the responsibilities of exporting and importing countries, such as issuing health certificates...... recognizing all known VHSV isolates, were prepared earlier. In the present study, more new genotype specific monoclonal antibodies against VHSV were produced, aiming at establishing a complete immunoassay for typing of VHSV according to genotype. BALb-c mice were immunized with purified preparations of 7...

  3. Virulence of viral haemorrhagic septicaemia virus (VHSV) genotype III in rainbow trout.

    Science.gov (United States)

    Ito, Takafumi; Kurita, Jun; Mori, Koh-ichiro; Olesen, Niels J

    2016-01-08

    In general, viral haemorrhagic septicaemia virus (VHSV) isolates from marine fish species in European waters (genotypes GIb, GII and GIII) are non- to low virulent in rainbow trout. However, a VHSV isolation was made in 2007 from a disease outbreak in sea farmed rainbow trout in Norway. The isolate, named NO-2007-50-385, was demonstrated to belong to GIII. This isolate has attracted attention to assess which of the viral genome/proteins might be associated with the virulence in rainbow trout. In this study, we describe the difference of virulence in rainbow trout between the NO-2007-50-385 and 4p168 isolates as representatives of virulent and non-virulent GIII isolates, respectively. Rainbow trout were bath challenged with VHSV NO-2007-50-385 for 1 and 6 h, resulting in cumulative mortalities of 5 and 35%, respectively. No mortality was observed in the rainbow trout groups immersed with the genotype III VHSV isolate 4p168 for 1 and 6 h. The viral titre in organs from fish challenged with NO-2007-50-385 for 6 h increased more rapidly than those exposed for 1 h. By in vitro studies it was demonstrated that the final titres of VHSV DK-3592B (GI), NO-2007-50-385 and 4p168 inoculated on EPC cells were very similar, whereas when inoculated on the rainbow trout cell line RTG-2 the titre of the non-virulent 4p168 isolate was 3-4 logs below the two other VHSV isolates. Based on a comparative analysis of the entire genome of the genotype III isolates, we suggest that substitutions of amino acids in positions 118-123 of the nucleo-protein are candidates for being related to virulence of VHSV GIII in rainbow trout.

  4. Virulence of viral haemorrhagic septicaemia virus (VHSV) genotype III in rainbow trout

    DEFF Research Database (Denmark)

    Ito, Takafumi; Kurita, Jun; Mori, Koh-Ichiro

    2016-01-01

    were very similar, whereas when inoculated on the rainbow trout cell line RTG-2 the titre of the non-virulent 4p168 isolate was 3-4 logs below the two other VHSV isolates. Based on a comparative analysis of the entire genome of the genotype III isolates, we suggest that substitutions of amino acids......In general, viral haemorrhagic septicaemia virus (VHSV) isolates from marine fish species in European waters (genotypes GIb, GII and GIII) are non- to low virulent in rainbow trout. However, a VHSV isolation was made in 2007 from a disease outbreak in sea farmed rainbow trout in Norway. The isolate...... with the genotype III VHSV isolate 4p168 for 1 and 6 h. The viral titre in organs from fish challenged with NO-2007-50-385 for 6 h increased more rapidly than those exposed for 1 h. By in vitro studies it was demonstrated that the final titres of VHSV DK-3592B (GI), NO-2007-50-385 and 4p168 inoculated on EPC cells...

  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

    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...

  6. Susceptibility of various Japanese freshwater fish species to an isolate of viral haemorrhagic septicaemia virus (VHSV) genotype IVb.

    Science.gov (United States)

    Ito, Takafumi; Olesen, Niels Jørgen

    2013-11-25

    Genotype IVb of viral haemorrhagic septicaemia virus (VHSV) was isolated for the first time in the Great Lakes basin in 2003, where it spread and caused mass mortalities in several wild fish species throughout the basin. In order to prevent further spreading of the disease and to assess risks of new genotypes invading new watersheds, basic microbiological information such as pathogenicity studies are essential. In this study, experimental infections were conducted on 7 indigenous freshwater fish species from Japan by immersion with a VHSV genotype IVb isolate. In Expt 1, cumulative mortalities in bluegill Lepomis macrochirus used as positive controls, Japanese fluvial sculpin Cottus pollux, and iwana Salvelinus leucomaenis pluvius were 50, 80 and 0%, respectively. In Expt 2, cumulative mortalities of 100, 100 and 10% were observed in Japanese fluvial sculpin C. pollux, Japanese rice fish Oryzias latipes and yoshinobori Rhinogobius sp., respectively. No mortality was observed in honmoroko Gnathopogon caerulescens, akaza Liobagrus reini or Japanese striped loach Cobitis biwae. VHSV was detected by RT-PCR from samples of kidney, spleen, and brain from all dead fish, and virus re-isolation by cell culture was successful from all dead fish. We detected the virus in the brain from a few surviving bluegill 50 d post exposure by both cell culture and RT-PCR. These results revealed that VHSV IVb could become a serious threat to wild freshwater fish species in Japan, and that some surviving fish might become healthy carriers of the virus.

  7. Genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV)

    DEFF Research Database (Denmark)

    Snow, M.; Bain, N.; Black, J.

    2004-01-01

    The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders...... this the most comprehensive molecular epidemiological study of marine VHSV conducted to date. Phylogenetic analysis of nucleoprotein gene sequences confirmed the existence of the 4 major genotypes previously identified based on N- and subsequent G-gene based analyses. The range of Genotype I included subgroups...... of isolates associated with rainbow trout aquaculture (Genotype la) and those from the Baltic marine environment (Genotype Ib) to emphasise the relatively close genetic relationship between these isolates. The existence of an additional genotype circulating within the Baltic Sea (Genotype II) was also...

  8. In vivo and in vitro phenotypic differences between Great Lakes VHSV genotype IVb isolates with sequence types vcG001 and vcG002

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    Imanse, Sierra M.; Cornwell, Emily R.; Getchell, Rodman G.; Kurath, Gael; Bowser, Paul R.

    2014-01-01

    Viral hemorrhagic septicemia virus (VHSV) is an aquatic rhabdovirus first recognized in farmed rainbow trout in Denmark. In the past decade, a new genotype of this virus, IVb was discovered in the Laurentian Great Lakes basin and has caused several massive die-offs in some of the 28 species of susceptible North American freshwater fishes. Since its colonization of the Great Lakes, several closely related sequence types within genotype IVb have been reported, the two most common of which are vcG001 and vcG002. These sequence types have different spatial distributions in the Great Lakes. The aim of this study was to determine whether the genotypic differences between representative vcG001 (isolate MI03) and vcG002 (isolate 2010-030 #91) isolates correspond to phenotypic differences in terms of virulence using both in vitro and in vivo approaches. In vitro infection of epithelioma papulosum cyprini (EPC), bluegill fry (BF-2), and Chinook salmon embryo (CHSE) cells demonstrated some differences in onset and rate of growth in EPC and BF-2 cells, without any difference in the quantity of RNA produced. In vivo infection of round gobies (Neogobius melanostomus) via immersion exposure to different concentrations of vcG001 or vcG002 caused a significantly greater mortality in round gobies exposed to 102 plaque forming units ml− 1 of vcG001. These experiments suggest that there are phenotypic differences between Great Lakes isolates of VHSV genotype IVb.

  9. Susceptibility of various Japanese freshwater fish species to an isolate of viral haemorrhagic septicaemia virus (VHSV) genotype IVb

    DEFF Research Database (Denmark)

    Ito, Takafumi; Olesen, Niels Jørgen

    2013-01-01

    mortalities in bluegill Lepomis macrochirus used as positive controls, Japanese fluvial sculpin Cottus pollux, and iwana Salvelinus leucomaenis pluvius were 50, 80 and 0%, respectively. In Expt 2, cumulative mortalities of 100, 100 and 10% were observed in Japanese fluvial sculpin C. pollux, Japanese rice...... fish Oryzias latipes and yoshinobori Rhinogobius sp., respectively. No mortality was observed in honmoroko Gnathopogon caerulescens, akaza Liobagrus reini or Japanese striped loach Cobitis biwae. VHSV was detected by RT-PCR from samples of kidney, spleen, and brain from all dead fish, and virus re......-isolation by cell culture was successful from all dead fish. We detected the virus in the brain from a few surviving bluegill 50 d post exposure by both cell culture and RT-PCR. These results revealed that VHSV IVb could become a serious threat to wild freshwater fish species in Japan, and that some surviving fish...

  10. Detection of Viral Hemorrhagic Septicemia virus (VHSV from the leech Myzobdella lugubris Leidy, 1851

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    Faisal Mohamed

    2009-09-01

    Full Text Available Abstract The leech Myzobdella lugubris is widespread in the Lake Erie Watershed, especially Lake St. Clair. However, its role in pathogen transmission is not fully understood. In this same watershed, several widespread fish mortalities associated with the Viral Hemorrhagic Septicemia virus (VHSV were recorded. Viral Hemorrhagic Septicemia is an emerging disease in the Great Lakes Basin that is deadly to the fish population, yet little is known about its mode of transmission. To assess the potential role of M. lugubris in VHSV transmission, leeches were collected from Lake St. Clair and Lake Erie and pooled into samples of five. Cell culture and reverse transcriptase polymerase chain reaction (RT-PCR were used to determine the presence of the virus and its identity. Results showed that 57 of the 91 pooled leech samples were positive by cell culture for VHSV and 66 of the 91 pooled leech samples were positive by RT-PCR for the VHSV. Two representative virus isolates were sequenced for further genetic confirmation and genotype classification. VHSV detected within M. lugubris was homologous to the Great Lakes strain of VHSV genotype IVb. This is the first record of the VHSV being detected from within a leech, specifically M. lugubris, and suggests the potential of M. lugubris being involved in VHSV transmission.

  11. Molecular characterization of the Great Lakes viral hemorrhagic septicemia virus (VHSV isolate from USA

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    Vakharia Vikram N

    2009-10-01

    Full Text Available Abstract Background Viral hemorrhagic septicemia virus (VHSV is a highly contagious viral disease of fresh and saltwater fish worldwide. VHSV caused several large scale fish kills in the Great Lakes area and has been found in 28 different host species. The emergence of VHS in the Great Lakes began with the isolation of VHSV from a diseased muskellunge (Esox masquinongy caught from Lake St. Clair in 2003. VHSV is a member of the genus Novirhabdovirus, within the family Rhabdoviridae. It has a linear single-stranded, negative-sense RNA genome of approximately 11 kbp, with six genes. VHSV replicates in the cytoplasm and produces six monocistronic mRNAs. The gene order of VHSV is 3'-N-P-M-G-NV-L-5'. This study describes molecular characterization of the Great Lakes VHSV strain (MI03GL, and its phylogenetic relationships with selected European and North American isolates. Results The complete genomic sequences of VHSV-MI03GL strain was determined from cloned cDNA of six overlapping fragments, obtained by RT-PCR amplification of genomic RNA. The complete genome sequence of MI03GL comprises 11,184 nucleotides (GenBank GQ385941 with the gene order of 3'-N-P-M-G-NV-L-5'. These genes are separated by conserved gene junctions, with di-nucleotide gene spacers. The first 4 nucleotides at the termini of the VHSV genome are complementary and identical to other novirhadoviruses genomic termini. Sequence homology and phylogenetic analysis show that the Great Lakes virus is closely related to the Japanese strains JF00Ehi1 (96% and KRRV9822 (95%. Among other novirhabdoviruses, VHSV shares highest sequence homology (62% with snakehead rhabdovirus. Conclusion Phylogenetic tree obtained by comparing 48 glycoprotein gene sequences of different VHSV strains demonstrate that the Great Lakes VHSV is closely related to the North American and Japanese genotype IVa, but forms a distinct genotype IVb, which is clearly different from the three European genotypes. Molecular

  12. Viral hemorrhagic septicemia virus (VHSV IVb) risk factors and association measures derived by expert panel

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    ,

    2010-01-01

    Viral hemorrhagic septicemia virus (VHSV) is an OIE-listed pathogen of fish, recently expanding in known host and geographic range in North America. Through a group process designed for subjective probability assessment, an international panel of fish health experts identified and weighted risk factors perceived important to the emergence and spread of the viral genotype, VHSV IVb, within and from the Great Lakes region of the US and Canada. Identified factors included the presence of known VHSV-susceptible species, water temperatures conducive for disease, hydrologic connectivity and proximity to known VHSV-positive areas, untested shipments of live or frozen fish from known positive regions, insufficient regulatory infrastructure for fish health oversight, and uncontrolled exposure to fomites associated with boat and equipment or fish wastes from known VHSV-positive areas. Results provide qualitative insights for use in VHSV surveillance and risk-management planning, and quantitative estimates of contextual risk for use in a Bayesian model combining multiple evidence streams for joint probability assessment of disease freedom status. Consistency checks suggest that the compiled factors positively reflect expert judgment of watershed risk for acquiring VHSV IVb. External validation is recommended as the availability of empirical data permits.

  13. Analysis of the nucleoprotein gene identifies three distinct lineages of viral haemorrhagic septicemia virus (VHSV) within the European marine environment

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    Snow, M.; Cunningham, C.O.; Melvin, W.T.; Kurath, G.

    1999-01-01

    A ribonuclease (RNase) protection assay (RPA) has been used to detect nucleotide sequence variation within the nucleoprotein gene of 39 viral haemorrhagic septicaemia virus (VHSV) isolates of European marine origin. The classification of VHSV isolates based on RPA cleavage patterns permitted the identification of ten distinct groups of viruses based on differences at the molecular level. The nucleotide sequence of representatives of each of these groupings was determined and subjected to phylogenetic analysis. This revealed grouping of the European marine isolates of VHSV into three genotypes circulating within distinct geographic areas. A fourth genotype was identified comprising isolates originating from North America. Phylogenetic analyses indicated that VHSV isolates recovered from wild caught fish around the British Isles were genetically related to isolates responsible for losses in farmed turbot. Furthermore, a relationship between naturally occurring marine isolates and VHSV isolates causing mortality among rainbow trout in continental Europe was demonstrated. Analysis of the nucleoprotein gene identifies distinct lineages of viral haemorrhagic septicaemia virus within the European marine environment. Virus Res. 63, 35-44. Available from: 

  14. Inactivation of VHSV by Percolation and Salt Under Experimental Conditions

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    Skall, Helle Frank; Olesen, Niels Jørgen; Jørgensen, Claus

    2012-01-01

    At the moment the only legal method in Denmark to sanitize wastewater from fish cutting plants is by percolation. To evaluate the inactivation effect of percolation on VHSV an experimental examination was initiated. A column packed with gravel as top- and bottom layer (total of 22 cm) and a mid...... method to sanitize VHSV infected water. Changes in temperature, pH, earth types in the area used for percolation etc. may change the virus reduction, though. As some of the fish cutting plants are also smoking rainbow trout fillets, the question arose whether a brine solution will inactivate VHSV...

  15. Inactivation of VHSV by infiltration and salt under experimental conditions

    DEFF Research Database (Denmark)

    Skall, Helle Frank; Jørgensen, Claus; Olesen, Niels Jørgen

    2014-01-01

    At the moment the only legal method in Denmark to sanitize wastewater from fish cutting plants is by infiltration. To evaluate the inactivation effect of infiltration on VHSV an experimental examination was initiated. A column packed with gravel as top- and bottom layer (total of 22 cm) and a mid...... be a valuable method to sanitize VHSV infected water. Changes in temperature, pH, earth types in the area used for infiltration etc. may change the virus reduction, though. As some of the fish cutting plants are also smoking rainbow trout fillets, the question arose whether a brine solution will inactivate VHSV...

  16. Identifying potential virulence determinants in viral haemorrhagic septicaemia virus (VHSV) for rainbow trout

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    Campbell, Scott; Collet, Bertrand; Einer-Jensen, Katja

    2009-01-01

    We identified viral haemorrhagic septicaemia virus (VHSV) isolates classified within Genotype Ib which are genetically similar (>99.4% glycoprotein amino acid identity) yet, based on their isolation history, were suspected to differ in virulence in juvenile rainbow trout. The virulence...... of an isolate recovered in 2000 from a viral haemorrhagic septicaemia disease episode in a marine rainbow trout farm in Sweden (SE-SVA-1033) was evaluated in juvenile rainbow trout via intraperitoneal injection and immersion challenge alongside 3 isolates recovered from wild-caught marine fish (DK-4p37, DK-5e59...

  17. Genetic stability of the VHSV consensus sequence of G-gene in diagnostic samples from an acute outbreak

    DEFF Research Database (Denmark)

    Einer-Jensen, Katja; Ahrens, Peter; Lorenzen, Niels

    2006-01-01

    of RT-PCR products for epidemiological analysis. Focus was put on a specific case story involving an acute outbreak of VHS in a Danish rainbow trout farm which otherwise had been free of VHSV during the previous 5 years. Tissue materials from individual fish were collected during routine inspection...... collected tissue material as well as from inoculated cell culture. No nucleotide substitutions where identified when aligning the obtained sequence data for the two sample types. The presented data indicate that the overall consensus sequence of the virus outbreak was stable during the survey......, and that initial passage of the virus on BF-2 cells did not result in changes within the G-gene at a detectable level. The results suggest that genotyping of VHSV isolates based on RT-PCR products amplified from infected primary tissues material is a reliable tool for epidemiological studies....

  18. Outbreak of viral haemorrhagic septicaemic (VHS) in seawater-farmed rainbow trout in Norway caused by VHS virus genotype III

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    Dale, Ole Bendik; Ørpetveit, Irene; Lyngstad, Trude Marie

    2009-01-01

    , and the diagnosis was confirmed by the detection of VHSV in brain and internal tissues by immunohistochemistry, cell culture and reverse transcriptase PCR (RT-PCR). Sequence analysis of the G-gene revealed that the isolated virus clustered with VHSV Genotype III and that the Norwegian isolate represents a unique...

  19. Performance Comparison of the Versant HCV Genotype 2.0 Assay (LiPA) and the Abbott Realtime HCV Genotype II Assay for Detecting Hepatitis C Virus Genotype 6

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    Yang, Ruifeng; Cong, Xu; Du, Shaocai; Fei, Ran; Rao, Huiying

    2014-01-01

    The Versant HCV genotype 2.0 assay (line probe assay [LiPA] 2.0), based on reverse hybridization, and the Abbott Realtime HCV genotype II assay (Realtime II), based on genotype-specific real-time PCR, have been widely used to analyze hepatitis C virus (HCV) genotypes. However, their performances for detecting HCV genotype 6 infections have not been well studied. Here, we analyzed genotype 6 in 63 samples from the China HCV Genotyping Study that were originally identified as genotype 6 using the LiPA 2.0. The genotyping results were confirmed by nonstructural 5B (NS5B) or core sequence phylogenetic analysis. A total of 57 samples were confirmed to be genotype 6 (51 genotype 6a, 5 genotype 6n, and 1 genotype 6e). Four samples identified as a mixture of genotypes 6 and 4 by the LiPA 2.0 were confirmed to be genotype 3b. The remaining two samples classified as genotype 6 by the LiPA 2.0 were confirmed to be genotype 1b, which were intergenotypic recombinants and excluded from further comparison. In 57 genotype 6 samples detected using the Realtime II version 2.00 assay, 47 genotype 6a samples were identified as genotype 6, one 6e sample was misclassified as genotype 1, and four 6a and five 6n samples yielded indeterminate results. Nine nucleotide profiles in the 5′ untranslated region affected the performances of both assays. Therefore, our analysis shows that both assays have limitations in identifying HCV genotype 6. The LiPA 2.0 cannot distinguish some 3b samples from genotype 6 samples. The Realtime II assay fails to identify some 6a and all non-6a subtypes, and it misclassifies genotype 6e as genotype 1. PMID:25100817

  20. HPV genotype-specific concordance between EuroArray HPV, Anyplex II HPV28 and Linear Array HPV Genotyping test in Australian cervical samples

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    Alyssa M. Cornall

    2017-12-01

    Full Text Available Purpose: To compare human papillomavirus genotype-specific performance of two genotyping assays, Anyplex II HPV28 (Seegene and EuroArray HPV (EuroImmun, with Linear Array HPV (Roche. Methods: DNA extracted from clinican-collected cervical brush specimens in PreservCyt medium (Hologic, from 403 women undergoing management for detected cytological abnormalities, was tested on the three assays. Genotype-specific agreement were assessed by Cohen's kappa statistic and Fisher's z-test of significance between proportions. Results: Agreement between Linear Array and the other 2 assays was substantial to almost perfect (κ = 0.60 − 1.00 for most genotypes, and was almost perfect (κ = 0.81 – 0.98 for almost all high-risk genotypes. Linear Array overall detected most genotypes more frequently, however this was only statistically significant for HPV51 (EuroArray; p = 0.0497, HPV52 (Anyplex II; p = 0.039 and HPV61 (Anyplex II; p=0.047. EuroArray detected signficantly more HPV26 (p = 0.002 and Anyplex II detected more HPV42 (p = 0.035 than Linear Array. Each assay performed differently for HPV68 detection: EuroArray and LA were in moderate to substantial agreement with Anyplex II (κ = 0.46 and 0.62, respectively, but were in poor disagreement with each other (κ = −0.01. Conclusions: EuroArray and Anyplex II had similar sensitivity to Linear Array for most high-risk genotypes, with slightly lower sensitivity for HPV 51 or 52. Keywords: Human papillomavirus, Genotyping, Linear Array, Anyplex II, EuroArray, Cervix

  1. Mycobacterium massiliense Type II genotype leads to higher level of colony forming units and TNF-α secretion from human monocytes than Type I genotype.

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    Kim, Byoung-Jun; Shim, Tae Sun; Yi, Su-Yeon; Kim, Ho-Cheol; Kim, Bo-Ram; Lee, So-Young; Kook, Yoon-Hoh; Kim, Bum-Joon

    2015-10-01

    Recently, we introduced a novel Mycobacterium massiliense Type II genotype from Korean patients, in which all isolates showed only a rough (R) colony morphotype. In this study, we sought to compare clinical factors and virulence potentials of two genotypes of M. massiliense, Type I and Type II. Patients infected with Type II tend to be younger at infection than those infected with Type I (56.7 vs 62.3, p = 0.051). Type II was more significantly related to R colony type than Type I (34.1% vs 94.1%, p < 0.001). The Type II strain showed significantly more colony forming units (CFUs) and higher levels of TNF-α secretion in infection of human monocytes than the Type I strain. The challenge of extracted glycopeptidolipid (GPL) into human monocytes indicated that the loss of GPL from the cell wall of the Type II genotype led to a higher level of TNF-α secretion in a toll-like receptor 2(TLR2)-dependent manner. Taken together, our data suggest that the M. massiliense Type II genotype shows higher virulence than Type I, which may be due to the induction of TNF-α via the loss of GPL from the Type II cell wall. © 2015 APMIS. Published by John Wiley & Sons Ltd.

  2. Analytical performance evaluation of Anyplex II HPV28 and Euroarray HPV for genotyping of cervical samples.

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    Latsuzbaia, Ardashel; Tapp, Jessica; Nguyen, Trung; Fischer, Marc; Arbyn, Marc; Weyers, Steven; Mossong, Joël

    2016-07-01

    Analytically accurate human papillomavirus (HPV) genotyping methods are required to assess the impact of HPV vaccination. The aim of this study was to evaluate the analytical performance of Anyplex II HPV28 (Seegene, Korea) and Euroarray HPV (Euroimmun, Germany) genotyping kits, for conducting a future HPV vaccine efficacy monitoring study in Luxembourg. A total number of 150 cervical swabs were collected from women with mean age 31.4 years. Agreements for detecting any HPV between Aptima/Anyplex (88.0%) and Aptima/Euroarray (90.7%) were similar. Agreement of Anyplex/EuroArray with Aptima was higher for Genotypes 16, 18 or 45 than for the other 11 HPVs. The average number of HPV genotypes detected per sample was similar with 2.6 and 2.5, for Anyplex and EuroArray, respectively. In conclusion, Anyplex and Euroarray showed high agreement in general and in particular for detecting genotypes contained in HPV vaccines. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Comparison of quantitative RT-PCR with cell culture to detect viral hemorrhagic septicemia virus (VHSV) IVb infections in the Great Lakes.

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    Hope, Kristine M; Casey, Rufina N; Groocock, Geoffrey H; Getchell, Rodman G; Bowser, Paul R; Casey, James W

    2010-03-01

    Viral hemorrhagic septicemia virus (VHSV) is an important pathogen of cultured and wild fish in marine and freshwater environments. A new genotype, VHSV IVb, was isolated from a fish collected from the Great Lakes in 2003. Since the first isolation, VHSV IVb has been confirmed in 28 species, signaling the early invasion and continued spread of this Office International des Epizooties-reportable agent. For surveillance of this virus in both wild and experimental settings, we have developed a rapid and sensitive one-step quantitative real-time polymerase chain reaction (qRT-PCR) assay that amplifies a 100-base-pair conserved segment from both the genomic negative strand and the mRNA positive strand of the nucleoprotein (N) gene of VHSV IVb. This assay is linear over seven orders of magnitude, with an analytical capability of detecting a single copy of viral RNA and reproducibility at 100 copies. The assay is approximately linear with RNA input from 50 to 1000 ng per assay and works equally well with RNA prepared from a column-based or phenol-chloroform-based method. In wild-caught fish, 97% of the cases were found to be more than three orders of magnitude more sensitive using qRT-PCR than using cell culture. Of the 1,428 fish from the Great Lakes region tested in 2006 and 2007, 24% were positive by qRT-PCR whereas only 5% were positive by cell culture. All of the fish that were positive by cell culture were also positive by qRT-PCR. Importantly, qRT-PCR sensitivity is comparable to that of cell culture detection when comparing VHSV viral RNA levels with viral titer stocks, confirming that the high qRT-PCR signals obtained with diagnostic samples are due to the accumulation of N gene mRNA by transcriptional attenuation. The qRT-PCR assay is particularly valuable for rapid and high-throughput prescreening of fish before confirmatory testing by cell culture or sequencing tissue-derived amplicons and especially in detecting infection in fish that do not show clinical

  4. Characterization of the complete genomic sequence of genotype II hepatitis A virus (CF53/Berne isolate).

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    Lu, Ling; Ching, Karen Z; de Paula, Vanessa Salete; Nakano, Tatsunori; Siegl, Gunter; Weitz, Manfred; Robertson, Betty H

    2004-10-01

    The complete genomic sequence of hepatitis A virus (HAV) CF53/Berne strain was determined. Pairwise comparison with other complete HAV genomic sequences demonstrated that the CF53/Berne isolate is most closely related to the single genotype VII strain, SLF88. This close relationship was confirmed by phylogenetic analyses of different genomic regions, and was most pronounced within the capsid region. These data indicated that CF53/Berne and SLF88 isolates are related more closely to each other than are subtypes IA and IB. A histogram of the genetic differences between HAV strains revealed four separate peaks. The distance values for CF53/Berne and SLF88 isolates fell within the peak that contained strains of the same subtype, showing that they should be subtypes within a single genotype. The complete genomic data indicated that genotypes II and VII should be considered a single genotype, based upon the complete VP1 sequence, and it is proposed that the CF53/Berne isolate be classified as genotype IIA and strain SLF88 as genotype IIB. The CF53/Berne isolate is cell-adapted, and therefore its sequence was compared to that of two other strains adapted to cell culture, HM-175/7 grown in MK-5 and GBM grown in FRhK-4 cells. Mutations found at nucleotides 3889, 4087 and 4222 that were associated with HAV attenuation and cell adaptation in HM175/7 and GMB strains were not present in the CF53/Berne strain. Deletions found in the 5'UTR and P3A regions of the CF53/Berne isolate that are common to cell-adapted HAV isolates were identified, however.

  5. Characterization of Toxoplasma gondii isolates from herds of sheep in southern Brazil reveals the archetypal type II genotype and new non-archetypal genotypes.

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    da Silva Ramos, Tatiana; de Jesus Pena, Hilda Fátima; Dos Santos Junior, Alceu Gonçalves; de Faria Santos, Laura Maria Jorge; Cademartori, Beatris Gonzales; Oliveira, Solange; Gennari, Solange Maria; da Silva Ramos Rocha, Andréa; da Rosa Farias, Nara Amélia

    2018-02-01

    Recent studies have demonstrated that, in Brazil and South America, strains of Toxoplasma gondii are often genotypically and biologically different from those found in countries on other continents. The objective of this study was to genotypically characterize T. gondii isolates from naturally infected sheep in herds in the southern region of the state of Rio Grande do Sul, Brazil, by means of the polymerase chain reaction with restriction fragment length polymorphism (PCR-RFLP). Five T. gondii isolates obtained from sheep in five municipalities in the state of Rio Grande do Sul were used. Application of multilocus PCR-RFLP multilocus using 12 genetic markers (SAG1, 5'3' SAG2, alt. SAG2, SAG3, BTUB, c22-8, c29-2, GRA6, L358, PK1, APICO and CS3) revealed four different genotypes in the five isolates studied: clonal type II (TgOvBrRS4), type BrIV (TgOvBrRS2 and TgOvBrRS3) and two new non-archetypal genotypes, ToxoDB-RFLP#270 and #271 (TgOvBrRS1 and TgOvBrRS5, respectively). The genotype structure found in the T. gondii isolates from naturally infected sheep in the southern region of Brazil was revealed to have high diversity. This study confirms the presence of rare circulation of the clonal type II genotype in Brazil. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Search for genetic virulence markers in viral haemorrhagic septicaemia virus (VHSV) using a reverse genetics approach

    DEFF Research Database (Denmark)

    Stegmann, Anders; Biacchesi, S.; Bremont, M.

    2011-01-01

    VHSV is a negative strand RNA virus causing serious disease in farmed rainbow trout. Although VHSV has been eradicated by stamping out procedures in several fresh water bodies, recently including all streams in Denmark, the wildlife marine reservoir still represents a threat against rainbow trout...... farming. Particularly in Scandinavia, outbreaks of VHS in sea reared rainbow trout have demonstrated that although marine variants of VHSV are considered to be avirulent to rainbow trout, the virus is potentially able to adapt to this host and cause disease. Limited knowledge about the genetic background...... for virulence to rainbow trout makes it difficult to differentiate between dangerous and harmless VHSV variants. With the aim of identification of genetic virulence markers, we have implemented reverse genetics technology for generation of hybrid virus variants. By substituting different regions in the genome...

  7. Comparison of treatments to inactivate viral hemorrhagic septicemia virus (VHSV-IVb) in frozen baitfish

    National Research Council Canada - National Science Library

    Phelps, Nicholas B D; Goodwin, Andrew E; Marecaux, Emily; Goyal, Sagar M

    ...) through movement restrictions of live fish; however, they largely ignore the potential for the virus to be spread through commercial distribution and use of frozen baitfish from VHSV-IVb-positive regions...

  8. Comparison of treatments to inactivate viral hemorrhagic septicemia virus (VHSV-IVb) in frozen baitfish.

    Science.gov (United States)

    Phelps, Nicholas B D; Goodwin, Andrew E; Marecaux, Emily; Goyal, Sagar M

    2013-02-28

    Current US state and federal fish health regulations target the spread of viral hemorrhagic septicemia virus-IVb (VHSV-IVb) through movement restrictions of live fish; however, they largely ignore the potential for the virus to be spread through commercial distribution and use of frozen baitfish from VHSV-IVb-positive regions. Some state laws do require treatment of frozen baitfish to inactivate VHSV, and additional methods have been proposed, but few scientific studies have examined the efficacy of these treatments. In this study, bluegills Lepomis macrochirus were challenged with VHSV-IVb and frozen to represent standard industry methods, disinfected by various treatments, and tested for infectious VHSV-IVb using virus isolation. The virus was isolated from 70% of fish subjected to 3 freeze/thaw cycles. All other treatment methods were effective in inactivating the virus, including treatment with isopropyl alcohol, mineral oil, salt and borax, and dehydration. Dehydration followed by rehydration is rapid and effective, and therefore, seems to be the best option for inactivating VHSV-IVb present in frozen baitfish while maintaining their usefulness as bait.

  9. Genotyping of the fish rhabdovirus, viral haemorrhagic septicaemia virus, by restriction fragment length polymorphisms

    DEFF Research Database (Denmark)

    Einer-Jensen, Katja; Winton, J.; Lorenzen, Niels

    2005-01-01

    -gene by a set of three restriction enzymes was predicted to accurately enable the assignment of the VHSV isolates into the four major genotypes discovered to date. Further sub-typing of the isolates into the recently described sub-lineages of genotype I was possible by applying three additional enzymes......The aim of this study was to develop a standardized molecular assay that used limited resources and equipment for routine genotyping of isolates of the fish rhabdovirus, viral haemorrhagic septicaemia virus (VHSV). Computer generated restriction maps, based on 62 unique full-length (1524 nt......) sequences of the VHSV glycoprotein (G) gene, were used to predict restriction fragment length polymorphism (RFLP) patterns that were subsequently grouped and compared with a phylogenetic analysis of the G-gene sequences of the same set of isolates. Digestion of PCR amplicons from the full-length G...

  10. Spread of the Emerging Viral Hemorrhagic Septicemia Virus Strain, Genotype IVb, in Michigan, USA

    Science.gov (United States)

    Faisal, Mohamed; Shavalier, Megan; Kim, Robert K.; Millard, Elena V.; Gunn, Michelle R.; Winters, Andrew D.; Schulz, Carolyn A.; Eissa, Alaa; Thomas, Michael V.; Wolgamood, Martha; Whelan, Gary E.; Winton, James

    2012-01-01

    In 2003, viral hemorrhagic septicemia virus (VHSV) emerged in the Laurentian Great Lakes causing serious losses in a number of ecologically and recreationally important fish species. Within six years, despite concerted managerial preventive measures, the virus spread into the five Great Lakes and to a number of inland waterbodies. In response to this emerging threat, cooperative efforts between the Michigan Department of Natural Resources (MI DNR), the Michigan State University Aquatic Animal Health Laboratory (MSU-AAHL), and the United States Department of Agriculture-Animal and Plant Health Inspection Services (USDA-APHIS) were focused on performing a series of general and VHSV-targeted surveillances to determine the extent of virus trafficking in the State of Michigan. Herein we describe six years (2005–2010) of testing, covering hundreds of sites throughout Michigan’s Upper and Lower Peninsulas. A total of 96,228 fish representing 73 species were checked for lesions suggestive of VHSV and their internal organs tested for the presence of VHSV using susceptible cell lines. Of the 1,823 cases tested, 30 cases from 19 fish species tested positive for VHSV by tissue culture and were confirmed by reverse transcriptase polymerase chain reaction (RT-PCR). Gene sequence analyses of all VHSV isolates retrieved in Michigan demonstrated that they belong to the emerging sublineage “b” of the North American VHSV genotype IV. These findings underscore the complexity of VHSV ecology in the Great Lakes basin and the critical need for rigorous legislation and regulatory guidelines in order to reduce the virus spread within and outside of the Laurentian Great Lakes watershed. PMID:22754647

  11. Spread of the Emerging Viral Hemorrhagic Septicemia Virus Strain, Genotype IVb, in Michigan, USA

    Directory of Open Access Journals (Sweden)

    James Winton

    2012-05-01

    Full Text Available In 2003, viral hemorrhagic septicemia virus (VHSV emerged in the Laurentian Great Lakes causing serious losses in a number of ecologically and recreationally important fish species. Within six years, despite concerted managerial preventive measures, the virus spread into the five Great Lakes and to a number of inland waterbodies. In response to this emerging threat, cooperative efforts between the Michigan Department of Natural Resources (MI DNR, the Michigan State University Aquatic Animal Health Laboratory (MSU-AAHL, and the United States Department of Agriculture-Animal and Plant Health Inspection Services (USDA-APHIS were focused on performing a series of general and VHSV-targeted surveillances to determine the extent of virus trafficking in the State of Michigan. Herein we describe six years (2005–2010 of testing, covering hundreds of sites throughout Michigan’s Upper and Lower Peninsulas. A total of 96,228 fish representing 73 species were checked for lesions suggestive of VHSV and their internal organs tested for the presence of VHSV using susceptible cell lines. Of the 1,823 cases tested, 30 cases from 19 fish species tested positive for VHSV by tissue culture and were confirmed by reverse transcriptase polymerase chain reaction (RT-PCR. Gene sequence analyses of all VHSV isolates retrieved in Michigan demonstrated that they belong to the emerging sublineage “b” of the North American VHSV genotype IV. These findings underscore the complexity of VHSV ecology in the Great Lakes basin and the critical need for rigorous legislation and regulatory guidelines in order to reduce the virus spread within and outside of the Laurentian Great Lakes watershed.

  12. Rainbow trout surviving infections of viral haemorrhagic septicemia virus (VHSV) show lasting antibodies to recombinant G protein fragments

    DEFF Research Database (Denmark)

    Encinas, P.; Gomez-Casado, E.; Grandes, Fregeneda

    2011-01-01

    sera from trout infected with the homologous VHSV isolate but also with the VHSV-DK-201433 heterologous isolate, which had 13 amino acid changes. Sera from healthy trout and/or from trout surviving infectious haematopoietic necrosis virus (IHNV) infection, were used to calculate cut-off absorbances...... refinements of the frg-ELISA could allow detection of anti-VHSV trout Abs in natural outbreaks caused by different heterologous VHSV isolates. The homologous frg-ELISA method could be useful to follow G immunization attempts during vaccine development and/or to best understand the fish Ab response during VHSV...... infections. The viral frgs approach might also be used with other fish species and/or viruses....

  13. Direct genetic characterization of Toxoplasma gondii from clinical samples from Denmark: not only genotypes II and III.

    Science.gov (United States)

    Jokelainen, P; Murat, J-B; Nielsen, H V

    2018-03-01

    Genetic variation within Toxoplasma gondii can have both clinical and epidemiological significance, while the genotypes circulating in many parts of the world, including the Nordic country Denmark, are still unknown. We genetically characterized T. gondii strains that had been detected in human clinical samples in Denmark in 2011-2016. Samples that had tested positive for T. gondii DNA and had a quantification cycle value <33 were included in this study and subjected to direct genetic characterization of T. gondii based on length-polymorphism of 15 microsatellite markers. A total of 23 DNA samples from 22 individual patients were analyzed. The results were consistent with genotype II with 15/15 markers amplified from seven samples from the central nervous system (CNS) including two samples from one patient, four ocular samples, and one unspecified sample; with genotype III with 15/15 markers amplified from two ocular samples; with genotype Africa 1 with 15/15 markers amplified from one amniotic fluid sample and from one CNS-sample; with atypical genotype with 15/15 markers amplified from one CNS-sample and with 11/15 markers amplified from one CNS-sample; and with HG12-like genotype with 9/15 markers amplified from one CNS-sample. Genotype II, which is endemic in Europe, was predominant, but more than a third of the successfully genotyped strains were non-type-II. The possibility that clinical toxoplasmosis is caused by a strain that is not considered endemic to the region is definitely not negligible.

  14. Increased frequency of the DI genotype of the angiotensin-I converting enzyme and association of the II genotype with insulin resistance in polycystic ovary syndrome.

    Science.gov (United States)

    Koika, Vasiliki; Georgopoulos, Neoklis A; Piouka, Athanasia; Roupas, Nikolaos D; Karela, Anastasia; Armeni, Anastasia K; Katsantoni, Eleni; Panidis, Dimitrios

    2012-04-01

    The polycystic ovary syndrome (PCOS) is a common and complex disease with unclear pattern of inheritance, characterized by an androgen excess, while hyperinsulinemia and insulin resistance (IR) are common features of the syndrome. The angiotensin I converting enzyme (ACE) insertion (I)/deletion (D) gene polymorphism was proved to be involved in many pathophysiological conditions, including hypertension and IR. The purpose of this study was to evaluate the involvement of the ACE gene polymorphism in the pathogenesis of PCOS. In a case-control association study involving 801 PCOS women and 266 healthy controls, hormonal determinations and ACE polymorphism genotyping were performed. The PCOS women were classified into three groups: Group A presented biochemical hyperandrogenism, combined with anovulation and polycystic ovarian morphology; Group B, clinical hyperandrogenism combined with anovulation and polycystic ovarian morphology; and Group C, chronic anovulation and polycystic ovarian morphology. A significant increase in the frequency of the DI genotype of the ACE polymorphism was detected in PCOS women as a whole (P=0.035), in PCOS Group A (P=0.039) and Group B (P=0.010), while there was no difference in Group C (P=0.939). Significant difference was also observed in hyperandrogenic PCOS women as a whole (Group A+B) (P=0.017). The II genotype was positively correlated with HOMA-IR and QUICKI and with fasting insulin and glucose/insulin ratio in these groups. The association study of the ACE I/D polymorphism in PCOS women demonstrates an increase in the DI genotype incidence and an association of the II genotype with IR.

  15. Development and Application of Quantitative Detection Method for Viral Hemorrhagic Septicemia Virus (VHSV) Genogroup IVa

    Science.gov (United States)

    Kim, Jong-Oh; Kim, Wi-Sik; Kim, Si-Woo; Han, Hyun-Ja; Kim, Jin Woo; Park, Myoung Ae; Oh, Myung-Joo

    2014-01-01

    Viral hemorrhagic septicemia virus (VHSV) is a problematic pathogen in olive flounder (Paralichthys olivaceus) aquaculture farms in Korea. Thus, it is necessary to develop a rapid and accurate diagnostic method to detect this virus. We developed a quantitative RT-PCR (qRT-PCR) method based on the nucleocapsid (N) gene sequence of Korean VHSV isolate (Genogroup IVa). The slope and R2 values of the primer set developed in this study were −0.2928 (96% efficiency) and 0.9979, respectively. Its comparison with viral infectivity calculated by traditional quantifying method (TCID50) showed a similar pattern of kinetic changes in vitro and in vivo. The qRT-PCR method reduced detection time compared to that of TCID50, making it a very useful tool for VHSV diagnosis. PMID:24859343

  16. Development and Application of Quantitative Detection Method for Viral Hemorrhagic Septicemia Virus (VHSV Genogroup IVa

    Directory of Open Access Journals (Sweden)

    Jong-Oh Kim

    2014-05-01

    Full Text Available Viral hemorrhagic septicemia virus (VHSV is a problematic pathogen in olive flounder (Paralichthys olivaceus aquaculture farms in Korea. Thus, it is necessary to develop a rapid and accurate diagnostic method to detect this virus. We developed a quantitative RT-PCR (qRT-PCR method based on the nucleocapsid (N gene sequence of Korean VHSV isolate (Genogroup IVa. The slope and R2 values of the primer set developed in this study were −0.2928 (96% efficiency and 0.9979, respectively. Its comparison with viral infectivity calculated by traditional quantifying method (TCID50 showed a similar pattern of kinetic changes in vitro and in vivo. The qRT-PCR method reduced detection time compared to that of TCID50, making it a very useful tool for VHSV diagnosis.

  17. Sarcoidosis HLA class II genotyping distinguishes differences of clinical phenotype across ethnic groups

    Science.gov (United States)

    Sato, Hiroe; Woodhead, Felix A.; Ahmad, Tariq; Grutters, Jan C.; Spagnolo, Paolo; van den Bosch, Jules M.M.; Maier, Lisa A.; Newman, Lee S.; Nagai, Sonoko; Izumi, Takateru; Wells, Athol U.; du Bois, Roland M.; Welsh, Kenneth I.

    2010-01-01

    The HLA class II (DRB1 and DQB1) associations with sarcoidosis have been studied by several groups but often without consistent results. In this paper, we consider the hypothesis that observed inconsistencies relate to distinct, genetically encoded disease phenotypes which differ in prevalence between centres. We therefore typed HLA-DRB1 and DQB1 in 340 UK, 139 Dutch and 163 Japanese sarcoidosis patients and, respectively, 354, 218 and 168 healthy controls from these populations. We applied consistent phenotyping and genotyping and investigated associations between HLA class II alleles and distinct disease phenotypes within and between ethnic groups. DRB1*01 and DQB1*0501 are protective against all manifestations of sarcoidosis. Lung-predominant sarcoidosis is associated with DRB1*12 and *14. Löfgren's syndrome is a common sarcoidosis phenotype in the Dutch and is strongly associated with the DRB1*0301 allele. This phenotype is not seen among the Japanese in whom DRB1*0301 is absent. The same allele is protective for UK uveitis. Sarcoid uveitis is common in Japan. The DRB1*04–DQB1*0301 haplotype is a risk factor for this disease manifestation in Japanese and UK subjects but protective for sarcoidosis overall. We show that distinct sarcoidosis phenotypes have similar genetic associations across ethnic groups. The disease case mix differs between centres and may be explained by different ethnic allelic frequencies. PMID:20685690

  18. Comparison of Seegene Anyplex II HPV28 with the PGMY-CHUV Assay for Human Papillomavirus Genotyping.

    OpenAIRE

    Estrade, C.; Sahli, R

    2014-01-01

    The Anyplex II HPV28 (H28; Seegene) is a new semiquantitative real-time multiplex PCR assay for screening and genotyping 28 human papillomaviruses (HPV) in only 2 reaction wells. H28 was compared to the PGMY-CHUV assay (PG) with 309 archival DNA samples from cervical smears collected over 8 years in our laboratory. H28 and PG were fully concordant at the genotypic level on 228 (73.8%) out of 309 samples: 27 HPV negative and 201 HPV positive. The 201 fully concordant positive samples correspon...

  19. Establishment and partial characterization of a cell line from burbot Lota lota maculosa: susceptibility to IHNV, IPNV and VHSV.

    Science.gov (United States)

    Batts, William N.; Polinski, Mark P.; Drennan, John D.; Ireland, Susan C.; Cain, Kenneth D.

    2010-01-01

    This study describes the development and partial characterization of a continuous fibroblastic-like cell line (BEF-1) developed from late stage embryos of North American burbot Lota lota maculosa. This cell line has been maintained for over 5 yr and 100 passages in vitro. Cells were cultured using Eagle’s minimum essential medium with Earle’s salts (MEM) supplemented with GlutaMAX™, and 10% fetal bovine serum (FBS), pH 7.4. The addition of penicillin-streptomycin-neomycin (PSN) antibiotic mixture (0.05, 0.05, 0.1 mg ml–1, respectively) did not negatively influence cell replication; however, the antimycotic Fungizone™ (2.5 µg ml–1, amphotericin B) caused cell rounding and resulted in a severe decrease in cell proliferation. Optimal incubation temperature has been observed between 15 and 23°C, and at these temperatures cultures are routinely passed using standard trypsinization methods every 5 to 7 d at a split ratio of 1:3 or 1:4. The cell line was susceptible to isolates of the M and U North American genotypes of infectious hematopoietic necrosis virus (IHNV), and to isolates of genotypes I, IVa, and IVb of viral hemorrhagic septicemia virus (VHSV). In contrast, the cell line was refractory to infection by 2 North American isolates of infectious pancreatic necrosis virus (IPNV) from serotypes A1 and A9. This cell line provides a new laboratory tool, will allow further investigation into viral diseases of burbot and possibly other species, and is the first immortalized cell line reported from a species in the Gadidae (cod) family.

  20. Establishment and partial characterization of a cell line from burbot Lota lota maculosa: susceptibility to IHNV, IPNV and VHSV.

    Science.gov (United States)

    Polinski, Mark P; Drennan, John D; Batts, William N; Ireland, Susan C; Cain, Kenneth D

    2010-05-18

    This study describes the development and partial characterization of a continuous fibroblastic-like cell line (BEF-1) developed from late stage embryos of North American burbot Lota lota maculosa. This cell line has been maintained for over 5 yr and 100 passages in vitro. Cells were cultured using Eagle's minimum essential medium with Earle's salts (MEM) supplemented with GlutaMAX, and 10% fetal bovine serum (FBS), pH 7.4. The addition of penicillin-streptomycin-neomycin (PSN) antibiotic mixture (0.05, 0.05, 0.1 mg m(-1), respectively) did not negatively influence cell replication; however, the antimycotic FungizoneTM (2.5 microg m(-1), amphotericin B) caused cell rounding and resulted in a severe decrease in cell proliferation. Optimal incubation temperature has been observed between 15 and 23 degrees C, and at these temperatures cultures are routinely passed using standard trypsinization methods every 5 to 7 d at a split ratio of 1:3 or 1:4. The cell line was susceptible to isolates of the M and U North American genotypes of infectious hematopoietic necrosis virus (IHNV), and to isolates of genotypes I, IVa, and IVb of viral hemorrhagic septicemia virus (VHSV). In contrast, the cell line was refractory to infection by 2 North American isolates of infectious pancreatic necrosis virus (IPNV) from serotypes A1 and A9. This cell line provides a new laboratory tool, will allow further investigation into viral diseases of burbot and possibly other species, and is the first immortalized cell line reported from a species in the Gadidae (cod) family.

  1. Comparison of Seegene Anyplex II HPV28 with the PGMY-CHUV assay for human papillomavirus genotyping.

    Science.gov (United States)

    Estrade, C; Sahli, R

    2014-02-01

    The Anyplex II HPV28 (H28; Seegene) is a new semiquantitative real-time multiplex PCR assay for screening and genotyping 28 human papillomaviruses (HPV) in only 2 reaction wells. H28 was compared to the PGMY-CHUV assay (PG) with 309 archival DNA samples from cervical smears collected over 8 years in our laboratory. H28 and PG were fully concordant at the genotypic level on 228 (73.8%) out of 309 samples: 27 HPV negative and 201 HPV positive. The 201 fully concordant positive samples corresponded to single infections (n = 145) and to multiple infections (2 genotypes, n = 38; 3 to 5 genotypes, n = 18). The remaining 81 samples (26.2%) were either partially concordant (n = 64, 20.7%) or fully discordant (n = 17, 5.5%). While genotype-specific agreement was nearly perfect (κ = 0.877), HPV51 was significantly less well detected by H28 and the converse was observed for HPV40, -42, -54, and -68. Sequencing of PG amplicons confirmed HPV51 discordants and suggested the involvement of a possibly local HPV51 subtype. Mismatches in the PGMY09 primers to HPV68a explained most of the HPV68 discordants, confirming the specificity of H28 toward HPV68. With PG as a reference, the sensitivity and specificity of H28 were 93.4% and 99.0%, respectively. Considering H28 as a reference, the sensitivity and specificity of PG were 83.8% and 99.6%, respectively. H28 is a very sensitive and specific HPV genotyping assay suitable for research and clinical use as an adjunct to a clinically validated test. H28 semiquantitative readout ought to be evaluated for primary cervical cancer screening.

  2. Emergence of dengue virus 4 genotype II in Guangzhou, China, 2010: Survey and molecular epidemiology of one community outbreak

    Directory of Open Access Journals (Sweden)

    Jing Qin-Long

    2012-04-01

    Full Text Available Abstract Background The re-emergence of dengue virus 4 (DENV-4 has become a public health concern in South America, Southeast Asia and South Asia. However, it has not been known to have caused a local outbreak in China for the past 20 years. The purpose of this study was to elucidate the epidemiology of one local community outbreak caused by DENV-4 in Guangzhou city, China, in 2010; and to determine the molecular characteristics of the genotype II virus involved. Case presentations During September and October of 2010, one imported case, a Guangzhou resident who travelled back from Thailand, resulted in 18 secondary autochthonous cases in Guangzhou City, with an incidence rate of 5.53 per 10,000 residents. In indigenous cases, 14 serum samples tested positive for IgM against DENV and 7 for IgG from a total of 15 submitted serum samples, accompanied by 5 DENV-4 isolates. With identical envelope gene nucleotide sequences, the two isolates (D10168-GZ from the imported index case and Guangzhou 10660 from the first isolate in the autochthonous cases were grouped into DENV-4 genotype II after comparison to 32 previous DENV-4 isolates from GenBank that originated from different areas. Conclusions Based on epidemiological and phylogenetic analyses, the outbreak, which was absent for 20 years after the DENV-4 genotype I outbreak in 1990, was confirmed as DENV-4 genotype II and initially traced to the imported index case, a Guangzhou resident who travelled back from Thailand.

  3. Investigation of wild caught whitefish, Coregonus lavaretus (L.), for infection with viral haemorrhagic septicaemia virus (VHSV) and experimental challenge of whitefish with VHSV

    DEFF Research Database (Denmark)

    Skall, Helle Frank; Kjær, Torben Egil; Olesen, Niels Jørgen

    2004-01-01

    into contact with farmed rainbow trout. All samples were examined on cell cultures. No viruses were isolated. Three viral haemorrhagic septicaemia virus (VHSV) isolates of different origin were tested in infection trials by immersion and intraperitoneal (IP) injection, using 1.5 g farmed whitefish: an isolate...... from wild caught marine fish, a farmed rainbow trout isolate with a suspected marine origin and a classical freshwater isolate. The isolates were highly pathogenic by IP injection where 99-100% of the whitefish died. Using an immersion challenge the rainbow trout isolates were moderately pathogenic...

  4. Changes in microRNAs expression profile of olive flounder (Paralichthys olivaceus) in response to viral hemorrhagic septicemia virus (VHSV) infection.

    Science.gov (United States)

    Najib, Abdellaoui; Kim, Min Sun; Choi, Seung Hyuk; Kang, Yue Jai; Kim, Ki Hong

    2016-04-01

    To know the effect of viral hemorrhagic septicemia virus (VHSV) infection on the cellular microRNA expression profile in olive flounder (Paralichthys olivaceus), fish were infected with VHSV, and cellular microRNAs expression was analyzed at 0 (control), 6, 12, 24, 48 and 72 h post-infection (h.p.i.) by the high-throughput sequencing. A total of 372 mature miRNAs were identified, and, among them, 63 miRNAs were differentially expressed during VHSV infection. The differentially expressed microRNAs number was greatly increased from 24 h.p.i. compared to the number at 6 and 12 h.p.i., suggesting that the alteration of microRNAs expression by VHSV infection may be related to the progression of VHSV disease. The target prediction analysis, the GO enrichment analysis, and the KEGG pathway analysis of the predicted target genes showed that various biological pathways could be affected by VHSV infection through the down-regulation or up-regulation of host miRNAs. The present results provide a basic information on the microRNAs related to VHSV infection in olive flounder. Considering broad effects of microRNAs on various biological pathways, data in this study can be used to interpret the mechanism of VHSV pathogenesis, which, vice versa, can be used to develop control measures against VHSV. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. QCM DNA biosensor for the diagnosis of a fish pathogenic virus VHSV.

    Science.gov (United States)

    Hong, Sung-Rok; Jeong, Hyun-Do; Hong, Suhee

    2010-08-15

    Viral haemorrhagic septicaemia (VHS) is one of the most serious viral diseases damaging both fresh and marine fish species. VHS caused by VHSV and diagnosis of VHSV has been dependent on the conventional methods, such as cell culture and RT-PCR, which takes a few days or several hours. This study demonstrates a rapid and sensitive QCM biosensor for diagnosis of VHSV infection in fish. The QCM biosensor was developed to detect a main viral RNA encoding G protein in VHSV using the specific DNA probe. To maximize the sensitivity of the biosensor, we prepared three different DNA probes which modified 3' end of DNA by thiol, amine, or biotin and compared three different immobilisation methods on quartz surface coated with gold: immobilisation of thiol labelled probe DNA on naked gold surface, immobilisation of amino labelled probe DNA on gold surface prepared as carboxyl chip using MPA followed by EDC/NHS activation, and immobilisation of biotin labelled probe DNA on gold surface after immobilising avidin on carboxyl chip prior to biotin. As a result, immobilisation method using avidin-biotin interaction was most efficient to immobilise probe DNA and to detect target DNA. The QCM biosensor system using biotinylated probe DNA was stable enough to withstand 32 times of repeated regenerations and the detection limit was 0.0016muM. Diagnosis using the QCM biosensor system was more sensitive and much faster than a conventional RT-PCR analysis in detecting the viral RNA. Copyright 2010 Elsevier B.V. All rights reserved.

  6. Antiviral activity produced by an IPNV-carrier EPC cell culture confers resistance to VHSV infection.

    Science.gov (United States)

    Jurado, María Teresa; García-Valtanen, Pablo; Estepa, Amparo; Perez, Luis

    2013-10-25

    Infectious pancreatic necrosis virus (IPNV), a fish birnavirus, can establish a persistent infection on epithelioma papulosum cyprinid (EPC) cells producing a carrier state where a small fraction of IPNV-infected cells is maintained in the culture after continuous subculture. The EPC(IPNV) cells are resistant to challenge with IPNV as well as to challenge with viral hemorrhagic septicemia virus (VHSV), a rhabdovirus. In this work, the antiviral effect of the IPNV carrier culture conditioned medium (EPC(IPNV)-CM) was tested and analyzed in detail. EPC cells treated with the carrier culture supernatant become protected against VHSV challenge. Size-fractionation by filtration and acid and heat treatment showed that the IPNV persistently infected cells release an acid-resistant soluble factor in the molecular weight fraction bellow 50 kDa. The capacity of the EPC(IPNV)-CM to induce cytokine genes in EPC cells was also determined by real-time RT-PCR. We found that there is a positive correlation between up-regulation of mx gene expression in EPC cells treated with EPC(IPNV)-CM and protection against VHSV challenge. Our findings indicate that the control of IPNV multiplication in the carrier culture as well as the interference with rhabdovirus replication are connected to the production and release of an antiviral (interferon-like) factor to the medium. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. Genotyping of samples from German patients with ocular, cerebral and systemic toxoplasmosis reveals a predominance of Toxoplasma gondii type II.

    Science.gov (United States)

    Herrmann, Daland C; Maksimov, Pavlo; Hotop, Andrea; Groß, Uwe; Däubener, Walter; Liesenfeld, Oliver; Pleyer, Uwe; Conraths, Franz J; Schares, Gereon

    2014-10-01

    Toxoplasmosis is an important zoonosis transmitted from animals to humans world-wide. In order to determine Toxoplasma gondii genotypes in individuals living in Germany and to compare findings with those in animals, we analysed nine independent and unlinked genetic markers (nSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico) by PCR-RFLP in 83 archived T. gondii-positive DNA samples from patients with ocular toxoplasmosis (n=35), toxoplasmic encephalitis (n=32), systemic toxoplasmosis after bone-marrow transplantation (n=15) and congenital toxoplasmosis (n=1). In 46 of these 83 samples the presence of T. gondii DNA was confirmed by conventional end-point PCR. Among these, 17 T. gondii-positive samples were typed at all nine loci. The majority (15/17, 88.2%) of these samples were of T. gondii type II (i.e., including both, the Apico type II and Apico type I variants). In addition, in one sample a T. gondii type II/type III allele combination and in another sample a T. gondii genotype displaying type III alleles at all markers was observed. In the remaining 11 samples, in which T. gondii could only be partially typed, exclusively type II (n=10) or type III (n=1) alleles were observed. Results of the present study suggest that the majority of patients in Germany are infected with type II T. gondii regardless of the clinical manifestation of toxoplasmosis. This finding is in accord with the predominance of type II T. gondii in oocysts isolated from cats and in tissues of other intermediate hosts in Germany. Copyright © 2014 Elsevier GmbH. All rights reserved.

  8. Differentiation of Trypanosoma cruzi I (TcI) and T. cruzi II (TcII) genotypes using genes encoding serine carboxypeptidases.

    Science.gov (United States)

    de Araújo, Catarina Andréa Chaves; Mayer, Christoph; Waniek, Peter Josef; Azambuja, Patricia; Jansen, Ana Maria

    2016-11-01

    The parasite Trypanosoma cruzi (Kinetoplastida, Trypanosomatidae) can be classified based on biochemical and molecular markers, into six lineages or discrete typing units (DTUs), T. cruzi I-VI (TcI-VI), from which TcI and TcII are the parental genotypes. Trying to understand the dispersion of the subpopulations of T. cruzi in nature and its complex transmission cycles, the serine carboxypeptidase genes of T. cruzi were used as a molecular marker in the present study. DTUs of 25 T. cruzi isolates derived from different hosts and from different regions of Brazil were classified. Using specific primers, the complete serine carboxypeptidase open reading frame of 1401 bp was sequenced. The obtained data shows significant differences in the sequences of TcI and TcII. The analysis of the T. cruzi significantly different serine carboxypeptidase genes allowed distinguishing between the parental DTUs TcI to TcII and the hybrid DTU TcVI which grouped within the latter branch. The sequence diversity within the T. cruzi subpopulations was rather low. The analysis using the genes encoding proteases seems to be an interesting approach for the reconstruction of the origin and genotype evolution of T. cruzi.

  9. Interspecific pine hybrids II. genotype by environment interactions across Australia, Swaziland, and Zimbabwe

    Science.gov (United States)

    H. S. Dungey; M. J. Dieters; D. P. Gwaze; P. G. Toon; D. G. Nikles

    2000-01-01

    Collaborative research trials of Queensland-bred pine hybrids have been established in many sites outside Australia. These trials enable the estimation of genotype x environment effects, which are important in determining the level of regionalisation needed in any breeding program. Correlations across sites testing hybrids between Pinus caribaea var...

  10. Genotype and toxicity relationships among Hyalella azteca: II. Acute exposure to fluoranthene-contaminated sediment

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Y.; Guttman, S.I.; Oris, J.T.; Huang, X.; Burton, G.A.

    2000-05-01

    This study examined the genotypic responses of Hyalella azteca to the toxicity of sediment contaminated by the polycyclic aromatic hydrocarbon (PAH) fluoranthene. The authors monitored the time to death for 696 H. azteca exposed to ultraviolet light and sediment spiked with fluoranthene. The survival distribution functions within the genotypes at each of these variable allozyme loci (acid phosphatase [ACP*], glucose-6-phosphate isomerase [GPI*], and phosphoglucomutase [PGM*]) were compared using a long-rank test. Results showed significant differences among SDFs at all three loci. No association of heterozygosity with time to death was observed. The homozygote ACP*-CC was associated with decreased survivorship compared with ACP*-AA, ACP*-BB, and ACP*-AB. However, GPI*-AA was associated with increased survivorship compared with GPI*-BB, GPI*-CC, and GPI*-BC. Significant differences in resistance also were observed for PGM*-BB versus either PGM*-AC or PGM*-BC. These results indicate that differential resistance to PAH phototoxicity was genetically related, producing significant alteration in the frequencies of several genotypes in the population.

  11. Inter-species transmission of viral hemorrhagic septicemia virus (VHSV) from turbot (Scophthalmus maximus) to rainbow trout (Onchorhynchus mykiss)

    DEFF Research Database (Denmark)

    Schönherz, Anna Amanda; Lorenzen, Niels; Einer-Jensen, Katja

    2013-01-01

    barriers. The viral hemorrhagic septicemia virus (VHSV), a rhabdovirus with high economic impact on the aquaculture industry, has developed an exceptionally wide host range across marine and freshwater environments. Transmission of VHSV between host species therefore represents a potential risk......Successful viral infection is a complex mechanism, involving many host–pathogen interactions that developed during coevolution of host and pathogen, and often result in host-species specificity. Nevertheless, many viruses are able to infect several host species and sporadically cross species...... for aquaculture, which currently is not addressed in biosecurity managements. The objective of this study was to investigate the inter-species transmission potential of VHSV and evaluate whether infected marine wild fish pose a potential risk on marine cultured rainbow trout. A cohabitation infection trial...

  12. A novel multiplex RT-qPCR method based on dual-labelled probes suitable for typing all known genotypes of viral haemorrhagic septicaemia virus

    DEFF Research Database (Denmark)

    Vázquez, D.; López-Vázquez, C.; Skall, Helle Frank

    2016-01-01

    relationship. In this study, we have designed and validated a new procedure – named binary multiplex RT-qPCR (bmRT-qPCR) – for simultaneous detection and typing of all four genotypes of VHSV by real-time RT-PCR based on dual-labelled probes and composed by two multiplex systems designed for European......, resulting in a correct detection and typing of all strains. The analytical sensitivity was evaluated in a comparative assay with titration in cell culture, observing that both methods provided similar limits of detection. The proposed method can be a powerful tool for epidemiological analysis of VHSV...

  13. GENETIC CONSEQUENCES OF OUTCROSSING IN THE CLEISTOGAMOUS ANNUAL, IMPATIENS CAPENSIS. II. OUTCROSSING RATES AND GENOTYPIC CORRELATIONS.

    Science.gov (United States)

    Waller, Donald M; Knight, Susan E

    1989-07-01

    The genetic consequences of a plant's mating system depend on both the degree of outcrossing and the genetic relationship between mates. We examined the electrophoretic genotypes of seeds derived from cleistogamous (CL) and chasmogamous (CH) flowers in six populations of the facultatively cleistogamous annual, Impatiens capensis. Multilocus estimates of the outcrossing rates for the strongly protandrous CH flowers ranged from 0.29 to 0.71 and were higher than estimates based on single-locus data. Such results suggest that the CH flowers experience variable levels of both geitonogamous self-fertilization and biparental inbreeding. A new and generally applicable technique based on the relative level of inbreeding within progeny groups provided direct estimates of the correlation between the genotypic values of outcrossed mates. These correlations varied widely among populations and contributed up to half of the inbreeding observed among the CH progeny. Such biparental inbreeding biases estimates of the outcrossing rate based on the mixed-mating model downward and influences mating-system evolution by decreasing the "cost of meiosis." © 1989 The Society for the Study of Evolution.

  14. Sequence Analysis of the Capsid Gene during a Genotype II.4 Dominated Norovirus Season in One University Hospital

    DEFF Research Database (Denmark)

    Holzknecht, Barbara Juliane; Franck, Kristina Træholt; Nielsen, Rikke Thoft

    2015-01-01

    Norovirus (NoV) is a leading cause of gastroenteritis and genotype II.4 (GII.4) is responsible for the majority of nosocomial NoV infections. Our objective was to examine whether sequencing of the capsid gene might be a useful tool for the hospital outbreak investigation to define possible....... Sequences of the capsid gene (1412 nucleotides) were obtained from the first available sample from 55 patients. From six immunocompromised patients with persistent infections a second sample was also included. As a control for a point-source outbreak, five samples from a foodborne outbreak caused...... by the same GII.4 variant were analyzed. Forty-seven of the inpatients (85%) were infected with the GII.4 variant Den Haag 2006b. Phylogenetic analysis of the Den Haag 2006b sequences identified four distinct outbreaks in different departments and a fifth outbreak with possible inter-department spread...

  15. Correlation of mRNA Profiles, miRNA Profiles, and Functional Immune Response in Rainbow Trout (Oncorrhynkus Mykiss) During Infection With Viral Hemorrhagic Septicemia Virus (VHSV) and in Fish Vaccinated With an Anti-VHSV DNA Vaccine

    DEFF Research Database (Denmark)

    Bela-Ong, Dennis; Schyth, Brian Dall; Lorenzen, Niels

    This project seeks to characterize molecular genetic and immunological mechanisms involved in rainbow trout (Oncorhynchus mykiss) immunity towards Viral hemorrhagic septicemia virus (VHSV). To do so, we consider both relevant genes and the newly discovered small double-stranded RNAs called microR...

  16. Genotype of UGT1A1 and phenotype correlation between Crigler-Najjar syndrome type II and Gilbert syndrome.

    Science.gov (United States)

    Maruo, Yoshihiro; Nakahara, Sayuri; Yanagi, Takahide; Nomura, Akitaka; Mimura, Yu; Matsui, Katsuyuki; Sato, Hiroshi; Takeuchi, Yoshihiro

    2016-02-01

    Hereditary unconjugated hyperbilirubinemias, Crigler-Najjar syndrome type I, Crigler-Najjar syndrome type II (CN-2), and Gilbert syndrome (GS) all result from mutations of the bilirubin uridine 5'-diphosphate (UDP)-glucuronosyltransferase gene (UGT1A1). Often, to distinguish between CN-2 and GS is difficult because the borderline of the two syndromes is unclear. We analyzed the genotypes and phenotypes of 163 Japanese patients with CN-2 or GS. Japanese patients (99 males and 64 females) with unconjugated hyperbilirubinemia were analyzed. Their serum bilirubin concentrations varied from 1.2 to 22.2 mg/dL (20 to 379 μM). Genetic analysis of UGT1A1 was performed by PCR-amplified direct sequencing. Association between serum bilirubin concentrations and genotypes group (typical CN-2, intermediate group, and typical GS) was studied. Most patients had biallelic mutations of UGT1A1. Moreover, many of them (78.5%) had multiple mutations. The mutation in typical CN-2 was a homozygous double missense mutation of p.[G71R:Y486D]. In typical GS group, four prevalent genotypes were detected: homozygous UGT1A1*28, UGT1A1*6/UGT1A1*28, and homozygous UGT1A1*6, and UGT1A1*27/UGT1A1*28. In the intermediate group, three genotypes, p.[G71R:Y486D]/UGT1A1*7, p.[G71R:Y486D]/UGT1A1*6, and homozygous UGT1A1*7, were detected. Serum bilirubin concentrations of typical CN-2, intermediate group, and typical GS are respectively 12.9 ± 5.1, 5.2 ± 2.2, and 2.8 ± 1.1 mg/dL. Serum bilirubin concentration among the three groups is statistically different (P syndromes. Clinically, it is difficult to distinguish clearly between the two syndromes. © 2015 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

  17. Development and evaluation of novel one-step TaqMan realtime RT-PCR assays for the detection and direct genotyping of genogroup I and II noroviruses

    DEFF Research Database (Denmark)

    Schultz, Anna Charlotte; Vega, Everado; Dalsgaard, Anders

    2011-01-01

    BackgroundCurrent detection and genotyping methods of genogroup (G) I and II noroviruses (NoVs) consist of a 2-step approach including detection of viral RNA by TaqMan realtime RT-PCR (RT-qPCR) followed by conventional RT-PCR and sequencing of partial regions of ORF1 or ORF2. ObjectiveTo develop...

  18. Relative predispositional effects of HLA class II DRB1-DQB1 haplotypes and genotypes on type 1 diabetes : a meta-analysis

    NARCIS (Netherlands)

    Thomson, G.; Valdes, A. M.; Noble, J. A.; Kockum, I.; Grote, M. N.; Najman, J.; Erlich, H. A.; Cucca, F.; Pugliese, A.; Steenkiste, A.; Dorman, J. S.; Caillat-Zucman, S.; Hermann, R.; Ilonen, J.; Lambert, A. P.; Bingley, P. J.; Gillespie, K. M.; Lernmark, A.; Sanjeevi, C. B.; Ronningen, K. S.; Undlien, D. E.; Thorsby, E.; Petrone, A.; Buzzetti, R.; Koeleman, B. P. C.; Roep, B. O.; Saruhan-Direskeneli, G.; Uyar, F. A.; Gunoz, H.; Gorodezky, C.; Alaez, C.; Boehm, B. O.; Mlynarski, W.; Ikegami, H.; Berrino, M.; Fasano, M. E.; Dametto, E.; Israel, S.; Brautbar, C.; Santiago-Cortes, A.; de Llado, T. Frazer; She, J.-X.; Bugawan, T. L.; Rotter, J. I.; Raffel, L.; Zeidler, A.; Leyva-Cobian, F.; Hawkins, B. R.; Chan, S. H.; Castano, L.; Pociot, F.; Nerup, J.

    The direct involvement of the human leukocyte antigen class II DR-DQ genes in type 1 diabetes (T1D) is well established, and these genes display a complex hierarchy of risk effects at the genotype and haplotype levels. We investigated, using data from 38 studies, whether the DR-DQ haplotypes and

  19. Detection of rainbow trout antibodies against viral haemorrhagic septicaemia virus (VHSV) by neutralisation test is highly dependent on the virus isolate used

    DEFF Research Database (Denmark)

    Fregeneda-Grandes, J.M.; Olesen, Niels Jørgen

    2007-01-01

    Three serological tests, enzyme linked immunosorbent assay (ELISA), 50 % plaque neutralisation test (50%PNT) and Western blotting (WB), were used to detect antibodies against viral haemorrhagic septicaerma virus (VHSV) in 50 rainbow trout broodstock from a rainbow trout farm endemically infected...... %PNT, 90 % of the fish were found to be positive. By examining a panel of different VHSV isolates in 50 %PNT, it was demonstrated that the virus isolate used as test antigen could significantly affect the sensitivity and titre determination in 50 %PNT for detection of rainbow trout antibodies against...... VHSV. When the sera were examined for the presence of VHSV antibodies by ELISA or WB, 61 % were found to be positive. When conducting WB analysis, the viral glycoprotein was the protein most frequently recognized, followed by the viral nucleoprotein....

  20. Isolation of viral haemorrhagic septicaemia virus (VHSV) from wild marine fish species in the Baltic Sea, Kattegat, Skagerrak and the North Sea

    DEFF Research Database (Denmark)

    Mortensen, Helle Frank; Heuer, Ole Eske; Lorenzen, Niels

    1999-01-01

    ), rockling Rhinonemus cimbrius (one isolate), Norway pout Trisopterus esmarkii (one isolate), blue whiting Micromesistius poutassou (one isolate), whiting Merlangius merlangus (two isolates) and lesser argentine Argentina sphyraena (one isolate). VHSV has previously been reported from cod and herring...

  1. Study comparing human papillomavirus (HPV) real-time multiplex PCR and Hybrid Capture II INNO-LiPA v2 HPV genotyping PCR assays

    DEFF Research Database (Denmark)

    Iftner, Thomas; Germ, Liesje; Swoyer, Ryan

    2009-01-01

    Human papillomavirus (HPV) DNA genotyping is an essential test to establish efficacy in HPV vaccine clinical trials and HPV prevalence in natural history studies. A number of HPV DNA genotyping methods have been cited in the literature, but the comparability of the outcomes from the different...... methods has not been well characterized. Clinically, cytology is used to establish possible HPV infection. We evaluated the sensitivity and specificity of HPV multiplex PCR assays compared to those of the testing scheme of the Hybrid Capture II (HCII) assay followed by an HPV PCR/line hybridization assay...

  2. Dual DNA vaccination of rainbow trout (Oncorhynchus mykiss) against two different rhabdoviruses, VHSV and IHNV, induces specific divalent protection

    DEFF Research Database (Denmark)

    Einer-Jensen, Katja; Delgado, L.; Lorenzen, Ellen

    2009-01-01

    DNA vaccines encoding the glycoprotein genes of the salmonid rhabdoviruses VHSV and IHNV are very efficient in eliciting protective immune responses against their respective diseases in rainbow trout (Oncorhynchus mykiss). The early anti-viral response (EAVR) provides Protection by 4 days post...... vaccination and is non-specific and transient while the specific anti-viral response (SAVR) is long lasting and highly specific. Since both VHSV and IHNV are endemic in rainbow trout in several geographical regions of Europe and Atlantic salmon (Salmo salar) on the Pacific coast of North America, co-vaccination...... against the two diseases would be a preferable option. In the present study we demonstrated that a single injection of mixed DNA vaccines induced long-lasting protection against both individual and a simultaneous virus challenge 80 days post vaccination. Transfected muscle cells at the injection site...

  3. Performance of Different Tomato Genotypes in the Arid Tropics of Sudan during the Summer Season. II. Generative Development

    Directory of Open Access Journals (Sweden)

    Adil H.A. Abdelmageed

    2009-10-01

    Full Text Available Eleven tomato genotypes of diverse origin were grown in Shambat, University of Khartoum, Sudan, in a randomized block design with three replications for two successive seasons (2002/2003, 2003/2004. The same genotypes were firstly evaluated under glasshouse conditions at the Humboldt University of Berlin, Germany during 2002. Highly significant differences were encountered among the different genotypes for most of the generative characters, such as number of days to flowering, number of flowers per plant, number of fruits per plant, fruit fresh weight per plant and fruit set percentage. Based on results obtained from this study, the genotype ‘Summerset’ proved to be high yielding under high temperature conditions in comparison to other genotypes.

  4. Association of the transcobalamin II gene 776C → G polymorphism with Alzheimer's type dementia: dependence on the 5, 10-methylenetetrahydrofolate reductase 1298A → C polymorphism genotype.

    Science.gov (United States)

    Cascalheira, José F; Gonçalves, Mónica; Barroso, Madalena; Castro, Rita; Palmeira, Manuela; Serpa, André; Dias-Cabral, Ana C; Domingues, Fernanda C; Almeida, Sofia

    2015-07-01

    Decreased serum concentrations of vitamin B12 are associated with Alzheimer's type dementia. The transcobalamin II gene (TCN2) 776C → G polymorphism affects transcobalamin II function as a carrier of vitamin B12 and might modify its availability. The association of the TCN2 776C → G polymorphism with Alzheimer's type dementia is unclear and was investigated in the present study. Case-control study including 27 individuals diagnosed with Alzheimer's type dementia and 28 healthy controls. Serum concentrations of vitamin B12, homocysteine and other analytes were determined and the presence of TCN2 776C → G and 5, 10-methylenetetrahydrofolate reductase 1298A → C polymorphisms genotypes was ascertained by polymerase chain reaction-restriction fragment length polymorphism. Serum concentrations of vitamin B12 were lower while those of homocysteine were higher in patients than in controls (P Alzheimer's type dementia (OR = 0.17 versus CC genotype, P Alzheimer's type dementia together with higher concentrations of homocysteine, cholesterol and uric acid and lower concentrations of oestradiol. Association of TCN2 776C → G polymorphism with Alzheimer's type dementia was observed for individuals carrying the 5,10-methylenetetrahydrofolate reductase 1298AA genotype but not the AC or CC genotypes, indicating interaction between the two polymorphisms. The TCN2 776C → G polymorphism is negatively associated with Alzheimer's type dementia, suggesting a protective role against the disease in subjects with the 5, 10-methylenetetrahydrofolate reductase 1298AA genotype. © The Author(s) 2015 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  5. A one-step duplex rRT-PCR assay for the simultaneous detection of grass carp reovirus genotypes I and II.

    Science.gov (United States)

    Zeng, Weiwei; Wang, Yingying; Liang, Hongru; Liu, Cun; Song, Xinjian; Shi, Chunbin; Wu, Shuqin; Wang, Qing

    2014-12-15

    Hemorrhagic disease of grass carp, caused by grass carp reovirus (GCRV), leads to severe economic losses in the grass carp farming industry in China. GCRV has been divided into three genotypes based on genome sequence. Genotypes I and II (GCRV-1 and GCRV-II, respectively) are the dominant genotypes and co-infections of GCRV-I and GCRV-II are common in grass carp aquaculture. A one-step duplex real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assay was developed for simultaneous detection of GCRV-I and GCRV-II. The PCR assay is suitable for early diagnosis of grass carp hemorrhagic disease and for epidemiological surveillance. The detection limit of the assay is 10 copies for both GCRV-I and GCRV-II, which is as high as single-target rRT-PCR and higher than conventional RT-PCR. No cross reactivity with other GCRV subtypes or other viruses was observed. One hundred and twelve samples from grass carp suspected of hemorrhagic disease were collected from South and Central China. Eleven samples were positive for GCRV-I by RT-PCR alone, and fourteen samples were positive by single-target and duplex rRT-PCR. Forty two samples were positive for GCRV-II by RT-PCR alone and forty seven samples were positive by single-target and duplex rRT-PCR. Mixed infections were found in eight samples when analyzed by RT-PCR alone and in ten samples analyzed by single-target and duplex rRT-PCR. The duplex rRT-PCR system provides a sensitive and specific method to detect and differentiate between GCRV-I and GCRV-II in a single sample. This rRT-PCR assay could be a useful tool for the routine diagnosis of these two viruses and for epidemiology studies in grass carp aquaculture. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Susceptibility of various Japanese freshwater fish species to an isolate of viral haemorrhagic septicaemia virus (VHSV) genotype IVb

    National Research Council Canada - National Science Library

    Ito, Takafumi; Olesen, Niels Jørgen

    2013-01-01

    .... In Expt 1, cumulative mortalities in bluegill Lepomis macrochirus used as positive controls, Japanese fluvial sculpin Cottus pollux, and iwana Salvelinus leucomaenis pluvius were 50, 80 and 0%, respectively...

  7. Live vaccine of viral hemorrhagic septicemia virus (VHSV) for Japanese flounder at fish rearing temperature of 21°C instead of Poly(I:C) administration.

    Science.gov (United States)

    Nishizawa, Toyohiko; Takami, Ikuo; Yang, Minji; Oh, Myung-Joo

    2011-10-26

    The process of "Poly(I:C) immunization" involves immunization of fish with a pathogenic live virus, followed by administration of Poly(I:C), which induces a transient, non-specific antiviral state. As a result, fish in an antiviral state survive the initial immunization with live virus. Moreover, these fish are able to mount a specific protective immune response against the injected pathogenic virus. In the present study, we investigated the optimum temperature for Poly(I:C) immunization of Japanese flounder Paralichthys olivaceus with live viral hemorrhagic septicemia virus (VHSV). It was revealed that the optimum temperature was around at 17°C for Poly(I:C) immunization in Japanese flounder. Furthermore, the protection efficacy of Poly(I:C) immunization was significantly decreased by elevation of fish rearing temperature, and no efficacy was observed at a fish rearing temperature of 25°C. Interestingly, no mortality by VHSV infection was observed in fish reared at 21°C and 25°C even when those fish were not administered Poly(I:C). All of the survivors from the first VHSV-challenge at 21°C were strongly protected from re-challenge with VHSV. However, almost all of the survivors (≥82.6%) from the first challenge at 25°C were lost by the second challenge with VHSV. It was thus concluded that by rearing fish at 21°C and challenging with live VHSV, it is possible to induce strong specific immunity in Japanese flounder without Poly(I:C) administration. Copyright © 2011 Elsevier Ltd. All rights reserved.

  8. Existence of Paenibacillus larvae genotypes ERIC I-ST2, ERIC I-ST15 and ERIC II-ST10 in the western region of Aichi prefecture, Japan.

    Science.gov (United States)

    Hirai, Yuko; Suzuki, Toshinari; Inaba, Nanami; Minoguchi, Naokazu; Takamatsu, Daisuke

    2016-08-01

    American foulbrood is the most destructive honeybee bacterial disease. The etiological agent, Paenibacillus larvae, has been classified into four genotypes by a repetitive-element PCR (ERIC I-IV) and 21 sequence types by multilocus sequence typing (ST1-21). In this study, we genotyped Japanese P. larvae isolates for the first time and revealed the presence of three genotypes (ERIC I-ST2, ERIC I-ST15 and ERIC II-ST10) in the western region of Aichi prefecture. ERIC I-ST15 and ERIC II-ST10 are globally distributed types, whereas the ERIC I-ST2 isolate was the first isolate of this genotype identified outside the native range of the European honeybee. The ERIC I and II isolates differed in phenotypes including cell morphology, and these may be useful for predicting ERIC types.

  9. Evolutionary Mechanisms Involved in Emergence of Viral Haemorrhagic Septicaemia Virus (VHSV) into Cultured Rainbow Trout, Oncorhynchus mykiss

    DEFF Research Database (Denmark)

    Schönherz, Anna A.

    virulence, causing extensive losses to the aquacultre industry. Cross-species transmission and subsequent adaptation to cultured raibow trout is observed occasionally. However, the biological background facilitationg VHSV emergense has yet to be identified. In the present PhD project potential mechanisms...... host species. Main findings comprise the conformation of an oral transmission route and its potential importance as founder event for cross-species transmission, the potential of marine fish species to function as viral vector for rainbow trout adaptied isolates, recombination as possible source...

  10. Vurdering af hygiejniseringseffekten af nedsivning af viral hæmorrhagisk septikæmi virus (VHSV) under eksperimentelle forhold

    DEFF Research Database (Denmark)

    Skall, Helle Frank; Olesen, Niels Jørgen; Jørgensen, Claus

    2011-01-01

    prøver fra udløbet til virologisk undersøgelse. Prøveudtagningen var mest intensiv i den periode hvor der var størst risiko for at VHSV kom ud af i bunden søjlen. Der blev ikke påvist virus ved den virologiske undersøgelse. Da den virologiske undersøgelses følsomhed var 13,9 TCID50/ml kunne der påvises...

  11. Evaluation of the effect of percolation and NaCl solutions on viral haemorrhagic septicaemia virus (VHSV) under experimental conditions

    DEFF Research Database (Denmark)

    Skall, Helle Frank; Jørgensen, Claus; Olesen, Niels Jørgen

    2015-01-01

    from any of the outlet samples. As the sensitivity of the virological examination was 13.9 TCID50/ml a reduction of >4 log was shown at the outlet. Percolation thus seems to be a usable method for sanitation of water contaminated with VHSV. Changes in temperature, pH, earth types etc. may potentially...... this is an approved method to get rid of the wastewater. To our knowledge, for fish pathogenic viruses, this kind of investigation has never been published before and the presented knowledge is therefore new and valuable. (C) 2015 Elsevier B.V. All rights reserved....

  12. Assessment of a commercial kit collection for diagnosis of the fish viruses: IHNV, IPNV, SVCV and VHSV

    DEFF Research Database (Denmark)

    Ariel, Ellen; Olesen, Niels Jørgen

    2001-01-01

    A commercial kit collection for the detection of the fish pathogenic viruses, VHSV, IHNV, IPNV, and SVCV, was assessed for its ability to detect isolates in selected panels of the respective viruses. The kit collection, which was based on fluorescence staining of infected cell cultures in tissue ...... culture plates, fulfilled the promised requirements for the IHN kit only. The IPN, the SVC and especially the VHS kit were lacking in either specificity or sensitivity. The findings stress the need for commercial companies to carry out proper validation before market release....

  13. Studies on herd-immunity and primary versus secondary infection of VHSV in challenge and vaccination trials with rainbow trout

    DEFF Research Database (Denmark)

    Lorenzen, Ellen; Kjær, Torben Egil; Lorenzen, Niels

    Abstract for Scofda meeting 4-5.11.09 Studies on herd-immunity effect and primary versus secondary infection of VHSV by Ellen Lorenzen, Torben Eigil Kjær & Niels Lorenzen, National Veterinary Laboratory, Århus The phenomenon of “herd-immunity” is one of the basal principles behind vaccination...... as well as selective breeding, i.e. the more non-susceptible individuals in a population, the lower the risk of disease among susceptible individuals. Thus as part of a recent field trial with a VHS-DNA-vaccine vaccinated as well as naïve fish from a Danish fish farm were brought to the laboratory...

  14. Ledipasvir/sofosbuvir-based treatment of patients with chronic genotype-1 HCV infection and cirrhosis: results from two Phase II studies.

    Science.gov (United States)

    Lawitz, Eric; Poordad, Fred; Hyland, Robert H; Wang, Jing; Liu, Lin; Dvory-Sobol, Hadas; Brainard, Diana M; McHutchison, John G; Gutierrez, Julio A

    2016-01-01

    Ledipasvir/sofosbuvir ± ribavirin administered for 12 weeks to patients with genotype-1 HCV infection and compensated cirrhosis is effective and well-tolerated. The Phase II TRILOGY-1 and TRILOGY-2 studies investigated whether ledipasvir/sofosbuvir plus the non-nucleotide NS5B inhibitor GS-9669 or the NS3/4A protease inhibitor vedroprevir could reduce treatment duration and/or eliminate the need for ribavirin in genotype-1 HCV-infected patients with compensated cirrhosis. In TRILOGY-1, 100 cirrhotic patients were randomized (1:1:1) to 8 weeks of ledipasvir/sofosbuvir plus ribavirin, ledipasvir/sofosbuvir plus GS-9669 250 mg or ledipasvir/sofosbuvir plus GS-9669 500 mg. In TRILOGY-2, 46 previously treated cirrhotic patients were randomized (1:1) to 8 weeks of ledipasvir/sofosbuvir plus vedroprevir ± ribavirin. The primary end points were the proportion of patients with sustained virological response 12 weeks after treatment discontinuation (SVR12) and safety. In both studies, most patients were male (each 65%) and white (92-96%), infected with HCV genotype-1a (62-70%) and had IL28B non-CC genotypes (82-87%). In total, 37-39% of patients were Hispanic or Latino. SVR12 rates were similar across treatment arms in TRILOGY-1 (82-91%) and TRILOGY-2 (88-95%); no patient had on-treatment virological failure. Two serious adverse events (acute myocardial infarction and cardiomyopathy) were reported in two patients participating in TRILOGY-1, both of whom had pre-existing cardiac conditions. Laboratory abnormalities were infrequent. All ledipasvir/sofosbuvir-based regimens were well-tolerated. To shorten therapy and eliminate ribavirin, use of a more potent third agent or a third agent with a different mechanism of action may be required.

  15. Dual DNA vaccination of rainbow trout (Oncorhynchus mykiss) against two different rhabdoviruses, VHSV and IHNV, induces specific divalent protection.

    Science.gov (United States)

    Einer-Jensen, Katja; Delgado, Lourdes; Lorenzen, Ellen; Bovo, Giuseppe; Evensen, Øystein; Lapatra, Scott; Lorenzen, Niels

    2009-02-18

    DNA vaccines encoding the glycoprotein genes of the salmonid rhabdoviruses VHSV and IHNV are very efficient in eliciting protective immune responses against their respective diseases in rainbow trout (Oncorhynchus mykiss). The early anti-viral response (EAVR) provides protection by 4 days post vaccination and is non-specific and transient while the specific anti-viral response (SAVR) is long lasting and highly specific. Since both VHSV and IHNV are endemic in rainbow trout in several geographical regions of Europe and Atlantic salmon (Salmo salar) on the Pacific coast of North America, co-vaccination against the two diseases would be a preferable option. In the present study we demonstrated that a single injection of mixed DNA vaccines induced long-lasting protection against both individual and a simultaneous virus challenge 80 days post vaccination. Transfected muscle cells at the injection site expressed both G proteins. This study confirms the applied potential of using a combined DNA vaccination for protection of fish against two different rhabdoviral diseases.

  16. PTPN22 Trp620 explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes.

    Science.gov (United States)

    Smyth, Deborah J; Cooper, Jason D; Howson, Joanna M M; Walker, Neil M; Plagnol, Vincent; Stevens, Helen; Clayton, David G; Todd, John A

    2008-06-01

    The disease association of the common 1858C>T Arg620Trp (rs2476601) nonsynonymous single nucleotide polymorphism (SNP) of protein tyrosine phosphatase; nonreceptor type 22 (PTPN22) on chromosome 1p13 has been confirmed in type 1 diabetes and also in other autoimmune diseases, including rheumatoid arthritis and Graves' disease. Some studies have reported additional associated SNPs independent of rs2476601/Trp(620), suggesting that it may not be the sole causal variant in the region and that the relative risk of rs2476601/Trp(620) is greater in lower risk by HLA class II genotypes than in the highest risk class II risk category. We resequenced PTPN22 and used these and other data to provide >150 SNPs to evaluate the association of the PTPN22 gene and its flanking chromosome region with type 1 diabetes in a minimum of 2,000 case subjects and 2,400 control subjects. Due to linkage disequilibrium, we were unable to distinguish between rs2476601/Trp(620) (P = 2.11 x10(-87)) and rs6679677 (P = 3.21 x10(-87)), an intergenic SNP between the genes putative homeodomain transcription factor 1 and round spermatid basic protein 1. None of the previously reported disease-associated SNPs proved to be independent of rs2476601/Trp(620). We did not detect any interaction with age at diagnosis or sex. However, we found that rs2476601/Trp(620) has a higher relative risk in type 1 diabetic case subjects carrying lower risk HLA class II genotypes than in those carrying higher risk ones (P = 1.36 x 10(-4) in a test of interaction). In our datasets, there was no evidence for allelic heterogeneity at the PTPN22 locus in type 1 diabetes, indicating that the SNP rs2476601/Trp(620) remains the best candidate in this chromosome region in European populations. The heterogeneity of rs2476601/Trp(620) disease risk by HLA class II genotype is consistent with previous studies, and the joint effect of the two loci is still greater in the high-risk group.

  17. Virus isolation vs RT-PCR: which method is more successful in detecting VHSV and IHNV in fish tissue sampled under field conditions?

    DEFF Research Database (Denmark)

    Knüsel, R.; Bergmann, S. M.; Einer-Jensen, Katja

    2007-01-01

    (total of 859 fish) originating from a field survey on the occurrence of VHSV and IHNV in farmed and wild salmonids in Switzerland. These samples represented all sites with fish that were either identified as virus-positive by means of virus isolation (three sites, four positive tissue sample pools) and...

  18. Absence of viral hemorrhagic septicemia virus (VHSV) and infectious hemorrhagic necrosis virus (INHV) in a Tunisian fish farm: a case study.

    Science.gov (United States)

    Cherif, N; Hammami, S

    2012-01-01

    Beyond the obvious problems related to the sustainable management of wild stocks, current fish farming practices in the Mediterranean area entail important environmental risks and potential outbreaks of fish diseases linked to massive translocations across regional boundaries. Viral haemorrhagic septicaemia (VHS) and infectious hematopoietic necrosis (IHN) are well-known fish diseases caused by the VHSV and IHNV viruses, and positive cases are subject to obligatory reporting to the World Organisation for Animal Health (OIE). In August 2004, the OIE published the first record of a VHS outbreak in a sea bass (Dicentrarchus labrax) aquaculture facility on the coast of the Mediterranean Sea. However, D. labrax is not considered as a susceptible host species for viral hemorrhagic septicaemia according to OIE's International Aquatic Animal Health Code (2009) and VHSV was not previously reported in the Mediterranean. In this sense and given the high risk of disease translocation associated with farmed fish in marine aquaculture, the present study was aimed at investigating the presence of VHSV and IHNV in stocks of sea bass and sea bream (Sparus aurata) reared inside a Tunisian coastal fish farm. Cell culture, IFAT and RT-PCR were applied to screen for both VHSV and IHNV in 69 pooled samples of sea bass and 24 pooled samples of sea bream. All three techniques showed the absence of both viruses within fish at the selected site.

  19. High Prevalence of Helicobacter pylori hopQ II Genotype Isolated from Iranian Patients with Gastroduodenal Disorders

    Directory of Open Access Journals (Sweden)

    Amin Talebi Bezmin Abadi

    2014-01-01

    Full Text Available Helicobacter pylori plays an important role in the pathogenesis of chronic gastritis, peptic ulceration, and noncardia gastric cancer. Several putative virulence factors for H. pylori have been identified including vacA, babA, and iceA. HopQ is one of the outer membrane proteins involved in bacterial adherence to gastric mucosa and has been suggested to also play a role in the virulence of H. pylori. Due to the substantial geographic differences in the prevalence of H. pylori virulence factors reported, the main purpose of the current study was to investigate the association between different H. pylori virulence hopQ alleles (types I and II and patients with gastroduodenal disorders. The presence of H. pylori and hopQ alleles in gastric biopsy specimens was identified by specific PCR assays. H. pylori type II hopQ was found to be significantly associated with gastric cancer patients (odds ratio: 3.47, 95% CI: 1.56–5.89. Information about the prevalence of H. pylori hopQ type II can be used for determining the high-risk diseases type which is actually colonized by H. pylori hopQ type II positive strains. The presence of H. pylori hopQ type II should be investigated in different geographical regions as confirmatory findings may provide a definite biomarker attributed to the pathogenesis of certain severe digestive diseases.

  20. Genotype imputation for African Americans using data from HapMap phase II versus 1000 genomes projects.

    Science.gov (United States)

    Sung, Yun J; Gu, C Charles; Tiwari, Hemant K; Arnett, Donna K; Broeckel, Ulrich; Rao, Dabeeru C

    2012-07-01

    Genotype imputation provides imputation of untyped single nucleotide polymorphisms (SNPs) that are present on a reference panel such as those from the HapMap Project. It is popular for increasing statistical power and comparing results across studies using different platforms. Imputation for African American populations is challenging because their linkage disequilibrium blocks are shorter and also because no ideal reference panel is available due to admixture. In this paper, we evaluated three imputation strategies for African Americans. The intersection strategy used a combined panel consisting of SNPs polymorphic in both CEU and YRI. The union strategy used a panel consisting of SNPs polymorphic in either CEU or YRI. The merge strategy merged results from two separate imputations, one using CEU and the other using YRI. Because recent investigators are increasingly using the data from the 1000 Genomes (1KG) Project for genotype imputation, we evaluated both 1KG-based imputations and HapMap-based imputations. We used 23,707 SNPs from chromosomes 21 and 22 on Affymetrix SNP Array 6.0 genotyped for 1,075 HyperGEN African Americans. We found that 1KG-based imputations provided a substantially larger number of variants than HapMap-based imputations, about three times as many common variants and eight times as many rare and low-frequency variants. This higher yield is expected because the 1KG panel includes more SNPs. Accuracy rates using 1KG data were slightly lower than those using HapMap data before filtering, but slightly higher after filtering. The union strategy provided the highest imputation yield with next highest accuracy. The intersection strategy provided the lowest imputation yield but the highest accuracy. The merge strategy provided the lowest imputation accuracy. We observed that SNPs polymorphic only in CEU had much lower accuracy, reducing the accuracy of the union strategy. Our findings suggest that 1KG-based imputations can facilitate discovery of

  1. A sensitive one-step TaqMan amplification approach for detection of rubella virus clade I and II genotypes in clinical samples.

    Science.gov (United States)

    Claus, C; Bergs, S; Emmrich, N C; Hübschen, J M; Mankertz, A; Liebert, U G

    2017-02-01

    Although teratogenic rubella virus (RV) causes a vaccine-preventable disease, it is still endemic in several countries worldwide. Thus, there is a constant risk of RV importation into non-endemic areas. RV monitoring, especially during measles and Zika virus outbreaks, requires reliable diagnostic tools. For this study, a TaqMan-based one-step reverse transcription-quantitative PCR (RT-qPCR) assay, with the p90 gene as a novel and so far unexplored target for detection of clade I and II genotypes, was developed and evaluated. Automated nucleic acid extraction was carried out. Performance characteristics of the TaqMan RT-qPCR assay were determined for a RV plasmid standard and RNA extracted from virus-infected cell culture supernatants representing clade I and II genotypes. Diagnostic specificity and sensitivity were validated against other RNA and DNA viruses, relevant for RV diagnostic approaches and for RV-positive clinical samples, respectively. The assay is specific and highly sensitive with a limit of detection as low as five to one copies per reaction or 200 infectious virus particles per ml. The coefficients of variation (CV) were specified as intra- (within one run) and inter- (between different runs) assay variation, and calculated based on the standard deviations for the obtained Ct values of the respective samples. Intra- and inter-assay CV values were low, with a maximum of 3.4% and 2.4%, respectively. The assay was shown to be suitable and specific for the analysis of clinical samples. With p90 as a novel target, the highly sensitive and specific TaqMan assay outlined in this study is suitable for RV diagnosis worldwide.

  2. Performance of TcI/TcVI/TcII Chagas-Flow ATE-IgG2a for universal and genotype-specific serodiagnosis of Trypanosoma cruzi infection

    Science.gov (United States)

    Alessio, Glaucia Diniz; de Araújo, Fernanda Fortes; Côrtes, Denise Fonseca; Sales Júnior, Policarpo Ademar; Lima, Daniela Cristina; Gomes, Matheus de Souza; do Amaral, Laurence Rodrigues; Xavier, Marcelo Antônio Pascoal; Teixeira-Carvalho, Andréa; Martins-Filho, Olindo Assis; de Lana, Marta

    2017-01-01

    Distinct Trypanosoma cruzi genotypes have been considered relevant for patient management and therapeutic response of Chagas disease. However, typing strategies for genotype-specific serodiagnosis of Chagas disease are still unavailable and requires standardization for practical application. In this study, an innovative TcI/TcVI/TcII Chagas Flow ATE-IgG2a technique was developed with applicability for universal and genotype-specific diagnosis of T. cruzi infection. For this purpose, the reactivity of serum samples (percentage of positive fluorescent parasites-PPFP) obtained from mice chronically infected with TcI/Colombiana, TcVI/CL or TcII/Y strain as well as non-infected controls were determined using amastigote-AMA, trypomastigote-TRYPO and epimastigote-EPI in parallel batches of TcI, TcVI and TcII target antigens. Data demonstrated that “α-TcII-TRYPO/1:500, cut-off/PPFP = 20%” presented an excellent performance for universal diagnosis of T. cruzi infection (AUC = 1.0, Se and Sp = 100%). The combined set of attributes “α-TcI-TRYPO/1:4,000, cut-off/PPFP = 50%”, “α-TcII-AMA/1:1,000, cut-off/PPFP = 40%” and “α-TcVI-EPI/1:1,000, cut-off/PPFP = 45%” showed good performance to segregate infections with TcI/Colombiana, TcVI/CL or TcII/Y strain. Overall, hosts infected with TcI/Colombiana and TcII/Y strains displayed opposite patterns of reactivity with “α-TcI TRYPO” and “α-TcII AMA”. Hosts infected with TcVI/CL strain showed a typical interweaved distribution pattern. The method presented a good performance for genotype-specific diagnosis, with global accuracy of 69% when the population/prototype scenario include TcI, TcVI and TcII infections and 94% when comprise only TcI and TcII infections. This study also proposes a receiver operating reactivity panel, providing a feasible tool to classify serum samples from hosts infected with distinct T. cruzi genotypes, supporting the potential of this method for universal and genotype

  3. A new StaRT-PCR approach to detect and quantify fish Viral Hemorrhagic Septicemia virus (VHSv): enhanced quality control with internal standards.

    Science.gov (United States)

    Pierce, Lindsey R; Willey, James C; Crawford, Erin L; Palsule, Vrushalee V; Leaman, Douglas W; Faisal, Mohamed; Kim, Robert K; Shepherd, Brian S; Stanoszek, Lauren M; Stepien, Carol A

    2013-04-01

    Viral Hemorrhagic Septicemia virus (VHSv) causes one of the world's most important finfish diseases, killing >80 species across Eurasia and North America. A new and especially virulent strain (IVb) emerged in the North American Great Lakes in 2003, threatening fisheries, baitfish, and aquaculture industries. Weeks-long and costly cell culture is the OIE and USDA-APHIS approved diagnostic. A new Standardized Reverse Transcriptase Polymerase Chain Reaction (StaRT-PCR) assay that uniquely incorporates internal standards to improve accuracy and prevent false negatives was developed and evaluated for its ability to detect and quantify VHSv. Results from StaRT-PCR, SYBR(®) green real time qRT-PCR, and cell culture were compared, as well as the effects of potential PCR inhibitors (EDTA and high RNA). Findings show that StaRT-PCR is sensitive, detecting a single molecule, with 100% accuracy at six molecules, and had no false negatives. In comparison, false negatives ranged from 14 to 47% in SYBR(®) green real time qRT-PCR tests, and 47-70% with cell culture. StaRT-PCR uniquely controlled for EDTA and RNA interference. Range of VHSv quantitation by StaRT-PCR was 1.0×10(0)-1.2×10(5) VHSv/10(6)actb1 molecules in wild caught fishes and 1.0×10(0)-8.4×10(5) molecules in laboratory challenged specimens. In the latter experiments, muskellunge with skin lesions had significantly more viral molecules (mean=1.9×10(4)) than those without (1.1×10(3)) (p<0.04). VHSv infection was detected earlier in injection than in immersion challenged yellow perch (two versus three days), with molecule numbers in both being comparable and relatively consistent over the remaining course of the experiment. Our results show that the StaRT-PCR test accurately and reliably detects and quantifies VHSv. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Pathotypic and Sequence Characterization of Newcastle Disease Viruses from Vaccinated Chickens Reveals Circulation of Genotype II, IV and XIII and in India.

    Science.gov (United States)

    Jakhesara, S J; Prasad, V V S P; Pal, J K; Jhala, M K; Prajapati, K S; Joshi, C G

    2016-10-01

    Newcastle disease virus (NDV) causes a highly contagious disease which continuously haunts the global poultry industry. The nature and molecular epidemiology of NDVs prevalent in recent outbreaks in India is poorly understood. This study aimed to characterize NDVs prevalent in vaccinated flocks in India using whole-genome sequencing and biological pathotyping. Twelve field isolates were collected from outbreaks which occurred in different parts of India and characterized as velogenic based on their intracerebral pathogenicity index (ICPI) and amino acid sequence at the F protein cleavage site. All 12 of the field isolates and five commonly used vaccine strains were selected for whole-genome sequencing using Ion Torrent PGM technology, yielding complete genome sequences for ten field isolates and all vaccine strains. The genome of all isolates was found to be 15 192 nt long with a high level of conservation across multiple genomic features with APMV-I viruses. Phylogenetic analysis and evolutionary distance calculations placed the isolates in genotypes II, IV and XIII. Revisiting other recently reported strains provided preliminary evidence of genotypes VI, VII and XVIII circulating in India. Comparison between the field and vaccine virus sequences revealed unique genomic and amino acid differences in important antigenic regions of the F and hemagglutinin-neuraminidase (HN) genes which can be targeted for site directed mutagenesis to evaluate the impact of these substitutions on virus pathogenicity. This study highlights the requirement to evaluate current vaccines through systematic protection assays to determine protection efficacy against field isolates. © 2014 Blackwell Verlag GmbH.

  5. Genotypic and phenotypic characterization of Clostridium perfringens isolates from Darmbrand cases in post-World War II Germany.

    Science.gov (United States)

    Ma, Menglin; Li, Jihong; McClane, Bruce A

    2012-12-01

    Clostridium perfringens type C strains are the only non-type-A isolates that cause human disease. They are responsible for enteritis necroticans, which was termed Darmbrand when occurring in post-World War II Germany. Darmbrand strains were initially classified as type F because of their exceptional heat resistance but later identified as type C strains. Since only limited information exists regarding Darmbrand strains, this study genetically and phenotypically characterized seven 1940s era Darmbrand-associated strains. Results obtained indicated the following. (i) Five of these Darmbrand isolates belong to type C, carry beta-toxin (cpb) and enterotoxin (cpe) genes on large plasmids, and express both beta-toxin and enterotoxin. The other two isolates are cpe-negative type A. (ii) All seven isolates produce highly heat-resistant spores with D(100) values (the time that a culture must be kept at 100°C to reduce its viability by 90%) of 7 to 40 min. (iii) All of the isolates surveyed produce the same variant small acid-soluble protein 4 (Ssp4) made by type A food poisoning isolates with a chromosomal cpe gene that also produce extremely heat-resistant spores. (iv) The Darmbrand isolates share a genetic background with type A chromosomal-cpe-bearing isolates. Finally, it was shown that both the cpe and cpb genes can be mobilized in Darmbrand isolates. These results suggest that C. perfringens type A and C strains that cause human food-borne illness share a spore heat resistance mechanism that likely favors their survival in temperature-abused food. They also suggest possible evolutionary relationships between Darmbrand strains and type A strains carrying a chromosomal cpe gene.

  6. Recombinant hybrid infectious hematopoietic necrosis virus (IHNV) carrying viral haemorrhagic septicaemia virus (VHSV) G or NV genes show different virulence properities

    DEFF Research Database (Denmark)

    Einer-Jensen, Katja; Biacchesi, S.; Stegmann, Anders

    in host range (to include rainbow trout) likely have occurred several times. Virus from the marine environment therefore continues to represent a threat to the expanding trout aquaculture industry in the marine environment. Identification of potential virulence markers are therefore of great importance......Viral haemorrhagic septicaemia virus (VHSV) is the economically most important viral disease in European rainbow trout farming. The virus was introduced to fresh water farms in the 1950ies from a reservoir of VHSV in the marine environment. Isolates from wild marine fish and fresh water farms...... are difficult to distinguish serologically but they show different virulence profiles: marine isolates typically cause little or no mortality in rainbow trout fry following experimental waterborne challenge, while freshwater isolates often kill the majority of the fish. Genetic analysis reveal that the change...

  7. Optimization of a Plaque Neutralization Test (PNT) to identify the exposure history of Pacific Herring to viral hemorrhagic septicemia virus (VHSV)

    Science.gov (United States)

    Hart, Lucas; Mackenzie, Ashley; Purcell, Maureen; Thompson, Rachel L.; Hershberger, Paul

    2017-01-01

    Methods for a plaque neutralization test (PNT) were optimized for the detection and quantification of viral hemorrhagic septicemia virus (VHSV) neutralizing activity in the plasma of Pacific Herring Clupea pallasii. The PNT was complement dependent, as neutralizing activity was attenuated by heat inactivation; further, neutralizing activity was mostly restored by the addition of exogenous complement from specific-pathogen-free Pacific Herring. Optimal methods included the overnight incubation of VHSV aliquots in serial dilutions (starting at 1:16) of whole test plasma containing endogenous complement. The resulting viral titers were then enumerated using a viral plaque assay in 96-well microplates. Serum neutralizing activity was virus-specific as plasma from viral hemorrhagic septicemia (VHS) survivors demonstrated only negligible reactivity to infectious hematopoietic necrosis virus, a closely related rhabdovirus. Among Pacific Herring that survived VHSV exposure, neutralizing activity was detected in the plasma as early as 37 d postexposure and peaked at approximately 64 d postexposure. The onset of neutralizing activity was slightly delayed in fish reared at 7.4°C relative to those in warmer temperatures (9.9°C and 13.1°C); however, neutralizing activity persisted for at least 345 d postexposure in all temperature treatments. It is anticipated that this novel ability to assess VHSV neutralizing activity in Pacific Herring will enable retrospective comparisons between prior VHS infections and year-class recruitment failures. Additionally, the optimized PNT could be employed as a forecasting tool capable of identifying the potential for future VHS epizootics in wild Pacific Herring populations.

  8. Interferon-induced protein 56 (IFI56) is induced by VHSV infection but not by bacterial infection in olive flounder (Paralichthys olivaceus).

    Science.gov (United States)

    Hwang, Jee Youn; Ahn, Sang Jung; Kwon, Mun-Gyeong; Seo, Jung Soo; Hwang, Seong Don; Son, Maeng-Hyun

    2017-07-01

    Interferon-inducible protein 56 (IFI56, also known as ISG56/IFIT1, interferon-induced protein with tetratricopeptide repeats 1) is strongly induced in response to interferon and a potent inhibitor of viral replication and translational initiation. Here, we describe the identification of IFI56 (OfIFI56) in olive flounder, its characteristic features, and expression levels in various tissues before and after viral hemorrhagic septicemia virus (VHSV) infection. The full-length OfIFI56 sequence was identified from rapid amplification of cDNA ends PCR. The complete coding sequence of OfIFI56 is 1971 bp in length and encodes 431 amino acids. The putative OfIFI56 protein has multiple tetratricopeptide (TPR) motifs, which regulate diverse biological processes, such as organelle targeting, protein import, and vesicle fusion. Based on sequence analysis, the Larimichthys crocea IFI56 protein (61%) had the highest sequence homology to OfIFI56. In healthy olive flounder, OfIFI56 mRNA expression was detected in many tissues such as intestine, gill, head kidney, heart, spleen, and trunk kidney tissues. After VHSV challenge, OfIFI56 mRNA was significantly up-regulated in these tissues. Additionally, OfIFI56 expression was induced by poly I:C but not by Streptococcus parauberis and S. iniae infection or lipopolysaccharide injection in kidney and spleen tissues of olive flounder. These results demonstrate that piscine OfIFI56 expression is not induced by bacterial infection but is selectively induced by viral infection, especially VHSV, and that OfIFI56 may play an important role in the host response against VHSV infection. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Induction of anti-viral genes during acute infection with Viral hemorrhagic septicemia virus (VHSV) genogroup IVa in Pacific herring (Clupea pallasii)

    Science.gov (United States)

    Hansen, John D.; Woodson, James C.; Hershberger, Paul K.; Grady, Courtney; Gregg, Jacob L.; Purcell, Maureen K.

    2012-01-01

    Infection with the aquatic rhabdovirus Viral hemorrhagic septicemia virus (VHSV) genogroup IVa results in high mortality in Pacific herring (Clupea pallasii) and is hypothesized to be a potential limiting factor for herring recovery. To investigate anti-viral immunity in the Pacific herring, four immune response genes were identified: the myxovirus resistance (Clpa-Mx), a major histocompatibility complex IB (named Clpa-UAA.001), the inducible immunoproteosome subunit 9 (Clpa-PSMB9) and the neutrophil chemotactic factor (Clpa-LECT2). Reverse transcriptase quantitative PCR (RT-qPCR) assays were developed based on these gene sequences to investigate the host immune response to acute VHSV infection following both injection and immersion challenge. Virus levels were measured by both plaque assay and RT-qPCR and peaked at day 6 during the 10-day exposure period for both groups of fish. The interferon stimulated genes (Clpa-Mx, −UAA.001, and −PSMB9) were significantly up-regulated in response to VHSV infection at both 6 and 10 days post-infection in both spleen and fin. Results from this study indicate that Pacific herring mount a robust, early antiviral response in both fin and spleen tissues. The immunological tools developed in this study will be useful for future studies to investigate antiviral immunity in Pacific herring.

  10. Protective effect of a recombinant VHSV-G vaccine using poly(I:C) loaded nanoparticles as an adjuvant in zebrafish (Danio rerio) infection model.

    Science.gov (United States)

    Kavaliauskis, Arturas; Arnemo, Marianne; Speth, Martin; Lagos, Leidy; Rishovd, Anne-Lise; Estepa, Amparo; Griffiths, Gareth; Gjøen, Tor

    2016-08-01

    There is a constant need to increase the efficiency of vaccines in the aquaculture industry. Although several nano-based vaccine formulations have been reported, to the best of our knowledge so far only one of them have been implemented in the industry. Here we report on chitosan-poly(I:C) nanoparticles (NPs) that could be used as a non-specific adjuvant in antiviral vaccines in aquaculture. We have characterized the physical parameters of the NPs, studied the in vivo and in vitro bio-distribution of fluorescent NPs and verified NP uptake by zebrafish leucocytes. We used the zebrafish model to test the protective efficiency of the recombinant glycoprotein G (rgpG) of VHSV compared to inactivated whole virus (iV) against VHSV using NPs as an adjuvant in both formulations. In parallel we tested free poly(I:C) and rgpG (pICrgpG), and free chitosan and rgpG (CSrgpG) vaccine formulations. While the iV group (with NP adjuvant) provided the highest overall survival, all vaccine formulations with poly(I:C) provided a significant protection against VHSV; possibly through an early induction of an anti-viral state. Our results suggest that chitosan-poly(I:C) NPs are a promising adjuvant candidate for future vaccine formulations. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Angiotensin-converting enzyme and angiotensin II receptor subtype 2 genotypes in type 1 diabetes and severe hypoglycaemia requiring emergency treatment: a case cohort study

    DEFF Research Database (Denmark)

    Pedersen-Bjergaard, Ulrik; Nielsen, Søren L; Akram, Kamran

    2009-01-01

    AIMS: In type 1 diabetes, individual susceptibility to severe hypoglycaemia is likely to be influenced by genetic factors. We have previously reported an association of the deletion (D-) allele of the angiotensin-converting enzyme (ACE) insertion/deletion (I/D) polymorphism and the A-allele of th......AIMS: In type 1 diabetes, individual susceptibility to severe hypoglycaemia is likely to be influenced by genetic factors. We have previously reported an association of the deletion (D-) allele of the angiotensin-converting enzyme (ACE) insertion/deletion (I/D) polymorphism and the A......-allele of the angiotensin II receptor subtype 2 (AT2R) 1675 G>A polymorphism with risk of severe hypoglycaemia in such patients. The aim of this study was to test the hypothesis that these alleles are more frequent in patients suffering from the most severe episodes of hypoglycaemia requiring medical emergency treatment....... METHODS: The case cohort study consisted of 108 cases of type 1 diabetic patients with severe hypoglycaemia requiring medical emergency treatment during a 1-year period and 262 consecutive controls without such events. ACE I/D and AT2R 1675G>A genotype distributions were compared between cases...

  12. Viral hemorrhagic septicemia virus (VHSV) infection-mediated sequential changes in microRNAs profile of Epithelioma papulosum cyprini (EPC) cells.

    Science.gov (United States)

    Najib, Abdellaoui; Kim, Min Sun; Kim, Ki Hong

    2017-02-01

    MicroRNAs are small non-coding RNAs and are involved in the regulation of wide biological processes. Viral hemorrhagic septicemia virus (VHSV) is the causative agent of viral hemorrhagic septicemia (VHS) disease causing a heavy loss in aquaculture farms. In this study, we tried to explore the effect of VHSV infection on microRNAs profile of Epithelioma papulosum cyprini (EPC) cells at different points of time (0, 3, 12, 24, and 48 h post infection). A total of 355 conserved microRNAs and 3 novel microRNAs were identified, and among them, 103 microRNAs were differentially expressed. The number of differentially expressed microRNAs was highly increased at 24 h.p.i compared to 3 h.p.i and 12 h.p.i., suggesting that EPC cells might not actively respond to VHSV infection at an early infection period, which can allow viruses to transcript and translate their genes enough to produce viral particles that can infect to another cells. Among the differentially expressed microRNAs, 2 miRNAs (miR-735 and miR-738) that were reported only in fish species were highly upregulated, and based on the target prediction, they could regulate several immune pathways. Furthermore, the present results showed the upregulation of representative immune regulating microRNAs such as miR-146a, miR-155, and miR-99. The target prediction of differentially expressed miRNAs, GO, and KEGG pathways analysis revealed that several biological processes and different pathways were affected by the viral infection. The present dynamical changing patterns of differentially expressed microRNAs in response to the progression of VHSV infection suggest that microRNA profile that was analyzed at one time point cannot provide enough information for the interpretation of the disease mechanism. Considering the wide and complex interactions between microRNAs and genes expression, the present results provide the basis for the understanding of VHSV infection-mediated cellular responses and for future investigations

  13. The use of a one-step real-time reverse transcription polymerase chain reaction (rRT-PCR) for the surveillance of viral hemorrhagic septicemia virus (VHSV) in Minnesota.

    Science.gov (United States)

    Phelps, Nicholas B D; Patnayak, Devi P; Jiang, Yin; Goyal, Sagar M

    2012-12-01

    Viral hemorrhagic septicemia virus (VHSV) is a highly contagious and pathogenic virus of fish. The virus infects more than 70 fish species worldwide, in both fresh and salt water. A new viral strain (VHSV-IVb) has proven both virulent and persistent, spreading throughout the Great Lakes of North America and to inland water bodies in the region. To better understand the geographic distribution of the virus, we used a modified real-time reverse transcription polymerase chain reaction (rRT-PCR) assay for high-throughput testing of fish for VHSV. The assay was shown to be twice as sensitive as the gold standard, virus isolation, and did not cross react with other viruses found in fish. In addition, the diagnostic turnaround time was reduced from 28 to 30 d for virus isolation to 2-4 d for rRT-PCR. To demonstrate the usefulness of the rRT-PCR assay, 115 high-priority water bodies in Minnesota were tested by both methods from April 2010 to June 2011. All survey sites tested negative for VHSV by both methods. The survey results have informed fisheries managers on the absence of VHSV in Minnesota and have better prepared them for the eventual arrival of the disease. In addition, the results demonstrate the value of this rRT-PCR as a surveillance tool to rapidly identify an outbreak so that it can be controlled in a timely manner.

  14. In vitro antiproliferative and apoptosis-inducing properties of a mononuclear copper(II) complex with dppz ligand, in two genotypically different breast cancer cell lines.

    Science.gov (United States)

    Dhivya, Rajakumar; Jaividhya, Paramasivam; Riyasdeen, Anvarbatcha; Palaniandavar, Mallayan; Mathan, Ganeshan; Akbarsha, Mohammad Abdulkader

    2015-10-01

    In the background that there is concerted effort to discover newer metal-based cancer chemotherapeutic agents that could overcome the limitations in cisplatin and that copper, a biocompatible and redox-active metal, offers potential as alternative to cisplatin, the present study was undertaken to investigate the in vitro anti-proliferative properties of the mononuclear copper(II)complex [Cu(L)(diimine)] + where LH = 2-[(2-dimethylaminoethylimino)methyl]phenol and diimine = dipyrido[3,2-a:2',3'-c]phenazine (dppz) using breast cancer cell lines MCF-7 (ER(+ve) and p53(WT)) and MDA-MB-231(ER(-ve) and p53(mutant)) when cisplatin was used as positive control. The complex affected the viability of both the cell lines in dose-as well as duration-dependent manner as revealed in the MTT assay. The 24 and 48 h IC50 of the complex were several times lesser than those of cisplatin, and within this huge difference the efficacy of the complex was much superior with MCF-7 cell compared to MDA-MB-231 cell. The cell death was preferentially apoptosis, though necrosis also occurred to a certain extent. These inferences were substantiated by AO/EB fluorescent staining, Hoechst staining, assessment of mitochondrial transmembrane potential, comet assay for DNA damage, DCFH assay for reactive oxygen species (ROS) generation and Western blot of apoptosis-related proteins. Thus, the copper(II) dppz complex under investigation is much more efficient than cisplatin in affecting viability of the breast cancer cells. The underlying mechanism appears to be DNA damage-primed (in view of the known intercalation mode of binding of the complex with DNA) and ROS-associated mitochondria-mediated intrinsic apoptosis to a great extent but necrosis also has a role to a certain extent, which may also be a PARP-mediated cell death independent of apoptosis. Within the purview of this conclusion, the results indicate that the ER and/or p53 genotypes have a bearing on the efficacy of the complex as a

  15. Accurate detection and quantification of the fish viral hemorrhagic Septicemia virus (VHSv with a two-color fluorometric real-time PCR assay.

    Directory of Open Access Journals (Sweden)

    Lindsey R Pierce

    Full Text Available Viral Hemorrhagic Septicemia virus (VHSv is one of the world's most serious fish pathogens, infecting >80 marine, freshwater, and estuarine fish species from Eurasia and North America. A novel and especially virulent strain - IVb - appeared in the Great Lakes in 2003, has killed many game fish species in a series of outbreaks in subsequent years, and shut down interstate transport of baitfish. Cell culture is the diagnostic method approved by the USDA-APHIS, which takes a month or longer, lacks sensitivity, and does not quantify the amount of virus. We thus present a novel, easy, rapid, and highly sensitive real-time quantitative reverse transcription PCR (qRT-PCR assay that incorporates synthetic competitive template internal standards for quality control to circumvent false negative results. Results demonstrate high signal-to-analyte response (slope = 1.00±0.02 and a linear dynamic range that spans seven orders of magnitude (R(2 = 0.99, ranging from 6 to 6,000,000 molecules. Infected fishes are found to harbor levels of virus that range to 1,200,000 VHSv molecules/10(6 actb1 molecules with 1,000 being a rough cut-off for clinical signs of disease. This new assay is rapid, inexpensive, and has significantly greater accuracy than other published qRT-PCR tests and traditional cell culture diagnostics.

  16. Accurate detection and quantification of the fish viral hemorrhagic Septicemia virus (VHSv) with a two-color fluorometric real-time PCR assay.

    Science.gov (United States)

    Pierce, Lindsey R; Willey, James C; Palsule, Vrushalee V; Yeo, Jiyoun; Shepherd, Brian S; Crawford, Erin L; Stepien, Carol A

    2013-01-01

    Viral Hemorrhagic Septicemia virus (VHSv) is one of the world's most serious fish pathogens, infecting >80 marine, freshwater, and estuarine fish species from Eurasia and North America. A novel and especially virulent strain - IVb - appeared in the Great Lakes in 2003, has killed many game fish species in a series of outbreaks in subsequent years, and shut down interstate transport of baitfish. Cell culture is the diagnostic method approved by the USDA-APHIS, which takes a month or longer, lacks sensitivity, and does not quantify the amount of virus. We thus present a novel, easy, rapid, and highly sensitive real-time quantitative reverse transcription PCR (qRT-PCR) assay that incorporates synthetic competitive template internal standards for quality control to circumvent false negative results. Results demonstrate high signal-to-analyte response (slope = 1.00±0.02) and a linear dynamic range that spans seven orders of magnitude (R(2) = 0.99), ranging from 6 to 6,000,000 molecules. Infected fishes are found to harbor levels of virus that range to 1,200,000 VHSv molecules/10(6) actb1 molecules with 1,000 being a rough cut-off for clinical signs of disease. This new assay is rapid, inexpensive, and has significantly greater accuracy than other published qRT-PCR tests and traditional cell culture diagnostics.

  17. Expression of the glycoprotein of viral haemorrhagic septicaemia virus (VHSV) on the surface of the fish cell line RTG-P1 induces type 1 interferon expression in neighbouring cells

    DEFF Research Database (Denmark)

    Acosta, F.; Collet, B.; Lorenzen, Niels

    2006-01-01

    In the present study using a luciferase/Mx promoter reporter system, it was shown that the rainbow trout gonad cell line (RTG-P1), a fibroblastic cell line, produces IFN when transfected with a plasmid encoding the glycoprotein of VHSV but not with plasmid vector alone. Only a small percentage...

  18. Prevalence and genotyping of

    Directory of Open Access Journals (Sweden)

    Jawahir Alghamdi

    2016-11-01

    Full Text Available Introduction: Toxoplasma gondii (T. gondii is an intracellular protozoan that can infect all mammals, who serve as intermediate host. It causes congenital, neurological, eyes complications and mild or asymptomatic infections in humans. Purpose of this study: To investigate not only the prevalence of T. gondii, but also to find out its genotyping using multiple sequential molecular methods to predict exactly the precise genotyping of T. gondii among Saudi pregnant women. Methods: A cross-sectional study was conducted using multi-stage methods. Initial stage involved enrolment of 250 Saudi pregnant women from multi-centre healthcare and community based settings in the capital of Saudi Arabia Riyadh. The second stage was embracement of the laboratory investigation that included Enzyme immunoassay (ELISA, DNA extraction, PCR, nested-PCR assay, and genotyping of the seropositive cases. Results: 203 women agreed to take part in our study with a response rate of 81.2% (203/250. Using ELISA, we found that the prevalence of Toxoplasma gondii IgG and IgM antibodies was 32.5% and 6.4%, respectively. We found that 29 samples (80.6% were of genotype II; however 7 samples (19.4% were of genotype III. Conclusion: Defining the population structure of T. gondii from Saudi Arabia has important implications for transmission, immunogenicity, pathogenesis, and in planning preventive strategies. Relationship between such variation in structure and disease manifestation in pregnant women is still difficult to assess due to the role of host immune status and genetic background on the control of infection, and of other parasitic features such as the infecting dose or parasite stage. Our finding of the genotyping of T. gondii might facilitate and inform future studies on comparative genomics and identification of genes that control important biological phenotypes including pathogenesis and transmission among Saudi women.

  19. Toxoplasma gondii sexual cross in a single naturally infected feline host: Generation of highly mouse-virulent and avirulent clones, genotypically different from clonal types I, II and III

    Directory of Open Access Journals (Sweden)

    Herrmann Daland C

    2012-04-01

    Full Text Available Abstract Tachyzoite clones obtained from a single Toxoplasma gondii oocyst field sample were genotyped and characterized regarding mouse virulence. PCR-RFLP genotyping of tachyzoites initially isolated from interferon-γ-knockout (GKO mice, BALB/c mice and VERO cell culture using the nine independent, unlinked genetic markers nSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico revealed mixed T. gondii infections showing combinations of type II and type III alleles at different loci. Forty-five individual clones were obtained from all mixed T. gondii tachyzoite cell cultures by limiting dilution. Sixteen T. gondii clones showed type III alleles at all loci and 29 clones displayed a combination of type II and type III alleles at different loci. Five clone groups were identified in total, four of which include T. gondii clones that showed a non-canonical allele pattern and have never been described in natural infections before. All tested clones, except two, were highly virulent in BALB/c mice. The isolation of different non-canonical T. gondii clones originating from an oocyst sample of a single naturally infected cat demonstrate that sexual recombination as well as re-assortment of chromosomes via a sexual cross of T. gondii occur under natural conditions and result in the emergence of clones with increased virulence in mice.

  20. Validation of real time RT-PCR applied to cell culture for diagnosis of any known genotype of viral haemorrhagic septicaemia virus.

    Science.gov (United States)

    Cutrín, J M; Olveira, J G; Bandín, I; Dopazo, C P

    2009-12-01

    Viral haemorrhagic septicaemia virus (VHSV), a member of the Rhabdoviridae family, is a major viral pathogen of cultured salmonid fish, and also infects a wide range of marine fish species. In the present study, two real time PCR protocols (based on SYBR Green and TaqMan) were developed for the detection of strains belonging to all known genotypes of VHSV. Validation of the procedure, in terms of sensitivity, specificity and repeatability/reproducibility (R&R), was also performed. For this purpose, several pairs of primer amplifying regions corresponding to viral G and N genes were assayed. In the SYBR Green-based real time PCR, these primers failed to detect strains from some of the genotypes and/or showed low R&R. In order to improve the detection capacity, a multiplex procedure was designed, which enabled detection of all strains, with high R&R. The sensitivity of the procedure was measured, and a detection limit of 1 fg/microl of viral RNA or 10 copies of cloned plasmid was established. On the other hand, the TaqMan probe-based multiplex real time PCR detected all European strains, with similar levels of sensitivity and R&R, but failed to detect the American types.

  1. Vitamin D receptor biochemical and genetic profiling and HLA-class II genotyping among Lebanese with multiple sclerosis - A pilot study.

    Science.gov (United States)

    Yamout, Bassem; Karaky, Nathalie M; Mahfouz, Rami A R; Jaber, Fadel; Estaitieh, Nour; Shamaa, Dina; Abbas, Fatmeh; Hoteit, Rouba; Daher, Rose T

    2016-04-15

    Multiple sclerosis (MS) is an autoimmune demyelinating disease affecting mostly young adult females with multifactorial etiology. Recent studies suggested that adequate vitamin D levels may lower the risk of developing MS. Our aim was to explore the relationship between vitamin D receptor (VDR) polymorphism, HLA-DR locus genotype, and serum vitamins D and A levels in the Lebanese population. Fifty MS patients were recruited for this study. The control group consisted of 48 healthy and 51 patients with other neurological disorders (non-MS). Biochemical analysis included serum 25 hydroxyvitamin D (25OHD) and vitamin A. Molecular analysis targeted VDR genotypes (ApaI, TaqI and BsmI) and low resolution HLA typing for DRB1 locus. Healthy and non-MS groups had comparable parameters and were combined into one control group. No significant differences were found between MS and control groups for VDR genotypes. The frequency of HLA-DRB1*15 was significantly higher in MS patients (22%) compared to controls (8%) (p=0.018). Odds ratio for MS in the presence of DRB1*15 allele was 3.21 (p=0.018). Cosegregation with A (ApaI) and b (BsmI) alleles did not influence the risk for MS. 25OHD levels were significantly higher in MS patients compared to controls (p=0.002), due to more frequent oral supplementation (p=0.005). Vitamin A levels were comparable between the two groups. When all parameters were included in a logistic regression model adjusted for supplementation, only HLA-DRB1*15 (OR=3.42; p=0.027) contributed significantly to MS risk. There was no association between serum vitamin D or A or VDR genotypes and MS. HLA-DRB1*15 was the major factor imposing more than 3 folds greater risk for developing MS among Lebanese. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Genetic and epigenetic transgenerational implications related to omega-3 fatty acids. Part II: maternal FADS2 rs174575 genotype and DNA methylation predict toddler cognitive performance.

    Science.gov (United States)

    Cheatham, Carol L; Lupu, Daniel S; Niculescu, Mihai D

    2015-11-01

    Maternal transfer of fatty acids is important to fetal brain development. The prenatal environment may differentially affect the substrates supporting declarative memory abilities, as the level of fatty acids transferred across the placenta may be affected by the maternal fatty acid desaturase 2 (FADS2) rs174575 single nucleotide polymorphism. In this study, we hypothesized that toddler and maternal rs174575 genotype and FADS2 promoter methylation would be related to the toddlers' declarative memory performance. Seventy-one 16-month-old toddlers participated in an imitation paradigm designed to test immediate and long-term declarative memory abilities. FADS2 rs174575 genotype was determined and FADS2 promoter methylation was quantified from blood by bisulfite pyrosequencing for the toddlers and their natural mothers. Toddlers of GG mothers at the FADS2 rs174575 single nucleotide polymorphism did not perform as well on memory assessments as toddlers of CC or CG mothers when controlling for plasma α-linolenic acid and child genotype. Toddler methylation status was related to immediate memory performance, whereas maternal methylation status was related to delayed memory performance. Thus, prenatal experience and maternal FADS2 status have a pervasive, long-lasting influence on the brain development of the offspring, but as the postnatal environment becomes more primary, the offsprings' own biology begins to have an effect. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Association of a microsatellite in FASL to type II diabetes and of the FAS-670G>A genotype to insulin resistance

    DEFF Research Database (Denmark)

    Nolsøe, R L; Hamid, Y H; Pociot, F

    2006-01-01

    Type II diabetes is caused by a failure of the pancreatic beta-cells to compensate for insulin resistance leading to hyperglycaemia. There is evidence for an essential role of an increased beta-cell apoptosis in type II diabetes. High glucose concentrations induce IL-1beta production in human beta...... in the 3' UTR of FASL for association to type II diabetes in 549 type II diabetic patients and 525 normal-glucose-tolerant (NGT) control subjects. Furthermore, we have tested these polymorphisms for association to estimates of beta-cell function and insulin resistance in NGT subjects. We found significant...... association to type II diabetes for the allele distribution of the FASL microsatellite (P-value 0.02, Bonferroni corrected). The FAS-670G>A was associated with homeostasis model assessment insulin resistance index and body mass index (P-values 0.02 and 0.02). We conclude that polymorphisms of FASL and FAS...

  4. Autophagy-inducing peptides from mammalian VSV and fish VHSV rhabdoviral G glycoproteins (G) as models for the development of new therapeutic molecules.

    Science.gov (United States)

    García-Valtanen, Pablo; Ortega-Villaizán, María Del Mar; Martínez-López, Alicia; Medina-Gali, Regla; Pérez, Luis; Mackenzie, Simon; Figueras, Antonio; Coll, Julio M; Estepa, Amparo

    2014-09-01

    It has not been elucidated whether or not autophagy is induced by rhabdoviral G glycoproteins (G) in vertebrate organisms for which rhabdovirus infection is lethal. Our work provides the first evidence that both mammalian (vesicular stomatitis virus, VSV) and fish (viral hemorrhagic septicemia virus, VHSV, and spring viremia carp virus, SVCV) rhabdoviral Gs induce an autophagic antiviral program in vertebrate cell lines. The transcriptomic profiles obtained from zebrafish genetically immunized with either Gsvcv or Gvhsv suggest that autophagy is induced shortly after immunization and therefore, it may be an important component of the strong antiviral immune responses elicited by these viral proteins. Pepscan mapping of autophagy-inducing linear determinants of Gvhsv and Gvsv showed that peptides located in their fusion domains induce autophagy. Altogether these results suggest that strategies aimed at modulating autophagy could be used for the prevention and treatment of rhabdoviral infections such as rabies, which causes thousands of human deaths every year.

  5. Bioavailability of polyglutamyl folic acid relative to that of monoglutamyl folic acid in subjects with different genotypes of the glutamate carboxypeptidase II gene

    NARCIS (Netherlands)

    Boonstra, A.; Lievers, K.J.A.; Blom, H.J.; Verhoef, P.

    2004-01-01

    Background: Before dietary folate is absorbed, polyglutamate folates are deconjugated to monoglutamates by folylpoly-gamma-glutamyl carboxypeptidase in the small intestine. The 1561T allele of the glutamate carboxypeptidase II gene (GCPII), which codes for folylpoly-gamma-glutamyl carboxypeptidase,

  6. Bioavailability of polyglutamyl folic acid relative to that of monoglutamyl folic acid in subjects with different genotypes of the glutamate carboxypeptidase II gene.

    NARCIS (Netherlands)

    Melse-Boonstra, A.; Lievers, K.J.; Blom, H.J.; Verhoef, P.

    2004-01-01

    BACKGROUND: Before dietary folate is absorbed, polyglutamate folates are deconjugated to monoglutamates by folylpoly-gamma-glutamyl carboxypeptidase in the small intestine. The 1561T allele of the glutamate carboxypeptidase II gene (GCPII), which codes for folylpoly-gamma-glutamyl carboxypeptidase,

  7. Enhancement of glycoprotein-based DNA vaccine for viral hemorrhagic septicemia virus (VHSV) via addition of the molecular adjuvant, DDX41.

    Science.gov (United States)

    Lazarte, Jassy Mary S; Kim, Young Rim; Lee, Jung Seok; Im, Se Pyeong; Kim, Si Won; Jung, Jae Wook; Kim, Jaesung; Lee, Woo Jai; Jung, Tae Sung

    2017-03-01

    The use of molecular adjuvants to improve the immunogenicity of DNA vaccines has been thoroughly studied in recent years. Glycoprotein (G)-based DNA vaccines had been proven to be effective in combating infection against Rhabdovirus (especially infectious hematopoietic necrosis virus, IHNV) in salmonids. DDX41 is a helicase known to induce antiviral and inflammatory responses by inducing a type I IFN innate immune response. To gain more information regarding G-based DNA vaccines in olive flounder (Paralicthys olivaceus), we tried to develop a more efficient G-based DNA vaccine by adding a molecular adjuvant, DDX41. We designed a DNA vaccine in which the VHSV glycoprotein (G-protein) and DDX41 were driven by the EF-1α and CMV promoters, respectively. Olive flounders were intramuscularly immunized with 1 μg of plasmids encoding the G-based DNA vaccine alone (pEF-G), the molecular adjuvant alone (pEF-D), or the vaccine-adjuvant construct (pEF-GD). At two different time points, 15 and 30 days later, the fish were intraperitoneally infected with VHSV (100 μL; 1 × 10 6 TCID 50 /mL). Our assays revealed that the plasmid constructs showed up-regulated expression of IFN-1 and its associated genes at day 3 post-vaccination in both kidney and spleen samples. Specifically, pEF-GD showed statistically higher expression of immune response genes than pEF-G and pEF-D treated group (p pEF-GD showed higher survival rate than the pEF-G treated group, though difference was not statistically significant in the 15 dpv challenged group however in the 30 dpv challenged group, the difference was statistically significant (p < 0.05). Together, these results clearly demonstrate that DDX41 is an effective adjuvant for the G-based DNA vaccine in olive flounder. Our novel findings could facilitate the development of more effective DNA vaccines for the aquaculture industry. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Tipos de resistência a Alabama argillacea (Huebner, 1818 (Lepidoptera: Noctuidae envolvidos em genótipos de algodoeiro: II. Antibiose Evaluation of cotton genotypes resistance to Alabama argillacea (Huebner, 1818 (Lepidoptera: Noctuidae: II. Antibiosis

    Directory of Open Access Journals (Sweden)

    ALVEMAR FERREIRA

    1999-01-01

    Full Text Available Objetivou-se verificar a ocorrência do tipo de resistência antibiose em genótipos de algodoeiro (Gossypium hirsutum L. em relação a Alabama argillacea (Huebner, 1818, em experimentos de laboratório (27 ± 2oC, 70 ± 10% de U.R. e fotofase de 14 horas. Folhas dos genótipos T 1122-13-1, STO 285 N, JPM 157, T 953-13-4-2, CNPA 9211-21 e CNPA 9211-31 foram fornecidas às larvas, diariamente, verificando-se a duração de cada fase do inseto, avaliando-se a massa de larvas aos 3 e aos 8 dias de idade, a massa de pupas e as porcentagens de mortalidade larval, pré-pupal e pupal. O delineamento utilizado foi inteiramente casualizado, com dez repetições, cada uma com dez larvas/genótipo. Em comparação com STO 285 N, todos os genótipos provocaram períodos mais longos de larva a adulto em A. argillacea; entretanto, os menores valores de massa de larvas com 3 dias e de massa média de pupas, e os maiores valores de duração do período larval e de mortalidade de larva a adulto foram verificados em CNPA 9211-31 e CNPA 9211-21, evidenciando que antibiose é um dos tipos de resistência presentes em ambos os genótipos.Cotton genotypes resistance to Alabama argillacea (Huebner, 1818 due to antibiosis has been evaluated in laboratory trials (at 27 ± 2oC, 70 ± 10% relative humidity and 14 hours photoperiod. Six different genetic materials (T 1122-13-1, STO 285 N, JPM 157, T 953-13-4-2, CNPA 9211-21, and CNPA 9211-31 have been tested in a completely randomized experimental design, with ten replications, each one with ten larvae/genotype. Larvae have been supplied with leaves daily. The following variables have been scored: time length of several insect stages (from larvae to adult, average mass of larvae and pupae as well as average larval, pre-pupal and pupal mortality rates. All genotypes have revealed longer overall average time length of stage duration from larvae to adult, as compared to STO 285 N; however, CNPA 9211-31 and CNPA 9211-21 have

  9. Efficacy, safety, and pharmacokinetics of simeprevir, daclatasvir, and ribavirin in patients with recurrent hepatitis C virus genotype 1b infection after orthotopic liver transplantation: The Phase II SATURN study.

    Science.gov (United States)

    Forns, Xavier; Berenguer, Marina; Herzer, Kerstin; Sterneck, Martina; Donato, Maria Francesca; Andreone, Pietro; Fagiuoli, Stefano; Cieciura, Tomasz; Durlik, Magdalena; Calleja, Jose Luis; Mariño, Zoe; Shukla, Umesh; Verbinnen, Thierry; Lenz, Oliver; Ouwerkerk-Mahadevan, Sivi; Peeters, Monika; Janssen, Katrien; Kalmeijer, Ronald; Jessner, Wolfgang

    2017-06-01

    Recurrent hepatitis C virus (HCV) infection following liver transplantation is associated with accelerated progression to graft failure and reduced patient survival. The Phase II, open-label SATURN study (NCT01938625) investigated the combination of simeprevir (SMV), daclatasvir (DCV), and ribavirin (RBV) administered for 24 weeks in 35 patients with recurrent HCV genotype (GT) 1b infection after orthotopic liver transplantation (OLT). High rates of both on-treatment and sustained virologic response 12 weeks after end of treatment (SVR12) were achieved in patients who were either treatment-naïve or had failed post-OLT treatment with peginterferon and RBV. Overall, 91% of patients (32/35) achieved SVR12. The combination was generally well tolerated, with an adverse event profile consistent with that observed in previous clinical trials of SMV or DCV separately. Co-administration of SMV with cyclosporine resulted in significantly increased SMV plasma exposures, which was not the case with the co-administration of SMV with tacrolimus. Therefore, the concomitant use of SMV with cyclosporine is not recommended. The interferon-free combination of SMV, DCV, and RBV administered for 24 weeks was shown to be effective and well tolerated in the treatment of post-OLT HCV GT1b-infected patients. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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

    Science.gov (United States)

    Mello, Francisco C A; Souto, Francisco J D; Nabuco, Leticia C; Villela-Nogueira, Cristiane A; Coelho, Henrique Sergio M; Franz, Helena Cristina F; Saraiva, Joao Carlos P; Virgolino, Helaine A; Motta-Castro, Ana Rita C; Melo, Mabel M M; Martins, Regina M B; Gomes, Selma A

    2007-11-23

    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. 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. 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 isolates belonged to cluster II, the presence of some

  11. 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

  12. Characterization of a novel arginine catabolic mobile element (ACME) and staphylococcal chromosomal cassette mec composite island with significant homology to Staphylococcus epidermidis ACME type II in methicillin-resistant Staphylococcus aureus genotype ST22-MRSA-IV.

    LENUS (Irish Health Repository)

    Shore, Anna C

    2011-05-01

    The arginine catabolic mobile element (ACME) is prevalent among methicillin-resistant Staphylococcus aureus (MRSA) isolates of sequence type 8 (ST8) and staphylococcal chromosomal cassette mec (SCCmec) type IVa (USA300) (ST8-MRSA-IVa isolates), and evidence suggests that ACME enhances the ability of ST8-MRSA-IVa to grow and survive on its host. ACME has been identified in a small number of isolates belonging to other MRSA clones but is widespread among coagulase-negative staphylococci (CoNS). This study reports the first description of ACME in two distinct strains of the pandemic ST22-MRSA-IV clone. A total of 238 MRSA isolates recovered in Ireland between 1971 and 2008 were investigated for ACME using a DNA microarray. Twenty-three isolates (9.7%) were ACME positive, and all were either MRSA genotype ST8-MRSA-IVa (7\\/23, 30%) or MRSA genotype ST22-MRSA-IV (16\\/23, 70%). Whole-genome sequencing and comprehensive molecular characterization revealed the presence of a novel 46-kb ACME and staphylococcal chromosomal cassette mec (SCCmec) composite island (ACME\\/SCCmec-CI) in ST22-MRSA-IVh isolates (n=15). This ACME\\/SCCmec-CI consists of a 12-kb DNA region previously identified in ACME type II in S. epidermidis ATCC 12228, a truncated copy of the J1 region of SCCmec type I, and a complete SCCmec type IVh element. The composite island has a novel genetic organization, with ACME located within orfX and SCCmec located downstream of ACME. One PVL locus-positive ST22-MRSA-IVa isolate carried ACME located downstream of SCCmec type IVa, as previously described in ST8-MRSA-IVa. These results suggest that ACME has been acquired by ST22-MRSA-IV on two independent occasions. At least one of these instances may have involved horizontal transfer and recombination events between MRSA and CoNS. The presence of ACME may enhance dissemination of ST22-MRSA-IV, an already successful MRSA clone.

  13. Vaccine Adjuvants in Fish Vaccines Make a Difference: Comparing Three Adjuvants (Montanide ISA763A Oil, CpG/Poly I:C Combo and VHSV Glycoprotein Alone or in Combination Formulated with an Inactivated Whole Salmonid Alphavirus Antigen

    Directory of Open Access Journals (Sweden)

    Hanna L. Thim

    2014-03-01

    Full Text Available Most commercial vaccines offered to the aquaculture industry include inactivated antigens (Ag formulated in oil adjuvants. Safety concerns are related to the use of oil adjuvants in multivalent vaccines for fish, since adverse side effects (e.g., adhesions can appear. Therefore, there is a request for vaccine formulations for which protection will be maintained or improved, while the risk of side effects is reduced. Here, by using an inactivated salmonid alphavirus (SAV as the test Ag, the combined use of two Toll-like receptor (TLR ligand adjuvants, CpG oligonucleotides (ODNs and poly I:C, as well as a genetic adjuvant consisting of a DNA plasmid vector expressing the viral haemorrhagic septicaemia virus (VHSV glycoprotein (G was explored. VHSV-G DNA vaccine was intramuscularly injected in combination with intraperitoneal injection of either SAV Ag alone or combined with the oil adjuvant, Montanide ISA763, or the CpG/polyI:C combo. Adjuvant formulations were evaluated for their ability to boost immune responses and induce protection against SAV in Atlantic salmon, following cohabitation challenge. It was observed that CpG/polyI:C-based formulations generated the highest neutralizing antibody titres (nAbs before challenge, which endured post challenge. nAb responses for VHSV G-DNA- and oil-adjuvanted formulations were marginal compared to the CpG/poly I:C treatment. Interestingly, heat-inactivated sera showed reduced nAb titres compared to their non-heated counterparts, which suggests a role of complement-mediated neutralization against SAV. Consistently elevated levels of innate antiviral immune genes in the CpG/polyI:C injected groups suggested a role of IFN-mediated responses. Co-delivery of the VHSV-G DNA construct with either CpG/polyI:C or oil-adjuvanted SAV vaccine generated higher CD4 responses in head kidney at 48 h compared to injection of this vector or SAV Ag alone. The results demonstrate that a combination of pattern recognizing

  14. Species specific inhibition of viral replication using dicer substrate siRNAs (DsiRNAs) targeting the viral nucleoprotein of the fish pathogenic rhabdovirus viral hemorrhagic septicemia virus (VHSV)

    DEFF Research Database (Denmark)

    Bohle, Harry; Lorenzen, Niels; Schyth, Brian Dall

    2011-01-01

    Gene knock down by the use of small interfering RNAs (siRNAs) is widely used as a method for reducing the expression of specific genes in eukaryotic cells via the RNA interference pathway. But, the effectivity of siRNA induced gene knock down in cells from fish has in several studies been...... for dicer for the generation of siRNAs targeting the nucleoprotein N gene of viral hemorrhagic septicemia virus (VHSV). This rhabdovirus infects salmonid fish and is responsible for large yearly losses in aquaculture production. Specificity of the DsiRNA is assured in two ways: first, by using...

  15. Characterization of a Novel Arginine Catabolic Mobile Element (ACME) and Staphylococcal Chromosomal Cassette mec Composite Island with Significant Homology to Staphylococcus epidermidis ACME type II in Methicillin-Resistant Staphylococcus aureus Genotype ST22-MRSA-IV.

    LENUS (Irish Health Repository)

    Shore, Anna C

    2011-02-22

    The arginine catabolic mobile element (ACME) is prevalent among ST8-MRSA-IVa (USA300) isolates and evidence suggests that ACME enhances the ability of ST8-MRSA-IVa to grow and survive on its host. ACME has been identified in a small number of isolates belonging to other MRSA clones but is widespread among coagulase-negative staphylococci (CoNS). This study reports the first description of ACME in two distinct strains of the pandemic ST22-MRSA-IV clone. A total of 238 MRSA isolates recovered in Ireland between 1971 and 2008 were investigated for ACME using a DNA microarray. Twenty-three isolates (9.7%) were ACME-positive, all were either MRSA genotype ST8-MRSA-IVa (7\\/23, 30%) or ST22-MRSA-IV (16\\/23, 70%). Whole-genome sequencing and comprehensive molecular characterization revealed the presence of a novel 46-kb ACME and SCCmec composite island (ACME\\/SCCmec-CI) in ST22-MRSA-IVh isolates (n = 15). This ACME\\/SCCmec-CI consists of a 12-kb DNA region previously identified in ACME type II in S. epidermidis ATCC 12228, a truncated copy of the J1 region of SCCmec I and a complete SCCmec IVh element. The composite island has a novel genetic organization with ACME located within orfX and SCCmec located downstream of ACME. One pvl-positive ST22-MRSA-IVa isolate carried ACME located downstream of SCCmec IVa as previously described in ST8-MRSA-IVa. These results suggest that ACME has been acquired by ST22-MRSA-IV on two independent occasions. At least one of these instances may have involved horizontal transfer and recombination events between MRSA and CoNS. The presence of ACME may enhance dissemination of ST22-MRSA-IV, an already successful MRSA clone.

  16. Genotype adaptability and stability

    Directory of Open Access Journals (Sweden)

    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. .

  17. Distribution of hepatitis delta virus genotypes in mashhad, northeast iran.

    Science.gov (United States)

    Sadeghian, Hamid; Varasteh, Naiemeh; Esmaeelzadeh, Abbas; Nomani, Hosein; Alimardani, Maliheh; Davoodnejad, Mahdieh; Meshkat, Mojtaba; Ahadi, Mitra; Sepahi, Samaneh; Rostami, Sina; Meshkat, Zahra

    2015-02-01

    Hepatitis delta virus (HDV) is dependent on the hepatitis B virus for transmission and propagation. Based on isolated HDV sequences from different parts of the world, at least three major different genotypes with different geographic distributions are suggested. Studies have shown that genotype 1 is the predominant genotype of HDV in different parts of Iran; however, the genotype distribution of this virus has not been identified in Mashhad, northeast Iran. This current study determines the frequency of HDV major genotypes in Mashhad, Iran. Twenty-five participants were enrolled in this study. All samples were positive for HBsAg (determined by Enzyme-linked immunosorbent assay (ELISA)) and anti-HDV. RNA extraction and cDNA synthesis was performed. Then, PCR was performed and HDV genotypes were determined by restriction fragment length polymorphism (RFLP). Of 25 patients, 12 (48%) were positive for HDV RNA. Genotype analysis of HDV RNA revealed that the prevalence of HDV genotypes I and II was 83.3% (n = 10) and 16.7% (n = 2), respectively. This study showed that the most prevalent genotype of HDV in Mashhad was genotype I. It was of interest that in contrast to other provinces of Iran, HDV genotype 2 was observed in Mashhad. Similar studies with larger sample sizes could provide valuable information regarding the molecular epidemiology and geographical distribution. It may also help control and prevent the spread of hepatitis D virus infections. In addition, the genotyping of HDV may predict the severity of the disease.

  18. Genotype to phenotype

    National Research Council Canada - National Science Library

    Malcolm, Sue; Goodship, Timothy H. J

    2001-01-01

    ... Disorders Molecular Genetics of Hypertension Human Gene EvolutionAnalysis of Multifactorial Disease Transcription Factors Molecular Genetics of Cancer, Second edition Genotype to Phenotype, second e...

  19. Porphyromonas gingivalis Fim-A genotype distribution among Colombians.

    Science.gov (United States)

    Moreno, Sandra; Jaramillo, Adriana; Parra, Beatriz; Botero, Javier Enrique; Contreras, Adolfo

    2015-09-30

    Porphyromonas gingivalis is associated with periodontitis and exhibit a wide array of virulence factors, including fimbriae which is encoded by the FimA gene representing six known genotypes. To identify FimA genotypes of P. gingivalis in subjects from Cali-Colombia, including the co-infection with Aggregatibacter actinomycetemcomitans, Treponema denticola, and Tannerella forsythia. Subgingival samples were collected from 151 people exhibiting diverse periodontal condition. The occurrence of P. gingivalis, FimA genotypes and other bacteria was determined by PCR. P. gingivalis was positive in 85 patients. Genotype FimA II was more prevalent without reach significant differences among study groups (54.3%), FimA IV was also prevalent in gingivitis (13.0%). A high correlation (p= 0.000) was found among P. gingivalis, T. denticola, and T. forsythia co-infection. The FimA II genotype correlated with concomitant detection of T. denticola and T. forsythia. Porphyromonas gingivalis was high even in the healthy group at the study population. A trend toward a greater frequency of FimA II genotype in patients with moderate and severe periodontitis was determined. The FimA II genotype was also associated with increased pocket depth, greater loss of attachment level, and patients co-infected with T. denticola and T. forsythia.

  20. Porphyromonas gingivalis Fim-A genotype distribution among Colombians

    Science.gov (United States)

    Jaramillo, Adriana; Parra, Beatriz; Botero, Javier Enrique; Contreras, Adolfo

    2015-01-01

    Introduction: Porphyromonas gingivalis is associated with periodontitis and exhibit a wide array of virulence factors, including fimbriae which is encoded by the FimA gene representing six known genotypes. Objetive: To identify FimA genotypes of P. gingivalis in subjects from Cali-Colombia, including the co-infection with Aggregatibacter actinomycetemcomitans, Treponema denticola, and Tannerella forsythia. Methods: Subgingival samples were collected from 151 people exhibiting diverse periodontal condition. The occurrence of P. gingivalis, FimA genotypes and other bacteria was determined by PCR. Results: P. gingivalis was positive in 85 patients. Genotype FimA II was more prevalent without reach significant differences among study groups (54.3%), FimA IV was also prevalent in gingivitis (13.0%). A high correlation (p= 0.000) was found among P. gingivalis, T. denticola, and T. forsythia co-infection. The FimA II genotype correlated with concomitant detection of T. denticola and T. forsythia. Conclusions: Porphyromonas gingivalis was high even in the healthy group at the study population. A trend toward a greater frequency of FimA II genotype in patients with moderate and severe periodontitis was determined. The FimA II genotype was also associated with increased pocket depth, greater loss of attachment level, and patients co-infected with T. denticola and T. forsythia. PMID:26600627

  1. The pathogenic role of different Blastocystis hominis genotypes isolated from patients with irritable bowel syndrome.

    Science.gov (United States)

    Fouad, Shawky A; Basyoni, Maha M A; Fahmy, Reham A; Kobaisi, Mohamed H

    2011-12-01

    The pathogenic role of Blastocystis hominis is still regarded by some as controversial. Studies have been in progress for years to evaluate the role of blastocystosis in irritable bowel syndrome (IBS) and demonstrated that faecal carriage of B. hominis was frequent in these patients. This study attempted to distinguish different genotypes of B. hominis isolates obtained from patients with IBS and to evaluate their pathogenic potentials. One hundred subjects (51 patients with IBS and 49 asymptomatic infected subjects) harbouring B. hominis were investigated by a direct smear examination and in vitro culture of stool samples followed by genotyping of B. hominis by PCR using STS primers. Sigmoidoscopy was done in all subjects and biopsies were taken and subjected to histopathologic examination. Genotyping proved that only four genotypes of B. hominis were identified. In patients with IBS, genotypes III, I, and IV were detected (28, 15 and 14 isolates, respectively). On the other hand, genotypes III, IV, and II were identified in asymptomatic infected individuals (21, 19 and 13 isolates, respectively). The degrees of chronic inflammatory changes in sigmoidoscopic biopsies caused by B. hominis genotypes among IBS patients revealed that severe inflammation was present mainly in patients harboring genotype I isolates (4/15) (26.66%), while genotype III caused severe inflammation only in 9.09%. Genotype II isolates were not detected in IBS cases. Asymptomatic infected individuals harboring genotypes II, III and IV exhibited mild to moderate inflammatory changes. Genotype I isolates were not detected in asymptomatic infected group. The correlation between different B. hominis genotypes and degree of inflammation was statistically insignificant. Genotype I was the most pathogenic genotype of B. hominis isolates in patients with IBS while genotype II was not detected among those patients. Also, our results suggest the presence of pathogenic and non-pathogenic strains among

  2. Contributions…uterine environment and piglet genotype on weaning survivability potential: II. Piglet growth, lactation performance, milk composition…blood profiles…lactation…reciprocal embryo transfers…Meishan and White…gilts

    Science.gov (United States)

    Crossbreeding studies between Meishan (MS) and Large White (LW) pigs have illustrated that increased piglet growth prior to weaning is attributed to the maternal genotype of LW dams. The objective of this study was to determine the contributions of the maternal uterine environment (MUE), piglet geno...

  3. APOE Genotyping, Cardiovascular Disease

    Science.gov (United States)

    ... Resources For Health Professionals Subscribe Search APOE Genotyping, Cardiovascular Disease Send Us Your Feedback Choose Topic At ... help understand the role of genetic factors in cardiovascular disease . However, the testing is sometimes used in ...

  4. HIV Genotypic Resistance Testing

    Science.gov (United States)

    ... High-sensitivity C-reactive Protein (hs-CRP) Histamine Histone Antibody HIV Antibody and HIV Antigen (p24) HIV ... antiretroviral drugs. With genotypic resistance testing, the genetic code of the HIV a person has been infected ...

  5. 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.

  6. Sequence variation of the glycoprotein gene identifies three distinct lineages within field isolates of viral hemorrhagic septicemia virus, a fish rhabdovirus

    Science.gov (United States)

    Benmansour, A.; Bascuro, B.; Monnier, A.F.; Vende, P.; Winton, J.R.; de Kinkelin, P.

    1997-01-01

    To evaluate the genetic diversity of viral haemorrhagic septicaemia virus (VHSV), the sequence of the glycoprotein genes (G) of 11 North American and European isolates were determined. Comparison with the G protein of representative members of the family Rhabdoviridae suggested that VHSV was a different virus species from infectious haemorrhagic necrosis virus (IHNV) and Hirame rhabdovirus (HIRRV). At a higher taxonomic level, VHSV, IHNV and HIRRV formed a group which was genetically closest to the genus Lyssavirus. Compared with each other, the G genes of VHSV displayed a dissimilar overall genetic diversity which correlated with differences in geographical origin. The multiple sequence alignment of the complete G protein, showed that the divergent positions were not uniformly distributed along the sequence. A central region (amino acid position 245-300) accumulated substitutions and appeared to be highly variable. The genetic heterogeneity within a single isolate was high, with an apparent internal mutation frequency of 1.2 x 10(-3) per nucleotide site, attesting the quasispecies nature of the viral population. The phylogeny separated VHSV strains according to the major geographical area of isolation: genotype I for continental Europe, genotype II for the British Isles, and genotype III for North America. Isolates from continental Europe exhibited the highest genetic variability, with sub-groups correlated partially with the serological classification. Neither neutralizing polyclonal sera, nor monoclonal antibodies, were able to discriminate between the genotypes. The overall structure of the phylogenetic tree suggests that VHSV genetic diversity and evolution fit within the model of random change and positive selection operating on quasispecies.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. Axiom turkey genotyping array

    Science.gov (United States)

    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...

  9. 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.

  10. Phenotypic characterization and ERIC-PCR based genotyping of Paenibacillus larvae isolates recovered from American foulbrood outbreaks in honey bees from Italy.

    Science.gov (United States)

    Bassi, Stefano; Formato, Giovanni; Milito, Marcella; Trevisiol, Karin; Salogni, Cristian; Carra, Elena

    2015-03-01

    Paenibacillus larvae is the etiological agent of American foulbrood (AFB), a widespread and severe bacterial brood disease of honey bees. The genomic characterization of P. larvae strains by enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) is able to differentiate four genotypes (ERIC I, ERIC II, ERIC III, ERIC IV). The information on the presence of P. larvae ERIC genotypes worldwide is few. We have characterized P. larvae strains isolated in Italy from AFB outbreaks to obtain information on ERIC genotypes and phenotypes of the strains circulating in the country. A total of 117 P. larvae isolates from 115 AFB outbreaks occurring in 2008-2012 were subjected to phenotypic and genetic characterization. The genomic characterization allowed the identification of ERIC I and ERIC II genotypes. Examining the data of Northern and Central Italy separately it was noted that in Northern Italy most outbreaks were caused by the ERIC I genotype (78.6%), followed by the ERIC II genotype (18.6%) and by co-infections (ERIC I + ERIC II) (2.6%). In Central Italy, only outbreaks caused by the ERIC I genotype were observed. With regard to phenotypic characteristics all examined strains of ERIC II genotype fermented fructose while no strains of ERIC I genotype possessed this ability. Both P. larvae ERIC I and ERIC II genotypes were isolated from the AFB outbreaks, but ERIC II genotype was isolated only in Northern Italy. The fermentation of fructose seems to be a genotype-specific biochemical marker.

  11. Contributions of the maternal uterine environment and piglet genotype on weaning survivability potential: II. Piglet growth, lactation performance, milk composition, and piglet blood profiles during lactation following reciprocal embryo transfers between Meishan and White crossbred gilts.

    Science.gov (United States)

    Miles, J R; Vallet, J L; Ford, J J; Freking, B A; Oliver, W T; Rempel, L A

    2015-04-01

    Crossbreeding studies between Meishan (MS) and Large White (LW) pigs have illustrated that increased piglet growth before weaning is attributed to the maternal genotype of LW dams. The objective of this study was to determine the contributions of the maternal uterine environment (MUE), piglet genotype (PigG), piglet age (PA), and their interactions on piglet growth, lactation performance, milk composition, and piglet blood profiles during lactation following reciprocal embryo transfers between MS and White crossbred (WC) gilts. Twenty-five successful pregnancies were generated by embryo transfer in 2 farrowing years representing all MUE × PigG combinations: MS × MS (n = 4 litters), MS × WC (n = 7 litters), WC × MS (n = 7 litters), and WC × WC (n = 7 litters). At d 1 and 10 and at weaning, piglets (n = 147, n = 96, and n = 94, respectively) were weighed and blood samples were collected and measured for hematocrit, hemoglobin, glucose, nitrogen, NEFA, albumin, lactate, and cortisol. In addition, sows were manually milked from a medial mammary gland to determine milk composition. All data were analyzed by ANOVA using MIXED model procedures with the fixed effects of MUE, PigG, PA, and their interactions. Piglet weight was greater (P lactation. However, milk composition was greater (P lactation and in MS piglets from MS dams at d 10 of lactation. Blood glucose was greater (P = 0.01) at d 1 in piglets from WC dams regardless of PigG but, at weaning, glucose was greater (P = 0.01) in WC piglets regardless of MUE. Serum NEFA levels were greater (P = 0.02) in piglets from MS dams throughout the lactation period. This study demonstrated that WC dams were superior to MS dams for piglet growth during lactation, in agreement with previous crossbreeding studies. However, blood components measured displayed complex interactions between the piglet and maternal breed, which signify possible mechanisms for improved preweaning survivability but slower lactational growth of MS

  12. Parallel phylogenetic analyses using the N, G or Nv gene from a fixed group of VHSV isolates reveal the same overall genetic typing

    DEFF Research Database (Denmark)

    Einer-Jensen, Katja; Ahrens, Peter; Lorenzen, Niels

    2005-01-01

    by a G gene fragment (nt 360 to 720) or the Nv gene (366 nt), although these regions had different characteristics with respect to resolution of Genotype I sublineages and resolution within Sub-lineage Ia. Phylogenetic analysis based on the deduced amino acid sequences was also performed....... The phylogenetic relationship between the nucleotide and amino acid sequences of the isolates corresponded best in the case of the N gene/protein. For the 6 other genomic regions, genetically distant isolates occasionally grouped together when compared at protein levels. No clear relationship between the G gene...

  13. GENOTYPE X ENVIRONMENT INTERACTION AND STABILITY ...

    African Journals Online (AJOL)

    GENOTYPE X ENVIRONMENT INTERACTION AND STABILITY ANALYSIS OF SEED YIELD IN NAVY BEAN GENOTYPES. ... Abstract. Genotype x environment interactions, genotype response to environments and stability for seed yield of navy bean genotypes (Phaseolus vulgaris L.) were studied. Sixteen genotypes were ...

  14. Genotype � Environment Interaction and Stability Analysis of Seed Yield of Durum Wheat Genotypes in Dryland Conditions

    Directory of Open Access Journals (Sweden)

    Mohtasham MOHAMMADI

    2012-08-01

    Full Text Available The objective of this investigation was to evaluate seed yield of twenty durum wheat (Triticum turgidum spp. durum genotypes. Evaluation of genotype � environment interaction and stability were also carried out at five diverse locations during the 2007-2009 growing seasons. Significant differences were found among the genotypes for seed yield on individual years and combined over years, in all locations. Genotype � environment interaction showed significance (p>0.001 for seed yield. According to the coefficients of linear regression and deviations from the regression model, genotypes G2, G7 and G8 proved to be the most stable while based on ? and ? parameters, genotypes G7, G12 and G13 were identified the most stable. Clustering genotypes based on all stability methods and mean yield divided them into four major classes, which Class II had relatively high stability and high mean yield performance. To compare relationships among stability statistics, hierarchical clustering procedure showed that the ten stability statistics and mean yield could be categorized into three major groups, which methods of Group C indicated dynamic concept of yield stability. The genotypic stability, stability variance, superiority index and desirability index provide information for reaching definitive conclusions. Also, the best recommended genotypes, according to the present investigation, were G2 (2697.18 kg ha-1, G7 (2644.70 kg ha-1, G8 (2580.16 kg ha-1 and G10 (2637.43 kg ha-1, which had high mean yield and were the most stable genotypes based on the above mentioned stability statistics.

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

    African Journals Online (AJOL)

    SARAH

    2014-08-31

    Aug 31, 2014 ... General Background: Niger seed [(Guizotia abyssinica (L.F.) Cass.), 2n = 30] and Linseed [(Linum usitatissimum L.), n=15] are ... Objectives: The objectives of the study were to (i) assess genotype by environment interaction (G x E) and (ii) identify stable and adaptable Linseed and Niger seed varieties for ...

  16. Toxoplasma gondii Type I, predominant genotype isolated from sheep in South of Iran

    Directory of Open Access Journals (Sweden)

    Belal Armand

    2017-04-01

    Full Text Available Aim: This study was performed to determine the genetic diversity of Toxoplasma gondii in sheep using nested-polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP in Southern Iran. Materials and Methods: The tissue samples of diaphragm and heart from 125 sheep were collected from the main slaughterhouses of Jahrom district in South of Fars province, Iran, between Aprils and June 2013. The DNA were extracted and analyzed by nested-PCR using specific primers for SAG2 and GRA6 loci. RFLP was used to classify strains into one of the three major lineages of T. gondii. Results: T. gondii Type I was predominant in this area. The data obtained from both loci demonstrated that the frequency of each genotype was 72% Type I, 2.4% Type III, 7.2% mixed Type I and II, 16.8% mixed Type I and III, 0.8% mixed Type II and III, and 0.8% mixed Type I, II and III. Conclusion: Although the previously published data indicated that Type II is the predominant T. gondii genotype in sheep in the other parts of the world, this study showed that genotype I is the dominant genotype of T. gondii in the southern Iran; however, other genotypes were detected. High diversity of T. gondii genotypes including mix genotypes in lambs is of importance for the public health. These studies depict a new mapping of T. gondii genotypes pattern which could be very helpful in toxoplasmosis control and prevention.

  17. Genotyping sleep disorders patients.

    Science.gov (United States)

    Kripke, Daniel F; Shadan, Farhad F; Dawson, Arthur; Cronin, John W; Jamil, Shazia M; Grizas, Alexandra P; Koziol, James A; Kline, Lawrence E

    2010-03-01

    The genetic susceptibility factors underlying sleep disorders might help us predict prognoses and responses to treatment. Several candidate polymorphisms for sleep disorders have been proposed, but there has as yet inadequate replication or validation that the candidates may be useful in the clinical setting. To assess the validity of several candidate associations, we obtained saliva deoxyribonucleic acid (DNA) samples and clinical information from 360 consenting research participants who were undergoing clinical polysomnograms. Ten single nucleotide polymorphisms (SNPs) were genotyped. These were thought to be related to depression, circadian sleep disorders, sleep apnea, restless legs syndrome (RLS), excessive sleepiness, or to slow waves in sleep. With multivariate generalized linear models, the association of TEF rs738499 with depressive symptoms was confirmed. Equivocal statistical evidence of association of rs1801260 (the C3111T SNP in the CLOCK gene) with morningness/eveningness and an association of Apolipoprotein E (APOE) rs429358 with the Epworth Sleepiness Scale (ESS) were obtained, but these associations were not strong enough to be of clinical value by themselves. Predicted association of SNPs with sleep apnea, RLS, and slow wave sleep were not confirmed. The SNPs tested would not, by themselves, be of use for clinical genotyping in a sleep clinic.

  18. Genotypic and phenotypic heterogeneity in Streptococcus mutans isolated from diabetic patients in Rome, Italy

    National Research Council Canada - National Science Library

    De, Arpan; Pasquantonio, Guido; Cerroni, Loredana; Petrelli, Dezemona; Lauro, Davide; Longhi, Marta; Vitali, Luca A

    2016-01-01

    Our study focuses on the antimicrobial susceptibility, genotypic and phenotypic heterogeneity, and serotype classification of the Streptococcus mutans isolated from type II diabetic patients (n = 25; age 42–68...

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

    Science.gov (United States)

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

    2011-01-01

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

  20. Overlapping Toxoplasma gondii genotypes circulating in domestic animals and humans in Southeastern Brazil.

    Science.gov (United States)

    Silva, Letícia A; Andrade, Renata O; Carneiro, Ana Carolina A V; Vitor, Ricardo W A

    2014-01-01

    Although several Toxoplasma gondii genotyping studies have been performed in Brazil, studies of isolates from animals in the state of Minas Gerais are rare. The objective of this study was to conduct a genotypic characterization of T. gondii isolates obtained from dogs, free-range chickens, and humans in Minas Gerais and to verify whether the T. gondii genotypes circulating in domestic animals correspond to the genotypes detected in humans. Genetic variability was assessed by restricted fragment length polymorphism at 11 loci (SAG1, 5'+3'SAG2, SAG2 alt, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). Twelve different genotypes were identified among the 24 isolates studied, including 8 previously identified genotypes and 4 new genotypes. The genetic relationship of the 24 T. gondii isolates, together with the genotypes previously described from 24 human newborns with congenital toxoplasmosis, revealed a high degree of similarity among the genotypes circulating in humans and animals in Minas Gerais. The most common genotypes among these species were BrII, BrIII, ToxoDB #108, and ToxoDB #206. Restricted fragment length polymorphism at the CS3 locus of these 48 isolates showed that the majority of isolates presented alleles I (50%) or II (27%). Isolates harboring allele III at the CS3 locus presented low virulence for mice, whereas those harboring alleles I or II presented higher virulence. These results confirm the utility of marker CS3 for predicting the virulence of Brazilian isolates of T. gondii in mice. No association was found between the allele type and clinical manifestations of human congenital toxoplasmosis. This is the first report of T. gondii genotyping that verifies the overlapping genotypes of T. gondii from humans and animals in the same geographic region of Brazil. Our results suggest that there is a common source of infection to the species studied, most likely oocysts contaminating the environment.

  1. 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 availabil......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....

  2. Hepatitis C virus genotype 4: Genotype 1's little brother.

    Science.gov (United States)

    Llaneras, J; Riveiro-Barciela, M; Buti, M; Esteban, R

    2017-01-01

    Treatment for hepatitis C virus genotype 4 infection has undergone a major advance over the past 5 years with the emergence of direct-acting antiviral agents. Previously, genotype 4 treatment had been limited to the combination of pegylated interferon and ribavirin, with low rates of sustained virological response. The combinations of new direct-acting agents have resulted in a radical improvement in hepatitis C therapy. Much of the currently available efficacy and safety information in the treatment of genotype 4 has been extrapolated through the results of genotype 1. In this report, we review the efficacy and safety data obtained in recent studies focusing on genotype 4 patients, including special populations, such as those with decompensated cirrhosis. © 2016 John Wiley & Sons Ltd.

  3. Molecular epidemiology of dengue in Jamaica dengue virus genotypes in Jamaica, 2007.

    Science.gov (United States)

    Brown, M G; Salas, R A; Vickers, I E; Heslop, O D; Smikle, M F

    2011-03-01

    The genotypes of dengue viruses (DENV) isolated from patients with dengue in Jamaica during 2007 were determined using DNA sequencing and phylogenetic analysis of the C-prM gene junction. The 17 DENV analysed included strains of DENVserotypes 1 (DENV-1, n = 3), DENV-2 (n = 7) and DENV-4 (n = 7). All strains ofDENV-1 were classified as genotype III, while 1 of 7 strains of DENV-2 belonged to the Asian American/Asian genotype, genotype I/III (Jamaica genotype), 2 were genotype V, the American genotype and 4 strains clustered with reference strains belonging to genotype IV. The 6 DENV-4 strains from Jamaica and the control strain clustered together in a separate clade from Caribbean/American reference strains, which belong to genotype II and Asian strains, classified as genotypes I and III. There has been little evolution in the DENV-1 strains circulating in Jamaica over the years and this might reduce the risk of outbreaks due to this serotype. In contrast, the high genetic diversity in strains of DENV-2 viruses in circulation, the presence of more recently introduced genotypes and a new clade of DENV-4 might contribute to the epidemic potential of these DENV serotypes. These preliminary data clearly indicate the need to maintain laboratory surveillance, and other control measures against hyperendemicity of dengue in Jamaica.

  4. 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

  5. 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.

  6. 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.

  7. [Genetic diversity of a rare hepatitis A virus genotype].

    Science.gov (United States)

    Desbois, D; Couturier, E; Graube, A; Letort, M-J; Dussaix, E; Roque-Afonso, A-M

    2011-02-01

    Very few is known on genotype II hepatitis A virus (HAV) since it is rarely isolated. From 2002 to 2007, the French observatory of HAV identified six sub-genotype IIA strains of which one from a patient having travelled to West Africa. To investigate the possible African origin of sub-genotype IIA, we determined its prevalence among French travellers in 2008 and characterised its genetic variability. The 2008 mandatory notification records were screened for travel to Africa. Viral genotype was determined on the nucleotide sequencing of the VP1/2A junction region. The P1 region coding for capsid proteins was used to compare the genetic diversity of IIA isolates to those of other genotypes. In 2008, five out of 54 patients returning from West Africa were infected by IIA strains and an additional "autochthonous" case was identified. Two more African cases were identified in 2009. A total of 14 IIA isolates (eight African and six "autochthonous") were analysed. Nucleotide and amino-acid variability of IIA sequences was lower than that of the other genotypes. Phylogenetic analysis revealed the clustering of two "autochthonous" cases with African isolates whereas the other ones belonged to a different lineage. Most IIA strains isolated in France are imported by travellers returning from West Africa. However, the unexplained contamination mode of some "autochthonous" cases suggests another geographical origin to discover or a French reservoir to explore. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

  8. Genotype Specification Language.

    Science.gov (United States)

    Wilson, Erin H; Sagawa, Shiori; Weis, James W; Schubert, Max G; Bissell, Michael; Hawthorne, Brian; Reeves, Christopher D; Dean, Jed; Platt, Darren

    2016-06-17

    We describe here the Genotype Specification Language (GSL), a language that facilitates the rapid design of large and complex DNA constructs used to engineer genomes. The GSL compiler implements a high-level language based on traditional genetic notation, as well as a set of low-level DNA manipulation primitives. The language allows facile incorporation of parts from a library of cloned DNA constructs and from the "natural" library of parts in fully sequenced and annotated genomes. GSL was designed to engage genetic engineers in their native language while providing a framework for higher level abstract tooling. To this end we define four language levels, Level 0 (literal DNA sequence) through Level 3, with increasing abstraction of part selection and construction paths. GSL targets an intermediate language based on DNA slices that translates efficiently into a wide range of final output formats, such as FASTA and GenBank, and includes formats that specify instructions and materials such as oligonucleotide primers to allow the physical construction of the GSL designs by individual strain engineers or an automated DNA assembly core facility.

  9. Flapjack--graphical genotype visualization.

    Science.gov (United States)

    Milne, Iain; Shaw, Paul; Stephen, Gordon; Bayer, Micha; Cardle, Linda; Thomas, William T B; Flavell, Andrew J; Marshall, David

    2010-12-15

    New software tools for graphical genotyping are required that can routinely handle the large data volumes generated by the high-throughput single-nucleotide polymorphism (SNP) platforms, genotyping-by-sequencing and other comparable genotyping technologies. Flapjack has been developed to facilitate analysis of these data, providing real time rendering with rapid navigation and comparisons between lines, markers and chromosomes, with visualization, sorting and querying based on associated data, such as phenotypes, quantitative trait loci or other mappable features. Flapjack is freely available for Microsoft Windows, Mac OS X, Linux and Solaris, and can be downloaded from http://bioinf.scri.ac.uk/flapjack .

  10. Nutrient uptake of soybean genotypes under aluminum toxicity

    Directory of Open Access Journals (Sweden)

    Heru Kuswantoro

    2014-09-01

    Full Text Available The objective of this research was to study the nutrient uptake of soybean exposed to aluminium (Al toxicity. The factorial design consisted of two treatments arranged in a randomized block design with three replications. Liming was the first factor which consisted of four levels, i.e. i without liming; ii liming with 0.5×Al(exchangeable/ec; iii liming with 1×Al(ec; and iv liming with 1.5×Al(ec. Five genotypes were used as second factor, i.e. three tolerant genotypes (W3898- 14-3, Wilis, and Kawi, and two sensitve genotypes (MLG 3209 and MLG 3083. It was found that two tolerant genotypes, W3898-14-3 and Kawi, had a higher potassium (K and sodium (Na uptake than susceptible genotypes. Liming affected significantly the ratio of Al/[calcium (Ca + magnesium (Mg] in roots and leaves, the content of Ca and Mg in the roots and the content of Mg in the leaves. The K content in the roots and the content of Ca, K, and Na in the leaves were unresponsive to the alteration of pH and Al saturation.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    O'Farrell, Brian; Haase, Jana K; Velayudhan, Vimalkumar; Murphy, Ronan A; Achtman, Mark

    2012-01-01

    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.

  13. Influence of oxygen administration on pulmonary haemodynamics and tissue oxygenation during exercise in COPD patients with different ACE genotypes.

    Science.gov (United States)

    Kanazawa, Hiroshi; Hirata, Kazuto; Yoshikawa, Junichi

    2003-11-01

    We previously found that the angiotensin-converting enzyme (ACE) DD genotype is associated with exaggerated pulmonary hypertension and disturbance of tissue oxygenation during exercise in chronic obstructive pulmonary disease (COPD) patients. This study was designed to compare the effect of oxygen administration on pulmonary haemodynamics and tissue oxygenation during exercise in COPD patients with different ACE genotypes. Forty-three COPD patients (II=16, ID=12, DD=15) underwent right heart catheterization, and then performed an exercise test with room air or oxygen. We measured pulmonary haemodynamic variables and indices of tissue oxygenation such as mixed venous oxygen tension (PVO2) and arterial lactate concentration, both at rest and after exercise. The magnitude of difference in mean pulmonary arterial pressure and pulmonary vascular resistance after exercise between breathing of room air and breathing of oxygen did not significantly differ among the three groups. PVO2 after exercise with room air or oxygen was significantly higher in patients with the II genotype than in those with the ID or DD genotype. In contrast, lactate concentration after exercise with room air or oxygen was significantly lower in patients with the II genotype than in those with the ID or DD genotype. Moreover, the magnitude of difference in PVO2 and lactate concentration after exercise between breathing of room air and breathing of oxygen was the II>ID>DD genotype. These findings suggest that the ability of oxygen administration to improve tissue oxygenation during exercise is associated with the ACE genotypes in COPD patients.

  14. Potential distribution of the viral haemorrhagic septicaemia virus in the Great Lakes region

    Science.gov (United States)

    Escobar, Luis E.; Kurath, Gael; Escobar-Dodero, Joaquim; Craft, Meggan E.; Phelps, Nicholas B.D.

    2017-01-01

    Viral haemorrhagic septicaemia virus (VHSV) genotype IVb has been responsible for large-scale fish mortality events in the Great Lakes of North America. Anticipating the areas of potential VHSV occurrence is key to designing epidemiological surveillance and disease prevention strategies in the Great Lakes basin. We explored the environmental features that could shape the distribution of VHSV, based on remote sensing and climate data via ecological niche modelling. Variables included temperature measured during the day and night, precipitation, vegetation, bathymetry, solar radiation and topographic wetness. VHSV occurrences were obtained from available reports of virus confirmation in laboratory facilities. We fit a Maxent model using VHSV-IVb reports and environmental variables under different parameterizations to identify the best model to determine potential VHSV occurrence based on environmental suitability. VHSV reports were generated from both passive and active surveillance. VHSV occurrences were most abundant near shore sites. We were, however, able to capture the environmental signature of VHSV based on the environmental variables employed in our model, allowing us to identify patterns of VHSV potential occurrence. Our findings suggest that VHSV is not at an ecological equilibrium and more areas could be affected, including areas not in close geographic proximity to past VHSV reports.

  15. Deviations from hardy-weinberg equilibrium in parental and unaffected sibling genotype data.

    Science.gov (United States)

    Li, Bingshan; Leal, Suzanne M

    2009-01-01

    Genotyping error can increase both type I and II errors. In order to elucidate potential genotyping errors, data quality control often includes testing genotype data for deviations from Hardy-Weinberg Equilibrium (HWE). The Hardy-Weinberg Disequilibrium (HWD) coefficient and the ability to reject the null hypothesis of HWE were calculated analytically for genotype data from parents and unaffected siblings of affected probands. Genotype data from parents and unaffected siblings display deviations from HWE when functional or markers in LD with functional locus are tested. For the parental genotype data all deviations from HWE are negative, indicating an excess of heterozygous genotypes with the strongest deviations from HWE observed for the multiplicative model. In contrast, for affected proband genotype data, there is no deviation from HWE under the multiplicative model and the deviations from HWE for the recessive model are positive. For the unaffected sibling data, patterns of deviation from HWE are similar to those observed in the proband data with the exception of the multiplicative model where the HWD coefficient although close to 0 can be either positive or negative depending on the allele frequency. Deviations from HWE in parental and unaffected sibling genotype data could be due to an association with the functional locus. However these deviations for genotypic relative risk < or =2.0 are not large and therefore the power to detect them is usually low. Testing for deviations from HWE in parental and unaffected sibling genotype data is still beneficial for quality control even though functional loci, in parental and unaffected sibling genotype data, can produce an association signal. Copyright 2008 S. Karger AG, Basel.

  16. Phenotypic and genotypic screening of rice genotypes at seedling ...

    African Journals Online (AJOL)

    of 11 genotypes was done in hydroponic system using salinized (EC 12 dS/m) nutrient solution. IRRI standard protocol was followed to evaluate salinity tolerance. Large variation in salinity tolerance among the rice germplasms was detected. Plant height and total dry matter of tolerant lines were reduced by 19.0 and 40.6%, ...

  17. Genotype networks in metabolic reaction spaces

    Science.gov (United States)

    2010-01-01

    Background A metabolic genotype comprises all chemical reactions an organism can catalyze via enzymes encoded in its genome. A genotype is viable in a given environment if it is capable of producing all biomass components the organism needs to survive and reproduce. Previous work has focused on the properties of individual genotypes while little is known about how genome-scale metabolic networks with a given function can vary in their reaction content. Results We here characterize spaces of such genotypes. Specifically, we study metabolic genotypes whose phenotype is viability in minimal chemical environments that differ in their sole carbon sources. We show that regardless of the number of reactions in a metabolic genotype, the genotypes of a given phenotype typically form vast, connected, and unstructured sets -- genotype networks -- that nearly span the whole of genotype space. The robustness of metabolic phenotypes to random reaction removal in such spaces has a narrow distribution with a high mean. Different carbon sources differ in the number of metabolic genotypes in their genotype network; this number decreases as a genotype is required to be viable on increasing numbers of carbon sources, but much less than if metabolic reactions were used independently across different chemical environments. Conclusions Our work shows that phenotype-preserving genotype networks have generic organizational properties and that these properties are insensitive to the number of reactions in metabolic genotypes. PMID:20302636

  18. Pooled DNA genotyping on Affymetrix SNP genotyping arrays

    Directory of Open Access Journals (Sweden)

    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.

  19. Do imports of rainbow trout carcasses risk introducing viral haemorrhagic septicaemia virus into England and Wales?

    Science.gov (United States)

    Pearce, F M; Oidtmann, B C; Thrush, M A; Dixon, P F; Peeler, E J

    2014-06-01

    A qualitative import risk assessment was undertaken to assess the likelihood of introduction and establishment of viral haemorrhagic septicaemia virus (VHSV) genotype 1a in England and Wales (E&W), via the processing of imported rainbow trout (Oncorhynchus mykiss) carcasses from continental Europe. The likelihood was estimated for one import from an infected farm. Four main routes by which susceptible populations could be exposed to VHSV via processing waste were considered: (i) run-off from solid waste to watercourses, (ii) contamination of birds or rodents with VHSV by scavenging solid waste, (iii) discharge of liquid waste to mains drainage, and (iv) discharge of liquid waste directly to watercourses. Data on the biophysical characteristics of VHSV, its epidemiology, fish processing practices and waste management were collected. Likelihoods for each step of the four pathways were estimated. Pathway 4 (discharge of liquid waste to a watercourse) was judged as the most likely to result in infection of susceptible individuals. Levels of virus entering the aquatic environment via pathways 1-3 were judged to be many times lower than pathway 4 due mainly to the treatment of solid waste (pathways 1 and 2) and high levels of dilution (pathways 1, 2 and 3). Thirty-four trout farms process fish, of which seven have imported carcasses for processing. Compared with other processing facilities, on-farm processing results in a higher likelihood of VHSV exposure and establishment via all four pathways. Data availability was an issue; the analysis was particularly constrained by a lack of data on the prevalence of VHSV in Europe, volume of trade of carcasses into the UK and processing practices in E&W. It was concluded that the threat of VHSV introduction into E&W could be reduced by treatment of liquid effluent from processing plants and by sourcing carcasses for on-farm processing only from approved VHSV free areas. © 2012 Crown copyright. Transboundary and Emerging Diseases

  20. SCREENING SOYBEAN GENOTYPES FOR PROMISCUOUS ...

    African Journals Online (AJOL)

    ACSS

    2016-02-25

    Feb 25, 2016 ... symbiotic association with Bradyrhizobium sp. in order to identify genotypes with potential to be used as parents to initiate a breeding ... 5N as potential parental materials for subsequent breeding work. Key Words: Glycine max, nodules, ..... Journal of Systematic and Evolutionary. Microbiology50: 225-234.

  1. (Nigella sativa L.) genotypes from

    African Journals Online (AJOL)

    ajl yemi

    2011-10-26

    Oct 26, 2011 ... nutritional characteristics revealed five distinct clusters with genotypes which were markedly different. Thus, all clusters were ... Key words: Biodiversity, black seed, cluster analyses, kalonji, physico-chemical traits, principal components' analysis. ...... industry and thus may enhance farmers' productivity.

  2. 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

  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. SCREENING SOYBEAN GENOTYPES FOR PROMISCUOUS ...

    African Journals Online (AJOL)

    ACSS

    2016-02-25

    Feb 25, 2016 ... The current low soybean (Glycine max L. Merrill) yields in Sub-Saharan Africa can be alleviated by developing promiscuous genotypes. The research trend in Africa is towards developing promiscuous varieties for less labour and high yields in soybean production. A greenhouse experiment was conducted ...

  5. Response of different genotypes of faba bean plant to drought stress.

    Science.gov (United States)

    Siddiqui, Manzer H; Al-Khaishany, Mutahhar Y; Al-Qutami, Mohammed A; Al-Whaibi, Mohamed H; Grover, Anil; Ali, Hayssam M; Al-Wahibi, Mona S; Bukhari, Najat A

    2015-05-05

    Drought stress is one of the major abiotic stresses that are a threat to crop production worldwide. Drought stress impairs the plants growth and yield. Therefore, the aim of the present experiment was to select the tolerant genotype/s on the basis of moprpho-physiological and biochemical characteristics of 10 Vicia faba genotypes (Zafar 1, Zafar 2, Shebam, Makamora, Espan, Giza Blanka, Giza 3, C4, C5 and G853) under drought stress. We studied the effect of different levels of drought stress i.e., (i) normal irrigation (ii) mild stress (iii) moderate stress, and (iv) severe stress on plant height (PH) plant-1, fresh weight (FW) and dry weight (DW) plant-1, area leaf-1, leaf relative water content (RWC), proline (Pro) content, total chlorophyll (Total Chl) content, electrolyte leakage (EL), malondialdehyde (MDA), hydrogen peroxide (H2O2) content, and activities of catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD) of genotypes of faba bean. Drought stress reduced all growth parameters and Total Chl content of all genotypes. However, the deteriorating effect of drought stress on the growth performance of genotypes "C5" and "Zafar 1" were relatively low due to its better antioxidant enzymes activities (CAT, POD and SOD), and accumulation of Pro and Total Chl, and leaf RWC. In the study, genotype "C5" and "Zafar 1" were found to be relatively tolerant to drought stress and genotypes "G853" and "C4" were sensitive to drought stress.

  6. Genotyping of polymorphic effectors of Toxoplasma gondii isolates from China

    Directory of Open Access Journals (Sweden)

    Weisheng Cheng

    2017-11-01

    Full Text Available Abstract Background Toxoplasma gondii is an opportunistic protozoan apicomplexan and obligate intracellular parasite that infects a wide range of animals and humans. Rhoptry proteins 5 (ROP5, ROP16, ROP18 and dense granules 15 (GRA15 are the important effectors secreted by T. gondii which link to the strain virulence for mice and modulate the host’s response to the parasite. Little has been known about these molecules as well as GRA3 in type Chinese 1 strains that show polymorphism among strains of archetypical genotypes. This study examined the genetic diversity of these effectors and its correlated virulence in mice among T. gondii isolates from China. Results Twenty-one isolates from stray cats were detected, of which 15 belong to Chinese 1, and 6 to ToxoDB #205. Wh6 isolate, a Chinese 1 strain, has an avirulent phenotype. PCR-RFLP results of ROP5 and ROP18 presented few variations among the strains. Genotyping of GRA15 and ROP16 revealed that all the strains belong to type II allele except Xz7 which carries type I allele. ROP16 amino acid alignment at 503 locus demonstrated that 17 isolates are featured as type I or type III (ROP16I/III, and the other 4 as type II (ROP16II. The strains investigated may be divided into four groups based on GRA3 amino acid alignment, and all isolates of type Chinese 1 belong to the μ-1 allele except Wh6 which is identical to type II strain. Conclusions PCR-RFLP and sequence alignment analyses of ROP5, ROP16, ROP18, GRA3, and GRA15 in T. gondii revealed that strains with the same genotype may have variations in some of their key genes. GRA3 variation exhibited by Wh6 strain may be associated with the difference in phenotype and pathogenesis.

  7. Univariate stability analysis methods for determining genotype ...

    African Journals Online (AJOL)

    However, superior genotypes are recommended for use by farmers in semi-arid areas. Finally, based on most statistics, mean yield and dynamic concept of stability genotype G13 was stable and favorable and is recommended for national release in rain-fed lands of Iran. Regression method's slopes, genotypic stability (D2) ...

  8. Genetic relationships among Ethiopian mustard genotypes based ...

    African Journals Online (AJOL)

    Genetic relationships among Ethiopian mustard genotypes based on oil content and fatty acid composition. ... Quantification and classification of genetic diversity among genotypes is essential for parental selection in breeding programs. The objective of this study was to classify and cluster Ethiopian mustard genotypes ...

  9. Genotype x environment interaction and optimum resource ...

    African Journals Online (AJOL)

    Dry yield and yield components from 6 multilocational trials of cassava genotypes conducted for 3 years in Nigeria were used to study the nature and magnitude of genotype x environment (G x E) interaction and to determine the optimum resource allocation for cassava yield trials. The effects of environment, genotype and G ...

  10. Compensatory and Susceptive Responses of Cowpea Genotypes...

    African Journals Online (AJOL)

    User

    turing genotypes of cowpea. Control of aphid's infestation in early maturing cowpea genotypes should not be delayed up to two weeks after infestation (28 days after planting) to avoid yield loss. Aphid infestation period for studies in susceptive response in medium to late matur- ing genotypes should go beyond 28 days after.

  11. Compensatory and Susceptive Responses of Cowpea Genotypes...

    African Journals Online (AJOL)

    User

    the seedlings of cowpea and causes direct dam- age on the crop by sucking ... Description of the 10 genotypes of cowpea by parentage or source. Genotype. Description. APAGBAALA. Prima/TVu. 4552/California. Blackeye. No.5//7977. Cultivar, released in ... genotypes started showing symptoms of dam- age. When the ...

  12. Genetic variation in V gene of class II Newcastle disease virus.

    Science.gov (United States)

    Hao, Huafang; Chen, Shengli; Liu, Peng; Ren, Shanhui; Gao, Xiaolong; Wang, Yanping; Wang, Xinglong; Zhang, Shuxia; Yang, Zengqi

    2016-01-01

    The genetic variation and molecular evolution of the V gene of the class II Newcastle disease virus (NDV) isolates with genotypes I-XVIII were determined using bioinformatics. Results indicated that low homology existed in different genotype viruses, whereas high homology often for the same genotypes, exception may be existed within genotypes I, V, VI, and XII. Sequence analysis showed that the genetic variation of V protein was consistent with virus genotype, and specific signatures on the V protein for nine genotypes were identified. Phylogenetic analysis demonstrated that the phylogenetic trees were highly consistent between the V and F genes, with slight discrepancies in the sub-genotypes. Evolutionary rate analyses based on V and F genes revealed the evolution rates varied in genotypes. These data indicate that the genetic variation of V protein is genotype-related and will help in elucidating the molecular evolution of NDV. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Genotypes and mouse virulence of Toxoplasma gondii isolates from animals and humans in China.

    Directory of Open Access Journals (Sweden)

    Lin Wang

    Full Text Available BACKGROUND: Recent population structure studies of T. gondii revealed that a few major clonal lineages predominated in different geographical regions. T. gondii in South America is genetically and biologically divergent, whereas this parasite is remarkably clonal in North America and Europe with a few major lineages including Types I, II and III. Information on genotypes and mouse virulence of T. gondii isolates from China is scarce and insufficient to investigate its population structure, evolution, and transmission. METHODOLOGY/PRINCIPAL FINDINGS: Genotyping of 23 T. gondii isolates from different hosts using 10 markers for PCR-restriction fragment length polymorphism analyses (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico revealed five genotypes; among them three genotypes were atypical and two were archetypal. Fifteen strains belong to the Chinese 1 lineage, which has been previously reported as a widespread lineage from swine, cats, and humans in China. Two human isolates fall into the type I and II lineages and the remaining isolates belong to two new atypical genotypes (ToxoDB#204 and #205 which has never been reported in China. Our results show that these genotypes of T. gondii isolates are intermediately or highly virulent in mice except for the strain TgCtwh6, which maintained parasitemia in mice for 35 days post infection although it possesses the uniform genotype of Chinese 1. Additionally, phylogenetic network analyses of all isolates of genotype Chinese 1 are identical, and there is no variation based on the sequence data generated for four introns (EF1, HP2, UPRT1 and UPRT7 and two dense granule proteins (GRA6 and GRA7. CONCLUSION/SIGNIFICANCE: A limited genetic diversity was found and genotype Chinese 1 (ToxoDB#9 is dominantly circulating in mainland China. The results will provide a useful profile for deep insight to the population structure, epidemiology and biological characteristics of T. gondii in China.

  14. FTO genotype and weight loss

    DEFF Research Database (Denmark)

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

    2016-01-01

    : 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...... 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.......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...

  15. 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

  16. Quantifying uncertainty in genotype calls.

    Science.gov (United States)

    Carvalho, Benilton S; Louis, Thomas A; Irizarry, Rafael A

    2010-01-15

    Genome-wide association studies (GWAS) are used to discover genes underlying complex, heritable disorders for which less powerful study designs have failed in the past. The number of GWAS has skyrocketed recently with findings reported in top journals and the mainstream media. Microarrays are the genotype calling technology of choice in GWAS as they permit exploration of more than a million single nucleotide polymorphisms (SNPs) simultaneously. The starting point for the statistical analyses used by GWAS to determine association between loci and disease is making genotype calls (AA, AB or BB). However, the raw data, microarray probe intensities, are heavily processed before arriving at these calls. Various sophisticated statistical procedures have been proposed for transforming raw data into genotype calls. We find that variability in microarray output quality across different SNPs, different arrays and different sample batches have substantial influence on the accuracy of genotype calls made by existing algorithms. Failure to account for these sources of variability can adversely affect the quality of findings reported by the GWAS. We developed a method based on an enhanced version of the multi-level model used by CRLMM version 1. Two key differences are that we now account for variability across batches and improve the call-specific assessment of each call. The new model permits the development of quality metrics for SNPs, samples and batches of samples. Using three independent datasets, we demonstrate that the CRLMM version 2 outperforms CRLMM version 1 and the algorithm provided by Affymetrix, Birdseed. The main advantage of the new approach is that it enables the identification of low-quality SNPs, samples and batches. Software implementing of the method described in this article is available as free and open source code in the crlmm R/BioConductor package. Supplementary data are available at Bioinformatics online.

  17. [Molecular genotyping: development and limits].

    Science.gov (United States)

    Delpech, M

    2003-06-01

    Kits dedicated to molecular genotyping are now commercially available and are routinely used for diagnosis purpose. In the future these kits that use the classical reverse dot-blot approach will be replaced by micro-arrays, DNA chips and Labs on a chip. Some systems and DNA chips designed for medical diagnosis are already available. The present main problem is their very high cost.

  18. 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.

  19. Development of genotype-specific primers for differentiation of genotypes A and B of Aichi viruses.

    Science.gov (United States)

    Pham, Ngan Thi Kim; Trinh, Quang Duy; Nguyen, Tuan Anh; Dey, Shuvra Kanti; Phan, Tung Gia; Hoang, Le Phuc; Khamrin, Pattara; Maneekarn, Niwat; Okitsu, Shoko; Mizuguchi, Masashi; Ushijima, Hiroshi

    2009-03-01

    A nested polymerase chain reaction method using genotype-specific primers based on the capsid gene was developed to differentiate between genotypes A and B of Aichi viruses. Results of the study showed that the PCR using newly designed genotype-specific primers could generate appropriate PCR products from all 17 samples tested, the newly developed primers could differentiate genotype A from genotype B, and all matched those obtained by nucleotide sequencing of the capsid regions. The nested PCR method using genotype-specific primers is useful and can be used for genotyping of Aichi viruses isolated from epidemiological studies.

  20. Molecular epidemiology of American/Asian genotype DENV-2 in Peru.

    Science.gov (United States)

    Cruz, Cristhopher D; Forshey, Brett M; Juarez, Diana S; Guevara, Carolina; Leguia, Mariana; Kochel, Tadeusz J; Halsey, Eric S

    2013-08-01

    During the past decade, countries in South America have reported dengue hemorrhagic fever (DHF) associated with American/Asian genotype of dengue virus serotype 2 (DENV-2). DENV-2 strains have been associated with large outbreaks of dengue fever and DHF in numerous regions of Peru since the mid-1990s, but studies to address the origins, distribution, and genetic diversity of DENV-2 strains have been limited. To address this knowledge gap, we sequenced the envelope gene region of DENV-2 isolates from Peru, Ecuador, Paraguay, and Bolivia. Sequences were aligned and compared to a global sample of DENV-2 viruses. Phylogenetic analysis confirmed the circulation of two DENV-2 genotypes in Peru: American (prior to 2001) and American/Asian (2000 to present). American/Asian genotype variants can be classified into two lineages, and these were introduced into Peru from the north (Ecuador, Colombia, and/or Venezuela) and the east (Brazil and Bolivia). American/Asian lineage II replaced lineage I after 2009. We estimate the time to the most recent common ancestor for American/Asian DENV-2 genotype in the Americas was in 1980, and 1984 and 1989 for lineages I and II, respectively. In light of evidence for increased virulence of lineage II of American/Asian DENV-2, our results support the need for continuous monitoring for the emergence of new DENV genotypes that may be associated with severe disease. Copyright © 2013. Published by Elsevier B.V.

  1. A SNP Genotyping Array for Hexaploid Oat

    Directory of Open Access Journals (Sweden)

    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.

  2. Determination of Trichomonas vaginalis Genotypes Using PCR-Restriction Fragment Length Polymorphism (RFLP).

    Science.gov (United States)

    Demirağ, Serpil; Malatyalı, Erdoğan; Ertuğ, Sema; Ertabaklar, Hatice

    2017-12-01

    Trichomonas vaginalis is an anaerobic protozoon and the most common non-viral sexually transmitted pathogen. The present study was designed to determine the genotypes of T. vaginalis using polymerase chain reaction (PCR)-restriction fragment length polymorphism of actin gene. A total of 20 isolates from symptomatic females isolated and cryopreserved at Adnan Menderes University, Research and Training Hospital Parasitology Laboratory were included. The isolates from liquid nitrogen were thawed and grown in trypticase-yeast extract-maltose medium prior to the study. Following nucleic acid extraction, the actin gene of T. vaginalis was amplified using nested PCR and amplicons were concentrated with phenol-chloroform-isoamyl alcohol precipitation. The final products were digested with HindII, MseI, and RsaI and were visualized using agarose gel electrophoresis. Most isolates were actin genotype E (n=9, 45%). The remaining isolates were genotype G (n=7, 35%), genotype N (n=1, 5%), and genotype H (n=1, 5%); two were mixed genotypes of E and H (10%). To the best of our knowledge, this study is the first to provide data on T. vaginalis genotypes in Turkey. However, further studies should be conducted to understand the molecular epidemiology of T. vaginalis at the national and global levels.

  3. Molecular characterization of arabica and Conilon coffee plants genotypes by SSR and ISSR markers

    Directory of Open Access Journals (Sweden)

    Ludymila Brandão Motta

    2014-10-01

    Full Text Available The molecular characterization of ten genotypes of the Coffea arabica plants and of seven genotypes of C. canephora having interesting features for coffee breeding programs was carried to select the parents for breeding. A total of 40 SSR and 29 ISSR primers were used. The primers generated a total of 331 (307 polymorphic and 24 monomorphic bands. Analysis of genetic diversity presented dissimilarity intervals ranging from 0.22 to 0.44 between the Conilon genotypes, from 0.02 to 0.28 between the Arabica genotypes, and from 0.49 to 0.60 between the genotypes of the two species in the joint analysis. Four groups were formed: I = genotypes of C. arabica, II = four progenies of C. canephora, Conilon group, and one non defined C. canephora (Conilon or Robusta, III = one progeny of un-defined C. canephora (Conilon or Robusta and IV = one progeny of C. canephora of Robusta group. The grouping formed was consistent with the origins of each group. High stabilities of the bifurcations were found by bootstrap analysis. The use of molecular markers of the SSR and ISSR types in the diversity study was efficient in distinguishing genotypes between and within C. arabica and C. canephora.

  4. Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes

    Directory of Open Access Journals (Sweden)

    Vaishali P. Waman

    2016-08-01

    Full Text Available Background Dengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae. There are four serotypes of Dengue Virus (DENV-1 to DENV-4, each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages. Methods Complete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches. Results DENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach. Discussion Complete genome-based analysis

  5. Decoding noises in HIV computational genotyping.

    Science.gov (United States)

    Jia, MingRui; Shaw, Timothy; Zhang, Xing; Liu, Dong; Shen, Ye; Ezeamama, Amara E; Yang, Chunfu; Zhang, Ming

    2017-11-01

    Lack of a consistent and reliable genotyping system can critically impede HIV genomic research on pathogenesis, fitness, virulence, drug resistance, and genomic-based healthcare and treatment. At present, mis-genotyping, i.e., background noises in molecular genotyping, and its impact on epidemic surveillance is unknown. For the first time, we present a comprehensive assessment of HIV genotyping quality. HIV sequence data were retrieved from worldwide published records, and subjected to a systematic genotyping assessment pipeline. Results showed that mis-genotyped cases occurred at 4.6% globally, with some regional and high-risk population heterogeneities. Results also revealed a consistent mis-genotyping pattern in gp120 in all studied populations except the group of men who have sex with men. Our study also suggests novel virus diversities in the mis-genotyped cases. Finally, this study reemphasizes the importance of implementing a standardized genotyping pipeline to avoid genotyping disparity and to advance our understanding of virus evolution in various epidemiological settings. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. (II) complexes

    African Journals Online (AJOL)

    activities of Schiff base tin (II) complexes. Neelofar1 ... Conclusion: All synthesized Schiff bases and their Tin (II) complexes showed high antimicrobial and ...... Singh HL. Synthesis and characterization of tin (II) complexes of fluorinated Schiff bases derived from amino acids. Spectrochim Acta Part A: Molec Biomolec.

  7. Joint genome-wide prediction in several populations accounting for randomness of genotypes: A hierarchical Bayes approach. II: Multivariate spike and slab priors for marker effects and derivation of approximate Bayes and fractional Bayes factors for the complete family of models.

    Science.gov (United States)

    Martínez, Carlos Alberto; Khare, Kshitij; Banerjee, Arunava; Elzo, Mauricio A

    2017-03-21

    This study corresponds to the second part of a companion paper devoted to the development of Bayesian multiple regression models accounting for randomness of genotypes in across population genome-wide prediction. This family of models considers heterogeneous and correlated marker effects and allelic frequencies across populations, and has the ability of considering records from non-genotyped individuals and individuals with missing genotypes in any subset of loci without the need for previous imputation, taking into account uncertainty about imputed genotypes. This paper extends this family of models by considering multivariate spike and slab conditional priors for marker allele substitution effects and contains derivations of approximate Bayes factors and fractional Bayes factors to compare models from part I and those developed here with their null versions. These null versions correspond to simpler models ignoring heterogeneity of populations, but still accounting for randomness of genotypes. For each marker loci, the spike component of priors corresponded to point mass at 0 in R S , where S is the number of populations, and the slab component was a S-variate Gaussian distribution, independent conditional priors were assumed. For the Gaussian components, covariance matrices were assumed to be either the same for all markers or different for each marker. For null models, the priors were simply univariate versions of these finite mixture distributions. Approximate algebraic expressions for Bayes factors and fractional Bayes factors were found using the Laplace approximation. Using the simulated datasets described in part I, these models were implemented and compared with models derived in part I using measures of predictive performance based on squared Pearson correlations, Deviance Information Criterion, Bayes factors, and fractional Bayes factors. The extensions presented here enlarge our family of genome-wide prediction models making it more flexible in the

  8. Heterogeneous recombination among Hepatitis B virus genotypes.

    Science.gov (United States)

    Castelhano, Nadine; Araujo, Natalia M; Arenas, Miguel

    2017-10-01

    The rapid evolution of Hepatitis B virus (HBV) through both evolutionary forces, mutation and recombination, allows this virus to generate a large variety of adapted variants at both intra and inter-host levels. It can, for instance, generate drug resistance or the diverse viral genotypes that currently exist in the HBV epidemics. Concerning the latter, it is known that recombination played a major role in the emergence and genetic diversification of novel genotypes. In this regard, the quantification of viral recombination in each genotype can provide relevant information to devise expectations about the evolutionary trends of the epidemic. Here we measured the amount of this evolutionary force by estimating global and local recombination rates in >4700 HBV complete genome sequences corresponding to nine (A to I) HBV genotypes. Counterintuitively, we found that genotype E presents extremely high levels of recombination, followed by genotypes B and C. On the other hand, genotype G presents the lowest level, where recombination is almost negligible. We discuss these findings in the light of known characteristics of these genotypes. Additionally, we present a phylogenetic network to depict the evolutionary history of the studied HBV genotypes. This network clearly classified all genotypes into specific groups and indicated that diverse pairs of genotypes are derived from a common ancestor (i.e., C-I, D-E and, F-H) although still the origin of this virus presented large uncertainty. Altogether we conclude that the amount of observed recombination is heterogeneous among HBV genotypes and that this heterogeneity can influence on the future expansion of the epidemic. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Coxiella burnetii Genotypes in Iberian Wildlife.

    Science.gov (United States)

    González-Barrio, David; Hagen, Ferry; Tilburg, Jeroen J H C; Ruiz-Fons, Francisco

    2016-11-01

    To investigate if Coxiella burnetii, the causative agent of Q fever, genotypes circulating in wildlife are associated with those infecting livestock and humans, multiple-locus variable number tandem-repeat analysis (MLVA-6-marker) was carried out over C. burnetii obtained from red deer (Cervus elaphus), Eurasian wild boar (Sus scrofa), European wild rabbit (Oryctolagus cuniculus), black rat (Rattus rattus), and wood mouse (Apodemus sylvaticus). MLVA typing was performed by using six variable loci in C. burnetii: Ms23, Ms24, Ms27, Ms28, Ms33, and Ms34. The C. burnetii cooperative database from MLVABank 5.0 was employed to compare genotypes found in this study with 344 isolates of diverse origin. Twenty-two genotypes from wildlife and two genotypes from domestic goats were identified. Some MLVA genotypes identified in wildlife or in farmed game clustered with genotypes of human Q fever clinical cases, supporting the idea that humans and wildlife share C. burnetii genotypes. The major part of genotypes identified in coexisting red deer and rabbits clustered according to their host of origin, suggesting host specificity for particular C. burnetii genotypes. These findings provide important insights to understand the epidemiology of C. burnetii at the wildlife-livestock-human interface.

  10. Additional novel Cryptosporidium genotypes in ornamental fishes.

    Science.gov (United States)

    Morine, M; Yang, R; Ng, J; Kueh, S; Lymbery, A J; Ryan, U M

    2012-12-21

    Current knowledge on the prevalence and genotypes of Cryptosporidium in fishes is still limited. This study investigated the prevalence of Cryptosporidium species in 171 ornamental fishes, belonging to 33 species, collected from 8 commercial aquariums around Perth, Western Australia. All samples were screened by nested PCR targeting the 18S rRNA locus. A total of 6 positives were identified by PCR at the 18S locus from 4 different species of fishes (red eye tetra, Moenkhausia sanctaefilomenae; gold gourami, Trichogaster trichopterus; neon tetra, Paracheirodon innesi; goldfish, Carassius auratus auratus), giving an overall prevalence of 3.5% (6/171). Four different genotypes were identified, only one of which has been previously reported in fish; piscine genotype 4 in a neon tetra isolate, a rat genotype III-like isolate in a goldfish, a novel genotype in three isolates from red eye (piscine genotype 7) which exhibited a 3.5% genetic distance from piscine genotype 1 and a piscine genotype 6-like from a gold gourami (1% genetic distance). Further biological and genetic characterisation is required to determine the relationship of these genotypes to established species and strains of Cryptosporidium. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. Genotypic Diversity of Iranian strains of Ralstonia solanacearum

    Directory of Open Access Journals (Sweden)

    Mahsa IZADIYAN

    2011-09-01

    Full Text Available Normal 0 14 false false false During 2007–2009, 170 bacterial isolates were obtained from wilting potato and tomato plants from Iran. Specific polymerase chain reaction (PCR analyses identified all the isolates as Ralstonia solanacearum. Diversity among the Iranian isolates was determined by a study based on biovar determination, pathogenicity, repetitive sequence PCR and phylotype classification. On the basis of  genotypic, phenotypic and pathogenic characteristics two distinct clusters obtained. Cluster I comprised all biovar 2 isolates and cluster II comprised all biovar N2 (2T isolates. Phylotype-specifi c multiplex PCR (pmx-PCR indicated that all biovar 2 and N2 belong to phylotype II. This is the first report of phylotype determination of biovars of R. solanacearum with pmx-PCR in Iran.

  12. Performance of genotype imputations using data from the 1000 Genomes Project.

    Science.gov (United States)

    Sung, Yun Ju; Wang, Lihua; Rankinen, Tuomo; Bouchard, Claude; Rao, D C

    2012-01-01

    Genotype imputations based on 1000 Genomes (1KG) Project data have the advantage of imputing many more SNPs than imputations based on HapMap data. It also provides an opportunity to discover associations with relatively rare variants. Recent investigations are increasingly using 1KG data for genotype imputations, but only limited evaluations of the performance of this approach are available. In this paper, we empirically evaluated imputation performance using 1KG data by comparing imputation results to those using the HapMap Phase II data that have been widely used. We used three reference panels: the CEU panel consisting of 120 haplotypes from HapMap II and 1KG data (June 2010 release) and the EUR panel consisting of 566 haplotypes also from 1KG data (August 2010 release). We used Illumina 324,607 autosomal SNPs genotyped in 501 individuals of European ancestry. Our most important finding was that both 1KG reference panels provided much higher imputation yield than the HapMap II panel. There were more than twice as many successfully imputed SNPs as there were using the HapMap II panel (6.7 million vs. 2.5 million). Our second most important finding was that accuracy using both 1KG panels was high and almost identical to accuracy using the HapMap II panel. Furthermore, after removing SNPs with MACH Rsq Project is still underway, we expect that later versions will provide even better imputation performance. Copyright © 2011 S. Karger AG, Basel.

  13. Multivariate approach in popcorn genotypes using the Ward-MLM strategy: morpho-agronomic analysis and incidence of Fusarium spp.

    Science.gov (United States)

    Kurosawa, R N F; do Amaral Junior, A T; Silva, F H L; Dos Santos, A; Vivas, M; Kamphorst, S H; Pena, G F

    2017-02-08

    The multivariate analyses are useful tools to estimate the genetic variability between accessions. In the breeding programs, the Ward-Modified Location Model (MLM) multivariate method has been a powerful strategy to quantify variability using quantitative and qualitative variables simultaneously. The present study was proposed in view of the dearth of information about popcorn breeding programs under a multivariate approach using the Ward-MLM methodology. The objective of this study was thus to estimate the genetic diversity among 37 genotypes of popcorn aiming to identify divergent groups associated with morpho-agronomic traits and traits related to resistance to Fusarium spp. To this end, 7 qualitative and 17 quantitative variables were analyzed. The experiment was conducted in 2014, at Universidade Estadual do Norte Fluminense, located in Campos dos Goytacazes, RJ, Brazil. The Ward-MLM strategy allowed the identification of four groups as follows: Group I with 10 genotypes, Group II with 11 genotypes, Group III with 9 genotypes, and Group IV with 7 genotypes. Group IV was distant in relation to the other groups, while groups I, II, and III were near. The crosses between genotypes from the other groups with those of group IV allow an exploitation of heterosis. The Ward-MLM strategy provided an appropriate grouping of genotypes; ear weight, ear diameter, and grain yield were the traits that most contributed to the analysis of genetic diversity.

  14. Mutant DD genotype of NFKB1 gene is associated with the susceptibility and severity of coronary artery disease.

    Science.gov (United States)

    Luo, Jun-Yi; Li, Xiao-Mei; Zhou, Yun; Zhao, Qiang; Chen, Bang-Dang; Liu, Fen; Chen, Xiao-Cui; Zheng, Hong; Ma, Yi-Tong; Gao, Xiao-Ming; Yang, Yi-Ning

    2017-02-01

    Nuclear factor κappa B (NF-κB) is an important transcription factor in the development and progression of coronary artery disease (CAD). Recent evidence suggests that -94 ATTG ins/del mutant in the promoter of NFKB1 gene is an essential functional mutant. The present study demonstrated the frequencies of the del/del (DD) genotype and del (D) allele were significantly higher in CAD patients than in controls. CAD patients carrying mutant DD genotype had worse stenosis of diseased coronary arteries compared to those carrying ins/ins (II) or ins/del (ID) genotype. Plasma levels of endothelial nitric oxide synthase (eNOS) were lower, while inflammatory cytokine incnterlukin-6 (IL-6) was higher in CAD patients with DD genotype than those with II or ID genotype (both PDD genotype HUVECs) were more susceptible to H 2 O 2 -induced apoptosis, which was accompanied with a decreased Bcl-2 expression. Further, mutant HUVECs had lower eNOS but higher IL-6 mRNA levels and decreased phosphorylation of eNOS under H 2 O 2 -stimulation (both PDD genotype of NFKB1 gene is associated with the risk and severity of CAD. Dwonregulation of NF-κB p50 subunit leads to exacerbated endothelial dysfunction and apoptosis and enhanced inflammatory response that is the potential underlying mechanism. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. DD genotype of ACE gene in boys: may it be a risk factor for minimal change nephrotic syndrome?

    Science.gov (United States)

    Alasehirli, Belgin; Balat, Ayşe; Büyükçelik, Mithat

    2012-01-01

    It has been shown that angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism affects the circulating and cellular levels of ACE and may be a risk factor in several renal diseases. We analyzed the association of ACE gene I/D polymorphism with the clinical presentation of minimal change nephrotic syndrome (MCNS) in a Turkish child population. This study consisted of 97 children with MCNS and 144 healthy controls. Genotyping of ACE gene was performed using polymerase chain reaction (PCR). The distributions of ACE genotypes were II in 13%, ID in 49%, and DD in 38% in patient group, and 9%, 49%, and 42% in control group, respectively. The frequency of the D allele was 63% and that of the I allele was 37% in patients. There were no relevant differences in the allele frequencies and genotypes of ACE I/D polymorphism between patients and controls. However, DD genotype was higher in boys in children with MCNS (78.4%. vs. 50.0%, p = 0.004). The frequencies of DD genotype and D allele in boys were 7.25 and 2.56 times higher than II genotype and I allele in the patient group, respectively. We suggest that DD genotype in boys may be one of the risk factors for MCNS.

  16. DNA detection and genotypic identification of potentially human-pathogenic microsporidia from asymptomatic pet parrots in South Korea as a risk factor for zoonotic emergence.

    Science.gov (United States)

    Lee, So-Young; Lee, Sung-Seok; Lyoo, Young S; Park, Hee-Myung

    2011-12-01

    We detected and identified genotypes of human-pathogenic microsporidia in fecal samples from 51 asymptomatic captive-bred pet parrots in South Korea. Microsporidia were identified in 8 samples (15.7%); 7 parrots tested positive for Encephalitozoon hellem, and 1 parrot tested positive for both E. hellem and Encephalitozoon cuniculi. In genotypic identifications, E. hellem was present in genotypes 1A and 2B and E. cuniculi was present in genotype II. Pet parrots might be a source of human microsporidian infection.

  17. DNA Detection and Genotypic Identification of Potentially Human-Pathogenic Microsporidia from Asymptomatic Pet Parrots in South Korea as a Risk Factor for Zoonotic Emergence ▿

    Science.gov (United States)

    Lee, So-Young; Lee, Sung-Seok; Lyoo, Young S.; Park, Hee-Myung

    2011-01-01

    We detected and identified genotypes of human-pathogenic microsporidia in fecal samples from 51 asymptomatic captive-bred pet parrots in South Korea. Microsporidia were identified in 8 samples (15.7%); 7 parrots tested positive for Encephalitozoon hellem, and 1 parrot tested positive for both E. hellem and Encephalitozoon cuniculi. In genotypic identifications, E. hellem was present in genotypes 1A and 2B and E. cuniculi was present in genotype II. Pet parrots might be a source of human microsporidian infection. PMID:21965400

  18. Genetic relationship among Musa genotypes revealed by ...

    African Journals Online (AJOL)

    enoh

    2012-03-29

    Mar 29, 2012 ... Selangor, Malaysia. Accepted 4 March, 2011. A banana germplasm was established containing 44 Musa genotypes collected from various locations in Malaysia. To detect ... number of new species in Malaysia has increased recently. ..... markers where nine primers allowed discrimination of all genotypes.

  19. AFLP analysis among Ethiopian arabica coffee genotypes ...

    African Journals Online (AJOL)

    African Journal of Biotechnology ... The genetic relationship of 28 Coffea arabica genotypes from Ethiopia was assessed using 10 Amplified ... All genotypes were independently distinguished and did not cluster according to collection region, demonstrating the presence of coffee genetic resource diversity within each region ...

  20. Phenotype and genotype differentiation between flathead grey ...

    African Journals Online (AJOL)

    This study aimed to study the phenotype and genotype differentiation and to compare the amount of differences in phenotype based on morphometric character indices and meristic counts with the amount of differences in genotype based on random amplified polymorphic DNA (RAPD) fingerprinting between two Mugilidae, ...

  1. Disentangling pooled triad genotypes for association studies.

    Science.gov (United States)

    Shi, Min; Umbach, David M; Weinberg, Clarice R

    2014-09-01

    Association studies that genotype affected offspring and their parents (triads) offer robustness to genetic population structure while enabling assessments of maternal effects, parent-of-origin effects, and gene-by-environment interaction. We propose case-parents designs that use pooled DNA specimens to make economical use of limited available specimens. One can markedly reduce the number of genotyping assays required by randomly partitioning the case-parent triads into pooling sets of h triads each and creating three pools from every pooling set, one pool each for mothers, fathers, and offspring. Maximum-likelihood estimation of relative risk parameters proceeds via log-linear modeling using the expectation-maximization algorithm. The approach can assess offspring and maternal genetic effects and accommodate genotyping errors and missing genotypes. We compare the power of our proposed analysis for testing offspring and maternal genetic effects to that based on a difference approach and that of the gold standard based on individual genotypes, under a range of allele frequencies, missing parent proportions, and genotyping error rates. Power calculations show that the pooling strategies cause only modest reductions in power if genotyping errors are low, while reducing genotyping costs and conserving limited specimens. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

  2. genotype by environment interaction of advanced generation

    African Journals Online (AJOL)

    facilitating a rapid response to selection. This multi-environment trial (MET) used. Additive Main effects and Multiplicative. Interactions (AMMI) and Genotype main effects plus genotype-by-environment interaction (GGE) to (i) determine the adaptability and stability of advanced generation soybean breeding lines in different ...

  3. Genetic relationship among Musa genotypes revealed by ...

    African Journals Online (AJOL)

    Genetic relationship among Musa genotypes revealed by microsatellite markers. NAP Abdullah, GB Saleh, ETS Putra, ZB Wahab. Abstract. A banana germplasm was established containing 44 Musa genotypes collected from various locations in Malaysia. To detect their genetic variation and to rule out duplicates among ...

  4. Genotypically defined lissencephalies show distinct pathologies.

    Science.gov (United States)

    Forman, Mark S; Squier, Waney; Dobyns, William B; Golden, Jeffrey A

    2005-10-01

    Lissencephaly is traditionally divided into 2 distinct pathologic forms: classic (type I) and cobblestone (type II). To date, mutations in 4 genes, LIS1, DCX, RELN, and ARX, have been associated with distinct type I lissencephaly syndromes. Each of these genes has been shown to play a role in normal cell migration, consistent with the presumed pathogenesis of type I lissencephaly. Based on these data, we hypothesized that all forms of radiographically defined type I lissencephaly independent of genotype would be pathologically similar. To test this hypothesis, we examined brains from 16 patients, including 15 lissencephalic patients and one patient with subcortical band heterotopia. Of these 16 patients, 6 had LIS1 deletions, 2 had DCX mutations, and 2 had ARX mutations. In addition, 6 patients had no defined genetic defect, although the patient with subcortical band heterotopia exhibited the same pattern of malformation expected with an XLIS mutation. In all cases, the cortex was thickened; however, the topographic distribution of the cortical pathology varied, ranging from frontal- to occipital-biased pathology to diffuse involvement of the neocortex. Although brains with LIS1 deletions exhibited the classic 4-layer lissencephalic architecture, patients with DCX and ARX mutations each had unique cytoarchitectural findings distinct from LIS1. Furthermore, 2 of the 5 patients with no known genetic defect showed a fourth type of histopathology characterized by a 2-layered cortex. Interestingly, the 2 brains with the fourth type of lissencephaly showed profound brainstem and cerebellar abnormalities. In summary, we identified at least 4 distinct histopathologic subtypes of lissencephaly that stratify with the underlying genetic defect. Based on these data, a new classification for lissencephaly is proposed that incorporates both pathologic and genetic findings.

  5. Angiotensin-converting enzyme genotype and physical performance during US Army basic training.

    Science.gov (United States)

    Sonna, L A; Sharp, M A; Knapik, J J; Cullivan, M; Angel, K C; Patton, J F; Lilly, C M

    2001-09-01

    Prior studies have suggested that angiotensin I-converting enzyme (ACE) genotype correlates with superior physical performance in highly selected populations. This study assessed whether such an association exists in a heterogeneous population. Using polymerase chain reaction techniques, we determined the ACE genotypes (insertion/insertion, deletion/insertion, or deletion/deletion) of 62 male and 85 female US Army recruits. Before and after 8 wk of basic training, we determined peak oxygen uptake and performance on the Army Physical Fitness Test (APFT), which includes standardized measures of muscular endurance (sit-ups, push-ups) and a 2-mile run. Subjects of different ACE genotypes had similar peak oxygen uptakes and APFT scores, both before and after training. Subjects with genotype II had higher APFT scores than others, but the differences were not statistically significant. Furthermore, no ACE genotype group had a performance advantage in analyses that adjusted for baseline fitness. We conclude that ACE genotype does not have a strong effect on aerobic power or muscular endurance in healthy, young American adults drawn from an ethnically and geographically diverse population.

  6. Comparison of Three Different Commercial Kits for the Human Papilloma Virus Genotyping.

    Science.gov (United States)

    Lim, Yong Kwan; Choi, Jee-Hye; Park, Serah; Kweon, Oh Joo; Park, Ae Ja

    2016-11-01

    High-risk type human papilloma virus (HPV) is the most important cause of cervical cancer. Recently, real-time polymerase chain reaction and reverse blot hybridization assay-based HPV DNA genotyping kits are developed. So, we compared the performances of different three HPV genotyping kits using different analytical principles and methods. Two hundred positive and 100 negative cervical swab specimens were used. DNA was extracted and all samples were tested by the MolecuTech REBA HPV-ID, Anyplex II HPV28 Detection, and HPVDNAChip. Direct sequencing was performed as a reference method for confirming high-risk HPV genotypes 16, 18, 45, 52, and 58. Although high-level agreement results were observed in negative samples, three kits showed decreased interassay agreement as screening setting in positive samples. Comparing the genotyping results, three assays showed acceptable sensitivity and specificity for the detection of HPV 16 and 18. Otherwise, various sensitivities showed in the detection of HPV 45, 52, and 58. The three assays had dissimilar performance of HPV screening capacity and exhibited moderate level of concordance in HPV genotyping. These discrepant results were unavoidable due to difference in type-specific analytical sensitivity and lack of standardization; therefore, we suggested that the efforts to standardization of HPV genotyping kits and adjusting analytical sensitivity would be important for the best clinical performance. © 2016 Wiley Periodicals, Inc.

  7. Evidence of independent evolution of genotype XIII Newcastle disease viruses in India.

    Science.gov (United States)

    Das, Moushumee; Kumar, Sachin

    2017-04-01

    Despite the prevalence of Newcastle disease virus (NDV) outbreaks in India through the decades, there has been little genetic characterisation of the virulent strains circulating in Northeast India. In 2014, a poultry farm in the Kamrup district of Assam reported an ND outbreak. In this study, genetic analysis and clinicopathological tests showed the virulent nature of the isolate Kamrup. Based on prudent classification criteria, the virulent strain Kamrup was found to be most closely related to members of genotype XIII of class II NDV. A phylogenetic analysis of NDV strains suggested three sub-genotypes: XIIIa, XIIIb and XIIIc. NDV strain Kamrup belonged to sub-genotype XIIIc. Sub-genotype XIIIc isolates were similar to the 1982 isolate from cockatoo and appeared to have evolved parallel to the preceding genotype XIII viruses circulating in India. The high genetic diversity and frequency of mutations observed in the envelope glycoproteins of strain Kamrup demonstrate the evolution of the pandemic genotype XIII NDV in India, which further undermines and complicates of NDV management in India.

  8. ACE DD genotype is unfavorable to Korean short-term muscle power athletes.

    Science.gov (United States)

    Kim, C-H; Cho, J-Y; Jeon, J Y; Koh, Y G; Kim, Y-M; Kim, H-J; Park, M; Um, H-S; Kim, C

    2010-01-01

    The purpose of this study was to test the hypothesis that the ACE DD genotype is unfavorably associated with the ultimate power-oriented performance. To test the hypothesis we recruited a total of 848 subjects including 55 international level power-oriented athletes (High-performance), 100 national level power-oriented athletes (Mid-performance) and 693 healthy controls (Control) in Korea. Then the distributions of ACE polymorphism throughout these groups were analyzed. As a result, there was a gradual decrease of frequencies of the DD genotype with advancing levels of performance (Control vs. Mid-performance vs. High-performance=17.2% vs. 10.0% vs. 5.5%, p=0.002). Also, the frequencies of D allele decreased gradually with advancing levels of performance (Control vs. Mid-performance vs. High-performance=42.6% vs. 35.0% vs. 30.9%, pDD genotype and the D allele. This finding gave 3.83 times lower probability of success in power-oriented sports for individuals with the DD genotype than those with the II+ ID genotype. In conclusion, these results indicate that Korean power-oriented athletes with a lower frequency of the DD genotype had a lower probability of success in power-oriented sports. Georg Thieme Verlag KG Stuttgart, New York.

  9. [Evaluation of genotyping of human papilomavirus by a new DNA liquid chip based on Luminex XMAP].

    Science.gov (United States)

    Deng, Xiao-mei; Liu, Min; Zheng, Gui-xi; Wang, Chuan-xin; Zhang, Jian; Li, Wei

    2009-12-01

    To evaluate the diagnostic value of Luminex XMAP liquid chip for HPV detection. Detect HPV DNA with the liquid chip and HC II in 264 cases, including 231 of cervical cancer and 33 of cervical scrapes. The accordance of two methods were compared and DNA sequencing was performed in conflicting samples and single (infection samples. There is an excellent agreement between the methods. The overall incidence of HPV was 82.95%, the most common genotypes were HPV 16, 52, 58, 18, 11, 31, 6, 39, 33, 56, 70. Among all the positive types, 117 were single type and 102 were multiple types, and 87.43% were high-risk HPV genotypes and 12.57% were low-risk genotypes. Based on the criteria of histology and pathology, the sensitivity, specificity, positive and negative-predictive value of HPV liquid chip and HC II for detecting all cases of CIN II, III and carcinomas were respectively 93.07%, 87.88%, 98.17%, 64.44% and 94.81%, 87.88%, 98.21%, 70.73%. The common types of HPV infection are 16, 52, 58, 18, 11, 6, 56 and 31. Multiplex HPV genotyping by Luminex XMAP liquid chip appears to be highly suitable for diagnostic screening and large-scale epidemiological studies.

  10. High prevalence of ACE DD genotype among north Indian end stage renal disease patients

    Directory of Open Access Journals (Sweden)

    Pandirikkal Baburajan Vinod

    2006-10-01

    Full Text Available Abstract Background The Renin-Angiotensin system (RAS is a key regulator of both blood pressure and kidney functions and their interaction. In such a situation, genetic variability in the genes of different components of RAS is likely to contribute for its heterogeneous association in the renal disease patients. Angiotensin converting enzyme-1 (ACE-1 is an important component of RAS which determines the vasoactive peptide Angiotensin-II. Methods In the present study, we have investigated 127 ESRD patients and 150 normal healthy controls from north India to deduce the association between ACE gene polymorphism and ESRD. The inclusion criteria for patients included a constantly elevated serum creatinine level above normal range (ranging from 3.4 to 15.8 and further the patients were recommended for renal transplantation. A total of 150 normal healthy controls were also genotyped for ACE I/D polymorphism. The criterion of defining control sample as normal was totally based on the absence of any kidney disease determined from the serum creatinin level. Genotyping of ACE I/D were assayed by polymerase chain reaction (PCR based DNA amplification using specific flanking primers Based on the method described elsewhere. Results The difference of DD and II genotypes was found highly significant among the two groups (p = 0.025; OR = 3.524; 95%CI = 1.54-8.07. The combined genotype DD v/s ID+II comparison validated that DD genotype is a high risk genotype for ESRD (p = 0.001; OR = 5.74; 95%CI limit = 3.4-8.5. However, no correlation was obtained for different biochemical parameters of lipid profile and renal function among DD and non DD genotype. Interestingly, ~87% of the DD ESRD patients were found hypertensive in comparison to the 65% patients of non DD genotype Conclusion Based on these observations we conclude that ACE DD genotype implicate a strong possible role in the hypertensive state and in renal damage among north Indians. The study will help in

  11. Copper (II)

    African Journals Online (AJOL)

    CLEMENT O BEWAJI

    ABSTRACT: A Schiff base was prepared from the reaction of 2 - amino - 3 – methylbutanoic acid and 2, 4 - pentanedione. The reaction of the prepared Schiff base with ethanolic solution of copper (II) chloride formed diaquo bis( N – 2 – amino – 3 - methylbutyl - 2, 4 - pentanedionato) copper (II) complex. The Schiff base is ...

  12. Seroprevalence and genotypes of Toxoplasma gondii isolated from pigs intended for human consumption in Liaoning province, northeastern China.

    Science.gov (United States)

    Wang, Dawei; Liu, Yan; Jiang, Tiantian; Zhang, Guoxin; Yuan, Gaoming; He, Jianbin; Su, Chunlei; Yang, Na

    2016-04-29

    Genetic information for Toxoplasma gondii isolates from pigs in eastern, south, and southwestern regions of China has been reported previously. However, there are no data from pigs in the northeastern area of the country. To better understand the epidemiology of T. gondii, we determined the seroprevalence and genotypes of T. gondii from pigs slaughtered for human consumption in Liaoning province, northeastern China. Out of 2063 pigs examined, 233 (11.26%) were seropositive for T. gondii by the modified agglutination test (MAT), and viable parasites were isolated by bioassay in mice from 23 (9.87%) of the 233 seropositive pigs. Fifteen out of 23 isolates were genotyped using 10 PCR-restriction fragment length polymorphism (RFLP) genetic markers including SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico. One isolate was identified as ToxoDB genotype #3 (type II-variant), and one was genotype #1 or #3. The other 13 isolates were ToxoDB #9 (type Chinese 1). To our knowledge, this is the first report of T. gondii isolation and genotyping from pigs in northeastern China. This study indicates that pigs are a potential source for transmission of T. gondii to humans, therefore poses a potential public health concern. The genotyping results revealed the presence of genotype Chinese 1 in northeastern China, enriching the scope of T. gondii genotypes distribution in eastern Asia.

  13. 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

  14. The effect of serum angiotensin II and angiotensin II type 1 receptor ...

    African Journals Online (AJOL)

    Objective: To measure serum Ang II and the frequency of AT1 receptor CC genotype among a group of Egyptian patients with pediatric onset lupus nephritis (pLN). Methods: This is a case-control cross sectional study which included 24 patients with pLN and 24 age and sex-matched healthy subjects as controls. Clinical ...

  15. Response of Different Genotypes of Faba Bean Plant to Drought Stress

    Directory of Open Access Journals (Sweden)

    Manzer H. Siddiqui

    2015-05-01

    Full Text Available Drought stress is one of the major abiotic stresses that are a threat to crop production worldwide. Drought stress impairs the plants growth and yield. Therefore, the aim of the present experiment was to select the tolerant genotype/s on the basis of moprpho-physiological and biochemical characteristics of 10 Vicia faba genotypes (Zafar 1, Zafar 2, Shebam, Makamora, Espan, Giza Blanka, Giza 3, C4, C5 and G853 under drought stress. We studied the effect of different levels of drought stress i.e., (i normal irrigation (ii mild stress (iii moderate stress, and (iv severe stress on plant height (PH plant−1, fresh weight (FW and dry weight (DW plant−1, area leaf−1, leaf relative water content (RWC, proline (Pro content, total chlorophyll (Total Chl content, electrolyte leakage (EL, malondialdehyde (MDA, hydrogen peroxide (H2O2 content, and activities of catalase (CAT, peroxidase (POD and superoxide dismutase (SOD of genotypes of faba bean. Drought stress reduced all growth parameters and Total Chl content of all genotypes. However, the deteriorating effect of drought stress on the growth performance of genotypes “C5” and “Zafar 1” were relatively low due to its better antioxidant enzymes activities (CAT, POD and SOD, and accumulation of Pro and Total Chl, and leaf RWC. In the study, genotype “C5” and “Zafar 1” were found to be relatively tolerant to drought stress and genotypes “G853” and “C4” were sensitive to drought stress.

  16. Hepatitis C virus genotypes in Tirana, Albania.

    Science.gov (United States)

    Haldeda, Migena; Baume, Julien; Tamalet, Catherine; Bizhga, Melpomeni; Colson, Philippe

    2014-01-01

    Hepatitis C virus (HCV) infection is a worldwide concern. Knowledge of the HCV genotype is clinically important because it predicts the rate of response to therapy and guides the treatment duration. Moreover, it allows molecular epidemiology to be performed. To our knowledge, the prevalence of HCV genotypes has been assessed only once in Albania, using a line probe genotyping assay. We determined HCV genotypes by population sequencing of HCV-infected patients in Tirana, Albania. HCV genotype and sequence analyses were performed for serum samples collected from January 2011 through May 2012 from 61 HCV-seropositive patients using population sequencing of the NS3 protease gene and alternatively the NS5b gene and the 5' untranslated region (UTR). HCV RNA was retrieved from the blood samples of 50 patients. The HCV NS3 protease gene was sequenced for 28 patients and NS5b and/or 5'UTR fragments were sequenced for an additional 22 patients. The predominant genotype was 1b in 25 patients (50%), followed by genotypes 2c, 4a, 3a, and 1a in 18%, 14%, 8%, and 6% of cases, respectively. Best matches for these HCV RNAs in GenBank were obtained in different countries worldwide. One NS3 protease naturally harbored an amino acid conferring minor drug resistance to newly available HCV protease inhibitors. In conclusion, HCV-1b was predominant in the present Albanian population, as in southeastern Europe. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

  17. Structural properties of genotype-phenotype maps.

    Science.gov (United States)

    Ahnert, S E

    2017-07-01

    The map between genotype and phenotype is fundamental to biology. Biological information is stored and passed on in the form of genotypes, and expressed in the form of phenotypes. A growing body of literature has examined a wide range of genotype-phenotype (GP) maps and has established a number of properties that appear to be shared by many GP maps. These properties are 'structural' in the sense that they are properties of the distribution of phenotypes across the point-mutation network of genotypes. They include: a redundancy of genotypes, meaning that many genotypes map to the same phenotypes, a highly non-uniform distribution of the number of genotypes per phenotype, a high robustness of phenotypes and the ability to reach a large number of new phenotypes within a small number of mutational steps. A further important property is that the robustness and evolvability of phenotypes are positively correlated. In this review, I give an overview of the study of GP maps with particular emphasis on these structural properties, and discuss a model that attempts to explain why these properties arise, as well as some of the fundamental ways in which the structure of GP maps can affect evolutionary outcomes. © 2017 The Author(s).

  18. Helicobacter pylori Genotypes May Determine Gastric Histopathology

    Science.gov (United States)

    Nogueira, Cristina; Figueiredo, Céu; Carneiro, Fátima; Taveira Gomes, António; Barreira, Raul; Figueira, Paulo; Salgado, Céu; Belo, Luis; Peixoto, António; Bravo, Juan C.; Bravo, Luis E.; Realpe, Jose L.; Plaisier, Anton P.; Quint, Wim G. V.; Ruiz, Bernardo; Correa, Pelayo; van Doorn, Leen-Jan

    2001-01-01

    The outcome of Helicobacter pylori infection has been associated with specific virulence-associated bacterial genotypes. The present study aimed to investigate the gastric histopathology in Portuguese and Colombian patients infected with H. pylori and to assess its relationship with bacterial virulence-associated vacA, cagA, and iceA genotypes. A total of 370 patients from Portugal (n = 192) and Colombia (n = 178) were studied. Corpus and antrum biopsy specimens were collected from each individual. Histopathological features were recorded and graded according to the updated Sydney system. H. pylori vacA, cagA, and iceA genes were directly genotyped in the gastric biopsy specimens by polymerase chain reaction and reverse hybridization. Despite the significant differences between the Portuguese and Colombian patient groups, highly similar results were observed with respect to the relation between H. pylori genotypes and histopathology. H. pylori vacA s1, vacA m1, cagA+ genotypes were significantly associated with a higher H. pylori density, higher degrees of lymphocytic and neutrophilic infiltrates, atrophy, the type of intestinal metaplasia, and presence of epithelial damage. The iceA1 genotype was only associated with epithelial damage in Portuguese patients. These findings show that distinct H. pylori genotypes are strongly associated with histopathological findings in the stomach, confirming their relevance for the development of H. pylori-associated gastric pathology. PMID:11159201

  19. Trade practices are main factors involved in the transmission of viral haemorrhagic septicaemia

    DEFF Research Database (Denmark)

    Reichert, M.; Matras, M.; Skall, Helle Frank

    2013-01-01

    Viral haemorrhagic septicaemia (VHS), caused by the novirhabdovirus viral haemorrhagic septicaemia virus (VHSV), causes significant economic problems to European rainbow trout, Oncorhynchus mykiss (Walbaum), production. The virus isolates can be divided into four distinct genotypes with additiona...... cause of virus transmission appears to be movement of fish. At least in Polish circumstances trading practices appear to have significant impact on spreading of VHSV infection....

  20. Phenotypic and genotypic diversity of organisms previously classified as maltose positive Pasteurella multocida.

    Science.gov (United States)

    Petersen, K D; Christensen, J P; Bisgaard, M

    1998-07-01

    Fifteen isolates tentatively classified as maltose positive Pasteurella multocida have been characterized in 79 biochemical tests and by ribotyping using HindIII and HpaII for digestion of DNA. Phenotypic and genotypic results were analysed using the computer programmes NTSYS and GelCompar, respectively. Two strains were classified as maltose positive P. multocida ssp. multocida while six strains were classified as maltose positive P. multocida ssp. septica. The remaining strains clustered with P. volantium and P. gallinarum, but remained unclassified. With the exception of a single isolate correlation was observed between phenotypic and genotypic results. The unclassified isolates which represented three different sources were heterogenous according to both phenotypic and genotypic results. The findings obtained support the 16S rRNA sequencing results indicating that the genus Pasteurella sensu stricto might represent two or more genera.

  1. 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.

  2. in common bean ( Phaseolus Vulgaris L.) genotypes

    African Journals Online (AJOL)

    Bako, Boshe and Gute) and years (2004 – 2005) with the objective of identifying high yielding, stable and adaptable varieties for western parts of Ethiopia. Regression and AMMI analysis were computed to identify stable genotypes across ...

  3. (AMMI) and genotype by environment interaction

    African Journals Online (AJOL)

    SARAH

    2014-04-30

    , stable and high yielding genotypes under varying environmental conditions prior to release as a cultivar is the first and foremost steps for plant breedingr and this has direct bearing on the adoption of the variety, ...

  4. ApoE (Apolipoprotein E) Genotyping

    Science.gov (United States)

    ... Questions Related Content View Sources Formal Name Apolipoprotein E Genotyping This article was last reviewed on March ... They Mean . What is being tested? Apolipoprotein (Apo) E is produced under the direction of the APOE ...

  5. 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...

  6. 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,...

  7. Micropropagation of Jatropha curcas superior genotypes and ...

    African Journals Online (AJOL)

    Micropropagation of Jatropha curcas superior genotypes and evaluation of clonal fidelity by target region amplification polymorphism (TRAP) molecular marker and flow cytometry. MC Franco, DA Marques, WJ Siqueira, RR Latado ...

  8. 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...

  9. 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....

  10. Selection of Gossypium hirsutum genotypes for interspecific ...

    African Journals Online (AJOL)

    FORRESTER

    hybridization. INTRODUCTION. Tetraploid upland cotton, Gossypium hirsutum L., is comprised of over 90% of global cotton production (Zhao et al., 2015). Cultivated G. hirsutum genotypes are considered to have a narrow genetic base, due in part to.

  11. 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.......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....

  12. Pancreaticobiliary cancers with deficient methylenetetrahydrofolate reductase genotypes.

    Science.gov (United States)

    Matsubayashi, Hiroyuki; Skinner, Halcyon G; Iacobuzio-Donahue, Christine; Abe, Tadayoshi; Sato, Norihiro; Riall, Taylor Sohn; Yeo, Charles J; Kern, Scott E; Goggins, Michael

    2005-08-01

    Methyl group deficiency might promote carcinogenesis by inducing DNA breaks and DNA hypomethylation. We hypothesized that deficient methylenetetrahydrofolate reductase (MTHFR) genotypes could promote pancreatic cancer development. First, we performed a case-control study of germline MTHFR polymorphisms (C677T, A1298C) in 303 patients with pancreatic cancer and 305 matched control subjects. Pancreatic neoplasms frequently lose an MTHFR allele during tumorigenesis; we hypothesized that such loss could promote carcinogenesis. We therefore evaluated the cancer MTHFR genotypes of 82 patients with pancreaticobiliary cancers and correlated them to genome-wide measures of chromosomal deletion by using 386 microsatellite markers. Finally, MTHFR genotypes were correlated with global DNA methylation in 68 cancer cell lines. Germline MTHFR polymorphisms were not associated with an increased likelihood of having pancreatic cancer. Fractional allelic loss (a measure of chromosomal loss) trended higher in cancers with 677T genotypes than in cancers with other genotypes (P = .055). Among cancers with loss of an MTHFR allele, cancers with 677T MTHFR alleles had more deletions at folate-sensitive fragile sites (36.9%) and at tumor suppressor gene loci (68.5%) than 677C cancers (28.7% and 47.8%, P = .079 and .014, respectively). LINE1 methylation was lower in cancers with less functional 677T/TT genotypes (24.4%) than in those with 677CT (26.0%) and CC/C genotypes (32.5%) (P = .014). Cancers with defective MTHFR genotypes have more DNA hypomethylation and more chromosomal losses. Deficient MTHFR function due to loss of an MTHFR allele by an evolving neoplasm might, by promoting chromosomal losses, accelerate cancer development.

  13. Effect of Mahanarva fimbriolata (Hemiptera: Cercopidae) Attack on Photosynthetic Parameters of Sugarcane Genotypes of Contrasting Susceptibility.

    Science.gov (United States)

    Soares, Bruno Oliveira; Chaves, Vinicius de Vicente; Tomaz, Adriano Cirino; Kuki, Kacilda Naomi; Peternelli, Luiz Alexandre; Barbosa, Márcio Henrique Pereira

    2017-12-05

    The aim of this study was to compare the effect of spittlebug Mahanarva fimbriolata Stål (Hemiptera: Cercopidae) on photosynthetic parameters of both a susceptible (SP81-3250) and a resistant (H.Kawandang) sugarcane genotype. In the first assay, the susceptibility level of genotypes to spittlebug was confirmed by comparing damage score and chlorophyll content of the plants. In the second assay, the effect of spittlebug nymphs on photosynthetic characteristics was assessed using the following parameters: Net photosynthetic rate (A), carboxylation efficiency (A/Ci), stomata conductance (gS), transpiration (E), electron transport rate (ETR), maximum quantum yield of Photosystem 2 (PSII) (FV/FM), effective quantum yield (Y(II)), photochemical quenching (Y(NPQ)), and nonphotochemical quenching (Y(NO)). Spittlebug nymphs affected the photosynthetic process of the susceptible genotype SP81-3250 by decreasing the Chl content, ETR, FV/FM, and Y(II). However, this genotype was able to maintain A probably due to its ability to maintain stomata aperture, increase the carboxylation efficiency of Rubisco, and dissipate excess energy through the xanthophyll cycle, as Y(NPQ) increased under the spittlebug attack. On the other hand, the spittlebug did not affect Chl content and FV/FM of the H.Kawandang genotype. Furthermore, H.Kawandang increased A to compensate for the sink demand by the spittlebug by increasing stomatal aperture and carboxylation efficiency and increasing efficiency of the photochemical apparatus in converting light energy into chemical products. We can conclude that the feeding habits of spittlebug nymphs have different impacts on photosynthesis of susceptible and resistant sugarcane genotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Sequence-based in silico analysis of well studied Hepatitis C Virus epitopes and their variants in other genotypes (particularly genotype 5a against South African human leukocyte antigen backgrounds

    Directory of Open Access Journals (Sweden)

    Prabdial-Sing Nishi

    2012-12-01

    Full Text Available Abstract Background Host genetics influence the outcome of HCV disease. HCV is also highly mutable and escapes host immunity. HCV genotypes are geographically distributed and HCV subtypes have been shown to have distinct repertoires of HLA-restricted viral epitopes which explains the lack of cross protection across genotypes observed in some studies. Despite this, immune databases and putative epitope vaccines concentrate almost exclusively on HCV genotype 1 class I-epitopes restricted by the HLA-A*02 allele. While both genotype and allele predominate in developed countries, we hypothesise that HCV variation and population genetics will affect the efficacy of proposed epitope vaccines in South Africa. This in silico study investigates HCV viral variability within well-studied epitopes identified in genotype 1 and uses algorithms to predict the immunogenicity of their variants from other less studied genotypes and thus rate the most promising vaccine candidates for the South African population. Six class I- and seven class II- restricted epitope sequences within the core, NS3, NS4B and NS5B regions were compared across the six HCV genotypes using local genotype 5a sequence data together with global data. Common HLA alleles in the South African population are A30:01, A02:01, B58:02, B07:02; DRB1*13:01 and DRB1*03:01. Epitope binding to 13 class I- and 8 class –II alleles were described using web-based prediction servers, Immune Epitope Database, (IEDB and Propred. Online population coverage tools were used to assess vaccine efficacy. Results Despite the homogeneity of genotype 1 and genotype 5 over the epitopes, there was limited promiscuity to local HLA-alleles.Host differences will make a putative vaccine less effective in South Africa. Of the 6 well-characterized class I- epitopes, only 2 class I- epitopes were promiscuous and 3 of the 7 class-II epitopes were better conserved and promiscuous. By fine tuning the putative vaccine using an

  15. Genotype-specific interactions between parasitic arthropods.

    Science.gov (United States)

    Orsucci, M; Navajas, M; Fellous, S

    2017-03-01

    Despite the ubiquity of coinfection, we know little of the effects of intra-specific genetic variability on coinfection by distinct parasite species. Here we test the hypothesis that parasite multiplication depends on the combination of parasite genotypes that coinfect the host (that is Genotype.parasite × Genotype.parasite interaction). To that aim, we infected tomato leaves with the ecto-parasitic mites Tetranychus urticae and Tetranychus evansi. We tested all possible combinations between four T. urticae and two T. evansi populations sampled on different hosts or localities. There was no universal (that is genotype-independent) effect of coinfection on mite multiplication; in many cases the two species had no effect on each other. However, several combinations of T. evansi and T. urticae populations led to elevated T. evansi numbers. Similarly, T. urticae reproduction largely depended on the interaction between T. urticae and T. evansi populations. This evidence for genotype-by-genotype interaction between coinfecting parasites indicates that the effect of coinfection on parasite epidemiology and evolution may vary in space according to the genetic composition of local parasite populations; it further suggests the possibility of coevolution between parasites species that share the same hosts.

  16. Monitoring coyote population dynamics by genotyping faeces.

    Science.gov (United States)

    Prugh, L R; Ritland, C E; Arthur, S M; Krebs, C J

    2005-04-01

    Reliable population estimates are necessary for effective conservation and management, and faecal genotyping has been used successfully to estimate the population size of several elusive mammalian species. Information such as changes in population size over time and survival rates, however, are often more useful for conservation biology than single population estimates. We evaluated the use of faecal genotyping as a tool for monitoring long-term population dynamics, using coyotes (Canis latrans) in the Alaska Range as a case study. We obtained 544 genotypes from 56 coyotes over 3 years (2000-2002). Tissue samples from all 15 radio-collared coyotes in our study area had > or = 1 matching faecal genotypes. We used flexible maximum-likelihood models to study coyote population dynamics, and we tested model performance against radio telemetry data. The staple prey of coyotes, snowshoe hares (Lepus americanus), dramatically declined during this study, and the coyote population declined nearly two-fold with a 1(1/2)-year time lag. Survival rates declined the year after hares crashed but recovered the following year. We conclude that long-term monitoring of elusive species using faecal genotyping is feasible and can provide data that are useful for wildlife conservation and management. We highlight some drawbacks of standard open-population models, such as low precision and the requirement of discrete sampling intervals, and we suggest that the development of open models designed for continuously collected data would enhance the utility of faecal genotyping as a monitoring tool.

  17. Lactose intolerance: lactose tolerance test versus genotyping.

    Science.gov (United States)

    Ridefelt, Peter; Håkansson, Lena D

    2005-07-01

    Adult lactose intolerance, which affects the majority of the population in the world, has been associated with a single nucleotide polymorphism, C-13910T, located upstream of the lactase gene. Adult patients undergoing lactose tolerance tests with lactose challenge and plasma glucose measurements were included in the study comprising 44 Swedes and 7 non-Swedish individuals. A real-time PCR method was established for the genotyping. Out of 51 patients 48 had concordant results on genotyping and lactose tolerance tests, e.g. -13910T/T and -13910C/T genotypes had high glucose elevations. All patients with the heterozygous genotype, -13910C/T, had high glucose elevations, and no gene-dose relationship was observed when comparing maximal glucose increases for cases with -13910C/T and -13910T/T genotypes. Genotyping could replace lactose challenge as a first-stage screening test in adults of European descent, but should be used together with tolerance tests in children and patients where secondary lactose intolerance is suspected.

  18. Genetic heterogeneity of Usher syndrome type II.

    Science.gov (United States)

    Pieke Dahl, S; Kimberling, W J; Gorin, M B; Weston, M D; Furman, J M; Pikus, A; Möller, C

    1993-01-01

    Usher syndrome is an autosomal recessive disorder characterised by retinitis pigmentosa and congenital sensorineural hearing loss. A gene for Usher syndrome type II (USH2) has been localised to chromosome 1q32-q41. DNA from a family with four of seven sibs affected with clinical characteristics of Usher syndrome type II was genotyped using markers spanning the 1q32-1q41 region. These included D1S70 and D1S81, which are believed to flank USH2. Genotypic results and subsequent linkage analysis indicated non-linkage of this family to these markers. The A test analysis for heterogeneity with this family and 32 other Usher type II families was statistically significant at p < 0.05. Further clinical evaluation of this family was done in light of the linkage results to determine if any phenotypic characteristics would allow for clinical identification of the unlinked type. No clear phenotypic differences were observed; however, this unlinked family may represent a previously unreported subtype of Usher type II characterised by a milder form of retinitis pigmentosa and mild vestibular abnormalities. Heterogeneity of Usher syndrome type II complicates efforts to isolate and clone Usher syndrome genes using linkage analysis and limits the use of DNA markers in early detection of Usher type II. Images PMID:7901420

  19. 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

  20. Estrogen receptor alpha XbaI GG genotype was associated with severe preeclampsia.

    Science.gov (United States)

    Salimi, Saeedeh; Farajian-Mashhadi, Farzaneh; Tabatabaei, Ehsan; Shahrakipour, Mahnaz; Yaghmaei, Minoo; Mokhtari, Mojgan

    2017-01-01

    Estrogen receptor-α (ERα) plays an essential role in the adaptation of increased uterine blood flow during gestation. Therefore, ERα gene could be a possible candidate for preeclampsia (PE) susceptibility. In current study we aimed to investigate the association of the ERα gene polymorphisms and PE in an Iranian population. A total of 192 pregnant women with PE and 186 normotensive women were genotyped for ERα gene (PvuII and XbaI) polymorphisms by polymerase chain reaction-restriction fragment length polymorphism method. The frequencies of alleles and genotypes of ERα PvuII and XbaI polymorphisms were not different between PE and normotensive control women. However, higher frequency of GG genotype was observed in women with severe PE compared to mild PE (OR, 1.8 [95% CI, 1.1 to 3]; p = 0.02) and in severe PE compared to normotensive women [OR = 1.8 (1.1-3), p = 0.02] after adjusting for age, ethnicity, and primiparity. The GG genotype of ERα XbaI polymorphism could be a genetic risk factor for PE predisposition.

  1. Human Cytomegalovirus and Epstein-Barr Virus Genotypes in Apical Periodontitis Lesions.

    Science.gov (United States)

    Jakovljevic, Aleksandar; Andric, Miroslav; Knezevic, Aleksandra; Soldatovic, Ivan; Nikolic, Nadja; Karalic, Danijela; Milasin, Jelena

    2015-11-01

    Different genotypes of human cytomegalovirus (HCMV) and Epstein-Barr virus (EBV) possess specific pathogenic abilities because of various interactions with the host's immune system and differences in cell tropism. The aim of this study was to determine the distribution of HCMV and EBV genotypes in apical periodontitis lesions in relation to their clinical and histopathologic features. One hundred samples of apical periodontitis lesions and 25 control samples (healthy pulp tissue) were collected. The presence of HCMV glycoprotein B (gB) and EBV nuclear antigen-2 genotypes was analyzed by nested polymerase chain reaction and restriction fragment length polymorphisms analysis. EBV and HCMV were detected in apical periodontitis lesions at significantly higher frequencies than in healthy pulp controls (P = .020 and P = .020, respectively). HCMV gB type II was significantly more frequent compared with gB type I in the examined groups (P = .036). No HCMV gB type III or IV products were found. In both periapical lesions and controls, EBV-1 occurred more often compared with EBV-2 (P = .001). Dual EBV and HCMV coinfection was more frequently detected in large-size periapical lesions (P = .038). Both HCMV and EBV are associated with inflammatory processes of periapical bone destruction. HCMV gB type II and EBV-1 are the most prevalent genotypes in apical periodontitis lesions. Copyright © 2015 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  2. Isolation and RFLP genotyping of Toxoplasma gondii from the gray wolf (Canis lupus).

    Science.gov (United States)

    Dubey, J P; Choudhary, S; Ferreira, L R; Kwok, O C H; Butler, E; Carstensen, M; Yu, L; Su, C

    2013-11-08

    Little is known of the genetic diversity of Toxoplasma gondii circulating in wildlife. In the present study feral gray wolves (Canis lupus) from Minnesota were examined for T. gondii infection. Antibodies to T. gondii were detected in 130 (52.4%) of 248 wolves tested by the modified agglutination test (cut-off titer of 25). Tissues (hearts, brains or both) of 109 wolves were bioassayed in mice for protozoal isolation. Viable T. gondii was isolated from 25 and the isolates were further propagated in cell culture. T. gondii DNA from these isolates was characterized using 10 PCR-RFLP markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico). Four genotypes were detected. Twenty-one isolates were Type 12 (ToxoDB PCR-RFLP genotype #5), 2 were Type II clonal (ToxoDB #1), 1 was Type II variant (ToxoDB #3), and 1 was a new genotype designated as ToxoDB genotype #219. Published by Elsevier B.V.

  3. Genotyping of Pseudomonas aeruginosa strains isolated from burn patients by RAPD-PCR.

    Science.gov (United States)

    Nanvazadeh, Fatemeh; Khosravi, Azar Dokht; Zolfaghari, Mohammad Reza; Parhizgari, Najmeh

    2013-11-01

    Pseudomonas aeruginosa is one of the important causes of nosocomial infections that easily gains resistance to many antibiotics. This opportunistic pathogen is a major health hazard particularly in immunodeficient patients, patients in intensive care units (ICU) and burn units with life threatening outcome. The bacterium may be originated from different or common sources, and comprises a high colonization and transmission capacity. The aim of present study was to investigate the genotypic variation of Pseudomonas aeroginosa strains isolated from burn patients by using Random Amplified Polymorphic DNA (RAPD) method. Totally 70 clinical samples were collected from burn patients in Taleghani Burn Hospital of Ahvaz. Fifty out of total samples were positive for P. aeruginosa by application of conventional culture and biochemical identification tests. DNA was extracted from the isolates and the RAPD-PCR method was applied to the DNA extracts according to standard method using a short single primer of 272. The technique created repetitive electrophoresis patterns which was used for genotypic differentiation. RAPD-PCR, created 9 genotypic profiles designated as I-IX with base pair length ranging from 180 to 2700. Each genotype showed between 3 and 6 different weight DNA bands. Genotype I was the most prevalent, identified in 10 bacterial isolates (20%). Genotypes I, II and VI were mostly common in patients with more severe burn, and were mainly isolated from wound and blood samples obtained from the same patients. In present study, we found RAPD-PCR technique as a useful tool for investigation of the genetic variation among P. aeruginosa strains. This is a rapid, low cost, genotypic method with high discriminatory power. The results could assist to screen for the original of infection caused by this organism with subsequent control of colonization and transmission. Copyright © 2013 Elsevier Ltd and ISBI. All rights reserved.

  4. New coxsackievirus B4 genotype circulating in Inner Mongolia Autonomous Region, China.

    Directory of Open Access Journals (Sweden)

    Xiaoling Tian

    Full Text Available Hand, foot, and mouth disease (HFMD surveillance was initiated in the Inner Mongolia Autonomous Region of China in 2007, a crucial scrutiny for monitoring the prevalence of enterovirus serotypes associated with HFMD patients. However, this surveillance mostly focused on enterovirus 71 (EV-A71 and coxsackievirus A16; therefore, information on other enterovirus serotypes is limited. To identify the other circulating enterovirus serotypes in the HFMD outbreaks in Inner Mongolia in 2010, clinical samples from HFMD patients were investigated. Six coxsackievirus B4 (CVB4 strains were isolated and phylogenetic analyses of VP1 sequences were performed. Full-length genome sequences of two representative CVB4 isolates were acquired and similarity plot and bootscanning analyses were performed. The phylogenetic dendrogram indicated that all CVB4 strains could be divided into 5 genotypes (Genotypes I-V with high bootstrap support (90-100%. The CVB4 prototype strain (JVB was the sole member of genotype I. CVB4 strains belonging to genotype II, which were once common in Europe and the Americas, seemingly disappeared and gave way to genotype III and IV strains, which appear to be the dominant circulating strains in the world. All Chinese CVB4 strains belonged to Genotype V, a newly identified genotype supported by a high bootstrap value (100%, and are circulating only in mainland of China. Intertypic recombination occurred in the Chinese CVB4 strains with novel unknown serotype EV-B donor sequences. Two Chinese CVB4 strains had a virulent residue at position 129 of VP1, and one strain also had a virulent residue at position 16 of VP4. Increased surveillance is needed to monitor the emergence of new genetic lineages of enteroviruses in areas that are often associated with large-scale outbreaks. In addition, continued monitoring of enteroviruses by clinical surveillance and genetic characterization should be enhanced.

  5. A multi-site study using high-resolution HLA genotyping by next generation sequencing.

    Science.gov (United States)

    Holcomb, C L; Höglund, B; Anderson, M W; Blake, L A; Böhme, I; Egholm, M; Ferriola, D; Gabriel, C; Gelber, S E; Goodridge, D; Hawbecker, S; Klein, R; Ladner, M; Lind, C; Monos, D; Pando, M J; Pröll, J; Sayer, D C; Schmitz-Agheguian, G; Simen, B B; Thiele, B; Trachtenberg, E A; Tyan, D B; Wassmuth, R; White, S; Erlich, H A

    2011-03-01

    The high degree of polymorphism at human leukocyte antigen (HLA) class I and class II loci makes high-resolution HLA typing challenging. Current typing methods, including Sanger sequencing, yield ambiguous typing results because of incomplete genomic coverage and inability to set phase for HLA allele determination. The 454 Life Sciences Genome Sequencer (GS FLX) next generation sequencing system coupled with conexio atf software can provide very high-resolution HLA genotyping. High-throughput genotyping can be achieved by use of primers with multiplex identifier (MID) tags to allow pooling of the amplicons generated from different individuals prior to sequencing. We have conducted a double-blind study in which eight laboratory sites performed amplicon sequencing using GS FLX standard chemistry and genotyped the same 20 samples for HLA-A, -B, -C, DPB1, DQA1, DQB1, DRB1, DRB3, DRB4, and DRB5 (DRB3/4/5) in a single sequencing run. The average sequence read length was 250 base pairs and the average number of sequence reads per amplicon was 672, providing confidence in the allele assignments. Of the 1280 genotypes considered, assignment was possible in 95% of the cases. Failure to assign genotypes was the result of researcher procedural error or the presence of a novel allele rather than a failure of sequencing technology. Concordance with known genotypes, in cases where assignment was possible, ranged from 95.3% to 99.4% for the eight sites, with overall concordance of 97.2%. We conclude that clonal pyrosequencing using the GS FLX platform and CONEXIO ATF software allows reliable identification of HLA genotypes at high resolution. © 2011 John Wiley & Sons A/S.

  6. Comparison of genotypes I and III in Japanese encephalitis virus reveals distinct differences in their genetic and host diversity.

    Science.gov (United States)

    Han, Na; Adams, James; Chen, Ping; Guo, Zhen-yang; Zhong, Xiang-fu; Fang, Wei; Li, Na; Wen, Lei; Tao, Xiao-yan; Yuan, Zhi-ming; Rayner, Simon

    2014-10-01

    Japanese encephalitis (JE) is an arthropod-borne disease associated with the majority of viral encephalitis cases in the Asia-Pacific region. The causative agent, Japanese encephalitis virus (JEV), has been phylogenetically divided into five genotypes. Recent surveillance data indicate that genotype I (GI) is gradually replacing genotype III (GIII) as the dominant genotype. To investigate the mechanism behind the genotype shift and the potential consequences in terms of vaccine efficacy, human cases, and virus dissemination, we collected (i) all full-length and partial JEV molecular sequences and (ii) associated genotype and host information comprising a data set of 873 sequences. We then examined differences between the two genotypes at the genetic and epidemiological level by investigating amino acid mutations, positive selection, and host range. We found that although GI is dominant, it has fewer sites predicted to be under positive selection, a narrower host range, and significantly fewer human isolates. For the E protein, the sites under positive selection define a haplotype set for each genotype that shows striking differences in their composition and diversity, with GIII showing significantly more variety than GI. Our results suggest that GI has displaced GIII by achieving a replication cycle that is more efficient but is also more restricted in its host range. Japanese encephalitis is an arthropod-borne disease associated with the majority of viral encephalitis cases in the Asia-Pacific region. The causative agent, Japanese encephalitis virus (JEV), has been divided into five genotypes based on sequence similarity. Recent data indicate that genotype I (GI) is gradually replacing genotype III (GIII) as the dominant genotype. Understanding the reasons behind this shift and the potential consequences in terms of vaccine efficacy, human cases, and virus dissemination is important for controlling the spread of the virus and reducing human fatalities. We

  7. Genotyping of Norovirus strains detected in outbreaks between April 2002 and March 2003 in Osaka City, Japan.

    Science.gov (United States)

    Seto, Yoshiyuki; Iritani, Nobuhiro; Kubo, Hideyuki; Kaida, Atsushi; Murakami, Tsukasa; Haruki, Kosuke; Nishio, Osamu; Ayata, Minoru; Ogura, Hisashi

    2005-01-01

    Noroviruses (NVs) are the major cause of food- and waterborne nonbacterial gastroenteritis in Japan. Between April 2002 and March 2003, a total of 111 fecal specimens from 40 outbreaks of acute nonbacterial gastroenteritis in Osaka City, Japan were subject to NV detection. Seventy-two samples (64.9%) from 31 outbreaks (77.5%) were NV positive by a real time reverse transcription (RT)-PCR assay. To further determine the genotype of individual NV strains, we sequenced the capsid N-terminal/shell (N/S) domain of some representative strains from each outbreak. The 51 NV strains detected in this study were segregated into 15 genotypes (6 in genogroup I and 9 in genogroup II), and GII/5 genotype NV was a dominant outbreak genotype.

  8. Genotype-dependent Burst of Transposable Element Expression in Crowns of Hexaploid Wheat (Triticum aestivum L. during Cold Acclimation

    Directory of Open Access Journals (Sweden)

    Debbie Laudencia-Chingcuanco

    2012-01-01

    Full Text Available The expression of 1,613 transposable elements (TEs represented in the Affymetrix Wheat Genome Chip was examined during cold treatment in crowns of four hexaploid wheat genotypes that vary in tolerance to cold and in flowering time. The TE expression profiles showed a constant level of expression throughout the experiment in three of the genotypes. In winter Norstar, the most cold-hardy of the four genotypes, a subset of the TEs showed a burst of expression after vernalization saturation was achieved. About 47% of the TEs were expressed, and both Class I (retrotransposons and Class II (DNA transposons types were well represented. Gypsy and Copia were the most represented among the retrotransposons while CACTA and Mariner were the most represented DNA transposons. The data suggests that the Vrn-A1 region plays a role in the stage-specific induction of TE expression in this genotype.

  9. Assessment of two flexible and compatible SNP genotyping platforms: TaqMan SNP Genotyping Assays and the SNPlex Genotyping System.

    Science.gov (United States)

    De la Vega, Francisco M; Lazaruk, Katherine D; Rhodes, Michael D; Wenz, Michael H

    2005-06-03

    In this review we describe the principles, protocols, and applications of two commercially available SNP genotyping platforms, the TaqMan SNP Genotyping Assays and the SNPlex Genotyping System. Combined, these two technologies meet the requirements of multiple SNP applications in genetics research and pharmacogenetics. We also describe a set of SNP selection tools and validated assay resources which we developed to accelerate the cycle of experimentation on these platforms. Criteria for selecting the more appropriate of these two genotyping technologies are presented: the genetic architecture of the trait of interest, the throughput required, and the number of SNPs and samples needed for a successful study. Overall, the TaqMan assay format is suitable for low- to mid-throughput applications in which a high assay conversion rate, simple assay workflow, and low cost of automation are desirable. The SNPlex Genotyping System, on the other hand, is well suited for SNP applications in which throughput and cost-efficiency are essential, e.g., applications requiring either the testing of large numbers of SNPs and samples, or the flexibility to select various SNP subsets.

  10. Screening for viral hemorrhagic septicemia virus in marine fish along the Norwegian coastal line.

    Science.gov (United States)

    Sandlund, Nina; Gjerset, Britt; Bergh, Øivind; Modahl, Ingebjørg; Olesen, Niels Jørgen; Johansen, Renate

    2014-01-01

    Viral hemorrhagic septicemia virus (VHSV) infects a wide range of marine fish species. To study the occurrence of VHSV in wild marine fish populations in Norwegian coastal waters and fjord systems a total of 1927 fish from 39 different species were sampled through 5 research cruises conducted in 2009 to 2011. In total, VHSV was detected by rRT-PCR in twelve samples originating from Atlantic herring (Clupea harengus), haddock (Melanogrammus aeglefinus), whiting (Merlangius merlangus) and silvery pout (Gadiculus argenteus). All fish tested positive in gills while four herring and one silvery pout also tested positive in internal organs. Successful virus isolation in cell culture was only obtained from one pooled Atlantic herring sample which shows that today's PCR methodology have a much higher sensitivity than cell culture for detection of VHSV. Sequencing revealed that the positive samples belonged to VHSV genotype Ib and phylogenetic analysis shows that the isolate from Atlantic herring and silvery pout are closely related. All positive fish were sampled in the same area in the northern county of Finnmark. This is the first detection of VHSV in Atlantic herring this far north, and to our knowledge the first detection of VHSV in silvery pout. However, low prevalence of VHSV genotype Ib in Atlantic herring and other wild marine fish are well known in other parts of Europe. Earlier there have been a few reports of disease outbreaks in farmed rainbow trout with VHSV of genotype Ib, and our results show that there is a possibility of transfer of VHSV from wild to farmed fish along the Norwegian coast line. The impact of VHSV on wild fish is not well documented.

  11. Screening for viral hemorrhagic septicemia virus in marine fish along the Norwegian coastal line.

    Directory of Open Access Journals (Sweden)

    Nina Sandlund

    Full Text Available Viral hemorrhagic septicemia virus (VHSV infects a wide range of marine fish species. To study the occurrence of VHSV in wild marine fish populations in Norwegian coastal waters and fjord systems a total of 1927 fish from 39 different species were sampled through 5 research cruises conducted in 2009 to 2011. In total, VHSV was detected by rRT-PCR in twelve samples originating from Atlantic herring (Clupea harengus, haddock (Melanogrammus aeglefinus, whiting (Merlangius merlangus and silvery pout (Gadiculus argenteus. All fish tested positive in gills while four herring and one silvery pout also tested positive in internal organs. Successful virus isolation in cell culture was only obtained from one pooled Atlantic herring sample which shows that today's PCR methodology have a much higher sensitivity than cell culture for detection of VHSV. Sequencing revealed that the positive samples belonged to VHSV genotype Ib and phylogenetic analysis shows that the isolate from Atlantic herring and silvery pout are closely related. All positive fish were sampled in the same area in the northern county of Finnmark. This is the first detection of VHSV in Atlantic herring this far north, and to our knowledge the first detection of VHSV in silvery pout. However, low prevalence of VHSV genotype Ib in Atlantic herring and other wild marine fish are well known in other parts of Europe. Earlier there have been a few reports of disease outbreaks in farmed rainbow trout with VHSV of genotype Ib, and our results show that there is a possibility of transfer of VHSV from wild to farmed fish along the Norwegian coast line. The impact of VHSV on wild fish is not well documented.

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

    DEFF Research Database (Denmark)

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

    for 72h was appropriate to induce genotype dependent variation in Fv/Fm. This standardized protocol was used to phenotype wheat genotypes until the variation in the genotypes was consistently high with increased heritability for the trait, Fv/Fm. Mass screening of 1273 wheat genotypes in a milder stress...

  13. Genotype x environment interactions and yield stability of stress ...

    African Journals Online (AJOL)

    Genotype x environment interactions are inherent in multilocational trials and complicate identification of superior genotypes. The aim of the study was to determine yield performance and stability of 13 maize genotypes in five locations of the Eastern Cape province, South Africa. The genotypes assessed were: ZM305, ...

  14. Effect of phosphorus nutrition on growth of potato genotypes with ...

    African Journals Online (AJOL)

    Effect of phosphorus nutrition on growth of potato genotypes with contrasting phosphorus effeciency. ... and inefficient genotypes. P-efficient genotype CGN 17903 allocated more dry matter yield to the leaf which might have enabled higher light harvesting, hence contributing to high biomass accumulation of this genotype.

  15. The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping.

    Science.gov (United States)

    Tobler, Andreas R; Short, Sabine; Andersen, Mark R; Paner, Teodoro M; Briggs, Jason C; Lambert, Stephen M; Wu, Priscilla P; Wang, Yiwen; Spoonde, Alexander Y; Koehler, Ryan T; Peyret, Nicolas; Chen, Caifu; Broomer, Adam J; Ridzon, Dana A; Zhou, Hui; Hoo, Bradley S; Hayashibara, Kathleen C; Leong, Lilley N; Ma, Congcong N; Rosenblum, Barnet B; Day, Joseph P; Ziegle, Janet S; De La Vega, Francisco M; Rhodes, Michael D; Hennessy, Kevin M; Wenz, H Michael

    2005-12-01

    We developed the SNPlex Genotyping System to address the need for accurate genotyping data, high sample throughput, study design flexibility, and cost efficiency. The system uses oligonucleotide ligation/polymerase chain reaction and capillary electrophoresis to analyze bi-allelic single nucleotide polymorphism genotypes. It is well suited for single nucleotide polymorphism genotyping efforts in which throughput and cost efficiency are essential. The SNPlex Genotyping System offers a high degree of flexibility and scalability, allowing the selection of custom-defined sets of SNPs for medium- to high-throughput genotyping projects. It is therefore suitable for a broad range of study designs. In this article we describe the principle and applications of the SNPlex Genotyping System, as well as a set of single nucleotide polymorphism selection tools and validated assay resources that accelerate the assay design process. We developed the control pool, an oligonucleotide ligation probe set for training and quality-control purposes, which interrogates 48 SNPs simultaneously. We present performance data from this control pool obtained by testing genomic DNA samples from 44 individuals. in addition, we present data from a study that analyzed 521 SNPs in 92 individuals. Combined, both studies show the SNPlex Genotyping system to have a 99.32% overall call rate, 99.95% precision, and 99.84% concordance with genotypes analyzed by TaqMan probe-based assays. The SNPlex Genotyping System is an efficient and reliable tool for a broad range of genotyping applications, supported by applications for study design, data analysis, and data management.

  16. 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.

  17. Improved haplotype assembly using Xor genotypes.

    Science.gov (United States)

    Mousavi, Sayyed R

    2012-04-07

    Given a set of aligned fragments, haplotype assembly is the problem of finding the haplotypes from which the fragments have been read. The problem is important because haplotypes contain SNP information, which is essential to many genomic analyses such as the analysis of potential association between certain diseases and genetic variations. The current state-of-the-art haplotype assembly algorithm, HapSAT, does not exploit genotype information and only receives a read matrix as input. However, the imminent importance of haplotypes and inexpensiveness of genotype information motivate for exploiting genotype information to obtain more accurate haplotypes. In this paper, an improved haplotype assembly method, xGenHapSAT, is proposed, which exploits xor genotype information for more accurate haplotype assembly. Xor genotype information is even less expensive than full genotype information, e.g., using the Denaturing High-Performance Liquid Chromatography (DHPLC) technique. It is shown that using this inexpensively obtainable information significantly improves the accuracy of the assembled haplotypes. In addition, a new, more efficient, Max-2-SAT formulation is adopted in xGenHapSAT, which, on average, increases the speed of the algorithm. Moreover, the proposed xGenHapSAT method replaces the current state-of-the-art haplotype assembly method based on genotype information. Finally, our state-of-the-art haplotype assembly software, HapSoft, which includes both xGenHapSAT and HapSAT, is made freely available for research purposes. Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. Warfarin dose and INR related to genotypes of CYP2C9 and VKORC1 in patients with myocardial infarction

    Directory of Open Access Journals (Sweden)

    Seljeflot Ingebjørg

    2008-06-01

    Full Text Available Abstract Background Warfarin treatment has a narrow therapeutic range, requiring meticulous monitoring and dosage titration. Individual dosage requirement has recently partly been explained by genetic variation of the warfarin metabolizing enzyme CYP2C9 and the Vitamin K-activating enzyme VKORC1. In the WARIS-II study, comparing three different antithrombotic regimens after myocardial infarction, warfarin treatment reduced thrombotic events, but was associated with more frequent bleeding than use of acetylsalisylic acid (ASA alone. Aims The primary aim of the present study was to investigate the relation between genotypes of CYP2C9 and VKORC1 and warfarin maintenance dose in myocardial infarction. The secondary aim was to relate the genotypes to international normalized ratio (INR. Methods Genotyping was performed in 212 myocardial infarction patients from the WARIS-II study by robotic isolation of DNA from EDTA whole blood (MagNa Pure LC before PCR amplification (LightCycler and melting point analysis. Results The 420 C>T substitution of CYP2C9*2, the 1075 A>C substitution of CYP2C9*3 and the 1173 C>T substitution of VKORC1 had minor allele frequencies of, 11.3%, 5.7% and 36.6% respectively. Warfarin weekly dose varied between 17 mg and 74 mg among the patients. INR did not vary between genotypes. Warfarin dosage requirement was significantly associated with CYP2C9 and VKORC1 genotypes, treatment group and age. The VKORC1 genotype contributed 24.5% to the interindividual variation in warfarin dosage, whereas the combined CYP2C9 genotypes were only responsible for 7.2% of the dose variation. Conclusion CYP2C9 and VKORC1 genotype frequencies in myocardial infarction patients appear similar to other patient groups and have similar impact on warfarin maintenance dose.

  19. Ni(II), Mn(II), Zn(II)

    Indian Academy of Sciences (India)

    Unknown

    Abstract. Neutral tetradentate N2O2 type complexes of Cu(II), Ni(II), Mn(II),. Zn(II) and VO(II) have been synthesised using a Schiff base formed by the condensation of o-phenylenediamine with acetoacetanilide in alcohol medium. All the complexes were characterised on the basis of their microanalytical data, molar.

  20. Sequence analysis of the core gene of 14 hepatitis C virus genotypes.

    Science.gov (United States)

    Bukh, J; Purcell, R H; Miller, R H

    1994-01-01

    We previously sequenced the 5' noncoding region of 44 isolates of hepatitis C virus (HCV), as well as the envelope 1 (E1) gene of 51 HCV isolates, and provided evidence for the existence of at least 6 major genetic groups consisting of at least 12 minor genotypes of HCV (i.e., genotypes I/1a, II/1b, III/2a, IV/2b, 2c, V/3a, 4a-4d, 5a, and 6a). We now report the complete nucleotide sequence of the putative core (C) gene of 52 HCV isolates that represent all of these 12 genotypes as well as two additional genotypes provisionally designated 4e and 4f that we identified in this study. The phylogenetic analysis of the C gene sequences was in agreement with that of the E1 gene sequences. A major division in the genetic distance was observed between HCV isolates of genotype 2 and those of the other genotypes in analysis of both the E1 and C genes. The C gene sequences of 9 genotypes have not been reported previously (i.e., genotypes 2c, 4a-4f, 5a, and 6a). Our analysis indicates that the C gene-based methods currently used to determine the HCV genotype, such as PCR with genotype-specific primers, should be revised in light of these data. We found that the predicted C gene was exactly 573 nt long in all 52 HCV isolates, with an N-terminal start codon and no in-frame stop codons. The nucleotide and predicted amino acid identities of the C gene sequences were in the range of 79.4-99.0% and 85.3-100%, respectively. Furthermore, we mapped universally conserved, as well as genotype-specific, nucleotide and deduced amino acid sequences of the C gene. The predicted C proteins of the different HCV genotypes shared the following features: (i) high content of proline residues, (ii) high content of arginine and lysine residues located primarily in three domains with 10 such residues invariant at positions 39-62, (iii) a cluster of 5 conserved tryptophan residues, (iv) two nuclear localization signals and a DNA-binding motif, (v) a potential phosphorylation site with a serine

  1. Genotyping Reveals the Presence of a Predominant Genotype of Coxiella burnetii in Consumer Milk Products

    NARCIS (Netherlands)

    Tilburg, J.J.H.C.; Roest, H.I.J.; Nabuurs-Fransen, M.H.; Horrevorts, A.M.; Klaassen, C.H.W.

    2012-01-01

    Real-time PCR shows the widespread presence of Coxiella burnetii DNA in a broad range of commercially available milk and milk products. MLVA genotyping shows that this is the result of the presence of a predominant C. burnetii genotype in the dairy cattle population.

  2. Lactobacillus buchneri Genotyping on the Basis of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Locus Diversity

    Science.gov (United States)

    Briner, Alexandra E.

    2014-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) in combination with associated sequences (cas) constitute the CRISPR-Cas immune system, which uptakes DNA from invasive genetic elements as novel “spacers” that provide a genetic record of immunization events. We investigated the potential of CRISPR-based genotyping of Lactobacillus buchneri, a species relevant for commercial silage, bioethanol, and vegetable fermentations. Upon investigating the occurrence and diversity of CRISPR-Cas systems in Lactobacillus buchneri genomes, we observed a ubiquitous occurrence of CRISPR arrays containing a 36-nucleotide (nt) type II-A CRISPR locus adjacent to four cas genes, including the universal cas1 and cas2 genes and the type II signature gene cas9. Comparative analysis of CRISPR spacer content in 26 L. buchneri pickle fermentation isolates associated with spoilage revealed 10 unique locus genotypes that contained between 9 and 29 variable spacers. We observed a set of conserved spacers at the ancestral end, reflecting a common origin, as well as leader-end polymorphisms, reflecting recent divergence. Some of these spacers showed perfect identity with phage sequences, and many spacers showed homology to Lactobacillus plasmid sequences. Following a comparative analysis of sequences immediately flanking protospacers that matched CRISPR spacers, we identified a novel putative protospacer-adjacent motif (PAM), 5′-AAAA-3′. Overall, these findings suggest that type II-A CRISPR-Cas systems are valuable for genotyping of L. buchneri. PMID:24271175

  3. Lactobacillus buchneri genotyping on the basis of clustered regularly interspaced short palindromic repeat (CRISPR) locus diversity.

    Science.gov (United States)

    Briner, Alexandra E; Barrangou, Rodolphe

    2014-02-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) in combination with associated sequences (cas) constitute the CRISPR-Cas immune system, which uptakes DNA from invasive genetic elements as novel "spacers" that provide a genetic record of immunization events. We investigated the potential of CRISPR-based genotyping of Lactobacillus buchneri, a species relevant for commercial silage, bioethanol, and vegetable fermentations. Upon investigating the occurrence and diversity of CRISPR-Cas systems in Lactobacillus buchneri genomes, we observed a ubiquitous occurrence of CRISPR arrays containing a 36-nucleotide (nt) type II-A CRISPR locus adjacent to four cas genes, including the universal cas1 and cas2 genes and the type II signature gene cas9. Comparative analysis of CRISPR spacer content in 26 L. buchneri pickle fermentation isolates associated with spoilage revealed 10 unique locus genotypes that contained between 9 and 29 variable spacers. We observed a set of conserved spacers at the ancestral end, reflecting a common origin, as well as leader-end polymorphisms, reflecting recent divergence. Some of these spacers showed perfect identity with phage sequences, and many spacers showed homology to Lactobacillus plasmid sequences. Following a comparative analysis of sequences immediately flanking protospacers that matched CRISPR spacers, we identified a novel putative protospacer-adjacent motif (PAM), 5'-AAAA-3'. Overall, these findings suggest that type II-A CRISPR-Cas systems are valuable for genotyping of L. buchneri.

  4. Pb II

    African Journals Online (AJOL)

    Windows User

    used was oven-dried till constant weight and were ground to fine powder in a pestle and mortar. RESULTS AND DISCUSSION. Screening for lead sorption. 15 fungal isolates were screened for Pb(II) biosorption potential at initial pH value of 4.5 and temperature 30°C by incubating freshly harvested wet biomass corres-.

  5. Rapid and precise genotyping of porcine microsatellites.

    Science.gov (United States)

    Yue, G H; Beeckmann, P; Bartenschlager, H; Moser, G; Geldermann, H

    1999-11-01

    Microsatellites are useful markers for genetic mapping and linkage analysis because they are highly polymorphic, abundant in genomes and relatively easily scored with polymerase chain reaction (PCR). A rapid genotyping system for microsatellites was developed, which included multiplex PCRs, multiple use of Hydrolink gels, automated fluorescent detection of fragments on an A.L.F. DNA sequencer, automatic assignment of alleles to each locus and verification of genotypes with a self-developed computer program "Fragtest". Eight multiplex PCRs have been developed to genotype 29 microsatellites for genetic and quantitative trait loci (QTL) mapping on pig chromosomes 6, 7, 12 and 13. Three to six microsatellites could be amplified in one multiplex PCR. Each multiplex reaction required only different concentrations of each pair of primers and a low concentration of dNTP (100 microM). A dNTP concentration of 100 microM proved to be optimal for the coamplification of microsatellites under the concentration of 1.5 mM MgCl2. Using four internal size standards added in each sample, the 5% Hydrolink gel could subsequently be used up to five times (total running time of 500 min) on the A.L.F. automated sequencer without significant loss of resolution and precision of fragment length analysis. Automatic assignment of alleles on each locus using "Fragtest" significantly increased the efficiency and precision of the genotyping. This system is thus a rapid, cheap, and highly discriminating genotyping system.

  6. 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.

  7. 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

    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...... to recover the correct labels. Here we describe a statistical method which given a few extra independent genotypes (barcode genotypes) detects mislabeled samples and recovers the correct labels for sample mix-ups. We have implemented the method in a program (named Wunderbar) and we evaluate the reliability...

  8. COMT genotype, gambling activity, and cognition

    DEFF Research Database (Denmark)

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

    2015-01-01

    Neuropsychological studies of adults with problem gambling indicate impairments across multiple cognitive domains. Catechol-O-methyltransferase (COMT) plays a unique role in the regulation of dopamine in the prefrontal cortex, and has been implicated in the cognitive dysfunction evident in problem...... 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...... samples for genotyping COMT val158met (rs4680). All subjects underwent clinical evaluations and neurocognitive assessment of decision-making, working memory, and impulsivity. The Val/Val COMT genotype was associated with the largest percentage of subjects with gambling disorder (31.8%), a rate...

  9. 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.

  10. HPV detection and genotyping as an earlier approach in cervical cancer screening of the female genital tract.

    Science.gov (United States)

    Krambeck, W M; Cadidé, R M; Dalmarco, E M; de Cordova, C M M

    2008-01-01

    Human papillomavirus (HPV) infection is the leading risk factor for cervical intraepithelial neoplasia (CIN) and cervical cancer. More than 100 virus genotypes have been identified so far, some of them strongly associated with the development of neoplasia. The aim of this study was to evaluate the prevalence of the different HPV genotypes in women presenting no cytological alterations in cervical cells, in women presenting light alterations, and in women presenting severe alterations at routine gynecological examination. We retrospectively analyzed 97 HPV results of women submitted to cervical cancer screening compared to their Papanicolaou and colposcopy examinations. Data were analyzed individually and within groups to correlate the HPV genotypes identified by polymerase chain reaction (PCR) and the respective alterations in cervical cells. Among the nine cases diagnosed as CIN I (9.3%), two were positive for low-risk HPV genotypes (22%), and the other seven were negative for HPV by PCR (78%). CIN II or CIN III diagnoses were associated with positive HPV results by PCR in four cases (36%), for high-risk as well as low-risk genotypes. There were two patients with severe cytological alterations in cervical cells, but with an indeterminate HPV genotype (18%), and one case with a negative HPV result (9%). Among the 57 cases without cytological alterations, seven were positive for low-risk HPV (12%) and two for high-risk HPV genotypes (3.5%). In the 48 remaining cases, we observed one with an indeterminate HPV genotype (2%), and the other 47 were negative for HPV by PCR (47%). Our study demonstrates an important prevalence of high- and low-risk HPV genotypes in our population, including those not present in the commercially available vaccine, even in patients with no evidence of cytological alterations in cervical cells. These results highlight the usefulness of HPV detection and typing as an early approach for cervical cancer screening and prevention.

  11. Oilseed rape genotypes response to boron toxicity

    Directory of Open Access Journals (Sweden)

    Savić Jasna

    2013-01-01

    Full Text Available Response of 16 oilseed rape genotypes to B (boron toxicity was analyzed by comparing the results of two experiments conducted in a glasshouse. In Experiment 1 plants were grown in standard nutrient solutions with 10 µMB (control and 1000 µM B. Relative root and shoot growth varied from 20-120% and 31-117%, respectively. Variation in B concentration in shoots was also wide (206.5-441.7 µg B g-1 DW as well as total B uptake by plant (62.3-281.2 µg B g1. Four selected genotypes were grown in Experiment 2 in pots filled with high B soil (8 kg ha-1 B; B8. Shoot growth was not affected by B8 treatment, while root and shoot B concentration was significantly increased compared to control. Genotypes Panther and Pronto which performed low relative root and shoot growth and high B accumulation in plants in Experiment 1, had good growth in B8 treatment. In Experiment 2 genotype NS-L-7 had significantly lower B concentration in shots under treatment B8, but also very high B accumulation in Experiment 1. In addition, cluster analyses classified genotypes in three groups according to traits contrasting in their significance for analyzing response to B toxicity. The first group included four varieties based on their shared characteristics that have small value for the relative growth of roots and shoots and large values of B concentration in shoot. In the second largest group were connected ten genotypes that are heterogeneous in traits and do not stand out on any characteristic. Genotypes NS-L-7 and Navajo were separated in the third group because they had big relative growth of root and shoot, but also a high concentration of B in the shoot, and high total B uptake. Results showed that none of tested genotypes could not be recommended for breeding process to tolerance for B toxicity. [Projekat Ministarstva nauke Republike Srbije, br. OI 173028

  12. Association between the 5-HTTLPR Genotype and Childhood Characteristics in Mood Disorders.

    Science.gov (United States)

    Eun, Tae Kyung; Jeong, Seong Hoon; Lee, Kyu Young; Kim, Se Hyun; Ahn, Yong Min; Bang, Yang Weon; Joo, Eun-Jeong

    2016-02-29

    The features of childhood attention deficit hyperactivity disorder (ADHD) are significantly associated with adult mood disorders. Some genetic factors may be common to both ADHD and mood disorders underlie the association between these two phenotypes. The present study aimed to determine whether a genetic role may be played by the serotonin transporter-linked polymorphic region (5-HTTLPR) in the childhood ADHD features of adult patients with mood disorders. The present study included 232 patients with major depressive disorder (MDD), 154 patients with bipolar disorder (BPD), and 1,288 normal controls. Childhood ADHD features were assessed with the Korean version of the Wender Utah Rating Scale (WURS-K). The total score and the scores of three factors (impulsivity, inattention, and mood instability) from the WURS-K were analyzed to determine whether they were associated with the 5-HTTLPR genotype. In the BPD type II group, the 5-HTTLPR genotype was significantly associated with the total score (p=0.029) and the impulsivity factor (p=0.004) on the WURS-K. However, the inattention and mood instability factors were not associated with the 5-HTTLPR genotype. BPD type I, MDD and normal control groups did not exhibit any significant associations between the WURS-K scores and the 5-HTTLPR genotype. The findings suggest that the 5-HTTLPR genotype may play a role in the impulsivity component of childhood ADHD in patients with BPD type II. Because of a small sample size and a single candidate gene, further studies investigating other candidate genes using a larger sample are warranted to determine any common genetic links.

  13. Toxoplasma gondii seroprevalence and genotype diversity in select wildlife species from the southeastern United States

    Directory of Open Access Journals (Sweden)

    Richard W. Gerhold

    2017-10-01

    Full Text Available Abstract Background Toxoplasma gondii is a widespread protozoan parasite that infects humans and other animals. Previous studies indicate some genotypes of T. gondii are more frequently isolated in wildlife than agricultural animals, suggesting a wild/feral animal diversity model. To determine seroprevalence and genetic diversity of T. gondii in southeastern US wildlife, we collected sera from 471 wild animals, including 453 mammals and 18 birds, between 2011 and 2014. These serum samples were assayed for T. gondii infection using the modified agglutination test (MAT. Heart or tongue tissues from 66 seropositive animals were bioassayed in mice and 19 isolates were obtained. The isolated parasites were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP method employing 10 genetic markers. Results One hundred and ninety-six of 471 samples (41.6% had a titer ≥1:32 and were considered positive for T. gondii infection. Of 453 mammals, 195 (43% were seropositive, whereas only one (5.6% of 18 birds was seropositive. The seroprevalence in mammals was significantly higher than in the birds. Mammalian hosts with adequate samples size (≥ 20 comprised white-tailed deer (n = 241, feral hogs (n = 100, raccoons (n = 34 and coyotes (n = 22, with seroprevalences of 41.0%, 51.0%, 50.0% and 72.7%, respectively. Coyotes had significantly higher seroprevalence than the white-tailed deer. Genotyping revealed five distinct genotypes, including the ToxoDB PCR-RFLP genotype #5 (a.k.a type 12 for 15 isolates, genotype #3 (a.k.a. type II for 1 isolate, and genotypes #154, #167 and #216, each for 1 isolate. The results showed moderate to high infection rates of T. gondii in white-tailed deer, feral hogs, raccoons and coyotes. Genotyping results indicated limited genetic diversity and a dominance of genotype #5, which has been reported as a major type in wildlife in North America. Conclusions We conclude that T. gondii

  14. Prevalence of hepatitis C virus genotypes in mashhad, northeast iran.

    Science.gov (United States)

    Vossughinia, H; Goshayeshi, LA; Bayegi, H Rafatpanah; Sima, H; Kazemi, A; Erfani, S; Abedini, S; Goshayeshi, LE; Ghaffarzadegan, K; Nomani, H; Jamehdar, S Amel

    2012-01-01

    Hepatitis C is a disease with significant global impact. The distribution of hepatitis C virus (HCV) genotypes in Mashhad (the Northeast and the biggest city after the capital of Iran) is unknown. The purpose of this study was to determine the prevalence of HCV genotypes among HCV seropositive patients, and to study the relationship between types, virologic and demographic features of patients in Mashhad. Three hundred and eighty-two clinical specimens obtained from HCV-infected patients referred to Ghaem Hospital in Mashhad during a period of 2009 to 2010 were selected. HCV genotype was determined by Nested PCR amplification of HCV core gene using genotype specific primers. Totally, 299 patients were male (79.9%). The most common HCV genotype was genotype 3a, with 150 (40%) of subjects. Genotype 1a was the other frequent genotype, with 147(39.2%) subjects. Frequency of genotypes for 1b, 5 and 2 was 41(10.9%), 13(3.4%) and 9(2.4%), respectively. Mix genotype including 1a+1b in 4 (1.04%), 1a+3a in 3 (0.8%) was found in 7 patients. Four percent out of these samples had an undetermined genotype. Among the hemophilia patient, there were 13(48.1%) genotypes as 1a, 3(11.1%) 1b and 10(37%) 3a, respectively. The dominant HCV genotype among patients living in Mashhad was 3a. This study gives added evidence of the predominant HCV genotypes in Iran.

  15. Restriction Fragment Length Polymorphisms and Sequence Analysis: an Approach for Genotyping Infectious Pancreatic Necrosis Virus Reference Strains and Other Aquabirnaviruses Isolated from Northwestern Spain†

    Science.gov (United States)

    Cutrín, J. M.; Barja, J. L.; Nicholson, B. L.; Bandín, I.; Blake, S.; Dopazo, C. P.

    2004-01-01

    Reference strains of infectious pancreatic necrosis virus resembling the 10 recognized serotypes and local isolates of aquabirnaviruses isolated in northwestern Spain from reservoirs (mollusks) and from asymptomatic and carrier cultured fish were genotyped by restriction fragment length polymorphism (RFLP) and nucleic acid sequence analyses. The RFLP analysis yielded seven genogroups, each of which was clearly correlated with a serotype. Sequence analysis of the three open reading frames provided quite similar results in terms of genogrouping. Based on the results of this study and in order to unify the two types of assays, we propose placing aquabirnaviruses into six genogroups, four of which can be subdivided into two genotypes based on a two-step restriction analysis. The genotyping corresponds with serotyping as follows: genogroup I includes two genotypes corresponding to serotypes A9 (genotype I.1) and A1 (genotype I.2); genogroup II corresponds to serotype A3; genogroup III includes genotypes III.1 (serotype A2) and III.2 (serotype B1); genogroups IV and V include two genotypes, each corresponding to serotypes A5, A6, A7, and A8 (genotypes IV.1, IV.2, V.1, and V.2, respectively);and genogroup VI corresponds to serotype A4. As expected, most local isolates belonged to genotype III.1 and genogroup II. However, a few local isolates corresponded to the American types of genogroup I. Finally, based on the results of this study and due to its simplicity, the two-step restriction analysis assay is proposed as a method for typing new isolates of aquabirnaviruses, and the results correspond to the results of conventional serotyping. PMID:14766589

  16. Prevalence and genotyping ofToxoplasma gondii among Saudi pregnant women in Saudi Arabia.

    Science.gov (United States)

    Alghamdi, Jawahir; Elamin, Maha Hussein; Alhabib, Samia

    2016-11-01

    Introduction: Toxoplasma gondii (T. gondii) is an intracellular protozoan that can infect all mammals, who serve as intermediate host. It causes congenital, neurological, eyes complications and mild or asymptomatic infections in humans. Purpose of this study: To investigate not only the prevalence of T. gondii, but also to find out its genotyping using multiple sequential molecular methods to predict exactly the precise genotyping of T. gondii among Saudi pregnant women. Methods: A cross-sectional study was conducted using multi-stage methods. Initial stage involved enrolment of 250 Saudi pregnant women from multi-centre healthcare and community based settings in the capital of Saudi Arabia Riyadh. The second stage was embracement of the laboratory investigation that included Enzyme immunoassay (ELISA), DNA extraction, PCR, nested-PCR assay, and genotyping of the seropositive cases. Results: 203 women agreed to take part in our study with a response rate of 81.2% (203/250). Using ELISA, we found that the prevalence of Toxoplasma gondii IgG and IgM antibodies was 32.5% and 6.4%, respectively. We found that 29 samples (80.6%) were of genotype II; however 7 samples (19.4%) were of genotype III. Conclusion: Defining the population structure of T. gondii from Saudi Arabia has important implications for transmission, immunogenicity, pathogenesis, and in planning preventive strategies. Relationship between such variation in structure and disease manifestation in pregnant women is still difficult to assess due to the role of host immune status and genetic background on the control of infection, and of other parasitic features such as the infecting dose or parasite stage. Our finding of the genotyping of T. gondii might facilitate and inform future studies on comparative genomics and identification of genes that control important biological phenotypes including pathogenesis and transmission among Saudi women.

  17. Using msa-2b as a molecular marker for genotyping Mexican isolates of Babesia bovis.

    Science.gov (United States)

    Genis, Alma D; Perez, Jocelin; Mosqueda, Juan J; Alvarez, Antonio; Camacho, Minerva; Muñoz, Maria de Lourdes; Rojas, Carmen; Figueroa, Julio V

    2009-12-01

    Variable merozoite surface antigens of Babesia bovis are exposed glycoproteins having a role in erythrocyte invasion. Members of this gene family include msa-1 and msa-2 (msa-2c, msa-2a(1), msa-2a(2) and msa-2b). To determine the sequence variation among B. bovis Mexican isolates using msa-2b as a genetic marker, PCR amplicons corresponding to msa-2b were cloned and plasmids carrying the corresponding inserts were purified and sequenced. Comparative analysis of nucleotide and deduced amino acid sequences revealed distinct degrees of variability and identity among the coding gene sequences obtained from 16 geographically different Mexican B. bovis isolates and a reference strain. Clustal-W multiple alignments of the MSA-2b deduced amino acid sequences performed with the 17 B. bovis Mexican isolates, revealed the identification of three genotypes with a distinct set each of amino acid residues present at the variable region: Genotype I represented by the MO7 strain (in vitro culture-derived from the Mexico isolate) as well as RAD, Chiapas-1, Tabasco and Veracruz-3 isolates; Genotype II, represented by the Jalisco, Mexico and Veracruz-2 isolates; and Genotype III comprising the sequences from most of the isolates studied, Tamaulipas-1, Chiapas-2, Guerrero-1, Nayarit, Quintana Roo, Nuevo Leon, Tamaulipas-2, Yucatan and Guerrero-2. Moreover, these three genotypes could be discriminated against each other by using a PCR-RFLP approach. The results suggest that occurrence of indels within the variable region of msa-2b sequences can be useful markers for identifying a particular genotype present in field populations of B. bovis isolated from infected cattle in Mexico.

  18. 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...

  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

    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...... 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. Characterisation of genotype VII Newcastle disease virus (NDV) isolated from NDV vaccinated chickens, and the efficacy of LaSota and recombinant genotype VII vaccines against challenge with velogenic NDV.

    Science.gov (United States)

    Roohani, Kiarash; Tan, Sheau Wei; Yeap, Swee Keong; Ideris, Aini; Bejo, Mohd Hair; Omar, Abdul Rahman

    2015-01-01

    A Newcastle disease virus (NDV) isolate designated IBS002 was isolated from a commercial broiler farm in Malaysia. The virus was characterised as a virulent strain based on the multiple basic amino acid motif of the fusion (F) cleavage site (112)RRRKGF(117) and length of the C-terminus extension of the hemagglutinin-neuraminidase (HN) gene. Furthermore, IBS002 was classified as a velogenic NDV with mean death time (MDT) of 51.2 h and intracerebral pathogenicity index (ICPI) of 1.76. A genetic distance analysis based on the full-length F and HN genes showed that both velogenic viruses used in this study, genotype VII NDV isolate IBS002 and genotype VIII NDV isolate AF2240-I, had high genetic variations with genotype II LaSota vaccine. In this study, the protection efficacy of the recombinant genotype VII NDV inactivated vaccine was also evaluated when added to an existing commercial vaccination program against challenge with velogenic NDV IBS002 and NDV AF2240-I in commercial broilers. The results indicated that both LaSota and recombinant genotype VII vaccines offered full protection against challenge with AF2240-I. However, the LaSota vaccine only conferred partial protection against IBS002. In addition, significantly reduced viral shedding was observed in the recombinant genotype VII-vaccinated chickens compared to LaSota-vaccinated chickens.

  1. Ni(II), Cu(II) and Zn(II)

    African Journals Online (AJOL)

    Chemical speciation of citric acid complexes of Co(II), Ni(II), Cu(II) and Zn(II) was investigated pH-metrically in 0.0-2.5% anionic, cationic and neutral micellar media. The primary alkalimetric data were pruned with SCPHD program. The existence of different binary species was established from modeling studies using the ...

  2. Ni(II), Cu(II) and Zn(II)

    African Journals Online (AJOL)

    NICO

    2010-06-15

    Jun 15, 2010 ... physico-chemical techniques. A square planar geometry was suggested for Cu(II) and octahedral geometry proposed for Co(II),. Ni(II) and Zn(II). TG curves indicated that the complexes decompose in three to four steps. The presence of coordinated water in metal complexes was confirmed by thermal and ...

  3. GENOTYPES IN THE CENTRAL HIGHLANDS OF ETHIOPIA

    African Journals Online (AJOL)

    Eight promising bread wheat lines and one standard check cultivar were evaluated for grain yield performance, stability and adaptation across nine environments of the central highlands of Ethiopia. Results of the combined analysis of variance for grain yield showed highly significant effects of genotypes, environments, and ...

  4. Genotypic identification and technological characterization of lactic ...

    African Journals Online (AJOL)

    enoh

    African Journal of Biotechnology Vol. 11(28), pp. 7218-7226, 5 April, 2012 ... Key words: Lactic acid bacteria, genotypic characterization, technological characterization, tulum cheese. INTRODUCTION. Kargi tulum ... traditional production method of Kargi tulum cheese begins with fresh raw milk that is coagulated by adding.

  5. Genetic diversity evaluation of rapeseed genotypes ( Brassica ...

    African Journals Online (AJOL)

    Path analysis showed that number of pods per main branch had the highest direct effect on seed yield. Stepwise regressing showed numbers of pods per main branch was entered as the first variable in the model and explained 79% of seed yield variation. Phenotypic cluster showed that genotypes were divided into 4 ...

  6. genotype by environment interaction of advanced generation ...

    African Journals Online (AJOL)

    recommended as primary testing centres for new soybean genotypes. ACKNOWLEDGEMENT. This research was supported by Alliance for a. Green Revolution in Africa (AGRA) and Vegetable. Oil Development Project, of the Ministry of. Agriculture Animal Industry and Fisheries,. Uganda. We thank Makerere University and.

  7. genotyping methods in routine clinical practice

    African Journals Online (AJOL)

    milcah

    2013-05-08

    May 8, 2013 ... Pharmacogenetics requires robust and affordable tests to determine genetic variability. This study compares three genotyping methods: gene re-sequencing, real time polymerase chain reaction (PCR) allelic discrimination and PCR-RFLP for the detection of a genetic variation (516G>T) in the gene which.

  8. AFLP analysis among Ethiopian arabica coffee genotypes

    African Journals Online (AJOL)

    STORAGESEVER

    2008-09-17

    Sep 17, 2008 ... AFLP analysis among Ethiopian arabica coffee genotypes. Yigzaw Dessalegn1*, L. Herselman2 and M. T. Labuschagne2. 1IPMS Project, Bure PLW, P.O. Box 03, Bure, Ethiopia. 2University of the Free State, Department of Plant Sciences, P.O. Box 339, Bloemfontein 9300, Republic of South Africa.

  9. (Saccharum officinarum L) genotypes to callus induction ...

    African Journals Online (AJOL)

    Jane

    2010-12-20

    Dec 20, 2010 ... Cultivar CSSG-668 was found to be the best genotype yielding maximum embryogenic callus and regeneration whereas cultivar CPF-. 245 exhibited lowest callus induction frequency. Five different concentrations (0 ..... Planta, 89: 299-302. Bower R, Birch RG (1992). Transgenic sugarcane plants via micro-.

  10. Camelina: Adaptation and performance of genotypes

    Science.gov (United States)

    Camelina (Camelina sativa L. Crantz) has shown potential as an alternative and biofuel crop in cereal-based cropping systems. Our study investigated the adaption, performance, and yield stability among camelina genotypes across diverse US Pacific Northwest (PNW) environments. Seven named camelina ge...

  11. Phenotypic and Genotypic Characterization of Nosocomial Isolates ...

    African Journals Online (AJOL)

    Phenotypic and Genotypic Characterization of Nosocomial. Isolates of Staphylococcus aureus with Reference to. Methicillin Resistance. Mounir M Salem-Bekhit1,2. 1Kayyali Chair for Pharmaceutical Industries, Department of Pharmaceutics, College of Pharmacy, King Saud University, PO. Box 2457, Riyadh 11451, Saudi ...

  12. Human papillomavirus genotyping by multiplex pyrosequencing in ...

    Indian Academy of Sciences (India)

    Cervical cancer is a leading cause of cancer-related deaths among women in India. Human papillomavirus (HPV) infection is the causative agent of cervical cancer; and infection with the high-risk genotypes, predominantly HPV16 and 18, is the biggest risk factor. Vaccines targeting HPV16 and 18 have been found to confer ...

  13. Probabilistic Transcriptome Assembly and Variant Graph Genotyping

    DEFF Research Database (Denmark)

    Sibbesen, Jonas Andreas

    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...

  14. Morphometric characteristics of Lotus corniculatus L. genotypes ...

    African Journals Online (AJOL)

    The aim of this study was to examine the degree of variability in morphological and agronomic characteristics of 20 Lotus corniculatus L. local genotypes, and also to set aside germplasm that will be used as a source of genetic basis for improvement of the studied properties. In poor quality soils, L. corniculatus L. plays an ...

  15. Assessment of antibiotic susceptibilities, genotypic characteristics ...

    African Journals Online (AJOL)

    This study was designed to evaluate the antibiotic susceptibilities, genotypic characteristics and biofilm formation abilities of antibiotic-sensitive Staphylococcus aureus KACC 13236 (SAS), multiple antibiotic-resistant S. aureus CCARM 3080 (SAR), antibiotic-sensitive Salmonella Typhimurium KCCM 40253 (STS) and ...

  16. Heritability Studies of Some Cassava Genotypes

    African Journals Online (AJOL)

    komla

    82/00058, 82/00661, 82/00942 and 900942. These genotypes were grown under rainfed conditions in a randomized complete design with four replicates (Fig. 1). No fertilizers or any other agrochemicals were applied to the experimental plots. Plants were planted. 50 , West AfricanJournal of Applied Ecology, vol. 3, 2002 ...

  17. EFFECT OF TEMPERATURE AND HOST GENOTYPE ON ...

    African Journals Online (AJOL)

    Disease development in plants involves various inter-related processes each of which may be. influenced by environmental factors as well as host and pathogen genotypes Temperature in the range of 20~25°C was reported to be optimum for urediniospore germination of groundnut rust. (Subrahmanyam and McDonald ...

  18. Human papillomavirus genotyping by multiplex pyrosequencing in ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR G

    known, together accounting for about 90% of all cervical cancer cases worldwide. HPV 31, 33 and 45 account for a high proportion of HPV16/18-negative cervical cancer cases. (Pretet et al 2007a, b) and to complete the representative spectrum of HPV genotypes, two low-risk HPV types, namely HPV6 and 11, known to be ...

  19. Fruit characteristics of the selected fig genotypes

    African Journals Online (AJOL)

    GREGORY

    2010-09-13

    Sep 13, 2010 ... Key words: Ficus carica L., genotype, fruit characteristics, quality, selection. INTRODUCTION. Turkey is the world's largest fig producing country. According to FAO statistics, world fig production is. 1.056,820 tonnes. Turkey's production of 285.000 tonnes is 27% of the world's total production and its 177.900.

  20. Morphometric characteristics of Lotus corniculatus L. genotypes

    African Journals Online (AJOL)

    LAB-89 sjemenarstvo

    2013-08-28

    Aug 28, 2013 ... Variability of productive characteristics and fodder quality of selected Birdsfoot Trefoil (Lotus corniculatus L.) genotypes. A. Periodical of Scientific Research on Field and Vegetable Crops, Novi. Sad, Serbia. 44 (1):45-50. Rumbaugh MD, Caddel JL, Rowe DE(1988). Breeding and Quantitative. Genetics.

  1. Participatory selection of mungbean genotypes in Uganda ...

    African Journals Online (AJOL)

    We captured twenty five traits during farmer interviews out of which six traits were identified (through group discussions) as the most often used by farmers when selecting the best mungbean genotypes. The traits were; yield, overall performance, seed size, seed colour, marketability and early maturity. Nine out of eleven ...

  2. Screening soybean genotypes for promiscuous symbiotic ...

    African Journals Online (AJOL)

    The current low soybean (Glycine max L. Merrill) yields in Sub-Saharan Africa can be alleviated by developing promiscuous genotypes. The research trend in Africa is towards developing promiscuous varieties for less labour and high yields in soybean production. A greenhouse experiment was conducted at Makerere ...

  3. Carbon isotope fractionation for cotton genotype selection

    Directory of Open Access Journals (Sweden)

    Giovani Greigh de Brito

    2014-09-01

    Full Text Available The objective of this work was to evaluate the carbon isotope fractionation as a phenomic facility for cotton selection in contrasting environments and to assess its relationship with yield components. The experiments were carried out in a randomized block design, with four replicates, in the municipalities of Santa Helena de Goiás (SHGO and Montividiu (MONT, in the state of Goiás, Brazil. The analysis of carbon isotope discrimination (Δ was performed in 15 breeding lines and three cultivars. Subsequently, the root growth kinetic and root system architecture from the selected genotypes were determined. In both locations, Δ analyses were suitable to discriminate cotton genotypes. There was a positive correlation between Δ and seed-cotton yield in SHGO, where water deficit was more severe. In this site, the negative correlations found between Δ and fiber percentage indicate an integrative effect of gas exchange on Δ and its association with yield components. As for root robustness and growth kinetic, the GO 05 809 genotype performance contributes to sustain the highest values of Δ found in MONT, where edaphoclimatic conditions were more suitable for cotton. The use of Δ analysis as a phenomic facility can help to select cotton genotypes, in order to obtain plants with higher efficiency for gas exchange and water use.

  4. Simple methodology to directly genotype Trypanosoma cruzi discrete typing units in single and mixed infections from human blood samples.

    Science.gov (United States)

    Bontempi, Iván A; Bizai, María L; Ortiz, Sylvia; Manattini, Silvia; Fabbro, Diana; Solari, Aldo; Diez, Cristina

    2016-09-01

    Different DNA markers to genotype Trypanosoma cruzi are now available. However, due to the low quantity of parasites present in biological samples, DNA markers with high copy number like kinetoplast minicircles are needed. The aim of this study was to complete a DNA assay called minicircle lineage specific-PCR (MLS-PCR) previously developed to genotype the T. cruzi DTUs TcV and TcVI, in order to genotype DTUs TcI and TcII and to improve TcVI detection. We screened kinetoplast minicircle hypervariable sequences from cloned PCR products from reference strains belonging to the mentioned DTUs using specific kDNA probes. With the four highly specific sequences selected, we designed primers to be used in the MLS-PCR to directly genotype T. cruzi from biological samples. High specificity and sensitivity were obtained when we evaluated the new approach for TcI, TcII, TcV and TcVI genotyping in twenty two T. cruzi reference strains. Afterward, we compared it with hybridization tests using specific kDNA probes in 32 blood samples from chronic chagasic patients from North Eastern Argentina. With both tests we were able to genotype 94% of the samples and the concordance between them was very good (kappa=0.855). The most frequent T. cruzi DTUs detected were TcV and TcVI, followed by TcII and much lower TcI. A unique T. cruzi DTU was detected in 18 samples meantime more than one in the remaining; being TcV and TcVI the most frequent association. A high percentage of mixed detections were obtained with both assays and its impact was discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Association between single nucleotide polymorphism of apoVLDL-II ...

    African Journals Online (AJOL)

    ONOS

    2010-07-05

    Jul 5, 2010 ... polymorphism on chicken growth and body composition traits. Genomic DNAs were extracted from 400 chickens from four different commercial broiler lines. Genotyping for the apoVLDL-II gene by using. PCR-RFLP method and SfcI restriction endonuclease showed a mutation in 492-bp fragment located on.

  6. Genetic characterization of Toxoplasma gondii revealed highly diverse genotypes for isolates from newborns with congenital toxoplasmosis in southeastern Brazil.

    Science.gov (United States)

    Carneiro, Ana Carolina Aguiar Vasconcelos; Andrade, Gláucia Manzan; Costa, Júlia Gatti Ladeia; Pinheiro, Breno Veloso; Vasconcelos-Santos, Daniel Vitor; Ferreira, Adriana Melo; Su, Chunlei; Januário, José Nélio; Vitor, Ricardo Wagner Almeida

    2013-03-01

    Recent studies of Toxoplasma gondii isolates from animals in Brazil have revealed high genetic diversity. Many of these isolates are virulent to mice. It is speculated that these isolates may also be virulent to humans. However, there is very limited data regarding T. gondii strains from human infection. Therefore, it is not clear whether there is any association between parasite genotypes and disease phenotypes. In this study, a total of 27 T. gondii strains were isolated from humans with congenital toxoplasmosis in Minas Gerais state, Brazil. The genetic variability was assessed by restricted fragment length polymorphism in 11 loci (SAG1, 5' plus 3' SAG2, alternative [alt.] SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). Genetic analysis of 24 strains revealed 14 different genotypes, including 7 previously identified from animals and 7 new types. The widespread genotype BrII accounted for 29% (7/24) of the isolates and was the dominant genotype involved in this study. This is the first report of genotyping of T. gondii isolates obtained from blood samples from newborns with congenital toxoplasmosis. Genotypic characterization of these isolates suggests high genetic diversity of T. gondii in this human population in Brazil. Future studies are needed to determine the source of contamination of this human population.

  7. DD Genotype of ACE I/D Polymorphism Might Confer Protection against Dental Caries in Polish Children.

    Science.gov (United States)

    Olszowski, Tomasz; Adler, Grażyna; Janiszewska-Olszowska, Joanna; Safranow, Krzysztof; Chlubek, Dariusz

    2015-01-01

    The aim of the study was to examine the frequencies of the genotypes and alleles of ACE insertion/deletion (I/D) polymorphism and their association with dental caries in a sample of Polish children. The study subjects were 120 children with dental caries experience (cases) and 41 caries-free individuals (controls). The genotyping was performed using polymerase chain reaction. The genotype distributions of ACE I/D polymorphism were not statistically different between carious and control children. However, we found a borderline overrepresentation of the II + ID genotypes versus the DD genotype in the carious compared to the control group (69.2% and 51.2%, respectively, p = 0.057). Logistic regression analysis adjusted for age and sex revealed that I allele carriage was a significant predictor of dental caries susceptibility (OR = 2.14, 95% CI = 1.02-4.49, p = 0.041). In conclusion, the DD genotype of ACE I/D polymorphism might be protective against dental caries in Polish children. © 2015 S. Karger AG, Basel.

  8. Frequency and genotypic distribution of GB virus C (GBV-C) among Colombian population with Hepatitis B (HBV) or Hepatitis C (HCV) infection.

    Science.gov (United States)

    Alvarado-Mora, Mónica V; Botelho, Livia; Nishiya, Anna; Neto, Raymundo A; Gomes-Gouvêa, Michele S; Gutierrez, Maria F; Carrilho, Flair J; Pinho, João Rr

    2011-07-11

    GB virus C (GBV-C) is an enveloped positive-sense ssRNA virus belonging to the Flaviviridae family. Studies on the genetic variability of the GBV-C reveals the existence of six genotypes: genotype 1 predominates in West Africa, genotype 2 in Europe and America, genotype 3 in Asia, genotype 4 in Southwest Asia, genotype 5 in South Africa and genotype 6 in Indonesia. The aim of this study was to determine the frequency and genotypic distribution of GBV-C in the Colombian population. Two groups were analyzed: i) 408 Colombian blood donors infected with HCV (n = 250) and HBV (n = 158) from Bogotá and ii) 99 indigenous people with HBV infection from Leticia, Amazonas. A fragment of 344 bp from the 5' untranslated region (5' UTR) was amplified by nested RT PCR. Viral sequences were genotyped by phylogenetic analysis using reference sequences from each genotype obtained from GenBank (n = 160). Bayesian phylogenetic analyses were conducted using Markov chain Monte Carlo (MCMC) approach to obtain the MCC tree using BEAST v.1.5.3. Among blood donors, from 158 HBsAg positive samples, eight 5.06% (n = 8) were positive for GBV-C and from 250 anti-HCV positive samples, 3.2%(n = 8) were positive for GBV-C. Also, 7.7% (n = 7) GBV-C positive samples were found among indigenous people from Leticia. A phylogenetic analysis revealed the presence of the following GBV-C genotypes among blood donors: 2a (41.6%), 1 (33.3%), 3 (16.6%) and 2b (8.3%). All genotype 1 sequences were found in co-infection with HBV and 4/5 sequences genotype 2a were found in co-infection with HCV. All sequences from indigenous people from Leticia were classified as genotype 3. The presence of GBV-C infection was not correlated with the sex (p = 0.43), age (p = 0.38) or origin (p = 0.17). It was found a high frequency of GBV-C genotype 1 and 2 in blood donors. The presence of genotype 3 in indigenous population was previously reported from Santa Marta region in Colombia and in native people from Venezuela and

  9. Frequency and genotypic distribution of GB virus C (GBV-C among Colombian population with Hepatitis B (HBV or Hepatitis C (HCV infection

    Directory of Open Access Journals (Sweden)

    Carrilho Flair J

    2011-07-01

    Full Text Available Abstract Background GB virus C (GBV-C is an enveloped positive-sense ssRNA virus belonging to the Flaviviridae family. Studies on the genetic variability of the GBV-C reveals the existence of six genotypes: genotype 1 predominates in West Africa, genotype 2 in Europe and America, genotype 3 in Asia, genotype 4 in Southwest Asia, genotype 5 in South Africa and genotype 6 in Indonesia. The aim of this study was to determine the frequency and genotypic distribution of GBV-C in the Colombian population. Methods Two groups were analyzed: i 408 Colombian blood donors infected with HCV (n = 250 and HBV (n = 158 from Bogotá and ii 99 indigenous people with HBV infection from Leticia, Amazonas. A fragment of 344 bp from the 5' untranslated region (5' UTR was amplified by nested RT PCR. Viral sequences were genotyped by phylogenetic analysis using reference sequences from each genotype obtained from GenBank (n = 160. Bayesian phylogenetic analyses were conducted using Markov chain Monte Carlo (MCMC approach to obtain the MCC tree using BEAST v.1.5.3. Results Among blood donors, from 158 HBsAg positive samples, eight 5.06% (n = 8 were positive for GBV-C and from 250 anti-HCV positive samples, 3.2%(n = 8 were positive for GBV-C. Also, 7.7% (n = 7 GBV-C positive samples were found among indigenous people from Leticia. A phylogenetic analysis revealed the presence of the following GBV-C genotypes among blood donors: 2a (41.6%, 1 (33.3%, 3 (16.6% and 2b (8.3%. All genotype 1 sequences were found in co-infection with HBV and 4/5 sequences genotype 2a were found in co-infection with HCV. All sequences from indigenous people from Leticia were classified as genotype 3. The presence of GBV-C infection was not correlated with the sex (p = 0.43, age (p = 0.38 or origin (p = 0.17. Conclusions It was found a high frequency of GBV-C genotype 1 and 2 in blood donors. The presence of genotype 3 in indigenous population was previously reported from Santa Marta region in

  10. Thymidylate synthase genotype-directed chemotherapy for patients with gastric and gastroesophageal junction cancers.

    Directory of Open Access Journals (Sweden)

    Laura W Goff

    Full Text Available Retrospective studies indicate associations between TSER (thymidylate synthase enhancer region genotypes and clinical outcomes in patients receiving 5-FU based chemotherapy, but well-controlled prospective validation has been lacking.In this phase II study (NCT00515216 registered through ClinicalTrials.gov, http://clinicaltrials.gov/show/NCT00515216, patients with "good risk" TSER genotypes (at least one TSER*2 allele were treated with FOLFOX chemotherapy to determine whether prospective patient selection can improve overall response rates (ORR in patients with gastric and gastroesophageal junction (GEJ cancers, compared with historical outcomes in unselected patients (estimated 43%.The ORR in genotype-selected patients was 39.1% (9 partial responses out of 23 evaluable patients, 95% CI, 22.2 to 59.2, not achieving the primary objective of improving ORR. An encouraging disease control rate (DCR, consisting of partial responses and stable diseases of 95.7% was noted and patients with homozygous TSER*2 genotype showed better tumor response.In this first prospective, multi-institutional study in patients with gastric or GEJ cancers, selecting patients with at least one TSER*2 allele did not improve the ORR but led to an encouraging DCR. Further studies are needed to investigate the utility of selecting patients homozygous for the TSER*2 allele and additional genomic markers in improving clinical outcomes for patients with gastric and GEJ cancers.ClinicalTrials.gov NCT00515216.

  11. Tunisian Toxoplasma gondii strains genotyping by the use of AK69 marker

    Directory of Open Access Journals (Sweden)

    Aoun Karim

    2011-08-01

    Full Text Available Abstract Background Clinical manifestation due to infection by Toxoplasma gondii is closely linked to the infecting strain of the parasite. Several genetic markers are available to determinate its genotype but few of them are able to discriminate between the three predominant lineages, namely types I, II and III. The number of markers decreases when atypical, recombinant/mixed genotypes need to be identified. Findings In our study, the contribution of sequence polymorphisms in the AK69 gene as typing markers for T. gondii was investigated for the first time in an epidemiological study. The coding region of the marker was amplified, sequenced and aligned for different Toxoplasma strains. The identified nucleotide polymorphism at 12 positions was able to highly discriminate between the different congenital toxoplasmosis Tunisian strains. Moreover the high detection sensitivity level of the marker enabled unambiguous identification of mixed/recombinant genotypes directly. Conclusion It can be, thus, very useful for direct typing in areas where such genotypes are frequently encountered, mainly in the African continent.

  12. Renin-angiotensin-aldosterone genotype influences ventricular remodeling in infants with single ventricle.

    Science.gov (United States)

    Mital, Seema; Chung, Wendy K; Colan, Steven D; Sleeper, Lynn A; Manlhiot, Cedric; Arrington, Cammon B; Cnota, James F; Graham, Eric M; Mitchell, Michael E; Goldmuntz, Elizabeth; Li, Jennifer S; Levine, Jami C; Lee, Teresa M; Margossian, Renee; Hsu, Daphne T

    2011-05-31

    We investigated the effect of polymorphisms in the renin-angiotensin-aldosterone system (RAAS) genes on ventricular remodeling, growth, renal function, and response to enalapril in infants with single ventricle. Single ventricle infants enrolled in a randomized trial of enalapril were genotyped for polymorphisms in 5 genes: angiotensinogen, angiotensin-converting enzyme, angiotensin II type 1 receptor, aldosterone synthase, and chymase. Alleles associated with renin-angiotensin-aldosterone system upregulation were classified as risk alleles. Ventricular mass, volume, somatic growth, renal function using estimated glomerular filtration rate, and response to enalapril were compared between patients with ≥2 homozygous risk genotypes (high risk), and those with SCPC) and at age 14 months. Of 230 trial subjects, 154 were genotyped: Thirty-eight were high risk, and 116 were low risk. Ventricular mass and volume were elevated in both groups pre-SCPC. Ventricular mass and volume decreased and estimated glomerular filtration rate increased after SCPC in the low-risk (PSCPC surgery, less improvement in renal function, and impaired somatic growth, the latter especially in patients receiving enalapril. Renin-angiotensin-aldosterone system genotype may identify a high-risk subgroup of single ventricle patients who fail to fully benefit from volume-unloading surgery. Follow-up is warranted to assess long-term impact. http://www.clinicaltrials.gov. Unique identifier: NCT00113087.

  13. CXCL12 chemokine genotypes as predictive biomarkers of ovarian cancer outcome.

    Science.gov (United States)

    Coelho, Ana; Pereira, Deolinda; Nogal, Ana; Pinto, Daniela; Catarino, Raquel; Araújo, António; Medeiros, Rui

    2009-01-01

    Ovarian cancer is an aggressive disease with high mortality. The CXCL12 chemokine has been associated with the development of this neoplasia. The aim of this study was to evaluate the genetic influence of the CXCL12-3'A polymorphism as a prognostic/predictive factor in ovarian cancer patients treated with platinum/paclitaxel chemotherapy. The mean survival rates for early stages (I/II) of the disease were statistically different according to patient genotype (96 months for GG and 57 months for A carrier genotypes; p=0.017). The mean progression-free interval was statistically lower in patients with early stages (I/II) of the tumour carrying the A allele (55 months) than in those carrying the GG genotype (91 months; P=0.009). The CXCL12-3'A polymorphism leads to a poorer response to chemotherapy with cisplatin/paclitaxel, and diminishes the mean survival rate and the progression-free interval in patients with ovarian cancer. CXCL12-3'A may therefore serve as an important predictive biomarker for the determination of outcome in ovarian cancer.

  14. Worldwide Genotyping in the Planktonic Foraminifer Globoconella inflata: Implications for Life History and Paleoceanography

    Science.gov (United States)

    Morard, Raphaël; Quillévéré, Frédéric; Douady, Christophe J.; de Vargas, Colomban; de Garidel-Thoron, Thibault; Escarguel, Gilles

    2011-01-01

    The planktonic foraminiferal morpho-species Globoconella inflata is widely used as a stratigraphic and paleoceanographic index. While G. inflata was until now regarded as a single species, we show that it rather constitutes a complex of two pseudo-cryptic species. Our study is based on SSU and ITS rDNA sequence analyses and genotyping of 497 individuals collected at 49 oceanic stations covering the worldwide range of the morpho-species. Phylogenetic analyses unveil the presence of two divergent genotypes. Type I inhabits transitional and subtropical waters of both hemispheres, while Type II is restricted to the Antarctic subpolar waters. The two genetic species exhibit a strictly allopatric distribution on each side of the Antarctic Subpolar Front. On the other hand, sediment data show that G. inflata was restricted to transitional and subtropical environments since the early Pliocene, and expanded its geographic range to southern subpolar waters ∼700 kyrs ago, during marine isotopic stage 17. This datum may correspond to a peripatric speciation event that led to the partition of an ancestral genotype into two distinct evolutionary units. Biometric measurements performed on individual G. inflata from plankton tows north and south of the Antarctic Subpolar Front indicate that Types I and II display slight but significant differences in shell morphology. These morphological differences may allow recognition of the G. inflata pseudo-cryptic species back into the fossil record, which in turn may contribute to monitor past movements of the Antarctic Subpolar Front during the middle and late Pleistocene. PMID:22028935

  15. Genotype-Phenotype Correlations of β-Thalassemia Mutations in an Azerbaijani Population

    Directory of Open Access Journals (Sweden)

    Chingiz Asadov

    2017-09-01

    Full Text Available β-Thalassemia is the most common inherited disorder in Azerbaijan. The aim of our study was to reveal genotype-to-phenotype correlations of the most common β-thalassemia mutations in an Azerbaijani population. Patients with codon 8 (-AA, IVS-I-6 (T>C, and IVS-II-1 (G>A mutations, which are reportedly the most common β-globin gene mutations among the local population, were tested for hematologic parameters. Fifty-five previously tested patients with known genotypes were included in the study. Hematologic indices and hemoglobin fractions were tested in order to reveal the phenotypic manifestation of the mutations. The results obtained indicate that clinical presentation varies between different β-globin gene mutations: individuals with IVS-I-6 (T>C mutations showed milder presentation than those with codon 8 (-AA and IVS-II-1 (G>A, which is associated with the molecular basis of the mutations. These data can be of assistance to predict clinical presentation and select the best possible therapeutic approach via early genotype identification.

  16. Detection of human papillomavirus genotypes in cervical intraepithelial neoplasia and invasive cancer patients: Sharkia Governorate, Egypt.

    Science.gov (United States)

    Abd El-Azim, Shymaa; Lotfy, Mohamed; Omr, Ayman

    2011-01-01

    Cervical cancer (CCA) is the 2nd most common cancer among women worldwide. For approximately 2 years now, CCA has been converted from an oncological disease to an infectious disease, almost certainly caused by Human papillomavirus (HPV). Development of effective vaccines against the virus has created considerable issue world-wide and has major implications for both primary and secondary prevention strategies. The objective of this study was to establish the prevalence and genotype distribution of HPV in preinvasive, cervical intraepithelial neoplasia (CIN II and III) and invasive CCA in Sharkia governorate, Egypt. This study included 42 patients with CIN II and III, 30 patients with invasive CCA, and 45 controls who had undergone hysterectomy for any cause other than CCA. HPV detection and genotyping in cervical biopsies by Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism (RFLP). HPV DNA was detected in 85.7% (36/42) patients with CIN II and III. HPV genotypes were arranged in order of decreasing frequency as follows: HPV 16 being detected in 50.0% (21/42), HPV 45 in 143% (6/42) HPV 33 in 11.9% (5/42), HPV 18 in 9.5% (4/42) and HPV 31 in 7.1% (3/42) cases. In patients with invasive CCA, 93.3% (28/30) were positive for HPV DNA. In order of decreasing frequency, HPV genotypes were: HPV 16 being detected in 66.7% (20/30), HPV 18 in 16.7% (5/30), HPV 33 in 10.0% (3 /30) and both HPV 31 and HPV 45 in 6.7% (2/30) cases. About 13.3% invasive cervical cancer and 7.1% CIN II & III specimens exhibited multiple infections without significant difference (P > 0.05). HPV 16 and 33 infections show a higher risk for development of advanced stages of invasive CCA but without a statistically significant difference. The high prevalence of HPV genotypes 16, 18, and 45 in Sharkia governorate, Egypt, deserves attention as it has important implications for the usefulness of vaccine in prevention of a significant proportion of CCA and the choice of diagnostic

  17. 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.

  18. Daclatasvir plus simeprevir with or without ribavirin for the treatment of chronic hepatitis C virus genotype 1 infection.

    Science.gov (United States)

    Zeuzem, Stefan; Hézode, Christophe; Bronowicki, Jean-Pierre; Loustaud-Ratti, Veronique; Gea, Francisco; Buti, Maria; Olveira, Antonio; Banyai, Tivadar; Al-Assi, M Tarek; Petersen, Joerg; Thabut, Dominique; Gadano, Adrian; Pruitt, Ronald; Makara, Mihály; Bourlière, Marc; Pol, Stanislas; Beumont-Mauviel, Maria; Ouwerkerk-Mahadevan, Sivi; Picchio, Gaston; Bifano, Marc; McPhee, Fiona; Boparai, Navdeep; Cheung, Kin; Hughes, Eric A; Noviello, Stephanie

    2016-02-01

    We evaluated the combination of daclatasvir (pan-genotypic NS5A inhibitor) and simeprevir (NS3/4A protease inhibitor), with or without ribavirin, in hepatitis C virus genotype 1-infected patients. This phase II, open-label study enrolled treatment-naive patients or prior null responders with genotype 1b (n=147) or 1a (n=21) infection. Genotype 1b-infected patients were randomized 1:1 to receive daclatasvir 30mg plus simeprevir 150mg once daily with or without ribavirin; those who completed the initial 12-week treatment were re-randomized 1:1 to stop treatment or continue treatment through to week 24. Genotype 1a-infected patients received daclatasvir plus simeprevir with ribavirin for 24weeks. The primary endpoint was the proportion of patients with sustained virologic response at posttreatment week 12 (SVR12). For genotype 1b, 84.9% (45/53) and 74.5% (38/51) of treatment-naive patients and 69.6% (16/23) and 95.0% (19/20) of prior null responders to peginterferon and ribavirin achieved SVR12 with daclatasvir plus simeprevir alone and with ribavirin, respectively. Treatment duration did not have a well-defined impact on response. For genotype 1a, daclatasvir plus simeprevir with ribavirin provided a 66.7% (8/12) response rate in treatment-naive patients and was not effective in prior null responders. Data suggest that baseline resistance polymorphisms influenced SVR12 rates. Daclatasvir plus simeprevir was well tolerated with or without ribavirin with low incidences of serious adverse events and adverse events leading to discontinuation. Daclatasvir plus simeprevir, with or without ribavirin, was effective with a 12- or 24-week duration in genotype 1b-infected patients and was well tolerated. ClinicalTrials.gov identifier: NCT01628692. Copyright © 2015 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

  19. Molecular surveillance of Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi by genotyping and subtyping parasites in wastewater.

    Directory of Open Access Journals (Sweden)

    Na Li

    Full Text Available BACKGROUND: Despite their wide occurrence, cryptosporidiosis and giardiasis are considered neglected diseases by the World Health Organization. The epidemiology of these diseases and microsporidiosis in humans in developing countries is poorly understood. The high concentration of pathogens in raw sewage makes the characterization of the transmission of these pathogens simple through the genotype and subtype analysis of a small number of samples. METHODOLOGY/PRINCIPAL FINDINGS: The distribution of genotypes and subtypes of Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi in 386 samples of combined sewer systems from Shanghai, Nanjing and Wuhan and the sewer system in Qingdao in China was determined using PCR-sequencing tools. Eimeria spp. were also genotyped to assess the contribution of domestic animals to Cryptosporidium spp., G. duodenalis, and E. bieneusi in wastewater. The high occurrence of Cryptosporidium spp. (56.2%, G. duodenalis (82.6%, E. bieneusi (87.6%, and Eimeria/Cyclospora (80.3% made the source attribution possible. As expected, several human-pathogenic species/genotypes, including Cryptosporidium hominis, Cryptosporidium meleagridis, G. duodenalis sub-assemblage A-II, and E. bieneusi genotype D, were the dominant parasites in wastewater. In addition to humans, the common presence of Cryptosporidium spp. and Eimeria spp. from rodents indicated that rodents might have contributed to the occurrence of E. bieneusi genotype D in samples. Likewise, the finding of Eimeria spp. and Cryptosporidium baileyi from birds indicated that C. meleagridis might be of both human and bird origins. CONCLUSIONS/SIGNIFICANCE: The distribution of Cryptosporidium species, G. duodenalis genotypes and subtypes, and E. bieneusi genotypes in urban wastewater indicates that anthroponotic transmission appeared to be important in epidemiology of cryptosporidiosis, giardiasis, and microsporidiosis in the study areas. The finding of

  20. Role of CYP2E1 genotypes in susceptibility to colorectal cancer in the Kashmiri population

    Directory of Open Access Journals (Sweden)

    Sameer A

    2011-10-01

    Full Text Available Abstract Cytochrome P450 2E1 (CYP2E1 is a key enzyme involved in the metabolic activation of procarcinogens such as N-nitrosoamines and low-molecular-weight organic compounds. The main aim of this study was to determine whether CYP450 2E1 polymorphisms are associated with the risk of colorectal cancer (CRC. We investigated the genotype distribution of the CYP2E1 gene RsaI and a 96-base pair (bp insertion in 86 CRC cases in comparison with 160 healthy subjects. We found the frequency of the CYP2E1 RsaI genotype to be 53.5 per cent (46/86 for c1/c1, 17.4 per cent (15/86 for c1/c2 and 29.1 per cent (25/86 for c2/c2, and the CYP2E1 98-bp insertion frequencies to be 63.9 per cent (55/86 for non-insertion (i/i, 22.1 per cent (19/86 for heterozygous insertion (i/I and 36.0 per cent (12/86 for homozygous insertion (I/I among CRC cases. We also found the CYP2E1 RsaI c2/c2 and CYP2E1 98-bp heterozygous i/I genotypes to be significantly associated with an increased risk of CRC (p = 0.01. We suggest that CYP2E1 polymorphisms are involved in the susceptibility to developing CRC in the ethnic Kashmiri population.

  1. 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.......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....

  2. Comparison of the digene HPV genotyping LQ test and the PANArray HPV genotyping chip for detection of high-risk or probable high-risk human papillomavirus genotypes.

    Science.gov (United States)

    Park, Kyung Sun; Kim, Ji-Youn; Ki, Chang-Seok; Lee, Nam Yong

    2014-07-01

    We evaluated the performance of two different array-based techniques, a bead-based multiplex genotyping method (LQ; digene HPV Genotyping LQ Test, QIAGEN, Germany) and a DNA chip-based method using peptide nucleic acid probes (PANArray; PANArray HPV Genotyping Chip, Panagene, Korea), for detection of human papillomavirus (HPV) and genotyping of high-risk (HR) or probable high-risk (PHR) HPVs in healthy patients who visited a health-promotion center. We obtained 508 unselected, consecutive cervicovaginal swab specimens. All specimens were examined by using the PANArray and LQ tests. All HPV-positive samples were then analyzed by multiplex PCR and direct sequencing. The LQ test detected 47 HPV-positive cases (9.3%) with HR or PHR genotypes and the PANArray test identified 36 cases (7.1%). When the results of LQ and PANArray were compared by using comprehensive genotyping (integrated interpretation of the results of LQ, PANArray, multiplex PCR, and direct sequencing) for the detection of HR or PHR genotypes, the kappa values were 0.44 and 0.30 for LQ and PANArray, respectively. In comparison to comprehensive genotyping, the LQ test yielded 53 (60.0%) concordant and 12 (13.5%) compatible results, and the PANArray yielded 36 (40.4%) concordant and three (3.4%) compatible results. The results of the LQ test had higher concordance and/or greater compatibility with those of comprehensive genotyping for the detection of HR or PHR genotypes than those of the PANArray test.

  3. HLA class II haplotypes differentiate between the adult autoimmune polyglandular syndrome types II and III.

    Science.gov (United States)

    Flesch, B K; Matheis, N; Alt, T; Weinstock, C; Bux, J; Kahaly, G J

    2014-01-01

    Genetics of the adult autoimmune polyglandular syndrome (APS) is poorly understood. The aim of this study was to gain further insight into the genetics of the adult APS types. SITE: The study was conducted at a university referral center. The human leukocyte antigen (HLA) class II alleles, haplotypes, and genotypes were determined in a large cohort of patients with APS, autoimmune thyroid disease (AITD), and type 1 diabetes and in healthy controls by the consistent application of high-resolution typing at a four-digit level. Comparison of the allele and haplotype frequencies significantly discriminated patients with APS vs AITD and controls. The HLA class II alleles DRB1*03:01 *04:01, DQA1*03:01, *05:01, DQB1*02:01, and *03:02 were observed more frequently (Pdisease (APS type II) and those without Addison's disease but including type 1 diabetes and AITD (APS type III) demonstrated DR3-DQ2/DRB1*04:01-DQ8 as a susceptibility genotype in APS III (Pctype II (Pctypes II and III. Susceptible haplotypes favor the development of polyglandular autoimmunity in patients with AITD.

  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. 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

  6. Effect of Genotype and Age on Some Morphometric, Body Linear ...

    African Journals Online (AJOL)

    A population of 231 roosters of the Nigerian indigenous chickens of normal feathered frizzle feathered and naked neck genotypes was evaluated for the effect of genotype and age on some morphometric body linear measurements and semen characteristics of three Nigerian chicken genotypes. 20 roosters from each ...

  7. Genotype by environment interactions and yield stability of stem ...

    African Journals Online (AJOL)

    GREGORY

    2011-06-01

    Jun 1, 2011 ... In a maize breeding program, potential genotypes are usually evaluated in different environments before desirable ones are selected. Genotype x environment (G x E) interaction is associated with the differential performance of genotypes tested at different locations and in different years, and influences ...

  8. Grain yield assessment of six pigeonpea genotypes in production ...

    African Journals Online (AJOL)

    Five improved pigeonpea genotypes obtained from ICRISAT of short- and medium-duration and a Nsukka local long-duration genotype were assessed for their grain yield in mixtures with two maize genotypes (hybrid and open pollinated types) and as sole crops in 2006 at Nsukka, Nigeria. The 2006 pigeonpea plants were ...

  9. Hepatitis B virus Genotypes in West Azarbayjan Province, Northwest Iran

    Directory of Open Access Journals (Sweden)

    Mohammad Hasan Khadem Ansari

    2017-12-01

    CONCLUSIONS: The results reveal that D genotype is the main genotype of HBV in West Azarbayjan province. Presence of this genotype conformed with the low rate of acute liver diseases caused by hepatitis B chronic infection, cirrhosis of the liver and hepatocellular carcinoma.

  10. Characterization of Kenyan sweet potato genotypes for SPVD ...

    African Journals Online (AJOL)

    had an average polymorphic information content (PIC) of 0.47. The average number of alleles within the 89 genotypes across the 6 loci was 13.52. Cluster analyses revealed a 50% variation among the 89 genotypes. The dendrogram did not reveal any unique clustering of the genotypes according to dry matter content and ...

  11. Core Gene Expression and Association of Genotypes with Viral ...

    African Journals Online (AJOL)

    Purpose: To determine genotypic distribution, ribonucleic acid (RNA) RNA viral load and express core gene from Hepatitis C Virus (HCV) infected patients in Punjab, Pakistan. Methods: A total of 1690 HCV RNA positive patients were included in the study. HCV genotyping was tested by type-specific genotyping assay, viral ...

  12. Genotype x Environment Interaction for Tuber Yield, Dry Matter ...

    African Journals Online (AJOL)

    A study was conducted to determine stability of tuber yield, dry matter content and specific gravity, and the nature and magnitude of genotype x environment (G x E) interaction in elite tetraploid potato genotypes. Eleven potato genotypes including two standard checks were evaluated in the eastern part of Ethiopia at ...

  13. Introduction to a special issue on genotype by environment interaction

    Science.gov (United States)

    Expression of a phenotype is a function of the genotype, the environment, and the differential sensitivity of certain genotypes to different environments, also known as genotype by environment (G × E) interaction. This special issue of Crop Science includes a collection of manuscripts that reviews t...

  14. Genotype by environment interactions and yield stability of stem ...

    African Journals Online (AJOL)

    In a maize breeding program, potential genotypes are usually evaluated in different environments before desirable ones are selected. Genotype x environment (G x E) interaction is associated with the differential performance of genotypes tested at different locations and in different years, and influences selection and ...

  15. Genotype-based personalised nutrition for obesity prevention and ...

    African Journals Online (AJOL)

    Typically, genotype-based personalised nutrition involves genotyping for a number of susceptibility SNPs associated with the prevention, or management, of a particular disease. Dietary advice is then personalised to the individual's genotype to ensure optimal prevention or treatment outcomes. To ensure evidence-based ...

  16. Genotype identification and inference of genetic relatedness among ...

    African Journals Online (AJOL)

    The unweighted Neighbour-Joining tree generated using DARwin 5.0 software classified the germplasm into three different clusters. The grouping of the different genotypes in the tree had distinct order. Genotypes derived from the same species were in one group, while the genotypes having both or one parents common in ...

  17. Reactions of some potato genotypes to late blight in Cameroon ...

    African Journals Online (AJOL)

    Reactions of some potato genotypes to late blight in Cameroon. D. K. Njualem, P. Demo, H. A. Mendoza, J. T. Koi, S. F. Nana. Abstract. Field experiments were conducted in Cameroon in 1995 and 1996 to evaluate reactions of different potato genotypes to late blight. There were significant differences among genotypes for ...

  18. Assessment of rice genotypes for salt tolerance using microsatellite ...

    African Journals Online (AJOL)

    The results of phenotypic response of rice genotypes to salinity stress at the seedling stage indicated the varied genotypic responses. The genotypes were classified into five groups from highly tolerant (score 1) to highly sensitive (score 9). Number of alleles of the SSR markers ranged from 3 for RM10702 to 14 for RM8094.

  19. relationship of status of polymorphic rapd bands with genotypic

    African Journals Online (AJOL)

    jen

    Department of Plant Breeding and Genetics, College of Agriculture, Orissa University of Agriculture and. Technology ... millet may give some indication about specific adaptability of genotypes to poor environments. ... ments. These findings may help to predict the genotypic adaptation of different genotypes before going for.

  20. genotype by environment interaction and grain yield stability

    African Journals Online (AJOL)

    Preferred Customer

    IPCA, γgn is the genotype eigenvector for axis n, and δen is the environment eigenvector; εger is error term and ρge is PCA residual. Accordingly, genotypes with low magnitude regardless of the sign of interaction principal component analysis scores have general or wider adaptability while genotypes with high magnitude ...

  1. Genotype x row spacing and environment interaction of cowpea in ...

    African Journals Online (AJOL)

    Genotype x within row spacing interaction effects were not significant, suggesting that selection at low densities would be effective in identifying superior and productive genotypes for further testing in either within row spacing. Because of significant genotype x environment and WRS interaction effects, this effectiveness ...

  2. 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. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  3. Learning monotonic genotype-phenotype maps.

    Science.gov (United States)

    Beerenwinkel, Niko; Knupfer, Patrick; Tresch, Achim

    2011-01-01

    Evolutionary escape of pathogens from the selective pressure of immune responses and from medical interventions is driven by the accumulation of mutations. We introduce a statistical model for jointly estimating the dynamics and dependencies among genetic alterations and the associated phenotypic changes. The model integrates conjunctive Bayesian networks, which define a partial order on the occurrences of genetic events, with isotonic regression. The resulting genotype-phenotype map is non-decreasing in the lattice of genotypes. It describes evolutionary escape as a directed process following a phenotypic gradient, such as a monotonic fitness landscape. We present efficient algorithms for parameter estimation and model selection. The model is validated using simulated data and applied to HIV drug resistance data. We find that the effect of many resistance mutations is non-linear and depends on the genetic background in which they occur.

  4. 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

    . 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......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...... explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the zoonotic potential of G. duodenalis is evident, evidence on the contribution and frequency is (still) lacking. This newly developed molecular database has...

  5. 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

  6. Genome structural variation discovery and genotyping

    OpenAIRE

    Alkan, Can; Coe, Bradley P.; Eichler, Evan E.

    2011-01-01

    Comparisons of human genomes show that more base pairs are altered as a result of structural variation — including copy number variation — than as a result of point mutations. Here we review advances and challenges in the discovery and genotyping of structural variation. The recent application of massively parallel sequencing methods has complemented microarray-based methods and has led to an exponential increase in the discovery of smaller structural-variation events. Some glo...

  7. Genotype and phenotype data analysis and visualization

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    Alma Molytė

    2013-09-01

    Full Text Available In this paper, we present a comparative analysis of hierarchical clustering and multidimensional scaling methods for genotype and phenotype data analysis. Fisher's exact test was applied to determinate dependencies between congenital anomalies. In order to determine the relationship between the dependences of congenital anomalies, deformations, these systems’ micro anomalies and congenital anomalies associated with orofacial clefs, the Spearman and Kendall correlation coefficients were applied. It has been detected which methods are better for genetic data visualization.

  8. Canine hip dysplasia is predictable by genotyping.

    Science.gov (United States)

    Guo, G; Zhou, Z; Wang, Y; Zhao, K; Zhu, L; Lust, G; Hunter, L; Friedenberg, S; Li, J; Zhang, Y; Harris, S; Jones, P; Sandler, J; Krotscheck, U; Todhunter, R; Zhang, Z

    2011-04-01

    To establish a predictive method using whole genome genotyping for early intervention in canine hip dysplasia (CHD) risk management, for the prevention of the progression of secondary osteoarthritis (OA), and for selective breeding. Two sets of dogs (six breeds) were genotyped with dense SNPs covering the entire canine genome. The first set contained 359 dogs upon which a predictive formula for genomic breeding value (GBV) was derived by using their estimated breeding value (EBV) of the Norberg angle (a measure of CHD) and their genotypes. To investigate how well the formula would work for an individual dog with genotype only (without using EBV), a cross validation was performed by masking the EBV of one dog at a time. The genomic data and the EBV of the remaining dogs were used to predict the GBV for the single dog that was left out. The second set of dogs included 38 new Labrador retriever dogs, which had no pedigree relationship to the dogs in the first set. The cross validation showed a strong correlation (R>0.7) between the EBV and the GBV. The independent validation showed a moderate correlation (R=0.5) between GBV for the Norberg angle and the observed Norberg angle (no EBV was available for the new 38 dogs). Sensitivity, specificity, positive and negative predictive values of the genomic data were all above 70%. Prediction of CHD from genomic data is feasible, and can be applied for risk management of CHD and early selection for genetic improvement to reduce the prevalence of CHD in breeding programs. The prediction can be implemented before maturity, at which age current radiographic screening programs are traditionally applied, and as soon as DNA is available. Copyright © 2010 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

  9. Canine Hip Dysplasia is Predictable by Genotyping

    Science.gov (United States)

    Guo, Gang; Zhou, Zhengkui; Wang, Yachun; Zhao, Keyan; Zhu, Lan; Lust, George; Hunter, Linda; Friedenberg, Steven; Li, Junya; Zhang, Yuan; Harris, Stephen; Jones, Paul; Sandler, Jody; Krotscheck, Ursula; Todhunter, Rory; Zhang, Zhiwu

    2011-01-01

    Summary Objective To establish a predictive method using whole genome genotyping for early intervention in canine hip dysplasia (CHD) risk management, for the prevention of the progression of secondary osteoarthritis (OA), and for selective breeding. Design Two sets of dogs (6 breeds) were genotyped with dense SNPs covering the entire canine genome. The first set contained 359 dogs upon which a predictive formula for genomic breeding value (GBV) was derived by using their estimated breeding value (EBV) of the Norberg angle (a measure of CHD) and their genotypes. To investigate how well the formula would work for an individual dog with genotype only (without using EBV or phenotype), a cross validation was performed by masking the EBV of one dog at a time. The genomic data and the EBV of the remaining dogs were used to predict the GBV for the single dog that was left out. The second set of dogs included 38 new Labrador retriever dogs, which had no pedigree relationship to the dogs in the first set. Results The cross validation showed a strong correlation (r>0.7) between the EBV and the GBV. The independent validation showed a strong correlation (r=0.5) between GBV for the Norberg angle and the observed Norberg angle (no EBV was available for the new 38 dogs). Sensitivity, specificity, positive, and negative predictive value of the genomic data were all above 70%. Conclusions Prediction of CHD from genomic data is feasible, and can be applied for risk management of CHD and early selection for genetic improvement to reduce the prevalence of CHD in breeding programs. The prediction can be implemented before maturity, at which age current radiographic screening programs are traditionally applied, and as soon as DNA is available. PMID:21215318

  10. Intraspecies genotypic heterogeneity among Mycoplasma gallisepticum strains.

    OpenAIRE

    Santha, M; Lukacs, K; Burg, K; Bernath, S; Rasko, I; Stipkovits, L.

    1988-01-01

    The DNA cleavage patterns and protein profiles of six Mycoplasma gallisepticum strains from various parts of the world were compared. Obvious differences among the strains were obtained by DNA restriction analysis. Reflection of genotypic variations in the polypeptide patterns was less pronounced; slight differences in the protein profiles of the strains were found. The data presented here indicate that some intraspecies polymorphism exists among M. gallisepticum strains.

  11. Intraspecies genotypic heterogeneity among Mycoplasma gallisepticum strains.

    Science.gov (United States)

    Santha, M; Lukacs, K; Burg, K; Bernath, S; Rasko, I; Stipkovits, L

    1988-01-01

    The DNA cleavage patterns and protein profiles of six Mycoplasma gallisepticum strains from various parts of the world were compared. Obvious differences among the strains were obtained by DNA restriction analysis. Reflection of genotypic variations in the polypeptide patterns was less pronounced; slight differences in the protein profiles of the strains were found. The data presented here indicate that some intraspecies polymorphism exists among M. gallisepticum strains. PMID:2895605

  12. Wheat genotypes under different seeding rates

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    Luís César Vieira Tavares

    2014-06-01

    Full Text Available The wheat tillering capacity defines yield and yield components, being affected by seeding rate. This study aimed at evaluating wheat genotypes under different seeding rates, in Londrina and Ponta Grossa, Paraná State, Brazil, in 2009 and 2010. A completely randomized blocks design, in a factorial scheme, with four replications, was used. The agronomic traits of three wheat genotypes (PF 014384, BRS Tangará and BRS Pardela were evaluated under the seeding rates of 150 pl m-2, 250 pl m-2, 350 pl m-2 and 450 pl m-2. In Londrina, the maximum yield was observed at densities close to 270 pl m-2, while in Ponta Grossa (2009 there was a linear fit. There was no adjustment for plant height, concerning seeding rate. The number of ears per area (ears m-2 was higher in Ponta Grossa (2009 and did not differ between the locations, in 2010. In Ponta Grossa (2010, the highest one thousand seeds weight was estimated at the density of 341 pl m-2, while in Londrina (2010 it was estimated at 150 pl m-2 and 450 pl m-2. The seeding rate affected grain yield, depending on place and year. In Londrina, there was a limit for yield, concerning seeding rate. The one thousand seeds weight was influenced by seeding rate, depending on year and location. Plant height was affected by genotype and growing area.

  13. Screening cotton genotypes for seedling drought tolerance

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    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.

  14. The genotype role in maize competitive ability

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    Simić Milena

    2009-01-01

    Full Text Available Growing competitive crops is an important component of the integrated weed management system, although selection of genotypes with the increased competitive ability is rather difficult. The possibility of reducing weed infestation by increasing the competitive activity of crops by growing genotypes, i.e. hybrids that better 'endure' a greater density, depends on the FAO maturity group and morphological properties of a genotype, environmental conditions and the growing regions. The competition between maize and weeds varies over the modified crop arrangement pattern. The greatest weed infestation is recorded in the crops of the sparse-spaced plants, while the height and the weight of weeds are significantly lower in closely-spaced plants. The height, growth intensity in the initial stages, embryo vigour and leaf area of the plant are important for a greater competitive ability, as they are components of competitive effects of crops on weeds. Weed infestation and maize hybrids yielding were studied in dependence on the hybrids arrangement pattern and the application of herbicides. Obtained results show statistically significant differences in the weed fresh weight, but only in certain years and in accordance with differences in the height and the leaf area of ZP maize hybrids.

  15. Morpho-physiological characterization of soybean genotypes under subtropical environment

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    Al-Hadi Gaffar M.A.

    2017-01-01

    Full Text Available Soybean is a promising oilseed crop in rice-based cropping systems in South and Southeast Asia. In spite of immense scope of its expansion, the crop is not being popular to the farmers because of poor yield of the existing cultivars. Therefore, this study evaluated eighty-soybean genotypes of diverse growth habits with a view to searching genotype(s of desirable morpho-physiological characters and high yield potential. Sixteen quantitative plant traits were evaluated to classify the genotypes into different groups using various multivariate methods. A wide range of variation was found in almost all qualitative plant traits. The study reveals that plants tend to become taller as the phenological cycle is longer. Seed yield was the product of the number of pods per plant, pod weight and seeds per pod. The first three components of principal component analysis explained 75% of the total variations of the soybean genotypes. Using Dendrogram from cluster analysis, the genotypes were grouped into six clusters. The maximum number of genotypes was concentrated in cluster 5 followed by clusters 4. The phenology, plant height, the number of pods and seed yield were the important discriminating variables in grouping the genotypes. The number of pods per plant displayed the principal role in explaining the maximum variance in the genotypes. The clustering pattern of the genotypes revealed that the genotypes under cluster 2 and cluster 6 were long statures, late maturing and produced higher seed yield. The genotype G00003 under cluster 2 is the best entry giving the highest seed yield. From cluster 6, the genotype G00209 could be the better choice for much better seed yield. The cluster 3 genotypes were comparatively early maturing and gave reasonable yield. It is concluded that the genotypes under clusters 2 and 6 and 3 can be important resources for developing a high yielding variety and sustainability of growing soybean in the subtropical conditions.

  16. THE EFFECT OF GENOTYPE AND SEX ON PORK QUALITY

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    Marjeta Furman

    2007-06-01

    Full Text Available The effects of genotype and sex on the most important factors for technological meat quality were analyzed. In the experiment 63 gilts and 57 barrows of three different boar genotypes (44, 54 and 74 were included. Slaughter was carried out in two groups, the first was about 100 kg and the second group was about 125 kg of live weight. After the slaughter colour of meat, pH value, drip loss and conductivity were measured and intramuscular fat was defined in laboratory. Statistical analysis of data was done with statistical package SAS/STAT with last square method where procedure for general linear models (GLM was used. The effects were genotype, sex and carcass weight as regression. The results showed that barrows had significant higher content of intramuscular fat than gilts at 100 kg (p=0.0019 and 125 kg (p<0.0001 of live weight, respectively. In other traits sex did not have an influence. Genotype had no effect on intramuscular fat content. Genotype 74 had darker meat (lower value L* in both groups. Genotype 44 had significant higher value a* and value b*. There were no differences between genotype in pH and conductivity in the first group. In the second group genotype 44 had lower pH value as genotype 54 (p=0.0345 and genotype 74 (p=0.0188 and higher conductivity (p=0.0004 and p=0.0001 on m. longissimus dorsi. On m. semimembranossus genotype 54 had higher pH than genotype 44 (p=0.0160 and lower than genotype 74 (p=0.0148. Drip loss on both muscles was higher in genotype 44 in the first group and higher than genotype 74 in the second group.

  17. Identification of polymorphic inversions from genotypes

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    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

  18. Identification of zoonotic genotypes of Giardia duodenalis.

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    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

  19. Inaccurate identification of rotavirus genotype G9 as genotype G3 strains due to primer mismatch

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    Mitui Marcelo

    2012-08-01

    Full Text Available Abstract Reverse transcription (RT-PCR is now the standard method for typing group A rotaviruses (RVA to monitor the circulating genotypes in a population. Selection of primers that can accurately type the circulating genotypes is crucial in the context of vaccine introduction and correctly interpreting the impact of vaccination on strain distribution. To our knowledge this study is the first report from Asia of misidentification of genotype G9 as G3 due to a primer-template mismatch. We tested two published G-genotype specific primers sets, designed by Gouvea and colleagues (Set A and Iturriza‐Gomara and colleagues (Set B on RVA from Hong Kong and Sri Lanka. Among 52 rotaviruses typed as G3 by set A primers, 36 (69.2% were identified as G9 by nucleotide sequencing and set B primers. Moreover, of 300 rotaviruses tested, 28.3% were untypable by set A primers whereas only 12.3% were untypable by set B primers. Our findings reinforce the need to periodically monitor the primers used for RVA genotyping.

  20. Genotyping of HCV RNA Reveals That 3a Is the Most Prevalent Genotype in Mardan, Pakistan

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    Sajid Ali

    2014-01-01

    Full Text Available The clinical outcomes of patients infected with hepatitis C virus (HCV range from acute resolving hepatitis to chronic liver diseases such as liver cirrhosis or hepatocellular carcinoma. Identification of the infecting virus genotype is indispensable for the exploration of many aspects of HCV infection, including epidemiology, pathogenesis, and response to antiviral therapy. 1419 individuals were screened for anti-HCV in this study, of which 166 (11.7% were found reactive by ICT (Immunochromatographic test. These 166 anti-HCV positive and 26 normal individuals were further analyzed. RNA was extracted from serum and reverse-transcribed to cDNA and the core region of HCV genome was targeted and amplified by multiplex PCR. HCV RNA was detected in 121 individuals, of which 87 were male and 34 were female. Genotype 3a was the most prevalent among all the genotypes observed followed by 3b. Genotypes 1a, 2a, and 2b were found in 10.89%, 13.22%, and 6.61% patients, respectively. 25.41% of the HCV RNA positive samples were not typed. 6.05% of patients were found having mixed genotypes. These findings will not only help the physicians to prescribe more appropriate treatment for the HCV infection but will also draw the attention of health-related policy makers to devise strategies to curb the disease more effectively.

  1. Inaccurate identification of rotavirus genotype G9 as genotype G3 strains due to primer mismatch.

    Science.gov (United States)

    Mitui, Marcelo Takahiro; Chandrasena, Tga Nilmini; Chan, Paul Ks; Rajindrajith, Shaman; Nelson, E Anthony S; Leung, Ting Fan; Nishizono, Akira; Ahmed, Kamruddin

    2012-08-03

    Reverse transcription (RT)-PCR is now the standard method for typing group A rotaviruses (RVA) to monitor the circulating genotypes in a population. Selection of primers that can accurately type the circulating genotypes is crucial in the context of vaccine introduction and correctly interpreting the impact of vaccination on strain distribution. To our knowledge this study is the first report from Asia of misidentification of genotype G9 as G3 due to a primer-template mismatch. We tested two published G-genotype specific primers sets, designed by Gouvea and colleagues (Set A) and Iturriza-Gomara and colleagues (Set B) on RVA from Hong Kong and Sri Lanka. Among 52 rotaviruses typed as G3 by set A primers, 36 (69.2%) were identified as G9 by nucleotide sequencing and set B primers. Moreover, of 300 rotaviruses tested, 28.3% were untypable by set A primers whereas only 12.3% were untypable by set B primers. Our findings reinforce the need to periodically monitor the primers used for RVA genotyping.

  2. Angiotensin-converting enzyme genotype and late respiratory complications of mustard gas exposure

    Science.gov (United States)

    Hosseini-khalili, Ali Reza; Thompson, Julian; Kehoe, Anthony; Hopkinson, Nicholas S; Khoshbaten, A; Soroush, Mohammad Reza; Humphries, Steve E; Montgomery, Hugh; Ghanei, Mostafa

    2008-01-01

    Background Exposure to mustard gas frequently results in long-term respiratory complications. However the factors which drive the development and progression of these complications remain unclear. The Renin Angiotensin System (RAS) has been implicated in lung inflammatory and fibrotic responses. Genetic variation within the gene coding for the Angiotensin Converting Enzyme (ACE), specifically the Insertion/Deletion polymorphism (I/D), is associated with variable levels of ACE and with the severity of several acute and chronic respiratory diseases. We hypothesized that the ACE genotype might influence the severity of late respiratory complications of mustard gas exposure. Methods 208 Kurdish patients who had suffered high exposure to mustard gas, as defined by cutaneous lesions at initial assessment, in Sardasht, Iran on June 29 1987, underwent clinical examination, spirometric evaluation and ACE Insertion/Deletion genotyping in September 2005. Results ACE genotype was determined in 207 subjects. As a continuous variable, FEV1 % predicted tended to be higher in association with the D allele 68.03 ± 20.5%, 69.4 ± 21.4% and 74.8 ± 20.1% for II, ID and DD genotypes respectively. Median FEV1 % predicted was 73 and this was taken as a cut off between groups defined as having better or worse lung function. The ACE DD genotype was overrepresented in the better spirometry group (Chi2 4.9 p = 0.03). Increasing age at the time of exposure was associated with reduced FEV1 %predicted (p = 0.001), whereas gender was not (p = 0.43). Conclusion The ACE D allele is associated with higher FEV1 % predicted when assessed 18 years after high exposure to mustard gas. PMID:18702808

  3. Angiotensin-converting enzyme genotype and late respiratory complications of mustard gas exposure

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    Humphries Steve E

    2008-08-01

    Full Text Available Abstract Background Exposure to mustard gas frequently results in long-term respiratory complications. However the factors which drive the development and progression of these complications remain unclear. The Renin Angiotensin System (RAS has been implicated in lung inflammatory and fibrotic responses. Genetic variation within the gene coding for the Angiotensin Converting Enzyme (ACE, specifically the Insertion/Deletion polymorphism (I/D, is associated with variable levels of ACE and with the severity of several acute and chronic respiratory diseases. We hypothesized that the ACE genotype might influence the severity of late respiratory complications of mustard gas exposure. Methods 208 Kurdish patients who had suffered high exposure to mustard gas, as defined by cutaneous lesions at initial assessment, in Sardasht, Iran on June 29 1987, underwent clinical examination, spirometric evaluation and ACE Insertion/Deletion genotyping in September 2005. Results ACE genotype was determined in 207 subjects. As a continuous variable, FEV1 % predicted tended to be higher in association with the D allele 68.03 ± 20.5%, 69.4 ± 21.4% and 74.8 ± 20.1% for II, ID and DD genotypes respectively. Median FEV1 % predicted was 73 and this was taken as a cut off between groups defined as having better or worse lung function. The ACE DD genotype was overrepresented in the better spirometry group (Chi2 4.9 p = 0.03. Increasing age at the time of exposure was associated with reduced FEV1 %predicted (p = 0.001, whereas gender was not (p = 0.43. Conclusion The ACE D allele is associated with higher FEV1 % predicted when assessed 18 years after high exposure to mustard gas.

  4. Joint effect of glutathione S-transferase genotypes and cigarette smoking on idiopathic male infertility.

    Science.gov (United States)

    Yarosh, S L; Kokhtenko, E V; Churnosov, M I; Solodilova, M A; Polonikov, A V

    2015-11-01

    Inconsistent results of association studies investigated the role of glutathione S-transferase genes in idiopathic male infertility may be explained by ethnical differences in gene-gene and gene-environment interactions. In this study, we investigated a joint contribution of GSTM1, GSTT1 and GSTP1 gene polymorphisms and cigarette smoking to the risk of idiopathic infertility in Russian men. DNA samples from 203 infertile and 227 fertile men were genotyped by a multiplex polymerase chain reaction (GSTM1 and GSTT1 deletions) and PCR-restriction fragment length polymorphism (GSTP1 I105V) methods. The GSTP1 genotype 105IV was associated with increased risk of male infertility (OR = 1.50 95% CI 1.02-2.20 P = 0.04). Genotype combinations GSTP1 105II/GSTT1 del (G1), GSTM1 del/GSTT1 del (G2) and GSTM1 + /GSTT1 del (G3) were associated with decreased risk of male infertility (P ≤ 0.003), whereas a genotype combination GSTP1 105IV/GSTT1 + (G4) was associated with increased disease risk (P = 0.001). The genotype combinations G3 and G4 showed a significant association with infertility in smokers; however, nonsmokers carriers did show the disease risk. In conclusion, GSTM1, GSTT1 and GSTP1 genes are collectively involved in the development of idiopathic male infertility and their phenotypic effects on the disease risk are potentiated by cigarette smoking. © 2014 Blackwell Verlag GmbH.

  5. Genotypic Differences in Architectural and Physiological Responses to Water Restriction in Rose Bush

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    Camille eLi-Marchetti

    2015-05-01

    Full Text Available The shape and, therefore, the architecture of the plant are dependent on genetic and environmental factors such as water supply. The architecture determines the visual quality, a key criterion underlying the decision to purchase an ornamental potted plant. The aim of this study was to analyze genotypic responses of eight rose bush cultivars to alternation of water restriction and re-watering periods, with soil water potential of -20kPa and -10 kPa respectively. Responses were evaluated at the architectural level through 3D digitalization using six architectural variables and at the physiological level by measuring stomatal conductance, water content, hormones (abscisic acid, auxin, cytokinins, jasmonic acid and salicylic acid, sugars (sucrose, fructose and glucose and proline. Highly significant genotype and watering effects were revealed for all the architectural variables measured, as well as genotype x watering interaction, with three distinct genotypic architectural responses to water restriction - weak, moderate and strong - represented by Hw336, ‘Baipome’ and ‘The Fairy’, respectively. The physiological analysis explained, at least in part, the more moderate architectural response of ‘Baipome’ compared to ‘The Fairy’, but not that of Hw336 which is an interspecific hybrid. Such physiological responses could be related to: (i the maintenance of the stimulation of budbreak and photosynthetic activity in ‘Baipome’ during water restriction periods due to a higher concentration in conjugated cytokinins (cCK and to a lower concentration in salicylic acid (SA; (ii a better resumption of budbreak during the re-watering periods due to a lower concentration in abscisic acid (ABA during this period. When associated with the six architectural descriptors, cCK, SA and ABA, which explained the genotypic differences in this study, could be used as selection criteria for breeding programs aimed at improving plant shape and tolerance to

  6. Citrus tristeza virus: Evolution of complex and varied genotypic groups

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    Scott J Harper

    2013-04-01

    Full Text Available 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.

  7. 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.

  8. Genotypic diversity of root and shoot characteristics of

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    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

  9. Hepatitis B virus genotype E variability in Africa.

    Science.gov (United States)

    Hübschen, Judith M; Andernach, Iris E; Muller, Claude P

    2008-12-01

    In sub-Saharan Africa, genotype E is the predominant genotype throughout a vast region spanning from Senegal to Namibia and extending to the Central African Republic in the East. Despite its wide geographic distribution and the high prevalence throughout this genotype E crescent, this genotype has a very low genetic diversity. Here we review our current understanding of genotype E reanalysing all currently available sequences of the S gene and the complete genome. Phylogenetic analysis of the complete genome sequences confirmed a previously suggested South-West/Central African cluster and several lineages of West African sequences. The overall mean genetic distance was 1.71%, with the more Southern countries of the genotype E crescent exhibiting lower distances than the Northern countries. Genotype E seems to have a longer natural history in the Northern part of the genotype E crescent than in the Southern countries. As genotype E is essentially absent from the Americas despite the Afro-American slave trade until at least the beginning of the 19th century, genotype E strains may have been introduced into the general African population only within the past 200 years. How the virus may have spread throughout the genotype E crescent warrants further investigation.

  10. 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

  11. Genotyping by genome reducing and sequencing for outbred animals.

    Directory of Open Access Journals (Sweden)

    Qiang Chen

    Full Text Available Next-generation sequencing (NGS approaches are widely used in genome-wide genetic marker discovery and genotyping. However, current NGS approaches are not easy to apply to general outbred populations (human and some major farm animals for SNP identification because of the high level of heterogeneity and phase ambiguity in the haplotype. Here, we reported a new method for SNP genotyping, called genotyping by genome reducing and sequencing (GGRS to genotype outbred species. Through an improved procedure for library preparation and a marker discovery and genotyping pipeline, the GGRS approach can genotype outbred species cost-effectively and high-reproducibly. We also evaluated the efficiency and accuracy of our approach for high-density SNP discovery and genotyping in a large genome pig species (2.8 Gb, for which more than 70,000 single nucleotide polymorphisms (SNPs can be identified for an expenditure of only $80 (USD/sample.

  12. Pathotyping and Phylogenetic Characterization of Newcastle Disease Viruses Isolated in Peru: Defining Two Novel Subgenotypes Within Genotype XII.

    Science.gov (United States)

    Chumbe, Ana; Izquierdo-Lara, Ray; Tataje, Luis; Gonzalez, Rosa; Cribillero, Giovana; González, Armando E; Fernández-Díaz, Manolo; Icochea, Eliana

    2017-03-01

    Infections of poultry with virulent strains of avian paramyxovirus 1 (APMV-1), also known as Newcastle disease viruses (NDVs), cause Newcastle disease (ND). This highly contagious disease affects poultry and many other species of birds worldwide. In countries where the disease is prevalent, constant monitoring and characterization of isolates causing outbreaks are necessary. In this study, we report the results of pathogenicity testing and phylogenetic analyses of seven NDVs isolated from several regions of Peru between 2004 and 2015. Six viruses had intracerebral pathogenicity indices (ICPIs) of between 1.75 and 1.88, corresponding to a velogenic pathotype. The remaining virus had an ICPI of 0.00, corresponding to a lentogenic pathotype. These results were consistent with amino acid sequences at the fusion protein (F) cleavage site. All velogenic isolates had the polybasic amino acid sequence (112)RRQKR↓F(117) at the F cleavage site. Phylogenetic analyses of complete F gene sequences showed that all isolates are classified in class II of APMV-1. The velogenic viruses are classified in genotype XII, while the lentogenic virus is classified in genotype II, closely related to the LaSota vaccine strain. Moreover, tree topology, bootstrap values, and genetic distances observed within genotype XII resulted in the identification of novel subgenotypes XIIa (in South America) and XIIb (in China) and possibly two clades within genotype XIIa. All velogenic Peruvian viruses belonged to subgenotype XIIa. Overall, our results confirm the presence of genotype XII in Peru and suggest that it is the prevalent genotype currently circulating in our country. The phylogenetic characterization of these isolates helps to characterize the evolution of NDV and may help with the development of vaccines specific to our regional necessities.

  13. Global genotype flow in Cercospora beticola populations confirmed through genotyping-by-sequencing.

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    Niloofar Vaghefi

    Full Text Available Genotyping-by-sequencing (GBS was conducted on 333 Cercospora isolates collected from Beta vulgaris (sugar beet, table beet and swiss chard in the USA and Europe. Cercospora beticola was confirmed as the species predominantly isolated from leaves with Cercospora leaf spot (CLS symptoms. However, C. cf. flagellaris also was detected at a frequency of 3% in two table beet fields in New York. Resolution of the spatial structure and identification of clonal lineages in C. beticola populations using genome-wide single nucleotide polymorphisms (SNPs obtained from GBS was compared to genotyping using microsatellites. Varying distance thresholds (bitwise distance = 0, 1.854599 × 10-4, and 1.298 × 10-3 were used for delineation of clonal lineages in C. beticola populations. Results supported previous reports of long distance dispersal of C. beticola through genotype flow. The GBS-SNP data set provided higher resolution in discriminating clonal lineages; however, genotype identification was impacted by filtering parameters and the distance threshold at which the multi-locus genotypes (MLGs were contracted to multi-locus lineages. The type of marker or different filtering strategies did not impact estimates of population differentiation and structure. Results emphasize the importance of robust filtering strategies and designation of distance thresholds for delineating clonal lineages in population genomics analyses that depend on individual assignment and identification of clonal lineages. Detection of recurrent clonal lineages shared between the USA and Europe, even in the relaxed-filtered SNP data set and with a conservative distance threshold for contraction of MLGs, provided strong evidence for global genotype flow in C. beticola populations. The implications of intercontinental migration in C. beticola populations for CLS management are discussed.

  14. SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels

    Directory of Open Access Journals (Sweden)

    Franke Andre

    2010-12-01

    Full Text Available Abstract Background Expression levels for 47294 transcripts in lymphoblastoid cell lines from all 270 HapMap phase II individuals, and genotypes (both HapMap phase II and III of 3.96 million single nucleotide polymorphisms (SNPs in the same individuals are publicly available. We aimed to generate a user-friendly web based tool for visualization of the correlation between SNP genotypes within a specified genomic region and a gene of interest, which is also well-known as an expression quantitative trait locus (eQTL analysis. Results SNPexp is implemented as a server-side script, and publicly available on this website: http://tinyurl.com/snpexp. Correlation between genotype and transcript expression levels are calculated by performing linear regression and the Wald test as implemented in PLINK and visualized using the UCSC Genome Browser. Validation of SNPexp using previously published eQTLs yielded comparable results. Conclusions SNPexp provides a convenient and platform-independent way to calculate and visualize the correlation between HapMap genotypes within a specified genetic region anywhere in the genome and gene expression levels. This allows for investigation of both cis and trans effects. The web interface and utilization of publicly available and widely used software resources makes it an attractive supplement to more advanced bioinformatic tools. For the advanced user the program can be used on a local computer on custom datasets.

  15. Isolation and Genotyping of Toxoplasma gondii in Brazilian Dogs

    Science.gov (United States)

    da Silva, Jamille Rodrigues; Maciel, Bianca Mendes; de Santana Souza Santos, Luana Karla Nogueira; Carvalho, Fábio Santos; de Santana Rocha, Daniele; Lopes, Carlos Wilson Gomes; Albuquerque, George Rêgo

    2017-01-01

    Strains of Toxoplasma gondii in Brazil are highly genetically diverse compared to strains from North America and Europe. Dogs are epidemiologically important because they act as sentinels for T. gondii infections in humans and are good indicators of environmental contamination. The aim of this study was to isolate and genetically characterize T. gondii strains from tissues of naturally infected Brazilian dogs. For this study, 21 blood samples were collected from dogs at the Zoonosis Control Centers of Ilhéus and Itabuna cities, Bahia, Brazil. The sera were examined for T. gondii antibodies using the indirect hemagglutination test. Brains and hearts of seropositive dogs were bioassayed in mice to isolate and characterize T. gondii parasites by PCR-RFLP using 10 genetic markers (SAG1, newSAG2, SAG3, BTUB, c22-8, c29-2, GRA6, PK1, APICO, and L358). However, T. gondii was isolated from only 4 (57.1%) dogs, designated TgDgBr6, 13, 17, and 21. All strains were virulent, causing clinical changes (rough hair coat, lethargy, and abdominal distention) and the death of all mice within 8–20 days after inoculation. Genetic analysis of these 4 T. gondii isolates revealed 4 distinct genotypes with different clonal lineage combinations (types I, II, and III) and 2 atypical alleles. Using PCR-RFLP with several markers, this study contributes to evaluations of the genetic diversity of strains circulating in Brazil. PMID:28719948

  16. IDH Mutations: Genotype-Phenotype Correlation and Prognostic Impact

    Directory of Open Access Journals (Sweden)

    Xiao-Wei Wang

    2014-01-01

    Full Text Available IDH1/2 mutation is the most frequent genomic alteration found in gliomas, affecting 40% of these tumors and is one of the earliest alterations occurring in gliomagenesis. We investigated a series of 1305 gliomas and showed that IDH mutation is almost constant in 1p19q codeleted tumors. We found that the distribution of IDH1R132H, IDH1nonR132H, and IDH2 mutations differed between astrocytic, mixed, and oligodendroglial tumors, with an overrepresentation of IDH2 mutations in oligodendroglial phenotype and an overrepresentation of IDH1nonR132H in astrocytic tumors. We stratified grade II and grade III gliomas according to the codeletion of 1p19q and IDH mutation to define three distinct prognostic subgroups: 1p19q and IDH mutated, IDH mutated—which contains mostly TP53 mutated tumors, and none of these alterations. We confirmed that IDH mutation with a hazard ratio = 0.358 is an independent prognostic factor of good outcome. These data refine current knowledge on IDH mutation prognostic impact and genotype-phenotype associations.

  17. Differences in genotype frequencies of salt-sensitive genes between fishing and nonfishing communities in Japan

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    Harada M

    2016-04-01

    Full Text Available Masanori Harada,1 Taro Takeshima,2 Masanobu Okayama,2,3 Eiji Kajii,21Department for Support of Rural Health Care, Yamaguchi Grand Medical Center, Hofu, Yamaguchi, 2Division of Community and Family Medicine, Center for Community Medicine, Jichi Medical University, Shimotsuke, 3Division of Community Medicine and Medical Education, Kobe University Graduate School of Medicine, Kobe, Japan Purpose: To identify the differences in genotype frequencies of salt-sensitive genes between residents of fishing communities (FCs and nonfishing communities (NFCs. Methods: The subjects included 18,156 individuals (8,043 males [44%] and 10,113 females [56%]; average age: 57.2±16.1 years from the general population who were registered with large-scale genome banks and resided in 30 prefectures and 78 different regions in Japan. The measurement items were age, sex, blood pressure, presence or absence of hypertension, body mass index, alcohol consumption, and smoking habit. Furthermore, to analyze the genotype frequencies of salt-sensitive genes, α-adducin 1 (ADD1, angiotensinogen (AGT, angiotensin II receptor type 1 (AT1, and guanine nucleotide-binding protein β  peptide 3 (GNB3 were measured. According to the 2004 government classification of municipalities (cities, towns, and villages, communities existing in areas bordering an ocean and with an ocean port were defined as FCs (28 areas. The others were defined as NFCs (50 areas. A logistic regression model was used for comparison of genotype frequencies between subjects residing in FCs and NFCs. Results: Of the included subjects, 4,916 (27.0% and 13,240 (73.0% resided in FCs and NFCs, respectively. In FCs, the mean age was 59.4±16.7 years and men accounted for 41.0% of the cohort (n=2,015. In NFCs, the mean age was 56.4±15.8 years and men accounted for 45.5% of the cohort (n=6,028. The adjusted odds ratios of the AA and AG genotypes compared with the GG genotype for AGT were 0.80 (95% confidence interval [CI

  18. First report of genotyping of Toxoplasma gondii isolates from wild birds in China.

    Science.gov (United States)

    Huang, Si-Yang; Cong, Wei; Zhou, Peng; Zhou, Dong-Hui; Wu, Song-Ming; Xu, Min-Jun; Zou, Feng-Cai; Song, Hui-Qun; Zhu, Xing-Quan

    2012-06-01

    Toxoplasma gondii is an important cosmopolitan opportunistic protozoan parasite, which threatens the health of human beings and animals. Genetic characterization of isolates from South America has revealed high genetic diversity. In contrast, isolates from North America and Europe were highly clonal, with 3 major lineages known as the Types I, II, and III. However, limited information on T. gondii genotypes has been reported in The People's Republic of China. Here we conducted a survey to determine genetic diversity of this parasite in wild birds of China. In total, tissues from breast muscle of 178 wild birds, including 98 common pheasants ( Phasianus colchicus ), 35 tree sparrows ( Passer montanus ), 22 house sparrows ( Passer domesticus ), 20 saxaul sparrows ( Passer ammodendri ), and 1 cinnamon sparrow ( Passer rutilans ), were tested for T. gondii infection, 4 of which were found to be positive for the T. gondii B1 gene by PCR amplification. These positive DNA samples were typed at 10 genetic markers, including 9 nuclear loci, i.e., SAG1, 5'- and 3'-SAG2, alternative SAG2, SAG3, GRA6, L358, PK1, c22-8, c29-2, and an apicoplast locus Apico. Of these, 3 isolates were genotyped with complete data for all loci, and 2 genotypes (Type I and Type II variant) were identified. This is the first report of genetic typing of T. gondii isolates from wild birds from different regions in China. The results suggest that the Type I and II variant strains are circulating in wild birds in China, and these birds are potential reservoirs for T. gondii transmission.

  19. 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

  20. Potent acid inhibition by vonoprazan in comparison with esomeprazole, with reference to CYP2C19 genotype.

    Science.gov (United States)

    Kagami, T; Sahara, S; Ichikawa, H; Uotani, T; Yamade, M; Sugimoto, M; Hamaya, Y; Iwaizumi, M; Osawa, S; Sugimoto, K; Miyajima, H; Furuta, T

    2016-05-01

    Acid inhibitory effects of proton pump inhibitors (PPIs) are influenced by CYP2C19 genotype. In contrast, the potent acid inhibition of vonoprazan is not influenced by CYP2C19 genotype. To compare the acid inhibitory effects of vonoprazan and esomeprazole in relation to CYP2C19 genotype. Twenty-eight healthy Japanese volunteers [7 CYP2C19 poor metabolisers (PMs), 11 intermediate metabolisers (IMs) and 10 rapid metabolisers (RMs)] received four different regimens in a randomised crossover manner: (i) vonoprazan 20 mg twice daily (b.d.), (ii) vonoprazan 20 mg daily, (iii) esomeprazole 20 mg b.d. and (iv) esomeprazole 20 mg daily. The timing of each dosing was 1 h before a meal. Twenty-four-hour intragastric pH monitoring was performed on day 7 on each regimen. In the overall genotype group, pH ≥4 holding time ratios (pH 4 HTRs) with vonoprazan b.d., vonoprazan daily, esomeprazole b.d. and esomeprazole daily were 100%, 95%, 91%, and 68% respectively. pH 5 HTRs were 99%, 91%, 84% and 54% respectively. Vonoprazan b.d. potently suppressed acid for 24 h, and was significantly superior to other regimens irrespective of CYP2C19 genotype. Vonoprazan daily was equivalent to esomeprazole b.d. in IMs and PMs, but superior in RMs. CYP2C19 genotype-dependent differences were observed in esomeprazole daily but not in vonoprazan b.d. or daily. Vonoprazan 20 mg b.d. inhibits acid irrespective of CYP2C19 genotype, more potently than esomeprazole 20 mg b.d., pH 4 and 5 holding time ratios reached 100% and 99%, respectively. © 2016 John Wiley & Sons Ltd.

  1. Understanding the role of dogs (Canis lupus familiaris) in the transmission dynamics of Trypanosoma cruzi genotypes in Colombia.

    Science.gov (United States)

    Ramírez, Juan David; Turriago, Brenda; Tapia-Calle, Gabriela; Guhl, Felipe

    2013-09-01

    The dog (Canis lupus familiaris) is the most important domestic reservoir of Chagas disease, a zoonosis that affects more than 10 million people in Latin America. Trypanosoma cruzi, the etiologic agent of the disease, displays remarkable genetic variability, as indicated by its six genotypes (TcI-TcVI). A pilot study was conducted to establish the prevalence of T. cruzi among the canine population by analyzing 80 dogs. We report the identification of the TcI, TcII, TcIV and TcVI genotypes as single infections. TcI/TcII and TcI/TcIV presented as mixed infections and included the presence of Trypanosoma angel. The implications of this distribution are herein discussed. Based on the molecular epidemiology findings, this study suggests a plausible role for canine synanthropism in the transmission of T. cruzi. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Effect of different soil water content effect on genotype expession in photosynthetic efficiency and leaf temperature in sunflower

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    Markulj-Kulundžić Antonela

    2016-01-01

    Full Text Available Sunflower (Helianthus annuus L. has high needs for water but can tolerate drought very well because, under stress conditions, its well developed root system can supply water and mineral nutrients from deeper soil layers. Reduced water content in soil affects plant growth and development, photosynthetic rate and causes rapid leaf senescence. In this study, we measured maximum quantum yield of photosystem II (Fv/Fm, photosynthetic performance index (PIABS and leaf temperature (LT on 13 sunflower genotypes at different soil water contents. By calculating stress tolerance indices (STI of Fv/Fm and PIABS parameters we evaluated drought tolerance for every tested sunflower genotype at given soil water contents. The experiment was set up in vegetation pots in two treatments with different soil water contents (60% and 80% of field water capacity in three replications. Based on the obtained results for Fv/Fm and PIABS and STI values of Fv/Fm and PIABS parameters, we concluded that genotypes 5 and 12 had higher tolerance at both treatments, as opposed to genotypes 2 and 13 which were less tolerant. These analyses will help breeders to select genotypes adapted to different farming areas which is, along with the use of recommended production practices, the background for profitable sunflower production.

  3. Relationship Between Genotype Variants Follicle-stimulating Hormone Receptor Gene Polymorphisms (FSHR) and Morphology of Oocytes Prior to ICSI Procedures

    Science.gov (United States)

    Gashi, Zafer; Elezaj, Shkelzen; Zeqiraj, Afrim; Grabanica, Driton; Shabani, Isak; Gruda, Bujar; Gashi, Fitore

    2016-01-01

    Introduction: This study investigated association of Asn680Ser FSHR polymorphism with the ovarian response in 104 women of Albanian ethnic population enrolled in ICSI program. The reason of infertility in all cases has been identified as male factor. Methods: Analysis of the Asn680Ser polymorphism was performed using TaqMan® SNP Genotyping Assay. Clinical and endocrinologic parameters were analyzed based on the genotype, age, BMI, oocyte yield, number of transferred embryos and pregnancy rate. Results: The frequencies of the Asn680 Ser genotype variants were as follows: Asn/Asn 22.1%, Asn/Ser 47.1%, and Ser/Ser 30.8%, respectively. BMI was significantly higher in the Ser/Ser group as compared to those from the Asn/Ser or the Asn/Asn group (p= 0.0010). The genotype variants Ser/Ser indicates a higher rate of oocyte retrieval (25.9%) in the immature form, metaphase I (MI) as opposed to the other two groups (Asn/Asn 23.7 % vs. Asn/Ser 21.9%), which was statistically significant (p = 0.3020). Conclusions: FSH receptor polymorphism is associated with different ovarian response to controlled ovarian stimulation (COS), but is not an important factor in increasing the degree of pregnancy. Polymorphisms of the FSH receptor is associated with normal morphology and genetic maturation (metaphase II) oocytes in dependence of genotypic variation polymorphisms. PMID:27994298

  4. Relationship Between Genotype Variants Follicle-stimulating Hormone Receptor Gene Polymorphisms (FSHR) and Morphology of Oocytes Prior to ICSI Procedures.

    Science.gov (United States)

    Gashi, Zafer; Elezaj, Shkelzen; Zeqiraj, Afrim; Grabanica, Driton; Shabani, Isak; Gruda, Bujar; Gashi, Fitore

    2016-10-01

    This study investigated association of Asn680Ser FSHR polymorphism with the ovarian response in 104 women of Albanian ethnic population enrolled in ICSI program. The reason of infertility in all cases has been identified as male factor. Analysis of the Asn680Ser polymorphism was performed using TaqMan® SNP Genotyping Assay. Clinical and endocrinologic parameters were analyzed based on the genotype, age, BMI, oocyte yield, number of transferred embryos and pregnancy rate. The frequencies of the Asn680 Ser genotype variants were as follows: Asn/Asn 22.1%, Asn/Ser 47.1%, and Ser/Ser 30.8%, respectively. BMI was significantly higher in the Ser/Ser group as compared to those from the Asn/Ser or the Asn/Asn group (p= 0.0010). The genotype variants Ser/Ser indicates a higher rate of oocyte retrieval (25.9%) in the immature form, metaphase I (MI) as opposed to the other two groups (Asn/Asn 23.7 % vs. Asn/Ser 21.9%), which was statistically significant (p = 0.3020). FSH receptor polymorphism is associated with different ovarian response to controlled ovarian stimulation (COS), but is not an important factor in increasing the degree of pregnancy. Polymorphisms of the FSH receptor is associated with normal morphology and genetic maturation (metaphase II) oocytes in dependence of genotypic variation polymorphisms.

  5. Vitamin D and estrogen receptor-alpha genotype and indices of bone mass and bone turnover in Danish girls

    DEFF Research Database (Denmark)

    Cusack, S.; Mølgaard, C.; Michaelsen, K. F.

    2006-01-01

    Peak bone mass is a major determinant of osteoporosis risk in later life. It is under strong genetic control; however, little is known about the identity of the genes involved. In the present study, we investigated the relationship between polymorphisms in the genes encoding the vitamin D recepto...... (VDR) (FokI, TaqI) and estrogen receptor-alpha (ER alpha) (PvuII, XbaI), and bone mineral density (BMD), bone mineral content (BMC), and markers of bone turnover in 224 Danish girls aged 11-12 years. BMD and BMC were measured by dual-energy X-ray absorptiometry. Serum osteocalcin, 25(OH......(OH)D, or PTH among genotype groups. BMD or BMC of lumbar spine or whole body (adjusted for body and bone size and pubertal status) were not associated with VDR or ER alpha genotypes or the combination of these genotypes. This lack of association remained even after adjustment for dietary...... and environmental factors. VDR genotypes had no effect on bone turnover markers. XX and PP ER alpha genotypes were associated (P

  6. DD genotype of angiotensin-converting enzyme in type 2 diabetes mellitus with renal disease in Mexican Mestizos.

    Science.gov (United States)

    Palomo-Piñón, Silvia; Gutiérrez-Rodríguez, Margarita E; Díaz-Flores, Margarita; Sánchez-Barrera, Reyna; Valladares-Salgado, Adán; Utrera-Barillas, Dolores; Durán-Reyes, Genoveva; Galván-Duarte, Rosa E; Trinidad-Ramos, Pedro; Cruz, Miguel

    2009-04-01

    The DD genotype of angiotensin-converting enzyme (ACE) has been suggested as a major contributor of diabetic nephropathy in several populations. The purpose of the present study was to determine whether micro/macroalbuminuria is associated with ACE insertion/deletion (I/D) polymorphism in Mexican Mestizos with type 2 diabetes mellitus. A total of 435 patients with type 2 diabetes mellitus, of whom 233 had albuminuria, were characterized for the ACE I/D polymorphism by the polymerase chain reaction method. Clinical and biochemical characteristics and frequencies according to DD, ID and II genotypes in patients with and without albuminuria showed no significant differences. However, only females with micro/macroalbuminuria showed higher frequency of a DD genotype than those without albuminuria (27.9%, 21.2% and 10.5%, respectively; P DD genotype is a risk factor for the development of renal disease in Mexican Mestizo females with type 2 diabetes, indicating a possible DD genotype-associated sex effect in renal disease.

  7. Indirect genetic effects and sexual conflicts: Partner genotype influences multiple morphological and behavioral reproductive traits in a flatworm.

    Science.gov (United States)

    Marie-Orleach, Lucas; Vogt-Burri, Nadja; Mouginot, Pierick; Schlatter, Aline; Vizoso, Dita B; Bailey, Nathan W; Schärer, Lukas

    2017-05-01

    The expression of an individual's phenotypic traits can be influenced by genes expressed in its social partners. Theoretical models predict that such indirect genetic effects (IGEs) on reproductive traits should play an important role in determining the evolutionary outcome of sexual conflict. However, empirical tests of (i) whether reproductive IGEs exist, (ii) how they vary among genotypes, and (iii) whether they are uniform for different types of reproductive traits are largely lacking. We addressed this in a series of experiments in the simultaneously hermaphroditic flatworm Macrostomum lignano. We found strong evidence for IGEs on both morphological and behavioral reproductive traits. Partner genotype had a significant impact on the testis size of focal individuals-varying up to 2.4-fold-suggesting that IGEs could mediate sexual conflicts that target the male sex function. We also found that time to first copulation was affected by a genotype × genotype interaction between mating partners, and that partner genotype affected the propensity to copulate and perform the postcopulatory suck behavior, which may mediate conflicts over the fate of received ejaculate components. These findings provide clear empirical evidence for IGEs on multiple behavioral and morphological reproductive traits, which suggests that the evolutionary dynamics of these traits could be altered by genes contained in the social environment. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  8. Genotyping of Toxoplasma gondii by Multiplex PCR and Peptide-Based Serological Testing of Samples from Infants in Poland Diagnosed with Congenital Toxoplasmosis

    OpenAIRE

    Nowakowska, Dorota; Colón, Iris; Remington, Jack S.; Grigg, Michael; Golab, Elzbieta; Wilczynski, J.; Sibley, L. David

    2006-01-01

    Toxoplasma gondii has a clonal population genetic structure with three (I, II, and III) lineages that predominate in North America and Europe. Type II strains cause most cases of symptomatic human infections in France and the United States, although few other regions have been adequately sampled. Here we determined the parasite genotype in amniotic fluid and cerebrospinal fluid samples from congenital toxoplasmosis cases in Poland. Nineteen confirmed congenital cases of toxoplasmosis were ana...

  9. SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Xiaowen Sun

    Full Text Available Large-scale genotyping plays an important role in genetic association studies. It has provided new opportunities for gene discovery, especially when combined with high-throughput sequencing technologies. Here, we report an efficient solution for large-scale genotyping. We call it specific-locus amplified fragment sequencing (SLAF-seq. SLAF-seq technology has several distinguishing characteristics: i deep sequencing to ensure genotyping accuracy; ii reduced representation strategy to reduce sequencing costs; iii pre-designed reduced representation scheme to optimize marker efficiency; and iv double barcode system for large populations. In this study, we tested the efficiency of SLAF-seq on rice and soybean data. Both sets of results showed strong consistency between predicted and practical SLAFs and considerable genotyping accuracy. We also report the highest density genetic map yet created for any organism without a reference genome sequence, common carp in this case, using SLAF-seq data. We detected 50,530 high-quality SLAFs with 13,291 SNPs genotyped in 211 individual carp. The genetic map contained 5,885 markers with 0.68 cM intervals on average. A comparative genomics study between common carp genetic map and zebrafish genome sequence map showed high-quality SLAF-seq genotyping results. SLAF-seq provides a high-resolution strategy for large-scale genotyping and can be generally applicable to various species and populations.

  10. Immature tassels as alternative explants in somatic embryogenesis and plant regeneration in south Brazilian maize genotypes - doi: 10.4025/actasciagron.v35i1.15545

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    Magali Ferrari Grando

    2012-08-01

    Full Text Available Somatic embryogenesis and in vitro plant regeneration are fundamental processes in the obtainment of transgenic maize plants. Explant, genotype and culture medium are determining factors in these processes. Immature embryo explants and the American Hi-II genotype have been widely employed to acquire genetically modified plants in this species. However, the use of more readily available explants is desired as well as the development of genetic transformation protocols for productive genotypes adapted to local conditions. This study provides an evaluation of immature tassel explants in relation to embryogenic callus production and plant regeneration in South Brazilian maize genotypes for their use in genetic transformation experiments. Immature tassels from 5 hybrids were cultivated in different callus-induction media. The frequency and the fresh mass of embryogenic calli were evaluated. The frequency was influenced by genotype, and the fresh mass was influenced by genotype and culture medium. In plant regeneration, shoots, complete seedlings and acclimatized and fertile plants were quantified. Treatments producing long term embryogenic calli from immature tassels of South Brazilian genotypes with the capacity to regenerate were identified.

  11. Genotypic Response of Dry Bean (Phaseolus vulgaris L. to Natural Field Infection of Ascochyta Blight (Phoma exigua var. diversispora (Bubak Boerema under Diverse Environmental Conditions in Rwanda

    Directory of Open Access Journals (Sweden)

    Clement Urinzwenimana

    2017-12-01

    Full Text Available Ascochyta blight, caused by Phoma exigua var. diversispora (Bubak Boerema, is a serious constraint in the cultivation of the common bean (Phaseolus vulgaris L. in Rwanda, particularly in the cool and wet highland production areas. In order to identify resistant genotypes, a germplasm evaluation study was conducted to quantify the impact of the disease on phenotypic and agronomic traits under natural conditions. Field screening trials of 39 bush (Types I, II and III and 36 climbing (Type IV genotypes from different accessions within and outside the country were conducted at three sites, namely, Rwerere, Nyamagabe and Musanze Research Stations, for two seasons. The relative area under the disease progress curve (RAUDPC based on evaluations of the disease severity (percentage leaf area infected, was used to evaluate the genotypes. Thirteen genotypes were identified with some level of ascochyta resistance. The study revealed Rwandan genotypes G 2333 and SMC 18 as new sources of resistance to Ascochyta blight. Additional results showed a negative relationship (r = −0.42 and −0.51 for Seasons A and B, respectively between ascochyta infection and yield. Further relationships were identified between the plant flower colour and seed size to ascochyta resistance. Some of the identified resistant genotypes can be used to introgress ascochyta resistance into susceptible Rwandan market classes of common bean genotypes.

  12. NUTRITIONAL AND ROTI QUALITY OF SORGHUM GENOTYPES

    Directory of Open Access Journals (Sweden)

    U.D. Chavan

    2016-10-01

    Full Text Available Sorghum grains are mostly used for the roti preparation. The M 35-1 (Maldhandi a sorghum cultivar is known for its good quality of roti due to having pearly white grain color, its flour having higher water holding capacity, and good organoleptic taste. However, this cultivar is low yielder. To evolve sorghum high yielding genotype coupled with this good roti qualities, systematic breeding program was planned and executed to overcome this problem. Twenty local land races, 92 genotypes, and seven improved cultivars of sorghum along with check M 35-1 were studied for various nutritional quality parameters, with special reference to the roti quality. Considering nutritional quality and organoleptic evaluation parameters studied for roti quality, the local land races viz., RSLG 428-1, RSLG 1238, RSLG 1275 and the genotypes viz., RSV 290, RSV 292, RSV 858, RSV 859, RSV 861, RSV 868, RSV 894, RSV 985, RSV 992, RSV 995, RSV 999 were found to be promising for protein, sugar, water absorption, and soluble protein content. Therefore, they can be used for further improvement in nutritional quality through breeding program. Among the improved cultivars, Phule Vasudha (RSV 423, CSV 22, and Phule Chitra (SPV 1546 werefound to be most promising for roti quality. The maximum score for overall acceptability was found for Phule Vasudha followed by Phule Anuradha (RSV 458, Phule Yeshoda (RSLG 262, and Phule Maulee (CSV 216.

  13. 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.

  14. Multilocus genotyping of Giardia duodenalis in Malaysia.

    Science.gov (United States)

    Huey, Choy Seow; Mahdy, Mohammed A K; Al-Mekhlafi, Hesham M; Nasr, Nabil A; Lim, Yvonne A L; Mahmud, Rohela; Surin, Johari

    2013-07-01

    Giardia duodenalis is considered the most common intestinal parasite in humans worldwide. In Malaysia, many studies have been conducted on the epidemiology of giardiasis. However, there is a scarcity of information on the genetic diversity and the dynamics of transmission of G. duodenalis. The present study was conducted to identify G. duodenalis assemblages and sub-assemblages based on multilocus analysis of the glutamate dehydrogenase (gdh), beta-giardin (bg) and triose phosphate isomerase (tpi) genes. Faecal specimens were collected from 484 Orang Asli children with a mean age of 7 years and examined using light microscopy. Specimens positive for Giardia were subjected to PCR analysis of the three genes and subsequent sequencing in both directions. Sequences were edited and analysed by phylogenetic analysis. G. duodenalis was detected in 17% (84 of 484) of the examined specimens. Among them, 71 were successfully sequenced using at least one locus. Genotyping results showed that 30 (42%) of the isolates belonged to assemblage A, 32 (45%) belonged to assemblage B, while discordant genotype results were observed in 9 specimens. Mixed infections were detected in 43 specimens using a tpi-based assemblage specific protocol. At the sub-assemblages level, isolates belonged to assemblage A were AII. High nucleotide variation found in isolates of assemblage B made subtyping difficult to achieve. The finding of assemblage B and the anthroponotic genotype AII implicates human-to-human transmission as the most possible mode of transmission among Malaysian aborigines. The high polymorphism found in isolates of assemblage B warrants a more defining tool to discriminate assemblage B at the sub-assemblage level. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Audioprofiles and antioxidant enzyme genotypes in presbycusis.

    Science.gov (United States)

    Angeli, Simon I; Bared, Anthony; Ouyang, Xiaomei; Du, Li Lin; Yan, Denise; Zhong Liu, Xue

    2012-11-01

    Audiometric patterns have been shown to indirectly provide information regarding the pathophysiology of presbycusis and be useful in the phenotyping of hereditary deafness. Hospital-based cohort study of adults with presbycusis, comparing the association of audiometric patterns and polymorphisms of antioxidant enzymes that have been linked to presbycusis: GSTT1, GSTM1 and NAT2. All subjects underwent a clinical evaluation and completed questionnaires regarding ototoxicity and noise exposure. Pure-tone threshold audiometry was obtained and subjects' audiograms were classified into specific patterns. DNA was extracted from blood and the polymorphisms of GSTT1, GSTM1, and the NAT2 variants (NAT2* 5A; NAT2* 6A,B) were analyzed by PCR. The audiometric patterns that were more prevalent in our cohort were "High-Frequency Steeply Sloping" or HFSS (33%), "High-Frequency Gently Sloping" or HFGS (31%), and "Flat" (27%), with other patterns being rare. We did not find a statistical significant effect of gender, age, hearing level, and ear side on the audiometric pattern. Subjects with mutant alleles for GSTT1 were more likely to have a HFSS audiogram than subjects with the wild type genotype. In this cohort, there was a similar prevalence for the three audiometric configurations HFSS, HFGS, and Flat, with other configurations being rare. Subjects with mutant alleles for GSTT1 were more likely to have a HFSS audiogram than subjects with the wild type genotype, suggesting that the basal turn of the cochlea is susceptible to GSTT1 regulated oxidative stress. However, further studies of audioprofiles with larger sample sizes may be needed to establish phenotype-genotype correlations in presbycusis. Copyright © 2012 The American Laryngological, Rhinological, and Otological Society, Inc.

  16. 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.

  17. Coffee Berry Borer Resistance in Coffee Genotypes

    Directory of Open Access Journals (Sweden)

    Gustavo Hiroshi Sera

    2010-04-01

    Full Text Available The aim of this study was to evaluate the coffee germplasm of the Paraná Agronomic Institute (IAPAR for resistance to the coffee-berry-borer. Preliminary field evaluation was performed in August 2004 and the fruits of less damaged genotypes in the field were evaluated under controlled condition with obligated and free choice experiments established in a randomized complete design with three replications. The genotypes were evaluated fifteen days after infestation with one borer per fruit in Petri dishes. The data were analyzed by the Scott-Knott means test at 1 % and by the χ2 test. Statistical analysis indicated that Coffea kapakata, Psilanthus bengalensis, C. eugenioides and genotypes with C. eugenioides genes were resistant. These genotypes presented low frequency of bored grains. C. eugenioides and C. kapakata could present resistance at epicarp level but not in the grain. P. bengalensis could present resistance also in the grains.O objetivo deste trabalho foi identificar fontes de resistência genética a H. hampei em diferentes espécies de café do banco de germoplasma do Instituto Agronômico do Paraná (IAPAR, Londrina, PR. Foram realizadas avaliações preliminares de campo, para posterior testes de confinamento e de livre escolha, em laboratório, instalados em delineamento inteiramente casualizado com três repetições. Os genótipos foram avaliados quinze dias após a infestação com uma broca por fruto em placas de petri. Os dados foram analisados pelo teste de médias Scott-Knott a 1 % e pelo teste de χ2. Foi observado que C. eugenioides, C. kapakata e P. bengalensis constituem importantes fontes de resistência à broca, pois apresentaram menor freqüência de grãos brocados. Os dois primeiros podem apresentar substâncias voláteis antagônicas à broca na casca e a resistência de P. bengalensis pode estar também no grão.

  18. Single molecule genotyping by TIRF microscopy.

    Science.gov (United States)

    Rüttinger, Steffen; Lamarre, Baptiste; Knight, Alex E

    2008-09-01

    As part of a programme to develop a metrological framework for single molecule measurements in biology, we have investigated the applications of single molecule imaging to genomics. Specifically, we have developed a technique for measuring the frequencies of single nucleotide polymorphisms (SNPs) in complex or pooled samples of DNA. We believe that this technique has applications to statistical genotyping-the identification of correlations between SNP frequencies and particular phenotypes-and other areas where it is desirable to track the frequencies of SNPs in complex DNA populations.

  19. First report of typical Brazilian Toxoplasma gondii genotypes from isolates of free-range chickens (Gallus gallus domesticus) circulating in the state of Paraíba, Northeast Brazil.

    Science.gov (United States)

    Feitosa, Thais Ferreira; Vilela, Vinícius Longo Ribeiro; de Almeida-Neto, João Leite; de Melo, Lídio Ricardo Bezerra; de Morais, Dayana Firmino; Alves, Bruna Farias; Nakashima, Fabiana; Gennari, Solange Maria; Athayde, Ana Célia Rodrigues; de Jesus Pena, Hilda Fátima

    2017-08-01

    This study evaluated, for the first time, the genetic diversity of Toxoplasma gondii isolates from free-range chickens from the state of Paraíba, Northeast Brazil. Tissue samples from 33 chickens from properties in five municipalities of Paraíba (Esperança, Olho d'Água, Malta, Monteiro, and Patos) were bioassayed in mice. The brains of mice infected with T. gondii cysts were used for DNA extraction and genotyping. Genotyping was performed using 11 PCR-RFLP markers and 15 microsatellite (MS) markers. Complete genotyping results were obtained for 29 isolates, with nine genotypes detected by RFLP and 15 genotypes identified by MS. Three genotypes (#273, #274, and #277) have only been recently identified from pigs in the region. Brazilian clonal types BrII and BrIII were identified from one isolate each. Clonal types I, II, and III were not detected by RFLP. Genotype #13 (Caribbean 1), detected in 48.3% (14/29) of isolates from four of the five municipalities investigated, was the most prevalent genotype in the state of Paraíba. However, the MS analysis showed that of these 14 isolates, only four were unique genotypes, and considering the distance between the municipalities from where they were collected, it is possible that only seven are independent isolates while the others are clones. The other genotypes were restricted to different microregions. The results indicate that the Caribbean 1 lineage of T. gondii is circulating widely in Northeast Brazil. The genotypic diversity of T. gondii in the state of Paraíba is high, and microsatellite analysis revealed this diversity with higher resolution than PCR-RFLP.

  20. Prevalence of hepatitis C virus genotypes in Mexican patients.

    Science.gov (United States)

    Dehesa-Violante, Margarita; Bosques-Padilla, Francisco; Kershenobich-Stalnikowitz, David

    2007-01-01

    Worldwide HCV studies have documented its large genetic variability; HCV has major genetic groups called genotypes that are designated from 1 to 6, as well as > 50 subtypes. This is very important considering that treatment response varies according to genotype. The purpose of this trial was to ascertain prevalence of HCV genotypes in a group of patients from 10 states in Mexico. This study enrolled patients from 22 hospitals throughout the country. Patients tested positive to hepatitis C antibody and genotyping was preformed by Lipa method. To carry out a comparison, two regions were arbitrarily defined, the northern region embodied the cities of Culiacan, Torreón, Monterrey, Ciudad Obregón, and Tijuana, while the central-southern region embodied Mexico City, Guadalajara, León, Puebla, and Veracruz. The test was performed on a total of 421 patients. The most frequently found genotype was genotype 1, present in 70.55% of cases. The majority (40.1%) corresponded to genotype 1b, 17.81% to 1a, and genotype 2a/2c (11.64%). A total of 29.4% of samples corresponded to genotypes non-1. Genotype 1 was found in 72.34 (northern region) and 70.03% (central-southern) of the two regions, and genotypes non-1 in 27.66 and 29.97%, respectively. We conclude that the most frequent genotype in Mexico is 1b, followed by 1a, and, in third place 1b1a, for a total of 70.55%; the remaining 29.45% had genotypes other than 1.

  1. 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.

  2. (ii) and ni (ii) complexes with n

    African Journals Online (AJOL)

    DR. AMINU

    II) complexes with a. Schiff base derived from. 4-dimetylamino benzaldehyde and primary amines. The chemical analysis data showed the formation of (1:1) metal - ligand ratio and a square planar geometry was suggested for Co(II) and Ni(II) ...

  3. manganese(II) and uranyl(II)

    African Journals Online (AJOL)

    Paper electrophoresis is used for the study of equilibria in binary complex systems in solution. The stability constants of ML and ML2 complex species of some metal ions copper(II), manganese(II) and uranyl(II) with a-aminobutenoic acid and hydroxyproline were determined at an ionic strength of 0.1 M and 35 ºC.

  4. Toxoplasma gondii in foxes and rodents from the German Federal States of Brandenburg and Saxony-Anhalt: seroprevalence and genotypes.

    Science.gov (United States)

    Herrmann, D C; Maksimov, P; Maksimov, A; Sutor, A; Schwarz, S; Jaschke, W; Schliephake, A; Denzin, N; Conraths, F J; Schares, G

    2012-04-30

    Data on the genotypes of Toxoplasma gondii circulating in wildlife are scarce. In the present study, foxes and rodents from two Federal States in Central or Eastern Germany were examined for T. gondii infections. Body fluids were collected at necropsy or fluids were obtained from frozen tissues of naturally exposed red foxes (Vulpes vulpes), voles (Microtus arvalis), shrews (Neomys anomalus) and a striped field mouse (Apodemus agrarius) and tested for T. gondii by serology. DNA isolated from tissues of seropositive foxes and all the rodents was examined by PCR. In the German Federal States of Brandenburg and Saxony-Anhalt 152/204 (74.5%) and 149/176 (84.7%) of foxes, respectively, but none of the rodents (0/72) had antibodies to T. gondii. Only 28/152 (18.4%) and 20/149 (13.4%) of seropositive foxes from Brandenburg and Saxony-Anhalt, respectively, but none of the rodents tested PCR-positive for T. gondii. The complete T. gondii genotype could be determined for twelve samples using nine PCR-restriction fragment length polymorphism (PCR-RFLP) markers (newSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, PK1, L358 and Apico). In addition to T. gondii clonal type II (Apico II) and type II (Apico I), type III and T. gondii genotypes showing non-canonical allele patterns were observed in foxes. This suggests that, while T. gondii type II prevails in foxes, other genotypes circulate in wildlife. The population structure of T. gondii in Germany may be more diverse than previously thought. Copyright © 2011 Elsevier B.V. All rights reserved.

  5. Genotypic Characterization of Toxoplasma gondii Strains Associated with Human Toxoplasmosis in Spain: Direct Analysis from Clinical Samples

    OpenAIRE

    Fuentes, Isabel; Rubio, Jose M; Ramírez, Carmen; Alvar, Jorge

    2001-01-01

    Genetic analysis of the SAG2 locus was performed to determine the prevalence of the different genotypes of Toxoplasma gondii (strain types I, II, and III) associated with human toxoplasmosis in Spain. This determination was made directly from primary clinical samples, obviating the previous process of isolation in mice or cell culture. A total of 34 isolates of T. gondii, collected from immunocompromised patients and congenital infection cases, were analyzed. Restriction fragment length polym...

  6. Elizabeth II uus kunstigalerii

    Index Scriptorium Estoniae

    1999-01-01

    Tähistamaks oma troonile asumise 50. aastapäeva, avab Elizabeth II 6. II 2002 Buckinghami palees uue kunstigalerii, mis ehitatakse palee tiibhoonena. Arhitekt John Simpson. Elizabeth II kunstikogust

  7. Interaction of ACE genotype and salt intake on hypertension among Chinese Kazakhs: results from a population-based cross-sectional study.

    Science.gov (United States)

    Wang, Yuyan; Zhang, Biao; Hou, Lei; Han, Wei; Xue, Fang; Wang, Yanhong; Tang, Yong; Liang, Shaohua; Wang, Weizhi; Asaiti, Kuliqian; Wang, Zixing; Hu, Yaoda; Wang, Lei; Qiu, Changchun; Zhang, Mingtao; Jiang, Jingmei

    2017-05-17

    To explore the effect of interaction between ACE genotype and salt intake on hypertension among Chinese Kazakhs, and to compare applications of interactions between logistic model and generalised partially linear tree-based regression (GPLTR) model. Population-based cross-sectional study. Hong Dun, North Xinjiang, China. Non-consanguineous Chinese Kazakh participants (n=916, 342 men and 574 women) aged ≥30 years. Association between ACE genotype and hypertension, association between salt intake and hypertension, and interaction of ACE genotype and salt intake on hypertension in two models. Associations between salt intake and hypertension were different in ACE genotype of II and ID+DD. Under the logistic models, main and interaction effects were not observed for men, but effects were present in opposite directions for women (main effect of ACE: OR=0.20, p=0.003; interaction effect: OR=1.07, p=0.027). Under the GPLTR model, Bayesian information criterion trees included both salt intake and ACE genotype as split variables. Individuals with a salt intake ≥19.5 g/day and ID+DD genotypes had a 3.99-fold (p=0.004) higher risk of hypertension compared with the II genotype for men, whereas salt intake ACE genotype and salt intake on hypertension was observed among Chinese Kazakhs but in different ways according to sex. The GPLTR model appears to be more suitable for an exploration of interactions in complex diseases. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  8. Randomized Trial Evaluating the Impact of Ribavirin Mono-Therapy and Double Dosing on Viral Kinetics, Ribavirin Pharmacokinetics and Anemia in Hepatitis C Virus Genotype 1 Infection

    DEFF Research Database (Denmark)

    Waldenström, Jesper; Westin, Johan; Nyström, Kristina

    2016-01-01

    In this pilot study (RibaC), 58 hepatitis C virus (HCV) genotype 1 infected treatment-naïve patients were randomized to (i) 2 weeks ribavirin double dosing concomitant with pegylated interferon-α (pegIFN-α), (ii) 4 weeks ribavirin mono-therapy prior to adding pegIFN-α, or (iii) standard-of-care (...

  9. HPV genotypes co-infections associated with cervical carcinoma: Special focus on phylogenetically related and non-vaccine targeted genotypes.

    Science.gov (United States)

    Senapati, Rashmirani; Nayak, Bhagyalaxmi; Kar, Shantanu Kumar; Dwibedi, Bhagirathi

    2017-01-01

    HPV is the major causative agent for cervical cancer. Study on the risk of cervical cancer associated with different hr-HPV genotypes would be useful for disease management and new vaccine strategy. With limited reports available, the present study aimed to investigate the pattern of HPV genotypes coinfections and risk of cervical carcinoma associated with them in Indian population. 15 HPV genotypes were detected by E6/E7 multiplex nested type-specific PCR in the HPV-positive cervical samples of 172 cervical cancer cases and 174 subjects with normal cytology. Association between the genotypes and cervical cancer was estimated by calculating the Odds ratio and 95% confidence interval. Risk of cervical carcinoma was associated with multiple genotypes excluding HPV16 (OR:5.87; 95% CI-1.28-26-29; p = .02), multiple genotypes excluding HPV18 (OR = 2.5; 95% CI = 1.09-6.05; p = .03), multiple genotypes of α9 species(OR = 5.3 95% CI = 1.14-24.03; p = .007), and multiple genotypes of α7 species (OR = 2.5; 95% CI = .49-13.45; p = .2). Genotypes not targeted by quadrivalent vaccine types (OR = 2.94 95% CI = 1.48-5.80; p = .001) conferred 2.94 fold higher risk of cervical carcinoma. Cases those coinfected with phylogenetically related genotypes (OR = 2.29; 95% CI(.69-7.59) p = .17) were at 2.9 fold higher risk of invasive cervical carcinoma than those infected with other genotypes although it is not statistically significant. Whereas phylogenetically unrelated genotypes coinfection is negatively associated with cervical carcinoma (OR = .44 95% CI (.244-.8) p = .007) and it is statistically significant.Genotypes not targeted by 9-valent vaccines (OR = .40; 95% CI = .19-.85; p = .017) associated with lesser risk of cervical carcinoma as compared to other genotypes. Subjects infected with any HPV genotype/genotypes excluding HPV16 in association with HPV 18 (OR = 4.1; 95% CI = 1.81-9.25 P = < .001) were at 4.1 fold higher risk of developing invasive cervical carcinoma

  10. Genotype harmonizer : automatic strand alignment and format conversion for genotype data integration

    NARCIS (Netherlands)

    Deelen, Patrick; Bonder, Marc Jan; van der Velde, K Joeri; Westra, Harm-Jan; Winder, Erwin; Hendriksen, Dennis; Franke, Lude; Swertz, Morris A

    2014-01-01

    BACKGROUND: To gain statistical power or to allow fine mapping, researchers typically want to pool data before meta-analyses or genotype imputation. However, the necessary harmonization of genetic datasets is currently error-prone because of many different file formats and lack of clarity about

  11. Advantages of continuous genotype values over genotype classes for GWAS in higher polyploids

    NARCIS (Netherlands)

    Grandke, Fabian; Singh, Priyanka; Heuven, Henri C.M.; Haan, de Jorn R.; Metzler, Dirk

    2016-01-01

    Background: Association studies are an essential part of modern plant breeding, but are limited for polyploid crops. The increased number of possible genotype classes complicates the differentiation between them. Available methods are limited with respect to the ploidy level or data producing

  12. Genotypic correlation and path analysis in early and super-early maize genotypes.

    Science.gov (United States)

    Alves, B M; Cargnelutti Filho, A

    2017-05-25

    The aims of this study were to assess the linear relationships between agronomic and nutritional traits and to identify promising traits for indirect selection in early and super-early maturing maize genotypes. Two trials were run in the 2009/2010 agricultural year, each consisting of a randomized block design with three replications. One trial was run on 36 early maturing maize genotypes and the other on 22 super-early maturing genotypes. Six agronomic traits, 11 protein-nutritional traits, and four energetic-nutritional traits were measured. Error normality assumptions were verified using the Kolmogorov-Smirnov test and residual variance homogeneity assumptions using the Levene test. Analysis of variance and the F-test were run for each of the 21 traits. Next, the genotype correlation coefficient matrix was estimated for the 21 traits and each trial. Ridge path analysis was based on values of k = 0.00 and k = 0.10 on the diagonal of X'X correlation matrix, taking the nutritional traits as principal variables and agronomic traits as explanatory variables. The number of days from sowing to male flowering, the number of days from sowing to female flowering, plant height, ear insertion height, ear weight and grain yield can be used in indirect selection as indicators of grain nutritional quality.

  13. Genotypic Characterization of Toxoplasma gondii Strains Associated with Human Toxoplasmosis in Spain: Direct Analysis from Clinical Samples

    Science.gov (United States)

    Fuentes, Isabel; Rubio, Jose M.; Ramírez, Carmen; Alvar, Jorge

    2001-01-01

    Genetic analysis of the SAG2 locus was performed to determine the prevalence of the different genotypes of Toxoplasma gondii (strain types I, II, and III) associated with human toxoplasmosis in Spain. This determination was made directly from primary clinical samples, obviating the previous process of isolation in mice or cell culture. A total of 34 isolates of T. gondii, collected from immunocompromised patients and congenital infection cases, were analyzed. Restriction fragment length polymorphism in PCR-amplified SAG2 products was used to group strains into one of the three genotypes of T. gondii. Complete characterization of the SAG2 gene was successful in 76.5% of the cases, demonstrating the feasibility of direct genotype analysis from clinical samples of different origins. Strains of T. gondii type II were the most prevalent in immunocompromised patients, with 52% of cases, while strains of type I were present in 75% of the congenital infection cases. These data differ from previous reports that show type II strains to be mostly associated with all kinds of human toxoplasmosis. These differences might be an effect of selection in the process of culture and isolation of the samples performed by other researchers prior to strain characterization. PMID:11283088

  14. 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.

  15. Associating Symptom Phenotype and Genotype in Preeclampsia.

    Science.gov (United States)

    Founds, Sandra A; Tsigas, Eleni; Ren, Dianxu; Barmada, M Michael

    2018-03-01

    Preeclampsia is a complex genetic disorder with an incompletely understood pathogenesis. Its phenotype may be better elucidated by integrating symptoms. This study aimed to identify symptoms by gestational age and associations with novel preeclampsia candidate genes. Women with a history of preeclampsia recruited from The Preeclampsia Registry completed clinical/demographic, symptom surveys and provided medical records. DNA extracted from saliva was processed with multiplexed assays for eight single-nucleotide polymorphisms (SNPs) selected to tag candidate genes and/or located in symptom susceptibility regions. Groups with versus without symptoms were compared using χ 2 . Associations between SNPs and symptoms were analyzed as genotype categories and presence/absence of the variant allele. Logistic regression modeling was conducted with exploratory p = .05. In 114 participants, 113 reported at least 1 of the 18 symptoms. Symptoms varied by trimester. Nine symptoms were associated with seven SNPs. Visual disturbances were associated with three SNPs and nausea/vomiting with two SNPs. Modeling adjustment for maternal age and parity resulted in 15 associations between 9 symptoms and 8 SNPs. Medical records demonstrated 100% concordance with self-reported diagnosis and 48% concordance with reported severity. Findings indicated novel symptom-genotype associations in preeclampsia. The small sample was self-selected, but results support future studies including medical records review. When validated, these results may lead to holistic phenotyping of women to characterize subsets of preeclampsia. This approach may optimize health in pregnancy and later life for mothers and offspring through prediction, prevention, and precision nursing care.

  16. Genotypic richness predicts phenotypic variation in an endangered clonal plant

    Directory of Open Access Journals (Sweden)

    Suzanna M. Evans

    2016-02-01

    Full Text Available Declines in genetic diversity within a species can affect the stability and functioning of populations. The conservation of genetic diversity is thus a priority, especially for threatened or endangered species. The importance of genetic variation, however, is dependent on the degree to which it translates into phenotypic variation for traits that affect individual performance and ecological processes. This is especially important for predominantly clonal species, as no single clone is likely to maximise all aspects of performance. Here we show that intraspecific genotypic diversity as measured using microsatellites is a strong predictor of phenotypic variation in morphological traits and shoot productivity of the threatened, predominantly clonal seagrass Posidonia australis, on the east coast of Australia. Biomass and surface area variation was most strongly predicted by genotypic richness, while variation in leaf chemistry (phenolics and nitrogen was unrelated to genotypic richness. Genotypic richness did not predict tissue loss to herbivores or epiphyte load, however we did find that increased herbivore damage was positively correlated with allelic richness. Although there was no clear relationship between higher primary productivity and genotypic richness, variation in shoot productivity within a meadow was significantly greater in more genotypically diverse meadows. The proportion of phenotypic variation explained by environmental conditions varied among different genotypes, and there was generally no variation in phenotypic traits among genotypes present in the same meadows. Our results show that genotypic richness as measured through the use of presumably neutral DNA markers does covary with phenotypic variation in functionally relevant traits such as leaf morphology and shoot productivity. The remarkably long lifespan of individual Posidonia plants suggests that plasticity within genotypes has played an important role in the longevity of

  17. Genotype-Specific Evolution of Hepatitis E Virus

    Science.gov (United States)

    Brayne, Adam B.; Dearlove, Bethany L.; Lester, James S.; Kosakovsky Pond, Sergei L.

    2017-01-01

    ABSTRACT Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis globally. HEV comprises four genotypes with different geographic distributions and host ranges. We utilize this natural case-control study for investigating the evolution of zoonotic viruses compared to single-host viruses, using 244 near-full-length HEV genomes. Genome-wide estimates of the ratio of nonsynonymous to synonymous evolutionary changes (dN/dS ratio) located a region of overlapping reading frames, which is subject to positive selection in genotypes 3 and 4. The open reading frames (ORFs) involved have functions related to host-pathogen interaction, so genotype-specific evolution of these regions may reflect their fitness. Bayesian inference of evolutionary rates shows that genotypes 3 and 4 have significantly higher rates than genotype 1 across all ORFs. Reconstruction of the phylogenies of zoonotic genotypes demonstrates significant intermingling of isolates between hosts. We speculate that the genotype-specific differences may result from cyclical adaptation to different hosts in genotypes 3 and 4. IMPORTANCE Hepatitis E virus (HEV) is increasingly recognized as a pathogen that affects both the developing and the developed world. While most often clinically mild, HEV can be severe or fatal in certain demographics, such as expectant mothers. Like many other viral pathogens, HEV has been classified into several distinct genotypes. We show that most of the HEV genome is evolutionarily constrained. One locus of positive selection is unusual in that it encodes two distinct protein products. We are the first to detect positive selection in this overlap region. Genotype 1, which infects humans only, appears to be evolving differently from genotypes 3 and 4, which infect multiple species, possibly because genotypes 3 and 4 are unable to achieve the same fitness due to repeated host jumps. PMID:28202767

  18. Genotype-Specific Evolution of Hepatitis E Virus.

    Science.gov (United States)

    Brayne, Adam B; Dearlove, Bethany L; Lester, James S; Kosakovsky Pond, Sergei L; Frost, Simon D W

    2017-05-01

    Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis globally. HEV comprises four genotypes with different geographic distributions and host ranges. We utilize this natural case-control study for investigating the evolution of zoonotic viruses compared to single-host viruses, using 244 near-full-length HEV genomes. Genome-wide estimates of the ratio of nonsynonymous to synonymous evolutionary changes (dN/dS ratio) located a region of overlapping reading frames, which is subject to positive selection in genotypes 3 and 4. The open reading frames (ORFs) involved have functions related to host-pathogen interaction, so genotype-specific evolution of these regions may reflect their fitness. Bayesian inference of evolutionary rates shows that genotypes 3 and 4 have significantly higher rates than genotype 1 across all ORFs. Reconstruction of the phylogenies of zoonotic genotypes demonstrates significant intermingling of isolates between hosts. We speculate that the genotype-specific differences may result from cyclical adaptation to different hosts in genotypes 3 and 4.IMPORTANCE Hepatitis E virus (HEV) is increasingly recognized as a pathogen that affects both the developing and the developed world. While most often clinically mild, HEV can be severe or fatal in certain demographics, such as expectant mothers. Like many other viral pathogens, HEV has been classified into several distinct genotypes. We show that most of the HEV genome is evolutionarily constrained. One locus of positive selection is unusual in that it encodes two distinct protein products. We are the first to detect positive selection in this overlap region. Genotype 1, which infects humans only, appears to be evolving differently from genotypes 3 and 4, which infect multiple species, possibly because genotypes 3 and 4 are unable to achieve the same fitness due to repeated host jumps. Copyright © 2017 American Society for Microbiology.

  19. Hepatitis B virus genotypes A and D in Uganda.

    Science.gov (United States)

    Zirabamuzale, Jackie T; Opio, Christopher K; Bwanga, Freddie; Seremba, Emmanuel; Apica, Betty S; Colebunders, Robert; Ocama, Ponsiano

    2016-01-01

    The prevalence of hepatitis B virus (HBV) infection in Uganda is 10%. Hepatitis B virus genotypes impact on treatment response, rate of spontaneous recovery and progression of chronic HBV infection and hepatocellular carcinoma. There is little information on the HBV genotypic distribution in Uganda. To determine HBV genotypes in Uganda. The MBN clinical laboratory performs HBV viral load and genotype testing in Uganda. It receives hepatitis B surface antigen (HBsAg)-positive samples from all over the country for additional HBV testing. Samples are stored for 6 months before being discarded. Our study used delinked stored samples. PCR-positive samples had DNA extracted and used as template for HBV genome amplification by nested PCR. Reverse hybridisation was performed and genotypes were determined by the line probe assay method (INNO-LiPA). One hundred stored HBsAg-positive plasma samples with detectable viral loads were analysed. Of these, 93 samples showed PCR amplification products and gave genotype-specific probe lines on the INNO-LiPA assay. Of the patients, where gender was recorded, 60.9% were female, and the overall median age (IQR) was 25 (2-60) years. There was a predominance of HBV genotype D (47 patients; 50.5%), followed by genotype A, (16 patients; 17.2%). One patient (1.1%) had genotype E. In 28% of the samples mixed infections were detected with genotypes A/E (9.7%) and A/D (6.5%) being most common. Genotypes B, C, E and H only occurred as part of mixed infections. Hepatitis B genotypes D and A were predominant in our study population.

  20. Deep Sequencing Analysis of HBV Genotype Shift and Correlation with Antiviral Efficiency during Adefovir Dipivoxil Therapy

    Science.gov (United States)

    Shan, Youlan; Huang, Wenxiang; Zhang, Dazhi; Zen, Aizhong; Zhou, Xin; Zhao, Yao; Gong, Xuyang; Xu, Ge; Zhang, Xiuyu; Chen, Juan; Huang, Ailong

    2015-01-01

    Background Viral genotype shift in chronic hepatitis B (CHB) patients during antiviral therapy has been reported, but the underlying mechanism remains elusive. Methods 38 CHB patients treated with ADV for one year were selected for studying genotype shift by both deep sequencing and Sanger sequencing method. Results 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. Conclusions 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. PMID:26110616

  1. Detecting and genotyping Escherichia coli O157:H7 using multiplexed PCR and nucleic acid microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Call, Douglas R.; Brockman, Fred J.; Chandler, Darrell P.

    2001-07-05

    Rapid detection and characterization of food borne pathogens such as Escherichia coli O157:H7 is crucial for epidemiological investigations and food safety surveillance. As an alternative to conventional technologies, we examined the sensitivity and specificity of nucleic acid microarrays for detecting and genotyping E. coli O157:H7. The array was composed of oligonucleotide probes (25-30 mer) complementary to four virulence loci (intimin, Shiga-like toxins I and II, and hemolysin A). Target DNA was amplified from whole cells or from purified DNA via single or multiplexed polymerase chain reaction (PCR), and PCR products were hybridized to the array without further modification or purification. The array was 32-fold more sensitive than gel electrophoresis and capable of detecting amplification products from < 1 cell equivalent of genomic DNA (1 fg). Immunomagnetic capture, PCR and a microarray were subsequently used to detect 55 CFUs ml-1 (E. coli O157:H7) from chicken rinsate without the aid of pre-enrichment. Four isolates of E. coli O157:H7 and one isolate of O91:H2, for which genotypic data were available, were unambiguously genotyped with this array. Glass based microarrays are relatively simple to construct and provide a rapid and sensitive means to detect multiplexed PCR products and the system is amenable to automation.

  2. Detecting and Genotyping Escherichia coli O157:H7 using multiplexed PCR and nucleic acid microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Call, Douglas R.(Michigan, Univ Of - Ann Arbor); Brockman, Fred J.(BATTELLE (PACIFIC NW LAB)); Chandler, Darrell P.(Pacific Northwest National Laboratory)

    2000-12-01

    Rapid detection and characterization of food borne pathogens such as Escherichia coli O157:H7 is crucial for epidemiological investigations and food safety surveillance. As an alternative to conventional technologies, we examined the sensitivity and specificity of nucleic acid microarrays for detecting and genotyping E. coli O157:H7. The array was composed of oligonucleotide probes (25-30 mer) complementary to four virulence loci (intimin, Shiga-like toxins I and II, and hemolysin A). Target DNA was amplified from whole cells or from purified DNA via single or multiplexed polymerase chain reaction (PCR), and PCR products were hybridized to the array without further modification or purification. The array was 32-fold more sensitive than gel electrophoresis and capable of detecting amplification products from < 1 cell equivalent of genomic DNA (1 fg). Immunomagnetic capture, PCR and a microarray were subsequently used to detect 55 CFU ml-1 (E. coli O157:H7) from chicken rinsate without the aid of pre-enrichment. Four isolates of E. coli O157:H7 and one isolate of O91:H2, for which genotypic data were available, were unambiguously genotyped with this array. Glass based microarrays are relatively simple to construct and provide a rapid and sensitive means to detect multiplexed PCR products and the system is amenable to automation.

  3. Heritability and Genetic Advance among Chili Pepper Genotypes for Heat Tolerance and Morphophysiological Characteristics

    Directory of Open Access Journals (Sweden)

    Magaji G. Usman

    2014-01-01

    Full Text Available High temperature tolerance is an important component of adaptation to arid and semiarid cropping environment in chili pepper. Two experiments were carried out to study the genetic variability among chili pepper for heat tolerance and morphophysiological traits and to estimate heritability and genetic advance expected from selection. There was a highly significant variation among the genotypes in response to high temperature (CMT, photosynthesis rate, plant height, disease incidence, fruit length, fruit weight, number of fruits, and yield per plant. At 5% selection intensity, high genetic advance as percent of the mean (>20% was observed for CMT, photosynthesis rate, fruit length, fruit weight, number of fruits, and yield per plant. Similarly, high heritability (>60% was also observed indicating the substantial effect of additive gene more than the environmental effect. Yield per plant showed strong to moderately positive correlations (r=0.23–0.56 at phenotypic level while at genotypic level correlation coefficient ranged from 0.16 to 0.72 for CMT, plant height, fruit length, and number of fruits. Cluster analysis revealed eight groups and Group VIII recorded the highest CMT and yield. Group IV recorded 13 genotypes while Groups II, VII, and VIII recorded one each. The results showed that the availability of genetic variance could be useful for exploitation through selection for further breeding purposes.

  4. The presence of PAI-1 4G/5G and ACE DD genotypes increases the risk of early-stage AVF thrombosis in hemodialysis patients.

    Science.gov (United States)

    Güngör, Yahya; Kayataş, Mansur; Yıldız, Gürsel; Özdemir, Öztürk; Candan, Ferhan

    2011-01-01

    In this study, we investigated the relationship between early arteriovenous fistula (AVF) thrombosis with angiotensin-converting enzyme (ACE) gene and thrombophilic factor gene polymorphisms. Thirty-five patients who suffered from three or more fistula thrombosis episodes in the early period after AVF operation and 33 control patients with no history of thrombosis for at least 3 years were enrolled in this study. Factor V G1691A Leiden, factor V H1299R (R2), prothrombin G20210A, factor XIIIV34L, β-fibrinogen-455 G-A, glycoprotein IIIa L33P human platelet antigens (HPA-1), methylenetetrahydrofolate reductase C677T, and methylenetetrahydrofolate reductase A1298C gene polymorphisms were similar in both groups (p > 0.05). Plasminogen activator inhibitor 1 (PAI-1) 4G/5G genotype in the study group and 4G/4G genotype in the control group were significantly higher (p = 0.014). No significant difference was detected in terms of the 5G/5G genotype. With regard to the ACE gene polymorphism, the control group showed more ID genotype (19/33, 57.6%), whereas the study group showed more DD genotype (17/35, 48.6%). II genotype was similar in both groups (x(2) = 7.40, p = 0.025). The rate of ACE inhibitor-angiotensin II receptor blockers use was 5/35 in the study group (14.3%) and 5/33 in the control group (15.2%). Individuals with PAI-1 4G/5G genotype showed 5.03 times more risk of thrombosis when compared with 4G/4G and 5G/5G genotypes [p = 0.008, OR = 5.03, 95% confidence interval (1.44:17.64)]. Individuals with ACE DD genotype showed 4.25 times more risk of thrombosis when compared with II and ID [p = 0.008, OR = 4.25, 95% confidence interval (1.404:12.83)]. PAI-1 4G/5G and ACE DD genotypes are associated with increased risk for early AVF thrombosis.

  5. Cryptosporidium parvum: infectivity and pathogenicity of the 'porcine' genotype

    DEFF Research Database (Denmark)

    Enemark, Heidi L.; Ahrens, Peter; Bille-Hansen, Vivi

    2003-01-01

    Genetic studies have demonstrated profound differences between the 'porcine' genotype of Cryptosporidium parvum, versus 'human' and 'bovine' genotypes. The study analysed infectivity and pathogenicity of the 'porcine' genotype (CPP-13 isolate) of C. parvum, and compared the results with published...... data on the 'bovine' genotype (CPB-0 isolate). This was investigated in calves and piglets from commercial herds. Piglets were mildly affected by the CPP-13 isolate, contrary to piglets infected with the CPB-0 isolate, which caused diarrhoea of a mean duration of 3.5 days. CPP-13 produced no or very...

  6. Genotype and Phenotype Analysis in Pediatric Patients with Cystinuria.

    Science.gov (United States)

    Kim, Ji Hyun; Park, Eujin; Hyun, Hye Sun; Lee, Beom Hee; Kim, Gu Hwan; Lee, Joo Hoon; Park, Young Seo; Kang, Hee Gyung; Ha, Il Soo; Cheong, Hae Il

    2017-02-01

    Cystinuria is an inherited disorder characterized by defective renal reabsorption of cystine and dibasic amino acids leading to nephrolithiasis. This study was conducted to analyze the genotypes and phenotypes of pediatric patients with cystinuria. Eight children from Seoul National University Hospital and Asan Medical Center presenting with cystinuria from January 2003 to June 2016 were retrospectively analyzed. Mutational studies were performed by direct sequencing. Two of the 8 were male and 6 were female. The median ages at onset and diagnosis were 1.5 (range, 0.3-13.6) and 2.6 (range, 0.7-16.7) years, respectively. The median followed up was 7.7 (range, 3.4-14.0) years. Mutational analyses were performed in 7 patients and revealed biallelic SLC3A1 mutations (AA genotype) in 4 patients, a single heterozygous SLC3A1 mutation (A- genotype) in 1 patient, biallelic SLC7A9 mutations (BB genotype) in 1 patient, and a single heterozygous SLC7A9 mutation (B- genotype) in 1 patient. Two of the mutations were novel. No genotype-phenotype correlations were observed, except for earlier onset age in patients with non-AA genotypes than in patients with the AA genotype. All patients suffered from recurrent attacks of symptomatic nephrolithiasis, which lead to urologic interventions. At the last follow-up, 3 patients had a mild-to-moderate degree of renal dysfunction. This is the first study of genotypic and phenotypic analyses of patients with cystinuria in Korea.

  7. Genotype Calling from Population-Genomic Sequencing Data

    Science.gov (United States)

    Maruki, Takahiro; Lynch, Michael

    2017-01-01

    Genotype calling plays important roles in population-genomic studies, which have been greatly accelerated by sequencing technologies. To take full advantage of the resultant information, we have developed maximum-likelihood (ML) methods for calling genotypes from high-throughput sequencing data. As the statistical uncertainties associated with sequencing data depend on depths of coverage, we have developed two types of genotype callers. One approach is appropriate for low-coverage sequencing data, and incorporates population-level information on genotype frequencies and error rates pre-estimated by an ML method. Performance evaluation using computer simulations and human data shows that the proposed framework yields less biased estimates of allele frequencies and more accurate genotype calls than current widely used methods. Another type of genotype caller applies to high-coverage sequencing data, requires no prior genotype-frequency estimates, and makes no assumption on the number of alleles at a polymorphic site. Using computer simulations, we determine the depth of coverage necessary to accurately characterize polymorphisms using this second method. We applied the proposed method to high-coverage (mean 18×) sequencing data of 83 clones from a population of Daphnia pulex. The results show that the proposed method enables conservative and reasonably powerful detection of polymorphisms with arbitrary numbers of alleles. We have extended the proposed method to the analysis of genomic data for polyploid organisms, showing that calling accurate polyploid genotypes requires much higher coverage than diploid genotypes. PMID:28108551

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

    National Research Council Canada - National Science Library

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

    2013-01-01

    .... We exposed seven genetically different but concurrent strains of the diatom Asterionella formosa to one genotype of its naturally co-occurring chytrid parasite Zygorhizidium planktonicum across five...

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

    Science.gov (United States)

    Ruocco, Silvia; Stefanini, Marco; Stanstrup, Jan; Perenzoni, Daniele; Mattivi, Fulvio; Vrhovsek, Urska

    2017-08-01

    Wild American genotypes represent an important part of the Vitis germplasm in relation to grape improvement. Today, these genotypes are currently involved in breeding programmes in order to introgress traits resistant to pests and diseases in V. vinifera cultivars. Nevertheless, the metabolic 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 genotypes. As regards the composition of anthocyanins, not all wild genotypes contained both mono- and di-glucoside derivatives. Wild genotype 41B and V. vinifera cultivars contained only monoglucoside anthocyanins. The proanthocyanidins of non-V. vinifera genotypes were mainly rich in oligomers and short-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. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. 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.

  11. Phenotype and genotype in 103 patients with tricho-rhino-phalangeal syndrome

    DEFF Research Database (Denmark)

    Maas, Saskia M; Shaw, Adam C; Bikker, Hennie

    2015-01-01

    to delineate phenotype, natural history, variability, and genotype-phenotype correlations in more detail. We gathered information on 103 cytogenetically or molecularly confirmed affected individuals. TRPS I was present in 85 individuals (22 missense mutations, 62 other mutations), TRPS II in 14, and in 5...... it remained uncertain whether TRPS1 was partially or completely deleted. Main features defining the facial phenotype include fine and sparse hair, thick and broad eyebrows, especially the medial portion, a broad nasal ridge and tip, underdeveloped nasal alae, and a broad columella. The facial manifestations...... in severity. Missense mutations are located exclusively in exon 6 and 7 of TRPS1. Other mutations are located anywhere in exons 4-7. Whole gene deletions are common but have variable breakpoints. Most of the phenotype in patients with TRPS II is explained by the deletion of TRPS1 and EXT1...

  12. Genotyping of Toxoplasma gondii isolates in meningo-encephalitis affected striped dolphins (Stenella coeruleoalba) from Italy.

    Science.gov (United States)

    Di Guardo, Giovanni; Di Cesare, Angela; Otranto, Domenico; Casalone, Cristina; Iulini, Barbara; Mignone, Walter; Tittarelli, Cristiana; Meloni, Silvana; Castagna, Giuseppe; Forster, Fiona; Kennedy, Seamus; Traversa, Donato

    2011-12-29

    This study reports the occurrence of Toxoplasma gondii in the brain of three striped dolphins (Stenella ceoruleoalba) found stranded on the Ligurian Sea coast of Italy between 2007 and 2008. These animals showed a severe, subacute to chronic, non-purulent, multifocal meningo-encephalitis, with the cerebral parenchyma of two dolphins harbouring protozoan cysts and zoites immunohistochemically linked to T. gondii. Molecular, phylogenetic and mutation scanning analyses showed the occurrence of Type II and of an atypical Type II T. gondii isolates in one and two dolphins, respectively. In spite of the different molecular patterns characterizing the above T. gondii genotypes, the brain lesions observed in the three animals showed common microscopic features, with no remarkable differences among them. The role of T. gondii in causing the meningo-encephalitis is herein discussed. Copyright © 2011 Elsevier B.V. All rights reserved.

  13. [High-risk HPV genotyping PCR testing as a means of cervical cancer and precancerous lesions early screening].

    Science.gov (United States)

    Ma, Li; Cong, Xiao; Bian, Meilu; Shi, Mai; Wang, Xiuhong; Liu, Jun; Liu, Haiyan

    2015-04-01

    To explored high-risk HPV genotyping PCR testing whether as a feasible means for the early screening of cervical cancer and precancerous lesions. From January 2013 to June 2014, 15,192 outpatients in China-Japan Friendship Hospital voluntary were tested by high-risk type HPV genotyping PCR. The average age of them were (33±8) years old. High-risk HPV types genotyping PCR tested by fluorescence PCR technology, in which 13 kinds of high-risk HPV subtypes were detected, including HPV16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59 and 68. A total of 4,315 cases of them were tested by the liquid-based cytology (LCT), among them with positive of high-risk HPV genotyping tested by PCR (n=2,366) were biopsy under colposcope (648 cases) in those LCT results were positive or LCT negative but HPV16 positive or LCT negative but had the clear clinical symptoms or and non-HPV16 positive but with clear clinical symptoms. (1) Analysis high-risk HPV infection status of 15 192 women. (2) As the pathological diagnosis was the gold standard in the diagnosis of cervical lesions, analysis of the relationship among high-risk HPV infection, virus loads and cervical lesions. (3) To evaluated the value of high-risk HPV genotyping PCR tested method in screening of cervical cancer and precancerous lesions. ⑴ Of 15,192 cases tested by high-risk HPV genotyping PCR, 2,366 cases were HPV positive (HPV infection), the overall infection rate was 15.57% (2,366/15,192), in which a single subtype of HPV infection in 1,767 cases, infection rate was 11.63% (1,767/15,192), and multiple subtypes of HPV infection (two and more subtypes HPV infection) in 599 cases, infection rate was 3.94% (599/15,192). The HPV16, 52 and 58 infections were the most common HPV subtypes in 13 subtypes, the infection rate was 3.95% (600/15,192), 2.86% (435/15,192) and 2.67% (406/15,192), respectively. (2) The most relevant subtypes with cervical intraepithelial neoplasia (CIN) II and even higher lesion were HPV16, 52 and 58

  14. and ni(ii)

    African Journals Online (AJOL)

    userpc

    with nickel(II) and cobalt(II) chloride in 2:1 mole ratio yielded Ni(II) and Co(II) complexes respectively. The synthesized compounds were characterized based on melting point/decomposition temperature, solubility, molar conductance, magnetic susceptibility and infrared spectral analyses. The complexes have low molar ...

  15. Preparation and Antimicrobial Screeningof Cu (II, Ni (II, Zn (II Cd (II Complexes

    Directory of Open Access Journals (Sweden)

    R. M. Desai

    2006-01-01

    Full Text Available The metal complexes of Ni(II, Cu(II, Zn(II Cd(II with organic ligands viz Hydrazine hydrate, 1,2-N,N'-Bisammonium thiocarbamoyl ethane and 1,4-N,N'-Bisammonium thiocarbamoyl benzene have been prepared. These ligands and metal complexes of dithiocarbamates were screened for their antimicrobial activity against various microbs.

  16. Copper (II), cobalt (II), nickel (II) and zinc (II) complexes of Schiff ...

    Indian Academy of Sciences (India)

    Abstract. New Schiff base chelates of Cu(II), Co(II), Ni(II) and Zn(II) derived from benzil-2,4-dinitrophenylhydrazone with aniline have been synthesised. Microanalytical data, molar conductance, and magnetic susceptibility values have been obtained, and IR, 1H NMR, 13C NMR, UV-Vis, CV and EPR spectral studies have ...

  17. Molecular surveillance of dengue in Semarang, Indonesia revealed the circulation of an old genotype of dengue virus serotype-1.

    Directory of Open Access Journals (Sweden)

    Sukmal Fahri

    Full Text Available Dengue disease is currently a major health problem in Indonesia and affects all provinces in the country, including Semarang Municipality, Central Java province. While dengue is endemic in this region, only limited data on the disease epidemiology is available. To understand the dynamics of dengue in Semarang, we conducted clinical, virological, and demographical surveillance of dengue in Semarang and its surrounding regions in 2012. Dengue cases were detected in both urban and rural areas located in various geographical features, including the coastal and highland areas. During an eight months' study, a total of 120 febrile patients were recruited, of which 66 were serologically confirmed for dengue infection using IgG/IgM ELISA and/or NS1 tests. The cases occurred both in dry and wet seasons. Majority of patients were under 10 years old. Most patients were diagnosed as dengue hemorrhagic fever, followed by dengue shock syndrome and dengue fever. Serotyping was performed in 31 patients, and we observed the co-circulation of all four dengue virus (DENV serotypes. When the serotypes were correlated with the severity of the disease, no direct correlation was observed. Phylogenetic analysis of DENV based on Envelope gene sequence revealed the circulation of DENV-2 Cosmopolitan genotype and DENV-3 Genotype I. A striking finding was observed for DENV-1, in which we found the co-circulation of Genotype I with an old Genotype II. The Genotype II was represented by a virus strain that has a very slow mutation rate and is very closely related to the DENV strain from Thailand, isolated in 1964 and never reported in other countries in the last three decades. Moreover, this virus was discovered in a cool highland area with an elevation of 1,001 meters above the sea level. The discovery of this old DENV strain may suggest the silent circulation of old virus strains in Indonesia.

  18. Noninvasive fetal RhD genotyping

    DEFF Research Database (Denmark)

    Clausen, Frederik Banch; Damkjær, Merete Berthu; Dziegiel, Morten Hanefeld

    2014-01-01

    Immunization against RhD is the major cause of hemolytic disease of the fetus and newborn (HDFN), which causes fetal or neonatal death. The introduction of postnatal immune prophylaxis in the 1960s drastically reduced immunization incidents in pregnant, D-negative women. In several countries......, antenatal prophylaxis is combined with postnatal prophylaxis to further minimize the immunization risk. Due to lack of knowledge of the fetal RhD type, antenatal prophylaxis is given to all D-negative women. In the European population, approximately 40% of pregnant women carry a D-negative fetus...... and are thus at no risk of immunization. Noninvasive fetal RhD genotyping enables antenatal prophylaxis to be targeted to only those women carrying a D-positive fetus to avoid unnecessary treatment. Based on an analysis of cell-free fetal DNA from the plasma of pregnant women, this approach has recently...

  19. Genome structural variation discovery and genotyping.

    Science.gov (United States)

    Alkan, Can; Coe, Bradley P; Eichler, Evan E

    2011-05-01

    Comparisons of human genomes show that more base pairs are altered as a result of structural variation - including copy number variation - than as a result of point mutations. Here we review advances and challenges in the discovery and genotyping of structural variation. The recent application of massively parallel sequencing methods has complemented microarray-based methods and has led to an exponential increase in the discovery of smaller structural-variation events. Some global discovery biases remain, but the integration of experimental and computational approaches is proving fruitful for accurate characterization of the copy, content and structure of variable regions. We argue that the long-term goal should be routine, cost-effective and high quality de novo assembly of human genomes to comprehensively assess all classes of structural variation.

  20. Genotypic Variation in Wheat Flour Lysophospholipids

    Directory of Open Access Journals (Sweden)

    Lei Liu

    2017-05-01

    Full Text Available Lysophospholipids (LPLs are the most abundant polar lipids in wheat endosperm and naturally complex with amylose, affecting starch physicochemical properties. We analyzed LPLs in wheat flour from 58 cultivars which differ by grain hardness using liquid chromatography mass spectrometry (LCMS. There were significant differences in LPL content between cultivars, demonstrating that genotype rather than environment contributes most to the total variance in wheat endosperm LPLs. Polar lipids such as LPLs may play a role in grain hardness through their interaction with puroindoline proteins, however, no strong correlation between kernel hardness and LPLs was detected. This may reflect the location of LPLs within the starch granule as opposed to the puroindoline proteins outside starch granules. LPLs may have an indirect relationship with kernel hardness as they could share the same origin as polar lipids that interact with puroindoline on the starch granule surface.

  1. Medulloblastoma Genotype Dictates Blood Brain Barrier Phenotype.

    Science.gov (United States)

    Phoenix, Timothy N; Patmore, Deanna M; Boop, Scott; Boulos, Nidal; Jacus, Megan O; Patel, Yogesh T; Roussel, Martine F; Finkelstein, David; Goumnerova, Liliana; Perreault, Sebastien; Wadhwa, Elizabeth; Cho, Yoon-Jae; Stewart, Clinton F; Gilbertson, Richard J

    2016-04-11

    The childhood brain tumor, medulloblastoma, includes four subtypes with very different prognoses. Here, we show that paracrine signals driven by mutant β-catenin in WNT-medulloblastoma, an essentially curable form of the disease, induce an aberrant fenestrated vasculature that permits the accumulation of high levels of intra-tumoral chemotherapy and a robust therapeutic response. In contrast, SHH-medulloblastoma, a less curable disease subtype, contains an intact blood brain barrier, rendering this tumor impermeable and resistant to chemotherapy. The medulloblastoma-endothelial cell paracrine axis can be manipulated in vivo, altering chemotherapy permeability and clinical response. Thus, medulloblastoma genotype dictates tumor vessel phenotype, explaining in part the disparate prognoses among medulloblastoma subtypes and suggesting an approach to enhance the chemoresponsiveness of other brain tumors. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Sources of Wilhelm Johannsen's genotype theory.

    Science.gov (United States)

    Roll-Hansen, Nils

    2009-01-01

    This paper describes the historical background and early formation of Wilhelm Johannsen's distinction between genotype and phenotype. It is argued that contrary to a widely accepted interpretation (For instance, W. Provine, 1971. The Origins of Theoretical Population Genetics. Chicago: The University of Chicago Press; Mayr, 1973; F. B. Churchill, 1974. Journal of the History of Biology 7: 5-30; E. Mayr, 1982. The Growth of Biological Thought, Cambridge: Harvard University Press; J. Sapp, 2003. Genesis. The Evolution of Biology. New York: Oxford University Press) his concepts referred primarily to properties of individual organisms and not to statistical averages. Johannsen's concept of genotype was derived from the idea of species in the tradition of biological systematics from Linnaeus to de Vries: An individual belonged to a group - species, subspecies, elementary species - by representing a certain underlying type (S. Müller-Wille and V. Orel, 2007. Annals of Science 64: 171-215). Johannsen sharpened this idea theoretically in the light of recent biological discoveries, not least those of cytology. He tested and confirmed it experimentally combining the methods of biometry, as developed by Francis Galton, with the individual selection method and pedigree analysis, as developed for instance by Louis Vilmorin. The term "genotype" was introduced in W. Johannsen's 1909 (Elemente der Exakten Erblichkeitslehre. Jena: Gustav Fischer) treatise, but the idea of a stable underlying biological "type" distinct from observable properties was the core idea of his classical bean selection experiment published 6 years earlier (W. Johannsen, 1903. Ueber Erblichkeit in Populationen und reinen Linien. Eine Beitrag zur Beleuchtung schwebender Selektionsfragen, Jena: Gustav Fischer, pp. 58-59). The individual ontological foundation of population analysis was a self-evident presupposition in Johannsen's studies of heredity in populations from their start in the early 1890s till his

  3. Genotyping-by-Sequencing and Its Exploitation for Forage and Cool-Season Grain Legume Breeding

    Directory of Open Access Journals (Sweden)

    Paolo Annicchiarico

    2017-05-01

    Full Text Available Genotyping-by-Sequencing (GBS may drastically reduce genotyping costs compared with single nucleotide polymorphism (SNP array platforms. However, it may require optimization for specific crops to maximize the number of available markers. Exploiting GBS-generated markers may require optimization, too (e.g., to cope with missing data. This study aimed (i to compare elements of GBS protocols on legume species that differ for genome size, ploidy, and breeding system, and (ii to show successful applications and challenges of GBS data on legume species. Preliminary work on alfalfa and Medicago truncatula suggested the greater interest of ApeKI over PstI:MspI DNA digestion. We compared KAPA and NEB Taq polymerases in combination with primer extensions that were progressively more selective on restriction sites, and found greater number of polymorphic SNP loci in pea, white lupin and diploid alfalfa when adopting KAPA with a non-selective primer. This protocol displayed a slight advantage also for tetraploid alfalfa (where SNP calling requires higher read depth. KAPA offered the further advantage of more uniform amplification than NEB over fragment sizes and GC contents. The number of GBS-generated polymorphic markers exceeded 6,500 in two tetraploid alfalfa reference populations and a world collection of lupin genotypes, and 2,000 in different sets of pea or lupin recombinant inbred lines. The predictive ability of GBS-based genomic selection was influenced by the genotype missing data threshold and imputation, as well as by the genomic selection model, with the best model depending on traits and data sets. We devised a simple method for comparing phenotypic vs. genomic selection in terms of predicted yield gain per year for same evaluation costs, whose application to preliminary data for alfalfa and pea in a hypothetical selection scenario for each crop indicated a distinct advantage of genomic selection.

  4. Light response of sunflower and canola as affected by plant density, plant genotype and N fertilization.

    Science.gov (United States)

    Soleymani, A

    2017-08-01

    Crop response to light is an important parameter determining crop growth. Three field (split plots) experiments were conducted to investigate the effects of plant density, plant genotype and N fertilization on the light absorption and light extinction of sunflower (Helianthus annuus L.) and canola (Brassica napus L.). A detailed set of plant growth, light absorption and crop yield and oil related parameters were determined. Light was measured at noon during the sunny days with clear sky. In experiment I, although the plant density (PD) of 14 resulted in the highest rate of sunflower light absorption (31.37%) and light extinction (0.756), the highest rate of grain yield and grain oil yield was resulted at PD12 at 3639 and 1457.9kg/ha, respectively; as well as by genotype SUP.A. In experiment II (canola), PD80 resulted in the highest rate of light absorption (13.13%), light extinction (0.63), grain yield (2189.4kg/ha) and grain oil yield (556.54kg/ha). This was also the case for Genotype H. In experiment III (canola), although N150 resulted in the highest rate of light absorption (10.74%) and light extinction (0.48), the highest rate of grain yield (3413.6kg/ha) and grain oil yield (891.86kg/ha) was resulted at N100 as well as by Genotype H401. Results indicate how light properties, crop growth and yield of sunflower and canola can be affected by plant and environmental parameters, which are also of practical use by farmers. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Genotype Imputation with Thousands of Genomes

    Science.gov (United States)

    Howie, Bryan; Marchini, Jonathan; Stephens, Matthew

    2011-01-01

    Genotype imputation is a statistical technique that is often used to increase the power and resolution of genetic association studies. Imputation methods work by using haplotype patterns in a reference panel to predict unobserved genotypes in a study dataset, and a number of approaches have been proposed for choosing subsets of reference haplotypes that will maximize accuracy in a given study population. These panel selection strategies become harder to apply and interpret as sequencing efforts like the 1000 Genomes Project produce larger and more diverse reference sets, which led us to develop an alternative framework. Our approach is built around a new approximation that uses local sequence similarity to choose a custom reference panel for each study haplotype in each region of the genome. This approximation makes it computationally efficient to use all available reference haplotypes, which allows us to bypass the panel selection step and to improve accuracy at low-frequency variants by capturing unexpected allele sharing among populations. Using data from HapMap 3, we show that our framework produces accurate results in a wide range of human populations. We also use data from the Malaria Genetic Epidemiology Network (MalariaGEN) to provide recommendations for imputation-based studies in Africa. We demonstrate that our approximation improves efficiency in large, sequence-based reference panels, and we discuss general computational strategies for modern reference datasets. Genome-wide association studies will soon be able to harness the power of thousands of reference genomes, and our work provides a practical way for investigators to use this rich information. New methodology from this study is implemented in the IMPUTE2 software package. PMID:22384356

  6. 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.

  7. [Phenotype-genotype correlation analysis of 12 cases with Angelman/Prader-Willi syndrome].

    Science.gov (United States)

    Chen, Chen; Peng, Ying; Xia, Yan; Li, Haoxian; Zhu, Huimin; Pan, Qian; Yin, Fei; Wu, Lingqian

    2014-12-01

    To investigate the genotype-phenotype correlation in patients with Angelman syndrome/Prader-Willi syndrome (AS/PWS) and assess the application value of high-resolution single nucleotide polymorphism microarrays (SNP array) for such diseases. Twelve AS/PWS patients were diagnosed through SNP array, fluorescence in situ hybridization (FISH) and karyotype analysis. Clinical characteristics were analyzed. Deletions ranging from 4.8 Mb to 7.0 Mb on chromosome 15q11.2-13 were detected in 11 patients. Uniparental disomy (UPD) was detected in only 1 patient. Patients with deletions could be divided into 2 groups, including 7 cases with class I and 4 with class II. The two groups however had no significant phenotypic difference. The UPD patient had relatively better development and language ability. Deletions of 6 patients were confirmed by FISH to be of de novo in origin. The risk to their sibs was determined to be less than 1%. The phenotypic differences between AS/PWS patients with class I and class II deletion need to be further studied. SNP array is useful in detecting and distinguishing of patients with deletion or UPD. This method may be applied for studying the genotype-phenotype association and the mechanism underlying AS/PWS.

  8. Application of molecular genotyping to determine prevalence of HPV strains in Pap smears of Kazakhstan women.

    Science.gov (United States)

    Niyazmetova, Luiza; Aimagambetova, Gulzhanat; Stambekova, Nazigul; Abugalieva, Zaurech; Seksembayeva, Korlukain; Ali, Syed; Azizan, Azliyati

    2017-01-01

    Human papillomavirus is the main causative agent for cervical cancer. However, few data are available about HPV prevalence in Kazakhstan. The aims of this study were to genotype HPV DNA in Pap smear samples of women to determine prevalence of carcinogenic HPV types in Astana, Kazakhstan and to analyze the association between HPV positivity and the cytology results of patient samples. Pap smear materials were obtained from 140 patients aged 18-59, who visited the outpatient gynecological clinic. Microscopic examination was done to detect dysplasia, and HPV genotyping was done using real-time multiplex PCR. HPV testing showed that among 61 HPV positive patients, the most prevalent types were 16 and 18. Microscopic examination showed that 79% of the samples had normal cytology, while 13% had CIN grade I, 5% had CIN grade II, and 3% had CIN grade III. The analysis revealed that 12% of the samples had CIN cytology and presence of HPV. Approximately 31% had HPV without cervical dysplasia, while 8% of samples were CIN positive without HPV infection. A statistically significant relationship between HPV 16 and HPV 33 positive samples and CIN grade II and III was found. Overall, this study will help to strengthen and guide health policy implementation of primary and secondary cervical cancer prevention strategies in Kazakhstan. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  9. A SNP genotyping array for hexaploid oat

    Science.gov (United States)

    Recognizing a need in cultivated hexaploid oat (Avena sativa L.) for a reliable set of reference SNPs, we have developed a 6K BeadChip design containing 257 Infinium I and 5,486 Infinium II designs corresponding to 5,743 SNPs. Of those, 4,975 SNPs yielded successful assays after array manufacturing...

  10. Incidence of rotavirus and circulating genotypes in Northeast Brazil during 7 years of national rotavirus vaccination.

    Directory of Open Access Journals (Sweden)

    Ricardo Q Gurgel

    Full Text Available BACKGROUND AND AIMS: Rotavirus causes severe diarrhoea and Brazil introduced the Rotarix G1P[8] vaccine in 2006. We aimed to describe changes in rotavirus incidence and diarrhoea epidemiology before and after vaccine introduction. METHODS: DESIGN: (i hospital-based survey of children with diarrhoea (2006-2012; (ii diarrhea-mortality and hospitalization surveillance (1999-2012. SETTING: (i Aracaju and (ii state and national level. RESULTS: 1841 children were enrolled and 231 (12.5% had rotavirus. Rotavirus was less frequent from January-June than from July-December (9.4% versus 20.9%, p<0.01, but the seasonal variation was less defined after 2009. Very few rotavirus cases (8-3.9% were detected in 2011, with an increase in 2012 (13-18.5%. In 2006, unvaccinated children were more likely to have rotavirus, but thereafter unvaccinated and vaccinated children had equally low incidence. Older children and those with rotavirus were more likely to have severe diarrhea episodes. The most frequent genotype from 2006 to 2010 was G2P[4]; except in 2009, when most cases were G1P[8]. Very few G2P[4] were detected from 2011 and 50% cases in 2012 were G8P[4]. Diarrhoea-hospitalizations decreased nationally from 89,934 (2003 to 53,705 (2012; 40.3% reduction and in the state from 1729 to 748 (56.7% reduction. Diarrhoea-deaths decreased nationally from 4368 in 1999 to 697 in 2012 (84% reduction, p<0.001 and in the state from 132 to 18 (86% reduction. These changes were much larger after vaccine introduction. CONCLUSIONS: The vaccine was associated with substantial reductions in rotavirus incidence and diarrhoea-hospitalizations and deaths. The G2P[4] genotype predominance disappeared over time and may be replaced by other heterotypic genotypes.

  11. Comparative analysis of full genomic sequences among different genotypes of dengue virus type 3

    Directory of Open Access Journals (Sweden)

    Lin Ting-Hsiang

    2008-05-01

    Full Text Available Abstract Background Although the previous study demonstrated the envelope protein of dengue viruses is under purifying selection pressure, little is known about the genetic differences of full-length viral genomes of DENV-3. In our study, complete genomic sequencing of DENV-3 strains collected from different geographical locations and isolation years were determined and the sequence diversity as well as selection pressure sites in the DENV genome other than within the E gene were also analyzed. Results Using maximum likelihood and Bayesian approaches, our phylogenetic analysis revealed that the Taiwan's indigenous DENV-3 isolated from 1994 and 1998 dengue/DHF epidemics and one 1999 sporadic case were of the three different genotypes – I, II, and III, each associated with DENV-3 circulating in Indonesia, Thailand and Sri Lanka, respectively. Sequence diversity and selection pressure of different genomic regions among DENV-3 different genotypes was further examined to understand the global DENV-3 evolution. The highest nucleotide sequence diversity among the fully sequenced DENV-3 strains was found in the nonstructural protein 2A (mean ± SD: 5.84 ± 0.54 and envelope protein gene regions (mean ± SD: 5.04 ± 0.32. Further analysis found that positive selection pressure of DENV-3 may occur in the non-structural protein 1 gene region and the positive selection site was detected at position 178 of the NS1 gene. Conclusion Our study confirmed that the envelope protein is under purifying selection pressure although it presented higher sequence diversity. The detection of positive selection pressure in the non-structural protein along genotype II indicated that DENV-3 originated from Southeast Asia needs to monitor the emergence of DENV strains with epidemic potential for better epidemic prevention and vaccine development.

  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. Trait associations in common bean genotypes grown under drought stress and field infestation by BSM bean fly

    Directory of Open Access Journals (Sweden)

    Daniel Ambachew

    2015-08-01

    Full Text Available Understanding functional relations among plant traits and their modulation by growing conditions is imperative in designing selection strategies for breeding programs. This study assessed trait relationships among 196 common bean genotypes exposed to stresses for drought and field infestation of bean fly or bean stem maggot (BSM. The study was carried out at two locations and data was analyzed with linear correlation, path coefficient and genotype × trait biplot analyses. Multiple trait data related to mechanisms of drought and bean fly tolerance were collected on 196 genotypes grown under i water deficit at mid-pod fill, or ii unprotected against bean fly; iii irrigated, well watered conditions, or iv bean fly protection with chemicals. Seed yield exhibited positive and significant correlations with leaf chlorophyll content, vertical root pulling resistance, pod harvest index, pods per plant and seeds per pod at both phenotypic and genotypic levels under stress and non-stress conditions. Genotypic correlations of traits with seed yield were greater than their respective phenotypic correlations across environments indicating the greater contribution of genotypic factors to the trait correlation. Pods per plant and seeds per pod had high positive direct effects on seed yield both under stress and non-stress whereas pods per plant had the highest indirect effect on seed yield through pod harvest index under stress. In general, our results suggest that vertical root pulling resistance and pod harvest index are important selection objectives for improving seed yield in common beans under non-stress and stress conditions, and particularly useful for drought and BSM tolerance evaluation.

  14. Biological and Phylogenetic Characterization of a Genotype VII Newcastle Disease Virus from Venezuela: Efficacy of Field Vaccination

    Science.gov (United States)

    Perozo, Francisco; Marcano, Rosmar

    2012-01-01

    Here we report the biological and molecular characterization of a virulent genotype VII Newcastle disease virus (NDV) circulating in Venezuela and the assessment of the vaccination efficacy under field conditions compared to controlled rearing conditions. Biological pathotyping showed a mean embryo dead time of 50 h and an intracerebral pathogenicity index of 1.86. Sequence-based phylogenetic analysis demonstrated that the virus belongs to genotype VII in class II (a genotype often found in Asia and Africa), representing the first report of the presence of this genotype in the continent of South America. A vaccine-challenge trial in commercial broilers reared in fields or in a experimental setting included dual (live/killed) priming of 1-day-old chicks plus two live NDV and infectious bursal disease virus (IBDV) field vaccinations at days 7 and 17, followed by a very stringent genotype VII NDV challenge at day 28. Serology for NDV and IBDV, bursal integrity, and protection against NDV lethal challenge were assessed. At 28 days, field vaccinates showed significantly lower NDV (1,356 versus 2,384) and higher IBD (7,295 versus 1,489) enzyme-linked immunosorbent assay (ELISA) antibody titers than the experimentally reared birds. A lower bursal size and bursa-body weight ratio (P < 0.05) and higher bursa lesion score were also detected in the field set. Only 57.1% of field vaccinates survived the lethal challenge, differing (P < 0.05) from 90.5% survival in the experimental farm. Overall, results confirmed the presence of the genotype VII viruses in South America and suggest that field-associated factors such as immunosuppression compromise the efficacy of the vaccination protocols implemented. PMID:22238433

  15. 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.

  16. FishPathogens.eu/vhsv: A user-friendly Viral Haemorrhagic Septicaemia Virus (VHSV) isolate and sequence database

    DEFF Research Database (Denmark)

    Jonstrup, Søren Peter; Gray, Tanya; Kahns, Søren

    A database has been created, www.FishPathogens.eu, with the aim of providing a single repository for collating important information on significant pathogens of aquaculture, relevant to their control and management. This database will be developed, maintained and managed as part of the European...

  17. Large SNP arrays for genotyping in crop plants

    Indian Academy of Sciences (India)

    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 ...

  18. SURVIVAL OF NORTH AMERICAN GENOTYPES OF TRICHINELLA IN FROZEN PORK

    Science.gov (United States)

    North American genotypes of Trichinella (T. nativa (T-2), T. pseudospiralis (T-4), T. murrelli (T-5), and Trichinella (T-6)) were examined for susceptibility to freezing in pork using established parameters for control of T. spiralis. Pig infections with these Trichinella genotypes were established ...

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

    African Journals Online (AJOL)

    Seeds from each harvest were subjected to different seed quality tests and data generated were analyzed. Seed quality traits were considerably affected by the genotypes and growing conditions i.e. plant population and cropping seasons. Genotypes with superior seed quality were prevalent at 166.667 and 266.667 plants ...

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

    African Journals Online (AJOL)

    symbiotic fixation). A set of 52 random lines from a broad-based reference population was evaluated for 2 years with and without B.japonicum inoculation in a split-plot design. Inoculation increased ... Genotype x: Inoculation Interactions, Nitrogen fixation ..... genotype x N treatment interaction was non significant each year ...

  1. CYP2D6 genotype determination in the Danish population

    DEFF Research Database (Denmark)

    Brøsen, K; Nielsen, P N; Brusgaard, K

    1994-01-01

    CYP2D6 genotyping was carried out by XbaI restriction fragment length polymorphism analysis and polymerase chain reaction in 168 healthy Danish volunteers, 77 extensive metabolizers (EM) and 91 poor metabolizers (PM) of sparteine. All EM were genotyped correctly as heterozygous or homozygous...

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

    African Journals Online (AJOL)

    cntaganda

    main branches using UPGMA clustering method based on Nei's (1978) genetic distance (Figure 3). The first branch had only one genotype 12158, a gene bank accession. The other 12 genotypes were found in the second branch which had four sub clusters. In the first sub cluster, Mbeere 1 and Mbeere 2 had the least.

  3. Application of mixed models for the assessment genotype and ...

    African Journals Online (AJOL)

    In the process of introducing cotton cultivars, it is essential to assess their productive behavior for different environments for which they will be recommended. Knowledge of the magnitude of the genotype interaction with environment allows the evaluation of the stability and adaptability of genotypes where one intends to ...

  4. 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...

  5. Efficiency and response of conilon coffee genotypes to nitrogen supply

    African Journals Online (AJOL)

    The objective of the study was to differentiate genotypes with higher efficiency and responsiveness to nitrogen supply, to understand how the nitrogen supply can impact the dry matter allocation and the accumulation of this nutrient in the different plant compartments of genotypes of conilon coffee, cultivated under ...

  6. 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.

  7. Efficiency and response of conilon coffee genotypes to nitrogen supply

    African Journals Online (AJOL)

    Lindomar

    2016-08-31

    Aug 31, 2016 ... The objective of the study was to differentiate genotypes with higher efficiency and responsiveness to nitrogen supply, to understand how the nitrogen supply can impact the dry matter allocation and the accumulation of this nutrient in the different plant compartments of genotypes of conilon coffee, cultivated ...

  8. Screening of Wheat Genotypes for Boron Efficiency in Bangladesh

    Science.gov (United States)

    A number of Bangladeshi wheat genotypes (varieties and advanced lines) have been tested for boron efficiency through sand culture experiments over two years (2007-08 & 2008-09) against two Thai check varieties ‘Fang 60’ (boron efficient) and ‘SW41’ (boron inefficient). Performances of the genotypes ...

  9. Monotonicity is a key feature of genotype-phenotype maps

    Science.gov (United States)

    Gjuvsland, Arne B.; Wang, Yunpeng; Plahte, Erik; Omholt, Stig W.

    2013-01-01

    It was recently shown that monotone gene action, i.e., order-preservation between allele content and corresponding genotypic values in the mapping from genotypes to phenotypes, is a prerequisite for achieving a predictable parent-offspring relationship across the whole allele frequency spectrum. Here we test the consequential prediction that the design principles underlying gene regulatory networks are likely to generate highly monotone genotype-phenotype maps. To this end we present two measures of the monotonicity of a genotype-phenotype map, one based on allele substitution effects, and the other based on isotonic regression. We apply these measures to genotype-phenotype maps emerging from simulations of 1881 different 3-gene regulatory networks. We confirm that in general, genotype-phenotype maps are indeed highly monotonic across network types. However, regulatory motifs involving incoherent feedforward or positive feedback, as well as pleiotropy in the mapping between genotypes and gene regulatory parameters, are clearly predisposed for generating non-monotonicity. We present analytical results confirming these deep connections between molecular regulatory architecture and monotonicity properties of the genotype-phenotype map. These connections seem to be beyond reach by the classical distinction between additive and non-additive gene action. PMID:24223579

  10. Performance of Bemisia tabaci Biotype B on Soybean Genotypes.

    Science.gov (United States)

    Cruz, P L; Baldin, E L L

    2017-04-01

    Bemisia tabaci (Genn.) (Hemiptera: Aleyrodidae) has been recognized as an important pest of many agricultural systems including soybean [Glycine max (L.) Merrill] crops. As an alternative to chemical control, the use of resistant genotypes represents an important tool for integrated pest management (IPM). This study aimed to evaluate the biological development of Bemisia tabaci biotype B confined on 13 soybean genotypes under greenhouse conditions. Initially, the nymphal period, complete development period (egg-adult), and the viability of the silverleaf whitefly nymphs were evaluated in all genotypes. Then, four genotypes promising for resistance ('Jackson,' UX-2569-159, 'P98Y11,' and 'TMG132 RR') and a susceptible genotype (PI-227687) were selected for further assays, where two insect populations were compared: a first population from the initial rearing (cabbage plants) and another corresponding to insects previously reared out on the selected genotypes. In addition to the parameters evaluated in preliminary tests, we also determined the viability and incubation period of eggs. Moderate levels of resistance (antibiosis/antixenosis) to B. tabaci biotype B were found in three genotypes. 'P98Y11' and 'TMG132 RR' were less suitable for insect development, extending the development cycle, and UX-2569-159 caused high nymphal mortality. We did not observe a significant increase in the level of plant resistance by the use of previously stressed insects. This suggests that the evaluation of a single whitefly generation may be sufficient to make correct decisions on promising soybean genotypes.

  11. Molecular investigation of two contrasting genotypes of Medicago ...

    African Journals Online (AJOL)

    The EST-SSRs markers were polymorphic with an average of 1.33 alleles per primers and gave moderate values of polymorphic information content (PIC) that ranged from 0 to 0.267. The analysis of polymorphism loci for each genotype showed that the tolerant genotype (Tru 131) population had two alleles; genetic ...

  12. Influence of genotype and plant growth regulator on somatic ...

    African Journals Online (AJOL)

    USER

    2010-06-28

    Jun 28, 2010 ... Two genotypes of Brassica napus species (Talayeh and RGS003) and the explants segment (hypocotyls and cotyledon) were tested for their potential to produce somatic embryos in in vitro condition. The effect of genotype, different explants and also different concentrations of plant growth regulators.

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

    African Journals Online (AJOL)

    AJL

    2012-01-26

    Jan 26, 2012 ... genotypes. 3D graphs, Bi-plot and cluster analysis confirmed these results. Principal components analysis showed two components which explained 98.0% variation. Genotypes were grouped in cluster analysis (using Ward's method) based on Yp, Ys and quantitative indices of drought tolerance. Finally,.

  14. Screening upland rice ( Oryza sativa L. ssp. indica ) genotypes for ...

    African Journals Online (AJOL)

    Screening upland rice (Oryza sativa L. ssp. indica) genotypes for salt-tolerance using multivariate cluster analysis. S Cha-um, M Ashraf, C Kirdmanee. Abstract. Seedlings of thirteen genotypes of rice were photoautotrophically grown on MS medium and subsequently exposed to 0 (control) or 200 mM NaCl (salt stress) for 14 ...

  15. Genotype-dependent responses of wheat ( Triticum aestivum L ...

    African Journals Online (AJOL)

    Genotype-dependent responses of wheat ( Triticum aestivum L.) seedlings to drought, UV-B radiation and their combined stresses. ... and ascobate acid, AsA) exhibited differences under the tested stressful conditions in the two genotypes, indicating that they play significant roles in plant responses to these stresses.

  16. Assessment of rice genotypes for salt tolerance using microsatellite ...

    African Journals Online (AJOL)

    SERVER

    2008-03-18

    Mar 18, 2008 ... homeostasis in the rice shoots. To test the usefulness of microsatellite (SSR) markers associated with Saltol QTL, a collection of 36 diverse rice genotypes were used. Phenotypic response of the genotypes to salt stress with EC=12 was assessed under controlled environmental conditions at seedling stage ...

  17. Genetic analysis of some Egyptian rice genotypes using RAPD, SSR ...

    African Journals Online (AJOL)

    nformation of genetic similarities and diversity among superior Egyptian rice genotypes is necessary for future rice breeding programs and derivation of plant lines. Genetic variability and relationships among seven Egyptian rice genotypes namely Giza 178, Giza177, Giza 175, Giza171 Giza 172, Sakha 102, and Sakha 101 ...

  18. Influence of genotype and plant growth regulator on somatic ...

    African Journals Online (AJOL)

    Two genotypes of Brassica napus species (Talayeh and RGS003) and the explants segment (hypocotyls and cotyledon) were tested for their potential to produce somatic embryos in in vitro condition. The effect of genotype, different explants and also different concentrations of plant growth regulators (PGRs) including: ...

  19. Evaluation of promising sweetpotato genotypes for high altitude ...

    African Journals Online (AJOL)

    Eighteen genotypes from the NationalSweetpotato Programme were evaluated for their fresh storage root yield and reaction to stem and leafbUght (Alternaria bataticola) at Kachwckano (2000 metres above sea level) in Southwest. Uganda. The trials were set up to identify sweetpotato genotypes with adaptation to highland ...

  20. Genetic evaluation of spring wheat (Triticum aestivum L.) genotypes ...

    African Journals Online (AJOL)

    SAM

    2014-04-30

    Apr 30, 2014 ... yield (g) was observed in genotypes WH1132 and WH 1131. Grain yield per plot (g) .... Genotype. Pedigree. Source. Amber 28. WG5669/2/MACS2496/BOW. KSPL,Jalna (M.H). WCW 2009-06. PBW 343/WH 147. SVBPUA&T, Merrut (U.P). HUW 660 .... cient analysis was accessed by Dewey and Lu (1959).

  1. The nutritive value of forage sorghum genotypes developed for the ...

    African Journals Online (AJOL)

    Jack Ouda

    for all genotypes after 24 h incubation but Lan-12 had the highest methane production after 72 h incubation. After 24 h and 72 h incubation all the genotypes produced a .... The rumen fluid used was collected from cannulated sheep kept on a maintenance diet with a 60:40 forage to concentrate composition. The forage was ...

  2. Haemoglobin genotype of children with severe malaria seen at the ...

    African Journals Online (AJOL)

    Prof Ezechukwu

    2011-10-23

    Oct 23, 2011 ... Abstract: Introduction: Types of haemoglobin (Hb) genotype have been found to be crucial to the rate of red blood cell parasite invasion, multiplication, and destruction as well as outcome of malaria disease. In a bid to provide more informa- tion on the relationship between Hb genotype and level of ...

  3. Crossbreeding of large white and Nsukka local pigs: Genotype and ...

    African Journals Online (AJOL)

    Crossbreeding of large white and Nsukka local pigs: Genotype and age are related changes in haematological parameters. ... Nigerian Journal of Animal Science ... However, significant genotype x age interactions were found for RBC, MCH, WBC, lymphocytes, monicytes and eosinophils which limit the inferences made on ...

  4. Leveraging from genotype by environment interaction for bread ...

    African Journals Online (AJOL)

    Developing high yielding and stable genotypes for wide and specific adaptation is important in wheat (Triticum aestivum L.) production. The objective of this study was to exploit the gains from genotype by environment interaction for increased bread wheat production in eastern Africa. Thirty-three advanced bread wheat ...

  5. Genotype dependent callus induction and shoot regeneration in ...

    African Journals Online (AJOL)

    This study aims to observe the effect of genotype, hormone and culture conditions on sunflower (Helianthus annuus L.) callus induction and indirect plant regeneration. Calli were obtained from hypocotyl and cotyledon explants of five different sunflower genotypes; Trakya 80, Trakya 129, Trakya 259, Trakya 2098 and ...

  6. Responses of some selected Malaysian rice genotypes to callus ...

    African Journals Online (AJOL)

    user

    2011-01-17

    Jan 17, 2011 ... genotype performance for in vitro salt stress responses in some selected Malaysian rice genotypes. Differences in culture conditions, ... stress, which prevents the crop from reaching its full genetic potential as well as .... hydrolysates did not respond to callus induction, but only resulted in seed germination.

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

    African Journals Online (AJOL)

    ACSS

    Genotype by environment analysis methods for yield-related traits of pearl millet probably no stand-alone method exists. (Kaya et al., 2006). ... percentage of productive tillers (PRO) at plot level. Data analysis was conducted using the ...... Haussmann, B.I.G. 2014. Patterns of pearl millet genotype-by-environment interaction ...

  8. Evaluation of sorghum genotypes under drought stress conditions ...

    African Journals Online (AJOL)

    Seven genotypes of sorghum (Sorghum bicolour (L.) Moench) were studied in both drought and normal conditions. In each condition, the genotypes were evaluated using a split plot based randomized complete block design with three replications. Drought tolerance indices including stability tolerance index (STI), mean ...

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

    African Journals Online (AJOL)

    Markers OPA-05, OPF-06, OPF-09, OPF-17, OPG-17, OPG-18, OPG-19, OPH-18, OPK-12, P-265-550 and P-286-350 found linked to blast resistance in most of the resistant genotypes could be considered as potent molecular markers in the selection of blast resistant genotypes. Amplification with RAPD and SCAR primers ...

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

    African Journals Online (AJOL)

    A simple crop physiological model was employed to study the yield basis and environmental effects on 31cowpea genotypes of early, medium and late maturities. The tests were carried out at four sites in northern Ghana between 1992 and 1994. Genotypic variations observed for pod yields (Y), reproductive duration (RD), ...

  11. Genotype x Environment interaction for quality traits in durum wheat ...

    African Journals Online (AJOL)

    To evaluate the effects of genotype, environment and genotype x environment interaction on quality traits such as vitreousness, SDS sedimentation test, yellow pigment index, protein content and test weight, twelve Moroccan durum wheat cultivars representing a range of agronomic adaptation were tested in five locations ...

  12. Application of mixed models for the assessment genotype and ...

    African Journals Online (AJOL)

    SAM

    2014-05-07

    May 7, 2014 ... In the process of introducing cotton cultivars, it is essential to assess their productive behavior for different environments for which they will be recommended. Knowledge of the magnitude of the genotype interaction with environment allows the evaluation of the stability and adaptability of genotypes where ...

  13. Characteristics of Streptococcus mutans genotypes and dental caries in children.

    Science.gov (United States)

    Cheon, Kyounga; Moser, Stephen A; Wiener, Howard W; Whiddon, Jennifer; Momeni, Stephanie S; Ruby, John D; Cutter, Gary R; Childers, Noel K

    2013-06-01

    This longitudinal cohort study evaluated the diversity, commonality, and stability of Streptococcus mutans genotypes associated with dental caries history. Sixty-seven 5- and 6-yr-old children, considered as being at high caries risk, had plaque collected from baseline through 36 months for S. mutans isolation and genotyping using repetitive extragenic palindromic-PCR (4,392 total isolates). Decayed, missing, or filled surfaces (dmfs (primary teeth)/DMFS (secondary teeth)) for each child were recorded at baseline. At baseline, 18 distinct genotypes were found among 911 S. mutans isolates from 67 children (diversity), and 13 genotypes were shared by at least two children (commonality). The number of genotypes per individual was positively associated with the proportion of decayed surfaces (p-ds) at baseline. Twenty-four of the 39 children who were available at follow-up visits maintained a predominant genotype for the follow-up periods (stability) and this was negatively associated with the p-ds. The observed diversity, commonality, and stability of S. mutans genotypes represent a pattern of dental caries epidemiology in this high-caries-risk community, which suggests that fewer decayed surfaces are significantly associated with lower diversity and higher stability of S. mutans genotypes. © 2013 Eur J Oral Sci.

  14. stability analysis of food barley genotypes in northern ethiopia ...

    African Journals Online (AJOL)

    ACSS

    interaction principal component axis, AMMI- additive main effect and multiplicative interaction. Figure 1. AMMI1 biplot for grain yield (t ha-1) and IPCA1of food barley genotypes grown in northern Ethiopia. Stability analysis for genotypic performance. AMMI Stability Value (ASV). Table 5 shows. AMMI stability values for ...

  15. Genotype x environment interactions for seed yield in sesame in ...

    African Journals Online (AJOL)

    As sesame is a short day plant and sensitive to light, heat, and moisture stress the yield is not stable. The selection of stable genotypes that interact less with the varying environment in which they are to be grown is required. The extent of genotype by environment interaction indicates the likelihood of adaptation of a given ...

  16. Screening ten genotypes of natural rubber seedlings ( Hevea ...

    African Journals Online (AJOL)

    A field study was conducted in 2012 and 2013 cropping season at the Research Farm of National Root Crops Research Institute, (NRCRI) Umudike, in Abia State, to screen 10 rubber genotypes collected from Rubber Research Institute of Nigeria for tolerant to drought conditions. The aim was to select tolerant genotypes for ...

  17. Variation of meat quality traits among five genotypes of chicken.

    Science.gov (United States)

    Tang, H; Gong, Y Z; Wu, C X; Jiang, J; Wang, Y; Li, K

    2009-10-01

    The main objective of this study was to examine the diversity of meat quality traits among 5 chicken genotypes. The genotypes included 2 Chinese native breeds (Wenchang,WCH, and Xianju), 1 commercial broiler line (Avian, AV), 1 commercial layer line (Hy-Line Brown, HLB), and 1 Chinese commercial broiler line (Lingnanhuang, LNH) synthesized by exotic and native breeds, which were slaughtered at their market ages: 16, 7, 16, and 8 wk, respectively. The effects of genotype, muscle type, and sex on meat quality traits were examined. Birds from slow-growing genotypes (WCH, Xianju, and HLB) exhibited higher shear value, inosine-5'-monophosphate concentration, lower cook loss, and more fat than those from fast-growing genotypes (AV and LNH). Chickens from WCH possessed the lowest expressible moisture, cook loss, and the highest lipid (%) among the 3 slow-growing genotypes. The HLB birds were intermediate in expressible moisture and cook loss and lowest in lipid among all genotypes. The LNH cross birds were similar to AV broilers in most meat quality parameters, although they had a lower shear force value and higher fat content than AV broilers. Breast muscle had higher expressible moisture, shear force, protein (%), inosine-5'-monophosphate content, lower cook loss, and lipid (%) than leg muscle. Muscles from male chickens had higher expressible moisture than those from the females. Variability of meat quality characteristics is mainly related to genotype and muscle type differences.

  18. Magnitude of genotype x environment interaction for bacterial leaf ...

    African Journals Online (AJOL)

    Magnitude of genotype x environment interaction for bacterial leaf blight resistance in rice growing areas of Uganda. ... Low attack was observed on pyramided genotypes in all locations and two with single gene, i.e. IRBB8 and IRBB21, respectively. Interestingly, IR24 was as resistant as any of the pyramided combinations.

  19. Prevalence of heamoglobin genotype screening and awareness of ...

    African Journals Online (AJOL)

    Even though majority of the respondents (72.3%) had fair knowledge of the disease, only a quarter (28.2%) of them had ever done their genotype test prior to the study. Factors that positively influenced respondents' practice of premarital genotype screening included; age, being married, parental educational background ...

  20. Genotype X environment interactions and stability of soybean for ...

    African Journals Online (AJOL)

    Soybean Glycine max (L.) Merrill] is the world's leading source of oil and protein. It has the highest protein content of all food crops and is second only to groundnut in terms of oil content among food legumes. Study on genotype x enviroment interaction (GE) and stability of twenty soybean [Glycine max (L.) Merrill] genotypes ...