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Sample records for nontoxigenic variants isolated

  1. Genetic diversity among toxigenic and nontoxigenic Vibrio cholerae O1 isolated from the Western Hemisphere.

    PubMed Central

    Chen, F.; Evins, G. M.; Cook, W. L.; Almeida, R.; Hargrett-Bean, N.; Wachsmuth, K.

    1991-01-01

    Multilocus enzyme electrophoresis was used to examine genetic relationships among and between toxigenic and non-toxigenic isolates of Vibrio cholerae O1 obtained from patients and the environment in the US Gulf Coast and surrounding areas. A total of 23 toxigenic and 23 non-toxigenic strains were examined. All the toxigenic and 7 of the non-toxigenic strains had the same alleles at 16 enzyme loci, whereas the balance of the nontoxigenic strains had 9 distinct combinations of alleles. This study suggests that all of the toxigenic strains belong to a single clone, and that while some of the non-toxigenic isolates were related, most were of diverse origin. PMID:1879486

  2. NON-TOXIGENIC ASPERGILLUS FLAVUS ISOLATES FOR REDUCING AFLATOXIN IN MISSISSIPPI DELTA CORN

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The potential for two non-toxigenic isolates of Aspergillus flavus CT3 and K49 isolated from the Mississippi Delta to reduce aflatoxin contamination of corn was assessed in a field study. These two isolates exhibited comparable growth and aggressiveness as the toxigenic A. flavus isolate F3W4. The...

  3. Isolation of nontoxigenic Vibrio cholerae O1 from a human wound infection.

    PubMed Central

    Johnston, J M; McFarland, L M; Bradford, H B; Caraway, C T

    1983-01-01

    Vibrio cholerae serotype O1 organisms that do not produce cholera toxin and, in fact, lack the genetic material encoding the enterotoxin have recently been detected in coastal regions of the United States. Although these organisms have been assumed to be nonpathogenic, they have been considered a potential reservoir of toxigenic V. cholerae. In 1979, nontoxigenic V. cholerae O1 was isolated from a leg wound of an accident victim residing in New Orleans. The only known risk factors of the patient, besides his debilitated condition, were alcoholism and the consumption of raw oysters before recognition of his wound infection. Coincident with the identification of the isolate from the leg wound, an identical nontoxigenic V. cholerae O1 isolate was cultured from the sewage system serving the residence of this patient. Nontoxigenic V. cholerae O1 seems to be capable of multiplying in human tissue and may produce extraintestinal infection. This indigenous inhabitant of temperate coastal regions may not be avirulent and may be of public health significance. PMID:6863510

  4. Isolation of culturable mycobiota from agricultural soils and determination of tolerance to glyphosate of nontoxigenic Aspergillus section Flavi strains.

    PubMed

    Carranza, Cecilia S; Barberis, Carla L; Chiacchiera, Stella M; Dalcero, Ana María; Magnoli, Carina E

    2016-01-01

    Glyphosate-based herbicides are extensively used in Argentina's agricultural system to control undesirable weeds. This study was conducted to evaluate the culturable mycobiota [colony forming units (CFU) g(-1) and frequency of fungal genera or species] from an agricultural field exposed to pesticides. In addition, we evaluated the tolerance of A. oryzae and nontoxigenic A. flavus strains to high concentrations (100 to 500 mM - 17,000 to 84,500 ppm) of a glyphosate commercial formulation. The analysis of the mycobiota showed that the frequency of the main fungal genera varied according to the analyzed sampling period. Aspergillus spp. or Aspergillus section Flavi strains were isolated from 20 to 100% of the soil samples. Sterilia spp. were also observed throughout the sampling (50 to 100%). Aspergillus section Flavi tolerance assays showed that all of the tested strains were able to develop at the highest glyphosate concentration tested regardless of the water availability conditions. In general, significant reductions in growth rates were observed with increasing concentrations of the herbicide. However, a complete inhibition of fungal growth was not observed with the concentrations assayed. This study contributes to the knowledge of culturable mycobiota from agricultural soils exposed to pesticides and provides evidence on the effective growth ability of A. oryzae and nontoxigenic A. flavus strains exposed to high glyphosate concentrations in vitro. PMID:26549415

  5. Field Assessment of Non-toxigenic Aspergillus flavus Strain K49 in Competitive Displacement of Toxigenic Isolates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Non-toxigenic strains of Aspergillus flavus offer the potential to control aflatoxin contamination by competitive displacement of indigenous populations of A. flavus colonizing corn grain. Two sets of experiments were conducted to assess the competitiveness of strain K49 when challenged against two...

  6. Nontoxigenic Vibrio parahaemolyticus Strains Causing Acute Gastroenteritis

    PubMed Central

    Leoni, Francesca; Serra, Roberto; Serracca, Laura; Decastelli, Lucia; Rocchegiani, Elena; Masini, Laura; Canonico, Cristina; Talevi, Giulia; Carraturo, Antonio

    2012-01-01

    We investigated the virulence properties of four Vibrio parahaemolyticus strains causing acute gastroenteritis following consumption of indigenous mussels in Italy. The isolated strains were cytotoxic and adhesive but, surprisingly, lacked tdh, trh, and type three secretion system 2 (T3SS2) genes. We emphasize that nontoxigenic V. parahaemolyticus can induce acute gastroenteritis, highlighting the need for more investigation of the pathogenicity of this microorganism. PMID:23052317

  7. Inhibition of adhesion of Clostridium difficile to human intestinal cells after treatment with serum and intestinal fluid isolated from mice immunized with nontoxigenic C. difficile membrane fraction.

    PubMed

    Senoh, Mitsutoshi; Iwaki, Masaaki; Yamamoto, Akihiko; Kato, Haru; Fukuda, Tadashi; Shibayama, Keigo

    2015-04-01

    Diarrhea and pseudomembrane colitis caused by Clostridium difficile infection is a global health concern because of the high recurrence rate after standard antibiotic therapy. Vaccination presents a powerful countermeasure against disease recurrence. In this study, mice vaccinated with the nontoxigenic C. difficile membrane fraction generated a marked immune response to the antigen, as demonstrated by the serum IgG and intestinal fluid IgA levels. Significantly, pretreatment with harvested IgG- and IgA-containing fluids was sufficient to prevent in vitro adhesion of C. difficile to human Caco-2 intestinal cells. These results highlight the potential of nontoxigenic C. difficile membrane fraction as a vaccine candidate for C. difficile infection. PMID:25745878

  8. Molecular characterization of environmental and nontoxigenic strains of Vibrio cholerae.

    PubMed Central

    Kaper, J B; Moseley, S L; Falkow, S

    1981-01-01

    Environmental and nontoxigenic strains of Vibrio cholerae 0-1 were examined for genes homologous to genes encoding Escherichia coli heat-labile enterotoxin (LT). Restriction fragments encoding LT A and B subunits were isolated from the recombinant plasmid EWD299 and labeled in vitro with 32P. These probes were then hybridized to deoxyribonucleic acid extracted from strains of V. cholerae and visualized by autoradiography. None of the nontoxigenic strains of V. cholerae 0-1 from Louisiana, Alabama, Maryland, Guam, Brazil, Bangladesh, or Great Britain hybridized with the LT probes, whereas all toxigenic strains exhibited homology. In addition, strains of V. cholerae non-0-1, "group F" vibrios, V. vulnificus, and Aeromonas hydrophila were tested, and all were negative except two strains of V. cholerae non-0-1. The presence of plasmids did not correlate with toxigenicity or nontoxigenicity in any of the species examined. Thus, it appears that these strains are not simple nontoxigenic mutants, but rather do not possess any genetic material encoding cholera toxin. Such strains therefore cannot revert and serve as a reservoir of cholera. Images PMID:7251142

  9. Nontoxigenic tox-bearing Corynebacterium ulcerans Infection among Game Animals, Germany

    PubMed Central

    Kutzer, Peter; Peters, Martin; Sing, Andreas; Contzen, Matthias; Rau, Jörg

    2014-01-01

    Corynebacterium ulcerans may cause diphtheria in humans and caseous lymphadenitis in animals. We isolated nontoxigenic tox-bearing C. ulcerans from 13 game animals in Germany. Our results indicate a role for game animals as reservoirs for zoonotic C. ulcerans. PMID:24572455

  10. Nontoxigenic Vibrio cholerae Non-O1/O139 Isolate from a Case of Human Gastroenteritis in the U.S. Gulf Coast

    PubMed Central

    Hasan, Nur A.; Rezayat, Talayeh; Blatz, Peter J.; Choi, Seon Young; Griffitt, Kimberly J.; Rashed, Shah M.; Huq, Anwar; Conger, Nicholas G.; Colwell, Rita R.

    2014-01-01

    An occurrence of Vibrio cholerae non-O1/O139 gastroenteritis in the U.S. Gulf Coast is reported here. Genomic analysis revealed that the isolate lacked known virulence factors associated with the clinical outcome of a V. cholerae infection but did contain putative genomic islands and other accessory virulence factors. Many of these factors are widespread among environmental strains of V. cholerae, suggesting that there might be additional virulence factors in non-O1/O139 V. cholerae yet to be determined. Phylogenetic analysis revealed that the isolate belonged to a phyletic lineage of environmental V. cholerae isolates associated with sporadic cases of gastroenteritis in the Western Hemisphere, suggesting a need to monitor non-O1/O139 V. cholerae in the interest of public health. PMID:25339398

  11. Volatile profiles and aflatoxin production by toxigenic and non-toxigenic isolates of Aspergillus flavus grown on sterile and non-sterile cracked corn

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aspergillus flavus is a saprophytic fungus which can grow on corn and produce aflatoxins which render it unsafe for food and feed consumption. In this study, aflatoxin and non-aflatoxin producing isolates of A. flavus were grown separately on wet (20% water added), sterile or non-sterile cracked co...

  12. Isolation of genotypic variants of Autographa californica nuclear polyhedrosis virus.

    PubMed Central

    Lee, H H; Miller, L K

    1978-01-01

    A nuclear polyhedrosis virus (MNPV) isolated from a lepidopteran (Noctuidae) insect, Autographa californica, was cloned by successive plaque purification using virions containing only one nucleocapsid per envelope as inoculum. The ability to clone the virus by this method was demonstrated by the isolation of nondefective, genotypic variants of the virus with similar but not identical restriction endonuclease fragment patterns. Five distinct variants were identified by genotypic analysis with HindIII, EcoRI, SalI, and Bam HI restriction endonucleases. The characteristic genotype of each variant was maintained upon passage in insect larvae. The isolation of these virus variants demonstrates (i) the heterogeneity of the uncloned virus preparation and (ii) the ability to clone MNPVs by plaque purification of media-derived nonoccluded virions. The A. californica MNPV is being considered for commercial use as a pesticide in the United States, and the cloning of the virus, in view of the heterogeneity detected, may be advisable. The cloning and genotype analyses are also significant with regard to understanding the genetic nature of multiply embedded NPVs (those NPVs containing more than one nucleocapsid per envelope in the occluded form of the virus) and indicate that further genetic analysis of these viruses is possible. Images PMID:359831

  13. Internalization of non-toxigenic Corynebacterium diphtheriae by cultured human respiratory epithelial cells.

    PubMed

    Bertuccini, Lucia; Baldassarri, Lucilla; von Hunolstein, Christina

    2004-09-01

    Although infection by Corynebacterium diphtheriae is a model of extracellular mucosal pathogenesis, and diphtheria is one of the most worried diseases, this microorganism can be associated also with invasive infections such as endocarditis, septic arthritis, and osteomyelitis. Invasive infections are usually caused by non-toxigenic C. diphtheriae strains. Over the last years severe pharyngitis/tonsillitis associated with the isolation of non-toxigenic C. diphtheriae have been described. Penicillin treatment failure of these infections could only partially be explained by penicillin tolerance of the causing strain. Thus, we examined the in vitro ability of non-toxigenic C. diphtheriae throat clinical isolates to adhere to, and enter human respiratory epithelial cells. Trasmission and scanning electron microscopy demonstrated intracellular C. diphtheriae in laryngeal (HEp-2 cells) and pharyngeal (Detroit D562 cells) tissue culture. Live intracellular bacteria were detectable up to 48 h post-infection. Using a variety of compound that act on eukariotic cell structures, the internalization of C. diphtheriae seems to occur via a zipper-like mechanism. It is likely that internalization of C. diphtheriae can be involved in throat colonization contributing to bacterial eradication failure and asymptomatic carriage. PMID:15351033

  14. IGF1R Variants Associated with Isolated Single Suture Craniosynostosis

    PubMed Central

    Cunningham, Michael L.; Horst, Jeremy A.; Rieder, Mark J.; Hing, Anne V.; Stanaway, Ian B.; Park, Sarah S.; Samudrala, Ram; Speltz, Matthew L.

    2010-01-01

    The genetic contribution to the pathogenesis of isolated single suture craniosynostosis is poorly understood. The role of mutations in genes known to be associated with syndromic synostosis appears to be limited. We present our findings of a candidate gene resequencing approach to identify rare variants associated with the most common forms of isolated craniosynostosis. Resequencing of the coding regions, splice junction sites, and 5? and 3? untranslated regions of 27 candidate genes in 186 cases of isolated nonsyndromic single suture synostosis revealed three novel and two rare sequence variants (R406H, R595H, N857S, P190S, M446V) in insulin-like growth factor I receptor (IGF1R) that are enriched relative to control samples. Mapping the resultant amino acid changes to the modeled homodimer protein structure suggests a structural basis for segregation between these and other disease-associated mutations found in IGF1R. These data suggest that IGF1R mutations may contribute to the risk and in some cases cause single suture craniosynostosis. PMID:21204214

  15. Isolating potentiated Hsp104 variants using yeast proteinopathy models.

    PubMed

    Jackrel, Meredith E; Tariq, Amber; Yee, Keolamau; Weitzman, Rachel; Shorter, James

    2014-01-01

    Many protein-misfolding disorders can be modeled in the budding yeast Saccharomyces cerevisiae. Proteins such as TDP-43 and FUS, implicated in amyotrophic lateral sclerosis, and α-synuclein, implicated in Parkinson's disease, are toxic and form cytoplasmic aggregates in yeast. These features recapitulate protein pathologies observed in patients with these disorders. Thus, yeast are an ideal platform for isolating toxicity suppressors from libraries of protein variants. We are interested in applying protein disaggregases to eliminate misfolded toxic protein conformers. Specifically, we are engineering Hsp104, a hexameric AAA+ protein from yeast that is uniquely capable of solubilizing both disordered aggregates and amyloid and returning the proteins to their native conformations. While Hsp104 is highly conserved in eukaryotes and eubacteria, it has no known metazoan homologue. Hsp104 has only limited ability to eliminate disordered aggregates and amyloid fibers implicated in human disease. Thus, we aim to engineer Hsp104 variants to reverse the protein misfolding implicated in neurodegenerative disorders. We have developed methods to screen large libraries of Hsp104 variants for suppression of proteotoxicity in yeast. As yeast are prone to spontaneous nonspecific suppression of toxicity, a two-step screening process has been developed to eliminate false positives. Using these methods, we have identified a series of potentiated Hsp104 variants that potently suppress the toxicity and aggregation of TDP-43, FUS, and α-synuclein. Here, we describe this optimized protocol, which could be adapted to screen libraries constructed using any protein backbone for suppression of toxicity of any protein that is toxic in yeast. PMID:25407485

  16. Aspergillus flavus genetic diversity of corn fields treated with non-toxigenic strain afla-guard in the southern U.S

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aspergillus flavus genetic diversity of corn fields treated with the non-toxigenic strain Afla-Guard (NRRL 21882) was determined for 384 A. flavus isolates from 14 locations within 6 states in the southern U.S. ELISA test has determined low levels of toxigenic strains (only 91 positive). Nearly hal...

  17. Comparative genomics of toxigenic and non-toxigenic Staphylococcus hyicus.

    PubMed

    Leekitcharoenphon, Pimlapas; Pamp, Sünje Johanna; Andresen, Lars Ole; Aarestrup, Frank M

    2016-03-15

    The most common causative agent of exudative epidermitis (EE) in pigs is Staphylococcus hyicus. S. hyicus can be grouped into toxigenic and non-toxigenic strains based on their ability to cause EE in pigs and specific virulence genes have been identified. A genome wide comparison between non-toxigenic and toxigenic strains has never been performed. In this study, we sequenced eleven toxigenic and six non-toxigenic S. hyicus strains and performed comparative genomic and phylogenetic analysis. Our analyses revealed two genomic regions encoding genes that were predominantly found in toxigenic strains and are predicted to encode for virulence determinants for EE. All toxigenic strains encoded for one of the exfoliative toxins ExhA, ExhB, ExhC, or ExhD. In addition, one of these regions encoded for an ADP-ribosyltransferase (EDIN, epidermal cell differentiation inhibitor) and a novel putative RNase toxin (polymorphic toxin) and was associated with the gene encoding ExhA. A clear differentiation between toxigenic and non-toxigenic strains based on genomic and phylogenetic analyses was not apparent. The results of this study support the observation that exfoliative toxins of S. hyicus and S. aureus are located on genetic elements such as pathogenicity islands, phages, prophages and plasmids. PMID:26931389

  18. Complete Genome Sequence of a Variant Pseudorabies Virus Strain Isolated in Central China

    PubMed Central

    Xiang, Shuangshuang; Zhou, Zhi; Hu, Xule; Li, Yingying; Zhang, Chaolin; Wang, Juan; Li, Xiangdong

    2016-01-01

    Pseudorabies virus (PRV) variants have been prevalent in China since 2011 and have caused huge economic losses to the Chinese pig industry. Here, we report the genome sequence of a PRV variant HN1201 that was isolated from diseased animals in central China in 2011. PMID:26988055

  19. Two novel Salmonella genomic island 1 variants in Proteus mirabilis isolates from swine farms in China.

    PubMed

    Lei, Chang-Wei; Zhang, An-Yun; Liu, Bi-Hui; Wang, Hong-Ning; Yang, Li-Qin; Guan, Zhong-Bin; Xu, Chang-Wen; Zhang, Dong-Dong; Yang, Yong-Qiang

    2015-07-01

    Four different Salmonella genomic island 1 (SGI1) variants, including two novel variants, were characterized in one Salmonella enterica serovar Rissen sequence type ST1917 isolate and three Proteus mirabilis isolates from swine farms in China. One novel variant was derived from SGI1-B with the backbone gene S021 disrupted by a 12.72-kb IS26 composite transposon containing the dfrA17-aadA5 cassettes and macrolide inactivation gene cluster mphA-mrx-mphR. The other one was an integron-free SGI1 and contained a 183-bp truncated S025 next to IS6100 and S044. PMID:25918148

  20. Variants of Triticum mosaic virus isolated from wheat in Colorado

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Triticum mosaic virus (TriMV) is a recently discovered virus infecting wheat. We compared the Colorado isolates C10-492 and C11-775 with the 06-123 isolate of TriMV from Kansas (TriMV-K). Comparisons were made using enzyme-linked immunosorbent assay (ELISA), infectivity assay, host range, dry weig...

  1. Molecular characterization of cloned variants of Coxiella burnetii isolated in China.

    PubMed

    Ning, Z; Yu, S R; Quan, Y G; Xue, Z

    1992-03-01

    To study the molecular properties of Coxiella burnetii phase variants we cloned the phase variants of C. burnetii Qiyi (CBQY) strain by the red plaque technique. Three cloned strains, CBQYIC3 (phase I), CBQYIIC7 (phase II) and CBQYIIC5 (semirough-phase) were analysed by SDS-PAGE, immunoblot assay, plasmid isolation and agarose gel electrophoresis of DNA restriction fragments. The results suggest that the unique phase-dependent substance is a lipopolysaccharide and that most protein components of phase I and phase II cells are shared. No significant differences of DNA restriction fragments were found between clonal isolates of phase I and phase II C. burnetii CBQY strains. A plasmid of approximately 56 Kb was isolated from both phase I and phase II variants indicating that phase variation probably could not be attributed to its presence or absence. PMID:1359769

  2. Novel THAP1 variants in Brazilian patients with idiopathic isolated dystonia.

    PubMed

    da Silva-Junior, Francisco Pereira; dos Santos, Camila Oliveira; Silva, Sonia Maria Cesar Azevedo; Barbosa, Egberto Reis; Borges, Vanderci; Ferraz, Henrique Ballalai; Limongi, João Carlos Papaterra; Rocha, Maria Sheila Guimarães; de Carvalho Aguiar, Patricia

    2014-09-15

    THAP1 mutations are associated with idiopathic isolated dystonia in different ethnicities, but the importance of this gene as a cause of dystonia in the Brazilian population has not been determined. The aim of this study was to investigate the prevalence of THAP1 variants in Brazilian patients with idiopathic dystonia and to describe their clinical characteristics including non-motor symptoms. One hundred and ten unrelated patients with non-TOR1A (DYT1) idiopathic isolated dystonia and family members were evaluated and screened for genetic variants. Variants with a potential pathological role were observed in 9.0% of families studied, of which four were novel. The variants were identified in approximately 12% of patients with the age of onset below 40 years. In most of the patients, the onset of the disease was before early adulthood. The upper limb was the most common site of the onset, and approximately half of the patients had dysphonia. Pain, anxiety, and sleep-onset insomnia were the most prevalent non-motor symptoms, and their prevalence was not different from that observed in THAP1-negative patients. Therefore, THAP1 variants are an important cause of dystonia among individuals with an early-onset disease and a positive family history. The phenotypical heterogeneity among patients carrying similar variants shows that other factors may be modulating the disease. PMID:24976531

  3. Novel VIM metallo-beta-lactamase variant, VIM-24, from a Klebsiella pneumoniae isolate from Colombia.

    PubMed

    Montealegre, Maria Camila; Correa, Adriana; Briceño, David F; Rosas, Natalia C; De La Cadena, Elsa; Ruiz, Sory J; Mojica, Maria F; Camargo, Ruben Dario; Zuluaga, Ivan; Marin, Adriana; Quinn, John P; Villegas, Maria Virginia

    2011-05-01

    We report the emergence of a novel VIM variant (VIM-24) in a Klebsiella pneumoniae isolate in Colombia. The isolate displays MICs for carbapenems below the resistance breakpoints, posing a real challenge for its detection. The blaVIM-24 gene was located within a class 1 integron carried on a large plasmid. Further studies are needed to clarify its epidemiological and clinical impact. PMID:21282438

  4. Novel VIM Metallo-?-Lactamase Variant, VIM-24, from a Klebsiella pneumoniae Isolate from Colombia?

    PubMed Central

    Montealegre, Maria Camila; Correa, Adriana; Briceño, David F.; Rosas, Natalia C.; De La Cadena, Elsa; Ruiz, Sory J.; Mojica, Maria F.; Camargo, Ruben Dario; Zuluaga, Ivan; Marin, Adriana; Quinn, John P.; Villegas, Maria Virginia

    2011-01-01

    We report the emergence of a novel VIM variant (VIM-24) in a Klebsiella pneumoniae isolate in Colombia. The isolate displays MICs for carbapenems below the resistance breakpoints, posing a real challenge for its detection. The blaVIM-24 gene was located within a class 1 integron carried on a large plasmid. Further studies are needed to clarify its epidemiological and clinical impact. PMID:21282438

  5. Characterization of Small-Colony Variants of Enterococcus faecalis Isolated from Chickens with Amyloid Arthropathy▿

    PubMed Central

    Petersen, Andreas; Chadfield, Mark S.; Christensen, Jens P.; Christensen, Henrik; Bisgaard, Magne

    2008-01-01

    In this study we report the isolation and characterization of normal-sized and small-colony variants of Enterococcus faecalis from outbreaks of amyloid arthropathy in chickens. Postmortem examinations of 59 chickens revealed orange deposits in the knee joints, typical for amyloid arthropathy. Bacterial cultures from 102 joints and 43 spleens exhibited pure (n = 88) and mixed (n = 11) cultures of normal (n = 60) and pinpoint (n = 28) colonies of E. faecalis. Pulsed-field gel electrophoresis of 62 isolates demonstrated seven different band patterns with at most two band size variations, and multilocus sequence typing demonstrated two different sequence types, sharing six out of seven alleles, suggesting a close evolutionary relationship between isolates obtained from four outbreaks. In addition, all isolates were clonally related to an amyloid arthropathy reference strain from The Netherlands, previously shown to be globally dispersed. Initial investigation of the isolated small-colony variant phenotype revealed no difference in whole-cell protein profiling between normal and pinpoint colonies. However, the pinpoint colony isolates appeared to be more virulent in an in vivo challenge model in chickens than their normal-sized-colony counterparts. In addition, pinpoint morphology and associated slow growth were expressed without reversion after in vitro and in vivo passage, suggesting a genuine altered phenotype, and in some instances normal colonies converted to pinpoint morphology postinfection. In conclusion, small-colony variants of E. faecalis are described for the first time from veterinary clinical sources and in relation to amyloid arthropathy in chickens. PMID:18579713

  6. Neutralizing monoclonal antibodies recognize antigenic variants among isolates of infectious hematopoietic necrosis virus

    USGS Publications Warehouse

    Winton, J.R.; Arakawa, C.N.; Lannan, C.N.; Fryer, J.L.

    1988-01-01

    eutralizing monoclonal antibodies were developed against strains of infectious hematopoietic necrosis virus (IHNV) from steelhead trout Salmo gairdneri in the Deschutes River of Oregon, chinook salmon Oncorhynchus tshawytscha in the Sacramento River of California, and rainbow trout Salmo gairdneri reared in the Hagerman Valley of Idaho, USA. These antibodies were tested for neutralization of 12 IHNV isolates obtained from salmonids in Japan, Alaska, Washington, Oregon, California, and Idaho. The antibodies recognized antigenic variants among the isolates and could be used to separate the viruses into 4 groups. The members of each group tended to be related by geographic area rather than by source host species, virulence, or date of isolation.

  7. A rare functional cardioprotective APOC3 variant has risen in frequency in distinct population isolates

    PubMed Central

    Tachmazidou, Ioanna; Dedoussis, George; Southam, Lorraine; Farmaki, Aliki-Eleni; Ritchie, Graham R. S.; Xifara, Dionysia K.; Matchan, Angela; Hatzikotoulas, Konstantinos; Rayner, Nigel W.; Chen, Yuan; Pollin, Toni I.; O’Connell, Jeffrey R.; Yerges-Armstrong, Laura M.; Kiagiadaki, Chrysoula; Panoutsopoulou, Kalliope; Schwartzentruber, Jeremy; Moutsianas, Loukas; Tsafantakis, Emmanouil; Tyler-Smith, Chris; McVean, Gil; Xue, Yali; Zeggini, Eleftheria

    2013-01-01

    Isolated populations can empower the identification of rare variation associated with complex traits through next generation association studies, but the generalizability of such findings remains unknown. Here we genotype 1,267 individuals from a Greek population isolate on the Illumina HumanExome Beadchip, in search of functional coding variants associated with lipids traits. We find genome-wide significant evidence for association between R19X, a functional variant in APOC3, with increased high-density lipoprotein and decreased triglycerides levels. Approximately 3.8% of individuals are heterozygous for this cardioprotective variant, which was previously thought to be private to the Amish founder population. R19X is rare (<0.05% frequency) in outbred European populations. The increased frequency of R19X enables discovery of this lipid traits signal at genome-wide significance in a small sample size. This work exemplifies the value of isolated populations in successfully detecting transferable rare variant associations of high medical relevance. PMID:24343240

  8. Homozygous loss-of-function variants in European cosmopolitan and isolate populations

    PubMed Central

    Kaiser, Vera B.; Svinti, Victoria; Prendergast, James G.; Chau, You-Ying; Campbell, Archie; Patarcic, Inga; Barroso, Inês; Joshi, Peter K.; Hastie, Nicholas D.; Miljkovic, Ana; Taylor, Martin S.; Enroth, Stefan; Memari, Yasin; Kolb-Kokocinski, Anja; Wright, Alan F.; Gyllensten, Ulf; Durbin, Richard; Rudan, Igor; Campbell, Harry; Polašek, Ozren; Johansson, Åsa; Sauer, Sascha; Porteous, David J.; Fraser, Ross M.; Drake, Camilla; Vitart, Veronique; Hayward, Caroline; Semple, Colin A.; Wilson, James F.

    2015-01-01

    Homozygous loss of function (HLOF) variants provide a valuable window on gene function in humans, as well as an inventory of the human genes that are not essential for survival and reproduction. All humans carry at least a few HLOF variants, but the exact number of inactivated genes that can be tolerated is currently unknown—as are the phenotypic effects of losing function for most human genes. Here, we make use of 1432 whole exome sequences from five European populations to expand the catalogue of known human HLOF mutations; after stringent filtering of variants in our dataset, we identify a total of 173 HLOF mutations, 76 (44%) of which have not been observed previously. We find that population isolates are particularly well suited to surveys of novel HLOF genes because individuals in such populations carry extensive runs of homozygosity, which we show are enriched for novel, rare HLOF variants. Further, we make use of extensive phenotypic data to show that most HLOFs, ascertained in population-based samples, appear to have little detectable effect on the phenotype. On the contrary, we document several genes directly implicated in disease that seem to tolerate HLOF variants. Overall HLOF genes are enriched for olfactory receptor function and are expressed in testes more often than expected, consistent with reduced purifying selection and incipient pseudogenisation. PMID:26173456

  9. Glucans of Pleurotus florida blue variant: isolation, purification, characterization and immunological studies.

    PubMed

    Dey, Biswajit; Bhunia, Sanjoy K; Maity, Kankan K; Patra, Sukesh; Mandal, Soumitra; Maiti, Swatilekha; Maiti, Tapas K; Sikdar, Samir R; Islam, Syed S

    2012-04-01

    Two different glucans (PS-I and PS-II) were isolated from the alkaline extract of the fruiting bodies of an edible mushroom, Pleurotus florida blue variant and the PS-I showed macrophage, splenocyte and thymocyte activations. On the basis of sugar analysis, methylation analysis, periodate oxidation, and NMR studies ((1)H, (13)C, DEPT-135, DQF-COSY, TOCSY, NOESY, ROESY, HMQC and HMBC), the structure of the repeating unit of these polysaccharides were established. PMID:22322111

  10. Emergence of an Invasive Clone of Nontoxigenic Corynebacterium diphtheriae in the Urban Poor Population of Vancouver, Canada

    PubMed Central

    Romney, M. G.; Roscoe, D. L.; Bernard, K.; Lai, S.; Efstratiou, A.; Clarke, A. M.

    2006-01-01

    Invasive disease due to Corynebacterium diphtheriae is rare in North America. Here we describe the emergence of a predominant clone of a nontoxigenic strain of C. diphtheriae in the impoverished population of Vancouver's downtown core. This clone has caused significant morbidity and contributed to at least two deaths. Over a 5-year period, seven cases of bacteremia due to C. diphtheriae were detected in patients admitted to Vancouver hospitals. Injection drug use, diabetes mellitus, skin colonization/infection with C. diphtheriae, and homelessness all appeared to be related to the development of bacteremia with the organism. Ribotyping of isolates recovered from blood culture revealed a predominant ribotype pattern that has not previously been reported in North America. PMID:16672385

  11. Isolation and characterization of a variant porcine epidemic diarrhea virus in China

    PubMed Central

    2012-01-01

    An outbreak of diarrhea in pigs started in Guangdong, South China in January 2011. Cases were characterized by watery diarrhea, dehydration and vomiting, with 80–100% morbidity and 50–90% mortality in suckling piglets. The causative agent of the diarrhea was ultimately identified as porcine epidemic diarrhea virus (PEDV). In this study, we isolated a PEDV strain designated CHGD-01 from piglet intestines using Vero cell cultures, and its specific cytopathic effects were confirmed in susceptible cells by direct immunofluorescence testing and electron microscopy. The complete genome of CHGD-01 was shown to be 28,035 nucleotides in length, with a similar structure to that of PEDV reference strains. Phylogenetic analyses based on the whole genome revealed that CHGD-01 shared nucleotide sequence identities of 98.2–98.4% with two other Chinese isolates reported in the same year, thus constituting a new cluster. Amino acid sequence analysis based on individual virus genes indicated a close relationship between the spike protein gene of CHGD-01 and the field strain KNU0802 in Korea. Its ORF3 and nucleoprotein genes, however, were divergent from all other sequenced PEDV isolate clusters and therefore formed a new group, suggesting a new variant PEDV isolate in China. Further studies will be required to determine the immunogenicity and pathogenicity of this new variant. PMID:22967434

  12. Characterization of a Small Plaque Variant of West Nile Virus Isolated in New York in 2000

    PubMed Central

    Jia, Yongqing; Moudy, Robin M.; Dupuis, Alan P.; Ngo, Kiet A.; Maffei, Joseph G.; Jerzak, Greta V. S.; Franke, Mary A.; Kauffman, Elizabeth B.; Kramer, Laura D.

    2007-01-01

    A small-plaque variant (SP) of West Nile virus (WNV) was isolated in Vero cell culture from kidney tissue of an American crow collected in New York in 2000. The in vitro growth of the SP and parental (WT) strains was characterized in mammalian (Vero), avian (DF-1 and PDE) and mosquito (C6/36) cells. The SP variant replicated less efficiently than did the WT in Vero cells. In avian cells, SP growth was severely restricted at high temperatures, suggesting that the variant is temperature sensitive. In mosquito cells, growth of SP and WT was similar, but in vivo in Culex pipiens (L.) there were substantial differences. Relative to WT, SP exhibited reduced replication following intrathoracic inoculation and lower infection, dissemination and transmission rates following oral infection. Analysis of the full length sequence of the SP variant identified sequence differences which led to only two amino acid substitutions relative to WT, prM P54S and NS2A V61A. PMID:17617432

  13. Isolation of Protein-Tyrosine Phosphatase-like Member-a Variant from Cementum

    PubMed Central

    Valdés De Hoyos, A.; Hoz-Rodríguez, L.; Arzate, H.; Narayanan, A.S.

    2012-01-01

    Cementum has been shown to contain unique polypeptides that participate in cell recruitment and differentiation during cementum formation. We report the isolation of a cDNA variant for protein-tyrosine phosphatase-like (proline instead of catalytic arginine) member-a (PTPLA) from cementum. A cementifying fibroma-derived ?-ZAP expression library was screened by panning with a monoclonal antibody to cementum attachment protein (CAP), and 1435 bp cDNA (gb AC093525.3) was isolated. This cDNA encodes a 140-amino-acid polypeptide, and its N-terminal 125 amino acids are identical to those of PTPLA. This isoform, designated as PTPLA-CAP, results from a read-through of the PTPLA exon 2 splice donor site, truncating after the second putative transmembrane domain. It contains 15 amino acids encoded within the intron between PTPLA exons 2 and 3, which replace the active site for PTPLA phosphatase activity. The recombinant protein, rhPTPLA-CAP, has Mr 19 kDa and cross-reacts with anti-CAP antibody. Anti-rhPTPLA-CAP antibody immunostained cementum cells, cementum, heart, and liver. Quantitative RT-PCR showed that PTPLA was expressed in all periodontal cells; however, PTPLA-CAP expression was limited to cementum cells. The rhPTPLA-CAP promoted gingival fibroblast attachment. We conclude that PTPLA-CAP is a splice variant of PTPLA, and that, in the periodontium, cementum and cementum cells express this variant. PMID:22067203

  14. Charge Variants of an Avastin Biosimilar Isolation, Characterization, In Vitro Properties and Pharmacokinetics in Rat.

    PubMed

    Zhao, Yan-Yan; Wang, Ning; Liu, Wan-Hui; Tao, Wen-Jie; Liu, Li-Li; Shen, Zhen-Duo

    2016-01-01

    The similarity between a proposed biosimilar product and the reference product can be affected by many factors. This study is designed to examine whether any subtle difference in the distribution of the charge variants of an Avastin biosimilar can affect its in vitro potency and in vivo PK. Here, the acidic, basic and main peak fractions of a biosimilar product were isolated using high-performance cation-exchange chromatography and were subjected to various studies to compare their in vitro properties and in vivo PK profile. A serial of analytical methods, including size exclusion chromatography (SEC), imaged capillary isoelectric focusing (icIEF) capillary zone electrophoresis (CZE) and cation-exchange chromatography (CEX-HPLC) were also used to characterize the isolated charge variants. The kinetics constant was measured using a Biacore X100 system. The study indicates the biosimilar product has a high similarity with avastin in physicochemical properties. The potency in vitro and PK profile in rat of charge variants and biosimilar product are consistent with avastin. PMID:26987122

  15. Charge Variants of an Avastin Biosimilar Isolation, Characterization, In Vitro Properties and Pharmacokinetics in Rat

    PubMed Central

    Liu, Wan-Hui; Tao, Wen-Jie; Liu, Li-Li; Shen, Zhen-Duo

    2016-01-01

    The similarity between a proposed biosimilar product and the reference product can be affected by many factors. This study is designed to examine whether any subtle difference in the distribution of the charge variants of an Avastin biosimilar can affect its in vitro potency and in vivo PK. Here, the acidic, basic and main peak fractions of a biosimilar product were isolated using high-performance cation-exchange chromatography and were subjected to various studies to compare their in vitro properties and in vivo PK profile. A serial of analytical methods, including size exclusion chromatography (SEC), imaged capillary isoelectric focusing (icIEF) capillary zone electrophoresis (CZE) and cation-exchange chromatography (CEX-HPLC) were also used to characterize the isolated charge variants. The kinetics constant was measured using a Biacore X100 system. The study indicates the biosimilar product has a high similarity with avastin in physicochemical properties. The potency in vitro and PK profile in rat of charge variants and biosimilar product are consistent with avastin. PMID:26987122

  16. Segregation of distinct variants from Citrus tristeza virus isolate SY568 using aphid transmission.

    PubMed

    Velazquez-Monreal, J J; Mathews, D M; Dodds, J A

    2009-10-01

    A well-studied severe isolate of Citrus tristeza virus (CTV) known as SY568 has previously been shown to contain multiple variants of the virus which differ in their genetic and biological characters. Aphid transmission was used in an attempt to segregate some of these variants for further characterization. Resulting infections gave symptoms which varied from asymptomatic to more severe than the inoculum source. RNase protection assays (RPAs) were used to compare nine regions of the CTV genome and determine whether unique strains could be identified. Five aphid-transmitted subcultures, with fingerprints that were different from those of the inoculum sources in at least one genomic area, were then cloned, sequenced, and compared with known isolates. An asymptomatic strain was shown to be different in every area of the CTV genome when examined by RPA and sequencing of selected regions. Mixed-infection studies using graft transmission of the asymptomatic subculture and two of the more severe aphid-transmitted subcultures showed that the mild strain was not able to compete well when in the presence of any of the severe variants tested, and its titer was significantly reduced from that seen in single infection. The mild strain and a selected severe strain were singly graft inoculated into five different citrus hosts (sweet orange, grapefruit, sour orange, lemon, and lime), where they maintained their distinct biological and genetic characteristics. PMID:19740030

  17. Variants of the obligate methanotroph isolate 761M capable of growth on glucose in the absence of methane

    SciTech Connect

    Zhao, S.J.; Hanson, R.S.

    1984-10-01

    Isolate 761M is an unusual type I methanotroph that possess a complete tricarboxylic acid cycle. Variants of this methanotroph that were capable of growth with methanol (isolate 761AR) or glucose (isolate 761H) have been isolated. Cultures of isolate 761H grown with glucose and casein hydrolysate as the sole carbon and energy sources retained the ability to grow on methane, contained methane monooxygenase and 3-hexulose phosphate synthase, and possessed intracytoplasmic membranes similar to those found in thin sections of isolate 761M grown on methane. Methane monooxygenase was also present in cultures of isolate 761AR grown on methanol and casein hydrolysate. 18 references, 4 figures, 2 tables.

  18. Genetic analysis of maize streak virus isolates from Uganda reveals widespread distribution of a recombinant variant.

    PubMed

    Owor, Betty E; Martin, Darren P; Shepherd, Dionne N; Edema, Richard; Monjane, Adérito L; Rybicki, Edward P; Thomson, Jennifer A; Varsani, Arvind

    2007-11-01

    Maize streak virus (MSV) contributes significantly to the problem of extremely low African maize yields. Whilst a diverse range of MSV and MSV-like viruses are endemic in sub-Saharan Africa and neighbouring islands, only a single group of maize-adapted variants - MSV subtypes A(1)-A(6) - causes severe enough disease in maize to influence yields substantially. In order to assist in designing effective strategies to control MSV in maize, a large survey covering 155 locations was conducted to assess the diversity, distribution and genetic characteristics of the Ugandan MSV-A population. PCR-restriction fragment-length polymorphism analyses of 391 virus isolates identified 49 genetic variants. Sixty-two full-genome sequences were determined, 52 of which were detectably recombinant. All but two recombinants contained predominantly MSV-A(1)-like sequences. Of the ten distinct recombination events observed, seven involved inter-MSV-A subtype recombination and three involved intra-MSV-A(1) recombination. One of the intra-MSV-A(1) recombinants, designated MSV-A(1)UgIII, accounted for >60 % of all MSV infections sampled throughout Uganda. Although recombination may be an important factor in the emergence of novel geminivirus variants, it is demonstrated that its characteristics in MSV are quite different from those observed in related African cassava-infecting geminivirus species. PMID:17947543

  19. Isolation and characterization of novel RECK tumor suppressor gene splice variants

    PubMed Central

    Trombetta-Lima, Marina; Winnischofer, Sheila Maria Brochado; Demasi, Marcos Angelo Almeida; Filho, Renato Astorino; Carreira, Ana Claudia Oliveira; Wei, Beiyang; de Assis Ribas, Thais; Konig, Michelle Silberspitz; Bowman-Colin, Christian; Oba-Shinjo, Sueli Mieko; Marie, Suely Kazue Nagahashi; Stetler-Stevenson, William; Sogayar, Mari Cleide

    2015-01-01

    Glioblastoma multiforme is the most common and lethal of the central nervous system glial-derived tumors. RECK suppresses tumor invasion by negatively regulating at least three members of the matrix metalloproteinase family: MMP-9, MMP-2, and MT1-MMP. A positive correlation has been observed between the abundance of RECK expression in tumor samples and a more favorable prognosis for patients with several types of tumors. In the present study, novel alternatively spliced variants of the RECK gene: RECK-B and RECK-I were isolated by RT-PCR and sequenced. The expression levels and profiles of these alternative RECK transcripts, as well as canonical RECK were determined in tissue samples of malignant astrocytomas of different grades and in a normal tissue RNA panel by qRT-PCR. Our results show that higher canonical RECK expression, accompanied by a higher canonical to alternative transcript expression ratio, positively correlates with higher overall survival rate after chemotherapeutic treatment of GBM patients. U87MG and T98G cells over-expressing the RECK-B alternative variant display higher anchorage-independent clonal growth and do not display modulation of, respectively, MMP-2 and MMP-9 expression. Our findings suggest that RECK transcript variants might have opposite roles in GBM biology and the ratio of their expression levels may be informative for the prognostic outcome of GBM patients. PMID:26431549

  20. Forced expression of AID facilitates the isolation of class switch variants from hybridoma cells.

    PubMed

    Iglesias-Ussel, Maria D; Fan, Manxia; Li, Ziqiang; Martin, Alberto; Scharff, Matthew D

    2006-10-20

    Monoclonal antibodies are used in the treatment and diagnosis of diseases and to study the protective and adverse functions of antibodies in vitro and in vivo. Since the isotype determines the effector function, half-life in the serum and distribution throughout the body, it would be useful to have a battery of antibodies with the same binding site associated with different isotypes. However, since hybridomas switch isotypes at very low frequencies in tissue culture, it has been difficult and very labor intensive to isolate panels of class switch variants. We show here that stable transfection of activation-induced cytidine deaminase (AID) in hybridomas increased their frequency of switching to a level that greatly facilitated the isolation of subclones expressing monoclonal antibodies of different isotypes. Although forced expression of AID also increased the frequency of somatic hypermutation in the immunoglobulin variable regions that encode the antigen binding site, antigen recognition was retained in the isotype switched antibodies. PMID:16997317

  1. Distribution of allelic variants of the chromosomal gene bla OXA-114-like in Achromobacter xylosoxidans clinical isolates.

    PubMed

    Traglia, German Matías; Almuzara, Marisa; Merkier, Andrea Karina; Papalia, Mariana; Galanternik, Laura; Radice, Marcela; Vay, Carlos; Centrón, Daniela; Ramírez, María Soledad

    2013-11-01

    Achromobacter xylosoxidans is increasingly being documented in cystic fibrosis patients. The bla(OXA-114) gene has been recognized as a naturally occurring chromosomal gene, exhibiting different allelic variants. In the population under study, the bla(OXA-114)-like gene was found in 19/19 non-epidemiological-related clinical isolates of A. xylosoxidans with ten different alleles including 1 novel OXA-114 variant. PMID:23771548

  2. Genomic analysis of a nontoxigenic, invasive Corynebacterium diphtheriae strain from Brazil

    PubMed Central

    Encinas, Fernando; Marin, Michel A; Ramos, Juliana N; Vieira, Verônica V; Mattos-Guaraldi, Ana Luiza; Vicente, Ana Carolina P

    2015-01-01

    We report the complete genome sequence and analysis of an invasive Corynebacterium diphtheriae strain that caused endocarditis in Rio de Janeiro, Brazil. It was selected for sequencing on the basis of the current relevance of nontoxigenic strains for public health. The genomic information was explored in the context of diversity, plasticity and genetic relatedness with other contemporary strains. PMID:26517665

  3. Bloodstream Infection Caused by Nontoxigenic Corynebacterium diphtheriae in an Immunocompromised Host in the United States

    PubMed Central

    Wojewoda, Christina M.; Koval, Christine E.; Wilson, Deborah A.; Chakos, Mary H.

    2012-01-01

    Corynebacterium species are well-known causes of catheter-related bloodstream infections. Toxigenic strains of Corynebacterium diphtheriae cause respiratory diphtheria. We report a bloodstream infection caused by a nontoxigenic strain of C. diphtheriae and discuss the epidemiology, possible sources of the infection, and the implications of rapid species identification of corynebacteria. PMID:22493337

  4. Identification and characterization of porcine kobuvirus variant isolated from suckling piglet in Gansu province, China.

    PubMed

    Fan, Shengtao; Sun, Heting; Ying, Ying; Gao, Xiaolong; Wang, Zheng; Yu, Yicong; Li, Yuanguo; Wang, Tiecheng; Yu, Zhijun; Yang, Songtao; Zhao, Yongkun; Qin, Chuan; Gao, Yuwei; Xia, Xianzhu

    2013-10-01

    Kobuviruses comprise three species, the Aichivirus A, Aichivirus B, and Aichivirus C (porcine kobuvirus). Porcine kobuvirus is endemic to pig farms and is not restricted geographically but, rather, is distributed worldwide. The complete genomic sequences of four porcine kobuvirus strains isolated during a diarrhea outbreak in piglets in the Gansu province of China were determined. Two of these strains exhibited variations relative to the traditional strains. The potential 3C/3D cleavage sites of the variant strains were Q/C, which differed from the Q/S in the traditional porcine kobuvirus genome. A 90-nucleotide deletion in the 2B protein and a single nucleotide insertion in the 3'UTR were found in the variant strains. The VP1 regions of all four porcine kobuviruses in our study were highly variable (81%-86%). Ten common amino acid mutations were found specifically at certain positions within the VP1 region. Significant recombination sites were identified using SimPlot scans of whole genome sequences. Porcine kobuviruses were also detected in pig serum, indicating that the virus can escape the gastrointestinal tract and travel to the circulatory system. These findings suggest that mutations and recombination events may have contributed to the high level of genetic diversity of porcine kobuviruses and serve as a driving force in its evolution. PMID:24145960

  5. Identification and Characterization of Porcine Kobuvirus Variant Isolated from Suckling Piglet in Gansu Province, China

    PubMed Central

    Fan, Shengtao; Sun, Heting; Ying, Ying; Gao, Xiaolong; Wang, Zheng; Yu, Yicong; Li, Yuanguo; Wang, Tiecheng; Yu, Zhijun; Yang, Songtao; Zhao, Yongkun; Qin, Chuan; Gao, Yuwei; Xia, Xianzhu

    2013-01-01

    Kobuviruses comprise three species, the Aichivirus A, Aichivirus B, and Aichivirus C (porcine kobuvirus). Porcine kobuvirus is endemic to pig farms and is not restricted geographically but, rather, is distributed worldwide. The complete genomic sequences of four porcine kobuvirus strains isolated during a diarrhea outbreak in piglets in the Gansu province of China were determined. Two of these strains exhibited variations relative to the traditional strains. The potential 3C/3D cleavage sites of the variant strains were Q/C, which differed from the Q/S in the traditional porcine kobuvirus genome. A 90-nucleotide deletion in the 2B protein and a single nucleotide insertion in the 3′UTR were found in the variant strains. The VP1 regions of all four porcine kobuviruses in our study were highly variable (81%–86%). Ten common amino acid mutations were found specifically at certain positions within the VP1 region. Significant recombination sites were identified using SimPlot scans of whole genome sequences. Porcine kobuviruses were also detected in pig serum, indicating that the virus can escape the gastrointestinal tract and travel to the circulatory system. These findings suggest that mutations and recombination events may have contributed to the high level of genetic diversity of porcine kobuviruses and serve as a driving force in its evolution. PMID:24145960

  6. Pathogenic mitochondrial mt-tRNA(Ala) variants are uniquely associated with isolated myopathy.

    PubMed

    Lehmann, Diana; Schubert, Kathrin; Joshi, Pushpa R; Hardy, Steven A; Tuppen, Helen A L; Baty, Karen; Blakely, Emma L; Bamberg, Christian; Zierz, Stephan; Deschauer, Marcus; Taylor, Robert W

    2015-12-01

    Pathogenic mitochondrial DNA (mtDNA) point mutations are associated with a wide range of clinical phenotypes, often involving multiple organ systems. We report two patients with isolated myopathy owing to novel mt-tRNA(Ala) variants. Muscle biopsy revealed extensive histopathological findings including cytochrome c oxidase (COX)-deficient fibres. Pyrosequencing confirmed mtDNA heteroplasmy for both mutations (m.5631G>A and m.5610G>A) whilst single-muscle fibre segregation studies (revealing statistically significant higher mutation loads in COX-deficient fibres than in COX-positive fibres), hierarchical mutation segregation within patient tissues and decreased steady-state mt-tRNA(Ala) levels all provide compelling evidence of pathogenicity. Interestingly, both patients showed very high-mutation levels in all tissues, inferring that the threshold for impairment of oxidative phosphorylation, as evidenced by COX deficiency, appears to be extremely high for these mt-tRNA(Ala) variants. Previously described mt-tRNA(Ala) mutations are also associated with a pure myopathic phenotype and demonstrate very high mtDNA heteroplasmy thresholds, inferring at least some genotype:phenotype correlation for mutations within this particular mt-tRNA gene. PMID:25873012

  7. Campylobacter hyointestinalis Isolated from Pigs Produces Multiple Variants of Biologically Active Cytolethal Distending Toxin.

    PubMed

    Kamei, Kazumasa; Hatanaka, Noritoshi; Asakura, Masahiro; Somroop, Srinuan; Samosornsuk, Worada; Hinenoya, Atsushi; Misawa, Naoaki; Nakagawa, Shinsaku; Yamasaki, Shinji

    2015-11-01

    Campylobacter hyointestinalis isolated from swine with proliferative enteritis often is considered to be pathogenic. While the precise virulence mechanisms of this species remain unclear, we have recently identified a cytolethal distending toxin (cdt) gene cluster in C. hyointestinalis isolated from a patient with diarrhea (W. Samosornsuk et al., J Med Microbiol, 27 July 2015, http://dx.doi.org/10.1099/jmm.0.000145). However, the sequences of the cdt genes in C. hyointestinalis were found to be significantly different and the gene products are immunologically distinct from those of other Campylobacter species. In this study, we demonstrate the presence of a second variant of the cdt gene cluster in C. hyointestinalis, designated cdt-II, while the former is named cdt-I. Sequencing of the cdt-II gene cluster and deduced amino acid sequences revealed that homologies between the subunits CdtA, CdtB, and CdtC of ChCDT-I and ChCDT-II are 25.0, 56.0, and 24.8%, respectively. Furthermore, the CdtB subunit of ChCDT-II was found to be immunologically unrelated to that of ChCDT-I by Ouchterlony double gel diffusion test. Recombinant ChCDT-II also induced cell distention and death of HeLa cells by blocking the cell cycle at G2/M phase. Interestingly, the cdt-II genes were detected in all 23 animal isolates and in 1 human isolate of C. hyointestinalis, and 21 of these strains carried both cdt-I and cdt-II gene clusters. Altogether, our results indicate that ChCDT-II is an important virulence factor of C. hyointestinalis in animals. PMID:26283337

  8. Low-Pass Genome-Wide Sequencing and Variant Inference Using Identity-by-Descent in an Isolated Human Population

    PubMed Central

    Gusev, A.; Shah, M. J.; Kenny, E. E.; Ramachandran, A.; Lowe, J. K.; Salit, J.; Lee, C. C.; Levandowsky, E. C.; Weaver, T. N.; Doan, Q. C.; Peckham, H. E.; McLaughlin, S. F.; Lyons, M. R.; Sheth, V. N.; Stoffel, M.; De La Vega, F. M.; Friedman, J. M.; Breslow, J. L.

    2012-01-01

    Whole-genome sequencing in an isolated population with few founders directly ascertains variants from the population bottleneck that may be rare elsewhere. In such populations, shared haplotypes allow imputation of variants in unsequenced samples without resorting to complex statistical methods as in studies of outbred cohorts. We focus on an isolated population cohort from the Pacific Island of Kosrae, Micronesia, where we previously collected SNP array and rich phenotype data for the majority of the population. We report identification of long regions with haplotypes co-inherited between pairs of individuals and methodology to leverage such shared genetic content for imputation. Our estimates show that sequencing as few as 40 personal genomes allows for inference in up to 60% of the 3000-person cohort at the average locus. We ascertained a pilot data set of whole-genome sequences from seven Kosraean individuals, with average 5× coverage. This assay identified 5,735,306 unique sites of which 1,212,831 were previously unknown. Additionally, these variants are unusually enriched for alleles that are rare in other populations when compared to geographic neighbors (published Korean genome SJK). We used the presence of shared haplotypes between the seven Kosraen individuals to estimate expected imputation accuracy of known and novel homozygous variants at 99.6% and 97.3%, respectively. This study presents whole-genome analysis of a homogenous isolate population with emphasis on optimal rare variant inference. PMID:22135348

  9. Vibrio cholerae O1 El Tor variant and emergence of Haitian ctxB variant in the strains isolated from South India.

    PubMed

    Bhattacharya, Debdutta; Dey, Shuchismita; Pazhani, Gururaja Perumal; Ramamurthy, Thandavarayan; Parande, Mahantesh V; Kholkute, Sanjiva D; Roy, Subarna

    2016-04-01

    Cholera still continues to be an important cause of human infection, especially in developing countries that lack access to safe drinking water and proper sanitation. In the present study, we report the emergence of new variant form of V. cholerae O1 El Tor biotype with a novel mutation in ctxB in strains isolated from various outbreaks during 2010-2014 in Belgaum situated in north-west Karnataka, India. A total of 14 occurrences of cholera were documented from Belgaum Division of North Karnataka during the 4-year period from 2010 to 2014. All the V. cholerae O1 isolates were subjected to DAMA PCR to detect the three different allelic subtypes of ctxB and PCR-based detection of virulent genes, and subsequently, 14 strains (one strain from each outbreak or sporadic case) were subjected to ctxB gene sequence and pulsed-field gel electrophoresis (PFGE) analysis. A total of 54 V. cholerae O1 strains were obtained of which 21 strains isolated during 2010-2011 had classical ctxB and remaining 33 strains isolated during 2012-2014 belonged to Haitian variant. In the cluster analysis, the PFGE profiles were divided into clades A with and B. Clade A contained eight strains with 94 % similarity and Haitian type of ctxB. Clade B contained six strains and had Haitian type of ctxB except one with classical ctxB. To the best of our knowledge, this is the first report of the Haitian variant of V. cholerae O1 Ogawa causing outbreaks and sporadic cases of cholera in South India. PMID:26337047

  10. A new variant of rabbit hemorrhagic disease virus G2-like strain isolated in China.

    PubMed

    Hu, Bo; Fan, Zhiyu; Wang, Fang; Song, Yanhua; Wei, Houjun; Liu, Xing; Qiu, Rulong; Xu, Weizhong; Yuan, Wanzhe; Xue, Jiabin

    2016-04-01

    To investigate the genetic variability and evolution of rabbit hemorrhagic disease virus (RHDV) strains in China, VP60 gene sequences of eight new isolates collected from farms with RHD occurrences in China between 2009 and 2014 were analyzed, and compared with the reference sequence of the vaccine strain WF/China/2007. We conducted a comprehensive analysis of the Chinese RHDV strains, including hemagglutination tests, western blot and immunosassays of capsid proteins, and phylogenetic analysis, and identified a new distinct antigenic variant. Specifically, strain HB/2014 collected in North China was identified as a non-hemagglutinating strain, and belongs to the original RHDV (G1-G5) group. The other seven isolates were classified in genogroup G6 (RHDVa), which was widely distributed across China before 2014, and was thought to replace the earlier groups. Antigenic characterization of the VP60 genes revealed a large degree of nucleotide sequence divergence between HB/2014 and the other Chinese strains. However, the current vaccine showed complete cross-protection against HB/2014 challenge in inoculated rabbits. Collectively, these data provide new tools and insight for further understanding the molecular evolution of RHDV in China. PMID:26827930

  11. Generation of HIV-1 primary isolates representative of plasma variants using the U87.CD4 cell line.

    PubMed

    Heeregrave, Edwin J; Ampofo, William K; Tetteh, John K A; Ofori, Michael; Ofori, Sampson B; Shah, Akram S; Pollakis, Georgios; Paxton, William A

    2010-11-01

    In order to obtain HIV-1 primary isolates in settings with limited access to donor PBMCs, a culture method was developed where patient PBMCs infected with HIV-1 were cultured together with U87.CD4 cells. Using this non-laborious method, it is possible to harvest virus solely on the basis of syncytia formation and circumventing monitoring of viral replication by CA-p24 ELISA. Primary isolates from 23 out of 33 patients (70%) were isolated successfully. From PCR amplification and sequencing of the V1V5 region of the viral gp120 envelope gene, primary isolates were compared with variants obtained from plasma and PBMCs of 13 patients. The primary isolates of seven patients (54%) resembled closely the plasma viral quasispecies, whereas different variants were isolated from the other patients (46%). Three patients harboured a dual infection, while this remained unnoticed from sequencing the plasma or PBMC compartment. The primary isolates were highly infectious for TZM-bl cells and could infect CD4-enriched lymphocytes. This study demonstrates that it is possible to grow viral isolates using a non-laborious and simple method. These isolates may be used in the field for studies on antiretroviral therapy or for vaccine trials. PMID:20705104

  12. Genetic characterization of Greek population isolates reveals strong genetic drift at missense and trait-associated variants

    PubMed Central

    Panoutsopoulou, Kalliope; Hatzikotoulas, Konstantinos; Xifara, Dionysia Kiara; Colonna, Vincenza; Farmaki, Aliki-Eleni; Ritchie, Graham R. S.; Southam, Lorraine; Gilly, Arthur; Tachmazidou, Ioanna; Fatumo, Segun; Matchan, Angela; Rayner, Nigel W.; Ntalla, Ioanna; Mezzavilla, Massimo; Chen, Yuan; Kiagiadaki, Chrysoula; Zengini, Eleni; Mamakou, Vasiliki; Athanasiadis, Antonis; Giannakopoulou, Margarita; Kariakli, Vassiliki-Eirini; Nsubuga, Rebecca N.; Karabarinde, Alex; Sandhu, Manjinder; McVean, Gil; Tyler-Smith, Chris; Tsafantakis, Emmanouil; Karaleftheri, Maria; Xue, Yali; Dedoussis, George; Zeggini, Eleftheria

    2014-01-01

    Isolated populations are emerging as a powerful study design in the search for low-frequency and rare variant associations with complex phenotypes. Here we genotype 2,296 samples from two isolated Greek populations, the Pomak villages (HELIC-Pomak) in the North of Greece and the Mylopotamos villages (HELIC-MANOLIS) in Crete. We compare their genomic characteristics to the general Greek population and establish them as genetic isolates. In the MANOLIS cohort, we observe an enrichment of missense variants among the variants that have drifted up in frequency by more than fivefold. In the Pomak cohort, we find novel associations at variants on chr11p15.4 showing large allele frequency increases (from 0.2% in the general Greek population to 4.6% in the isolate) with haematological traits, for example, with mean corpuscular volume (rs7116019, P=2.3 × 10−26). We replicate this association in a second set of Pomak samples (combined P=2.0 × 10−36). We demonstrate significant power gains in detecting medical trait associations. PMID:25373335

  13. Charge variants in IgG1: Isolation, characterization, in vitro binding properties and pharmacokinetics in rats.

    PubMed

    Khawli, Leslie A; Goswami, Sirj; Hutchinson, Ryan; Kwong, Zephania W; Yang, Jihong; Wang, Xiangdan; Yao, Zhenling; Sreedhara, Alavattam; Cano, Tony; Tesar, Devin; Nijem, Ihsan; Allison, David E; Wong, Pin Yee; Kao, Yung-Hsiang; Quan, Cynthia; Joshi, Amita; Harris, Reed J; Motchnik, Paul

    2010-01-01

    Antibody charge variants have gained considerable attention in the biotechnology industry due to their potential influence on stability and biological activity. Subtle differences in the relative proportions of charge variants are often observed during routine biomanufacture or process changes and pose a challenge to demonstrating product comparability. To gain further insights into the impact on biological activity and pharmacokinetics (PK) of monoclonal antibody (mAb) charge heterogeneity, we isolated the major charge forms of a recombinant humanized IgG1 and compared their in vitro properties and in vivo PK. The mAb starting material had a pI range of 8.7-9.1 and was composed of about 20% acidic variants, 12% basic variants, and 68% main peak. Cation exchange displacement chromatography was used to isolate the acidic, basic, and main peak fractions for animal studies. Detailed analyses were performed on the isolated fractions to identify specific chemical modification contributing to the charge differences, and were also characterized for purity and in vitro potency prior to being administered either subcutaneously (SC) or intravenously (IV) in rats. All isolated materials had similar potency and rat FcRn binding relative to the starting material. Following IV or SC administration (10 mg/kg) in rats, no difference in serum PK was observed, indicating that physiochemical modifications and pI differences among charge variants were not sufficient to result in PK changes. Thus, these results provided meaningful information for the comparative evaluation of charge-related heterogeneity of mAbs, and suggested that charge variants of IgGs do not affect the in vitro potency, FcRn binding affinity, or the PK properties in rats. PMID:20818176

  14. A new variant of cytolethal distending toxin in a clinical isolate of Campylobacter hyointestinalis.

    PubMed

    Samosornsuk, Worada; Kamei, Kazumasa; Hatanaka, Noritoshi; Taguchi, Takashi; Asakura, Masahiro; Somroop, Srinuan; Sugimoto, Norihiko; Chaicumpa, Wanpen; Yamasaki, Shinji

    2015-10-01

    Increasing numbers of Campylobacter hyointestinalis have been isolated from humans and animals with gastroenteritis, although the virulence mechanism of this species remains largely unknown. Here, we show that C. hyointestinalis isolated from a patient with diarrhoea in Thailand produced a novel variant of cytolethal distending toxin (CDT). Sequencing of a 13 965 bp genomic region of C. hyointestinalis carrying the genes coding for Ch-CDT revealed three ORFs of 798, 804 and 537 bp, which code for the Ch-CdtA, Ch-CdtB and Ch-CdtC subunits, respectively. The deduced amino acid sequence of Ch-CdtA showed ∼38.9 % homology with the CdtA of Campylobacter coli, but sequences of Ch-CdtB and Ch-CdtC were homologous to CdtB (65.7 %) and CdtC (33.1 %) of Campylobacter upsaliensis, respectively. Filter-sterilized sonic lysate of C. hyointestinalis demonstrated distension and death of HeLa cells by arresting the cell cycle at the G(2)/M phase and phosphorylation of host histone H2AX, a sensitive marker of DNA double-strand breaks. Rabbit antiserum raised against recombinant Ch-CdtB was not reactive against the recombinant CdtB protein of Campylobacter jejuni. A reconstituted Ch-CDT holotoxin prepared using each of the recombinant subunit proteins demonstrated distension and death of HeLa cells, suggesting that the C. hyointestinalis isolate indeed produced functionally active Ch-CDT. Furthermore, the immunological distinctiveness of the Ch-CDT produced by C. hyointestinalis and the increasing prevalence of the species in patients and animals with gastroenteritis suggest that this species may be an important emerging zoonotic pathogen. PMID:26220191

  15. Molecular characterization of "inconsistent" variants of Salmonella Typhimurium isolated in Italy.

    PubMed

    Barco, Lisa; Longo, Alessandra; Lettini, Antonia Anna; Cortini, Enzo; Saccardin, Cristina; Minorello, Claudio; Olsen, John Elmerdahl; Ricci, Antonia

    2014-06-01

    Salmonella 4,[5],12:i:- is a variant of Salmonella Typhimurium, which lacks the expression of phase-2 flagellar antigen, generally associated with the deletion of the fljB gene. Additional mechanisms involving the fljAB operon ( fljA, fljB, and hin genes) lead to the lack of expression of phase-2 flagellar antigens also in Salmonella strains harboring the fljB gene. For 20 S. 4,[5],12:i:- strains, defined as "inconsistent" Salmonella Typhimurium variants since they had phenotypically behaved as monophasic, even though the fljB gene was conserved, the fljAB operon was characterized in order to explain the ineffective expression of the phase-2 flagellar antigen. The monophasic phenotype for a first group of strains (9) was likely due to the absence of the hin gene, leading to the inhibited switch between the expression of phase-1 and phase-2 flagellar genes. For a second group of strains (5), the monophasic phenotype could be attributed to nonconservative point mutations identified in fljA and hin genes, which could hamper the proper expression of invertase gene and the fljA, acting as repressor of the phase-1 flagellar gene. Finally, for a last group of inconsistent strains (6), a plausible reason for their monophasic phenotype was not found, since the genes involved in the expression of phase-2 flagellar antigen were fully conserved. Moreover, the collection of inconsistent Salmonella Typhimurium isolates investigated were characterized by distinct molecular profiles, as demonstrated by multiple-locus variable-number tandem repeat analysis, and phenotype variability, as demonstrated by phage-typing. This study highlights the usefulness of investigating the entire fljAB operon when a definitive identification of the monophasic or biphasic status of Salmonella Typhimurium strains is needed (for instance, in the context of epidemiological investigations aimed to identify the relatedness among strains). PMID:24666380

  16. Pseudomonas aeruginosa variants isolated from patients with cystic fibrosis are killed by a bactericidal protein from human polymorphonuclear leukocytes.

    PubMed Central

    Siefferman, C M; Regelmann, W E; Gray, B H

    1991-01-01

    The susceptibility of paired mucoid and nonmucoid variants of Pseudomonas aeruginosa isolated from 13 patients with cystic fibrosis (CF) to killing by a 55,000-Da bactericidal protein (BP55) from human polymorphonuclear leukocytes was studied. Mucoid and nonmucoid variants were equally sensitive to killing by BP55 at both pH 5.6 and pH 7.2. Eleven of the isolates were resistant to the bactericidal activity of 10% normal human serum but were as sensitive as the serum-sensitive isolates to BP55. Similarly, the 15 isolates with lipopolysaccharides (LPS) containing O-polysaccharide side chains (smooth LPS) were as sensitive to BP55 as those isolates with rough LPS.P. aeruginosa isolates from patients in poor clinical condition were more likely to have LPS of the smooth type and to be resistant to killing by 10% human serum than the isolates from patients in good clinical condition. We have concluded that the susceptibility of the P. aeruginosa isolates from patients with CF to killing by BP55 does not correlate with mucoid or nonmucoid variations, with the presence or absence of smooth LPS, or with the sensitivity or resistance to killing by normal human serum. Images PMID:1903774

  17. Exome sequencing in an admixed isolated population indicates NFXL1 variants confer a risk for specific language impairment.

    PubMed

    Villanueva, Pía; Nudel, Ron; Hoischen, Alexander; Fernández, María Angélica; Simpson, Nuala H; Gilissen, Christian; Reader, Rose H; Jara, Lillian; Echeverry, María Magdalena; Echeverry, Maria Magdalena; Francks, Clyde; Baird, Gillian; Conti-Ramsden, Gina; O'Hare, Anne; Bolton, Patrick F; Hennessy, Elizabeth R; Palomino, Hernán; Carvajal-Carmona, Luis; Veltman, Joris A; Cazier, Jean-Baptiste; De Barbieri, Zulema; Fisher, Simon E; Newbury, Dianne F

    2015-03-01

    Children affected by Specific Language Impairment (SLI) fail to acquire age appropriate language skills despite adequate intelligence and opportunity. SLI is highly heritable, but the understanding of underlying genetic mechanisms has proved challenging. In this study, we use molecular genetic techniques to investigate an admixed isolated founder population from the Robinson Crusoe Island (Chile), who are affected by a high incidence of SLI, increasing the power to discover contributory genetic factors. We utilize exome sequencing in selected individuals from this population to identify eight coding variants that are of putative significance. We then apply association analyses across the wider population to highlight a single rare coding variant (rs144169475, Minor Allele Frequency of 4.1% in admixed South American populations) in the NFXL1 gene that confers a nonsynonymous change (N150K) and is significantly associated with language impairment in the Robinson Crusoe population (p = 2.04 × 10-4, 8 variants tested). Subsequent sequencing of NFXL1 in 117 UK SLI cases identified four individuals with heterozygous variants predicted to be of functional consequence. We conclude that coding variants within NFXL1 confer an increased risk of SLI within a complex genetic model. PMID:25781923

  18. Exome Sequencing in an Admixed Isolated Population Indicates NFXL1 Variants Confer a Risk for Specific Language Impairment

    PubMed Central

    Villanueva, Pía; Nudel, Ron; Hoischen, Alexander; Fernández, María Angélica; Simpson, Nuala H.; Gilissen, Christian; Reader, Rose H.; Jara, Lillian; Echeverry, Maria Magdalena; Francks, Clyde; Baird, Gillian; Conti-Ramsden, Gina; O’Hare, Anne; Bolton, Patrick F.; Hennessy, Elizabeth R.; Palomino, Hernán; Carvajal-Carmona, Luis; Veltman, Joris A.; Cazier, Jean-Baptiste; De Barbieri, Zulema

    2015-01-01

    Children affected by Specific Language Impairment (SLI) fail to acquire age appropriate language skills despite adequate intelligence and opportunity. SLI is highly heritable, but the understanding of underlying genetic mechanisms has proved challenging. In this study, we use molecular genetic techniques to investigate an admixed isolated founder population from the Robinson Crusoe Island (Chile), who are affected by a high incidence of SLI, increasing the power to discover contributory genetic factors. We utilize exome sequencing in selected individuals from this population to identify eight coding variants that are of putative significance. We then apply association analyses across the wider population to highlight a single rare coding variant (rs144169475, Minor Allele Frequency of 4.1% in admixed South American populations) in the NFXL1 gene that confers a nonsynonymous change (N150K) and is significantly associated with language impairment in the Robinson Crusoe population (p = 2.04 × 10–4, 8 variants tested). Subsequent sequencing of NFXL1 in 117 UK SLI cases identified four individuals with heterozygous variants predicted to be of functional consequence. We conclude that coding variants within NFXL1 confer an increased risk of SLI within a complex genetic model. PMID:25781923

  19. Isolation of a Variant Strain of Pleurotus eryngii and the Development of Specific DNA Markers to Identify the Variant Strain

    PubMed Central

    Lee, Hyun-Jun; Kim, Sang-Woo; Ryu, Jae-San; Lee, Chang-Yun

    2014-01-01

    A degenerated strain of Pleurotus eryngii KNR2312 was isolated from a commercial farm. Random amplified polymorphic DNA analysis performed on the genomic DNA of the normal and degenerated strains of this species revealed differences in the DNA banding pattern. A unique DNA fragment (1.7 kbp), which appeared only in the degenerated strain, was isolated and sequenced. Comparing this sequence with the KNR2312 genomic sequence showed that the sequence of the degenerated strain comprised three DNA regions that originated from nine distinct scaffolds of the genomic sequence, suggesting that chromosome-level changes had occurred in the degenerated strain. Using the unique sequence, three sets of PCR primers were designed that targeted the full length, the 5' half, and the 3' half of the DNA. The primer sets P2-1 and P2-2 yielded 1.76 and 0.97 kbp PCR products, respectively, only in the case of the degenerated strain, whereas P2-3 generated a 0.8 kbp product in both the normal and the degenerated strains because its target region was intact in the normal strain as well. In the case of the P2-1 and P2-2 sets, the priming regions of the forward and reverse primers were located at distinct genomic scaffolds in the normal strain. These two primer sets specifically detected the degenerate strain of KNR2312 isolated from various mushrooms including 10 different strains of P. eryngii, four strains of P. ostreatus, and 11 other wild mushrooms. PMID:24808734

  20. Isolation and molecular characterization of newly emerging avian reovirus variants and novel strains in Pennsylvania, USA, 2011-2014.

    PubMed

    Lu, Huaguang; Tang, Yi; Dunn, Patricia A; Wallner-Pendleton, Eva A; Lin, Lin; Knoll, Eric A

    2015-01-01

    Avian reovirus (ARV) infections of broiler and turkey flocks have caused significant clinical disease and economic losses in Pennsylvania (PA) since 2011. Most of the ARV-infected birds suffered from severe arthritis, tenosynovitis, pericarditis and depressed growth or runting-stunting syndrome (RSS). A high morbidity (up to 20% to 40%) was observed in ARV-affected flocks, and the flock mortality was occasionally as high as 10%. ARV infections in turkeys were diagnosed for the first time in PA in 2011. From 2011 to 2014, a total of 301 ARV isolations were made from affected PA poultry. The molecular characterization of the Sigma C gene of 114 field isolates, representing most ARV outbreaks, revealed that only 21.93% of the 114 sequenced ARV isolates were in the same genotyping cluster (cluster 1) as the ARV vaccine strains (S1133, 1733, and 2048), whereas 78.07% of the sequenced isolates were in genotyping clusters 2, 3, 4, 5, and 6 (which were distinct from the vaccine strains) and represented newly emerging ARV variants. In particular, genotyping cluster 6 was a new ARV genotype that was identified for the first time in 10 novel PA ARV variants of field isolates. PMID:26469681

  1. Isolation and molecular characterization of newly emerging avian reovirus variants and novel strains in Pennsylvania, USA, 2011–2014

    PubMed Central

    Lu, Huaguang; Tang, Yi; Dunn, Patricia A.; Wallner-Pendleton, Eva A.; Lin, Lin; Knoll, Eric A.

    2015-01-01

    Avian reovirus (ARV) infections of broiler and turkey flocks have caused significant clinical disease and economic losses in Pennsylvania (PA) since 2011. Most of the ARV-infected birds suffered from severe arthritis, tenosynovitis, pericarditis and depressed growth or runting-stunting syndrome (RSS). A high morbidity (up to 20% to 40%) was observed in ARV-affected flocks, and the flock mortality was occasionally as high as 10%. ARV infections in turkeys were diagnosed for the first time in PA in 2011. From 2011 to 2014, a total of 301 ARV isolations were made from affected PA poultry. The molecular characterization of the Sigma C gene of 114 field isolates, representing most ARV outbreaks, revealed that only 21.93% of the 114 sequenced ARV isolates were in the same genotyping cluster (cluster 1) as the ARV vaccine strains (S1133, 1733, and 2048), whereas 78.07% of the sequenced isolates were in genotyping clusters 2, 3, 4, 5, and 6 (which were distinct from the vaccine strains) and represented newly emerging ARV variants. In particular, genotyping cluster 6 was a new ARV genotype that was identified for the first time in 10 novel PA ARV variants of field isolates. PMID:26469681

  2. Identification of interleukin-26 in the dromedary camel (Camelus dromedarius): Evidence of alternative splicing and isolation of novel splice variants.

    PubMed

    Premraj, Avinash; Nautiyal, Binita; Aleyas, Abi G; Rasool, Thaha Jamal

    2015-10-01

    Interleukin-26 (IL-26) is a member of the IL-10 family of cytokines. Though conserved across vertebrates, the IL-26 gene is functionally inactivated in a few mammals like rat, mouse and horse. We report here the identification, isolation and cloning of the cDNA of IL-26 from the dromedary camel. The camel cDNA contains a 516 bp open reading frame encoding a 171 amino acid precursor protein, including a 21 amino acid signal peptide. Sequence analysis revealed high similarity with other mammalian IL-26 homologs and the conservation of IL-10 cytokine family domain structure including key amino acid residues. We also report the identification and cloning of four novel transcript variants produced by alternative splicing at the Exon 3-Exon 4 regions of the gene. Three of the alternative splice variants had premature termination codons and are predicted to code for truncated proteins. The transcript variant 4 (Tv4) having an insertion of an extra 120 bp nucleotides in the ORF was predicted to encode a full length protein product with 40 extra amino acid residues. The mRNA transcripts of all the variants were identified in lymph node, where as fewer variants were observed in other tissues like blood, liver and kidney. The expression of Tv2 and Tv3 were found to be up regulated in mitogen induced camel peripheral blood mononuclear cells. IL-26-Tv2 expression was also induced in camel fibroblast cells infected with Camel pox virus in-vitro. The identification of the transcript variants of IL-26 from the dromedary camel is the first report of alternative splicing for IL-26 in a species in which the gene has not been inactivated. PMID:26190308

  3. Complete genome sequence of two rabbit hemorrhagic disease virus variant b isolates detected on the Iberian Peninsula.

    PubMed

    Dalton, K P; Abrantes, J; Lopes, A M; Nicieza, I; Álvarez, Á L; Esteves, P J; Parra, F

    2015-03-01

    We report the complete genome sequences of two isolates (RHDV-N11 and CBVal16) of variant rabbit hemorrhagic disease virus (RHDVb). Isolate N11 was detected in young domestic animals during a rabbit hemorrhagic disease (RHD) outbreak that occurred in 2011 on a rabbit farm in Navarra, Spain, while CBVal16 was isolated from a wild rabbit found dead in Valpaços, Northern Portugal, a year later. The viral sequences reported show 84.8-85.1 % and 78.3-78.5 % identity to RHDVAst/89 and RCV-A1 MIC-07, representative members of the pathogenic genogroup 1 RHDV and apathogenic rabbit calicivirus, respectively. In comparison with other RHDV isolates belonging to the previously known genogroups 1-6, RHDVb shows marked phenotypic differences, as it causes disease preferentially in young rabbits under 40 days of age and shows modified red blood cell agglutination profiles as well as antigenic differences that allow this variant to escape protection by the currently available vaccines. PMID:25577166

  4. Patients with cystic fibrosis have a high carriage rate of non-toxigenic Clostridium difficile.

    PubMed

    Bauer, M P; Farid, A; Bakker, M; Hoek, R A S; Kuijper, E J; van Dissel, J T

    2014-07-01

    Thirty-year-old observations report frequent asymptomatic Clostridium difficile carriage among cystic fibrosis (CF) patients. In this case-control study, we found more carriers among CF patients than controls (47% versus 11%), but most strains carried by CF patients were non-toxigenic (77% versus 17%). Among CF patients, carriers were younger, with more severe pulmonary disease than non-carriers. Strains belonged to multiple PCR-ribotypes, suggesting that these CF patients did not acquire strains from each other. PMID:24286342

  5. Exome sequencing identifies recessive CDK5RAP2 variants in patients with isolated agenesis of corpus callosum.

    PubMed

    Jouan, Loubna; Ouled Amar Bencheikh, Bouchra; Daoud, Hussein; Dionne-Laporte, Alexandre; Dobrzeniecka, Sylvia; Spiegelman, Dan; Rochefort, Daniel; Hince, Pascale; Szuto, Anna; Lassonde, Maryse; Barbelanne, Marine; Tsang, William Y; Dion, Patrick A; Théoret, Hugo; Rouleau, Guy A

    2016-04-01

    Agenesis of the corpus callosum (ACC) is a common brain malformation which can be observed either as an isolated condition or as part of numerous congenital syndromes. Therefore, cognitive and neurological involvements in patients with ACC are variable, from mild linguistic and behavioral impairments to more severe neurological deficits. To date, the underlying genetic causes of isolated ACC remains elusive and causative genes have yet to be identified. We performed exome sequencing on three acallosal siblings from the same non-consanguineous family and identified compound heterozygous variants, p.[Gly94Arg];[Asn1232Ser], in the protein encoded by the CDK5RAP2 gene, also known as MCPH3, a gene previously reported to cause autosomal recessive primary microcephaly. Our findings suggest a novel role for this gene in the pathogenesis of isolated ACC. PMID:26197979

  6. Prevention of porcine Clostridium difficile-associated disease by competitive exclusion with nontoxigenic organisms.

    PubMed

    Songer, J Glenn; Jones, Randy; Anderson, Michael A; Barbara, Angelique J; Post, Karen W; Trinh, Hien T

    2007-10-01

    Clostridium difficile is widely known as a cause of disease in humans, and has emerged as an important problem in neonatal swine. No commercial product is available for immunoprophylaxis of C. difficile-associated disease, but success in preventing experimental infections in hamsters by use of nontoxigenic strains to competitively exclude toxigenic strains led us to try this method in neonatal pigs. Spores were administered orally to newborn pigs or were sprayed onto perineum and teats of dams. Significantly more piglets were weaned among litters receiving spores orally, and average weaning weights were significantly higher for both treatment groups than for controls. Toxins A and B were detected in 44.8% of litters and 16.5% of piglets born to sprayed sows and 58.3% of litters and 15.4% of piglets in the control group. However, toxins were detected in only 13.8% of litters and 3.4% of piglets given spores orally. These data support a contention that precolonization by a nontoxigenic strain can ameliorate the pre-weaning growth retardation associated with C. difficile infection in piglets. PMID:17493774

  7. Isolation of a variant Porphyromonas sp. from polymicrobial infections in central bearded dragons (Pogona vitticeps).

    PubMed

    Bemis, David A; Greenacre, Cheryl B; Bryant, Mary Jean; Jones, Rebekah D; Kania, Stephen A

    2011-01-01

    Isolates of gram-negative anaerobic bacteria from reptiles have only occasionally been identified to the genus and species level in the veterinary medical literature. In particular, reports identifying Porphyromonas spp. from infections in reptiles are scarce. The present report describes unique Porphyromonas isolates obtained from necrosuppurative infections in central bearded dragons (Pogona vitticeps). The isolates grew in the presence of oxygen, were strongly hemolytic, and did not produce detectable black, iron porphyrin pigment. Biochemical identification kit numeric biocodes gave high but unreliable probabilities (>99.9%) for identification as Porphyromonas gingivalis. Partial 16S ribosomal RNA gene sequences of the isolates were identical to each other and shared 91% identity with those of Porphyromonas gulae. The isolates may represent a new reptile-associated Porphyromonas species. PMID:21217036

  8. Biochemical Characterization of VIM-39, a VIM-1-Like Metallo-?-Lactamase Variant from a Multidrug-Resistant Klebsiella pneumoniae Isolate from Greece.

    PubMed

    Papagiannitsis, Costas C; Pollini, Simona; De Luca, Filomena; Rossolini, Gian Maria; Docquier, Jean-Denis; Hrabák, Jaroslav

    2015-12-01

    VIM-39, a VIM-1-like metallo-?-lactamase variant (VIM-1 Thr33Ala His224Leu) was identified in a clinical isolate of Klebsiella pneumoniae belonging to sequence type 147. VIM-39 hydrolyzed ampicillin, cephalothin, and imipenem more efficiently than did VIM-1 and VIM-26 (a VIM-1 variant with the His224Leu substitution) because of higher turnover rates. PMID:26369975

  9. Variants of a genomic island in Aeromonas salmonicida subsp. salmonicida link isolates with their geographical origins.

    PubMed

    Emond-Rheault, Jean-Guillaume; Vincent, Antony T; Trudel, Mélanie V; Brochu, Francis; Boyle, Brian; Tanaka, Katherine H; Attéré, Sabrina A; Jubinville, Éric; Loch, Thomas P; Winters, Andrew D; Faisal, Mohamed; Frenette, Michel; Derome, Nicolas; Charette, Steve J

    2015-01-30

    Aeromonas salmonicida subsp. salmonicida is a fish pathogen. Analysis of its genomic characteristics is required to determine the worldwide distribution of the various populations of this bacterium. Genomic alignments between the 01-B526 pathogenic strain and the A449 reference strain have revealed a 51-kb chromosomal insertion in 01-B526. This insertion (AsaGEI1a) has been identified as a new genomic island (GEI) bearing prophage genes. PCR assays were used to detect this GEI in a collection of 139 A. salmonicida subsp. salmonicida isolates. Three forms of this GEI (AsaGEI1a, AsaGEI1b, AsaGEI2a) are now known based on this analysis and the sequencing of the genomes of seven additional isolates. A new prophage (prophage 3) associated with AsaGEI2a was also discovered. Each GEI appeared to be strongly associated with a specific geographic region. AsaGEI1a and AsaGEI2a were exclusively found in North American isolates, except for one European isolate bearing AsaGEI2a. The majority of the isolates bearing AsaGEI1b or no GEI were from Europe. Prophage 3 has also a particular geographic distribution and was found only in North American isolates. We demonstrated that A. salmonicida subsp. salmonicida possesses unsuspected elements of genomic heterogeneity that could be used as indicators to determine the geographic origins of isolates of this bacterium. PMID:25480167

  10. Identification of the genetic basis for clinical menadione-auxotrophic small-colony variant isolates of Staphylococcus aureus.

    PubMed

    Lannergård, Jonas; von Eiff, Christof; Sander, Gunnar; Cordes, Tina; Seggewiss, Jochen; Peters, Georg; Proctor, Richard A; Becker, Karsten; Hughes, Diarmaid

    2008-11-01

    Small-colony variants (SCVs) of Staphylococcus aureus are associated with persistent infections and may be selectively enriched during antibiotic therapy. Three pairs of clonally related S. aureus isolates were recovered from patients receiving systemic antibiotic therapy. Each pair consisted of an isolate with a normal phenotype and an isolate with an SCV phenotype. These SCVs were characterized by reduced susceptibility to gentamicin, reduced hemolytic activity, slow growth, and menadione auxotrophy. Sequencing of the genes involved in menadione biosynthesis revealed mutations in menB, the gene encoding naphthoate synthase, in all three strains with the SCV phenotype. The menB mutations were (i) a 9-bp deletion from nucleotides 55 to 63, (ii) a frameshift mutation that resulted in a premature stop codon at position 230, and (iii) a point mutation that caused the amino acid substitution Gly to Val at codon 233. Fluctuation tests showed that growth-compensated mutants arose in the SCV population of one strain, strain OM1b, at a rate of 1.8 x 10(-8) per cell per generation. Sequence analyses of 23 independently isolated growth-compensated mutants of this strain revealed alterations in the menB sequence in every case. These alterations included reversions to the wild-type sequence and intragenic second-site mutations. Each of the growth-compensated mutants showed a restoration of normal growth and a loss of menadione auxotrophy, increased susceptibility to gentamicin, and restored hemolytic activity. These data show that mutations in menB cause the SCV phenotype in these clinical isolates. This is the first report on the genetic basis of menadione-auxotrophic SCVs determined in clinical S. aureus isolates. PMID:18779359

  11. Triclosan-Induced Aminoglycoside-Tolerant Listeria monocytogenes Isolates Can Appear as Small-Colony Variants

    PubMed Central

    Kastbjerg, Vicky G.; Hein-Kristensen, Line

    2014-01-01

    Exposure of the human food-borne pathogen Listeria monocytogenes to sublethal concentrations of triclosan can cause resistance to several aminoglycosides. Aminoglycoside-resistant isolates exhibit two colony morphologies: normal-size and pinpoint colonies. The purposes of the present study were to characterize the small colonies of L. monocytogenes and to determine if specific genetic changes could explain the triclosan-induced aminoglycoside resistance in both pinpoint and normal-size isolates. Isolates from the pinpoint colonies grew poorly under aerated conditions, but growth was restored by addition of antibiotics. Pinpoint isolates had decreased hemolytic activity under stagnant conditions and a changed spectrum of carbohydrate utilization compared to the wild type and isolates from normal-size colonies. Genome sequence comparison revealed that all seven pinpoint isolates had a mutation in a heme gene, and addition of heme caused the pinpoint isolates to revert to normal colony size. Triclosan-induced gentamicin-resistant isolates had mutations in several different genes, and it cannot be directly concluded how the different mutations caused gentamicin resistance. However, since many of the mutations affected proteins involved in respiration, it seems likely that the mutations affected the active transport of the antibiotic and thereby caused resistance by decreasing the amount of aminoglycoside that enters the bacterial cell. Our study emphasizes that triclosan likely has more targets than just fabI and that exposure to triclosan can cause resistance to antibiotics that enters the cell via active transport. Further studies are needed to elucidate if L. monocytogenes pinpoint isolates could have any clinical impact, e.g., in persistent infections. PMID:24637686

  12. Phylogenetic analysis and molecular characteristics of seven variant Chinese field isolates of PRRSV

    PubMed Central

    2010-01-01

    Background Porcine reproductive and respiratory syndrome (PRRS) has now been widely recognized as an economically important disease. The objective of this study was to compare the molecular and biological characteristics of porcine reproductive and respiratory syndrome virus (PRRSV) field isolates in China to those of the modified live virus (MLV) PRRS vaccine and its parent strain (ATCC VR2332). Results Five genes (GP2, GP3, GP4, GP5 and NSP2) of seven isolates of PRRSV from China, designated LS-4, HM-1, HQ-5, HQ-6, GC-2, GCH-3 and ST-7/2008, were sequenced and analyzed. Phylogenetic analyses based on the nucleotide sequence of the ORF2-5 and NSP2 showed that the seven Chinese isolates belonged to the same genetic subgroup and were related to the North American PRRSV genotype. Comparative analysis with the relevant sequences of another Chinese isolate (BJ-4) and North American (VR2332 and MLV) viruses revealed that these isolates have 80.8-92.9% homology with VR-2332, and 81.3-98.8% identity with MLV and 80.7-92.9% with BJ-4. All Nsp2 nonstructural protein of these seven isolates exhibited variations (a 29 amino acids deletion) in comparison with other North American PRRSV isolates. Therefore, these isolates were novel strain with unique amino acid composition. However, they all share more than 97% identity with other highly pathogenic Chinese PRRSV strains. Additionally, there are extensive amino acid (aa) mutations in the GP5 protein and the Nsp2 protein when compared with the previous isolates. Conclusions These results might be useful to study the genetic diversity of PRRSV in China and to track the infection sources as well as for vaccines development. PMID:20482897

  13. Mitochondrial DNA Variant in COX1 Subunit Significantly Alters Energy Metabolism of Geographically Divergent Wild Isolates in Caenorhabditis elegans

    PubMed Central

    Dingley, Stephen D.; Polyak, Erzsebet; Ostrovsky, Julian; Srinivasan, Satish; Lee, Icksoo; Rosenfeld, Amy B.; Tsukikawa, Mai; Xiao, Rui; Selak, Mary A.; Coon, Joshua J.; Hebert, Alexander S.; Grimsrud, Paul A.; Kwon, Young Joon; Pagliarini, David J.; Gai, Xiaowu; Schurr, Theodore G.; Hüttemann, Maik; Nakamaru-Ogiso, Eiko; Falk, Marni J.

    2014-01-01

    Mitochondrial DNA (mtDNA) sequence variation can influence the penetrance of complex diseases and climatic adaptation. While studies in geographically defined human populations suggest that mtDNA mutations become fixed when they have conferred metabolic capabilities optimally suited for a specific environment, it has been challenging to definitively assign adaptive functions to specific mtDNA sequence variants in mammals. We investigated whether mtDNA genome variation functionally influences Caenorhabditis elegans wild isolates of distinct mtDNA lineages and geographic origins. We found that, relative to N2 (England) wild-type nematodes, CB4856 wild isolates from a warmer native climate (Hawaii) had a unique p.A12S amino acid substitution in the mtDNA-encoded COX1 core catalytic subunit of mitochondrial complex IV (CIV). Relative to N2, CB4856 worms grown at 20 °C had significantly increased CIV enzyme activity, mitochondrial matrix oxidant burden, and sensitivity to oxidative stress but had significantly reduced lifespan and mitochondrial membrane potential. Interestingly, mitochondrial membrane potential was significantly increased in CB4856 grown at its native temperature of 25 °C. A transmitochondrial cybrid worm strain, chpIR (M, CB4856 > N2), was bred as homoplasmic for the CB4856 mtDNA genome in the N2 nuclear background. The cybrid strain also displayed significantly increased CIV activity, demonstrating that this difference results from the mtDNA-encoded p.A12S variant. However, chpIR (M, CB4856 > N2) worms had significantly reduced median and maximal lifespan relative to CB4856, which may relate to their nuclear– mtDNA genome mismatch. Overall, these data suggest that C. elegans wild isolates of varying geographic origins may adapt to environmental challenges through mtDNA variation to modulate critical aspects of mitochondrial energy metabolism. PMID:24534730

  14. Glycosylation of chicken haptoglobin: isolation and characterization of three molecular variants and studies of their distribution in hen plasma before and after turpentine-induced inflammation.

    PubMed

    Delers, F; Strecker, G; Engler, R

    1988-03-01

    Chicken haptoglobin (Hp), a hemoglobin-binding protein isolated from chicken plasma, is composed of three molecular variants that react differently with concanavalin A (ConA). These glycosylation variants of chicken Hp have been isolated by affinity chromatography using Sepharose-bound ConA. They differ in their molecular weight, as determined by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. Analysis of the glycopeptides obtained after pronase digestion of these variants yielded two types of structures: one, reactive with ConA, corresponded to a biantennary N-linked carbohydrate unit and one, unreactive with ConA, corresponded to a triantennary unit. The strongly ConA-reactive Hp variant bears only two biantennary units and the nonreactive Hp variant bears only two triantennary units; the weakly reactive Hp variant bears equal amounts of both units. The distribution of Hp glycosylation variant does not show any significant difference when obtained from the plasma of laying hens before and after turpentine-induced inflammation. PMID:3132955

  15. Apolipoprotein A-I amyloidogenic variant L174S, expressed and isolated from stably transfected mammalian cells, is associated with fatty acids.

    PubMed

    Monti, Daria Maria; Di Gaetano, Sonia; Del Giudice, Rita; Giangrande, Chiara; Amoresano, Angela; Monti, Maria; Arciello, Angela; Piccoli, Renata

    2012-03-01

    Sixteen variants of apolipoprotein A-I (ApoA-I) are associated with hereditary systemic amyloidoses, characterized by amyloid deposition in peripheral organs of patients. As these are heterozygous for the amyloidogenic variants, their isolation from plasma is impracticable and recombinant expression systems are needed. Here we report the expression of recombinant ApoA-I amyloidogenic variant Leu174 with Ser (L174S) in stably transfected Chinese hamster ovary-K1 cells. ApoA-I variant L174S was found to be efficiently secreted in the culture medium, from which it was isolated following a one-step purification procedure. Mass spectrometry analyses allowed the qualitative and quantitative definition of the amyloidogenic variant lipid content, which was found to consist of two saturated and two monounsaturated fatty acids. Interestingly, the same lipid species were found to be associated with the wild-type ApoA-I, expressed and isolated using the same cell system, with lower values of the lipid to protein molar ratios with respect to the amyloidogenic variant. A possible role of fatty acids in trafficking and secretion of apolipoproteins may be hypothesized. PMID:22295944

  16. Characterization of H5N1 Influenza Virus Variants with Hemagglutinin Mutations Isolated from Patients

    PubMed Central

    Arai, Yasuha; Daidoji, Tomo; Kawashita, Norihito; Ibrahim, Madiha S.; El-Gendy, Emad El-Din M.; Hiramatsu, Hiroaki; Kubota-Koketsu, Ritsuko; Takagi, Tatsuya; Murata, Takeomi; Takahashi, Kazuo; Okuno, Yoshinobu; Nakaya, Takaaki; Suzuki, Yasuo; Ikuta, Kazuyoshi

    2015-01-01

    ABSTRACT A change in viral hemagglutinin (HA) receptor binding specificity from α2,3- to α2,6-linked sialic acid is necessary for highly pathogenic avian influenza (AI) virus subtype H5N1 to become pandemic. However, details of the human-adaptive change in the H5N1 virus remain unknown. Our database search of H5N1 clade 2.2.1 viruses circulating in Egypt identified multiple HA mutations that had been selected in infected patients. Using reverse genetics, we found that increases in both human receptor specificity and the HA pH threshold for membrane fusion were necessary to facilitate replication of the virus variants in human airway epithelia. Furthermore, variants with enhanced replication in human cells had decreased HA stability, apparently to compensate for the changes in viral receptor specificity and membrane fusion activity. Our findings showed that H5N1 viruses could rapidly adapt to growth in the human airway microenvironment by altering their HA properties in infected patients and provided new insights into the human-adaptive mechanisms of AI viruses. PMID:25852160

  17. Isolation of novel variants of infectious bursal disease virus from different outbreaks in Northeast India.

    PubMed

    Morla, Sudhir; Deka, Pankaj; Kumar, Sachin

    2016-04-01

    Infectious bursal disease virus (IBDV) is a highly infectious disease of young chicken that predominantly affects the immune system. In the present study, we are reporting first comprehensive study of IBDV outbreaks from the Northeastern part of India. Northeast India shares a porous border with four different countries; and as a rule any outbreak in the neighboring countries substantially affects the poultry population in the adjoining states. Nucleotide sequence analysis of the VP2 gene of the IBDV isolates from the Northeastern part of India suggested the extreme virulent nature of the virus. The virulent marker amino acids (A222, I242, Q253, I256 and S299) in the hypervariable region of the Northeastern isolates were found identical with the reported very virulent strains of IBDV. A unique insertion of I/L294V was recorded in all the isolates of the Northeastern India. The study will be useful in understanding the circulating pathotypes of IBDV in India. PMID:26854869

  18. Mycobacterium canettii, the smooth variant of M. tuberculosis, isolated from a Swiss patient exposed in Africa.

    PubMed

    Pfyffer, G E; Auckenthaler, R; van Embden, J D; van Soolingen, D

    1998-01-01

    An exceptionally smooth and glossy morphotype of Mycobacterium tuberculosis complex was isolated from a 56-year-old Swiss patient with mesenteric tuberculosis. Direct 16S rRNA sequence analysis of the hypervariable signature gene regions revealed a 100% homology to the specific M. tuberculosis complex sequence. Spoligotyping and restriction fragment length polymorphism analyses using the insertion sequences IS6110 and IS1081 and the polymorphic GC-rich sequence as additional genetic markers identified the isolate as the novel taxon M. canettii. Like a Somali child with a similar case, this patient probably contracted the infection in Africa, which raises questions about the geographic distribution of M. canettii. PMID:9866740

  19. Genetic Diversity of Tropical Isolates and Color Variants of Aureobasidium pullulans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The polymorphic fungus Aureobasidium pullulans was isolated from many provinces in tropical Thailand and cultured in pullulan production medium (PM) containing sucrose and peptone as carbon and nitrogen sources, respectively. Liquid PM cultures varied in color from cream to pale pink, light burgund...

  20. Isolation of Two Plaque Variants from the Adenovirus Type 2-Simian Virus 40 Hybrid Population Which Differ in Their Efficiency in Yielding Simian Virus 40

    PubMed Central

    Lewis, Andrew M.; Rowe, Wallace P.

    1970-01-01

    Studies on the adenovirus type 2-simian virus 40 (SV40) hybrid population demonstrated two genetically stable variants within this population, which were isolated by plaquing in African green monkey kidney cells. These variants were similar in that each induced SV40 T antigen in human embryonic kidney cells and contained similar concentrations of nonhybrid adenovirus type 2 virions and adenovirus-encapsidated particles containing the infectious SV40 genome. These variants differed markedly, however, in their ability to produce SV40 viral antigen in human embryonic kidney cells and the efficiency with which they produce SV40 plaques in monkey cell monolayers. It is postulated that the differences in SV40-yielding efficiency between these variants lie in the nature of the recombinant deoxyribonucleic acid composing the genome of the hybrid particles. PMID:4318083

  1. De Novo Copy Number Variants Identify New Genes and Loci in Isolated, Sporadic Tetralogy of Fallot

    PubMed Central

    Greenway, Steven C; Pereira, Alexandre C; Lin, Jennifer C; DePalma, Steven R; Israel, Samuel J; Mesquita, Sonia M; Ergul, Emel; Conta, Jessie R; Korn, Joshua M; McCarroll, Steven A; Gorham, Joshua M; Gabriel, Stacey; Altshuler, David A; de Lourdes Quintanilla-Dieck, Maria; Artunduaga, Maria Alexandra; Eavey, Roland D; Plenge, Robert M; Shadick, Nancy A; Weinblatt, Michael E; De Jager, Philip L; Hafler, David A; Breitbart, Roger E; Seidman, J G; Seidman, Christine E

    2009-01-01

    Tetralogy of Fallot (TOF), the most common severe congenital heart malformation, occurs sporadically, without other anomaly, and from unknown cause in 70% of cases. A genome-wide survey of 114 TOF patients and their unaffected parents identified 11 de novo copy number variants (CNVs) that were absent or extremely rare (<0.1%) in 2,265 controls. A second, independent TOF cohort (n = 398) was then examined for additional CNVs at these loci. In 1% (5/512, p = 0.0002, OR = 22.3) of non-syndromic sporadic TOF cases we identified CNVs at chromosome 1q21.1. Recurrent CNVs were also identified at 3p25.1, 7p21.3 and 22q11.2. CNVs in a single TOF case occurred at six loci, two that encode known (NOTCH1, JAG1) disease genes. Our data predicts that at least 10% (4.5–15.5, 95% CI) of sporadic, non-syndromic TOF reflects de novo CNVs and implicates mutations within these loci as etiologic in other cases of TOF. PMID:19597493

  2. Characterization of Staphylococcus aureus small colony variant strains isolated from Italian patients attending a regional cystic fibrosis care centre.

    PubMed

    Morelli, Patrizia; De Alessandri, Alessandra; Manno, Graziana; Marchese, Anna; Bassi, Marta; Lobello, Raffaele; Minicucci, Laura; Bandettini, Roberto

    2015-04-01

    Small colony variant (SCV) Staphylococcus aureus are a subpopulation of auxotroph, slow-growing strains causing persisting and relapsing infections in cystic fibrosis (CF) patients. Twenty-eight SCV and 29 normal S. aureus strains were isolated from 42 out of 222 Italian CF patients. The isolates were characterized for: susceptibility to antibiotics, methicillin-resistance (MR), Panton Valentine leukocidin, auxotrophy, hypermutability and biofilm formation. Clonal identity of SCV and normal strains was determined by pulsed-field gel electrophoresis. We found that 27 out of 28 SCVs were thymidine-dependent. Furthermore, in contrast to normal phenotype, SCVs were characterized by antibiotic resistance. We also found that 39.3% SCV vs 20.7% normal strains were strong mutators. Moreover, SCVs showed a higher capability to form biofilm compared to normal strains (100% vs 59%). Importantly, we found evidence of clonal spread of SCV strain among CF patients. Using molecular typing, we found that five patients shared the same type A and five out of seven MR-SCV belonged to the same clone (Clone C). The particular virulence and spreading ability of MR-SCV observed highlights the importance of accurate identification and susceptibility testing of these strains. It is important to adopt the optimal approach to treat patients and to prevent cross-infection in CF centres. PMID:25938748

  3. Draft Genome Sequence of a Bordetella pertussis Strain with the Virulence-Associated Allelic Variant ptxP3, Isolated in Italy

    PubMed Central

    Anselmo, A.; Buttinelli, G.; Ciammaruconi, A.; Midulla, F.; Nicolai, A.; Fortunato, A.; Palozzi, A.; Fillo, S.; Lista, F.

    2015-01-01

    Despite a universal immunization program, pertussis has persisted and resurged, and is of particular concern for infants in terms of morbidity and mortality. Here, we report the genome sequence a of Bordetella pertussis strain with the virulence-associated allelic variant ptxP3, isolated from a 45-day-old infant. PMID:26358588

  4. A novel cloning strategy for isolating, genotyping and phenotyping genetic variants of geminiviruses

    PubMed Central

    Urbino, Cica; Thébaud, Gael; Granier, Martine; Blanc, Stéphane; Peterschmitt, Michel

    2008-01-01

    Background Viruses of the genus Begomovirus (Geminiviridae) are emerging economically important plant viruses with a circular, single-stranded DNA genome. Previous studies have shown that geminiviruses and RNA viruses exhibit similar mutation frequencies, although geminiviruses are replicated by host DNA polymerases and RNA viruses by their own virus-encoded error-prone RNA-dependent RNA-polymerase. However, the phenotypic effects of naturally occurring mutations have never been extensively investigated in geminiviruses, particularly because, to be infectious, cloned viral genomes usually require sub-cloning as complete or partial tandem repeats into a binary vector from Agrobacterium tumefaciens. Results Using Tomato yellow leaf curl virus (TYLCV), we show here that infectivity can be obtained when only a 41-nucleotide region containing a highly conserved stem-loop is repeated. A binary vector containing this 41-nt region and a unique restriction site was created, allowing direct cloning of infectious monomeric viral genomes provided that they harbour the same restriction site at the corresponding nucleotide position. This experimental system, which can be transferable to other geminiviruses, was validated by analysis of the phenotypic effect of mutations appearing in TYLCV genomes in a single tomato host plant originally inoculated with a unique viral sequence. Fourteen full-length infectious genomes extracted from this plant were directly cloned and sequenced. The mutation frequency was 1.38 × 10-4 mutation per nucleotide sequenced, similar to that found previously for another begomovirus by sequencing PCR-amplified partial sequences. Interestingly, even in this minimal pool of analysed genomes, mutants with altered properties were readily identified, one of them being fitter and reducing plant biomass more drastically than the parental clone. Conclusion The cloning strategy presented here is useful for any extensive phenotyping of geminivirus variants and particularly of artificially generated mutants or recombinants. PMID:18976479

  5. Novel VIM metallo-beta-lactamase variant from clinical isolates of Enterobacteriaceae from Algeria.

    PubMed

    Robin, Frédéric; Aggoune-Khinache, Nadjet; Delmas, Julien; Naim, Malek; Bonnet, Richard

    2010-01-01

    Five different strains of bacteria belonging to the family Enterobacteriaceae were isolated from two patients hospitalized in the intensive care unit of the Central Military Hospital of Algiers, Algeria. All five strains, one Providencia stuartii strain, two Escherichia coli strains, and two Klebsiella pneumoniae strains, were intermediate or resistant to all beta-lactams, including carbapenems. Synergy between imipenem and EDTA was observed for all five strains. The results of the PCR experiment confirmed the presence of a bla(VIM) gene in all five strains. The bla(VIM) genes were located as part of a class 1 integron on a 180-kb conjugative plasmid. They encoded a novel metallo-beta-lactamase designated VIM-19, which differed from the parental enzyme VIM-1 by only two substitutions: Ser228Arg, previously observed in the closely related enzyme VIM-4, and Asn215Lys, not previously observed in other VIM-type carbapenemases. VIM-19 was further characterized after purification through determination of its kinetic constants. This enzyme was inhibited by EDTA and hydrolyzed penicillins, cephalosporins, and carbapenems, as observed for other VIM-type carbapenemases but with greater catalytic efficiency against penicillins than VIM-1. VIM-19 is the first carbapenemase enzyme identified from an isolate from Algeria. These results confirm the emergence of VIM-4-like enzymes in members of the family Enterobacteriaceae from Mediterranean countries. PMID:19901092

  6. Isolation of sulfite reductase variants of a commercial wine yeast with significantly reduced hydrogen sulfide production.

    PubMed

    Cordente, Antonio G; Heinrich, Anthony; Pretorius, Isak S; Swiegers, Jan H

    2009-05-01

    The production of hydrogen sulfide (H(2)S) during fermentation is a common and significant problem in the global wine industry as it imparts undesirable off-flavors at low concentrations. The yeast Saccharomyces cerevisiae plays a crucial role in the production of volatile sulfur compounds in wine. In this respect, H(2)S is a necessary intermediate in the assimilation of sulfur by yeast through the sulfate reduction sequence with the key enzyme being sulfite reductase. In this study, we used a classical mutagenesis method to develop and isolate a series of strains, derived from a commercial diploid wine yeast (PDM), which showed a drastic reduction in H(2)S production in both synthetic and grape juice fermentations. Specific mutations in the MET10 and MET5 genes, which encode the catalytic alpha- and beta-subunits of the sulfite reductase enzyme, respectively, were identified in six of the isolated strains. Fermentations with these strains indicated that, in comparison with the parent strain, H(2)S production was reduced by 50-99%, depending on the strain. Further analysis of the wines made with the selected strains indicated that basic chemical parameters were similar to the parent strain except for total sulfite production, which was much higher in some of the mutant strains. PMID:19236486

  7. Concomitant Isolation of the Pulmonary Veins and Posterior Wall Using a Box Lesion Set in a Patient with Persistent Atrial Fibrillation and Variant Pulmonary Venous Anatomy.

    PubMed

    Roberts, Jason D; Gerstenfeld, Edward P

    2016-03-01

    Variant pulmonary venous anatomy is common and its pre-procedural recognition through cardiac imaging facilitates a personalized approach to ablation tailored to the individual patient. Close juxtaposition of the right and left pulmonary veins is an anatomic variation that serves as an ideal substrate for creation of a single box lesion set that concomitantly isolates the pulmonary veins and posterior wall. Isolation of the posterior wall may serve as an adjunctive ablative strategy in addition to pulmonary vein isolation that facilitates maintenance of sinus rhythm among patients with persistent atrial fibrillation. PMID:26920183

  8. A novel experimental platform for toxigenic and non-toxigenic Corynebacterium ulcerans infection in mice.

    PubMed

    Mochizuki, Yu; Saeki, Honami; Iwaki, Masaaki; Takagi, Hitrotaka; Shibayama, Keigo; Amao, Hiromi; Yamamoto, Akihiko

    2016-03-01

    Corynebacterium ulcerans is a zoonotic pathogen that can produce diphtheria toxin and causes an illness categorized as diphtheria in the European Union because its clinical appearance is similar to that of diphtheria caused by Corynebacterium diphtheriae. Despite the importance of the pathogen in public health, the organism's mechanism of infection has not been extensively studied, especially in experimental animal models. Therefore in the present study we constructed an intranasal infection system for mice. Mice are insensitive to diphtheria toxin and this has the advantage of excluding the cytotoxic effect of the toxin that might interfere with the analysis of the early stage of infection. Both the toxigenic and non-toxigenic C. ulcerans strains were capable of killing mice within 3 days after inoculation at 10(7) colony-forming units per mouse. In experimentally infected animals, C. ulcerans was detected in the respiratory tract but not in the intestinal tract. The bacterium was also detected in peripheral blood and it disseminated into the lung, kidney and spleen to produce a systemic infection. This experimental infection system provides a platform for analyzing the virulence of C. ulcerans in future studies. PMID:26607400

  9. Isolation of two physiologically induced variant strains of Bacillus stearothermophilus NRS 2004/3a and characterization of their S-layer lattices.

    PubMed Central

    Sára, M; Pum, D; Küpcü, S; Messner, P; Sleytr, U B

    1994-01-01

    During growth of Bacillus stearothermophilus NRS 2004/3a in continuous culture on complex medium, the chemical properties of the S-layer glycoprotein and the characteristic oblique lattice were maintained only if glucose was used as the sole carbon source. With increased aeration, amino acids were also metabolized, accompanied by liberation of ammonium and by changes in the S-layer protein. Depending on the stage of fermentation at which oxygen limitation was relieved, two different variants, one with a more delicate oblique S-layer lattice (variant 3a/V1) and one with a square S-layer lattice (variant 3a/V2), were isolated. During the switch from the wild-type strain to a variant or from variant 3a/V2 to variant 3a/V1, monolayers of two types of S-layer lattices could be demonstrated on the surfaces of single cells. S-layer proteins from variants had different molecular sizes and a significantly lower carbohydrate content than S-layer proteins from the wild-type strain did. Although the S-layer lattices from the wild-type and variant strains showed quite different protein mass distributions in two- and three-dimensional reconstructions, neither the amino acid composition nor the pore size, as determined by permeability studies, was significantly changed. Peptide mapping and N-terminal sequencing results strongly indicated that the three S-layer proteins are encoded by different genes and are not derived from a universal precursor form. Images PMID:8300538

  10. A major EBNA1 variant from Asian EBV isolates shows enhanced transcriptional activity compared to prototype B95.8.

    PubMed

    Do, Nguyen-Van; Ingemar, Ernberg; Phi, Phan-Thi Phi; Jenny, Almqvist; Chinh, Tran-Thi; Zeng, Yixin; Hu, Lifu

    2008-03-01

    Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) has an instrumental role in maintaining EBV latent infection by controlling EBV episome replication and regulating viral transcription. It is a ubiquitously expressed protein during latent viral infection and in EBV-associated tumors. The EBNA1 C-terminus interacts functionally with the Qp and Cp that control viral gene expression in latency I/II and III, respectively. EBNA1 has been classified into five subtypes due to sequence variation in the DNA-interacting C-terminus. By DNA sequence analysis of its C-terminus, we detected a main sub-variant (V-val-v1) of EBNA1 with valine located in both positions 487 and 528 from matched samples including NPC biopsies and peripheral blood taken from Vietnamese (9), Chinese (12) NPC patients and healthy donors (5). In the FR-region of oriP from nine NPC biopsies from Vietnam we also frequently found substitutions, deletions and variable numbers of repeats. Using a luciferase reporter system, EBNA1 and FR both derived from Asian isolates induced higher transcriptional activity than those from B95-8 virus. PMID:18096263

  11. Variants of Coconut cadang-cadang viroid isolated from an African oil palm (Elaies guineensis Jacq.) in Malaysia.

    PubMed

    Vadamalai, G; Hanold, D; Rezaian, M A; Randles, J W

    2006-07-01

    Variants of Coconut cadang-cadang viroid have been identified in a plantation oil palm growing in Malaysia. Three size classes are described, comprising 297, 293, and 270 nt. Compared with the 296-nt form of coconut cadang-cadang viroid (CCCVd), all variants substituted C31 --> U in the pathogenicity domain and A175 --> C in the right-hand terminus. Other mutations and deletions accounted for the different sizes. These are the first sequences reported for variants of Coconut cadang-cadang viroid in a species other than coconut palm, and this is the first evidence that variants closely related to CCCVd occur outside the Philippines. PMID:16470341

  12. The Kiss2 receptor (Kiss2r) gene in Southern Bluefin Tuna, Thunnus maccoyii and in Yellowtail Kingfish, Seriola lalandi - functional analysis and isolation of transcript variants.

    PubMed

    Nocillado, J N; Biran, J; Lee, Y Y; Levavi-Sivan, B; Mechaly, A S; Zohar, Y; Elizur, A

    2012-10-15

    The kisspeptin system plays an essential role in reproductive function in vertebrates, particularly in the onset of puberty. We investigated the kisspeptin system in two Perciform teleosts, the Southern Bluefin Tuna (SBT; Thunnus maccoyii), and the Yellowtail Kingfish (YTK; Seriola lalandi), by characterising their kisspeptin 2 receptor (Kiss2r) genes. In addition to the full length Kiss2r cDNA sequences, we have isolated from SBT and YTK a transcript variant that retained an intron. We have further obtained three ytkKiss2r transcript variants that contained deletions. In vitro functional analysis of the full length SBT and YTK Kiss2r showed higher response to Kiss2-10 than to Kiss1-10, with stronger transduction via PKC than PKA. The full length ytkKiss2r and two deletion variants were differentially expressed in the brain of male, but not in female, juvenile YTK treated with increasing doses of Kiss2-10 peptide. In the gonads, the expression level of the ytkKiss2r transcripts did not vary significantly either in the male or female fish. This is the first time that transcript variants of the Kiss2r gene that contain deletions and show responsiveness to treatments with kisspeptin have been reported in any teleost. PMID:22824208

  13. A cleavable ligand column for the rapid isolation of large quantities of homogeneous and functional neurotensin receptor 1 variants from E. coli.

    PubMed

    Egloff, Pascal; Deluigi, Mattia; Heine, Philipp; Balada, Stefanie; Plückthun, Andreas

    2015-04-01

    G protein-coupled receptors (GPCRs) are key players of cell signaling, thus representing important drug targets for the treatment of human diseases. Since inherent difficulties in receptor production and handling have precluded the application of many in vitro experiments, major questions about GPCR mechanisms and dynamics remain elusive to date. We recently used directed evolution in Escherichia coli on neurotensin receptor 1 (NTR1) for the generation of GPCR variants with greatly elevated functional expression levels and with excellent stability in detergent micelles. In this work we outline a highly efficient purification method for our evolved receptor variants, which is based on the application of an inexpensive, disposable high-affinity ligand column as the initial purification step. The ligand resin allows isolation of correctly folded GPCR variants directly from whole E. coli cell lysates at the scale of 10mg and it permits preparations of agonist- and antagonist-bound receptor samples. The purification principle presented here was key to the first structures of signaling-active NTR1 variants (Egloff et al., 2014). Since E. coli is uniquely suitable for the production of fully deuterated proteins, our method provides the basis for an array of NMR experiments that were not feasible for GPCRs to date, but which will shed light on novel aspects of receptor function and dynamics. PMID:25461958

  14. Clinical Isolates of Vibrio cholerae O1 El Tor Ogawa of 2009 from Kolkata, India: Preponderance of SXT Element and Presence of Haitian ctxB Variant

    PubMed Central

    Kutar, Braj M. R. N. S.; Rajpara, Neha; Upadhyay, Hardik; Ramamurthy, Thandavarayan; Bhardwaj, Ashima K.

    2013-01-01

    Background Increase in the number of multidrug resistant pathogens and the accompanied rise in case fatality rates has hampered the treatment of many infectious diseases including cholera. Unraveling the mechanisms responsible for multidrug resistance in the clinical isolates of Vibrio cholerae would help in understanding evolution of these pathogenic bacteria and their epidemic potential. This study was carried out to identify genetic factors responsible for multiple drug resistance in clinical isolates of Vibrio cholerae O1, serotype Ogawa, biotype El Tor isolated from the patients admitted to the Infectious Diseases Hospital, Kolkata, India, in 2009. Methodology/Principal Findings One hundred and nineteen clinical isolates of V. cholerae were analysed for their antibiotic resistance phenotypes. Antibiogram analysis revealed that majority of the isolates showed resistance to co-trimoxazole, nalidixic acid, polymixin B and streptomycin. In PCR, SXT integrase was detected in 117 isolates and its sequence showed 99% identity notably to ICEVchInd5 from Sevagram, India, ICEVchBan5 from Bangladesh and VC1786ICE sequence from Haiti outbreak among others. Antibiotic resistance traits corresponding to SXT element were transferred from the parent Vibrio isolate to the recipient E. coli XL-1 Blue cells during conjugation. Double-mismatch-amplification mutation assay (DMAMA) revealed the presence of Haitian type ctxB allele of genotype 7 in 55 isolates and the classical ctxB allele of genotype 1 in 59 isolates. Analysis of topoisomerase sequences revealed the presence of mutation Ser83 ? Ile in gyrA and Ser85? Leu in parC. This clearly showed the circulation of SXT-containing V. cholerae as causative agent for cholera in Kolkata. Conclusions There was predominance of SXT element in these clinical isolates from Kolkata region which also accounted for their antibiotic resistance phenotype typical of this element. DMAMA PCR showed them to be a mixture of isolates with different ctxB alleles like classical, El Tor and Haitian variants. PMID:23431378

  15. Holotoxin Activity of Botulinum Neurotoxin Subtype A4 Originating from a Nontoxigenic Clostridium botulinum Expression System

    PubMed Central

    Bradshaw, Marite; Tepp, William H.; Whitemarsh, Regina C. M.; Pellett, Sabine

    2014-01-01

    Clostridium botulinum subtype A4 neurotoxin (BoNT/A4) is naturally expressed in the dual-toxin-producing C. botulinum strain 657Ba at 100× lower titers than BoNT/B. In this study, we describe purification of recombinant BoNT/A4 (rBoNT/A4) expressed in a nonsporulating and nontoxigenic C. botulinum expression host strain. The rBoNT/A4 copurified with nontoxic toxin complex components provided in trans by the expression host and was proteolytically cleaved to the active dichain form. Activity of the recombinant BoNT/A4 in mice and in human neuronal cells was about 1,000-fold lower than that of BoNT/A1, and the recombinant BoNT/A4 was effectively neutralized by botulism heptavalent antitoxin. A previous report using recombinant truncated BoNT/A4 light chain (LC) expressed in Escherichia coli has indicated reduced stability and activity of BoNT/A4 LC compared to BoNT/A1 LC, which was surmounted by introduction of a single-amino-acid substitution, I264R. In order to determine whether this mutation would also affect the holotoxin activity of BoNT/A4, a recombinant full-length BoNT/A4 carrying this mutation as well as a second mutation predicted to increase solubility (L260F) was produced in the clostridial expression system. Comparative analyses of the in vitro, cellular, and in vivo activities of rBoNT/A4 and rBoNT/A4-L260F I264R showed 1,000-fold-lower activity than BoNT/A1 in both the mutated and nonmutated BoNT/A4. This indicates that these mutations do not alter the activity of BoNT/A4 holotoxin. In summary, a recombinant BoNT from a dual-toxin-producing strain was expressed and purified in an endogenous clostridial expression system, allowing analysis of this toxin. PMID:25239905

  16. In vitro Isolation and Identification of Human Immunodeficiency Virus (HIV) Variants with Reduced Sensitivity to C-2 Symmetrical Inhibitors of HIV Type 1 Protease

    NASA Astrophysics Data System (ADS)

    Otto, M. J.; Garber, S.; Winslow, D. L.; Reid, C. D.; Aldrich, P.; Jadhav, P. K.; Patterson, C. E.; Hodge, C. N.; Cheng, Y.-S. E.

    1993-08-01

    Protease inhibitors are another class of compounds for treatment of human immunodeficiency virus (HIV)-caused disease. The emergence of resistance to the current anti-HIV drugs makes the determination of potential resistance to protease inhibitors imperative. Here we describe the isolation of an HIV type 1 (HIV-1) resistant to an HIV-protease inhibitor. Serial passage of HIV-1 (strain RF) in the presence of the inhibitor, [2-pyridylacetylisoleucylphenylalanyl-psi(CHOH)]_2 (P9941), failed to yield a stock of virus with a resistance phenotype. However, variants of the virus with 6- to 8-fold reduced sensitivity to P9941 were selected by using a combination of plaque assay and endpoint titration. Genetic analysis and computer modeling of the variant proteases revealed a single change in the codon for amino acid 82 (Val -> Ala), which resulted in a protease with lower affinity and reduced sensitivity to this inhibitor and certain, but not all, related inhibitors.

  17. A rapid and simple method for the isolation of mutant variants regulating tissue-specific expression of the TnI gene through drug selection

    SciTech Connect

    Lee, Youngwon; Kim, Myoung Hee; Emerson, C.P. Jr.

    1995-12-01

    TnINEO fusion gene was constructed by fusing 3.4-kbp of quail TnI genomic DNA sequences spanning the promoter to exon 5 and a neo gene in frame. A myoblast cell line was established after transfection of pTnINEO. Since this cell line was passaged several times, a high frequency of neomycin (G418) sensitivity conversion was detected. Two drug-resistant variants were analyzed through genomic Southern blot and S1 nuclease protection assay. One variant has a mutation(s) in the regulatory element that activated the dormant TnI promoter-enhancer in myoblast, and the other has shown the geonomic rearrangement. This result presented the possibility of isolating factor(s) that activate the muscle-specific TnI promoter simply by screening drug-resistant cells having appropriate mutations. 12 refs., 4 fig.

  18. Prevalence of Smqnr and plasmid-mediated quinolone resistance determinants in clinical isolates of Stenotrophomonas maltophilia from Japan: novel variants of Smqnr

    PubMed Central

    Kanamori, H.; Yano, H.; Tanouchi, A.; Kakuta, R.; Endo, S.; Ichimura, S.; Ogawa, M.; Shimojima, M.; Inomata, S.; Ozawa, D.; Aoyagi, T.; Weber, D.J.; Kaku, M.

    2015-01-01

    Stenotrophomonas maltophilia is an important pathogen in healthcare-associated infections. S. maltophilia may contain Smqnr, a quinolone resistance gene encoding the pentapeptide repeat protein, which confers low-level quinolone resistance upon expression in a heterologous host. We investigated the prevalence of Smqnr and plasmid-mediated quinolone resistance (PMQR) determinants in S. maltophilia isolates from Japan. A total of 181 consecutive and nonduplicate clinical isolates of S. maltophilia were collected from four areas of Japan. The antimicrobial susceptibility profiles for these strains were determined. PCR was conducted for Smqnr and PMQR genes, including qnrA, qnrB, qnrC, qnrS,aac(6?)-Ib and qepA. PCR products for Smqnr and aac(6?)-Ib were sequenced. For the S. maltophilia isolates containing Smqnr, pulsed-field gel electrophoresis (PFGE) was performed using XbaI. Resistance rates to ceftazidime, levofloxacin, trimethoprim–sulfamethoxazole, chloramphenicol and minocycline were 67.4%, 6.1%, 17.7%, 8.8% and 0%, respectively. The minimum inhibitory concentration required to inhibit the growth of 50% and 90% of organisms were 0.5 and 2 mg/L for moxifloxacin but 1 and 4 mg/L for levofloxacin, respectively. Smqnr was detected in 104 of the 181 S. maltophilia isolates (57.5%), and the most frequent was Smqnr6, followed by Smqnr8 and Smqnr11. Eleven novel variants from Smqnr48 to Smqnr58 were detected. The 24 Smqnr-containing S. maltophilia isolates were typed by PFGE and divided into 21 unique types. Nine S. maltophilia isolates (5.0%) carried aac(6?)-Ib-cr. No qnr or qepA genes were detected. This study describes a high prevalence of Smqnr and novel variants of Smqnr among S. maltophilia from Japan. Continuous antimicrobial surveillance and further molecular epidemiological studies on quinolone resistance in S. maltophilia are needed. PMID:26110061

  19. Prevalence and genetic diversity of arginine catabolic mobile element (ACME) in clinical isolates of coagulase-negative staphylococci: identification of ACME type I variants in Staphylococcus epidermidis.

    PubMed

    Onishi, Mayumi; Urushibara, Noriko; Kawaguchiya, Mitsuyo; Ghosh, Souvik; Shinagawa, Masaaki; Watanabe, Naoki; Kobayashi, Nobumichi

    2013-12-01

    Arginine catabolic mobile element (ACME), a genomic island consisting of the arc and/or opp3 gene clusters found in staphylococcal species, is related to increased bacterial adaptability to hosts. Staphylococcus epidermidis is considered a major ACME reservoir; however, prevalence and genetic diversity of ACME in coagulase-negative staphylococci (CNS) have not yet been well characterized for clinical isolates in Japan. A total of 271 clinical isolates of CNS in a Japanese hospital were investigated for the presence and genotype of ACME and SCCmec. The prevalence of ACME-arcA was significantly higher (p<0.001) in S. epidermidis (45.8%) than in other CNS species (3.7%). ACME in S. epidermidis isolates (n=87) were differentiated into type I (n=33), variant forms of type I (?I, n=26) newly identified in this study, type II (n=6), and type ?II (n=19). ACME-type ?I, which were further classified into three subtypes, lacked some genetic components between the arc and opp3 clusters in archetypal type I, whereas the arc and opp3 clusters were intact. The arc cluster exhibited high sequence identity (95.8-100%) to that of type I ACME; in contrast, the opp3 cluster was highly diverse, and showed relatively lower identities (94.8-98.7%) to the identical regions in type I ACME. Twenty-one isolates of ?I ACME-carrying S. epidermidis possessed SCCmec IVa and belonged to ST5 (clonal complex 2). Phylogenetic analysis revealed that isolates harboring ACME ?I in this study clustered with previously reported S. epidermidis strains with other lineges, suggesting that S. epidermidis originally had some genetic variations in the opp3 cluster. In summary, ACME type ?I, a truncated variant of ACME-I, was first identified in S. epidermidis, and revealed to be prevalent in ST5 MRSE clinical isolates with SCCmec IVa. PMID:24113082

  20. Aminoglycoside 6?-N-Acetyltransferase Variants of the Ib Type with Altered Substrate Profile in Clinical Isolates of Enterobacter cloacae and Citrobacter freundii

    PubMed Central

    Casin, Isabelle; Bordon, Florence; Bertin, Philippe; Coutrot, Anne; Podglajen, Isabelle; Brasseur, Robert; Collatz, Ekkehard

    1998-01-01

    Three clinical isolates, Enterobacter cloacae EC1562 and EC1563 and Citrobacter freundii CFr564, displayed an aminoglycoside resistance profile evocative of low-level 6?-N acetyltransferase type II [AAC(6?)-II] production, which conferred reduced susceptibility to gentamicin but not to amikacin or isepamicin. Aminoglycoside acetyltransferase assays suggested the synthesis in the three strains of an AAC(6?) which acetylated amikacin practically as well as it acetylated gentamicin in vitro. Both compounds, however, as well as isepamicin, retained good bactericidal activity against the three strains. The aac genes were borne by conjugative plasmids (pLMM562 and pLMM564 of ca. 100 kb and pLMM563 of ca. 20 kb). By PCR mapping and nucleotide sequence analysis, an aac(6?)-Ib gene was found in each strain upstream of an ant(3")-I gene in a sulI-type integron. The size of the AAC(6?)-Ib variant encoded by pLMM562 and pLMM564, AAC(6?)-Ib7, was deduced to be 184 (or 177) amino acids long, whereas in pLMM563 a 21-bp duplication allowing the recruitment of a start codon resulted in the translation of a variant, AAC(6?)-Ib8, of 196 amino acids, in agreement with size estimates obtained by Western blot analysis. Both variants had at position 119 a serine instead of the leucine typical for the AAC(6?)-Ib variants conferring resistance to amikacin. By using methods that predict the secondary structure, these two amino acids appear to condition an ?-helical structure within a putative aminoglycoside binding domain of AAC(6?)-Ib variants. PMID:9527761

  1. Clostridium botulinum Group II Isolate Phylogenomic Profiling Using Whole-Genome Sequence Data

    PubMed Central

    Weedmark, K. A.; Mabon, P.; Hayden, K. L.; Lambert, D.; Van Domselaar, G.; Austin, J. W.

    2015-01-01

    Clostridium botulinum group II isolates (n = 163) from different geographic regions, outbreaks, and neurotoxin types and subtypes were characterized in silico using whole-genome sequence data. Two clusters representing a variety of botulinum neurotoxin (BoNT) types and subtypes were identified by multilocus sequence typing (MLST) and core single nucleotide polymorphism (SNP) analysis. While one cluster included BoNT/B4/F6/E9 and nontoxigenic members, the other comprised a wide variety of different BoNT/E subtype isolates and a nontoxigenic strain. In silico MLST and core SNP methods were consistent in terms of clade-level isolate classification; however, core SNP analysis showed higher resolution capability. Furthermore, core SNP analysis correctly distinguished isolates by outbreak and location. This study illustrated the utility of next-generation sequence-based typing approaches for isolate characterization and source attribution and identified discrete SNP loci and MLST alleles for isolate comparison. PMID:26116673

  2. Clostridium botulinum Group II Isolate Phylogenomic Profiling Using Whole-Genome Sequence Data.

    PubMed

    Weedmark, K A; Mabon, P; Hayden, K L; Lambert, D; Van Domselaar, G; Austin, J W; Corbett, C R

    2015-09-01

    Clostridium botulinum group II isolates (n = 163) from different geographic regions, outbreaks, and neurotoxin types and subtypes were characterized in silico using whole-genome sequence data. Two clusters representing a variety of botulinum neurotoxin (BoNT) types and subtypes were identified by multilocus sequence typing (MLST) and core single nucleotide polymorphism (SNP) analysis. While one cluster included BoNT/B4/F6/E9 and nontoxigenic members, the other comprised a wide variety of different BoNT/E subtype isolates and a nontoxigenic strain. In silico MLST and core SNP methods were consistent in terms of clade-level isolate classification; however, core SNP analysis showed higher resolution capability. Furthermore, core SNP analysis correctly distinguished isolates by outbreak and location. This study illustrated the utility of next-generation sequence-based typing approaches for isolate characterization and source attribution and identified discrete SNP loci and MLST alleles for isolate comparison. PMID:26116673

  3. First isolation of oleate-dependent Enterococcus faecalis small-colony variants from the umbilical exudate of a paediatric patient with omphalitis.

    PubMed

    Kubota, Noriko; Kuzumoto, Kei; Hidaka, Eiko; Yoshizawa, Katsumi; Yumoto, Kayoko; Oana, Kozue; Ogiso, Yoshifumi; Nakamura, Tomohiko; Kawakami, Yoshiyuki

    2013-12-01

    An oleate-dependent Enterococcus faecalis isolate representing small-colony variants (SCVs) was isolated from the umbilical exudate of a 31-month-old Japanese male patient in Nagano Children's Hospital, Azumino, Japan. The patient had been suffering from recurrent omphalitis since early infancy. The initial E. faecalis SCV isolate formed small colonies on sheep blood agar plates and tiny colonies on chocolate and modified Drigalski agar, although no visible growth was observed in HK-semi solid medium after 48 h incubation in ambient air. Moreover, the SCV isolate, the colonial morphology of which was reminiscent of Streptococcus species, could not be identified using the MicroScan WalkAway-40 and API 20 Strep systems, both of which yielded profile numbers that did not correspond to any bacterial species, probably as a result of insufficient growth of the isolate. The SCV isolate was subsequently identified as E. faecalis based on its morphological, cultural and biochemical properties, and this was confirmed by sequencing the 16S rRNA gene of the organism. Investigations revealed that the addition of oleate, an unsaturated fatty acid, enabled the isolate to grow on every medium with normal-sized colony morphology. Although it has long been known that long-chain fatty acids, especially unsaturated oleic acid, have a major inhibitory effect on the growth of a variety of microorganisms, including not only mycobacteria but also streptococci, this is, to the best of our knowledge, the first clinical isolation of an oleate-dependent E. faecalis SCV isolate. In addition, oleic acid might be considered to affect the cell membrane permeability of carbohydrates or antimicrobial agents such as β-lactams. PMID:24072765

  4. An Atypical Clostridium Strain Related to the Clostridium botulinum Group III Strain Isolated from a Human Blood Culture

    PubMed Central

    Ruimy, Raymond; Bouchier, Christiane; Faucher, Nathalie; Mazuet, Christelle; Popoff, Michel R.

    2014-01-01

    A nontoxigenic strain isolated from a fatal human case of bacterial sepsis was identified as a Clostridium strain from Clostridium botulinum group III, based on the phenotypic characters and 16S rRNA gene sequence, and was found to be related to the mosaic C. botulinum D/C strain according to a multilocus sequence analysis of 5 housekeeping genes. PMID:24088855

  5. NDM-12, a Novel New Delhi Metallo-?-Lactamase Variant from a Carbapenem-Resistant Escherichia coli Clinical Isolate in Nepal

    PubMed Central

    Tada, Tatsuya; Shrestha, Basudha; Miyoshi-Akiyama, Tohru; Shimada, Kayo; Ohara, Hiroshi; Pokhrel, Bharat M.

    2014-01-01

    A novel New Delhi metallo-?-lactamase variant, NDM-12, was identified in a carbapenem-resistant Escherichia coli clinical isolate obtained from a urine sample from a patient in Nepal. NDM-12 differed from NDM-1 by two amino acid substitutions (M154L and G222D). The enzymatic activities of NDM-12 against ?-lactams were similar to those of NDM-1, although NDM-12 showed lower kcat/Km ratios for all ?-lactams tested except doripenem. The blaNDM-12 gene was located in a plasmid of 160 kb. PMID:25092693

  6. Molecular characterization and expression of buffalo (Bubalus bubalis) DEAD-box family VASA gene and mRNA transcript variants isolated from testis tissue.

    PubMed

    Kaushik, Ramakant; Singh, Karn Pratap; Bahuguna, Vivek; Rameshbabu, K; Singh, Manoj Kumar; Manik, Radhey Shyam; Palta, Prabhat; Singla, Suresh Kumar; Chauhan, Manmohan Singh

    2015-11-01

    VASA is a member of the DEAD-box protein family that plays an indispensable role in mammalian spermatogenesis, particularly during meiosis. In the present study, we isolated, sequenced, and characterized VASA gene in buffalo testis. Here, we demonstrated that VASA mRNA is expressed as multiple isoforms and uses four alternative transcriptional start sites (TSSs) and four different polyadenylation sites. The TSSs identified by 5'-RNA ligase-mediated rapid amplification of cDNA ends (RLM-5'-RACE) were positioned at 48, 53, 85, and 88 nucleotides upstream relative to the translation initiation codon. 3'-RACE experiment revealed the presence of tandem polyadenylation signals, which lead to the expression of at least four different 3'-untranslated regions (209, 233, 239 and 605 nucleotides). The full-length coding region of VASA was 2190 bp, which encodes a 729 amino acid (aa) protein containing nine consensus regions of the DEAD box protein family. VASA variants are highly expressed in testis of adult buffalo. We found five variants, one full length VASA (729 aa) and four splice variants VASA 2, 4, 5, 6 (683, 685, 679, 703 aa). The expression level of VASA 1 was significantly higher than rest of all (P < 0.05) except VASA 6. The relative ratio for VASA 1:2:4:5:6 was 100:1.0:1.6:0.9:48. PMID:26127001

  7. Isolation and functional assessment of common, polymorphic variants of the B-MYB proto-oncogene associated with a reduced cancer risk.

    PubMed

    Schwab, R; Bussolari, R; Corvetta, D; Chayka, O; Santilli, G; Kwok, J M-M; Ferrari-Amorotti, G; Amorotti, G F; Tonini, G P; Iacoviello, L; Bertorelle, R; Menin, C; Hubank, M; Calabretta, B; Sala, A

    2008-05-01

    The B-MYB proto-oncogene is a transcription factor belonging to the MYB family that is frequently overexpressed or amplified in different types of human malignancies. While it is suspected that B-MYB plays a role in human cancer, there is still no direct evidence of its causative role. Looking for mutations of the B-MYB gene in human cell lines and primary cancer samples, we frequently isolated two nonsynonymous B-MYB polymorphic variants (rs2070235 and rs11556379). Compared to the wild-type protein, the B-MYB isoforms display altered conformation, impaired regulation of target genes and decreased antiapoptotic activity, suggesting that they are hypomorphic variants of the major allele. Importantly, the B-MYB polymorphisms are common; rs2070235 and rs11556379 are found, depending on the ethnic background, in 10-50% of human subjects. We postulated that, if B-MYB activity is important for transformation, the presence of common, hypomorphic variants might modify cancer risk. Indeed, the B-MYB polymorphisms are underrepresented in 419 cancer patients compared to 230 controls (odds ratio 0.53; (95%) confidence interval 0.385-0.755; P=0.001). This data imply that a large fraction of the human population is carrier of B-MYB alleles that might be associated with a reduced risk of developing neoplastic disease. PMID:18026132

  8. Characterization of a variant of human T-lymphotropic virus type I isolated from a healthy member of a remote, recently contacted group in Papua New Guinea.

    PubMed Central

    Yanagihara, R; Nerurkar, V R; Garruto, R M; Miller, M A; Leon-Monzon, M E; Jenkins, C L; Sanders, R C; Liberski, P P; Alpers, M P; Gajdusek, D C

    1991-01-01

    We report the characterization of a variant of human T-lymphotropic virus type I (HTLV-I) isolated from an interleukin 2-dependent, CD8+ T-cell line derived from peripheral blood mononuclear cells of a healthy member of a remote, recently contacted hunter-horticulturalist group (Hagahai) in Madang province of Papua New Guinea. Antigenic characterization of this variant, designated PNG-1, by immunofluorescence, indicated no expression of gag-encoded proteins p19 and p24 (even after incubation with 5-bromo-2'-deoxyuridine), using monoclonal and polyclonal antibodies against HTLV-I gag gene products. Virus-specific proteins of 15, 19, 46, 53, and 61/68 kDa were demonstrated by Western blot analysis, using sera from patients with serologically and/or virologically confirmed HTLV-I myeloneuropathy, sera from HTLV-I-infected rabbits, and antibodies prepared against the C terminus of the major envelope glycoprotein gp46. Restriction endonuclease maps of PNG-1 proviral DNA differed from that of a prototype strain of HTLV-I (MT-2), but, as verified by polymerase chain reaction, PNG-1 was definitely HTLV-I, not HTLV-II. Nucleotide sequencing and further molecular genetic studies of this variant may provide insights into the origin and evolution of HTLV-I. Images PMID:1996344

  9. A novel triplex quantitative PCR strategy for quantification of toxigenic and nontoxigenic Vibrio cholerae in aquatic environments.

    PubMed

    Bliem, Rupert; Schauer, Sonja; Plicka, Helga; Obwaller, Adelheid; Sommer, Regina; Steinrigl, Adolf; Alam, Munirul; Reischer, Georg H; Farnleitner, Andreas H; Kirschner, Alexander

    2015-05-01

    Vibrio cholerae is a severe human pathogen and a frequent member of aquatic ecosystems. Quantification of V. cholerae in environmental water samples is therefore fundamental for ecological studies and health risk assessment. Beside time-consuming cultivation techniques, quantitative PCR (qPCR) has the potential to provide reliable quantitative data and offers the opportunity to quantify multiple targets simultaneously. A novel triplex qPCR strategy was developed in order to simultaneously quantify toxigenic and nontoxigenic V. cholerae in environmental water samples. To obtain quality-controlled PCR results, an internal amplification control was included. The qPCR assay was specific, highly sensitive, and quantitative across the tested 5-log dynamic range down to a method detection limit of 5 copies per reaction. Repeatability and reproducibility were high for all three tested target genes. For environmental application, global DNA recovery (GR) rates were assessed for drinking water, river water, and water from different lakes. GR rates ranged from 1.6% to 76.4% and were dependent on the environmental background. Uncorrected and GR-corrected V. cholerae abundances were determined in two lakes with extremely high turbidity. Uncorrected abundances ranged from 4.6×10(2) to 2.3×10(4) cell equivalents liter(-1), whereas GR-corrected abundances ranged from 4.7×10(3) to 1.6×10(6) cell equivalents liter(-1). GR-corrected qPCR results were in good agreement with an independent cell-based direct detection method but were up to 1.6 log higher than cultivation-based abundances. We recommend the newly developed triplex qPCR strategy as a powerful tool to simultaneously quantify toxigenic and nontoxigenic V. cholerae in various aquatic environments for ecological studies as well as for risk assessment programs. PMID:25724966

  10. A Novel Triplex Quantitative PCR Strategy for Quantification of Toxigenic and Nontoxigenic Vibrio cholerae in Aquatic Environments

    PubMed Central

    Bliem, Rupert; Schauer, Sonja; Plicka, Helga; Obwaller, Adelheid; Sommer, Regina; Steinrigl, Adolf; Alam, Munirul; Reischer, Georg H.; Farnleitner, Andreas H.

    2015-01-01

    Vibrio cholerae is a severe human pathogen and a frequent member of aquatic ecosystems. Quantification of V. cholerae in environmental water samples is therefore fundamental for ecological studies and health risk assessment. Beside time-consuming cultivation techniques, quantitative PCR (qPCR) has the potential to provide reliable quantitative data and offers the opportunity to quantify multiple targets simultaneously. A novel triplex qPCR strategy was developed in order to simultaneously quantify toxigenic and nontoxigenic V. cholerae in environmental water samples. To obtain quality-controlled PCR results, an internal amplification control was included. The qPCR assay was specific, highly sensitive, and quantitative across the tested 5-log dynamic range down to a method detection limit of 5 copies per reaction. Repeatability and reproducibility were high for all three tested target genes. For environmental application, global DNA recovery (GR) rates were assessed for drinking water, river water, and water from different lakes. GR rates ranged from 1.6% to 76.4% and were dependent on the environmental background. Uncorrected and GR-corrected V. cholerae abundances were determined in two lakes with extremely high turbidity. Uncorrected abundances ranged from 4.6 × 102 to 2.3 × 104 cell equivalents liter−1, whereas GR-corrected abundances ranged from 4.7 × 103 to 1.6 × 106 cell equivalents liter−1. GR-corrected qPCR results were in good agreement with an independent cell-based direct detection method but were up to 1.6 log higher than cultivation-based abundances. We recommend the newly developed triplex qPCR strategy as a powerful tool to simultaneously quantify toxigenic and nontoxigenic V. cholerae in various aquatic environments for ecological studies as well as for risk assessment programs. PMID:25724966

  11. Identification of Two Novel Mycobacterium avium Allelic Variants in Pig and Human Isolates from Brazil by PCR-Restriction Enzyme Analysis

    PubMed Central

    Leão, Sylvia Cardoso; Briones, Marcelo R. S.; Sircili, Marcelo Palma; Balian, Simone Carvalho; Mores, Nelson; Ferreira-Neto, José Soares

    1999-01-01

    Mycobacterium avium complex (MAC) is composed of environmental mycobacteria found widely in soil, water, and aerosols that can cause disease in animals and humans, especially disseminated infections in AIDS patients. MAC consists of two closely related species, M. avium and M. intracellulare, and may also include other, less-defined groups. The precise differentiation of MAC species is a fundamental step in epidemiological studies and for the evaluation of possible reservoirs for MAC infection in humans and animals. In this study, which included 111 pig and 26 clinical MAC isolates, two novel allelic M. avium PCR-restriction enzyme analysis (PRA) variants were identified, differing from the M. avium PRA prototype in the HaeIII digestion pattern. Mutations in HaeIII sites were confirmed by DNA sequencing. Identification of these isolates as M. avium was confirmed by PCR with DT1-DT6 and IS1245 primers, nucleic acid hybridization with the AccuProbe system, 16S ribosomal DNA sequencing, and biochemical tests. The characterization of M. avium PRA variants can be useful in the elucidation of factors involved in mycobacterial virulence and routes of infection and also has diagnostic significance, since they can be misidentified as M. simiae II and M. kansasii I if the PRA method is used in the clinical laboratory for identification of mycobacteria. PMID:10405407

  12. Two variants of Pepino mosaic virus isolated from imported tomato seed from Chile share high levels of sequence identity with the U.S. isolates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pepino mosaic virus (PepMV), a member of the genus Potexvirus, was first described on pepino (Solanum muricatum A.) grown in South America. In recent years PepMV was reported to infect greenhouse-grown tomatoes. European isolates showed high sequence identity (>99%). On the other hand, two US isol...

  13. Prevalence of Smqnr and plasmid-mediated quinolone resistance determinants in clinical isolates of Stenotrophomonas maltophilia from Japan: novel variants of Smqnr.

    PubMed

    Kanamori, H; Yano, H; Tanouchi, A; Kakuta, R; Endo, S; Ichimura, S; Ogawa, M; Shimojima, M; Inomata, S; Ozawa, D; Aoyagi, T; Weber, D J; Kaku, M

    2015-09-01

    Stenotrophomonas maltophilia is an important pathogen in healthcare-associated infections. S. maltophilia may contain Smqnr, a quinolone resistance gene encoding the pentapeptide repeat protein, which confers low-level quinolone resistance upon expression in a heterologous host. We investigated the prevalence of Smqnr and plasmid-mediated quinolone resistance (PMQR) determinants in S. maltophilia isolates from Japan. A total of 181 consecutive and nonduplicate clinical isolates of S. maltophilia were collected from four areas of Japan. The antimicrobial susceptibility profiles for these strains were determined. PCR was conducted for Smqnr and PMQR genes, including qnrA, qnrB, qnrC, qnrS, aac(6')-Ib and qepA. PCR products for Smqnr and aac(6')-Ib were sequenced. For the S. maltophilia isolates containing Smqnr, pulsed-field gel electrophoresis (PFGE) was performed using XbaI. Resistance rates to ceftazidime, levofloxacin, trimethoprim-sulfamethoxazole, chloramphenicol and minocycline were 67.4%, 6.1%, 17.7%, 8.8% and 0%, respectively. The minimum inhibitory concentration required to inhibit the growth of 50% and 90% of organisms were 0.5 and 2 mg/L for moxifloxacin but 1 and 4 mg/L for levofloxacin, respectively. Smqnr was detected in 104 of the 181 S. maltophilia isolates (57.5%), and the most frequent was Smqnr6, followed by Smqnr8 and Smqnr11. Eleven novel variants from Smqnr48 to Smqnr58 were detected. The 24 Smqnr-containing S. maltophilia isolates were typed by PFGE and divided into 21 unique types. Nine S. maltophilia isolates (5.0%) carried aac(6')-Ib-cr. No qnr or qepA genes were detected. This study describes a high prevalence of Smqnr and novel variants of Smqnr among S. maltophilia from Japan. Continuous antimicrobial surveillance and further molecular epidemiological studies on quinolone resistance in S. maltophilia are needed. PMID:26110061

  14. Isolated cerebellar variant of adrenoleukodystrophy with a de novo adenosine triphosphate-binding cassette D1 (ABCD1) gene mutation.

    PubMed

    Kang, Joon Won; Lee, Sang Mi; Koo, Kyo Yeon; Lee, Young-Mock; Nam, Hyo Suk; Quan, Zhejiu; Kang, Hoon-Chul

    2014-07-01

    X-linked adrenoleukodystrophy (X-ALD) shows a wide range of phenotypic expression, but clinical presentation as an isolated lesion of the cerebellar white matter and dentate nuclei has not been reported. We report an unusual presentation of X-ALD only with an isolated lesion of the cerebellar white matter and dentate nuclei. The proband, a 37-year-old man presented with bladder incontinence, slurred speech, dysmetria in all limbs, difficulties in balancing, and gait ataxia. Brain magnetic resonance imaging showed an isolated signal change of white matter around the dentate nucleus in cerebellum. With high level of very long chain fatty acid, gene study showed a de novo mutation in exon 1 at nucleotide position c.277_296dup20 (p.Ala100Cysfs*10) of the adenosine triphosphate-binding cassette D1 gene. It is advised to consider X-ALD as a differential diagnosis in patients with isolated cerebellar degeneration symptoms. PMID:24954351

  15. Prevalence of Factor H–Binding Protein Variants and NadA among Meningococcal Group B Isolates from the United States: Implications for the Development of a Multicomponent Group B Vaccine

    PubMed Central

    Beernink, Peter T.; Welsch, Jo Anne; Harrison, Lee H.; Leipus, Arunas; Kaplan, Sheldon L.; Granoff, Dan M.

    2008-01-01

    Background Two promising recombinant meningococcal protein vaccines are in development. One contains factor H–binding protein (fHBP) variants (v.) 1 and 2, whereas the other contains v.1 and 4 other antigens discovered by genome mining (5 component [5C]). Antibodies against fHBP are bactericidal against strains within a variant group. There are limited data on the prevalence of strains expressing different fHBP variants in the United States. Methods A total of 143 group B isolates from patients hospitalized in the United States were tested for fHBP variant by quantitative polymerase chain reaction, for reactivity with 6 anti-fHBP monoclonal antibodies (MAb) by dot immunoblotting, and for susceptibility to bactericidal activity of mouse antisera. Results fHBP v.1 isolates predominated in California (83%), whereas isolates expressing v.1 (53%) or v.2 (42%) were common in 9 other states. Isolates representative of 5 anti-fHBP MAb–binding phenotypes (70% of isolates) were highly susceptible to anti–fHBP v.1 or v.2 bactericidal activity, whereas 3 phenotypes were ~50% susceptible. Collectively, antibodies against the fHBP v.1 and v.2 vaccine and the 5C vaccine killed 76% and 83% of isolates, respectively. Conclusions Susceptibility to bactericidal activity can be predicted, in part, on the basis of fHBP phenotypes. Both vaccines have the potential to prevent most group B disease in the United States. PMID:17436227

  16. First Complete Genome Sequence of Clostridium sporogenes DSM 795T, a Nontoxigenic Surrogate for Clostridium botulinum, Determined Using PacBio Single-Molecule Real-Time Technology.

    PubMed

    Nakano, Kazuma; Terabayashi, Yasunobu; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

    2015-01-01

    The first complete genome sequence of Clostridium sporogenes DSM 795(T), a nontoxigenic surrogate for Clostridium botulinum, was determined in a single contig using the PacBio single-molecule real-time technology. The genome (4,142,990 bp; G+C content, 27.98%) included 86 sets of >1,000-bp identical sequence pairs and 380 tandem repeats. PMID:26227598

  17. First Complete Genome Sequence of Clostridium sporogenes DSM 795T, a Nontoxigenic Surrogate for Clostridium botulinum, Determined Using PacBio Single-Molecule Real-Time Technology

    PubMed Central

    Terabayashi, Yasunobu; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

    2015-01-01

    The first complete genome sequence of Clostridium sporogenes DSM 795T, a nontoxigenic surrogate for Clostridium botulinum, was determined in a single contig using the PacBio single-molecule real-time technology. The genome (4,142,990 bp; G+C content, 27.98%) included 86 sets of >1,000-bp identical sequence pairs and 380 tandem repeats. PMID:26227598

  18. Pharmacogenetic impact of VKORC1 and CYP2C9 allelic variants on warfarin dose requirements in a hispanic population isolate.

    PubMed

    Palacio, Lina; Falla, Diana; Tobon, Ignacio; Mejia, Fernando; Lewis, John E; Martinez, Ariel F; Arcos-Burgos, Mauricio; Camargo, Mauricio

    2010-02-01

    Warfarin is the most prescribed oral anticoagulant worldwide. Because of the complexity of warfarin therapy, we attempted to dissect genetic from bioenvironmental factors influencing warfarin dose responses in individuals of a genetic isolate of Hispanic ancestry. A total of 191 patients with standard values of international normalized ratio were recruited. Three groups with a significantly different warfarin dose response were identified, that is, sensitive (2.28 +/- 0.50 mg/d), intermediate (4.2 +/- 0.76 mg/d), and resistant (7.40 +/- 1.54 mg/d; Tukey test, P < .001). Age had a significant inverse correlation with warfarin dose (P < .001; effective dose diminished 0.56 mg/d/decade). Required doses were higher for individuals with CYP2C9 variants containing the allele *1 compared to those individuals with variants composed of other alleles (P = .006). Similarly, individuals with VKORC1-1639GG and VKORC1-1639GA genotypes also required higher doses compared to the AA genotype (P < .001). Evaluation of potential gene-gene interactions between CYP2C9 and VKORC1 polymorphisms showed significant differences in dosing for CYP2C9 genotypes within the VKORC1-1639G/A subgroup (P = .013). A stepwise multivariate linear regression analysis showed that 38.2% of the warfarin dose response variance was accounted for by a model involving age (20.9%), VKORC1-1639G/A (11.3%), and CYP2C9*1, *2, and *3 variants (7.1%). These results corroborate previous findings on warfarin pharmacogenetics and define a contrastable gene-bioenvironment interaction model suited to be used in Hispanic populations. PMID:19567378

  19. MLVA Subtyping of Genovar E Chlamydia trachomatis Individualizes the Swedish Variant and Anorectal Isolates from Men who Have Sex with Men

    PubMed Central

    Peuchant, Olivia; Le Roy, Chloé; Herrmann, Björn; Clerc, Maithé; Bébéar, Cécile; de Barbeyrac, Bertille

    2012-01-01

    This study describes a new multilocus variable number tandem-repeat (VNTR) analysis (MLVA) typing system for the discrimination of Chlamydia trachomatis genovar D to K isolates or specimens. We focused our MLVA scheme on genovar E which predominates in most populations worldwide. This system does not require culture and therefore can be performed directly on DNA extracted from positive clinical specimens. Our method was based on GeneScan analysis of five VNTR loci labelled with fluorescent dyes by multiplex PCR and capillary electrophoresis. This MLVA, called MLVA-5, was applied to a collection of 220 genovar E and 94 non-E genovar C. trachomatis isolates and specimens obtained from 251 patients and resulted in 38 MLVA-5 types. The genetic stability of the MLVA-5 scheme was assessed for results obtained both in vitro by serial passage culturing and in vivo using concomitant and sequential isolates and specimens. All anorectal genovar E isolates from men who have sex with men exhibited the same MLVA-5 type, suggesting clonal spread. In the same way, we confirmed the clonal origin of the Swedish new variant of C. trachomatis. The MLVA-5 assay was compared to three other molecular typing methods, ompA gene sequencing, multilocus sequence typing (MLST) and a previous MLVA method called MLVA-3, on 43 genovar E isolates. The discriminatory index was 0.913 for MLVA-5, 0.860 for MLST and 0.622 for MLVA-3. Among all of these genotyping methods, MLVA-5 displayed the highest discriminatory power and does not require a time-consuming sequencing step. The results indicate that MLVA-5 enables high-resolution molecular epidemiological characterisation of C. trachomatis genovars D to K infections directly from specimens. PMID:22363667

  20. In vitro isolation and identification of human immunodeficiency virus (HIV) variants with reduced sensitivity to C-2 symmetrical inhibitors of HIV type 1 protease.

    PubMed Central

    Otto, M J; Garber, S; Winslow, D L; Reid, C D; Aldrich, P; Jadhav, P K; Patterson, C E; Hodge, C N; Cheng, Y S

    1993-01-01

    Protease inhibitors are another class of compounds for treatment of human immunodeficiency virus (HIV)-caused disease. The emergence of resistance to the current anti-HIV drugs makes the determination of potential resistance to protease inhibitors imperative. Here we describe the isolation of an HIV type 1 (HIV-1) resistant to an HIV-protease inhibitor. Serial passage of HIV-1 (strain RF) in the presence of the inhibitor, [2-pyridylacetylisoleucylphenylalanyl-psi (CHOH)]2 (P9941), failed to yield a stock of virus with a resistance phenotype. However, variants of the virus with 6- to 8-fold reduced sensitivity to P9941 were selected by using a combination of plaque assay and endpoint titration. Genetic analysis and computer modeling of the variant proteases revealed a single change in the codon for amino acid 82 (Val-->Ala), which resulted in a protease with lower affinity and reduced sensitivity to this inhibitor and certain, but not all, related inhibitors. Images Fig. 2 PMID:8356053

  1. Multidrug-resistant Salmonella enterica Serovar Typhimurium Monophasic Variant 4,12:i:- Isolated from Asymptomatic Wildlife in a Catalonian Wildlife Rehabilitation Center, Spain.

    PubMed

    Molina-López, Rafael A; Vidal, Anna; Obón, Elena; Martín, Marga; Darwich, Laila

    2015-07-01

    Wildlife can act as long-term asymptomatic reservoirs for zoonotic bacteria, such as Salmonella. The prevalence and antimicrobial-susceptibility profiles of Salmonella spp. were assessed in 263 cases in wildlife from 22 animal orders from a wildlife rehabilitation center in Catalonia (NE Spain), September 2013-May 2014. Eleven of 263 tested animals were positive for Salmonella spp., representing an overall prevalence of 4.2%. Prevalences by taxonomic categories were 2% in mammals, 4.7% in birds, and 4.5% in reptiles. By species, one each of European hedgehog (Erinaceus europeus; from a sample of n = 26), Eurasian Eagle Owl (Bubo bubo; n = 2), Barn Owl (Tyto alba; n = 3), Tawny Owl (Strix aluco; n = 20), Egyptian Vulture (Neophron percnopterus; n = 1), Griffon Vulture (Gyps fulvus; n = 1), and Hoopoe (Upupa epops; n = 2), and two each Common Kestrels (Falco tinnunculus; n = 16) and pond sliders (Trachemys scripta; n = 25) were positive for Salmonella. By serotyping, seven of eleven isolates were classified as S. enterica subsp. enterica serovar Typhimurium, and five of seven belonged to the monophasic variant 4,12:i:-. All the monophasic variants were isolated from birds (4/5 in raptors) and showed a multidrug-resistance (MDR) profile to at least ampicillin, streptomycin, sulfonamide, and tetracycline (R-type ASSuT), and up to 12 antibiotics. The large proportion of S. Typhimurium monophasic MDR strains detected in wildlife never treated with antibiotics, especially in raptors, adds more complexity to the epidemiologic control of one of the most frequent serovars involved in human and livestock infection. PMID:25973627

  2. Genome Sequence of the Small-Colony Variant Pseudomonas aeruginosa MH27, Isolated from a Chronic Urethral Catheter Infection.

    PubMed

    Tielen, Petra; Wibberg, Daniel; Blom, Jochen; Rosin, Nathalie; Meyer, Ann-Kathrin; Bunk, Boyke; Schobert, Max; Tüpker, Reinhilde; Schatschneider, Sarah; Rückert, Christian; Albersmeier, Andreas; Goesmann, Alexander; Vorhölter, Frank-Jörg; Jahn, Dieter; Pühler, Alfred

    2014-01-01

    Pseudomonas aeruginosa is a notable nosocomial pathogen causing severe chronic infections. Here we present the draft genome sequence of P. aeruginosa MH27, isolated from a patient with a chronic hospital-acquired catheter-associated urinary tract infection. The 7.1-Mb genome sequence organized in 24 scaffolds contributes to the understanding of biofilm formation and antibiotic resistance. PMID:24459261

  3. Genome Sequence of the Small-Colony Variant Pseudomonas aeruginosa MH27, Isolated from a Chronic Urethral Catheter Infection

    PubMed Central

    Tielen, Petra; Wibberg, Daniel; Blom, Jochen; Rosin, Nathalie; Meyer, Ann-Kathrin; Bunk, Boyke; Schobert, Max; Tüpker, Reinhilde; Schatschneider, Sarah; Rückert, Christian; Albersmeier, Andreas; Goesmann, Alexander; Vorhölter, Frank-Jörg; Pühler, Alfred

    2014-01-01

    Pseudomonas aeruginosa is a notable nosocomial pathogen causing severe chronic infections. Here we present the draft genome sequence of P. aeruginosa MH27, isolated from a patient with a chronic hospital-acquired catheter-associated urinary tract infection. The 7.1-Mb genome sequence organized in 24 scaffolds contributes to the understanding of biofilm formation and antibiotic resistance. PMID:24459261

  4. Full genome sequence analysis of a wild, non-MLV-related type 2 Hungarian PRRSV variant isolated in Europe.

    PubMed

    Balka, Gyula; Wang, Xiong; Olasz, Ferenc; Bálint, Ádám; Kiss, István; Bányai, Krisztián; Rusvai, Miklós; Stadejek, Tomasz; Marthaler, Douglas; Murtaugh, Michael P; Zádori, Zoltán

    2015-03-16

    Porcine reproductive and respiratory syndrome virus (PRRSV) is a widespread pathogen of pigs causing significant economic losses to the swine industry. The expanding diversity of PRRSV strains makes the diagnosis, control and eradication of the disease more and more difficult. In the present study, the authors report the full genome sequencing of a type 2 PRRSV strain isolated from piglet carcasses in Hungary. Next generation sequencing was used to determine the complete genome sequence of the isolate (PRRSV-2/Hungary/102/2012). Recombination analysis performed with the available full-length genome sequences showed no evidence of such event with other known PRRSV. Unique deletions and an insertion were found in the nsp2 region of PRRSV-2/Hungary/102/2012 when it was compared to the highly virulent VR2332 and JXA-1 prototype strains. The majority of amino acid alterations in GP4 and GP5 of the virus were in the known antigenic regions suggesting an important role for immunological pressure in PRRSV-2/Hungary/102/2012 evolution. Phylogenetic analysis revealed that it belongs to lineage 1 or 2 of type 2 PRRSV. Considering the lack of related PRRSV in Europe, except for a partial sequence from Slovakia, the ancestor of PRRSV-2/Hungary/102/2012 was most probably transported from North-America. It is the first documented type 2 PRRSV isolated in Europe that is not related to the Ingelvac MLV. PMID:25616050

  5. Neonatal, urogenital isolates of biotype 4 nontypeable Haemophilus influenzae express a variant P6 outer membrane protein molecule.

    PubMed Central

    Murphy, T F; Kirkham, C; Sikkema, D J

    1992-01-01

    The P6 outer membrane protein is a highly conserved molecule which is present on the surface of all strains of Haemophilus influenzae. Sixty strains of nontypeable H. influenzae which caused invasive disease or colonized the female urogenital tract were studied with monoclonal antibodies 7F3 and 4G4, which recognize different surface-exposed epitopes on the P6 molecule. All 60 strains expressed the epitope recognized by 4G4, whereas 47 of 60 strains expressed the epitope recognized by antibody 7F3. The 7F3-nonreactive strains were all biotype 4 and were recovered from the blood of neonates or postpartum women or from the female urogenital tract. The P6 genes from two 7F3-nonreactive strains were cloned, and the nucleotide sequences were determined. Analysis of amino acid sequences, immunoassays with synthetic peptides, and site-directed mutation of the P6 gene indicate that the epitope recognized by antibody 7F3 is conformational and that the sequence Asp-Ile-Thr is critical in maintaining the conformation of the epitope. We conclude that the unusually virulent clone family of biotype 4 strains of nontypeable H. influenzae express a variant P6 molecule which has an alteration in a highly conserved surface-exposed epitope. Images PMID:1373403

  6. Maternal MTHFR variant forms increase the risk in offspring of isolated nonsyndromic cleft lip with or without cleft palate.

    PubMed

    Pezzetti, F; Martinelli, M; Scapoli, L; Carinci, F; Palmieri, A; Marchesini, J; Carinci, P; Caramelli, E; Rullo, R; Gombos, F; Tognon, M

    2004-07-01

    The pathogenesis of cleft lip with or without cleft palate (CL/P) is complex; its onset could be due to the interaction of various genetic and environmental factors. Recently MTHFR functional polymorphisms were found to increase the risk of this common malformation; however, this finding is still debated. We investigated 110 sporadic CL/P patients, their parents and 289 unrelated controls for c.665C>T (commonly known as 677C>T; p.Ala222Val) and c.1286A>C (known as 1298A>C; p.Glu429Ala) polymorphism in the MTHFR gene. Transmission disequilibrium test (TDT) showed no distortion in allele transmission. Nevertheless, association studies revealed significant differences in allele frequencies between mothers of CL/P patients and controls. This work supports the hypothesis that a lower MTHFR enzyme activity in pregnant women, mostly related to the c.665C>T variant form, is responsible for a higher risk of having CL/P affected offspring. PMID:15221800

  7. Non-toxigenic Clostridium sordellii: clinical and microbiological features of a case of cholangitis-associated bacteremia

    PubMed Central

    Walk, Seth T.; Jain, Ruchika; Trivedi, Itishree; Grossman, Sylvia; Newton, Duane W.; Thelen, Tennille; Hao, Yibai; Songer, J. Glenn; Carter, Glen P.; Lyras, Dena; Young, Vincent B.; Aronoff, David M.

    2011-01-01

    Toxigenic C. sordellii strains are increasingly recognized to cause highly lethal infections in humans that are typified by a toxic shock syndrome (TSS). Two glucosylating toxins, lethal toxin (TcsL) and hemorrhagic toxin (TcsH) are believed to be important in the pathogenesis of TSS. While non-toxigenic strains of C. sordellii demonstrate reduced cytotoxicity in vitro and lower virulence in animal models of infection, there are few data regarding their behavior in humans. Here we report a non-TSS C. sordellii infection in the context of a polymicrobial bacterial cholangitis. The C. sordellii strain associated with this infection did not carry either the TcsL-encoding tcsL gene or the tcsH gene for TcsH. In addition, the strain was neither cytotoxic in vitro nor lethal in a murine sepsis model. These results provide additional correlative evidence that TcsL and TcsH increase the risk of mortality during C. sordellii infections. PMID:21726656

  8. Identification of a novel NDM variant, NDM-13, from a multidrug-resistant Escherichia coli clinical isolate in Nepal.

    PubMed

    Shrestha, Basudha; Tada, Tatsuya; Miyoshi-Akiyama, Tohru; Shimada, Kayo; Ohara, Hiroshi; Kirikae, Teruo; Pokhrel, Bharat M

    2015-09-01

    A novel New Delhi metallo-?-lactamase, NDM-13, was identified in a carbapenem-resistant Escherichia coli clinical isolate obtained from the urine of a patient in Nepal. The enzymatic activity of NDM-13 against ?-lactams was similar to that of NDM-1. However, NDM-13 displayed significantly higher k cat/Km ratios for cefotaxime. The genetic environment of bla NDM-13 was determined to be tnpA-IS30-bla NDM-13-ble MBL-trpF-dsbC-cutA-groES-groL, with bla NDM-13 located within the chromosome. PMID:26169399

  9. Cyclin-dependent kinase inhibitor 1B (CDKN1B) gene variants in AIP mutation-negative familial isolated pituitary adenoma kindreds.

    PubMed

    Tichomirowa, Maria A; Lee, Misu; Barlier, Anne; Daly, Adrian F; Marinoni, Ilaria; Jaffrain-Rea, Marie-Lise; Naves, Luciana A; Rodien, Patrice; Rohmer, Vincent; Faucz, Fabio Rueda; Caron, Philippe; Estour, Bruno; Lecomte, Pierre; Borson-Chazot, Françoise; Penfornis, Alfred; Yaneva, Maria; Guitelman, Mirtha; Castermans, Emily; Verhaege, Catherine; Wémeau, Jean-Louis; Tabarin, Antoine; Fajardo Montañana, Carmen; Delemer, Brigitte; Kerlan, Veronique; Sadoul, Jean-Louis; Cortet Rudelli, Christine; Archambeaud, Françoise; Zacharieva, Sabine; Theodoropoulou, Marily; Brue, Thierry; Enjalbert, Alain; Bours, Vincent; Pellegata, Natalia S; Beckers, Albert

    2012-06-01

    Familial isolated pituitary adenoma (FIPA) occurs in families and is unrelated to multiple endocrine neoplasia type 1 and Carney complex. Mutations in AIP account only for 15-25% of FIPA families. CDKN1B mutations cause MEN4 in which affected patients can suffer from pituitary adenomas. With this study, we wanted to assess whether mutations in CDKN1B occur among a large cohort of AIP mutation-negative FIPA kindreds. Eighty-eight AIP mutation-negative FIPA families were studied and 124 affected subjects underwent sequencing of CDKN1B. Functional analysis of putative CDKN1B mutations was performed using in silico and in vitro approaches. Germline CDKN1B analysis revealed two nucleotide changes: c.286A>C (p.K96Q) and c.356T>C (p.I119T). In vitro, the K96Q change decreased p27 affinity for Grb2 but did not segregate with pituitary adenoma in the FIPA kindred. The I119T substitution occurred in a female patient with acromegaly. p27(I119T) shows an abnormal migration pattern by SDS-PAGE. Three variants (p.S56T, p.T142T, and c.605+36C>T) are likely nonpathogenic because In vitro effects were not seen. In conclusion, two patients had germline sequence changes in CDKN1B, which led to functional alterations in the encoded p27 proteins in vitro. Such rare CDKN1B variants may contribute to the development of pituitary adenomas, but their low incidence and lack of clear segregation with affected patients make CDKN1B sequencing unlikely to be of use in routine genetic investigation of FIPA kindreds. However, further characterization of the role of CDKN1B in pituitary tumorigenesis in these and other cases could help clarify the clinicopathological profile of MEN4. PMID:22291433

  10. A neurotoxic phospholipase A2 variant: isolation and characterization from eastern regional Indian cobra (Naja naja) venom.

    PubMed

    Shashidharamurthy, R; Kemparaju, K

    2006-06-01

    CM-Sephadex C-25 column chromatography profile of Indian cobra (Naja naja) venom from eastern region showed a distinct and a dominant phospholipase peak, peak-10, while it was not seen in either southern or western venom samples. Peak-10 was subjected to CM-Sephadex C-25 and Sephadex G-50 column chromatography to isolate NN-X-PLA(2). NN-X-PLA(2) is a single chain protein with the relative molecular weight of 10kDa by SDS-PAGE. It was toxic to mice with an LD(50) value 0.098 mg/kg body weight (i.p.) and the mice exhibited acute neurotoxic symptoms. Upon indirect stimulation, it inhibited the twitching of frog's gastrocnemius muscle in a dose dependent manner. NN-X-PLA(2) was weakly anticoagulant and devoid of cytotoxicity, myotoxicity, hemorrhage, edema inducing, and directlytic activities and effects on platelet aggregation process. Upon chemical modification independently with p-bromophenacyl bromide and acetic anhydride, NN-X-PLA(2) lost both enzymatic and toxic properties. PMID:16574178

  11. Identification and Quantification of a Toxigenic and Non-Toxigenic Aspergillus flavus Strain in Contaminated Maize Using Quantitative Real-Time PCR.

    PubMed

    Mylroie, J Erik; Ozkan, Seval; Shivaji, Renuka; Windham, Gary L; Alpe, Michael N; Williams, W Paul

    2016-01-01

    Aflatoxins, which are produced by Aspergillus flavus, are toxic to humans, livestock, and pets. The value of maize (Zea mays) grain is markedly reduced when contaminated with aflatoxin. Plant resistance and biological control using non-toxin producing strains are considered effective strategies for reducing aflatoxin accumulation in maize grain. Distinguishing between the toxin and non-toxin producing strains is important in determining the effectiveness of bio-control strategies and understanding inter-strain interactions. Using polymorphisms found in the fungal rRNA intergenic spacer region (IGS) between a toxigenic strain of A. flavus (NRRL 3357) and the non-toxigenic strain used in the biological control agent Afla-Guard(®) (NRRL 21882), we developed a set of primers that allows for the identification and quantification of the two strains using quantitative PCR. This primer set has been used to screen maize grain that was inoculated with the two strains individually and co-inoculated with both strains, and it has been shown to be effective in both the identification and quantification of both strains. Screening of co-inoculated ears from multiple resistant and susceptible genotypic crosses revealed no significant differences in fungal biomass accumulation of either strain in the field tests from 2010 and 2011 when compared across the means of all genotypes. Only one genotype/year combination showed significant differences in strain accumulation. Aflatoxin accumulation analysis showed that, as expected, genotypes inoculated with the toxigenic strain accumulated more aflatoxin than when co-inoculated with both strains or inoculated with only the non-toxigenic strain. Furthermore, accumulation of toxigenic fungal mass was significantly correlated with aflatoxin accumulation while non-toxigenic fungal accumulation was not. This primer set will allow researchers to better determine how the two fungal strains compete on the maize ear and investigate the interaction between different maize lines and these A. flavus strains. PMID:26742074

  12. Identification and Quantification of a Toxigenic and Non-Toxigenic Aspergillus flavus Strain in Contaminated Maize Using Quantitative Real-Time PCR

    PubMed Central

    Mylroie, J. Erik; Ozkan, Seval; Shivaji, Renuka; Windham, Gary L.; Alpe, Michael N.; Williams, W. Paul

    2016-01-01

    Aflatoxins, which are produced by Aspergillus flavus, are toxic to humans, livestock, and pets. The value of maize (Zea mays) grain is markedly reduced when contaminated with aflatoxin. Plant resistance and biological control using non-toxin producing strains are considered effective strategies for reducing aflatoxin accumulation in maize grain. Distinguishing between the toxin and non-toxin producing strains is important in determining the effectiveness of bio-control strategies and understanding inter-strain interactions. Using polymorphisms found in the fungal rRNA intergenic spacer region (IGS) between a toxigenic strain of A. flavus (NRRL 3357) and the non-toxigenic strain used in the biological control agent Afla-Guard® (NRRL 21882), we developed a set of primers that allows for the identification and quantification of the two strains using quantitative PCR. This primer set has been used to screen maize grain that was inoculated with the two strains individually and co-inoculated with both strains, and it has been shown to be effective in both the identification and quantification of both strains. Screening of co-inoculated ears from multiple resistant and susceptible genotypic crosses revealed no significant differences in fungal biomass accumulation of either strain in the field tests from 2010 and 2011 when compared across the means of all genotypes. Only one genotype/year combination showed significant differences in strain accumulation. Aflatoxin accumulation analysis showed that, as expected, genotypes inoculated with the toxigenic strain accumulated more aflatoxin than when co-inoculated with both strains or inoculated with only the non-toxigenic strain. Furthermore, accumulation of toxigenic fungal mass was significantly correlated with aflatoxin accumulation while non-toxigenic fungal accumulation was not. This primer set will allow researchers to better determine how the two fungal strains compete on the maize ear and investigate the interaction between different maize lines and these A. flavus strains. PMID:26742074

  13. Subtypes of intimin among non-toxigenic Escherichia coli from diarrheic calves in Brazil.

    PubMed Central

    Aidar, L; Penteado, A S; Trabulsi, L R; Blanco, J E; Blanco, M; Blanco, J; Pestana de Castro, A F

    2000-01-01

    One hundred and five strains of Escherichia coli that were isolated from calves with diarrhea in the state of São Paulo, Brazil, and were negative for enterotoxins and cytotoxins, were examined for the eae gene. Four (3.8%) strains were positive by polymerase chain reaction (PCR) and were shown to produce intimin by using Western blot with specific antiserum against the conserved N-terminal region of intimin. Subtyping of the intimins was done by PCR with specific primers and by Western blot with specific antisera against the C-terminal variable region of the protein. Three of these isolates (O?:H11, O26:H-, O123:H1) produced the beta subtype of intimin, and the 4th (0103:H2) produced intimin that was not typable. The 0103:H2 and the O26:H-isolates adhered to HEp-2 cells with diffuse adherence and localized-like adherence patterns, respectively. The other strains did not adhere to HEp-2 cells. To our knowledge, this is the first report of the occurrence of a subtype of intimin described for human enteropathogenic E. coli among bovine diarrheogenic E. coli. It is also the first report from Brazil demonstrating the presence of bovine E. coli harboring the eae gene. Images Figure 1. Figure 2. Figure 3. Figure 4. Figure 5. Figure 6. PMID:10680651

  14. Clostridium Difficile Colonization in Hematopoietic Stem Cell Transplant Recipients: A Prospective Study of the Epidemiology and Outcomes Involving Toxigenic and Nontoxigenic Strains.

    PubMed

    Jain, Tania; Croswell, Christopher; Urday-Cornejo, Varinia; Awali, Reda; Cutright, Jessica; Salimnia, Hossein; Reddy Banavasi, Harsha Vardhan; Liubakka, Alyssa; Lephart, Paul; Chopra, Teena; Revankar, Sanjay G; Chandrasekar, Pranatharthi; Alangaden, George

    2016-01-01

    Clostridium difficile is a leading cause of infectious diarrhea in hematopoietic stem cell transplant (HSCT) recipients. Asymptomatic colonization of the gastrointestinal tract occurs before development of C. difficile infection (CDI). This prospective study examines the rates, risk factors, and outcomes of colonization with toxigenic and nontoxigenic strains of C. difficile in HSCT patients. This 18-month study was conducted in the HSCT unit at the Karmanos Cancer Center and Wayne State University in Detroit. Stool samples from the patients who consented for the study were taken at admission and weekly until discharge. Anaerobic culture for C. difficile and identification of toxigenic strains by PCR were performed on the stool samples. Demographic information and clinical and laboratory data were collected. Of the 150 patients included in the study, 29% were colonized with C. difficile at admission; 12% with a toxigenic strain and 17% with a nontoxigenic strain. Over a 90-day follow-up, 12 of 44 (26%) patients colonized with any C. difficile strain at admission developed CDI compared with 13 of 106 (12%) of patients not colonized (odds ratio [OR], 2.70; 95% confidence interval [95% CI], 1.11 to 6.48; P = .025). Eleven of 18 (61%) patients colonized with the toxigenic strain and 1 of 26 (4%) of those colonized with nontoxigenic strain developed CDI (OR, 39.30; 95% CI, 4.30 to 359.0; P < .001) at a median of 12 days. On univariate and multivariate analyses, none of the traditional factors associated with high risk for C. difficile colonization or CDI were found to be significant. Recurrent CDI occurred in 28% of cases. Asymptomatic colonization with C. difficile at admission was high in our HSCT population. Colonization with toxigenic C. difficile was predictive of CDI, whereas colonization with a nontoxigenic C. difficile appeared protective. These findings may have implications for infection control strategies and for novel approaches for the prevention and preemptive treatment of CDI in the HSCT patient population. PMID:26211988

  15. Comparative genome analysis of non-toxigenic non-O1 versus toxigenic O1 Vibrio cholerae

    PubMed Central

    Mukherjee, Munmun; Kakarla, Prathusha; Kumar, Sanath; Gonzalez, Esmeralda; Floyd, Jared T.; Inupakutika, Madhuri; Devireddy, Amith Reddy; Tirrell, Selena R.; Bruns, Merissa; He, Guixin; Lindquist, Ingrid E.; Sundararajan, Anitha; Schilkey, Faye D.; Mudge, Joann; Varela, Manuel F.

    2015-01-01

    Pathogenic strains of Vibrio cholerae are responsible for endemic and pandemic outbreaks of the disease cholera. The complete toxigenic mechanisms underlying virulence in Vibrio strains are poorly understood. The hypothesis of this work was that virulent versus non-virulent strains of V. cholerae harbor distinctive genomic elements that encode virulence. The purpose of this study was to elucidate genomic differences between the O1 serotypes and non-O1 V. cholerae PS15, a non-toxigenic strain, in order to identify novel genes potentially responsible for virulence. In this study, we compared the whole genome of the non-O1 PS15 strain to the whole genomes of toxigenic serotypes at the phylogenetic level, and found that the PS15 genome was distantly related to those of toxigenic V. cholerae. Thus we focused on a detailed gene comparison between PS15 and the distantly related O1 V. cholerae N16961. Based on sequence alignment we tentatively assigned chromosome numbers 1 and 2 to elements within the genome of non-O1 V. cholerae PS15. Further, we found that PS15 and O1 V. cholerae N16961 shared 98% identity and 766 genes, but of the genes present in N16961 that were missing in the non-O1 V. cholerae PS15 genome, 56 were predicted to encode not only for virulence–related genes (colonization, antimicrobial resistance, and regulation of persister cells) but also genes involved in the metabolic biosynthesis of lipids, nucleosides and sulfur compounds. Additionally, we found 113 genes unique to PS15 that were predicted to encode other properties related to virulence, disease, defense, membrane transport, and DNA metabolism. Here, we identified distinctive and novel genomic elements between O1 and non-O1 V. cholerae genomes as potential virulence factors and, thus, targets for future therapeutics. Modulation of such novel targets may eventually enhance eradication efforts of endemic and pandemic disease cholera in afflicted nations. PMID:25722857

  16. Continuing evolution of canine parvovirus in China: Isolation of novel variants with an Ala5Gly mutation in the VP2 protein.

    PubMed

    Wang, Jianke; Lin, Peng; Zhao, Hang; Cheng, Yuening; Jiang, Zhong; Zhu, Hongwei; Wu, Hua; Cheng, Shipeng

    2016-03-01

    Canine parvovirus (CPV) type 2c is a new antigenic variant of CPV-2. Since the year 2000 it has spread to several countries, causing severe hemorrhagic enteritis in dogs. In 2014 and 2015, 58 fecal samples were collected from dogs in Beijing with suspected CPV infection. Regardless of the vaccination status of the dogs, 43 samples were found positive for CPV according to PCR results; i.e., 18, 7, and 18 respectively belonged to antigenic types new CPV-2a, new CPV-2b, and CPV-2c. A phylogenetic tree based on their VP2 gene sequences indicated that the Chinese CPV-2c strains form a separate cluster. In addition to synonymous mutations, the CPV-2c strains also contain a unique coding mutation in VP2 that leads to glycine at residue 5, instead of the highly conserved alanine at this position in all other CPV-2c strains sequenced to date. Using F81 cells, several novel isolates of CPV-2c, each with the Ala5Gly mutation, were obtained. One of these was used to infect experimentally beagle dogs, which subsequently developed the typical clinical symptoms of CPV infection. Hence, it appears that CPV-2c is still evolving in China, a finding that warrants continuous surveying and the eventual adaptation of current vaccines. PMID:26692471

  17. Characterization of a genetic and antigenic variant of avian paramyxovirus 6 isolated from a migratory wild bird, the red-necked stint (Calidris ruficollis).

    PubMed

    Bui, Vuong Nghia; Mizutani, Tetsuya; Nguyen, Tung Hoang; Trinh, Dai Quang; Awad, Sanaa S A; Minoungou, Germaine L; Yamamoto, Yu; Nakamura, Kikuyasu; Saito, Keisuke; Watanabe, Yukiko; Runstadler, Jonathan; Huettmann, Falk; Ogawa, Haruko; Imai, Kunitoshi

    2014-11-01

    A hemagglutinating virus (8KS0813) was isolated from a red-necked stint. Hemagglutination inhibition and neutralization tests indicated that 8KS0813 was antigenically related to a prototype strain, APMV-6/duck/Hong Kong/18/199/77, but with an 8- and 16-fold difference, respectively, in their titers. The full genome sequence of 8KS0813 showed 98.6 % nucleotide sequence identity to that of APMV-6/duck/Italy/4524-2/07, which has been reported to belong to an APMV-6 subgroup, and showed less similarity to that of the prototype strain (70.6 % similarity). The growth of 8KS0813 and the prototype strain in four different cell cultures was greatly enhanced by adding trypsin. Interestingly, this virus induced syncytia only in Vero cells. 8KS0813 was identified as APMV-6/red-necked stint/Japan/8KS0813/08, but it is antigenically and genetically distinguishable from the prototype strain, suggesting that variant APMV-6 is circulating in migratory birds. PMID:25000900

  18. Cellulase variants

    DOEpatents

    Blazej, Robert; Toriello, Nicholas; Emrich, Charles; Cohen, Richard N.; Koppel, Nitzan

    2015-07-14

    This invention provides novel variant cellulolytic enzymes having improved activity and/or stability. In certain embodiments the variant cellulotyic enzymes comprise a glycoside hydrolase with or comprising a substitution at one or more positions corresponding to one or more of residues F64, A226, and/or E246 in Thermobifida fusca Cel9A enzyme. In certain embodiments the glycoside hydrolase is a variant of a family 9 glycoside hydrolase. In certain embodiments the glycoside hydrolase is a variant of a theme B family 9 glycoside hydrolase.

  19. Variant surface glycoproteins from Venezuelan trypanosome isolates are recognized by sera from animals infected with either Trypanosoma evansi or Trypanosoma vivax

    PubMed Central

    Camargo, Rocío; Izquier, Adriana; Uzcanga, Graciela L.; Perrone, Trina; Acosta-Serrano, Alvaro; Carrasquel, Liomary; Arias, Laura P.; Escalona, José L.; Cardozo, Vanessa; Bubis, José

    2015-01-01

    Salivarian trypanosomes sequentially express only one variant surface glycoprotein (VSG) on their cell surface from a large repertoire of VSG genes. Seven cryopreserved animal trypanosome isolates known as TeAp-ElFrio01, TEVA1 (or TeAp-N/D1), TeGu-N/D1, TeAp-Mantecal01, TeGu-TerecayTrino, TeGu-Terecay03 and TeGu-Terecay323, which had been isolated from different hosts identified in several geographical areas of Venezuela were expanded using adult albino rats. Soluble forms of predominant VSGs expressed during the early infection stages were purified and corresponded to concanavalin A-binding proteins with molecular masses of 48–67 kDa by sodium dodecyl sulfate-polyacrylamide gel electropohoresis, and pI values between 6.1 and 7.5. The biochemical characterization of all purified soluble VSGs revealed that they were dimers in their native form and represented different gene products. Sequencing of some of these proteins yielded peptides homologous to VSGs from Trypanosoma (Trypanozoon) brucei and Trypanosoma (Trypanozoon) evansi and established that they most likely are mosaics generated by homologous recombination. Western blot analysis showed that all purified VSGs were cross-reacting antigens that were recognized by sera from animals infected with either T. evansi or Trypanosoma (Dutonella) vivax. The VSG glycosyl-phosphatidylinositol cross-reacting determinant epitope was only partially responsible for the cross-reactivity of the purified proteins, and antibodies appeared to recognize cross-reacting conformational epitopes from the various soluble VSGs. ELISA experiments were performed using infected bovine sera collected from cattle in a Venezuelan trypanosome-endemic area. In particular, soluble VSGs from two trypanosome isolates, TeGu-N/D1 and TeGu-TeracayTrino, were recognized by 93.38% and 73.55% of naturally T. vivax-infected bovine sera, respectively. However, approximately 70% of the sera samples did not recognize all seven purified proteins. Hence, the use of a combination of various VSGs for the diagnosis of animal trypanosomosis is recommended. PMID:25468674

  20. Detection of ST772 Panton-Valentine leukocidin-positive methicillin-resistant Staphylococcus aureus (Bengal Bay clone) and ST22 S. aureus isolates with a genetic variant of elastin binding protein in Nepal

    PubMed Central

    Pokhrel, R.H.; Aung, M.S.; Thapa, B.; Chaudhary, R.; Mishra, S.K.; Kawaguchiya, M.; Urushibara, N.; Kobayashi, N.

    2016-01-01

    Genetic characteristics were analysed for recent clinical isolates of methicillin-resistant and -susceptible Staphylococcus aureus (MRSA and MSSA respectively) in Kathmandu, Nepal. MRSA isolates harbouring Panton-Valentine leukocidin (PVL) genes were classified into ST1, ST22 and ST88 with SCCmec-IV and ST772 with SCCmec-V (Bengal Bay clone), while PVL-positive MSSA into ST22, ST30 and ST772. ST22 isolates (PVL-positive MRSA and MSSA, PVL-negative MRSA) possessed a variant of elastin binding protein gene (ebpS) with an internal deletion of 180 bp, which was similar to that reported for ST121 S. aureus previously outside Nepal. Phylogenetic analysis indicated that the ebpS variant in ST22 might have occurred independently of ST121 strains. This is the first report of ST772 PVL-positive MRSA in Nepal and detection of the deletion variant of ebpS in ST22 S. aureus. PMID:27014464

  1. Antiviral Susceptibility of Variant Influenza A(H3N2)v Viruses Isolated in the United States from 2011 to 2013

    PubMed Central

    Sleeman, K.; Mishin, V. P.; Guo, Z.; Garten, R. J.; Balish, A.; Fry, A. M.; Villanueva, J.; Stevens, J.

    2014-01-01

    Since 2011, outbreaks caused by influenza A(H3N2) variant [A(H3N2)v] viruses have become a public health concern in the United States. The A(H3N2)v viruses share the A(H1N1)pdm09 M gene containing the marker of M2 blocker resistance, S31N, but do not contain any known molecular markers associated with resistance to neuraminidase (NA) inhibitors (NAIs). Using a fluorescent NA inhibition (NI) assay, the susceptibilities of recovered A(H3N2)v viruses (n = 168) to FDA-approved (oseltamivir and zanamivir) and other (peramivir, laninamivir, and A-315675) NAIs were assessed. All A(H3N2)v viruses tested, with the exception of a single virus strain, A/Ohio/88/2012, isolated from an untreated patient, were susceptible to the NAIs tested. The A/Ohio/88/2012 virus contained two rare substitutions, S245N and S247P, in the NA and demonstrated reduced inhibition by oseltamivir (31-fold) and zanamivir (66-fold) in the NI assay. Using recombinant NA (recNA) proteins, S247P was shown to be responsible for the observed altered NAI susceptibility, in addition to an approximately 60% reduction in NA enzymatic activity. The S247P substitution has not been previously reported as a molecular marker of reduced susceptibility to the NAIs. Using cell culture assays, the investigational antiviral drugs nitazoxanide, favipiravir, and fludase were shown to inhibit the replication of A(H3N2)v viruses, including the virus with the S247P substitution in the NA. This report demonstrates the importance of continuous monitoring of susceptibility of zoonotic influenza viruses to available and investigational antiviral drugs. PMID:24449767

  2. Genome-wide association analysis on five isolated populations identifies variants of the HLA-DOA gene associated with white wine liking.

    PubMed

    Pirastu, Nicola; Kooyman, Maarten; Traglia, Michela; Robino, Antonietta; Willems, Sara M; Pistis, Giorgio; Amin, Najaf; Sala, Cinzia; Karssen, Lennart C; van Duijn, Cornelia M; Toniolo, Daniela; Gasparini, Paolo

    2015-12-01

    Wine is the most popular alcoholic beverage around the world and because of its importance in society has been widely studied. Understanding what drives its flavor has been a quest for decades but much is still unknown and will be determined at least in part by individual taste preferences. Recently studies in the genetics of taste have uncovered the role of different genes in the determination of food preferences giving new insight on its physiology. In this context we have performed a genome-wide association study on red and white wine liking using three isolated populations collected in Italy, and replicated our results on two additional populations coming from the Netherland and Central Asia for a total of 3885 samples. We have found a significant association (P=2.1 × 10(-8)) between white wine liking and rs9276975:C>T a polymorphism in the HLA-DOA gene encoding a non-canonical MHC II molecule, which regulates other MHC II molecules. The same association was also found with red wine liking (P=8.3 × 10(-6)). Sex-separated analysis have also revealed that the effect of HLA-DOA is twice as large in women as compared to men suggesting an interaction between this polymorphism and gender. Our results are one of the first examples of genome-wide association between liking of a commonly consumed food and gene variants. Moreover, our results suggest a role of the MHC system in the determination of food preferences opening new insight in this field in general. PMID:25758996

  3. A molecular surveillance reveals the prevalence of Vibrio cholerae O139 isolates in China from 1993 to 2012.

    PubMed

    Zhang, Ping; Zhou, Haijian; Diao, Baowei; Li, Fengjuan; Du, Pengcheng; Li, Jie; Kan, Biao; Morris, J Glenn; Wang, Duochun

    2014-04-01

    Vibrio cholerae serogroup O139 was first identified in 1992 in India and Bangladesh, in association with major epidemics of cholera in both countries; cases were noted shortly thereafter in China. We characterized 211 V. cholerae O139 isolates that were isolated at multiple sites in China between 1993 and 2012 from patients (n = 92) and the environment (n = 119). Among clinical isolates, 88 (95.7%) of 92 were toxigenic, compared with 47 (39.5%) of 119 environmental isolates. Toxigenic isolates carried the El Tor CTX prophage and toxin-coregulated pilus A gene (tcpA), as well as the Vibrio seventh pandemic island I (VSP-I) and VSP-II. Among a subset of 42 toxigenic isolates screened by multilocus sequence typing (MLST), all were in the same sequence type as a clinical isolate (MO45) from the original Indian outbreak. Nontoxigenic isolates, in contrast, generally lacked VSP-I and -II, and fell within 13 additional sequence types in two clonal complexes distinct from the toxigenic isolates. In further pulsed-field gel electrophoresis (PFGE) (with NotI digestion) studies, toxigenic isolates formed 60 pulsotypes clustered in one group, while the nontoxigenic isolates formed 43 pulsotypes which clustered into 3 different groups. Our data suggest that toxigenic O139 isolates from widely divergent geographic locations, while showing some diversity, have maintained a relatively tight clonal structure across a 20-year time span. Nontoxigenic isolates, in contrast, exhibited greater diversity, with multiple clonal lineages, than did their toxigenic counterparts. PMID:24452176

  4. Efflux-mediated fluoroquinolone resistance in the multidrug-resistant Pseudomonas aeruginosa clinical isolate PA7: identification of a novel MexS variant involved in upregulation of the mexEF-oprN multidrug efflux operon

    PubMed Central

    Morita, Yuji; Tomida, Junko; Kawamura, Yoshiaki

    2014-01-01

    The emergence of multidrug-resistant Pseudomonas aeruginosa has become a serious problem in medical settings. P. aeruginosa clinical isolate PA7 is resistant to fluoroquinolones, aminoglycosides, and most β-lactams but not imipenem. In this study, enhanced efflux-mediated fluoroquinolone resistance of PA7 was shown to reflect increased expression of two resistance nodulation cell division (RND) -type multidrug efflux operons, mexEF-oprN and mexXY-oprA. Such a clinical isolate has rarely been reported because MexEF-OprN-overproducing mutants often increase susceptibility to aminoglycosides apparently owing to impairment of the MexXY system. A mutant of PA7 lacking three RND-type multidrug efflux operons (mexAB-oprM, mexEF-oprN, and mexXY-oprA) was susceptible to all anti-pseudomonas agents we tested, supporting an idea that these RND-type multidrug efflux transporters are molecular targets to overcome multidrug resistance in P. aeruginosa. mexEF-oprN-upregulation in P. aeruginosa PA7 was shown due to a MexS variant harboring the Valine-155 amino acid residue. This is the first genetic evidence shown that a MexS variant causes mexEF-oprN-upregulation in P. aeruginosa clinical isolates. PMID:25653649

  5. Vibrio cholerae Serogroup O139: Isolation from Cholera Patients and Asymptomatic Household Family Members in Bangladesh between 2013 and 2014

    PubMed Central

    Chowdhury, Fahima; Mather, Alison E.; Begum, Yasmin Ara; Asaduzzaman, Muhammad; Baby, Nabilah; Sharmin, Salma; Biswas, Rajib; Ikhtear Uddin, Muhammad; LaRocque, Regina C.; Harris, Jason B.; Calderwood, Stephen B.; Ryan, Edward T.; Clemens, John D.; Thomson, Nicholas R.; Qadri, Firdausi

    2015-01-01

    Background Cholera is endemic in Bangladesh, with outbreaks reported annually. Currently, the majority of epidemic cholera reported globally is El Tor biotype Vibrio cholerae isolates of the serogroup O1. However, in Bangladesh, outbreaks attributed to V. cholerae serogroup O139 isolates, which fall within the same phylogenetic lineage as the O1 serogroup isolates, were seen between 1992 and 1993 and in 2002 to 2005. Since then, V. cholerae serogroup O139 has only been sporadically isolated in Bangladesh and is now rarely isolated elsewhere. Methods Here, we present case histories of four cholera patients infected with V. cholerae serogroup O139 in 2013 and 2014 in Bangladesh. We comprehensively typed these isolates using conventional approaches, as well as by whole genome sequencing. Phenotypic typing and PCR confirmed all four isolates belonging to the O139 serogroup. Findings Whole genome sequencing revealed that three of the isolates were phylogenetically closely related to previously sequenced El Tor biotype, pandemic 7, toxigenic V. cholerae O139 isolates originating from Bangladesh and elsewhere. The fourth isolate was a non-toxigenic V. cholerae that, by conventional approaches, typed as O139 serogroup but was genetically divergent from previously sequenced pandemic 7 V. cholerae lineages belonging to the O139 or O1 serogroups. Conclusion These results suggest that previously observed lineages of V. cholerae O139 persist in Bangladesh and can cause clinical disease and that a novel disease-causing non-toxigenic O139 isolate also occurs. PMID:26562418

  6. Association Analysis of Bitter Receptor Genes in Five Isolated Populations Identifies a Significant Correlation between TAS2R43 Variants and Coffee Liking

    PubMed Central

    Pirastu, Nicola; Kooyman, Maarten; Traglia, Michela; Robino, Antonietta; Willems, Sara M.; Pistis, Giorgio; d’Adamo, Pio; Amin, Najaf; d’Eustacchio, Angela; Navarini, Luciano; Sala, Cinzia; Karssen, Lennart C.; van Duijn, Cornelia; Toniolo, Daniela; Gasparini, Paolo

    2014-01-01

    Coffee, one of the most popular beverages in the world, contains many different physiologically active compounds with a potential impact on people’s health. Despite the recent attention given to the genetic basis of its consumption, very little has been done in understanding genes influencing coffee preference among different individuals. Given its markedly bitter taste, we decided to verify if bitter receptor genes (TAS2Rs) variants affect coffee liking. In this light, 4066 people from different parts of Europe and Central Asia filled in a field questionnaire on coffee liking. They have been consequently recruited and included in the study. Eighty-eight SNPs covering the 25 TAS2R genes were selected from the available imputed ones and used to run association analysis for coffee liking. A significant association was detected with three SNP: one synonymous and two functional variants (W35S and H212R) on the TAS2R43 gene. Both variants have been shown to greatly reduce in vitro protein activity. Surprisingly the wild type allele, which corresponds to the functional form of the protein, is associated to higher liking of coffee. Since the hTAS2R43 receptor is sensible to caffeine, we verified if the detected variants produced differences in caffeine bitter perception on a subsample of people coming from the FVG cohort. We found a significant association between differences in caffeine perception and the H212R variant but not with the W35S, which suggests that the effect of the TAS2R43 gene on coffee liking is mediated by caffeine and in particular by the H212R variant. No other significant association was found with other TAS2R genes. In conclusion, the present study opens new perspectives in the understanding of coffee liking. Further studies are needed to clarify the role of the TAS2R43 gene in coffee hedonics and to identify which other genes and pathways are involved in its genetics. PMID:24647340

  7. Prevalence of Met-203 type spaA variant in Erysipelothrix rhusiopathiae isolates and the efficacy of swine erysipelas vaccines in Japan.

    PubMed

    Uchiyama, Mariko; Yamamoto, Kinya; Ochiai, Mariko; Yamamoto, Tsukasa; Hirano, Fumiya; Imamura, Saiki; Nagai, Hidetaka; Ohishi, Kouji; Horiuchi, Noriyuki; Kijima, Mayumi

    2014-03-01

    Since 2009, erysipelas infection among pigs in Japan has been increasing. This study investigated the prevalence, and characteristics of Erysipelothrix rhusiopathiae isolates in Japan from 2008 to 2010 and assessed the efficacy of current commercial erysipelas vaccines. Based on polymorphisms in a 432-bp hypervariable region in the surface protective antigen A (spaA) gene, 34 isolates were classified into three groups: (i) Group 1 with methionine at position 203 (Met-203) and isoleucine at position 257 (Ile-257) (18 isolates of serotype 1a and one untypable isolate). (ii) Group 2 with Ile-257 (12 isolates of serotypes 1a, 1b, 2, 10 and 11), and (iii) Group 3 with alanine at position 195 (Ala-195) and Ile-257 (three isolates of serotype 1a). Isolates with Met-203 were highly pathogenic in mice and pigs, causing death in the pig and LD50 values of 0.45-1.45 CFU per mouse. One live and three inactivated commercial E. rhusiopathiae vaccines were evaluated for efficacy against a Met-203 isolate. Almost all mice and pigs that received vaccine survived, while non-vaccinated controls all died within 5 days of the challenge. This indicates that swine erysipelas vaccines might be still effective in protecting animals against the recently prevalent Met-203 isolates in Japan. PMID:24405986

  8. Clade C HIV-1 isolates circulating in Southern Africa exhibit a greater frequency of dicysteine motif-containing Tat variants than those in Southeast Asia and cause increased neurovirulence

    PubMed Central

    2013-01-01

    Background HIV-1 Clade C (Subtype C; HIV-1C) is responsible for greater than 50% of infections worldwide. Unlike clade B HIV-1 (Subtype B; HIV-1B), which is known to cause HIV associated dementia (HAD) in approximately 15% to 30% of the infected individuals, HIV-1C has been linked with lower prevalence of HAD (0 to 6%) in India and Ethiopia. However, recent studies report a higher prevalence of HAD in South Africa, Zambia and Botswana, where HIV-1C infections predominate. Therefore, we examined whether Southern African HIV-1C is genetically distinct and investigated its neurovirulence. HIV-1 Tat protein is a viral determinant of neurocognitive dysfunction. Therefore, we focused our study on the variations seen in tat gene and its contribution to HIV associated neuropathogenesis. Results A phylogenetic analysis of tat sequences of Southern African (South Africa and Zambia) HIV isolates with those from the geographically distant Southeast Asian (India and Bangladesh) isolates revealed that Southern African tat sequences are distinct from Southeast Asian isolates. The proportion of HIV − 1C variants with an intact dicysteine motif in Tat protein (C30C31) was significantly higher in the Southern African countries compared to Southeast Asia and broadly paralleled the high incidence of HAD in these countries. Neuropathogenic potential of a Southern African HIV-1C isolate (from Zambia; HIV-1C1084i), a HIV-1C isolate (HIV-1IndieC1) from Southeast Asia and a HIV-1B isolate (HIV-1ADA) from the US were tested using in vitro assays to measure neurovirulence and a SCID mouse HIV encephalitis model to measure cognitive deficits. In vitro assays revealed that the Southern African isolate, HIV-1C1084i exhibited increased monocyte chemotaxis and greater neurotoxicity compared to Southeast Asian HIV-1C. In neurocognitive tests, SCID mice injected with MDM infected with Southern African HIV-1C1084i showed greater cognitive dysfunction similar to HIV-1B but much higher than those exposed to Southeast Asian HIV − 1C. Conclusions We report here, for the first time, that HIV-1C from Southern African countries is genetically distinct from Southeast Asian HIV-1C and that it exhibits a high frequency of variants with dicysteine motif in a key neurotoxic HIV protein, Tat. Our results indicate that Tat dicysteine motif determines neurovirulence. If confirmed in population studies, it may be possible to predict neurocognitive outcomes of individuals infected with HIV-1C by genotyping Tat. PMID:23758766

  9. AsaGEI2b: a new variant of a genomic island identified in the Aeromonas salmonicida subsp. salmonicida JF3224 strain isolated from a wild fish in Switzerland.

    PubMed

    Emond-Rheault, Jean-Guillaume; Vincent, Antony T; Trudel, Mélanie V; Frey, Joachim; Frenette, Michel; Charette, Steve J

    2015-07-01

    Aeromonas salmonicida subsp. salmonicida is the causal agent of furunculosis in salmonids. We recently identified a group of genomic islands (AsaGEI) in this bacterium. AsaGEI2a, one of these genomic islands, has almost exclusively been identified in isolates from North America. To date, Aeromonas salmonicida subsp. salmonicida JF3224, a strain isolated from a wild brown trout (Salmo trutta) caught in Switzerland, was the only European isolate that appeared to bear AsaGEI2a. We analyzed the genome of JF3224 and showed that the genomic island in JF3224 is a new variant of AsaGEI, which we have called AsaGEI2b. While AsaGEI2b shares the same integrase gene and insertion site as AsaGEI2a, it is very different in terms of many other features. Additional genomic investigations combined with PCR genotyping revealed that JF3224 is sensitive to growth at 25°C, leading to insertion sequence-dependent rearrangement of the locus on the pAsa5 plasmid that encodes a type three secretion system, which is essential for the virulence of the bacterium. The analysis of the JF3224 genome confirmed that AsaGEIs are accurate indicators of the geographic origins of A. salmonicida subsp. salmonicida isolates and is another example of the susceptibility of the pAsa5 plasmid to DNA rearrangements. PMID:26048417

  10. Isolation and characterization of Clostridium difficile from pet dogs in Assam, India.

    PubMed

    Hussain, Isfaqul; Sharma, R K; Borah, P; Rajkhowa, S; Hussain, Iftikar; Barkalita, L M; Hasin, D; Choudhury, M; Rupnik, M; Deka, N K; Saikia, G K

    2015-12-01

    One hundred and seventeen faecal samples from pet dogs (pup = 21 and adult = 96) brought for treatment to a veterinary clinic were examined for Clostridium difficile. A total of 16 (13.67%) samples were positive. Nine (56.25%) isolates were obtained from 17 adult dogs undergoing antibiotic treatment and this was significantly higher (p < 0.01) as compared to isolates from dogs without antibiotic treatment. Ten isolates (62.5%) were toxigenic (all toxinotype 0) and six were non-toxigenic. None of the isolates were positive for binary toxin genes. PCR ribotyping revealed three different ribotypes (012, 014 and 046) among A(+)B(+) isolates and five different ribotypes (010, SLO 131, and ACD 001 to ACD 003) among A(-)B(-) isolates. The PFGE analysis of toxigenic isolates revealed three different pulsotypes corresponding to the PCR ribotypes. PMID:26393292

  11. Aspergillus oryzae NRRL 35191 from coffee, a non-toxigenic endophyte with the ability to synthesize kojic acid

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aspergillus oryzae was isolated as an endophyte from coffee leaves and found to produce kojic acid in culture. When inoculated in cacao seedlings (Theobroma cacao L.), A. oryzae grew endophytically and synthesize kojic acid in planta. Cacao seedlings inoculated with A. oryzae produced higher levels...

  12. Complete Genome Sequence of a Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Variant with a New Insertion in Glycoprotein 5, Isolated from a Stillborn Fetus

    PubMed Central

    Liu, Can; Zhang, Lei

    2015-01-01

    Here, we report the complete genome sequence of strain GD-2011, a highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) that was isolated from a stillborn fetus. The GD-2011 strain is characterized by a discontinuous 30–amino acid deletion in the nonstructural protein 2. In addition, GD-2011 had a 1–amino acid insertion in glycoprotein 5, which does not exist in any other HP-PRRSV strains. PMID:26607885

  13. Complete Genome Sequence of a Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Variant with a New Insertion in Glycoprotein 5, Isolated from a Stillborn Fetus.

    PubMed

    Liu, Can; Zhang, Lei; Ning, Yi-Bao

    2015-01-01

    Here, we report the complete genome sequence of strain GD-2011, a highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) that was isolated from a stillborn fetus. The GD-2011 strain is characterized by a discontinuous 30-amino acid deletion in the nonstructural protein 2. In addition, GD-2011 had a 1-amino acid insertion in glycoprotein 5, which does not exist in any other HP-PRRSV strains. PMID:26607885

  14. Extraintestinal Infections Caused by Non-toxigenic Vibrio cholerae non-O1/non-O139

    PubMed Central

    Chowdhury, Goutam; Joshi, Sangeeta; Bhattacharya, Sanjay; Sekar, Uma; Birajdar, Balaji; Bhattacharyya, Arpita; Shinoda, Sumio; Ramamurthy, Thandavarayan

    2016-01-01

    Vibrio cholerae is an aerobic, sucrose fermentative Gram-negative bacterium that generally prevails in the environment. Pathogenic V. cholerae is well-known as causative agent of acute diarrhea. Apart from enteric infections, V. cholerae may also cause other diseases. However, their role in causing extraintestinal infections is not fully known as it needs proper identification and evaluation. Four cases of extraintestinal infections due to V. cholerae non-O1/non-O139 have been investigated. The isolates were screened for phenotypic and genetic characteristics with reference to their major virulence genes. Serologically distinct isolates harbored rtx, msh, and hly but lacked enteric toxin encoding genes that are generally present in toxigenic V. cholerae. Timely detection of this organism can prevent fatalities in hospital settings. The underlying virulence potential of V. cholerae needs appropriate testing and intervention. PMID:26904017

  15. Extraintestinal Infections Caused by Non-toxigenic Vibrio cholerae non-O1/non-O139.

    PubMed

    Chowdhury, Goutam; Joshi, Sangeeta; Bhattacharya, Sanjay; Sekar, Uma; Birajdar, Balaji; Bhattacharyya, Arpita; Shinoda, Sumio; Ramamurthy, Thandavarayan

    2016-01-01

    Vibrio cholerae is an aerobic, sucrose fermentative Gram-negative bacterium that generally prevails in the environment. Pathogenic V. cholerae is well-known as causative agent of acute diarrhea. Apart from enteric infections, V. cholerae may also cause other diseases. However, their role in causing extraintestinal infections is not fully known as it needs proper identification and evaluation. Four cases of extraintestinal infections due to V. cholerae non-O1/non-O139 have been investigated. The isolates were screened for phenotypic and genetic characteristics with reference to their major virulence genes. Serologically distinct isolates harbored rtx, msh, and hly but lacked enteric toxin encoding genes that are generally present in toxigenic V. cholerae. Timely detection of this organism can prevent fatalities in hospital settings. The underlying virulence potential of V. cholerae needs appropriate testing and intervention. PMID:26904017

  16. Determination of common genetic variants within the non-structural proteins of foot-and-mouth disease viruses isolated in sub-Saharan Africa.

    PubMed

    Nsamba, P; de Beer, T A P; Chitray, M; Scott, K; Vosloo, W; Maree, F F

    2015-05-15

    The non-structural proteins of foot-and-mouth disease virus (FMDV) are responsible for RNA replication, proteolytic processing of the viral polyprotein precursor, folding and assembly of the structural proteins and modification of the cellular translation apparatus. Investigation of the amino acid heterogeneity of the non-structural proteins of seventy-nine FMDV isolates of SAT1, SAT2, SAT3, A and O serotypes revealed between 29 and 62% amino acid variability. The Leader protease (L(pro)) and 3A proteins were the most variable whilst the RNA-dependent RNA polymerase (3D(pol)) the most conserved. Phylogeny based on the non-structural protein-coding regions showed separate clusters for southern African viruses for both the L(pro) and 3C protease (3C(pro)) and sequences unique to this group of viruses, e.g. in the 2C and 3C(pro) proteins. These groupings were unlike serotype groupings based on structural protein-coding regions. The amino acid substitutions and the nature of the naturally occurring substitutions provide insight into the functional domains and regions of the non-structural proteins that are critical for structure-function. The L(pro) of southern African SAT type isolates differed from A, O and SAT isolates in northern Africa, particularly in the auto-processing region. Three-dimensional structures of the 3C protease (3C(pro)) and 3D(pol) showed that the observed variation does not affect the enzymatic active sites or substrate binding sites. Variation in the 3C(pro) cleavage sites demonstrates broad substrate specificity. PMID:25818579

  17. Nontoxigenic Clostridium difficile Protects Hamsters against Challenge with Historic and Epidemic Strains of Toxigenic BI/NAP1/027 C. difficile

    PubMed Central

    Nagaro, Kristin J.; Phillips, S. Tyler; Cheknis, Adam K.; Sambol, Susan P.; Zukowski, Walter E.

    2013-01-01

    Nontoxigenic Clostridium difficile (NTCD) has been shown to prevent fatal C. difficile infection in the hamster model when hamsters are challenged with standard toxigenic C. difficile strains. The purpose of this study was to determine if NTCD can prevent C. difficile infection in the hamster model when hamsters are challenged with restriction endonuclease analysis group BI C. difficile strains. Groups of 10 hamsters were given oral clindamycin, followed on day 2 by 106 CFU of spores of NTCD strain M3 or T7, and were challenged on day 5 with 100 CFU of spores of BI1 or BI6. To conserve animals, results for control hamsters challenged with BI1 or BI6 from the present study and controls from previous identical experiments were combined for statistical comparisons. NTCD strains M3 and T7 achieved 100% colonization and were 100% protective against challenge with BI1 (P ? 0.001). M3 colonized 9/10 hamsters and protected against BI6 challenge in the colonized hamsters (P = 0.0003). T7 colonized 10/10 hamsters, but following BI6 challenge, cocolonization occurred in 5 hamsters, 4 of which died, for protection of 6/10 animals (P = 0.02). NTCD colonization provides protection against challenge with toxigenic BI group strains. M3 is more effective than T7 in preventing C. difficile infection caused by the BI6 epidemic strain. Prevention of C. difficile infection caused by the epidemic BI6 strain may be more challenging than that of infections caused by historic BI1 and non-BI C. difficile strains. PMID:23939887

  18. Protection conferred by live infectious bronchitis vaccine viruses against variant Middle East IS/885/00-like and IS/1494/06-like isolates in commercial broiler chicks

    PubMed Central

    Awad, Faez; Forrester, Anne; Baylis, Matthew; Lemiere, Stephane; Ganapathy, Kannan

    2015-01-01

    The ability of the infectious bronchitis H120 (a Massachusetts strain) and CR88 (a 793B strain) live attenuated vaccine viruses to protect from two Middle East infectious bronchitis virus isolates, IS/885/00-like (IS/885) and IS/1494/06-like (IS/1494) in broiler chicks was investigated. Day-old chicks were separated into three groups, (I) vaccinated with H120 at day-old followed by CR88 at 14 days-old, (II) vaccinated with H120 and CR88 simultaneously at day-old and again with CR88 at 14?days-old, (III) control unvaccinated. At 30?days-old, each of the groups was challenged with virulent IS/885 or IS/1494. Protection was evaluated based on the clinical signs, tracheal and kidney gross lesions and tracheal ciliostasis. Results showed that administering combined live H120 and CR88 vaccines simultaneously at day-old followed by CR88 vaccine at 14?days-old gave more than 80 per cent tracheal ciliary protection from both of the Middle East isolates. In addition, this programme conferred 100 per cent protection from clinical signs and tracheal or kidney lesions. The other vaccination programme, H120 at day-old followed by CR88 at 14 days-old, the tracheal ciliary protection conferred were 60 per cent and 80 per cent from IS/885/00-like and IS/1494/06-like, respectively. PMID:26392909

  19. In Vitro Selection of Highly Darunavir-Resistant and Replication-Competent HIV-1 Variants by Using a Mixture of Clinical HIV-1 Isolates Resistant to Multiple Conventional Protease Inhibitors▿ †

    PubMed Central

    Koh, Yasuhiro; Amano, Masayuki; Towata, Tomomi; Danish, Matthew; Leshchenko-Yashchuk, Sofiya; Das, Debananda; Nakayama, Maki; Tojo, Yasushi; Ghosh, Arun K.; Mitsuya, Hiroaki

    2010-01-01

    We attempted to select HIV-1 variants resistant to darunavir (DRV), which potently inhibits the enzymatic activity and dimerization of protease and has a high genetic barrier to HIV-1 development of resistance to DRV. We conducted selection using a mixture of 8 highly multi-protease inhibitor (PI)-resistant, DRV-susceptible clinical HIV-1 variants (HIV-1MIX) containing 9 to 14 PI resistance-associated amino acid substitutions in protease. HIV-1MIX became highly resistant to DRV, with a 50% effective concentration (EC50) ∼333-fold greater than that against HIV-1NL4-3. HIV-1MIX at passage 51 (HIV-1MIXP51) replicated well in the presence of 5 μM DRV and contained 14 mutations. HIV-1MIXP51 was highly resistant to amprenavir, indinavir, nelfinavir, ritonavir, lopinavir, and atazanavir and moderately resistant to saquinavir and tipranavir. HIV-1MIXP51 had a resemblance with HIV-1C of the HIV-1MIX population, and selection using HIV-1C was also performed; however, its DRV resistance acquisition was substantially delayed. The H219Q and I223V substitutions in Gag, lacking in HIV-1CP51, likely contributed to conferring a replication advantage on HIV-1MIXP51 by reducing intravirion cyclophilin A content. HIV-1MIXP51 apparently acquired the substitutions from another HIV-1 strain(s) of HIV-1MIX through possible homologous recombination. The present data suggest that the use of multiple drug-resistant HIV-1 isolates is of utility in selecting drug-resistant variants and that DRV would not easily permit HIV-1 to develop significant resistance; however, HIV-1 can develop high levels of DRV resistance when a variety of PI-resistant HIV-1 strains are generated, as seen in patients experiencing sequential PI failure, and ensuing homologous recombination takes place. HIV-1MIXP51 should be useful in elucidating the mechanisms of HIV-1 resistance to DRV and related agents. PMID:20810732

  20. Serotypes of attachment pili of enterotoxigenic Escherichia coli isolated from humans.

    PubMed Central

    Deneke, C F; Thorne, G M; Gorbach, S L

    1981-01-01

    Pili from enterotoxigenic Escherichia coli isolated from humans have been partially purified, and antisera have been prepared. These pili were initially attached to erythrocytes and then removed by thermal elution for purification. Three distinct antigenic types of pili have been identified. Antisera against these three pili types reacted with 60 of 106 (56%) enterotoxigenic E. coli isolated from humans but not with nontoxigenic, normal human fecal isolates of E. coli nor with enterotoxigenic E. coli strains isolated from animals. There was no correlation between pili serogroup and any of the following toxin production (heat labile, heat stable, or both), O antigenic type, geographical source of isolation, or mannose-resistant hemagglutination patterns of various erythrocyte types. Images PMID:6114039

  1. Characterization of a cluster of oncogenic mutations in E6 of a human papillomavirus 83 variant isolated from a high-grade squamous intraepithelial lesion.

    PubMed

    Cannavo, Isabelle; Benchetrit, Maxime; Loubatier, Céline; Michel, Gregory; Lemichez, Emmanuel; Giordanengo, Valérie

    2011-10-01

    We previously isolated human papillomavirus 83 (HPV83m) from a cervical smear. Sequence analysis of E6 and E7 proteins highlighted five mutations located in the second putative zinc-finger region of E6 (E6m), an important domain for protein-protein or protein-DNA interactions. Here, we show that E6m of HPV83m can trigger human primary cell proliferation and anchorage-independent growth properties, similarly to E6 of HPV16, a high-risk HPV (HR-HPV). Interestingly, we demonstrate that, in contrast to E6 of HPV16, E6m corrupts neither p53 stability nor telomerase activity, but acts as a specific modulator of the transcriptional machinery. By studying E6m reversion mutants, we confirmed the importance of the second zinc-finger domain in triggering the observed upregulation of cell growth and of the transcriptional machinery. Reversion of these mutations in E6m (to yield strain E6r) fully abolished the oncogenic potential of E6m, transforming the phenotype of E6 from a high-risk to a low-risk phenotype. Importantly, our data define the importance of a cluster of mutations in the second zinc finger of E6m in increasing the oncogenic potential of HPV83. PMID:21752964

  2. Characterization of Microbulbifer strain CMC-5, a new biochemical variant of Microbulbifer elongatus type strain DSM6810T isolated from decomposing seaweeds.

    PubMed

    Jonnadula, RaviChand; Verma, Pankaj; Shouche, Yogesh S; Ghadi, Sanjeev C

    2009-12-01

    A Gram-negative, rod-shaped, non-spore forming, non-motile and moderate halophilic bacteria designated as strain CMC-5 was isolated from decomposing seaweeds by enrichment culture. The growth of strain CMC-5 was assessed in synthetic seawater-based medium containing polysaccharide. The bacterium degraded and utilized agar, alginate, carrageenan, xylan, carboxymethyl cellulose and chitin. The strain was characterized using a polyphasic approach for taxonomic identification. Cellular fatty acid analysis showed the presence of iso-C(15:0) as major fatty acid and significant amounts of iso-C(17:1x9c) and C(18:1x7c). Phylogenetic analysis based on 16S rDNA sequence indicated that strain CMC-5 is phylogenetically related to Microbulbifer genus and 99% similar to type strain Microbulbifer elongatus DSM6810T. However in contrast to Microbulbifer elongatus DSM6810T, strain CMC-5 is non-motile, utilizes glucose, galactose, inositol and xylan, does not utilize fructose and succinate nor does it produce H2S. Further growth of bacterial strain CMC-5 was observed when inoculated in seawater-based medium containing sterile pieces of Gracilaria corticata thalli. The bacterial growth was associated with release of reducing sugar in the broth suggesting its role in carbon recycling of polysaccharides from seaweeds in marine ecosystem. PMID:19701665

  3. Risk Factors of Fecal Toxigenic or Non-Toxigenic Clostridium difficile Colonization: Impact of Toll-Like Receptor Polymorphisms and Prior Antibiotic Exposure

    PubMed Central

    Wu, Tai-Chieh; Liu, Hsiu-Chuan; Lee, Jen-Chieh; Lee, Chih-I; Wu, Yi-Hui; Wan, Lei; Tsai, Pei-Jane; Ko, Wen-Chien

    2013-01-01

    Background This study is to investigate the significance and risk factors of fecal toxigenic (tCdC) or non-toxigenic Clostridium difficile colonization (ntCdC) among hospitalized patients. Methods Adults admitted to medical wards in a district hospital between January 2011 and June 2012 were enrolled, and those with a history of colectomy, C. difficile fecal colonization or infection or receipt of either metronidazole or oral vancomycin within 3 months, were excluded. Stools collected within 48 hours after admission and every week during hospitalization were cultured for C. difficile. Findings Among the 441 enrolled patients, 84 (20.0%) had CdC at initial screening, including 58 (13.2%) with tCdC and 26 (6.8%) with ntCdC. Among patients with initial negative fecal screening for CdC, it took an average of 70.6 days or 66.5 days to develop tCdC or ntCdC during the study period. Finally 78 (17.7%) had tCdC and 34 (7.7%) had ntCdC. During the follow-up period, the patients with tCdC had a higher risk of CDAD (11/79, 14.1%) than those without CdC (3/328, 0.9%) and those with ntCdC (0/34, 0%) (P<0.001). In multivariate analysis, the TLR4 rs1927914 polymorphism (GG genotype) (odds ratio [OR] 4.4, 95% confidence interval [CI] 1.6–11.8, P = 0.003) and recent cefepime therapy (OR 5.3, 95% CI 2.1–13.2, P<0.001) were independently associated with tCdC, whereas recent cefuroxime (OR 11.7, 95% CI 2.3–60.2, P = 0.003) and glycopeptide therapy (OR 10.9, CI: 2.1–57.2, P = 0.005) associated with ntCdC. Conclusion The incidence of CDAD is highest in patients with tCdC and lowest in patients with ntCdC, and the TLR4 rs1927914 polymorphism GG genotype and recent cefepime therapy were independently associated with tCdC. PMID:23936050

  4. Efficacy of commercial produce sanitizers against nontoxigenic Escherichia coli O157:H7 during processing of iceberg lettuce in a pilot-scale leafy green processing line.

    PubMed

    Davidson, Gordon R; Buchholz, Annemarie L; Ryser, Elliot T

    2013-11-01

    Chemical sanitizers are routinely used during commercial flume washing of fresh-cut leafy greens to minimize cross-contamination from the water. This study assessed the efficacy of five commercial sanitizer treatments against Escherichia coli O157:H7 on iceberg lettuce, in wash water, and on equipment during simulated commercial production in a pilot-scale processing line. Iceberg lettuce (5.4 kg) was inoculated to contain 10(6) CFU/g of a four-strain cocktail of nontoxigenic, green fluorescent protein-labeled, ampicillin-resistant E. coli O157:H7 and processed after 1 h of draining at ~22 °C. Lettuce was shredded using a commercial slicer, step-conveyed to a flume tank, washed for 90 s using six different treatments (water alone, 50 ppm of peroxyacetic acid, 50 ppm of mixed peracid, or 50 ppm of available chlorine either alone or acidified to pH 6.5 with citric acid [CA] or T-128), and then dried using a shaker table and centrifugal dryer. Various product (25-g) and water (50-ml) samples collected during processing along with equipment surface samples (100 cm(2)) from the flume tank, shaker table, and centrifugal dryer were homogenized in neutralizing buffer and plated on tryptic soy agar. During and after iceberg lettuce processing, none of the sanitizers were significantly more effective (P ≤ 0.05) than water alone at reducing E. coli O157:H7 populations on lettuce, with reductions ranging from 0.75 to 1.4 log CFU/g. Regardless of the sanitizer treatment used, the centrifugal dryer surfaces yielded E. coli O157:H7 populations of 3.49 to 4.98 log CFU/100 cm(2). Chlorine, chlorine plus CA, and chlorine plus T-128 were generally more effective (P ≤ 0.05) than the other treatments, with reductions of 3.79, 5.47, and 5.37 log CFU/ml after 90 s of processing, respectively. This indicates that chlorine-based sanitizers will likely prevent wash water containing low organic loads from becoming a vehicle for cross-contamination. PMID:24215685

  5. Characterization of rabies virus isolates in Bolivia.

    PubMed

    Favi, Myriam; Nina, Aleida; Yung, Verónica; Fernández, Jorge

    2003-11-01

    In Latin America, rabies is still an important public health problem. Canine rabies, and wild animal rabies, especially transmitted by hematofagous and insectivorous bats, has become an emerging problem in the countries of this region. We received 363 samples with a laboratory-confirmed rabies diagnosis from Bolivia during l997-2001. From these, we could obtain 222 rabies virus isolates by intra-cerebral inoculation in mice. By antigenic characterization we could identify 147 isolates as variant 1, 2 isolates as variant 2, 3 isolates as variant 3, and 1 isolate as variant 5. Phylogenetic analysis of 84 isolates established that they segregated in 3 different branches, corresponding to 3 genetic variants, 78 isolates corresponding to antigenic variant 1 segregated in the same lineage as the antigenic variant 5, 2 isolates corresponding to antigenic variant 2 segregated in another lineage, and 3 isolates from antigenic variant 3 segregated in a different lineage.The genetic variant that mainly circulates in Bolivia is maintained in a cycle whose main reservoir are dogs, but it is not possible to discard the presence of other cycles, in which different species of bats or other wild mammals could be participating. PMID:14602205

  6. Characterizations of clinical isolates of clostridium difficile by toxin genotypes and by susceptibility to 12 antimicrobial agents, including fidaxomicin (OPT-80) and rifaximin: a multicenter study in Taiwan.

    PubMed

    Liao, Chun-Hsing; Ko, Wen-Chien; Lu, Jang-Jih; Hsueh, Po-Ren

    2012-07-01

    A total of 403 nonduplicate isolates of Clostridium difficile were collected at three major teaching hospitals representing northern, central, and southern Taiwan from January 2005 to December 2010. Of these 403 isolates, 170 (42.2%) were presumed to be nontoxigenic due to the absence of genes for toxins A or B or binary toxin. The remaining 233 (57.8%) isolates carried toxin A and B genes, and 39 (16.7%) of these also had binary toxin genes. The MIC(90) of all isolates for fidaxomicin and rifaximin was 0.5 ?g/ml (range, ? 0.015 to 0.5 ?g/ml) and >128 ?g/ml (range, ? 0.015 to >128 ?g/ml), respectively. All isolates were susceptible to metronidazole (MIC(90) of 0.5 ?g/ml; range, ? 0.03 to 4 ?g/ml). Two isolates had reduced susceptibility to vancomycin (MICs, 4 ?g/ml). Only 13.6% of isolates were susceptible to clindamycin (MIC of ? 2 ?g/ml). Nonsusceptibility to moxifloxacin (n = 81, 20.1%) was accompanied by single or multiple mutations in gyrA and gyrB genes in all but eight moxifloxacin-nonsusceptible isolates. Two previously unreported gyrB mutations might independently confer resistance (MIC, 16 ?g/ml), Ser416 to Ala and Glu466 to Lys. Moxifloxacin-resistant isolates were cross-resistant to ciprofloxacin and levofloxacin, but some moxifloxacin-nonsusceptible isolates remained susceptible to gemifloxacin or nemonoxacin at 0.5 ?g/ml. This study found the diversity of toxigenic and nontoxigenic strains of C. difficile in the health care setting in Taiwan. All isolates tested were susceptible to metronidazole and vancomycin. Fidaxomicin exhibited potent in vitro activity against all isolates tested, while the more than 10% of Taiwanese isolates with rifaximin MICs of ? 128 ?g/ml raises concerns. PMID:22508299

  7. Characterizations of Clinical Isolates of Clostridium difficile by Toxin Genotypes and by Susceptibility to 12 Antimicrobial Agents, Including Fidaxomicin (OPT-80) and Rifaximin: a Multicenter Study in Taiwan

    PubMed Central

    Liao, Chun-Hsing; Ko, Wen-Chien; Lu, Jang-Jih

    2012-01-01

    A total of 403 nonduplicate isolates of Clostridium difficile were collected at three major teaching hospitals representing northern, central, and southern Taiwan from January 2005 to December 2010. Of these 403 isolates, 170 (42.2%) were presumed to be nontoxigenic due to the absence of genes for toxins A or B or binary toxin. The remaining 233 (57.8%) isolates carried toxin A and B genes, and 39 (16.7%) of these also had binary toxin genes. The MIC90 of all isolates for fidaxomicin and rifaximin was 0.5 ?g/ml (range, ?0.015 to 0.5 ?g/ml) and >128 ?g/ml (range, ?0.015 to >128 ?g/ml), respectively. All isolates were susceptible to metronidazole (MIC90 of 0.5 ?g/ml; range, ?0.03 to 4 ?g/ml). Two isolates had reduced susceptibility to vancomycin (MICs, 4 ?g/ml). Only 13.6% of isolates were susceptible to clindamycin (MIC of ?2 ?g/ml). Nonsusceptibility to moxifloxacin (n = 81, 20.1%) was accompanied by single or multiple mutations in gyrA and gyrB genes in all but eight moxifloxacin-nonsusceptible isolates. Two previously unreported gyrB mutations might independently confer resistance (MIC, 16 ?g/ml), Ser416 to Ala and Glu466 to Lys. Moxifloxacin-resistant isolates were cross-resistant to ciprofloxacin and levofloxacin, but some moxifloxacin-nonsusceptible isolates remained susceptible to gemifloxacin or nemonoxacin at 0.5 ?g/ml. This study found the diversity of toxigenic and nontoxigenic strains of C. difficile in the health care setting in Taiwan. All isolates tested were susceptible to metronidazole and vancomycin. Fidaxomicin exhibited potent in vitro activity against all isolates tested, while the more than 10% of Taiwanese isolates with rifaximin MICs of ?128 ?g/ml raises concerns. PMID:22508299

  8. Characterization of an Acholeplasma laidlawii variant with a REP- phenotype.

    PubMed Central

    Nowak, J A; Das, J; Maniloff, J

    1976-01-01

    An Acholeplasma laidlawii variant has been isolated that has a REP- phenotype. The properties of this variant, relative to parental cells, are: (i) it exhibits no change in cell growth kinetics; (ii) it does not propagate single-stranded deoxyribonucleic acid (DNA) mycoplasmaviruses but does propagate double-stranded DNA mycoplasmaviruses; (iii) it converts parental circular single-stranded mycoplasmavirus DNA to double-stranded replicative forms that are not replicated further; (iv) it exhibits no change in host modification and restriction; and (v) it has an increased ultraviolet light sensitivity. The REP- isolate is the first stable mycoplasma variant to which a physiological defect has been attributed. PMID:956119

  9. The [PSI+] Prion Exists as a Dynamic Cloud of Variants

    PubMed Central

    Bateman, David A.; Wickner, Reed B.

    2013-01-01

    [PSI+] is an amyloid-based prion of Sup35p, a subunit of the translation termination factor. Prion “strains” or “variants” are amyloids with different conformations of a single protein sequence, conferring different phenotypes, but each relatively faithfully propagated. Wild Saccharomyces cerevisiae isolates have SUP35 alleles that fall into three groups, called reference, ?19, and E9, with limited transmissibility of [PSI+] between cells expressing these different polymorphs. Here we show that prion transmission pattern between different Sup35 polymorphs is prion variant-dependent. Passage of one prion variant from one Sup35 polymorph to another need not change the prion variant. Surprisingly, simple mitotic growth of a [PSI+] strain results in a spectrum of variant transmission properties among the progeny clones. Even cells that have grown for >150 generations continue to vary in transmission properties, suggesting that simple variant segregation is insufficient to explain the results. Rather, there appears to be continuous generation of a cloud of prion variants, with one or another becoming stochastically dominant, only to be succeeded by a different mixture. We find that among the rare wild isolates containing [PSI+], all indistinguishably “weak” [PSI+], are several different variants based on their transmission efficiencies to other Sup35 alleles. Most show some limitation of transmission, indicating that the evolved wild Sup35 alleles are effective in limiting the spread of [PSI+]. Notably, a “strong [PSI+]” can have any of several different transmission efficiency patterns, showing that “strong” versus “weak” is insufficient to indicate prion variant uniformity. PMID:23382698

  10. The [PSI+] prion exists as a dynamic cloud of variants.

    PubMed

    Bateman, David A; Wickner, Reed B

    2013-01-01

    [PSI(+)] is an amyloid-based prion of Sup35p, a subunit of the translation termination factor. Prion "strains" or "variants" are amyloids with different conformations of a single protein sequence, conferring different phenotypes, but each relatively faithfully propagated. Wild Saccharomyces cerevisiae isolates have SUP35 alleles that fall into three groups, called reference, ?19, and E9, with limited transmissibility of [PSI(+)] between cells expressing these different polymorphs. Here we show that prion transmission pattern between different Sup35 polymorphs is prion variant-dependent. Passage of one prion variant from one Sup35 polymorph to another need not change the prion variant. Surprisingly, simple mitotic growth of a [PSI(+)] strain results in a spectrum of variant transmission properties among the progeny clones. Even cells that have grown for >150 generations continue to vary in transmission properties, suggesting that simple variant segregation is insufficient to explain the results. Rather, there appears to be continuous generation of a cloud of prion variants, with one or another becoming stochastically dominant, only to be succeeded by a different mixture. We find that among the rare wild isolates containing [PSI(+)], all indistinguishably "weak" [PSI(+)], are several different variants based on their transmission efficiencies to other Sup35 alleles. Most show some limitation of transmission, indicating that the evolved wild Sup35 alleles are effective in limiting the spread of [PSI(+)]. Notably, a "strong [PSI(+)]" can have any of several different transmission efficiency patterns, showing that "strong" versus "weak" is insufficient to indicate prion variant uniformity. PMID:23382698

  11. Human papillomavirus variants among Inuit women in northern Quebec, Canada

    PubMed Central

    Gauthier, Barbara; Coutlée, Francois; Franco, Eduardo L.; Brassard, Paul

    2015-01-01

    Background Inuit communities in northern Quebec have high rates of human papillomavirus (HPV) infection, cervical cancer and cervical cancer–related mortality as compared to the Canadian population. HPV types can be further classified as intratypic variants based on the extent of homology in their nucleotide sequences. There is limited information on the distribution of intratypic variants in circumpolar areas. Objective Our goal was to describe the HPV intratypic variants and associated baseline characteristics. Design We collected cervical cell samples in 2002–2006 from 676 Inuit women between the ages of 15 and 69 years in Nunavik. DNA isolates from high-risk HPVs were sequenced to determine the intratypic variant. Results There were 149 women that were positive for HPVs 16, 18, 31, 33, 35, 45, 52, 56 or 58 during follow-up. There were 5 different HPV16 variants, all of European lineage, among the 57 women positive for this type. There were 8 different variants of HPV18 present and all were of European lineage (n=21). The majority of samples of HPV31 (n=52) were of lineage B. The number of isolates and diversity of the other HPV types was low. Age was the only covariate associated with HPV16 variant category. Conclusions These frequencies are similar to what was seen in another circumpolar region of Canada, although there appears to be less diversity as only European variants were detected. This study shows that most variants were clustered in one lineage for each HPV type. PMID:26653084

  12. Mucopolysaccharidosis: A New Variant?

    ERIC Educational Resources Information Center

    Primrose, D. A.

    1972-01-01

    Described is a possibly new variant of mucopolysaccharidosis characterized by progressive mental and motor deficiency, bone abnormalities, a generalized skin lesion, and abnormal mucopolysaccharides in the urine as seen in a 20-year-old female. (DB)

  13. Effect of indigenous mycobiota on ochratoxin A production by Aspergillus carbonarius isolated from soil: ochratoxin in mixed cultures.

    PubMed

    Barberis, Carla L; Pena, Gabriela; Carranza, Cecilia; Magnoli, Carina E

    2014-02-01

    This study determined the biotic interaction between 30 non-toxigenic indigenous strains of Aspergillus niger aggregate, Aspergillus flavus, Trichoderma spp., Mucor spp., Cladosporium spp., Ulocladium spp., Curvularia spp., Absidia spp., Geotrichum spp. and Acremonium spp., isolated from soil destined for maize crops, with respect to their ability to prevent ochratoxin A (OTA) production by A. carbonarius on "in vitro" assay, on liquid and solid medium. OTA production was completely inhibited when A. carbonarius was inoculated in a interactive mixed culture with all A. niger aggregate strains assayed, a 80 % of Trichoderma spp. strains, a 40 % of Cladosporium spp. strains, Acremonium spp and Geotrichum spp; only one strain of A. flavus tested was able to completely inhibit the mycotoxin accumulation. OTA production increased when A. carbonarius ACS 8 was growing on liquid interactive mixed culture with Mucor spp strains. These results demonstrated that OTA production by Aspergillua carbonarius strain was significantly influenced by the presence of different non-toxigenic fungal strains when growing together on paired cultures. PMID:24155120

  14. Biotic and abiotic variables affecting internalization and fate of Escherichia coli O157:H7 isolates in leafy green roots.

    PubMed

    Erickson, Marilyn C; Webb, Cathy C; Davey, Lindsey E; Payton, Alison S; Flitcroft, Ian D; Doyle, Michael P

    2014-06-01

    Preharvest internalization of Escherichia coli O157:H7 into the roots of leafy greens is a food safety risk because the pathogen may be systemically transported to edible portions of the plant. In this study, both abiotic (degree of soil moisture) and biotic (E. coli O157:H7 exposure, presence of Shiga toxin genes, and type of leafy green) factors were examined to determine their potential effects on pathogen internalization into roots of leafy greens. Using field soil that should have an active indigenous microbial community, internalized populations in lettuce roots were 0.8 to 1.6 log CFU/g after exposure to soil containing E. coli O157:H7 at 5.6 to 6.1 log CFU/g. Internalization of E. coli O157:H7 into leafy green plant roots was higher when E. coli O157:H7 populations in soil were increased to 7 or 8 log CFU/g or when the soil was saturated with water. No differences were noted in the extent to which internalization of E. coli O157:H7 occurred in spinach, lettuce, or parsley roots; however, in saturated soil, maximum levels in parsley occurred later than did those in spinach or lettuce. Translocation of E. coli O157:H7 from roots to leaves was rare; therefore, decreases observed in root populations over time were likely the result of inactivation within the plant tissue. Shiga toxin-negative (nontoxigenic) E. coli O157:H7 isolates were more stable than were virulent isolates in soil, but the degree of internalization of E. coli O157:H7 into roots did not differ between isolate type. Therefore, these nontoxigenic isolates could be used as surrogates for virulent isolates in field trials involving internalization. PMID:24853507

  15. A survey of metronidazole and vancomycin resistance in strains of Clostridium difficile isolated in Warsaw, Poland.

    PubMed

    Pituch, Hanna; Obuch-Woszczaty?ski, Piotr; Wulta?ska, Dorota; Meisel-Miko?ajczyk, Felicja; ?uczak, Miros?aw

    2005-08-01

    The drug of choice used to treat Clostridium difficile-associated diarroea (CDAD) are metronidazole and vancomycin. Information about emergence of antimicrobial resistance among C. difficile strains to metronidazole and intermediate resistance to vancomycin in some countries are alarming. This study was performed to determine the susceptibility to metronidazole and vancomycin of 193 C. difficile strains isolated in our diagnostic laboratory between year 1998 and 2003 from patients adults and children suffering from CDAD. Among these strains, 142 produced toxin A and B (TcdA(+)TcdB(+)), 43 only B (TcdA(-)TcdB(+)) and 8 were nontoxigenic. We have not observed any differences in susceptibility to metronidazole and vancomycin between all C. difficile strains under investigation (toxinogenic and non-toxinogenic). Resistance to metronidazole and vancomycin was not observed. PMID:16701568

  16. Searching for missing heritability: Designing rare variant association studies

    PubMed Central

    Zuk, Or; Schaffner, Stephen F.; Samocha, Kaitlin; Do, Ron; Hechter, Eliana; Kathiresan, Sekar; Daly, Mark J.; Neale, Benjamin M.; Sunyaev, Shamil R.; Lander, Eric S.

    2014-01-01

    Genetic studies have revealed thousands of loci predisposing to hundreds of human diseases and traits, revealing important biological pathways and defining novel therapeutic hypotheses. However, the genes discovered to date typically explain less than half of the apparent heritability. Because efforts have largely focused on common genetic variants, one hypothesis is that much of the missing heritability is due to rare genetic variants. Studies of common variants are typically referred to as genomewide association studies, whereas studies of rare variants are often simply called sequencing studies. Because they are actually closely related, we use the terms common variant association study (CVAS) and rare variant association study (RVAS). In this paper, we outline the similarities and differences between RVAS and CVAS and describe a conceptual framework for the design of RVAS. We apply the framework to address key questions about the sample sizes needed to detect association, the relative merits of testing disruptive alleles vs. missense alleles, frequency thresholds for filtering alleles, the value of predictors of the functional impact of missense alleles, the potential utility of isolated populations, the value of gene-set analysis, and the utility of de novo mutations. The optimal design depends critically on the selection coefficient against deleterious alleles and thus varies across genes. The analysis shows that common variant and rare variant studies require similarly large sample collections. In particular, a well-powered RVAS should involve discovery sets with at least 25,000 cases, together with a substantial replication set. PMID:24443550

  17. Splicing variants of porcine synphilin-1?

    PubMed Central

    Larsen, Knud; Madsen, Lone Bruhn; Farajzadeh, Leila; Bendixen, Christian

    2015-01-01

    Parkinson's disease (PD), idiopathic and familial, is characterized by degradation of dopaminergic neurons and the presence of Lewy bodies (LB) in the substantia nigra. LBs contain aggregated proteins of which ?-synuclein is the major component. The protein synphilin-1 interacts and colocalizes with ?-synuclein in LBs. The aim of this study was to isolate and characterize porcine synphilin-1 and isoforms hereof with the future perspective to use the pig as a model for Parkinson's disease. The porcine SNCAIP cDNA was cloned by reverse transcriptase PCR. The spatial expression of SNCAIP mRNA was investigated by RNAseq. The presented work reports the molecular cloning and characterization of the porcine (Sus scrofa) synphilin-1 cDNA (SNCAIP) and three splice variants hereof. The porcine SNCAIP cDNA codes for a protein (synphilin-1) of 919 amino acids which shows a high similarity to human (90%) and to mouse (84%) synphilin-1. Three shorter transcript variants of the synphilin-1 gene were identified, all lacking one or more exons. SNCAIP transcripts were detected in most examined organs and tissues and the highest expression was found in brain tissues and lung. Conserved splicing variants and a novel splice form of synhilin-1 were found in this study. All synphilin-1 isoforms encoded by the identified transcript variants lack functional domains important for protein degradation. PMID:26101749

  18. Splicing variants of porcine synphilin-1.

    PubMed

    Larsen, Knud; Madsen, Lone Bruhn; Farajzadeh, Leila; Bendixen, Christian

    2015-09-01

    Parkinson's disease (PD), idiopathic and familial, is characterized by degradation of dopaminergic neurons and the presence of Lewy bodies (LB) in the substantia nigra. LBs contain aggregated proteins of which ?-synuclein is the major component. The protein synphilin-1 interacts and colocalizes with ?-synuclein in LBs. The aim of this study was to isolate and characterize porcine synphilin-1 and isoforms hereof with the future perspective to use the pig as a model for Parkinson's disease. The porcine SNCAIP cDNA was cloned by reverse transcriptase PCR. The spatial expression of SNCAIP mRNA was investigated by RNAseq. The presented work reports the molecular cloning and characterization of the porcine (Sus scrofa) synphilin-1 cDNA (SNCAIP) and three splice variants hereof. The porcine SNCAIP cDNA codes for a protein (synphilin-1) of 919 amino acids which shows a high similarity to human (90%) and to mouse (84%) synphilin-1. Three shorter transcript variants of the synphilin-1 gene were identified, all lacking one or more exons. SNCAIP transcripts were detected in most examined organs and tissues and the highest expression was found in brain tissues and lung. Conserved splicing variants and a novel splice form of synhilin-1 were found in this study. All synphilin-1 isoforms encoded by the identified transcript variants lack functional domains important for protein degradation. PMID:26101749

  19. LRP5 variants may contribute to ADPKD.

    PubMed

    Cnossen, Wybrich R; Te Morsche, René Hm; Hoischen, Alexander; Gilissen, Christian; Venselaar, Hanka; Mehdi, Soufi; Bergmann, Carsten; Losekoot, Monique; Breuning, Martijn H; Peters, Dorien Jm; Veltman, Joris A; Drenth, Joost Ph

    2016-02-01

    Mutations in Polycystic Kidney Disease proteins (PKD1 or PKD2) are causative for autosomal dominant polycystic kidney disease (ADPKD). However, a small subset of ADPKD probands do not harbor a mutation in any of the known genes. Low density lipoprotein Receptor-related Protein 5 (LRP5) was recently associated with hepatic cystogenesis in isolated polycystic liver disease (PCLD). Here, we demonstrate that this gene may also have a role in unlinked and sporadic ADPKD patients. In a cohort of 79 unrelated patients with adult-onset ADPKD, we identified a total of four different LRP5 variants that were predicted to be pathogenic by in silico tools. One ADPKD patient has a positive family history for ADPKD and variant LRP5 c.1680G>T; p.(Trp560Cys) segregated with the disease. Although also two PKD1 variants probably affecting protein function were identified, luciferase activity assays presented for three LRP5 variants significant decreased signal activation of canonical Wnt signaling. This study contributes to the genetic spectrum of ADPKD. Introduction of the canonical Wnt signaling pathway provides new avenues for the study of the pathophysiology. PMID:25920554

  20. Antigenic stability of foot-and-mouth disease virus variants on serial passage in cell culture.

    PubMed Central

    Gonzalez, M J; Saiz, J C; Laor, O; Moore, D M

    1991-01-01

    Two neutralizing monoclonal antibody (MAb)-resistant variants selected from an isolate of foot-and-mouth disease virus (FMDV) type A5 were repeatedly passaged in cell culture and monitored for susceptibility to neutralization by the selecting MAb. A variant isolated with a MAb to a conformational epitope (1-OG2) lost resistance in 20 passages, while a variant isolated with a MAb to a linear epitope (1-HA6) persisted for 30 passages. In both cases, the virus population emerging after passage was antigenically and genetically indistinguishable from the original wild-type parental virus (FMDV A5 Spain-86). Coinfection assays with the wild type and each variant, and between the variants, showed rapid conversion to a homogeneous population. Wild-type virus prevailed over the variants and for coinfection between the variants, the linear epitope variant 1-HA6. While both variants arose from a single nucleotide substitution and reversion to wild type occurred for each, it appears that the variant based on the continuous epitope (1-HA6) was more stable. We discuss the implications of these results for the antigenic diversity of FMDV and its relationship to virus evolution. PMID:1645803

  1. Parenteral Adjuvant Effects of an Enterotoxigenic Escherichia coli Natural Heat-Labile Toxin Variant.

    PubMed

    Braga, Catarina J M; Rodrigues, Juliana F; Medina-Armenteros, Yordanka; Farinha-Arcieri, Luís E; Ventura, Armando M; Boscardin, Silvia B; Sbrogio-Almeida, Maria E; Ferreira, Luís C S

    2014-01-01

    Native type I heat-labile toxins (LTs) produced by enterotoxigenic Escherichia coli (ETEC) strains exert strong adjuvant effects on both antibody and T cell responses to soluble and particulate antigens following co-administration via mucosal routes. However, inherent enterotoxicity and neurotoxicity (following intra-nasal delivery) had reduced the interest in the use of these toxins as mucosal adjuvants. LTs can also behave as powerful and safe adjuvants following delivery via parenteral routes, particularly for activation of cytotoxic lymphocytes. In the present study, we evaluated the adjuvant effects of a new natural LT polymorphic form (LT2), after delivery via intradermal (i.d.) and subcutaneous (s.c.) routes, with regard to both antibody and T cell responses. A recombinant HIV-1 p24 protein was employed as a model antigen for determination of antigen-specific immune responses while the reference LT (LT1), produced by the ETEC H10407 strain, and a non-toxigenic LT form (LTK63) were employed as previously characterized LT types. LT-treated mice submitted to a four dose-base immunization regimen elicited similar p24-specific serum IgG responses and CD4(+) T cell activation. Nonetheless, mice immunized with LT1 or LT2 induced higher numbers of antigen-specific CD8(+) T cells and in vivo cytotoxic responses compared to mice immunized with the non-toxic LT derivative. These effects were correlated with stronger activation of local dendritic cell populations. In addition, mice immunized with LT1 and LT2, but not with LTK63, via s.c. or i.d. routes developed local inflammatory reactions. Altogether, the present results confirmed that the two most prevalent natural polymorphic LT variants (LT1 or LT2) display similar and strong adjuvant effects for subunit vaccines administered via i.d. or s.c. routes. PMID:24432018

  2. Variants of glycoside hydrolases

    SciTech Connect

    Teter, Sarah; Ward, Connie; Cherry, Joel; Jones, Aubrey; Harris, Paul; Yi, Jung

    2013-02-26

    The present invention relates to variants of a parent glycoside hydrolase, comprising a substitution at one or more positions corresponding to positions 21, 94, 157, 205, 206, 247, 337, 350, 373, 383, 438, 455, 467, and 486 of amino acids 1 to 513 of SEQ ID NO: 2, and optionally further comprising a substitution at one or more positions corresponding to positions 8, 22, 41, 49, 57, 113, 193, 196, 226, 227, 246, 251, 255, 259, 301, 356, 371, 411, and 462 of amino acids 1 to 513 of SEQ ID NO: 2 a substitution at one or more positions corresponding to positions 8, 22, 41, 49, 57, 113, 193, 196, 226, 227, 246, 251, 255, 259, 301, 356, 371, 411, and 462 of amino acids 1 to 513 of SEQ ID NO: 2, wherein the variants have glycoside hydrolase activity. The present invention also relates to nucleotide sequences encoding the variant glycoside hydrolases and to nucleic acid constructs, vectors, and host cells comprising the nucleotide sequences.

  3. Variants of glycoside hydrolases

    DOEpatents

    Teter, Sarah (Davis, CA); Ward, Connie (Hamilton, MT); Cherry, Joel (Davis, CA); Jones, Aubrey (Davis, CA); Harris, Paul (Carnation, WA); Yi, Jung (Sacramento, CA)

    2011-04-26

    The present invention relates to variants of a parent glycoside hydrolase, comprising a substitution at one or more positions corresponding to positions 21, 94, 157, 205, 206, 247, 337, 350, 373, 383, 438, 455, 467, and 486 of amino acids 1 to 513 of SEQ ID NO: 2, and optionally further comprising a substitution at one or more positions corresponding to positions 8, 22, 41, 49, 57, 113, 193, 196, 226, 227, 246, 251, 255, 259, 301, 356, 371, 411, and 462 of amino acids 1 to 513 of SEQ ID NO: 2 a substitution at one or more positions corresponding to positions 8, 22, 41, 49, 57, 113, 193, 196, 226, 227, 246, 251, 255, 259, 301, 356, 371, 411, and 462 of amino acids 1 to 513 of SEQ ID NO: 2, wherein the variants have glycoside hydrolase activity. The present invention also relates to nucleotide sequences encoding the variant glycoside hydrolases and to nucleic acid constructs, vectors, and host cells comprising the nucleotide sequences.

  4. Genetic Variability of Aspergillus flavus Isolates from a Mississippi Corn Field

    PubMed Central

    Solorzano, Cesar D.; Abbas, Hamed K.; Zablotowicz, Robert M.; Chang, Perng-Kuang; Jones, Walker A.

    2014-01-01

    A nontoxigenic Aspergillus flavus strain, K49, is currently being tested as a biological control agent in corn fields in the Mississippi Delta. However, little is known about the overall genetic diversity of A. flavus from year to year in corn fields and specifically in Mississippi. Our objective was to assess the genetic variability of A. flavus isolates from different seasons, inoculum sources, and years, from a no-till corn field. Of the 175 A. flavus isolates examined, 74 and 97 had the typical norB-cypA type I (1.5?kb) and type II (1.0?kb) deletion patterns, respectively. Variability in the sequence of the omtA gene of the majority of the field isolates (n = 118) was compared to strain K49. High levels of haplotypic diversity (24 omtA haplotypes; Hd = 0.61 ± 0.04) were found. Among the 24 haplotypes, two were predominant, H1 (n = 71), which consists of mostly toxigenic isolates, and H49 (n = 18), which consists of mostly atoxigenic isolates including K49. Toxigenic isolates were prevalent (60%) in this natural population. Nonetheless, about 15% of the population likely shared the same ancestral origin with K49. This study provides valuable information on the diversity of A. flavus. This knowledge can be further used to develop additional biological control strains. PMID:25478591

  5. Isolation and characterization of Clostridium difficile associated with beef cattle and commercially produced ground beef.

    PubMed

    Kalchayanand, Norasak; Arthur, Terrance M; Bosilevac, Joseph M; Brichta-Harhay, Dayna M; Shackelford, Steven D; Wells, James E; Wheeler, Tommy L; Koohmaraie, Mohammad

    2013-02-01

    The incidence of Clostridium difficile infection has recently increased in North American and European countries. This pathogen has been isolated from retail pork, turkey, and beef products and reported associated with human illness. This increase in infections has been attributed to the emergence of a toxigenic strain designated North America pulsed-field gel electrophoresis type 1 (NAP1). The NAP1 strain has been isolated from calves as well as ground meat products, leading to speculation of illness from consumption of contaminated meat products. However, information on C. difficile associated with beef cattle during processing and commercially produced ground beef is limited. To address this data gap, samples from various steps during beef production were collected. Samples from hides (n = 525), preevisceration carcasses (n = 475), postintervention carcasses (n = 471), and 956 commercial ground beef samples were collected from across the United States. The prevalence of C. difficile spores on hides was 3.2%. C. difficile spores were not detected on preevisceration and postintervention carcasses or in commercially produced ground beef. Phenotypic and genetic characterizations were carried out for all 18 isolates collected from hide samples. Twenty-two percent of the isolates were nontoxigenic strains, while 78% of the isolates were toxigenic. Toxinotyping and PCR ribotyping patterns revealed that 6 and 33% of the isolates were identified as NAP1 and NAP7 strains, respectively. This article evidences that the prevalence of C. difficile, specifically pathogenic strains, in the U.S. beef production chain is low. PMID:23433373

  6. Association of the nibrin gene (NBN) variants with breast cancer

    PubMed Central

    UZUNOGLU, HAKAN; KORAK, TUGCAN; ERGUL, EMEL; UREN, NIHAL; SAZCI, ALI; UTKAN, N. ZAFER; KARGI, ERTUĞRUL; TRIYAKI, ÇAĞRI; YIRMIBESOGLU, OKTAY

    2016-01-01

    Nibrin, encoded by the NBN gene, participates in DNA repair. Mutations in the NBN gene lead to Nijemen breakage syndrome, which may result in several types of diseases, particularly susceptibility to cancer, including breast cancer. Polymorphic variants and defective mutations occurring in the NBN gene increase the risk of breast cancer through the double-stranded break repair mechanism. The aim of the present study was to investigate a possible association between breast cancer and NBN genetic variants, NBN 924 T>C, 8360 G>C and 30537 G>C, in women with breast cancer. Locus-specific primers were designed to study 3 genetic variants in DNA samples isolated from peripheral blood samples of 101 women with breast cancer and 115 healthy controls. Subsequently, 3 polymerase chain reaction-restriction fragment length polymorphism methods were performed and the obtained results were statistically analysed. The NBN gene 924 T>C variant was found to be significantly associated with breast cancer (χ2=5.722, P=0.017). There were no statistically significant differences between cases and controls in the NBN gene 8360 G>C variant (χ2=1,125, P=0.570) or the NBN gene 30537 G>C variant (χ2=4.301, P=0.116). In conclusion, the NBN gene 924 T>C variant may be a genetic risk factor for breast cancer development in women with breast cancer.

  7. Impact of Pathogen Population Heterogeneity and Stress-Resistant Variants on Food Safety.

    PubMed

    Abee, T; Koomen, J; Metselaar, K I; Zwietering, M H; den Besten, H M W

    2016-01-01

    This review elucidates the state-of-the-art knowledge about pathogen population heterogeneity and describes the genotypic and phenotypic analyses of persister subpopulations and stress-resistant variants. The molecular mechanisms underlying the generation of persister phenotypes and genetic variants are identified. Zooming in on Listeria monocytogenes, a comparative whole-genome sequence analysis of wild types and variants that enabled the identification of mutations in variants obtained after a single exposure to lethal food-relevant stresses is described. Genotypic and phenotypic features are compared to those for persistent strains isolated from food processing environments. Inactivation kinetics, models used for fitting, and the concept of kinetic modeling-based schemes for detection of variants are presented. Furthermore, robustness and fitness parameters of L. monocytogenes wild type and variants are used to model their performance in food chains. Finally, the impact of stress-resistant variants and persistence in food processing environments on food safety is discussed. PMID:26772414

  8. The Phylloplane as a Source of Bacillus thuringiensis Variants

    PubMed Central

    Smith, Robert A.; Couche, Graham A.

    1991-01-01

    Novel variants of Bacillus thuringiensis were isolated from the phylloplane of deciduous and conifer trees as well as of other plants. These isolates displayed a range of toxicity towards Trichoplusia ni. Immunoblot and toxin protein analysis indicate that these strains included representatives of the three principal B. thuringiensis pathotypes active against larvae of the orders Lepidoptera, Diptera, and Coleoptera. We propose that B. thuringiensis be considered part of the common leaf microflora of many plants. Images PMID:16348400

  9. DNA vectors encoding a novel human growth hormone-variant protein

    SciTech Connect

    Seeburg, P.H.

    1987-06-02

    This patent describes a replicable cloning vehicle comprising an inserted DNA sequence, the inserted DNA sequence encoding a human growth hormone variant protein having an amino acid sequence. A DNA isolate is described consisting essentially of a DNA sequence encoding an amino-terminal presequence-containing human growth hormone variant protein of an amino acid sequence.

  10. COLOR VARIABILITY AND PULLULAN PRODUCTION FROM TROPICAL VARIANTS AUREOBASIDIUM PULLULANS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Diverse tropical variant strains of the polymorphic fungus Aureobasidium pullulans were isolated from many provinces in Thailand. They were cultured from leaves, painted walls, and wood surfaces. Most colonies were smooth, moist, cream or pale pink on YMA (yeast malt agar) medium, while budding ye...

  11. EMCD, a hypoglycemic triterpene isolated from Momordica charantia wild variant, attenuates TNF-?-induced inflammation in FL83B cells in an AMP-activated protein kinase-independent manner.

    PubMed

    Cheng, Hsueh-Ling; Kuo, Ching-Yi; Liao, Yun-Wen; Lin, Chen-Chen

    2012-08-15

    Insulin resistance is a causative factor for type 2 diabetes, whereas the development of insulin resistance is closely related to chronic inflammation induced by factors such as tumor necrosis factor-? (TNF-?). Momordica charantia, also known as bitter melon, has been used as an herbal medicine and reported to ameliorate inflammation and hyperglycemia. Previously, a triterpene 5?,19-epoxy-25-methoxy-cucurbita-6,23-diene-3?,19-diol (EMCD), purified from M. charantia L. wild variant WB24, was found to activate AMP-activated protein kinase (AMPK) and have a hypoglycaemic effect in TNF-?-treated FL83B cells. AMPK has been a target for developing anti-diabetic medicine and suggested to play a role in anti-inflammation. The current study aims to investigate if EMCD might repress TNF-?-induced inflammation via AMPK. TNF-?-induced inflammation in FL83B cells was characterized using Western blotting and reverse transcriptase-polymerase chain reaction. Consequently, the expression of inflammatory markers including inducible nitric oxide synthase (iNOS), the p65 subunit of nuclear factor-?B (NF-?B), protein-tyrosine phosphatase-1B, TNF-? and interleukin-1? were significantly elevated by TNF-? in the cell, and EMCD obviously suppressed the TNF-?-induced expression of these markers. When the effect of EMCD was tested simultaneously with epigallocatechin-3-gallate (EGCG), a catechin from green tea reported to be anti-inflammatory, EMCD showed a more obvious anti-inflammatory activity than EGCG did. Investigation of the underlying mechanism suggested that EMCD inhibited the activation of the I?B kinase (IKK) complex and the NF-?B pathway, and the effect was likely independent of AMPK. Collectively, the multiple functions of EMCD suggest it to be a potential agent in treating diabetic complications and other inflammation-related disorders. PMID:22683870

  12. Phenylketonuria variants in Ontario.

    PubMed Central

    1976-01-01

    Since mass screening of the newborn population for phenylketonuria (PKU) by the Guthrie test was begun in Ontario in July 1965 many variants of PKU have been recognized in the 96 to 97% screened. Seventy-one cases of classic PKU were detected (four were missed). Of 48 cases of persistent hyperphenylalaninemia discovered, 18 were classified as atypical PKU and 30 as persistent benign hyperphenylalaninemia. Numerous infants with transient hyperphenylalaninemia (initial values over 10 mg/dl in 12), in many instances the result of transient neonatal tyrosinemia, were discovered. There was a slight predominance of males. Serum phenylalanine values of up to 15 mg/dl seemed to be harmless to the developing brain. A survey of 67 247 adults in the general population revealed 1 person with PKU and 1 with persistent benign hyperphenylalaninemia; both had normal intelligence quotients. Of 1548 mothers of retarded children tested, none had hyperphenylalaninemia. PMID:953933

  13. [Rare keratoacanthoma variants].

    PubMed

    Jasnoch, V; Ernst, K; Hundeiker, M

    1995-04-01

    Keratoacanthomas are made up of the same spinocellular differentiated cell material as squamous cell carcinomas, but they differ from the latter in origin and growth properties. The majority--in our series 98% of 741 examined cases--are of the "crateriform" type, which after rapid growth during the initial stage give way to spontaneous regression, mostly with complete restoration of the cutaneous structure. Less than 2% belong to the rare destructive variants with disturbed or absent regression and persistent invasive growth. Keratoacanthoma marginatum centrifugum, mutilating keratoacanthomas and aggregated keratoacanthomas can lead to extremely severe defects. None of the "conservative" treatment methods recommended in the literature up to now has proved effective, with the exception of surgery and radiotherapy with tumour ratio doses. Many publications are obviously based on uncritically interpreted individual observations. PMID:7790189

  14. Oxidation of linear terpenes and squalene variants by Arthrobacter sp.

    PubMed Central

    Yamada, Y; Kusuhara, N; Okada, H

    1977-01-01

    Cells of Arthrobacter sp. that had been isolated from soil were used to study oxidation of some linear terpenes and squalene variants. The cells oxidized geraniol, nerol, and farnesol to the corresponding aldehydes, with partial conversion of the geometrical isomerism of the alpha,beta-double bond. The squalene variant, squalene-2,3-oxide, was cleaved to 9,10-epoxygeranylacetone and geranylacetone. Squalene-2,3-22,23-dioxide was cleaved to 9,10-epoxygeranylacetone. These products were optically active, and their stereochemistry and optical purity were determined. PMID:869527

  15. Characteristics of Helicobacter pylori variants selected for urease deficiency.

    PubMed Central

    Pérez-Pérez, G I; Olivares, A Z; Cover, T L; Blaser, M J

    1992-01-01

    The urease of Helicobacter pylori is suspected to play a role in the pathogenesis of gastritis. Although all clinical isolates of H. pylori are urease positive (U+), we have selected and characterized several spontaneously arising urease-negative (U-) variants from wild-type strain 60190. Urease-negative variants were identified by growth in medium containing 60 mM urea and arose at a frequency of 10(-5) to 10(-6). The urease activity of the wild-type strain inhibited growth of this strain in the presence of 60 mM urea. U- variants retained the U- phenotype for more than 100 passages on medium with or without urea. The urease activities of the original U+ and derived U- cells were 9.55 to 16.7 and 0.01 to 0.17 U/mg of protein, respectively. Colonial growth and other biochemical characteristics were identical for the strains. U- variants showed three classes of whole-cell sodium dodecyl sulfate-polyacrylamide gel electrophoresis profiles: (i) identical to U+; (ii) change in the migration of the 61-kDa urease subunit; and (iii) lack of 61- and 30-kDa subunits. These differences were confirmed by immunoblotting and by protein separation using fast protein liquid chromatography. The U+ strain but not U- variants tolerated exposure to pH 4.0 for 60 min in the presence of urea. Supernatants of the U+ strain and U- variants contained vacuolating cytotoxin activity for HeLa cells in similar titers. By enzyme-linked immunosorbent assay, human serum samples recognized water extract from the U+ strain significantly better than extract from a U- variant lacking urease subunits. In conclusion, this study demonstrates that U- H. pylori variants may arise spontaneously, that urease activity enhances survival at acid pH, and that urease and cytotoxin activities are disparate phenotypes. Images PMID:1500174

  16. Swine Influenza/Variant Influenza Viruses

    MedlinePLUS

    ... Past Newsletters Information on Swine Influenza/Variant Influenza Viruses Language: English Español Recommend on Facebook Tweet ... the Spread of Influenza A Viruses Variant Influenza Viruses in Humans Variant (Swine Origin) Influenza Viruses in ...

  17. Cellobiohydrolase variants and polynucleotides encoding the same

    DOEpatents

    Wogulis, Mark

    2014-09-09

    The present invention relates to variants of a parent cellobiohydrolase. The present invention also relates to polynucleotides encoding the cellobiohydrolase variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the cellobiohydrolase variants.

  18. Cellobiohydrolase variants and polynucleotides encoding same

    DOEpatents

    Wogulis, Mark

    2013-09-24

    The present invention relates to variants of a parent cellobiohydrolase II. The present invention also relates to polynucleotides encoding the variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the variants.

  19. Cellobiohydrolase variants and polynucleotides encoding same

    SciTech Connect

    Wogulis, Mark

    2014-10-14

    The present invention relates to variants of a parent cellobiohydrolase II. The present invention also relates to polynucleotides encoding the variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the variants.

  20. Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture.

    PubMed

    Xue, Katherine S; Hooper, Kathryn A; Ollodart, Anja R; Dingens, Adam S; Bloom, Jesse D

    2016-01-01

    RNA viruses rapidly diversify into quasispecies of related genotypes. This genetic diversity has long been known to facilitate adaptation, but recent studies have suggested that cooperation between variants might also increase population fitness. Here, we demonstrate strong cooperation between two H3N2 influenza variants that differ by a single mutation at residue 151 in neuraminidase, which normally mediates viral exit from host cells. Residue 151 is often annotated as an ambiguous amino acid in sequenced isolates, indicating mixed viral populations. We show that mixed populations grow better than either variant alone in cell culture. Pure populations of either variant generate the other through mutation and then stably maintain a mix of the two genotypes. We suggest that cooperation arises because mixed populations combine one variant's proficiency at cell entry with the other's proficiency at cell exit. Our work demonstrates a specific cooperative interaction between defined variants in a viral quasispecies. PMID:26978794

  1. Rare Copy Number Variants

    PubMed Central

    Grozeva, Detelina; Kirov, George; Ivanov, Dobril; Jones, Ian R.; Jones, Lisa; Green, Elaine K.; St Clair, David M.; Young, Allan H.; Ferrier, Nicol; Farmer, Anne E.; McGuffin, Peter; Holmans, Peter A.; Owen, Michael J.; O’Donovan, Michael C.; Craddock, Nick

    2015-01-01

    Context Recent studies suggest that copy number variation in the human genome is extensive and may play an important role in susceptibility to disease, including neuropsychiatric disorders such as schizophrenia and autism. The possible involvement of copy number variants (CNVs) in bipolar disorder has received little attention to date. Objectives To determine whether large (>100 000 base pairs) and rare (found in <1% of the population) CNVs are associated with susceptibility to bipolar disorder and to compare with findings in schizophrenia. Design A genome-wide survey of large, rare CNVs in a case-control sample using a high-density microarray. Setting The Wellcome Trust Case Control Consortium. Participants There were 1697 cases of bipolar disorder and 2806 nonpsychiatric controls. All participants were white UK residents. Main Outcome Measures Overall load of CNVs and presence of rare CNVs. Results The burden of CNVs in bipolar disorder was not increased compared with controls and was significantly less than in schizophrenia cases. The CNVs previously implicated in the etiology of schizophrenia were not more common in cases with bipolar disorder. Conclusions Schizophrenia and bipolar disorder differ with respect to CNV burden in general and association with specific CNVs in particular. Our data are consistent with the possibility that possession of large, rare deletions may modify the phenotype in those at risk of psychosis: those possessing such events are more likely to be diagnosed as having schizophrenia, and those without them are more likely to be diagnosed as having bipolar disorder. PMID:20368508

  2. Variants of beta-glucosidases

    SciTech Connect

    Fidantsef, Ana; Lamsa, Michael; Gorre-Clancy, Brian

    2014-10-07

    The present invention relates to variants of a parent beta-glucosidase, comprising a substitution at one or more positions corresponding to positions 142, 183, 266, and 703 of amino acids 1 to 842 of SEQ ID NO: 2 or corresponding to positions 142, 183, 266, and 705 of amino acids 1 to 844 of SEQ ID NO: 70, wherein the variant has beta-glucosidase activity. The present invention also relates to nucleotide sequences encoding the variant beta-glucosidases and to nucleic acid constructs, vectors, and host cells comprising the nucleotide sequences.

  3. Variants of beta-glucosidase

    SciTech Connect

    Fidantsef, Ana; Lamsa, Michael; Gorre-Clancy, Brian

    2015-07-14

    The present invention relates to variants of a parent beta-glucosidase, comprising a substitution at one or more positions corresponding to positions 142, 183, 266, and 703 of amino acids 1 to 842 of SEQ ID NO: 2 or corresponding to positions 142, 183, 266, and 705 of amino acids 1 to 844 of SEQ ID NO: 70, wherein the variant has beta-glucosidase activity. The present invention also relates to nucleotide sequences encoding the variant beta-glucosidases and to nucleic acid constructs, vectors, and host cells comprising the nucleotide sequences.

  4. Variants of beta-glucosidase

    DOEpatents

    Fidantsef, Ana (Davis, CA); Lamsa, Michael (Davis, CA); Gorre-Clancy, Brian (Elk Grove, CA)

    2009-12-29

    The present invention relates to variants of a parent beta-glucosidase, comprising a substitution at one or more positions corresponding to positions 142, 183, 266, and 703 of amino acids 1 to 842 of SEQ ID NO: 2 or corresponding to positions 142, 183, 266, and 705 of amino acids 1 to 844 of SEQ ID NO: 70, wherein the variant has beta-glucosidase activity. The present invention also relates to nucleotide sequences encoding the variant beta-glucosidases and to nucleic acid constructs, vectors, and host cells comprising the nucleotide sequences.

  5. Variants of beta-glucosidases

    DOEpatents

    Fidantsef, Ana; Lamsa, Michael; Clancy, Brian Gorre

    2008-08-19

    The present invention relates to variants of a parent beta-glucosidase, comprising a substitution at one or more positions corresponding to positions 142, 183, 266, and 703 of amino acids 1 to 842 of SEQ ID NO: 2 or corresponding to positions 142, 183, 266, and 705 of amino acids 1 to 844 of SEQ ID NO: 70, wherein the variant has beta-glucosidase activity. The present invention also relates to nucleotide sequences encoding the variant beta-glucosidases and to nucleic acid constructs, vectors, and host cells comprising the nucleotide sequences.

  6. Human AZU-1 gene, variants thereof and expressed gene products

    DOEpatents

    Chen, Huei-Mei; Bissell, Mina

    2004-06-22

    A human AZU-1 gene, mutants, variants and fragments thereof. Protein products encoded by the AZU-1 gene and homologs encoded by the variants of AZU-1 gene acting as tumor suppressors or markers of malignancy progression and tumorigenicity reversion. Identification, isolation and characterization of AZU-1 and AZU-2 genes localized to a tumor suppressive locus at chromosome 10q26, highly expressed in nonmalignant and premalignant cells derived from a human breast tumor progression model. A recombinant full length protein sequences encoded by the AZU-1 gene and nucleotide sequences of AZU-1 and AZU-2 genes and variant and fragments thereof. Monoclonal or polyclonal antibodies specific to AZU-1, AZU-2 encoded protein and to AZU-1, or AZU-2 encoded protein homologs.

  7. Gene Variants Reduce Opioid Risks

    MedlinePLUS

    ... Abused Drugs Charts Emerging Trends Alcohol Club Drugs Cocaine Hallucinogens Heroin Inhalants Marijuana MDMA (Ecstasy/Molly) Methamphetamine ... a decreased risk for addiction to heroin or cocaine. The other linked variants in two genes— OPRM1 , ...

  8. Are isolated wetlands isolated?

    USGS Publications Warehouse

    Smith, Loren M.; Euliss, Ned H.; Haukos, David A.

    2011-01-01

    While federal regulations during the past 10 years have treated isolated wetlands as unconnected to aquatic resources protected by the Clean Water Act, they provide critical ecosystem services to society that extend well beyond their wetland boundaries. The authors offer well-documented examples from the scientific literature on some of the ecosystem services provided by isolated wetlands to society and other ecosystems.

  9. Phylodynamic Analysis of Clinical and Environmental Vibrio cholerae Isolates from Haiti Reveals Diversification Driven by Positive Selection

    PubMed Central

    Azarian, Taj; Ali, Afsar; Johnson, Judith A.; Mohr, David; Prosperi, Mattia; Veras, Nazle M.; Jubair, Mohammed; Strickland, Samantha L.; Rashid, Mohammad H.; Alam, Meer T.; Weppelmann, Thomas A.; Katz, Lee S.; Tarr, Cheryl L.; Colwell, Rita R.

    2014-01-01

    ABSTRACT Phylodynamic analysis of genome-wide single-nucleotide polymorphism (SNP) data is a powerful tool to investigate underlying evolutionary processes of bacterial epidemics. The method was applied to investigate a collection of 65 clinical and environmental isolates of Vibrio cholerae from Haiti collected between 2010 and 2012. Characterization of isolates recovered from environmental samples identified a total of four toxigenic V. cholerae O1 isolates, four non-O1/O139 isolates, and a novel nontoxigenic V. cholerae O1 isolate with the classical tcpA gene. Phylogenies of strains were inferred from genome-wide SNPs using coalescent-based demographic models within a Bayesian framework. A close phylogenetic relationship between clinical and environmental toxigenic V. cholerae O1 strains was observed. As cholera spread throughout Haiti between October 2010 and August 2012, the population size initially increased and then fluctuated over time. Selection analysis along internal branches of the phylogeny showed a steady accumulation of synonymous substitutions and a progressive increase of nonsynonymous substitutions over time, suggesting diversification likely was driven by positive selection. Short-term accumulation of nonsynonymous substitutions driven by selection may have significant implications for virulence, transmission dynamics, and even vaccine efficacy. PMID:25538191

  10. [Isolation and characterization of Escherichia coli O157 in bovine meat products and cattle in the province of Tucuman].

    PubMed

    Jure, María A; Condorí, Marina S; Pérez Terrazzino, Gabriela; Catalán, Mariana G; López Campo, Alejandro; Zolezzi, Gisella; Chinen, Isabel; Rivas, Marta; Castillo, Marta

    2015-01-01

    Escherichia coli O157 is an emergent pathogen associated with diarrhea, hemorrhagic colitis and hemolytic uremic syndrome. Meat products constitute an important transmission source of this microorganism. The aims of this study were to characterize E. coli O157 isolated from cattle and meat products collected from abattoirs and retail stores, to establish the clonal relatedness among regional isolates and to compare them with those in the national database. Between 2004 and 2013, 169 minced meat, 35 sausage and 216 carcass samples were analyzed. Thirteen E. coli O157 isolates were identified; 6 of which were O157:H7 and characterized as stx2c(vh-a)/eae/ehxA (n = 5) and stx2/eae/ehxA (n = 1). The 7 remaining isolates were non-toxigenic E. coli strains, and serotyped as O157:NT (n = 4), O157:NM (n = 1), O157:ND (n = 1) and O157:H16 (n = 1). The strains yielded different XbaI-PFGE patterns. Compared to the E. coli O157 isolates in the National Database, none of these patterns have been previously detected in strains of different origin in Argentina. PMID:26026230

  11. White Matter atrophy in Alzheimer Disease variants

    PubMed Central

    Migliaccio, Raffaella; Agosta, Federica; Possin, Katherine L.; Rabinovici, Gil D.; Miller, Bruce L.; Gorno-Tempini, Maria Luisa

    2013-01-01

    Background In comparison to late-onset Alzheimer’s disease (LO-AD, onset > 65), early age-of-onset Alzheimer’s disease (EO-AD, onset<65 years) more often presents with language, visuospatial and/or executive impairment, often occurring earlier than a progressive memory deficit. The logopenic variant of primary progressive aphasia (lv-PPA) and the posterior cortical atrophy (PCA) have recently been described as possible atypical variants of EO-AD. Lv-PPA is characterized by isolated language deficit, while PCA is characterized by predominant visuospatial deficits. Severe hemispheric grey matter (GM) atrophy associated with EO-AD, lv-PPA and PCA has been described, but regional patterns of white matter (WM) damage are still poorly understood. Methods Using structural MRI and voxel-based morphometry, we investigated WM damage in 16 EO-AD, 13 PCA, 10 lv-PPA, and 14 LO-AD patients at presentation, and 72 age-matched controls. Results In EO-AD, PCA and lv-PPA patients, WM atrophy was centered on lateral temporal and parietal regions, including cingulum and posterior corpus callosum. Compared to controls, lv-PPA patients showed a more severe left parietal damage, and PCA showed a more severe occipital atrophy. Moreover, EO-AD had greater cingulum atrophy compared with LO-AD. LO-AD showed WM damage in medial temporal regions and less extensive hemispheric involvement. Conclusions Patterns of WM damage in EO-AD, lv-PPA and PCA are consistent with the clinical syndromes and GM atrophy patterns. WM injury in AD atypical variants may contribute to symptoms and disease pathogenesis. PMID:23021625

  12. Characterization of purified CuZn SOD variants from adult rat liver

    SciTech Connect

    Yano, S.; Kikkawa, Y.; Desai, U.; Mettler, N.

    1986-03-01

    Rat liver CuZn SOD was purified by chloroform-ethanol extraction, ion exchange and molecular seive gel filtration. On electrofocussing six variants of SOD with isoelectric points of 5.16, 4.88, 4.76, 4.65, 4.57 and 4.50 were isolated. Variant PI 4.88 was the major component, variants PI 4.57 and PI 4.50 were minor components. This pattern was also obtained from SOD isolated by acetone-powder method or ultrafiltration dialysis method and even from liver homogenates incubated at 37/sup 0/C for 4 hrs. All SOD variants had m.w. of 32 kDa and were inhibitable by cyanide and Tris-HcL buffer. All variants contained 1 mole each of Cu and Zn/mole SOD except for variant PI 4.88 which contained 3 moles of Cu and Zn/mole SOD. Specific activity of SOD was measured by xanthine-xanthine oxidase cytochrome c method. At pH 7.8 in phosphate buffer the variant PI 4.88 showed highest activity (11,927 units per mgm) and PI 4.57 variant the lowest (1170 units). At pH 10.0 in carbonate buffer all variants had enhanced activities, however PI 4.50 variant showed least increase enhancement. Thus, CuZn SOD in normal rat liver consists of six variants of varying behaviors. It is possible that changes in their relative contents may thus affect the outcome of oxidant injury.

  13. Characterization of a Mycobacterium intracellulare Variant Strain by Molecular Techniques

    PubMed Central

    Menendez, M. C.; Palenque, E.; Navarro, M. C.; Nuñez, M. C.; Rebollo, M. J.; Garcia, M. J.

    2001-01-01

    This paper describes a Mycobacterium intracellulare variant strain causing an unusual infection. Several isolates obtained from an immunocompromised patient were identified as members of the Mycobacterium avium complex (MAC) by the commercial AccuProbe system and biochemical standard identification. Further molecular approaches were undertaken for a more accurate characterization of the bacteria. Up to seven different genomic sequences were analyzed, ranging from conserved mycobacterial genes such as 16S ribosomal DNA to MAC-specific genes such as mig (macrophage-induced gene). The results obtained identify the isolates as a variant of M. intracellulare, an example of the internal variability described for members of the MAC, particularly within that species. The application of other molecular approaches is recommended for more accurate identification of bacteria described as MAC members. PMID:11724827

  14. Prevalence and antimicrobial resistance of Shigella flexneri serotype 2 variant in China

    PubMed Central

    Cui, Xianyan; Wang, Jian; Yang, Chaojie; Liang, Beibei; Ma, Qiuxia; Yi, Shengjie; Li, Hao; Liu, Hongbo; Li, Peng; Wu, Zhihao; Xie, Jing; Jia, Leili; Hao, Rongzhang; Wang, Ligui; Hua, Yuejin; Qiu, Shaofu; Song, Hongbin

    2015-01-01

    Shigella flexneri serotype 2 variant (II:3,4,7,8) was isolated in 2008 and first reported in China in 2013. In the present study, epidemiological surveillance from 2003 to 2013 in China suggested that this serotype first appeared in Guangxi in 2003; it then emerged in Shanghai and Xinjiang in 2004 and in Henan in 2008. Of the 1813 S. flexneri isolates, 58 S. flexneri serotype 2 variant strains were identified. Serotype 2 variant has emerged as a prominent serotype in recent years, with 2a (32.6%), X variant (25.2%), 1a (9.4%), X (6.3%), 2b (5.4%), and 1b (3.6%). According to phenotypic and genotypic analysis, the serotype 2 variant originated from 2a to 2b. A higher antibiotic resistance rate was observed between 2009 and 2013 than that between 2003 and 2008. Among 22 cephalosporin-resistant isolates, blaTEM-1, blaOXA-1, blaCTX-3, blaCTX-14, and blaCTX-79 were detected. Among 22 fluoroquinolone-resistant isolates, a Ser80Ile mutation in parC was present in all of the isolates. Moreover, 21 isolates had three gyrA point mutations (Ser83Leu, His211Tyr, Asp87Asn, or Gly) and one isolate had two gyrA point mutations (Ser83Leu and His211Tyr). The prevalence of His211Tyr in the fluoroquinolone-resistant isolates is concerning, and the mutation was first reported in China. Besides, 22 isolates harbored the aac(6?)-Ib-cr gene, and two isolates harbored qnrS1. In view of the increased epidemic frequency and multidrug-resistant strain emergence, continuous surveillance will be needed to understand the actual disease burden and provide guidance for shigellosis. PMID:25999941

  15. Complete Genome Sequences of Low-Passage Virulent and High-Passage Avirulent Variants of Pathogenic Leptospira interrogans Serovar Manilae Strain UP-MMC-NIID, Originally Isolated from a Patient with Severe Leptospirosis, Determined Using PacBio Single-Molecule Real-Time Technology.

    PubMed

    Satou, Kazuhito; Shimoji, Makiko; Tamotsu, Hinako; Juan, Ayaka; Ashimine, Noriko; Shinzato, Misuzu; Toma, Claudia; Nohara, Toshitsugu; Shiroma, Akino; Nakano, Kazuma; Teruya, Kuniko; Terabayashi, Yasunobu; Ohki, Shun; Koizumi, Nobuo; Okano, Shou; Suzuki, Toshihiko; Hirano, Takashi

    2015-01-01

    Here, we report the complete genome sequences of low-passage virulent and high-passage avirulent variants of pathogenic Leptospira interrogans serovar Manilae strain UP-MMC-NIID, a major causative agent of leptospirosis. While there were no major differences between the genome sequences, the levels of base modifications were higher in the avirulent variant. PMID:26272567

  16. Complete Genome Sequences of Low-Passage Virulent and High-Passage Avirulent Variants of Pathogenic Leptospira interrogans Serovar Manilae Strain UP-MMC-NIID, Originally Isolated from a Patient with Severe Leptospirosis, Determined Using PacBio Single-Molecule Real-Time Technology

    PubMed Central

    Shimoji, Makiko; Tamotsu, Hinako; Juan, Ayaka; Ashimine, Noriko; Shinzato, Misuzu; Toma, Claudia; Nohara, Toshitsugu; Shiroma, Akino; Nakano, Kazuma; Teruya, Kuniko; Terabayashi, Yasunobu; Ohki, Shun; Koizumi, Nobuo; Okano, Shou; Suzuki, Toshihiko; Hirano, Takashi

    2015-01-01

    Here, we report the complete genome sequences of low-passage virulent and high-passage avirulent variants of pathogenic Leptospira interrogans serovar Manilae strain UP-MMC-NIID, a major causative agent of leptospirosis. While there were no major differences between the genome sequences, the levels of base modifications were higher in the avirulent variant. PMID:26272567

  17. Integration over song classification replicates: song variant analysis in the hihi.

    PubMed

    Ranjard, Louis; Withers, Sarah J; Brunton, Dianne H; Ross, Howard A; Parsons, Stuart

    2015-05-01

    Human expert analyses are commonly used in bioacoustic studies and can potentially limit the reproducibility of these results. In this paper, a machine learning method is presented to statistically classify avian vocalizations. Automated approaches were applied to isolate bird songs from long field recordings, assess song similarities, and classify songs into distinct variants. Because no positive controls were available to assess the true classification of variants, multiple replicates of automatic classification of song variants were analyzed to investigate clustering uncertainty. The automatic classifications were more similar to the expert classifications than expected by chance. Application of these methods demonstrated the presence of discrete song variants in an island population of the New Zealand hihi (Notiomystis cincta). The geographic patterns of song variation were then revealed by integrating over classification replicates. Because this automated approach considers variation in song variant classification, it reduces potential human bias and facilitates the reproducibility of the results. PMID:25994687

  18. Histone variants in metazoan development

    PubMed Central

    Banaszynski, Laura A.; Allis, C. David; Lewis, Peter W.

    2010-01-01

    Embryonic development is regulated by both genetic and epigenetic mechanisms, with nearly all DNA-templated processes influenced by chromatin architecture. Sequence variations in histone proteins, core components of chromatin, provide a means to generate diversity in the chromatin structure, resulting in distinct and profound biological outcomes in the developing embryo. Emerging literature suggests that epigenetic contributions from histone variants play key roles in a number of developmental processes such as the initiation and maintenance of pericentric heterochromatin, X-inactivation, and germ cell differentiation. Here, we review the role of histone variants in the embryo with particular emphasis on early mammalian development. PMID:21074717

  19. Connected speech production in three variants of primary progressive aphasia

    PubMed Central

    Henry, Maya L.; Besbris, Max; Ogar, Jennifer M.; Dronkers, Nina F.; Jarrold, William; Miller, Bruce L.; Gorno-Tempini, Maria Luisa

    2010-01-01

    Primary progressive aphasia is a clinical syndrome defined by progressive deficits isolated to speech and/or language, and can be classified into non-fluent, semantic and logopenic variants based on motor speech, linguistic and cognitive features. The connected speech of patients with primary progressive aphasia has often been dichotomized simply as ‘fluent’ or ‘non-fluent’, however fluency is a multidimensional construct that encompasses features such as speech rate, phrase length, articulatory agility and syntactic structure, which are not always impacted in parallel. In this study, our first objective was to improve the characterization of connected speech production in each variant of primary progressive aphasia, by quantifying speech output along a number of motor speech and linguistic dimensions simultaneously. Secondly, we aimed to determine the neuroanatomical correlates of changes along these different dimensions. We recorded, transcribed and analysed speech samples for 50 patients with primary progressive aphasia, along with neurodegenerative and normal control groups. Patients were scanned with magnetic resonance imaging, and voxel-based morphometry was used to identify regions where atrophy correlated significantly with motor speech and linguistic features. Speech samples in patients with the non-fluent variant were characterized by slow rate, distortions, syntactic errors and reduced complexity. In contrast, patients with the semantic variant exhibited normal rate and very few speech or syntactic errors, but showed increased proportions of closed class words, pronouns and verbs, and higher frequency nouns, reflecting lexical retrieval deficits. In patients with the logopenic variant, speech rate (a common proxy for fluency) was intermediate between the other two variants, but distortions and syntactic errors were less common than in the non-fluent variant, while lexical access was less impaired than in the semantic variant. Reduced speech rate was linked with atrophy to a wide range of both anterior and posterior language regions, but specific deficits had more circumscribed anatomical correlates. Frontal regions were associated with motor speech and syntactic processes, anterior and inferior temporal regions with lexical retrieval, and posterior temporal regions with phonological errors and several other types of disruptions to fluency. These findings demonstrate that a multidimensional quantification of connected speech production is necessary to characterize the differences between the speech patterns of each primary progressive aphasic variant adequately, and to reveal associations between particular aspects of connected speech and specific components of the neural network for speech production. PMID:20542982

  20. Rhizosphere Selection of Highly Motile Phenotypic Variants of Pseudomonas fluorescens with Enhanced Competitive Colonization Ability

    PubMed Central

    Martínez-Granero, Francisco; Rivilla, Rafael; Martín, Marta

    2006-01-01

    Phenotypic variants of Pseudomonas fluorescens F113 showing a translucent and diffuse colony morphology show enhanced colonization of the alfalfa rhizosphere. We have previously shown that in the biocontrol agent P. fluorescens F113, phenotypic variation is mediated by the activity of two site-specific recombinases, Sss and XerD. By overexpressing the genes encoding either of the recombinases, we have now generated a large number of variants (mutants) after selection either by prolonged laboratory cultivation or by rhizosphere passage. All the isolated variants were more motile than the wild-type strain and appear to contain mutations in the gacA and/or gacS gene. By disrupting these genes and complementation analysis, we have observed that the Gac system regulates swimming motility by a repression pathway. Variants isolated after selection by prolonged cultivation formed a single population with a swimming motility that was equal to the motility of gac mutants, being 150% more motile than the wild type. The motility phenotype of these variants was complemented by the cloned gac genes. Variants isolated after rhizosphere selection belonged to two different populations: one identical to the population isolated after prolonged cultivation and the other comprising variants that besides a gac mutation harbored additional mutations conferring higher motility. Our results show that gac mutations are selected both in the stationary phase and during rhizosphere colonization. The enhanced motility phenotype is in turn selected during rhizosphere colonization. Several of these highly motile variants were more competitive than the wild-type strain, displacing it from the root tip within 2 weeks. PMID:16672487

  1. Growth requirements of some small-colony-forming variants of Staphylococcus aureus.

    PubMed Central

    Kaplan, M L; Dye, W

    1976-01-01

    Nine stable, auxotrophic, small-colony-forming variants of Staphylococcus aureus were isolated. They were of two types. One type, from broth cultures containing varying concentrations of gentamicin or kanamycin, required heme for normal growth. The second type, from the blood culture of a patient who had been treated with penicillin and oxacillin, required long-chain unsaturated fatty acids for normal growth. These small-colony-forming variants differed from their parents with respect to specific metabolic activities, many of which may be attributed to an impaired electron transport system and related functions. A laboratory procedure for detecting possible small-colony variants in clinical specimens was proposed. PMID:977733

  2. Application of the antibiotic batumin for accurate and rapid identification of staphylococcal small colony variants

    PubMed Central

    2012-01-01

    Background Staphylococcus aureus is a major human pathogen causing significant morbidity and mortality. The S. aureus colonies in osteomyelitis, in patients with cystic fibrosis and patients with endoprosthesis rejection frequently have an atypical morphology, i.e. staphylococcal small-colony variants, which form a naturally occurring subpopulation of clinically important staphylococci. Identification of these small colony variants is difficult, because of the loss of typical phenotypic characteristics of these variants. We wanted to improve and simplify the diagnosis of staphylococcal infection using a diagnostic preparation, consisting of 5 ?g batumin paper disks. Batumin possesses a unique selective activity against all studied Staphylococcus spp., whereas all other species tested thus far are batumin resistant. We assessed the efficacy of the batumin diagnostic preparation to identify staphylococcal small colony variants, isolated from osteomyelitis patients. Findings With the batumin diagnostic preparation, all 30 tested staphylococcal small-colony variants had a growth inhibition zone around the disk of minimum 25 mm, accordant with the inhibition zones of the parent strains, isolated from the same patients. Conclusions The batumin diagnostic preparation correctly identified the small-colony variants of S. aureus, S. haemolyticus and S. epidermidis as belonging to the genus Staphylococcus, which differ profoundly from parental strains and are difficult to identify with standard methods. Identification of staphylococcal small-colony variants with the batumin diagnostic preparation is technically simple and can facilitate practical laboratory work. PMID:22828414

  3. Genetic Variants Associated with Port-Wine Stains

    PubMed Central

    Wooderchak-Donahue, Whitney; Tan, Oon T.; Margraf, Rebecca; Stevenson, David A.; Grimmer, J. Fredrik; Bayrak-Toydemir, Pinar

    2015-01-01

    Background Port-wine stains (PWS) are capillary malformations, typically located in the dermis of the head and neck, affecting 0.3% of the population. Current theories suggest that port-wine stains are caused by somatic mutations that disrupt vascular development. Objectives Understanding PWS genetic determinants could provide insight into new treatments. Methods Our study used a custom next generation sequencing (NGS) panel and digital polymerase chain reaction to investigate genetic variants in 12 individuals with isolated port-wine stains. Importantly, affected and healthy skin tissue from the same individual were compared. A subtractive correction method was developed to eliminate background noise from NGS data. This allowed the detection of a very low level of mosaicism. Results A novel somatic variant GNAQ, c.547C>G, p.Arg183Gly was found in one case with 4% allele frequency. The previously reported GNAQ c.548G>A, p.Arg183Gln was confirmed in 9 of 12 cases with an allele frequency ranging from 1.73 to 7.42%. Digital polymerase chain reaction confirmed novel variants detected by next generation sequencing. Two novel somatic variants were also found in RASA1, although neither was predicted to be deleterious. Conclusions This is the second largest study on isolated, non-syndromic PWS. Our data suggest that GNAQ is the main genetic determinant in this condition. Moreover, isolated port-wine stains are distinct from capillary malformations seen in RASA1 disorders, which will be helpful in clinical evaluation. PMID:26192947

  4. Cloning and characterization of human immunodeficiency virus type 1 variants diminished in the ability to induce syncytium-independent cytolysis.

    PubMed Central

    Stevenson, M; Haggerty, S; Lamonica, C; Mann, A M; Meier, C; Wasiak, A

    1990-01-01

    The phenomenon of interference was exploited to isolate low-abundance noncytopathic human immunodeficiency virus type 1 (HIV-1) variants from a primary HIV-1 isolate from an asymptomatic HIV-1-seropositive hemophiliac. Successive rounds of virus infection of a cytolysis-susceptible CD4+ cell line and isolation of surviving cells resulted in selective amplification of an HIV-1 variant reduced in the ability to induce cytolysis. The presence of a PvuII polymorphism facilitated subsequent amplification and cloning of cytopathic and noncytopathic HIV-1 variants from the primary isolate. Cloned virus stocks from cytopathic and noncytopathic variants exhibited similar replication kinetics, infectivity, and syncytium induction in susceptible host cells. The noncytopathic HIV-1 variant was unable, however, to induce single-cell killing in susceptible host cells. Construction of viral hybrids in which regions of cytopathic and noncytopathic variants were exchanged indicated that determinants for the noncytopathic phenotype map to the envelope glycoprotein. Sequence analysis of the envelope coding regions indicated the absence of two highly conserved N-linked glycosylation sites in the noncytopathic HIV-1 variant, which accompanied differences in processing of precursor gp160 envelope glycoprotein. These results demonstrate that determinants for syncytium-independent single-cell killing are located within the envelope glycoprotein and suggest that single-cell killing is profoundly influenced by alterations in envelope sequence which affect posttranslational processing of HIV-1 envelope glycoprotein within the infected cell. Images PMID:1695254

  5. Variant (Swine Origin) Influenza Viruses in Humans

    MedlinePLUS

    ... Submit Button Past Newsletters Variant (Swine Origin) Influenza Viruses in Humans Language: English Español Recommend on ... United States since 2005 Background On Variant Influenza Viruses Swine flu viruses do not normally infect humans. ...

  6. Evaluation of Perceived Threat Differences Posed by Filovirus Variants

    PubMed Central

    Kuhn, Jens H.; Dodd, Lori E.; Wahl-Jensen, Victoria; Radoshitzky, Sheli R.; Bavari, Sina

    2011-01-01

    In the United States, filoviruses (ebolaviruses and marburgviruses) are listed as National Institute of Allergy and Infectious Diseases (NIAID) Category A Priority Pathogens, Select Agents, and Centers for Disease Control and Prevention (CDC) Category A Bioterrorism Agents. In recent months, U.S. biodefense professionals and policy experts have initiated discussions on how to optimize filovirus research in regard to medical countermeasure (ie, diagnostics, antiviral, and vaccine) development. Standardized procedures and reagents could accelerate the independent verification of research results across government agencies and establish baselines for the development of animal models acceptable to regulatory entities, such as the Food and Drug Administration (FDA), while being fiscally responsible. At the root of standardization lies the question of which filovirus strains, variants, or isolates ought to be the prototypes for product development, evaluation, and validation. Here we discuss a rationale for their selection. We conclude that, based on currently available data, filovirus biodefense research ought to focus on the classical taxonomic filovirus prototypes: Marburg virus Musoke in the case of marburgviruses and Ebola virus Mayinga in the case of Zaire ebolaviruses. Arguments have been made in various committees in favor of other variants, such as Marburg virus Angola, Ci67 or Popp, or Ebola virus Kikwit, but these rationales seem to be largely based on anecdotal or unpublished and unverified data, or they may reflect a lack of awareness of important facts about the variants' isolation history and genomic properties. PMID:22070137

  7. Evaluation of perceived threat differences posed by filovirus variants.

    PubMed

    Kuhn, Jens H; Dodd, Lori E; Wahl-Jensen, Victoria; Radoshitzky, Sheli R; Bavari, Sina; Jahrling, Peter B

    2011-12-01

    In the United States, filoviruses (ebolaviruses and marburgviruses) are listed as National Institute of Allergy and Infectious Diseases (NIAID) Category A Priority Pathogens, Select Agents, and Centers for Disease Control and Prevention (CDC) Category A Bioterrorism Agents. In recent months, U.S. biodefense professionals and policy experts have initiated discussions on how to optimize filovirus research in regard to medical countermeasure (ie, diagnostics, antiviral, and vaccine) development. Standardized procedures and reagents could accelerate the independent verification of research results across government agencies and establish baselines for the development of animal models acceptable to regulatory entities, such as the Food and Drug Administration (FDA), while being fiscally responsible. At the root of standardization lies the question of which filovirus strains, variants, or isolates ought to be the prototypes for product development, evaluation, and validation. Here we discuss a rationale for their selection. We conclude that, based on currently available data, filovirus biodefense research ought to focus on the classical taxonomic filovirus prototypes: Marburg virus Musoke in the case of marburgviruses and Ebola virus Mayinga in the case of Zaire ebolaviruses. Arguments have been made in various committees in favor of other variants, such as Marburg virus Angola, Ci67 or Popp, or Ebola virus Kikwit, but these rationales seem to be largely based on anecdotal or unpublished and unverified data, or they may reflect a lack of awareness of important facts about the variants' isolation history and genomic properties. PMID:22070137

  8. Variant Humicola grisea CBH1.1

    DOEpatents

    Goedegebuur, Frits; Gualfetti, Peter; Mitchinson, Colin; Larenas, Edmund

    2008-12-02

    Disclosed are variants of Humicola grisea Cel7A (CBH1.1), H. jecorina CBH1 variant or S. thermophilium CBH1, nucleic acids encoding the same and methods for producing the same. The variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted.

  9. Variant Humicola grisea CBH1.1

    DOEpatents

    Goedegebuur, Frits; Gualfetti, Peter; Mitchinson, Colin; Larenas, Edmund

    2014-03-18

    Disclosed are variants of Humicola grisea Cel7A (CBH1.1), H. jecorina CBH1 variant or S. thermophilium CBH1, nucleic acids encoding the same and methods for producing the same. The variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted.

  10. Variant Humicola grisea CBH1.1

    DOEpatents

    Goedegeburr, Frits; Gualfetti, Peter; Mitchinson, Colin; Larenas, Edmund

    2013-02-19

    Disclosed are variants of Humicola grisea Cel7A (CBH1.1), H. jecorina CBH1 variant or S. thermophilium CBH1, nucleic acids encoding the same and methods for producing the same. The variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted.

  11. Variant Humicola grisea CBH1.1

    DOEpatents

    Goedegebuur, Frits; Gualfetti, Peter; Mitchinson, Colin; Larenas, Edmund

    2012-08-07

    Disclosed are variants of Humicola grisea Cel7A (CBH1.1), H. jecorina CBH1 variant or S. thermophilium CBH1, nucleic acids encoding the same and methods for producing the same. The variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted.

  12. Variant humicola grisea CBH1.1

    DOEpatents

    Goedegebuur, Frits; Gualfetti, Peter; Mitchinson, Colin; Edmund, Larenas

    2014-09-09

    Disclosed are variants of Humicola grisea Cel7A (CBH1.1), H. jecorina CBH1 variant or S. thermophilium CBH1, nucleic acids encoding the same and methods for producing the same. The variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted.

  13. Variant Humicola grisea CBH1.1

    DOEpatents

    Goedegebuur, Frits; Gualfetti, Peter; Mitchinson, Colin; Larenas, Edmund

    2011-05-31

    Disclosed are variants of Humicola grisea Cel7A (CBH1.1), H. jecorina CBH1 variant or S. thermophilium CBH1, nucleic acids encoding the same and methods for producing the same. The variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted.

  14. Variant Humicola grisea CBH1.1

    DOEpatents

    Goedegebuur, Frits; Gualfetti, Peter; Mitchinson, Colin; Larenas, Edmund

    2011-08-16

    Disclosed are variants of Humicola grisea Cel7A (CBH1.1), H. jecorina CBH1 variant or S. thermophilium CBH1, nucleic acids encoding the same and methods for producing the same. The variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted.

  15. Population structural analysis of O1 El Tor Vibrio cholerae isolated in China among the seventh cholera pandemic on the basis of multilocus sequence typing and virulence gene profiles.

    PubMed

    Zhou, Haijian; Zhao, Xuan; Wu, Rui; Cui, Zhigang; Diao, Baowei; Li, Jie; Wang, Duochun; Kan, Biao; Liang, Weili

    2014-03-01

    Serogroup O1 Vibrio cholerae is the most common agents to cause epidemic and pandemic cholera disease. In this study, multilocus sequence typing (MLST) was performed on 160 serogroup O1 strains (including 42 toxigenic and 118 non-toxigenic), and the virulence/fitness gene profiles of 16 loci were further analysed for 60 strains of these. Eighty-four sequence types (STs) with 14 clonal complexes were distinguished, and 29 STs were unique. Except SD19771005, all toxigenic strains were well-separated from the non-toxigenic strains. While a group of non-toxigenic strains clustered closer to the toxigenic strains compared to the other strains. Overall the examined gene loci showed higher presence rates in the toxigenic strains compared to the non-toxigenic strains. It is worth noting that the presence rates of VPI, TLC, VSP-I and VSP-II in the non-toxigenic strains that were clustered closer to the toxigenic strains were much higher compared to the other non-toxigenic strains. Our study indicated the complex population structure of O1 strains, and parts of non-toxigenic strains are genetically more closely related to toxigenic strains than other non-toxigenic strains, suggesting that these strains may have a higher potential for infection with CTX? in the environment or host intestine and is more efficient to become new pathogenic or epidemic clones. PMID:24448269

  16. Genetic Variation of Citrus Tristeza Virus Isolates from California and Spain: Evidence for Mixed Infections and Recombination

    PubMed Central

    Rubio, Luis; Ayllón, María Angeles; Kong, Ping; Fernández, Andres; Polek, MaryLou; Guerri, José; Moreno, Pedro; Falk, Bryce W.

    2001-01-01

    We examined the population structure and genetic variation of four genomic regions within and between 30 Citrus tristeza virus (CTV) isolates from Spain and California. Our analyses showed that most isolates contained a population of sequence variants, with one being predominant. Four isolates showed two major sequence variants in some genomic regions. The two major variants of three of these isolates showed very low nucleotide identity to each other but were very similar to those of other isolates, suggesting the possibility of mixed infections with two divergent isolates. Incongruencies of phylogenetic relationships in the different genomic regions and statistical analyses suggested that the genomes of some CTV sequence variants originated by recombination events between diverged sequence variants. No correlation was observed between geographic origin and nucleotide distance, and thus from a genetic view, the Spanish and Californian isolates analyzed here could be considered members of the same population. PMID:11483750

  17. Pilus Gene Pool Variation and the Virulence of Corynebacterium diphtheriae Clinical Isolates during Infection of a Nematode

    PubMed Central

    Broadway, Melissa M.; Rogers, Elizabeth A.; Chang, Chungyu; Huang, I-Hsiu; Dwivedi, Prabhat; Yildirim, Suleyman; Schmitt, Michael P.; Das, Asis

    2013-01-01

    Toxigenic Corynebacterium diphtheriae strains cause diphtheria in humans. The toxigenic C. diphtheriae isolate NCTC13129 produces three distinct heterotrimeric pili that contain SpaA, SpaD, and SpaH, making up the shaft structure. The SpaA pili are known to mediate bacterial adherence to pharyngeal epithelial cells. However, to date little is known about the expression of different pili in various clinical isolates and their importance in bacterial pathogenesis. Here, we characterized a large collection of C. diphtheriae clinical isolates for their pilin gene pool by PCR and for the expression of the respective pilins by immunoblotting with antibodies against Spa pilins. Consistent with the role of a virulence factor, the SpaA-type pili were found to be prevalent among the isolates, and most significantly, corynebacterial adherence to pharyngeal epithelial cells was strictly correlated with isolates that were positive for the SpaA pili. By comparison, the isolates were heterogeneous for the presence of SpaD- and SpaH-type pili. Importantly, using Caenorhabditis elegans as a model host for infection, we show here that strain NCTC13129 rapidly killed the nematodes, the phenotype similar to isolates that were positive for toxin and all pilus types. In contrast, isogenic mutants of NCTC13129 lacking SpaA-type pili or devoid of toxin and SpaA pili exhibited delayed killing of nematodes with similar kinetics. Consistently, nontoxigenic or toxigenic isolates that lack one, two, or all three pilus types were also attenuated in virulence. This work signifies the important role of pili in corynebacterial pathogenesis and provides a simple host model to identify additional virulence factors. PMID:23772071

  18. Pigmented Porokeratosis. A Further Variant?

    PubMed

    Tan, Tracy S P; Tallon, Ben

    2016-03-01

    Porokeratosis is a clonal disorder of keratinization characterized by the presence of the cornoid lamella. A number of variants of porokeratosis have been described, based on the clinical features and histologic features of the lesions. The authors present a case of porokeratosis with prominent melanocytic hyperplasia, which was biopsied to clinically exclude melanoma. The authors retrospectively studied cases of porokeratosis to look for the presence of melanocytic hyperplasia. Melanocytic hyperplasia was identified in 8 of 31 cases (25.8%). All of the cases except the index case were clinically nonpigmented but arose in solar damaged skin. This case represents a distinct variant of porokeratosis, and the authors propose the designation pigmented porokeratosis. Melanocytic hyperplasia is a benign condition, and it is important that this is not histologically confused with melanoma in situ, particularly in a context of clinically pigmented lesion. Increased recognition of pigmented porokeratosis is essential to avoid an erroneous diagnosis of melanoma in situ. PMID:26894774

  19. Oncotator: cancer variant annotation tool.

    PubMed

    Ramos, Alex H; Lichtenstein, Lee; Gupta, Manaswi; Lawrence, Michael S; Pugh, Trevor J; Saksena, Gordon; Meyerson, Matthew; Getz, Gad

    2015-04-01

    Oncotator is a tool for annotating genomic point mutations and short nucleotide insertions/deletions (indels) with variant- and gene-centric information relevant to cancer researchers. This information is drawn from 14 different publicly available resources that have been pooled and indexed, and we provide an extensible framework to add additional data sources. Annotations linked to variants range from basic information, such as gene names and functional classification (e.g. missense), to cancer-specific data from resources such as the Catalogue of Somatic Mutations in Cancer (COSMIC), the Cancer Gene Census, and The Cancer Genome Atlas (TCGA). For local use, Oncotator is freely available as a python module hosted on Github (https://github.com/broadinstitute/oncotator). Furthermore, Oncotator is also available as a web service and web application at http://www.broadinstitute.org/oncotator/. PMID:25703262

  20. Mammalian expression, purification, and crystallization of rhodopsin variants.

    PubMed

    Mattle, Daniel; Singhal, Ankita; Schmid, Georg; Dawson, Roger; Standfuss, Jörg

    2015-01-01

    After 25 years of intensive research, the understanding of how photoreceptors in the eye perceive light and convert it into nerve signals has largely advanced. Central to this is the structural and mechanistic exploration of the G protein-coupled receptor rhodopsin acting as a dim-light sensing pigment in the retina. Investigation of rhodopsin by X-ray crystallographic, electron microscopic, and biochemical means depends on the ability to produce and isolate pure rhodopsin protein. Robust and well-defined protocols permit the production and crystallization of rhodopsin variants to investigate the inactive ground, the fully activated metarhodopsin II state, or disease-causing rhodopsin mutations. This chapter details how we express and purify biologically active variants of rhodopsin from HEK293S GnTI(-) cells in a quality and quantity suitable for biochemical assays, crystallization, and structure determination. PMID:25697515

  1. Microcystic Variant of Urothelial Carcinoma

    PubMed Central

    Venyo, Anthony Kodzo-Grey

    2013-01-01

    Background. Microcystic variant of urothelial carcinoma is one of the new variants of urothelial carcinoma that was added to the WHO classification in 2004. Aims. To review the literature on microcystic variant of urothelial carcinoma. Methods. Various internet search engines were used to identify reported cases of the tumour. Results. Microscopic features of the tumour include: (i) Conspicuous intracellular and intercellular lumina/microcysts encompassed by malignant urothelial or squamous cells. (ii) The lumina are usually empty; may contain granular eosinophilic debris, mucin, or necrotic cells. (iii) The cysts may be variable in size; round, or oval, up to 2?mm; lined by urothelium which are either flattened cells or low columnar cells however, they do not contain colonic epithelium or goblet cells; are infiltrative; invade the muscularis propria; mimic cystitis cystica and cystitis glandularis; occasionally exhibit neuroendocrine differentiation. (iv) Elongated and irregular branching spaces are usually seen. About 17 cases of the tumour have been reported with only 2 patients who have survived. The tumour tends to be of high-grade and high-stage. There is no consensus opinion on the best option of treatment of the tumour. Conclusions. It would prove difficult at the moment to be dogmatic regarding its prognosis but it is a highly aggressive tumour. New cases of the tumour should be reported in order to document its biological behaviour. PMID:24363668

  2. Variant-specific prion interactions

    PubMed Central

    Sharma, Jaya; Liebman, Susan W

    2013-01-01

    Prions are protein conformations that “self-seed” the misfolding of their non-prion iso-forms into prion, often amyloid, conformations. The most famous prion is the mammalian PrP protein that in its prion form causes transmissible spongiform encephalopathy. Curiously there can be distinct conformational differences even between prions of the same protein propagated in the same host species. These are called prion strains or variants. For example, different PrP variants are faithfully transmitted during self-seeding and are associated with distinct disease characteristics. Variant-specific PrP prion differences include the length of the incubation period before the disease appears and the deposition of prion aggregates in distinct regions of the brain.1 Other more common neurodegenerative diseases (e.g., Alzheimer disease, Parkinson disease, type 2 diabetes and ALS) are likewise caused by the misfolding of a normal protein into a self-seeding aggregate.2-4 One of the most important unanswered questions is how the first prion-like seed arises de novo, resulting in the pathological cascade. PMID:24475372

  3. Molecular basis of organ-specific selection of viral variants during chronic infection.

    PubMed Central

    Ahmed, R; Hahn, C S; Somasundaram, T; Villarete, L; Matloubian, M; Strauss, J H

    1991-01-01

    Viral variants of different phenotypes are present in the central nervous system (CNS) and lymphoid tissues of carrier mice infected at birth with the Armstrong strain of lymphocytic choriomeningitis virus. The CNS isolates are similar to the parental virus and cause acute infections in adult mice, whereas the lymphoid isolates cause chronic infections associated with suppressed T-cell responses. In this study, we provide a molecular basis for this organ-specific selection and identify a single amino acid change in the viral glycoprotein that correlates with the tissue specific selection and the persistent and immunosuppressive phenotype of the variants. This phenylalanine (F)-to-leucine (L) change at position 260 of the viral glycoprotein was seen in the vast majority (43 of 47) of the lymphoid isolates, and variants with L at this residue were selected in spleens of persistently infected mice. In striking contrast, isolates with the parental sequence (F at residue 260) predominated (48 of 59 isolates) in the CNS of the same carrier mice. Complete nucleotide sequence analysis of the major structural genes of several independently derived (from different mice) spleen isolates showed that these variants were greater than 99.8% identical to the parental virus. In fact, the only common change among these spleen isolates was the F----L mutation at residue 260 of the glycoprotein. These results show that an RNA virus can exhibit minimal genetic drift during chronic infection in its natural host, and yet a single or few mutations can result in the organ-specific selection of variants that are markedly different from the parental virus. Images PMID:2072451

  4. Re-sequencing Expands Our Understanding of the Phenotypic Impact of Variants at GWAS Loci

    PubMed Central

    Ramensky, Vasily; Yajnik, Pranav; Koboldt, Daniel C.; Larson, David E.; Zhang, Qunyuan; Lin, Ling; Welch, Ryan; Ding, Li; McLellan, Michael D.; O'Laughlin, Michele; Fronick, Catrina; Fulton, Lucinda L.; Magrini, Vincent; Swift, Amy; Elliott, Paul; Jarvelin, Marjo-Riitta; Kaakinen, Marika; McCarthy, Mark I.; Pouta, Anneli; Bonnycastle, Lori L.; Collins, Francis S.; Narisu, Narisu; Stringham, Heather M.; Tuomilehto, Jaakko; Ripatti, Samuli; Fulton, Robert S.; Sabatti, Chiara; Wilson, Richard K.; Boehnke, Michael; Freimer, Nelson B.

    2014-01-01

    Genome-wide association studies (GWAS) have identified >500 common variants associated with quantitative metabolic traits, but in aggregate such variants explain at most 20–30% of the heritable component of population variation in these traits. To further investigate the impact of genotypic variation on metabolic traits, we conducted re-sequencing studies in >6,000 members of a Finnish population cohort (The Northern Finland Birth Cohort of 1966 [NFBC]) and a type 2 diabetes case-control sample (The Finland-United States Investigation of NIDDM Genetics [FUSION] study). By sequencing the coding sequence and 5? and 3? untranslated regions of 78 genes at 17 GWAS loci associated with one or more of six metabolic traits (serum levels of fasting HDL-C, LDL-C, total cholesterol, triglycerides, plasma glucose, and insulin), and conducting both single-variant and gene-level association tests, we obtained a more complete understanding of phenotype-genotype associations at eight of these loci. At all eight of these loci, the identification of new associations provides significant evidence for multiple genetic signals to one or more phenotypes, and at two loci, in the genes ABCA1 and CETP, we found significant gene-level evidence of association to non-synonymous variants with MAF<1%. Additionally, two potentially deleterious variants that demonstrated significant associations (rs138726309, a missense variant in G6PC2, and rs28933094, a missense variant in LIPC) were considerably more common in these Finnish samples than in European reference populations, supporting our prior hypothesis that deleterious variants could attain high frequencies in this isolated population, likely due to the effects of population bottlenecks. Our results highlight the value of large, well-phenotyped samples for rare-variant association analysis, and the challenge of evaluating the phenotypic impact of such variants. PMID:24497850

  5. Genome Sequence of WAU86/88-1, a New Variant of Vaccinia Virus Lister Strain from Poland.

    PubMed

    Mavian, Carla; López-Bueno, Alberto; Alcamí, Antonio

    2014-01-01

    The poxviruses Warsaw Agricultural University 86 (WAU86) and 88-1 (WAU88-1) were isolated in 1986 to 1988 from separate outbreaks in laboratory mice in Poland and described as ectromelia virus isolates. The genome sequences of these poxviruses reveal that they are almost identical and represent a novel variant of the vaccinia virus Lister strain. PMID:24407630

  6. Characterization of 19A-like 19F pneumococcal isolates from Papua New Guinea and Fiji

    PubMed Central

    Dunne, E.M.; Tikkanen, L.; Balloch, A.; Gould, K.; Yoannes, M.; Phuanukoonnon, S.; Licciardi, P.V.; Russell, F.M.; Mulholland, E.K.; Satzke, C.; Hinds, J.

    2015-01-01

    Molecular identification of Streptococcus pneumoniae serotype 19F is routinely performed by PCR targeting the wzy gene of the capsular biosynthetic locus. However, 19F isolates with genetic similarity to 19A have been reported in the United States and Brazil. We screened 78 pneumococcal carriage isolates and found six 19F wzy variants that originated from children in Papua New Guinea and Fiji. Isolates were characterized using multilocus sequence typing and opsonophagocytic assays. The 19F wzy variants displayed similar susceptibility to anti-19F IgG antibodies compared to standard 19F isolates. Our findings indicate that these 19F variants may be more common than previously believed. PMID:26339490

  7. Post-GWAS methodologies for localisation of functional non-coding variants: ANGPTL3

    PubMed Central

    Oldoni, Federico; Palmen, Jutta; Giambartolomei, Claudia; Howard, Philip; Drenos, Fotios; Plagnol, Vincent; Humphries, Steve E.; Talmud, Philippa J.; Smith, Andrew J.P.

    2016-01-01

    Genome-wide association studies have confirmed the involvement of non-coding angiopoietin-like 3 (ANGPTL3) gene variants with coronary artery disease, levels of low-density lipoprotein cholesterol (LDL-C), triglycerides and ANGPTL3 mRNA transcript. Extensive linkage disequilibrium at the locus, however, has hindered efforts to identify the potential functional variants. Using regulatory annotations from ENCODE, combined with functional in vivo assays such as allele-specific formaldehyde-assisted isolation of regulatory elements, statistical approaches including eQTL/lipid colocalisation, and traditional in vitro methodologies including electrophoretic mobility shift assay and luciferase reporter assays, variants affecting the ANGPTL3 regulome were examined. From 253 variants associated with ANGPTL3 mRNA expression, and/or lipid traits, 46 were located within liver regulatory elements and potentially functional. One variant, rs10889352, demonstrated allele-specific effects on DNA-protein interactions, reporter gene expression and chromatin accessibility, in line with effects on LDL-C levels and expression of ANGPTL3 mRNA. The ANGPTL3 gene lies within DOCK7, although the variant is within non-coding regions outside of ANGPTL3, within DOCK7, suggesting complex long-range regulatory effects on gene expression. This study illustrates the power of combining multiple genome-wide datasets with laboratory data to localise functional non-coding variation and provides a model for analysis of regulatory variants from GWAS. PMID:26800306

  8. Post-GWAS methodologies for localisation of functional non-coding variants: ANGPTL3.

    PubMed

    Oldoni, Federico; Palmen, Jutta; Giambartolomei, Claudia; Howard, Philip; Drenos, Fotios; Plagnol, Vincent; Humphries, Steve E; Talmud, Philippa J; Smith, Andrew J P

    2016-03-01

    Genome-wide association studies have confirmed the involvement of non-coding angiopoietin-like 3 (ANGPTL3) gene variants with coronary artery disease, levels of low-density lipoprotein cholesterol (LDL-C), triglycerides and ANGPTL3 mRNA transcript. Extensive linkage disequilibrium at the locus, however, has hindered efforts to identify the potential functional variants. Using regulatory annotations from ENCODE, combined with functional in vivo assays such as allele-specific formaldehyde-assisted isolation of regulatory elements, statistical approaches including eQTL/lipid colocalisation, and traditional in vitro methodologies including electrophoretic mobility shift assay and luciferase reporter assays, variants affecting the ANGPTL3 regulome were examined. From 253 variants associated with ANGPTL3 mRNA expression, and/or lipid traits, 46 were located within liver regulatory elements and potentially functional. One variant, rs10889352, demonstrated allele-specific effects on DNA-protein interactions, reporter gene expression and chromatin accessibility, in line with effects on LDL-C levels and expression of ANGPTL3 mRNA. The ANGPTL3 gene lies within DOCK7, although the variant is within non-coding regions outside of ANGPTL3, within DOCK7, suggesting complex long-range regulatory effects on gene expression. This study illustrates the power of combining multiple genome-wide datasets with laboratory data to localise functional non-coding variation and provides a model for analysis of regulatory variants from GWAS. PMID:26800306

  9. Analysis of amino acid substitutions in AraC variants that respond to triacetic acid lactone.

    PubMed

    Frei, Christopher S; Wang, Zhiqing; Qian, Shuai; Deutsch, Samuel; Sutter, Markus; Cirino, Patrick C

    2016-04-01

    The Escherichia coli regulatory protein AraC regulates expression of ara genes in response to l-arabinose. In efforts to develop genetically encoded molecular reporters, we previously engineered an AraC variant that responds to the compound triacetic acid lactone (TAL). This variant (named "AraC-TAL1") was isolated by screening a library of AraC variants, in which five amino acid positions in the ligand-binding pocket were simultaneously randomized. Screening was carried out through multiple rounds of alternating positive and negative fluorescence-activated cell sorting. Here we show that changing the screening protocol results in the identification of different TAL-responsive variants (nine new variants). Individual substituted residues within these variants were found to primarily act cooperatively toward the gene expression response. Finally, X-ray diffraction was used to solve the crystal structure of the apo AraC-TAL1 ligand-binding domain. The resolved crystal structure confirms that this variant takes on a structure nearly identical to the apo wild-type AraC ligand-binding domain (root-mean-square deviation 0.93 Å), suggesting that AraC-TAL1 behaves similar to wild-type with regard to ligand recognition and gene regulation. Our results provide amino acid sequence-function data sets for training and validating AraC modeling studies, and contribute to our understanding of how to design new biosensors based on AraC. PMID:26749125

  10. PBHoney: identifying genomic variants via long-read discordance and interrupted mapping

    PubMed Central

    2014-01-01

    Background As resequencing projects become more prevalent across a larger number of species, accurate variant identification will further elucidate the nature of genetic diversity and become increasingly relevant in genomic studies. However, the identification of larger genomic variants via DNA sequencing is limited by both the incomplete information provided by sequencing reads and the nature of the genome itself. Long-read sequencing technologies provide high-resolution access to structural variants often inaccessible to shorter reads. Results We present PBHoney, software that considers both intra-read discordance and soft-clipped tails of long reads (>10,000 bp) to identify structural variants. As a proof of concept, we identify four structural variants and two genomic features in a strain of Escherichia coli with PBHoney and validate them via de novo assembly. PBHoney is available for download at http://sourceforge.net/projects/pb-jelly/. Conclusions Implementing two variant-identification approaches that exploit the high mappability of long reads, PBHoney is demonstrated as being effective at detecting larger structural variants using whole-genome Pacific Biosciences RS II Continuous Long Reads. Furthermore, PBHoney is able to discover two genomic features: the existence of Rac-Phage in isolate; evidence of E. coli’s circular genome. PMID:24915764

  11. A rigorous approach for selection of optimal variant sets for carrier screening with demonstration of clinical utility

    PubMed Central

    Perreault-Micale, Cynthia; Davie, Jocelyn; Breton, Benjamin; Hallam, Stephanie; Greger, Valerie

    2015-01-01

    Carrier screening for certain diseases is recommended by major medical and Ashkenazi Jewish (AJ) societies. Most carrier screening panels test only for common, ethnic-specific variants. However, with formerly isolated ethnic groups becoming increasingly intermixed, this approach is becoming inadequate. Our objective was to develop a rigorous process to curate all variants, for relevant genes, into a database and then apply stringent clinical validity classification criteria to each in order to retain only those with clear evidence for pathogenicity. The resulting variant set, in conjunction with next-generation DNA sequencing (NGS), then affords the capability for an ethnically diverse, comprehensive, highly specific carrier-screening assay. The clinical utility of our approach was demonstrated by screening a pan-ethnic population of 22,864 individuals for Bloom syndrome carrier status using a BLM variant panel comprised of 50 pathogenic variants. In addition to carriers of the common AJ founder variant, we identified 57 carriers of other pathogenic BLM variants. All variants reported had previously been curated and their clinical validity documented, or were of a type that met our stringent, preassigned validity criteria. Thus, it was possible to confidently report an increased number of Bloom’s syndrome carriers compared to traditional, ethnicity-based screening, while not reducing the specificity of the screening due to reporting variants of unknown clinical significance. PMID:26247052

  12. First Case of Human Rabies in Chile Caused by an Insectivorous Bat Virus Variant

    PubMed Central

    Favi, Myriam; Yung, Verónica; Chala, Evelyn; López, Luis R.

    2002-01-01

    The first human rabies case in Chile since 1972 occurred in March 1996 in a patient without history of known exposure. Antigenic and genetic characterization of the rabies isolate indicated that its reservoir was the insectivorous bat Tadarida brasiliensis. This is the first human rabies case caused by an insectivorous bat rabies virus variant reported in Latin America. PMID:11749754

  13. First genome characterization of a novel hepatitis C virus genotype 5 variant.

    PubMed

    Henquell, Cécile; Yameogo, Saydou; Sangaré, Lassana

    2016-04-01

    We report a new hepatitis C virus (HCV) genotype 5 variant from a woman living in Burkina Faso. Phylogenetic analysis of the near full-length genome sequence suggests that this isolate HCV5_BF16 could be the first reported strain belonging to a new HCV 5 subtype, distinct from the 5a subtype. PMID:26807921

  14. Nested variant of urothelial carcinoma.

    PubMed

    Venyo, Anthony Kodzo-Grey

    2014-01-01

    Background. Nested variant of urothelial carcinoma was added to the WHO's classification in 2004. Aims. To review the literature on nested variant of urothelial carcinoma. Results. About 200 cases of the tumour have been reported so far and it has the ensuing morphological features: large numbers of small confluent irregular nests of bland-appearing, closely packed, haphazardly arranged, and poorly defined urothelial cells infiltrating the lamina propria and the muscularis propria. The tumour has a bland histomorphologic appearance, has an aggressive biological behaviour, and has at times been misdiagnosed as a benign lesion which had led to a significant delay in the establishment of the correct diagnosis and contributing to the advanced stage of the disease. Immunohistochemically, the tumour shares some characteristic features with high-risk conventional urothelial carcinomas such as high proliferation index and loss of p27 expression. However, p53, bcl-2, or EGF-r immunoreactivity is not frequently seen. The tumour must be differentiated from a number of proliferative lesions of the urothelium. Conclusions. Correct and early diagnosis of this tumour is essential to provide early curative treatment to avoid diagnosis at an advanced stage. A multicentre trial is required to identify treatment options that would improve the outcome of this tumour. PMID:24587796

  15. Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies

    PubMed Central

    Field, Matthew A.; Cho, Vicky

    2015-01-01

    A diversity of tools is available for identification of variants from genome sequence data. Given the current complexity of incorporating external software into a genome analysis infrastructure, a tendency exists to rely on the results from a single tool alone. The quality of the output variant calls is highly variable however, depending on factors such as sequence library quality as well as the choice of short-read aligner, variant caller, and variant caller filtering strategy. Here we present a two-part study first using the high quality ‘genome in a bottle’ reference set to demonstrate the significant impact the choice of aligner, variant caller, and variant caller filtering strategy has on overall variant call quality and further how certain variant callers outperform others with increased sample contamination, an important consideration when analyzing sequenced cancer samples. This analysis confirms previous work showing that combining variant calls of multiple tools results in the best quality resultant variant set, for either specificity or sensitivity, depending on whether the intersection or union, of all variant calls is used respectively. Second, we analyze a melanoma cell line derived from a control lymphocyte sample to determine whether software choices affect the detection of clinically important melanoma risk-factor variants finding that only one of the three such variants is unanimously detected under all conditions. Finally, we describe a cogent strategy for implementing a clinical variant detection pipeline; a strategy that requires careful software selection, variant caller filtering optimizing, and combined variant calls in order to effectively minimize false negative variants. While implementing such features represents an increase in complexity and computation the results offer indisputable improvements in data quality. PMID:26600436

  16. Beyond Rare-Variant Association Testing: Pinpointing Rare Causal Variants in Case-Control Sequencing Study.

    PubMed

    Lin, Wan-Yu

    2016-01-01

    Rare-variant association testing usually requires some method of aggregation. The next important step is to pinpoint individual rare causal variants among a large number of variants within a genetic region. Recently Ionita-Laza et al. propose a backward elimination (BE) procedure that can identify individual causal variants among the many variants in a gene. The BE procedure removes a variant if excluding this variant can lead to a smaller P-value for the BURDEN test (referred to as "BE-BURDEN") or the SKAT test (referred to as "BE-SKAT"). We here use the adaptive combination of P-values (ADA) method to pinpoint causal variants. Unlike most gene-based association tests, the ADA statistic is built upon per-site P-values of individual variants. It is straightforward to select important variants given the optimal P-value truncation threshold found by ADA. We performed comprehensive simulations to compare ADA with BE-SKAT and BE-BURDEN. Ranking these three approaches according to positive predictive values (PPVs), the percentage of truly causal variants among the total selected variants, we found ADA?>?BE-SKAT?>?BE-BURDEN across all simulation scenarios. We therefore recommend using ADA to pinpoint plausible rare causal variants in a gene. PMID:26903168

  17. Beyond Rare-Variant Association Testing: Pinpointing Rare Causal Variants in Case-Control Sequencing Study

    PubMed Central

    Lin, Wan-Yu

    2016-01-01

    Rare-variant association testing usually requires some method of aggregation. The next important step is to pinpoint individual rare causal variants among a large number of variants within a genetic region. Recently Ionita-Laza et al. propose a backward elimination (BE) procedure that can identify individual causal variants among the many variants in a gene. The BE procedure removes a variant if excluding this variant can lead to a smaller P-value for the BURDEN test (referred to as “BE-BURDEN”) or the SKAT test (referred to as “BE-SKAT”). We here use the adaptive combination of P-values (ADA) method to pinpoint causal variants. Unlike most gene-based association tests, the ADA statistic is built upon per-site P-values of individual variants. It is straightforward to select important variants given the optimal P-value truncation threshold found by ADA. We performed comprehensive simulations to compare ADA with BE-SKAT and BE-BURDEN. Ranking these three approaches according to positive predictive values (PPVs), the percentage of truly causal variants among the total selected variants, we found ADA > BE-SKAT > BE-BURDEN across all simulation scenarios. We therefore recommend using ADA to pinpoint plausible rare causal variants in a gene. PMID:26903168

  18. Detection of toxins A/B and isolation of Clostridium difficile and Clostridium perfringens from dogs in Minas Gerais, Brazil

    PubMed Central

    Silva, Rodrigo Otávio Silveira; Santos, Renata Lara Resende; Pires, Prhiscylla Sadanã; Pereira, Luiz Carlos; Pereira, Silvia Trindade; Duarte, Marina Carvalho; de Assis, Ronnie Antunes; Lobato, Francisco Carlos Faria

    2013-01-01

    The objective of this study was to detect C. difficile A/B toxins and to isolate strains of C. perfringens and C. difficile from diarrheic and non-diarrheic dogs in Brazil. Stool samples were collected from 57 dogs, 35 of which were apparently healthy, and 22 of which were diarrheic. C. difficile A/B toxins were detected by ELISA, and C. perfringens and C. difficile were identified by multiplex PCR. C. difficile A/B toxins were detected in 21 samples (36.8%). Of these, 16 (76.2%) were from diarrheic dogs, and five (23.8%) were from non-diarrheic dogs. Twelve C. difficile strains (21.1%) were isolated, of which ten were A+B+ and two were A?B?. All non-toxigenic strains were isolated from non-diarrheic animals. The binary toxin gene cdtB was found in one strain, which was A+B+ and was derived from a non-diarrheic dog. C. perfringens strains were isolated from 40 samples (70.2%). Of these, 18 (45%) were from the diarrheic group, and 22 (55%) belonged to the non-diarrheic group. All isolates were classified as C. perfringens type A and there was an association between the detection of the cpe gene and the presence of diarrhea. Interestingly, ten strains (25%) were positive for the presence of the cpb2 gene. The high rate of detection of the A/B toxins in non-diarrheic dogs suggests the occurrence of subclinical disease in dogs or carriage of its toxins without disease. More studies are needed to elucidate the epidemiology of C. difficile and C. perfringens in dogs and to better our understanding of C. difficile as a zoonotic agent. This is the first study to report the binary toxin gene in C. difficile strains isolated from dogs in Brazil. PMID:24159295

  19. Pseudomonas aeruginosa induces pigment production and enhances virulence in a white phenotypic variant of Staphylococcus aureus

    PubMed Central

    Antonic, Vlado; Stojadinovic, Alexander; Zhang, Binxue; Izadjoo, Mina J; Alavi, Mohammad

    2013-01-01

    Staphyloxanthin is a virulence factor which protects Staphylococcus aureus in stress conditions. We isolated two pigment variants of S. aureus and one strain of Pseudomonas aeruginosa from a single wound infection. S. aureus variants displayed white and yellow colony phenotypes. The sequence of the operons for staphyloxanthin synthesis indicated that coding and promoter regions were identical between the two pigment variants. Quorum sensing controls pigment synthesis in some bacteria. It is also shown that P. aeruginosa quorum-sensing molecules affect S. aureus transcription. We explored whether the co-infecting P. aeruginosa can affect pigment production in the white S. aureus variant. In co-culture experiments between the white variants and a selected number of Gram-positive and Gram-negative bacteria, only P. aeruginosa induced pigment production in the white variant. Gene expression analysis of the white variant did not indicate upregulation of the crtM and other genes known to be involved in pigment production (sigB, sarA, farnesyl pyrophosphate synthase gene [FPP-synthase], hfq). In contrast, transcription of the catalase gene was significantly upregulated after co-culture. P. aeruginosa-induced pigment synthesis and catalase upregulation correlated with increased resistance to polymyxin B, hydrogen peroxide, and the intracellular environment of macrophages. Our data indicate the presence of silent but functional staphyloxanthin synthesis machinery in a white phenotypic variant of S. aureus which is activated by a co-infecting P. aeruginosa via inter-species communication. Another S. aureus virulence factor, catalase is also induced by this co-infecting bacterium. The resulting phenotypic changes are directly correlated with resistance of the white variant to stressful conditions. PMID:24232573

  20. Distribution and Medical Impact of Loss-of-Function Variants in the Finnish Founder Population

    PubMed Central

    Lim, Elaine T.; Würtz, Peter; Havulinna, Aki S.; Palta, Priit; Tukiainen, Taru; Rehnström, Karola; Esko, Tõnu; Mägi, Reedik; Inouye, Michael; Lappalainen, Tuuli; Chan, Yingleong; Salem, Rany M.; Lek, Monkol; Flannick, Jason; Sim, Xueling; Manning, Alisa; Ladenvall, Claes; Bumpstead, Suzannah; Hämäläinen, Eija; Aalto, Kristiina; Maksimow, Mikael; Salmi, Marko; Blankenberg, Stefan; Ardissino, Diego; Shah, Svati; Horne, Benjamin; McPherson, Ruth; Hovingh, Gerald K.; Reilly, Muredach P.; Watkins, Hugh; Goel, Anuj; Farrall, Martin; Girelli, Domenico; Reiner, Alex P.; Stitziel, Nathan O.; Kathiresan, Sekar; Gabriel, Stacey; Barrett, Jeffrey C.; Lehtimäki, Terho; Laakso, Markku; Groop, Leif; Kaprio, Jaakko; Perola, Markus; McCarthy, Mark I.; Boehnke, Michael; Altshuler, David M.; Lindgren, Cecilia M.; Hirschhorn, Joel N.; Metspalu, Andres; Freimer, Nelson B.; Zeller, Tanja; Jalkanen, Sirpa; Koskinen, Seppo; Raitakari, Olli; Durbin, Richard; MacArthur, Daniel G.; Salomaa, Veikko; Ripatti, Samuli

    2014-01-01

    Exome sequencing studies in complex diseases are challenged by the allelic heterogeneity, large number and modest effect sizes of associated variants on disease risk and the presence of large numbers of neutral variants, even in phenotypically relevant genes. Isolated populations with recent bottlenecks offer advantages for studying rare variants in complex diseases as they have deleterious variants that are present at higher frequencies as well as a substantial reduction in rare neutral variation. To explore the potential of the Finnish founder population for studying low-frequency (0.5–5%) variants in complex diseases, we compared exome sequence data on 3,000 Finns to the same number of non-Finnish Europeans and discovered that, despite having fewer variable sites overall, the average Finn has more low-frequency loss-of-function variants and complete gene knockouts. We then used several well-characterized Finnish population cohorts to study the phenotypic effects of 83 enriched loss-of-function variants across 60 phenotypes in 36,262 Finns. Using a deep set of quantitative traits collected on these cohorts, we show 5 associations (p<5×10?8) including splice variants in LPA that lowered plasma lipoprotein(a) levels (P?=?1.5×10?117). Through accessing the national medical records of these participants, we evaluate the LPA finding via Mendelian randomization and confirm that these splice variants confer protection from cardiovascular disease (OR?=?0.84, P?=?3×10?4), demonstrating for the first time the correlation between very low levels of LPA in humans with potential therapeutic implications for cardiovascular diseases. More generally, this study articulates substantial advantages for studying the role of rare variation in complex phenotypes in founder populations like the Finns and by combining a unique population genetic history with data from large population cohorts and centralized research access to National Health Registers. PMID:25078778

  1. Distribution and medical impact of loss-of-function variants in the Finnish founder population.

    PubMed

    Lim, Elaine T; Würtz, Peter; Havulinna, Aki S; Palta, Priit; Tukiainen, Taru; Rehnström, Karola; Esko, Tõnu; Mägi, Reedik; Inouye, Michael; Lappalainen, Tuuli; Chan, Yingleong; Salem, Rany M; Lek, Monkol; Flannick, Jason; Sim, Xueling; Manning, Alisa; Ladenvall, Claes; Bumpstead, Suzannah; Hämäläinen, Eija; Aalto, Kristiina; Maksimow, Mikael; Salmi, Marko; Blankenberg, Stefan; Ardissino, Diego; Shah, Svati; Horne, Benjamin; McPherson, Ruth; Hovingh, Gerald K; Reilly, Muredach P; Watkins, Hugh; Goel, Anuj; Farrall, Martin; Girelli, Domenico; Reiner, Alex P; Stitziel, Nathan O; Kathiresan, Sekar; Gabriel, Stacey; Barrett, Jeffrey C; Lehtimäki, Terho; Laakso, Markku; Groop, Leif; Kaprio, Jaakko; Perola, Markus; McCarthy, Mark I; Boehnke, Michael; Altshuler, David M; Lindgren, Cecilia M; Hirschhorn, Joel N; Metspalu, Andres; Freimer, Nelson B; Zeller, Tanja; Jalkanen, Sirpa; Koskinen, Seppo; Raitakari, Olli; Durbin, Richard; MacArthur, Daniel G; Salomaa, Veikko; Ripatti, Samuli; Daly, Mark J; Palotie, Aarno

    2014-07-01

    Exome sequencing studies in complex diseases are challenged by the allelic heterogeneity, large number and modest effect sizes of associated variants on disease risk and the presence of large numbers of neutral variants, even in phenotypically relevant genes. Isolated populations with recent bottlenecks offer advantages for studying rare variants in complex diseases as they have deleterious variants that are present at higher frequencies as well as a substantial reduction in rare neutral variation. To explore the potential of the Finnish founder population for studying low-frequency (0.5-5%) variants in complex diseases, we compared exome sequence data on 3,000 Finns to the same number of non-Finnish Europeans and discovered that, despite having fewer variable sites overall, the average Finn has more low-frequency loss-of-function variants and complete gene knockouts. We then used several well-characterized Finnish population cohorts to study the phenotypic effects of 83 enriched loss-of-function variants across 60 phenotypes in 36,262 Finns. Using a deep set of quantitative traits collected on these cohorts, we show 5 associations (p<5×10⁻⁸) including splice variants in LPA that lowered plasma lipoprotein(a) levels (P = 1.5×10⁻¹¹⁷). Through accessing the national medical records of these participants, we evaluate the LPA finding via Mendelian randomization and confirm that these splice variants confer protection from cardiovascular disease (OR = 0.84, P = 3×10⁻⁴), demonstrating for the first time the correlation between very low levels of LPA in humans with potential therapeutic implications for cardiovascular diseases. More generally, this study articulates substantial advantages for studying the role of rare variation in complex phenotypes in founder populations like the Finns and by combining a unique population genetic history with data from large population cohorts and centralized research access to National Health Registers. PMID:25078778

  2. The Expression of NPPA Splice Variants During Mouse Cardiac Development

    PubMed Central

    2015-01-01

    Natriuretic peptide precursor-A (NPPA) is an early and specific marker for functional myocardium of the embryonic heart. NPPA gene encodes for a precursor of atrial natriuretic peptide (ANP). So far, three alternatively spliced variants have been reported for NPPA in human. In mouse, no alternatively spliced transcript of NPPA has been reported. In the current study, we investigated the expression of NPPA gene during cardiac differentiation of mouse adipose-tissue-derived stem cells (ADSCs) and embryonic stem (ES) cells. As revealed by reverse-transcription polymerase chain reaction analysis, 2-week-differentiated cells expressed some cardiac-specific makers, including ANP. Three additional intron-retained splice variants of NPPA were also detected during cardiac differentiation of the ADSCs and ES cells. In addition, we detected three intron-retained splice variants of NPPA in 8.5-day mouse embryonic heart. In the mature cardiomyocytes of 1-week-old mice, only the correctly spliced isoform of NPPA gene was expressed. Freshly isolated stromal vascular fraction also expressed one intron-retained isoform of NPPA gene. In conclusion, our findings have provided evidence for the expression of intron-retained splices of NPPA mRNA during the early stages of mouse cardiogenesis as well as in the mouse adipose tissue. PMID:25260157

  3. [PSI(+) ] prion variant establishment in yeast.

    PubMed

    Sharma, Jaya; Liebman, Susan W

    2012-11-01

    Differences in the clinical pathology of mammalian prion diseases reflect distinct heritable conformations of aggregated PrP proteins, called prion strains. Here, using the yeast [PSI(+) ] prion, we examine the de novo establishment of prion strains (called variants in yeast). The [PSI(+) ] prion protein, Sup35, is efficiently induced to take on numerous prion variant conformations following transient overexpression of Sup35 in the presence of another prion, e.g. [PIN(+) ]. One hypothesis is that the first [PSI(+) ] prion seed to arise in a cell causes propagation of only that seed's variant, but that different variants could be initiated in different cells. However, we now show that even within a single cell, Sup35 retains the potential to fold into more than one variant type. When individual cells segregating different [PSI(+) ] variants were followed in pedigrees, establishment of a single variant phenotype generally occurred in daughters, granddaughters or great-granddaughters - but in 5% of the pedigrees cells continued to segregate multiple variants indefinitely. The data are consistent with the idea that many newly formed prions go through a maturation phase before they reach a single specific variant conformation. These findings may be relevant to mammalian PrP prion strain establishment and adaptation. PMID:22998111

  4. Rare high-impact disease variants: properties and identifications.

    PubMed

    Park, Leeyoung; Kim, Ju Han

    2016-01-01

    Although many genome-wide association studies have been performed, the identification of disease polymorphisms remains important. It is now suspected that many rare disease variants induce the association signal of common variants in linkage disequilibrium (LD). Based on recent development of genetic models, the current study provides explanations of the existence of rare variants with high impacts and common variants with low impacts. Disease variants are neither necessary nor sufficient due to gene-gene or gene-environment interactions. A new method was developed based on theoretical aspects to identify both rare and common disease variants by their genotypes. Common disease variants were identified with relatively small odds ratios and relatively small sample sizes, except for specific situations in which the disease variants were in strong LD with a variant with a higher frequency. Rare disease variants with small impacts were difficult to identify without increasing sample sizes; however, the method was reasonably accurate for rare disease variants with high impacts. For rare variants, dominant variants generally showed better Type II error rates than recessive variants; however, the trend was reversed for common variants. Type II error rates increased in gene regions containing more than two disease variants because the more common variant, rather than both disease variants, was usually identified. The proposed method would be useful for identifying common disease variants with small impacts and rare disease variants with large impacts when disease variants have the same effects on disease presentation. PMID:26996452

  5. Carriage and acquisition rates of Clostridium difficile in hospitalized horses, including molecular characterization, multilocus sequence typing and antimicrobial susceptibility of bacterial isolates.

    PubMed

    Rodriguez, C; Taminiau, B; Brévers, B; Avesani, V; Van Broeck, J; Leroux, A A; Amory, H; Delmée, M; Daube, G

    2014-08-01

    Clostridium difficile has been identified as a significant agent of diarrhoea and enterocolitis in both foals and adult horses. Hospitalization, antibiotic therapy or changes in diet may contribute to the development of C. difficile infection. Horses admitted to a care unit are therefore at greater risk of being colonized. The aim of this study was to investigate the carriage of C. difficile in hospitalized horses and the possible influence of some risk factors in colonization. During a seven-month period, faecal samples and data relating the clinical history of horses admitted to a veterinary teaching hospital were collected. C. difficile isolates were characterized through toxin profiles, cytotoxicity activity, PCR-ribotyping, antimicrobial resistance and multilocus sequence typing (MLST). Ten isolates were obtained with a total of seven different PCR-ribotypes, including PCR-ribotype 014. Five of them were identified as toxinogenic. A high resistance to gentamicin, clindamycin and ceftiofur was found. MLST revealed four different sequencing types (ST), which included ST11, ST26, ST2 and ST15, and phylogenetic analysis showed that most of the isolates clustered in the same lineage. Clinical history suggests that horses frequently harbour toxigenic and non-toxigenic C. difficile and that in most cases they are colonized regardless of the reason for hospitalization; the development of diarrhoea is more unusual. PMID:24894133

  6. Mitochondrial DNA variants in obesity.

    PubMed

    Knoll, Nadja; Jarick, Ivonne; Volckmar, Anna-Lena; Klingenspor, Martin; Illig, Thomas; Grallert, Harald; Gieger, Christian; Wichmann, Heinz-Erich; Peters, Annette; Wiegand, Susanna; Biebermann, Heike; Fischer-Posovszky, Pamela; Wabitsch, Martin; Völzke, Henry; Nauck, Matthias; Teumer, Alexander; Rosskopf, Dieter; Rimmbach, Christian; Schreiber, Stefan; Jacobs, Gunnar; Lieb, Wolfgang; Franke, Andre; Hebebrand, Johannes; Hinney, Anke

    2014-01-01

    Heritability estimates for body mass index (BMI) variation are high. For mothers and their offspring higher BMI correlations have been described than for fathers. Variation(s) in the exclusively maternally inherited mitochondrial DNA (mtDNA) might contribute to this parental effect. Thirty-two to 40 mtDNA single nucleotide polymorphisms (SNPs) were available from genome-wide association study SNP arrays (Affymetrix 6.0). For discovery, we analyzed association in a case-control (CC) sample of 1,158 extremely obese children and adolescents and 435 lean adult controls. For independent confirmation, 7,014 population-based adults were analyzed as CC sample of n = 1,697 obese cases (BMI ? 30 kg/m2) and n = 2,373 normal weight and lean controls (BMI<25 kg/m2). SNPs were analyzed as single SNPs and haplogroups determined by HaploGrep. Fisher's two-sided exact test was used for association testing. Moreover, the D-loop was re-sequenced (Sanger) in 192 extremely obese children and adolescents and 192 lean adult controls. Association testing of detected variants was performed using Fisher's two-sided exact test. For discovery, nominal association with obesity was found for the frequent allele G of m.8994G/A (rs28358887, p = 0.002) located in ATP6. Haplogroup W was nominally overrepresented in the controls (p = 0.039). These findings could not be confirmed independently. For two of the 252 identified D-loop variants nominal association was detected (m.16292C/T, p = 0.007, m.16189T/C, p = 0.048). Only eight controls carried the m.16292T allele, five of whom belonged to haplogroup W that was initially enriched among these controls. m.16189T/C might create an uninterrupted poly-C tract located near a regulatory element involved in replication of mtDNA. Though follow-up of some D-loop variants still is conceivable, our hypothesis of a contribution of variation in the exclusively maternally inherited mtDNA to the observed larger correlations for BMI between mothers and their offspring could not be substantiated by the findings of the present study. PMID:24788344

  7. Mitochondrial DNA Variants in Obesity

    PubMed Central

    Knoll, Nadja; Jarick, Ivonne; Volckmar, Anna-Lena; Klingenspor, Martin; Illig, Thomas; Grallert, Harald; Gieger, Christian; Wichmann, Heinz-Erich; Peters, Annette; Wiegand, Susanna; Biebermann, Heike; Fischer-Posovszky, Pamela; Wabitsch, Martin; Völzke, Henry; Nauck, Matthias; Teumer, Alexander; Rosskopf, Dieter; Rimmbach, Christian; Schreiber, Stefan; Jacobs, Gunnar; Lieb, Wolfgang; Franke, Andre; Hebebrand, Johannes; Hinney, Anke

    2014-01-01

    Heritability estimates for body mass index (BMI) variation are high. For mothers and their offspring higher BMI correlations have been described than for fathers. Variation(s) in the exclusively maternally inherited mitochondrial DNA (mtDNA) might contribute to this parental effect. Thirty-two to 40 mtDNA single nucleotide polymorphisms (SNPs) were available from genome-wide association study SNP arrays (Affymetrix 6.0). For discovery, we analyzed association in a case-control (CC) sample of 1,158 extremely obese children and adolescents and 435 lean adult controls. For independent confirmation, 7,014 population-based adults were analyzed as CC sample of n = 1,697 obese cases (BMI≥30 kg/m2) and n = 2,373 normal weight and lean controls (BMI<25 kg/m2). SNPs were analyzed as single SNPs and haplogroups determined by HaploGrep. Fisher's two-sided exact test was used for association testing. Moreover, the D-loop was re-sequenced (Sanger) in 192 extremely obese children and adolescents and 192 lean adult controls. Association testing of detected variants was performed using Fisher's two-sided exact test. For discovery, nominal association with obesity was found for the frequent allele G of m.8994G/A (rs28358887, p = 0.002) located in ATP6. Haplogroup W was nominally overrepresented in the controls (p = 0.039). These findings could not be confirmed independently. For two of the 252 identified D-loop variants nominal association was detected (m.16292C/T, p = 0.007, m.16189T/C, p = 0.048). Only eight controls carried the m.16292T allele, five of whom belonged to haplogroup W that was initially enriched among these controls. m.16189T/C might create an uninterrupted poly-C tract located near a regulatory element involved in replication of mtDNA. Though follow-up of some D-loop variants still is conceivable, our hypothesis of a contribution of variation in the exclusively maternally inherited mtDNA to the observed larger correlations for BMI between mothers and their offspring could not be substantiated by the findings of the present study. PMID:24788344

  8. Genetic diversity among isolates of Autographa californica multiple nucleopolyhedrovirus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Our knowledge of genetic variation at the nucleotide sequence level of Autographa californica multiple nucleopolyhedrovirus (AcMNPV; Baculoviridae: Alphabaculovirus) derives from complete genome sequences of the C6 clonal isolate of AcMNPV and the R1 and CL3 clonal isolates of AcMNPV variants Rachip...

  9. PULLULAN PRODUCTION BY TROPICAL ISOLATES OF AUREOBASIDIUM PULLULANS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tropical isolates of Aureobasidium pullulans previously isolated from distinct habitats in Thailand were characterized for their capacities to produce the valuable polysaccharide, pullulan. A. pullulans strain NRM2, a so-called "color variant" strain, was the best producer, yielding 25.1 g pullulan...

  10. Variability in alternanthera mosaic virus isolates from different hosts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have determined the complete genome sequences of Alternanthera mosaic virus phlox isolate PA (AltMV-PA) and four infectious clone variants derived from AltMV-SP, as well as partial sequences of other isolates from various types of phlox, and from portulaca, nandina, and cineraria. Phylogenetic co...

  11. Spontaneous resolution of isolated congenital megacystis: the incredible shrinking bladder

    PubMed Central

    Johnson, Emilie K.; Nelson, Caleb P.

    2014-01-01

    Isolated congenital megacystis represents a rare variant of fetal megacystis without other associated anomalies. The etiology is unclear, and various management strategies have been proposed. We report a case of isolated congenital megacystis that resolved over the first year of life with observation alone. Considerations for the evaluation and management of this rare entity are discussed. PMID:22910450

  12. [Frontal variant of frontotemporal dementia].

    PubMed

    Boutoleau-Bretonniere, Claire; Lebouvier, Thibaud; Vercelletto, Martine

    2014-03-01

    The behavioral variant of frontotemporal dementia (bvFTD), characterized by early behavioral disorders, is a rare disease (about 5.000 cases in France). Diagnostic criteria have been revised in 2011 and propose three levels of diagnostic probability. However, it still could be difficult to discriminate FTD from other cerebral affections or psychiatric diseases. Genetic and molecular research has greatly expanded during the past fifteen years. About ten mutations have been discovered, bringing to describe particular phenotypes. To date, there is no curative treatment. Memantine had aroused some hope but is now abandoned. Inhibitors of serotonine recapture often permit to temporarily reduce behavioral troubles. But the caregiver's burden is high. The evolution of the bvFTD is faster than that of AD, particularly when associated with motor neuron disease (15% of cases). The therapeutic hope relies today on potential disease modifying drugs which could ensue from genetic discoveries. PMID:24647240

  13. SMOC2 gene variant and the risk of vitiligo in Jordanian Arabs.

    PubMed

    Alkhateeb, Asem; Al-Dain Marzouka, Nour; Qarqaz, Firas

    2010-01-01

    Generalized vitiligo is a common autoimmune disorder, characterized by patchy loss of pigmentation due to melanocyte death. It is a multifactorial disorder in which multiple genes and environmental triggers contribute to the expression of the phenotype. Different genetic variants can have varying effects on having vitiligo. Recently, an SMOC2 variant (rs13208776) was reported to be associated with vitiligo in Caucasian patients from an isolated founder population. In this study, we investigate the association of SMOC2 variant with Jordanian Arab vitiligo patients. Forty-four patients with generalized vitiligo and 151 matched normal controls were recruited. DNA samples were obtained from patients and controls and samples were genotyped for SMOC2 variant by restriction fragment length polymorphism. Allelic frequency of the less common allele (A allele) was 29.5% in patients compared to 19.6% in the controls (p = 0.27). Genotypic frequency for AA was 4.5% in patients and 7.9% in controls while heterozygous genotypes were 50% for patients and 33.1% in controls. Genotypes did not show statistical difference in patients versus control (p = 0.12). Our data shows that the variant rs13208776 in SMOC2 gene does not play a major role in increasing the risk of vitiligo in Jordanian Arab patients. This is in contrast to the previous association reported for Caucasian patients from an isolated patient population in Romania. This signifies genetic differences in the two populations. PMID:20965805

  14. Variants in GATA4 Are a Rare Cause of Familial and Sporadic Congenital Diaphragmatic Hernia

    PubMed Central

    Yu, Lan; Wynn, Julia; Cheung, Yee Him; Shen, Yufeng; Mychaliska, George B.; Crombleholme, Timothy M.; Azarow, Kenneth S.; Lim, Foong Yen; Chung, Dai H.; Potoka, Douglas; Warner, Brad W.; Bucher, Brian; Stolar, Charles; Aspelund, Gudrun; Arkovitz, Marc S.; Chung, Wendy K.

    2012-01-01

    Congenital diaphragmatic hernia (CDH) is characterized by incomplete formation of the diaphragm, occurring as either an isolated defect or in association with other anomalies. Genetic factors including aneuploidies and copy number variants are important in the pathogenesis of many cases of CDH, but few single genes have been definitively implicated in human CDH. In this study, we used whole exome sequencing (WES) to identify a paternally inherited novel missense GATA4 variant (c. 754C>T, p. R252W) in a familial case of CDH with incomplete penetrance. Phenotypic characterization of the family included magnetic resonance imaging (MRI) of the chest and abdomen demonstrating asymptomatic defects in the diaphragm in the two “unaffected” missense variant carriers. Screening 96 additional CDH patients identified a de novo heterozygous GATA4 variant (c.848G>A; p.R283H) in a non-isolated CDH patient. In summary, GATA4 is implicated in both familial and sporadic CDH, and our data suggests that WES may be a powerful tool to discover rare variants for CDH. PMID:23138528

  15. Differences in Transcriptional Activity of Human Papillomavirus Type 6 Molecular Variants in Recurrent Respiratory Papillomatosis

    PubMed Central

    Measso do Bonfim, Caroline; Simão Sobrinho, João; Lacerda Nogueira, Rodrigo; Salgado Kupper, Daniel; Cardoso Pereira Valera, Fabiana; Lacerda Nogueira, Maurício; Villa, Luisa Lina; Rahal, Paula; Sichero, Laura

    2015-01-01

    A significant proportion of recurrent respiratory papillomatosis (RRP) is caused by human papillomavirus type 6 (HPV-6). The long control region (LCR) contains cis-elements for regulation of transcription. Our aim was to characterize LCR HPV-6 variants in RRP cases, compare promoter activity of these isolates and search for cellular transcription factors (TFs) that could explain the differences observed. The complete LCR from 13 RRP was analyzed. Transcriptional activity of 5 variants was compared using luciferase assays. Differences in putative TFs binding sites among variants were revealed using the TRANSFAC database. Chromatin immunoprecipation (CHIP) and luciferase assays were used to evaluate TF binding and impact upon transcription, respectively. Juvenile-onset RRP cases harbored exclusively HPV-6vc related variants, whereas among adult-onset cases HPV-6a variants were more prevalent. The HPV-6vc reference was more transcriptionally active than the HPV-6a reference. Active FOXA1, ELF1 and GATA1 binding sites overlap variable nucleotide positions among isolates and influenced LCR activity. Furthermore, our results support a crucial role for ELF1 on transcriptional downregulation. We identified TFs implicated in the regulation of HPV-6 early gene expression. Many of these factors are mutated in cancer or are putative cancer biomarkers, and must be further studied. PMID:26151558

  16. Rare copy number variants implicated in posterior urethral valves.

    PubMed

    Boghossian, Nansi S; Sicko, Robert J; Kay, Denise M; Rigler, Shannon L; Caggana, Michele; Tsai, Michael Y; Yeung, Edwina H; Pankratz, Nathan; Cole, Benjamin R; Druschel, Charlotte M; Romitti, Paul A; Browne, Marilyn L; Fan, Ruzong; Liu, Aiyi; Brody, Lawrence C; Mills, James L

    2016-03-01

    The cause of posterior urethral valves (PUV) is unknown, but genetic factors are suspected given their familial occurrence. We examined cases of isolated PUV to identify novel copy number variants (CNVs). We identified 56 cases of isolated PUV from all live-births in New York State (1998-2005). Samples were genotyped using Illumina HumanOmni2.5 microarrays. Autosomal and sex-linked CNVs were identified using PennCNV and cnvPartition software. CNVs were prioritized for follow-up if they were absent from in-house controls, contained ≥10 consecutive probes, were ≥20 Kb in size, had ≤20% overlap with variants detected in other birth defect phenotypes screened in our lab, and were rare in population reference controls. We identified 47 rare candidate PUV-associated CNVs in 32 cases; one case had a 3.9 Mb deletion encompassing BMP7. Mutations in BMP7 have been associated with severe anomalies in the mouse urethra. Other interesting CNVs, each detected in a single PUV case included: a deletion of PIK3R3 and TSPAN1, duplication/triplication in FGF12, duplication of FAT1-a gene essential for normal growth and development, a large deletion (>2 Mb) on chromosome 17q that involves TBX2 and TBX4, and large duplications (>1 Mb) on chromosomes 3q and 6q. Our finding of previously unreported novel CNVs in PUV suggests that genetic factors may play a larger role than previously understood. Our data show a potential role of CNVs in up to 57% of cases examined. Investigation of genes in these CNVs may provide further insights into genetic variants that contribute to PUV. © 2015 Wiley Periodicals, Inc. PMID:26663319

  17. Rare hemoglobin variants in Tunisian population.

    PubMed

    Zorai, A; Moumni, I; Mosbahi, I; Douzi, K; Chaouachi, D; Guemira, F; Abbes, S

    2015-04-01

    During the last 30 years, many studies concerning hemoglobinopathies were realized among Tunisians. More than twenty different thalassemic alleles were detected on the ?-globin gene, and less are affecting the ?-globin genes. Unusual hemoglobin (Hb) variants other than Hb S, Hb C, and Hb O-arab, which are the most frequent variants in Tunisia, were also detected. Eight Tunisian subjects were studied at phenotypic and molecular levels. Hematological indices and hemoglobin (Hb) pattern were performed by alkaline electrophoresis and isoelectric focusing (IEF),and the Hb fractions were quantitated by cation exchange HPLC. On genomic level, coding regions were amplified by polymerase chain reaction (PCR) followed by a sequencing of the purified PCR products using the dye terminator method. Seven uncommon Hb variants were detected and described for the first time among Tunisians. HbA2-Tunis [?46(CD5), Gly ? Glu, GGG ? GAG] is the newly described ?-chain variant in our laboratory, and some other variants (Hb Constant Spring, G San Jose, and Hb J-Bangkok) are very uncommon in the Mediterranean region. We present here an updated review of the Hb variants detected among Tunisians. Twenty-one rare Hb variants were detected affecting the ?1-, ?2-, ?-, ?-, and ?-globin genes, leading in some cases to a severe phenotype especially when the stability is completely altered. The ethnical history of Tunisia could explain this important variability of the observed rare Hb variants. PMID:24905386

  18. MTDH genetic variants in colorectal cancer patients

    PubMed Central

    Gnosa, Sebastian; Ticha, Ivana; Haapaniemi, Staffan; Sun, Xiao-Feng

    2016-01-01

    The colorectal carcinogenesis is a complex process encompassing genetic alterations. The oncoprotein AEG-1, encoded by the MTDH gene, was shown previously to be involved in colorectal cancer (CRC). The aim of this study was to determine the frequency and the spectrum of MTDH variants in tumor tissue, and their relationship to clinicopathological variables in CRC patients. The study included tumors from 356 unselected CRC patients. Mutation analysis of the MTDH gene, including coding region and adjacent intronic sequences, was performed by direct DNA sequencing. The corresponding normal colorectal tissue was analyzed in the carriers of exonic variant to confirm germline or somatic origin. We detected 42 intronic variants, where 25 were novel. Furthermore, we found 8 exonic variants of which four, one missense (c.977C > G-germline) and three frameshift mutations (c.533delA-somatic, c.1340dupA-unknown origin, c.1731delA-unknown origin), were novel. In silico prediction analyses suggested four deleterious variants (c.232G > T, c.533delA, c.1340dupA, and c.1731delA). There were no correlations between the MTDH variants and tumor stage, differentiation or patient survival. We described several novel exonic and intronic variants of the MTDH gene. The detection of likely pathogenic truncating mutations and alterations in functional protein domains indicate their clinical significance, although none of the variants had prognostic potential. PMID:26983693

  19. Association of Copy Number Variants With Specific Ultrasonographically Detected Fetal Anomalies

    PubMed Central

    Donnelly, Jennifer C; Platt, Lawrence D; Rebarber, Andrei; Zachary, Julia; Grobman, William A; Wapner, Ronald J

    2014-01-01

    Objective To evaluate the association of other-than-common benign copy number variants with specific fetal abnormalities detected by ultrasonogram. Methods Fetuses with structural anomalies were compared to fetuses without detected abnormalities for the frequency of other-than-common benign copy number variants. This is a secondary analysis from the previously published National Institute of Child Health and Human Development microarray trial. Ultrasound reports were reviewed and details of structural anomalies were entered into a nonhierarchical web-based database. The frequency of other-than-common benign copy number variants (ie, either pathogenic or variants of uncertain significance) not detected by karyotype was calculated for each anomaly in isolation and in the presence of other anomalies and compared to the frequency in fetuses without detected abnormalities. Results Of 1,082 fetuses with anomalies detected on ultrasound, 752 had a normal karyotype. Other-than-common benign copy number variants were present in 61 (8.1%) of these euploid fetuses. Fetuses with anomalies in more than one system had a 13.0% frequency of other-than-common benign copy number variants, which was significantly higher (p<0.001) than the frequency (3.6%) in fetuses without anomalies (n = 1966). Specific organ systems in which isolated anomalies were nominally significantly associated with other-than-common benign copy number variants were the renal (p= 0.036) and cardiac systems (p=0.012) but did not meet the adjustment for multiple comparisons. Conclusions When a fetal anomaly is detected on ultrasonogram, chromosomal microarray offers additional information over karyotype, the degree of which depends on the organ system involved. PMID:24901266

  20. Disease variants in genomes of 44 centenarians

    PubMed Central

    Freudenberg-Hua, Yun; Freudenberg, Jan; Vacic, Vladimir; Abhyankar, Avinash; Emde, Anne-Katrin; Ben-Avraham, Danny; Barzilai, Nir; Oschwald, Dayna; Christen, Erika; Koppel, Jeremy; Greenwald, Blaine; Darnell, Robert B; Germer, Soren; Atzmon, Gil; Davies, Peter

    2014-01-01

    To identify previously reported disease mutations that are compatible with extraordinary longevity, we screened the coding regions of the genomes of 44 Ashkenazi Jewish centenarians. Individual genome sequences were generated with 30× coverage on the Illumina HiSeq 2000 and single-nucleotide variants were called with the genome analysis toolkit (GATK). We identified 130 coding variants that were annotated as “pathogenic” or “likely pathogenic” based on the ClinVar database and that are infrequent in the general population. These variants were previously reported to cause a wide range of degenerative, neoplastic, and cardiac diseases with autosomal dominant, autosomal recessive, and X-linked inheritance. Several of these variants are located in genes that harbor actionable incidental findings, according to the recommendations of the American College of Medical Genetics. In addition, we found risk variants for late-onset neurodegenerative diseases, such as the APOE ?4 allele that was even present in a homozygous state in one centenarian who did not develop Alzheimer's disease. Our data demonstrate that the incidental finding of certain reported disease variants in an individual genome may not preclude an extraordinarily long life. When the observed variants are encountered in the context of clinical sequencing, it is thus important to exercise caution in justifying clinical decisions. In genome sequences of 44 Ashkenazi centenarians, we identified many coding variants that were annotated as “pathogenic” or “likely pathogenic” based on the ClinVar database. Our data demonstrate that the incidental finding of certain reported disease variants in an individual genome may not preclude an extraordinarily long life. When the observed variants are encountered in the context of clinical sequencing, it is thus important to exercise caution in justifying clinical decisions. PMID:25333069

  1. EKG isolator

    NASA Technical Reports Server (NTRS)

    Palmer, E.; Rasquin, J. R.; Smith, H. E.

    1971-01-01

    Light beam transmits heartbeat signal from electrodes on patient to electrocardiograph without exposing patient to possible severe electrical shock. System provides complete isolation between patient and EKG instrumentation.

  2. Systematic comparison of variant calling pipelines using gold standard personal exome variants.

    PubMed

    Hwang, Sohyun; Kim, Eiru; Lee, Insuk; Marcotte, Edward M

    2015-01-01

    The success of clinical genomics using next generation sequencing (NGS) requires the accurate and consistent identification of personal genome variants. Assorted variant calling methods have been developed, which show low concordance between their calls. Hence, a systematic comparison of the variant callers could give important guidance to NGS-based clinical genomics. Recently, a set of high-confident variant calls for one individual (NA12878) has been published by the Genome in a Bottle (GIAB) consortium, enabling performance benchmarking of different variant calling pipelines. Based on the gold standard reference variant calls from GIAB, we compared the performance of thirteen variant calling pipelines, testing combinations of three read aligners-BWA-MEM, Bowtie2, and Novoalign-and four variant callers-Genome Analysis Tool Kit HaplotypeCaller (GATK-HC), Samtools mpileup, Freebayes and Ion Proton Variant Caller (TVC), for twelve data sets for the NA12878 genome sequenced by different platforms including Illumina2000, Illumina2500, and Ion Proton, with various exome capture systems and exome coverage. We observed different biases toward specific types of SNP genotyping errors by the different variant callers. The results of our study provide useful guidelines for reliable variant identification from deep sequencing of personal genomes. PMID:26639839

  3. Systematic comparison of variant calling pipelines using gold standard personal exome variants

    PubMed Central

    Hwang, Sohyun; Kim, Eiru; Lee, Insuk; Marcotte, Edward M.

    2015-01-01

    The success of clinical genomics using next generation sequencing (NGS) requires the accurate and consistent identification of personal genome variants. Assorted variant calling methods have been developed, which show low concordance between their calls. Hence, a systematic comparison of the variant callers could give important guidance to NGS-based clinical genomics. Recently, a set of high-confident variant calls for one individual (NA12878) has been published by the Genome in a Bottle (GIAB) consortium, enabling performance benchmarking of different variant calling pipelines. Based on the gold standard reference variant calls from GIAB, we compared the performance of thirteen variant calling pipelines, testing combinations of three read aligners—BWA-MEM, Bowtie2, and Novoalign—and four variant callers—Genome Analysis Tool Kit HaplotypeCaller (GATK-HC), Samtools mpileup, Freebayes and Ion Proton Variant Caller (TVC), for twelve data sets for the NA12878 genome sequenced by different platforms including Illumina2000, Illumina2500, and Ion Proton, with various exome capture systems and exome coverage. We observed different biases toward specific types of SNP genotyping errors by the different variant callers. The results of our study provide useful guidelines for reliable variant identification from deep sequencing of personal genomes. PMID:26639839

  4. Molecular variation of hop mosaic virus isolates.

    PubMed

    Poke, Fiona S; Crowle, Damian R; Whittock, Simon P; Wilson, Calum R

    2010-10-01

    Hop mosaic virus (HpMV), a member of the genus Carlavirus, is importance to hop production worldwide. We identified variation in nucleic and amino acid sequences among 23 HpMV isolates from Australia, the USA, the Czech Republic, South Africa and Japan using a 1,455-bp fragment covering the 3' end of the virus genome including ORFs 4, 5 and 6. Three clusters of two or more isolates were identified in phylogenies of the total nucleotide sequence and the coat protein (ORF5) amino acid sequence. Two of these clusters combined in analyses of ORF4 and ORF6 amino acid sequences. Isolates from within and outside of Australia were found in each cluster, indicating that sequence variation was not associated with geographic source. Monitoring of HpMV variants in the field and evaluation of the impact of variants on vector association, rate of spread, and hop yield and quality can now be undertaken. PMID:20680359

  5. Studies on color type variants from mutagenized protoplasts of Porphyra haitanensis Chang et Zheng & P. Yezoensis ueda (rhodophycease)

    NASA Astrophysics Data System (ADS)

    Yan, Xinghong

    1993-09-01

    Isolated protoplasts from thalli of Porphyra haitanensis and Porphyra yezoensis were treated with colchicine or irradiated by ultraviolet (UV). Several types of color variants were observed among the protoplast offspring. After treatment with colchicine: (1) 0.04 0.09% of red type variants in P. haitanensis were obtained; (2) The rate of red type variants and the variegated chimeral thalli composed of red type and wild type of sectors were 0.31 1.11% in P. yezoensis. After irradiation with UV: (1) 3.5 10.5% of red type variants in P. yezoensis were obtained: (2) 0.5 2.0% of red type variants and the variegated chimeral thalli composed of red type and wild type of sectors were obtained in P. haitanensis. Colchicine and UV’s mutangenic effects on P. yezoensis protoplasts were stronger than those on P. haitanensis protoplasts. The most efficient concentration of colchicine was 0.05%. The optimal length of UV-radiation was 1/2 min (radiation distance 5 cm). The red type variants induced by colchicine treatment grew faster than the wild type thalli. The clones of vegetative propagation from protoplasts of red type variants were still red type thalli. The red type variants will be good materials for genetic studies and improvement of Porphyra strains.

  6. Genotypes Associated with Virulence in Environmental Isolates of Vibrio cholerae

    PubMed Central

    Rivera, Irma N. G.; Chun, Jongsik; Huq, Anwar; Sack, R. Brad; Colwell, Rita R.

    2001-01-01

    Vibrio cholerae is an autochthonous inhabitant of riverine and estuarine environments and also is a facultative pathogen for humans. Genotyping can be useful in assessing the risk of contracting cholera, intestinal, or extraintestinal infections via drinking water and/or seafood. In this study, environmental isolates of V. cholerae were examined for the presence of ctxA, hlyA, ompU, stn/sto, tcpA, tcpI, toxR, and zot genes, using multiplex PCR. Based on tcpA and hlyA gene comparisons, the strains could be grouped into Classical and El Tor biotypes. The toxR, hlyA, and ompU genes were present in 100, 98.6, and 87.0% of the V. cholerae isolates, respectively. The CTX genetic element and toxin-coregulated pilus El Tor (tcpA ET) gene were present in all toxigenic V. cholerae O1 and V. cholerae O139 strains examined in this study. Three of four nontoxigenic V. cholerae O1 strains contained tcpA ET. Interestingly, among the isolates of V. cholerae non-O1/non-O139, two had tcpA Classical, nine contained tcpA El Tor, three showed homology with both biotype genes, and four carried the ctxA gene. The stn/sto genes were present in 28.2% of the non-O1/non-O139 strains, in 10.5% of the toxigenic V. cholerae O1, and in 14.3% of the O139 serogroups. Except for stn/sto genes, all of the other genes studied occurred with high frequency in toxigenic V. cholerae O1 and O139 strains. Based on results of this study, surveillance of non-O1/non-O139 V. cholerae in the aquatic environment, combined with genotype monitoring using ctxA, stn/sto, and tcpA ET genes, could be valuable in human health risk assessment. PMID:11375146

  7. Cellular cytotoxicity mediated by isotype-switch variants of a monoclonal antibody to human neuroblastoma.

    PubMed Central

    d'Uscio, C. H.; Jungi, T. W.; Blaser, K.

    1991-01-01

    The biological property of an antibody is determined by its antigen binding characteristics and its isotype-related effector functions. We have established monoclonal antibodies of different isotypes by stepwise selection and cloning of the hybridoma CE7. The original CE7 secretes an IgG1/kappa (CE7 gamma 1) antibody that recognises a 185 kD cell surface glycoprotein expressed on all human sympatho-adrenomedullary cells. Isotype-switch variants were isolated in the following sequence: from the original CE7 gamma 1, CE7 gamma 2b variants were isolated, and from a CE7 gamma 2b variant CE7 gamma 2a variants were isolated. The antibodies of three different isotype variant cell lines possess identical antigen binding characteristics, but display distinct effector functions as demonstrated by antibody dependent cell-mediated cytotoxicity (ADCC). ADCC was performed with the neuroblastoma line IMR-32 as the target cells, and different FcR gamma positive cells were either freshly isolated from human peripheral blood leukocytes or cultured for 6-10 days and tested as potential effector cells. Tumour lysis mediated by monocyte-derived macrophages depended on the presence of CE7 gamma 2a antibodies; antibodies from the CE7 hybridomas of gamma 2b and gamma 1 isotypes were virtually inactive in ADCC assay. Pre-exposure of macrophages to rIFN-gamma enhanced their ADCC activity, a result that is compatible with the notion that the high affinity Fc IgG receptor (FcR gamma I/CD64) is involved in the triggering of ADCC in macrophages. In contrast to macrophages, mononuclear cells, nonadherent cells and monocytes displayed considerable non-specific lytic activity, which was little influenced by the presence of antibody regardless of the isotype added. PMID:1911183

  8. Classification of Histoplasma capsulatum isolates by restriction fragment polymorphisms.

    PubMed Central

    Vincent, R D; Goewert, R; Goldman, W E; Kobayashi, G S; Lambowitz, A M; Medoff, G

    1986-01-01

    Twenty isolates of the dimorphic, pathogenic fungus Histoplasma capsulatum were divided into three classes based on comparisons of restriction enzyme digests of their mitochondrial DNA and rDNA. The majority of isolates, including most North American strains and the African H. capsulatum var. duboisii variants, belong to class 2. Isolates from Central America and South America make up class 3. The attenuated Downs strain is the only member of class 1. Images PMID:3005239

  9. Rapid Detection of New Delhi Metallo-?-Lactamase Gene and Variants Coding for Carbapenemases with Different Activities by Use of a PCR-Based In Vitro Protein Expression Method

    PubMed Central

    Huang, Li; Hu, Xiumei; Zhou, Man; Yang, Yinmei; Qiao, Jinjuan; Wang, Dianbing; Yu, Junping; Cui, Zongqiang; Zhang, Zhiping; Zhang, Xian-En

    2014-01-01

    New Delhi metallo-?-lactamase (NDM)-producing bacteria are considered potential global health threats. It is necessary to monitor NDM-1 and its variants in clinical isolates in order to understand the NDM-1 epidemic and the impact of its variants on ?-lactam resistance. To reduce the lengthy time needed for cloning and expression of NDM-1 variants, a novel PCR-based in vitro protein expression (PCR-P) method was used to detect blaNDM-1 and its variants coding for carbapenemases with different activities (functional variants). The PCR-P method combined a long-fragment real-time quantitative PCR (LF-qPCR) with in vitro cell-free expression to convert the blaNDM-1 amplicons into NDM for carbapenemase assay. The method could screen for blaNDM-1 within 3 h with a detection limit of 5 copies and identify functional variants within 1 day. Using the PCR-P to analyze 5 recent blaNDM-1 variants, 2 functional variants, blaNDM-4 and blaNDM-5, were revealed. In the initial testing of 23 clinical isolates, the PCR-P assay correctly found 8 isolates containing blaNDM-1. This novel method provides the first integrated approach for rapidly detecting the full-length blaNDM-1 and revealing its functional variants in clinical isolates. PMID:24671780

  10. Histone H3 Variants in Trichomonas vaginalis

    PubMed Central

    Zubá?ová, Zuzana; Hostomská, Jitka

    2012-01-01

    The parabasalid protist Trichomonas vaginalis is a widespread parasite that affects humans, frequently causing vaginitis in infected women. Trichomonad mitosis is marked by the persistence of the nuclear membrane and the presence of an asymmetric extranuclear spindle with no obvious direct connection to the chromosomes. No centromeric markers have been described in T. vaginalis, which has prevented a detailed analysis of mitotic events in this organism. In other eukaryotes, nucleosomes of centromeric chromatin contain the histone H3 variant CenH3. The principal aim of this work was to identify a CenH3 homolog in T. vaginalis. We performed a screen of the T. vaginalis genome to retrieve sequences of canonical and variant H3 histones. Three variant histone H3 proteins were identified, and the subcellular localization of their epitope-tagged variants was determined. The localization of the variant TVAG_185390 could not be distinguished from that of the canonical H3 histone. The sequence of the variant TVAG_087830 closely resembled that of histone H3. The tagged protein colocalized with sites of active transcription, indicating that the variant TVAG_087830 represented H3.3 in T. vaginalis. The third H3 variant (TVAG_224460) was localized to 6 or 12 distinct spots at the periphery of the nucleus, corresponding to the number of chromosomes in G1 phase and G2 phase, respectively. We propose that this variant represents the centromeric marker CenH3 and thus can be employed as a tool to study mitosis in T. vaginalis. Furthermore, we suggest that the peripheral distribution of CenH3 within the nucleus results from the association of centromeres with the nuclear envelope throughout the cell cycle. PMID:22408228

  11. A Novel Binary Mixture of Helicoverpa armigera Single Nucleopolyhedrovirus Genotypic Variants Has Improved Insecticidal Characteristics for Control of Cotton Bollworms

    PubMed Central

    Arrizubieta, Maite; Simón, Oihane; Williams, Trevor

    2015-01-01

    The genotypic diversity of two Spanish isolates of Helicoverpa armigera single nucleopolyhedrovirus (HearSNPV) was evaluated with the aim of identifying mixtures of genotypes with improved insecticidal characteristics for control of the cotton bollworm. Two genotypic variants, HearSP1A and HearSP1B, were cloned in vitro from the most pathogenic wild-type isolate of the Iberian Peninsula, HearSNPV-SP1 (HearSP1-wt). Similarly, six genotypic variants (HearLB1 to -6) were obtained by endpoint dilution from larvae collected from cotton crops in southern Spain that died from virus disease during laboratory rearing. Variants differed significantly in their insecticidal properties, pathogenicity, speed of kill, and occlusion body (OB) production (OBs/larva). HearSP1B was ∼3-fold more pathogenic than HearSP1-wt and the other variants. HearLB1, HearLB2, HeaLB5, and HearLB6 were the fastest-killing variants. Moreover, although highly virulent, HearLB1, HearLB4, and HearLB5 produced more OBs/larva than did the other variants. The co-occluded HearSP1B:LB6 mixture at a 1:1 proportion was 1.7- to 2.8-fold more pathogenic than any single variant and other mixtures tested and also killed larvae as fast as the most virulent genotypes. Serial passage resulted in modified proportions of the component variants of the HearSP1B:LB6 co-occluded mixture, suggesting that transmissibility could be further improved by this process. We conclude that the improved insecticidal phenotype of the HearSP1B:LB6 co-occluded mixture underlines the utility of the genotypic variant dissection and reassociation approach for the development of effective virus-based insecticides. PMID:25841011

  12. A Novel Binary Mixture of Helicoverpa armigera Single Nucleopolyhedrovirus Genotypic Variants Has Improved Insecticidal Characteristics for Control of Cotton Bollworms.

    PubMed

    Arrizubieta, Maite; Simón, Oihane; Williams, Trevor; Caballero, Primitivo

    2015-06-15

    The genotypic diversity of two Spanish isolates of Helicoverpa armigera single nucleopolyhedrovirus (HearSNPV) was evaluated with the aim of identifying mixtures of genotypes with improved insecticidal characteristics for control of the cotton bollworm. Two genotypic variants, HearSP1A and HearSP1B, were cloned in vitro from the most pathogenic wild-type isolate of the Iberian Peninsula, HearSNPV-SP1 (HearSP1-wt). Similarly, six genotypic variants (HearLB1 to -6) were obtained by endpoint dilution from larvae collected from cotton crops in southern Spain that died from virus disease during laboratory rearing. Variants differed significantly in their insecticidal properties, pathogenicity, speed of kill, and occlusion body (OB) production (OBs/larva). HearSP1B was ∼3-fold more pathogenic than HearSP1-wt and the other variants. HearLB1, HearLB2, HeaLB5, and HearLB6 were the fastest-killing variants. Moreover, although highly virulent, HearLB1, HearLB4, and HearLB5 produced more OBs/larva than did the other variants. The co-occluded HearSP1B:LB6 mixture at a 1:1 proportion was 1.7- to 2.8-fold more pathogenic than any single variant and other mixtures tested and also killed larvae as fast as the most virulent genotypes. Serial passage resulted in modified proportions of the component variants of the HearSP1B:LB6 co-occluded mixture, suggesting that transmissibility could be further improved by this process. We conclude that the improved insecticidal phenotype of the HearSP1B:LB6 co-occluded mixture underlines the utility of the genotypic variant dissection and reassociation approach for the development of effective virus-based insecticides. PMID:25841011

  13. Filovirus RefSeq entries: evaluation and selection of filovirus type variants, type sequences, and names.

    PubMed

    Kuhn, Jens H; Andersen, Kristian G; Bào, Yīmíng; Bavari, Sina; Becker, Stephan; Bennett, Richard S; Bergman, Nicholas H; Blinkova, Olga; Bradfute, Steven; Brister, J Rodney; Bukreyev, Alexander; Chandran, Kartik; Chepurnov, Alexander A; Davey, Robert A; Dietzgen, Ralf G; Doggett, Norman A; Dolnik, Olga; Dye, John M; Enterlein, Sven; Fenimore, Paul W; Formenty, Pierre; Freiberg, Alexander N; Garry, Robert F; Garza, Nicole L; Gire, Stephen K; Gonzalez, Jean-Paul; Griffiths, Anthony; Happi, Christian T; Hensley, Lisa E; Herbert, Andrew S; Hevey, Michael C; Hoenen, Thomas; Honko, Anna N; Ignatyev, Georgy M; Jahrling, Peter B; Johnson, Joshua C; Johnson, Karl M; Kindrachuk, Jason; Klenk, Hans-Dieter; Kobinger, Gary; Kochel, Tadeusz J; Lackemeyer, Matthew G; Lackner, Daniel F; Leroy, Eric M; Lever, Mark S; Mühlberger, Elke; Netesov, Sergey V; Olinger, Gene G; Omilabu, Sunday A; Palacios, Gustavo; Panchal, Rekha G; Park, Daniel J; Patterson, Jean L; Paweska, Janusz T; Peters, Clarence J; Pettitt, James; Pitt, Louise; Radoshitzky, Sheli R; Ryabchikova, Elena I; Saphire, Erica Ollmann; Sabeti, Pardis C; Sealfon, Rachel; Shestopalov, Aleksandr M; Smither, Sophie J; Sullivan, Nancy J; Swanepoel, Robert; Takada, Ayato; Towner, Jonathan S; van der Groen, Guido; Volchkov, Viktor E; Volchkova, Valentina A; Wahl-Jensen, Victoria; Warren, Travis K; Warfield, Kelly L; Weidmann, Manfred; Nichol, Stuart T

    2014-09-01

    Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information's (NCBI's) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [ ()/<isolation host-suffix>///variant designation>-<isolate designation>], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences. PMID:25256396

  14. Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names

    PubMed Central

    Kuhn, Jens H.; Andersen, Kristian G.; Bào, Yīmíng; Bavari, Sina; Becker, Stephan; Bennett, Richard S.; Bergman, Nicholas H.; Blinkova, Olga; Bradfute, Steven; Brister, J. Rodney; Bukreyev, Alexander; Chandran, Kartik; Chepurnov, Alexander A.; Davey, Robert A.; Dietzgen, Ralf G.; Doggett, Norman A.; Dolnik, Olga; Dye, John M.; Enterlein, Sven; Fenimore, Paul W.; Formenty, Pierre; Freiberg, Alexander N.; Garry, Robert F.; Garza, Nicole L.; Gire, Stephen K.; Gonzalez, Jean-Paul; Griffiths, Anthony; Happi, Christian T.; Hensley, Lisa E.; Herbert, Andrew S.; Hevey, Michael C.; Hoenen, Thomas; Honko, Anna N.; Ignatyev, Georgy M.; Jahrling, Peter B.; Johnson, Joshua C.; Johnson, Karl M.; Kindrachuk, Jason; Klenk, Hans-Dieter; Kobinger, Gary; Kochel, Tadeusz J.; Lackemeyer, Matthew G.; Lackner, Daniel F.; Leroy, Eric M.; Lever, Mark S.; Mühlberger, Elke; Netesov, Sergey V.; Olinger, Gene G.; Omilabu, Sunday A.; Palacios, Gustavo; Panchal, Rekha G.; Park, Daniel J.; Patterson, Jean L.; Paweska, Janusz T.; Peters, Clarence J.; Pettitt, James; Pitt, Louise; Radoshitzky, Sheli R.; Ryabchikova, Elena I.; Saphire, Erica Ollmann; Sabeti, Pardis C.; Sealfon, Rachel; Shestopalov, Aleksandr M.; Smither, Sophie J.; Sullivan, Nancy J.; Swanepoel, Robert; Takada, Ayato; Towner, Jonathan S.; van der Groen, Guido; Volchkov, Viktor E.; Volchkova, Valentina A.; Wahl-Jensen, Victoria; Warren, Travis K.; Warfield, Kelly L.; Weidmann, Manfred; Nichol, Stuart T.

    2014-01-01

    Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information’s (NCBI’s) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [ ()/<isolation host-suffix>///variant designation>-<isolate designation>], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences. PMID:25256396

  15. Identification of a chicken anemia virus variant-related gyrovirus in stray cats in china, 2012.

    PubMed

    Zhang, Xinheng; Liu, Yuanjia; Ji, Jun; Chen, Feng; Sun, Baoli; Xue, Chunyi; Ma, Jingyun; Bi, Yingzuo; Xie, Qingmei

    2014-01-01

    The chicken anemia virus (CAV), is a known member of the genus Gyrovirus and was first isolated from chickens in Japan in 1979. Some reports have also demonstrated that CAV can be identified in human stool specimens. In this study, a variant of CAV was detected using PCR with CAV-based primers in fecal samples of stray cats. The genome of CAV variant was sequenced and the results suggest that it could be a recombinant viral strain from parental CAV strains JQ690762 and AF311900. Recombination is an important evolutionary mechanism that contributes to genetic diversification. These findings indicate that CAV variant might have originated from CAV-infected chickens. The epidemiology and pathogenesis of this novel virus remains to be elucidated. This study underscores the importance of CAV surveillance and it presents the first evidence suggesting the possibility of CAV homologous recombination in cat. PMID:24689034

  16. Induction of L-phase variants of Nocardia caviae within intact murine lungs.

    PubMed Central

    Beaman, B L

    1980-01-01

    The data presented show that cells of Nocardia caviae 112 were converted to cell wall-deficient microbial variants within the intact murine lung after intranasal administration. At the time that these L-phase variants were recovered in large numbers from the lung, there was a correspondingly enhanced inflammation leading to alveolar consolidation and animal death. During the peak of this response (at 1 week after infection), normal nocardial cells were neither isolated from nor seen within the lung. It is suggested that the conversion of these normal nocardial cells to their L-phase variant leads to this extensive pulmonary damage. Furthermore, the L-phase organisms appear to play an active role in this pathological effect since introduction of similar amounts of killed nocardial cells into the lungs of the mice failed to produce a similar response. Images Fig. 2 Fig. 3 Fig. 4 PMID:7399704

  17. Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1.

    PubMed

    Wan, Yu; Gorrie, Claire L; Jenney, Adam; Mirceta, Mirjana; Holt, Kathryn E

    2015-01-01

    Serratia marcescens strain AH0650_Sm1 is a clinical multidrug-resistant isolate from Australia. Here, we report its annotated draft genome comprising 20 contigs. We identified chromosomal antimicrobial resistance genes including a tet(41) variant, an aac(6')-Ic variant, ampC, a metallo-beta-lactamase, and several putative multidrug efflux pumps, as well as a novel prophage. PMID:26337895

  18. FTO variant associated with malformation syndrome.

    PubMed

    Rohena, Luis; Lawson, Michelle; Guzman, Edwin; Ganapathi, Mythily; Cho, Megan T; Haverfield, Eden; Anyane-Yeboa, Kwame

    2016-04-01

    Common FTO variants are associated with obesity. However, it has recently been shown that homozygous FTO c.947G>A variant, which predicts p.R316Q, and c.956C>T, which predicts p.S319F, are associated with a malformation syndrome inherited in an autosomal recessive pattern. We present a similar homozygous FTO c.965G>A variant that predicts p.R322Q, associated with a lethal malformation syndrome in a consanguineous Yemeni family. Functional studies showed that the p.R316Q, p.S219F, and p.R322Q variants render the FTO protein inactive. We further expand on the phenotype of homozygous FTO loss-of-function mutations to include eye abnormalities, gingival overgrowth, craniosynostosis, and cutaneous photosensitivity. © 2015 Wiley Periodicals, Inc. PMID:26697951

  19. Guillain-Barré Syndrome and Variants

    PubMed Central

    Barohn, Richard J.

    2014-01-01

    Synopsis Guillain-Barré syndrome (GBS) is characterized by rapidly evolving ascending weakness, mild sensory loss and hypo- or areflexia, progressing to a nadir over up to four weeks. Cerebrospinal fluid evaluation demonstrates albuminocytologic dissociation in 90% of cases. Acute inflammatory demyelinating polyneuropathy (AIDP) was the first to be recognized over a century ago and is the most common form of GBS. In AIDP, the immune attack is directed at peripheral nerve myelin with secondary by-stander axon loss. Axonal motor and sensorimotor variants have been described in the last 3 decades and are mediated by molecular mimicry targeting peripheral nerve motor axons. Besides the Miller-Fisher syndrome (MFS) and descending weakness, other rare phenotypic variants have been recently described with pure sensory variant, restricted autonomic manifestations and the pharyngeal-cervical-brachial pattern. It is important to recognize GBS and its variants due to the availability of equally effective therapies in the form of plasmapheresis and intravenous immunoglobulins. PMID:23642721

  20. Directed Evolution of Streptavidin Variants Using IVC

    PubMed Central

    Levy, M.; Ellington, A.D.

    2008-01-01

    Summary We have developed and implemented an in vitro compartmentalization (IVC) selection scheme for the identification of streptavidin (SA) variants with altered specificities for the biotin analog desthiobiotin. Wild-type SA and selected variants bind desthiobiotin with similar affinities (~10−13 M), but the variants have off-rates almost 50 times slower and a half-life for dissociation of 24 hours at 25°C. The utility of streptavidin variants with altered specificities and kinetic properties was demonstrated by constructing protein microarrays that could be used to differentially organize and immobilize DNAs bearing these ligands. The methods we have developed should prove to be generally useful for generating a variety of novel SA reagents, and for evolving other extremely high affinity protein:ligand couples. PMID:18804035

  1. TREM2 Variants in Alzheimer's Disease

    PubMed Central

    Guerreiro, Rita; Wojtas, Aleksandra; Bras, Jose; Carrasquillo, Minerva; Rogaeva, Ekaterina; Majounie, Elisa; Cruchaga, Carlos; Sassi, Celeste; Kauwe, John S.K.; Younkin, Steven; Hazrati, Lilinaz; Collinge, John; Pocock, Jennifer; Lashley, Tammaryn; Williams, Julie; Lambert, Jean-Charles; Amouyel, Philippe; Goate, Alison; Rademakers, Rosa; Morgan, Kevin; Powell, John; St. George-Hyslop, Peter; Singleton, Andrew; Hardy, John

    2013-01-01

    BACKGROUND Homozygous loss-of-function mutations in TREM2, encoding the triggering receptor expressed on myeloid cells 2 protein, have previously been associated with an autosomal recessive form of early-onset dementia. METHODS We used genome, exome, and Sanger sequencing to analyze the genetic variability in TREM2 in a series of 1092 patients with Alzheimer's disease and 1107 controls (the discovery set). We then performed a meta-analysis on imputed data for the TREM2 variant rs75932628 (predicted to cause a R47H substitution) from three genomewide association studies of Alzheimer's disease and tested for the association of the variant with disease. We genotyped the R47H variant in an additional 1887 cases and 4061 controls. We then assayed the expression of TREM2 across different regions of the human brain and identified genes that are differentially expressed in a mouse model of Alzheimer's disease and in control mice. RESULTS We found significantly more variants in exon 2 of TREM2 in patients with Alzheimer's disease than in controls in the discovery set (P = 0.02). There were 22 variant alleles in 1092 patients with Alzheimer's disease and 5 variant alleles in 1107 controls (P<0.001). The most commonly associated variant, rs75932628 (encoding R47H), showed highly significant association with Alzheimer's disease (P<0.001). Meta-analysis of rs75932628 genotypes imputed from genomewide association studies confirmed this association (P = 0.002), as did direct genotyping of an additional series of 1887 patients with Alzheimer's disease and 4061 controls (P<0.001). Trem2 expression differed between control mice and a mouse model of Alzheimer's disease. CONCLUSIONS Heterozygous rare variants in TREM2 are associated with a significant increase in the risk of Alzheimer's disease. (Funded by Alzheimer's Research UK and others.) PMID:23150934

  2. Conditionally replicating HIV and SIV variants.

    PubMed

    Das, Atze T; Berkhout, Ben

    2016-05-01

    Conditionally replicating human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) variants that can be switched on and off at will are attractive tools for HIV and SIV research. We constructed HIV and SIV variants in which the natural transcription control mechanism was replaced by the doxycycline (dox)-inducible Tet-On gene expression mechanism. These HIV-rtTA and SIV-rtTA variants are fully replication-competent, but replication is critically dependent on dox administration. We here describe how the dox-dependent virus variants may improve the safety of live-attenuated virus vaccines and how they can be used to study the immune responses that correlate with vaccine-induced protection. Furthermore, we review how these variants were initially designed and subsequently optimized by spontaneous viral evolution. These efforts yielded efficiently replicating and tightly dox-controlled HIV-rtTA and SIV-rtTA variants that replicate in a variety of cell and tissue culture systems, and in human immune system (HIS) mice and macaques, respectively. These viruses can be used as a tool in HIV and SIV biology studies and in vaccine research. We review how HIV-rtTA and SIV-rtTA were used to study the role of the viral TAR and Tat elements in virus replication. PMID:25982510

  3. Detection of variants in SLC6A8 and functional analysis of unclassified missense variants.

    PubMed

    Betsalel, Ofir T; Pop, Ana; Rosenberg, Efraim H; Fernandez-Ojeda, Matilde; Jakobs, Cornelis; Salomons, Gajja S

    2012-04-01

    Creatine transporter deficiency is an X-linked disorder caused by mutations in the SLC6A8 gene. Currently, 38 pathogenic, including 15 missense variants, are reported. In this study, we report 33 novel, including 6 missense variants. To classify all known missense variants, we transfected creatine deficient fibroblasts with the SLC6A8 ORF containing one of the unique variants and tested their ability to restore creatine uptake. This resulted in the definitive classification of 2 non-disease associated and 19 pathogenic variants of which 3 have residual activity. Furthermore, we report the development and validation of a novel DHPLC method for the detection of heterozygous SLC6A8 variants. The method was validated by analysis of DNAs that in total contained 67 unique variants of which 66 could be detected. Therefore, this rapid screening method may prove valuable for the analysis of large cohorts of females with mild intellectual disability of unknown etiology, since in this group heterozygous SLC6A8 mutations may be detected. DHPLC proved also to be important for the detection of somatic mosaicism in mothers of patients who have a pathogenic mutation in SLC6A8. All variants reported in the present and previous studies are included in the Leiden Open Source Variant Database (LOVD) of SLC6A8 (www.LOVD.nl/SLC6A8). PMID:22281021

  4. Hybrid & El Tor variant biotypes of Vibrio cholerae O1 in Thailand

    PubMed Central

    Na-Ubol, M.; Srimanote, P.; Chongsa-nguan, M.; Indrawattana, N.; Sookrung, N.; Tapchaisri, P.; Yamazaki, S.; Bodhidatta, L.; Eampokalap, B.; Kurazono, H.; Hayashi, H.; Nair, G.B.; Takeda, Y.; Chaicumpa, W.

    2011-01-01

    Background & objectives: El Tor Vibrio cholerae O1 carrying ctxBC trait, so-called El Tor variant that causes more severe symptoms than the prototype El Tor strain, first detected in Bangladesh was later shown to have emerged in India in 1992. Subsequently, similar V. cholerae strains were isolated in other countries in Asia and Africa. Thus, it was of interest to investigate the characteristics of V. cholerae O1 strains isolated chronologically (from 1986 to 2009) in Thailand. Methods: A total of 330 V. cholerae O1 Thailand strains from hospitalized patients with cholera isolated during 1986 to 2009 were subjected to conventional biotyping i.e., susceptibility to polymyxin B, chicken erythrocyte agglutination (CCA) and Voges-Proskauer (VP) test. The presence of ctxA, ctxB, zot, ace, toxR, tcpAC, tcpAE, hlyAC and hlyAE were examined by PCR. Mismatch amplification mutation assay (MAMA) - and conventional- PCRs were used for differentiating ctxB and rstR alleles. Results: All 330 strains carried the El Tor virulence gene signature. Among these, 266 strains were typical El Tor (resistant to 50 units of polymyxin B and positive for CCA and VP test) while 64 had mixed classical and El Tor phenotypes (hybrid biotype). Combined MAMA-PCR and the conventional biotyping methods revealed that 36 strains of 1986-1992 were either typical El Tor, hybrid, El Tor variant or unclassified biotype. The hybrid strains were present during 1986-2004. El Tor variant strains were found in 1992, the same year when the typical El Tor strains disappeared. All 294 strains of 1993-2009 carried ctxBC ; 237 were El Tor variant and 57 were hybrid. Interpretation & conclusions: In Thailand, hybrid V. cholerae O1 (mixed biotypes), was found since 1986. Circulating strains, however, are predominantly El Tor variant (El Tor biotype with ctxBC). PMID:21537091

  5. Glyco-variant library of the versatile enzyme horseradish peroxidase

    PubMed Central

    Capone, Simona; Pletzenauer, Robert; Maresch, Daniel; Metzger, Karl; Altmann, Friedrich; Herwig, Christoph; Spadiut, Oliver

    2014-01-01

    When the glycosylated plant enzyme horseradish peroxidase (HRP) is conjugated to specific antibodies, it presents a powerful tool for medical applications. The isolation and purification of this enzyme from plant is difficult and only gives low yields. However, HRP recombinantly produced in the yeast Pichia pastoris experiences hyperglycosylation, which impedes the use of this enzyme in medicine. Enzymatic and chemical deglycosylation are cost intensive and cumbersome and hitherto existing P. pastoris strain engineering approaches with the goal to avoid hyperglycosylation only resulted in physiologically impaired yeast strains not useful for protein production processes. Thus, the last resort to obtain less glycosylated recombinant HRP from P. pastoris is to engineer the enzyme itself. In the present study, we mutated all the eight N-glycosylation sites of HRP C1A. After determination of the most suitable mutation at each N-glycosylation site, we physiologically characterized the respective P. pastoris strains in the bioreactor and purified the produced HRP C1A glyco-variants. The biochemical characterization of the enzyme variants revealed great differences in catalytic activity and stability and allowed the combination of the most promising mutations to potentially give an unglycosylated, active HRP C1A variant useful for medical applications. Interestingly, site-directed mutagenesis proved to be a valuable strategy not only to reduce the overall glycan content of the recombinant enzyme but also to improve catalytic activity and stability. In the present study, we performed an integrated bioprocess covering strain generation, bioreactor cultivations, downstream processing and product characterization and present the biochemical data of the HRP glyco-library. PMID:24859724

  6. Emergence of an outbreak-associated Clostridium difficile variant with increased virulence.

    PubMed

    Quesada-Gómez, Carlos; López-Ureña, Diana; Acuña-Amador, Luis; Villalobos-Zúñiga, Manuel; Du, Tim; Freire, Rosemayre; Guzmán-Verri, Caterina; del Mar Gamboa-Coronado, María; Lawley, Trevor D; Moreno, Edgardo; Mulvey, Michael R; de Castro Brito, Gerly Anne; Rodríguez-Cavallini, Evelyn; Rodríguez, César; Chaves-Olarte, Esteban

    2015-04-01

    The prevalence of Clostridium difficile infections has increased due to the emergence of epidemic variants from diverse genetic lineages. Here we describe the emergence of a novel variant during an outbreak in a Costa Rican hospital that was associated with severe clinical presentations. This C. difficile variant elicited higher white blood cell counts and caused disease in younger patients than did other strains isolated during the outbreak. Furthermore, it had a recurrence rate, a 30-day attributable disease rate, and disease severity as great as those of the epidemic strain NAP1. Pulsed-field gel electrophoresis genotyping indicated that the outbreak strains belong to a previously undescribed variant, designated NAPCR1. Whole-genome sequencing and ribotyping indicated that the NAPCR1 variant belongs to C. difficile ribotype 012 and sequence type 54, as does the reference strain 630. NAPCR1 strains are resistant to fluoroquinolones due to a mutation in gyrA, and they possess an 18-bp deletion in tcdC that is characteristic of the epidemic, evolutionarily distinct, C. difficile NAP1 variant. NAPCR1 genomes contain 10% more predicted genes than strain 630, most of which are of hypothetical function and are present on phages and other mobile genetic elements. The increased virulence of NAPCR1 was confirmed by mortality rates in the hamster model and strong inflammatory responses induced by bacteria-free supernatants in the murine ligated loop model. However, NAPCR1 strains do not synthesize toxin A and toxin B at levels comparable to those in NAP1 strains. Our results suggest that the pathogenic potential of this emerging C. difficile variant is due to the acquisition of hypothetical functions associated with laterally acquired DNA. PMID:25653402

  7. Emergence of an Outbreak-Associated Clostridium difficile Variant with Increased Virulence

    PubMed Central

    Quesada-Gómez, Carlos; López-Ureña, Diana; Acuña-Amador, Luis; Villalobos-Zúñiga, Manuel; Du, Tim; Freire, Rosemayre; Guzmán-Verri, Caterina; Gamboa-Coronado, María del Mar; Lawley, Trevor D.; Moreno, Edgardo; Mulvey, Michael R.; Brito, Gerly Anne de Castro; Rodríguez-Cavallini, Evelyn; Rodríguez, César

    2015-01-01

    The prevalence of Clostridium difficile infections has increased due to the emergence of epidemic variants from diverse genetic lineages. Here we describe the emergence of a novel variant during an outbreak in a Costa Rican hospital that was associated with severe clinical presentations. This C. difficile variant elicited higher white blood cell counts and caused disease in younger patients than did other strains isolated during the outbreak. Furthermore, it had a recurrence rate, a 30-day attributable disease rate, and disease severity as great as those of the epidemic strain NAP1. Pulsed-field gel electrophoresis genotyping indicated that the outbreak strains belong to a previously undescribed variant, designated NAPCR1. Whole-genome sequencing and ribotyping indicated that the NAPCR1 variant belongs to C. difficile ribotype 012 and sequence type 54, as does the reference strain 630. NAPCR1 strains are resistant to fluoroquinolones due to a mutation in gyrA, and they possess an 18-bp deletion in tcdC that is characteristic of the epidemic, evolutionarily distinct, C. difficile NAP1 variant. NAPCR1 genomes contain 10% more predicted genes than strain 630, most of which are of hypothetical function and are present on phages and other mobile genetic elements. The increased virulence of NAPCR1 was confirmed by mortality rates in the hamster model and strong inflammatory responses induced by bacteria-free supernatants in the murine ligated loop model. However, NAPCR1 strains do not synthesize toxin A and toxin B at levels comparable to those in NAP1 strains. Our results suggest that the pathogenic potential of this emerging C. difficile variant is due to the acquisition of hypothetical functions associated with laterally acquired DNA. PMID:25653402

  8. Common Variants in UMOD Associate with Urinary Uromodulin Levels: A Meta-Analysis

    PubMed Central

    Olden, Matthias; Corre, Tanguy; Hayward, Caroline; Toniolo, Daniela; Ulivi, Sheila; Gasparini, Paolo; Pistis, Giorgio; Hwang, Shih-Jen; Bergmann, Sven; Campbell, Harry; Cocca, Massimiliano; Gandin, Ilaria; Girotto, Giorgia; Glaudemans, Bob; Hastie, Nicholas D.; Loffing, Johannes; Polasek, Ozren; Rampoldi, Luca; Rudan, Igor; Sala, Cinzia; Traglia, Michela; Vollenweider, Peter; Vuckovic, Dragana; Youhanna, Sonia; Weber, Julien; Wright, Alan F.; Kutalik, Zoltán; Bochud, Murielle; Fox, Caroline S.

    2014-01-01

    Uromodulin is expressed exclusively in the thick ascending limb and is the most abundant protein excreted in normal urine. Variants in UMOD, which encodes uromodulin, are associated with renal function, and urinary uromodulin levels may be a biomarker for kidney disease. However, the genetic factors regulating uromodulin excretion are unknown. We conducted a meta-analysis of urinary uromodulin levels to identify associated common genetic variants in the general population. We included 10,884 individuals of European descent from three genetic isolates and three urban cohorts. Each study measured uromodulin indexed to creatinine and conducted linear regression analysis of approximately 2.5 million single nucleotide polymorphisms using an additive model. We also tested whether variants in genes expressed in the thick ascending limb associate with uromodulin levels. rs12917707, located near UMOD and previously associated with renal function and CKD, had the strongest association with urinary uromodulin levels (P<0.001). In all cohorts, carriers of a G allele of this variant had higher uromodulin levels than noncarriers did (geometric means 10.24, 14.05, and 17.67 μg/g creatinine for zero, one, or two copies of the G allele). rs12446492 in the adjacent gene PDILT (protein disulfide isomerase-like, testis expressed) also reached genome-wide significance (P<0.001). Regarding genes expressed in the thick ascending limb, variants in KCNJ1, SORL1, and CAB39 associated with urinary uromodulin levels. These data indicate that common variants in the UMOD promoter region may influence urinary uromodulin levels. They also provide insights into uromodulin biology and the association of UMOD variants with renal function. PMID:24578125

  9. Sequence variation of human 28S rRNA and expression of variants in different tissues

    SciTech Connect

    Sylvester, J.E.; Gonzalez, I.L.; Gillespie, D.A.

    1994-09-01

    There are 400 or so copies of the ribosomal RNA (rRNA) gene in humans. Previous studies have shown that human 28S encoding rDNA, and therefore rRNAs, vary in sequence at specific locations termed variable regions; these variations appear in a population and within an individual. This study asked the following questions regarding one variable region (V5) within 28S rRNA gene sequence variation in a single individual: (1) what is the extent and nature of the sequence variation at the DNA level?; (2) are these variant rRNA genes expressed?; (3) does rRNA gene sequence variation result in rRNA structural variation?; (4) is there evidence of differential expression of variant rRNA genes?. To address these four questions, genomic copies of the V5 region were cloned from the individual and sequenced. Six unique sequences were found among seven V5 clones, each differing only in the number of repeats of simple sequences (CGG), (TG), (T), and (C) at a specific site of the V5 region. Computer-generated secondary structure models of each of these variants indicated that the basic structure was not compromised. To test for V5 variant expression in different tissues of an individual, RNAs isolated from different tissues were used to protect each of the cloned V5 variant probes in the RNase protection assay (RPA). We conclude from the RPA results that different variants are present in proportionately different amounts in each tissue tested; however, the relative proportion of variants are similar in these tissues.

  10. Pathologic Potential of Variant Clones of the Oshima Strain of Far-Eastern Subtype Tick-Borne Encephalitis Virus

    PubMed Central

    Luat, Le Xuan; Tun, Mya Myat Ngwe; Buerano, Corazon C.; Aoki, Kotaro; Morita, Kouichi; Hayasaka, Daisuke

    2014-01-01

    Tick-borne encephalitis virus (TBEV) is a zoonotic agent that causes acute central nervous system (CNS) disease in humans. We previously suggested that immune response in addition to CNS infection contribute to mouse mortality following TBEV infection. However, we did not examine the influence of virus variants in the previous study. Therefore, in this study, we investigated the biological and pathologic potentials of the variant clones in the TBEV Oshima strain. We isolated eight variant clones from the stock virus of the Oshima 5-10. These variants exhibited different plaque morphologies in BHK cells and pathogenic potentials in mice. Full sequences of viral genomes revealed that each of the variant clones except one had specific combinations of nucleotide and amino acid changes at certain positions different from the parent strain. We also showed that an amino acid substitution of Glu122?Gly in the E protein could have affected virus infection and replication in vivo, as well as the attenuated pathogenicity in mice. These data confirm the presence of virus variants or quasispecies from the parent strain. Further elucidation of the effect of each variant clone on immune responses such as the T-cell response is an important priority in the development of an effective vaccine and treatment strategies for tick-borne encephalitis. PMID:24808743

  11. Strategies for the selection and characterization of aluminum-resistant variants from cell cultures of Nicotiana plumbaginifolia.

    PubMed

    Conner, A J; Meredith, C P

    1985-12-01

    The development of strategies for selecting and characterizing aluminum-resistant variants from Nicotiana plumbaginifolia Viv. cell cultures is described. Plated cells, smeared callus, in-vitro-grown shoots, and seedlings of wild-type N. plumbaginifolia all showed similar responses to Al, with total growth inhibition at or above 600 μM Al. The strict control of both cell density and aggregate size is important in selection experiments for total inhibition of the growth of wild-type cells. Two approaches for the selection of Al-resistant variants were used. In a direct method, cells were plated onto medium containing 600 μM Al which inhibited growth and chlorophyll synthesis in wildtype cells. A double selection strategy based on both cell growth and greening was used to isolate 29 Al-resistant variants. In the other approach, a rescue method, suspensions were cultured for 10 d in medium containing 600 μM Al, then plated onto standard medium for recovery of survivors. Using this strategy, 217 Al-resistant variants were selected. After six to twelve weeks of growth in the absence of Al, each variant was cloned and reselected from single cells. Al resistance was retained in 31% and 51% of the variants selected by the direct and rescue strategies, respectively. Seedling segregation data are presented for the progeny (selfed and backcrossed) of plants regenerated from one of the variants and are consistent with those expected for a single dominant mutation. PMID:24241611

  12. Identification of carriers of a variant plasma prealbumin (transthyretin) associated with familial amyloidotic polyneuropathy type I.

    PubMed Central

    Benson, M D; Dwulet, F E

    1985-01-01

    A method is described for detecting carriers of a variant plasma prealbumin that is associated with familial amyloidotic polyneuropathy (FAP) type I. It is based on the finding of an extra methionine in the variant prealbumin, at position 30 from the amino terminals. Since normal prealbumin has only one methionine (position 13), treatment with cyanogen bromide (CNBr), which cleaves only at methionines, results in two peptides. CNBr treatment of the variant prealbumin gives three peptides. The extra can then be detected in two ways: by HPLC using a reverse phase C18 column, and by sequential Edman degradation. Each method can detect as little as 1% variant prealbumin in isolated plasma prealbumin, and therefore, can identify carriers of the gene for the variant protein. Since FAP type I usually is not manifest until after the childbearing years, this method to identify carriers of the gene offers a new approach for genetic counseling of families with this disease. To date, kindreds with hereditary amyloidosis that could benefit from these studies include those with FAP type I of Swedish, Japanese, and Portuguese origins. PMID:2981253

  13. Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture

    PubMed Central

    Xue, Katherine S; Hooper, Kathryn A; Ollodart, Anja R; Dingens, Adam S; Bloom, Jesse D

    2016-01-01

    RNA viruses rapidly diversify into quasispecies of related genotypes. This genetic diversity has long been known to facilitate adaptation, but recent studies have suggested that cooperation between variants might also increase population fitness. Here, we demonstrate strong cooperation between two H3N2 influenza variants that differ by a single mutation at residue 151 in neuraminidase, which normally mediates viral exit from host cells. Residue 151 is often annotated as an ambiguous amino acid in sequenced isolates, indicating mixed viral populations. We show that mixed populations grow better than either variant alone in cell culture. Pure populations of either variant generate the other through mutation and then stably maintain a mix of the two genotypes. We suggest that cooperation arises because mixed populations combine one variant’s proficiency at cell entry with the other’s proficiency at cell exit. Our work demonstrates a specific cooperative interaction between defined variants in a viral quasispecies. DOI: http://dx.doi.org/10.7554/eLife.13974.001 PMID:26978794

  14. Characterizing sialic acid variants at the glycopeptide level.

    PubMed

    Medzihradszky, Katalin F; Kaasik, Krista; Chalkley, Robert J

    2015-03-01

    Beam-type collision-induced dissociation (CID) data of intact glycopeptides isolated from mouse liver tissue are presented to illustrate characteristic fragmentation of differentially sialylated glycopeptides. Eight glycoforms of an O-linked glycopeptide from Nucleobindin-1 are distinguished on the basis of the precursor masses and characteristic oxonium ions. We report that all sialic acid variants are prone to neutral loss from the charge reduced species in electron-transfer dissociation (ETD) fragmentation. We show how changes in sialic acid composition affect reverse phase chromatographic retention times: sialic acid addition increases glycopeptide retention times significantly; replacing the N-acetylneuraminic acid with the N-glycolyl variant leads to slightly reduced retention times, while O-acetylated sialic acid-containing glycoforms are retained longer. We then demonstrate how MS-Filter in Protein Prospector can use these diagnostic oxonium ions to find glycopeptides, by showing that a wealth of different glycopeptides can be found in a published phosphopeptide data set. PMID:25654559

  15. Variants of hamster fibroblasts resistant to Ricinus communis toxin (ricin).

    PubMed

    Meager, A; Ungkitchanukit, A; Hughes, R C

    1976-01-15

    1. Variant baby-hamster kidney (BHK) cell lines were isolated that grow in the presence of high concentrations of ricin, the toxic lectin of castor beans (Ricinus communis). The variant lines were independently derived from several cultures of normal BHK cells which had been exposed to the mutagen, methyl-N-nitro-N-nitrosoguanidine, before selection by ricin. 2. The cell lines maintain a high degree of resistance to ricin after growth in lectin-free medium for prolonged periods and therefore exhibit stable phenotypes that are different from normal BHK cells. 3. A preliminary classification of the phenotypes was made. Several cell lines bind normal amounts of 125I-labelled ricin, whereas other bind the lectin poorly. 4. A loss of surface receptors for two other lectins, R. communis RCA and Axinella polyploides, which have specificities similar to ricin, was also found in some but not all of the cell lines showing decreased surface concentrations of ricin receptors. 5. The binding to the ricin-resistant cells of lectins of different sugar specificity, namely Lens culinaris lectin and concanavalin A, was similar to, or higher than, to normal BHK cells. 6. Several of the ricin-resistant cell lines were shown to be cross-resistant to the weak cytotoxicity of Phaseolus vulgaris lectin. By contrast, some cell lines were more sensitive to concanavalin A than were normal BHK cells. PMID:1275903

  16. Hereditary renal amyloidosis with a novel variant fibrinogen.

    PubMed Central

    Uemichi, T; Liepnieks, J J; Benson, M D

    1994-01-01

    Two families with hereditary renal amyloidosis were found to have a novel mutation in the fibrinogen A alpha chain gene. This form of amyloidosis is an autosomal dominant condition characterized by proteinuria, hypertension, and subsequent azotemia. DNAs of patients with amyloidosis were screened for a polymorphism in fibrinogen A alpha chain gene by single-strand conformation polymorphism analysis, and affected individuals from two kindreds were found to have a mutation. Both of these kindreds are American of Irish descent presenting with non-neuropathic, nephropathic amyloidosis in the fifth to the seventh decade of life. DNA sequencing showed a point mutation in the fibrinogen A alpha chain gene that is responsible for substitution of valine for glutamic acid at position 526. By restriction fragment length polymorphism analysis, 7 affected individuals and 14 asymptomatic individuals in these two kindreds were positive for the fibrinogen A alpha chain Val 526 gene. Fibrinogen was isolated from plasma of a heterozygous gene carrier and shown to contain approximately 50% variant fibrinogen. Discovery of this new mutation confirms the association between fibrinogen A alpha chain variant and hereditary renal amyloidosis and establishes a new biochemical subtype of amyloidosis. Images PMID:8113408

  17. Super Spy variants implicate flexibility in chaperone action.

    PubMed

    Quan, Shu; Wang, Lili; Petrotchenko, Evgeniy V; Makepeace, Karl At; Horowitz, Scott; Yang, Jianyi; Zhang, Yang; Borchers, Christoph H; Bardwell, James Ca

    2014-01-01

    Experimental study of the role of disorder in protein function is challenging. It has been proposed that proteins utilize disordered regions in the adaptive recognition of their various binding partners. However apart from a few exceptions, defining the importance of disorder in promiscuous binding interactions has proven to be difficult. In this paper, we have utilized a genetic selection that links protein stability to antibiotic resistance to isolate variants of the newly discovered chaperone Spy that show an up to 7 fold improved chaperone activity against a variety of substrates. These "Super Spy" variants show tighter binding to client proteins and are generally more unstable than is wild type Spy and show increases in apparent flexibility. We establish a good relationship between the degree of their instability and the improvement they show in their chaperone activity. Our results provide evidence for the importance of disorder and flexibility in chaperone function. DOI: http://dx.doi.org/10.7554/eLife.01584.001. PMID:24497545

  18. Super Spy variants implicate flexibility in chaperone action

    PubMed Central

    Quan, Shu; Wang, Lili; Petrotchenko, Evgeniy V; Makepeace, Karl AT; Horowitz, Scott; Yang, Jianyi; Zhang, Yang; Borchers, Christoph H; Bardwell, James CA

    2014-01-01

    Experimental study of the role of disorder in protein function is challenging. It has been proposed that proteins utilize disordered regions in the adaptive recognition of their various binding partners. However apart from a few exceptions, defining the importance of disorder in promiscuous binding interactions has proven to be difficult. In this paper, we have utilized a genetic selection that links protein stability to antibiotic resistance to isolate variants of the newly discovered chaperone Spy that show an up to 7 fold improved chaperone activity against a variety of substrates. These “Super Spy” variants show tighter binding to client proteins and are generally more unstable than is wild type Spy and show increases in apparent flexibility. We establish a good relationship between the degree of their instability and the improvement they show in their chaperone activity. Our results provide evidence for the importance of disorder and flexibility in chaperone function. DOI: http://dx.doi.org/10.7554/eLife.01584.001 PMID:24497545

  19. A Splice Variant of Bardet-Biedl Syndrome 5 (BBS5) Protein that Is Selectively Expressed in Retina

    PubMed Central

    Bolch, Susan N.; Dugger, Donald R.; Chong, Timothy; McDowell, J. Hugh; Smith, W. Clay

    2016-01-01

    Purpose Bardet-Biedl syndrome is a complex ciliopathy that usually manifests with some form of retinal degeneration, amongst other ciliary-related deficiencies. One of the genetic causes of this syndrome results from a defect in Bardet-Biedl Syndrome 5 (BBS5) protein. BBS5 is one component of the BBSome, a complex of proteins that regulates the protein composition in cilia. In this study, we identify a smaller molecular mass form of BBS5 as a variant formed by alternative splicing and show that expression of this splice variant is restricted to the retina. Methods Reverse transcription PCR from RNA was used to isolate and identify potential alternative transcripts of Bbs5. A peptide unique to the C-terminus of the BBS5 splice variant was synthesized and used to prepare antibodies that selectively recognized the BBS5 splice variant. These antibodies were used on immunoblots of tissue extracts to determine the extent of expression of the alternative transcript and on tissue slices to determine the localization of expressed protein. Pull-down of fluorescently labeled arrestin1 by immunoprecipitation of the BBS5 splice variant was performed to assess functional interaction between the two proteins. Results PCR from mouse retinal cDNA using Bbs5-specific primers amplified a unique cDNA that was shown to be a splice variant of BBS5 resulting from the use of cryptic splicing sites in Intron 7. The resulting transcript codes for a truncated form of the BBS5 protein with a unique 24 amino acid C-terminus, and predicted 26.5 kD molecular mass. PCR screening of RNA isolated from various ciliated tissues and immunoblots of protein extracts from these same tissues showed that this splice variant was expressed in retina, but not brain, heart, kidney, or testes. Quantitative PCR showed that the splice variant transcript is 8.9-fold (+/- 1.1-fold) less abundant than the full-length transcript. In the retina, the splice variant of BBS5 appears to be most abundant in the connecting cilium of photoreceptors, where BBS5 is also localized. Like BBS5, the binding of BBS5L to arrestin1 can be modulated by phosphorylation through protein kinase C. Conclusions In this study we have identified a novel splice variant of BBS5 that appears to be expressed only in the retina. The BBS5 splice variant is expressed at approximately 10% of full-length BBS5 level. No unique functional or localization properties could be identified for the splice variant compared to BBS5. PMID:26867008

  20. Complete Genome Sequence of the Porcine Kobuvirus Variant CH/HNXX-4/2012

    PubMed Central

    Cao, Weijun; Zhang, Keshan; Jin, Ye; Lv, Lv; Yang, Fan

    2012-01-01

    Porcine kobuvirus, an emerging virus, may be the underlying etiological cause of a large-scale outbreak of diarrhea in suckling piglets in China that started in 2010. We report the complete genome sequence of the porcine kobuvirus variant CH/HNXX-4/2012 with a 30-amino-acid deletion in its 2B-coding region that was isolated in this outbreak. This will help the phenotypic variation and evolutionary characteristics of porcine kobuvirus to be understood. PMID:23043177

  1. Complete genome sequence of the porcine kobuvirus variant CH/HNXX-4/2012.

    PubMed

    Cao, Weijun; Zheng, Haixue; Zhang, Keshan; Jin, Ye; Lv, Lv; Yang, Fan; Liu, Xiangtao

    2012-11-01

    Porcine kobuvirus, an emerging virus, may be the underlying etiological cause of a large-scale outbreak of diarrhea in suckling piglets in China that started in 2010. We report the complete genome sequence of the porcine kobuvirus variant CH/HNXX-4/2012 with a 30-amino-acid deletion in its 2B-coding region that was isolated in this outbreak. This will help the phenotypic variation and evolutionary characteristics of porcine kobuvirus to be understood. PMID:23043177

  2. Efficacy of commercial canarypox vaccine for protecting Hawai'i 'Amakihi from field isolates of Avipoxvirus

    USGS Publications Warehouse

    Atkinson, Carter T.; Wiegand, Kimberly C.; Triglia, Dennis; Jarvi, Susan I.

    2010-01-01

    At least three variants of avian pox virus are present in Hawai‘i - Fowlpox from domestic poultry and a group of genetically distinct viruses that cluster within two clades (Pox Variant 1 and Pox Variant 2) that are most similar to Canarypox based on DNA sequence of the virus 4b core protein gene. We tested whether Hawai‘i ‘Amakihi can be protected from wild virus isolates with an attenuated live Canarypox vaccine that is closely related to isolates that cluster within clade 1 (Pox Variant 1) based on sequence of the attenuated Canarypox virus 4b core protein. Thirty-one (31) Hawai`i ‘Amakihi (Hemignathus virens) with no prior physical evidence of pox infection were collected on Mauna Kea from xeric, high elevation habitats with low pox prevalence and randomly divided into two groups. One group of 16 was vaccinated with Poximmune C® while the other group received a sham vaccination with virus diluent. Four of 15 (27%) vaccinated birds developed potentially life-threatening disseminated lesions or lesions of unusually long duration, while one bird never developed a vaccine-associated lesion or "take". After vaccine-associated lesions healed, vaccinated birds were randomly divided into three groups of five and challenged with either a wild isolate of Fowlpox, a Hawai`i `Amakihi isolate of a Canarypox-like virus from clade 1 (Pox Variant 1) or a Hawai`i `Amakihi isolate of a Canarypox-like virus from clade 2 (Pox Variant 2). Similarly, three random groups of five unvaccinated ‘Amakihi were challenged with the same virus isolates. Vaccinated and unvaccinated ‘Amakihi challenged with Fowlpox had transient infections with no clinical signs of infection. Mortality in vaccinated ‘Amakihi that were challenged with Pox Variant 1 and Pox Variant 2 ranged from 0% (0/5) for Pox Variant 1 to 60% (3/5) for Pox Variant 2. Mortality in unvaccinated ‘Amakihi ranged from 40% (2/5) for Pox Variant 1 to 100% (5/5) for Pox Variant 2. While the vaccine provided some protection against Pox Variant 1, serious side effects and low efficacy against Pox Variant 2 make it risky to use in captive or wild honeycreepers.

  3. Yield of stool culture with isolate toxin testing versus a two-step algorithm including stool toxin testing for detection of toxigenic Clostridium difficile.

    PubMed

    Reller, Megan E; Lema, Clara A; Perl, Trish M; Cai, Mian; Ross, Tracy L; Speck, Kathleen A; Carroll, Karen C

    2007-11-01

    We examined the incremental yield of stool culture (with toxin testing on isolates) versus our two-step algorithm for optimal detection of toxigenic Clostridium difficile. Per the two-step algorithm, stools were screened for C. difficile-associated glutamate dehydrogenase (GDH) antigen and, if positive, tested for toxin by a direct (stool) cell culture cytotoxicity neutralization assay (CCNA). In parallel, stools were cultured for C. difficile and tested for toxin by both indirect (isolate) CCNA and conventional PCR if the direct CCNA was negative. The "gold standard" for toxigenic C. difficile was detection of C. difficile by the GDH screen or by culture and toxin production by direct or indirect CCNA. We tested 439 specimens from 439 patients. GDH screening detected all culture-positive specimens. The sensitivity of the two-step algorithm was 77% (95% confidence interval [CI], 70 to 84%), and that of culture was 87% (95% CI, 80 to 92%). PCR results correlated completely with those of CCNA testing on isolates (29/29 positive and 32/32 negative, respectively). We conclude that GDH is an excellent screening test and that culture with isolate CCNA testing detects an additional 23% of toxigenic C. difficile missed by direct CCNA. Since culture is tedious and also detects nontoxigenic C. difficile, we conclude that culture is most useful (i) when the direct CCNA is negative but a high clinical suspicion of toxigenic C. difficile remains, (ii) in the evaluation of new diagnostic tests for toxigenic C. difficile (where the best reference standard is essential), and (iii) in epidemiologic studies (where the availability of an isolate allows for strain typing and antimicrobial susceptibility testing). PMID:17804652

  4. Frequency of thermostability variants: estimation of total rare variant frequency in human populations

    SciTech Connect

    Mohrenweiser, H.W.; Neel, J.V.

    1981-09-01

    Eight erythrocyte enzymes were examine for thermostability in an unselected sample of 100 newborn infants. Three thermolabile variants, one each of lactate dehydrogenase, glucosephosphate isomerase, and glucose-6-phosphate dehydrogenase, were identified, none of which was detectable as a variant by standard electrophoretic techniques. All were inherited. This frequency of 3.8 heritable thermostability variants per 1000 determinations is to be compared with a frequency of electrophoretically detectable variants of 1.1 per 1000 determinations, a frequency of 2.4 enzyme-deficiency variants per 1000 determinations, and a frequency of individuals with rare enzyme deficiency or electrophoretic or thermostability (or both) variants at these loci is 8.4 per 1000 determinations. A similar distribution and frequency is seen when the comparison is limited to the seven loci studied by all techniques. it is clear that not all of the electrophoretic and thermostability variants present in the population are detected by the techniques used in this study. Accordingly, it is estimated that the true frequency of carriers of a rare variant for each of these enzyme-coding loci averages greater than 10/1000. Some implications of these frequencies for human disease are discussed.

  5. Molecular Insights into the Phenotypic Divergence in Natural Curli Variants of Escherichia coli O157:H7

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Escherichia coli O157:H7 (EcO157) causes severe disease including hemolytic uremic syndrome and contributes significantly to human infections and outbreaks. We previously reported that natural curli variants isolated from the same strain display distinct phenotypic differences: curli-deficient varia...

  6. Escherichia coli harboring Shiga toxin 2 gene variants: frequency and association with clinical symptoms.

    PubMed

    Friedrich, Alexander W; Bielaszewska, Martina; Zhang, Wen-Lan; Pulz, Matthias; Kuczius, Thorsten; Ammon, Andrea; Karch, Helge

    2002-01-01

    Shiga toxin (Stx)-producing Escherichia coli (STEC) from patients with hemolytic-uremic syndrome (HUS), patients with diarrhea without HUS, or asymptomatic subjects were genotyped to assess associations between stx2 variants and clinical manifestations of infection. Neither stx2d nor stx2e was found in 268 STEC isolates from patients with HUS. Of 262 STEC isolates from patients with diarrhea, stx(2d) was found in 41 (15.6%; P<.000001), and stx2e was found in 12 (4.6%; P=.0004). The stx2c genotype frequency was similar among isolates from patients with HUS (3.7%) and diarrhea (5.0%). The frequencies of stx2c, stx2d, and stx2e among 96 STEC isolates from asymptomatic subjects were comparable to those among isolates from patients with diarrhea. None of the 626 STEC isolates contained stx2f. All stx2d-positive or stx2e-positive STEC isolates were eae negative and originated from subjects older than those with STEC isolates with stx2c. stx2c-positive STEC isolates can cause HUS, but the presence of stx2d or stx2e may predict a milder disease with a minimal risk of HUS. PMID:11756984

  7. Identification of an antigenic and genetic variant of dengue-4 virus from the Caribbean.

    PubMed

    Henchal, E A; Repik, P M; McCown, J M; Brandt, W E

    1986-03-01

    Twenty-one dengue (DEN) viruses isolated from the Caribbean (Dominica and Jamaica) during the 1981-1982 epidemic year were distinct serological and genetic variants of DEN-4 virus. These isolates were clearly identified as DEN-4 viruses using type-specific monoclonal antibodies in indirect immunofluorescence assays. However, they either were not neutralized, or were neutralized poorly using hyperimmune mouse ascitic fluids (HMAF) or rhesus monkey serum directed against the H-241 prototype strain of DEN-4 virus isolated in the Philippines in 1956. HMAF prepared against a representative Caribbean isolate, however, neutralized with similar effectiveness the homologous virus, the H-241 prototype strain, and virus strains isolated from the Pacific and Southeast Asian areas from 1973 to 1984. The Caribbean isolate exhibited no more than 30% and 16% oligonucleotide spot homology with the H-241 and Bangkok viruses, respectively, by RNA fingerprint analysis, while demonstrating 82% and 89% homology with the Gilbert and Niue Island isolates, respectively. The isolation of dengue viruses which are serologically and genetically distinct from the prototype virus emphasizes the need for continued dengue virus surveillance. The recognition of unique dengue isolates should allow the selection of reference strains and vaccine candidate strains which will induce antibodies that are equally effective in neutralizing viruses from all geographic areas. PMID:3513650

  8. Nuclear receptor variants in liver disease.

    PubMed

    Zimmer, Vincent; Liebe, Roman; Lammert, Frank

    2015-01-01

    This snapshot reviews the current state of knowledge on genetic variants of nuclear receptors (NRs) involved in regulating various aspects of liver metabolism. Interindividual differences in responses to diet and other 'in-' and environmental stressors can be caused by variants in components of the NR regulatory gene network. We recapitulate recent evidence for the application of NRs in genetic diagnosis of monogenic liver disease. Genetic analysis of multifactorial liver diseases, such as nonalcoholic fatty liver disease and diabetes mellitus, pinpoints key players in disease predisposition and progression. In particular, NR1H4 variants have been associated with intrahepatic cholestasis of pregnancy and gallstone disease. Other examples include studies of NR1I2 and NR1I3 polymorphisms in patients with drug-induced liver injury and NR5A2 variation in cholangiocarcinoma. Associations of NR gene variants have been identified in patients with dyslipidemia and other metabolic syndrome-associated traits by genome-wide studies. Evidence from these analyses confirms a role for NR variation in common diseases, linking regulatory networks to complex and variable phenotypes. These new insights into the impact of NR variants offer perspectives for their future use in diagnosis and treatment of common diseases. PMID:26045277

  9. MUS-2, a novel variant of the chromosome-encoded ?-lactamase MUS-1, from Myroides odoratimimus

    PubMed Central

    Al-Bayssari, C.; Gupta, S. Kumar; Dabboussi, F.; Hamze, M.; Rolain, J.-M.

    2015-01-01

    The aim of the present study was to investigate the molecular mechanism of carbapenem resistance of three imipenem-resistant isolates of Myroides odoratimimus recovered from two livestock farms of cows and pigeons by rectal swab in Lebanon in January 2014. Investigation of imipenem resistance of these isolates using the modified Hodge test, the EDTA test, the modified CarbaNP test and the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Ultraflex assay showed a carbapenemase activity due to the presence of a chromosome-encoded ?-lactamase MUS, verified by PCR. However amplification and sequencing of this chromosomal gene showed a novel variant of it designated MUS-2 by the curators of the Lahey database of ?-lactamases (http://www.lahey.org/Studies/webt.asp). Cloning of the blaMUS-2 was performed, followed by protein expression in Escherichia coli TOP 10. Pulsed-field gel electrophoresis clearly showed that the three isolates belonged to the same clone. This study reports a novel variant of the chromosome-encoded blaMUS-1 associated with carbapenem resistance in Myroides odoratimimus and shows that animals may represent a reservoir of bacteria harbouring several variants of resistance genes. PMID:26257915

  10. Nephritis associated with infectious bronchitis virus Cal99 variant in game chickens.

    PubMed

    França, M; Woolcock, P R; Yu, M; Jackwood, M W; Shivaprasad, H L

    2011-09-01

    Infectious bronchitis virus (IBV) Cal99 variant was isolated from the kidneys of seven 2-5-mo-old game chickens with nephritis and respiratory disease. IBV Cal99 variant is usually associated with respiratory disease in broiler chickens in California. Macroscopically, the majority of the birds had moderately to severely enlarged and mottled pale kidneys, with increased urates in the ureters. Microscopically, most of the birds had acute nephrosis and interstitial nephritis. The birds also had sinusitis, tracheitis, bronchopneumonia, airsacculitis, salivary gland adenitis, and lymphoid depletion in the thymus and bursa of Fabricius. Immunohistochemistry was strongly positive for IBV antigen in the cytoplasm of tubular epithelial cells in the kidneys and also in the epithelium of the respiratory tract, salivary glands, proventriculus, intestine, and bursa of Fabricius. Infectious bronchitis virus was isolated from the trachea, lungs, kidneys, and cecal tonsils. Sequencing of the hypervariable region of the S1 gene of the kidney IBV isolate, designated IBV/CA99variant/07, revealed that the virus was 98% homologous to the Cal99 serotype of IBV. PMID:22017040

  11. MUS-2, a novel variant of the chromosome-encoded ?-lactamase MUS-1, from Myroides odoratimimus.

    PubMed

    Al-Bayssari, C; Gupta, S Kumar; Dabboussi, F; Hamze, M; Rolain, J-M

    2015-09-01

    The aim of the present study was to investigate the molecular mechanism of carbapenem resistance of three imipenem-resistant isolates of Myroides odoratimimus recovered from two livestock farms of cows and pigeons by rectal swab in Lebanon in January 2014. Investigation of imipenem resistance of these isolates using the modified Hodge test, the EDTA test, the modified CarbaNP test and the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Ultraflex assay showed a carbapenemase activity due to the presence of a chromosome-encoded ?-lactamase MUS, verified by PCR. However amplification and sequencing of this chromosomal gene showed a novel variant of it designated MUS-2 by the curators of the Lahey database of ?-lactamases (http://www.lahey.org/Studies/webt.asp). Cloning of the bla MUS-2 was performed, followed by protein expression in Escherichia coli TOP 10. Pulsed-field gel electrophoresis clearly showed that the three isolates belonged to the same clone. This study reports a novel variant of the chromosome-encoded bla MUS-1 associated with carbapenem resistance in Myroides odoratimimus and shows that animals may represent a reservoir of bacteria harbouring several variants of resistance genes. PMID:26257915

  12. ?IIb?3 variants defined by next-generation sequencing: predicting variants likely to cause Glanzmann thrombasthenia.

    PubMed

    Buitrago, Lorena; Rendon, Augusto; Liang, Yupu; Simeoni, Ilenia; Negri, Ana; Filizola, Marta; Ouwehand, Willem H; Coller, Barry S

    2015-04-14

    Next-generation sequencing is transforming our understanding of human genetic variation but assessing the functional impact of novel variants presents challenges. We analyzed missense variants in the integrin ?IIb?3 receptor subunit genes ITGA2B and ITGB3 identified by whole-exome or -genome sequencing in the ThromboGenomics project, comprising ?32,000 alleles from 16,108 individuals. We analyzed the results in comparison with 111 missense variants in these genes previously reported as being associated with Glanzmann thrombasthenia (GT), 20 associated with alloimmune thrombocytopenia, and 5 associated with aniso/macrothrombocytopenia. We identified 114 novel missense variants in ITGA2B (affecting ?11% of the amino acids) and 68 novel missense variants in ITGB3 (affecting ?9% of the amino acids). Of the variants, 96% had minor allele frequencies (MAF) < 0.1%, indicating their rarity. Based on sequence conservation, MAF, and location on a complete model of ?IIb?3, we selected three novel variants that affect amino acids previously associated with GT for expression in HEK293 cells. ?IIb P176H and ?3 C547G severely reduced ?IIb?3 expression, whereas ?IIb P943A partially reduced ?IIb?3 expression and had no effect on fibrinogen binding. We used receiver operating characteristic curves of combined annotation-dependent depletion, Polyphen 2-HDIV, and sorting intolerant from tolerant to estimate the percentage of novel variants likely to be deleterious. At optimal cut-off values, which had 69-98% sensitivity in detecting GT mutations, between 27% and 71% of the novel ?IIb or ?3 missense variants were predicted to be deleterious. Our data have implications for understanding the evolutionary pressure on ?IIb?3 and highlight the challenges in predicting the clinical significance of novel missense variants. PMID:25827233

  13. Allele Variants of Enterotoxigenic Escherichia coli Heat-Labile Toxin Are Globally Transmitted and Associated with Colonization Factors

    PubMed Central

    Joffré, Enrique; von Mentzer, Astrid; Abd El Ghany, Moataz; Oezguen, Numan; Savidge, Tor; Dougan, Gordon; Svennerholm, Ann-Mari

    2014-01-01

    Enterotoxigenic Escherichia coli (ETEC) is a significant cause of morbidity and mortality in the developing world. ETEC-mediated diarrhea is orchestrated by heat-labile toxin (LT) and heat-stable toxins (STp and STh), acting in concert with a repertoire of more than 25 colonization factors (CFs). LT, the major virulence factor, induces fluid secretion after delivery of a monomeric ADP-ribosylase (LTA) and its pentameric carrier B subunit (LTB). A study of ETEC isolates from humans in Brazil reported the existence of natural LT variants. In the present study, analysis of predicted amino acid sequences showed that the LT amino acid polymorphisms are associated with a geographically and temporally diverse set of 192 clinical ETEC strains and identified 12 novel LT variants. Twenty distinct LT amino acid variants were observed in the globally distributed strains, and phylogenetic analysis showed these to be associated with different CF profiles. Notably, the most prevalent LT1 allele variants were correlated with major ETEC lineages expressing CS1 + CS3 or CS2 + CS3, and the most prevalent LT2 allele variants were correlated with major ETEC lineages expressing CS5 + CS6 or CFA/I. LTB allele variants generally exhibited more-stringent amino acid sequence conservation (2 substitutions identified) than LTA allele variants (22 substitutions identified). The functional impact of LT1 and LT2 polymorphisms on virulence was investigated by measuring total-toxin production, secretion, and stability using GM1–enzyme-linked immunosorbent assays (GM1-ELISA) and in silico protein modeling. Our data show that LT2 strains produce 5-fold more toxin than LT1 strains (P < 0.001), which may suggest greater virulence potential for this genetic variant. Our data suggest that functionally distinct LT-CF variants with increased fitness have persisted during the evolution of ETEC and have spread globally. PMID:25404692

  14. Specificity of antigens on UV radiation-induced antigenic tumor cell variants measured in vitro and in vivo

    SciTech Connect

    Hostetler, L.W.; Romerdahl, C.A.; Kripke, M.L.

    1989-03-01

    The purpose of this study was to determine whether antigenic variants cross-react immunologically with the parental tumor and whether the UVR-associated antigen unique to UVR-induced tumors is also present on the variants. Antigenic (regressor) variants and nonimmunogenic (progressor) clones derived from UV-irradiated cultures of the C3H K1735 melanoma and SF19 spontaneous fibrosarcoma cell lines were used to address these questions. In an in vivo immunization and challenge assay, the antigenic variants did not induce cross-protection among themselves, but each induced immunity against the immunizing variant, the parent tumor cells, and nonimmunogenic clones derived from UV-irradiated parent cultures. Therefore, the variants can be used to induce in mice a protective immunity that prevents the growth of the parent tumor and nonimmunogenic clones, but not other antigenic variants. In contrast, immunization with cells of the parental tumor or the nonimmunogenic clones induced no protective immunity against challenge with any of the cell lines. Utilizing the K1735 melanoma-derived cell lines in vitro, T-helper (Th) cells isolated from tumor-immunized mice were tested for cross-reactivity by their ability to collaborate with trinitrophenyl-primed B-cells in the presence of trinitrophenyl-conjugated tumor cells. Also, the cross-reactivity of cytotoxic T-lymphocytes from tumor-immunized mice was assessed by a 4-h 51Cr-release assay. Antigenic variants induced cytotoxic T-lymphocytes and Th activity that was higher than that induced by the parent tumor and nonimmunogenic clones from the UVR-exposed parent tumor and cross-reacted with the parental tumor cells and nonimmunogenic clones, but not with other antigenic variants.

  15. Heat sensitivity in a bentgrass variant. Failure to accumulate a chloroplast heat shock protein isoform implicated in heat tolerance.

    PubMed

    Wang, Dongfang; Luthe, Dawn S

    2003-09-01

    Two variants of creeping bentgrass (Agrostis stolonifera cv palustris), developed using tissue culture, have been used to determine the roles of chloroplast-localized small heat shock proteins (CP-sHSPs) in heat tolerance. Results from previous research indicate that the heat-tolerant variant expressed two additional CP-sHSP isoforms not expressed in the heat-sensitive variant, that accumulation of the additional CP-sHSP isoforms was genetically linked to thermotolerance, and that the presence of the additional isoforms in the heat-tolerant variant provided greater protection to photosystem II during heat stress. To determine the basis of the differential expression, we isolated the genes encoding the CP-sHSPs from both variants and characterized their structure and expression. Two genes, ApHsp26.2 and ApHsp26.7a, were isolated from the heat-tolerant variant, and three genes, ApHsp26.2m, ApHsp26.8, and ApHsp26.7b, were isolated from the heat-sensitive variant. The sequence of ApHsp26.2m from the heat-sensitive variant was identical to ApHsp26.2, except for a point mutation that generated a premature stop codon. Therefore, the protein product of ApHsp26.2m did not accumulate in the heat-sensitive line. Mass spectrometry analysis confirmed that ApHsp26.2 encoded for the CP-sHSP isoforms unique to the heat-tolerant variant. An identical mutation was detected in one of the three parental lines used to develop the creeping bentgrass variants. This suggests that ApHsp26.2m was inherited from this parent and did not arise from a mutation that occurred during tissue culture. The presence of two isoforms encoded by the same gene might be due to differential processing of the N-terminal amino acids during or after import into the chloroplast. PMID:12970497

  16. Hemoglobin Variants: Biochemical Properties and Clinical Correlates

    PubMed Central

    Thom, Christopher S.; Dickson, Claire F.; Gell, David A.; Weiss, Mitchell J.

    2013-01-01

    Diseases affecting hemoglobin synthesis and function are extremely common worldwide. More than 1000 naturally occurring human hemoglobin variants with single amino acid substitutions throughout the molecule have been discovered, mainly through their clinical and/or laboratory manifestations. These variants alter hemoglobin structure and biochemical properties with physiological effects ranging from insignificant to severe. Studies of these mutations in patients and in the laboratory have produced a wealth of information on hemoglobin biochemistry and biology with significant implications for hematology practice. More generally, landmark studies of hemoglobin performed over the past 60 years have established important paradigms for the disciplines of structural biology, genetics, biochemistry, and medicine. Here we review the major classes of hemoglobin variants, emphasizing general concepts and illustrative examples. PMID:23388674

  17. Novel Human Butyrylcholinesterase Variants: Toward Organophosphonate Detoxication

    PubMed Central

    2015-01-01

    Human butyrylcholinesterase (hBChE) is currently being developed as a detoxication enzyme for stoichiometric binding and/or catalytic hydrolysis of organophosphates. Herein, we describe the use of a molecular evolution method to develop novel hBChE variants with increased resistance to stereochemically defined nerve agent model compounds of soman, sarin, and cyclosarin. Novel hBChE variants (Y332S, D340H, and Y332S/D340H) were identified with an increased resistance to nerve agent model compounds that retained robust intrinsic catalytic efficiency. Molecular dynamics simulations of these variants revealed insights into the mechanism by which these structural changes conferred nerve agent model compound resistance. PMID:24902043

  18. A phonetic explanation of pronunciation variant effects.

    PubMed

    Sumner, Meghan

    2013-07-01

    Effects of word-level phonetic variation on the recognition of words with different pronunciation variants (e.g., center produced with/(out) [t]) are investigated via the semantic- and pseudoword-priming paradigms. A bias favoring clearly articulated words with canonical variants ([nt]) is found. By reducing the bias, words with different variants show robust and equivalent lexical activation. The equivalence of different word forms highlights a snag for frequency-based theories of lexical access: How are words and word productions with vastly different frequencies recognized equally well by listeners? A process-based account is proposed, suggesting that careful speech induces bottom-up processing and casual speech induces top-down processing. PMID:23862902

  19. Rare Variants and Transcriptomics in Alzheimer disease.

    PubMed

    Humphries, Crystal; Kohli, Martin A

    2014-06-01

    Alzheimer disease (AD) is the most common dementia in the elderly, still without effective treatment. Early-onset AD (EOAD) is caused by mutations in the genes APP, PSEN1 and PSEN2. Genome-wide association studies have identified >20 late-onset AD (LOAD) susceptibility genes with common variants of small risk, with the exception of APOE. We review rare susceptibility variants in LOAD with larger effects that have been recently identified in the EOAD gene APP and the newly discovered AD genes TREM2 and PLD3. Human genetic studies now consistently support the amyloid hypothesis of AD for both EOAD and LOAD. Moreover, they identified biological processes that overlap with human transcriptomics studies in AD across different tissues, such as inflammation, cytoskeletal organization, synaptic functions, etc. Transcriptomic profiles of pre-symptomatic AD-associated variant carriers already reflect specific molecular mechanisms reminiscent to those of AD patients. This might provide an avenue for personalized medicine. PMID:25045597

  20. Copy number variants, aneuploidies, and human disease.

    PubMed

    Martin, Christa Lese; Kirkpatrick, Brianne E; Ledbetter, David H

    2015-06-01

    In the perinatal setting, chromosome imbalances cause a range of clinically significant disorders and increase the risk for other particular phenotypes. As technologies have improved to detect increasingly smaller deletions and duplications, collectively referred to as copy number variants (CNVs), clinicians are learning the significant role that these types of genomic variants play in human disease and their high frequency in ? 1% of all pregnancies. This article highlights key aspects of CNV detection and interpretation used during the course of clinical care in the prenatal and neonatal periods. Early diagnosis and accurate interpretation are important for targeted clinical management. PMID:26042902

  1. Tall cell variant of papillary thyroid cancer.

    PubMed

    Cortese, F; Boffo, V; Gargiani, M; Servetti, S; Argirò, G; Casciani, C U

    1998-12-01

    Papillary histologic type is the most common form of thyroid carcinoma amounting to 85% cases. This pathology presents a rather good prognosis, but a few years ago, new subtypes have been described. Some of these variants show a fairly good prognosis i.e follicular, macropapillary, encapsulated while others appear to have a decidedly worse one, columnar cells, diffused sclerosing, or even to be clearly malignant as in the case of the tall cell variant. The authors report a case treated by a combined surgical and radiometabolic therapy and evidence the main characteristics of this rare and underestimated neoplasia. PMID:10089078

  2. Anatomical variants and pathologies of the vermix

    PubMed Central

    Deshmukh, Swati; Verde, Franco; Johnson, Pamela T.; Fishman, Elliot K.

    2015-01-01

    The appendix may demonstrate a perplexing range of normal and abnormal appearances on imaging exams. Familiarity with the anatomy and anatomical variants of the appendix is helpful in identifying the appendix on ultrasound, computed tomography, and magnetic resonance imaging. Knowledge of the variety of pathologies afflicting the appendix and of the spectrum of imaging findings may be particularly useful to the emergency radiologist for accurate diagnosis and appropriate guidance regarding clinical and surgical management. In this pictorial essay, we review appendiceal embryology, anatomical variants such as Amyand hernias, and pathologies from appendicitis to carcinoid, mucinous, and nonmucinous epithelial neoplasms. PMID:24570122

  3. Role of non-coding sequence variants in cancer.

    PubMed

    Khurana, Ekta; Fu, Yao; Chakravarty, Dimple; Demichelis, Francesca; Rubin, Mark A; Gerstein, Mark

    2016-02-01

    Patients with cancer carry somatic sequence variants in their tumour in addition to the germline variants in their inherited genome. Although variants in protein-coding regions have received the most attention, numerous studies have noted the importance of non-coding variants in cancer. Moreover, the overwhelming majority of variants, both somatic and germline, occur in non-coding portions of the genome. We review the current understanding of non-coding variants in cancer, including the great diversity of the mutation types - from single nucleotide variants to large genomic rearrangements - and the wide range of mechanisms by which they affect gene expression to promote tumorigenesis, such as disrupting transcription factor-binding sites or functions of non-coding RNAs. We highlight specific case studies of somatic and germline variants, and discuss how non-coding variants can be interpreted on a large-scale through computational and experimental methods. PMID:26781813

  4. Diversity of black Aspergilli isolated from raisins in Argentina: Polyphasic approach to species identification and development of SCAR markers for Aspergillus ibericus.

    PubMed

    Giaj Merlera, G; Muñoz, S; Coelho, I; Cavaglieri, L R; Torres, A M; Reynoso, M M

    2015-10-01

    Aspergillus section Nigri is a heterogeneous fungal group including some ochratoxin A producer species that usually contaminate raisins. The section contains the Series Carbonaria which includes the toxigenic species Aspergillus carbonarius and nontoxigenic Aspergillus ibericus that are phenotypically undistinguishable. The aim of this study was to examine the diversity of black aspergilli isolated from raisins and to develop a specific genetic marker to distinguish A. ibericus from A. carbonarius. The species most frequently found in raisins in this study were Aspergillus tubingensis (35.4%) and A. carbonarius (32.3%), followed by Aspergillus luchuensis (10.7%), Aspergillus japonicus (7.7%), Aspergillus niger (6.2%), Aspergillus welwitschiae (4.6%) and A. ibericus (3.1%). Based on inter-simple sequence repeat (ISSR) fingerprinting profiles of major Aspergillus section Nigri members, a sequence-characterized amplified region (SCAR) marker was identified. Primers were designed based on the conserved regions of the SCAR marker and were utilized in a PCR for simultaneous identification of A. carbonarius and A. ibericus. The detection level of the SCAR-PCR was found to be 0.01 ng of purified DNA. The present SCAR-PCR is rapid and less cumbersome than conventional identification techniques and could be a supplementary strategy and a reliable tool for high-throughput sample analysis. PMID:26114593

  5. Analysis of aflatoxin regulatory factors in serial transfer-induced non-aflatoxigenic Aspergillus parasiticus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aflatoxins (AFs) are carcinogenic secondary metabolites of Aspergillus parasiticus. In previous studies, non-toxigenic A. parasiticus sec' (for secondary metabolism negative) variants were generated from their toxigenic sec+ (for secondary metabolism positive) parents for genetic and physiological ...

  6. Cutaneous infection due to a rough variant of Mycobacterium marinum.

    PubMed

    Smith, A G; Jiji, R M

    1975-08-01

    Spreading lesions clinically resembling lymphangitic sporotrichosis developed on the right arm and chest of a 60-year-old man with chronic lymphocytic leukemia. Acid-fast bacilli were seen in exudates from lesions and in biopsies, and were cultured from them. The isolant grew initially as a yellowish-orange scotochromogen on Lowenstein-Jensen medium at room temperature and at 35 C., but failed to grow at 37 C. It failed to grow on 7-H-10 medium. On repeated subculturing over a 2-year period it gradually converted to a photochromogen. Histologically, there was ulceration with extensive acute and chronic inflammation with fibrosis. Organisms occurred intracellularly as dense, compact, cigar-like packets resembling lepara bacilli. The appeared to have a predilection for the nucleus. The patient was anergic to PPD S, B, Y and G, and lacked antibodies to BCG phosphoglycolipids. The mycobacteriosis was alleviated by combined INH and ethambutol therapy. The isolant was identified as a rough variant of Mycobacterium marinum. It may have been transmitted by an insect vector. PMID:1098441

  7. Comparison of the pathogenicity in three different Korean canine parvovirus 2 (CPV-2) isolates.

    PubMed

    Moon, H-S; Lee, S-A; Lee, S-G; Choi, R; Jeoung, S-Y; Kim, D; Hyun, C

    2008-09-18

    Canine parvovirus type 2 (CPV-2) is a major pathogen inducing acute hemorrhagic gastroenteritis in dogs. Despite the identification of numerous CPV-2 variants (from CPV-2a to CPV-2c), the pathogenic differences among the CPV-2 variants in dogs have not been evaluated. The aim of this study was to compare the pathogenicity of CPV-2 variants (CPV-2a-I, CPV-2a-V and CPV-2b) isolated mainly from Korea. We evaluated the pathogenicity of three different CPV-2 variants, by performing clinical, hematological, serological and histopathological examinations after experimentally inoculating three types of CPV-2 variants into young puppies. We found that the overall pathogenicity of the CPV-2a variants (CPV-2a-I and 2a-V) was severer compared to the CPV-2b variant. In addition, there was no significant difference in pathogenicity between the two CPV-2a variants. Our findings indicate that there are differences in the pathogenicity of CPV-2 variants in dogs, which may be useful to understand the different pathobiology of the CPV-2 variants. PMID:18400421

  8. Prevalence of Vibrio cholerae O1 El Tor variant in a cholera-endemic zone of Kenya.

    PubMed

    Saidi, Suleiman M; Chowdhury, Nityananda; Awasthi, Sharda P; Asakura, Masahiro; Hinenoya, Atsushi; Iijima, Yoshio; Yamasaki, Shinji

    2014-03-01

    Since 2007, Kenya has experienced an increase in cholera outbreaks characterized by a high fatality rate. In this study, we characterized 81 Vibrio cholerae isolates from diarrhoeal stool samples in Nyanza, a cholera-endemic lake region of Kenya, for virulence properties, clonality and antibiotic susceptibility. Eighty of these isolates were V. cholerae O1 El Tor variants carrying the classical ctxB gene sequence, while one isolate was V. cholerae non-O1/O139. All of the El Tor variants were of clonal origin, as revealed by PFGE, and were susceptible to ampicillin, tetracycline, ciprofloxacin, fosfomycin, kanamycin and norfloxacin. However, the isolates showed resistance to sulfamethoxazole/trimethoprim and streptomycin, and intermediate resistance to nalidixic acid, chloramphenicol and imipenem. The non-O1/O139 isolate carried the cholix toxin II gene (chxA II) and was susceptible to all antimicrobials tested except ampicillin. We propose that an El Tor variant clone caused the Nyanza cholera outbreak of 2007-2008. PMID:24396087

  9. Variant Spellings in Modern American Dictionaries.

    ERIC Educational Resources Information Center

    Emery, Donald W.

    A record of how present-day desk dictionaries are recognizing the existence of variant or secondary spellings for many common English words, this reference list can be used by teachers of English and authors of spelling lists. Originally published in 1958, this revised edition uses two dictionaries not in existence then and the revised editions of…

  10. Cellobiohydrolase I gene and improved variants

    DOEpatents

    Adney, William S. (Golden, CO); Decker, Stephen R. (Berthoud, CO); Mc Carter, Suzanne (San Carlos, CA); Baker, John O. (Golden, CO); Nieves, Raphael (Lakewood, CO); Himmel, Michael E. (Littleton, CO); Vinzant, Todd B. (Golden, CO)

    2008-05-20

    The disclosure provides a method for preparing an active exoglucanase in a heterologous host of eukaryotic origin. The method includes mutagenesis to reduce glycosylation of the exoglucanase when expressed in a heterologous host. It is further disclosed a method to produce variant cellobiohydrolase that is stable at high temperature through mutagenesis.

  11. Truncated variants of apolipoprotein B cause hypobetalipoproteinaemia.

    PubMed Central

    Collins, D R; Knott, T J; Pease, R J; Powell, L M; Wallis, S C; Robertson, S; Pullinger, C R; Milne, R W; Marcel, Y L; Humphries, S E

    1988-01-01

    Familial hypobetalipoproteinaemia is a rare autosomal dominant disorder in which levels of apo-B-containing plasma lipoproteins are approximately half-normal in heterozygotes and virtually absent in homozygotes. Here we describe mutations of the apo-B gene that cause two different truncated variants of apo-B in unrelated individuals with hypobetalipoproteinaemia. One variant, apo-B(His1795----Met-Trp-Leu-Val-Thr-Term) is predicted to be 1799 amino acids long and arises from deletion of a single nucleotide (G) from leucine codon 1794. This protein was found at low levels in very low density and low density lipoprotein fractions in the blood. The second, shorter variant, apo-B(Arg1306----Term), is caused by mutation of a CpG dinucleotide in arginine codon 1306 converting it to a stop codon and predicting a protein of 1305 residues. The product of this allele could not be detected in the circulation. The differences in size and behaviour of these two variants compared to apo-B100 or apo-B48 point to domains that may be important for the assembly, secretion or stability of apo-B-containing lipoproteins. Images PMID:2843815

  12. Regional Phonological Variants in Louisiana Speech.

    ERIC Educational Resources Information Center

    Rubrecht, August Weston

    Based on tape recorded conversations of 28 informants in 18 Louisiana communities, this study investigated regional phonological variants in Louisiana speech. On the basis of settlement history and previous dialect studies, four regions are defined: northern Louisiana, the Florida Parishes, French Louisiana, and New Orleans. The informants are all…

  13. Progress in methods for rare variant association.

    PubMed

    Santorico, Stephanie A; Hendricks, Audrey E

    2016-01-01

    Empirical studies and evolutionary theory support a role for rare variants in the etiology of complex traits. Given this motivation and increasing affordability of whole-exome and whole-genome sequencing, methods for rare variant association have been an active area of research for the past decade. Here, we provide a survey of the current literature and developments from the Genetics Analysis Workshop 19 (GAW19) Collapsing Rare Variants working group. In particular, we present the generalized linear regression framework and associated score statistic for the 2 major types of methods: burden and variance components methods. We further show that by simply modifying weights within these frameworks we arrive at many of the popular existing methods, for example, the cohort allelic sums test and sequence kernel association test. Meta-analysis techniques are also described. Next, we describe the 6 contributions from the GAW19 Collapsing Rare Variants working group. These included development of new methods, such as a retrospective likelihood for family data, a method using genomic structure to compare cases and controls, a haplotype-based meta-analysis, and a permutation-based method for combining different statistical tests. In addition, one contribution compared a mega-analysis of family-based and population-based data to meta-analysis. Finally, the power of existing family-based methods for binary traits was compared. We conclude with suggestions for open research questions. PMID:26866487

  14. New genetic variants associated with prostate cancer

    Cancer.gov

    Researchers have newly identified 23 common genetic variants -- one-letter changes in DNA known as single-nucleotide polymorphisms or SNPs -- that are associated with risk of prostate cancer. These results come from an analysis of more than 10 million SNP

  15. Regional Phonological Variants in Louisiana Speech.

    ERIC Educational Resources Information Center

    Rubrecht, August Weston

    Based on tape recorded conversations of 28 informants in 18 Louisiana communities, this study investigated regional phonological variants in Louisiana speech. On the basis of settlement history and previous dialect studies, four regions are defined: northern Louisiana, the Florida Parishes, French Louisiana, and New Orleans. The informants are all…

  16. Atypical phenotypes associated with pathogenic CHD7 variants and a proposal for broadening CHARGE syndrome clinical diagnostic criteria.

    PubMed

    Hale, Caitlin L; Niederriter, Adrienne N; Green, Glenn E; Martin, Donna M

    2016-02-01

    CHARGE syndrome (Coloboma of the eye, Heart defects, Atresia of the choanae, Retardation of growth and/or development, Genital and/or urinary anomalies, and Ear malformations, including deafness and vestibular disorders) is a genetic condition characterized by a specific and recognizable pattern of features. Heterozygous pathogenic variants in the chromodomain helicase DNA-binding protein 7 (CHD7) are the major cause of CHARGE syndrome, and have been identified in 70-90% of individuals fulfilling clinical diagnostic criteria. Since 2004, when CHD7 was discovered as the causative gene for CHARGE syndrome, the phenotypic spectrum associated with pathogenic CHD7 variants has expanded. Predicted pathogenic CHD7 variants have been identified in individuals with isolated features of CHARGE including autism and hypogonadotropic hypogonadism. Here, we present genotype and phenotype data from a cohort of 28 patients who were considered for a diagnosis of CHARGE syndrome, including one patient with atypical presentations and a pathogenic CHD7 variant. We also summarize published literature on pathogenic CHD7 variant positive individuals who have atypical clinical presentations. Lastly, we propose a revision to current clinical diagnostic criteria, including broadening of the major features associated with CHARGE syndrome and addition of pathogenic CHD7 variant status as a major criterion. © 2015 Wiley Periodicals, Inc. PMID:26590800

  17. Dynamic Bayesian Testing of Sets of Variants in Complex Diseases

    PubMed Central

    Zhang, Yu; Ghosh, Soumitra; Hakonarson, Hakon

    2014-01-01

    Rare genetic variants have recently been studied for genome-wide associations with human complex diseases. Existing rare variant methods are based on the hypothesis-testing framework that predefined variant sets need to be tested separately. The power of those methods is contingent upon accurate selection of variants for testing, and frequently, common variants are left out for separate testing. In this article, we present a novel Bayesian method for simultaneous testing of all genome-wide variants across the whole frequency range. The method allows for much more flexible grouping of variants and dynamically combines them for joint testing. The method accounts for correlation among variant sets, such that only direct associations with the disease are reported, whereas indirect associations due to linkage disequilibrium are not. Consequently, the method can obtain much improved power and flexibility and simultaneously pinpoint multiple disease variants with high resolution. Additional covariates of categorical, discrete, and continuous values can also be added. We compared our method with seven existing categories of approaches for rare variant mapping. We demonstrate that our method achieves similar power to the best methods available to date when testing very rare variants in small SNP sets. When moderately rare or common variants are included, or when testing a large collection of variants, however, our method significantly outperforms all existing methods evaluated in this study. We further demonstrate the power and the usage of our method in a whole-genome resequencing study of type 1 diabetes. PMID:25217050

  18. Examination of candidate exonic variants for association to Alzheimer disease in the Amish.

    PubMed

    D'Aoust, Laura N; Cummings, Anna C; Laux, Renee; Fuzzell, Denise; Caywood, Laura; Reinhart-Mercer, Lori; Scott, William K; Pericak-Vance, Margaret A; Haines, Jonathan L

    2015-01-01

    Alzheimer disease (AD) is the most common cause of dementia. As with many complex diseases, the identified variants do not explain the total expected genetic risk that is based on heritability estimates for AD. Isolated founder populations, such as the Amish, are advantageous for genetic studies as they overcome heterogeneity limitations associated with complex population studies. We determined that Amish AD cases harbored a significantly higher burden of the known risk alleles compared to Amish cognitively normal controls, but a significantly lower burden when compared to cases from a dataset of unrelated individuals. Whole-exome sequencing of a selected subset of the overall study population was used as a screening tool to identify variants located in the regions of the genome that are most likely to contribute risk. By then genotyping the top candidate variants from the known AD genes and from linkage regions implicated previous studies in the full dataset, new associations could be confirmed. The most significant result (p = 0.0012) was for rs73938538, a synonymous variant in LAMA1 within the previously identified linkage peak on chromosome 18. However, this association is specific to the Amish and did not generalize when tested in a dataset of unrelated individuals. These results suggest that additional risk variation in the Amish remains to be identified and likely resides outside of the classical protein coding gene regions. PMID:25668194

  19. Examination of Candidate Exonic Variants for Association to Alzheimer Disease in the Amish

    PubMed Central

    D’Aoust, Laura N.; Cummings, Anna C.; Laux, Renee; Fuzzell, Denise; Caywood, Laura; Reinhart-Mercer, Lori; Scott, William K.; Pericak-Vance, Margaret A.; Haines, Jonathan L.

    2015-01-01

    Alzheimer disease (AD) is the most common cause of dementia. As with many complex diseases, the identified variants do not explain the total expected genetic risk that is based on heritability estimates for AD. Isolated founder populations, such as the Amish, are advantageous for genetic studies as they overcome heterogeneity limitations associated with complex population studies. We determined that Amish AD cases harbored a significantly higher burden of the known risk alleles compared to Amish cognitively normal controls, but a significantly lower burden when compared to cases from a dataset of unrelated individuals. Whole-exome sequencing of a selected subset of the overall study population was used as a screening tool to identify variants located in the regions of the genome that are most likely to contribute risk. By then genotyping the top candidate variants from the known AD genes and from linkage regions implicated previous studies in the full dataset, new associations could be confirmed. The most significant result (p = 0.0012) was for rs73938538, a synonymous variant in LAMA1 within the previously identified linkage peak on chromosome 18. However, this association is specific to the Amish and did not generalize when tested in a dataset of unrelated individuals. These results suggest that additional risk variation in the Amish remains to be identified and likely resides outside of the classical protein coding gene regions. PMID:25668194

  20. Variant Creutzfeldt-Jakob Disease (vCJD)

    MedlinePLUS

    ... The CDC Cancel Submit Search The CDC Variant Creutzfeldt-Jakob Disease (vCJD) Note: Javascript is disabled or ... gov . Recommend on Facebook Tweet Share Compartir Variant Creutzfeldt-Jakob disease (vCJD) is a prion disease that ...

  1. Distribution of Bartonella henselae Variants in Patients, Reservoir Hosts and Vectors in Spain

    PubMed Central

    Gil, Horacio; Escudero, Raquel; Pons, Inmaculada; Rodríguez-Vargas, Manuela; García-Esteban, Coral; Rodríguez-Moreno, Isabel; García-Amil, Cristina; Lobo, Bruno; Valcárcel, Félix; Pérez, Azucena; Jiménez, Santos; Jado, Isabel; Juste, Ramón; Segura, Ferrán; Anda, Pedro

    2013-01-01

    We have studied the diversity of B. henselae circulating in patients, reservoir hosts and vectors in Spain. In total, we have fully characterized 53 clinical samples from 46 patients, as well as 78 B. henselae isolates obtained from 35 cats from La Rioja and Catalonia (northeastern Spain), four positive cat blood samples from which no isolates were obtained, and three positive fleas by Multiple Locus Sequence Typing and Multiple Locus Variable Number Tandem Repeats Analysis. This study represents the largest series of human cases characterized with these methods, with 10 different sequence types and 41 MLVA profiles. Two of the sequence types and 35 of the profiles were not described previously. Most of the B. henselae variants belonged to ST5. Also, we have identified a common profile (72) which is well distributed in Spain and was found to persist over time. Indeed, this profile seems to be the origin from which most of the variants identified in this study have been generated. In addition, ST5, ST6 and ST9 were found associated with felines, whereas ST1, ST5 and ST8 were the most frequent sequence types found infecting humans. Interestingly, some of the feline associated variants never found on patients were located in a separate clade, which could represent a group of strains less pathogenic for humans. PMID:23874563

  2. Emergence of Influenza A Virus Variants after Prolonged Shedding from Pheasants▿

    PubMed Central

    Humberd, Jennifer; Boyd, Kelli; Webster, Robert G.

    2007-01-01

    We previously demonstrated the susceptibility of pheasants to infection with influenza A viruses of 15 hemagglutinin (HA) subtypes: 13/23 viruses tested were isolated for ≥14 days, all in the presence of serum-neutralizing antibodies; one virus (H10) was shed for 45 days postinfection. Here we confirmed that 20% of pheasants shed low-pathogenic influenza viruses for prolonged periods. We aimed to determine why the antibody response did not clear the virus in the usual 3 to 10 days, because pheasants serve as a long-term source of influenza viruses in poultry markets. We found evidence of virus replication and histological changes in the large intestine, bursa of Fabricius, and cecal tonsil. The virus isolated 41 days postinfection was antigenically distinct from the parental H10 virus, with corresponding changes in the HA and neuraminidase. Ten amino acid differences were found between the parental H10 and the pheasant H10 virus; four were in potential antigenic sites of the HA molecule. Prolonged shedding of virus by pheasants results from a complex interplay between the diversity of virus variants and the host response. It is often argued that vaccination pressure is a mechanism that contributes to the generation of antigenic-drift variants in poultry. This study provided evidence that drift variants can occur naturally in pheasants after prolonged shedding of virus, thus strengthening our argument for the removal of pheasants from live-bird retail markets. PMID:17267493

  3. A condition assessment method for time-variant structures with incomplete measurements

    NASA Astrophysics Data System (ADS)

    Ding, Y.; Zhao, B. Y.; Wu, B.; Xu, G. S.; Lin, Q.; Jiang, H. B.; Miao, Q. S.

    2015-06-01

    The structural damage incurred in a seismic event is always time-variant. In this paper, a new time-variant structural system identification method is proposed based on a two-stage strategy and incomplete structural acceleration responses. In the first stage, an external excitation identification method is developed for a time-variant structural system. The unknown structural response could be re-constructed with the average acceleration discrete algorithm in this stage. In the second stage, structural parameter is identified and updated with a reduced extended Kalman filter which can improve the computational effort. The re-constructed structural response and identified external excitation are used in the second stage for the damage identification and model updating. The proposed method is validated numerically with the simulation of a fifteen-storey shear frame structure subject to earthquake excitation. A model of a fourteen-storey concrete shear wall building was also studied experimentally with shaking table tests to further validate the proposed method. This shear wall building has a two-storey steel frame on top with base isolation. Both the stiffness of the model and the interface force in the isolator at the bottom of the steel frame during the seismic excitation were estimated with the proposed method. Results from both numerical simulations and laboratory tests indicate that the proposed method can be used to identify structural parameters and external excitations effectively based on a few number of polluted structural acceleration measurements.

  4. Distribution of Bartonella henselae variants in patients, reservoir hosts and vectors in Spain.

    PubMed

    Gil, Horacio; Escudero, Raquel; Pons, Inmaculada; Rodríguez-Vargas, Manuela; García-Esteban, Coral; Rodríguez-Moreno, Isabel; García-Amil, Cristina; Lobo, Bruno; Valcárcel, Félix; Pérez, Azucena; Jiménez, Santos; Jado, Isabel; Juste, Ramón; Segura, Ferrán; Anda, Pedro

    2013-01-01

    We have studied the diversity of B. henselae circulating in patients, reservoir hosts and vectors in Spain. In total, we have fully characterized 53 clinical samples from 46 patients, as well as 78 B. henselae isolates obtained from 35 cats from La Rioja and Catalonia (northeastern Spain), four positive cat blood samples from which no isolates were obtained, and three positive fleas by Multiple Locus Sequence Typing and Multiple Locus Variable Number Tandem Repeats Analysis. This study represents the largest series of human cases characterized with these methods, with 10 different sequence types and 41 MLVA profiles. Two of the sequence types and 35 of the profiles were not described previously. Most of the B. henselae variants belonged to ST5. Also, we have identified a common profile (72) which is well distributed in Spain and was found to persist over time. Indeed, this profile seems to be the origin from which most of the variants identified in this study have been generated. In addition, ST5, ST6 and ST9 were found associated with felines, whereas ST1, ST5 and ST8 were the most frequent sequence types found infecting humans. Interestingly, some of the feline associated variants never found on patients were located in a separate clade, which could represent a group of strains less pathogenic for humans. PMID:23874563

  5. Human Papillomavirus 16 Non-European Variants Are Preferentially Associated with High-Grade Cervical Lesions

    PubMed Central

    Freitas, Luciana Bueno; Chen, Zigui; Muqui, Elaine Freire; Boldrini, Neide Aparecida Tosato; Miranda, Angélica Espinosa; Spano, Liliana Cruz; Burk, Robert D.

    2014-01-01

    HPV16 accounts for 50–70% of cervical cancer cases worldwide. Characterization of HPV16 variants previously indicated that they differ in risks for viral persistence, progression to cervical precancer and malignant cancer. The aim of this study was to examine the association of severity of disease with HPV16 variants identified in specimens (n?=?281) obtained from a Cervical Pathology and Colposcopy outpatient clinic in the University Hospital of Espírito Santo State, Southeastern Brazil, from April 2010 to November 2011. All cytologic and histologic diagnoses were determined prior to definitive treatment. The DNA was isolated using QIAamp DNA Mini Kit and HPV was detected by amplification with PGMY09/11 primers and positive samples were genotyped by RFLP analyses and reverse line blot. The genomes of the HPV16 positive samples were sequenced, from which variant lineages were determined. Chi2 statistics was performed to test the association of HPV16 variants between case and control groups. The prevalence of HR-HPV types in variants. Classification of disease into CIN3+ vs. variants with an increased risk of CIN3+ is consistent with an HPV16 genetically determined enhanced oncogenicity. The prevalence of genetic variants of HPV16 is distributed across different geographical areas and with recent population admixture, only empiric data will provide information on the highest risk HPV16 variants within a given population. PMID:24983739

  6. Multilocus Phylogenetic Analyses, Pullulan Production and Xylanase Activity of Tropical Isolates of Aureobasidium pullulans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aureobasidium pullulans is the source of the commercial polysaccharide, pullulan, and the enzyme, xylanase (EC 3.2.1.8). Isolates are typically off-white to black on solid media, while some tropical isolates have been described as "color variants" with bright pigments of red, yellow, or purple. In...

  7. Processing of No-Release Variants in Connected Speech

    ERIC Educational Resources Information Center

    LoCasto, Paul C.; Connine, Cynthia M.

    2011-01-01

    The cross modal repetition priming paradigm was used to investigate how potential lexically ambiguous no-release variants are processed. In particular we focus on segmental regularities that affect the variant's frequency of occurrence (voicing of the critical segment) and phonological context in which the variant occurs (status of the following…

  8. Identifying Causal Variants at Loci with Multiple Signals of Association

    PubMed Central

    Hormozdiari, Farhad; Kostem, Emrah; Kang, Eun Yong; Pasaniuc, Bogdan; Eskin, Eleazar

    2014-01-01

    Although genome-wide association studies have successfully identified thousands of risk loci for complex traits, only a handful of the biologically causal variants, responsible for association at these loci, have been successfully identified. Current statistical methods for identifying causal variants at risk loci either use the strength of the association signal in an iterative conditioning framework or estimate probabilities for variants to be causal. A main drawback of existing methods is that they rely on the simplifying assumption of a single causal variant at each risk locus, which is typically invalid at many risk loci. In this work, we propose a new statistical framework that allows for the possibility of an arbitrary number of causal variants when estimating the posterior probability of a variant being causal. A direct benefit of our approach is that we predict a set of variants for each locus that under reasonable assumptions will contain all of the true causal variants with a high confidence level (e.g., 95%) even when the locus contains multiple causal variants. We use simulations to show that our approach provides 20–50% improvement in our ability to identify the causal variants compared to the existing methods at loci harboring multiple causal variants. We validate our approach using empirical data from an expression QTL study of CHI3L2 to identify new causal variants that affect gene expression at this locus. CAVIAR is publicly available online at http://genetics.cs.ucla.edu/caviar/. PMID:25104515

  9. Variant Influenza Associated with Live Animal Markets, Minnesota.

    PubMed

    Choi, M J; Morin, C A; Scheftel, J; Vetter, S M; Smith, K; Lynfield, R

    2015-08-01

    Variant influenza viruses are swine-origin influenza A viruses that cause illness in humans. Surveillance for variant influenza A viruses, including characterization of exposure settings, is important because of the potential emergence of novel influenza viruses with pandemic potential. In Minnesota, we have documented variant influenza A virus infections associated with swine exposure at live animal markets. PMID:24931441

  10. The association between genetic variants in hMLH1 and hMSH2 and the development of sporadic colorectal cancer in the Danish population

    PubMed Central

    Christensen, Lise Lotte; Madsen, Bo E; Wikman, Friedrik P; Wiuf, Carsten; Koed, Karen; Tjønneland, Anne; Olsen, Anja; Syvänen, Ann-Christine; Andersen, Claus L; Ørntoft, Torben F

    2008-01-01

    Background Mutations in the mismatch repair genes hMLH1 and hMSH2 predispose to hereditary non-polyposis colorectal cancer (HNPCC). Genetic screening of more than 350 Danish patients with colorectal cancer (CRC) has led to the identification of several new genetic variants (e.g. missense, silent and non-coding) in hMLH1 and hMSH2. The aim of the present study was to investigate the frequency of these variants in hMLH1 and hMSH2 in Danish patients with sporadic colorectal cancer and in the healthy background population. The purpose was to reveal if any of the common variants lead to increased susceptibility to colorectal cancer. Methods Associations between genetic variants in hMLH1 and hMSH2 and sporadic colorectal cancer were evaluated using a case-cohort design. The genotyping was performed on DNA isolated from blood from the 380 cases with sporadic colorectal cancer and a sub-cohort of 770 individuals. The DNA samples were analyzed using Single Base Extension (SBE) Tag-arrays. A Bonferroni corrected Fisher exact test was used to test for association between the genotypes of each variant and colorectal cancer. Linkage disequilibrium (LD) was investigated using HaploView (v3.31). Results Heterozygous and homozygous changes were detected in 13 of 35 analyzed variants. Two variants showed a borderline association with colorectal cancer, whereas the remaining variants demonstrated no association. Furthermore, the genomic regions covering hMLH1 and hMSH2 displayed high linkage disequilibrium in the Danish population. Twenty-two variants were neither detected in the cases with sporadic colorectal cancer nor in the sub-cohort. Some of these rare variants have been classified either as pathogenic mutations or as neutral variants in other populations and some are unclassified Danish variants. Conclusion None of the variants in hMLH1 and hMSH2 analyzed in the present study were highly associated with colorectal cancer in the Danish population. High linkage disequilibrium in the genomic regions covering hMLH1 and hMSH2, indicate that common genetic variants in the two genes in general are not involved in the development of sporadic colorectal cancer. Nevertheless, some of the rare unclassified variants in hMLH1 and hMSH2 might be involved in the development of colorectal cancer in the families where they were originally identified. PMID:18547406

  11. Two Naturally Occurring Nuclear Polyhedrosis Virus Variants of Neodiprion sertifer Geoffr. (Hymenoptera; Diprionidae)

    PubMed Central

    Brown, David A.

    1982-01-01

    Two isolates of Neodiprion sertifer (Geoffr.) nuclear polyhedrosis virus from Britain and North America were compared using three biochemical techniques. Alkaline protease assays of polyhedra revealed the presence of endogenous enzyme activity in the British isolate but not in the North American isolate. Sodium dodecyl sulfate polyacrylamide gel electrophoresis of virus particle structural polypeptides revealed only minor differences, with the exception that the North American virus was contaminated with polyhedral protein. The restriction endonucleases SalI, HindIII, and HpaII were used as a definitive method of distinguishing the two variants, with all endonucleases achieving this to a greater or lesser extent. The possible significance of all of these observations is discussed in terms of their possible influence on the registration and field application of this virus. Images PMID:16345930

  12. Superluminescent variants of marine luciferases for bioassays.

    PubMed

    Kim, Sung Bae; Suzuki, Hideyuki; Sato, Moritoshi; Tao, Hiroaki

    2011-11-15

    In this study, a rational synthesis of superluminescent variants from marine luciferases with prolonged bioluminescence has been demonstrated. A putative active site of a model marine luciferase, Gaussia princeps Luciferase (GLuc), was assigned and modified by a site-directed mutagenesis. The potent variants were found to generate up to 10 times stronger bioluminescence, emitting red shifts of up to 33 nm with natural coelenterazine than native GLuc, rendering an efficient optical signature in bioassays. The advantageous properties were demonstrated with mammalian two-hybrid assays, single-chain probes, and metastases of murine B16 melanoma in BALB/c nude mice. The unique ideas for engineering GLuc are proved to be valid even for other marine luciferases. PMID:21951281

  13. Nuclear Receptor Variants in Liver Disease

    PubMed Central

    Müllenbach, Roman; Weber, Susanne N.; Lammert, Frank

    2012-01-01

    This review aims to provide a snapshot of the actual state of knowledge on genetic variants of nuclear receptors (NR) involved in regulating important aspects of liver metabolism. It recapitulates recent evidence for the application of NR in genetic diagnosis of monogenic (“Mendelian”) liver disease and their use in clinical diagnosis. Genetic analysis of multifactorial liver diseases such as viral hepatitis or fatty liver disease identifies key players in disease predisposition and progression. Evidence from these analyses points towards a role of NR polymorphisms in common diseases, linking regulatory networks to complex and variable phenotypes. The new insights into NR variants also offer perspectives and cautionary advice for their use as handles towards diagnosis and treatment. PMID:22523693

  14. The Saccharomyces Genome Database Variant Viewer

    PubMed Central

    Sheppard, Travis K.; Hitz, Benjamin C.; Engel, Stacia R.; Song, Giltae; Balakrishnan, Rama; Binkley, Gail; Costanzo, Maria C.; Dalusag, Kyla S.; Demeter, Janos; Hellerstedt, Sage T.; Karra, Kalpana; Nash, Robert S.; Paskov, Kelley M.; Skrzypek, Marek S.; Weng, Shuai; Wong, Edith D.; Cherry, J. Michael

    2016-01-01

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer. PMID:26578556

  15. The Saccharomyces Genome Database Variant Viewer.

    PubMed

    Sheppard, Travis K; Hitz, Benjamin C; Engel, Stacia R; Song, Giltae; Balakrishnan, Rama; Binkley, Gail; Costanzo, Maria C; Dalusag, Kyla S; Demeter, Janos; Hellerstedt, Sage T; Karra, Kalpana; Nash, Robert S; Paskov, Kelley M; Skrzypek, Marek S; Weng, Shuai; Wong, Edith D; Cherry, J Michael

    2016-01-01

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer. PMID:26578556

  16. Wham: Identifying Structural Variants of Biological Consequence.

    PubMed

    Kronenberg, Zev N; Osborne, Edward J; Cone, Kelsey R; Kennedy, Brett J; Domyan, Eric T; Shapiro, Michael D; Elde, Nels C; Yandell, Mark

    2015-12-01

    Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools-Lumpy, Delly and SoftSearch-and demonstrate Wham's ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/. PMID:26625158

  17. Wham: Identifying Structural Variants of Biological Consequence

    PubMed Central

    Kronenberg, Zev N.; Osborne, Edward J.; Cone, Kelsey R.; Kennedy, Brett J.; Domyan, Eric T.; Shapiro, Michael D.; Elde, Nels C.; Yandell, Mark

    2015-01-01

    Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools–Lumpy, Delly and SoftSearch–and demonstrate Wham’s ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/. PMID:26625158

  18. Isolation of Clostridium difficile from faecal specimens--a comparison of chromID C. difficile agar and cycloserine-cefoxitin-fructose agar.

    PubMed

    Carson, Kerry C; Boseiwaqa, Lusiana V; Thean, Sara K; Foster, Niki F; Riley, Thomas V

    2013-09-01

    The culture of toxigenic Clostridium difficile from stool specimens is still seen as the gold standard for the laboratory diagnosis of C. difficile infection (CDI). bioMérieux have released ChromID Cdiff chromogenic agar (CDIF) for the isolation and identification of C. difficile in 24 h. In this study, we compared CDIF to pre-reduced cycloserine-cefoxitin-fructose agar with sodium taurocholate (TCCFA) in the examination of glutamate dehydrogenase-positive faecal specimens that were either GeneOhm positive or negative, using direct culture or culture following alcohol shock. Direct culture on CDIF had a sensitivity of 100 % and recovery of 94 % while for TCCFA these were 87 % and 82 %, respectively. For GeneOhm-positive alcohol-shocked faecal samples, sensitivity and recovery on CDIF was similar to direct culture while on TCCFA they were about 10 % higher. For direct culture, there was a significant difference between growth on CDIF at 24 h and TCCFA at 48 h (P = 0.001) and between the two media at 48 h (P<0.001). A total of 142 strains of C. difficile were recovered in pure culture from all GeneOhm-positive samples used in this study and 11 (7.7 %) of these were A(-)B(-)CDT(-) and may represent mixed infections of toxigenic and non-toxigenic C. difficile. The most dominant ribotype was UK 014 (14.7 %) followed by 002 (11.9 %) and 020 (11.9 %), and 36 % of toxigenic isolates, including an A(-)B(+)CDT(-) strain, could not be assigned a UK ribotype. CDIF outperformed pre-reduced TCCFA by negating the need for alcohol shock treatment and by giving a time saving of 24 h in the isolation of C. difficile. CDIF plates were also more selective than TCCFA and C. difficile colonies were easy to identify and subculture prior to strain typing. PMID:23579394

  19. Uterine artery emerging variants - angiographic aspects

    PubMed Central

    ALBULESCU, DANA; CONSTANTIN, C.; CONSTANTIN, CONSTANTIN

    2014-01-01

    Uterine artery embolization as a therapeutic method in fibromyoma requires a good knowledge of the origin of the uterine artery to the success of this procedure involving selective catheterization. This study presents a classification of anatomical variants of uterine artery as a retrospective review of consecutive arteriogram, complete with various aspects of the origin of the uterine artery in cadaver dissection, in the Department of Anatomy. PMID:25729609

  20. MRI anatomical variants of mammillary bodies.

    PubMed

    Tagliamonte, Micaela; Sestieri, Carlo; Romani, Gian Luca; Gallucci, Massimo; Caulo, Massimo

    2015-01-01

    The mammillary bodies (MBs) are classically defined as a pair of small round structures located on the undersurface of the diencephalon. The systematic observation of MR brain images of patients with neurological diseases, but also of healthy subjects enrolled in research protocols, reveals, however, a greater anatomical variability. The aim of the present study was to define the spectrum of such variability using spatial normalized 3D TFE T1-weighted MR images in a group of 151 healthy right-handed young subjects (78 females, age range 16-39 years). The MBs were identified on reformatted coronal and axial images and classified according to morphological, positional and numerical criteria. On the basis of coronal images, MBs were first divided into symmetrical (86.1 %) and asymmetrical (13.9 %), depending on their respective height. Symmetrical MBs were further subdivided into three variants [type A (2.7 %), B (76.2 %), C (7.3 %)] according to the depth of the intermammillary sulcus. Two morphological variants were defined on axial images, depending on whether the MBs were circular (63.6 %) or elliptic (36.4 %). This latter group was further divided in two subgroups, depending on whether the MBs were parallel (21.9 %) or convergent (14.6 %). Finally, two subjects (1.3 %) presented a supernumeral MB. The transverse size of the third ventricle was greater in the type A compared to the type B and C groups. Gender did not significantly affect the frequency of MBs variants, except for the three symmetrical subgroups in which the variants A and C were more frequent in males than in females. These findings suggest the presence of an anatomical variability of the MBs, in contrast to their classical definition. Therefore, atypical presentation of MBs can be the expression of this variability rather than a marker of neurological disorders (i.e. cerebral malformation, mesial temporal sclerosis, Wernicke-Korsakoff syndrome). PMID:24072163

  1. Variant anatomy of internal jugular vein branching

    PubMed Central

    Deepak, Chris A.; Sarvadnya, Jagadish J.; Sabitha, K. S.

    2015-01-01

    The knowledge of both normal and abnormal anatomy of the veins of the neck is important for clinicians performing catheterization and surgeons operating in the region of the neck. The presence of such anomalous communications may also be important for radiologists performing angiographic and sonographic studies. This study presents three cases of variant anatomy in posterior branching and abnormal branching of internal jugular vein found during our routine neck dissection.

  2. Time Variant Floating Mean Counting Algorithm

    Energy Science and Technology Software Center (ESTSC)

    1999-06-03

    This software was written to test a time variant floating mean counting algorithm. The algorithm was developed by Westinghouse Savannah River Company and a provisional patent has been filed on the algorithm. The test software was developed to work with the Val Tech model IVB prototype version II count rate meter hardware. The test software was used to verify the algorithm developed by WSRC could be correctly implemented with the vendor''s hardware.

  3. Aggressive Angiomyolipomas: the Clandestine Epithelioid Variant

    PubMed Central

    Maré, Anton; Wickramasinghe, Shehan; Ilie, Victor; Mulcahy, Maurice

    2016-01-01

    Epithelioid angiomyolipoma is a rare mesenchymal derived neoplasm of the kidney. Thought to be a variant of classical angiomyolipoma, a benign tumour, its malignant potential has been highlighted by case reports of loco-regional and distant metastasis. Given the potentially adverse clinical course associated with epithelioid angiomyolipoma compared to classical angiomyolipoma, the distinction and comprehensive histological characterisation of this rare entity is essential. PMID:26989374

  4. Clock gene variants differentiate mood disorders.

    PubMed

    Dmitrzak-Weglarz, Monika Paulina; Pawlak, Joanna Maria; Maciukiewicz, Malgorzata; Moczko, Jerzy; Wilkosc, Monika; Leszczynska-Rodziewicz, Anna; Zaremba, Dorota; Hauser, Joanna

    2015-01-01

    Genetic variations in clock-related genes were hypothesized to be involved to in the susceptibility of mood disorders MD (both unipolar (UPD) and bipolar (BPD) disorders). In our work we investigated role of gene variants form four core period proteins: CLOCK, ARNTL, TIM and PER3. The total sample comprised from 744 mood disorders inpatients (UPD = 229, BPD = 515) and 635 healthy voluntary controls. The 42 SNPs from four genes of interest were genotyped. We used single polymorphisms, haplotypes, SNPs interactions and prediction analysis using classical statistical and machine learning methods. We observed association between two polymorphisms of CLOCK (rs1801260 and rs11932595) with BPDII and two polymorphisms of TIM (rs2291739, rs11171856) with UPD. We also detected ARNTL haplotype variant (rs1160996C/rs11022779G/rs1122780T) to be associated with increased risk of MD, BPD (both types). We established significant epistatic interaction between PER3 (rs2172563) and ARNTL (rs4146388 and rs7107287) in case of BPD. Additionally relation between PER3 (rs2172563) and CLOCK (rs1268271 and rs3805148) appeared in case of UPD. Classification and Regression Trees (C and RT) showed significant predictive value for 10 polymorphisms in all analyzed genes. However we failed to obtain model with sufficient predictive power. During analyses of sleep disturbances sample, we found carriers of homozygote variants (ARNTL: rs11022778 TT, rs1562438 TT, rs1982350 AA and PER3: rs836755 CC) showing more frequent falling asleep difficulties when compare to other genotypes carriers. Our study suggested a putative role of the CLOCK, TIM, ARNTL and PER3 and polymorphisms in MD susceptibility. In our analyses we showed association of specific gene variants with particular types of MD. We also confirmed necessity of performing separate analyzes for BPD and UPD patients. Comprehensive statistical approach is required even with individual symptoms analyses. PMID:25258123

  5. Random Plant Viral Variants Attain Temporal Advantages During Systemic Infections and in Turn Resist other Variants of the Same Virus

    PubMed Central

    Zhang, Xiao-Feng; Guo, Jiangbo; Zhang, Xiuchun; Meulia, Tea; Paul, Pierce; Madden, Laurence V.; Li, Dawei; Qu, Feng

    2015-01-01

    Infection of plants with viruses containing multiple variants frequently leads to dominance by a few random variants in the systemically infected leaves (SLs), for which a plausible explanation is lacking. We show here that SL dominance by a given viral variant is adequately explained by its fortuitous lead in systemic spread, coupled with its resistance to superinfection by other variants. We analyzed the fate of a multi-variant turnip crinkle virus (TCV) population in Arabidopsis and N. benthamiana plants. Both wild-type and RNA silencing-defective plants displayed a similar pattern of random dominance by a few variant genotypes, thus discounting a prominent role for RNA silencing. When introduced to plants sequentially as two subpopulations, a twelve-hour head-start was sufficient for the first set to dominate. Finally, SLs of TCV-infected plants became highly resistant to secondary invasions of another TCV variant. We propose that random distribution of variant foci on inoculated leaves allows different variants to lead systemic movement in different plants. The leading variants then colonize large areas of SLs, and resist the superinfection of lagging variants in the same areas. In conclusion, superinfection resistance is the primary driver of random enrichment of viral variants in systemically infected plants. PMID:26481091

  6. Random Plant Viral Variants Attain Temporal Advantages During Systemic Infections and in Turn Resist other Variants of the Same Virus.

    PubMed

    Zhang, Xiao-Feng; Guo, Jiangbo; Zhang, Xiuchun; Meulia, Tea; Paul, Pierce; Madden, Laurence V; Li, Dawei; Qu, Feng

    2015-01-01

    Infection of plants with viruses containing multiple variants frequently leads to dominance by a few random variants in the systemically infected leaves (SLs), for which a plausible explanation is lacking. We show here that SL dominance by a given viral variant is adequately explained by its fortuitous lead in systemic spread, coupled with its resistance to superinfection by other variants. We analyzed the fate of a multi-variant turnip crinkle virus (TCV) population in Arabidopsis and N. benthamiana plants. Both wild-type and RNA silencing-defective plants displayed a similar pattern of random dominance by a few variant genotypes, thus discounting a prominent role for RNA silencing. When introduced to plants sequentially as two subpopulations, a twelve-hour head-start was sufficient for the first set to dominate. Finally, SLs of TCV-infected plants became highly resistant to secondary invasions of another TCV variant. We propose that random distribution of variant foci on inoculated leaves allows different variants to lead systemic movement in different plants. The leading variants then colonize large areas of SLs, and resist the superinfection of lagging variants in the same areas. In conclusion, superinfection resistance is the primary driver of random enrichment of viral variants in systemically infected plants. PMID:26481091

  7. Genetic characterization of MHC class II DQB exon 2 variants in gayal (Bos frontalis)

    PubMed Central

    Sun, Yongke; Xi, Dongmei; Li, Guozhi; Hao, Tiantian; Chen, Yuhan; Yang, Yuai

    2014-01-01

    In the present study, exon 2 of major histocompatibility complex (MHC) class II DQB gene from 39 gayals (Bos frontalis) was isolated, characterized and compared with previously reported patterns for other bovidae. It was revealed by sequence analyses that there are 36 DQB exon 2 variants among 39 gayals. These variants exhibited a high degree of nucleotide and amino acid substitutions with most amino acid variations occurring at positions forming the peptide-binding sites (PBS). The DQB loci were analysed for patterns of synonymous (d S) and non-synonymous (d N) substitution. The gayals were observed to be under strong balancing selection in the DQB exon 2 PBS (d N = 0.094, P = 0.001). It appears that this variability among gayals could confer the ability to mount immune responses to a wide variety of peptides or pathogens. PMID:26019566

  8. Amino acid sequence of a variant pro-form of insulin-like growth factor II.

    PubMed Central

    Zumstein, P P; Lüthi, C; Humbel, R E

    1985-01-01

    Human serum contains, in addition to the "classical" 7.5-kDa insulin-like growth factors (IGFs) I and II, small amounts of larger IGF-II. A 10-kDa IGF-II was isolated by gel filtration, immunoaffinity chromatography, and reversed-phase HPLC. Upon amino acid sequence determination, a substitution of Cys-Gly-Asp for Ser-33 was found as well as a COOH-terminal extension of 21 residues (E peptide). These sequence differences suggest that 10-kDa IGF-II is a precursor of a variant IGF-II. Since the substitution is not located at a known intron/exon hinge region, the finding of this variant IGF-II is evidence for the presence of more than one gene for IGF-II. PMID:3889903

  9. High-accuracy biodistribution analysis of adeno-associated virus variants by double barcode sequencing

    PubMed Central

    Marsic, Damien; Méndez-Gómez, Héctor R; Zolotukhin, Sergei

    2015-01-01

    Biodistribution analysis is a key step in the evaluation of adeno-associated virus (AAV) capsid variants, whether natural isolates or produced by rational design or directed evolution. Indeed, when screening candidate vectors, accurate knowledge about which tissues are infected and how efficiently is essential. We describe the design, validation, and application of a new vector, pTR-UF50-BC, encoding a bioluminescent protein, a fluorescent protein and a DNA barcode, which can be used to visualize localization of transduction at the organism, organ, tissue, or cellular levels. In addition, by linking capsid variants to different barcoded versions of the vector and amplifying the barcode region from various tissue samples using barcoded primers, biodistribution of viral genomes can be analyzed with high accuracy and efficiency. PMID:26793739

  10. Middle East Respiratory Syndrome Coronavirus Intra-Host Populations Are Characterized by Numerous High Frequency Variants

    PubMed Central

    Borucki, Monica K.; Lao, Victoria; Hwang, Mona; Gardner, Shea; Adney, Danielle; Munster, Vincent; Bowen, Richard; Allen, Jonathan E.

    2016-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging human pathogen related to SARS virus. In vitro studies indicate this virus may have a broad host range suggesting an increased pandemic potential. Genetic and epidemiological evidence indicate camels serve as a reservoir for MERS virus but the mechanism of cross species transmission is unclear and many questions remain regarding the susceptibility of humans to infection. Deep sequencing data was obtained from the nasal samples of three camels that had been experimentally infected with a human MERS-CoV isolate. A majority of the genome was covered and average coverage was greater than 12,000x depth. Although only 5 mutations were detected in the consensus sequences, 473 intrahost single nucleotide variants were identified. Many of these variants were present at high frequencies and could potentially influence viral phenotype and the sensitivity of detection assays that target these regions for primer or probe binding. PMID:26790002

  11. Variant-specific prion interactions: Complicating factors.

    PubMed

    Sharma, Jaya; Liebman, Susan W

    2013-01-01

    Prions are protein conformations that "self-seed" the misfolding of their non-prion iso-forms into prion, often amyloid, conformations. The most famous prion is the mammalian PrP protein that in its prion form causes transmissible spongiform encephalopathy. Curiously there can be distinct conformational differences even between prions of the same protein propagated in the same host species. These are called prion strains or variants. For example, different PrP variants are faithfully transmitted during self-seeding and are associated with distinct disease characteristics. Variant-specific PrP prion differences include the length of the incubation period before the disease appears and the deposition of prion aggregates in distinct regions of the brain.(1) Other more common neurodegenerative diseases (e.g., Alzheimer disease, Parkinson disease, type 2 diabetes and ALS) are likewise caused by the misfolding of a normal protein into a self-seeding aggregate.(2) (-) (4) One of the most important unanswered questions is how the first prion-like seed arises de novo, resulting in the pathological cascade. PMID:24475372

  12. Association of genetic variants with diabetic nephropathy

    PubMed Central

    Rizvi, Saliha; Raza, Syed Tasleem; Mahdi, Farzana

    2014-01-01

    Diabetic nephropathy accounts for the most serious microvascular complication of diabetes mellitus. It is suggested that the prevalence of diabetic nephropathy will continue to increase in future posing a major challenge to the healthcare system resulting in increased morbidity and mortality. It occurs as a result of interaction between both genetic and environmental factors in individuals with both type 1 and type 2 diabetes. Genetic susceptibility has been proposed as an important factor for the development and progression of diabetic nephropathy, and various research efforts are being executed worldwide to identify the susceptibility gene for diabetic nephropathy. Numerous single nucleotide polymorphisms have been found in various genes giving rise to various gene variants which have been found to play a major role in genetic susceptibility to diabetic nephropathy. The risk of developing diabetic nephropathy is increased several times by inheriting risk alleles at susceptibility loci of various genes like ACE, IL, TNF-?, COL4A1, eNOS, SOD2, APOE, GLUT, etc. The identification of these genetic variants at a biomarker level could thus, allow the detection of those individuals at high risk for diabetic nephropathy which could thus help in the treatment, diagnosis and early prevention of the disease. The present review discusses about the various gene variants found till date to be associated with diabetic nephropathy. PMID:25512783

  13. Negative feedback buffers effects of regulatory variants

    PubMed Central

    Bader, Daniel M; Wilkening, Stefan; Lin, Gen; Tekkedil, Manu M; Dietrich, Kim; Steinmetz, Lars M; Gagneur, Julien

    2015-01-01

    Mechanisms conferring robustness against regulatory variants have been controversial. Previous studies suggested widespread buffering of RNA misexpression on protein levels during translation. We do not find evidence that translational buffering is common. Instead, we find extensive buffering at the level of RNA expression, exerted through negative feedback regulation acting in trans, which reduces the effect of regulatory variants on gene expression. Our approach is based on a novel experimental design in which allelic differential expression in a yeast hybrid strain is compared to allelic differential expression in a pool of its spores. Allelic differential expression in the hybrid is due to cis-regulatory differences only. Instead, in the pool of spores allelic differential expression is not only due to cis-regulatory differences but also due to local trans effects that include negative feedback. We found that buffering through such local trans regulation is widespread, typically compensating for about 15% of cis-regulatory effects on individual genes. Negative feedback is stronger not only for essential genes, indicating its functional relevance, but also for genes with low to middle levels of expression, for which tight regulation matters most. We suggest that negative feedback is one mechanism of Waddington's canalization, facilitating the accumulation of genetic variants that might give selective advantage in different environments. PMID:25634765

  14. Novel RNA variants in colorectal cancers.

    PubMed

    Hoff, Andreas M; Johannessen, Bjarne; Alagaratnam, Sharmini; Zhao, Sen; Nome, Torfinn; Løvf, Marthe; Bakken, Anne C; Hektoen, Merete; Sveen, Anita; Lothe, Ragnhild A; Skotheim, Rolf I

    2015-11-01

    With an annual estimated incidence of 1.4 million, and a five-year survival rate of 60%, colorectal cancer (CRC) is a major clinical burden. To identify novel RNA variants in CRC, we analyzed exon-level microarray expression data from a cohort of 202 CRCs. We nominated 25 genes with increased expression of their 3' parts in at least one cancer sample each. To efficiently investigate underlying transcript structures, we developed an approach using rapid amplification of cDNA ends followed by high throughput sequencing (RACE-seq). RACE products from the targeted genes in 23 CRC samples were pooled together and sequenced. We identified VWA2-TCF7L2, DHX35-BPIFA2 and CASZ1-MASP2 as private fusion events, and novel transcript structures for 17 of the 23 other candidate genes. The high-throughput approach facilitated identification of CRC specific RNA variants. These include a recurrent read-through fusion transcript between KLK8 and KLK7, and a splice variant of S100A2. Both of these were overrepresented in CRC tissue and cell lines from external RNA-seq datasets. PMID:26474385

  15. Short communication: Genetic variants of Sarcocystis cruzi in infected Malaysian cattle based on 18S rDNA.

    PubMed

    Ng, Yit Han; Fong, Mun Yik; Subramaniam, Vellayan; Shahari, Shahhaziq; Lau, Yee Ling

    2015-12-01

    Sarcocystis species are pathogenic parasites that infect a wide range of animals, including cattle. A high prevalence of cattle sarcocystosis has been reported worldwide, but its status is unknown in Malaysia. This study focused on utilizing 18S rDNA to identify Sarcocystis species in Malaysian cattle and to determine their genetic variants. In this study, only Sarcocystis cruzi was detected in Malaysian cattle. The intra-species S. cruzi phylogenetic tree analysis and principal coordinate analysis (PCoA), respectively displayed two minor groups among the parasite isolates. This finding was supported by high Wright FST value (FST=0.647). The definitive hosts (dogs) may play a fundamental role in the development of S. cruzi genetic variants. Additionally, the existence of microheterogeneity within the S. cruzi merozoites and/or distinct genetic variants arisen from independent merozoites in mature sarcocysts, possibly contributed to the existence of intra-species variations within the population. PMID:26679818

  16. [Selection of Bvg- variants of Bordetella pertussis].

    PubMed

    Passerini de Rossi, B N; Friedman, L E; Darnaud, S; de Torres, R A; Franco, M A

    1997-01-01

    Bordetella pertussis virulent strains (Bvg+) produce a wide array of virulence factors. The production of these factors is coordinately regulated by the locus bvg in response to environmental signals in a process known as antigenic modulation. Mutations in the bvg locus originate avirulent variants (Bvg-) that are unable to express virulence factors regardless of growth conditions. In this paper we have obtained spontaneous variants Bvg- of B. pertussis Tohama I and 10536, which would be useful for studying virulence markers, using the selective media Stainer-Scholte agar supplemented with 1% Casamino-acids (SSA-CAS) and Jones-Kendrick with 0.20 microgram of erythromycin per ml (JK-Ery). We have also studied the efficiency of plating of B. pertussis Tohama I, 10536 and 40103 cells (Bvg+ strains) and of Bvg- strain 347 (control of the avirulent phenotype) on SSA-CAS and Stainer-Scholte agar (SSA), and we have analyzed the phenotype of the cells recovered from these media. The bacterial phenotype was characterized by using the following virulence markers: hemolysis production, hemagglutinin production, and outer membrane protein (OMP) enriched profiles. The three Bvg+ strains showed different behaviour in these selective media. B. pertussis Tohama I and 10536 could not be recovered on SSA, whereas on SSA-CAS the efficiency of plating was poor, less than 0.001%, but nevertheless allowed the selection of stable Bvg- variants of Tohama I since the OMP profile of this stain did not change after subculture in Cyclodextrin liquid medium. By contrast, strain 10536 grown on SSA-CAS suffered the process of antigenic modulation since this strain recovered the virulent phenotype when it was subcultured in Bordet-Gengou. Stable Bvg- variants from Tohama I and 10536 were obtained on JK-Ery. On the other hand, Bvg+ strain 40103 showed a high efficiency of plating on SSA and SSA-CAS and retained the virulent phenotype in all the selective media. Bvg- strain 347, in spite of being an avirulen variant, showed a poor efficiency of plating in SSA and a scant growth in JK-Ery, in agreement with the findings of other investigators which suggest that not all avirulent strains posses the ability to grow on media that inhibit most of virulent strains. PMID:9424628

  17. Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins.

    PubMed

    Yourshaw, Michael; Taylor, S Paige; Rao, Aliz R; Martín, Martín G; Nelson, Stanley F

    2015-03-01

    High-throughput DNA sequencing has become a mainstay for the discovery of genomic variants that may cause disease or affect phenotype. A next-generation sequencing pipeline typically identifies thousands of variants in each sample. A particular challenge is the annotation of each variant in a way that is useful to downstream consumers of the data, such as clinical sequencing centers or researchers. These users may require that all data storage and analysis remain on secure local servers to protect patient confidentiality or intellectual property, may have unique and changing needs to draw on a variety of annotation data sets and may prefer not to rely on closed-source applications beyond their control. Here we describe scalable methods for using the plugin capability of the Ensembl Variant Effect Predictor to enrich its basic set of variant annotations with additional data on genes, function, conservation, expression, diseases, pathways and protein structure, and describe an extensible framework for easily adding additional custom data sets. PMID:24626529

  18. The computer-assisted differentiation of hemoglobin variants.

    PubMed

    Barwick, R C; Schneider, R G

    Using a TRS-80 Radio Shack microcomputer system, we have computerized the differentiation of hemoglobin variants according to their mobilities in four methods of zone electrophoresis, each measuring a somewhat different aspect of molecular structure. In the identification routine of the program, the electrophoretic mobilities of an unknown variant are compared mathematically to the mobilities of previously analyzed variants; the computer prints out those known variants whose mobilities are within a specifiable interval on either side of the mobilities of the unknown variant. Properly specifying this interval is essential to the effectiveness of the identification. Another routine in the program classifies the variants according to any of ten molecular variables. Computerizing the identification and the information output provides a way to differentiate many variants, allows convenient handling of a large number of data on them, and facilitates their structural analysis. PMID:7034266

  19. Microsatellite Instability Use in Mismatch Repair Gene Sequence Variant Classification

    PubMed Central

    Thompson, Bryony A.; Spurdle, Amanda B.

    2015-01-01

    Inherited mutations in the DNA mismatch repair genes (MMR) can cause MMR deficiency and increased susceptibility to colorectal and endometrial cancer. Microsatellite instability (MSI) is the defining molecular signature of MMR deficiency. The clinical classification of identified MMR gene sequence variants has a direct impact on the management of patients and their families. For a significant proportion of cases sequence variants of uncertain clinical significance (also known as unclassified variants) are identified, constituting a challenge for genetic counselling and clinical management of families. The effect on protein function of these variants is difficult to interpret. The presence or absence of MSI in tumours can aid in determining the pathogenicity of associated unclassified MMR gene variants. However, there are some considerations that need to be taken into account when using MSI for variant interpretation. The use of MSI and other tumour characteristics in MMR gene sequence variant classification will be explored in this review. PMID:25831438

  20. Stability and Cu(II) binding of prion protein variants related to inherited human prion diseases.

    PubMed

    Cereghetti, Grazia M; Schweiger, Arthur; Glockshuber, Rudi; Van Doorslaer, Sabine

    2003-03-01

    All inherited forms of human prion diseases are linked with mutations in the prion protein (PrP) gene. Here we have investigated the stability and Cu(II) binding properties of three recombinant variants of murine full-length PrP(23-231)-containing destabilizing point mutations that are associated with human Gerstmann-Sträussler-Scheinker disease (F198S), Creutzfeld-Jakob disease (E200K), and fatal familial insomnia (D178N) by electron paramagnetic resonance and circular dichroism spectroscopy. Furthermore, we analyzed the variants H140S, H177S, and H187S of the isolated C-terminal domain of murine PrP, mPrP(121-231), to test a role of the histidine residues in Cu(II) binding. The F198S and E200K variants of PrP(23-231) differed in Cu(II) binding from the wild-type mPrP(23-231). However, circular dichroism spectroscopy indicated that the variants and the wild type did not undergo conformational changes in the presence of Cu(II). The D178N variant showed a high tendency to aggregate at pH 7.4 both with and without Cu(II). At lower pH values, it showed the same Cu(II) binding behavior as the wild type. The analysis allowed for a better location of the Cu(II) binding sites in the C-terminal part of the protein. Our present data indicate that hereditary forms of prion diseases cannot be rationalized on the basis of altered Cu(II) binding or mutation-induced protein destabilization alone. PMID:12609901

  1. Runx3-regulated expression of two Ntrk3 transcript variants in dorsal root ganglion neurons.

    PubMed

    Ogihara, Yuuki; Masuda, Tomoyuki; Ozaki, Shigeru; Yoshikawa, Masaaki; Shiga, Takashi

    2016-03-01

    Somatosensation is divided into proprioception and cutaneous sensation. Dorsal root ganglion (DRG) neurons project their fibers toward peripheral targets including muscles and skin, and centrally to the spinal cord. Proprioceptive DRG neurons transmit information from muscle spindles and Golgi tendon organs to the spinal cord. We previously showed that Runt-related transcription factor 3 (Runx3) is expressed in these neurons and their projections to the ventral spinal cord and muscle spindles are lost in Runx3-deficient (Runx3(-/-) ) mouse embryos. Although Runx3 is likely to contribute to the fate decision and projection of proprioceptive DRG neurons, the precise roles for Runx3 in these phenomena are unknown. To identify genes regulated by Runx3 in embryonic DRGs, we performed microarray analyses using cDNAs isolated from wild-type and Runx3(-/-) DRGs of embryonic day (E) 12.5 and selected two transcript variants of the tyrosine kinase receptor C (TrkC) gene. These variants, Ntrk3 variant 1 (Ntrk3-v1) and variant 2 (Ntrk3-v2), encode full-length and truncated receptors of neurotrophin-3, respectively. Using double in situ hybridization, we found that most of Ntrk3-v1 mRNA expression in E14.5 DRGs depended on Runx3 but that more than half of Ntrk3-v2 mRNA one were expressed in a Runx3-independent manner. Furthermore, our data revealed that the rate of Ntrk3-v1 and Ntrk3-v2 colocalization in DRGs changed from E14.5 to E18.5. Together, our data suggest that Runx3 may play a crucial role in the development of DRGs by regulating the expression of Ntrk3 variants and that DRG neurons expressing Ntrk3-v1 but not Ntrk3-v2 may differentiate into proprioceptive ones. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 76: 313-322, 2016. PMID:26061886

  2. Monocytotropic human immunodeficiency virus type 1 (HIV-1) variants detectable in all stages of HIV-1 infection lack T-cell line tropism and syncytium-inducing ability in primary T-cell culture.

    PubMed Central

    Schuitemaker, H; Kootstra, N A; de Goede, R E; de Wolf, F; Miedema, F; Tersmette, M

    1991-01-01

    We previously demonstrated a correlation between the presence of syncytium-inducing (SI) human immunodeficiency virus type 1 (HIV-1) variants showing tropism for cell line H9 and the occurrence of rapid CD4 cell decline and progression to AIDS. In contrast, in stable asymptomatic individuals, we detected only isolates with low replication rates that were non-syncytium-inducing (NSI) and nontropic for the H9 cell line. Here, we investigated the monocytotropism of established HIV-1 isolates with a panel of isolates and with biological HIV-1 clones with distinct phenotypes. Moreover, the prevalence and biological phenotypes of monocytotropic HIV-1 variants in the course of HIV-1 infection were analyzed in comparative primary isolation studies on peripheral blood lymphocytes (PBL) and monocyte-derived macrophages (MDM). In cell-free infection studies with MDM from eight blood donors, 13 of 17 NSI isolates but only 4 of 14 SI isolates were able to infect MDM. NSI isolates also infected significantly more different donors than SI variants (median, 3 of 8 versus 0 of 8). This enhanced monocytotropism of NSI isolates was confirmed in experiments with biological HIV-1 clones with distinct phenotypes recovered from the same donor. To investigate the prevalence and biological phenotypes of monocytotropic variants in different stages of HIV-1 infection, sequential isolates from peripheral blood mononuclear cell samples from nine asymptomatic individuals, five of whom progressed to AIDS and seven of whom had a known time of seroconversion, were recovered by cocultivation with both PBL and MDM. Monocytotropic variants were obtained from 37 of 42 time points. All monocytotropic variants were NSI in PBL culture and non-T-cell-line tropic, even when SI, T-cell-line-tropic HIV-1 variants could be recovered from the same patient sample by cocultivation with PBL. We conclude that monocytotropic HIV-1 variants mostly have an NSI phenotype in PBL and, in contrast to SI variants, are present at all stages of HIV-1 infection. These results suggest an important role for monocytotropic variants in the persistence of HIV-1 infection. PMID:1985204

  3. Phenotypic variation of Staphylococcus epidermidis isolated from a patient with native valve endocarditis.

    PubMed Central

    Deighton, M; Pearson, S; Capstick, J; Spelman, D; Borland, R

    1992-01-01

    Two colonial variants of Staphylococcus epidermidis were isolated from the valvular tissue of a patient with native valve endocarditis. In addition to differing in colonial morphology, the two variants differed in hemolysis on blood-containing media, in adherence capacity, and in the expression of certain enzymes. Under suitable conditions, both variants were themselves capable of phenotypic variation, although they differed in the rate at which variants were generated. The variants yielded identical profiles on restriction endonuclease analysis of plasmid DNA and pulsed-field gel electrophoresis of whole-cell DNA. This report suggests a possible role for phenotypic variation in coagulase-negative staphylococcal virulence. Congo red agar would be an excellent medium for studying the contribution of variation to the virulence of these organisms. Images PMID:1401003

  4. Modified antimicrobial disc susceptibility testing for nutritionally-variant streptococci.

    PubMed

    Tantimavanich, Srisurang; Nilakul, Churairatana; Sukroongreung, Samaniya

    2002-03-01

    Streptococci that were dependent for their growth upon staphylococci were isolated from a patient with sub-acute bacterial endocarditis and subsequently identified as nutritionally-variant streptococci (NVS). Failure of the isolate to grow on agar media supplemented with pyridoxal hydrochloride or L-cysteine, the known supporting growth factors for NVS, made conventional antimicrobial disc diffusion assay impossible. We modified the assay by co-inoculating Staphylococcus aureus resistant to the drugs being tested as a helper to support the growth of the NVS. Streaking S. aureus closely to the antibiotic discs that were placed above NVS resulted in the growth of satellite colonies of NVS that orbited the S. aureus and that produced a pattern of interrupted zones of growth inhibition. Using an alternative method--adding staphylococcal secreting factor(s) to a 10% staphylococcal cell-free culture supernatant and adding this to an antibiotic susceptibility testing medium,--we found that the NVS formed colonies that formed clear zones of growth inhibition around the disc. When the sizes of the growth inhibition zones produced by both these methods were compared with those recommened by the NCCLS, the NVS were found to be susceptible to penicillin, vancomycin, erythromycin, chloramphenicol, cefoperazone, cefamandole and ofloxacin and resistant to co-trimoxazole, gentamicin and tetracycline. Based on these findings, vancomycin was selected for treatment and the patient was cured of endocarditis. The correlation between the in vitro drug susceptibility testing and the in vivo clinical response indicated that the modified antibiotic susceptibility test is an appropriate method for establishing antibiotic regimens. PMID:12118443

  5. Oligogenic basis of isolated gonadotropin-releasing hormone deficiency

    PubMed Central

    Sykiotis, Gerasimos P.; Plummer, Lacey; Hughes, Virginia A.; Au, Margaret; Durrani, Sadia; Nayak-Young, Sadhana; Dwyer, Andrew A.; Quinton, Richard; Hall, Janet E.; Gusella, James F.; Seminara, Stephanie B.; Crowley, William F.; Pitteloud, Nelly

    2010-01-01

    Between the genetic extremes of rare monogenic and common polygenic diseases lie diverse oligogenic disorders involving mutations in more than one locus in each affected individual. Elucidating the principles of oligogenic inheritance and mechanisms of genetic interactions could help unravel the newly appreciated role of rare sequence variants in polygenic disorders. With few exceptions, however, the precise genetic architecture of oligogenic diseases remains unknown. Isolated gonadotropin-releasing hormone (GnRH) deficiency caused by defective secretion or action of hypothalamic GnRH is a rare genetic disease that manifests as sexual immaturity and infertility. Recent reports of patients who harbor pathogenic rare variants in more than one gene have challenged the long-held view that the disorder is strictly monogenic, yet the frequency and extent of oligogenicity in isolated GnRH deficiency have not been investigated. By systematically defining genetic variants in large cohorts of well-phenotyped patients (n = 397), family members, and unaffected subjects (n = 179) for the majority of known disease genes, this study suggests a significant role of oligogenicity in this disease. Remarkably, oligogenicity in isolated GnRH deficiency was as frequent as homozygosity/compound heterozygosity at a single locus (2.5%). Among the 22% of patients with detectable rare protein-altering variants, the likelihood of oligogenicity was 11.3%. No oligogenicity was detected among controls (P < 0.05), even though deleterious variants were present. Viewing isolated GnRH deficiency as an oligogenic condition has implications for understanding the pathogenesis of its reproductive and nonreproductive phenotypes; deciphering the etiology of common GnRH-related disorders; and modeling the genetic architecture of other oligogenic and multifactorial diseases. PMID:20696889

  6. Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans.

    PubMed

    Casals, Ferran; Hodgkinson, Alan; Hussin, Julie; Idaghdour, Youssef; Bruat, Vanessa; de Maillard, Thibault; Grenier, Jean-Christophe; Grenier, Jean-Cristophe; Gbeha, Elias; Hamdan, Fadi F; Girard, Simon; Spinella, Jean-François; Larivière, Mathieu; Saillour, Virginie; Healy, Jasmine; Fernández, Isabel; Sinnett, Daniel; Michaud, Jacques L; Rouleau, Guy A; Haddad, Elie; Le Deist, Françoise; Awadalla, Philip

    2013-01-01

    Whole-exome or gene targeted resequencing in hundreds to thousands of individuals has shown that the majority of genetic variants are at low frequency in human populations. Rare variants are enriched for functional mutations and are expected to explain an important fraction of the genetic etiology of human disease, therefore having a potential medical interest. In this work, we analyze the whole-exome sequences of French-Canadian individuals, a founder population with a unique demographic history that includes an original population bottleneck less than 20 generations ago, followed by a demographic explosion, and the whole exomes of French individuals sampled from France. We show that in less than 20 generations of genetic isolation from the French population, the genetic pool of French-Canadians shows reduced levels of diversity, higher homozygosity, and an excess of rare variants with low variant sharing with Europeans. Furthermore, the French-Canadian population contains a larger proportion of putatively damaging functional variants, which could partially explain the increased incidence of genetic disease in the province. Our results highlight the impact of population demography on genetic fitness and the contribution of rare variants to the human genetic variation landscape, emphasizing the need for deep cataloguing of genetic variants by resequencing worldwide human populations in order to truly assess disease risk. PMID:24086152

  7. Fluoroquinolone Efflux by the Plasmid-Mediated Multidrug Efflux Pump QacB Variant QacBIII in Staphylococcus aureus?

    PubMed Central

    Nakaminami, Hidemasa; Noguchi, Norihisa; Sasatsu, Masanori

    2010-01-01

    Plasmids that carry the multidrug efflux genes qacA and qacB are widely distributed in methicillin-resistant Staphylococcus aureus (MRSA). Although the QacA and QacB proteins are similar to each other, their respective substrate specificities may differ. We investigated the variability and structure-function relationships of QacA and QacB in MRSA isolates. The amino acid sequences of 7 QacA and 25 QacB proteins showed that QacB was present in three variants, designated QacBII, QacBIII, and QacBIV, that were different from the prototypic QacB variant encoded by plasmid pSK23, which was named QacBI, while QacA was present in two variants. When cloned and expressed in S. aureus, the strain carrying qacBIII exhibited higher susceptibility to dyes and decreased susceptibility to norfloxacin and ciprofloxacin compared to strains carrying the other QacB variants. Site-directed mutagenesis experiments revealed that the residue at position 320 in QacB plays an important role in the resistance phenotypes to dyes and fluoroquinolones. Furthermore, the accumulation of norfloxacin and ciprofloxacin in the strain carrying qacBIII was significantly decreased. Our data demonstrate that the plasmid-mediated multidrug efflux pump QacB variant QacBIII confers the capability for fluoroquinolone efflux on S. aureus. PMID:20660673

  8. Genetic variants of bovine ?- and ?-casein result in different immunoglobulin E-binding epitopes after in vitro gastrointestinal digestion.

    PubMed

    Lisson, M; Lochnit, G; Erhardt, G

    2013-09-01

    Immunoglobulin E-mediated allergy to cow milk is a common allergy in industrialized countries, mainly affecting young children and infants. ?-Casein (CN) and ?-CN belong to the major allergens in cow milk. Within these milk proteins, genetic polymorphisms occur, which are characterized by substitutions or deletions of AA, resulting in different variants for each protein. Until now, these variants have not been considered when discussing the allergenic potential of bovine milk. In this study, the focus was placed on the arising peptide pattern after in vitro gastrointestinal digestion of several ?- and ?-CN variants to determine resistant fragments containing IgE-binding epitopes and to identify potential differences between these variants. ?-Casein A(1), A(2), and B, as well as ?-CN A, B, and E, were separated and isolated from milk of cows homozygous for these variants and digested with an in vitro gastrointestinal digestion model. The resulting peptides were identified using mass spectrometry and compared with previously determined epitopes. Seven ?-CN and 4 ?-CN peptides, common in all ?- or ?-CN variants, remained of sufficient size to harbor IgE-binding epitopes. In addition, some peptides and, consequently, epitopes differ from each other due to the AA substitution occurring in the individual variants. The distinct peptides AA 108 to 129 of ?-CN A(1) and A(2), AA 103 to 123 of ?-CN B, as well as AA 59 to 72, AA 59 to 80, and AA 58 to 80 of all 3 ?-CN variants correspond to the IgE-binding epitopes AA 107 to 120 and AA 55 to 70, respectively. In ?-CN, the 2 variant-specific peptides AA 136 to 149 (?-CN A, E) and AA 134 to 150 (?-CN B) are congruent with the IgE-binding epitope AA 137 to 148. The present study shows that genetic polymorphisms affected the arising peptide pattern of the caseins and thus modifications in the IgE-binding epitopes occurred. As a consequence, the casein variants could show differences in their allergenicity. Studies investigating the allergenic potential of these different peptides are currently in progress. PMID:23871370

  9. Infection of chickens with antimicrobial-resistant Salmonella enterica Typhimurium DT193 and monophasic Salmonella Typhimurium-like variants: an emerging risk to the poultry industry?

    PubMed

    Parsons, B N; Crayford, G; Humphrey, T J; Wigley, P

    2013-01-01

    Antimicrobial-resistant Salmonella enterica poses a particular risk to public health, and in particular isolates belonging to clonal lineages such as Salmonella Typhimurium DT104 cause epidemics across species including poultry. In recent years, antimicrobial-resistant S. Typhimurium DT193 and specifically the monophasic S. Typhimurium-like variants of this phage type, serotypes 4,12:i:- and 4,5,12:i:-, have become an increasing risk to public health in Europe and the USA and now account for nearly one-half of human S. Typhimurium infections in the UK. Unlike S. Typhimurium that possesses two forms of flagella which can vary between phase 1 and phase 2 during infection, monophasic variants possess only phase 1 flagella. These monophasic antimicrobial-resistant variants have become a major problem in pig production but human cases have also been associated with poultry consumption and have been found in UK flocks through surveillance schemes since 2010. In this study we determined the ability of antimicrobial-resistant DT193 serotype 4,12:i:- and 4,5,12:i:- isolates from pigs to infect chickens. All isolates were found to colonize the caeca and liver. All but one isolate of serotype 4,5,12:i:- also infected the spleen. Levels of infection and pathology were comparable with those found with the virulent S. Typhimurium isolate 4/74. These findings indicate that both S. Typhimurium DT193 and monophasic variants of this phage type usually associated with pigs are capable of colonizing the chicken. This shows that both S. Typhimurium DT193 and monophasic variants represent a significant and potential emerging threat to poultry production from "spill-over" of these isolates from the pig industry or other sources. PMID:23930753

  10. Rare genetic variants and the risk of cancer.

    PubMed

    Bodmer, Walter; Tomlinson, Ian

    2010-06-01

    There are good reasons to expect that common genetic variants do not explain all of the inherited risk of the common cancers, not least of these being the relatively low proportion of familial relative risk that common cancer SNPs currently explain. One promising source of the unexplained risk is rare, low-penetrance genetic variants, a class that ranges from low-frequency polymorphisms (allele frequency < 5%) through subpolymorphic variants (frequency 0.1-1.0%) to very low frequency or 'private' variants with frequencies of 0.1% or less. Examples of rare cancer variants include breast cancer susceptibility loci CHEK2, BRIP1 and PALB2. There are considerable challenges associated with the discovery and testing of rare predisposition alleles, many of which are illustrated by the issues associated with variants of unknown significance in the Mendelian cancer predisposition genes. However, whilst cost constraints remain, the technological barriers to rare variant discovery and large-scale genotyping no longer exist. If each individual carries many disease-causing rare variants, the so-called missing heritability of cancer might largely be explained. Whether or not rare variants do end up filling the heritability gap, it is imperative to look for them along side common variants. PMID:20554195

  11. Population genetics identifies challenges in analyzing rare variants.

    PubMed

    Johnston, Henry Richard; Hu, Yijuan; Cutler, David J

    2015-03-01

    Geneticists have, for years, understood the nature of genome-wide association studies using common genomic variants. Recently, however, focus has shifted to the analysis of rare variants. This presents potential problems for researchers, as rare variants do not always behave in the same way common variants do, sometimes rendering decades of solid intuition moot. In this paper, we present examples of the differences between common and rare variants. We show why one must be significantly more careful about the origin of rare variants, and how failing to do so can lead to highly inflated type I error. We then explain how to best avoid such concerns with careful understanding and study design. Additionally, we demonstrate that a seemingly low error rate in next-generation sequencing can dramatically impact the false-positive rate for rare variants. This is due to the fact that rare variants are, by definition, seen infrequently, making it hard to distinguish between errors and real variants. Compounding this problem is the fact that the proportion of errors is likely to get worse, not better, with increasing sample size. One cannot simply scale their way up in order to solve this problem. Understanding these potential pitfalls is a key step in successfully identifying true associations between rare variants and diseases. PMID:25640419

  12. Mutation Update: The Spectra of Nebulin Variants and Associated Myopathies

    PubMed Central

    Lehtokari, Vilma-Lotta; Kiiski, Kirsi; Sandaradura, Sarah A.; Laporte, Jocelyn; Repo, Pauliina; Frey, Jennifer A.; Donner, Kati; Marttila, Minttu; Saunders, Carol; Barth, Peter G.; den Dunnen, Johan T.; Beggs, Alan H.; Clarke, Nigel F.; North, Kathryn N.; Laing, Nigel G.; Romero, Norma B.; Winder, Thomas L.; Pelin, Katarina; Wallgren-Pettersson, Carina

    2015-01-01

    A mutation update on the nebulin gene (NEB) is necessary because of recent developments in analysis methodology, the identification of increasing numbers and novel types of variants, and a widening in the spectrum of clinical and histological phenotypes associated with this gigantic, 183 exons containing gene. Recessive pathogenic variants in NEB are the major cause of nemaline myopathy (NM), one of the most common congenital myopathies. Moreover, pathogenic NEB variants have been identified in core-rod myopathy and in distal myopathies. In this update, we present the disease-causing variants in NEB in 159 families, 143 families with NM, and 16 families with NM-related myopathies. Eighty-eight families are presented here for the first time. We summarize 86 previously published and 126 unpublished variants identified in NEB. Furthermore, we have analyzed the NEB variants deposited in the Exome Variant Server (http://evs.gs.washington.edu/EVS/), identifying that pathogenic variants are a minor fraction of all coding variants (~7%). This indicates that nebulin tolerates substantial changes in its amino acid sequence, providing an explanation as to why variants in such a large gene result in relatively rare disorders. Lastly, we discuss the difficulties of drawing reliable genotype–phenotype correlations in NEB-associated disease. PMID:25205138

  13. Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1

    PubMed Central

    Gorrie, Claire L.; Jenney, Adam; Mirceta, Mirjana

    2015-01-01

    Serratia marcescens strain AH0650_Sm1 is a clinical multidrug-resistant isolate from Australia. Here, we report its annotated draft genome comprising 20 contigs. We identified chromosomal antimicrobial resistance genes including a tet(41) variant, an aac(6′)-Ic variant, ampC, a metallo-beta-lactamase, and several putative multidrug efflux pumps, as well as a novel prophage. PMID:26337895

  14. A three-dimensional interactive atlas of cerebral arterial variants.

    PubMed

    Nowinski, Wieslaw L; Thirunavuukarasuu, A; Volkau, Ihar; Marchenko, Yevgen; Aminah, Bivi; Puspitasari, Fiftarina; Runge, Val M

    2009-12-01

    The knowledge of cerebrovascular variants is essential in education, training, diagnosis and treatment. The current way of presentation of vasculature and, particularly, vascular variants is insufficient. Our purpose is to construct a three-dimensional (3D) interactive atlas of cerebral arterial variants along with exploration tools allowing the investigator just with a few clicks to better and faster understand the variants and their spatial relationships. A 3D model of the cerebral arterial system created earlier, fully labeled with names and diameters, is used as a reference. As the vast material about vascular variability is incomplete and not fully documented, our approach synthesizes variants in 3D based on existing knowledge. The variants are created from literature using a dedicated vascular editor and embedded into the reference model. Sixty 3D variants and branching patterns are created including the internal carotid, middle cerebral, anterior cerebral, posterior cerebral, vertebral and basilar arteries, and circle of Willis. Their prevalence rates are given. The atlas is developed to explore the variants individually or embedded into the reference vasculature. Real-time interactive manipulation of variants and reference vasculature (rotate/zoom/pan/view) is provided. This atlas facilitates the investigator to easily get familiarized with the variants and rapidly explore them. It aids in presentation of vascular variants and understanding their spatial relationships either individually or embedded into the surrounding reference cerebrovasculature. It is useful for medical students, educators to prepare teaching materials, and clinicians for scan interpretation. It is easily extensible with additional variant instances, new variants, branching patterns, and supporting textual materials. PMID:19957055

  15. Attenuated variants of Lesch-Nyhan disease

    PubMed Central

    Ceballos-Picot, Irene; Torres, Rosa J.; Visser, Jasper E.; Schretlen, David J.; Verdu, Alfonso; Laróvere, Laura E.; Chen, Chung-Jen; Cossu, Antonello; Wu, Chien-Hui; Sampat, Radhika; Chang, Shun-Jen; de Kremer, Raquel Dodelson; Nyhan, William; Harris, James C.; Reich, Stephen G.; Puig, Juan G.

    2010-01-01

    Lesch–Nyhan disease is a neurogenetic disorder caused by deficiency of the enzyme hypoxanthine–guanine phosphoribosyltransferase. The classic form of the disease is described by a characteristic syndrome that includes overproduction of uric acid, severe generalized dystonia, cognitive disability and self-injurious behaviour. In addition to the classic disease, variant forms of the disease occur wherein some clinical features are absent or unusually mild. The current studies provide the results of a prospective and multi-centre international study focusing on neurological manifestations of the largest cohort of Lesch–Nyhan disease variants evaluated to date, with 46 patients from 3 to 65 years of age coming from 34 families. All had evidence for overproduction of uric acid. Motor abnormalities were evident in 42 (91%), ranging from subtle clumsiness to severely disabling generalized dystonia. Cognitive function was affected in 31 (67%) but it was never severe. Though none exhibited self-injurious behaviours, many exhibited behaviours that were maladaptive. Only three patients had no evidence of neurological dysfunction. Our results were compared with a comprehensive review of 78 prior reports describing a total of 127 Lesch–Nyhan disease variants. Together these results define the spectrum of clinical features associated with hypoxanthine–guanine phosphoribosyltransferase deficiency. At one end of the spectrum are patients with classic Lesch–Nyhan disease and the full clinical phenotype. At the other end of the spectrum are patients with overproduction of uric acid but no apparent neurological or behavioural deficits. Inbetween are patients with varying degrees of motor, cognitive, or behavioural abnormalities. Recognition of this spectrum is valuable for understanding the pathogenesis and diagnosis of all forms of hypoxanthine–guanine phosphoribosyltransferase deficiency. PMID:20176575

  16. Space variant deconvolution for optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Prashanth, R.; Bhattacharya, Shanti

    2011-12-01

    We present a method for mitigating space variant blur occurring in the images acquired using Optical coherence tomography (OCT). The effect of Gaussian beam divergence on the image resolution is analyzed mathematically to develop space dependent two dimensional point spread functions that define the blurring kernel. Two standard deconvolution algorithms are used to deblur the images using the space dependent point spread functions. We show that the deconvolution method is effective in improving the transverse resolution of cross sectional OCT images at regions up to several times as deep as the confocal region of the Gaussian beam.

  17. Rare Variant of Lycanthropy and Ecstasy

    PubMed Central

    Nasirian, Mansoureh; Banazadeh, Nabi; Kheradmand, Ali

    2009-01-01

    Background: Lycanthropy is an unusual belief or delusion in which the patient thinks that he/she has been transformed into an animal. In rare cases, the patient believes that another person has been transformed into an animal. Case Report: We report a patient with an uncommon variant of lycanthropy is introduced. The symptoms appeared after consumption of ecstasy. This shows the occurrences of uncommon and rare psychosis after ecstasy drug use especially in patients susceptible to schizophrenia. Ecstasy drug can induce paranoid psychosis similar to schizophrenia. In the presented case, ecstasy seemed to have a role in patient's underlying susceptibility to schizophrenia. PMID:24494083

  18. Two ATM variants and breast cancer risk.

    PubMed

    Thompson, Deborah; Antoniou, Antonis C; Jenkins, Mark; Marsh, Anna; Chen, Xiaoqing; Wayne, Tierney; Tesoriero, Andrea; Milne, Roger; Spurdle, Amanda; Thorstenson, Yvonne; Southey, Melissa; Giles, Graham G; Khanna, Kum Kum; Sambrook, Joseph; Oefner, Peter; Goldgar, David; Hopper, John L; Easton, Doug; Chenevix-Trench, Georgia

    2005-06-01

    The ATM gene is mutated in ataxia-telangiectasia (AT). Heterozygote female relatives of AT cases have a 2-7fold increased risk of breast cancer. We previously reported high risks of breast cancer associated with certain ATM variants. To estimate the risks more precisely, we have examined two ATM variants, c.1066-6T>G (IVS10-6T>G) and c.4258C>T (p.Leu1420Phe), in additional cases and controls from the same Australian cohorts previously used to estimate the risk of breast cancer associated with c.1066-6T>G. A total of 775 and 84 population-based controls were genotyped for the c.1066-6T>G and c.4258C>T ATM variants respectively, as were index cases from 378 and 373 non-BRCA1/2 breast cancer families. Penetrance was estimated by Bayes factor analysis. The allele frequencies of ATM c.1066-6T>G and c.4258C>T estimated from controls were 0.005 (95% CI=0.002 to 0.009) and 0.012 (95% CI=0.001 to 0.042), respectively. We identified three new breast cancer families with c.1066-6T>G, and seven families with c.4258C>T. Combining with the two c.1066-6T>G families previously reported, the estimated penetrance to age 70 of c.1066-6T>G was 17.2% (95% CI=4.7% to 37.5%). For c.4258C>T, the estimated average penetrance was 4.8% (95% CI 1.7% to 10.1%). In conclusion, we found no evidence that the ATM c.4258C>T variant increases breast cancer risk, and little evidence that c.1066-6T>G confers an elevated risk. Analysis of additional families will be necessary to define more precisely the risk, if any, associated with c.1066-6T>G. PMID:15880680

  19. Trabecular Variant of Juvenile Aggressive Ossifying Fibroma.

    PubMed

    Rahman, Tabishur; Hashmi, Ghulam Sarwar; Ansari, Hena

    2015-05-01

    Juvenile aggressive ossifying fibroma (JAOF) is an uncommon benign lesion which is distinctly aggressive in behavior with high tendency for recurrence. It appears in early age and in 79% of patients is diagnosed before 15. It has two histological variants: psammomatoid and trabecular, with the latter being less common with a stronger tendency to recur. In this article, we present a case of trabecular JAOF, in which treatment could not be given despite the availability of all requisites for surgery and good financial status, due to parental indifference and negligence. PMID:26266018

  20. Trabecular Variant of Juvenile Aggressive Ossifying Fibroma

    PubMed Central

    Rahman, Tabishur; Hashmi, Ghulam Sarwar; Ansari, Hena

    2015-01-01

    Juvenile aggressive ossifying fibroma (JAOF) is an uncommon benign lesion which is distinctly aggressive in behavior with high tendency for recurrence. It appears in early age and in 79% of patients is diagnosed before 15. It has two histological variants: psammomatoid and trabecular, with the latter being less common with a stronger tendency to recur. In this article, we present a case of trabecular JAOF, in which treatment could not be given despite the availability of all requisites for surgery and good financial status, due to parental indifference and negligence. PMID:26266018

  1. Selection of variant neuroblastoma clones with missing or altered sodium channels.

    PubMed Central

    West, G J; Catterall, W A

    1979-01-01

    Neurotoxins that cause persistent activation of voltage-sensitive sodium channels are highly cytotoxic to electrically excitable neuroblastoma cells. These toxins were used as selective agents to isolate variant neuroblastoma clones with missing or altered sodium channels. Of ten resistant clones analyzed, seven lacked functional sodium channels and one had a specific 40-fold increase Kd for scorpion toxin and altered voltage dependence of scorpion toxin binding. The phenotypes of these cell clones were stable for more than 100 generations, indicating that they were the result of stable genetic change. PMID:291071

  2. [The ultrastructural characteristics of Neisseria meningitidis strains isolated in different forms of infection].

    PubMed

    Vysotski?, V V; Smirnova-Mutusheva, M A; Mishina, A I

    1995-01-01

    The electron microscopic study of cell populations of the first generation of several N.meningitidis strains, isolated from humans and grown on artificial culture medium (Hottinger's serum agar) has made it possible to establish that these organisms are morphologically heterogeneous. It was manifested by the presence of 7 morphological variants of cells in their cultures (different strains have different proportions of these variants): (a) "normal" and similar to normal diplococcal variants; (b) atypically dividing cells; (c) spheroplastic forms; (d) protoplastic forms (typical and atypical); (e) variably gemmating forms; (f) microforms and (g) gigantic forms. These data are of interest for the microbiological diagnosis of meningitis. PMID:9381865

  3. Population Structure of KPC-Producing Klebsiella pneumoniae Isolates from Midwestern U.S. Hospitals

    PubMed Central

    Wright, Meredith S.; Perez, Federico; Brinkac, Lauren; Jacobs, Michael R.; Kaye, Keith; Cober, Eric; van Duin, David; Marshall, Steven H.; Hujer, Andrea M.; Rudin, Susan D.; Hujer, Kristine M.

    2014-01-01

    Genome sequencing of carbapenem-resistant Klebsiella pneumoniae isolates from regional U.S. hospitals was used to characterize strain diversity and the blaKPC genetic context. A phylogeny based on core single-nucleotide variants (SNVs) supports a division of sequence type 258 (ST258) into two distinct groups. The primary differences between the groups are in the capsular polysaccharide locus (cps) and their plasmid contents. A strict association between clade and KPC variant was found. The blaKPC gene was found on variants of two plasmid backbones. This study indicates that highly similar K. pneumoniae subpopulations coexist within the same hospitals over time. PMID:24913165

  4. Coagulase gene typing of Staphylococcus aureus isolated from cows with mastitis in southeastern Brazil

    PubMed Central

    2005-01-01

    Abstract A typing procedure based on polymorphism of the coagulase gene (coa) was used to discriminate Staphylococcus aureus isolated from Minas Gerais dairy cows with mastitis. Amplification of the gene from the 64 S. aureus isolates produced 27 different polymerase chain reaction (PCR) products; 60 isolates showed only 1 amplicon, and 4 showed 2 amplicons. The isolates were grouped into 49 types by analyzing the restriction fragment length polymorphism (RFLP) of the coa gene; the 10 most common types accounted for 39% of the isolates. The results demonstrate that many variants of the coa gene are present in the studied region, although only a few predominate. PMID:16479723

  5. Determination of a novel integron-located variant (blaOXA -320 ) of Class D β-lactamase in Proteus mirabilis.

    PubMed

    Cicek, Aysegul Copur; Duzgun, Azer Ozad; Saral, Aysegul; Sandalli, Cemal

    2014-10-01

    Proteus mirabilis (P. mirabilis) is one of Gram-negative pathogens encountered in clinical specimens. A clinical isolate (TRP41) of P. mirabilis was isolated from a Turkish patient in Turkey. The isolate was identified using the API 32GN system and 16S rRNA gene sequencing and it was found resistant to ampicillin/sulbactam, piperacillin, tetracycline, and trimethoprim/sulfamethoxazole. This isolate was harboring a Class 1 integron gene cassette and its DNA sequence analysis revealed a novel blaOXA variant exhibiting one amino acid substitution (Asn266Ile) from blaOXA-1 . This new variant of OXA was located on Class 1 integron together with aadA1 gene encoding aminoglycoside-modifying enzymes. According to sequence records, the new variant was named as blaOXA-320 . Cassette array and size of integron were found as blaOXA-320 -aadA1 and 2086 bp, respectively. The blaOXA-320 gene is not transferable according to conjugation experiment. In this study, we report the first identification of blaOXA-320 -aadA1 gene cassette, a novel variant of Class D β-lactamase, in P. mirabilis from Turkey. PMID:24027220

  6. Characterization of influenza virus variants with different sizes of the non-structural (NS) genes and their potential as live influenza vaccine in poultry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The influenza virus isolate A/turkey/Oregon/71-delNS1 (H7N3) has a 10 nucleotide deletion in the coding region of the NS1 gene and as a result produces a truncated NS1 protein. From a stock of this virus, we found that several variants with different sizes of the NS genes exist. The number of varian...

  7. The distribution of serotype-specific plasmids among different subgroups of strains of Salmonella enterica serotype Enteritidis: characterization of molecular variants by restriction enzyme fragmentation patterns.

    PubMed Central

    Rankin, S. C.; Benson, C. E.; Platt, D. J.

    1995-01-01

    Four hundred and thirty-four isolates of Salmonella enterica serotype Enteritidis were studied. They were grouped into five subsets defined by either the collection criteria or the parameter which formed the basis for subsequent analysis. Seventy-seven per cent harboured the serotype-specific plasmid (SSP). In 55% of the isolates this was the sole plasmid. Molecular variation in the SSP was detected in 17 (5%) of the isolates on the basis of restriction enzyme fragmentation pattern (REFP) analysis using Pst I and Sma I. The SSP variants were further characterized using additional restriction enzymes chosen to optimize the information content and analysed using a coefficient of similarity. A variant SSP designated pOG690 showed greater resemblance to the SSP of Salmonella enterica serotype Typhimurium than Enteritidis; 89% and 68% respectively for Pst I and 79% and 55% respectively for Sma I. In respect of the Pst I data pOG690 shared at least 55 kb of DNA with the Typhimurium SSP and 37 kb with the SSP of Enteritidis. This variant was associated with poultry (duck, goose, chicken) and all isolates belonged to phage type 9b. Other variants were associated with phage types 4, 6, 6a, 9a, 11, 15 and 24. The epidemiological implications of these results are discussed. Images Fig. 1 PMID:7867741

  8. Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster

    PubMed Central

    Santoni, Federico A.; Makrythanasis, Periklis; Nikolaev, Sergey; Guipponi, Michel; Robyr, Daniel; Bottani, Armand; Antonarakis, Stylianos E.

    2014-01-01

    There is increasing interest in clinical genetics pertaining to the utilization of high-throughput sequencing data for accurate diagnoses of monogenic diseases. Moreover, massive whole-exome sequencing of tumors has provided significant advances in the understanding of cancer development through the recognition of somatic driver variants. To improve the identification of the variants from HTS, we developed VariantMaster, an original program that accurately and efficiently extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation in a family, as well as the probability of it being de novo or somatic. In familial cases, various modes of inheritance are considered: X-linked, autosomal dominant, and recessive (homozygosity or compound heterozygosity). Moreover, VariantMaster integrates phenotypes and genotypes, and employs Annovar to produce additional information such as allelic frequencies in the general population and damaging scores to further reduce the number of putative variants. As a proof of concept, we successfully applied VariantMaster to identify (1) de novo mutations in a previously described data set, (2) causative variants in a rare Mendelian genetic disease, and (3) known and new “driver” mutations in previously reported cancer data sets. Our results demonstrate that VariantMaster is considerably more accurate in terms of precision and sensitivity compared with previously published algorithms. PMID:24389049

  9. A rare variant association test based on combinations of single-variant tests.

    PubMed

    Sha, Qiuying; Zhang, Shuanglin

    2014-09-01

    Next generation sequencing technologies make direct testing rare variant associations possible. However, the development of powerful statistical methods for rare variant association studies is still underway. Most of existing methods are burden and quadratic tests. Recent studies show that the performance of each of burden and quadratic tests depends strongly upon the underlying assumption and no test demonstrates consistently acceptable power. Thus, combined tests by combining information from the burden and quadratic tests have been proposed recently. However, results from recent studies (including this study) show that there exist tests that can outperform both burden and quadratic tests. In this article, we propose three classes of tests that include tests outperforming both burden and quadratic tests. Then, we propose the optimal combination of single-variant tests (OCST) by combining information from tests of the three classes. We use extensive simulation studies to compare the performance of OCST with that of burden, quadratic and optimal single-variant tests. Our results show that OCST either is the most powerful test or has similar power with the most powerful test. We also compare the performance of OCST with that of the two existing combined tests. Our results show that OCST has better power than the two combined tests. PMID:25065727

  10. A Rare Variant Association Test Based on Combinations of Single-Variant Tests

    PubMed Central

    Sha, Qiuying; Zhang, Shuanglin

    2014-01-01

    Next generation sequencing technologies make directly testing rare variant associations possible. However, the development of powerful statistical methods for rare variant association studies is still underway. Most of existing methods are burden and quadratic tests. Recent studies show that the performance of each of burden and quadratic tests depends strongly upon the underlying assumption and no test demonstrates consistently acceptable power. Thus, combined tests by combining information from the burden and quadratic tests have been proposed recently. However, results from recent studies (including this study) show that there exist tests that can outperform both burden and quadratic tests. In this article, we propose three classes of tests that include tests outperforming both burden and quadratic tests. Then, we propose the optimal combination of single-variant tests (OCST) by combining information from tests of the three classes. We use extensive simulation studies to compare the performance of OCST with that of burden, quadratic and optimal single-variant tests. Our results show that OCST either is the most powerful test or has similar power with the most powerful test. We also compare the performance of OCST with that of the two existing combined tests. Our results show that OCST has better power than the two combined tests. PMID:25065727

  11. False discovery rates for rare variants from sequenced data

    PubMed Central

    Seshan, Venkatraman E.

    2016-01-01

    The detection of rare deleterious variants is the pre-eminent current technical challenge in statistical genetics. Sorting the deleterious from neutral variants at a disease locus is challenging because of the sparseness of the evidence for each individual variant. Hierarchical modeling and Bayesian model uncertainty are two techniques that have been shown to be promising in pinpointing individual rare variants that may be driving the association. Interpreting the results from these techniques from the perspective of multiple testing is a challenge and the goal of this article is to better understand their false discovery properties. Using simulations, we conclude that accurate false discovery control cannot be achieved in this framework unless the magnitude of the variants’ risk is large and the hierarchical characteristics have high accuracy in distinguishing deleterious from neutral variants. PMID:25556339

  12. Variants in CUL4B are Associated with Cerebral Malformations

    PubMed Central

    Vulto-van Silfhout, Anneke T.; Nakagawa, Tadashi; Bahi-Buisson, Nadia; Haas, Stefan A.; Hu, Hao; Bienek, Melanie; Vissers, Lisenka E.L.M.; Gilissen, Christian; Tzschach, Andreas; Busche, Andreas; Müsebeck, Jörg; Rump, Patrick; Mathijssen, Inge B.; Avela, Kristiina; Somer, Mirja; Doagu, Fatma; Philips, Anju K.; Rauch, Anita; Baumer, Alessandra; Voesenek, Krysta; Poirier, Karine; Vigneron, Jacqueline; Amram, Daniel; Odent, Sylvie; Nawara, Magdalena; Obersztyn, Ewa; Lenart, Jacek; Charzewska, Agnieszka; Lebrun, Nicolas; Fischer, Ute; Nillesen, Willy M.; Yntema, Helger G.; Järvelä, Irma; Ropers, Hans-Hilger; de Vries, Bert B.A.; Brunner, Han G.; van Bokhoven, Hans; Raymond, F. Lucy; Willemsen, Michèl A.A.P.; Chelly, Jamel; Xiong, Yue; Barkovich, A. James; Kalscheuer, Vera M.; Kleefstra, Tjitske; de Brouwer, Arjan P.M.

    2015-01-01

    Variants in cullin 4B (CUL4B) are a known cause of syndromic X-linked intellectual disability. Here, we describe an additional 25 patients from 11 families with variants in CUL4B. We identified nine different novel variants in these families and confirmed the pathogenicity of all nontruncating variants. Neuroimaging data, available for 15 patients, showed the presence of cerebral malformations in ten patients. The cerebral anomalies comprised malformations of cortical development (MCD), ventriculomegaly, and diminished white matter volume. The phenotypic heterogeneity of the cerebral malformations might result from the involvement of CUL-4B in various cellular pathways essential for normal brain development. Accordingly, we show that CUL-4B interacts with WDR62, a protein in which variants were previously identified in patients with microcephaly and a wide range of MCD. This interaction might contribute to the development of cerebral malformations in patients with variants in CUL4B. PMID:25385192

  13. False discovery rates for rare variants from sequenced data.

    PubMed

    Capanu, Marinela; Seshan, Venkatraman E

    2015-02-01

    The detection of rare deleterious variants is the preeminent current technical challenge in statistical genetics. Sorting the deleterious from neutral variants at a disease locus is challenging because of the sparseness of the evidence for each individual variant. Hierarchical modeling and Bayesian model uncertainty are two techniques that have been shown to be promising in pinpointing individual rare variants that may be driving the association. Interpreting the results from these techniques from the perspective of multiple testing is a challenge and the goal of this article is to better understand their false discovery properties. Using simulations, we conclude that accurate false discovery control cannot be achieved in this framework unless the magnitude of the variants' risk is large and the hierarchical characteristics have high accuracy in distinguishing deleterious from neutral variants. PMID:25556339

  14. Clinical relevance of hepatitis B virus variants

    PubMed Central

    Gao, Shan; Duan, Zhong-Ping; Coffin, Carla S

    2015-01-01

    The hepatitis B virus (HBV) is a global public health problem with more than 240 million people chronically infected worldwide, who are at risk for end-stage liver disease and hepatocellular carcinoma. There are an estimated 600000 deaths annually from complications of HBV-related liver disease. Antiviral therapy with nucleos/tide analogs (NA) targeting the HBV polymerase (P) can inhibit disease progression by long-term suppression of HBV replication. However, treatment may fail with first generation NA therapy due to the emergence of drug-resistant mutants, as well as incomplete medication adherence. The HBV replicates via an error-prone reverse transcriptase leading to quasispecies. Due to overlapping open reading frames mutations within the HBV P can cause concomitant changes in the HBV surface gene (S) and vice versa. HBV quasispecies diversity is associated with response to antiviral therapy, disease severity and long-term clinical outcomes. Specific mutants have been associated with antiviral drug resistance, immune escape, liver fibrosis development and tumorgenesis. An understanding of HBV variants and their clinical relevance may be important for monitoring chronic hepatitis B disease progression and treatment response. In this review, we will discuss HBV molecular virology, mechanism of variant development, and their potential clinical impact. PMID:26052397

  15. Clinical relevance of hepatitis B virus variants.

    PubMed

    Gao, Shan; Duan, Zhong-Ping; Coffin, Carla S

    2015-05-18

    The hepatitis B virus (HBV) is a global public health problem with more than 240 million people chronically infected worldwide, who are at risk for end-stage liver disease and hepatocellular carcinoma. There are an estimated 600000 deaths annually from complications of HBV-related liver disease. Antiviral therapy with nucleos/tide analogs (NA) targeting the HBV polymerase (P) can inhibit disease progression by long-term suppression of HBV replication. However, treatment may fail with first generation NA therapy due to the emergence of drug-resistant mutants, as well as incomplete medication adherence. The HBV replicates via an error-prone reverse transcriptase leading to quasispecies. Due to overlapping open reading frames mutations within the HBV P can cause concomitant changes in the HBV surface gene (S) and vice versa. HBV quasispecies diversity is associated with response to antiviral therapy, disease severity and long-term clinical outcomes. Specific mutants have been associated with antiviral drug resistance, immune escape, liver fibrosis development and tumorgenesis. An understanding of HBV variants and their clinical relevance may be important for monitoring chronic hepatitis B disease progression and treatment response. In this review, we will discuss HBV molecular virology, mechanism of variant development, and their potential clinical impact. PMID:26052397

  16. Genomic variant representation in a Chlamydia population is dynamic and adaptive with dependence on in vitro and in vivo passage.

    PubMed

    Jasper, Deana K; Sigar, Ira M; Schripsema, Justin H; Sainvil, Carlyn K; Smith, Christopher L; Yeruva, Laxmi; Rank, Roger G; Murthy, Ashlesh K; Widder, Jared R; Ramsey, Kyle H

    2015-02-01

    We have previously shown that Chlamydia muridarum has multiple genomic variants that concomitantly vary in their in vitro and in vivo phenotype. Herein, we used real-time polymerase chain reaction-based genotyping assays to query plaque-cloned isolates of C. muridarum for the frequency of eight selected polymorphisms. These strains had no history of passage in vivo since their original isolation from laboratory mice. There was significant variance in the frequency of two of the eight polymorphisms assessed with the remaining exhibiting a low rate of variance. To determine if any of these polymorphisms were more favorable for in vivo conditions, we blindly passaged non-clonal C. muridarum three times at 7-day intervals through the urogenital tract of mice. Seven of the eight polymorphisms varied in frequency following in vivo passage and four of these varied between C. muridarum strains. Selected isolates displayed variable growth rates and cytopathic effect in vitro. We conclude that multiple genotypic variants are present within the existing known C. muridarum strains and that the frequency of these variants changes upon introduction into the mouse host. These findings lend support to the concept that genotypic proportional representation in a chlamydial population is dynamic and adaptive. PMID:25673672

  17. Complete nucleotide sequence analysis of the norovirus GII.17: A newly emerging and dominant variant in China, 2015.

    PubMed

    Wang, Hai-Bo; Wang, Qi; Zhao, Jun-Hua; Tu, Cheng-Ning; Mo, Qiu-Hua; Lin, Ji-Can; Yang, Ze

    2016-03-01

    Norovirus is an important pathogen which accounts for majority of the viral related acute gastroenteritis. Recently, a variant of genotype GII.17 was reported to be predominant over GII.4 and accounted for several acute gastroenteritis outbreaks in Asia. In the current study, the full genome of a norovirus strain ZHITHC-12 isolated during this outbreak period in China was identified and characterized. The viral genome was 7557 nucleotides in length and a phylogenetic analysis based on full length genome sequences indicated that ZHITHC-12 belonged to GII.17 genotype. A further phylogenetic analysis based on all available polymerase and capsid sequences showed that ZHITHC-12 was in Cluster III on both phylogenetic trees and grouped with other strains also isolated during 2013 to 2015. Moreover, homology modeling analysis based on GII norovirus capsid 5BSX template revealed that substitutions, mutations, and more importantly, deletions and insertions, occurred at or near the putative epitopes and histo-blood group antigen (HBGA) binding sites in its protruding P2 domain, which might confer new antigenic or biological properties for this novel variant. In summary, the first full genome and capsid protein structure of a novel norovirus GII.17 variant isolated in China was extensively characterized. The data would be helpful not only for the epidemiology study, but also for the diagnostic tool development and effective vaccine design in the future. PMID:26687061

  18. [Transferrin variants: significance and identification in paternity cases (author's transl)].

    PubMed

    Mauff, G; Doppelfeld, E; Weber, W

    1975-08-01

    Transferrin phenotypes were determined in 3380 sera of unrelated persons of the western region of Germany with 97.60 percent for TfC and 2.40 percent for Tf variants. Identification was achieved by immunochemical means or through autoradiography. Relative mobilities in some variants were measured using Tf B2C (0.7) as reference. Application of Tf variants is demonstrated in paternity cases. PMID:171873

  19. Improving coeliac disease risk prediction by testing non-HLA variants additional to HLA variants

    PubMed Central

    Romanos, Jihane; Rosén, Anna; Kumar, Vinod; Trynka, Gosia; Franke, Lude; Szperl, Agata; Gutierrez-Achury, Javier; van Diemen, Cleo C; Kanninga, Roan; Jankipersadsing, Soesma A; Steck, Andrea; Eisenbarth, Georges; van Heel, David A; Cukrowska, Bozena; Bruno, Valentina; Mazzilli, Maria Cristina; Núñez, Concepcion; Bilbao, Jose Ramon; Mearin, M Luisa; Barisani, Donatella; Rewers, Marian; Norris, Jill M; Ivarsson, Anneli; Boezen, H Marieke; Liu, Edwin; Wijmenga, Cisca

    2014-01-01

    Background The majority of coeliac disease (CD) patients are not being properly diagnosed and therefore remain untreated, leading to a greater risk of developing CD-associated complications. The major genetic risk heterodimer, HLA-DQ2 and DQ8, is already used clinically to help exclude disease. However, approximately 40% of the population carry these alleles and the majority never develop CD. Objective We explored whether CD risk prediction can be improved by adding non-HLA-susceptible variants to common HLA testing. Design We developed an average weighted genetic risk score with 10, 26 and 57 single nucleotide polymorphisms (SNP) in 2675 cases and 2815 controls and assessed the improvement in risk prediction provided by the non-HLA SNP. Moreover, we assessed the transferability of the genetic risk model with 26 non-HLA variants to a nested case–control population (n=1709) and a prospective cohort (n=1245) and then tested how well this model predicted CD outcome for 985 independent individuals. Results Adding 57 non-HLA variants to HLA testing showed a statistically significant improvement compared to scores from models based on HLA only, HLA plus 10 SNP and HLA plus 26 SNP. With 57 non-HLA variants, the area under the receiver operator characteristic curve reached 0.854 compared to 0.823 for HLA only, and 11.1% of individuals were reclassified to a more accurate risk group. We show that the risk model with HLA plus 26 SNP is useful in independent populations. Conclusions Predicting risk with 57 additional non-HLA variants improved the identification of potential CD patients. This demonstrates a possible role for combined HLA and non-HLA genetic testing in diagnostic work for CD. PMID:23704318

  20. Natural Variants of C. elegans Demonstrate Defects in Both Sperm Function and Oogenesis at Elevated Temperatures

    PubMed Central

    Petrella, Lisa N.

    2014-01-01

    The temperature sensitivity of the germ line is conserved from nematodes to mammals. Previous studies in C. briggsae and Drosophila showed that isolates originating from temperate latitudes lose fertility at a lower temperature than strains originating from tropical latitudes. In order to investigate these relationships in C. elegans, analysis of the fertility of 22 different wild-type isolates of C. elegans isolated from equatorial, tropical and temperate regions was undertaken. It was found that there are significant temperature, genotype and temperature × genotype effects on fertility but region of isolation showed no significant effect on differences in fertility. For most isolates 100% of the population maintained fertility from 20°C to 26°C, but there was a precipitous drop in the percentage of fertile hermaphrodites at 27°C. In contrast, all isolates show a progressive decrease in brood size as temperature increases from 20°C to 26°C, followed by a brood size near zero at 27°C. Temperature shift experiments were performed to better understand the causes of high temperature loss of fertility. Males up-shifted to high temperature maintained fertility, while males raised at high temperature lost fertility. Down-shifting males raised at high temperature generally did not restore fertility. This result differs from that observed in Drosophila and suggested that in C. elegans spermatogenesis or sperm function is irreversibly impaired in males that develop at high temperature. Mating and down-shifting experiments with hermaphrodites were performed to investigate the relative contributions of spermatogenic and oogenic defects to high temperature loss of fertility. It was found that the hermaphrodites of all isolates demonstrated loss in both spermatogenic and oogenic germ lines that differed in their relative contribution by isolate. These studies uncovered unexpectedly high variation in both the loss of fertility and problems with oocyte function in natural variants of C. elegans at high temperature. PMID:25380048

  1. Isolated sleep paralysis

    MedlinePLUS

    Sleep paralysis - isolated; Parasomnia - isolated sleep paralysis ... Episodes of isolated sleep paralysis last from a few seconds to 1 or 2 minutes. During these episodes the person is unable to move ...

  2. RcsB Contributes to the Distinct Stress Fitness among Escherichia coli O157:H7 Curli Variants of the 1993 Hamburger-Associated Outbreak Strains

    PubMed Central

    Parker, Craig T.; Louie, Jacqueline W.; Huynh, Steven; Fagerquist, Clifton K.; Mandrell, Robert E.

    2012-01-01

    Curli are adhesive fimbriae of Enterobactericaeae and are involved in surface attachment, cell aggregation, and biofilm formation. We reported previously that curli-producing (C+) variants of E. coli O157:H7 (EcO157) were much more acid sensitive than their corresponding curli-deficient (C−) variants; however, this difference was not linked to the curli fimbriae per se. Here, we investigated the underlying molecular basis of this phenotypic divergence. We identified large deletions in the rcsB gene of C+ variants isolated from the 1993 U.S. hamburger-associated outbreak strains. rcsB encodes the response regulator of the RcsCDB two-component signal transduction system, which regulates curli biogenesis negatively but acid resistance positively. Further comparison of stress fitness revealed that C+ variants were also significantly more sensitive to heat shock but were resistant to osmotic stress and oxidative damage, similar to C− variants. Transcriptomics analysis uncovered a large number of differentially expressed genes between the curli variants, characterized by enhanced expression in C+ variants of genes related to biofilm formation, virulence, catabolic activity, and nutrient uptake but marked decreases in transcription of genes related to various types of stress resistance. Supplying C+ variants with a functional rcsB restored resistance to heat shock and acid challenge in cells but blocked curli production, confirming that inactivation of RcsB in C+ variants was the basis of fitness segregation within the EcO157 population. This study provides an example of how genome instability of EcO157 promotes intrapopulation diversification, generating subpopulations carrying an array of distinct phenotypes that may confer the pathogen with survival advantages in diverse environments. PMID:22923406

  3. Multilocus variable-number tandem-repeat analysis of clinical isolates of Aspergillus flavus from Iran reveals the first cases of Aspergillus minisclerotigenes associated with human infection

    PubMed Central

    2014-01-01

    Background Aspergillus flavus is intensively studied for its role in infecting crop plants and contaminating produce with aflatoxin, but its role as a human pathogen is less well understood. In parts of the Middle East and India, A. flavus surpasses A. fumigatus as a cause of invasive aspergillosis and is a significant cause of cutaneous, sinus, nasal and nail infections. Methods A collection of 45 clinical and 10 environmental A. flavus isolates from Iran were analysed using Variable-Number Tandem-Repeat (VNTR) markers with MICROSAT and goeBURST to determine their genetic diversity and their relatedness to clinical and environmental A. flavus isolates from Australia. Phylogeny was assessed using partial β-tubulin and calmodulin gene sequencing, and mating type was determined by PCR. Antifungal susceptibility testing was performed on selected isolates using a reference microbroth dilution method. Results There was considerable diversity in the A. flavus collection, with no segregation on goeBURST networks according to source or geographic location. Three Iranian isolates, two from sinus infections and one from a paranasal infection grouped with Aspergillus minisclerotigenes, and all produced B and G aflatoxin. Phylogenic analysis using partial β-tubulin and calmodulin sequencing confirmed two of these as A. minisclerotigenes, while the third could not be differentiated from A. flavus and related species within Aspergillus section flavi. Based on epidemiological cut-off values, the A. minisclerotigens and A. flavus isolates tested were susceptible to commonly used antifungal drugs. Conclusions This is the first report of human infection due to A. minisclerotigenes, and it raises the possiblity that other species within Aspergillus section flavi may also cause clinical disease. Clinical isolates of A. flavus from Iran are not distinct from Australian isolates, indicating local environmental, climatic or host features, rather than fungal features, govern the high incidence of A. flavus infection in this region. The results of this study have important implications for biological control strategies that aim to reduce aflatoxin by the introduction of non-toxigenic strains, as potentially any strain of A. flavus, and closely related species like A. minisclerotigenes, might be capable of human infection. PMID:24986045

  4. Molecular Evidence of Cholera Outbreak Caused by a Toxigenic Vibrio cholerae O1 El Tor Variant Strain in Kelantan, Malaysia ?

    PubMed Central

    Ang, Geik Yong; Yu, Choo Yee; Balqis, Kamarudin; Elina, Husni Tan; Azura, Hussin; Hani, Mat Hussin; Yean, Chan Yean

    2010-01-01

    A total of 20 Vibrio cholerae isolates were recovered for investigation from a cholera outbreak in Kelantan, Malaysia, that occurred between November and December 2009. All isolates were biochemically characterized as V. cholerae serogroup O1 Ogawa of the El Tor biotype. They were found to be resistant to multiple antibiotics, including tetracycline, erythromycin, sulfamethoxazole-trimethoprim, streptomycin, penicillin G, and polymyxin B, with 35% of the isolates being resistant to ampicillin. All isolates were sensitive to ciprofloxacin, norfloxacin, chloramphenicol, gentamicin, and kanamycin. Multiplex PCR analysis confirmed the biochemical identification and revealed the presence of virulence genes, viz., ace, zot, and ctxA, in all of the isolates. Interestingly, the sequencing of the ctxB gene showed that the outbreak strain harbored the classical cholera toxin gene and therefore belongs to the newly assigned El Tor variant biotype. Clonal analysis by pulsed-field gel electrophoresis demonstrated that a single clone of a V. cholerae strain was responsible for this outbreak. Thus, we present the first molecular evidence that the toxigenic V. cholerae O1 El Tor variant has invaded Malaysia, highlighting the need for continuous monitoring to facilitate early interventions against any potential epidemic by this biotype. PMID:20826646

  5. A casein variant in cow's milk is atherogenic.

    PubMed

    Tailford, Kristy A; Berry, Celia L; Thomas, Anita C; Campbell, Julie H

    2003-09-01

    Casein is a major protein in cow's milk that occurs in several variant forms, two of which are beta-casein A1 and beta-casein A2. The levels of these two proteins vary considerably in milk dependent on the breed of cow, and epidemiology studies suggest that there is a relationship between their consumption and the degree of atherosclerosis. In the present study, the direct effect of consumption of beta-casein A1 vs beta-casein A2 on atherosclerosis development was examined in a rabbit model. Sixty rabbits had their right carotid artery balloon de-endothelialised at t=0, divided randomly into 10 groups (n=6 per group), then for 6 weeks fed a diet containing 0, 5, 10 or 20% casein isolate, either beta-casein variant A1 or A2, made up to 20% milk protein with whey. Some groups had their diets supplemented with 0.5% cholesterol. Blood samples were collected at t=0, 3 and 6 weeks and rabbits were sacrificed at t=6 weeks. In the absence of dietary cholesterol, beta-casein A1 produced significantly higher (P<0.05) serum cholesterol, LDL, HDL and triglyceride levels than whey diet alone, which in turn produced higher levels than beta-casein A2. Rabbits fed beta-casein A1 had a higher percent surface area of aorta covered by fatty streaks than those fed beta-casein A2 (5.2+/-0.81 vs 1.1+/-0.39, P<0.05) and the thickness of the fatty streak lesions in the aortic arch was significantly higher (0.04+/-0.010 vs 0.00, P<0.05). Similarly, the intima to media ratio (I:M) of the balloon injured carotid arteries in A1 fed animals (0.77+/-0.07) was higher than in those that consumed A2 (0.57+/-0.04) or whey (0.58+/-0.04), but this did not reach significance. In the presence of 0.5% dietary cholesterol, the thickness of the aortic arch lesions was higher (P<0.05) in 5, 10 and 20% casein A1 fed animals compared with their A2 counterparts, while other parameters were not significantly different. It is concluded that beta-casein A1 is atherogenic compared with beta-casein A2. PMID:12957678

  6. Identifying rare variants associated with complex traits via sequencing

    PubMed Central

    Li, Bingshan; Liu, Dajiang J.; Leal, Suzanne M.

    2013-01-01

    Although genome-wide association studies have been successful in detecting associations with common variants, there is currently an increasing interest in identifying low frequency and rare variants associated with complex traits. Next-generation sequencing technologies make it feasible to survey the full spectrum of genetic variation in coding regions or the entire genome. Due to the low frequency of rare variants, coupled with allelic heterogeneity, however, the association analysis for rare variants is challenging and traditional methods are ineffective. Recently a battery of new statistical methods has been proposed for identifying rare variants associated with complex traits. These methods test for associations by aggregating multiple rare variants across a gene or a genomic region, or a group of variants in the genome. In this Unit, we describe key concepts for rare variant association for complex traits, survey some of the recent methods and discuss their statistical power under various scenarios, and provide practical guidance on analyzing next-generation sequencing data for identifying rare variants associated with complex traits. PMID:23853079

  7. Neutral and weakly nonneutral sequence variants may define individuality

    PubMed Central

    Bromberg, Yana; Kahn, Peter C.; Rost, Burkhard

    2013-01-01

    Large-scale computational analyses of the growing wealth of genome-variation data consistently tell two distinct stories. The first is expected: coding variants reported in disease-related databases significantly alter the function of affected proteins. The second is surprising: the genomes of healthy individuals appear to carry many variants that are predicted to have some effect on function. As long as the complete experimental analysis of all human genome variants remains impossible, computational methods, such as PolyPhen, SNAP, and SIFT, might provide important insights. These methods capture the effects of particular variants very well and can highlight trends in populations of variants. Diseases are, arguably, extreme phenotypic variations and are often attributable to one or a few severely functionally disruptive variants. Our findings suggest a genomic basis of the different nondisease phenotypes. Prediction methods indicate that variants in seemingly healthy individuals tend to be neutral or weakly disruptive for protein molecular function. These variant effects are predicted to be largely either experimentally undetectable or are not deemed significant enough to be published. This may suggest that nondisease phenotypes arise through combinations of many variants whose effects are weakly nonneutral (damaging or enhancing) to the molecular protein function but fall within the wild-type range of overall physiological function. PMID:23940345

  8. A unified phylogeny-based nomenclature for histone variants

    PubMed Central

    2012-01-01

    Histone variants are non-allelic protein isoforms that play key roles in diversifying chromatin structure. The known number of such variants has greatly increased in recent years, but the lack of naming conventions for them has led to a variety of naming styles, multiple synonyms and misleading homographs that obscure variant relationships and complicate database searches. We propose here a unified nomenclature for variants of all five classes of histones that uses consistent but flexible naming conventions to produce names that are informative and readily searchable. The nomenclature builds on historical usage and incorporates phylogenetic relationships, which are strong predictors of structure and function. A key feature is the consistent use of punctuation to represent phylogenetic divergence, making explicit the relationships among variant subtypes that have previously been implicit or unclear. We recommend that by default new histone variants be named with organism-specific paralog-number suffixes that lack phylogenetic implication, while letter suffixes be reserved for structurally distinct clades of variants. For clarity and searchability, we encourage the use of descriptors that are separate from the phylogeny-based variant name to indicate developmental and other properties of variants that may be independent of structure. PMID:22650316

  9. VIRUS NOMENCLATURE BELOW THE SPECIES LEVEL: A STANDARDIZED NOMENCLATURE FOR LABORATORY ANIMAL-ADAPTED STRAINS AND VARIANTS OF VIRUSES ASSIGNED TO THE FAMILY FILOVIRIDAE

    PubMed Central

    Kuhn, Jens H.; Bao, Yiming; Bavari, Sina; Becker, Stephan; Bradfute, Steven; Brister, J. Rodney; Bukreyev, Alexander A.; Caì, Yíngyún; Chandran, Kartik; Davey, Robert A.; Dolnik, Olga; Dye, John M.; Enterlein, Sven; Gonzalez, Jean-Paul; Formenty, Pierre; Freiberg, Alexander N.; Hensley, Lisa E.; Honko, Anna N.; Ignatyev, Georgy M.; Jahrling, Peter B.; Johnson, Karl M.; Klenk, Hans-Dieter; Kobinger, Gary; Lackemeyer, Matthew G.; Leroy, Eric M.; Lever, Mark S.; Lofts, Loreen L.; Mühlberger, Elke; Netesov, Sergey V.; Olinger, Gene G.; Palacios, Gustavo; Patterson, Jean L.; Paweska, Janusz T.; Pitt, Louise; Radoshitzky, Sheli R.; Ryabchikova, Elena I.; Saphire, Erica Ollmann; Shestopalov, Aleksandr M.; Smither, Sophie J.; Sullivan, Nancy J.; Swanepoel, Robert; Takada, Ayato; Towner, Jonathan S.; van der Groen, Guido; Volchkov, Viktor E.; Wahl-Jensen, Victoria; Warren, Travis K.; Warfield, Kelly L.; Weidmann, Manfred; Nichol, Stuart T.

    2013-01-01

    The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of viruses into taxa, but is not responsible for the nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and nomenclature for filoviruses. Subsequently, and together with numerous other filovirus experts, a consistent nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoviruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filovirus genetic variant naming ( <isolation host-suffix>///variant designation>-<isolate designation>) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology “Vector” to cause disease in guinea pigs after seven passages would be akin to “Ebola virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7”. As was proposed for the names of natural filovirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as “EBOV VECTOR/C.por/COD/76/May-GPA-P7”) and abbreviations (such as “EBOV/May-GPA-P7”) could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed. PMID:23358612

  10. Production of bacteriolytic activity in the oral cavity by nutritionally variant streptococci.

    PubMed Central

    Pompei, R; Caredda, E; Piras, V; Serra, C; Pintus, L

    1990-01-01

    Microorganisms from the oral flora were examined for the production of bacteriolytic substances. Among human viridans group streptococci, only one group of strains with thiol-dependent properties was shown to secrete enzymes with bacteriolytic activity on heat-killed cells of Micrococcus luteus on double-layer nutrient agar plates. By morphology, culture requirements, and biochemical properties, they were found to conform to descriptions of nutritionally variant streptococci (NVS). Bacteriolytic activity was shown to be a constant property of all of the human oral NVS isolated and a property of some reference strains of NVS from clinical sources. No other known species of viridans group streptococci demonstrated bacteriolytic activity. Analysis of bacteriolytic activity could be a useful tool for both the isolation and identification of this fastidious group of microorganisms. Images PMID:2380384

  11. Association of FTO variants with BMI and fat mass in the self-contained population of Sorbs in Germany

    PubMed Central

    Tönjes, Anke; Zeggini, Eleftheria; Kovacs, Peter; Böttcher, Yvonne; Schleinitz, Dorit; Dietrich, Kerstin; Morris, Andrew P; Enigk, Beate; Rayner, Nigel W; Koriath, Moritz; Eszlinger, Markus; Kemppinen, Anu; Prokopenko, Inga; Hoffmann, Katrin; Teupser, Daniel; Thiery, Joachim; Krohn, Knut; McCarthy, Mark I; Stumvoll, Michael

    2010-01-01

    The association between common variants in the FTO gene with weight, adiposity and body mass index (BMI) has now been widely replicated. Although the causal variant has yet to be identified, it most likely maps within a 47?kb region of intron 1 of FTO. We performed a genome-wide association study in the Sorbian population and evaluated the relationships between FTO variants and BMI and fat mass in this isolate of Slavonic origin resident in Germany. In a sample of 948 Sorbs, we could replicate the earlier reported associations of intron 1 SNPs with BMI (eg, P-value=0.003, ?=0.02 for rs8050136). However, using genome-wide association data, we also detected a second independent signal mapping to a region in intron 2/3 about 40–60?kb away from the originally reported SNPs (eg, for rs17818902 association with BMI P-value=0.0006, ?=?0.03 and with fat mass P-value=0.0018, ?=?0.079). Both signals remain independently associated in the conditioned analyses. In conclusion, we extend the evidence that FTO variants are associated with BMI by putatively identifying a second susceptibility allele independent of that described earlier. Although further statistical analysis of these findings is hampered by the finite size of the Sorbian isolate, these findings should encourage other groups to seek alternative susceptibility variants within FTO (and other established susceptibility loci) using the opportunities afforded by analyses in populations with divergent mutational and/or demographic histories. PMID:19584900

  12. Characterization of Human Influenza Virus Variants Selected In Vitro in the Presence of the Neuraminidase Inhibitor GS 4071

    PubMed Central

    Tai, Chun Y.; Escarpe, Paul A.; Sidwell, Robert W.; Williams, Matthew A.; Lew, Willard; Wu, Huiwei; Kim, Choung U.; Mendel, Dirk B.

    1998-01-01

    An oral prodrug of GS 4071, a potent and selective inhibitor of influenza neuraminidases, is currently under clinical development for the treatment and prophylaxis of influenza virus infections in humans. To investigate the potential development of resistance during the clinical use of this compound, variants of the human influenza A/Victoria/3/75 (H3N2) virus with reduced susceptibility to the neuraminidase inhibitor GS 4071 were selected in vitro by passaging the virus in MDCK cells in the presence of inhibitor. After eight passages, variants containing two amino acid substitutions in the hemagglutinin (A28T in HA1 and R124M in HA2) but no changes in the neuraminidase were isolated. These variants exhibited a 10-fold reduction in susceptibility to GS 4071 and zanamivir (GG167) in an in vitro plaque reduction assay. After 12 passages, a second variant containing these hemagglutinin mutations and a Lys substitution for the conserved Arg292 of the neuraminidase was isolated. The mutant neuraminidase enzyme exhibited high-level (30,000-fold) resistance to GS 4071, but only moderate (30-fold) resistance to zanamivir and 4-amino-Neu5Ac2en, the amino analog of zanamivir. The mutant enzyme had weaker affinity for the fluorogenic substrate 2?-(4-methylumbelliferyl)-?-d-N-acetylneuraminic acid and lower enzymatic activity compared to the wild-type enzyme. The viral variant containing the mutant neuraminidase did not replicate as well as the wild-type virus in culture and was 10,000-fold less infectious than the wild-type virus in a mouse model. These results suggest that although the R292K neuraminidase mutation confers high-level resistance to GS 4071 in vitro, its effect on viral virulence is likely to render this mutation of limited clinical significance. PMID:9835519

  13. Spontaneous Variants of the [RNQ+] Prion in Yeast Demonstrate the Extensive Conformational Diversity Possible with Prion Proteins

    PubMed Central

    Huang, Vincent J.; Stein, Kevin C.; True, Heather L.

    2013-01-01

    Prion strains (or variants) are structurally distinct amyloid conformations arising from a single polypeptide sequence. The existence of prion strains has been well documented in mammalian prion diseases. In many cases, prion strains manifest as variation in disease progression and pathology, and in some cases, these prion strains also show distinct biochemical properties. Yet, the underlying basis of prion propagation and the extent of conformational possibilities available to amyloidogenic proteins remain largely undefined. Prion proteins in yeast that are also capable of maintaining multiple self-propagating structures have provided much insight into prion biology. Here, we explore the vast structural diversity of the yeast prion [RNQ+] in Saccharomyces cerevisiae. We screened for the formation of [RNQ+] in vivo, allowing us to calculate the rate of spontaneous formation as ~2.96x10-6, and successfully isolate several different [RNQ+] variants. Through a comprehensive set of biochemical and biological analyses, we show that these prion variants are indeed novel. No individual property or set of properties, including aggregate stability and size, was sufficient to explain the physical basis and range of prion variants and their resulting cellular phenotypes. Furthermore, all of the [RNQ+] variants that we isolated were able to facilitate the de novo formation of the yeast prion [PSI+], an epigenetic determinant of translation termination. This supports the hypothesis that [RNQ+] acts as a functional amyloid in regulating the formation of [PSI+] to produce phenotypic diversity within a yeast population and promote adaptation. Collectively, this work shows the broad spectrum of available amyloid conformations, and thereby expands the foundation for studying the complex factors that interact to regulate the propagation of distinct aggregate structures. PMID:24205387

  14. Rare Complement Factor H Variant Associated With Age-Related Macular Degeneration in the Amish

    PubMed Central

    Hoffman, Joshua D.; CookeBailey, Jessica N.; D'Aoust, Laura; Cade, William; Ayala-Haedo, Juan; Fuzzell, Denise; Laux, Renee; Adams, Larry D.; Reinhart-Mercer, Lori; Caywood, Laura; Whitehead-Gay, Patrice; Agarwal, Anita; Wang, Gaofeng; Scott, William K.; Pericak-Vance, Margaret A.; Haines, Jonathan L.

    2014-01-01

    Purpose. Age-related macular degeneration is the leading cause of blindness among the adult population in the developed world. To further the understanding of this disease, we have studied the genetically isolated Amish population of Ohio and Indiana. Methods. Cumulative genetic risk scores were calculated using the 19 known allelic associations. Exome sequencing was performed in three members of a small Amish family with AMD who lacked the common risk alleles in complement factor H (CFH) and ARMS2/HTRA1. Follow-up genotyping and association analysis was performed in a cohort of 973 Amish individuals, including 95 with self-reported AMD. Results. The cumulative genetic risk score analysis generated a mean genetic risk score of 1.12 (95% confidence interval [CI]: 1.10, 1.13) in the Amish controls and 1.18 (95% CI: 1.13, 1.22) in the Amish cases. This mean difference in genetic risk scores is statistically significant (P = 0.0042). Exome sequencing identified a rare variant (P503A) in CFH. Association analysis in the remainder of the Amish sample revealed that the P503A variant is significantly associated with AMD (P = 9.27 × 10?13). Variant P503A was absent when evaluated in a cohort of 791 elderly non-Amish controls, and 1456 non-Amish cases. Conclusions. Data from the cumulative genetic risk score analysis suggests that the variants reported by the AMDGene consortium account for a smaller genetic burden of disease in the Amish compared with the non-Amish Caucasian population. Using exome sequencing data, we identified a novel missense mutation that is shared among a densely affected nuclear Amish family and located in a gene that has been previously implicated in AMD risk. PMID:24906858

  15. [Phenotypic and genetic features of cultural-morphologic variants of Bacillus anthracis].

    PubMed

    Tsygankova, O I; Eremenko, E I; Tsygankova, E A; Buravtseva, N P; Riazanova, A G

    2008-01-01

    Comparative analysis of MVLA-genotypes of 6 Bacillus anthracis strains and 40 their variants differing on capsule- and toxin synthesis, hemolytic, proteolytic and lecitinase activity, nutritional requirements, susceptibility to anthrax bacteriophages, virulence, immunogenicity, and presence of genes for capsule and toxin synthesis was performed. Results of phylogenetic analysis of 5 chromosome locuses and plasmid locus pXO1aat which are variable for this sample of B. anthracis cultures showed that all strains divided on 2 main clusters - A and B. Cluster A consisted of 5 genotypes whereas cluster B - of 1 genotype. All highly virulent original strains and variants with characteristic phenotype Cap(CO2)(+)(O2)(-)Tox(+)ProtA(+)Hly(+) Lec(-)Trp(+) had identical genotype in 4 groups and in 5th group differences were present only in vrrA locus. All original strains and variants with the most atypical complex of phenotypic characteristics Cap (CO2)(+)(O2)(+)Tox(-)ProtA(-)Hly(-)Lec(-)Trp(-) also had the same genotype belonging to cluster B and diverged on characteristic of 5 chromosomal VNTR locuses and pXO1aat locus from typical strains. Absence of toxin production in vitro was not related to loss of genetic determinants of toxin components. Cultures with typical characteristics, one of which was ability to produce toxin in vitro, had larger sizes of amplicons of pXO1aat locus (135 and 132 nbp), whereas atoxigenic original strains and variants with complex of atypical characteristics and identical chromosome genotype had the smallest sizes (123 bnp). All original cultures were isolated in Russia, their genotypes are described for the first time. PMID:18822496

  16. Genetic divergence of Chikungunya virus plaque variants from the Comoros Island (2005).

    PubMed

    Wasonga, Caroline; Inoue, Shingo; Rumberia, Cecilia; Michuki, George; Kimotho, James; Ongus, Juliette R; Sang, Rosemary; Musila, Lillian

    2015-12-01

    Chikungunya virus (CHIKV) from a human sample collected during the 2005 Chikungunya outbreak in the Comoros Island, showed distinct and reproducible large (L2) and small (S7) plaques which were characterized in this study. The parent strain and plaque variants were analysed by in vitro growth kinetics in different cell lines and their genetic similarity assessed by whole genome sequencing, comparative sequence alignment and phylogenetic analysis. In vitro growth kinetic assays showed similar growth patterns of both plaque variants in Vero cells but higher viral titres of S7 compared to L2 in C6/36 cells. Amino acids (AA) alignments of the CHIKV plaque variants and S27 African prototype strain, showed 30 AA changes in the non-structural proteins (nsP) and 22 AA changes in the structural proteins. Between L2 and S7, only two AAs differences were observed. A missense substitution (C642Y) of L2 in the nsP2, involving a conservative AA substitution and a nonsense substitution (R524X) of S7 in the nsP3, which has been shown to enhance O'nyong-nyong virus infectivity and dissemination in Anopheles mosquitoes. The phenotypic difference observed in plaque size could be attributed to one of these AA substitutions. Phylogenetic analysis showed that the parent strain and its variants clustered closely together with each other and with Indian Ocean CHIKV strains indicating circulation of isolates with close evolutionary relatedness in the same outbreak. These observations pave way for important functional studies to understand the significance of the identified genetic changes in virulence and viral transmission in mosquito and mammalian hosts. PMID:26347221

  17. A genome-wide survey of CD4+ lymphocyte regulatory genetic variants identifies novel asthma genes

    PubMed Central

    Sharma, Sunita; Zhou, Xiaobo; Thibault, Derek M.; Himes, Blanca E.; Liu, Andy; Szefler, Stanley J.; Strunk, Robert; Castro, Mario; Hansel, Nadia N.; Diette, Gregory B.; Vonakis, Becky M.; Adkinson, N. Franklin; Avila, Lydiana; Soto-Quiros, Manuel; Barraza-Villareal, Albino; Lemanske, Robert F.; Solway, Julian; Krishnan, Jerry; White, Steven R.; Cheadle, Chris; Berger, Alan E.; Fan, Jinshui; Boorgula, Meher Preethi; Nicolae, Dan; Gilliland, Frank; Barnes, Kathleen; London, Stephanie J.; Martinez, Fernando; Ober, Carole; Celedón, Juan C.; Carey, Vincent J.; Weiss, Scott T.; Raby, Benjamin A.

    2014-01-01

    Background Genome-wide association studies have yet to identify the majority of genetic variants involved in asthma. We hypothesized that expression quantitative trait locus (eQTL) mapping can identify novel asthma genes by enabling prioritization of putative functional variants for association testing. Objective We evaluated 6,706 cis-acting expression-associated variants (eSNP) identified through a genome-wide eQTL survey of CD4+ lymphocytes for association with asthma. Methods eSNP were tested for association with asthma in 359 asthma cases and 846 controls from the Childhood Asthma Management Program, with verification using family-based testing. Significant associations were tested for replication in 579 parent-child trios with asthma from Costa Rica. Further functional validation was performed by Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE)-qPCR and Chromatin-Immunoprecipitation (ChIP)-PCR in lung derived epithelial cell lines (Beas-2B and A549) and Jurkat cells, a leukemia cell line derived from T lymphocytes. Results Cis-acting eSNP demonstrated associations with asthma in both cohorts. We confirmed the previously-reported association of ORMDL3/GSDMB variants with asthma (combined p=2.9 × 108). Reproducible associations were also observed for eSNP in three additional genes: FADS2 (p=0.002), NAGA (p=0.0002), and F13A1 (p=0.0001). We subsequently demonstrated that FADS2 mRNA is increased in CD4+ lymphocytes in asthmatics, and that the associated eSNPs reside within DNA segments with histone modifications that denote open chromatin status and confer enhancer activity. Conclusions Our results demonstrate the utility of eQTL mapping in the identification of novel asthma genes, and provide evidence for the importance of FADS2, NAGA, and F13A1 in the pathogenesis of asthma. PMID:24934276

  18. [A telangiectatic clinical variant of mastocytosis].

    PubMed

    Kasimov, N

    1990-01-01

    Six cases of telangiectatic clinical variant of mastocytosis (TMV) are reported. Patients' age varied from 33 to 62, there were 2 men and 4 women. A number of clinical features of TMV were detected in the course of follow-up: a generalized type of the skin process; abundant maculopapular eruptions colored brownish, sometimes with a cyanotic shade, liable to fuse and form diffuse foci of involvement; development of telangiectasias on the surface of these eruptions; symptoms of elevated blood histamin levels, i.e. regular blood congestion, enhanced itching, tachycardia, gastrointestinal events, etc.; systemic mastocytosis (3 of the 6 patients developed lymphadenopathy and hepatomegaly). The detected features of the condition permit considering TMV as an individual clinical variety of mastocytosis. PMID:2288158

  19. Juvenile Spring Eruption: A Variant of Perniosis?

    PubMed

    Nabatian, Adam S; Rosman, Ilana S; Sturza, Jeffrey; Jacobson, Mark

    2015-09-01

    Juvenile spring eruption (JSE) is a unique condition that typically affects the helices of the ears of boys and young men. The classical clinical picture of JSE includes the abrupt onset of lesions after spending time outdoors in the early spring. Because of the papulovesicular nature of the rash and the history of sun exposure, JSE is considered a variant of polymorphous light eruption. In addition to the term "juvenile spring eruption," this entity has also been described under other less common terms such as "perniosis juvenilis vernalis aurium" or "spring perniosis," which emphasizes the onset in the spring and the possible pathogenic role of cold weather. We present a case of likely JSE with histopathologic features more consistent with perniosis than polymorphous light eruption and present a review the literature. PMID:26291421

  20. Keratoameloblastoma: complex histologic variant of ameloblastoma.

    PubMed

    Sisto, John M; Olsen, Gregory G

    2012-04-01

    Keratoameloblastoma is a rare subtype of ameloblastoma that has been reported only 12 times previously in the literature. Ameloblastomas are benign, locally aggressive neoplasms that constitute approximately 1% of odontogenic neoplasms. The mandible is involved in 80% of cases and the maxilla 20%. Clinically, these appear as solid, unicystic, multicystic, and mixed solid and multicystic tumors. Histologically, these are classified as follicular, plexiform, acanthomatous, and granular cell. Less common histologic variants are clear cell, desmoplastic, basal cell, papilliferous, and keratoameloblastoma. This report presents a new case to the literature, reviews histologic findings and radiographic appearance, and discusses the clinical significance of this tumor with respect to treatment based on currently available literature. PMID:21798640

  1. Variant terminology. [for aerospace information systems

    NASA Technical Reports Server (NTRS)

    Buchan, Ronald L.

    1991-01-01

    A system called Variant Terminology Switching (VTS) is set forth that is intended to provide computer-assisted spellings for terms that have American and British versions. VTS is based on the use of brackets, parentheses, and other symbols in conjunction with letters that distinguish American and British spellings. The symbols are used in the systems as indicators of actions such as deleting, adding, and replacing letters as well as replacing entire words and concepts. The system is shown to be useful for the intended purpose and also for the recognition of misspellings and for the standardization of computerized input/output. The VTS system is of interest to the development of international retrieval systems for aerospace and other technical databases that enhance the use by the global scientific community.

  2. Possible new variant of Nijmegen breakage syndrome

    SciTech Connect

    Der Kaloustian, V.M.; Booth, A.; Elliott, A.M.

    1996-10-02

    We report on a child with microcephaly, small facial and body size, and immune deficiency. The phenotype is consistent with Nijmegen breakage syndrome (NBS), with additional clinical manifestations and laboratory findings not reported heretofore. Most investigations, including the results of radiation-resistant DNA synthesis, concurred with the diagnosis of NBS. Cytogenetic analysis documented abnormalities in virtually all cells examined. Along with the high frequency of breaks and rearrangements of chromosomes 7 and 14, we found breakage and monosomies involving numerous other chromosomes. Because of some variation in the clinical presentation and some unusual cytogenetic findings, we suggest that our patient may represent a new variant of Nijmegen breakage syndrome. 34 refs., 3 figs., 7 tabs.

  3. Aequorin variants with improved bioluminescence properties

    PubMed Central

    Dikici, E.; Qu, X.; Rowe, L.; Millner, L.; Logue, C.; Deo, S.K.; Ensor, M.; Daunert, S.

    2009-01-01

    The photoprotein aequorin has been widely used as a bioluminescent label in immunoassays, for the determination of calcium concentrations in vivo, and as a reporter in cellular imaging. It is composed of apoaequorin (189 amino acid residues), the imidazopyrazine chromophore coelenterazine and molecular oxygen. The emission characteristics of aequorin can be changed by rational design of the protein to introduce mutations in its structure, as well as by substituting different coelenterazine analogues to yield semi-synthetic aequorins. Variants of aequorin were created by mutating residues His16, Met19, Tyr82, Trp86, Trp108, Phe113 and Tyr132. Forty-two aequorin mutants were prepared and combined with 10 different coelenterazine analogues in a search for proteins with different emission wavelengths, altered decay kinetics and improved stability. This spectral tuning strategy resulted in semi-synthetic photoprotein mutants with significantly altered bioluminescent properties. PMID:19168563

  4. Right temporal lobe variant of frontotemporal dementia.

    PubMed

    González-Caballero, G; Abellán-Miralles, I; Sáenz-Sanjuan, M J

    2015-07-01

    We present two women with the right temporal lobe variant (RTLV) of frontotemporal dementia (FTD) and analyse the clinical features that are determined by the anatomical distribution of atrophy. Each of our patients displayed different clinical and radiological profiles which were in line with findings reported by other authors. One of two patients carries a novel mutation in the granulin gene. FTD is heterogeneous with regard to clinical manifestation, genetics, distribution of cortical atrophy and underlying disease. Its clinical manifestations are related to the distribution of the cortical atrophy. The RTLV of FTD is an uncommon entity. There is no consensus about its name despite the fact that its clinical and radiological features are well-defined and distinguish it from other types of FTD including semantic dementia. PMID:25981552

  5. Genomic characteristics of miscarriage copy number variants.

    PubMed

    Bagheri, Hani; Mercier, Eloi; Qiao, Ying; Stephenson, Mary D; Rajcan-Separovic, Evica

    2015-08-01

    Studies of copy number variants (CNVs) in miscarriages are rare in comparison to post-natal cases with developmental abnormalities. The overall characteristics of miscarriage CNVs (size, gene content and function) are therefore largely unexplored. Our goal was to assess and compare the characteristics of CNVs identified in 101 euploid miscarriages from four high-resolution array studies that documented both common miscarriage CNVs (i.e. CNVs found in controls from the Database of Genomic Variants, DGV) and rare miscarriage CNVs (not reported in DGV). Our miscarriage analysis included 24 rare CNVs with 93 genes, and 372 common CNVs (merged into 119 common CNV regions; CNVRs) with 354 genes. The rare and common CNVs were comparable in size (median size of ? 0.16 and 0.14 Mb, respectively); however, rare CNVs showed a significantly higher gene density, with 56 genes/Mb in rare and 24 genes/Mb in common CNVs (P = 0.03). Rare CNVs also had two times more genes with mouse knock-out models which were reported for 42% of rare and 19% of common CNV genes. No specific pathway enrichment was noted for 24 rare CNV genes, but common CNV genes showed significant enrichment in genes from immune-response related pathways and pregnancy/reproduction-related biological processes. Our analysis of CNVs from euploid miscarriages suggests that both rare and common CNVs could have a role in miscarriage by impacting pregnancy-related genes or pathways. Cataloguing of all CNVs and detailed description of their characteristics (e.g. gene content, genomic breakpoints) is desirable in the future for better understanding of their relevance to pregnancy loss. PMID:26071097

  6. Genetic variants associated with protein C levels

    PubMed Central

    Vossen, C.Y.; Koeleman, B.P.; Hasstedt, S.J.; Nijman, I.J.; Renkens, I.J.; Callas, P.W.; Rosendaal, F.R.; Bovill, E.G.

    2013-01-01

    Summary Background Normal protein C (PC) plasma levels range widely in the general population. Factors influencing normal PC levels are thought to influence the risk of venous thrombosis. Little is known about the underlying genetic variants. Objectives We performed a genome scan of normal PC levels to identify genes that regulate normal PC levels. Patients/Methods We performed a variance components linkage analysis for normal PC levels in 275 individuals from a single, large family. We then sequenced candidate genes under the identified linkage peak in eight family members: four with high and four with low, but normal PC levels. For variants showing a difference in carriers between those with high and low PC levels, we re-evaluated linkage in the 275 family members conditional on the measured genotype effect. Genotype-specific mean PC levels were determined using likelihood analysis. Findings were replicated in the Leiden Thrombophilia Study (LETS). Results We identified a quantitative trait locus at chromosome 5q14.1 affecting normal PC plasma level variability. Next-generation sequencing of 113 candidate genes under the linkage peak revealed four SNPs in BHMT2, ACOT12, SSBP2 and XRCC4, which significantly increased PC levels in our thrombophilic family, but not in LETS. Conclusions We identified four genes at chromosome 5q14.1 that might influence normal PC levels. BHMT2 seems the most likely candidate to regulate PC levels via homocysteine, a competitive inhibitor to thrombin. Failure to replicate our findings in LETS might be due to differences between the studies in genetic background and linkage disequilibrium patterns. PMID:23387557

  7. Generation of an Attenuated, Cross-Protective Pepino mosaic virus Variant Through Alignment-Guided Mutagenesis of the Viral Capsid Protein.

    PubMed

    Chewachong, Godwill M; Miller, Sally A; Blakeslee, Joshua J; Francis, David M; Morris, T Jack; Qu, Feng

    2015-01-01

    Mild variants of many viruses are able to protect infected plants from subsequent invasion by more severe variants of the same viruses through a process known as cross-protection. In the past, the cross-protective viral variants were commonly derived from mild field isolates that were sometimes genetically heterogeneous, providing variable levels of cross-protection. Here, we report a novel approach to rapidly generate cross-protective variants of the tomato-infecting Pepino mosaic virus (PepMV) independently of the availability of mild field isolates. Our approach sought to attenuate PepMV by mutating less conserved amino acid residues of the abundantly produced capsid protein (CP). These less-conserved amino acid residues were identified through multiple alignments of CPs of six potexviruses including PepMV, and were altered systematically to yield six PepMV mutants. These mutants were subsequently inoculated onto the model plant Nicotiana benthamiana, as well as tomato, to evaluate their accumulation levels, symptom severities, and cross-protection potentials. The mutant KD, in which the threonine (T) and alanine (A) residues at CP positions 66 and 67 were replaced with lysine (K) and aspartic acid (D), respectively, were found to accumulate to low levels in infected plants, cause very mild symptoms, and effectively protect both N. benthamiana and tomato against secondary infections by wild-type PepMV. These data suggest that our approach represents a simple, fast, and reliable way of generating attenuated viral variants capable of cross-protection. PMID:25496364

  8. The IBO germination quantitative trait locus encodes a phosphatase 2C-related variant with a nonsynonymous amino acid change that interferes with abscisic acid signaling.

    PubMed

    Amiguet-Vercher, Amélia; Santuari, Luca; Gonzalez-Guzman, Miguel; Depuydt, Stephen; Rodriguez, Pedro L; Hardtke, Christian S

    2015-02-01

    Natural genetic variation is crucial for adaptability of plants to different environments. Seed dormancy prevents precocious germination in unsuitable conditions and is an adaptation to a major macro-environmental parameter, the seasonal variation in temperature and day length. Here we report the isolation of IBO, a quantitative trait locus (QTL) that governs c. 30% of germination rate variance in an Arabidopsis recombinant inbred line (RIL) population derived from the parental accessions Eilenburg-0 (Eil-0) and Loch Ness-0 (Lc-0). IBO encodes an uncharacterized phosphatase 2C-related protein, but neither the Eil-0 nor the Lc-0 variant, which differ in a single amino acid, have any appreciable phosphatase activity in in vitro assays. However, we found that the amino acid change in the Lc-0 variant of the IBO protein confers reduced germination rate. Moreover, unlike the Eil-0 variant of the protein, the Lc-0 variant can interfere with the activity of the phosphatase 2C ABSCISIC ACID INSENSITIVE 1 in vitro. This suggests that the Lc-0 variant possibly interferes with abscisic acid signaling, a notion that is supported by physiological assays. Thus, we isolated an example of a QTL allele with a nonsynonymous amino acid change that might mediate local adaptation of seed germination timing. PMID:25490966

  9. Human Cytomegalovirus variant peptides adapt by decreasing their total coordination upon binding to a T cell receptor

    PubMed Central

    Antipas, Georgios S.E.; Germenis, Anastasios E.

    2015-01-01

    The tertiary structure of the native Cytomegalovirus peptide (NLV) presented by HLA-A2 and bound to the RA14 T cell receptor was used as a reference for the calculation of atomic coordination differences of both the NLV as well as of a number of singly substituted NLV variants in the absence of TCR. Among the pMHC complexes, the native peptide was found to exhibit the highest total coordination difference in respect to the reference structure, suggesting that it experienced the widest structural adaptation upon recognition by the TCR. In addition, the peptide on the isolated NLV-MHC complex was over-coordinated as compared to the rest of the variants. Moreover, the trend was found to account for a set of measured dissociation constants and critical concentrations for target-cell lysis for all variants in complexation with RA14: functionally, all variant peptides were established to be either weak agonists or null peptides, while, at the same time, our current study established that they were also under-coordinated in respect to NLV. It could, thus, be argued that the most ‘efficient’ structural adaptation upon pMHC recognition by the TCR requires of the peptide to undergo the widest under-coordination possible. The main structural characteristic which differentiated the NLV in respect to the variants was a the presence of 16 oxygen atoms (waters) in the former׳s second coordination shell which accounted for over-coordination of roughly 100% and 30% in the O–O and C–O partials respectively. In fact, in the absence of second shell oxygens, the NLV peptide was decidedly under-coordinated in respect to all of the variants, as also suggested by the C–C partial.

  10. Revisiting the Heidenhain Variant of Creutzfeldt-Jakob Disease: Evidence for Prion Type Variability Influencing Clinical Course and Laboratory Findings.

    PubMed

    Baiardi, Simone; Capellari, Sabina; Ladogana, Anna; Strumia, Silvia; Santangelo, Mario; Pocchiari, Maurizio; Parchi, Piero

    2015-12-01

    The Heidenhain variant defines a peculiar clinical presentation of sporadic Creutzfeldt-Jakob disease (sCJD) characterized by isolated visual disturbances at disease onset and reflecting the early targeting of prions to the occipital cortex. Molecular and histopathological typing, thus far performed in 23 cases, has linked the Heidenhain variant to the MM1 sCJD type. To contribute a comprehensive characterization of cases with the Heidenhain variant, we reviewed a series of 370 definite sCJD cases. Eighteen patients (4.9%) fulfilled the selection criteria. Fourteen of them belonging to sCJD types MM1 or MM1+2C had a short duration of isolated visual symptoms and overall clinical disease, a high prevalence of periodic sharp-wave complexes in EEG, and a marked increase of cerebrospinal fluid proteins t-tau and 14-3-3 levels. In contrast, three cases of the MM 2C or MM 2+1C types showed a longer duration of isolated visual symptoms and overall clinical disease, non-specific EEG findings, and cerebrospinal fluid concentration below threshold for the diagnosis of "probable" CJD of both 14-3-3 and t-tau. However, a brain DWI-MRI disclosed an occipital cortical hyperintensity in the majority of examined cases of both groups. While confirming the strong linkage with the methionine genotype at the polymorphic codon 129 of the prion protein gene, our results definitely establish that the Heidenhain variant can also be associated with the MM 2C sCJD type in addition to the more common MM1 type. Likewise, our results highlight the significant differences in clinical evolution and laboratory findings between cases according to the dominant PrPSc type (type 1 versus type 2). PMID:26682685

  11. Identification of a new splice variant of BDNF in chicken

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Brain-derived neurotrophic factor (BDNF) appears to be involved in the central regulation of energy homeostasis. BDNF splicing variants were discovered in vertebrates. Results from human, mouse and rat suggest that alternative BDNF splicing variants potentially play a role in fat deposition. Using t...

  12. CBH1 homologs and variant CBH1 cellulases

    DOEpatents

    Goedegebuur, Frits; Gualfetti, Peter; Mitchinson, Colin; Neefe, Paulien

    2008-11-18

    Disclosed are a number of homologs and variants of Hypocrea jecorina Cel7A (formerly Trichoderma reesei cellobiohydrolase I or CBH1), nucleic acids encoding the same and methods for producing the same. The homologs and variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted and/or deleted.

  13. CBH1 homologs and variant CBH1 cellulases

    DOEpatents

    Goedegebuur, Frits; Gualfetti, Peter; Mitchinson, Colin; Neefe, Paulien

    2011-05-31

    Disclosed are a number of homologs and variants of Hypocrea jecorina Cel7A (formerly Trichoderma reesei cellobiohydrolase I or CBH1), nucleic acids encoding the same and methods for producing the same. The homologs and variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted and/or deleted.

  14. The Structural Determinants behind the Epigenetic Role of Histone Variants

    PubMed Central

    Cheema, Manjinder S.; Ausió, Juan

    2015-01-01

    Histone variants are an important part of the histone contribution to chromatin epigenetics. In this review, we describe how the known structural differences of these variants from their canonical histone counterparts impart a chromatin signature ultimately responsible for their epigenetic contribution. In terms of the core histones, H2A histone variants are major players while H3 variant CenH3, with a controversial role in the nucleosome conformation, remains the genuine epigenetic histone variant. Linker histone variants (histone H1 family) haven’t often been studied for their role in epigenetics. However, the micro-heterogeneity of the somatic canonical forms of linker histones appears to play an important role in maintaining the cell-differentiated states, while the cell cycle independent linker histone variants are involved in development. A picture starts to emerge in which histone H2A variants, in addition to their individual specific contributions to the nucleosome structure and dynamics, globally impair the accessibility of linker histones to defined chromatin locations and may have important consequences for determining different states of chromatin metabolism. PMID:26213973

  15. Exploring the basis of [PIN(+)] variant differences in [PSI(+)] induction.

    PubMed

    Sharma, Jaya; Liebman, Susan W

    2013-09-01

    Certain soluble proteins can form amyloid-like prion aggregates. Indeed, the same protein can make different types of aggregates, called variants. Each variant is heritable because it attracts soluble homologous protein to join its aggregate, which is then broken into seeds (propagons) and transmitted to daughter cells. [PSI(+)] and [PIN(+)] are respectively prion forms of Sup35 and Rnq1. Curiously, [PIN(+)] enhances the de novo induction of [PSI(+)]. Different [PIN(+)] variants do this to dramatically different extents. Here, we investigate the mechanism underlying this effect. Consistent with a heterologous prion cross-seeding model, different [PIN(+)] variants preferentially promoted the appearance of different variants of [PSI(+)]. However, we did not detect this specificity in vitro. Also, [PIN(+)] variant cross-seeding efficiencies were not proportional to the level of Rnq1 coimmunocaptured with Sup35 or to the number of [PIN(+)] propagons characteristic for that variant. This leads us to propose that [PIN(+)] variants differ in the cross-seeding quality of their seeds, following the Sup35/[PIN(+)] binding step. PMID:23770111

  16. Exploring the basis of [PIN+] variant differences in [PSI+] induction

    PubMed Central

    Sharma, Jaya; Liebman, Susan W.

    2013-01-01

    Certain soluble proteins can form amyloid-like prion aggregates. Indeed, the same protein can make different types of aggregates, called variants. Each variant is heritable because it attracts soluble homologous protein to join its aggregate, which is then broken into seeds (propagons) and transmitted to daughter cells. [PSI+] and [PIN+] are respectively prion forms of Sup35 and Rnq1. Curiously, [PIN+] enhances the de novo induction of [PSI+]. Different [PIN+] variants do this to dramatically different extents. Here we investigate the mechanism underlying this effect. Consistent with a heterologous prion cross-seeding model, different [PIN+] variants preferentially promoted the appearance of different variants of [PSI+]. However, we did not detect this specificity in vitro. Also, [PIN+] variant cross-seeding efficiencies were not proportional to the level of Rnq1 coimmunocaptured with Sup35, nor to the number of [PIN+] propagons characteristic for that variant. This leads us to propose that [PIN+] variants differ in the cross-seeding quality of their seeds, following the Sup35/[PIN+] binding step. PMID:23770111

  17. Genetics Home Reference: GM2-gangliosidosis, AB variant

    MedlinePLUS

    ... and may include treatment providers. Genetic Testing Registry: Tay-Sachs disease, variant AB You might also find information on ... AB variant Activator Deficiency/GM2 Gangliosidosis Activator-deficient Tay-Sachs disease GM2 Activator Deficiency Disease GM2 gangliosidosis, type AB ...

  18. Cryogenic Faraday isolator

    SciTech Connect

    Zheleznov, D S; Zelenogorskii, V V; Katin, E V; Mukhin, I B; Palashov, O V; Khazanov, Efim A

    2010-05-26

    A Faraday isolator is described in which thermal effects are suppressed by cooling down to liquid nitrogen temperatures. The principal scheme, main characteristics and modifications of the isolator are presented. The isolation degree is studied experimentally for the subkilowatt average laser radiation power. It is shown that the isolator can be used at radiation powers up to tens of kilowatts. (quantum electronic devices)

  19. Improved RF Isolation Amplifier

    NASA Technical Reports Server (NTRS)

    Stevens, G. L.; Macconnell, J.

    1985-01-01

    Circuit has high reverse isolation and wide bandwidth. Wideband isolation amplifier has low intermodulation distortion and high reverse isolation. Circuit does not require selected or matched components or directional coupling device. Circuit used in applications requiring high reverse isolation such as receiver intermediate-frequency (IF) strips and frequency distribution systems. Also applicable in RF and video signaling.

  20. Comparison of mammalian and bacterial expression library screening to detect recombinant alpha-1 proteinase inhibitor variants with enhanced thrombin inhibitory capacity.

    PubMed

    Gierczak, Richard F; Bhakta, Varsha; Xie, Michael; Sheffield, William P

    2015-08-20

    Serpins are a widely distributed family of serine proteases. A key determinant of their specificity is the reactive centre loop (RCL), a surface motif of ∼20 amino acids in length. Expression libraries of variant serpins could be rapidly probed with proteases to develop novel inhibitors if optimal systems were available. The serpin variant alpha-1 proteinase inhibitor M358R (API M358R) inhibits the coagulation protease thrombin, but at sub-maximal rates compared to other serpins. Here we compared two approaches to isolate functional API variants from serpin expression libraries, using the same small library of API randomized at residue 358 (M358X): flow cytometry of transfected HEK 293 cells expressing membrane-displayed API; and a thrombin capture assay (TCA) performed on pools of bacterial lysates expressing soluble API. No enrichment for specific P1 residues was observed when the RCL codons of the 1% of sorted transfected 293 cells with the highest fluorescent thrombin-binding signals were subcloned and sequenced. In contrast, screening of 16 pools of bacterial API-expressing transformants led to the facile identification of API M358R and M358K as functional variants. Kinetic characterization showed that API M358R inhibited thrombin 17-fold more rapidly than API M358K. Reducing the incubation time with immobilized thrombin improved the sensitivity of TCA to detect supra-active API M358R variants and was used to screen a hypervariable library of API variants expressing 16 different amino acids at residues 352-357. The most active variant isolated, with TLSATP substituted for FLEAI, inhibited thrombin 2.9-fold more rapidly than API M358R. Our results indicate that flow cytometric approaches used in protein engineering of antibodies are not appropriate for serpins, and highlight the utility of the optimized TCA for serpin protein engineering. PMID:26043905

  1. Diversity of acid stress resistant variants of Listeria monocytogenes and the potential role of ribosomal protein S21 encoded by rpsU.

    PubMed

    Metselaar, Karin I; den Besten, Heidy M W; Boekhorst, Jos; van Hijum, Sacha A F T; Zwietering, Marcel H; Abee, Tjakko

    2015-01-01

    The dynamic response of microorganisms to environmental conditions depends on the behavior of individual cells within the population. Adverse environments can select for stable stress resistant subpopulations. In this study, we aimed to get more insight in the diversity within Listeria monocytogenes LO28 populations, and the genetic basis for the increased resistance of stable resistant fractions isolated after acid exposure. Phenotypic cluster analysis of 23 variants resulted in three clusters and four individual variants and revealed multiple-stress resistance, with both unique and overlapping features related to stress resistance, growth, motility, biofilm formation, and virulence indicators. A higher glutamate decarboxylase activity correlated with increased acid resistance. Whole genome sequencing revealed mutations in rpsU, encoding ribosomal protein S21 in the largest phenotypic cluster, while mutations in ctsR, which were previously shown to be responsible for increased resistance of heat and high hydrostatic pressure resistant variants, were not found in the acid resistant variants. This underlined that large population diversity exists within one L. monocytogenes strain and that different adverse conditions drive selection for different variants. The finding that acid stress selects for rpsU variants provides potential insights in the mechanisms underlying population diversity of L. monocytogenes. PMID:26005439

  2. Diversity of acid stress resistant variants of Listeria monocytogenes and the potential role of ribosomal protein S21 encoded by rpsU

    PubMed Central

    Metselaar, Karin I.; den Besten, Heidy M. W.; Boekhorst, Jos; van Hijum, Sacha A. F. T.; Zwietering, Marcel H.; Abee, Tjakko

    2015-01-01

    The dynamic response of microorganisms to environmental conditions depends on the behavior of individual cells within the population. Adverse environments can select for stable stress resistant subpopulations. In this study, we aimed to get more insight in the diversity within Listeria monocytogenes LO28 populations, and the genetic basis for the increased resistance of stable resistant fractions isolated after acid exposure. Phenotypic cluster analysis of 23 variants resulted in three clusters and four individual variants and revealed multiple-stress resistance, with both unique and overlapping features related to stress resistance, growth, motility, biofilm formation, and virulence indicators. A higher glutamate decarboxylase activity correlated with increased acid resistance. Whole genome sequencing revealed mutations in rpsU, encoding ribosomal protein S21 in the largest phenotypic cluster, while mutations in ctsR, which were previously shown to be responsible for increased resistance of heat and high hydrostatic pressure resistant variants, were not found in the acid resistant variants. This underlined that large population diversity exists within one L. monocytogenes strain and that different adverse conditions drive selection for different variants. The finding that acid stress selects for rpsU variants provides potential insights in the mechanisms underlying population diversity of L. monocytogenes. PMID:26005439

  3. Genetic variants of human serum albumin in Italy: point mutants and a carboxyl-terminal variant.

    PubMed Central

    Madison, J; Galliano, M; Watkins, S; Minchiotti, L; Porta, F; Rossi, A; Putnam, F W

    1994-01-01

    Of the > 50 different genetic variants of human serum albumin (alloalbumins) that have been characterized by amino acid or DNA sequence analysis, almost half have been identified in Italy through a long-term electrophoretic survey of serum. Previously we have reported structural studies of 11 Italian alloalbumins with point mutations, 2 different carboxyl-terminal variants, and 1 case of analbuminemia in an Italian family. This article describes confirmation by DNA sequencing of mutations previously inferred from protein sequencing of 4 of the above alloalbumins; it also reports the mutations identified by protein and DNA sequence analysis of 4 other Italian alloalbumins not previously recorded: albumin Larino, His3-->Tyr; Tradate-2 (protein sequencing only), Lys225-->Gln; Caserta, Lys276-->Asn; and Bazzano, a carboxyl-terminal variant. The first 3 have point mutations that produce a single amino acid substitution, but a nucleotide deletion causes a frameshift and an altered and truncated carboxyl-terminal sequence in albumin Bazzano. In these 4 instances the expression of the alloalbumin is variable, ranging from 10% to 70% of the total albumiN, in contrast to the usual 50% each for the normal and mutant albumin. The distribution of point mutations in the albumin gene is nonrandom; most of the 47 reported point substitutions involve charged amino acid residues on the surface of the molecule that are not concerned with ligand-binding sites. Images PMID:8022807

  4. Temporal Variant Frontotemporal Dementia Is Associated with Globular Glial Tauopathy

    PubMed Central

    Clark, Camilla N.; Lashley, Tammaryn; Mahoney, Colin J.; Warren, Jason D.; Revesz, Tamas

    2015-01-01

    Frontotemporal dementia (FTD) is a clinically and pathologically heterogeneous neurodegenerative disorder associated with atrophy of the frontal and temporal lobes. Most patients with focal temporal lobe atrophy present with either the semantic dementia subtype of FTD or the behavioral variant subtype. For patients with temporal variant FTD, the most common cause found on post-mortem examination has been a TDP-43 (transactive response DNA-binding protein 43 kDa) proteinopathy, but tauopathies have also been described, including Pick’s disease and mutations in the microtubule-associated protein tau (MAPT) gene. We report the clinical and imaging features of 2 patients with temporal variant FTD associated with a rare frontotemporal lobar degeneration pathology known as globular glial tauopathy. The pathologic diagnosis of globular glial tauopathy should be considered in patients with temporal variant FTD, particularly those who have atypical semantic dementia or an atypical parkinsonian syndrome in association with the right temporal variant. PMID:26102999

  5. Acute Promyelocytic Leukemia: A Review and Discussion of Variant Translocations.

    PubMed

    Adams, Julia; Nassiri, Mehdi

    2015-10-01

    The majority of patients with acute promyelocytic leukemia (APL) manifest the t(15;17)(q24.1;q21.2) translocation; however, a minor but significant proportion of patients with APL harbor complex, cryptic, or variant translocations, which typically involve RARA. With the exception of ZBTB16/RARA, these variants have similar morphologic and immunophenotypic features as classic APL. Study of the variant forms of APL not only gives insight into the pathogenesis of APL but also allows us to understand the mechanism of retinoid therapy. It is important to identify these cryptic and variant translocations because certain variants, including ZBTB16/RARA and STAT5B/RARA, are resistant to treatment with all-trans retinoic acid, arsenic trioxide, and anthracyclines. PMID:26414475

  6. Clinical and laboratory update on the DEL variant.

    PubMed

    Nuchnoi, Pornlada; Thongbus, Jairak; Srisarin, Apapan; Kerdpin, Usanee; Prachayasittikul, Virapong

    2014-01-01

    Serological assays for the RhD blood group are based on detection of the RhD antigen on human red blood cells using a specific anti-D antibody. The weak expression of the RhD antigen in the DEL variant hinders the sensitivity of conventional serological assays. Evidence of anti-D immunization in patients with D-negativity who have received DEL-variant blood units has been reported in various populations. This observation has prompted the need for genetic epidemiological and clinical data on the DEL variant in the development of DEL molecular diagnostic testing. This review highlights the molecular features of the DEL variant, the clinical consequences of DEL-blood transfusion, and current approaches for detection of the DEL-variant for donor screening and transfusion. PMID:25316658

  7. Temporal Variant Frontotemporal Dementia is Associated with Globular Glial Tauopathy.

    PubMed

    Clark, Camilla N; Lashley, Tammaryn; Mahoney, Colin J; Warren, Jason D; Revesz, Tamas; Rohrer, Jonathan D

    2015-06-01

    Frontotemporal dementia (FTD) is a clinically and pathologically heterogeneous neurodegenerative disorder associated with atrophy of the frontal and temporal lobes. Most patients with focal temporal lobe atrophy present with either the semantic dementia subtype of FTD or the behavioral variant subtype. For patients with temporal variant FTD, the most common cause found on post-mortem examination has been a TDP-43 (transactive response DNA-binding protein 43 kDa) proteinopathy, but tauopathies have also been described, including Pick's disease and mutations in the microtubule-associated protein tau (MAPT) gene. We report the clinical and imaging features of 2 patients with temporal variant FTD associated with a rare frontotemporal lobar degeneration pathology known as globular glial tauopathy. The pathologic diagnosis of globular glial tauopathy should be considered in patients with temporal variant FTD, particularly those who have atypical semantic dementia or an atypical parkinsonian syndrome in association with the right temporal variant. PMID:26102999

  8. Release of ?-casomorphin-7/5 during simulated gastrointestinal digestion of milk ?-casein variants from Indian crossbred cattle (Karan Fries).

    PubMed

    Ul Haq, Mohammad Raies; Kapila, Rajeev; Kapila, Suman

    2015-02-01

    Crossbred Karan Fries (KF) cows, among the best yielders of milk in India are carriers of A1 and A2 alleles. These genetic variants have been established as the source of ?-casomorphins (BCMs) bioactive peptides that are implicated with various physiological and health issues. Therefore, the present study was aimed to investigate the release of BCM-7/5 from ?-casein variants of KF by simulated gastrointestinal digestion (SGID) performed with proteolytic enzymes, in vitro. ?-Casein variants (A1A1, A1A2 and A2A2) were isolated from milk samples of genotyped Karan Fries animals and subjected to hydrolysis by SGID using proteolytic enzymes (pepsin, trypsin, chymotrypsin and pancreatin), in vitro. Detection of BCMs were carried out in two peptide fractions (A and B) of RP-HPLC collected at retention time (RT) 24 and 28min respectively corresponding to standard BCM-5 and BCM-7 by MS-MS and competitive ELISA. One of the RP-HPLC fractions (B) showed the presence of 14 amino acid peptide (VYPFPGPIHNSLPQ) having encrypted internal BCMs sequence while no such peptide or precursor was observed in fraction A by MS-MS analysis. Further hydrolysis of fraction B of A1A1 and A1A2 variants of ?-casein with elastase and leucine aminopeptidase revealed the release of BCM-7 by competitive ELISA. The yield of BCM-7 (0.20±0.02mg/g ?-casein) from A1A1 variant was observed to be almost 3.2 times more than A1A2 variant of ?-casein. However, release of BCM-7/5 could not be detected from A2A2 variant of ?-casein. The biological activity of released peptides on rat ileum by isolated organ bath from A1A1 (IC50=0.534-0.595?M) and A1A2 (IC50=0.410-0.420?M) hydrolysates further confirmed the presence of opioid peptide BCM-7. PMID:25172685

  9. Detection of mixed populations of wild-type and YMDD hepatitis B variants by pyrosequencing in acutely and chronically infected patients

    PubMed Central

    2012-01-01

    Background Lamivudine (LAM) is associated with the highest known rate of resistance mutations among nucleotide analogs used to treat chronic hepatitis B virus (HBV) infection. Despite this, LAM continues in widespread use, especially in combination therapies. The primary LAM resistance mutation (rtM204V/I) occurs in the YMDD motif of HBV polymerase. The aim of this study was to characterize Brazilian HBV isolates from acute and chronic cases by direct sequencing, and to identify HBV quasispecies in the YMDD motif using a pyrosequencing method capable of detecting single-nucleotide polymorphisms. HBV DNA from serum samples of 20 individuals with acute HBV infection and 44 with chronic infection undergoing antiviral therapies containing LAM were analyzed by direct sequencing and pyrosequencing methods. Results Phylogenic analyses of direct-sequenced isolates showed the expected genotypes (A, D and F) for the Brazilian population in both acute and chronic infections. However, within genotype A isolates, subgenotype A2 was more frequently detected in acute cases than in chronic cases (P?=?0.012). As expected, none of the individuals with acute hepatitis B had LAM-resistant isolates as a dominant virus population, whether detected by direct sequencing or pyrosequencing. However, pyrosequencing analyses showed that 45% of isolates (9/20) had minor subpopulations (4-17%) of LAM-resistant isolates. Among chronic patients undergoing LAM treatment, YMDD mutants were frequently found as a dominant virus population. In cases where wild-type virus was the dominant population, subpopulations of YMDD variants were usually found, demonstrating the complexity of HBV quasispecies. Conclusions YMDD variants were frequently detected as a minor population in acute HBV infection. The occurrence of pre-existing variants may lead to a high frequency of resistant mutants during antiviral therapy in the chronic phase. In chronic infection, detection of YMDD variants before virological or biochemical breakthrough might contribute to making better therapy choices and thus improving treatment outcome. PMID:22672436

  10. Detecting Association of Rare Variants by Testing an Optimally Weighted Combination of Variants for Quantitative Traits in General Families

    PubMed Central

    Fang, Shurong; Zhang, Shuanglin

    2013-01-01

    Although next-generation sequencing technology allows sequencing the whole genome of large groups of individuals, the development of powerful statistical methods for rare variant association studies is still underway. Even though many statistical methods have been developed for mapping rare variants, most of these methods are for unrelated individuals only, whereas family data have been shown to improve power to detect rare variants. The majority of the existing methods for unrelated individuals are essentially testing the effect of a weighted combination of variants with different weighting schemes. The performance of these methods depends on the weights being used. Recently, Sha et al. [Genet Epidemiol, 2012] proposed a test for Testing the effect of an Optimally Weighted combination of variants (TOW) for unrelated individuals. In this article, we extend our previously developed TOW for unrelated individuals to family-based data and propose a novel test for Testing the effect of an Optimally Weighted combination of variants for Family-based designs (TOW-F). The optimal weights are analytically derived. The results of extensive simulation studies show that TOW-F is robust to population stratification in a wide range of population structures, is robust to the direction and magnitude of the effects of causal variants, and is relatively robust to the percentage of neutral variants. PMID:23968488

  11. OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization

    PubMed Central

    Antanaviciute, Agne; Watson, Christopher M.; Harrison, Sally M.; Lascelles, Carolina; Crinnion, Laura; Markham, Alexander F.; Bonthron, David T.; Carr, Ian M.

    2015-01-01

    Motivation: Exome sequencing has become a de facto standard method for Mendelian disease gene discovery in recent years, yet identifying disease-causing mutations among thousands of candidate variants remains a non-trivial task. Results: Here we describe a new variant prioritization tool, OVA (ontology variant analysis), in which user-provided phenotypic information is exploited to infer deeper biological context. OVA combines a knowledge-based approach with a variant-filtering framework. It reduces the number of candidate variants by considering genotype and predicted effect on protein sequence, and scores the remainder on biological relevance to the query phenotype. We take advantage of several ontologies in order to bridge knowledge across multiple biomedical domains and facilitate computational analysis of annotations pertaining to genes, diseases, phenotypes, tissues and pathways. In this way, OVA combines information regarding molecular and physical phenotypes and integrates both human and model organism data to effectively prioritize variants. By assessing performance on both known and novel disease mutations, we show that OVA performs biologically meaningful candidate variant prioritization and can be more accurate than another recently published candidate variant prioritization tool. Availability and implementation: OVA is freely accessible at http://dna2.leeds.ac.uk:8080/OVA/index.jsp Supplementary information: Supplementary data are available at Bioinformatics online. Contact: umaan@leeds.ac.uk PMID:26272982

  12. A novel homozygous variant in the dsp gene underlies the first case of non-syndromic form of alopecia.

    PubMed

    Jan, Abid; Basit, Sulman; Wakil, Salma M; Ramzan, Khushnooda; Ahmad, Wasim

    2015-11-01

    Autosomal recessive forms of hair loss (alopecia) disorders have previously been associated with variants in at least five different genes including hairless (HR), desmoglein-4 (DSG4), desmocollin-3 (DSC3), lipase-H (LIPH), and lysophosphatidic acid receptor 6 (LPAR6). Here, we report the first familial case of alopecia resulting from a novel homozygous variant in the DSP gene. Since previous reports indicated the presence of heart abnormalities in patients carrying variants in the DSP gene; therefore, the echocardiographic evaluations of all affected members were performed. The results clearly excluded the presence of any form of heart abnormality in patients of the present family. Human genome scan mapped a disease locus on chromosome 6p25.1-p23, harboring DSP gene. Sequence analysis identified a novel homozygous missense variant [c.1493C > T (p.Pro498Leu)] in the DSP gene as the underlying genetic cause of non-syndromic alopecia in the family. The transition alters the completely conserved Pro498 residue in the SH3 domain of plakin that contributes to the stability and rigidity of this subfamily of spectrin repeats (SRs) containing proteins. Our study strengthens the evidence that hereditary hair loss disorders are genetically heterogeneous and imply that isolated form of alopecia is allelic with cardiocutaneous syndromes. PMID:26148547

  13. Comparative Genomic Analysis of Classical and Variant Virulent Parental/Attenuated Strains of Porcine Epidemic Diarrhea Virus

    PubMed Central

    Chen, Fangzhou; Zhu, Yinxing; Wu, Meizhou; Ku, Xugang; Ye, Shiyi; Li, Zhonghua; Guo, Xiaozhen; He, Qigai

    2015-01-01

    Since 2010, the variant porcine epidemic diarrhea virus (PEDV) has been the etiological agent responsible for the outbreak of porcine epidemic diarrhea (PED) worldwide. In this study, a variant PEDV strain YN1 was isolated, serially propagated on the Vero cells and was characterized for 200 passages. To better elucidate the molecular basis of Vero cell adaptation of variant PEDV strains, we sequenced, compared, and analyzed the full-genome sequences of parental YN1 and passages 15, 30, 60, 90, 144, and 200. The results showed that the variations increased with the viral passage. The nucleotides sequences of non-structural protein (NSP)2, NSP4-7, NSP10, NSP12 and NSP13 genes did not change during the Vero cell adaptation process. After comparison of the variation characteristic of classical, variant virulent/attenuated strains, it was found that attenuation of PEDV virus was associated with 9?26 amino acid (aa) changes in open reading frames (ORF) 1a/b and S protein, early termination in ORF3, 1–3 aa changes in E, M and N protein and some nucleotide sequences’ synonymous mutations. The aa deletion at about 144 aa of S protein could be the attenuation marker for the PEDV. The pig study showed that the early termination in ORF3 was more important for virus cell adaptation than virus attenuation. PMID:26512689

  14. Allelic variants of the Melanocortin 4 receptor (MC4R) gene in a South African study group.

    PubMed

    Logan, Murray; Van der Merwe, Maria-Teresa; Dodgen, Tyren M; Myburgh, Renier; Eloff, Arinda; Alessandrini, Marco; Pepper, Michael S

    2016-01-01

    Obesity is a global epidemic that results in significant morbidity and mortality. Mutations in the melanocortin 4 receptor (MC4R) gene, which codes for a G-protein-coupled receptor responsible for postprandial satiety signaling, have been associated with monogenic obesity. The prevalence of obesity is on the increase in South Africa, and it is hypothesized that mutations in MC4R are a contributing factor. The aim of this study was to perform a retrospective assessment of the relationship between allelic variants of MC4R and BMI in a South African study cohort. DNA was isolated from a demographically representative cohort of 297 individuals and the entire MC4R gene sequenced by Sanger sequencing. Eight previously reported MC4R variants were identified in 42 of the 297 (14.1%) study participants. The most frequently observed MC4R alleles were V103I (4.0%), I170V (1.5%), and I198I (1.2%), while the remaining five variants together constituted 1.18%. Five compound heterozygotes were also detected. Although MC4R variants were rare, the majority of variation was observed in individuals of Black African ancestry. No statistically significant associations with BMI were reported. Given that lifestyle interventions have limited success in decreasing obesity, there is an urgent need to perform large-scale population studies to further elucidate the molecular underpinnings of this disease. PMID:26788538

  15. Two variants of the Drosophila melanogaster retrotransposon gypsy (mdg4): structural and functional differences, and distribution in fly stocks.

    PubMed

    Lyubomirskaya, N V; Smirnova, J B; Razorenova, O V; Karpova, N N; Surkov, S A; Avedisov, S N; Kim, A I; Ilyin, Y V

    2001-04-01

    Two variants of the Drosophila melanogaster retrotransposon gypsy were subjected to detailed structural and functional analysis. A series of hybrid constructs containing various combinations of "active" and "inactive" gypsy copies were tested for their ability to produce new DNA copies in cultured cells by means of reverse transcription. It was shown that the previously demonstrated variations in retrotranspositional activity are associated with either one or both of two amino acid substitutions at the beginning of ORF2. The first substitution is located at the boundary between the putative protease and reverse transcriptase domains and, hence, may influence the processing of the polyprotein. The other substitution may alter reverse transcriptase activity since it is located in the second of the seven conserved domains of the RT gene. To address the question of the evolutionary relationship between the two gypsy variants, their distribution was analyzed in among various fly stocks. Southern analysis revealed that all D. melanogaster strains studied so far contain the "inactive" gypsy variant, while the "active" copies are present only in some strains; most of the latter were established from flies recently isolated from natural populations. Finally, in stocks carrying the flamenco mutation the "active" gypsy variant is much more abundant than the "inactive" form. Possible scenarios for the orgin of the "active" form of gypsy are discussed. PMID:11361349

  16. Conformational characterization of the charge variants of a human IgG1 monoclonal antibody using H/D exchange mass spectrometry

    PubMed Central

    Tang, Liangjie; Sundaram, Shanmuuga; Zhang, Jingming; Carlson, Ping; Matathia, Alice; Parekh, Babita; Zhou, Qinwei; Hsieh, Ming-Ching

    2013-01-01

    MAb1, a human IgG1 monoclonal antibody produced in a NS0 cell line, exhibits charge heterogeneity because of the presence of variants formed by processes such as N-terminal glutamate cyclization, C-terminal lysine truncation, deamidation, aspartate isomerization and sialylation in the carbohydrate moiety. Four major charge variants of MAb1 were isolated and the conformations of these charge variants were studied using hydrogen/deuterium exchange mass spectrometry, including the H/D exchange time course (HX-MS) and the stability of unpurified proteins from rates of H/D exchange (SUPREX) techniques. HX-MS was used to evaluate the conformation and solution dynamics of MAb1 charge variants by measuring their deuterium buildup over time at the peptide level. The SUPREX technique evaluated the unfolding profile and relative stability of the charge variants by measuring the exchange properties of globally protected amide protons in the presence of a chemical denaturant. The H/D exchange profiles from both techniques were compared among the four charge variants of MAb1. The two techniques together offered extensive understanding about the local and subglobal/global unfolding of the charge variants of MAb1. Our results demonstrated that all four charge variants of MAb1 were not significantly different in conformation, solution dynamics and chemical denaturant-induced unfolding profile and stability, which aids in understanding the biofunctions of the molecules. The analytical strategy used for conformational characterization may also be applicable to comparability studies done for antibody therapeutics. PMID:23222183

  17. Conformational characterization of the charge variants of a human IgG1 monoclonal antibody using H/D exchange mass spectrometry.

    PubMed

    Tang, Liangjie; Sundaram, Shanmuuga; Zhang, Jingming; Carlson, Ping; Matathia, Alice; Parekh, Babita; Zhou, Qinwei; Hsieh, Ming-Ching

    2013-01-01

    MAb1, a human IgG1 monoclonal antibody produced in a NS0 cell line, exhibits charge heterogeneity because of the presence of variants formed by processes such as N-terminal glutamate cyclization, C-terminal lysine truncation, deamidation, aspartate isomerization and sialylation in the carbohydrate moiety. Four major charge variants of MAb1 were isolated and the conformations of these charge variants were studied using hydrogen/deuterium exchange mass spectrometry, including the H/D exchange time course (HX-MS) and the stability of unpurified proteins from rates of H/D exchange (SUPREX) techniques. HX-MS was used to evaluate the conformation and solution dynamics of MAb1 charge variants by measuring their deuterium buildup over time at the peptide level. The SUPREX technique evaluated the unfolding profile and relative stability of the charge variants by measuring the exchange properties of globally protected amide protons in the presence of a chemical denaturant. The H/D exchange profiles from both techniques were compared among the four charge variants of MAb1. The two techniques together offered extensive understanding about the local and subglobal/global unfolding of the charge variants of MAb1. Our results demonstrated that all four charge variants of MAb1 were not significantly different in conformation, solution dynamics and chemical denaturant-induced unfolding profile and stability, which aids in understanding the biofunctions of the molecules. The analytical strategy used for conformational characterization may also be applicable to comparability studies done for antibody therapeutics. PMID:23222183

  18. Glycosylation Variants of a ?-Glucosidase Secreted by a Taiwanese Fungus, Chaetomella raphigera, Exhibit Variant-Specific Catalytic and Biochemical Properties

    PubMed Central

    Yoneda, Aki; Kuo, Hsion-Wen David; Ishihara, Mayumi; Azadi, Parastoo; Yu, Su-May; Ho, Tuan-hua David

    2014-01-01

    Cellulosic biomass is an abundant and promising energy source. To make cellulosic biofuels competitive against conventional fuels, conversion of rigid plant materials into sugars must become efficient and cost-effective. During cellulose degradation, cellulolytic enzymes generate cellobiose (?-(1?4)-glucose dimer) molecules, which in turn inhibit such enzymes by negative feedback. ?-Glucosidases (BGLs) cleave cellobiose into glucose monomers, assisting overall cellulolytic activities. Therefore, BGLs are essential for efficient conversion of cellulosic biomass into biofuels, and it is important to characterize newly isolated BGLs for useful traits. Here, we report our discovery that the indigenous Taiwanese fungus Chaetomella raphigera strain D2 produces two molecular weight variants of a single BGL, D2-BGL (shortened to “D2”), which differ in O-glycosylation. The more extensively O-glycosylated form of native D2 (nD2L) has increased activity toward the natural substrate, cellobiose, compared to the less O-glycosylated form (nD2S). nD2L is more stable at 60°C, in acidic pH, and in the presence of the ionic detergent sodium dodecyl sulfate than nD2S. Furthermore, unlike nD2S, nD2L does not display s