Sample records for nontoxigenic variants isolated

  1. 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...

  2. 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

  3. Culture-negative prosthetic valve endocarditis with concomitant septicemia due to a nontoxigenic Corynebacterium diphtheriae biotype gravis isolate in a patient with multiple risk factors.

    PubMed

    Clinton, Lani Kai; Bankowski, Matthew J; Shimasaki, Teppei; Sae-Ow, Wichit; Whelen, A Christian; O'Connor, Norman; Kim, Wesley; Young, Royden

    2013-11-01

    A 54-year-old female with a prosthetic mitral valve presented with a 3-day history of dizziness, subjective fever, and chills. Blood cultures were positive for a pleomorphic Gram-positive rod. Initial phenotypic testing could only support the identification of a Corynebacterium species. Nucleic acid sequencing (16S rRNA) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) were conclusive for Corynebacterium diphtheriae. Definitive phenotypic testing classified the strain as nontoxigenic C. diphtheriae biotype Gravis. PMID:24006007

  4. 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

  5. Toxigenic Corynebacterium ulcerans in human and non-toxigenic Corynebacterium diphtheriae in cat

    PubMed Central

    Detemmerman, L; Rousseaux, D; Efstratiou, A; Schirvel, C; Emmerechts, K; Wybo, I; Soetens, O; Piérard, D

    2013-01-01

    Corynebacterium diphtheriae and Corynebacterium ulcerans are rarely isolated from clinical samples in Belgium. A case of toxigenic C. ulcerans in a woman is described, which confirms that this pathogen is still present. During investigation of the patient's cats, only a non-toxigenic toxin-bearing C. diphtheriae strain was detected. PMID:25356320

  6. 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...

  7. 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...

  8. 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 ?-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 ?-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

  9. A new method for isolating host-independent variants of Bdellovibrio bacteriovorus using E. coli auxotrophs.

    PubMed

    Dashiff, Aliza; Kadouri, Daniel E

    2009-01-01

    Bdellovibrios are Gram-negative bacteria that are characterized by predatory behavior. Although Bdellovibrios exhibit an obligatory parasitic life cycle, it is possible to isolate Bdellovibrio variants that no longer require host cells for their growth. In this study, a new method for isolating Bdellovibrio bacteriovorus host-independent (HI) variants was developed. Filtered B. bacteriovorus prey cells were cultured with E. coli diaminopimelic acid (DAP) auxotrophs as host cells. Thereafter, the lysate was plated on DAP minus media, allowing only HI colonies to develop. Using this method, we have isolated numerous HI variants and demonstrated that the emergence of HI variants may be occurring at a higher frequency than was previously suggested. PMID:19590595

  10. Isolation of BamHI variants with reduced cleavage activities.

    PubMed

    Xu, S Y; Schildkraut, I

    1991-03-01

    Derivation of the bamhIR sequence (Brooks, J. E., Nathan, P.D., Landry, D., Sznyter, L.A., Waite-Rees, P., Ives, C. C., Mazzola, L. M., Slatko, B. E., and Benner, J. S. (1991) Nucleic Acids Res., in press), the gene coding for BamHI endonuclease, has facilitated construction of an Escherichia coli strain that overproduces BamHI endonuclease (W. E. Jack, L. Greenough, L. F. Dorner, S. Y. Xu, T. Strezelecka, A. K. Aggarwal, and I. Schildkraut, submitted for publication). As expected, low-level constitutive expression of the bamhIR gene in E. coli from the Ptac promotor construct is lethal to the host unless the bamHIM gene, which encodes the BamHI methylase, is also expressed within the cell. We identified four classes of BamHI endonuclease variants deficient in catalysis by selecting for survival of a host deficient for bamHIM gene, transformed with mutagenized copies of the bamhIR gene, and then screening the surviving cell extracts for DNA cleavage and binding activities. Class I variants (G56S, G91S/T153I, T114I, G130R, E135K, T153I, T157I, G194D) displayed 0.1-1% of the wild-type cleavage activity; class II variant (D94N) lacked cleavage activity but retained wild-type DNA binding specificity; class III variants (E77K, E113K) lacked cleavage activity but bound DNA more tightly; class IV variants (G56D, G90D, G91S, R122H, R155H) lacked both binding and cleavage activities. Variants with residual cleavage activities induced the E. coli SOS response and thus are presumed to cleave chromosomal DNA in vivo. We conclude that Glu77, Asp94, and Glu113 residues are essential for BamHI catalytic function. PMID:1999426

  11. Comparisons of some Properties of Two Laboratory Variants of Raspberry bushy dwarf virus (RBDV) with those of Three Previously Characterised RBDV Isolates

    Microsoft Academic Search

    A. Teifion Jones; Wendy J. McGavin; M. A. Mayo; J. E. Angel-Diaz; S. O. Kärenlampi; H. Kokko

    2000-01-01

    The properties of two laboratory variants of Raspberry bushy dwarf virus (RBDV), genus Idaeovirus, were compared with those of their parental sources and with two naturally occurring variants. Isolate RB is a natural variant able to overcome the resistance to RBDV present in some red raspberry cultivars. Isolate M is a serological variant from black raspberry. Laboratory variant D1, was

  12. Horizontal gene transfer converts non-toxigenic Clostridium difficile strains into toxin producers

    PubMed Central

    Brouwer, Michael S.M.; Roberts, Adam P.; Hussain, Haitham; Williams, Rachel J.; Allan, Elaine; Mullany, Peter

    2013-01-01

    Clostridium difficile is a major nosocomial pathogen and the main causative agent of antibiotic-associated diarrhoea. The organism produces two potent toxins, A and B, which are its major virulence factors. These are chromosomally encoded on a region termed the pathogenicity locus (PaLoc), which also contains regulatory genes, and is absent in non-toxigenic strains. Here we show that the PaLoc can be transferred from the toxin-producing strain, 630?erm, to three non-toxigenic strains of different ribotypes. One of the transconjugants is shown by cytotoxicity assay to produce toxin B at a similar level to the donor strain, demonstrating that a toxigenic C. difficile strain is capable of converting a non-toxigenic strain to a toxin producer by horizontal gene transfer. This has implications for the treatment of C. difficile infections, as non-toxigenic strains are being tested as treatments in clinical trials. PMID:24131955

  13. 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

  14. Isolation and Characterization of Brewer's Yeast Variants with Improved Fermentation Performance under High-Gravity Conditions?

    PubMed Central

    Blieck, Lies; Toye, Geert; Dumortier, Françoise; Verstrepen, Kevin J.; Delvaux, Freddy R.; Thevelein, Johan M.; Van Dijck, Patrick

    2007-01-01

    To save energy, space, and time, today's breweries make use of high-gravity brewing in which concentrated medium (wort) is fermented, resulting in a product with higher ethanol content. After fermentation, the product is diluted to obtain beer with the desired alcohol content. While economically desirable, the use of wort with an even higher sugar concentration is limited by the inability of brewer's yeast (Saccharomyces pastorianus) to efficiently ferment such concentrated medium. Here, we describe a successful strategy to obtain yeast variants with significantly improved fermentation capacity under high-gravity conditions. We isolated better-performing variants of the industrial lager strain CMBS33 by subjecting a pool of UV-induced variants to consecutive rounds of fermentation in very-high-gravity wort (>22° Plato). Two variants (GT336 and GT344) showing faster fermentation rates and/or more-complete attenuation as well as improved viability under high ethanol conditions were identified. The variants displayed the same advantages in a pilot-scale stirred fermenter under high-gravity conditions at 11°C. Microarray analysis identified several genes whose altered expression may be responsible for the superior performance of the variants. The role of some of these candidate genes was confirmed by genetic transformation. Our study shows that proper selection conditions allow the isolation of variants of commercial brewer's yeast with superior fermentation characteristics. Moreover, it is the first study to identify genes that affect fermentation performance under high-gravity conditions. The results are of interest to the beer and bioethanol industries, where the use of more-concentrated medium is economically advantageous. PMID:17158628

  15. 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

  16. Isolation and Characterization of Small-Colony Variants of Ornithobacterium rhinotracheale

    PubMed Central

    Zahra, Mohammad; Ferreri, Miro; Alkasir, Rashad; Yin, Jinhua

    2013-01-01

    Ornithobacterium rhinotracheale is a Gram-negative bacterium associated with respiratory diseases in many avian species, with worldwide distribution, and it causes significant economic loss to the poultry industry. In this study, the isolation and characterization of O. rhinotracheale small-colony variants (SCVs) are described for the first time. O. rhinotracheale isolates (n = 27) were recovered from tracheal samples (n = 321) collected from different avian species with clinical signs of respiratory disease. Of the 27 O. rhinotracheale isolates, 21 (77.8%) showed SCVs in their primary cultures. Five O. rhinotracheale SCV isolates showed high levels of stability and were chosen for further characterization with their wild-type (WT) isolates. Stable O. rhinotracheale SCVs were oxidase negative, while their WT isolates were positive. Growth curves for stable O. rhinotracheale SCVs indicated lower growth rates and longer lag phases than for their WT isolates. Furthermore, it was possible to increase the efficacy of the broth medium in supporting the growth of O. rhinotracheale WT isolates by supplementing it with 5% fetal bovine serum (FBS) and 2% IsoVitaleX Enrichment. Antibiotic susceptibility tests showed that O. rhinotracheale SCVs had higher MIC values than their WT isolates. This study suggests that successful antibiotic treatment of respiratory diseases associated with O. rhinotracheale must take into consideration the resistance patterns of O. rhinotracheale SCVs. Intracellular persistence in murine RAW 264.7 macrophages revealed that O. rhinotracheale SCV28 had higher survival rates than its WT isolate. Finally, small-colony variants may be important contributors to the pathogenesis of O. rhinotracheale. PMID:23863572

  17. Contributions of PTCH Gene Variants to Isolated Cleft Lip and Palate

    PubMed Central

    Mansilla, M.A.; Cooper, M.E.; Goldstein, T.; Castilla, E.E.; Camelo, J.S. Lopez; Marazita, M.L.; Murray, J.C.

    2007-01-01

    Objective Mutations in patched (PTCH) cause the nevoid basal cell carcinoma syndrome (NBCCS), or Gorlin syndrome. Nevoid basal cell carcinoma syndrome may present with developmental anomalies, including rib and craniofacial abnormalities, and predisposes to several tumor types, including basal cell carcinoma and medulloblastoma. Cleft palate is found in 4% of individuals with nevoid basal cell carcinoma syndrome. Because there might be specific sequence alterations in PTCH that limit expression to orofacial clefting, a genetic study of PTCH was undertaken in cases with cleft lip and/or palate (CL/P) known not to have nevoid basal cell carcinoma syndrome. Results Seven new normal variants spread along the entire gene and three missense mutations were found among cases with cleft lip and/or palate. One of these variants (P295S) was not found in any of 1188 control samples. A second variant was found in a case and also in 1 of 1119 controls. The third missense (S827G) was found in 5 of 1369 cases and in 5 of 1104 controls and is likely a rare normal variant. Linkage and linkage desequilibrium also was assessed using normal variants in and adjacent to the PTCH gene in 220 families (1776 individuals), each with two or more individuals with isolated clefting. Although no statistically significant evidence of linkage (multipoint HLOD peak = 2.36) was uncovered, there was borderline evidence of significant transmission distortion for one haplotype of two single nucleotide polymorphisms located within the PTCH gene (p = .08). Conclusion Missense mutations in PTCH may be rare causes of isolated cleft lip and/or palate. An as yet unidentified variant near PTCH may act as a modifier of cleft lip and/or palate. PMID:16405370

  18. Novel ctxB variants of Vibrio cholerae O1 isolates, China.

    PubMed

    Zhang, Ping; Zhou, Haijian; Kan, Biao; Wang, Duochun

    2013-12-01

    We screened 650 isolates from historical collection of Vibrio cholerae O1 during the 7th cholera pandemic in China, by amplifying and sequencing the cholera toxin subunit gene ctxB. Ten isolates were identified as harboring three novel ctxB genotypes based on amino acid residue substitutions. Within them one isolate from a patient in 1964 was similar to the El Tor genotype, except for an 11 amino acid repeat sequence (LAGKREMAIIT) that was inserted after position 62. Six environmental isolates from different regions and years were identified as the Australia El Tor genotype, except at positions 36(T?A), 39(H?Y), and 55(K?N), while three environmental isolates were similar to genotype 5, except at position 24(Q?H). Sequencing of rstR, the marker gene for the CTX? allele typing, revealed that two isolates carried the rstR gene of the El Tor type, five carried the classical type rstR, while other isolates carried the rstR232 type. All 10 isolates contained the repeat in the toxin gene rtxC, an El Tor biotype-specific marker, and the El Tor toxin-coregulated pili subunit A gene tcpA, showing the El Tor traits of these isolates. Additionally, by phenotypic biotyping (susceptibility to polymyxin B, positive for chicken erythrocyte agglutination, and Voges-Proskauer test), all isolates except two were typical of the prototype El Tor isolate, while these two isolates had mixed classical phenotypes (hybrid biotype). Furthermore, pulsed-field gel electrophoresis analysis suggested that the new ctxB altered isolates possessed potential transmissibility and thatthey propagated in the local region(s). Taken together, these novel ctxB variants of V. cholerae O1 experienced complex hybrid and genetic exchange but belong to the El Tor lineage, and the pathogenic and epidemic potential of these lineages should be monitored. PMID:23954417

  19. High incidence of recurrent copy number variants in patients with isolated and syndromic Müllerian aplasia

    PubMed Central

    Nik-Zainal, Serena; Strick, Reiner; Storer, Mekayla; Huang, Ni; Rad, Roland; Willatt, Lionel; Fitzgerald, Tomas; Martin, Vicki; Sandford, Richard; Carter, Nigel P; Janecke, Andreas R; Renner, Stefan P; Oppelt, Patricia G; Oppelt, Peter; Schulze, Christine; Brucker, Sara; Hurles, Matthew; Beckmann, Matthias W; Strissel, Pamela L; Shaw-Smith, Charles

    2012-01-01

    Background Congenital malformations involving the Müllerian ducts are observed in around 5% of infertile women. Complete aplasia of the uterus, cervix, and upper vagina, also termed Müllerian aplasia or Mayer–Rokitansky–Kuster–Hauser (MRKH) syndrome, occurs with an incidence of around 1 in 4500 female births, and occurs in both isolated and syndromic forms. Previous reports have suggested that a proportion of cases, especially syndromic cases, are caused by variation in copy number at different genomic loci. Methods In order to obtain an overview of the contribution of copy number variation to both isolated and syndromic forms of Müllerian aplasia, copy number assays were performed in a series of 63 cases, of which 25 were syndromic and 38 isolated. Results A high incidence (9/63, 14%) of recurrent copy number variants in this cohort is reported here. These comprised four cases of microdeletion at 16p11.2, an autism susceptibility locus not previously associated with Müllerian aplasia, four cases of microdeletion at 17q12, and one case of a distal 22q11.2 microdeletion. Microdeletions at 16p11.2 and 17q12 were found in 4/38 (10.5%) cases with isolated Müllerian aplasia, and at 16p11.2, 17q12 and 22q11.2 (distal) in 5/25 cases (20%) with syndromic Müllerian aplasia. Conclusion The finding of microdeletion at 16p11.2 in 2/38 (5%) of isolated and 2/25 (8%) of syndromic cases suggests a significant contribution of this copy number variant alone to the pathogenesis of Müllerian aplasia. Overall, the high incidence of recurrent copy number variants in all forms of Müllerian aplasia has implications for the understanding of the aetiopathogenesis of the condition, and for genetic counselling in families affected by it. PMID:21278390

  20. 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

  1. Isolation and characterization of a succinimide variant of methionyl human growth hormone.

    PubMed

    Teshima, G; Stults, J T; Ling, V; Canova-Davis, E

    1991-07-25

    Deamidation of asparagine and glutamine residues, isomerization of aspartic acid side chains, and racemization of the L- to the D-form of the amino acids are common spontaneous chemical reactions known to occur in proteins. Previous studies have implicated succinimides as intermediates in these reactions; however, the evidence has been indirect. Our results demonstrate, for the first time, the presence of a succinimide intermediate in an intact protein. The succinimide (cyclic imide) variant was isolated from thermally stressed recombinant methionyl human growth hormone (hGH) by high performance anion-exchange chromatography, further purified by reversed-phase high performance liquid chromatography, and analyzed by tryptic mapping. A later eluting tryptic peptide, compared with the native T12 peptide (residues 128-134, Leu-Glu-Asp-Gly-Ser-Pro-Arg), was analyzed by mass spectrometry (MS). This variant had a protonated molecular mass of 755.3 atomic mass units (u), as compared with 773.3 u for the native T12 peptide. A difference of 18 u, a loss of water, is consistent with the formation of a succinimide intermediate at Asp-130 of methionyl hGH. MS/MS analysis of the cyclic imide-containing peptide verified that the modification occurred at Asp-130. A difference of 18 u was also observed for the intact cyclic imide methionyl hGH variant (22,238 u), as measured by electrospray mass spectrometry, compared with native methionyl hGH (22,256 u). PMID:1856190

  2. 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

  3. Novel Allelic Variants of Mycobacteria Isolated in Brazil as Determined by PCR-Restriction Enzyme Analysis of hsp65

    Microsoft Academic Search

    A. da Silva Rocha; A. M. Werneck Barreto; C. E. Dias Campos; M. Villas-Boas da Silva; L. Fonseca; M. H. Saad; W. M. Degrave; P. N. Suffys

    2002-01-01

    Human isolates of Mycobacterium collected in 16 different states of Brazil were submitted to PCR-restriction analysis (PRA) of a 439-bp fragment of the hsp65 gene with HaeIII and BstEII. Fourteen allelic variants not described in clinical isolates so far were observed among 36 (10%) of 356 Brazilian strains, including a new pattern for Mycobacterium scrofulaceum, M. intracellulare, and M. flavescens,

  4. 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

  5. Nontoxigenic Vibrio cholerae 01 serotype Inaba biotype El Tor associated with a cluster of cases of cholera in southern India.

    PubMed Central

    Saha, P K; Koley, H; Mukhopadhyay, A K; Bhattacharya, S K; Nair, G B; Ramakrishnan, B S; Krishnan, S; Takeda, T; Takeda, Y

    1996-01-01

    Thirteen strains of Vibrio cholerae 01 belonging to the Inaba serotype El Tor biotype isolated from patients during an outbreak of cholera in the town of Warangal in southern India were found to be nontoxigenic (NT), since they did not produce cholera toxin or hybridize with DNA probes specific for cholera toxin, Zot, or Ace. The unheated and heated culture supernatants of the NT V. cholerae 01 evoked a rapid cell-rounding effect when introduced on confluent layers of CHO and HeLa cells which could not be inhibited by antiserum against known toxins. Culture supernatants of two representative NT V. cholerae 01 strains caused an increase in short-circuit current in rabbit ileal tissue mounted on an Ussing chamber, and the pattern of increase in short-circuit current was consistent with the presence of a quickly acting toxin like stable toxin. None of the strains of NT V. cholerae 01 hybridized with a DNA probe specific for the heat-stable enterotoxin of V. cholerae non-01, nor did the factor produced by NT V. cholerae 01 resemble the recently described heat-stable enterotoxin produced by enteroaggregative Escherichia coli as determine by a PCR assay. To our knowledge, this is the first report of NT V. cholerae 01 being associated with a cluster of cases of cholera, and it appears that a clone of NT V. cholerae 01 has the potential to cause localized outbreaks of cholera. PMID:8727886

  6. A variant of unknown significance in the GLA gene causing diagnostic uncertainty in a young female with isolated hypertrophic cardiomyopathy.

    PubMed

    Al-Thihli, Khalid; Ebrahim, Hatim; Hughes, Derralynn A; Patel, Millan; Tipple, Marion; Salvarinova, Ramona; Gardiner, Jane; Vallance, Hilary; Waters, Paula J

    2012-04-15

    Hypertrophic cardiomyopathy (HCM) is genetically heterogeneous, and largely caused by mutations in genes encoding sarcomere proteins. However, GLA mutations causing Fabry disease, an X-linked lysosomal storage disorder, may also present with isolated HCM. As HCM genetic testing panels are increasingly being used clinically, variants of unknown significance (VUS) are encountered, leading to challenges in interpretation. We present an illustrative case: a 10-year-old girl with isolated HCM who, on testing with a HCM multi-gene panel, was found to carry a maternally inherited p.W24R variant in GLA. Attempts to evaluate the significance of this variant, by direct biochemical testing of patient specimens, gave inconclusive results. Subsequent in vitro protein expression studies suggested that the variant is unlikely to be pathogenic. This case highlights diagnostic dilemmas that can be provoked by VUS in general, and specifically raises a question whether GLA sequencing should be included in first-line diagnostic testing for female children with isolated hypertrophic cardiomyopathy. PMID:22336178

  7. Novel Atomic Force Microscopy Based Biopanning for Isolation of Morphology Specific Reagents against TDP-43 Variants in Amyotrophic Lateral Sclerosis.

    PubMed

    Williams, Stephanie M; Venkataraman, Lalitha; Tian, Huilai; Khan, Galam; Harris, Brent T; Sierks, Michael R

    2015-01-01

    Because protein variants play critical roles in many diseases including TDP-43 in Amyotrophic Lateral Sclerosis (ALS), alpha-synuclein in Parkinson's disease and beta-amyloid and tau in Alzheimer's disease, it is critically important to develop morphology specific reagents that can selectively target these disease-specific protein variants to study the role of these variants in disease pathology and for potential diagnostic and therapeutic applications. We have developed novel atomic force microscopy (AFM) based biopanning techniques that enable isolation of reagents that selectively recognize disease-specific protein variants. There are two key phases involved in the process, the negative and positive panning phases. During the negative panning phase, phages that are reactive to off-target antigens are eliminated through multiple rounds of subtractive panning utilizing a series of carefully selected off-target antigens. A key feature in the negative panning phase is utilizing AFM imaging to monitor the process and confirm that all undesired phage particles are removed. For the positive panning phase, the target antigen of interest is fixed on a mica surface and bound phages are eluted and screened to identify phages that selectively bind the target antigen. The target protein variant does not need to be purified providing the appropriate negative panning controls have been used. Even target protein variants that are only present at very low concentrations in complex biological material can be utilized in the positive panning step. Through application of this technology, we acquired antibodies to protein variants of TDP-43 that are selectively found in human ALS brain tissue. We expect that this protocol should be applicable to generating reagents that selectively bind protein variants present in a wide variety of different biological processes and diseases. PMID:25742170

  8. 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, 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

  9. 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

  10. Prothymosin ? Variants Isolated From CD8+ T Cells and Cervicovaginal Fluid Suppress HIV-1 Replication Through Type I Interferon Induction.

    PubMed

    Teixeira, Avelino; Yen, Benjamin; Gusella, Gabriele Luca; Thomas, Albert G; Mullen, Michael P; Aberg, Judith; Chen, Xintong; Hoshida, Yujin; van Bakel, Harm; Schadt, Eric; Basler, Christopher F; García-Sastre, Adolfo; Mosoian, Arevik

    2015-05-01

    Soluble factors from CD8(+) T cells and cervicovaginal mucosa of women are recognized as important in controlling human immunodeficiency virus type 1 (HIV-1) infection and transmission. Previously, we have shown the strong anti-HIV-1 activity of prothymosin ? (ProT?) derived from CD8(+) T cells. ProT? is a small acidic protein with wide cell distribution, to which several functions have been ascribed, depending on its intracellular or extracellular localization. To date, activities of ProT? have been attributed to a single protein known as isoform 2. Here we report the isolation and identification of 2 new ProT? variants from CD8(+) T cells and cervicovaginal lavage with potent anti-HIV-1 activity. The first is a splice variant of the ProT? gene, known as isoform CRA_b, and the second is the product of a ProT? gene, thus far classified as a pseudogene 7. Native or recombinant ProT? variants potently restrict HIV-1 replication in macrophages through the induction of type I interferon. The baseline expression of interferon-responsive genes in primary human cervical tissues positively correlate with high levels of intracellular ProT?, and the knockdown of ProT? variants by small interfering RNA leads to downregulation of interferon target genes. Overall, these findings suggest that ProT? variants are innate immune mediators involved in immune surveillance. PMID:25404520

  11. 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

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

    PubMed

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

    2014-03-01

    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

  13. Genetic Variants Modulating CRIPTO Serum Levels Identified by Genome-Wide Association Study in Cilento Isolates

    PubMed Central

    Ruggiero, Daniela; Nappo, Stefania; Nutile, Teresa; Sorice, Rossella; Talotta, Francesco; Giorgio, Emilia; Bellenguez, Celine; Leutenegger, Anne-Louise; Liguori, Giovanna L.; Ciullo, Marina

    2015-01-01

    Cripto, the founding member of the EGF-CFC genes, plays an essential role in embryo development and is involved in cancer progression. Cripto is a GPI-anchored protein that can interact with various components of multiple signaling pathways, such as TGF-?, Wnt and MAPK, driving different processes, among them epithelial-mesenchymal transition, cell proliferation, and stem cell renewal. Cripto protein can also be cleaved and released outside the cell in a soluble and still active form. Cripto is not significantly expressed in adult somatic tissues and its re-expression has been observed associated to pathological conditions, mainly cancer. Accordingly, CRIPTO has been detected at very low levels in the plasma of healthy volunteers, whereas its levels are significantly higher in patients with breast, colon or glioblastoma tumors. These data suggest that CRIPTO levels in human plasma or serum may have clinical significance. However, very little is known about the variability of serum levels of CRIPTO at a population level and the genetic contribution underlying this variability remains unknown. Here, we report the first genome-wide association study of CRIPTO serum levels in isolated populations (n = 1,054) from Cilento area in South Italy. The most associated SNPs (p-value<5*10-8) were all located on chromosome 3p22.1-3p21.3, in the CRIPTO gene region. Overall six CRIPTO associated loci were replicated in an independent sample (n = 535). Pathway analysis identified a main network including two other genes, besides CRIPTO, in the associated regions, involved in cell movement and proliferation. The replicated loci explain more than 87% of the CRIPTO variance, with 85% explained by the most associated SNP. Moreover, the functional analysis of the main associated locus identified a causal variant in the 5’UTR of CRIPTO gene which is able to strongly modulate CRIPTO expression through an AP-1-mediate transcriptional regulation. PMID:25629528

  14. Novel variant serotype of streptococcus suis isolated from piglets with meningitis.

    PubMed

    Pan, Zihao; Ma, Jiale; Dong, Wenyang; Song, Wenchao; Wang, Kaicheng; Lu, Chengping; Yao, Huochun

    2015-02-01

    Streptococcus suis is an emerging zoonotic pathogen causing severe infections in pigs and humans. In previous studies, 33 serotypes of S. suis have been identified using serum agglutination. Here, we describe a novel S. suis strain, CZ130302, isolated from an outbreak of acute piglet meningitis in eastern China. Strong pathogenicity of meningitis caused by strain CZ130302 was reproduced in the BALB/c mouse model. The strain showed a high fatality rate (8/10), higher than those for known virulent serotype 2 strains P1/7 (1/10) and 9801 (2/10). Cell adhesion assay results with bEnd.3 and HEp2 cells showed that CZ130302 was significantly close to P1/7 and 9801. Both the agglutination test and its complementary test showed that strain CZ130302 had no strong cross-reaction with the other 33 S. suis serotypes. The multiplex PCR assays revealed no specified bands for all four sets used to detect the other 33 serotypes. In addition, genetic analysis of the whole cps gene clusters of all serotypes was performed in this study. The results of comparative genomics showed that the cps gene cluster of CZ130302, which was not previously reported, showed no homology to the gene sequences of the other strains. Especially, the wzy, wzx, and acetyltransferase genes of strain CZ130302 are phylogenetically distinct from strains of the other 33 serotypes. Therefore, this study suggested that strain CZ130302 represents a novel variant serotype of S. suis (designated serotype Chz) which has a high potential to be virulent and associated with meningitis in animals. PMID:25416757

  15. Genetic variants modulating CRIPTO serum levels identified by genome-wide association study in Cilento isolates.

    PubMed

    Ruggiero, Daniela; Nappo, Stefania; Nutile, Teresa; Sorice, Rossella; Talotta, Francesco; Giorgio, Emilia; Bellenguez, Celine; Leutenegger, Anne-Louise; Liguori, Giovanna L; Ciullo, Marina

    2015-01-01

    Cripto, the founding member of the EGF-CFC genes, plays an essential role in embryo development and is involved in cancer progression. Cripto is a GPI-anchored protein that can interact with various components of multiple signaling pathways, such as TGF-?, Wnt and MAPK, driving different processes, among them epithelial-mesenchymal transition, cell proliferation, and stem cell renewal. Cripto protein can also be cleaved and released outside the cell in a soluble and still active form. Cripto is not significantly expressed in adult somatic tissues and its re-expression has been observed associated to pathological conditions, mainly cancer. Accordingly, CRIPTO has been detected at very low levels in the plasma of healthy volunteers, whereas its levels are significantly higher in patients with breast, colon or glioblastoma tumors. These data suggest that CRIPTO levels in human plasma or serum may have clinical significance. However, very little is known about the variability of serum levels of CRIPTO at a population level and the genetic contribution underlying this variability remains unknown. Here, we report the first genome-wide association study of CRIPTO serum levels in isolated populations (n = 1,054) from Cilento area in South Italy. The most associated SNPs (p-value<5*10-8) were all located on chromosome 3p22.1-3p21.3, in the CRIPTO gene region. Overall six CRIPTO associated loci were replicated in an independent sample (n = 535). Pathway analysis identified a main network including two other genes, besides CRIPTO, in the associated regions, involved in cell movement and proliferation. The replicated loci explain more than 87% of the CRIPTO variance, with 85% explained by the most associated SNP. Moreover, the functional analysis of the main associated locus identified a causal variant in the 5'UTR of CRIPTO gene which is able to strongly modulate CRIPTO expression through an AP-1-mediate transcriptional regulation. PMID:25629528

  16. Isolating and characterizing three alternatively spliced mu opioid receptor variants: mMOR-1A, mMOR-1O and mMOR-1P

    PubMed Central

    Xu, Jin; Xu, Mingming; Bolan, Elizabeth; Gilbert, Annie-Kim; Pasternak, Gavril W.; Pan, Ying-Xian

    2014-01-01

    Extensive alternative pre-mRNA splicing of the mu opioid receptor gene, OPRM1, has demonstrated an array of splice variants in mouse, rat and human. Three classes of splice variants have been identified: full length 7 transmembrane (TM) domain variants with C-terminal splicing, truncated 6TM variants and single TM variants. The current studies isolates and characterizes an additional three full length C-terminal splice variants generated from the mouse OPRM1 gene: mMOR-1A, mMOR-1O and mMOR-1P. Using RT-qPCR, we demonstrated differential expression of these variants' mRNAs among selected brain regions, supporting region-specific alternative splicing. When expressed in Chinese Hamster Ovary cells, all the variants displayed high mu binding affinity and selectivity with subtle differences in the affinities toward some agonists. [35S]?GTP binding assays revealed marked differences in agonist-induced G protein activation in both potency and efficacy among the variants. Together with the previous studies of mu agonist-induced phosphorylation and internalization in several carboxyl terminal splice variants, the current studies further suggest the existence of biased signaling of various agonists within each individual variant and/or among different variants. PMID:24375714

  17. 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

  18. Isolation of a thermostable enzyme variant by cloning and selection in a thermophile.

    PubMed

    Liao, H; McKenzie, T; Hageman, R

    1986-02-01

    We developed a method for rapidly generating thermostable enzyme variants. Our strategy is to introduce the gene coding for a given enzyme from a mesophilic organism into a thermophile, Bacillus stearothermophilus. Variants that retain the enzymatic activity at the higher growth temperatures of the thermophile are then selected. This strategy was applied to kanamycin nucleotidyltransferase, which confers resistance to the antibiotic kanamycin. B. stearothermophilus carrying the wild-type enzyme is resistant to the antibiotic at 47 degrees C but not at 55 degrees C and above. Variants that were kanamycin resistant at 63 degrees C were obtained by selection of spontaneous mutants, by passage of a shuttle plasmid through the Escherichia coli mutD5 mutator strain and introduction into B. stearothermophilus by transformation, and by growing the thermophile in a chemostat. The kanamycin nucleotidyltransferases purified from these variants were all more resistant to irreversible thermal inactivation than is the wild-type enzyme, and all have the same single amino acid replacement, aspartate to tyrosine at position 80. Mutants that are even more heat stable were derived from the first variant by selecting for kanamycin resistance at 70 degrees C, and these carry the additional change of threonine to lysine at position 130. This strategy is applicable to other enzymatic activities that are selectable in thermophiles or that can be screened for by plate assays. PMID:3003740

  19. Isolation of a variant human adenovirus identified based on phylogenetic analysis during an outbreak of acute keratoconjunctivitis in Chennai

    PubMed Central

    Janani, M.K.; Malathi, J.; Madhavan, H.N.

    2012-01-01

    Background & objectives: Though several viruses are responsible for conjunctivitis, but human adenovirus (HAdV) is by far the most common cause. Epidemic conjunctivitis causes morbidity and early detection of aetiological agent is essential in preventing spread of disease as some of serotypes of adenoviruses cause a severe form of conjunctivitis. This study was undertaken to identify the causative agent of conjunctivitis outbreak in Chennai in 2010. Methods: Conjunctival samples collected from 17 patients with conjunctivitis were subjected to virological investigations. Culture and PCR for detection of adenovirus and enterovirus were carried out. PCR positive products were further subjected for DNA sequencing. The nucleotide sequences of the hexons of isolates were analyzed by comparison with all 51 human adenovirus strains. Phylogenetic tree was constructed using DAMBE software. Results: Among 17 patients, seven were positive for adenovirus by PCR on the direct specimen, none was positive for enterovirus. Eleven of 30 conjunctival swabs showed cytopathic effect in HEp-2 cell line and were confirmed as HAdV by PCR. The DNA sequence data of the 11 isolates had equal percentage of homology with HAdV 6 and 2 on blast analysis. On phylogenetic analysis with GeneBank data of 51 adenovirus strains, 11 isolates from patients during the outbreak of conjunctivitis formed a separate clade indicating a new variant strain. Interpretation & conclusions: Based on phylogenetic analysis it was concluded that the recent conjunctivitis outbreak that occurred in Chennai was caused by a variant adenovirus strain. PMID:22960893

  20. Pathogenicity and genomic characterization of a pseudorabies virus variant isolated from Bartha-K61-vaccinated swine population in China.

    PubMed

    Luo, Yuzi; Li, Na; Cong, Xin; Wang, Chun-Hua; Du, Min; Li, Lin; Zhao, Bibo; Yuan, Jin; Liu, Dan-Dan; Li, Su; Li, Yongfeng; Sun, Yuan; Qiu, Hua-Ji

    2014-11-01

    Pseudorabies (PR) or Aujeszky's disease (AD), caused by pseudorabies virus (PRV), is an economically important viral disease worldwide. Recently, PR outbreaks occurred in a large number of Bartha-K61-vaccinated swine herds in many regions of China. Here, we isolated a PRV variant, named TJ strain, from a Bartha-K61-vaccinated pig farm in China, evaluated the pathogenicity of the TJ strain in susceptible animals and analyzed its complete genomic sequence obtained by 454 pyrosequencing. Vaccination-challenge experiment in sheep showed that the classical Bartha-K61 vaccine could not provide complete protection against the challenge with the PRV TJ strain. In mice, the 50% lethal dose (LD50) of the TJ strain (10(2.3) TCID50) was lower than that of the classical PRV SC strain (10(3.0) TCID50). Furthermore, the TJ strain displayed higher mortality for pigs, as compared with the SC strain. The PRV TJ strain genome was determined to be 143,642 bp in length, encoding 67 open reading frames. The TJ strain was clustered to an independent branch together with some recent PRV isolates in China in the phylogenetic tree, which was relatively distant from previous PRV isolates. The TJ strain showed unique variations in the viral proteins that play key roles in the viral replication cycle. Taken together, the TJ strain is a highly pathogenic PRV variant with unique molecular signatures. Further studies are needed to explore the relevance of the sequence differences to the virulence alteration of the PRV variant. PMID:25293398

  1. De novo copy number variants identify new genes and loci in isolated sporadic tetralogy of Fallot

    Microsoft Academic Search

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

    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. Through a genome-wide survey of 114 subjects with TOF and their unaffected parents, we identified 11 de novo copy number variants (CNVs) that were absent or extremely rare (o0.1%) in 2,265 controls. We then examined a

  2. Existence of variant strains Fowlpox virus integrated with Reticuloendotheliosis virus in its genome in field isolates in Tanzania.

    PubMed

    Mzula, Alexanda; Masola, Selemani N; Kasanga, Christopher J; Wambura, Philemon N

    2014-06-01

    Fowlpox virus (FPV) is one example of poultry viruses which undergoes recombination with Reticuloendotheliosis virus (REV). Trepidation had been raised, and it was well established on augmented pathogenicity of the FPV upon integration of the full intact REV. In this study, we therefore intended at assessing the integration of REV into FPV genome of the field isolates obtained in samples collected from different regions of Tanzania. DNA extraction of 85 samples (scabs) was performed, and FPV-specific PCR was done by the amplification of the highly conserved P4b gene. Evaluation of FPV-REV recombination was done to FPV-specific PCR positively identified samples by amplifying the env gene and REV long terminal repeats (5' LTR). A 578-bp PCR product was amplified from 43 samples. We are reporting for the first time in Tanzania the existence of variant stains of FPV integrated with REV in its genome as 65 % of FPV identified isolates were having full intact REV integration, 21 % had partial FPV-REV env gene integration and 5 % had partial 5' LTR integration. Despite of the fact that FPV-REV integrated stains prevailed, FPV-REV-free isolates (9 %) also existed. In view of the fact that full intact REV integration is connected with increased pathogenicity of FPV, its existence in the FPV genome of most field isolates could have played a role in increased endemic, sporadic and recurring outbreaks in selected areas in Tanzania. PMID:24557589

  3. Novel Allelic Variants of Mycobacteria Isolated in Brazil as Determined by PCR-Restriction Enzyme Analysis of hsp65

    PubMed Central

    da Silva Rocha, A.; Werneck Barreto, A. M.; Dias Campos, C. E.; Villas-Bôas da Silva, M.; Fonseca, L.; Saad, M. H.; Degrave, W. M.; Suffys, P. N.

    2002-01-01

    Human isolates of Mycobacterium collected in 16 different states of Brazil were submitted to PCR-restriction analysis (PRA) of a 439-bp fragment of the hsp65 gene with HaeIII and BstEII. Fourteen allelic variants not described in clinical isolates so far were observed among 36 (10%) of 356 Brazilian strains, including a new pattern for Mycobacterium scrofulaceum, M. intracellulare, and M. flavescens, two new patterns for M. fortuitum, three new patterns each for M. gordonae and M. terrae, and one new pattern for M. avium complex-like strains. Two unidentified strains each also presented a new pattern, strongly suggesting that Mycobacterium genotypes are distributed biogeographically. The PRA procedure was also performed with 43 reference isolates belonging to 34 species, adding a further six new patterns to the identification algorithm. A database containing the normalized restriction patterns of both enzymes was constructed. Patterns available on the Internet can be introduced into this database, which will make possible the comparison of genotypes from isolates from different parts of the world. PMID:12409396

  4. 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

  5. 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

  6. Diversity within inc genes of clinical Chlamydia trachomatis variant isolates that occupy non-fusogenic inclusions

    Microsoft Academic Search

    Daniel D. Rockey; Wasna Viratyosin; John P. Bannantine; Robert J. Suchland; Walter E. Stamm

    2002-01-01

    The obligately intracellular chlamydiae are bacterial pathogens that occupy intracellular vacuoles, termed inclusions, as they develop and multiply. Typical Chlamydia trachomatis isolates occupy inclusions that fuse with other C. trachomatis inclusions within cells infected with multiple elementary bodies (wild-type phenotype). The authors of this study have recently described C. trachomatis isolates that form multiply-lobed, non-fusogenic inclusions within single cells infected

  7. Temporal Expression and Localization Patterns of Variant Surface Antigens in Clinical Plasmodium falciparum Isolates during Erythrocyte Schizogony

    PubMed Central

    Bachmann, Anna; Petter, Michaela; Tilly, Ann-Kathrin; Biller, Laura; Uliczka, Karin A.; Duffy, Michael F.; Tannich, Egbert; Bruchhaus, Iris

    2012-01-01

    Avoidance of antibody-mediated immune recognition allows parasites to establish chronic infections and enhances opportunities for transmission. The human malaria parasite Plasmodium falciparum possesses a number of multi-copy gene families, including var, rif, stevor and pfmc-2tm, which encode variant antigens believed to be expressed on the surfaces of infected erythrocytes. However, most studies of these antigens are based on in vitro analyses of culture-adapted isolates, most commonly the laboratory strain 3D7, and thus may not be representative of the unique challenges encountered by P. falciparum in the human host. To investigate the expression of the var, rif-A, rif-B, stevor and pfmc-2tm family genes under conditions that mimic more closely the natural course of infection, ex vivo clinical P. falciparum isolates were analyzed using a novel quantitative real-time PCR approach. Expression patterns in the clinical isolates at various time points during the first intraerythrocytic developmental cycle in vitro were compared to those of strain 3D7. In the clinical isolates, in contrast to strain 3D7, there was a peak of expression of the multi-copy gene families rif-A, stevor and pfmc-2tm at the young ring stage, in addition to the already known expression peak in trophozoites. Furthermore, most of the variant surface antigen families were overexpressed in the clinical isolates relative to 3D7, with the exception of the pfmc-2tm family, expression of which was higher in 3D7 parasites. Immunofluorescence analyses performed in parallel revealed two stage-dependent localization patterns of RIFIN, STEVOR and PfMC-2TM. Proteins were exported into the infected erythrocyte at the young trophozoite stage, whereas they remained inside the parasite membrane during schizont stage and were subsequently observed in different compartments in the merozoite. These results reveal a complex pattern of expression of P. falciparum multi-copy gene families during clinical progression and are suggestive of diverse functional roles of the respective proteins. PMID:23166704

  8. A new genetic variant of La Crosse virus (bunyaviridae) isolated from New England.

    PubMed

    Armstrong, Philip M; Andreadis, Theodore G

    2006-09-01

    La Crosse virus (LACV) is found primarily in the Midwestern and Appalachian regions of the United States where it is a leading cause of mosquito-borne encephalitis in children. To determine whether the distribution of this virus extends further east into New England, we analyzed a bunyavirus that was isolated from a pool of eastern tree-hole mosquitoes, Ochlerotatus triseriatus (= Aedes triseriatus), collected from Fairfield, Connecticut (CT) in 2005. Nucleotide and encoded amino acid sequences from portions of the S, M, and L segments were more similar to the prototype strain of La Crosse virus than that of closely related snowshoe hare virus. Phylogenetic analysis of sequences from the M segment indicated that the CT isolate represents a distinct lineage of La Crosse virus, diverging earliest from other strains found in southeastern, central, and northeastern United States. Despite low sequence homology with other viral strains, the CT isolate was antigenically similar to the prototype strain of LACV by plaque-reduction neutralization tests with polyclonal and monoclonal antibodies. This represents the first isolation of LACV in New England to our knowledge and suggests long-term independent evolution of the CT isolate. PMID:16968927

  9. 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...

  10. Association between ?-Lactamase-Encoding blaOXA-51 Variants and DiversiLab Rep-PCR-Based Typing of Acinetobacter baumannii Isolates

    PubMed Central

    Zander, Esther; Nemec, Alexandr; Seifert, Harald

    2012-01-01

    This study investigated the correlation between blaOXA-51 variants and Acinetobacter baumannii worldwide clonal lineages 1 to 8 (WW1 to -8). The blaOXA-51-like genes of 102 A. baumannii isolates were sequenced. Using DiversiLab repetitive-sequence-based PCR (rep-PCR) typing, 92 of these isolates had previously been assigned to WW1 to -8 and 10 were unclustered. Clustering of DNA sequences was performed using the neighbor-joining method and the Jukes-Cantor phylogenetic correction. blaOXA-51 variants were in good correlation with DiversiLab-defined clonal lineages. Sequence-based typing of blaOXA-51 variants has the potential to be applied for epidemiologic characterization of A. baumannii and to identify worldwide clonal lineages 1 to 8. PMID:22422849

  11. Association between ?-lactamase-encoding bla(OXA-51) variants and DiversiLab rep-PCR-based typing of Acinetobacter baumannii isolates.

    PubMed

    Zander, Esther; Nemec, Alexandr; Seifert, Harald; Higgins, Paul G

    2012-06-01

    This study investigated the correlation between bla(OXA-51) variants and Acinetobacter baumannii worldwide clonal lineages 1 to 8 (WW1 to -8). The bla(OXA-51-like) genes of 102 A. baumannii isolates were sequenced. Using DiversiLab repetitive-sequence-based PCR (rep-PCR) typing, 92 of these isolates had previously been assigned to WW1 to -8 and 10 were unclustered. Clustering of DNA sequences was performed using the neighbor-joining method and the Jukes-Cantor phylogenetic correction. bla(OXA-51) variants were in good correlation with DiversiLab-defined clonal lineages. Sequence-based typing of bla(OXA-51) variants has the potential to be applied for epidemiologic characterization of A. baumannii and to identify worldwide clonal lineages 1 to 8. PMID:22422849

  12. Isolation and characterization of novel variants of BBI coding genes from the legume Lathyrus sativus.

    PubMed

    De Paola, Domenico; Blanco, Emanuela; Pierri, Ciro Leonardo; Sonnante, Gabriella

    2012-08-01

    A pool of twelve cDNA sequences coding for Bowman-Birk inhibitors (BBIs) was identified in the legume grass pea (Lathyrus sativus L.). The corresponding amino acid sequences showed a canonical first anti-trypsin domain, predicted according to the identity of the determinant residue P(1). A more variable second binding loop was observed allowing to identify three groups based on the identity of residue P(1): two groups (Ls_BBI_1 and Ls_BBI_2) carried a second reactive site specific for chymotrypsin, while a third group (Ls_BBI_3) was predicted to inhibit elastase. A fourth variant carrying an Asp in the P(1) position of the second reactive site was identified only from genomic DNA. A phylogenetic tree constructed using grass pea BBIs with their homologs from other legume species revealed grouping based on taxonomy and on specificity of the reactive sites. Five BBI sequences, representing five different second reactive sites, were heterologously expressed in the yeast Pichia pastoris. The recombinant proteins demonstrated to be active against trypsin, while three of them were also active against chymotrypsin, and one against human leukocyte elastase. Comparative modeling and protein docking were used to further investigate interactions between two grass pea BBI isoforms and their target proteases. Thus two reliable 3D models have been proposed, representing two potential ternary complexes, each constituted of an inhibitor and its target enzymes. PMID:22677449

  13. Effect of light intensity on the relative dominance of toxigenic and nontoxigenic strains of Microcystis aeruginosa.

    PubMed

    Leblanc Renaud, Susan; Pick, Frances R; Fortin, Nathalie

    2011-10-01

    In aquatic ecosystems, the factors that regulate the dominance of toxin-producing cyanobacteria over non-toxin-producing strains of the same species are largely unknown. One possible hypothesis is that limiting resources lead to the dominance of the latter because of the metabolic costs associated with toxin production. In this study, we tested the effect of light intensity on the performance of a microcystin-producing strain of Microcystis aeruginosa (UTCC 300) when grown in mixed cultures with non-microcystin-producing strains with similar intrinsic growth rates (UTCC 632 and UTCC 633). The endpoints measured included culture growth rates, microcystin concentrations and composition, and mcyD gene copy numbers determined using quantitative PCR (Q-PCR). In contrast to the predicted results, under conditions of low light intensity (20 ?mol·m(-2)·s(-1)), the toxigenic strain became dominant in both of the mixed cultures based on gene copy numbers and microcystin concentrations. When grown under conditions of high light intensity (80 ?mol·m(-2)·s(-1)), the toxigenic strain still appeared to dominate over nontoxigenic strain UTCC 632 but less so over strain UTCC 633. Microcystins may not be so costly to produce that toxigenic cyanobacteria are at a disadvantage in competition for limiting resources. PMID:21841026

  14. A bacterial one-hybrid system to isolate homing endonuclease variants with altered DNA target specificities.

    PubMed

    Joshi, Rakesh; Gimble, Frederick S

    2014-01-01

    Chromosomal cleavage near the site of mutations that cause disease can facilitate the targeted repair of the locus. Gene therapy protocols therefore require the engineering of DNA endonucleases that target specific genomic loci. Here, we describe a bacterial one-hybrid selection system that has been used to isolate derivatives of the I-SceI homing endonuclease from combinatorial libraries that display altered DNA recognition specificities. The construction of plasmid expression libraries, the development of reporter strains, and the utilization of these components in the bacterial one-hybrid system are detailed. PMID:24557906

  15. 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

  16. Novel VIM Metallo-?-Lactamase Variant from Clinical Isolates of Enterobacteriaceae from Algeria ?

    PubMed Central

    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 ?-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 blaVIM gene in all five strains. The blaVIM genes were located as part of a class 1 integron on a 180-kb conjugative plasmid. They encoded a novel metallo-?-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

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

    PubMed

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

    1994-02-01

    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. PMID:8300538

  18. Isolation and functional analysis of yeast ubiquitin ligase Rsp5 variants that alleviate the toxicity of human ?-synuclein.

    PubMed

    Wijayanti, Indah; Watanabe, Daisuke; Oshiro, Satoshi; Takagi, Hiroshi

    2015-04-01

    The essential ubiquitin ligase Rsp5 is a key enzyme involved in the degradation of abnormal or unfavourable proteins in the yeast Saccharomyces cerevisiae. Overexpression of human ?-synuclein (?-syn), a small lipid-binding protein implicated in several neurodegenerative diseases, in S. cerevisiae leads to growth inhibition due to many intracellular defects, including accumulation of reactive oxygen species (ROS). Here, to understand the mechanism of Rsp5-mediated detoxification of ?-syn, we isolated novel Rsp5 variants (T255A, D295G, P343S and N427D), which conferred ?-syn tolerance to yeast cells. Interestingly, these mutants were phenotypically distinguished from our previously identified RSP5(T357A) mutation, which increases ubiquitination of the general amino acid permease Gap1. Among them, the RSP5(P343S) substitution accelerated the degradation of ?-syn, suppressed the accumulation of intracellular ROS and enhanced the interaction with ?-syn and its ubiquitination. In contrast, the RSP5(T255A) mutation did not contribute to degradation of ?-syn, but improved cell growth under acetate stress conditions, possibly leading to alleviation of the ?-syn toxicity. Thus, these novel mutations might be useful not only in elucidating the molecular basis by which disused proteins are specifically recognized and effectively removed but also in screening drug candidates for neurodegenerative diseases or in improving ethanol production under acidic fermentation conditions. PMID:25398992

  19. Isolation of recent variant influenza types A(H3N2), A (H1N1) & B strains in Pune, India.

    PubMed

    Rao, B L; Kadam, S S; Pawar, M S

    2001-11-01

    A total of 293 patients with influenza like illness were investigated during the course of continuous surveillance on influenza in Pune, India in 2000. The throat/nasal swab specimens collected from these patients were inoculated in MDCK cell culture and influenza types A(H3N2), A(H1N1) and type B strains were isolated. They were identified as similar to the recently prevalent variant strains; A/Sydney/05/97(H3N2), A/New Caledonia/20/99(H1N1) and B/Sichuan/379/99. The latter two were the new variant strains reported for the first time in Pune. It is important to note that A(H1N1) strains were isolated in Pune during 2000 after a gap of 10 yr. PMID:12025254

  20. Isolation of highly fusogenic variants of simian virus 5 from persistently infected cells that produce and respond to interferon.

    PubMed Central

    Young, D F; Didcock, L; Randall, R E

    1997-01-01

    A series of experiments were undertaken to examine how interferon and neutralizing antibodies influence the ability of simian virus 5 (SV5) (strain W3) to establish and maintain persistent infections in murine cells. In contrast to the rapid decline in SV5 protein synthesis observed in murine BALB/c fibroblasts (BF cells), which produce and respond to interferon, between 24 and 48 h postinfection there was no inhibition of virus protein synthesis in MSFI- cells, skin fibroblasts derived from alpha/beta-interferon receptor knockout BALB/c mice. Furthermore, the addition of anti-interferon antibodies to the culture medium of infected BF cells significantly reduced the observed decline in virus protein synthesis. Following infection of untreated BF cells, the majority replicated virus but survived the infection and eventually cleared the virus after 8 to 15 days. However, not all the cells were cured, and the cultures became persistently infected. Upon passage of persistently infected cultures, the virus fluxed between active and repressed states as a consequence of interferon production. This resulted in a balance being reached in which only 5 to 20% of the cells were infected at any one time. After 30 passages of the persistently infected cells, highly fusogenic virus variants arose (one of which was isolated and termed W3-f). W3-f remained as sensitive to interferon as the parental W3 isolate but, in the absence of interferon, spread much more rapidly than the parental W3 strain through BF cell monolayers. Sequence analysis revealed no deduced amino acid differences between the F proteins of W3 and W3-f. BF cell cultures persistently infected with W3-f were rapidly cleared of virus by the addition of virus-neutralizing antibodies to the culture medium. In contrast, neutralizing antibodies had little effect on the numbers of cells persistently infected with W3 over several passages. These results suggest that the ability of paramyxoviruses to cause cell-cell fusion may be selected for in vivo as a consequence of their adaptation to the interferon response rather than their need to escape from neutralizing antibodies. The significance of these observations with regard to persistent parainfluenza virus infections in vivo is further discussed. PMID:9371592

  1. 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

  2. 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

  3. 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

  4. 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 [Korea Research Institute of Bioscience and Biotechnology, Taejon (Korea, Republic of); Emerson, C.P. Jr. [Fox Chase Cancer Center, Philadelphia, PA (United States)

    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.

  5. 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.

  6. Engineering of the yeast ubiquitin ligase Rsp5: isolation of a new variant that induces constitutive inactivation of the general amino acid permease Gap1.

    PubMed

    Haitani, Yutaka; Nakata, Maiko; Sasaki, Toshiya; Uchida, Akiko; Takagi, Hiroshi

    2009-02-01

    Rsp5 is an essential ubiquitin-protein ligase in Saccharomyces cerevisiae. We found previously that the Ala401Glu rsp5 mutant is hypersensitive to various stresses that induce protein misfolding, suggesting that Rsp5 is a key enzyme for yeast cell growth under stress conditions. To isolate new Rsp5 variants as suppressors of the A401E mutant, PCR random mutagenesis was used in the rsp5(A401E) gene, and the mutagenized plasmid library was introduced into rsp5(A401E) cells. As a phenotypic suppressor of rsp5(A401E) cells, we isolated a quadruple variant (Thr357Ala/Glu401Gly/Lys764Glu/Glu767Gly) on a minimal medium containing the toxic proline analogue azetidine-2-carboxylate (AZC). Site-directed mutagenesis experiments showed that the rsp5(T357A/K764E) cells were much more tolerant to AZC than the wild-type cells, due to the smaller amounts of intracellular AZC. However, the T357A/K764E variant Rsp5 did not reverse the hypersensitivity of rsp5(A401E) cells to other stresses such as high growth temperature, ethanol, and freezing treatment. Interestingly, immunoblot and localization analyses indicated that the general amino acid permease Gap1, which is involved in AZC uptake, was absent on the plasma membrane and degraded in the vacuole of rsp5(T357A/K764E) cells before the addition of ammonium ions. These results suggest that the T357A/K764E variant Rsp5 induces constitutive inactivation of Gap1. PMID:19054125

  7. 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

  8. The Thymidine-Dependent Small-Colony-Variant Phenotype Is Associated with Hypermutability and Antibiotic Resistance in Clinical Staphylococcus aureus Isolates?

    PubMed Central

    Besier, Silke; Zander, Johannes; Kahl, Barbara C.; Kraiczy, Peter; Brade, Volker; Wichelhaus, Thomas A.

    2008-01-01

    Thymidine-dependent small-colony variants (TD-SCVs) of Staphylococcus aureus can be isolated from the airway secretions of patients suffering from cystic fibrosis (CF) and are implicated in persistent and treatment-resistant infections. These characteristics, as well as the variety of mutations in the thymidylate synthase-encoding thyA gene which are responsible for thymidine dependency, suggest that these morphological variants are hypermutable. To prove this hypothesis, we analyzed the mutator phenotype of different S. aureus phenotypes, in particular CF-derived TD-SCVs, CF-derived isolates with a normal phenotype (NCVs), and non-CF NCVs. The comparative analysis revealed that the CF isolates had significantly higher mutation rates than the non-CF isolates. The TD-SCVs, in turn, harbored significantly more strong hypermutators (mutation rate ? 10?7) than the CF and non-CF NCVs. In addition, antimicrobial resistance to non-beta-lactam antibiotics, including gentamicin, ciprofloxacin, erythromycin, fosfomycin, and rifampin, was significantly more prevalent in TD-SCVs than in CF and non-CF NCVs. Interestingly, macrolide resistance, which is usually mediated by mobile genetic elements, was conferred in half of the macrolide-resistant TD-SCVs by the point mutation A2058G or A2058T in the genes encoding the 23S rRNA. Sequence analysis of mutS and mutL, which are involved in DNA mismatch repair in gram-positive bacteria, revealed that in hypermutable CF isolates and especially in TD-SCVs, mutL was often truncated due to frameshift mutations. In conclusion, these data provide direct evidence that TD-SCVs are hypermutators. This hypermutability apparently favors the acquisition of antibiotic resistance and facilitates bacterial adaptation during long-term persistence. PMID:18378706

  9. Molecular epidemiology and antimicrobial susceptibility of Clostridium difficile isolated from a university teaching hospital in Japan.

    PubMed

    Kuwata, Y; Tanimoto, S; Sawabe, E; Shima, M; Takahashi, Y; Ushizawa, H; Fujie, T; Koike, R; Tojo, N; Kubota, T; Saito, R

    2015-04-01

    Clostridium difficile infection control strategies require an understanding of its epidemiology. In this study, we analysed the toxin genotypes of 130 non-duplicate clinical isolates of C. difficile from a university hospital in Tokyo, Japan. Multilocus sequence typing (MLST) and eBURST analysis were performed for these isolates and nine strains previously analysed by polymerase chain reaction (PCR) ribotyping. Minimum inhibitory concentrations (MICs) were determined for six antibiotics, and the bacterial resistance mechanisms were investigated. Ninety-five toxigenic strains (73 %), including seven tcdA-negative, tcdB-positive and cdtA/cdtB-negative strains (A(-)B(+)CDT(-)) and three A(+)B(+)CDT(+) strains, and 35 (27 %) non-toxigenic strains, were classified into 23 and 12 sequence types, respectively. Of these, sequence type (ST)17 (21.8 %) was the most predominant. MLST and eBURST analysis showed that 139 strains belonged to seven groups and singletons, and most A(+)B(+)CDT(-) strains (98 %, 89/91) were classified into group 1. All isolates were susceptible to metronidazole, vancomycin and meropenem; the ceftriaxone, clindamycin and ciprofloxacin resistance rates were 49, 59 and 99 %, respectively. Resistance rates to ceftriaxone and clindamycin were higher in toxigenic strains than in non-toxigenic strains (P?non-toxigenic strains in Japan, providing evidence that non-toxigenic and toxigenic strains exhibit high genetic diversity and that toxigenic strains are more likely than non-toxigenic strains to exhibit multidrug resistance. PMID:25471195

  10. A Novel New Delhi Metallo-?-Lactamase Variant, NDM-14, Isolated in a Chinese Hospital Possesses Increased Enzymatic Activity against Carbapenems.

    PubMed

    Zou, Dayang; Huang, Yong; Zhao, Xiangna; Liu, Wei; Dong, Derong; Li, Huan; Wang, Xuesong; Huang, Simo; Wei, Xiao; Yan, Xiabei; Yang, Zhan; Tong, Yigang; Huang, Liuyu; Yuan, Jing

    2015-04-01

    A novel New Delhi metallo-?-lactamase (NDM) variant, NDM-14, was identified in clinical isolate Acinetobacter lwoffii JN49-1, which was recovered from an intensive care unit patient at a local hospital in China. NDM-14, which differs from other existing enzymes by an amino acid substitution at position 130 (Asp130Gly), possesses enzymatic activity toward carbapenems that is greater than that of NDM-1. Kinetic data indicate that NDM-14 has a higher affinity for imipenem and meropenem. PMID:25645836

  11. 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

  12. Distribution of streptococcal inhibitor of complement variants in pharyngitis and invasive isolates in an epidemic of serotype M1 group A Streptococcus infection.

    PubMed

    Hoe, N P; Vuopio-Varkila, J; Vaara, M; Grigsby, D; De Lorenzo, D; Fu, Y X; Dou, S J; Pan, X; Nakashima, K; Musser, J M

    2001-02-15

    Streptococcal inhibitor of complement (Sic) is a highly polymorphic extracellular protein made predominantly by serotype M1 group A Streptococcus (GAS). New variants of the Sic protein frequently appear in M1 epidemics as a result of positive natural selection. To gain further understanding of the molecular basis of M1 epidemics, the sic gene was sequenced from 471 pharyngitis and 127 pyogenic and blood isolates recovered from 598 patients living in metropolitan Helsinki, Finland, during a 37-month population-based surveillance study. Most M1 GAS subclones recovered from pyogenic infections and blood were abundantly represented in the pool of subclones causing pharyngitis. Alleles shared among the pharyngitis, pyogenic, and blood samples were identified in throat isolates a mean of 9.8 months before their recovery from pyogenic infections and blood, which indicates that selection of most sic variants occurs on mucosal surfaces. In contrast, no variation was identified in the emm and covR/covS genes. PMID:11170990

  13. Isolated Cerebellar Variant of Adrenoleukodystrophy with a de novo Adenosine Triphosphate-Binding Cassette D1 (ABCD1) Gene Mutation

    PubMed Central

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

    2014-01-01

    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

  14. Identification of OXA-23 carbapenemases: novel variant OXA-239 in Acinetobacter baumannii ST758 clinical isolates in Mexico

    PubMed Central

    Tamayo-Legorreta, E M; Garza-Ramos, U; Barrios-Camacho, H; Sanchez-Perez, A; Galicia-Paredes, A; Meza-Chavez, A; Silva-Sanchez, J

    2014-01-01

    A collection of 15 carbapenem-resistance Acinetobacter baumannii clinical isolates was analysed on two tertiary hospitals in Mexico. The OXA-51 was identified in all isolates, followed by OXA-239 and OXA-58; OXA-239 is described as a new OXA-23-like allele. These carbapenemases were identified on four clonal groups, distributed between two neighbouring hospitals. Acinetobacter baumannii is poorly studied in Mexico; this situation urges the implementation of strategies to prevent its dissemination. PMID:25566396

  15. Multi-drug resistant Vibrio cholerae O1 variant El Tor isolated in northern Vietnam between 2007 and 2010.

    PubMed

    Tran, Huu Dat; Alam, Munirul; Trung, Nguyen Vu; Kinh, Nguyen Van; Nguyen, Hong Ha; Pham, Van Ca; Ansaruzzaman, Mohammad; Rashed, Shah Manzur; Bhuiyan, Nurul A; Dao, Tuyet Trinh; Endtz, Hubert P; Wertheim, Heiman F L

    2012-03-01

    Since 2007, there has been a re-emergence of cholera outbreaks in northern Vietnam. To understand the molecular epidemiological relatedness and determine the antibiotic susceptibility profiles of responsible V. cholerae O1 outbreak strains, a representative collection of 100 V. cholerae O1 strains was characterized. V. cholerae O1 strains isolated from diarrhoeal patients in northern Vietnam between 2007 and 2010 were investigated for antibiotic susceptibility and characterized by using phenotypic and genotypic tests, including PFGE analysis. Ten clinical V. cholerae O1 isolates from Bangladesh and Zimbabwe were included for comparison. The results revealed that all isolates were resistant to co-trimoxazole and nalidixic acid, 29?% were resistant to tetracycline and 1?% were resistant to azithromycin. All strains were susceptible to ampicillin-sulbactam, doxycycline, chloramphenicol and ciprofloxacin and 95?% were susceptible to azithromycin. MIC values did show reduced susceptibility to fluoroquinolones and 63?% of the strains were intermediately resistant to tetracycline. The isolates expressed phenotypic traits of both serogroup O1 Ogawa and El Tor and harboured an rstR El Tor and ctxB classical biotype. Among the outbreak isolates, only a single PFGE pattern was observed throughout the study period. This study shows that multi-drug resistant V. cholerae altered El Tor producing classical CT strains are now predominant in northern Vietnam. PMID:22016560

  16. Multi-drug resistant Vibrio cholerae O1 variant El Tor isolated in northern Vietnam between 2007 and 2010

    PubMed Central

    Alam, Munirul; Trung, Nguyen Vu; Van Kinh, Nguyen; Nguyen, Hong Ha; Pham, Van Ca; Ansaruzzaman, Mohammad; Rashed, Shah Manzur; Bhuiyan, Nurul A.; Dao, Tuyet Trinh; Endtz, Hubert P.; Wertheim, Heiman F. L.

    2012-01-01

    Since 2007, there has been a re-emergence of cholera outbreaks in northern Vietnam. To understand the molecular epidemiological relatedness and determine the antibiotic susceptibility profiles of responsible V. cholerae O1 outbreak strains, a representative collection of 100 V. cholerae O1 strains was characterized. V. cholerae O1 strains isolated from diarrhoeal patients in northern Vietnam between 2007 and 2010 were investigated for antibiotic susceptibility and characterized by using phenotypic and genotypic tests, including PFGE analysis. Ten clinical V. cholerae O1 isolates from Bangladesh and Zimbabwe were included for comparison. The results revealed that all isolates were resistant to co-trimoxazole and nalidixic acid, 29?% were resistant to tetracycline and 1?% were resistant to azithromycin. All strains were susceptible to ampicillin–sulbactam, doxycycline, chloramphenicol and ciprofloxacin and 95?% were susceptible to azithromycin. MIC values did show reduced susceptibility to fluoroquinolones and 63?% of the strains were intermediately resistant to tetracycline. The isolates expressed phenotypic traits of both serogroup O1 Ogawa and El Tor and harboured an rstR El Tor and ctxB classical biotype. Among the outbreak isolates, only a single PFGE pattern was observed throughout the study period. This study shows that multi-drug resistant V. cholerae altered El Tor producing classical CT strains are now predominant in northern Vietnam. PMID:22016560

  17. Isolation of a Hop-Sensitive Variant of Lactobacillus lindneri and Identification of Genetic Markers for Beer Spoilage Ability of Lactic Acid Bacteria

    PubMed Central

    Suzuki, Koji; Iijima, Kazumaru; Ozaki, Kazutaka; Yamashita, Hiroshi

    2005-01-01

    We have isolated a hop-sensitive variant of the beer spoilage bacterium Lactobacillus lindneri DSM 20692. The variant lost a plasmid carrying two contiguous open reading frames (ORF s) designated horBL and horCL that encode a putative regulator and multidrug transporter presumably belonging to the resistance-nodulation-cell division superfamily. The loss of hop resistance ability occurred with the loss of resistance to other drugs, including ethidium bromide, novobiocin, and cetyltrimethylammonium bromide. PCR and Southern blot analysis using 51 beer spoilage strains of various species of lactic acid bacteria (LAB) revealed that 49 strains possessed homologs of horB and horC. No false-positive results have been observed for nonspoilage LAB or frequently encountered brewery isolates. These features are superior to those of horA and ORF 5, previously reported genetic markers for determining the beer spoilage ability of LAB. It was further shown that the combined use of horB/horC and horA is able to detect all 51 beer spoilage strains examined in this study. Furthermore sequence comparison of horB and horC homologs identified in four different beer spoilage species indicates these homologs are 96.6 to 99.5% identical, which is not typical of distinct species. The wide and exclusive distribution of horB and horC homologs among beer spoilage LAB and their sequence identities suggest that the hop resistance ability of beer spoilage LAB has been acquired through horizontal gene transfer. These insights provide a foundation for applying trans-species genetic markers to differentiating beer spoilage LAB including previously unencountered species. PMID:16151091

  18. 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

  19. Full-length genome sequences of five hepatitis C virus isolates representing subtypes 3g, 3h, 3i and 3k, and a unique genotype 3 variant.

    PubMed

    Lu, Ling; Li, Chunhua; Yuan, Jie; Lu, Teng; Okamoto, Hiroaki; Murphy, Donald G

    2013-03-01

    We characterized the full-length genomes of five distinct hepatitis C virus (HCV)-3 isolates. These represent the first complete genomes for subtypes 3g and 3h, the second such genomes for 3k and 3i, and of one novel variant presently not assigned to a subtype. Each genome was determined from 18-25 overlapping fragments. They had lengths of 9579-9660 nt and each contained a single ORF encoding 3020-3025 aa. They were isolated from five patients residing in Canada; four were of Asian origin and one was of Somali origin. Phylogenetic analysis using 64 partial NS5B sequences differentiated 10 assigned subtypes, 3a-3i and 3k, and two additional lineages within genotype 3. From the data of this study, HCV-3 full-length sequences are now available for six of the assigned subtypes and one unassigned. Our findings should add insights to HCV evolutionary studies and clinical applications. PMID:23152370

  20. Ig isotype switching in B lymphocytes. Isolation and characterization of clonal variants of the murine Ly-1+ B cell lymphoma, CH12, expressing isotypes other than IgM.

    PubMed

    Arnold, L W; Grdina, T A; Whitmore, A C; Haughton, G

    1988-06-15

    We have selected and cloned variant cells from the murine B cell lymphoma, CH12, that produce a variety of other Ig isotypes in addition to or in place of the original IgM and IgD. Variants were selected by flow cytometry and automated cloning and isotype production was analyzed by membrane immunofluorescence and ELISA of culture fluids. Variants have been isolated that produce the single isotypes IgA, IgG2b, and IgG3, as well as variants that produce more than one isotype simultaneously, i.e., IgM, IgD, and IgA; IgG2b and IgA; IgG3 and IgA. All isotypes have been seen as cell surface proteins and all except IgD have been found in culture supernatants. All isotypes display the same idiotype and Ag-binding specificity for phosphatidyl choline as the original IgM and all are translated from the same VDJH and VJ kappa gene assemblies. Production of more than one isotype by a variant clone is due to simultaneous production of all the isotypes by each cell within the clone. The finding that the variants producing more than one isotype are all tetraploid suggests the interesting possibility that each isotype is derived from an independently switching chromosome. All isotype variants can be stimulated by LPS to secrete the appropriate Ig isotype at an increased rate similar to the IgM expressing parent. The variants differ in stability; some have remained stable for more than 9 months in culture, whereas other have undergone further isotype switching. The facts that some isotypes have not been seen, that multistep switching has occurred, and that many variants produce IgA in addition to another isotype are discussed in relation to current notions of isotype switching mechanisms. PMID:3131432

  1. Rough and smooth morphotypes isolated from Lactobacillus farciminis CNCM I-3699 are two closely-related variants.

    PubMed

    Tareb, Raouf; Bernardeau, Marion; Horvath, Philippe; Vernoux, Jean-Paul

    2015-01-16

    This study focused on a pleomorphic strain Lactobacillus farciminis CNCM I-3699 known as probiotic for animal applications. On plating, this strain was characterized by the presence of rough and smooth morphotypes depending on experimental conditions. Dominant smooth (S) form, bright white, having smooth edges with moist, ropy, and creamy along with rough (R) form, pale white, having irregular edges and a dry and granular aspect were always obtained from the parent strain under aerobic culture conditions. In anaerobic conditions, only S form growth was observed. Biochemical dosage of capsular exopolysaccharides showed a significant difference between S and R forms (p<0.01), in agreement with a ropy or non ropy phenotype for the S or R form, respectively. These differences were confirmed by transmission electronic microscopy. The auto-aggregation profile revealed major differences in cultural behaviors. The R morphotype presented a highly auto-aggregative ability contrary to the S morphotype. However, biochemical and molecular analyses revealed that R and S morphotypes: 1) shared the same sugar fermentation pattern; 2) belonged to L. farciminis species using 16S rDNA sequencing; 3) had identical PFGE patterns using NotI and ApaI endonucleases; and 4) had identical CRISPR loci but different from those of other L. farciminis strains. Furthermore, the novelty and uniqueness of CRISPR spacer sequences in CNCM I-3699 provides a genetic support for the development of a molecular tracking tool for CNCM I-3699 and its variants. In conclusion, L. farciminis CNCM I-3699 is a pleomorphic strain giving reproducibly rise to two phenotypically distinct morphotypes R and S. This phenomenon may explain survival and growth abilities in in vitro fluctuating aerobic-anaerobic conditions along with modulation of exopolysaccharide synthesis and autoaggregation profile. PMID:25462927

  2. Nontoxigenic protein A vaccine for methicillin-resistant Staphylococcus aureus infections in mice

    PubMed Central

    Kim, Hwan Keun; Cheng, Alice G.; Kim, Hye-Young; Missiakas, Dominique M.

    2010-01-01

    The current epidemic of hospital- and community-acquired methicillin-resistant Staphylococcus aureus (MRSA) infections has caused significant human morbidity, but a protective vaccine is not yet available. Prior infection with S. aureus is not associated with protective immunity. This phenomenon involves staphylococcal protein A (SpA), an S. aureus surface molecule that binds to Fc? of immunoglobulin (Ig) and to the Fab portion of VH3-type B cell receptors, thereby interfering with opsonophagocytic clearance of the pathogen and ablating adaptive immune responses. We show that mutation of each of the five Ig-binding domains of SpA with amino acid substitutions abolished the ability of the resulting variant SpAKKAA to bind Fc? or Fab VH3 and promote B cell apoptosis. Immunization of mice with SpAKKAA raised antibodies that blocked the virulence of staphylococci, promoted opsonophagocytic clearance, and protected mice against challenge with highly virulent MRSA strains. Furthermore, SpAKKAA immunization enabled MRSA-challenged mice to mount antibody responses to many different staphylococcal antigens. PMID:20713595

  3. Novel Variants of AbaR Resistance Islands with a Common Backbone in Acinetobacter baumannii Isolates of European Clone II

    PubMed Central

    Povilonis, Justas; Sužied?lien?, Edita

    2012-01-01

    In this study, the genetic organization of three novel genomic antibiotic resistance islands (AbaRs) in Acinetobacter baumannii isolates belonging to group of European clone II (EC II) comM integrated sequences of 18-, 21-, and 23-kb resistance islands were determined. These resistance islands carry the backbone of AbaR-type transposon structures, which are composed of the transposition module coding for potential transposition proteins and other genes coding for the intact universal stress protein (uspA), sulfate permease (sul), and proteins of unknown function. The antibiotic resistance genes strA, strB, tetB, and tetR and insertion sequence CR2 element were found to be inserted into the AbaR transposons. GenBank homology searches indicated that they are closely related to the AbaR sequences found integrated in comM in strains of EC II (A. baumannii strains 1656-2 and TCDC-AB0715) and AbaR4 integrated in another location of A. baumannii AB0057 (EC I). All of the AbaRs showed structural similarity to the previously described AbaR4 island and share a 12,008-bp backbone. AbaRs contain Tn1213, Tn2006, and the multiple fragments which could be derived from transposons Tn3, Tn10, Tn21, Tn1000, Tn5393, and Tn6020, the insertion sequences IS26, ISAba1, ISAba14, and ISCR2, and the class 1 integron. Moreover, chromosomal DNA was inserted into distinct regions of the AbaR backbone. Sequence analysis suggested that the AbaR-type transposons have evolved through insertions, deletions, and homologous recombination. AbaR islands, sharing the core structure similar to AbaR4, appeared to be distributed in isolates of EC I and EC II via integration into distinct genomic sites, i.e., pho and comM, respectively. PMID:22290980

  4. 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

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

    PubMed

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

    2015-01-15

    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

  6. 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

  7. Isolation of Clostridium botulinum type G from Swiss soil specimens by using sequential steps in an identification scheme.

    PubMed Central

    Sonnabend, W F; Sonnabend, U P; Krech, T

    1987-01-01

    After Clostridium botulinum type G organisms and toxin were identified in necropsy specimens in cases of unexplained death in adults and infants (O. Sonnabend, W. Sonnabend, R. Heinzle, T. Sigrist, R Dirnhofer, and U. Krech, J. Infect. Dis. 143:22-27, 1981), extensive research to detect C. botulinum type G in soil samples from Switzerland was done. A total of 41 specimens from virgin soil and from cultivated land were examined for the presence of C. botulinum type G and other toxin types. Because of the lack of the lipase marker in type G, the detection of C. botulinum type G was based on the demonstration of type G organisms in enrichment cultures by a type G-specific enzyme-linked immunosorbent assay to detect both the type G toxin and antigen; enrichment cultures in which type G toxin or antigen was identified by enzyme-linked immunosorbent assay were then tested by a type G-specific gel immunodiffusion agar procedure. This method not only isolated strains of type G but also strains of Clostridium subterminale, a nontoxigenic variant of C. botulinum type G. As a consequence of the observed cross-reactions caused by strains of C. subterminale within this test system, all isolates of type G had to be definitively confirmed by mouse bioassay. The sequential steps of these methods seem to be very useful for detecting C. botulinum type G organisms. C. botulinum type G strains were isolated in five soil samples from different locations in close association with cultivated land.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:3116935

  8. A Molecular Surveillance Reveals the Prevalence of Vibrio cholerae O139 Isolates in China from 1993 to 2012

    PubMed Central

    Zhang, Ping; Zhou, Haijian; Diao, Baowei; Li, Fengjuan; Du, Pengcheng; Li, Jie; Morris, J. Glenn

    2014-01-01

    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 within13 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

  9. 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

  10. Host Adaptation of Pigeon Isolates of Salmonella enterica subsp. enterica Serovar Typhimurium Variant Copenhagen Phage Type 99 Is Associated with Enhanced Macrophage Cytotoxicity

    Microsoft Academic Search

    Frank Pasmans; Filip Van Immerseel; Marc Heyndrickx; An Martel; Claudine Godard; Christa Wildemauwe; Richard Ducatelle; Freddy Haesebrouck

    2003-01-01

    Phage type 99 of Salmonella enterica subsp. enterica serovar Typhimurium variant Copenhagen strains iso- lated from pigeons were examined for the presence of genotypic and phenotypic characteristics. The pulsed- field gel electrophoresis patterns obtained with XbaI and BlnI from 38 pigeon strains were compared with those obtained from 89 porcine, poultry, and human strains of variant Copenhagen. Identical patterns with

  11. Isolation of a thermostable variant of Lip2 lipase from Yarrowia lipolytica by directed evolution and deeper insight into the denaturation mechanisms involved.

    PubMed

    Bordes, Florence; Tarquis, Laurence; Nicaud, Jean-Marc; Marty, Alain

    2011-11-10

    Lip2 lipase from Yarrowia lipolytica is a very promising lipase with many potential applications (e.g. resolution of racemic mixtures, production of fine chemicals). Unfortunately this potential is impeded by a very low thermostability for temperatures higher than 40°C. Error-prone PCR and screening of the library in a high-performance yeast expression system (Y. lipolytica) enabled a thermostable variant to be identified. This variant presents only one mutation, the free cysteine 244 is changed into an alanine. At 60°C, the half-life time of the purified variant was 127-fold increased compared to the WT enzyme (from 1.5 min to 3 h). Saturation mutagenesis experiment at position 244 demonstrated that the presence of a cysteine at this position was responsible for the thermal denaturation. It was demonstrated that WT Lip2 and the thermostable variant are both inactivated through aggregation mechanisms, but that the kinetics and the nature of the aggregation were different. For the WT enzyme, rapid intermolecular disulphide bridge interchanges triggered by the free cysteine 244 mediates aggregation. For the variant C244A, aggregation still occurred but much slower than for the WT lipase and was mainly driven by hydrophobic forces. PMID:21763359

  12. 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 ?-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

  13. 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

    Morita, Yuji; Tomida, Junko; Kawamura, Yoshiaki

    2015-01-01

    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 ?-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

  14. 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

  15. Metallo -Lactamases in Clinical Pseudomonas Isolates in Taiwan and Identification of VIM3, a Novel Variant of the VIM2 Enzyme

    Microsoft Academic Search

    JING-JOU YAN; PO-REN HSUEH; WEN-CHIEN KO; KWEN-TAY LUH; SHU-HUEI TSAI; HSIU-MEI WU; JIUNN-JONG WU

    2001-01-01

    A total of 209 clinical isolates of Pseudomonas (193 Pseudomonas aeruginosa ,1 0P. putida ,4 P. stutzeri, and 2 P. fluorescens isolates) with reduced susceptibilities to imipenem and\\/or ceftazidime were subjected to PCR assays with primers specific for blaIMP-1, blaIMP-2, blaVIM-1, and blaVIM-2 and sequence analysis to identify the metallo-b-lactamases (MBLs) prevalent among these organisms in Taiwan; and 21 isolates

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

    Microsoft Academic Search

    Youngwon Lee; Charles P. Emerson; Myoung Hee Kim

    1995-01-01

    TnINEO fusion gene was constructed by fusing 3.4-kbp of quailTnI genomic DNA sequences spanning the promoter to exon 5 and aneo gene in frame. A myoblast cell line was established after transfection of pTnINEO. Since this cell line was passaged several\\u000a times, a high frequency of neomycin (G418) sensitivity conversion was detected. Two drug-resistant variants were analyzed\\u000a through genomic Southern

  17. Abstract A genetic variant of the entomopathogenic fungus Metarhizium anisop-liae var. anisopliae, isolated from a soil in Alberta, Canada, from a location with a

    E-print Network

    Johnson, Dan L.

    % (LT50 = 4.1 days, LT90 = 5.8 days) mortality at 8 days in insects exposed to a commercial isolate of M) mortality in 9 days in insects treated with M. anisopliae var. acridum. Amplification of fungal genomic DNA, isolated from a soil in Alberta, Canada, from a location with a history of severe grasshopper infestations

  18. Draft Whole-Genome Sequence of a New Variant of Vibrio cholerae O1 El Tor Strain Isolated from a Cholera Patient in Russia.

    PubMed

    Smirnova, Nina I; Cherkasov, Alexander V; Krasnov, Yaroslav M; Agafonov, Dmitriy A; Kutyrev, Vladimir V

    2014-01-01

    Draft whole-genome sequencing of the Vibrio cholerae ?1 El Tor clinical strain L3226, isolated in Moscow in 2010, was carried out. Various mutations in the virulence-associated mobile elements were determined in its genome that differentiated this strain from the reference V. cholerae ?1 El Tor strain N16961. PMID:24874670

  19. Draft Whole-Genome Sequence of a New Variant of Vibrio cholerae O1 El Tor Strain Isolated from a Cholera Patient in Russia

    PubMed Central

    Smirnova, Nina I.; Krasnov, Yaroslav M.; Agafonov, Dmitriy A.; Kutyrev, Vladimir V.

    2014-01-01

    Draft whole-genome sequencing of the Vibrio cholerae ?1 El Tor clinical strain L3226, isolated in Moscow in 2010, was carried out. Various mutations in the virulence-associated mobile elements were determined in its genome that differentiated this strain from the reference V. cholerae ?1 El Tor strain N16961. PMID:24874670

  20. Presence of New mecA and mph(C) Variants Conferring Antibiotic Resistance in Staphylococcus spp. Isolated from the Skin of Horses before and after Clinic Admission

    Microsoft Academic Search

    Christina Schnellmann; Vinzenz Gerber; Alexandra Rossano; Valentine Jaquier; Yann Panchaud; Marcus G. Doherr; Andreas Thomann; Reto Straub; Vincent Perreten

    Because of the frequency of multiple antibiotic resistance, Staphylococcus species often represent a challenge in incisional infections of horses undergoing colic surgery. To investigate the evolution of antibiotic resistance patterns before and after preventative peri- and postoperative penicillin treatment, staphylococci were isolated from skin and wound samples at different times during hospitalization. Most staphylococci were normal skin commensals and belonged

  1. Nontoxigenic Clostridium difficile protects hamsters against challenge with historic and epidemic strains of toxigenic BI/NAP1/027 C. difficile.

    PubMed

    Nagaro, Kristin J; Phillips, S Tyler; Cheknis, Adam K; Sambol, Susan P; Zukowski, Walter E; Johnson, Stuart; Gerding, Dale N

    2013-11-01

    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 10(6) 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

  2. Migraine Variants in Children

    MedlinePLUS

    ... headaches . Home > Migraine Variants in Children Print Email Migraine Variants in Children ACHE Newsletter Sign up for ... newsletter by entering your e-mail address below. Migraine Variants in Children There are several disorders that ...

  3. Selection during Cefepime Treatment of a New Cephalosporinase Variant with Extended-Spectrum Resistance to Cefepime in an Enterobacter aerogenes Clinical Isolate

    Microsoft Academic Search

    G. Barnaud; Y. Benzerara; J. Gravisse; L. Raskine; M. J. Sanson-Le Pors; R. Labia; G. Arlet

    2004-01-01

    Enterobacter aerogenes resistant to cefepime (MIC, 32 g\\/ml) was isolated from a patient treated with cefepime for an infection caused by a strain of E. aerogenes overproducing its AmpC -lactamase (MIC of cefepime, 0.5 g\\/ml). The AmpC -lactamase of the resistant strain had an L-293-P amino acid substitution and a high kcat\\/Km ratio for cefepime. Both of these modifications were

  4. 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

  5. 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

  6. The intergenic-junction variant (genotype 2 isolate) of hepatitis E virus restores the CREX 'stem-loop' structural integrity, essential for viral life cycle.

    PubMed

    Parvez, Mohammad Khalid

    2015-04-01

    Among the known human HEV strains (genotypes 1, 2, 3 and 4), the genotype 2 Mexican isolate has two 'double-base' substitutions (5'U5100G5101?CU/3'C5117U5118?GG) flanking the conserved cis-reactive element (CRE) in the intergenic-junction sequences. While the 'C5100U5101' natural mutations in the upstream ORF1 coding region replace 'alanine' for the conserved 'valine', the 'G5117G5118' doublet resides in the downstream non-coding/promoter region of ORF3 gene. Though a stable 'stem-loop' structure containing CRE, critical for virus replication had been reported, the phenotypic effect of genotype 2 'CU/GG' variations were neither mentioned nor explored. In this study, the evolutionary significance of such tolerable mutations in the conserved regulatory-sequences was investigated. Multiple sequence alignment of intergenic-junction of human HEV strains showed further base conservations flanking the CRE sequences. In silico analysis of the conserved sequences (nts. 5099-5121) of the representative genotypes revealed a stable RNA 'stem-loop' structure (CREX). Of the four genotype-specific CREX, the Mexican mutant bases 'CU/GG' very interestingly, compensated and complemented themselves (5'C5100:3'G5118 and 5'U5101:3'G5117) in the 'lower-stem'. The substitution of 'GG' bases in the ORF3 promoter-region did not affect its 'optimal-context' and therefore, negated its regulatory role at 'nucleotide' level. Virtual mutations introduced to break the two base-pairings in the CREX 'lower-stem', completely destabilized the secondary structure. Further molecular characterization of the CREX mutants in HEV-SAR55 replicon background showed a drastic downregulation of viral RNA replication in S10-3 cells. Though the CREX-mutant RNA were encapsidated into trans-complemented viral capsids (ORF2), and produced virions, they were poorly infectious to naïve HepG2/C3A cells. In conclusion, the compensatory mutations in the intergenic-junction of Mexican isolate suggest strict conservation of the CREX 'stem-loop' structure, essential for HEV genome replication. This could have a greater regulatory role in viral life cycle, including RNA packaging. PMID:25597766

  7. Characterization of the amantadine-resistant H5N1 highly pathogenic avian influenza variants isolated from quails in Southern China.

    PubMed

    Dong, Guoying; Luo, Jing; Zhou, Kai; Wu, Bin; Peng, Chao; Ji, Guangju; He, Hongxuan

    2014-10-01

    Highly pathogenic H5N1 avian influenza viruses have spread in poultry and wild birds in Asia, Europe, and Africa since 2003. To evaluate the role of quails in the evolution of influenza A virus, we characterized three H5N1 viruses isolated from quails (QA viruses) in southern China. Phylogenetic analysis indicated that three QA viruses derived from the A/goose/Guangdong/1/96-like lineage and most closely related to HA clade 4 A/chicken/Hong Kong/31.4/02-like viruses. Molecular analysis suggested that QA viruses and clade 4 H5N1 viruses carried consistent residue signatures, such as the characteristic M2 Ser31Asn amantadine-resistance mutation, implying a common origin of these viruses. As revealed by viral pathogenicity tests, these QA viruses could replicate in intranasally infected mice, but were not lethal to them, showing low pathogenicity in mammals. However, they killed all intravenously inoculated chickens, showing high pathogenicity in poultry. Results from amantadine sensitivity tests of wild-type QA viruses and their reverse genetic viruses demonstrated that all QA viruses were resistant to amantadine, and the M2 Ser31Asn mutation was determined as the most likely cause of the increased amantadine-resistance of H5N1 QA viruses. Our study confirmed experimentally that the amino acid at residue 31 in the M2 protein plays a major role in determining the amantadine-resistance phenotype of H5N1 influenza viruses. Our findings provide further evidence that quails may play important roles in the evolution of influenza A viruses, which raises concerns over possible transmissions of H5N1 viruses among poultry, wild birds, and humans. PMID:24993865

  8. Space variant image processing

    Microsoft Academic Search

    Richard S. Wallace; Ping-wen Ong; Benjamin B. Bederson; Eric L. Schwartz

    1994-01-01

    This paper describes a graph-based approach to image processing, intended for use with images obtained from sensors having space variant sampling grids. The connectivity graph (CG) is presented as a fundamental framework for posing image operations in any kind of space variant sensor. Partially motivated by the observation that human vision is strongly space variant, a number of research groups

  9. 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

  10. HPV58 Molecular Variants Exhibit Different Transcriptional Activity

    Microsoft Academic Search

    Tainá Raiol; Regina Maria Santos de Amorim; Pedro Galante; Cláudia Renata Fernandes Martins; Luisa Lina Villa; Laura Sichero

    2011-01-01

    Early promoter activity of HPV-58 molecular variants isolated from high-grade cervical lesions in Brazil was compared. Luciferase reporter assays were conducted in C33 cells transfected with the complete long control region of 3 molecular variants of HPV-58 as well as HPV-58, -18 or -16 prototypes. The HPV-58 prototype and Bsb-329 and Bsb-367 variants showed a promoter activity similar to that

  11. Pullulan production by color variant strains of Aureobasidium pullulans

    Microsoft Academic Search

    T. D. Leathers; G. W. Nofsinger; C. P. Kurtzman; R. J. Bothast

    1988-01-01

    Summary Naturally occurring ‘color variant’ strains ofAureobasidium pullulans are distinguished from typical strains by their brilliant pigmentation, overproduction of secreted enzymes (xylanase), and low DNA relatedness. Color variants have not previously been examined for pullulan secretion. Among five independently isolated color variants, strains NRRL Y-12,974 and YB-4026 made the greatest amounts of pullulan from cornstarch, with conversion efficiencies of about

  12. Hemoglobin variants in Cyprus.

    PubMed

    Kyrri, Andreani R; Felekis, Xenia; Kalogerou, Eleni; Wild, Barbara J; Kythreotis, Loukas; Phylactides, Marios; Kleanthous, Marina

    2009-01-01

    Cyprus, located at the eastern end of the Mediterranean region, has been a place of eastern and western civilizations, and the presence of various hemoglobin (Hb) variants can be considered a testimony to past colonizations of the island. In this study, we report the structural Hb variants identified in the Cypriot population (Greek Cypriots, Maronites, Armenians, and Latinos) during the thalassemia screening of 248,000 subjects carried out at the Thalassaemia Centre, Nicosia, Cyprus, over a period of 26 years. A sample population of 65,668 people was used to determine the frequency and localization of several of the variants identified in Cyprus. The localization of some of the variants in regions where the presence of foreign people was most prevalent provides important clues to the origin of the variants. Twelve structural variants have been identified by DNA sequencing, nine concerning the beta-globin gene and three concerning the alpha-globin gene. The most common beta-globin variants identified were Hb S (0.2%), Hb D-Punjab (0.02%), and Hb Lepore-Washington-Boston (Hb Lepore-WB) (0.03%); the most common alpha-globin variant was Hb Setif (0.1%). The presence of some of these variants is likely to be directly linked to the history of Cyprus, as archeological monuments have been found throughout the island which signify the presence for many years of the Greeks, Syrians, Persians, Arabs, Byzantines, Franks, Venetians, and Turks. PMID:19373583

  13. Histone variants and epigenetics.

    PubMed

    Henikoff, Steven; Smith, M Mitchell

    2015-01-01

    Histones package and compact DNA by assembling into nucleosome core particles. Most histones are synthesized at S phase for rapid deposition behind replication forks. In addition, the replacement of histones deposited during S phase by variants that can be deposited independently of replication provide the most fundamental level of chromatin differentiation. Alternative mechanisms for depositing different variants can potentially establish and maintain epigenetic states. Variants have also evolved crucial roles in chromosome segregation, transcriptional regulation, DNA repair, and other processes. Investigations into the evolution, structure, and metabolism of histone variants provide a foundation for understanding the participation of chromatin in important cellular processes and in epigenetic memory. PMID:25561719

  14. Genetic Studies on Small-colony Variants of Escherichia coli K-12

    Microsoft Academic Search

    R. C. CLOWES; D. ROWLEY

    1955-01-01

    SUMMARY: Stable small-colony variants of Escherichia coli K-12 and several of its auxotrophs were isolated by treatment of cultures with copper sulphate solutions. These variants did not show any associated changes in nutritional, fermentative or serological characters. The small-colony forms showed normal recombining character in two instances, but in one variant the F - form showed a lower recombination rate

  15. Studies on variants of Bacillus stearothermophilus strain NCA 1518.

    PubMed

    Humbert, R D; DeGuzman, A; Fields, M L

    1972-04-01

    The heat resistance, fermentation reactions, nutritional requirements, and phage sensitivity of 18 selected morphological variants of Bacillus stearothermophilus NCA 1518 were studied. It was found that when smooth variants mutated to rough colonial morphology, there was no concurrent change in fermentation reactions, nutritional requirements, or heat resistance. The smooth variant, and the rough mutants derived directly from it, presented a uniform pattern of biochemical capabilities which differed from the pattern presented by the rough variants isolated from the same stock culture. This led to the conclusion that the smooth and rough types previously observed in stocks of B. stearothermophilus NCA 1518 either were carried in the stock since the original isolation or represent a very profound and uncommon mutation, or that one of the variants has been introduced into the stock culture from an extraneous source sometime in the past. PMID:4553138

  16. Interpretation of genetic variants

    PubMed Central

    Sosnay, Patrick R; Cuttingu, Garry R

    2015-01-01

    Sequencing of the human genome and introduction of clinical next-generation sequencing enable discovery of all DNA variants carried by an individual. Variants may be solely responsible for disease, may contribute to disease, or may have no influence on the development of disease. lnterpreting the effect of these variants upon disease is a major chalIenge for medicine. Although the process is still evolving, certain methods are useful in discriminating the effect of variants upon phenotype. These methods have been employed to the greatest extent in Mendelian disorders where deleterious changes in one gene can cause disease. Here, we briefly review the relative merits of these methods, with emphasis on using a comprehensive approach modelIed after the analysis of variants that causes cystic fibrosis. PMID:24343785

  17. 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

  18. Maisonneuve-hyperplantarflexion variant ankle fracture.

    PubMed

    Hinds, Richard M; Tran, Wesley H; Lorich, Dean G

    2014-11-01

    Maisonneuve fractures are rare ankle injuries, accounting for up to 7% of all ankle fractures. They consist of a proximal third fibula fracture, syndesmotic disruption, and medial ankle injury (either a deltoid ligament disruption or a medial malleolus fracture), and are often successfully managed with nonoperative treatment of the proximal fibula fracture and open reduction and internal fixation (ORIF) of the medial ankle injury and syndesmotic disruption. The hyperplantarflexion variant ankle fracture comprises approximately 7% of all ankle fractures and features dual posterior tibial lip fractures featuring a posterolateral fragment and a posteromedial fragment. Good functional results have been reported in the literature after ORIF of both the posterolateral and posteromedial fragments of this variant fracture that is not described by the Lauge-Hansen classification. In this report, the authors present the unique case of an isolated ankle fracture demonstrating characteristics of both a Maisonneuve fracture and a hyperplantarflexion variant ankle fracture. They also highlight the diagnostic imaging characteristics, including magnetic resonance imaging (MRI) and preoperative radiograph findings, surgical treatment, and postoperative clinical outcome for this patient with a Maisonneuve-hyperplantarflexion variant ankle fracture. To the authors' knowledge, this unique fracture pattern has not been reported previously in the literature. The authors conclude that although good results were seen postoperatively in this case, the importance of ORIF of both the posteromedial and posterolateral fragments of variant fractures cannot be overstated. They also found MRI to be a particularly helpful adjunct in formulating the correct diagnosis and treatment plan. PMID:25361368

  19. Variation of DNA sequence in immediate-early gene of human herpesvirus 6 and variant identification by PCR.

    PubMed Central

    Yamamoto, T; Mukai, T; Kondo, K; Yamanishi, K

    1994-01-01

    The complete nucleotide sequence of one of the immediate-early genes of human herpesvirus 6 variant B was determined and compared with that of variant A reported by Martin et al. (M.D. Martin, J. Nicholas, B. J. Thomson, C. Newman, and R. W. Honess, J. Virol. 65:5381-5390, 1991). While it was reported that two open reading frames exist in this region of variant A, only one open reading frame was found in variant B and the putative coding region of variant B was 2,679 nucleotides long. Furthermore, two additive regions of 108 and 228 bp were found in variant B. Primers covering one of these regions deleted in variant A were synthesized and used for PCR amplification. Twelve isolates from patients were clearly classified into variants A and B by PCR amplification with these primers. All isolates from patients with exanthem subitum were variant B. Images PMID:8150960

  20. Occurrence of genetic variants of Listeria monocytogenes strains.

    PubMed

    Tham, Wilhem; Lopez-Valladares, Gloria; Helmersson, Seved; Wennström, Stefan; Österlund, Anders; Danielsson-Tham, Marie-Louise

    2013-09-01

    Isolates of Listeria monocytogenes saved from outbreaks of listeriosis, cases of sporadic listeriosis, and similar events do not always belong to a solitary genetic variant. Variants of the same strain may have evolved from a unique clone, and plasmid loss or gain and phage-mediated genetic changes are suggested as the main mechanism. Some of these reports are summarized in this short communication. PMID:23988078

  1. 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

  2. Transferable class C -lactamases in Escherichia coli strains isolated in Greek hospitals and characterization of two enzyme variants (LAT3 and LAT4) closely related to Citrobacter freundii AmpC -lactamase

    Microsoft Academic Search

    M. Gazouli; L. S. Tzouvelekis; A. C. Vatopoulos; E. Tzelepi

    1998-01-01

    Among 2133 isolates of Escherichia coli obtained during 1996 from 10 Greek hospitals, 63 (3%) were resistant to cefoxitin. Typing by ERIC2-PCR indicated that the cefoxitin-resistant (FOX r ) isolates were distinct. -Lactamase studies and hybridization experiments showed that most strains produced -lactamases related to the AmpC chromosomal cephalosporinase of Citrobacter freundii. The enzymes were encoded by similar non-self-transmissible plasmids.

  3. [Rare variants and demographic explosion].

    PubMed

    Jordan, Bertrand

    2014-04-01

    The abundance of rare variants in human DNA is the consequence of tremendous recent expansion of our population. Careful measurement of neutral variants in a European population points to more recent and more rapid expansion than previously believed. PMID:24801044

  4. 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

  5. New Iranian and Australian peach latent mosaic viroid variants and evidence for rapid sequence evolution.

    PubMed

    Yazarlou, Arezou; Jafarpour, Behrooz; Tarighi, Saeed; Habili, Nuredin; Randles, John W

    2012-02-01

    Peach latent mosaic viroid isolates from peach and plum in Iran have been compared with an Australian isolate from nectarine. Thirteen sequence variants 336-338 nt in size were obtained. All variants clustered phylogenetically with variants reported from several hosts and countries. A total nucleic acid extract, a slightly longer than full-length RT-PCR amplicon, and a recombinant plasmid clone from the Australian isolate were all infectious to, and symptomatic in, mechanically inoculated peach seedlings. The infectious clone generated two progeny viroid molecules, which each showed 10 different mutations compared with the parent clone inoculated 30 days previously. PMID:22075917

  6. 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

  7. 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.

  8. Variants of glycoside hydrolases

    SciTech Connect

    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.

  9. Frequent compartmentalization of hepatitis C virus variants in circulating B cells and monocytes

    Microsoft Academic Search

    Delphine Ducoulombier; Anne-Marie Roque-Afonso; Rachid Kara; Yolande Richard; Elisabeth Dussaix

    2004-01-01

    Differences in the composition of the hepatitis C virus (HCV) quasispecies between plasma and blood mononuclear cells (BMC) strongly suggest that BMCs support viral replication. We examined the frequency of such compartmentalization, the cell types involved, the constraints exerted on the different variants, and the role of immunoglobulin-complexed variants. We screened the hypervariable region (HVR1) of HCV isolates from 14

  10. Discrimination of geographical song variants by Darwin's finches

    E-print Network

    Podos, Jeff

    Discrimination of geographical song variants by Darwin's finches JEFFREY PODOS Department influence the processes of mate recognition and reproductive isolation. In Darwin's finches of the Gala The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. Keywords: Darwin's finches

  11. Functional analysis of organophosphorus hydrolase variants with high degradation

    E-print Network

    Chen, Wilfred

    ]. They act as cholinesterase inhibitors and in turn disrupt neuro- transmission in both insects and humans., 1994). Recently, a similar enzyme (OPDA) with 90% sequence identity to OPH has been isolated from have generated several OPH variants by DNA shuffling fo

  12. Teal fluorescent proteins: Characterization of a reversibly photoswitchable variant

    E-print Network

    Campbell, Robert E.

    bacteria to plants to mammals a functional (i.e. fluorescent) protein product is produced. The ability green fluorescent protein (GFP) in 1961 when he was isolating aequorin, a calciumTeal fluorescent proteins: Characterization of a reversibly photoswitchable variant Hui-wang Ai

  13. 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...

  14. 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

  15. 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

  16. Cellobiohydrolase variants and polynucleotides encoding same

    DOEpatents

    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.

  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. 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

  20. Heteromorphic variants of chromosome 9

    PubMed Central

    2013-01-01

    Background Heterochromatic variants of pericentromere of chromosome 9 are reported and discussed since decades concerning their detailed structure and clinical meaning. However, detailed studies are scarce. Thus, here we provide the largest ever done molecular cytogenetic research based on >300 chromosome 9 heteromorphism carriers. Results In this study, 334 carriers of heterochromatic variants of chromosome 9 were included, being 192 patients from Western Europe and the remainder from Easter-European origin. A 3-color-fluorescence in situ hybridization (FISH) probe-set directed against for 9p12 to 9q13~21.1 (9het-mix) and 8 different locus-specific probes were applied for their characterization. The 9het-mix enables the characterization of 21 of the yet known 24 chromosome 9 heteromorphic patterns. In this study, 17 different variants were detected including five yet unreported; the most frequent were pericentric inversions (49.4%) followed by 9qh-variants (23.9%), variants of 9ph (11.4%), cenh (8.2%), and dicentric- (3.8%) and duplication-variants (3.3%). For reasons of simplicity, a new short nomenclature for the yet reported 24 heteromorphic patterns of chromosome 9 is suggested. Six breakpoints involved in four of the 24 variants could be narrowed down using locus-specific probes. Conclusions Based on this largest study ever done in carriers of chromosome 9 heteromorphisms, three of the 24 detailed variants were more frequently observed in Western than in Eastern Europe. Besides, there is no clear evidence that infertility is linked to any of the 24 chromosome 9 heteromorphic variants. PMID:23547710

  1. HPV-58 molecular variants exhibit different transcriptional activity.

    PubMed

    Raiol, Tainá; de Amorim, Regina Maria Santos; Galante, Pedro; Martins, Cláudia Renata Fernandes; Villa, Luisa Lina; Sichero, Laura

    2011-01-01

    Early promoter activity of HPV-58 molecular variants isolated from high-grade cervical lesions in Brazil was compared. Luciferase reporter assays were conducted in C33 cells transfected with the complete long control region of 3 molecular variants of HPV-58 as well as HPV-58, -18 or -16 prototypes. The HPV-58 prototype and Bsb-329 and Bsb-367 variants showed a promoter activity similar to that of HPV-16, but lower than that of Bsb-295 and HPV-18. The introduction of the Bsb-295 7788 mutation into the HPV-58 prototype resulted in the enhancement of transcription closer to Bsb-295 and HPV-18. These results could impact the expression of E6 and E7 viral oncogenes. PMID:20948225

  2. A Cytopathogenic, Apoptosis-Inducing Variant of Hepatitis A Virus†

    PubMed Central

    Brack, Kerstin; Frings, Werner; Dotzauer, Andreas; Vallbracht, Angelika

    1998-01-01

    A cytopathogenic variant of hepatitis A virus (HAVcyt/HB1.1) was isolated from persistently infected BS-C-1 cells by serial passages in FRhK-4 cells. This virus shows a rapid replication pattern and high final titers are obtained, which are main characteristics of cytopathogenic HAVs. Sequencing of the nontranslated regions and the coding regions for 2ABC and 3AB revealed that mutations are distributed all over these regions and that certain mutated sites correspond to those in other cytopathogenic HAV variants. Investigating the mechanisms causing the cytopathic effect in FRhK-4 cells infected with this variant, we found that an apoptotic reaction takes place. PMID:9525664

  3. 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.

  4. Variants of beta-glucosidases

    DOEpatents

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

    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.

  5. Variants of beta-glucosidase

    SciTech Connect

    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.

  6. Variants of beta-glucosidases

    DOEpatents

    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.

  7. Phenotypic and Enzymatic Comparative Analysis of the Novel KPC Variant KPC5 and Its Evolutionary Variants, KPC2 and KPC4

    Microsoft Academic Search

    Daniel J. Wolter; Philip M. Kurpiel; Neil Woodford; Marie-France I. Palepou; Richard V. Goering; Nancy D. Hanson

    2009-01-01

    A novel Klebsiella pneumoniae carbapenemase (KPC) variant, designated blaKPC-5, was discovered in a carbapenem-resistant Pseudomonas aeruginosa clinical isolate from Puerto Rico. Characterization of the up- stream region of blaKPC-5 showed significant differences from the flanking regions of other blaKPC variants. Comparison of amino acid sequences with those of other KPC enzymes revealed that KPC-5 was an interme- diate between KPC-2

  8. A hepatitis E virus variant from the United States: molecular characterization and transmission in cynomolgus macaques

    Microsoft Academic Search

    James C. Erker; Suresh M. Desai; George G. Schlauder; George J. Dawson; Isa K. Mushahwar

    1999-01-01

    The partial sequence of a hepatitis E virus (HEV-US1) isolated from a patient in the United States (US), suffering from acute viral hepatitis with no known risk factors for acquiring HEV, has been reported. These sequences were significantly different from previously characterized HEV isolates, alluding to the existence of a distinct human variant. In this paper, we report the near

  9. Full-length genomes of 16 hepatitis C virus genotype 1 isolates representing subtypes 1c, 1d, 1e, 1g, 1h, 1i, 1j and 1k, and two new subtypes 1m and 1n, and four unclassified variants reveal ancestral relationships among subtypes.

    PubMed

    Lu, Ling; Li, Chunhua; Xu, Yan; Murphy, Donald G

    2014-07-01

    We characterized the full-length genomes of 16 distinct hepatitis C virus genotype 1 (HCV-1) isolates. Among them, four represented the first full-length genomes for subtypes 1d (QC103), 1i (QC181), 1j (QC329) and 1k (QC82), and another four corresponded to subtypes 1c (QC165), 1g (QC78), 1h (QC156) and 1e (QC172). Both QC196 and QC87 were assigned into a new subtype 1m, and QC113 and QC74 into another new subtype 1n. The remaining four (QC60, QC316, QC152 and QC180) did not classify among the established subtypes and corresponded to four new lineages. Subtypes 1j, 1k, 1m, 1n and the unclassified isolate QC60 were identified in Haitian immigrants. In the updated HCV nomenclature of 2005, a total of 12 subtypes of HCV-1 were designated. Including the data from the present study, all but subtype 1f now have their full-length genomes defined. Further analysis of partial NS5B sequences available in GenBank denoted a total of 21 unclassified lineages, indicating the taxonomic complexity of HCV-1. Among them, six have had their full-length genomes characterized. Based on the available full-length genome sequences, a timescale phylogenetic tree was reconstructed which estimated important time points in the evolution of HCV-1. It revealed that subtype 1a diverged from its nearest relatives 135 years ago and subtype 1b diverged from its nearest relatives 112 years ago. When subtypes 1a, 1j, 1k, 1m, 1n and six close relatives (all but one from Haitian immigrants) were considered as a whole, the divergence time was 176 years ago. This diversification was concurrent with the time period when the transatlantic slave trade was active. When taking all the HCV-1 isolates as a single lineage, the divergence time was 326 years ago. This analysis suggested the existence of a recent common ancestor for subtype 1a and the Haitian variants; a co-origin for subtypes 1b, 1i and 1d was also implied. PMID:24718832

  10. Piezotolerant Small-Colony Variants with Increased Thermotolerance, Antibiotic Susceptibility, and Low Invasiveness in a Clonal Staphylococcus aureus Population?

    PubMed Central

    Karatzas, Kimon A. G.; Zervos, Angelos; Tassou, Chrysoula C.; Mallidis, Costas G.; Humphrey, Tom J.

    2007-01-01

    Following a pressure treatment of a clonal Staphylococcus aureus culture with 400 MPa for 30 min, piezotolerant variants were isolated. Among 21 randomly selected survivors, 9 were piezotolerant and all formed small colonies on several agar media. The majority of the isolates showed increased thermotolerance, impaired growth, and reduced antibiotic resistance compared to the wild type. However, several nonpiezotolerant isolates also demonstrated impaired growth and the small-colony phenotype. In agglutination tests for the detection of protein A and fibrinogen, the piezotolerant variants showed weaker agglutination reactions than the wild type and the other isolates. All variants also showed defective production of the typical S. aureus golden color, a characteristic which has previously been linked with virulence. They were also less able to invade intestinal epithelial cells than the wild type. These S. aureus variants showed phenotypic similarities to previously isolated Listeria monocytogenes piezotolerant mutants that contained mutations in ctsR. Because of these similarities, possible alterations in the ctsR hypermutable regions of the S. aureus variants were investigated through amplified fragment length polymorphism analysis. No mutations were identified, and subsequently we sequenced the ctsR and hrcA genes of three representative variants, finding no mutations. This work demonstrates that S. aureus probably possesses a strategy resulting in an abundance of multiple-stress-resistant variants within clonal populations. This strategy, however, seems to involve genes and regulatory mechanisms different from those previously reported for L. monocytogenes. We are in the process of identifying these mechanisms. PMID:17259364

  11. Acute small fiber neuropathy following Mycoplasma infection: a rare variant of Guillain-Barré syndrome.

    PubMed

    Makonahalli, Rohitha; Seneviratne, Janaka; Seneviratne, Udaya

    2014-06-01

    Guillain-Barré syndrome (GBS) is a well-described condition involving the peripheral nervous system. The most well-known form of this disease is acute inflammatory demyelinating polyradiculoneuropathy. Among the different variants of GBS described in the literature, the sensory variant is scantily recognized. There has been a recent attempt to classify the sensory variants of the GBS and bring more objectivity to this diagnostic paradigm. We report a rare sensory variant of GBS presenting with isolated small nerve fiber involvement peripherally in the limbs and associated facial nerve palsy in a patient who had clinical and serological evidence of a preceding Mycoplasma pneumoniae infection. The symptoms resolved gradually with intravenous immunoglobulin therapy. This case adds to the growing literature of the rare form of acute small fiber neuropathy and GBS variants. PMID:24872212

  12. 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

  13. Variants of Human Papillomavirus Types 53, 58 and 66 Identified in Central Brazil

    Microsoft Academic Search

    Daniela Marreco Cerqueira; GeniNoceti de Lima Camara; Márcio Rojas da Cruz; Evandro Oliveira Silva; Marcelo de Macedo BrÍgido; LucianoGonçalves de Souza Carvalho; Cláudia Renata Fernandes Martins

    2003-01-01

    The present study on molecular characterization of human papillomaviruses occurring in Central Brazil, describes two variants each of HPV-53 and HPV-58 and one variant of HPV-66 detected in samples from smears of women showing cervical intraepithelial neoplasia grade II (CIN II). Samples were assayed by PCR using MY09\\/MY11 consensus primers, followed by restriction fragment length polymorphism typing. The five isolates

  14. Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates

    E-print Network

    Sim, Bernice Meng Qi; Chantratita, Narisara; Ooi, Wen Fong; Nandi, Tannistha; Tewhey, Ryan; Wuthiekanun, Vanaporn; Thaipadungpanit, Janjira; Tumapa, Sarinna; Ariyaratne, Pramila; Sung, Wing-Kin; Sem, Xiao Hui; Chua, Hui Hoon; Ramnarayanan, Kalpana; Lin, Chi Ho; Liu, Yichun; Feil, Edward J; Glass, Mindy B; Tan, Gladys; Peacock, Sharon J; Tan, Patrick

    2010-08-27

    genomic islands, while 26 regions were novel. Variant B. thailandensis isolates exhibited isolated acquisition of a capsular polysaccharide biosynthesis gene cluster (B. pseudomallei-like capsular polysaccharide) closely resembling a similar cluster in B...

  15. PULLULAN PRODUCTION BY TROPICAL ISOLATES OF AUREOBASIDIUM PULLULANS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tropical isolates of A. pullulans were obtained from distinct habitats in Thailand, from leaf to indoor surfaces. These isolates appeared to be so-called "color variant" strains, with pink, red, or yellow pigmentation. In order to obtain the highest pullulan - producing strain, isolates were optim...

  16. 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

  17. Gene variants influence insulin production

    Cancer.gov

    A new analytical tool has found three previously unknown gene variants relevant to diabetes, and researchers say it also may be useful in unraveling other complex diseases like obesity and cancer. In research published online December 23 in Nature Genetics, scientists say the relatively rare genetic variants influence insulin production,a finding that could offer new clues about the genetic factors behind diabetes. The study included participants from the University of North Carolina School of Medicine (home to the Lineberger Comprehensive Cancer Center), the University of Michigan (home to the University of Michigan Comprehensive Cancer Center), and the University of Eastern Finland.

  18. Fecal influenza in mammals: selection of novel variants.

    PubMed

    Koçer, Zeynep A; Obenauer, John; Zaraket, Hassan; Zhang, Jinghui; Rehg, Jerold E; Russell, Charles J; Webster, Robert G

    2013-11-01

    In aquatic birds, influenza A viruses mainly replicate in the intestinal tract without significantly affecting the health of the host, but in mammals, they replicate in the respiratory tract and often cause disease. Occasionally, influenza viruses have been detected in stool samples of hospitalized patients and in rectal swabs of naturally or experimentally infected mammals. In this study, we compared the biological and molecular differences among four wild-type avian H1N1 influenza viruses and their corresponding fecal and lung isolates in DBA/2J and BALB/cJ mice. All fecal and lung isolates were more pathogenic than the original wild-type viruses, when inoculated into mice of both strains. The increased virulence was associated with the acquisition of genetic mutations. Most of the novel genotypes emerged as PB2(E627K), HA(F128V), HA(F454L), or HA(H300P) variations, and double mutations frequently occurred in the same isolate. However, influenza virus strain- and host-specific differences were also observed in terms of selected variants. The avian H1N1 virus of shorebird origin appeared to be unique in its ability to rapidly adapt to BALB/cJ mice via the fecal route, compared to the adaptability of the H1N1 virus of mallard origin. Furthermore, a bimodal distribution in fecal shedding was observed in mice infected with the fecal isolates, while a normal distribution was observed after infection with the lung isolates or wild-type virus. Fecal isolates contained HA mutations that increased the activation pH of the HA protein. We conclude that influenza virus variants that emerge in fecal isolates in mammals might influence viral transmission, adaptation to mammals, and viral ecology or evolution. PMID:23966381

  19. Fecal Influenza in Mammals: Selection of Novel Variants

    PubMed Central

    Koçer, Zeynep A.; Obenauer, John; Zaraket, Hassan; Zhang, Jinghui; Rehg, Jerold E.; Russell, Charles J.

    2013-01-01

    In aquatic birds, influenza A viruses mainly replicate in the intestinal tract without significantly affecting the health of the host, but in mammals, they replicate in the respiratory tract and often cause disease. Occasionally, influenza viruses have been detected in stool samples of hospitalized patients and in rectal swabs of naturally or experimentally infected mammals. In this study, we compared the biological and molecular differences among four wild-type avian H1N1 influenza viruses and their corresponding fecal and lung isolates in DBA/2J and BALB/cJ mice. All fecal and lung isolates were more pathogenic than the original wild-type viruses, when inoculated into mice of both strains. The increased virulence was associated with the acquisition of genetic mutations. Most of the novel genotypes emerged as PB2E627K, HAF128V, HAF454L, or HAH300P variations, and double mutations frequently occurred in the same isolate. However, influenza virus strain- and host-specific differences were also observed in terms of selected variants. The avian H1N1 virus of shorebird origin appeared to be unique in its ability to rapidly adapt to BALB/cJ mice via the fecal route, compared to the adaptability of the H1N1 virus of mallard origin. Furthermore, a bimodal distribution in fecal shedding was observed in mice infected with the fecal isolates, while a normal distribution was observed after infection with the lung isolates or wild-type virus. Fecal isolates contained HA mutations that increased the activation pH of the HA protein. We conclude that influenza virus variants that emerge in fecal isolates in mammals might influence viral transmission, adaptation to mammals, and viral ecology or evolution. PMID:23966381

  20. Pilus gene pool variation and the virulence of Corynebacterium diphtheriae clinical isolates during infection of a nematode.

    PubMed

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

    2013-08-01

    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

  1. 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

  2. Flashlamp for NIF: Russian variant

    SciTech Connect

    Erlandson, A.C.; Nikiforov, V.G.; Nikolaevskii, V.G. [Troitsk Inst. for Innovation and Fusion Research (Russian Federation); Gerasimov, V.A. [Zenit Scientific Research Inst., Zelenograd (Russian Federation); Zapata, L.E. [Lawrence Livermore National Lab., CA (United States)

    1996-11-01

    A variant of the flashlamp for NIF was developed on the base of the experience of manufacture and application of high-power flashlamps in Russia. Features of flashlamp design as well as first test results of the experimental samples are presented.

  3. 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

  4. 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. ...

  5. Swine Influenza/Variant Influenza Viruses

    MedlinePLUS

    ... this? Submit What's this? Submit Button Information on Swine Influenza/Variant Influenza Viruses Language: English Español ... pigs and variant influenza virus infections in humans. Swine Flu in Swine (pigs) Swine Flu in Swine ( ...

  6. Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone?

    PubMed Central

    Miller, R.R.; Price, J.R.; Batty, E.M.; Didelot, X.; Wyllie, D.; Golubchik, T.; Crook, D.W.; Paul, J.; Peto, T.E.A.; Wilson, D.J.; Cule, M.; Ip, C.L.C.; Day, N.P.J.; Moore, C.E.; Bowden, R.; Llewelyn, M.J.

    2014-01-01

    Summary Background New strains of meticillin-resistant Staphylococcus aureus (MRSA) may be associated with changes in rates of disease or clinical presentation. Conventional typing techniques may not detect new clonal variants that underlie changes in epidemiology or clinical phenotype. Aim To investigate the role of clonal variants of MRSA in an outbreak of MRSA bacteraemia at a hospital in England. Methods Bacteraemia isolates of the major UK lineages (EMRSA-15 and -16) from before and after the outbreak were analysed by whole-genome sequencing in the context of epidemiological and clinical data. For comparison, EMRSA-15 and -16 isolates from another hospital in England were sequenced. A clonal variant of EMRSA-16 was identified at the outbreak hospital and a molecular signature test designed to distinguish variant isolates among further EMRSA-16 strains. Findings By whole-genome sequencing, EMRSA-16 isolates during the outbreak showed strikingly low genetic diversity (P < 1 × 10?6, Monte Carlo test), compared with EMRSA-15 and EMRSA-16 isolates from before the outbreak or the comparator hospital, demonstrating the emergence of a clonal variant. The variant was indistinguishable from the ancestral strain by conventional typing. This clonal variant accounted for 64/72 (89%) of EMRSA-16 bacteraemia isolates at the outbreak hospital from 2006. Conclusions Evolutionary changes in epidemic MRSA strains not detected by conventional typing may be associated with changes in disease epidemiology. Rapid and affordable technologies for whole-genome sequencing are becoming available with the potential to identify and track the emergence of variants of highly clonal organisms. PMID:24433924

  7. Eosinophilic variant of chromophobe renal cell carcinoma

    PubMed Central

    Yourshaw, Charles J.; Zhang, Haiying

    2015-01-01

    Chromophobe renal cell carcinoma is a distinct subtype of renal cell carcinoma that accounts for 5% of all renal tumors. This subtype is further subdivided into two variants, classic and eosinophilic, with the latter variant being less frequent. We report two cases of the eosinophilic variant of chromophobe renal cell carcinoma diagnosed at our institution between January 2008 and December 2012. PMID:25552800

  8. Configuration and Management of Process Variants

    E-print Network

    Pfeifer, Holger

    Configuration and Management of Process Variants Alena Hallerbach, Thomas Bauer Group Research the process context. Contemporary business process management tools do not adequately support the modeling and management of such process variants. Either the variants have to be specified in separate process models

  9. Variant Humicola grisea CBH1.1

    DOEpatents

    Goedegebuur, Frits (Vlaardingen, NL); Gualfetti, Peter (San Francisco, CA); Mitchinson, Colin (Half Moon Bay, CA); Larenas, Edmund (Moss Beach, CA)

    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.

  10. Variant Humicola grisea CBH1.1

    DOEpatents

    Goedegebuur, Frits (Vlaardingen, NL); Gualfetti, Peter (San Francisco, CA); Mitchinson, Colin (Half Moon Bay, CA); Larenas, Edmund (Moss Beach, CA)

    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.

  11. 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.

  12. Variant Humicola grisea CBH1.1

    DOEpatents

    Goedegebuur, Frits (Vlaardingen, NL); Gualfetti, Peter (San Francisco, CA); Mitchinson, Colin (Half Moon Bay, CA); Larenas, Edmund (Moss Beach, CA)

    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.

  13. Variant Humicola grisea CBH1.1

    DOEpatents

    Goedegebuur, Frits (Vlaardingen, NL); Gualfetti, Peter (San Francisco, CA); Mitchinson, Colin (Half Moon Bay, CA); Larenas, Edmund (Moss Beach, CA)

    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.

  14. 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.

  15. 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.

  16. 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

  17. Antigenic variants of influenza A virus obtained in vitro

    PubMed Central

    Haaheim, L. R.; Schild, G. C.

    1976-01-01

    The aim of this study was to investigate antigenic “drift” in the haemagglutinin and neuraminidase antigens of influenza A virus in vitro under immunological pressure. Variants of the “Asian” influenza strains A/England/12/64 (H2N2) and A/Tokyo/3/67 (H2N2) were isolated in the allantois-on-shell system in the presence of homologous postinfection ferret sera. For each of these two viruses three generations of variants were isolated and characterized. It was found that the successive antigenic variants of A/Eng/12/64 did not resemble A/Tokyo/3/67. Thus it is probable that the pathway of antigenic drift in vitro was not the same as that which occurred in nature during the evolution of A/Tokyo/3/67 from A/Eng/12/64. In addition, A/Tokyo/3/67, which was the last strain to be prevalent before the A/Hong Kong subtype appeared, underwent significant antigenic drift from “junior” to “senior” variants. This finding did not support the concept that, when antigenic drift occurs, resulting in the appearence of viruses with new haemagglutinin antigen subtypes, the previously prevalent strain has no capacity for further antigenic drift. The study did not result in the production of strains that were identifiable as “bridging” viruses between the H2 and H3 haemagglutinin subtypes. The present paper includes the first report of antigenic variation in the neuraminidase antigens of influenza A viruses occurring in vitro under immunological pressure. ImagesFig. 2Fig. 3Fig. 4 PMID:62624

  18. Genetic Variants in Male Infertility

    Microsoft Academic Search

    Mounia Tannour-Louet; Dolores J. Lamb

    \\u000a Different types of genetic variants are present in the genome. Single nucleotide polymorphisms, or SNPs, are minor variations\\u000a in the genetic sequence that differ between members of a species or even between paired chromosomes in an individual. There\\u000a are common SNPs that occur in at least 1% of a population. These SNPs may be specific to an ethnic group or

  19. 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

  20. Characterisation and Carriage Ratio of Clostridium difficile Strains Isolated from a Community-Dwelling Elderly Population in the United Kingdom

    PubMed Central

    Swale, Andrew; Price, Valerie; Jones, Maureen; Horan, Michael; Beeching, Nicholas; Brazier, Jonathan; Parry, Christopher; Pendleton, Neil; Pirmohamed, Munir

    2011-01-01

    Background Community-associated Clostridium difficile infection (CDI) appears to be an increasing problem. Reported carriage rates by C.difficile are debatable with suggestions that primary asymptomatic carriage is associated with decreased risk of subsequent diarrhoea. However, knowledge of potential reservoirs and intestinal carriage rates in the community, particularly in the elderly, the most susceptible group, is limited. We have determined the presence of C.difficile in the faeces of a healthy elderly cohort living outside of long-term care facilities (LCFs) in the United Kingdom. Methods Faecal samples from 149 community-based healthy elderly volunteers (median age 81 years) were screened for C.difficile using direct (Brazier's CCEY) and enrichment (Cooked Meat broth) culture methods and a glutamate dehydrogenase (GDH) immunoassay. Isolates were PCR-ribotyped and analysed for toxin production and the presence of toxin genes. Results Of 149 faecal samples submitted, six (4%) were found to contain C.difficile. One particular sample was positive by both the GDH immunoassay and direct culture, and concurrently produced two distinct strain types: one toxigenic and the other non-toxigenic. The other five samples were only positive by enrichment culture method. Overall, four C.difficile isolates were non-toxigenic (PCR-ribotypes 009, 026 (n?=?2) and 039), while three were toxigenic (PCR-ribotypes 003, 005 and 106). All individuals who had a positive culture were symptom-free and none of them had a history of CDI and/or antibiotics use in the 3 month period preceding recruitment. Conclusions To our knowledge, this is the first study of the presence of C.difficile in healthy elderly community-dwelling individuals residing outside of LCFs. The observed carriage rate is lower than that reported for individuals in LCFs and interestingly no individual carried the common epidemic strain PCR-ribotype 027 (NAP1/BI). Further follow-up of asymptomatic carriers in the community, is required to evaluate host susceptibility to CDI and identify dynamic changes in the host and microbial environment that are associated with pathogenicity. PMID:21886769

  1. High Prevalence of the EBER Variant EB-8m in Endemic Nasopharyngeal Carcinomas

    PubMed Central

    Shen, Zhi-chao; Luo, Bing; Chen, Jian-ning; Chao, Yan; Shao, Chun-kui; Liu, Qian-qian; Wang, Yun

    2015-01-01

    Epstein-Barr virus (EBV)-encoded small RNAs (EBERs) are the most highly expressed transcripts in all EBV-associated tumors and are involved in both lymphoid and epithelioid carcinogenesis. Our previous study on Chinese isolates from non-endemic area of nasopharyngeal carcinoma (NPC) identified new EBER variants (EB-8m and EB-10m) which were less common but relatively more frequent in NPC cases than healthy donors. In the present study, we determined the EBER variants in NPC cases and healthy donors from endemic and non-endemic areas of NPC within China and compared the EBER variants, in relation to the genotypes at BamHI F region (prototype F and f variant), between population groups and between two areas. According to the phylogenetic tree, four EBER variants (EB-6m, EB-8m, EB-10m and B95-8) were identified. EB-6m was dominant in all population groups except for endemic NPC group, in which EB-8m was dominant. EB-8m was more common in endemic NPC cases (82.0%, 41/50) than non-endemic NPC cases (33.7%, 32/95) (p<0.0001), and it was also more frequent in healthy donors from endemic area (32.4%, 24/74) than healthy donors from non-endemic area (1.1%, 1/92) (p<0.0001). More importantly, the EB-8m was more prevalent in NPC cases than healthy donors in both areas (p<0.0001). The f variant, which has been suggested to associate with endemic NPC, demonstrated preferential linkage with EB-8m in endemic isolates, however, the EB-8m variant seemed to be more specific to NPC isolates than f variant. These results reveal high prevalence of EBER EB-8m variant in endemic NPC cases, suggesting an association between NPC development and EBV isolates carrying EB-8m variant. Our finding identified a small healthy population group that shares the same viral strain which predominates in NPC cases. It could be interesting to carry extensive cohort studies following these individuals to evaluate the risk to develop NPC. PMID:25807550

  2. Small colony variants of Pseudomonas aeruginosa in chronic bacterial infection of the lung in cystic fibrosis.

    PubMed

    Evans, Thomas J

    2015-02-01

    ABSTRACT? Pseudomonas aeruginosa is the most common pathogen that colonizes the lungs of patients with cystic fibrosis. Isolates from sputum are typically all derived from the same strain of bacterium but show extensive phenotypic heterogeneity. One of these variants is the so-called small colony variant, which also shows increased ability to form a biofilm and is frequently resistant to multiple antibiotics. The presence of small colony variants in the sputum of patients with cystic fibrosis is associated with a worse clinical condition. The underlying mechanism responsible for generation of the small colony phenotype remains unclear, but a final common pathway would appear to be elevation of intracellular levels of cyclic di-GMP. This phenotypic variant is thus not just a laboratory curiosity, but a significant bacterial adaptation that favors survival within the lung of patients with cystic fibrosis and contributes to the pulmonary damage caused by P. aeruginosa. PMID:25689535

  3. 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

  4. 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

  5. First case of human rabies in chile caused by an insectivorous bat virus variant.

    PubMed

    Favi, Myriam; de Mattos, Carlos A; Yung, Verónica; Chala, Evelyn; López, Luis R; de Mattos, Cecilia C

    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

  6. Small Colony Variant of Methicillin-Resistant Staphylococcus pseudintermedius ST71 Presenting as a Sticky Phenotype

    PubMed Central

    Carretto, Edoardo; Polilli, Ennio; Marrollo, Roberta; Santarone, Stella; Fazii, Paolo; D'Antonio, Domenico; Rossano, Alexandra; Perreten, Vincent

    2014-01-01

    We first observed the phenomenon of small colony variants (SCVs) in a Staphylococcus pseudintermedius sequence type 71 (ST71) strain, isolated from a non-pet owner. Although we found that small-sized colonies share main features with Staphylococcus aureus SCVs, they nevertheless show a novel, particular, and sticky phenotype, whose expression was extremely stable, even after subcultivation. PMID:24452163

  7. First Report of Brain Abscess Caused by a Satelliting Phenotypic Variant of Helcococcus kunzii

    PubMed Central

    Sridhar, Siddharth; Chan, Jasper F. W.

    2014-01-01

    Helcococcus kunzii was isolated from a brain abscess in a diabetic patient with cholesteatoma and demonstrated satellitism around Staphylococcus aureus in culture. This is the first reported case of severe central nervous system infection due to H. kunzii and the first description of a satelliting phenotypic variant of this organism. PMID:24172152

  8. 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

  9. Isolation precautions

    MedlinePLUS

    Isolation precautions create barriers between people and germs. These types of precautions help prevent the spread of ... who visits a hospital patient who has an isolation sign outside their door should stop at the ...

  10. 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??) including splice variants in LPA that lowered plasma lipoprotein(a) levels (P?=?1.5×10?¹¹?). 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??), 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

  11. Nested Variant of Urothelial Carcinoma

    PubMed Central

    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

  12. 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...

  13. 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...

  14. Terpenoid aldehyde formation and lysigenous gland storage sites in cotton: variant with mature glands but suppressed levels of terpenoid aldehydes

    Microsoft Academic Search

    Chauncey R Benedict; Gail S Martin; Jinggao Liu; Lorraine Puckhaber; Clint W Magill

    2004-01-01

    A new cotton variant with reduced levels of terpenoid aldehydes (sesquiterpenoids and sesterterpenoids (heliocides)) was isolated from the progeny of hemizygous cotton (Gossypium hirsutum cv. Coker 312) transformed with antisense (+)-?-cadinene synthase cDNA. Southern analysis of leaf DNA digested with HindIII, Pst or KpnI restriction endonucleases did not detect any antisense cdn1-C1 DNA in the genome of the variant. The

  15. Novel Aggregative Adherence Fimbria Variant of Enteroaggregative Escherichia coli.

    PubMed

    Jønsson, Rie; Struve, Carsten; Boisen, Nadia; Mateiu, Ramona Valentina; Santiago, Araceli E; Jenssen, Håvard; Nataro, James P; Krogfelt, Karen A

    2015-04-01

    Enteroaggregative Escherichia coli (EAEC) organisms belong to a diarrheagenic pathotype known to cause diarrhea and can be characterized by distinct aggregative adherence (AA) in a stacked-brick pattern to cultured epithelial cells. In this study, we investigated 118 EAEC strains isolated from the stools of Danish adults with traveler's diarrhea. We evaluated the presence of the aggregative adherence fimbriae (AAFs) by a multiplex PCR, targeting the four known major subunit variants as well as their usher-encoding genes. Almost one-half (49/118) of the clinical isolates did not possess any known AAF major fimbrial subunit, despite the presence of other AggR-related loci. Further investigation revealed the presence of an AAF-related gene encoding a yet-uncharacterized adhesin, termed agg5A. The sequence of the agg5DCBA gene cluster shared fimbrial accessory genes (usher, chaperone, and minor pilin subunit genes) with AAF/III, as well as the signal peptide present in the beginning of the agg3A gene. The complete agg5DCBA gene cluster from a clinical isolate, EAEC strain C338-14, with the typical stacked-brick binding pattern was cloned, and deletion of the cluster was performed. Transformation to a nonadherent E. coli HB101 and complementation of the nonadherent C338-14 mutant with the complete gene cluster restored the AA adhesion. Overall, we found the agg5A gene in 12% of the 118 strains isolated from Denmark, suggesting that this novel adhesin represents an important variant. PMID:25624357

  16. 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

  17. Longitudinal studies on maternal HIV-1 variants by biological phenotyping, sequence analysis and viral load.

    PubMed

    Renta, J Y; Cadilla, C L; Vega, M E; Hillyer, G V; Estrada, C; Jiménez, E; Abreu, E; Méndez, I; Gandía, J; Meléndez-Guerrero, L M

    1997-11-01

    In this study, the HIV-1 variant viruses from ten pregnant women and their infants were isolated and characterized longitudinally in order to determine the role that viral envelope (gp120-V3 loop) gene variation and viral tropism play in vertical transmission. Biological phenotyping of each HIV variant was accomplished by growth in MT-2, and macrophages from healthy and non-HIV-infected donors. Genetic characterization of the variants was accomplished by DNA sequence analysis. All the women enrolled in this study received ZDV therapy. Virus was cultured from eight out of ten env V3-PCR positive mothers. HIV-1 isolates were all non-syncitium inducing variants. None of the mothers were found to transmit HIV, as determined by DNA PCR and quantitative co-cultures on their infants which were seronegative for HIV-1 through one year after birth. Viral cultures from infant blood samples were negative and infants were all healthy. However, nested env V3-PCR detected proviral DNA in five out of ten infants. In contrast, conventional gag-PCR was negative in the same five infants. Sequences of the five maternal-infant pairs were different, suggesting unique infant HIV-1 variants. The three highest maternal viral load values corresponded to infants that were env V3-PCR positive. These results suggest that HIV-1 particles are transmitted from ZDV-treated mothers to infants. Infant follow up is recommended to determine if HIV-1 has been inhibited by the immune system of the infants. PMID:9449544

  18. 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

  19. 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

  20. Frequency of Thermostability Variants: Estimation of Total ``Rare'' Variant frequency in Human Populations

    Microsoft Academic Search

    H. W. Mohrenweiser; J. V. Neel

    1981-01-01

    Eight erythrocyte enzymes were examined 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

  1. Frequency of thermostability variants: estimation of total rare variant frequency in human populations

    Microsoft Academic Search

    H. W. Mohrenweiser; J. V. Neel

    1981-01-01

    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

  2. Phenotypic and Enzymatic Comparative Analysis of the KPC Variants, KPC-2 and Its Recently Discovered Variant KPC-15

    PubMed Central

    Yang, Yijun

    2014-01-01

    Sixteen different variants (KPC-2 to KPC-17) in the KPC family have been reported, and most current studies are focusing on KPC-2 and KPC-3. The KPC-15 variant, which isolated from Klebsiella pneumoniae in a Chinese hospital, was a recently discovered KPC enzyme. To compare the characteristics of KPC-15 and KPC-2, the variants were determined by susceptibility testing, PCR amplification and sequencing, and study of kinetic parameters. The strain harboring the KPC-15 showed resistance to 18 conventional antimicrobial agents, especially to cabapenem antibiotics, and the strain involving the KPC-2 also indicated resistance to cabapenem antibiotics, but both strains were susceptible to polymyxin B and colistin. The conjugation experiments showed that the changes of MIC values to the antibiotics were due to the transferred plasmids. The differences of amino acids were characterised at sites of 119 leucine and 146 lysine with KPC-15 and KPC-2. The minimum evolution tree indicated the KPC alleles evolution, and showed that the KPC-15 appeared to be homogenous with KPC-4 closely. Steady-state kinetic parameters showed the catalytic efficiency of KPC-15 was higher than that of KPC-2 for all tested antibiotics in this study. The catalytic efficiency of KPC-15 caused resistance to ?-lactam antibiotics was higher than that of KPC-2. Meanwhile, an evolutionary transformation changed KPC from an efficient carbapenemase to its variants (KPC-15) with better ceftazidimase catalytic efficiency, and the old antibiotics polymyxin B and colistin might play a role in the therapy for multi-resistant strains. PMID:25360633

  3. Rare and common variants: twenty arguments

    Microsoft Academic Search

    Greg Gibson

    2012-01-01

    Genome-wide association studies have greatly improved our understanding of the genetic basis of disease risk. The fact that they tend not to identify more than a fraction of the specific causal loci has led to divergence of opinion over whether most of the variance is hidden as numerous rare variants of large effect or as common variants of very small

  4. 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

  5. Antigenic variants of rabies virus

    Microsoft Academic Search

    T. J. WIKTOR; H. KOPROWSKI

    1980-01-01

    Rabies viruses isolated from different animal species in various parts of the world were in the past considered to be antigenically closely related. Only when the antibodies produced in animals immunized with whole virions or viral components were assayed by the plaque reduction method, were some minor differences detected in the antigenic composition of various rabies strains (1). On the

  6. 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

  7. Decoding the androgen receptor splice variants

    PubMed Central

    Lu, Changxue; Luo, Jun

    2014-01-01

    In the past five years, multiple structurally and functionally distinct androgen receptor (AR) splice variants have been decoded and characterized. The mature transcripts for the majority of the fully decoded AR splice variants contain a transcribed “intronic” sequence, capable of encoding a short variant-specific peptide to replace the AR ligand-binding domain (LBD). Functionally, AR splice variants represent a diverse group of molecules often demonstrating cell context-specific genomic functions that may or may not be coupled with the functions of the canonical full-length AR (AR-FL). However, the full spectrum of their functional diversity and the underlying mechanistic basis remains very poorly characterized. In clinical specimens derived from men treated with a variety of hormone therapy regimens, AR splice variants are almost always expressed at detectable, yet lower levels when compared to that of AR-FL. In spite of the collective in vitro data supporting the putative role of AR splice variants in therapeutic resistance to hormone therapies, the extent to which AR splice variants mediate resistance to each individual regimen is not known and awaits thorough investigations in a clinically relevant setting using specimens from men undergoing treatments. Among the AR splice variants, AR-V7 is more abundantly and frequently expressed in castration-resistant prostate cancer (CRPC) and remains the most important variant identified so far. The relative importance of different AR molecules, including AR-FL, should be functionally dissected in the setting of castration-resistant prostate cancer, particularly in tumors resistant to more potent inhibitors of AR-FL recently approved by the FDA. In this review, we will focus on the discovery and characterization of AR splice variants, their putative functions and roles in mediating constitutively active AR signaling, and key areas of investigation that are necessary to establish their clinical relevance. PMID:25356377

  8. 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

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

    2014-06-01

    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

  9. Multiple Genetically Distinct Groups Revealed among Clinical Isolates Identified as Atypical Aspergillus fumigatus

    Microsoft Academic Search

    Margaret E. Katz; Annette M. Dougall; Brian F. Cheetham

    2005-01-01

    To investigate whether genetic variants of A. fumigatus are found among clinical isolates, four isolates that were originally identified as poorly sporulating strains of Aspergillus fumigatus were subjected to molecular analysis. DNA sequence analysis of the alkaline protease genes of these isolates showed that each is genetically distinct and each shows substantial variation (7 to 11%) from the A. fumigatus

  10. Genetic diversity of parvovirus isolates from dogs and wild animals in China.

    PubMed

    Chen, Xiao-ying; Xie, Zhi-jing; Zhao, Zhong-peng; Jiang, Shi-jin; Zhao, Hong-kun; Zhu, Yan-li; Zhang, Xing-xiao

    2011-10-01

    We isolated three new parvovirus variants in China. The isolate from a blue fox was related to feline parvovirus, but possessed a mutation of VP2 residue A300P. Isolates from a raccoon dog and a masked civet were antigenically similar to canine parvovirus-2a but had a substitution of VP2 residue G300S. PMID:22102680

  11. Tissue-specific splice variants of HARE/Stabilin-2 are expressed in bone marrow, lymph node, and spleen.

    PubMed

    Hare, Amanda K; Harris, Edward N

    2015-01-01

    The hyaluronan receptor for endocytosis (HARE), or Stabilin-2, is the mammalian endocytic clearance receptor for HA, heparin, advanced glycation end-products, acetylated and oxidized low-density lipoproteins and collagen N-terminal propeptides. This large 2551 amino acid receptor is encoded by a gene that covers over 180 kbp on human chromosome 12 and is predicted to be composed of 69 exons. Due to the expression profile of this gene and the number of exons it contains, we hypothesized that splice variants of stab2 are encoded in these tissues. In addition, a correlation between alternative splice variants and cancer progression has been shown in other HA receptors such as RHAMM and CD42. In this study, two methods were utilized in identifying and/or isolating the HARE splice variants. The first method used primer sets to amplify the 190-HARE encoding region that could contain splice junctions; therefore, they were purified from agarose gels and sequenced. Five splice variants were detected in that manner. In the second approach, the entire open reading frame of HARE was amplified. This allowed four splice variants with extensive exon splicing to be isolated. After the splice variants were sequenced, three were cloned into a mammalian expression vector. Next, stable cell lines expressing the variants were created in order to determine stable protein expression. In this study, the splice variants were found to be tissue specific in most cases. This suggests that tissue specific regulatory splicing mechanisms may lead to differences in functionality between the splice variants. PMID:25446080

  12. Sequence-dependent histone variant positioning signatures

    PubMed Central

    2010-01-01

    Background Nucleosome, the fundamental unit of chromatin, is formed by wrapping nearly 147bp of DNA around an octamer of histone proteins. This histone core has many variants that are different from each other by their biochemical compositions as well as biological functions. Although the deposition of histone variants onto chromatin has been implicated in many important biological processes, such as transcription and replication, the mechanisms of how they are deposited on target sites are still obscure. Results By analyzing genomic sequences of nucleosomes bearing different histone variants from human, including H2A.Z, H3.3 and both (H3.3/H2A.Z, so-called double variant histones), we found that genomic sequence contributes in part to determining target sites for different histone variants. Moreover, dinucleotides CA/TG are remarkably important in distinguishing target sites of H2A.Z-only nucleosomes with those of H3.3-containing (both H3.3-only and double variant) nucleosomes. Conclusions There exists a DNA-related mechanism regulating the deposition of different histone variants onto chromatin and biological outcomes thereof. This provides additional insights into epigenetic regulatory mechanisms of many important cellular processes. PMID:21143812

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

    PubMed Central

    Kuhn, Jens H.; Andersen, Kristian G.; Bào, Y?míng; 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

  14. 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

  15. Histological variants of cutaneous Kaposi sarcoma

    PubMed Central

    Grayson, Wayne; Pantanowitz, Liron

    2008-01-01

    This review provides a comprehensive overview of the broad clinicopathologic spectrum of cutaneous Kaposi sarcoma (KS) lesions. Variants discussed include: usual KS lesions associated with disease progression (i.e. patch, plaque and nodular stage); morphologic subtypes alluded to in the older literature such as anaplastic and telangiectatic KS, as well as several lymphedematous variants; and numerous recently described variants including hyperkeratotic, keloidal, micronodular, pyogenic granuloma-like, ecchymotic, and intravascular KS. Involuting lesions as a result of treatment related regression are also presented. PMID:18655700

  16. Human papillomavirus type 16 sequence variants: identification by E6 and L1 lineage-specific hybridization.

    PubMed Central

    Wheeler, C M; Yamada, T; Hildesheim, A; Jenison, S A

    1997-01-01

    A catalog of human papillomavirus (HPV) type 16 (HPV-16) E6 and L1 signature nucleotides was used to develop PCR-based oligonucleotide probe systems capable of distinguishing HPV-16 class and subclass variants. Twenty-three E6-specific oligonucleotide probes targeting 13 variant nucleotide positions and 12 L1-specific oligonucleotide probes targeting 6 variant nucleotide positions were used to characterize HPV-16-containing cervicovaginal lavage specimens. Nucleotide positions that could be distinguished included E6 nucleotides 109, 131, 132, 143, 145, 178, 183, 286, 289, 335, 350, 403, and 532 and L1 nucleotides 6695, 6721, 6803, 6854, 6862, and 6994. Combined hybridization patterns were assigned on the basis of the predicted HPV-16 class, subclass, or minor class variants described previously (T. Yamada, C. M. Wheeler, A. L. Halpern, A.-C. M. Stewart, A. Hildesheim, and S.A. Jenison, J. Virol. 69:7743-7753, 1995). The major HPV-16 variant lineages detected included European prototype-like (E-P), Asian (As), Asian-American (AA), and African (Af1 and Af2) lineages. In addition, E-G131, an E-class variant, and AA-G183, an AA-class variant, were also identified. For each clinical specimen, DNA hybridization results were compared to nucleotide sequence determinations. Targeted L1 and E6 marker nucleotides covaried within all HPV-16 variant isolates examined. These hybridization-based methods result in minimal misclassification error, are amenable to targeting additional lineage-specific nucleotide positions, and should facilitate the large-scale, low-cost analysis of HPV-16 variants in epidemiologic investigations. Specifically, these methods will facilitate epidemiologic studies of HPV-16 transmission and natural history, as well as studies of associations between HPV variants, host immune responses, and cervical neoplasia. PMID:8968874

  17. Gonococcal pilin variants in experimental gonorrhea

    PubMed Central

    1987-01-01

    When pilus+ Gc were introduced into a male subject's urethra, they gave rise to pilus+ variants whose pilin mRNAs differed from that of input Gc. The differences stemmed from the Gc genome's single complete pilin gene having undergone gene conversion by different partial pilin genes' sequences and by different length stretches of a single partial pilin gene. In some instances, the variant's pilin mRNA appeared to reflect two independent gene-conversion events that used sequences from two different partial pilin genes. The resulting variants' pilins exhibited antigenic differences compared with the pilin polypeptide of input Gc; these differences were discernible by immunoblotting with mAbs. Amino acid and antigenic changes occurred in a segment of the variants' pilin polypeptides that previously was thought to be conserved or constant in sequence. PMID:3106555

  18. [Direct-acting antiviral-resistant variant].

    PubMed

    Imamura, Michio; Chayama, Kazuaki

    2015-02-01

    Recently, IFN-free NS5A inhibitor daclatasvir and protease inhibitor asunaprevir combination treatment was approved for genotype 1b HCV-infected patients who were ineligible or who failed to respond to previous therapies. NS5A inhibitor-resistant variants occasionally exist in HCV-infected patients who have never been exposed to direct-acting antivirals. In Japanese HCV genotype 1b-infected patients, the frequency of NS5A inhibitor-resistant variants is approximately 11-23 %. The phase 3 study of daclatasvir and asunaprevir combination therapy showed that more patients with NS5A 31 and/or 93 resistance-associated variants experienced virological failure. Preexisting NS5A inhibitor-resistant variants should be evaluated carefully before choosing the drugs. PMID:25764690

  19. Prinzmetal's Angina, Variant Angina and Angina Inversa

    MedlinePLUS

    ... Stress Medicines that tighten or narrow blood vessels Smoking Cocaine use Symptoms of Variant (Prinzmetal) Angina: The pain or discomfort: Usually occurs while resting and during the night or early morning hours Are usually severe Can be relieved by ...

  20. Guillain-Barré syndrome and variants.

    PubMed

    Dimachkie, Mazen M; Barohn, Richard J

    2013-05-01

    Guillain-Barré syndrome (GBS) is characterized by rapidly evolving ascending weakness, mild sensory loss, and hyporeflexia or areflexia. Acute inflammatory demyelinating polyneuropathy was the first to be recognized over a century ago and is the most common form of GBS. Axonal motor and sensorimotor variants have been described in the last three decades and are mediated by molecular mimicry targeting peripheral nerve motor axons. 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 because of the availability of equally effective therapies in the form of plasmapheresis and intravenous immunoglobulins. PMID:23642721

  1. Comparison of Different DNA Fingerprinting Techniques for Molecular Typing of Bartonella henselae Isolates

    Microsoft Academic Search

    ANNA SANDER; MICHAEL RUESS; STEFAN BERESWILL; MARKUS SCHUPPLER; BERNHARD STEINBRUECKNER

    1998-01-01

    Seventeen isolates of Bartonella henselae from the region of Freiburg, Germany, obtained from blood cultures of domestic cats, were examined for their genetic heterogeneity. On the basis of different DNA fingerprinting methods, including pulsed-field gel electrophoresis (PFGE), enterobacterial repetitive intergenic consensus (ERIC)-PCR, repetitive extragenic palindromic (REP) PCR, and arbitrarily primed (AP)-PCR, three different variants were identified among the isolates (variants

  2. 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

  3. A divergent variant of Grapevine leafroll-associated virus 3 is present in California

    PubMed Central

    2012-01-01

    Background Grapevine leafroll-associated viruses are a problem for grape production globally. Symptoms are caused by a number of distinct viral species. During a survey of Napa Valley vineyards (California, USA), we found evidence of a new variant of Grapevine leafroll-associated virus 3 (GLRaV-3). We isolated its genome from a symptomatic greenhouse-raised plant and fully sequenced it. Findings In a maximum likelihood analysis of representative GLRaV-3 gene sequences, the isolate grouped most closely with a recently sequenced variant from South Africa and a partial sequence from New Zealand. These highly divergent GLRaV-3 variants have predicted proteins that are more than 10% divergent from other GLRaV-3 variants, and appear to be missing an open reading frame for the p6 protein. Conclusions This divergent GLRaV-3 phylogroup is already present in grape-growing regions worldwide and is capable of causing symptoms of leafroll disease without the p6 protein. PMID:23062082

  4. 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

  5. Isolated Aortitis

    MedlinePLUS

    ... are forms of large vessel vasculitis, most commonly giant cell arteritis and Takayasu arteritis. Other autoimmune diseases ... cases are due to a rheumatic cause like giant cell arteritis and Takayasu arteritis. Who gets Isolated ...

  6. Common variants in UMOD associate with urinary uromodulin levels: a meta-analysis.

    PubMed

    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; Devuyst, Olivier

    2014-08-01

    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 ?g/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

  7. 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; Gamboa-Coronado, María Del Mar; Lawley, Trevor D; Moreno, Edgardo; Mulvey, Michael R; Brito, Gerly Anne de Castro; 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

  8. Characterizing Genetic Variants for Clinical Action

    PubMed Central

    Ramos, Erin M.; Din-Lovinescu, Corina; Berg, Jonathan S.; Brooks, Lisa D.; Duncanson, Audrey; Dunn, Michael; Good, Peter; Hubbard, Tim; Jarvik, Gail P.; O'Donnell, Christopher; Sherry, Stephen T.; Aronson, Naomi; Biesecker, Leslie G.; Blumberg, Bruce; Calonge, Ned; Colhoun, Helen M.; Epstein, Robert S.; Flicek, Paul; Gordon, Erynn S.; Green, Eric D.; Green, Robert C.; Hurles, Matthew; Kawamoto, Kensaku; Knaus, William; Ledbetter, David H.; Levy, Howard P.; Lyon, Elaine; Maglott, Donna; McLeod, Howard L.; Rahman, Nazneen; Randhawa, Gurvaneet; Wicklund, Catherine; Manolio, Teri A.; Chisholm, Rex L.; Williams, Marc S.

    2014-01-01

    Genome-wide association studies, DNA sequencing studies, and other genomic studies are finding an increasing number of genetic variants associated with clinical phenotypes that may be useful in developing diagnostic, preventive, and treatment strategies for individual patients. However, few common variants have been integrated into routine clinical practice. The reasons for this are several, but two of the most significant are limited evidence about the clinical implications of the variants and a lack of a comprehensive knowledge base that captures genetic variants, their phenotypic associations, and other pertinent phenotypic information that is openly accessible to clinical groups attempting to interpret sequencing data. As the field of medicine begins to incorporate genome-scale analysis into clinical care, approaches need to be developed for collecting and characterizing data on the clinical implications of variants, developing consensus on their actionability, and making this information available for clinical use. The National Human Genome Research Institute (NHGRI) and the Wellcome Trust thus convened a workshop to consider the processes and resources needed to: 1) identify clinically valid genetic variants; 2) decide whether they are actionable and what the action should be; and 3) provide this information for clinical use. This commentary outlines the key discussion points and recommendations from the workshop. PMID:24634402

  9. Fidelity Variants of RNA Dependent RNA Polymerases Uncover an Indirect, Mutagenic Activity of Amiloride Compounds

    PubMed Central

    Beaucourt, Stéphanie; McPherson, Malia J.; Baron, Bruno; Arnold, Jamie J.; Vignuzzi, Marco

    2010-01-01

    In a screen for RNA mutagen resistance, we isolated a high fidelity RNA dependent RNA polymerase (RdRp) variant of Coxsackie virus B3 (CVB3). Curiously, this variant A372V is also resistant to amiloride. We hypothesize that amiloride has a previously undescribed mutagenic activity. Indeed, amiloride compounds increase the mutation frequencies of CVB3 and poliovirus and high fidelity variants of both viruses are more resistant to this effect. We hypothesize that this mutagenic activity is mediated through alterations in intracellular ions such as Mg2+ and Mn2+, which in turn increase virus mutation frequency by affecting RdRp fidelity. Furthermore, we show that another amiloride-resistant RdRp variant, S299T, is completely resistant to this mutagenic activity and unaffected by changes in ion concentrations. We show that RdRp variants resist the mutagenic activity of amiloride via two different mechanisms: 1) increased fidelity that generates virus populations presenting lower basal mutation frequencies or 2) resisting changes in divalent cation concentrations that affect polymerase fidelity. Our results uncover a new antiviral approach based on mutagenesis. PMID:21060812

  10. Genetic and functional analyses of ZIC3 variants in congenital heart disease

    PubMed Central

    Cowan, Jason; Tariq, Muhammad; Ware, Stephanie M.

    2013-01-01

    Mutations in zinc-finger in cerebellum 3 (ZIC3) result in heterotaxy or isolated congenital heart disease (CHD). The majority of reported mutations cluster in zinc-finger domains. We previously demonstrated that many of these lead to aberrant ZIC3 subcellular trafficking. A relative paucity of N- and C-terminal mutations has, however, prevented similar analyses in these regions. Notably, an N-terminal polyalanine expansion was recently identified in a patient with VACTERL, suggesting a potentially distinct function for this domain. Here, we report ZIC3 sequencing results from 440 unrelated patients with heterotaxy and CHD, the largest cohort yet examined. Variants were identified in 5.2% of sporadic male cases. This rate exceeds previous estimates of 1% and has important clinical implications for genetic testing and risk-based counseling. Eight of 11 were novel, including 5 N-terminal variants. Subsequent functional analyses included 4 additional reported but untested variants. Aberrant cytoplasmic localization and decreased luciferase transactivation were observed for all zinc-finger variants, but not for downstream or in-frame upstream variants, including both analyzed polyalanine expansions. Collectively, these results expand the ZIC3 mutational spectrum, support a higher than expected prevalence in sporadic cases, and suggest alternative functions for terminal mutations, highlighting a need for further study of these domains. PMID:24123890

  11. Delegated isolation

    Microsoft Academic Search

    Roberto Lublinerman; Jisheng Zhao; Zoran Budimli?; Swarat Chaudhuri; Vivek Sarkar

    2011-01-01

    Isolation---the property that a task can access shared data without interference from other tasks---is one of the most basic concerns in parallel programming. In this paper, we present Aida, a new model of isolated execution for parallel programs that perform frequent, irregular accesses to pointer-based shared data structures. The three primary benefits of Aida are dynamism, safety and liveness guarantees,

  12. 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

  13. 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

  14. Essential Oil Composition of a Citronella-like Variant of Lemongrass

    Microsoft Academic Search

    R. N. Kulkarni; G. R. Mallavarapu; K. Baskaran; S. Ramesh; Sushil Kumar

    1997-01-01

    A natural variant of lemongrass (Cymbopogon flexuosus), with a citronella-like odor which was isolated from cycle-4 population of a recurrent selection program in lemongrass, was studied for its essential oil composition by GC and GC\\/MS. The main components of the oil were geraniol (13.1%), citronellyl acetate (11.2%) and geranyl acetate (25.9%), while neral (3.7%) and geranial (5.8%) were minor constituents.

  15. Variants of Parvovirus B19: Bioinformatical Evaluation of Nested PCR Assays

    Microsoft Academic Search

    Massimiliano Bergallo; Cristina Costa; Francesca Sidoti; Mauro Novelli; Renata Ponti; Carlotta Castagnoli; Chiara Merlino; Maria Grazia Bernengo; Rossana Cavallo

    2008-01-01

    Variants of parvovirus B19 are currently grouped into three genotypes: 1 (reference B19 strains), 2 and 3. It has been evidenced that isolate K71 of genotype 2 is more prevalent in skin than the conventional B19 genotype 1. In this study we investigated the detection of parvovirus B19 genotypes by using two nested PCRs and evaluating the suitability of these

  16. Different splice variants of filamin-B affect myogenesis, subcellular distribution, and determine binding to integrinsubunits

    Microsoft Academic Search

    Arjan van der Flier; Ingrid Kuikman; Duco Kramer; Dirk Geerts; Maaike Kreft; Toshiro Takafuta; Sandor S. Shapiro; Arnoud Sonnenberg

    2002-01-01

    ntegrins connect the extracellular matrix with the cell interior, and transduce signals through interactions of their cytoplasmic tails with cytoskeletal and signaling proteins. Using the yeast two-hybrid system, we isolated a novel splice variant (filamin-B var-1 ) of the filamentous actin cross-linking protein, filamin-B, that interacts with the cytoplasmic domain of the integrin ? 1A and ? 1D subunits. RT-PCR

  17. Determination of a novel integron-located variant (blaOXA -320 ) of Class D ?-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 ?-lactamase, in P. mirabilis from Turkey. PMID:24027220

  18. Characterization of a Unique Variant of Bat Rabies Virus Responsible for Newly Emerging Human Cases in North America

    Microsoft Academic Search

    Kinjiro Morimoto; Menal Patel; Susanne Corisdeo; D. Craig Hooper; Zhen Fang Fu; Charles E. Rupprecht; Hilary Koprowski; Bernhard Dietzschold

    1996-01-01

    The silver-haired bat variant of rabies virus (SHBRV) has been identified as the etiological agent of a number of recent human rabies cases in the United States that are unusual in not having been associated with any known history of conventional exposure. Comparison of the different biological and biochemical properties of isolates of this virus with those of a coyote

  19. [The logopenic variant of primary progressive aphasia].

    PubMed

    Yoshino, Mariko

    2011-10-01

    The logopenic variant of primary progressive aphasia [also referred to as logopenic progressive aphasia (LPA)] is the most recently identified variant of primary progressive aphasia (PPA). This disorder, characterized by a unique speech and language profile, occurs due to damage to specific anatomical areas. An international panel of experts has established a set of diagnostic criteria for PPA and its clinical variants. The clinical diagnostic criteria for the logopenic variant include core features such as impaired single-word retrieval in spontaneous speech and impaired repetition of sentences and phrases. Additional features, of which at least 3 are essential for diagnosing the logopenic variant, include phonological errors in speech, spared single-word comprehension and object knowledge, spared motor speech, and lack of frank agrammatism. For a next imaging-supported diagnosis, the aforementioned clinical features must be accompanied by imaging findings revealing atrophy, hypoperfusion, or hypometabolism in the left temporo-parietal junction area. Finally, a pathology-confirmed case of the logopenic variant requires a clinical diagnosis of the syndrome accompanied by histopathological data or the presence of a known pathogenic mutation. Studies have clarified the clinical phenotype of this disorder, suggesting a prominent impairment of the phonological working memory. Several studies have provided evidences of a possible link between the logopenic phenotype and the specific pathological and genetic correlates. The diagnostic guidelines will enable a more accurate identification of the individuals with the logopenic variant, thus facilitating the documentation of the course of illness and, ultimately, the underlying pathological substrate in this patient group via the pathology-confirmed series. PMID:21987563

  20. Novel compound heterozygous NMNAT1 variants associated with Leber congenital amaurosis

    PubMed Central

    Siemiatkowska, Anna M.; van den Born, L. Ingeborgh; van Genderen, Maria M.; Bertelsen, Mette; Zobor, Ditta; Rohrschneider, Klaus; van Huet, Ramon A.C.; Nurohmah, Siska; Klevering, B. Jeroen; Kohl, Susanne; Faradz, Sultana M.H.; Rosenberg, Thomas; den Hollander, Anneke I.; Collin, Rob W.J.

    2014-01-01

    Purpose The gene encoding nicotinamide nucleotide adenylyltransferase 1 (NMNAT1) was recently found to be mutated in a subset of patients with Leber congenital amaurosis (LCA) with macular atrophy. The aim of this study was to determine the occurrence and frequency of NMNAT1 mutations and associated phenotypes in different types of inherited retinal dystrophies. Methods DNA samples of 161 patients with LCA without genetic diagnosis were analyzed for variants in NMNAT1 using Sanger sequencing. Variants in exon 5 of NMNAT1, which harbors the majority of the previously identified mutations, were screened in 532 additional patients with retinal dystrophies. This cohort encompassed 108 persons with isolated or autosomal recessive cone-rod dystrophy (CRD), 271 with isolated or autosomal recessive retinitis pigmentosa (RP), and 49 with autosomal dominant RP, as well as 104 persons with LCA in whom the causative mutation was previously identified. Results Compound heterozygous alterations were found in six patients with LCA and in one person with early-onset RP. All except one carried the common p.E257K variant on one allele. Macular atrophy was absent in one patient, who carried this variant in combination with a truncating mutation on the other allele. The p.E257K alteration was also found in a heterozygous state in five individuals with LCA and one with RP while no mutation was detected on the other allele. Two individuals with LCA carried other NMNAT1 variants in a heterozygous state, whereas no NMNAT1 variants in exon 5 were identified in individuals with CRD. The p.E257K variant was found to be enriched in a heterozygous state in individuals with LCA (0.94%) compared to Caucasian controls (0.18%), although the difference was statistically insignificant (p=0.12). Conclusions Although macular atrophy can occur in LCA and CRD, no NMNAT1 mutations were found in the latter cohort. NMNAT1 variants were also not found in a large group of patients with sporadic or autosomal recessive RP. The enrichment of p.E257K in a heterozygous state in patients with LCA versus controls suggests that this allele could act as a modifier in other genetic subtypes of LCA. PMID:24940029

  1. 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 ...

  2. Variants of parvovirus B19: bioinformatical evaluation of nested PCR assays.

    PubMed

    Bergallo, Massimiliano; Costa, Cristina; Sidoti, Francesca; Novelli, Mauro; Ponti, Renata; Castagnoli, Carlotta; Merlino, Chiara; Bernengo, Maria Grazia; Cavallo, Rossana

    2008-01-01

    Variants of parvovirus B19 are currently grouped into three genotypes: 1 (reference B19 strains), 2 and 3. It has been evidenced that isolate K71 of genotype 2 is more prevalent in skin than the conventional B19 genotype 1. In this study we investigated the detection of parvovirus B19 genotypes by using two nested PCRs and evaluating the suitability of these assays by BLAST search of parvovirus isolates. Subsequently, we analyze the present genotypes in skin biopsies. The two nested PCRs employed in this study allow to amplify 41 isolates as confirmed by bioinformatical validation. The molecular epidemiological characterization of our casistics confirmed the presence of isolate K71 in human skin. PMID:18431072

  3. Allele variants of enterotoxigenic Escherichia coli heat-labile toxin are globally transmitted and associated with colonization factors.

    PubMed

    Joffré, Enrique; von Mentzer, Astrid; Abd El Ghany, Moataz; Oezguen, Numan; Savidge, Tor; Dougan, Gordon; Svennerholm, Ann-Mari; Sjöling, Åsa

    2015-01-01

    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

  4. Signal Isolators

    NASA Astrophysics Data System (ADS)

    1991-01-01

    The City of Dubuque, Iowa's new Water Division computer system was experiencing failures of the analog inputs ranging from signals out of tolerance by more than 30 percent to intermittent and sometimes complete loss of signals. The problem stemmed from a lack of signal isolation of the analog input cards, which made the inputs vulnerable to interference from storms and machinery. Electronic technician Bob Ervolino read an article in Tech Briefs describing an Ames Research Center solution to a similar problem. He studied the Technical Support Package and contacted the vendor; the information saved the Water Division more than 50 percent of the cost of commercial isolators.

  5. ?IIb?3 variants defined by next-generation sequencing: Predicting variants likely to cause Glanzmann thrombasthenia

    PubMed Central

    Buitrago, Lorena; Rendon, Augusto; Liang, Yupu; Simeoni, Ilenia; Negri, Ana; Filizola, Marta; Ouwehand, Willem H.; Coller, Barry S.; Alessi, Marie-Christine; Ballmaier, Matthias; Bariana, Tadbir; Bellissimo, Daniel; Bertoli, Marta; Bray, Paul; Bury, Loredana; Carrell, Robin; Cattaneo, Marco; Collins, Peter; French, Deborah; Favier, Remi; Freson, Kathleen; Furie, Bruce; Germeshausen, Manuela; Ghevaert, Cedric; Gomez, Keith; Goodeve, Anne; Gresele, Paolo; Guerrero, Jose; Hampshire, Dan J.; Hadinnapola, Charaka; Heemskerk, Johan; Henskens, Yvonne; Hill, Marian; Hogg, Nancy; Johnsen, Jill; Kahr, Walter; Kerr, Ron; Kunishima, Shinji; Laffan, Michael; Natwani, Amit; Neerman-Arbez, Marguerite; Nurden, Paquita; Nurden, Alan; Ormiston, Mark; Othman, Maha; Ouwehand, Willem; Perry, David; Vilk, Shoshana Ravel; Reitsma, Pieter; Rondina, Matthew; Simeoni, Ilenia; Smethurst, Peter; Stephens, Jonathan; Stevenson, William; Szkotak, Artur; Turro, Ernest; Van Geet, Christel; Vries, Minka; Ward, June; Waye, John; Westbury, Sarah; Whiteheart, Sidney; Wilcox, David; Zhang, Bi

    2015-01-01

    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

  6. ?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

  7. The Thymocyte-Specific MAR Binding Protein, SATB1, Interacts in Vitro with a Novel Variant of DNA-Directed RNA Polymerase II, Subunit 11

    Microsoft Academic Search

    Linda K. Durrin; Theodore G. Krontiris

    2002-01-01

    A yeast two-hybrid screen of a Jurkat (T cell) derived cDNA library, using SATB1 (a matrix attachment region binding protein) as the bait, yielded four independent isolates of a novel variant of the DNA directed RNA polymerase II, subunit 11 (RPB11). Absence of lysine-17 from the amino terminus of this variant cannot be explained by alternative mRNA splicing. Instead, allele-specific

  8. Evolution of a Human Immunodeficiency Virus Type 1 Variant with Enhanced Replication in Pig-Tailed Macaque Cells by DNA Shuffling

    Microsoft Academic Search

    Katja Pekrun; Riri Shibata; Tatsuhiko Igarashi; Margaret Reed; Liana Sheppard; Philip A. Patten; Willem P. C. Stemmer; Malcolm A. Martin; Nay-Wei Soong

    2002-01-01

    DNA shuffling facilitated the evolution of a human immunodeficiency virus type 1 (HIV-1) variant with enhanced replication in pig-tailed macaque peripheral blood mononuclear cells (pt mPBMC). This variant consists exclusively of HIV-1-derived sequences with the exception of simian immunodeficiency virus (SIV) nef. Sequences spanning the gag-protease-reverse transcriptase (gag-pro-RT) region from several HIV-1 isolates were shuffled and cloned into a parental

  9. Novel human butyrylcholinesterase variants: toward organophosphonate detoxication.

    PubMed

    Dwyer, Mary; Javor, Sacha; Ryan, Daniel A; Smith, Emily M; Wang, Beilin; Zhang, Jun; Cashman, John R

    2014-07-15

    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

  10. 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

  11. Postnatally-transmitted HIV-1 Envelope variants have similar neutralization-sensitivity and function to that of nontransmitted breast milk variants

    PubMed Central

    2013-01-01

    Background Breastfeeding is a leading cause of infant HIV-1 infection in the developing world, yet only a minority of infants exposed to HIV-1 via breastfeeding become infected. As a genetic bottleneck severely restricts the number of postnatally-transmitted variants, genetic or phenotypic properties of the virus Envelope (Env) could be important for the establishment of infant infection. We examined the efficiency of virologic functions required for initiation of infection in the gastrointestinal tract and the neutralization sensitivity of HIV-1 Env variants isolated from milk of three postnatally-transmitting mothers (n=13 viruses), five clinically-matched nontransmitting mothers (n=16 viruses), and seven postnatally-infected infants (n = 7 postnatally-transmitted/founder (T/F) viruses). Results There was no difference in the efficiency of epithelial cell interactions between Env virus variants from the breast milk of transmitting and nontransmitting mothers. Moreover, there was similar efficiency of DC-mediated trans-infection, CCR5-usage, target cell fusion, and infectivity between HIV-1 Env-pseudoviruses from nontransmitting mothers and postnatal T/F viruses. Milk Env-pseudoviruses were generally sensitive to neutralization by autologous maternal plasma and resistant to breast milk neutralization. Infant T/F Env-pseudoviruses were equally sensitive to neutralization by broadly-neutralizing monoclonal and polyclonal antibodies as compared to nontransmitted breast milk Env variants. Conclusion Postnatally-T/F Env variants do not appear to possess a superior ability to interact with and cross a mucosal barrier or an exceptional resistance to neutralization that define their capability to initiate infection across the infant gastrointestinal tract in the setting of preexisting maternal antibodies. PMID:23305422

  12. Histone variants: dynamic punctuation in transcription

    PubMed Central

    Weber, Christopher M.; Henikoff, Steven

    2014-01-01

    Eukaryotic gene regulation involves a balance between packaging of the genome into nucleosomes and enabling access to regulatory proteins and RNA polymerase. Nucleosomes are integral components of gene regulation that restrict access to both regulatory sequences and the underlying template. Whereas canonical histones package the newly replicated genome, they can be replaced with histone variants that alter nucleosome structure, stability, dynamics, and, ultimately, DNA accessibility. Here we consider how histone variants and their interacting partners are involved in transcriptional regulation through the creation of unique chromatin states. PMID:24696452

  13. Rare and Common Variants: Twenty arguments

    PubMed Central

    Gibson, Greg

    2015-01-01

    Genome-wide association studies have greatly improved our understanding of the genetic basis of disease risk. The fact that they tend not to identify more than a fraction of the specific causal loci has led to divergence of opinion over whether most of the variance is hidden as numerous rare variants of large effect, or common variants of very small effect. Here I review 20 arguments for and against each of these models of the genetic basis of complex traits, and conclude that both classes of effect can be reconciled readily. PMID:22251874

  14. 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

  15. Atlas of nuclear medicine artifacts and variants

    SciTech Connect

    Yun Ryo, U.; Pinsky, S.; Bekerman, C.

    1985-01-01

    Atlas of Nuclear Medicine Artifacts and Variants is a guide to interpretation of nuclear images. Both common and uncommon problems that can confuse the nuclear physician or radiologist reading the images are illustrated. The authors have assembled an atlas comprising approximately 200 cases of variants and artifacts in images of the brain, lung, heart, liver, spleen, biliary system, vascular system, and thyroid gland. There is also a section of tumor and infectious disease imaging. Some of the cases include radiographs, CT, and ultrasonograms to correlate or verify the findings of nuclear medicine images where appropriate.

  16. Hypoxia-Induced Expression of VEGF Splice Variants and Protein in Four Retinal Cell Types

    PubMed Central

    Watkins, William M.; McCollum, Gary W.; Savage, Sara R.; Capozzi, Megan E.; Penn, John S.; Morrison, David G.

    2014-01-01

    The purpose of this study was to investigate the hypoxia-induced Vegf120, Vegf164 and Vegf188 mRNA expression profiles in rat Müller cells (MC), astrocytes, retinal pigmented epithelial cells (RPE) and retinal microvascular endothelial cells (RMEC) and correlate these findings to VEGF secreted protein. Cultured cells were exposed to normoxia or hypoxia. Total RNA was isolated from cell lysates and Vegf splice variant mRNA copy numbers were assayed by a validated qRT-PCR external calibration curve method. mRNA copy numbers were normalized to input total RNA. Conditioned medium was collected from cells and assayed for total VEGF protein by ELISA. Hypoxia increased total Vegf mRNA and secreted protein in all the retinal cell types, with the highest levels observed in MC and astrocytes ranking second. Total Vegf mRNA levels in hypoxic RPE and RMEC were comparable; however, the greatest hypoxic induction of each Vegf splice variant mRNA was observed in RMEC. RPE and RMEC ranked 3rd and 4th respectively, in terms of secreted total VEGF protein in hypoxia. The Vegf120, Vegf164 and Vegf188 mRNA splice variants were all increased in hypoxic cells compared to normoxic controls. In normoxia, the relative Vegf splice variant mRNA levels ranked from highest to lowest for each cell type were Vegf164>Vegf120>Vegf188. Hypoxic induction did not alter this ranking, although it did favor an increased stoichiometry of Vegf164 mRNA over the other two splice variants. MC and astrocytes are likely to be the major sources of total Vegf, and Vegf164 splice variant mRNAs, and VEGF protein in retinal hypoxia. PMID:24076411

  17. Isolated lichen planus of lower lip: a case report.

    PubMed

    Samal, Dillip Kumar; Behera, Ganakalyan; Gupta, Vikas; Majumdar, Kaushik; Khurana, Ujjawal

    2015-03-01

    Lichen planus is an idiopathic inflammatory condition, which may involve mucosa of the oral cavity, gastrointestinal tract, larynx or the cutaneous surface either in isolation or in combinations. Mucosal lichen planus is more common than the cutaneous variant. Isolated lip involvement is very rare and should be differentiated from other similar leukoplakic lesions. We are reporting a rare case of oral lichen planus in an elderly male that was exclusively localised to the lower lip. PMID:25621274

  18. Guidelines for investigating causality of sequence variants in human disease

    PubMed Central

    MacArthur, D. G.; Manolio, T. A.; Dimmock, D. P.; Rehm, H. L.; Shendure, J.; Abecasis, G. R.; Adams, D. R.; Altman, R. B.; Antonarakis, S. E.; Ashley, E. A.; Barrett, J. C.; Biesecker, L. G.; Conrad, D. F.; Cooper, G. M.; Cox, N. J.; Daly, M. J.; Gerstein, M. B.; Goldstein, D. B.; Hirschhorn, J. N.; Leal, S. M.; Pennacchio, L. A.; Stamatoyannopoulos, J. A.; Sunyaev, S. R.; Valle, D.; Voight, B. F.; Winckler, W.; Gunter, C.

    2014-01-01

    The discovery of rare genetic variants is accelerating, and clear guidelines for distinguishing disease-causing sequence variants from the many potentially functional variants present in any human genome are urgently needed. Without rigorous standards we risk an acceleration of false-positive reports of causality, which would impede the translation of genomic research findings into the clinical diagnostic setting and hinder biological understanding of disease. Here we discuss the key challenges of assessing sequence variants in human disease, integrating both gene-level and variant-level support for causality. We propose guidelines for summarizing confidence in variant pathogenicity and highlight several areas that require further resource development. PMID:24759409

  19. Characterisation of PCV2 isolates from Spain, Germany and France

    Microsoft Academic Search

    Annette Mankertz; Mariano Domingo; Josep M Folch; Pierre LeCann; André Jestin; Joaquim Segalés; Barbara Chmielewicz; Juan Plana-Durán; Dirk Soike

    2000-01-01

    The new isolated circovirus variant PCV-2 is discussed to be the etiological agent of a new emerging swine disease with a variable morbidity and high lethality, postweaning multisystemic wasting syndrome (PMWS). PMWS has been diagnosed in North America and West Europe. Clinical signs include dyspnea, loss of weight, lymph node enlargement and lymphocyte depletion in lymphoid tissues. This report describes

  20. PIN1 gene variants in Alzheimer's disease

    PubMed Central

    2009-01-01

    Background Peptidyl-prolyl isomerase, NIMA-interacting 1 (PIN1) plays a significant role in the brain and is implicated in numerous cellular processes related to Alzheimer's disease (AD) and other neurodegenerative conditions. There are confounding results concerning PIN1 activity in AD brains. Also PIN1 genetic variation was inconsistently associated with AD risk. Methods We performed analysis of coding and promoter regions of PIN1 in early- and late-onset AD and frontotemporal dementia (FTD) patients in comparison with healthy controls. Results Analysis of eighteen PIN1 common polymorphisms and their haplotypes in EOAD, LOAD and FTD individuals in comparison with the control group did not reveal their contribution to disease risk. In six unrelated familial AD patients four novel PIN1 sequence variants were detected. c.58+64C>T substitution that was identified in three patients, was located in an alternative exon. In silico analysis suggested that this variant highly increases a potential affinity for a splicing factor and introduces two intronic splicing enhancers. In the peripheral leukocytes of one living patient carrying the variant, a 2.82 fold decrease in PIN1 expression was observed. Conclusion Our data does not support the role of PIN1 common polymorphisms as AD risk factor. However, we suggest that the identified rare sequence variants could be directly connected with AD pathology, influencing PIN1 splicing and/or expression. PMID:19909517

  1. Psychiatric misdiagnoses in Dandy-Walker variant.

    PubMed

    Blaettner, C; Pfaffenberger, N M; Cartes-Zumelzu, F; Hofer, A

    2015-08-01

    Cases of intellectual impairment and aberrant behavior in patients with cerebellar diseases have been described since the early nineteenth century. Here, we report on a patient suffering from Dandy-Walker variant who presented with symptoms of obsessive compulsive disorder and delusional disorder. The current findings emphasize the potential relevance of focal cerebellar lesions as organic correlates of these disorders. PMID:25058305

  2. DISCRETE VARIANTS OF EVENING GROSBEAK FLIGHT CALLS

    Microsoft Academic Search

    Kendra Sewall; Rodd Kelsey; Thomas P. Hahn

    2004-01-01

    We describe four discrete variants of the frequency-modulated flight calls of Evening Grosbeaks (Coccothraustes vespertinus) in the United States and southwestern Canada. Each call type is aurally and spectrographically distinct, and individual birds appear to produce only one call type. The observed geograph- ic distributions of these call types are roughly concor- dant with described subspecies ranges. The long-term geographic

  3. Fuzzy Turing Machines: Variants and Universality

    Microsoft Academic Search

    Yongming Li

    2008-01-01

    In this paper, we study some variants of fuzzy Turing machines (FTMs) and universal FTM. First, we give several formulations of FTMs, including, in particular, deterministic FTMs (DFTMs) and nondeterministic FTMs (NFTMs). We then show that DFTMs and NFTMs are not equivalent as far as the power of recognizing fuzzy languages is concerned. This contrasts sharply with classical TMs. Second,

  4. Discovery of variants unmasked by hemizygous deletions

    PubMed Central

    Hochstenbach, Ron; Poot, Martin; Nijman, Isaac J; Renkens, Ivo; Duran, Karen J; van'T Slot, Ruben; van Binsbergen, Ellen; van der Zwaag, Bert; Vogel, Maartje J; Terhal, Paulien A; Ploos van Amstel, Hans Kristian; Kloosterman, Wigard P; Cuppen, Edwin

    2012-01-01

    Array-based genome-wide segmental aneuploidy screening detects both de novo and inherited copy number variations (CNVs). In sporadic patients de novo CNVs are interpreted as potentially pathogenic. However, a deletion, transmitted from a healthy parent, may be pathogenic if it overlaps with a mutated second allele inherited from the other healthy parent. To detect such events, we performed multiplex enrichment and next-generation sequencing of the entire coding sequence of all genes within unique hemizygous deletion regions in 20 patients (1.53?Mb capture footprint). Out of the detected 703 non-synonymous single-nucleotide variants (SNVs), 8 represented variants being unmasked by a hemizygous deletion. Although evaluation of inheritance patterns, Grantham matrix scores, evolutionary conservation and bioinformatic predictions did not consistently indicate pathogenicity of these variants, no definitive conclusions can be drawn without functional validation. However, in one patient with severe mental retardation, lack of speech, microcephaly, cheilognathopalatoschisis and bilateral hearing loss, we discovered a second smaller deletion, inherited from the other healthy parent, resulting in loss of both alleles of the highly conserved heat shock factor binding protein 1 (HSBP1) gene. Conceivably, inherited deletions may unmask rare pathogenic variants that may exert a phenotypic impact through a recessive mode of gene action. PMID:22258528

  5. 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…

  6. 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.

  7. Truncated variants of apolipoprotein B cause hypobetalipoproteinaemia

    SciTech Connect

    Collins, D.R.; Knott, T.J.; Pease, R.J.; Powell, L.M.; Wallis, S.C.; Robertson, S.; Pullinger, C.R.; Lloyd, K.; Miller, N.E.; Muller, D.; Scott, J. (MRC Clinical Research Centre, Harrow (England)); Humphries, S.E.; Talmud, P.J. (Charing Cross Sunley Research Centre, London (England)); Milne, R.W.; Marcel, Y.L. (Clinical Research Institute of Montreal, Quebec (Canada))

    1988-09-12

    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 the authors describe mutations of the apo-B gene that cause two different truncated variants of apo-B in unrelated individuals with hypobetalipoproteinaemia. One variant is predicted to be 1,799 amino acids long and arises from deletion of a single nucleotide (G) from leucine codon 1,794. This protein was found at low levels in very low density and low density lipoprotein fractions in the blood. The second, shorter variant is caused by mutation of a CpG dinucleotide in arginine codon 1,306 converting it to a stop codon and predicting a protein of 1,305 residues. The differences in size and behavior 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.

  8. Novel Streptococcus infantarius subsp. infantarius variants harboring lactose metabolism genes homologous to Streptococcus thermophilus.

    PubMed

    Jans, Christoph; Gerber, Andrea; Bugnard, Joséphine; Njage, Patrick Murigu Kamau; Lacroix, Christophe; Meile, Leo

    2012-08-01

    Streptococcus infantarius subsp. infantarius belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC) commonly associated with human and animal infections. We elucidated the lactose metabolism of S. infantarius subsp. infantarius predominant in African fermented milk products. S. infantarius subsp. infantarius isolates (n = 192) were identified in 88% of spontaneously fermented camel milk suusac samples (n = 24) from Kenya and Somalia at log?? 8.2-8.5 CFU mL?¹. African S. infantarius isolates excreted stoichiometric amounts of galactose when grown on lactose, exhibiting a metabolism similar to Streptococcus thermophilus and distinct from their type strain. African S. infantarius subsp. infantarius CJ18 harbors a regular gal operon with 99.7-100% sequence identity to S. infantarius subsp. infantarius ATCC BAA-102(T) and a gal-lac operon with 91.7-97.6% sequence identity to S. thermophilus, absent in all sequenced SBSEC strains analyzed. The expression and functionality of lacZ was demonstrated in a ?-galactosidase assay. The gal-lac operon was identified in 100% of investigated S. infantarius isolates (n = 46) from suusac samples and confirmed in Malian fermented cow milk isolates. The African S. infantarius variant potentially evolved through horizontal gene transfer of an S. thermophilus-homologous lactose pathway. Safety assessments are needed to identify any putative health risks of this novel S. infantarius variant. PMID:22475940

  9. 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

  10. Renal hypodysplasia associates with a WNT4 variant that causes aberrant canonical WNT signaling.

    PubMed

    Vivante, Asaf; Mark-Danieli, Michal; Davidovits, Miriam; Harari-Steinberg, Orit; Omer, Dorit; Gnatek, Yehudit; Cleper, Roxana; Landau, Daniel; Kovalski, Yael; Weissman, Irit; Eisenstein, Israel; Soudack, Michalle; Wolf, Haike Reznik; Issler, Naomi; Lotan, Danny; Anikster, Yair; Dekel, Benjamin

    2013-03-01

    Abnormal differentiation of the renal stem/progenitor pool into kidney tissue can lead to renal hypodysplasia (RHD), but the underlying causes of RHD are not well understood. In this multicenter study, we identified 20 Israeli pedigrees with isolated familial, nonsyndromic RHD and screened for mutations in candidate genes involved in kidney development, including PAX2, HNF1B, EYA1, SIX1, SIX2, SALL1, GDNF, WNT4, and WT1. In addition to previously reported RHD-causing genes, we found that two affected brothers were heterozygous for a missense variant in the WNT4 gene. Functional analysis of this variant revealed both antagonistic and agonistic canonical WNT stimuli, dependent on cell type. In HEK293 cells, WNT4 inhibited WNT3A induced canonical activation, and the WNT4 variant significantly enhanced this inhibition of the canonical WNT pathway. In contrast, in primary cultures of human fetal kidney cells, which maintain WNT activation and more closely represent WNT signaling in renal progenitors during nephrogenesis, this mutation caused significant loss of function, resulting in diminished canonical WNT/?-catenin signaling. In conclusion, heterozygous WNT4 variants are likely to play a causative role in renal hypodysplasia. PMID:23520208

  11. 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...

  12. Mouse p63 variants and chondrogenesis

    PubMed Central

    Gu, Junxia; Lu, Yaojuan; Qiao, Longwei; Ran, Deyuan; Li, Na; Cao, Hong; Gao, Yan; Zheng, Qiping

    2013-01-01

    As a critical member of the p53 family of transcription factors, p63 has been implicated a role in development than in tumor formation, because p63 is seldom mutated in human cancers, while p63 null mice exhibit severe developmental abnormalities without increasing cancer susceptibility. Notably, besides the major epithelial and cardiac defect, p63 deficient mice show severe limb and craniofacial abnormalities. In addition, humans with p63 mutations also show severe limb and digit defects, suggesting a putative role of p63 in skeletal development. There are eight p63 variants which encode for the TAp63 and ?Np63 isoforms by alternative promoters. How these isoforms function during skeletal development is currently largely unknown. Our recent transgenic studies suggest a role of TAP63?, but not ?NP63?, during embryonic long bone development. However, the moderate skeletal phenotypes in the TAP63? transgenic mice suggest requirement of additional p63 isoform(s) for the limb defects in p63 null mice. Here, we report analysis of mouse p63 variants in MCT and ATDC5 cells, two cell models undergo hypertrophic differentiation and mimic the process of endochondral bone formation upon growth arrest or induction. We detected increased level of p63 variants in hypertrophic MCT cells by regular RT-PCR analysis. Further analysis by qRT-PCR, we detected significantly upregulated level of ? variant (p<0.05), but not ? or ? variant (p>0.05), in hypertrophic MCT cells than in proliferative MCT cells. Moreover, we detected upregulated TAP63? in ATDC5 cells undergoing hypertrophic differentiation. Our results suggest that TAp63? plays a positive role during endochondral bone formation. PMID:24294373

  13. 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

  14. Characterization of the Two Intra-Individual Sequence Variants in the 18S rRNA Gene in the Plant Parasitic Nematode, Rotylenchulus reniformis

    PubMed Central

    Nyaku, Seloame T.; Sripathi, Venkateswara R.; Kantety, Ramesh V.; Gu, Yong Q.; Lawrence, Kathy; Sharma, Govind C.

    2013-01-01

    The 18S rRNA gene is fundamental to cellular and organismal protein synthesis and because of its stable persistence through generations it is also used in phylogenetic analysis among taxa. Sequence variation in this gene within a single species is rare, but it has been observed in few metazoan organisms. More frequently it has mostly been reported in the non-transcribed spacer region. Here, we have identified two sequence variants within the near full coding region of 18S rRNA gene from a single reniform nematode (RN) Rotylenchulus reniformis labeled as reniform nematode variant 1 (RN_VAR1) and variant 2 (RN_VAR2). All sequences from three of the four isolates had both RN variants in their sequences; however, isolate 13B had only RN variant 2 sequence. Specific variable base sites (96 or 5.5%) were found within the 18S rRNA gene that can clearly distinguish the two 18S rDNA variants of RN, in 11 (25.0%) and 33 (75.0%) of the 44 RN clones, for RN_VAR1 and RN_VAR2, respectively. Neighbor-joining trees show that the RN_VAR1 is very similar to the previously existing R. reniformis sequence in GenBank, while the RN_VAR2 sequence is more divergent. This is the first report of the identification of two major variants of the 18S rRNA gene in the same single RN, and documents the specific base variation between the two variants, and hypothesizes on simultaneous co-existence of these two variants for this gene. PMID:23593343

  15. Variant Influenza Associated with Live Animal Markets, Minnesota.

    PubMed

    Choi, M J; Morin, C A; Scheftel, J; Vetter, S M; Smith, K; Lynfield, R

    2014-06-16

    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

  16. GenOVa: a computer program to generate orientational variants

    PubMed Central

    Cayron, Cyril

    2007-01-01

    A computer program called GenOVa, written in Python, calculates the orientational variants, the operators (special types of misorientations between variants) and the composition table associated with a groupoid structure. The variants can be represented by three-dimensional shapes or by pole figures. PMID:19461844

  17. Spatially Variant Morphological Image Processing: Theory and Applications

    E-print Network

    Bouaynaya, Nidhal

    Spatially Variant Morphological Image Processing: Theory and Applications N. Bouaynaya and D under Euclidean translations. An interest in the extension of mathematical morphology to spatially-variant (image) processing. This paper presents a general theory of spatially-variant mathematical morphology

  18. Biological Sciences: Frequencies of Amylase Variants in Drosophila melanogaster

    Microsoft Academic Search

    G. de Jong; A. J. W. Hoorn; G. E. W. Thörig; W. Scharloo

    1972-01-01

    THE selective significance of enzyme polymorphisms remains unsettled1,2. The frequencies of some enzyme variants are correlated with environmental factors3, which might cause frequency changes by acting on closely linked genes. We therefore studied amylase variants in Drosophila melanogaster. A major function of amylase in Drosophila is in the digestion of starch. Genetical and physiological investigations on amylase variants were made

  19. Molecular epidemiology of hepatitis B virus vaccine variants in Singapore

    Microsoft Academic Search

    Chong-Jin Oon; Gek-Keow Lim; Zhao Ye; Kee-Tai Goh; Kim-Leong Tan; Sui-Lan Yo; Elaine Hopes; Tim J. Harrison; Arie J. Zuckerman

    1995-01-01

    Perinatal infection with variants of hepatitis B virus occurs despite combined immunoprophylaxis with hepatitis B immunoglobulin and currently licensed plasma-derived and recombinant yeast hepatitis B vaccines. Several variants have been detected during a large study of infants born to carrier mothers in Singapore. The most frequent variant was a virus in which a single amino acid substitution Gly to Arg

  20. 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…

  1. MARS Attacks! Preliminary Cryptanalysis of Reduced-Round MARS Variants

    E-print Network

    Schneier, Bruce

    MARS Attacks! Preliminary Cryptanalysis of Reduced-Round MARS Variants John Kelsey and Bruce,schneier}@counterpane.com Abstract. In this paper, we discuss ways to attack various reduced- round variants of MARS. We consider cryptanalysis of two reduced- round variants of MARS: MARS with the full mixing layers but fewer core rounds

  2. MARS Attacks! Preliminary Cryptanalysis of ReducedRound MARS Variants

    E-print Network

    Schneier, Bruce

    MARS Attacks! Preliminary Cryptanalysis of Reduced­Round MARS Variants John Kelsey and Bruce,schneier}@counterpane.com Abstract. In this paper, we discuss ways to attack various reduced­ round variants of MARS. We consider cryptanalysis of two reduced­ round variants of MARS: MARS with the full mixing layers but fewer core rounds

  3. Slow alpha variant during REM sleep.

    PubMed

    Gelisse, P; Crespel, A

    2008-02-01

    REM sleep resembles wakefulness or drowsiness. The pattern can be low-voltage, or else alpha-like. Alpha frequencies are present only during the tonic phases of REM sleep and, compared to wakefulness tracings, alpha activities are slightly slower by 1-2 Hz and are more monomorphic. The slow alpha-variant rhythm or subharmonic alpha pattern consists of rhythmic notched theta waves. It shares the same topography and reactivity with the alpha rhythm. We report its presence during the tonic phases of REM sleep without any modification in its morphology in the first case. In the second case, its morphology was similar to awakening but with slower amplitude. No alpha frequencies were found in REM sleep but only its slow alpha variant. This study provides evidence that REM sleep is a stage of sleep that contains rhythms similar to those seen during wakefulness and drowsiness. PMID:18329545

  4. Alphavirus Mutator Variants Present Host-Specific Defects and Attenuation in Mammalian and Insect Models

    PubMed Central

    Rozen-Gagnon, Kathryn; Stapleford, Kenneth A.; Mongelli, Vanesa; Blanc, Hervé; Failloux, Anna-Bella; Saleh, Maria-Carla; Vignuzzi, Marco

    2014-01-01

    Arboviruses cycle through both vertebrates and invertebrates, which requires them to adapt to disparate hosts while maintaining genetic integrity during genome replication. To study the genetic mechanisms and determinants of these processes, we use chikungunya virus (CHIKV), a re-emerging human pathogen transmitted by the Aedes mosquito. We previously isolated a high fidelity (or antimutator) polymerase variant, C483Y, which had decreased fitness in both mammalian and mosquito hosts, suggesting this residue may be a key molecular determinant. To further investigate effects of position 483 on RNA-dependent RNA-polymerase (RdRp) fidelity, we substituted every amino acid at this position. We isolated novel mutators with decreased replication fidelity and higher mutation frequencies, allowing us to examine the fitness of error-prone arbovirus variants. Although CHIKV mutators displayed no major replication defects in mammalian cell culture, they had reduced specific infectivity and were attenuated in vivo. Unexpectedly, mutator phenotypes were suppressed in mosquito cells and the variants exhibited significant defects in RNA synthesis. Consequently, these replication defects resulted in strong selection for reversion during infection of mosquitoes. Since residue 483 is conserved among alphaviruses, we examined the analogous mutations in Sindbis virus (SINV), which also reduced polymerase fidelity and generated replication defects in mosquito cells. However, replication defects were mosquito cell-specific and were not observed in Drosophila S2 cells, allowing us to evaluate the potential attenuation of mutators in insect models where pressure for reversion was absent. Indeed, the SINV mutator variant was attenuated in fruit flies. These findings confirm that residue 483 is a determinant regulating alphavirus polymerase fidelity and demonstrate proof of principle that arboviruses can be attenuated in mammalian and insect hosts by reducing fidelity. PMID:24453971

  5. A phylogenetic reconstruction of the epidemiological history of canine rabies virus variants in Colombia.

    PubMed

    Hughes, Gareth J; Páez, Andrés; Bóshell, Jorge; Rupprecht, Charles E

    2004-03-01

    Historically, canine rabies in Colombia has been caused by two geographically distinct canine variants of rabies virus (RV) which between 1992 and 2002 accounted for approximately 95% of Colombian rabies cases. Genetic variant 1 (GV1) has been isolated up until 1997 in the Central Region and the Department of Arauca, and is now considered extinct through a successful vaccination program. Genetic variant 2 (GV2) has been isolated from the northern Caribbean Region and continues to circulate at present. Here we have analyzed two sets of sequence data based upon either a 147 nucleotide region of the glycoprotein (G) gene or a 258 nucleotide region that combines a fragment of the non-coding intergenic region and a fragment of the polymerase gene. Using both maximum likelihood (ML) and Markov chain Monte Carlo (MCMC) methods we have estimated the time of the most recent common ancestor (MRCA) of the two variants to be between 1983 and 1988. Reconstructions of the population history suggest that GV2 has been circulating in Colombia since the 1960s and that GV1 evolved as a separate lineage from GV2. Estimations of the effective population size at present show the GV2 outbreak to be approximately 20 times greater than that of GV1. Demographic reconstructions were unable to detect a decrease in population size concurrent with the elimination of GV1. We find a raised rate of nucleotide substitution for GV1 gene sequences when compared to that of GV2, although all estimates have wide confidence limits. We demonstrate that phylogenetic reconstructions and sequence analysis can be used to support incidence data from the field in the assessment of RV epidemiology. PMID:15019589

  6. Genetic Characteristics of the Coxsackievirus A24 Variant Causing Outbreaks of Acute Hemorrhagic Conjunctivitis in Jiangsu, China, 2010

    PubMed Central

    Wu, Bin; Qi, Xian; Xu, Ke; Ji, Hong; Zhu, Yefei; Tang, Fenyang; Zhou, Minghao

    2014-01-01

    During September 2010, an outbreak of acute hemorrhagic conjunctivitis reemerged in Jiangsu, three years after the nationwide epidemic in China in 2007. In total, 2409 cases were reported, 2118 of which were reported in September; 79.8% of those affected were students or teachers, with a median age of 16 years. To identify and demonstrate the genetic characteristics of the etiological agent, 52 conjunctival swabs were randomly collected from four different cities. After detection and isolation, 43 patients were positive for coxsackievirus A24 variant according to PCR and 20 according to culture isolation. Neither adenovirus nor EV70 was detected. A phylogenetic study of the complete 3Cpro and VP1 regions showed that the Jiangsu isolates clustered into a new lineage, GIV-C5, with two uniform amino-acid mutations that distinguished them from all previous strains. Another new cluster, GIV-C4, formed by Indian isolates from 2007 and Brazilian isolates from 2009, was also identified in this study. Interestingly, our isolates shared greatest homology with the GIV-C4 strains, not with the isolates that were responsible for the nationwide acute hemorrhagic conjunctivitis epidemic in China in 2007. Although all our isolates were closely related, they could be differentiated into two subclusters within GIV-C5. In conclusion, our study suggests that a new cluster of coxsackievirus A24 variant that had already evolved into diverse strains was associated with the acute hemorrhagic conjunctivitis outbreaks in Jiangsu in September 2010. These viruses might have originated from the virus isolated in India in 2007, rather than from the epidemic strains isolated in China in 2007. PMID:24475191

  7. Characterization of variant forms of organophosphorus hydrolase

    E-print Network

    Rowe, Claire E.

    2013-02-22

    Colony Screening and Its Limitations The proposed colony screening procedure was designed to take advantage of the fact that one of the products of enzymatic degradation of paraoxon, p-nitrophenol, has a yellow color. This allows for simple visual... monitoring of the reaction by monitoring the appearance of p-nitrophenol's yellow color. The screening procedure was designed to identify variant forms of OPH with increased stability. Following transfer to a nitrocellulose membrane the enzyme could...

  8. Oral fibrolipoma: a rare histological variant.

    PubMed

    Pereira, Treville; Shetty, Subraj; Sapdhare, Swati; Tamgadge, Avinash

    2014-01-01

    Lipomas are benign soft tissue mesenchymal neoplasms. Fibrolipoma is a histological variant of lipoma that mostly affects the buccal mucosa and causes functional and cosmetic disabilities. The diagnosis and differentiation of fibrolipoma with clinically similar lesions such as fibroma and pleomorphic adenoma is very essential for a correct treatment plan and complete follow-up. This article presents a case of a 35-year-old female with a fibrolipoma on the lingual marginal gingiva of the mandibular left third molar. PMID:25511072

  9. Dot-Size Variant Visual Cryptography

    Microsoft Academic Search

    Jonathan Weir; Wei-Qi Yan

    2009-01-01

    In this paper, we propose a scheme by which a secure random share can be generated using a dot-size variant form of visual\\u000a cryptography (VC). We generate two extended style VC shares, when the share is viewed, it appears as a normal random visual\\u000a cryptography share. However, this scheme is designed with spatial filtering in mind, this is the dot-size

  10. Structural characteristics of aramid fibre variants

    Microsoft Academic Search

    M. G. Dobb; R. M. Robson

    1990-01-01

    Recently new types of high-performance aramid fibre based on poly(p-phenylene terephthalamide) have been developed. This paper reports on their very different tensile behaviour and structural character as revealed by electron microscope and X-ray diffraction studies. The relationship between mechanical performance and structure of the variants is explored in detail, and performance-limiting factors are identified with a view to understanding how

  11. Genetics in psychiatry: Common variant association studies

    E-print Network

    Buxbaum, Joseph D; Baron-Cohen, Simon; Devlin, Bernie

    2010-03-25

    EDITORIAL Open Access Genetics in psychiatry: common variant association studies Joseph D Buxbaum1*, Simon Baron-Cohen2, Bernie Devlin3 Abstract Many psychiatric conditions and traits are associated with significant heritability. Genetic risk... , Propping P, Vasilescu C, Maier W, Rietschel M, Zammit S, Schumacher J, Quinn EM, Schulze TG, Williams NM, Giegling I, Iwata N, Ikeda M, Darvasi A, Shifman S, He L, Duan J, Sanders AR, Levinson DF, Gejman PV, Cichon S, Nöthen MM, Gill M, Corvin A, Rujescu D...

  12. A Practical, Typed Variant Object Model

    E-print Network

    Smith, Scott F.

    object a { 2 } 1 let a = fun msg -> 2 match msg with 3 . . . #12;Variant-Based Encoding (Scala) (OCaml) 1 object a { 2 val v = 5 3 } 1 let v = ref 5 in 2 let a = fun msg -> 3 match msg with 4 . . . Fields+v } 5 def foo(x:Unit ){} 6 } 1 let v = ref 5 in 2 let a = fun msg -> 3 match msg with 4 | `mth (self ,x

  13. Human Prion Diseases with Variant Prion Protein

    Microsoft Academic Search

    Tetsuyuki Kitamoto; Jun Tateishi

    1994-01-01

    Recent molecular genetic studies revealed that the human prion protein (PrP) gene has a large repertoire of polymorphisms and mutations. Each variant PrP seems to correspond to a distinct type of prion diseases. We report herein that it is useful to classify prion diseases into plaque type or non-plaque type, based on the distribution of PrP in the central nervous

  14. New Genetic Variants Improve Personalized Breast Cancer Diagnosis

    PubMed Central

    Liu, Jie; Page, David; Peissig, Peggy; McCarty, Catherine; Onitilo, Adedayo A.; Trentham-Dietz, Amy; Burnside, Elizabeth

    2014-01-01

    Recent large-scale genome-wide association studies (GWAS) have identified a number of new genetic variants associated with breast cancer. However, the degree to which these genetic variants improve breast cancer diagnosis in concert with mammography remains unknown. We conducted a case-control study and collected mammography features and 77 genetic variants which reflect the state of the art GWAS findings on breast cancer. A naïve Bayes model was developed on the mammography features and these genetic variants. We observed that the incorporation of the genetic variants significantly improved breast cancer diagnosis based on mammographic findings. PMID:25717406

  15. Stability and Cu(II) Binding of Prion Protein Variants Related to Inherited Human Prion Diseases

    PubMed Central

    Cereghetti, Grazia M.; Schweiger, Arthur; Glockshuber, Rudi; Van Doorslaer, Sabine

    2003-01-01

    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

  16. 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

  17. 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

  18. Negative feedback buffers effects of regulatory variants.

    PubMed

    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

  19. Splicing analysis of 14 BRCA1 missense variants classifies nine variants as pathogenic.

    PubMed

    Ahlborn, Lise B; Dandanell, Mette; Steffensen, Ane Y; Jønson, Lars; Nielsen, Finn C; Hansen, Thomas V O

    2015-04-01

    Pathogenic germline mutations in the BRCA1 gene predispose carriers to early onset breast and ovarian cancer. Clinical genetic screening of BRCA1 often reveals variants with uncertain clinical significance, complicating patient and family management. Therefore, functional examinations are urgently needed to classify whether these uncertain variants are pathogenic or benign. In this study, we investigated 14 BRCA1 variants by in silico splicing analysis and mini-gene splicing assay. All 14 alterations were missense variants located within the BRCT domain of BRCA1 and had previously been examined by functional analysis at the protein level. Results from a validated mini-gene splicing assay indicated that nine BRCA1 variants resulted in splicing aberrations leading to truncated transcripts and thus can be considered pathogenic (c.4987A>T/p.Met1663Leu, c.4988T>A/p.Met1663Lys, c.5072C>T/p.Thr1691Ile, c.5074G>C/p.Asp1692His, c.5074G>A/p.Asp1692Asn, c.5074G>T/p.Asp1692Tyr, c.5332G>A/p.Asp1778Asn, c.5332G>T/p.Asp1778Tyr, and c.5408G>C/p.Gly1803Ala), whereas five BRCA1 variants had no effect on splicing (c.4985T>C/p.Phe1662Ser, c.5072C>A/p.Thr1691Lys, c.5153G>C/p.Trp1718Ser, c.5154G>T/p.Trp1718Cys, and c.5333A>G/p.Asp1778Gly). Eight of the variants having an effect on splicing (c.4987A>T/p.Met1663Leu, c.4988T>A/p.Met1663Lys, c.5074G>C/p.Asp1692His, c.5074G>A/p.Asp1692Asn, c.5074G>T/p.Asp1692Tyr, c.5332G>A/p.Asp1778Asn, c.5332G>T/p.Asp1778Tyr, and c.5408G>C/p.Gly1803Ala) were previously determined to have no or an uncertain effect on the protein level, whereas one variant (c.5072C>T/p.Thr1691Ile) were shown to have a strong effect on the protein level as well. In conclusion, our study emphasizes that in silico splicing prediction and mini-gene splicing analysis are important for the classification of BRCA1 missense variants located close to exon/intron boundaries. PMID:25724305

  20. Detecting Novel Genetic Variants Associated with Isoniazid-Resistant Mycobacterium tuberculosis

    PubMed Central

    Chan, Maurice K. L.; Ong, Danny C. T.; Tongyoo, Pumipat; Wong, Sin-Yew; Lee, Ann S. G.

    2014-01-01

    Background Isoniazid (INH) is a highly effective antibiotic central for the treatment of Mycobacterium tuberculosis (MTB). INH-resistant MTB clinical isolates are frequently mutated in the katG gene and the inhA promoter region, but 10 to 37% of INH-resistant clinical isolates have no detectable alterations in currently known gene targets associated with INH-resistance. We aimed to identify novel genes associated with INH-resistance in these latter isolates. Methodology/Principal Findings INH-resistant clinical isolates of MTB were pre-screened for mutations in the katG, inhA, kasA and ndh genes and the regulatory regions of inhA and ahpC. Twelve INH-resistant isolates with no mutations, and 17 INH-susceptible MTB isolates were subjected to whole genome sequencing. Phylogenetically related variants and synonymous mutations were excluded and further analysis revealed mutations in 60 genes and 4 intergenic regions associated with INH-resistance. Sanger sequencing verification of 45 genes confirmed that mutations in 40 genes were observed only in INH-resistant isolates and not in INH-susceptible isolates. The ratios of non-synonymous to synonymous mutations (dN/dS ratio) for the INH-resistance associated mutations identified in this study were 1.234 for INH-resistant and 0.654 for INH-susceptible isolates, strongly suggesting that these mutations are indeed associated with INH-resistance. Conclusion The discovery of novel targets associated with INH-resistance described in this study may potentially be important for the development of improved molecular detection strategies. PMID:25025225

  1. Characterisation of Toxoplasma gondii isolates using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) of the non-coding Toxoplasma gondii ( TGR)-gene sequences

    Microsoft Academic Search

    Estrid Høgdall; Jens Vuust; Peter Lind; Eskild Petersen

    2000-01-01

    The Toxoplasma gondii (TGR) genes constitute a family of non-coding sequences, three of which have been previously described as possible tools for typing of Toxoplasma gondii isolates. We obtained new isolates of T. gondii from domestic and wild animals, and used these to evaluate the possibility of using TGR gene variants as markers to distinguish among T. gondii isolates from

  2. Real-time PCR for differentiation of F18 variants among enterotoxigenic and Shiga toxin-producing Escherichia coli from piglets with diarrhoea and oedema disease.

    PubMed

    Byun, Jae-Won; Jung, Byeong Yeal; Kim, Ha-Young; Fairbrother, John M; Lee, Myoung-Heon; Lee, Wan-Kyu

    2013-11-01

    One-step real-time PCR using one set of primers and four probes was developed for differentiation of F18 variants (F18 common, F18ab, F18ac, F18new variant) of enterotoxigenic (ETEC) and Shiga toxin-producing (STEC) Escherichia coli from piglets with diarrhoea and oedema disease. The limits of detection for F18common, F18ab, F18ac, and F18new variant were 10(7), 10(7), 10(5) and 10(7)colony forming units/g faeces, respectively. Of 94 Korean isolates of E. coli encoding F18, 70 were F18ac (43 STEC/ETEC, 4 STEC and 23 ETEC), 15 were F18ab (all STEC) and nine were F18new variant (1 STEC/ETEC, 7 STEC, 1 ETEC). PMID:23992871

  3. The genetic variants of group-specific component (vitamin D-binding protein) possess different binding characteristics for immobilized Cibacron Blue 3-GA.

    PubMed Central

    Gianazza, E; Emerson, D L; Dykes, D; Arnaud, P

    1984-01-01

    The elution profiles of several variants of the Gc protein have been studied after chromatography on immobilized Cibacron Blue 3-GA. The allele products belonging to the Gcl type were retarded and eluted with a Ve/Vo at 1.5, as previously reported for the Gcl-1 phenotype [Chapuis-Cellier, Gianazza & Arnaud (1982) Biochim. Biophys. Acta 709, 353-357]. The allele products belonging to the Gc2 type were further retarded (Ve/Vo at 2.6), and both Gcl and Gc2 allele products were clearly separated in heterozygous individuals. This observation allows the isolation and purification of Gc variants in heterozygous individuals which carry the combination Gcl variant-Gc2, Gcl-Gc2 variant, or Gcl variant-Gc2 variant. In contrast, the corresponding holoproteins did not bind to the gel and were eluted in the void volume. This suggests that the interaction of Gc with immobilized Cibacron Blue 3-GA involves the binding site of the protein for 25-hydroxycholecalciferol and that the dye behaves as a 'pseudoligand' for the protein. In addition, our data suggest that the different elution profiles of the variants could reflect a different affinity of the gene products for the dye. Images Fig. 1. Fig. 2. Fig. 3. PMID:6336318

  4. Prevalence of genetic variants associated with cardiovascular disease risk and drug response in the Southern Indian population of Kerala

    PubMed Central

    Mahadevan, Lakshmi; Yesudas, Ancy; Sajesh, P. K.; Revu, S.; Kumar, Prasanna; Santhosh, Devi; Santhosh, Sam; Sashikumar, J. M.; Gopalakrishnan, V. K.; Boben, Joji; Rajesh, Changanamkandath

    2014-01-01

    BACKGROUND AND AIM: This study reports the prevalence of five clinically significant variants associated with increased risk of cardiovascular disorders, and variable responses of individuals to commonly prescribed cardiovascular drugs in a South Indian population from the state of Kerala. MATERIALS AND METHODS: Genomic DNA isolated from 100 out-patient samples from Kerala were sequenced to examine the frequency of clinically relevant polymorphisms in the genes MYBPC3 (cardiomyopathy), SLCO1B1 (statin-induced myopathy), CYP2C9, VKORC1 (response to warfarin) and CYP2C19 (response to clopidogrel). RESULTS: Our analyses revealed the frequency of a 25 bp deletion variant of MYBPC3 associated with risk of cardiomyopathy was 7%, and the SLCO1B1 “C” allele associated with risk for statin-induced myopathy was 15% in this sample group. Among the other variants associated with dose-induced toxicity of warfarin, VKORC1 (c.1639G>A), was detected at 22%, while CYP2C9*3 and CYP2C9*2 alleles were present at a frequency of 15% and 3% respectively. Significantly, the tested sample population showed high prevalence (66%) of CYP2C19*2 variant, which determines response to clopidogrel therapy. CONCLUSIONS: We have identified that certain variants associated with cardiovascular disease and related drug response in the five genes, especially those in VKORC1, CYP2C19 and MYBPC3, are highly prevalent in the Kerala population, with almost 2 times higher prevalence of CYP2C19*2 variant compared with other regions in the country. Since the variants chosen in this study have relevance in disease phenotype and/or drug response, and are detected at a higher frequency, this study is likely to encourage clinicians to perform genetic testing before prescribing therapy. PMID:25400347

  5. Geographical Distribution of the Herpes Simplex Virus Type 1 BgKL Variant in Japan Suggests Gradual Dispersion of the Virus from Shikoku Island to the Other Islands

    PubMed Central

    Ozawa, Shigeru; Eda, Hiroyuki; Hayashi, Kozaburo; Yoshino, Kamesaburo; Yanagi, Kazuo

    2006-01-01

    Restriction endonuclease fragment length polymorphism (RFLP) is useful for the epidemiological study of herpes simplex virus type 1 (HSV-1). We report here the identification of a major BglII RFLP variant of HSV-1, designated BgKL, found in 27.0% of 636 HSV-1 clinical isolates. We have also established its geographic distribution in Japan. BgKL has an unusually large BglII K fragment. SalI cleavage analyses showed that 97% of BgKL variant isolates lack both the SalI C-J and the F-J cleavage sites and have an unusually large SalI D or E fragment, and 91% of the BgKL variants lack both SalI G and H fragments. Furthermore, 96% of BgKL isolates have an unusually small KpnI M fragment. Therefore, BgKL is a marker for these five mutations in most HSV-1 isolates and is a useful HSV-1 RFLP marker. The BgKL variant was found in 59% of HSV-1 isolates from Shikoku Island, 44% of HSV-1 isolates from the Chugoku region of Honshu Island, 31% of HSV-1 isolates from Kyushu Island, 0% of HSV-1 isolates from Okinawa Island, 49% of HSV-1 isolates from Osaka, 27% of HSV-1 isolates from Shiga, 13% of HSV-1 isolates from the Chubu Region, and 9% of HSV-1 isolates from the Tohoku Region of Honshu Island. Differences in the frequency of BgKL between the Shikoku-Chugoku-Osaka area (49%) and Kyushu, between Kyushu and Okinawa, between the Shikoku-Chugoku-Osaka area and Shiga, and between Shiga and Tohoku are all statistically significant. The BgKL frequency decreases in a geographical gradient suggest that this HSV-1 variant was dispersed from Shikoku to the surrounding regions and then to more distant regions. The BgKL frequency in Tokyo was similar to the nationwide average. These are the first data to suggest a geographic and demographic dispersion pattern of HSV-1. Implications for the epidemiology and diversification of HSV-1 are discussed. PMID:16757606

  6. 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

  7. Selection of a thermostable variant of chloramphenicol acetyltransferase (Cat-86).

    PubMed

    Turner, S L; Ford, G C; Mountain, A; Moir, A

    1992-09-01

    The moderate thermophile Bacillus stearothermophilus was used as a host in which to detect more thermostable variants of the B.pumilus chloramphenicol acetyltransferase (Cat-86) protein. Seventeen mutants were isolated and detected by their ability to grow in the presence of chloramphenicol at a previously restrictive temperature (58 degrees C). The genes encoding these proteins were sequenced; all 17 mutants carried the same C to T transition that conferred an amino acid substitution of alanine by valine at position 203 of the protein sequence. The wild-type and one mutant Cat-86 protein were purified to homogeneity using affinity chromatography, and kinetic and thermal stability studies were undertaken. Both enzymes had similar sp. act. in the region of 215 U/mg, with Km values for chloramphenicol in the range 13.8-15.4 microM and for acetyl CoA in the range 13.6-15.5 microM. The A203V mutant shows greater stability than the wild-type Cat-86 protein at temperatures above 50 degrees C and appears to pass through a transition state between 48 and 50 degrees C. PMID:1438164

  8. In-vitro screening of cissus quadrangularis L. Variant ii against helicobacter pylori.

    PubMed

    Austin, Anoop; Jegadeesan, M; Gowrishankar, R

    2003-07-01

    Cissus quadrangularis L. variant II belonging to the family Vitaceae was screened for its activity Hellcobacter pylori (Hp) human isolates. Flowering and vegetative period samples were analyzed. Aqueous (hot and cold) and solvent extracts (acetone, chloroform and methanol) were screened. Among them chloroform was observed to recover bioactive principles with low MIC and MLC. MIC and MLC was 40 ?g/ml for flowering period. Whereas for vegetative period MIC was 40 ?g/ml and MLC was 40 ?g/ml respectively. Extracts from samples collected during flowering period were better than that of vegetative period. The results confirm the traditional use of the plant in PUD. PMID:22557114

  9. 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 ?-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 ?-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

  10. Human Metabotropic Glutamate Receptor 1: mRNA Distribution, Chromosome Localization and Functional Expression of Two Splice Variants

    Microsoft Academic Search

    DANIELLE STEPHAN; CHRISTELLE BON; JAMES A HOLZWARTH; MARTIN GALVAN; REBECCA M PRUSS

    1996-01-01

    We have isolated clones from a human brain cDNA library coding for two splice variants of mGluR1. The combined sequences account for 6864 base pairs (bp) of the ? 7 kilobase (kb) transcript seen on northern blots of human brain mRNA. The distribution of mGluR1 mRNA in human brain is similar to that found in rat brain and the gene

  11. Identification of a consistent pattern of mutations in neurovirulent variants derived from the sabin vaccine strain of poliovirus type 2.

    PubMed Central

    Equestre, M; Genovese, D; Cavalieri, F; Fiore, L; Santoro, R; Perez Bercoff, R

    1991-01-01

    Complete nucleotide sequencing of the RNAs of two unrelated neurovirulent isolates of Sabin-related poliovirus type 2 revealed that two nucleotides and one amino acid (amino acid 143 in the major capsid protein VP1) consistently departed from the sequences of the nonneurovirulent poliovirus type 2 712 and Sabin vaccine strains. This pattern of mutation appeared to be a feature common to all neurovirulent variants of poliovirus type 2. PMID:1850043

  12. Novel Variants of Clade 2.3.4 Highly Pathogenic Avian Influenza A(H5N1) Viruses, China

    PubMed Central

    Gu, Min; Zhao, Guo; Zhao, Kunkun; Zhong, Lei; Huang, Junqing; Wan, Hongquan; Wang, Xiaoquan; Liu, Wenbo; Liu, Huimou; Peng, Daxin

    2013-01-01

    We characterized 7 highly pathogenic avian influenza A(H5N1) viruses isolated from poultry in China during 2009–2012 and found that they belong to clade 2.3.4 but do not fit within the 3 defined subclades. Antigenic drift in subtype H5N1 variants may reduce the efficacy of vaccines designed to control these viruses in poultry. PMID:24274396

  13. Differential expression and response of growth factors in different metastatic variants of human pulmonary giant cell carcinoma

    Microsoft Academic Search

    Lingfang Zeng; Wen Cui; Weigang Fang; Jie Zheng; Bingquang Wu

    1997-01-01

    The cell lines PGbE1 and PGLH7, which have high and low metastatic potential respectively, were two different variants isolated\\u000a from human pulmonary giant cell carcinoma cell line PG. This study compared the expression and response of several growth\\u000a factors TGF?, TGF?, bFGF, IL-6, IL-8 and ANG in the two cell lines. By using RT-PCR analysis and [3H] thymidine incorporation assay,

  14. 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...

  15. 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

  16. 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

  17. Association of genetic variants of GRIN2B with autism

    PubMed Central

    Pan, Yongcheng; Chen, Jingjing; Guo, Hui; Ou, Jianjun; Peng, Yu; Liu, Qiong; Shen, Yidong; Shi, Lijuan; Liu, Yalan; Xiong, Zhimin; Zhu, Tengfei; Luo, Sanchuan; Hu, Zhengmao; Zhao, Jingping; Xia, Kun

    2015-01-01

    Autism (MIM 209850) is a complex neurodevelopmental disorder characterized by social communication impairments and restricted repetitive behaviors. It has a high heritability, although much remains unclear. To evaluate genetic variants of GRIN2B in autism etiology, we performed a system association study of common and rare variants of GRIN2B and autism in cohorts from a Chinese population, involving a total sample of 1,945 subjects. Meta-analysis of a triad family cohort and a case-control cohort identified significant associations of multiple common variants and autism risk (Pmin = 1.73 × 10?4). Significantly, the haplotype involved with the top common variants also showed significant association (P = 1.78 × 10?6). Sanger sequencing of 275 probands from a triad cohort identified several variants in coding regions, including four common variants and seven rare variants. Two of the common coding variants were located in the autism-related linkage disequilibrium (LD) block, and both were significantly associated with autism (P < 9 × 10?3) using an independent control cohort. Burden analysis and case-only analysis of rare coding variants identified by Sanger sequencing did not find this association. Our study for the first time reveals that common variants and related haplotypes of GRIN2B are associated with autism risk. PMID:25656819

  18. RVboost: RNA-seq variants prioritization using a boosting method

    PubMed Central

    Wang, Chen; Davila, Jaime I.; Baheti, Saurabh; Bhagwate, Aditya V.; Wang, Xue; Kocher, Jean-Pierre A.; Slager, Susan L.; Feldman, Andrew L.; Novak, Anne J.; Cerhan, James R.; Thompson, E. Aubrey; Asmann, Yan W.

    2014-01-01

    Motivation: RNA-seq has become the method of choice to quantify genes and exons, discover novel transcripts and detect fusion genes. However, reliable variant identification from RNA-seq data remains challenging because of the complexities of the transcriptome, the challenges of accurately mapping exon boundary spanning reads and the bias introduced during the sequencing library preparation. Method: We developed RVboost, a novel method specific for RNA variant prioritization. RVboost uses several attributes unique in the process of RNA library preparation, sequencing and RNA-seq data analyses. It uses a boosting method to train a model of ‘good quality’ variants using common variants from HapMap, and prioritizes and calls the RNA variants based on the trained model. We packaged RVboost in a comprehensive workflow, which integrates tools of variant calling, annotation and filtering. Results: RVboost consistently outperforms the variant quality score recalibration from the Genome Analysis Tool Kit and the RNA-seq variant-calling pipeline SNPiR in 12 RNA-seq samples using ground-truth variants from paired exome sequencing data. Several RNA-seq–specific attributes were identified as critical to differentiate true and false variants, including the distance of the variant positions to exon boundaries, and the percent of the reads supporting the variant in the first six base pairs. The latter identifies false variants introduced by the random hexamer priming during the library construction. Availability and implementation: The RVboost package is implemented to readily run in Mac or Linux environments. The software and user manual are available at http://bioinformaticstools.mayo.edu/research/rvboost/. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25170027

  19. 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

  20. 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

    2015-01-01

    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

  1. Possible new variant of Nijmegen breakage syndrome.

    PubMed

    Der Kaloustian, V M; Kleijer, W; Booth, A; Auerbach, A D; Mazer, B; Elliott, A M; Abish, S; Usher, R; Watters, G; Vekemans, M; Eydoux, P

    1996-10-01

    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. PMID:8914736

  2. [Necrobiosis lipoidica. Variants on a theme].

    PubMed

    Geissler, E; Laaff, H; Technau, K; Bruckner-Tuderman, L; Nashan, D

    2011-08-01

    A 69-year-old patient presented with different skin lesions all of which belonged to group of necrobiosis lipoidica. The initial histologic diagnosis was actinic granuloma O'Brien. A subsequent biopsy was interpreted as granulomatous necrobiosis lipoidica. The history of these necrobiotic variants is reviewed and exemplarily depicted with this case. Necrobiosis lipoidica is part of the spectrum of granulomatous skin disorders. Although its etiology is unclear, an association with diabetes mellitus is often discussed. Multiple therapeutic options exist, but standardized guidelines for treatment are missing. PMID:21732163

  3. 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

  4. Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster.

    PubMed

    Santoni, Federico A; Makrythanasis, Periklis; Nikolaev, Sergey; Guipponi, Michel; Robyr, Daniel; Bottani, Armand; Antonarakis, Stylianos E

    2014-02-01

    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

  5. 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

  6. Molecular variants of human papillomavirus type 16 from four continents suggest ancient pandemic spread of the virus and its coevolution with humankind.

    PubMed Central

    Chan, S Y; Ho, L; Ong, C K; Chow, V; Drescher, B; Dürst, M; ter Meulen, J; Villa, L; Luande, J; Mgaya, H N

    1992-01-01

    We have amplified by the polymerase chain reaction, cloned, and sequenced genomic segments of 118 human papillomavirus type 16 (HPV-16) isolates from 76 cervical biopsy, 14 cervical smear, 3 vulval biopsy, 2 penile biopsy, 2 anal biopsy, and 1 vaginal biopsy sample and two cell lines. The specimens were taken from patients in four countries--Singapore, Brazil, Tanzania, and Germany. The sequence of a 364-bp fragment of the long control region of the virus revealed 38 variants, most of which differed by one or several point mutations. Phylogenetic trees were constructed by distance matrix methods and a transformation series approach. The trees based on the long control region were supported by another set based on the complete E5 protein-coding region. Both sets had two main branches. Nearly all of the variants from Tanzania were assigned to one (African) branch, and all of the German and most of the Singaporean variants were assigned to the other (Eurasian) branch. While some German and Singaporean variants were identical, each group also contained variants that formed unique branches. In contrast to the group-internal homogeneity of the Singaporean, German, and Tanzanian variants, the Brazilian variants were clearly divided between the two branches. Exceptions to this were the seven Singaporean isolates with mutational patterns typical of the Tanzanian isolates. The data suggest that HPV-16 evolved separately for a long period in Africa and Eurasia. Representatives of both branches may have been transferred to Brazil via past colonial immigration. The comparable efficiencies of transfer of the African and the Eurasian variants to the New World suggest pandemic spread of HPV-16 in past centuries. Representatives of the African branch were possibly transferred to the Far East along old Arab and Indonesian sailing routes. Our data also support the view that HPV-16 is a well-defined virus type, since the variants show only a maximal genomic divergence of about 5%. The small amount of divergence in any one geographic location and the lack of marked divergence between the Tanzanian and Brazilian African genome variants two centuries after their likely introduction into the New World suggest a very slow rate of viral evolution. The phylogenetic tree therefore probably represents a minimum of several centuries of evolution, if not an age equal to that of the respective human races. PMID:1312620

  7. 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

  8. Genetic Variants Improve Breast Cancer Risk Prediction on Mammograms

    PubMed Central

    Liu, Jie; Page, David; Nassif, Houssam; Shavlik, Jude; Peissig, Peggy; McCarty, Catherine; Onitilo, Adedayo A.; Burnside, Elizabeth

    2013-01-01

    Several recent genome-wide association studies have identified genetic variants associated with breast cancer. However, how much these genetic variants may help advance breast cancer risk prediction based on other clinical features, like mammographic findings, is unknown. We conducted a retrospective case-control study, collecting mammographic findings and high-frequency/low-penetrance genetic variants from an existing personalized medicine data repository. A Bayesian network was developed using Tree Augmented Naive Bayes (TAN) by training on the mammographic findings, with and without the 22 genetic variants collected. We analyzed the predictive performance using the area under the ROC curve, and found that the genetic variants significantly improved breast cancer risk prediction on mammograms. We also identified the interaction effect between the genetic variants and collected mammographic findings in an attempt to link genotype to mammographic phenotype to better understand disease patterns, mechanisms, and/or natural history. PMID:24551380

  9. Variantes 2 IFT6299 H2014 UdeM Miklos Csuros VARIANTES G ENOMIQUES II

    E-print Network

    Csürös, Miklós

    = y2) ou h´et´erozygotes (y1 = y2) . . . #12;G´enotypes : Hardy-Weinberg Variantes 2 IFT6299 H2014 UdeM Mikl´os Csur¨os vi ´equilibre Hardy-Weinberg : population infinie g´en´erations discr`etes panmixie

  10. Association Between a Functional Variant Downstream of TNFAIP3 and Systemic Lupus Erythematosus

    PubMed Central

    Adrianto, Indra; Wen, Feng; Templeton, Amanda; Wiley, Graham; King, Jarrod B.; Lessard, Christopher J.; Bates, Jared S.; Hu, Yanqing; Kelly, Jennifer A.; Kaufman, Kenneth M.; Guthridge, Joel M.; Alarcón-Riquelme, Marta E.; Anaya, Juan-Manuel; Bae, Sang-Cheol; Bang, So-Young; Boackle, Susan A.; Brown, Elizabeth E.; Petri, Michelle A.; Gallant, Caroline; Ramsey-Goldman, Rosalind; Reveille, John D.; Vila, Luis M.; Criswell, Lindsey A.; Edberg, Jeffrey C.; Freedman, Barry I.; Gregersen, Peter K.; Gilkeson, Gary S.; Jacob, Chaim O.; James, Judith A.; Kamen, Diane L.; Kimberly, Robert P.; Martin, Javier; Merrill, Joan T.; Niewold, Timothy B.; Park, So-Yeon; Pons-Estel, Bernardo A.; Scofield, R. Hal; Stevens, Anne M.; Tsao, Betty P.; Vyse, Timothy J.; Langefeld, Carl D.; Harley, John B.; Moser, Kathy L.; Webb, Carol F.; Humphrey, Mary Beth; Montgomery, Courtney Gray; Gaffney, Patrick M.

    2011-01-01

    Systemic Lupus Erythematosus (SLE, OMIM 152700) is an autoimmune disease characterized by self-reactive antibodies resulting in systemic inflammation and organ failure. TNFAIP3, encoding the ubiquitin-modifying enzyme A20, is an established susceptibility locus for SLE. By fine mapping and genomic resequencing in ethnically diverse populations we fully characterized the TNFAIP3 risk haplotype and isolated a novel TT>A polymorphic dinucleotide associated with SLE in subjects of European (P = 1.58 × 10?8; odds ratio (OR) = 1.70) and Korean (P = 8.33 × 10?10; OR = 2.54) ancestry. This variant, located in a region of high conservation and regulatory potential, bound a nuclear protein complex comprised of NF-?B subunits with reduced avidity. Furthermore, compared with the non-risk haplotype, the haplotype carrying this variant resulted in reduced TNFAIP3 mRNA and A20 protein expression. These results establish this TT>A variant as the most likely functional polymorphism responsible for the association between TNFAIP3 and SLE. PMID:21336280

  11. Differences in crystallization of two LinB variants from Sphingobium japonicum UT26

    PubMed Central

    Degtjarik, Oksana; Chaloupkova, Radka; Rezacova, Pavlina; Kuty, Michal; Damborsky, Jiri; Kuta Smatanova, Ivana

    2013-01-01

    Haloalkane dehalogenases are microbial enzymes that convert a broad range of halogenated aliphatic compounds to their corresponding alcohols by the hydrolytic mechanism. These enzymes play an important role in the biodegradation of various environmental pollutants. Haloalkane dehalogenase LinB isolated from a soil bacterium Sphingobium japonicum UT26 has a relatively broad substrate specificity and can be applied in bioremediation and biosensing of environmental pollutants. The LinB variants presented here, LinB32 and LinB70, were constructed with the goal of studying the effect of mutations on enzyme functionality. In the case of LinB32 (L117W), the introduced mutation leads to blocking of the main tunnel connecting the deeply buried active site with the surrounding solvent. The other variant, LinB70 (L44I, H107Q), has the second halide-binding site in a position analogous to that in the related haloalkane dehalogenase DbeA from Bradyrhizobium elkanii USDA94. Both LinB variants were successfully crystallized and full data sets were collected for native enzymes as well as their complexes with the substrates 1,2-dibromoethane (LinB32) and 1-bromobutane (LinB70) to resolutions ranging from 1.6 to 2.8?Å. The two mutants crystallize differently from each other, which suggests that the mutations, although deep inside the molecule, can still affect the protein crystallizability. PMID:23519805

  12. Streptococcus equi with truncated M-proteins isolated from outwardly healthy horses.

    PubMed

    Chanter, N; Talbot, N C; Newton, J R; Hewson, D; Verheyen, K

    2000-06-01

    The M-protein genes of Streptococcus equi isolated from 17 outwardly healthy horses after 4 strangles outbreaks had ended, including a quarantined animal, were compared with those of S. equi isolates from 167 active cases of strangles across 4 countries. The healthy horses included 16 persistent S. equi carriers, at least one from each of the four outbreaks. These carriers, despite being outwardly healthy, had empyema of the guttural pouch(es), an enlargement of the equine Eustachian tube. A persistent carrier from two of these outbreaks, the quarantined animal and a healthy animal with normal guttural pouches, from which S. equi was isolated only once, were colonized by variant S. equi with truncated M-protein genes (24% of outwardly healthy animals with S. equi). The truncated M-protein genes had in-frame deletions in slightly different positions between the signal sequence and the central repeat region, equivalent to approximately 20% of the mature expressed protein. Immunoblotting with antibody to recombinant M-protein confirmed that the variants expressed a truncated form of the M-protein. In contrast to the outwardly healthy S. equi carriers, only 1/167 of S. equi isolates from strangles cases possessed a truncated M-protein gene (<1%; Fisher's exact test, P=0.0002). Compared with isolates from healthy horses with a truncated M-protein, much more of the N terminus of the truncated M-protein was retained in the variant S. equi from a strangles case. Variant S. equi from outwardly healthy animals were more susceptible to phagocytosis by neutrophils in vitro than typical isolates. This is the first report of detection of S. equi with a truncated M-protein. The distribution of the variants between strangles cases and carriers suggests that the 80% of the M-protein retained in the variants may contribute to colonization whilst the deleted portion of the gene may be needed for full virulence. PMID:10846214

  13. Solid variant of serous cystadenoma of the pancreas

    PubMed Central

    Yasuda, Akira; Sawai, Hirozumi; Ochi, Nobuo; Matsuo, Yoichi; Okada, Yuji; Takeyama, Hiromitsu

    2011-01-01

    We describe a case of a solid variant of serous cystadenoma of the pancreas. The preoperative examination results led to a diagnosis of a nonfunctional pancreatic islet cell tumour, and the patient underwent a pylorus-preserving pancreaticoduodenectomy. The tumour was diagnosed as a solid variant of serous cystadenoma by histopathological examination. Solid variant of serous cystadenoma of the pancreas is difficult to diagnose preoperatively. More cases must be accumulated and investigated to obtain clues for accurate diagnosis. PMID:22291781

  14. Pharmacognostical studies on Cissus quadrangularis L. variant I & II.

    PubMed

    Austin, Anoop; Kannan, R; Jegadeesan, M

    2004-04-01

    The aerial parts of Cissus quadrangularis L.Variant I and II are being used therapeutically for various ailments in indigenous system of medicine. Detailed pharmacognostical studies on the aerial parts were made. Variant I and II were analysed for their physiochemical, microscopical, fluorescent, qualitative and quantitative phytochemical, TLC and HPTLC characteristics. Quantitative variations were noted among seasonal samples and between variants and the results are presented. PMID:22557140

  15. Hfq variant with altered RNA binding functions

    PubMed Central

    Ziolkowska, Katarzyna; Derreumaux, Philippe; Folichon, Marc; Pellegrini, Olivier; Régnier, Philippe; Boni, Irina V.; Hajnsdorf, Eliane

    2006-01-01

    The interaction between Hfq and RNA is central to multiple regulatory processes. Using site-directed mutagenesis, we have found a missense mutation in Hfq (V43R) which strongly affects2 the RNA binding capacity of the Hfq protein and its ability to stimulate poly(A) tail elongation by poly(A)-polymerase in vitro. In vivo, overexpression of this Hfq variant fails to stimulate rpoS–lacZ expression and does not restore a normal growth rate in hfq null mutant. Cells in which the wild-type gene has been replaced by the hfqV43R allele exhibit a phenotype intermediate between those of the wild-type and of the hfq minus or null strains. This missense mutation derepresses Hfq synthesis. However, not all Hfq functions are affected by this mutation. For example, HfqV43R represses OppA synthesis as strongly as the wild-type protein. The dominant negative effect of the V43R mutation over the wild-type allele suggests that hexamers containing variant and genuine subunits are presumably not functional. Finally, molecular dynamics studies indicate that the V43R substitution mainly changes the position of the K56 and Y55 side chains involved in the Hfq–RNA interaction but has probably no effect on the folding and the oligomerization of the protein. PMID:16449205

  16. Kenny-Caffey syndrome: an Arab variant?

    PubMed

    Sabry, M A; Farag, T I; Shaltout, A A; Zaki, M; Al-Mazidi, Z; Abulhassan, S J; Al-Torki, N; Quishawi, A; Al Awadi, S A

    1999-01-01

    We describe 2 unrelated Bedouin girls who met the criteria for the diagnosis of Kenny-Caffey syndrome. The girls had some unusual features--microcephaly and psychomotor retardation--that distinguish the Kenny-Caffey syndrome profile in Arab children from the classical Kenny-Caffey syndrome phenotype characterized by macrocephaly and normal intelligence. The 2 girls did not harbor the 22q11 microdeletion (the hallmark of the DiGeorge cluster of diseases) that we previously reported in another Bedouin family with the Kenny-Caffey syndrome (Sabry et al. J Med Genet 1998: 35(1): 31-36). This indicates considerable genetic heterogeneity for this syndrome. We also review previously reported 44 Arab/Bedouin patients with the same profile of hypoparathyroidism, short stature, seizures, mental retardation and microcephaly. Our results suggest that these patients represent an Arab variant of Kenny-Caffey syndrome with characteristic microcephaly and psychomotor retardation. We suggest that all patients with Kenny-Caffey syndrome should be investigated for the 22q11 microdeletion. Other possible genetic causes for the Kenny-Caffey syndrome or its Arab variant include chromosome 10p abnormalities. PMID:10066031

  17. Interaction of human GTP cyclohydrolase I with its splice variants

    PubMed Central

    Pandya, Maya J.; Golderer, Georg; Werner, Ernst R.; Werner-Felmayer, Gabriele

    2006-01-01

    Tetrahydrobiopterin is an essential cofactor for aromatic amino acid hydroxylases, ether lipid oxidase and nitric oxide synthases. Its biosynthesis in mammals is regulated by the activity of the homodecameric enzyme GCH (GTP cyclohydrolase I; EC 3.5.4.16). In previous work, catalytically inactive human GCH splice variants differing from the wild-type enzyme within the last 20 C-terminal amino acids were identified. In the present study, we searched for a possible role of these splice variants. Gel filtration profiles of purified recombinant proteins showed that variant GCHs form high-molecular-mass oligomers similar to the wild-type enzyme. Co-expression of splice variants together with wild-type GCH in mammalian cells revealed that GCH levels were reduced in the presence of splice variants. Commensurate with these findings, the GCH activity obtained for wild-type enzyme was reduced 2.5-fold through co-expression with GCH splice variants. Western blots of native gels suggest that splice variants form decamers despite C-terminal truncation. Therefore one possible explanation for the effect of GCH splice variants could be that inactive variants are incorporated into GCH heterodecamers, decreasing the enzyme stability and activity. PMID:16848765

  18. 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

  19. 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

  20. Qualitative and Quantitative Analysis of the Binding of GII.4 Norovirus Variants onto Human Blood Group Antigens?

    PubMed Central

    de Rougemont, A.; Ruvoen-Clouet, N.; Simon, B.; Estienney, M.; Elie-Caille, C.; Aho, S.; Pothier, P.; Le Pendu, J.; Boireau, W.; Belliot, G.

    2011-01-01

    Noroviruses (NoVs) are one of the leading causes of gastroenteritis in children and adults. For the last 2 decades, genogroup II genotype 4 (GII.4) NoVs have been circulating worldwide. GII.4 NoVs can be divided into variants, and since 2002 they have circulated in the population before being replaced every 2 or 3 years, which raises questions about the role of their histo-blood group antigen (HBGA) ligands in their evolution. To shed light on these questions, we performed an analysis of the interaction between representative GII.4 variants and HBGAs, and we determined the role of selected amino acids in the binding profiles. By mutagenesis, we showed that there was a strict structural requirement for the amino acids, directly implicated in interactions with HBGAs. However, the ablation of the threonine residue at position 395 (?T395), an epidemiological feature of the post-2002 variants, was not deleterious to the binding of the virus-like particle (VLP) to the H antigen, while binding to A and B antigens was severely hampered. Nevertheless, the ?T395 VLPs gained the capacity to bind to the Lewis x and sialyl-Lewis x antigens in comparison with the wild-type VLP, demonstrating that amino acid residues outside the HBGA binding site can modify the binding properties of NoVs. We also analyzed the attachment of baculovirus-expressed VLPs from six variants (Bristol, US95/96, Hunter, Yerseke, Den Haag, and Osaka) that were isolated from 1987 to 2007 to phenotyped saliva samples and synthetic HBGAs. We showed that the six variants could all attach to saliva of secretors irrespective of the ABO phenotype and to oligosaccharides characteristic of the secretor phenotype. Interestingly, Den Haag and Osaka variants additionally bound to carbohydrates present in the saliva of Lewis-positive nonsecretors. The carbohydrate binding profile and the genetic and mutagenesis analysis suggested that GII.4 binding to Lewis x and sialyl-Lewis x antigens might be a by-product of the genetic variation of the amino acids located in the vicinity of the binding site. Analysis of the binding properties for the six variants by surface plasmon resonance showed that only post-2002 variants (i.e., Hunter, Yerseke, Den Haag, and Osaka) presented strong binding to A and B antigens, suggesting that the GII.4 evolution could be related to an increased affinity for HBGAs for the post-2002 variants. The combination of increased affinity for ABH antigens and of a newly acquired ability to recognize glycans from Lewis-positive nonsecretors could have contributed to the epidemiological importance of strains such as the Den Haag GII.4 subtype. PMID:21345963

  1. Biofilm formation in a hydrodynamic environment by novel fimh variants and ramifications for virulence.

    PubMed

    Schembri, M A; Klemm, P

    2001-03-01

    Type 1 fimbriae are surface-located adhesion organelles of Escherichia coli that are directly associated with virulence of the urinary tract. They mediate D-mannose-sensitive binding to different host surfaces by way of the minor fimbrial component FimH. Naturally occurring variants of FimH that bind strongly to terminally exposed monomannose residues have been associated with a pathogenicity-adaptive phenotype that enhances E. coli colonization of extraintestinal locations such as the urinary tract. The FimH adhesin also promotes biofilm formation in a mannose-inhibitable manner on abiotic surfaces under static growth conditions. In this study, we used random mutagenesis combined with a novel selection-enrichment technique to specifically identify mutations in the FimH adhesin that confer on E. coli the ability to form biofilms under hydrodynamic flow (HDF) conditions. We identified three FimH variants from our mutant library that could mediate an HDF biofilm formation phenotype to various degrees. This phenotype was induced by the cumulative effect of multiple changes throughout the receptor-binding region of the protein. Two of the HDF biofilm-forming FimH variants were insensitive to mannose inhibition and represent novel phenotypes not previously identified in naturally occurring isolates. Characterization of our enriched clones revealed some similarities to amino acid alterations that occur in urinary tract infection (UTI) strains. Subsequent screening of a selection of UTI FimH variants demonstrated that they too could promote biofilm formation on abiotic surfaces under HDF conditions. Interestingly, the same correlation was not observed for commensal FimH variants. FimH is a multifaceted protein prone to rapid microevolution. In addition to its previously documented roles in adherence and invasion, we have now demonstrated its function in biofilm formation on abiotic surfaces subjected to HDF conditions. The study indicates that UTI FimH variants possess adaptations that enhance biofilm formation and suggests a novel role for FimH in UTIs associated with medical implants such as catheters. PMID:11179294

  2. Early diagnostic value of survivin and its alternative splice variants in breast cancer

    PubMed Central

    2014-01-01

    Background The inhibitor of apoptosis (IAP) protein Survivin and its splice variants are differentially expressed in breast cancer tissues. Our previous work showed Survivin is released from tumor cells via small membrane-bound vesicles called exosomes. We, therefore, hypothesize that analysis of serum exosomal Survivin and its splice variants may provide a novel biomarker for early diagnosis of breast cancer. Methods We collected sera from forty breast cancer patients and ten control patients who were disease free for 5 years after treatment. In addition, twenty-three paired breast cancer tumor tissues from those same 40 patients were analyzed for splice variants. Serum levels of Survivin were analyzed using ELISA and exosomes were isolated from this serum using the commercially available ExoQuick kit, with subsequent Western blots and immunohistochemistry performed. Results Survivin levels were significantly higher in all the breast cancer samples compared to controls (p?variant expression and localization was identical in serum exosomes, differential expression of Survivin-2B protein existed in the exosomes. Similarly, Survivin and Survivin-?Ex3 proteins were the predominant forms detected in all of the breast cancer tissues evaluated in this study, whereas a more variable expression of Survivin-2B level was found at different cancer stages. Conclusion In this study we show for the first time that like Survivin, the Survivin splice variants are also exosomally packaged in the breast cancer patients’ sera, mimicking the survivin splice variant pattern that we also report in breast cancer tissues. Differential expression of exosomal-Survivin, particularly Survivin-2B, may serve as a diagnostic and/or prognostic marker, a “liquid biopsy” if you will, in early breast cancer patients. Furthermore, a more thorough understanding of the role of this prominent antiapoptotic pathway could lead to the development of potential therapeutics for breast cancer patients. PMID:24620748

  3. Clinical and microbiologic characteristics of tcdA-negative variant clostridium difficile infections

    PubMed Central

    2012-01-01

    Background The tcdA-negative variant (A-B+) of Clostridium difficile is prevalent in East Asian countries. However, the risk factors and clinical characteristics of A-B+C. difficile infections (CDI) are not clearly documented. The objective of this study was to investigate these characteristics. Methods From September 2008 through January 2010, the clinical characteristics, medication history and treatment outcomes of CDI patients were recorded prospectively. Toxin characterization and antibiotic susceptibility tests were performed on stool isolates of C. difficile. Results During the study period, we identified 22 cases of CDI caused by tcdA-negative tcdB-positive (A-B+) strains and 105 cases caused by tcdA-positive tcdB-positive (A+B+) strains. There was no significant difference in disease severity or clinical characteristics between the two groups. Previous use of clindamycin and young age were identified as significant risk factors for the acquisition of A-B+ CDI (OR?=?4.738, 95% CI 1.48–15.157, p?=?0.009 and OR?=?0.966, 95% CI 0.935–0.998, p?=?0.038, respectively) in logistic regression. Rates of resistance to clindamycin were 100% and 69.6% in the A-B+ and A+B+ isolates, respectively (p?=?0.006), and the ermB gene was identified in 17 of 21 A-B+ isolates (81%). Resistance to moxifloxacin was also more frequent in the A-B+ than in the A+B+ isolates (95.2% vs. 63.7%, p?=?0.004). Conclusions The clinical course of A-B+ CDI is not different from that of A+B+ CDI. Clindamycin use is a significant risk factor for the acquisition of tcdA-negative variant strains. PMID:22571633

  4. 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

  5. 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

  6. Histone Variants and Their Post-Translational Modifications in Primary Human Fat Cells

    PubMed Central

    Jufvas, Åsa; Strålfors, Peter; Vener, Alexander V.

    2011-01-01

    Epigenetic changes related to human disease cannot be fully addressed by studies of cells from cultures or from other mammals. We isolated human fat cells from subcutaneous abdominal fat tissue of female subjects and extracted histones from either purified nuclei or intact cells. Direct acid extraction of whole adipocytes was more efficient, yielding about 100 µg of protein with histone content of 60% –70% from 10 mL of fat cells. Differential proteolysis of the protein extracts by trypsin or ArgC-protease followed by nanoLC/MS/MS with alternating CID/ETD peptide sequencing identified 19 histone variants. Four variants were found at the protein level for the first time; particularly HIST2H4B was identified besides the only H4 isoform earlier known to be expressed in humans. Three of the found H2A potentially organize small nucleosomes in transcriptionally active chromatin, while two H2AFY variants inactivate X chromosome in female cells. HIST1H2BA and three of the identified H1 variants had earlier been described only as oocyte or testis specific histones. H2AFX and H2AFY revealed differential and variable N-terminal processing. Out of 78 histone modifications by acetylation/trimethylation, methylation, dimethylation, phosphorylation and ubiquitination, identified from six subjects, 68 were found for the first time. Only 23 of these modifications were detected in two or more subjects, while all the others were individual specific. The direct acid extraction of adipocytes allows for personal epigenetic analyses of human fat tissue, for profiling of histone modifications related to obesity, diabetes and metabolic syndrome, as well as for selection of individual medical treatments. PMID:21249133

  7. Molecular and Genetic Characterization of Natural HIV-1 Tat Exon-1 Variants from North India and Their Functional Implications

    PubMed Central

    Ronsard, Larance; Lata, Sneh; Singh, Jyotsna; Ramachandran, Vishnampettai G.; Das, Shukla; Banerjea, Akhil C.

    2014-01-01

    Background Designing an ideal vaccine against HIV-1 has been difficult due to enormous genetic variability as a result of high replication rate and lack of proofreading activity of reverse transcriptase leading to emergence of genetic variants and recombinants. Tat transactivates HIV-1 LTR, resulting in a remarkable increase in viral gene expression, and plays a vital role in pathogenesis. The aim of this study was to characterize the genetic variations of Tat exon-1 from HIV-1 infected patients from North India. Methods Genomic DNA was isolated from PBMCs and Tat exon-1 was PCR amplified with specific primers followed by cloning, sequencing and sequence analyses using bioinformatic tools for predicting HIV-1 subtypes, recombination events, conservation of domains and phosphorylation sites, and LTR transactivation by luciferase assay. Results Phylogenetic analysis of Tat exon-1 variants (n?=?120) revealed sequence similarity with South African Tat C sequences and distinct geographical relationships were observed for B/C recombinants. Bootscan analysis of our variants showed 90% homology to Tat C and 10% to B/C recombinants with a precise breakpoint. Natural substitutions were observed with high allelic frequencies which may be beneficial for virus. High amino acid conservation was observed in Tat among Anti Retroviral Therapy (ART) recipients. Barring few changes, most of the functional domains, predicted motifs and phosphorylation sites were well conserved in most of Tat variants. dN/dS analysis revealed purifying selection, implying the importance of functional conservation of Tat exon-1. Our Indian Tat C variants and B/C recombinants showed differential LTR transactivation. Conclusions The possible role of Tat exon-1 variants in shaping the current HIV-1 epidemic in North India was highlighted. Natural substitutions across conserved functional domains were observed and provided evidence for the emergence of B/C recombinants within the ORF of Tat exon-1. These events are likely to have implications for viral pathogenesis and vaccine formulations. PMID:24465566

  8. A Changing Gastric Environment Leads to Adaptation of Lipopolysaccharide Variants in Helicobacter pylori Populations during Colonization

    PubMed Central

    Nilsson, Christina; Björkholm, Britta; Normark, Staffan; Engstrand, Lars

    2009-01-01

    The human gastric pathogen Helicobacter pylori colonizes the stomachs of half of the human population, and causes development of peptic ulcer disease and gastric adenocarcinoma. H. pylori-associated chronic atrophic gastritis (ChAG) with loss of the acid-producing parietal cells, is correlated with an increased risk for development of gastric adenocarinoma. The majority of H. pylori isolates produce lipopolysaccharides (LPS) decorated with human-related Lewis epitopes, which have been shown to phase-vary in response to different environmental conditions. We have characterized the adaptations of H. pylori LPS and Lewis antigen expression to varying gastric conditions; in H. pylori isolates from mice with low or high gastric pH, respectively; in 482 clinical isolates from healthy individuals and from individuals with ChAG obtained at two time points with a four-year interval between endoscopies; and finally in isolates grown at different pH in vitro. Here we show that the gastric environment can contribute to a switch in Lewis phenotype in the two experimental mouse models. The clinical isolates from different human individuals showed that intra-individual isolates varied in Lewis antigen expression although the LPS diversity was relatively stable within each individual over time. Moreover, the isolates demonstrated considerable diversity in the levels of glycosylation and in the sizes of fucosylated O-antigen chains both within and between individuals. Thus our data suggest that different LPS variants exist in the colonizing H. pylori population, which can adapt to changes in the gastric environment and provide a means to regulate the inflammatory response of the host during disease progression. PMID:19517017

  9. Association of Low-Frequency and Rare Coding-Sequence Variants with Blood Lipids and Coronary Heart Disease in 56,000 Whites and Blacks

    PubMed Central

    Peloso, Gina M.; Auer, Paul L.; Bis, Joshua C.; Voorman, Arend; Morrison, Alanna C.; Stitziel, Nathan O.; Brody, Jennifer A.; Khetarpal, Sumeet A.; Crosby, Jacy R.; Fornage, Myriam; Isaacs, Aaron; Jakobsdottir, Johanna; Feitosa, Mary F.; Davies, Gail; Huffman, Jennifer E.; Manichaikul, Ani; Davis, Brian; Lohman, Kurt; Joon, Aron Y.; Smith, Albert V.; Grove, Megan L.; Zanoni, Paolo; Redon, Valeska; Demissie, Serkalem; Lawson, Kim; Peters, Ulrike; Carlson, Christopher; Jackson, Rebecca D.; Ryckman, Kelli K.; Mackey, Rachel H.; Robinson, Jennifer G.; Siscovick, David S.; Schreiner, Pamela J.; Mychaleckyj, Josyf C.; Pankow, James S.; Hofman, Albert; Uitterlinden, Andre G.; Harris, Tamara B.; Taylor, Kent D.; Stafford, Jeanette M.; Reynolds, Lindsay M.; Marioni, Riccardo E.; Dehghan, Abbas; Franco, Oscar H.; Patel, Aniruddh P.; Lu, Yingchang; Hindy, George; Gottesman, Omri; Bottinger, Erwin P.; Melander, Olle; Orho-Melander, Marju; Loos, Ruth J.F.; Duga, Stefano; Merlini, Piera Angelica; Farrall, Martin; Goel, Anuj; Asselta, Rosanna; Girelli, Domenico; Martinelli, Nicola; Shah, Svati H.; Kraus, William E.; Li, Mingyao; Rader, Daniel J.; Reilly, Muredach P.; McPherson, Ruth; Watkins, Hugh; Ardissino, Diego; Zhang, Qunyuan; Wang, Judy; Tsai, Michael Y.; Taylor, Herman A.; Correa, Adolfo; Griswold, Michael E.; Lange, Leslie A.; Starr, John M.; Rudan, Igor; Eiriksdottir, Gudny; Launer, Lenore J.; Ordovas, Jose M.; Levy, Daniel; Chen, Y.-D. Ida; Reiner, Alexander P.; Hayward, Caroline; Polasek, Ozren; Deary, Ian J.; Borecki, Ingrid B.; Liu, Yongmei; Gudnason, Vilmundur; Wilson, James G.; van Duijn, Cornelia M.; Kooperberg, Charles; Rich, Stephen S.; Psaty, Bruce M.; Rotter, Jerome I.; O’Donnell, Christopher J.; Rice, Kenneth; Boerwinkle, Eric; Kathiresan, Sekar; Cupples, L. Adrienne

    2014-01-01

    Low-frequency coding DNA sequence variants in the proprotein convertase subtilisin/kexin type 9 gene (PCSK9) lower plasma low-density lipoprotein cholesterol (LDL-C), protect against risk of coronary heart disease (CHD), and have prompted the development of a new class of therapeutics. It is uncertain whether the PCSK9 example represents a paradigm or an isolated exception. We used the “Exome Array” to genotype >200,000 low-frequency and rare coding sequence variants across the genome in 56,538 individuals (42,208 European ancestry [EA] and 14,330 African ancestry [AA]) and tested these variants for association with LDL-C, high-density lipoprotein cholesterol (HDL-C), and triglycerides. Although we did not identify new genes associated with LDL-C, we did identify four low-frequency (frequencies between 0.1% and 2%) variants (ANGPTL8 rs145464906 [c.361C>T; p.Gln121?], PAFAH1B2 rs186808413 [c.482C>T; p.Ser161Leu], COL18A1 rs114139997 [c.331G>A; p.Gly111Arg], and PCSK7 rs142953140 [c.1511G>A; p.Arg504His]) with large effects on HDL-C and/or triglycerides. None of these four variants was associated with risk for CHD, suggesting that examples of low-frequency coding variants with robust effects on both lipids and CHD will be limited. PMID:24507774

  10. A rare variant angioarchitecture of upper abdomen

    PubMed Central

    Anand, Mamta; Gupta, Smrity

    2014-01-01

    Vascular anomalies are frequently encountered in abdomen. But they are usually asymptomatic and diagnosed accidently during angiography or surgery leading into severe complications. Thus knowledge of angioarchitecture in abdomen, whether normal or variant, is considered prerequisite for successful, uncomplicated surgeries and interventional radiology. This case report describes one of such varying branching pattern of celiac trunk and superior mesenteric artery. During routine abdominal dissection, gastroduodenal artery was seen arising from celiac trunk along with its usual three branches. Common hepatic artery continued as left hepatic artery after giving rise the right gastric artery and a tortuous replaced right hepatic artery arose from superior mesenteric artery. An unusually long cystic artery arose from left hepatic artery and gave rise to 2-3 small anastomotic branches towards hepatic flexor of colon, in addition to its normal gallbladder supply. Awareness of such variations would certainly be helpful in upper abdominal surgeries. PMID:24693485

  11. Gene variant raises risk for colorectal cancer

    Cancer.gov

    A common genetic variant that affects one in three people significantly increases the risk of colorectal cancer from the consumption of red meat and processed meat, according to a study presented by researchers from the Keck School of Medicine of USC (home of the USC Norris Comprehensive Cancer Center) at the annual American Society of Human Genetics meeting. In addition to identifying a gene that raises risk for colorectal cancer from eating red or processed meat, the study — the first to identify the interactions of genes and diet on a genome-wide scale — also revealed another specific genetic variation that appears to modify whether eating more fruits, vegetables and fiber actually lowers your colorectal cancer risk.

  12. Glycolipid binding preferences of Shiga toxin variants.

    PubMed

    Karve, Sayali S; Weiss, Alison A

    2014-01-01

    The major virulence factor of Shiga toxin producing E. coli, is Shiga toxin (Stx), an AB5 toxin that consists of a ribosomal RNA-cleaving A-subunit surrounded by a pentamer of receptor-binding B subunits. The two major isoforms, Stx1 and Stx2, and Stx2 variants (Stx2a-h) significantly differ in toxicity. The exact reason for this toxicity difference is unknown, however different receptor binding preferences are speculated to play a role. Previous studies used enzyme linked immunosorbent assay (ELISA) to study binding of Stx1 and Stx2a toxoids to glycolipid receptors. Here, we studied binding of holotoxin and B-subunits of Stx1, Stx2a, Stx2b, Stx2c and Stx2d to glycolipid receptors globotriaosylceramide (Gb3) and globotetraosylceramide (Gb4) in the presence of cell membrane components such as phosphatidylcholine (PC), cholesterol (Ch) and other neutral glycolipids. In the absence of PC and Ch, holotoxins of Stx2 variants bound to mixtures of Gb3 with other glycolipids but not to Gb3 or Gb4 alone. Binding of all Stx holotoxins significantly increased in the presence of PC and Ch. Previously, Stx2a has been shown to form a less stable B-pentamer compared to Stx1. However, its effect on glycolipid receptor binding is unknown. In this study, we showed that even in the absence of the A-subunit, the B-subunits of both Stx1 and Stx2a were able to bind to the glycolipids and the more stable B-pentamer formed by Stx1 bound better than the less stable pentamer of Stx2a. B-subunit mutant of Stx1 L41Q, which shows similar stability as Stx2a B-subunits, lacked glycolipid binding, suggesting that pentamerization is more critical for binding of Stx1 than Stx2a. PMID:24983355

  13. Glycolipid Binding Preferences of Shiga Toxin Variants

    PubMed Central

    Karve, Sayali S.; Weiss, Alison A.

    2014-01-01

    The major virulence factor of Shiga toxin producing E. coli, is Shiga toxin (Stx), an AB5 toxin that consists of a ribosomal RNA-cleaving A-subunit surrounded by a pentamer of receptor-binding B subunits. The two major isoforms, Stx1 and Stx2, and Stx2 variants (Stx2a-h) significantly differ in toxicity. The exact reason for this toxicity difference is unknown, however different receptor binding preferences are speculated to play a role. Previous studies used enzyme linked immunosorbent assay (ELISA) to study binding of Stx1 and Stx2a toxoids to glycolipid receptors. Here, we studied binding of holotoxin and B-subunits of Stx1, Stx2a, Stx2b, Stx2c and Stx2d to glycolipid receptors globotriaosylceramide (Gb3) and globotetraosylceramide (Gb4) in the presence of cell membrane components such as phosphatidylcholine (PC), cholesterol (Ch) and other neutral glycolipids. In the absence of PC and Ch, holotoxins of Stx2 variants bound to mixtures of Gb3 with other glycolipids but not to Gb3 or Gb4 alone. Binding of all Stx holotoxins significantly increased in the presence of PC and Ch. Previously, Stx2a has been shown to form a less stable B-pentamer compared to Stx1. However, its effect on glycolipid receptor binding is unknown. In this study, we showed that even in the absence of the A-subunit, the B-subunits of both Stx1 and Stx2a were able to bind to the glycolipids and the more stable B-pentamer formed by Stx1 bound better than the less stable pentamer of Stx2a. B-subunit mutant of Stx1 L41Q, which shows similar stability as Stx2a B-subunits, lacked glycolipid binding, suggesting that pentamerization is more critical for binding of Stx1 than Stx2a. PMID:24983355

  14. Beam manipulating by metallic nano-slits with variant widths

    Microsoft Academic Search

    Haofei Shi; Changtao Wang; Chunlei Du; Xiangang Luo; Xiaochun Dong; Hongtao Gao

    2005-01-01

    A novel method is proposed to manipulate beam by modulating light phase through a metallic film with arrayed nano-slits, which have constant depth but variant widths. The slits transport electro-magnetic energy in the form of surface plasmon polaritons (SPPs) in nanometric waveguides and provide desired phase retardations of beam manipulating with variant phase propagation constant. Numerical simulation of an illustrative

  15. CBH1 homologs and variant CBH1 cellulases

    SciTech Connect

    Goedegebuur, Frits (Rozenlaan, NL); Gualfetti, Peter (San Francisco, CA); Mitchinson, Colin (Half Moon Bay, CA); Neefe, Paulien (Zoetermeer, NL)

    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.

  16. CBH1 homologs and variant CBH1 cellulases

    DOEpatents

    Goedegebuur, Frits (Rozenlaan, NL); Gualfetti, Peter (San Francisco, CA); Mitchinson, Colin (Half Moon Bay, CA); Neefe, Paulien (Zoetermeer, NL)

    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.

  17. The personal genome browser: visualizing functions of genetic variants

    PubMed Central

    Juan, Liran; Teng, Mingxiang; Zang, Tianyi; Hao, Yafeng; Wang, Zhenxing; Yan, Chengwu; Liu, Yongzhuang; Li, Jie; Zhang, Tianjiao; Wang, Yadong

    2014-01-01

    Advances in high-throughput sequencing technologies have brought us into the individual genome era. Projects such as the 1000 Genomes Project have led the individual genome sequencing to become more and more popular. How to visualize, analyse and annotate individual genomes with knowledge bases to support genome studies and personalized healthcare is still a big challenge. The Personal Genome Browser (PGB) is developed to provide comprehensive functional annotation and visualization for individual genomes based on the genetic–molecular–phenotypic model. Investigators can easily view individual genetic variants, such as single nucleotide variants (SNVs), INDELs and structural variations (SVs), as well as genomic features and phenotypes associated to the individual genetic variants. The PGB especially highlights potential functional variants using the PGB built-in method or SIFT/PolyPhen2 scores. Moreover, the functional risks of genes could be evaluated by scanning individual genetic variants on the whole genome, a chromosome, or a cytoband based on functional implications of the variants. Investigators can then navigate to high risk genes on the scanned individual genome. The PGB accepts Variant Call Format (VCF) and Genetic Variation Format (GVF) files as the input. The functional annotation of input individual genome variants can be visualized in real time by well-defined symbols and shapes. The PGB is available at http://www.pgbrowser.org/. PMID:24799434

  18. 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...

  19. Winding quotients and some variants of Fermat's Last Theorem

    E-print Network

    Darmon, Henri

    Winding quotients and some variants of Fermat's Last Theorem Henri Darmon at Montr´eal Lo¨ic Merel of the following variants of Fermat's equation xn + yn = zn : xn + yn = 2zn , (1) xn + yn = z2 , (2) xn + yn = z3 Fermat's Last Theorem to the Shimura-Taniyama conjecture (and the precise 1 #12;form of this conjecture

  20. Angiogenin variants in Parkinson disease and amyotrophic lateral sclerosis

    Microsoft Academic Search

    M. A. van Es; H. J. Schelhaas; P. W. van Vught; N. Ticozzi; P. M. Andersen; E. J. Groen; C. Schulte; H. M. Blauw; M. Koppers; F. P. Diekstra; K. Fumoto; A. L. Leclerc; P. Keagle; B. R. Bloem; H. Scheffer; B. F. L. van Nuenen; M. van Blitterswijk; W. van Rheenen; A. M. Wills; P. P. Lowe; G. F. Hu; W. Yu; H. Kishikawa; D. Wu; R. D. Folkerth; C. Mariani; S. Goldwurm; G. Pezzoli; P. van Damme; R. Lemmens; C. Dahlberg; A. Birve; R. Fernandez-Santiago; S. Waibel; C. Klein; M. Weber; A. J. van der Kooi; M. C. H. de Visser; D. Verbaan; J. J. van Hilten; P. Heutink; E. A. Hennekam; E. Cuppen; D. Van den Berg; R. H. Jr. Brown; V. Silani; T. Gasser; A. C. Ludolph; W. Robberecht; R. A. Ophoff; J. H. Veldink; R. J. Pasterkamp; P. I. de Bakker; J. E. Landers; B. P. C. van de Warrenburg; L. H. van den Berg

    2011-01-01

    OBJECTIVE: Several studies have suggested an increased frequency of variants in the gene encoding angiogenin (ANG) in patients with amyotrophic lateral sclerosis (ALS). Interestingly, a few ALS patients carrying ANG variants also showed signs of Parkinson disease (PD). Furthermore, relatives of ALS patients have an increased risk to develop PD, and the prevalence of concomitant motor neuron disease in PD

  1. Foodborne outbreak and nonmotile Salmonella enterica variant, France.

    PubMed

    Le Hello, Simon; Brisabois, Anne; Accou-Demartin, Marie; Josse, Adeline; Marault, Muriel; Francart, Sylvie; Da Silva, Nathalie Jourdan; Weill, François-Xavier

    2012-01-01

    We report a food-related outbreak of salmonellosis in humans caused by a nonmotile variant of Salmonella enterica serotype Typhimurium in France in 2009. This nonmotile variant had been circulating in laying hens but was not considered as Typhimurium and consequently escaped European poultry flock regulations. PMID:22257550

  2. Parental origin of sequence variants associated with complex diseases

    Microsoft Academic Search

    Valgerdur Steinthorsdottir; Gisli Masson; Gudmar Thorleifsson; Patrick Sulem; Soren Besenbacher; Aslaug Jonasdottir; Asgeir Sigurdsson; Kari Th. Kristinsson; Adalbjorg Jonasdottir; Michael L. Frigge; Arnaldur Gylfason; Pall I. Olason; Sigurjon A. Gudjonsson; Sverrir Sverrisson; Simon N. Stacey; Bardur Sigurgeirsson; Kristrun R. Benediktsdottir; Helgi Sigurdsson; Thorvaldur Jonsson; Rafn Benediktsson; Jon H. Olafsson; Oskar Th. Johannsson; Astradur B. Hreidarsson; Gunnar Sigurdsson; Benjamin F. Voight; Laura J. Scott; Christian Dina; Eleftheria Zeggini; Cornelia Huth; Yurii S. Aulchenko; Ryan P. Welch; Laura J. McCulloch; Teresa Ferreira; Harald Grallert; Najaf Amin; Guanming Wu; Cristen J. Willer; Soumya Raychaudhuri; Shaun Purcell; Steve A. McCarroll; Claudia Langenberg; Oliver M. Hoffmann; Josée Dupuis; Lu Qi; Ayellet V. Segrè; Mandy van Hoek; Pau Navarro; Kristin Ardlie; Beverley Balkau; Amanda J. Bennett; Roza Blagieva; Eric Boerwinkle; Lori L. Bonnycastle; Kristina Bengtsson Boström; Bert Bravenboer; Suzannah Bumpstead; Noël P. Burtt; Guillaume Charpentier; Peter S. Chines; Marilyn Cornelis; David J. Couper; Gabe Crawford; Alex S. F. Doney; Katherine S. Elliott; Amanda L. Elliott; Michael R. Erdos; Caroline S. Fox; Christopher S. Franklin; Martha Ganser; Christian Gieger; Niels Grarup; Todd Green; Simon Griffin; Christopher J. Groves; Candace Guiducci; Samy Hadjadj; Neelam Hassanali; Christian Herder; Bo Isomaa; Anne U. Jackson; Paul R. V. Johnson; Torben Jørgensen; Wen H. L. Kao; Norman Klopp; Peter Kraft; Johanna Kuusisto; Torsten Lauritzen; Man Li; Alouisius Lieverse; Cecilia M. Lindgren; Valeriya Lyssenko; Michel Marre; Thomas Meitinger; Kristian Midthjell; Mario A Morken; Narisu Narisu; Peter Nilsson; Katharine R. Owen; Felicity Payne; John R. B. Perry; Ann-Kristin Petersen; Carl Platou; Christine Proença; Inga Prokopenko; Wolfgang Rathmann; N. William Rayner; Neil R. Robertson; Ghislain Rocheleau; Michael Roden; Michael J. Sampson; Richa Saxena; Beverley M. Shields; Peter Shrader; Nicholas Smith; Thomas Sparsø; Klaus Strassburger; Heather M. Stringham; Qi Sun; Amy J. Swift; Barbara Thorand; Jean Tichet; Tiinamaija Tuomi; Rob van Dam; Thijs van Herpt; G. Bragi Walters; Michael N. Weedon; Jacqueline Witteman; Richard N. Bergman; Stephane Cauchi; Francis S. Collins; Anna L. Gloyn; Ulf Gyllensten; Torben Hansen; Winston A. Hide; Graham A. Hitman; Albert Hofman; David Hunter; Kristian Hveem; Markku Laakso; Karen L. Mohlke; Andrew D. Morris; Colin N. A. Palmer; Peter P. Pramstaller; Igor Rudan; Eric Sijbrands; Lincoln D. Stein; Jaakko Tuomilehto; Andre Uitterlinden; Mark Walker; Nicholas J. Wareham; Richard M. Watanabe; Goncalo R. Abecasis; Inês Barroso; Bernhard O. Boehm; Harry Campbell; Mark J. Daly; Jose C. Florez; Timothy M. Frayling; Leif Groop; Andrew T. Hattersley; Frank B. Hu; James B. Meigs; Andrew P. Morris; James S. Pankow; Oluf Pedersen; Rob Sladek; Unnur Thorsteinsdottir; H.-Erich Wichmann; James F. Wilson; Thomas Illig; Philippe Froguel; Cornelia M. van Duijn; David Altshuler; Michael Boehnke; Anne C. Ferguson-Smith; Daniel F. Gudbjartsson; Augustine Kong; Kari Stefansson

    2009-01-01

    Effects of susceptibility variants may depend on from which parent they are inherited. Although many associations between sequence variants and human traits have been discovered through genome-wide associations, the impact of parental origin has largely been ignored. Here we show that for 38,167 Icelanders genotyped using single nucleotide polymorphism (SNP) chips, the parental origin of most alleles can be determined.

  3. 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

  4. Histological variety of floral variant of follicular lymphoma.

    PubMed

    Kojima, Masaru; Yamanaka, Shouji; Yoshida, Takatomo; Shimizu, Ken; Murayama, Kayoko; Ohno, Yoshihiro; Itoh, Hideaki; Motoori, Tadashi; Masawa, Nobuhide; Nakamura, Shigeo

    2006-09-01

    To further clarify the histopathological findings of the floral variant of follicular lymphoma (FVFL), we studied 13 Japanese cases. Two histological subtypes of neoplastic follicles of FVFL have been described: (i) A macrogerminal center pattern where the mantle zone lymphocytes were invaginated into the neoplastic germinal center, often reminiscent of a floral design. (ii) A microgerminal center pattern where the massive invasion of mantle zone lymphocytes resulted in almost complete breakage of the neoplastic follicles. In the former pattern, the neoplastic germinal center usually contained large clusters of tumor cells, whereas in the latter, small clusters of up to 20 tumor cells or isolated tumor cells were observed in the neoplastic germinal centers. Moreover, occasional tumor cells showed a lymphocytic and/or histiocytic Reed-Sternberg cell (L&H cells)-like morphology. Both types of neoplastic follicles were observed to a varying degree in most cases. The macrogerminal center pattern was predominant in nine cases (70%), whilst the microgerminal center pattern was predominant in only four cases (30%). Three lesions (23%) had a marginal zone component. Immunohistochemistry showed that atypical follicular center cells, including L&H cells, were CD3-, CD5-, CD10+, CD20+, CD43-, bcl-2+, cyclinD1-. The overall histological findings of the macrogerminal center are similar to those of florid progressive transformation of germinal center (PTGC), whilst the microgerminal center pattern is similar to that of nodular lymphocyte-predominant Hodgkin lymphoma. Initially, the differential diagnosis between FVFL and florid PTGC was emphasized. However, the present study indicates that nodal marginal zone B-cell lymphoma possessing floral follicles and nodular lymphocyte-predominant Hodgkin lymphoma should be added to the differential diagnosis of FVFL. The germinal center B-cell nature of FVFL is most clearly recognizable by immunohistochemistry, though histological appearance alone may cause some diagnostic problems. PMID:16948815

  5. Revealing Histone Variant Induced Changes Via Quantitative Proteomics

    PubMed Central

    Arnaudo, Anna M.; Molden, Rosalynn C.; Garcia, Benjamin A.

    2011-01-01

    Histone variants are isoforms of linker and core histone proteins that differ in their amino acid sequences. These variants have distinct genomic locations and post-translational modifications, thus increasing the complexity of the chromatin architecture. Biological studies of histone variants indicate that they play a role in many processes including transcription, DNA damage response, and the cell cycle. The small differences in amino acid sequence and the diverse post-translational modification states that exist between histone variants make traditional analysis using immunoassay methods challenging. In recent years, a number of mass spectrometric techniques have been developed to identify and quantify histones at the whole protein or peptide levels. In this review we discuss the biology of histone variants and methods to characterize them using mass spectrometry-based proteomics. PMID:21526979

  6. Estimation of age and rate of increase of rare variants.

    PubMed Central

    Thompson, E A

    1976-01-01

    The problem considered is that of estimating the age or rate of increase of a variant on the basis of the present number of replicates observed in a population. In place of previous diffusion equation analyses of age probability distributions, the likelihood for the age is studied on the basis of a discrete branching process model. It is shown that variations inherent in the process of gene evolution in natural populations make it impossible to provide a reliable point estimate of the age of a specified variant, although the likelihood analysis provides a confidence interval which may place useful bounds on the period in which a variant originated. The observed distribution of numbers of several variants may also provide useful information. The problems of estimation are discussed with reference to rare variants arising in American Indian populations. PMID:984040

  7. 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

  8. 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

  9. 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

  10. Focal and segmental glomerulosclerosis: does prognosis vary with the variants?

    PubMed

    Swarnalatha, Guditi; Ram, R; Ismal, Kiran Mai; Vali, Sharmas; Sahay, Manisha; Dakshinamurty, K V

    2015-01-01

    Focal and segmental glomerulosclerosis (FSGS) is a clinicopathological entity. The following five FSGS variants: Collapsing, cellular, glomerular tip, peri-hilar and not otherwise specified (NOS) are recognized, which may have prognostic value. The aim of this study was to highlight the clinical course and outcome in the different pathological variants of FSGS and to evaluate the predictive risk factors of end-stage renal disease (ESRD). It was a retrospective analysis of biopsy-proven primary FSGS patients who presented over a period of three years. The data were collected from the clinical and biopsy records of the Nephrology Unit. There were 116 patients with biopsy-proven FSGS. The frequency of occurrence of FSGS among all cases of the nephrotic syndrome seen in our unit was 35.47%. NOS was the most common pathological variant (62.2%), followed by peri-hilar (11.2%), cellular (9.4%) and glomerular tip (7.7%), and the least common variant was collapsing (4.3%). Majority of patients with collapsing, NOS and glomerular tip variants had nephrotic range proteinuria. However, the amount of proteinuria was highest in the glomerular tip and collapsing variants. A higher percentage of patients with the collapsing and cellular variants had renal failure at the time of presentation. A higher rate of tubular and interstitial changes was seen in the collapsing and cellular variants. The collapsing and cellular variants showed lower response rate and higher rates of ESRD, while the glomerular tip lesion had the highest remission rate and the lowest rate of ESRD. Poor prognostic factors for ESRD in FSGS were initial renal insufficiency, severe tubulo-interstitial change, initial nonresponsiveness to steroids and collapsing histopathological variant. Our study suggests that histopathological classification of FSGS is of paramount importance in the management and in predicting the prognosis. PMID:25579744

  11. Small effective population size and genetic homogeneity in the Val Borbera isolate

    PubMed Central

    Colonna, Vincenza; Pistis, Giorgio; Bomba, Lorenzo; Mona, Stefano; Matullo, Giuseppe; Boano, Rosa; Sala, Cinzia; Viganò, Fiammetta; Torroni, Antonio; Achilli, Alessandro; Hooshiar Kashani, Baharak; Malerba, Giovanni; Gambaro, Giovanni; Soranzo, Nicole; Toniolo, Daniela

    2013-01-01

    Population isolates are a valuable resource for medical genetics because of their reduced genetic, phenotypic and environmental heterogeneity. Further, extended linkage disequilibrium (LD) allows accurate haplotyping and imputation. In this study, we use nuclear and mitochondrial DNA data to determine to what extent the geographically isolated population of the Val Borbera valley also presents features of genetic isolation. We performed a comparative analysis of population structure and estimated effective population size exploiting LD data. We also evaluated haplotype sharing through the analysis of segments of autozygosity. Our findings reveal that the valley has features characteristic of a genetic isolate, including reduced genetic heterogeneity and reduced effective population size. We show that this population has been subject to prolonged genetic drift and thus we expect many variants that are rare in the general population to reach significant frequency values in the valley, making this population suitable for the identification of rare variants underlying complex traits. PMID:22713810

  12. Glycosylation variants of a ?-glucosidase secreted by a Taiwanese fungus, Chaetomella raphigera, exhibit variant-specific catalytic and biochemical properties.

    PubMed

    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 substrate inhibition by an artificial substrate p-nitrophenyl glucopyranoside (pNPG), and the glucose feedback inhibition kinetics of nD2L is competitive (while it is non-competitive for nD2S), suggesting that these two glycovariants of D2 bind substrates differently. Interestingly, D2 produced in a heterologous system, Pichia pastoris, closely mimics properties of nD2S. Our studies suggest that O-glycosylation of D2 is important in determining its catalytic and biochemical properties. PMID:25180973

  13. 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 substrate inhibition by an artificial substrate p-nitrophenyl glucopyranoside (pNPG), and the glucose feedback inhibition kinetics of nD2L is competitive (while it is non-competitive for nD2S), suggesting that these two glycovariants of D2 bind substrates differently. Interestingly, D2 produced in a heterologous system, Pichia pastoris, closely mimics properties of nD2S. Our studies suggest that O-glycosylation of D2 is important in determining its catalytic and biochemical properties. PMID:25180973

  14. Emergence of a New Multidrug-Resistant Serotype X Variant in an Epidemic Clone of Shigella flexneri? †

    PubMed Central

    Ye, Changyun; Lan, Ruiting; Xia, Shengli; Zhang, Jin; Sun, Qiangzheng; Zhang, Shaomin; Jing, Huaiqi; Wang, Lei; Li, Zhenjun; Zhou, Zhemin; Zhao, Ailan; Cui, Zhigang; Cao, Jingjing; Jin, Dong; Huang, Lili; Wang, Yiting; Luo, Xia; Bai, Xuemei; Wang, Yan; Wang, Ping; Xu, Qiang; Xu, Jianguo

    2010-01-01

    Shigella spp. are the causative agent of shigellosis with Shigella flexneri serotype 2a being the most prevalent in developing countries. Epidemiological surveillance in China found that a new serotype of S. flexneri appeared in 2001 and replaced serotype 2a in 2003 as the most prevalent serotype in Henan Province. The new serotype also became the dominant serotype in 7 of the 10 other provinces under surveillance in China by 2007. The serotype was identified as a variant of serotype X. It differs from serotype X by agglutination to the monovalent anti-IV type antiserum and the group antigen-specific monoclonal antibody MASF IV-I. Genome sequencing of a serotype X variant isolate, 2002017, showed that it acquired a Shigella serotype conversion island, also as an SfX bacteriophage, containing gtr genes for type X-specific glucosylation. Multilocus sequence typing of 15 genes from 37 serotype X variant isolates and 69 isolates of eight other serotypes, 1a, 2a, 2b, 3a, 4a, 5b, X, and Y, found that all belong to a new sequence type (ST), ST91. Pulsed-field gel electrophoresis revealed 154 pulse types with 655 S. flexneri isolates analyzed and identified 57 serotype switching events. The data suggest that S. flexneri epidemics in China have been caused by a single epidemic clone, ST91, with frequent serotype switching to evade infection-induced immunity to serotypes to which the population was exposed previously. The clone has also acquired resistance to multiple antibiotics. These findings underscore the challenges to the current vaccine development and control strategies for shigellosis. PMID:19955273

  15. Molecular analysis of the thymidine-auxotrophic small colony variant phenotype of Staphylococcus aureus.

    PubMed

    Besier, Silke; Ludwig, Albrecht; Ohlsen, Knut; Brade, Volker; Wichelhaus, Thomas A

    2007-07-01

    Thymidine-auxotrophic small colony variants (SCVs) of Staphylococcus aureus are frequently isolated from the chronically infected airways of patients suffering from cystic fibrosis. To date, little is known regarding the molecular mechanisms leading to the formation of this special phenotype, but the auxotrophism for thymidine suggests that impaired thymidine metabolism might play a major role. Sequence analysis of the thymidylate synthase-encoding thyA gene of six clinical thymidine-auxotrophic S. aureus SCVs revealed that all isolates had mutations within thyA. In five isolates the function of the thymidylate synthase was definitely impaired: three of them showed a truncation of the thyA coding sequence by nonsense or frame-shift mutations, in one further isolate the active site of the enzyme was affected by an internal 12-bp deletion, and another isolate had a 173-bp deletion spanning the 5'-terminal region of thyA and the preceding DNA sequence. The sixth isolate showed two amino acid substitutions within the thyA gene product. To confirm the importance of impaired thymidylate synthase synthesis or activity for the formation of the thymidine-auxotrophic SCV phenotype, we constructed a thyA knock-out mutant of a wild-type S. aureus strain. This mutant showed all characteristics of clinical SCVs, such as slow growth, decreased pigment production, reduced hemolytic activity, auxotrophism for thymidine, resistance to trimethoprim/sulfamethoxazol, and reduced plasma coagulase activity. Complementation of the thyA knock-out mutant with intact thyA in trans nearly restored the normal phenotype. In conclusion, these data confirm at the molecular level that impaired thymidylate synthase function is causative for the formation of the thymidine-auxotrophic SCV phenotype in S. aureus. PMID:17412637

  16. Characteristics of Salmonella enterica Serovar 4,[5],12:i:- as a Monophasic Variant of Serovar Typhimurium

    PubMed Central

    Ido, Noriko; Lee, Ken-ichi; Iwabuchi, Kaori; Izumiya, Hidemasa; Uchida, Ikuo; Kusumoto, Masahiro; Iwata, Taketoshi; Ohnishi, Makoto; Akiba, Masato

    2014-01-01

    Salmonella enterica subspecies enterica serovar 4,[5],12:i:- (S. 4,[5]12:i:-) is believed to be a monophasic variant of S. enterica serovar Typhimurium (S. Typhimurium). This study was conducted to corroborate this hypothesis and to identify the molecular and phenotypic characteristics of the S. 4,[5]12:i:- isolates in Japan. A total of 51 S. 4,[5]12:i:- isolates derived from humans, cattle, swine, chickens, birds, meat (pork), and river water in 15 prefectures in Japan between 2000 and 2010 were analyzed. All the S. 4,[5],12:i:- isolates were identified as S. Typhimurium by two different polymerase chain reactions (PCR) for identification of S. Typhimurium. Of the 51 S. 4,[5],12:i:- isolates, 39 (76.5%) harbored a 94-kb virulence plasmid, which is known to be specific for S. Typhimurium. These data suggest that the S. 4,[5],12:i:- isolates are monophasic variants of S. Typhimurium. The flagellar phase variation is induced by three adjacent genes (fljA, fljB, and hin) in the chromosome. The results of PCR mapping of this region and comparative genomic hybridization analysis suggested that the deletion of the fljAB operon and its flanking region was the major genetic basis of the monophasic phenotype of S. 4,[5],12:i:-. The fljAB operon and hin gene were detectable in eight of the S. 4,[5],12:i:- isolates with common amino acid substitutions of A46T in FljA and R140L in Hin. The introduction of these mutations into S. Typhimurium isolates led to the loss of selectability of isolates expressing the phase 2 H antigen. These data suggested that a point mutation was the genetic basis, at least in part, of the S. 4,[5],12:i:- isolates. The results of phenotypic analysis suggested that the S. 4,[5],12:i:- isolates in Japan consist of multiple distinct clones. This is the first detailed characterization of the S. 4,[5],12:i:- isolates derived from various sources across Japan. PMID:25093666

  17. Handedness and language learning disability differentially distribute in progressive aphasia variants

    PubMed Central

    Mandelli, Maria Luisa; Rankin, Katherine P.; Henry, Maya L.; Babiak, Miranda C.; Frazier, Darvis T.; Lobach, Iryna V.; Bettcher, Brianne M.; Wu, Teresa Q.; Rabinovici, Gil D.; Graff-Radford, Neill R.; Miller, Bruce L.; Gorno-Tempini, Maria Luisa

    2013-01-01

    Primary progressive aphasia is a neurodegenerative clinical syndrome that presents in adulthood with an isolated, progressive language disorder. Three main clinical/anatomical variants have been described, each associated with distinctive pathology. A high frequency of neurodevelopmental learning disability in primary progressive aphasia has been reported. Because the disorder is heterogeneous with different patterns of cognitive, anatomical and biological involvement, we sought to identify whether learning disability had a predilection for one or more of the primary progressive aphasia subtypes. We screened the University of California San Francisco Memory and Aging Center's primary progressive aphasia cohort (n = 198) for history of language-related learning disability as well as hand preference, which has associations with learning disability. The study included logopenic (n = 48), non-fluent (n = 54) and semantic (n = 96) variant primary progressive aphasias. We investigated whether the presence of learning disability or non-right-handedness was associated with differential effects on demographic, neuropsychological and neuroimaging features of primary progressive aphasia. We showed that a high frequency of learning disability was present only in the logopenic group (?2 = 15.17, P < 0.001) and (?2 = 11.51, P < 0.001) compared with semantic and non-fluent populations. In this group, learning disability was associated with earlier onset of disease, more isolated language symptoms, and more focal pattern of left posterior temporoparietal atrophy. Non-right-handedness was instead over-represented in the semantic group, at nearly twice the prevalence of the general population (?2 = 6.34, P = 0.01). Within semantic variant primary progressive aphasia the right-handed and non-right-handed cohorts appeared homogeneous on imaging, cognitive profile, and structural analysis of brain symmetry. Lastly, the non-fluent group showed no increase in learning disability or non-right-handedness. Logopenic variant primary progressive aphasia and developmental dyslexia both manifest with phonological disturbances and posterior temporal involvement. Learning disability might confer vulnerability of this network to early-onset, focal Alzheimer’s pathology. Left-handedness has been described as a proxy for atypical brain hemispheric lateralization. As non-right-handedness was increased only in the semantic group, anomalous lateralization mechanisms might instead be related to frontotemporal lobar degeneration with abnormal TARDBP. Taken together, this study suggests that neurodevelopmental signatures impart differential trajectories towards neurodegenerative disease. PMID:24056533

  18. Genetic variability and pathological properties of Grapevine Leafroll-associated Virus 2 isolates

    Microsoft Academic Search

    Nadia Bertazzon; Michele Borgo; Stefano Vanin; Elisa Angelini

    2010-01-01

    The genetic variability among Grapevine leafroll-associated virus 2 (GLRaV-2) isolates was investigated in several grapevine accessions from various geographic origins in three genomic fragments,\\u000a which encode the 70 kDa heat-shock protein homologue, the coat protein and the ?60 kDa protein. The majority of the isolates\\u000a were identical or only slightly different from one another and formed a monophyletic group. Several other variants

  19. Adjustment of familial relatedness in association test for rare variants

    PubMed Central

    2014-01-01

    High-throughput sequencing technology allows researchers to test associations between phenotypes and all the variants identified throughout the genome, and is especially useful for analyzing rare variants. However, the statistical power to identify phenotype-associated rare variants is very low with typical genome-wide association studies because of their low allele frequencies among unrelated individuals. In contrast, a family-based design may have more power because rare variants are more likely to be enriched in families than among unrelated individuals. Regardless, an analysis of family-based association studies needs to account appropriately for relatedness between family members. We analyzed the observed quantitative trait systolic blood pressure as well as the simulated Q1 data in the Genetic Analysis Workshop 18 data set using 4 tests: (a) a single-variant test, (b) a collapsing test, (c) a single-variant test where familial relatedness was accounted for, and (d) a collapsing test where familial relatedness was accounted for. We then compared the results of the 4 methods and observed that adjusting for familial relatedness could appropriately control the false-positive rate while maintaining reasonable power to detect several strongly associated variants/genes. PMID:25519384

  20. Adjustment of familial relatedness in association test for rare variants.

    PubMed

    Li, Cong; Yang, Can; Chen, Mengjie; Chen, Xiaowei; Hou, Lin; Zhao, Hongyu

    2014-01-01

    High-throughput sequencing technology allows researchers to test associations between phenotypes and all the variants identified throughout the genome, and is especially useful for analyzing rare variants. However, the statistical power to identify phenotype-associated rare variants is very low with typical genome-wide association studies because of their low allele frequencies among unrelated individuals. In contrast, a family-based design may have more power because rare variants are more likely to be enriched in families than among unrelated individuals. Regardless, an analysis of family-based association studies needs to account appropriately for relatedness between family members. We analyzed the observed quantitative trait systolic blood pressure as well as the simulated Q1 data in the Genetic Analysis Workshop 18 data set using 4 tests: (a) a single-variant test, (b) a collapsing test, (c) a single-variant test where familial relatedness was accounted for, and (d) a collapsing test where familial relatedness was accounted for. We then compared the results of the 4 methods and observed that adjusting for familial relatedness could appropriately control the false-positive rate while maintaining reasonable power to detect several strongly associated variants/genes. PMID:25519384

  1. Rare variant analysis for family-based design.

    PubMed

    De, Gourab; Yip, Wai-Ki; Ionita-Laza, Iuliana; Laird, Nan

    2013-01-01

    Genome-wide association studies have been able to identify disease associations with many common variants; however most of the estimated genetic contribution explained by these variants appears to be very modest. Rare variants are thought to have larger effect sizes compared to common SNPs but effects of rare variants cannot be tested in the GWAS setting. Here we propose a novel method to test for association of rare variants obtained by sequencing in family-based samples by collapsing the standard family-based association test (FBAT) statistic over a region of interest. We also propose a suitable weighting scheme so that low frequency SNPs that may be enriched in functional variants can be upweighted compared to common variants. Using simulations we show that the family-based methods perform at par with the population-based methods under no population stratification. By construction, family-based tests are completely robust to population stratification; we show that our proposed methods remain valid even when population stratification is present. PMID:23341868

  2. Molecular Characterization of Hepatitis A Virus Isolates from a Transcontinental Shellfish-Borne Outbreak

    PubMed Central

    Sánchez, Glòria; Pintó, Rosa M.; Vanaclocha, Hermelinda; Bosch, Albert

    2002-01-01

    One hundred eighty-four serologically confirmed cases of hepatitis A were reported in eastern Spain in 1999. A matched case-control study implicated imported coquina clams complying with European Union shellfish standards as the source of infection; this implication was confirmed by the detection by reverse transcription-PCR of hepatitis A virus (HAV) RNA in shellfish samples. In spite of the recognized low variability of HAV, genetic characterization of the complete capsid region of virus isolates from patient serum samples revealed the existence of both synonymous and nonsynonymous variants. Two antigenic variants were detected, one in a discontinuous epitope defined by monoclonal antibody K3-4C8 and a second in a linear VP1 epitope of the virus. In spite of these antigenic variants, all isolates were assigned to genotype IB, providing further evidence that the outbreak originated from a common source, although multiple strains were likely to be involved. PMID:12409389

  3. Antigenic, morphologic, and molecular characterization of new Ehrlichia risticii isolates.

    PubMed Central

    Chaichanasiriwithaya, W; Rikihisa, Y; Yamamoto, S; Reed, S; Crawford, T B; Perryman, L E; Palmer, G H

    1994-01-01

    Ehrlichia risticii causes an acute infectious disease in horses called Potomac horse fever. To investigate the biological diversity of E. risticii organisms, nine E. risticii isolates derived from the peripheral blood monocytes of clinically sick horses in Ohio and Kentucky during the summers of 1991 and 1993 were compared with Illinois and Virginia isolates originally obtained from horses in Maryland in 1984. Seven of the nine isolates (081, 606, 380, 679, As, Co, and Ov) formed large morulae (tightly packed inclusions of ehrlichial organisms). The remaining isolates, including 1984 isolates, were individually dispersed or formed small morulae in the cytoplasm of P388D1 cells. In Western blot (immunoblot) analysis with four equine and one rabbit polyclonal anti-E. risticii sera, these recent E. risticii isolates showed patterns of antigenic proteins distinct from those of the 1984 isolates and could be divided into three groups: (i) 081; (ii) 606, 022, 067, 380, and 679; and (iii) As, Co, and Ov. By indirect fluorescent antibody labeling with two panels of murine anti-E. risticii (Illinois and Maryland isolates) monoclonal antibodies, isolate 081 was not labeled with any of 20 monoclonal antibodies tested. The remaining isolates were not labeled with several monoclonal antibodies. The digestion pattern with one of the restriction enzymes, AvaII, of the PCR-amplified partial 16S rRNA gene of E. risticii from all Kentucky isolates (As, Co, and Ov) was different from that of Illinois, Virginia, and six Ohio isolates. These results indicate the presence of distinct variants of E. risticii which vary significantly in morphology, antigenic composition, and the base sequence of the 16S rRNA gene. Images PMID:7533780

  4. VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data

    PubMed Central

    Horner, Neil; Assefa, Samuel; Campino, Susana; Auburn, Sarah; Zongo, Issaka; Ouedraogo, Jean-Bosco; Nosten, Francois; Anderson, Tim; Clark, Taane G.

    2012-01-01

    Summary: There is an immediate need for tools to both analyse and visualize in real-time single-nucleotide polymorphisms, insertions and deletions, and other structural variants from new sequence file formats. We have developed VarB software that can be used to visualize variant call format files in real time, as well as identify regions under balancing selection and informative markers to differentiate user-defined groups (e.g. populations). We demonstrate its utility using sequence data from 50 Plasmodium falciparum isolates comprising two different continents and confirm known signals from genomic regions that contain important antigenic and anti-malarial drug-resistance genes. Availability and implementation: The C++-based software VarB and user manual are available from www.pathogenseq.org/varb. Contact: taane.clark@lshtm.ac.uk PMID:22976080

  5. HIV-1 genetic diversity in Russia: CRF63_02A1, a new HIV type 1 genetic variant spreading in Siberia.

    PubMed

    Baryshev, Pavel B; Bogachev, Vladislav V; Gashnikova, Natalya M

    2014-06-01

    One of the factors determining a high degree of heterogeneity in the HIV population is recombination-based variation, which leads to the emergence of the virus variants with a mosaic genome. An example is CRF63_02A1, an HIV-1 variant currently spreading in the Siberian region of Russia. To prove that this HIV-1 variant is a new circulating recombinant form that had emerged as a result of repeated recombination between CRF02_AG and subtype A, we have isolated seven full-length HIV genomes and theoretically analyzed them, that is, reconstructed the phylogenetic relationships, determined recombination breakpoints and regions, and compared them with the regions known for CRF02_AG. PMID:24279614

  6. Detection and Impact of Rare Regulatory Variants in Human Disease

    PubMed Central

    Li, Xin; Montgomery, Stephen B.

    2013-01-01

    Advances in genome sequencing are providing unprecedented resolution of rare and private variants. However, methods which assess the effect of these variants have relied predominantly on information within coding sequences. Assessing their impact in non-coding sequences remains a significant contemporary challenge. In this review, we highlight the role of regulatory variation as causative agents and modifiers of monogenic disorders. We further discuss how advances in functional genomics are now providing new opportunity to assess the impact of rare non-coding variants and their role in disease. PMID:23755067

  7. Multiple Sodium Channel Variants in the Mosquito Culex quinquefasciatus

    PubMed Central

    He, Lin; Li, Ting; Zhang, Lee; Liu, Nannan

    2012-01-01

    Voltage-gated sodium channels are the target sites of both DDT and pyrethroid insecticides. The importance of alternative splicing as a key mechanism governing the structural and functional diversity of sodium channels and the resulting development of insecticide and acaricide resistance is widely recognized, as shown by the extensive research on characterizing alternative splicing and variants of sodium channels in medically and agriculturally important insect species. Here we present the first comparative study of multiple variants of the sodium channel transcripts in the mosquito Culex quinquefasciatus. The variants were classified into two categories, CxNa-L and CxNa-S based on their distinguishing sequence sizes of ~6.5 kb and ~4.0 kb, respectively, and generated via major extensive alternative splicing with minor small deletions/ insertions in susceptible S-Lab, low resistant HAmCqG0, and highly resistant HAmCqG8 Culex strains. Four alternative Cx-Na-L splice variants were identified, including three full length variants with three optional exons (2, 5, and 21i) and one with in-frame-stop codons. Large, multi-exon-alternative splices were identified in the CxNa-S category. All CxNa-S splicing variants in the S-Lab and HAmCqG0 strains contained in-frame stop codons, suggesting that any resulting proteins would be truncated. The ~1000 to ~3000-fold lower expression of these splice variants with stop codons compared with the CxNa-L splicing variants may support the lower importance of these variants in S-Lab and HAmCqG0. Interestingly, two alternative splicing variants of CxNa-S in HAmCqG8 included entire ORFs but lacked exons 5 to18 and these two variants had much higher expression levels in HAmCqG8 than in S-Lab and HAmCqG0. These results provide a functional basis for further characterizing how alternative splicing of a voltage-gated sodium channel contributes to diversity in neuronal signaling in mosquitoes in response to pyrethroids, and possibly indicates the role of these variants in the development of pyrethroid resistance. PMID:23139629

  8. Multi-Locus Analysis of a Citreoviridin-Producing Isolate Previously Identified as Penicillium NRRL 13013

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cole et al (1981) reported a citreoviridin-producing isolate of Penicillium charlesii (NRRL 13013) from molded pecans. Wicklow later identified it as a variant of Penicillium citreoviride, noting that it produced sclerotia, although the species as a whole is not known to do so. We sequenced the IT...

  9. Genomic sequence analysis of a nucleopolyhedrovirus isolated from the diamondback moth, Plutella xylostella.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The CL3 plaque isolate of Plutella xylostella multiple nucleopolyhedrovirus (PlxyMNPV-CL3) is a variant of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) but exhibits a much higher degree of virulence against the diamondback moth, Plutella xylostella. To identify genetic differences ...

  10. Antigenic and genetic variation in cytopathic hepatitis A virus variants arising during persistent infection: evidence for genetic recombination.

    PubMed

    Lemon, S M; Murphy, P C; Shields, P A; Ping, L H; Feinstone, S M; Cromeans, T; Jansen, R W

    1991-04-01

    Variants of hepatitis A virus (pHM175 virus) recovered from persistently infected green monkey kidney (BS-C-1) cells induced a cytopathic effect during serial passage in BS-C-1 or fetal rhesus kidney (FRhK-4) cells. Epitope-specific radioimmunofocus assays showed that this virus comprised two virion populations, one with altered antigenicity including neutralization resistance to monoclonal antibody K24F2, and the other with normal antigenic characteristics. Replication of the antigenic variant was favored over that of virus with the normal antigenic phenotype during persistent infection, while virus with the normal antigenic phenotype was selected during serial passage. Viruses of each type were clonally isolated; both were cytopathic in cell cultures and displayed a rapid replication phenotype when compared with the noncytopathic passage 16 (p16) HM175 virus which was used to establish the original persistent infection. The two cytopathic virus clones contained 31 and 34 nucleotide changes from the sequence of p16 HM175. Both shared a common 5' sequence (bases 30 to 1677), as well as sequence identity in the P2-P3 region (bases 3249 to 5303 and 6462 to 6781) and 3' terminus (bases 7272 to 7478). VP3, VP1, and 3Cpro contained different mutations in the two virus clones, with amino acid substitutions at residues 70 of VP3 and 197 and 276 of VP1 of the antigenic variant. These capsid mutations did not affect virion thermal stability. A comparison of the nearly complete genomic sequences of three clonally isolated cytopathic variants was suggestive of genetic recombination between these viruses during persistent infection and indicated that mutations in both 5' and 3' nontranslated regions and in the nonstructural proteins 2A, 2B, 2C, 3A, and 3Dpol may be related to the cytopathic phenotype. PMID:1705995

  11. Antigenic and genetic variation in cytopathic hepatitis A virus variants arising during persistent infection: evidence for genetic recombination.

    PubMed Central

    Lemon, S M; Murphy, P C; Shields, P A; Ping, L H; Feinstone, S M; Cromeans, T; Jansen, R W

    1991-01-01

    Variants of hepatitis A virus (pHM175 virus) recovered from persistently infected green monkey kidney (BS-C-1) cells induced a cytopathic effect during serial passage in BS-C-1 or fetal rhesus kidney (FRhK-4) cells. Epitope-specific radioimmunofocus assays showed that this virus comprised two virion populations, one with altered antigenicity including neutralization resistance to monoclonal antibody K24F2, and the other with normal antigenic characteristics. Replication of the antigenic variant was favored over that of virus with the normal antigenic phenotype during persistent infection, while virus with the normal antigenic phenotype was selected during serial passage. Viruses of each type were clonally isolated; both were cytopathic in cell cultures and displayed a rapid replication phenotype when compared with the noncytopathic passage 16 (p16) HM175 virus which was used to establish the original persistent infection. The two cytopathic virus clones contained 31 and 34 nucleotide changes from the sequence of p16 HM175. Both shared a common 5' sequence (bases 30 to 1677), as well as sequence identity in the P2-P3 region (bases 3249 to 5303 and 6462 to 6781) and 3' terminus (bases 7272 to 7478). VP3, VP1, and 3Cpro contained different mutations in the two virus clones, with amino acid substitutions at residues 70 of VP3 and 197 and 276 of VP1 of the antigenic variant. These capsid mutations did not affect virion thermal stability. A comparison of the nearly complete genomic sequences of three clonally isolated cytopathic variants was suggestive of genetic recombination between these viruses during persistent infection and indicated that mutations in both 5' and 3' nontranslated regions and in the nonstructural proteins 2A, 2B, 2C, 3A, and 3Dpol may be related to the cytopathic phenotype. Images PMID:1705995

  12. Integrated optical isolators

    E-print Network

    Zaman, Tauhid R

    2005-01-01

    Introduction: Optical isolators are important components in lasers. Their main function is to eliminate noise caused by back-reflections into these lasers. The need for integrated isolators comes from the continuing growth ...

  13. Base isolation case study

    E-print Network

    Ching, Kenneth A. (Kenneth Apostol)

    2008-01-01

    The primary objective of this thesis is the introduction of the current code, ASCE 7-05 into the base isolation design and the analysis of base isolation response due to seismic forces. An eight story irregular structure ...

  14. Psychopathology of social isolation

    PubMed Central

    Baek, Sang-Bin

    2014-01-01

    The most important defining factor of being human is the use of symbolic language. Language or communication problem occurs during the growth, the child will have a higher risk of social isolation and then the survival will be threatened constantly. Today, adolescents and youths are familiar with computer and smart-phone devices, and communication with others by these devices is easy than face-to-face communication. As adolescents and youths live in the comfortable and familiar cyber-world rather than actively participating real society, so they make social isolation. Extreme form of this isolation in adolescents and youths is so-called Socially Withdrawn Youth. In this study, the psychopathological factors inducing social isolation were discussed. Development stages of social isolation in relation with types of social isolation, Ego-syntonic isolation and Ego-dystonic isolation, were also considered. PMID:25061592

  15. Meta-analysis of gene-level associations for rare variants based on single-variant statistics.

    PubMed

    Hu, Yi-Juan; Berndt, Sonja I; Gustafsson, Stefan; Ganna, Andrea; Hirschhorn, Joel; North, Kari E; Ingelsson, Erik; Lin, Dan-Yu

    2013-08-01

    Meta-analysis of genome-wide association studies (GWASs) has led to the discoveries of many common variants associated with complex human diseases. There is a growing recognition that identifying "causal" rare variants also requires large-scale meta-analysis. The fact that association tests with rare variants are performed at the gene level rather than at the variant level poses unprecedented challenges in the meta-analysis. First, different studies may adopt different gene-level tests, so the results are not compatible. Second, gene-level tests require multivariate statistics (i.e., components of the test statistic and their covariance matrix), which are difficult to obtain. To overcome these challenges, we propose to perform gene-level tests for rare variants by combining the results of single-variant analysis (i.e., p values of association tests and effect estimates) from participating studies. This simple strategy is possible because of an insight that multivariate statistics can be recovered from single-variant statistics, together with the correlation matrix of the single-variant test statistics, which can be estimated from one of the participating studies or from a publicly available database. We show both theoretically and numerically that the proposed meta-analysis approach provides accurate control of the type I error and is as powerful as joint analysis of individual participant data. This approach accommodates any disease phenotype and any study design and produces all commonly used gene-level tests. An application to the GWAS summary results of the Genetic Investigation of ANthropometric Traits (GIANT) consortium reveals rare and low-frequency variants associated with human height. The relevant software is freely available. PMID:23891470

  16. Meta-analysis of Gene-Level Associations for Rare Variants Based on Single-Variant Statistics

    PubMed Central

    Hu, Yi-Juan; Berndt, Sonja I.; Gustafsson, Stefan; Ganna, Andrea; Berndt, Sonja I.; Gustafsson, Stefan; Mägi, Reedik; Ganna, Andrea; Wheeler, Eleanor; Feitosa, Mary F.; Justice, Anne E.; Monda, Keri L.; Croteau-Chonka, Damien C.; Day, Felix R.; Esko, Tõnu; Fall, Tove; Ferreira, Teresa; Gentilini, Davide; Jackson, Anne U.; Luan, Jian’an; Randall, Joshua C.; Vedantam, Sailaja; Willer, Cristen J.; Winkler, Thomas W.; Wood, Andrew R.; Workalemahu, Tsegaselassie; Hu, Yi-Juan; Lee, Sang Hong; Liang, Liming; Lin, Dan-Yu; Min, Josine L.; Neale, Benjamin M.; Thorleifsson, Gudmar; Yang, Jian; Albrecht, Eva; Amin, Najaf; Bragg-Gresham, Jennifer L.; Cadby, Gemma; den Heijer, Martin; Eklund, Niina; Fischer, Krista; Goel, Anuj; Hottenga, Jouke-Jan; Huffman, Jennifer E.; Jarick, Ivonne; Johansson, Åsa; Johnson, Toby; Kanoni, Stavroula; Kleber, Marcus E.; König, Inke R.; Kristiansson, Kati; Kutalik, Zoltán; Lamina, Claudia; Lecoeur, Cecile; Li, Guo; Mangino, Massimo; McArdle, Wendy L.; Medina-Gomez, Carolina; Müller-Nurasyid, Martina; Ngwa, Julius S.; Nolte, Ilja M.; Paternoster, Lavinia; Pechlivanis, Sonali; Perola, Markus; Peters, Marjolein J.; Preuss, Michael; Rose, Lynda M.; Shi, Jianxin; Shungin, Dmitry; Smith, Albert Vernon; Strawbridge, Rona J.; Surakka, Ida; Teumer, Alexander; Trip, Mieke D.; Tyrer, Jonathan; Van Vliet-Ostaptchouk, Jana V.; Vandenput, Liesbeth; Waite, Lindsay L.; Zhao, Jing Hua; Absher, Devin; Asselbergs, Folkert W.; Atalay, Mustafa; Attwood, Antony P.; Balmforth, Anthony J.; Basart, Hanneke; Beilby, John; Bonnycastle, Lori L.; Brambilla, Paolo; Bruinenberg, Marcel; Campbell, Harry; Chasman, Daniel I.; Chines, Peter S.; Collins, Francis S.; Connell, John M.; Cookson, William; de Faire, Ulf; de Vegt, Femmie; Dei, Mariano; Dimitriou, Maria; Edkins, Sarah; Estrada, Karol; Evans, David M.; Farrall, Martin; Ferrario, Marco M.; Ferrières, Jean; Franke, Lude; Frau, Francesca; Gejman, Pablo V.; Grallert, Harald; Grönberg, Henrik; Gudnason, Vilmundur; Hall, Alistair S.; Hall, Per; Hartikainen, Anna-Liisa; Hayward, Caroline; Heard-Costa, Nancy L.; Heath, Andrew C.; Hebebrand, Johannes; Homuth, Georg; Hu, Frank B.; Hunt, Sarah E.; Hyppönen, Elina; Iribarren, Carlos; Jacobs, Kevin B.; Jansson, John-Olov; Jula, Antti; Kähönen, Mika; Kathiresan, Sekar; Kee, Frank; Khaw, Kay-Tee; Kivimaki, Mika; Koenig, Wolfgang; Kraja, Aldi T.; Kumari, Meena; Kuulasmaa, Kari; Kuusisto, Johanna; Laitinen, Jaana H.; Lakka, Timo A.; Langenberg, Claudia; Launer, Lenore J.; Lind, Lars; Lindström, Jaana; Liu, Jianjun; Liuzzi, Antonio; Lokki, Marja-Liisa; Lorentzon, Mattias; Madden, Pamela A.; Magnusson, Patrik K.; Manunta, Paolo; Marek, Diana; März, Winfried; Leach, Irene Mateo; McKnight, Barbara; Medland, Sarah E.; Mihailov, Evelin; Milani, Lili; Montgomery, Grant W.; Mooser, Vincent; Mühleisen, Thomas W.; Munroe, Patricia B.; Musk, Arthur W.; Narisu, Narisu; Navis, Gerjan; Nicholson, George; Nohr, Ellen A.; Ong, Ken K.; Oostra, Ben A.; Palmer, Colin N.A.; Palotie, Aarno; Peden, John F.; Pedersen, Nancy; Peters, Annette; Polasek, Ozren; Pouta, Anneli; Pramstaller, Peter P.; Prokopenko, Inga; Pütter, Carolin; Radhakrishnan, Aparna; Raitakari, Olli; Rendon, Augusto; Rivadeneira, Fernando; Rudan, Igor; Saaristo, Timo E.; Sambrook, Jennifer G.; Sanders, Alan R.; Sanna, Serena; Saramies, Jouko; Schipf, Sabine; Schreiber, Stefan; Schunkert, Heribert; Shin, So-Youn; Signorini, Stefano; Sinisalo, Juha; Skrobek, Boris; Soranzo, Nicole; Stan?áková, Alena; Stark, Klaus; Stephens, Jonathan C.; Stirrups, Kathleen; Stolk, Ronald P.; Stumvoll, Michael; Swift, Amy J.; Theodoraki, Eirini V.; Thorand, Barbara; Tregouet, David-Alexandre; Tremoli, Elena; Van der Klauw, Melanie M.; van Meurs, Joyce B.J.; Vermeulen, Sita H.; Viikari, Jorma; Virtamo, Jarmo; Vitart, Veronique; Waeber, Gérard; Wang, Zhaoming; Widén, Elisabeth; Wild, Sarah H.; Willemsen, Gonneke; Winkelmann, Bernhard R.; Witteman, Jacqueline C.M.; Wolffenbuttel, Bruce H.R.; Wong, Andrew; Wright, Alan F.

    2013-01-01

    Meta-analysis of genome-wide association studies (GWASs) has led to the discoveries of many common variants associated with complex human diseases. There is a growing recognition that identifying “causal” rare variants also requires large-scale meta-analysis. The fact that association tests with rare variants are performed at the gene level rather than at the variant level poses unprecedented challenges in the meta-analysis. First, different studies may adopt different gene-level tests, so the results are not compatible. Second, gene-level tests require multivariate statistics (i.e., components of the test statistic and their covariance matrix), which are difficult to obtain. To overcome these challenges, we propose to perform gene-level tests for rare variants by combining the results of single-variant analysis (i.e., p values of association tests and effect estimates) from participating studies. This simple strategy is possible because of an insight that multivariate statistics can be recovered from single-variant statistics, together with the correlation matrix of the single-variant test statistics, which can be estimated from one of the participating studies or from a publicly available database. We show both theoretically and numerically that the proposed meta-analysis approach provides accurate control of the type I error and is as powerful as joint analysis of individual participant data. This approach accommodates any disease phenotype and any study design and produces all commonly used gene-level tests. An application to the GWAS summary results of the Genetic Investigation of ANthropometric Traits (GIANT) consortium reveals rare and low-frequency variants associated with human height. The relevant software is freely available. PMID:23891470

  17. October 1992 ISOLATOR-11

    E-print Network

    Kleinfeld, David

    generates both high voltage and high current and care should be taken in its operation in any environment The ISOLATOR-11 Stimulus Isolation Unit is a constant current source, and so the voltage it produces Tissues ...7 The Stimulus Artifact 7 Ganging Together Isolators ...8 Power Supply Voltage 9 Grounding

  18. Searching for Variants, Genes, and Pathways Involved in Hyperlipidemia

    E-print Network

    Haas, Blake Edwin

    2012-01-01

    association studies (GWAS) have been successful in identifying variants with low to moderate effects on serum lipid levels.association studies (GWAS) are a popular method of discovering common SNPs that are associated with serum lipid levels

  19. Statistical Analysis Strategies for Association Studies Involving Rare Variants

    PubMed Central

    Bansal, Vikas; Libiger, Ondrej; Torkamani, Ali; Schork, Nicholas J.

    2013-01-01

    The limitations of genome-wide association (GWA) studies that focus on the phenotypic influence of common genetic variants have motivated human geneticists to consider the contribution of rare variants to phenotypic expression. The increasing availability of high-throughput sequencing technology has enabled studies of rare variants, but will not be sufficient for their success since appropriate analytical methods are also needed. We consider data analysis approaches to testing associations between a phenotype and collections of rare variants in a defined genomic region or set of regions. Ultimately, although a wide variety of analytical approaches exist, more work is needed to refine them and determine their properties and power in different contexts. PMID:20940738

  20. Lobular Carcinoma in Situ, Classical Type and Unusual Variants

    Microsoft Academic Search

    Melissa Murray; Edi Brogi

    2009-01-01

    The morphologic spectrum of lobular carcinoma in situ (LCIS) includes the classical type and unusual variants recently described. In this article we review the morphology of LCIS and highlight ways to distinguish it from its morphologic mimickers.

  1. Frequency of enzyme deficiency variants in erythrocytes of newborn infants

    SciTech Connect

    Mohrenweiser, H.W.

    1981-08-01

    The frequency of enzyme deficiency variants, defined as alleles whose products are either absent or almost devoid of normal activity in erythrocytes, was determined for nine erythrocyte enzymes in some 675 newborn infants and in approximately 200 adults. Examples of this type of genetic abnormality, which in the homozygous condition are often associated with significant health consequences, were detected for seven of the nine enzymes studied. Fifteen inherited enzyme deficiency variants in 1809 determinations from adults were identified. Seven of the deficiency variants involved triosephosphate isomerase, a frequency of 0.01 in the newborn population. The average frequency of 2.4/1000 is 2 to 3 times the frequency observed for rare electrophoretic variants of erythrocyte enzymes in this same population.

  2. New insights into old methods for identifying causal rare variants.

    PubMed

    Wang, Haitian; Huang, Chien-Hsun; Lo, Shaw-Hwa; Zheng, Tian; Hu, Inchi

    2011-01-01

    The advance of high-throughput next-generation sequencing technology makes possible the analysis of rare variants. However, the investigation of rare variants in unrelated-individuals data sets faces the challenge of low power, and most methods circumvent the difficulty by using various collapsing procedures based on genes, pathways, or gene clusters. We suggest a new way to identify causal rare variants using the F-statistic and sliced inverse regression. The procedure is tested on the data set provided by the Genetic Analysis Workshop 17 (GAW17). After preliminary data reduction, we ranked markers according to their F-statistic values. Top-ranked markers were then subjected to sliced inverse regression, and those with higher absolute coefficients in the most significant sliced inverse regression direction were selected. The procedure yields good false discovery rates for the GAW17 data and thus is a promising method for future study on rare variants. PMID:22373518

  3. Techniques to access histone modifications and variants in cancer.

    PubMed

    Tyagi, Monica; Khan, Shafqat A; Bhattacharya, Saikat; Reddy, Divya; Sharma, Ajit K; Khade, Bharat; Gupta, Sanjay

    2015-01-01

    Recent years have witnessed an explosion of epigenetic research on the role of histone variants and modifications in cancer. To understand the global dynamics of chromatin structure and function, analysis of histone variants incorporated into the nucleosome and their covalent modifications, is required. The nucleosome is the fundamental structural unit of chromatin, contains an octamer of core histones H3, H4, H2A, and H2B. The differential alterations in diverse histone variants and their accompanying modifications patterns will provide a deeper insight into their biological role in structural and functional properties of chromatin. Here we provide a step-by-step protocol to investigate these aspects, the histone modifications and variants, their localization and dynamics within specific regions of chromatin under distinct condition and the recruitment/retention of epigenetic regulators at their target sites in chromatin to influence cell growth and differentiation. PMID:25421664

  4. Genetics Home Reference: GM2-gangliosidosis, AB variant

    MedlinePLUS

    ... Patients and Families Resources for Health Professionals What glossary definitions help with understanding GM2-gangliosidosis, AB variant? ... many other terms in the Genetics Home Reference Glossary . See also Understanding Medical Terminology . References (4 links) ...

  5. Leapfrog variants of iterative methods for linear algebra equations

    NASA Technical Reports Server (NTRS)

    Saylor, Paul E.

    1988-01-01

    Two iterative methods are considered, Richardson's method and a general second order method. For both methods, a variant of the method is derived for which only even numbered iterates are computed. The variant is called a leapfrog method. Comparisons between the conventional form of the methods and the leapfrog form are made under the assumption that the number of unknowns is large. In the case of Richardson's method, it is possible to express the final iterate in terms of only the initial approximation, a variant of the iteration called the grand-leap method. In the case of the grand-leap variant, a set of parameters is required. An algorithm is presented to compute these parameters that is related to algorithms to compute the weights and abscissas for Gaussian quadrature. General algorithms to implement the leapfrog and grand-leap methods are presented. Algorithms for the important special case of the Chebyshev method are also given.

  6. Identification of an atypical variant of logopenic progressive aphasia

    PubMed Central

    Machulda, Mary M.; Whitwell, Jennifer L.; Duffy, Joseph R.; Strand, Edythe; Dean, Pamela M.; Senjem, Matthew L.; Jack, Clifford R.; Josephs, Keith A.

    2013-01-01

    The purpose of this study was to examine the association between aphasia severity and neurocognitive function, disease duration and temporoparietal atrophy in 21 individuals with the logopenic variant of primary progressive aphasia (lvPPA). We found significant correlations between aphasia severity and neurocognitive severity as well as temporoparietal atrophy; but not disease duration. Cluster analysis identified three variants of lvPPA: (1) subjects with mild aphasia and short disease duration (mild typical lvPPA); (2) subjects with mild aphasia and long disease duration (mild atypical lvPPA); and, (3) subjects with severe aphasia and relatively long disease duration (severe typical lvPPA). All three variants showed temporoparietal atrophy, with the mild atypical group showing the least atrophy despite the longest disease duration. The mild atypical group also showed mild neuropsychological impairment. The subjects with mild aphasia and neuropsychological impairment despite long disease duration may represent a slowly progressive variant of lvPPA. PMID:23566690

  7. Variant of Usher Syndrome Gene Preserves Vision and Balance

    MedlinePLUS

    ... preserves vision and balance Variant of Usher Syndrome Gene Preserves Vision and Balance Usher syndrome, an inherited, ... mutant copy of any one of several different genes. But surprisingly, some mutations of the same genes ...

  8. Study on Variant Anatomy of Sciatic Nerve

    PubMed Central

    V, Sangeetha

    2014-01-01

    Introduction: Sciatic Nerve (SN) is the nerve of the posterior compartment of thigh formed in the pelvis from the ventral rami of the L4 to S3 spinal nerves. It leaves the pelvis via the greater sciatic foramen below piriformis and divides into Common Peroneal Nerve (CPN) and Tibial Nerve (TN) at the level of the upper angle of the popliteal fossa. Higher division of the sciatic nerve is the most common variation where the TN and CPN may leave the pelvis through different routes. Such variation may lead to compression of the nerve and lead to Non-discogenic sciatica. Materials and Methods: Fifty lower limbs were used for the study from Department of Anatomy, J.J.M.M.C Davangere, Karnataka, India. Observation and Results: In our study on 25 cadavers (50 lower limbs), we have observed 4 (8 %) lower limbs high division of sciatic nerve was noted. High division of sciatic nerve in the back of thigh was noted in one specimen (2%), while high division within the pelvis was noted in 3 specimens (6%), while in 46 (92%) it occurred outside the pelvis. Conclusion: Knowledge regarding such variation and differences in the course of SN is important for the surgeons to plan for various surgical interventions pertaining to the gluteal region. The variant anatomy of SN may cause piriformis syndrome and failure of SN block. Hence present study is undertaken to know the level of division, exit, course, relationship to piriformis and variations in the branching pattern of SN. PMID:25302181

  9. Two variants of minimum discarded fill ordering

    SciTech Connect

    D'Azevedo, E.F. (Oak Ridge National Lab., TN (USA)); Forsyth, P.A.; Tang, Wei-Pai (Waterloo Univ., ON (Canada). Dept. of Computer Science)

    1991-01-01

    It is well known that the ordering of the unknowns can have a significant effect on the convergence of Preconditioned Conjugate Gradient (PCG) methods. There has been considerable experimental work on the effects of ordering for regular finite difference problems. In many cases, good results have been obtained with preconditioners based on diagonal, spiral or natural row orderings. However, for finite element problems having unstructured grids or grids generated by a local refinement approach, it is difficult to define many of the orderings for more regular problems. A recently proposed Minimum Discarded Fill (MDF) ordering technique is effective in finding high quality Incomplete LU (ILU) preconditioners, especially for problems arising from unstructured finite element grids. Testing indicates this algorithm can identify a rather complicated physical structure in an anisotropic problem and orders the unknowns in the preferred'' direction. The MDF technique may be viewed as the numerical analogue of the minimum deficiency algorithm in sparse matrix technology. At any stage of the partial elimination, the MDF technique chooses the next pivot node so as to minimize the amount of discarded fill. In this work, two efficient variants of the MDF technique are explored to produce cost-effective high-order ILU preconditioners. The Threshold MDF orderings combine MDF ideas with drop tolerance techniques to identify the sparsity pattern in the ILU preconditioners. These techniques identify an ordering that encourages fast decay of the entries in the ILU factorization. The Minimum Update Matrix (MUM) ordering technique is a simplification of the MDF ordering and is closely related to the minimum degree algorithm. The MUM ordering is especially for large problems arising from Navier-Stokes problems. Some interesting pictures of the orderings are presented using a visualization tool. 22 refs., 4 figs., 7 tabs.

  10. Protein variants in Hiroshima and Nagasaki: tales of two cities.

    PubMed Central

    Neel, J V; Satoh, C; Smouse, P; Asakawa, J; Takahashi, N; Goriki, K; Fujita, M; Kageoka, T; Hazama, R

    1988-01-01

    The results of 1,465,423 allele product determinations based on blood samples from Hiroshima and Nagasaki, involving 30 different proteins representing 32 different gene products, are analyzed in a variety of ways, with the following conclusions: (1) Sibships and their parents are included in the sample. Our analysis reveals that statistical procedures designed to reduce the sample to equivalent independent genomes do not in population comparisons compensate for the familial cluster effect of rare variants. Accordingly, the data set was reduced to one representative of each sibship (937,427 allele products). (2) Both chi 2-type contrasts and a genetic distance measure (delta) reveal that rare variants (P less than .01) are collectively as effective as polymorphisms in establishing genetic differences between the two cities. (3) We suggest that rare variants that individually exhibit significant intercity differences are probably the legacy of tribal private polymorphisms that occurred during prehistoric times. (4) Despite the great differences in the known histories of the two cities, both the overall frequency of rare variants and the number of different rare variants are essentially identical in the two cities. (5) The well-known differences in locus variability are confirmed, now after adjustment for sample size differences for the various locus products; in this large series we failed to detect variants at only three of 29 loci for which sample size exceeded 23,000. (6) The number of alleles identified per locus correlates positively with subunit molecular weight. (7) Loci supporting genetic polymorphisms are characterized by more rare variants than are loci at which polymorphisms were not encountered. (8) Loci whose products do not appear to be essential for health support more variants than do loci the absence of whose product is detrimental to health. (9) There is a striking excess of rare variants over the expectation under the neutral mutation/drift/equilibrium theory. We suggest that this finding is primarily due to the relatively recent (in genetic time) agglomeration of previously separated tribal populations; efforts to test for agreement with the expectations of this theory by using data from modern cosmopolitan populations are exercises in futility. (10) All of these findings should characterize DNA variants in exons as more data become available, since the finding are the protein expression of such variants. PMID:3195587

  11. Prevalence and genetic diversity of Staphylococcus aureus small-colony variants in cystic fibrosis patients.

    PubMed

    Yagci, S; Hascelik, G; Dogru, D; Ozcelik, U; Sener, B

    2013-01-01

    Staphylococcus aureus small-colony variants (SCVs) are being isolated more frequently in cystic fibrosis (CF) patients. We aimed to determine the prevalence of S. aureus SCVs and their phenotypic and genotypic properties in CF patients admitted to a university hospital. Specimens of 248 patients were examined during a period of 11 months. Colonies supposed to be SCVs were evaluated on Columbia blood agar, mannitol salt agar, and brain-heart infusion agar with 5% NaCl (BHIA 5% NaCl). Strains were confirmed by S. aureus nucA PCR. Antibiotic susceptibilities of SCVs and simultaneously isolated S. aureus strains were determined for oxacillin, gentamicin, trimethoprim-sulphamethoxazole, vancomycin, ciprofloxacin, linezolid, and tigecycline. Genetic relatedness between SCVs and normal S. aureus strains was determined with a pulsed-field gel electrophoresis (PFGE) method. S. aureus SCVs were detected in 20 of 248 patients (8.1%). The highest SCV isolation rate was obtained with MSA, followed by BHIA 5% NaCl. Auxotrophism for thymidine was demonstrated in six SCVs. The tigecycline susceptibilities of 48 SCV strains isolated in this study showed higher MIC values than those of 33 simultaneously isolated normal S. aureus strains. Whereas SCVs and normal S. aureus strains showed identical genotypes in 14 of the patients, five patients showed different genotypes. This first study from Turkey evaluating S. aureus SCVs in CF patients has indicated the importance of considering and reporting SCVs in chronic infections such as CF. The presence of SCVs will probably indicate persistent infection, and this might impact on antibiotic treatment decisions, as they are more resistant to antibiotics. PMID:22284387

  12. Rare variant testing of imputed data: an analysis pipeline typified.

    PubMed

    Drichel, Dmitriy; Herold, Christine; Lacour, André; Ramirez, Alfredo; Jessen, Frank; Maier, Wolfgang; Noethen, Markus M; Leber, Markus; Vaitsiakhovich, Tatsiana; Becker, Tim

    2014-01-01

    Important methodological advancements in rare variant association testing have been made recently, among them collapsing tests, kernel methods and the variable threshold (VT) technique. Typically, rare variants from a region of interest are tested for association as a group ('bin'). Rare variant studies are already routinely performed as whole-exome sequencing studies. As an alternative approach, we propose a pipeline for rare variant analysis of imputed data and develop respective quality control criteria. We provide suggestions for the choice and construction of analysis bins in whole-genome application and support the analysis with implementations of standard burden tests (COLL, CMAT) in our INTERSNP-RARE software. In addition, three rare variant regression tests (REG, FRACREG and COLLREG) are implemented. All tests are accompanied with the VT approach which optimizes the definition of 'rareness'. We integrate kernel tests as implemented in SKAT/SKAT-O into the suggested strategies. Then, we apply our analysis scheme to a genome-wide association study of Alzheimer's disease. Further, we show that our pipeline leads to valid significance testing procedures with controlled type I error rates. Strong association signals surrounding the known APOE locus demonstrate statistical power. In addition, we highlight several suggestive rare variant association findings for follow-up studies, including genomic regions overlapping MCPH1, MED18 and NOTCH3. In summary, we describe and support a straightforward and cost-efficient rare variant analysis pipeline for imputed data and demonstrate its feasibility and validity. The strategy can complement rare variant studies with next generation sequencing data. PMID:25504234

  13. Measuring missing heritability: Inferring the contribution of common variants

    PubMed Central

    Golan, David; Lander, Eric S.; Rosset, Saharon

    2014-01-01

    Genome-wide association studies (GWASs), also called common variant association studies (CVASs), have uncovered thousands of genetic variants associated with hundreds of diseases. However, the variants that reach statistical significance typically explain only a small fraction of the heritability. One explanation for the “missing heritability” is that there are many additional disease-associated common variants whose effects are too small to detect with current sample sizes. It therefore is useful to have methods to quantify the heritability due to common variation, without having to identify all causal variants. Recent studies applied restricted maximum likelihood (REML) estimation to case–control studies for diseases. Here, we show that REML considerably underestimates the fraction of heritability due to common variation in this setting. The degree of underestimation increases with the rarity of disease, the heritability of the disease, and the size of the sample. Instead, we develop a general framework for heritability estimation, called phenotype correlation–genotype correlation (PCGC) regression, which generalizes the well-known Haseman–Elston regression method. We show that PCGC regression yields unbiased estimates. Applying PCGC regression to six diseases, we estimate the proportion of the phenotypic variance due to common variants to range from 25% to 56% and the proportion of heritability due to common variants from 41% to 68% (mean 60%). These results suggest that common variants may explain at least half the heritability for many diseases. PCGC regression also is readily applicable to other settings, including analyzing extreme-phenotype studies and adjusting for covariates such as sex, age, and population structure. PMID:25422463

  14. Uncommon variants of the scimitar syndrome in two siblings

    PubMed Central

    Bo, Ilaria; Daubeney, Piers E F; Rigby, Michael L

    2015-01-01

    The Scimitar syndrome is a complex association of cardiovascular and bronchopulmonary abnormalities, with the main feature a partial or total anomalous right pulmonary venous drainage to the inferior vena cava. A number of cases that lack of all the features of the typical syndrome have been described as Scimitar variant, but the incidence is rare. Familial occurrence is exceptional and limited to few cases in literature. We report two sibling diagnosed with an uncommon variant of the Scimitar syndrome. PMID:25684890

  15. Functional characterization of a natural variant of luteinizing hormone

    Microsoft Academic Search

    W. X. Liao; H. H. Goh; A. C. Roy

    2002-01-01

    Luteinizing hormone (LH) plays an important role in the gametogenesis in both sexes by promoting the production of sex steroid hormones in the testes and ovaries. We previously described a genetic variant (V) of LH resulted from a mutation (G1502A) in the LH #-subunit gene, causing the glycine102serine change in the protein hormone. This variant was subsequently found to be

  16. Bifurcations of travelling wave solutions in variant Boussinesq equations

    Microsoft Academic Search

    Yu-bo Yuan; Dong-mei Pu; Shu-min Li

    2006-01-01

    The bifurcations of solitary waves and kink waves for variant Boussinesq equations are studied by using the bifurcation theory\\u000a of planar dynamical systems. The bifurcation sets and the numbers of solitary waves and kink waves for the variant Boussinesq\\u000a equations are presented. Several types explicit formulas of solitary waves solutions and kink waves solutions are obtained.\\u000a In the end, several

  17. Training Neural Networks to Play Backgammon Variants Using Reinforcement Learning

    Microsoft Academic Search

    Nikolaos Papahristou; Ioannis Refanidis

    2011-01-01

    \\u000a Backgammon is a board game that has been studied considerably by computer scientists. Apart from standard backgammon, several\\u000a yet unexplored variants of the game exist, which use the same board, number of checkers, and dice but may have different rules\\u000a for moving the checkers, starting positions and movement direction. This paper studies two popular variants in Greece and\\u000a neighboring countries,

  18. Mouse Ribosomal RNA Genes Contain Multiple Differentially Regulated Variants

    Microsoft Academic Search

    Hung Tseng; Weichin Chou; Junwen Wang; Xiaohong Zhang; Shengliang Zhang; Richard M. Schultz; Peter Fraser

    2008-01-01

    Previous cytogenetic studies suggest that various rDNA chromosomal loci are not equally active in different cell types. Consistent with this variability, rDNA polymorphism is well documented in human and mouse. However, attempts to identify molecularly rDNA variant types, which are regulated individually (i.e., independent of other rDNA variants) and tissue-specifically, have not been successful. We report here the molecular cloning

  19. Mouse Ribosomal RNA Genes Contain Multiple Differentially Regulated Variants

    PubMed Central

    Tseng, Hung; Chou, Weichin; Wang, Junwen; Zhang, Xiaohong; Zhang, Shengliang; Schultz, Richard M.

    2008-01-01

    Previous cytogenetic studies suggest that various rDNA chromosomal loci are not equally active in different cell types. Consistent with this variability, rDNA polymorphism is well documented in human and mouse. However, attempts to identify molecularly rDNA variant types, which are regulated individually (i.e., independent of other rDNA variants) and tissue-specifically, have not been successful. We report here the molecular cloning and characterization of seven mouse rDNA variants (v-rDNA). The identification of these v-rDNAs was based on restriction fragment length polymorphisms (RFLPs), which are conserved among individuals and mouse strains. The total copy number of the identified variants is less than 100 and the copy number of each individual variant ranges from 4 to 15. Sequence analysis of the cloned v-rDNA identified variant-specific single nucleotide polymorphisms (SNPs) in the transcribed region. These SNPs were used to develop a set of variant-specific PCR assays, which permitted analysis of the v-rDNAs' expression profiles in various tissues. These profiles show that three v-rDNAs are expressed in all tissues (constitutively active), two are expressed in some tissues (selectively active), and two are not expressed (silent). These expression profiles were observed in six individuals from three mouse strains, suggesting the pattern is not randomly determined. Thus, the mouse rDNA array likely consists of genetically distinct variants, and some are regulated tissue-specifically. Our results provide the first molecular evidence for cell-type-specific regulation of a subset of rDNA. PMID:18365001

  20. HIV-1 genetic variants in the Russian Far East.

    PubMed

    Kazennova, Elena; Laga, Vita; Lapovok, Ilya; Glushchenko, Nataliya; Neshumaev, Dmitry; Vasilyev, Alexander; Bobkova, Marina

    2014-08-01

    A molecular analysis of HIV-1 subtypes and recombinants circulating in cities in the Russian Far East was performed. The study included samples from 201 outpatients from Vladivostok, Khabarovsk, and Blagoveshchensk. In most parts of Russia, patients are infected with HIV-1 subtype A, known as the IDU-A variant. Subtype B, including the IDU-B variant, is rare in Russia but widespread in the Ukraine, and the CRF02_AG is prevalent in Central Asian countries and Siberia, Russia. One of the challenges of this study in the Far East was to determine whether the molecular landscape of HIV infection in this region is influenced by the bordering countries, including China and Japan, where a distinct set of HIV subtypes is circulating, such as B', C, and CRF01_AE. The distribution of HIV-1 genetic variants in the cities studied was as follows: subtype A (IDU-A), 55.7%; subtype B, 25.3% (IDU-B variant-24.3%); subtype C, 10.0%; CRF02_AG, 1.5%; and CRF63_02A1, 7.5%. A phylogenetic analysis confirmed the relationship of subtype A viruses with the IDU-A variant predominating in Ukraine, Russia and other former Soviet Union (FSU) countries, of subtype B viruses with IDU-B in the Ukraine and of CRF02_AG variants with variants in Uzbekistan, Russia, and other former USSR countries. Subtype C sequences were not uniform, and most clustered between each other and HIV-1 sequences originating from Africa; there was only one sample possibly related to Chinese variants. Thus, despite close cultural and commercial relationships among Russia, China, and Japan, the distribution of HIV-1 subtypes in the Russian Far East is still primarily influenced by contacts with the countries of the former USSR. PMID:24773167

  1. Measuring missing heritability: inferring the contribution of common variants.

    PubMed

    Golan, David; Lander, Eric S; Rosset, Saharon

    2014-12-01

    Genome-wide association studies (GWASs), also called common variant association studies (CVASs), have uncovered thousands of genetic variants associated with hundreds of diseases. However, the variants that reach statistical significance typically explain only a small fraction of the heritability. One explanation for the "missing heritability" is that there are many additional disease-associated common variants whose effects are too small to detect with current sample sizes. It therefore is useful to have methods to quantify the heritability due to common variation, without having to identify all causal variants. Recent studies applied restricted maximum likelihood (REML) estimation to case-control studies for diseases. Here, we show that REML considerably underestimates the fraction of heritability due to common variation in this setting. The degree of underestimation increases with the rarity of disease, the heritability of the disease, and the size of the sample. Instead, we develop a general framework for heritability estimation, called phenotype correlation-genotype correlation (PCGC) regression, which generalizes the well-known Haseman-Elston regression method. We show that PCGC regression yields unbiased estimates. Applying PCGC regression to six diseases, we estimate the proportion of the phenotypic variance due to common variants to range from 25% to 56% and the proportion of heritability due to common variants from 41% to 68% (mean 60%). These results suggest that common variants may explain at least half the heritability for many diseases. PCGC regression also is readily applicable to other settings, including analyzing extreme-phenotype studies and adjusting for covariates such as sex, age, and population structure. PMID:25422463

  2. Analysis of interleukin-4 receptor ? chain variants in multiple sclerosis

    Microsoft Academic Search

    Holger Hackstein; Andreas Bitsch; Anette Bohnert; Henrike Hofmann; Frank Weber; Astrid Ohly; Chris Linington; Matthias Mäurer; Sigrid Poser; Peter Rieckmann; Gregor Bein

    2001-01-01

    A recent candidate gene study employing microsatellite markers suggested a possible linkage of multiple sclerosis (MS) with the interleukin-4 receptor (IL4R) gene. Consequently, we investigated the association of different IL4R variants with MS in 341 german MS patients and 305 healthy controls. Analysis of the first 100 MS patients for six IL4R variants showed an increased frequency of the R551

  3. Mouse ribosomal RNA genes contain multiple differentially regulated variants.

    PubMed

    Tseng, Hung; Chou, Weichin; Wang, Junwen; Zhang, Xiaohong; Zhang, Shengliang; Schultz, Richard M

    2008-01-01

    Previous cytogenetic studies suggest that various rDNA chromosomal loci are not equally active in different cell types. Consistent with this variability, rDNA polymorphism is well documented in human and mouse. However, attempts to identify molecularly rDNA variant types, which are regulated individually (i.e., independent of other rDNA variants) and tissue-specifically, have not been successful. We report here the molecular cloning and characterization of seven mouse rDNA variants (v-rDNA). The identification of these v-rDNAs was based on restriction fragment length polymorphisms (RFLPs), which are conserved among individuals and mouse strains. The total copy number of the identified variants is less than 100 and the copy number of each individual variant ranges from 4 to 15. Sequence analysis of the cloned v-rDNA identified variant-specific single nucleotide polymorphisms (SNPs) in the transcribed region. These SNPs were used to develop a set of variant-specific PCR assays, which permitted analysis of the v-rDNAs' expression profiles in various tissues. These profiles show that three v-rDNAs are expressed in all tissues (constitutively active), two are expressed in some tissues (selectively active), and two are not expressed (silent). These expression profiles were observed in six individuals from three mouse strains, suggesting the pattern is not randomly determined. Thus, the mouse rDNA array likely consists of genetically distinct variants, and some are regulated tissue-specifically. Our results provide the first molecular evidence for cell-type-specific regulation of a subset of rDNA. PMID:18365001

  4. A probabilistic method for identifying rare variants underlying complex traits

    PubMed Central

    2013-01-01

    Background Identifying the genetic variants that contribute to disease susceptibilities is important both for developing methodologies and for studying complex diseases in molecular biology. It has been demonstrated that the spectrum of minor allelic frequencies (MAFs) of risk genetic variants ranges from common to rare. Although association studies are shifting to incorporate rare variants (RVs) affecting complex traits, existing approaches do not show a high degree of success, and more efforts should be considered. Results In this article, we focus on detecting associations between multiple rare variants and traits. Similar to RareCover, a widely used approach, we assume that variants located close to each other tend to have similar impacts on traits. Therefore, we introduce elevated regions and background regions, where the elevated regions are considered to have a higher chance of harboring causal variants. We propose a hidden Markov random field (HMRF) model to select a set of rare variants that potentially underlie the phenotype, and then, a statistical test is applied. Thus, the association analysis can be achieved without pre-selection by experts. In our model, each variant has two hidden states that represent the causal/non-causal status and the region status. In addition, two Bayesian processes are used to compare and estimate the genotype, phenotype and model parameters. We compare our approach to the three current methods using different types of datasets, and though these are simulation experiments, our approach has higher statistical power than the other methods. The software package, RareProb and the simulation datasets are available at: http://www.engr.uconn.edu/~jiw09003. PMID:23369113

  5. Space Variant Representations for Mobile Platform Vision Applications

    Microsoft Academic Search

    Naveen Onkarappa; Angel D. Sappa

    \\u000a The log-polar space variant representation, motivated by biological vision, has been widely studied in the literature. Its\\u000a data reduction and invariance properties made it useful in many vision applications. However, due to its nature, it fails\\u000a in preserving features in the periphery. In the current work, as an attempt to overcome this problem, we propose a novel space-variant\\u000a representation. It

  6. Characterization of Randomly Time-Variant Linear Channels

    Microsoft Academic Search

    P. Bello

    1963-01-01

    This paper is concerned with various aspects of the characterization of randomly time-variant linear channels. At the outset it is demonstrated that time-varying linear channels (or filters) may be characterized in an interesting symmetrical manner in time and frequency variables by arranging system functions in (timefrequency) dual pairs. Following this a statistical characterization of randomly time-variant linear channels is carried

  7. Histone variant innovation in a rapidly evolving chordate lineage

    PubMed Central

    2011-01-01

    Background Histone variants alter the composition of nucleosomes and play crucial roles in transcription, chromosome segregation, DNA repair, and sperm compaction. Modification of metazoan histone variant lineages occurs on a background of genome architecture that shows global similarities from sponges to vertebrates, but the urochordate, Oikopleura dioica, a member of the sister group to vertebrates, exhibits profound modification of this ancestral architecture. Results We show that a histone complement of 47 gene loci encodes 31 histone variants, grouped in distinct sets of developmental expression profiles throughout the life cycle. A particularly diverse array of 15 male-specific histone variants was uncovered, including a testes-specific H4t, the first metazoan H4 sequence variant reported. Universal histone variants H3.3, CenH3, and H2A.Z are present but O. dioica lacks homologs of macroH2A and H2AX. The genome encodes many H2A and H2B variants and the repertoire of H2A.Z isoforms is expanded through alternative splicing, incrementally regulating the number of acetylatable lysine residues in the functionally important N-terminal "charge patch". Mass spectrometry identified 40 acetylation, methylation and ubiquitylation posttranslational modifications (PTMs) and showed that hallmark PTMs of "active" and "repressive" chromatin were present in O. dioica. No obvious reduction in silent heterochromatic marks was observed despite high gene density in this extraordinarily compacted chordate genome. Conclusions These results show that histone gene complements and their organization differ considerably even over modest phylogenetic distances. Substantial innovation among all core and linker histone variants has evolved in concert with adaptation of specific life history traits in this rapidly evolving chordate lineage. PMID:21756361

  8. Fitness of Isogenic Colony Morphology Variants of Pseudomonas aeruginosa in Murine Airway Infection

    PubMed Central

    Rakhimova, Elza; Munder, Antje; Wiehlmann, Lutz; Bredenbruch, Florian; Tümmler, Burkhard

    2008-01-01

    Chronic lung infections with Pseudomonas aeruginosa are associated with the diversification of the persisting clone into niche specialists and morphotypes, a phenomenon called ‘dissociative behaviour’. To explore the potential of P. aeruginosa to change its morphotype by single step loss-of–function mutagenesis, a signature-tagged mini-Tn5 plasposon library of the cystic fibrosis airway isolate TBCF10839 was screened for colony morphology variants under nine different conditions in vitro. Transposon insertion into 1% of the genome changed colony morphology into eight discernable morphotypes. Half of the 55 targets encode features of primary or secondary metabolism whereby quinolone production was frequently affected. In the other half the transposon had inserted into genes of the functional categories transport, regulation or motility/chemotaxis. To mimic dissociative behaviour of isogenic strains in lungs, pools of 25 colony morphology variants were tested for competitive fitness in an acute murine airway infection model. Six of the 55 mutants either grew better or worse in vivo than in vitro, respectively. Metabolic proficiency of the colony morphology variant was a key determinant for survival in murine airways. The most common morphotype of self-destructive autolysis did unexpectedly not impair fitness. Transposon insertions into homologous genes of strain PAO1 did not reproduce the TBCF10839 mutant morphotypes for 16 of 19 examined loci pointing to an important role of the genetic background on colony morphology. Depending on the chosen P. aeruginosa strain, functional genome scans will explore other areas of the evolutionary landscape. Based on our discordant findings of mutant phenotypes in P. aeruginosa strains PAO1, PA14 and TBCF10839, we conclude that the current focus on few reference strains may miss modes of niche adaptation and dissociative behaviour that are relevant for the microevolution of complex traits in the wild. PMID:18301762

  9. Development of a novel classification system for anatomical variants of the puboprostatic ligaments with expert validation

    PubMed Central

    Kim, Michael; Boyle, Shawna L.; Fernandez, Alfonso; Matsumoto, Edward D.; Pace, Kenneth T.; Anidjar, Maurice; Kozak, Gregory N.; Davé, Sumit; Welk, Blayne K.; Johnson, Marjorie I.; Pautler, Stephen E.

    2014-01-01

    Introduction: We propose a novel classification system with a validation study to help clinicians identify and typify commonly seen variants of the puboprostatic ligaments (PPL). Methods: A preliminary dissection of 6 male cadavers and a prospective dataset of over 300 robotic-assisted laparoscopic radical prostatectomies (RARP) recorded on video were used to identify 4 distinct ligament types. Then the prospectively collected database of surgical videos was used to isolate images of the PPL from RARP. Over 300 surgical videos were reviewed and classified with 1 to 5 pictures saved for reference of the type of PPL. To validate the new classification system, we selected 5 independent, blinded expert robotic surgeons to classify 100 ligaments based on morphology into a 4-type system: parallel, V-shaped, inverted V-shape, and fused. One week later, a subset of 25 photographs was sent to the same experts and classified. Statistical analyses were performed to determine both the intra-rater and inter-rater reliability of the proposed system. Results: Inverted V-shaped ligaments were noted most frequently (29.97%), parallel and V-shaped ligaments were found at 19.19% and 11.11%, respectively and fused ligaments were noted less frequently (6.06%). There was good intra-rater agreement (? = 0.66) and inter-rater agreement (? = 0.67) for the classification system. Conclusions: This classification system provided standardized descriptions of ligament variations that could be adopted universally to help clinicians categorize the variants. The system, validated by several blinded expert surgeons, demonstrated that surgeons were able to learn and correctly classify the variants. The system may be useful in helping to predict peri- and postoperative outcomes; however, this will require further study. PMID:25553158

  10. Engineering human interleukin-6 to obtain variants with strongly enhanced bioactivity.

    PubMed Central

    Toniatti, C; Cabibbo, A; Sporena, E; Salvati, A L; Cerretani, M; Serafini, S; Lahm, A; Cortese, R; Ciliberto, G

    1996-01-01

    Interleukin-6 (IL-6) triggers the formation of a high affinity receptor complex with the ligand binding subunit IL-6Ralpha and the signal transducing chain gp130. Since the intracytoplasmic region of the IL-6Ralpha does not contribute to signaling, soluble forms of the extracytoplasmic domain (sIL-6Ralpha), potentiate IL-6 bioactivity and induce a cytokine-responsive status in cells expressing gp130 only. This observation, together with the detection of high levels of circulating soluble human IL-6Ralpha (shIL-6Ralpha) in sera, suggests that the hIL-6-shIL-6Ralpha complex is an alternative form of the cytokine. Here we describe the generation of human IL-6 (hIL-6) variants with strongly enhanced shIL-6Ralpha binding activity and bioactivity. Homology modeling and site-directed mutagenesis of hIL-6 suggested that the binding interface for hIL-6Ralpha is constituted by the C-terminal portion of the D-helix and residues contained in the AB loop. Four libraries of hIL-6 mutants were generated by each time fully randomizing four different amino acids in the predicted AB loop. These libraries were displayed monovalently on filamentous phage surface and sorted separately for binding to immobilized shIL-6Ralpha. Mutants were selected which, when expressed as soluble proteins, showed a 10- to 40-fold improvement in shIL-6Ralpha binding; a further increase (up to 70-fold) was achieved by combining variants isolated from different libraries. Interestingly, high affinity hIL-6 variants show strongly enhanced bioactivity on cells expressing gp13O in the presence of shIL-6Ralpha at concentrations similar to those normally found in human sera. Images PMID:8654370

  11. Mapping Genetic Variants Underlying Differences in the Central Nitrogen Metabolism in Fermenter Yeasts

    PubMed Central

    García, Verónica; Salinas, Francisco; Aguilera, Omayra; Liti, Gianni; Martínez, Claudio

    2014-01-01

    Different populations within a species represent a rich reservoir of allelic variants, corresponding to an evolutionary signature of withstood environmental constraints. Saccharomyces cerevisiae strains are widely utilised in the fermentation of different kinds of alcoholic beverages, such as, wine and sake, each of them derived from must with distinct nutrient composition. Importantly, adequate nitrogen levels in the medium are essential for the fermentation process, however, a comprehensive understanding of the genetic variants determining variation in nitrogen consumption is lacking. Here, we assessed the genetic factors underlying variation in nitrogen consumption in a segregating population derived from a cross between two main fermenter yeasts, a Wine/European and a Sake isolate. By linkage analysis we identified 18 main effect QTLs for ammonium and amino acids sources. Interestingly, majority of QTLs were involved in more than a single trait, grouped based on amino acid structure and indicating high levels of pleiotropy across nitrogen sources, in agreement with the observed patterns of phenotypic co-variation. Accordingly, we performed reciprocal hemizygosity analysis validating an effect for three genes, GLT1, ASI1 and AGP1. Furthermore, we detected a widespread pleiotropic effect on these genes, with AGP1 affecting seven amino acids and nine in the case of GLT1 and ASI1. Based on sequence and comparative analysis, candidate causative mutations within these genes were also predicted. Altogether, the identification of these variants demonstrate how Sake and Wine/European genetic backgrounds differentially consume nitrogen sources, in part explaining independently evolved preferences for nitrogen assimilation and representing a niche of genetic diversity for the implementation of practical approaches towards more efficient strains for nitrogen metabolism. PMID:24466135

  12. Biochemical characterization of trans-sialidase TS1 variants from Trypanosoma congolense

    PubMed Central

    2011-01-01

    Background Animal African trypanosomiasis, sleeping sickness in humans and Nagana in cattle, is a resurgent disease in Africa caused by Trypanosoma parasites. Trans-sialidases expressed by trypanosomes play an important role in the infection cycle of insects and mammals. Whereas trans-sialidases of other trypanosomes like the American T. cruzi are well investigated, relatively little research has been done on these enzymes of T. congolense. Results Based on a partial sequence and an open reading frame in the WTSI database, DNA sequences encoding for eleven T. congolense trans-sialidase 1 variants with 96.3% overall amino acid identity were amplified. Trans-sialidase 1 variants were expressed as recombinant proteins, isolated and assayed for trans-sialylation activity. The purified proteins produced ?2,3-sialyllactose from lactose by desialylating fetuin, clearly demonstrating their trans-sialidase activity. Using an HPLC-based assay, substrate specificities and kinetic parameters of two variants were characterized in detail indicating differences in substrate specificities for lactose, fetuin and synthetic substrates. Both enzymes were able to sialylate asialofetuin to an extent, which was sufficient to reconstitute binding sites for Siglec-4. A mass spectrometric analysis of the sialylation pattern of glycopeptides from fetuin revealed clear but generally similar changes in the sialylation pattern of the N-glycans on fetuin catalyzed by the trans-sialidases investigated. Conclusions The identification and characterization of a trans-sialidase gene family of the African parasite T. congolense has opened new perspectives for investigating the biological role of these enzymes in Nagana and sleeping sickness. Based on this study it will be interesting to address the expression pattern of these genes and their activities in the different stages of the parasite in its infection cycle. Furthermore, these trans-sialidases have the biotechnological potential to be used for enzymatic modification of sialylated glycoconjugates. PMID:21801439

  13. GATA4 sequence variants in patients with congenital heart disease

    PubMed Central

    Tomita?Mitchell, A; Maslen, C L; Morris, C D; Garg, V; Goldmuntz, E

    2007-01-01

    Background Recent reports have identified mutations in the transcription factor GATA4 in familial cases of cardiac septal defects. The prevalence of GATA4 mutations in the population of patients with septal defects is unknown. Given that patients with septal and conotruncal defect can share a common genetic basis, it is unclear whether patients with additional types of CHD might also have GATA4 mutations. Aims To explore these questions by investigating a large population of 628 patients with either septal or conotruncal defects for GATA4 sequence variants. Methods The GATA4 coding region and exon–intron boundaries were investigated for sequence variants using denaturing high?performance liquid chromatography or conformation?sensitive gel electrophoresis. Samples showing peak or band shifts were reamplified from genomic DNA and sequenced. Results Four missense sequence variants (Gly93Ala, Gln316Glu, Ala411Val, Asp425Asn) were identified in five patients (two with atrial septal defect, two with ventricular septal defect and one with tetralogy of Fallot), which were not seen in a control population. All four affected amino acid residues are conserved across species, and two of the sequence variants lead to changes in polarity. Ten synonymous sequence variants were also identified in 18 patients, which were not seen in the control population. Conclusions These data suggest that non?synonymous GATA4 sequence variants are found in a small percentage of patients with septal defects and are very uncommonly found in patients with conotruncal defects. PMID:18055909

  14. Rare-Variant Association Analysis: Study Designs and Statistical Tests

    PubMed Central

    Lee, Seunggeung; Abecasis, Gonçalo R.; Boehnke, Michael; Lin, Xihong

    2014-01-01

    Despite the extensive discovery of trait- and disease-associated common variants, much of the genetic contribution to complex traits remains unexplained. Rare variants can explain additional disease risk or trait variability. An increasing number of studies are underway to identify trait- and disease-associated rare variants. In this review, we provide an overview of statistical issues in rare-variant association studies with a focus on study designs and statistical tests. We present the design and analysis pipeline of rare-variant studies and review cost-effective sequencing designs and genotyping platforms. We compare various gene- or region-based association tests, including burden tests, variance-component tests, and combined omnibus tests, in terms of their assumptions and performance. Also discussed are the related topics of meta-analysis, population-stratification adjustment, genotype imputation, follow-up studies, and heritability due to rare variants. We provide guidelines for analysis and discuss some of the challenges inherent in these studies and future research directions. PMID:24995866

  15. Human FABP1 T94A variant enhances cholesterol uptake.

    PubMed

    Huang, Huan; McIntosh, Avery L; Landrock, Kerstin K; Landrock, Danilo; Storey, Stephen M; Martin, Gregory G; Gupta, Shipra; Atshaves, Barbara P; Kier, Ann B; Schroeder, Friedhelm

    2015-07-01

    Although expression of the human liver fatty acid binding protein (FABP1) T94A variant alters serum lipoprotein cholesterol levels in human subjects, nothing is known whereby the variant elicits these effects. This issue was addressed by in vitro cholesterol binding assays using purified recombinant wild-type (WT) FABP1 T94T and T94A variant proteins and in cultured primary human hepatocytes expressing the FABP1 T94T (genotyped as TT) or T94A (genotyped as CC) proteins. The human FABP1 T94A variant protein had 3-fold higher cholesterol-binding affinity than the WT FABP1 T94T as shown by NBD-cholesterol fluorescence binding assays and by cholesterol isothermal titration microcalorimetry (ITC) binding assays. CC variant hepatocytes also exhibited 30% higher total FABP1 protein. HDL- and LDL-mediated NBD-cholesterol uptake was faster in CC variant than TT WT human hepatocytes. VLDL-mediated uptake of NBD-cholesterol did not differ between CC and TT human hepatocytes. The increased HDL- and LDL-mediated NBD-cholesterol uptake was not associated with any significant change in mRNA levels of SCARB1, LDLR, CETP, and LCAT encoding the key proteins in lipoprotein cholesterol uptake. Thus, the increased HDL- and LDL-mediated NBD-cholesterol uptake by CC hepatocytes may be associated with higher affinity of T94A protein for cholesterol and/or increased total T94A protein level. PMID:25732850

  16. Exploring the role of exposure frequency in recognizing pronunciation variants

    PubMed Central

    Pitt, Mark A.; Dilley, Laura; Tat, Michael

    2010-01-01

    Words can be pronounced in multiple ways in casual speech. Corpus analyses of the frequency with which these pronunciation variants occur (e.g., Patterson & Connine, 2001) show that typically, one pronunciation variant tends to predominate; this raises the question of whether variant recognition is aligned with exposure frequency. We explored this issue in words containing one of four phonological contexts, each of which favors one of four surface realizations of word-medial /t/: [t], [?], [?], or a deleted variant. The frequencies of the four realizations in all four contexts were estimated for a set of words in a production experiment. Recognition of all pronunciation variants was then measured in a lexical decision experiment. Overall, the data suggest that listeners are sensitive to variant frequency: Word classification rates closely paralleled production frequency. The exceptions to this were [t] realizations (i.e., canonical pronunciations of the words), a finding which confirms other results in the literature and indicates that factors other than exposure frequency affect word recognition. PMID:21822340

  17. Mutation update for GNE gene variants associated with GNE myopathy.

    PubMed

    Celeste, Frank V; Vilboux, Thierry; Ciccone, Carla; de Dios, John Karl; Malicdan, May Christine V; Leoyklang, Petcharat; McKew, John C; Gahl, William A; Carrillo-Carrasco, Nuria; Huizing, Marjan

    2014-08-01

    The GNE gene encodes the rate-limiting, bifunctional enzyme of sialic acid biosynthesis, uridine diphosphate-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE). Biallelic GNE mutations underlie GNE myopathy, an adult-onset progressive myopathy. GNE myopathy-associated GNE mutations are predominantly missense, resulting in reduced, but not absent, GNE enzyme activities. The exact pathomechanism of GNE myopathy remains unknown, but likely involves aberrant (muscle) sialylation. Here, we summarize 154 reported and novel GNE variants associated with GNE myopathy, including 122 missense, 11 nonsense, 14 insertion/deletions, and seven intronic variants. All variants were deposited in the online GNE variation database (http://www.dmd.nl/nmdb2/home.php?select_db=GNE). We report the predicted effects on protein function of all variants well as the predicted effects on epimerase and/or kinase enzymatic activities of selected variants. By analyzing exome sequence databases, we identified three frequently occurring, unreported GNE missense variants/polymorphisms, important for future sequence interpretations. Based on allele frequencies, we estimate the world-wide prevalence of GNE myopathy to be ?4-21/1,000,000. This previously unrecognized high prevalence confirms suspicions that many patients may escape diagnosis. Awareness among physicians for GNE myopathy is essential for the identification of new patients, which is required for better understanding of the disorder's pathomechanism and for the success of ongoing treatment trials. PMID:24796702

  18. Evaluation of the MTHFR A1298C variant in leukoaraiosis.

    PubMed

    Szolnoki, Zoltan; Szaniszlo, Istvan; Szekeres, Marta; Hitri, Krisztina; Kondacs, Andras; Mandi, Yvette; Nedo, Erika; Somogyvari, Ferenc

    2012-03-01

    Vascular demyelinization of the white matter of the brain is referred to as leukoaraiosis (LA). This very frequent entity is associated with a cognitive decline, thereby resulting in a deteriorating quality of life. Besides poorly controlled hypertension and aging, its development is reported to be associated with an elevated serum homocysteine level. Although the methylenetetrahydrofolate reductase (MTHFR) C677T genetic variant is associated with an elevated serum homocysteine level, it has not been proved to be an independent risk factor for LA. The aim of the present study was to examine whether the MTHFR A1298C genetic variant, which is also believed to be unfavorable, is associated with the presence of LA. The clinical and genetic data on 198 LA patients and 235 neuroimaging alteration-free controls were analyzed. The presence of the A1298C or the 1298CC variant was calculated to be a risk factor for LA, as compared with the absence of both of them. The clustering of the heterozygous A1298C and C677T variants was proved to involve the risk of LA. Our results suggest that the MTHFR A1298C variant confers an independent genetic risk of LA, and this pathological role may be amplified by the MTHFR C677T variant. PMID:21845428

  19. Integrated Analysis of Germline and Somatic Variants in Ovarian Cancer

    PubMed Central

    Kanchi, Krishna L.; Johnson, Kimberly J.; Lu, Charles; McLellan, Michael D.; Leiserson, Mark D.M.; Wendl, Michael C.; Zhang, Qunyuan; Koboldt, Daniel C.; Xie, Mingchao; Kandoth, Cyriac; McMichael, Joshua F.; Wyczalkowski, Matthew A.; Larson, David E.; Schmidt, Heather K.; Miller, Christopher A.; Fulton, Robert S.; Spellman, Paul T.; Mardis, Elaine R.; Druley, Todd E.; Graubert, Timothy A.; Goodfellow, Paul J.; Raphael, Benjamin J.; Wilson, Richard K.; Ding, Li

    2014-01-01

    We report the first large-scale exome-wide analysis of the combined germline-somatic landscape in ovarian cancer. Here we analyze germline and somatic alterations in 429 ovarian carcinoma cases and 557 controls. We identify 3,635 high confidence, rare truncation and 22,953 missense variants with predicted functional impact. We find germline truncation variants and large deletions across Fanconi pathway genes in 20% of cases. Enrichment of rare truncations is shown in BRCA1, BRCA2, and PALB2. Additionally, we observe germline truncation variants in genes not previously associated with ovarian cancer susceptibility (NF1, MAP3K4, CDKN2B, and MLL3). Evidence for loss of heterozygosity was found in 100% and 76% of cases with germline BRCA1 and BRCA2 truncations respectively. Germline-somatic interaction analysis combined with extensive bioinformatics annotation identifies 237 candidate functional germline truncation and missense variants, including 2 pathogenic BRCA1 and 1 TP53 deleterious variants. Finally, integrated analyses of germline and somatic variants identify significantly altered pathways, including the Fanconi, MAPK, and MLL pathways. PMID:24448499

  20. Evaluating LRRK2 Genetic Variants with Unclear Pathogenicity

    PubMed Central

    Refai, Fathima Shaffra; Ng, Shin Hui; Tan, Eng-King

    2015-01-01

    Mutations in the leucine-rich repeat kinase 2 (LRRK2) have been known to be a major genetic component affecting Parkinson's disease (PD). However, the pathogenicity of many of the LRRK2 variants is unclear because they have been detected in single patients or also in patients and controls. Here, we selected 5 exonic variants (L1165P, T1410M, M1646T, L2063X, and Y2189C) from each of the protein domain of LRRK2 and analysed their possible association with pathogenicity using in vitro functional assays. Point mutations representing each of these variants were incorporated into the LRRK2 gene, and functional aspects such as the percentage of cell survival upon application of stress and kinase activity were measured. Our results showed that all 5 variants had a significantly negative effect on the survival of cells, in both presence and absence of stress, as compared to the wild-type. In addition, there was also a slight increase in kinase activity in most of the variants in comparison to the wild-type. A negative correlation between cell survival and kinase activity was observed. These data suggest that most of the variants despite being located in different domains of LRRK2 appear to exert a potential pathogenic effect possibly through an increased kinase activity, supporting a gain of function mechanism. PMID:25821816

  1. Increased frequency of Mediterranean fever gene variants in multiple myeloma

    PubMed Central

    CELIK, SERKAN; TANGI, FATIH; OKTENLI, CAGATAY

    2014-01-01

    High frequencies of inherited variants in the Mediterranean fever (MEFV) gene have been identified in patients with multiple myeloma (MM). The sample size of the present pilot study was small, therefore, the actual frequency of inherited variants in the MEFV gene could be investigated in patients with MM. Twenty-eight patients with MM and 65 healthy controls were included in the study. Six heterozygous and one homozygous (E148Q/E148Q) variant was identified in patients with MM. None of the patients had a family history compatible with familial Mediterranean fever. In the healthy control group, 11 heterozygous variants were identified. The difference in the overall frequency of the inherited variants in the MEFV gene between the MM patients and the controls was statistically significant (?2=4.905; P=0.027). In conclusion, a high frequency of inherited variants in the MEFV gene was identified in patients with MM. Based on the current data, it is hypothesized that the MEFV gene is a cancer susceptibility gene. Additional evidence, such as familial aggregation, monozygotic versus dizygotic twin concordance, and tumors in genetically engineered model organisms, is required in order to support this hypothesis. PMID:25202401

  2. Insight into the complex genetic network of tetraploid Atlantic salmon (Salmo salar L.): description of multiple novel Pax-7 splice variants.

    PubMed

    Gotensparre, Susan M; Andersson, Eva; Wargelius, Anna; Hansen, Tom; Johnston, Ian A

    2006-05-24

    Paired box transcription factor 7 (Pax-7) cDNA was isolated from the skeletal muscle and brain of alevin and adult stages of Atlantic salmon, identifying 10 variants categorised as novel or established insertions (ins) or deletions (del). Two putative Pax-7 paralogs were identified (denoted Pax-7alpha and Pax-7beta) on the basis of the length and sequences of intron 3 (218 and 248 bp) and versions of ins1 and ins2. Pax-7beta contained a threonine variant of ins1 (GQY[T]GPEYVYCGT), and a shortened variant of ins2 (GEAS). Pattern identification revealed the threonine variant of ins1 includes a potential phosphorylation site (casein kinase II). Thus, the tetraploid Atlantic salmon genome appears to contain at least two putative copies and multiple splice variants of Pax-7. In situ hybridisation localised Pax-7 to mononuclear cells in the fast muscle of adult Atlantic salmon, while quantitative real-time PCR showed Pax-7alpha to be more highly expressed in brain than in skeletal muscle. PMID:16567062

  3. A variant in the sonic hedgehog regulatory sequence (ZRS) is associated with triphalangeal thumb and deregulates expression in the developing limb.

    PubMed

    Furniss, Dominic; Lettice, Laura A; Taylor, Indira B; Critchley, Paul S; Giele, Henk; Hill, Robert E; Wilkie, Andrew O M

    2008-08-15

    A locus for triphalangeal thumb, variably associated with pre-axial polydactyly, was previously identified in the zone of polarizing activity regulatory sequence (ZRS), a long range limb-specific enhancer of the Sonic Hedgehog (SHH) gene at human chromosome 7q36.3. Here, we demonstrate that a 295T>C variant in the human ZRS, previously thought to represent a neutral polymorphism, acts as a dominant allele with reduced penetrance. We found this variant in three independently ascertained probands from southern England with triphalangeal thumb, demonstrated significant linkage of the phenotype to the variant (LOD = 4.1), and identified a shared microsatellite haplotype around the ZRS, suggesting that the probands share a common ancestor. An individual homozygous for the 295C allele presented with isolated bilateral triphalangeal thumb resembling the heterozygous phenotype, suggesting that the variant is largely dominant to the wild-type allele. As a functional test of the pathogenicity of the 295C allele, we utilized a mutated ZRS construct to demonstrate that it can drive ectopic anterior expression of a reporter gene in the developing mouse forelimb. We conclude that the 295T>C variant is in fact pathogenic and, in southern England, appears to be the most common cause of triphalangeal thumb. Depending on the dispersal of the founding mutation, it may play a wider role in the aetiology of this disorder. PMID:18463159

  4. A variant in the sonic hedgehog regulatory sequence (ZRS) is associated with triphalangeal thumb and deregulates expression in the developing limb

    PubMed Central

    Furniss, Dominic; Lettice, Laura A.; Taylor, Indira B.; Critchley, Paul S.; Giele, Henk; Hill, Robert E.; Wilkie, Andrew O.M.

    2008-01-01

    A locus for triphalangeal thumb, variably associated with pre-axial polydactyly, was previously identified in the zone of polarizing activity regulatory sequence (ZRS), a long range limb-specific enhancer of the Sonic Hedgehog (SHH) gene at human chromosome 7q36.3. Here, we demonstrate that a 295T>C variant in the human ZRS, previously thought to represent a neutral polymorphism, acts as a dominant allele with reduced penetrance. We found this variant in three independently ascertained probands from southern England with triphalangeal thumb, demonstrated significant linkage of the phenotype to the variant (LOD = 4.1), and identified a shared microsatellite haplotype around the ZRS, suggesting that the probands share a common ancestor. An individual homozygous for the 295C allele presented with isolated bilateral triphalangeal thumb resembling the heterozygous phenotype, suggesting that the variant is largely dominant to the wild-type allele. As a functional test of the pathogenicity of the 295C allele, we utilized a mutated ZRS construct to demonstrate that it can drive ectopic anterior expression of a reporter gene in the developing mouse forelimb. We conclude that the 295T>C variant is in fact pathogenic and, in southern England, appears to be the most common cause of triphalangeal thumb. Depending on the dispersal of the founding mutation, it may play a wider role in the aetiology of this disorder. PMID:18463159

  5. An Escherichia coli Expression Assay and Screen for Human Immunodeficiency Virus Protease Variants with Decreased Susceptibility to Indinavir

    PubMed Central

    Melnick, Laurence; Yang, Shiow-Shong; Rossi, Rick; Zepp, Charlie; Heefner, Donald

    1998-01-01

    We have developed a recombinant Escherichia coli screening system for the rapid detection and identification of amino acid substitutions in the human immunodeficiency virus (HIV) protease associated with decreased susceptibility to the protease inhibitor indinavir (MK-639; Merck & Co.). The assay depends upon the correct processing of a segment of the HIV-1 HXB2 gag-pol polyprotein followed by detection of HIV reverse transcriptase activity by a highly sensitive, colorimetric enzyme-linked immunosorbent assay. The highly sensitive system detects the contributions of single substitutions such as I84V, L90M, and L63P. The combination of single substitutions further decreases the sensitivity to indinavir. We constructed a library of HIV protease variant genes containing dispersed mutations and, using the E. coli recombinant system, screened for mutants with decreased indinavir sensitivity. The discovered HIV protease variants contain amino acid substitutions commonly associated with indinavir resistance in clinical isolates, including the substitutions L90M, L63P, I64V, V82A, L24I, and I54T. One substitution, W6R, is also frequently found by the screen and has not been reported elsewhere. Of a total of 12,000 isolates that were screened, 12 protease variants with decreased sensitivity to indinavir were found. The L63P substitution, which is also associated with indinavir resistance, increases the stability of the isolated protease relative to that of the native HXB2 protease. The rapidity, sensitivity, and accuracy of this screen also make it useful for screening for novel inhibitors. We have found the approach described here to be useful for the detection of amino acid substitutions in HIV protease that have been associated with drug resistance as well as for the screening of novel compounds for inhibitory activity. PMID:9835523

  6. Candidate genes for congenital diaphragmatic hernia from animalmodels: sequencing of fog2 and pdgfra reveals rare variants indiaphragmatic hernia patients

    SciTech Connect

    Bleyl, S.B.; Moshrefi, A.; Shaw, G.M.; Saijoh, Y.; Schoenwolf,G.C.; Pennacchio, L.A.; Slavotinek, A.M.

    2007-05-11

    Congenital diaphragmatic hernia (CDH) is a common, lifethreatening birth defect. Although there is strong evidence implicatinggenetic factors in its pathogenesis, few causative genes have beenidentified, and in isolated CDH, only one de novo, nonsense mutation hasbeen reported in FOG2 in a female with posterior diaphragmaticeventration. We report here that the homozygous null mouse for the Pdgfragene has posterolateral diaphragmatic defects and thus is a model forhuman CDH. We hypothesized that mutations in this gene could cause humanCDH. We sequenced PDGFRa and FOG2 in 96 patients with CDH, of which 53had isolated CDH (55.2 percent), 36 had CDH and additional anomalies(37.5 percent), and 7 had CDH and known chromosome aberrations (7.3percent). For FOG2, we identified novel sequence alterations predictingp.M703L and p.T843A in two patients with isolated CDH that were absent in526 and 564 control chromosomes respectively. These altered amino acidswere highly conserved. However, due to the lack of available parental DNAsamples we were not able to determine if the sequence alterations were denovo. For PDGFRa, we found a single variant predicting p.L967V in apatient with CDH and multiple anomalies that was absent in 768 controlchromosomes. This patient also had one cell with trisomy 15 on skinfibroblast culture, a finding of uncertain significance. Although ourstudy identified sequence variants in FOG2 and PDGFRa, we have notdefinitively established the variants as mutations and we found noevidence that CDH commonly results from mutations in thesegenes.

  7. A role for chromosomal instability in the development of and selection for radioresistant cell variants

    NASA Technical Reports Server (NTRS)

    Limoli, C. L.; Corcoran, J. J.; Jordan, R.; Morgan, W. F.; Schwartz, J. L.

    2001-01-01

    Chromosome instability is a common occurrence in tumour cells. We examined the hypothesis that the elevated rate of mutation formation in unstable cells can lead to the development of clones of cells that are resistant to the cancer therapy. To test this hypothesis, we compared chromosome instability to radiation sensitivity in 30 independently isolated clones of GM10115 human-hamster hybrid cells. There was a broader distribution of radiosensitivity and a higher mean SF(2)in chromosomally unstable clones. Cytogenetic and DNA double-strand break rejoining assays suggest that sensitivity was a function of DNA repair efficiency. In the unstable population, the more radioresistant clones also had significantly lower plating efficiencies. These observations suggest that chromosome instability in GM10115 cells can lead to the development of cell variants that are more resistant to radiation. In addition, these results suggest that the process of chromosome breakage and recombination that accompanies chromosome instability might provide some selective pressure for more radioresistant variants. Copyright 2001 Cancer Research Campaign.

  8. Variant Salmonella Genomic Island 1 Antibiotic Resistance Gene Cluster in Salmonella enterica Serovar Albany

    PubMed Central

    Doublet, Benoît; Lailler, Renaud; Meunier, Danièle; Brisabois, Anne; Boyd, David; Mulvey, Michael R.; Chaslus-Dancla, Elisabeth

    2003-01-01

    Salmonella genomic island 1 (SGI1) contains an antibiotic resistance gene cluster and has been previously identified in multidrug-resistant Salmonella enterica serovars Typhimurium DT104, Agona, and Paratyphi B. We identified a variant SGI1 antibiotic-resistance gene cluster in a multidrug-resistant strain of S. enterica serovar Albany isolated from food fish from Thailand and imported to France. In this strain, the streptomycin resistance aadA2 gene cassette in one of the SGI1 integrons was replaced by a dfrA1 gene cassette, conferring resistance to trimethoprim and an open reading frame of unknown function. Thus, this serovar Albany strain represents the fourth S. enterica serovar in which SGI1 has been identified and the first SGI1 example where gene cassette replacement took place in one of its integron structures. The antibiotic resistance gene cluster of serovar Albany strain 7205.00 constitutes a new SGI1 variant; we propose a name of SGI1-F. PMID:12737743

  9. Structural, Catalytic and Stabilizing Consequences of Aromatic Cluster Variants in Human Carbonic Anhydrase II

    PubMed Central

    Boone, Christopher D.; Gill, Sonika; Tu, Chingkuang; Silverman, David N.; McKenna, Robert

    2015-01-01

    The presence of aromatic clusters has been found to be an integral feature of many proteins isolated from thermophilic microorganisms. Residues found in aromatic cluster interact via ?-? or C-H···? bonds between the phenyl rings, which are among the weakest interactions involved in protein stability. The lone aromatic cluster in human carbonic anhydrase II (HCA II) is centered on F226 with the surrounding aromatics F66, F95 and W97 located 12 Å posterior the active site; a location which could facilitate proper protein folding and active site construction. The role of F226 in the structure, catalytic activity and thermostability of HCA II was investigated via site-directed mutagenesis of three variants (F226I/L/W) into this position. The measured catalytic rates of the F226 variants via 18O-mass spectrometry were identical to the native enzyme, but differential scanning calorimetry studies revealed a 3-4 K decrease in their denaturing temperature. X-ray crystallographic analysis suggests that the structural basis of this destabilization is via disruption and/or removal of weak C-H···? interactions between F226 to F66, F95 and W97. This study emphasizes the importance of the delicate arrangement of these weak interactions among aromatic clusters in overall protein stability. PMID:24036123

  10. Evaluation of an indirect rapid immunohistochemistry test for the differentiation of rabies virus variants.

    PubMed

    Dyer, Jessie L; Niezgoda, Michael; Orciari, Lillian A; Yager, Pamela A; Ellison, James A; Rupprecht, Charles E

    2013-06-01

    Cost effective diagnostic tests are needed in rabies virus (RABV) enzootic areas to study the prevalence, distribution, and transmission of rabies virus among reservoir hosts. To reduce the associated costs of acquiring and maintaining specialized laboratory equipment, an indirect rapid immunohistochemistry test (IRIT), for the detection and differentiation of RABV variants, was evaluated by traditional light microscopy. The IRIT utilizes fresh frozen brain touch impressions or cell culture monolayers fixed in buffered formalin, a panel of murine anti-nucleoprotein monoclonal antibodies (mAb-N) and commercially available biotin-labeled goat anti-mouse antibody. In this study, 96 RABV isolates, representing 20 RABV variants previously determined by antigenic typing using a panel of mAb-N and the indirect fluorescent antibody test (IFA), and genetic sequence analysis were characterized by IRIT and the results compared. The IRIT results revealed distinct reactivity patterns associated with current and historical RABV reservoir hosts similar to IFA test and genetic sequence analysis. Evaluation of suspected RABV samples through IRIT does not require specialized equipment and is possible to perform in a field setting. Additionally, commercially available labeled secondary antibodies permit the use of a standard panel of unlabeled primary mAbs, without the need for fluorescence microscopy, and should augment existing attempts at antigenic characterization during canine rabies elimination campaigns in developed and developing countries. These results are useful in studying the epizootiology of rabies and inferring the source of infection when unknown. PMID:23541783

  11. Characterization of Fusarium wilt resistant somaclonal variants of banana cv. Rasthali by cDNA-RAPD.

    PubMed

    Ghag, Siddhesh B; Shekhawat, Upendra K S; Ganapathi, Thumballi R

    2014-12-01

    Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is counted among the most destructive diseases of crop plants in India. In the absence of any credible control measure to manage this disease, development of resistant cultivars is the best option. Somaclonal variations arising out of long term in vitro culture of plant tissues is an important source of genetic variability and the selection of somaclones having desired characteristics is a promising strategy to develop plants with improved characters. In the present study, we isolated a group of somaclonal variants of banana cv. Rasthali which showed efficient resistance towards Foc race 1 infection in repeated bioassays. cDNA-RAPD methodology using 96 decamer primers was used to characterize these somaclonal variants. Among the four differentially amplified bands obtained, one mapping to the coding region of a lipoxygenase gene was confirmed to be down regulated in the somaclones as compared to controls by real-time quantitative RT-PCR. Our results correlated well with earlier studies with lipoxygenase mutants in maize wherein reduced expression of lipoxygenase led to enhanced resistance towards Fusarium infection. PMID:25160909

  12. Extensive Genetic Variability Linked to IS26 Insertions in the fljB Promoter Region of Atypical Monophasic Variants of Salmonella enterica Serovar Typhimurium.

    PubMed

    Boland, Cécile; Bertrand, Sophie; Mattheus, Wesley; Dierick, Katelijne; Jasson, Vicky; Rosseel, Toon; Van Borm, Steven; Mahillon, Jacques; Wattiau, Pierre

    2015-05-01

    Fifty-nine monophasic Salmonella enterica serovar Typhimurium isolates, collected in Belgium during the period from 2008 to 2011, have been serotyped as 4,[5]:i:- and shown to harbor an fljB coding sequence. The genetic differences between these strains and phenotypically biphasic Salmonella Typhimurium were analyzed through PCR and DNA sequencing. Genetic alterations in the fljB promoter region affecting expression of the phase 2 flagellin were observed in 53 isolates. Other genetic events in the invertible region carrying the fljB promoter were observed in 2 isolates. For the remaining 4 isolates, no molecular differences with a reference biphasic Salmonella Typhimurium strain could be observed. Next-generation sequencing of one representative isolate affected in the fljB promoter region revealed a 26-kb IS26 composite transposon insertion along with a local genomic rearrangement. Several other IS26 element-mediated alterations of this genomic region were observed. This group of monophasic Salmonella Typhimurium isolates was genetically heterogeneous, as revealed by multilocus variable-number tandem-repeat analysis (MLVA), PCR, and sequencing. Pigs and pork represented a major source of such monophasic isolates in Belgium, as reported in other countries. Three out of 5 isolates of human origin presented genetic profiles identical to those of food isolates, demonstrating the pathogenic potential of the newly characterized variants and potential dissemination along the food chain. This study highlighted the key role played by IS26 insertions in the loss of phase 2 flagellin expression and the subsequent generation of multiple monophasic variant lineages from biphasic Salmonella Typhimurium ancestors. PMID:25724958

  13. GENDER-VARIANT TRANS QUEER G LESBIAN BISEXUAL TWO-SPIRIT INTE

    E-print Network

    Pulfrey, David L.

    GENDER-VARIANT TRANS QUEER G LESBIAN BISEXUAL TWO-SPIRIT INTE SEX GENDER-VARIANT TRANS QUEE GAY LESBIAN BISEXUAL TWO-SPIRIT INTERSEX GENDER-VARIANT TRANS QUEER GAY LESBIAN BISEXUAL TWO SPIRIT INTERSEX GENDER-VARIANT TRANS QUEER GAY LESBIAN BISEXU TWO-SPIRIT INTERSEX GENDER-VAR ANT TRANS QUEER GAY LESBIAN

  14. Cellulase variants with improved expression, activity and stability, and use thereof

    SciTech Connect

    Aehle, Wolfgang; Bott, Richard R; Bower, Benjamin; Caspi, Jonathan; Estell, David A; Goedegebuur, Frits; Hommes, Ronaldus W.J.; Kaper, Thijs; Kelemen, Bradley; Kralj, Slavko; Van Lieshout, Johan; Nikolaev, Igor; Van Stigt Thans, Sander; Wallace, Louise; Vogtentanz, Gudrun; Sandgren, Mats

    2014-03-25

    The present disclosure relates to cellulase variants. In particular the present disclosure relates to cellulase variants having improved expression, activity and/or stability. Also described are nucleic acids encoding the cellulase variants, compositions comprising the cellulase variants, and methods of use thereof.

  15. Small-plaque variant of canine herpesvirus with reduced pathogenicity for newborn pups.

    PubMed Central

    Carmichael, L E; Medic, B L

    1978-01-01

    The plaque characteristics of 13 field isolates of canine herpesvirus were found to be similar. After 312 passages of the F-205 strain in dog kidney cell cultures incubated at 35 degrees C, the virus still was virulent for newborn pups; it also had the macroplaque morphology of the wild-type virus. However, after 20 additional passages at 30 degrees C, a microplaque (mP) variant had emerged as the predominant type. Cloned mP virus retained the small-plaque characteristic after 66 transfers at 30 degrees C. The natural history of the mP strain and some of its biological properties are reported, the most significant being its lack of pathogenicity for newborn pups. Images PMID:208969

  16. Immunological selection of variant mouse lymphoid cells with altered glucocorticoid responsiveness.

    PubMed Central

    Danielsen, M; Peterson, D O; Stallcup, M R

    1983-01-01

    We have devised an immunological procedure to separate cells on the basis of expression of mouse mammary tumor virus (MMTV) gene products. Plastic petri dishes coated with specific antibodies against MMTV proteins bind cells with an efficiency that correlates with the level of MMTV gene expression. Glucocorticoid-sensitive mouse thymoma cell line W7 was infected with MMTV. Clones from the infected population retain the relatively slow cytolytic glucocorticoid response and, in addition, exhibit a rapid induction of MMTV-specific RNA and proteins. By combining our immunological selection with the selection for resistance to hormone-mediated cytolysis, we have isolated variant cells which are resistant to the cytotoxic effect of glucocorticoids but which retain the induction of viral gene products and must therefore have a functional glucocorticoid receptor protein. Images PMID:6310372

  17. Novel Chikungunya Virus Variant in Travelers Returning from Indian Ocean Islands

    PubMed Central

    Parola, Philippe; de Lamballerie, Xavier; Jourdan, Jacques; Rovery, Clarisse; Vaillant, Véronique; Minodier, Philippe; Brouqui, Philippe; Flahault, Antoine; Charrel, Rémi N.

    2006-01-01

    Chikungunya virus (CHIKV) emerged in Indian Ocean islands in 2005 and is causing an ongoing outbreak that involves >260,000 patients, including travelers returning home from these islands. We investigated cases in 4 patients returning from Mayotte and Reunion Islands with CHIKV infection and a nurse infected in metropolitan France after direct contact with the blood of a traveler. Four patients had tenosynovitis and pain at wrist pressure, and 1 had life-threatening manifestations. Four CHIKV strains were isolated, including 1 from the patient with the autochthonous case. The complete genomic sequence identified a new CHIKV variant emerging from the East/central African evolutionary lineage. Aedes albopictus, the implicated vector of CHIKV in Indian Ocean islands, has dispersed worldwide in recent decades. High viral loads in patients returning from Indian Ocean islands to countries where Ae. albopictus is prevalent may be a source of epidemics. PMID:17176562

  18. Development of a Hybridoma Cell Line Secreting Monoclonal Antibody Against S Protein of a Chinese Variant of PEDV.

    PubMed

    Lei, Ximei; Zhao, Jun; Wang, Xiaomeng; Zhao, Yongxiang; Wang, Chuanqing

    2015-02-01

    Gene encoding 22-380 aa of spike protein of porcine epidemic diarrhea virus (PEDV) isolate in China was cloned and expressed as a recombinant protein in Escherichia coli BL21(DE3). Female BALB/c mice were immunized with the purified recombinant S protein, and a monoclonal antibody (MAb) designated as 2D1 against S protein was achieved by hybridoma technique. MAb 2D1 reacted with S protein of PEDV specifically. The monoclonal antibody 2D1 may provide a useful tool as a specific diagnostic reagent for detecting S protein of the Chinese variant of PEDV and for further investigation into the virus' pathogenic mechanism. PMID:25723278

  19. Characterization of a variant of the polysaccharide acetan produced by a mutant of Acetobacter xylinum strain CR1/4.

    PubMed

    MacCormick, C A; Harris, J E; Gunning, A P; Morris, V J

    1993-02-01

    Acetobacter xylinum NRRL B42 (NCIB 40123) produces both cellulose and a complex anionic branched heteropolysaccharide called acetan. Chemical mutagenesis was used to isolate stable cellulose-minus Acetobacter xylinum mutants. Further chemical mutagenesis of these cellulose-minus A. xylinum bacteria was used to select mutants which secrete polysaccharides which are variants of the acetan structure. Preparation, purification and characterization of these polysaccharides are described. Methylation analysis of the polysaccharide structure CR1/4 suggests that the polysaccharide has an acetan structure with a truncated sidechain terminating in glucuronic acid. PMID:8444650

  20. Thermodynamic characterisation of the mutated isoenzyme A of ?- N-acetylhexosaminidase in GM2-gangliosidosis B1 variant

    Microsoft Academic Search

    Luis F. Pérez; Helena M. Ribeiro; J. Antonio Casal; Rui A. Pinto; M. Clara Sá Miranda; J. Carlos Tutor

    1999-01-01

    Here we report the determination of the activation energies of the plasma isoenzymes of ?-N-acetylhexosaminidase (Hex, EC 3.2.1.52), isolated by chromatography in DEAE-cellulose, using the neutral chromogenic substrate 3,3?dichlorophenylsulfonphthaleinyl-N-acetyl-?-d-glucosaminide. The activation energy of mutated Hex A isoenzyme (Ea?71.5 kJ\\/mol) from a patient with GM2-gangliosidosis B1 variant, homozygote for the G533?A (Argl78His) mutation, was significantly higher than that of normal Hex

  1. Potential forensic applications of minisatellite variant repeat (MVR) mapping using the polymerase chain reaction (PCR) at D1S8.

    PubMed

    Yamamoto, T; Tamaki, K; Kojima, T; Uchihi, R; Katsumata, Y

    1994-05-01

    Minisatellite variant repeat (MVR) mapping using the polymerase chain reaction (PCR) at D1S8 (MS32) was applied to samples from various human tissues. All DNA samples obtained from an individual's organs at autopsy consistently gave the same digital diploid codes. Even 1 ng of genomic DNA was sufficient to obtain authentic diploid MVR coding ladders. MVR-PCR could be reliably applied to DNA isolated from bloodstains, saliva stains, seminal stains and plucked hair roots, and should become a powerful tool for individual identification in forensic investigations. PMID:8006621

  2. Identifying Mendelian disease genes with the Variant Effect Scoring Tool

    PubMed Central

    2013-01-01

    Background Whole exome sequencing studies identify hundreds to thousands of rare protein coding variants of ambiguous significance for human health. Computational tools are needed to accelerate the identification of specific variants and genes that contribute to human disease. Results We have developed the Variant Effect Scoring Tool (VEST), a supervised machine learning-based classifier, to prioritize rare missense variants with likely involvement in human disease. The VEST classifier training set comprised ~ 45,000 disease mutations from the latest Human Gene Mutation Database release and another ~45,000 high frequency (allele frequency >1%) putatively neutral missense variants from the Exome Sequencing Project. VEST outperforms some of the most popular methods for prioritizing missense variants in carefully designed holdout benchmarking experiments (VEST ROC AUC = 0.91, PolyPhen2 ROC AUC = 0.86, SIFT4.0 ROC AUC = 0.84). VEST estimates variant score p-values against a null distribution of VEST scores for neutral variants not included in the VEST training set. These p-values can be aggregated at the gene level across multiple disease exomes to rank genes for probable disease involvement. We tested the ability of an aggregate VEST gene score to identify candidate Mendelian disease genes, based on whole-exome sequencing of a small number of disease cases. We used whole-exome data for two Mendelian disorders for which the causal gene is known. Considering only genes that contained variants in all cases, the VEST gene score ranked dihydroorotate dehydrogenase (DHODH) number 2 of 2253 genes in four cases of Miller syndrome, and myosin-3 (MYH3) number 2 of 2313 genes in three cases of Freeman Sheldon syndrome. Conclusions Our results demonstrate the potential power gain of aggregating bioinformatics variant scores into gene-level scores and the general utility of bioinformatics in assisting the search for disease genes in large-scale exome sequencing studies. VEST is available as a stand-alone software package at http://wiki.chasmsoftware.org and is hosted by the CRAVAT web server at http://www.cravat.us PMID:23819870

  3. Thymidine-Dependent Staphylococcus aureus Small-Colony Variants: Human Pathogens That Are Relevant Not Only in Cases of Cystic Fibrosis Lung Disease ?

    PubMed Central

    Besier, Silke; Zander, Johannes; Siegel, Ekkehard; Saum, Stephan H.; Hunfeld, Klaus-Peter; Ehrhart, Annabelle; Brade, Volker; Wichelhaus, Thomas A.

    2008-01-01

    We report the isolation of thymidine-dependent small-colony variants (TD-SCVs) of Staphylococcus aureus from unusual infection sites of patients with chronic soft tissue infection, tympanitis, bronchitis, peritonitis, and septicemia. Furthermore, we provide evidence that the essential growth factor for TD-SCVs, i.e., thymidine, and its metabolite dTMP are present in various human specimens. PMID:18832128

  4. Thymidine-dependent Staphylococcus aureus small-colony variants: human pathogens that are relevant not only in cases of cystic fibrosis lung disease.

    PubMed

    Besier, Silke; Zander, Johannes; Siegel, Ekkehard; Saum, Stephan H; Hunfeld, Klaus-Peter; Ehrhart, Annabelle; Brade, Volker; Wichelhaus, Thomas A

    2008-11-01

    We report the isolation of thymidine-dependent small-colony variants (TD-SCVs) of Staphylococcus aureus from unusual infection sites of patients with chronic soft tissue infection, tympanitis, bronchitis, peritonitis, and septicemia. Furthermore, we provide evidence that the essential growth factor for TD-SCVs, i.e., thymidine, and its metabolite dTMP are present in various human specimens. PMID:18832128

  5. Oral mucosal morphea: a new variant.

    PubMed

    Tang, M M; Bornstein, M M; Irla, N; Beltraminelli, H; Lombardi, T; Borradori, L

    2012-01-01

    Morphea is a cutaneous disorder characterized by an excessive collagen deposition. While in almost all cases the sclerosing process exclusively affects the skin, there are anecdotal cases in which associated mucosal involvement has been described. We here report the case of a woman developing a whitish indurated plaque over the left upper vestibular mucosa and hard palate leading to dental mobility and exposure of the roots of several teeth. Cone beam computed tomography of the left maxilla showed bone resorption involving the upper cuspid to the second molar region with widened periodontal ligament spaces, while light microscopy studies demonstrated epithelial atrophy and fibrosis of the dermis extending into the submucosa with hyalinization of subepithelial collagen. Our observation expands the spectrum of clinical presentations of morphea and provides the first example of isolated oral morphea. Its recognition is important to avoid significant local complications. PMID:22538799

  6. Prevalence and Clinical Significance of Staphylococcus aureus Small-Colony Variants in Cystic Fibrosis Lung Disease?

    PubMed Central

    Besier, Silke; Smaczny, Christina; von Mallinckrodt, Christian; Krahl, Andreas; Ackermann, Hanns; Brade, Volker; Wichelhaus, Thomas A.

    2007-01-01

    Small-colony variants (SCVs) of Staphylococcus aureus can be isolated from the chronically infected airways of patients suffering from cystic fibrosis (CF). These slow-growing morphological variants have been associated with persistent and antibiotic-resistant infections, such as osteomyelitis and device-related infections, but no information is available to date regarding the clinical significance of this special phenotype in CF lung disease. We therefore investigated the prevalence of S. aureus SCVs in CF lung disease in a 12-month prospective study and correlated the microbiological culture results with the patients' clinical data. A total of 252 patients were screened for the presence of SCVs. The prevalence rate was determined to be 17% (95% confidence interval, 10 to 25%) among S. aureus carriers. S. aureus isolates with the SCV phenotype showed significantly higher antibiotic resistance rates than those with the normal phenotype. Patients positive for SCVs were significantly older (P = 0.0099), more commonly cocolonized with Pseudomonas aeruginosa (P = 0.0454), and showed signs of more advanced disease, such as lower forced expiratory volume in 1 s (P = 0.0148) than patients harboring S. aureus with a solely normal phenotype. The logistic regression model determined lower weight (P = 0.016), advanced age (P = 0.000), and prior use of trimethoprim-sulfamethoxazole (P = 0.002) as independent risk factors for S. aureus SCV positivity. The clinical status of CF patients is known to be affected by multiple parameters. Nonetheless, the independent risk factors determined here point to the impact of S. aureus SCVs on chronic and persistent infections in advanced CF lung disease. PMID:17108072

  7. [Selection of heparin-sensitive dengue virus variants in BHK-21 cells].

    PubMed

    Celis, Argelia; Moros, Zoila; Gerder, Marlene; Pagano, Francesca; Vizzi, Esmeralda; Liprandi, Ferdinando

    2014-06-01

    Several studies have shown that adaptation of various viruses to grow in certain cell lines of vertebrates, leads to the selection of virus variants that bind heparan sulfate (HS) with high affinity. In this study we investigated the susceptibility of strains of dengue virus (DENV) to oversulfated heparin an analogue of HS after passages in BHK-21 cells. Field isolates of the four serotypes of DENV with a limited number of passes in mosquito cells C6/36HT were serially passaged eight times in BHK-21 cells. The adaptation of the DENV to the cell culture selected viral variants with an increased replicative capacity in BHK-21 cells and an increased susceptibility to heparin compared with the original not adapted strains, with a more significant inhibition of the infectivity in DENV-2 and DENV-4.The E protein of the adapted strains showed changes in the amino acid sequence, particularly at the position K204R to DENV-1, N67K to DENV-2, K308R and V452A for DENV-3 and E327G to DENV-4. These substitutions implicated a gain of basic residues that increased the net positive charge of the protein. These results suggest that adaptation of DENV strains to BHK-21 cells implies changes in the envelope protein, changes associated to the protein reactivity with heparin, the inhibitory effectiveness of this compound varying depending on the viral strain. In addition, these results suggest that the HS can play an important role in the infectivity of the DENV strains adapted to vertebrate cell culture, but not in the infectivity of non-adapted DENV isolates. PMID:24974631

  8. Genomic Architecture of Aggression: Rare Copy Number Variants in Intermittent Explosive Disorder

    PubMed Central

    Vu, Tiffany H; Coccaro, Emil F; Eichler, Evan E; Girirajan, Santhosh

    2011-01-01

    Copy number variants (CNVs) are known to be associated with complex neuropsychiatric disorders (e.g., schizophrenia and autism) but have not been explored in the isolated features of aggressive behaviors such as intermittent explosive disorder (IED). IED is characterized by recurrent episodes of aggression in which individuals act impulsively and grossly out of proportion from the involved stressors. Previous studies have identified genetic variants in the serotonergic pathway that play a role in susceptibility to this behavior, but additional contributors have not been identified. Therefore, to further delineate possible genetic influences, we investigated CNVs in individuals diagnosed with IED and/or personality disorder (PD). We carried out array comparative genomic hybridization on 113 samples of individuals with isolated features of IED (n = 90) or PD (n = 23). We detected a recurrent 1.35-Mbp deletion on chromosome 1q21.1 in one IED subject and a novel ?350-kbp deletion on chromosome 16q22.3q23.1 in another IED subject. While five recent reports have suggested the involvement of an ?1.6-Mbp 15q13.3 deletion in individuals with behavioral problems, particularly aggression, we report an absence of such events in our study of individuals specifically selected for aggression. We did, however, detect a smaller ?430-kbp 15q13.3 duplication containing CHRNA7 in one individual with PD. While these results suggest a possible role for rare CNVs in identifying genes underlying IED or PD, further studies on a large number of well-characterized individuals are necessary. © 2011 Wiley-Liss, Inc. PMID:21812102

  9. Normal Mutation Rate Variants Arise in a Mutator (Mut S) Escherichia coli Population

    PubMed Central

    Turrientes, María-Carmen; Baquero, Fernando; Levin, Bruce R.; Martínez, José-Luis; Ripoll, Aida; González-Alba, José-María; Tobes, Raquel; Manrique, Marina; Baquero, Maria-Rosario; Rodríguez-Domínguez, Mario-José; Cantón, Rafael; Galán, Juan-Carlos

    2013-01-01

    The rate at which mutations are generated is central to the pace of evolution. Although this rate is remarkably similar amongst all cellular organisms, bacterial strains with mutation rates 100 fold greater than the modal rates of their species are commonly isolated from natural sources and emerge in experimental populations. Theoretical studies postulate and empirical studies teort the hypotheses that these “mutator” strains evolved in response to selection for elevated rates of generation of inherited variation that enable bacteria to adapt to novel and/or rapidly changing environments. Less clear are the conditions under which selection will favor reductions in mutation rates. Declines in rates of mutation for established populations of mutator bacteria are not anticipated if such changes are attributed to the costs of augmented rates of generation of deleterious mutations. Here we report experimental evidence of evolution towards reduced mutation rates in a clinical isolate of Escherichia coli with an hyper-mutable phenotype due a deletion in a mismatch repair gene, (?mutS). The emergence in a ?mutS background of variants with mutation rates approaching those of the normal rates of strains carrying wild-type MutS was associated with increase in fitness with respect to ancestral strain. We postulate that such an increase in fitness could be attributed to the emergence of mechanisms driving a permanent “aerobic style of life”, the negative consequence of this behavior being regulated by the evolution of mechanisms protecting the cell against increased endogenous oxidative radicals involved in DNA damage, and thus reducing mutation rate. Gene expression assays and full sequencing of evolved mutator and normo-mutable variants supports the hypothesis. In conclusion, we postulate that the observed reductions in mutation rate are coincidental to, rather than, the selective force responsible for this evolution. PMID:24069167

  10. The sequence of a viroid from grapevine closely related to severe isolates of citrus exocortis viroid.

    PubMed

    García-Arenal, F; Pallás, V; Flores, R

    1987-05-26

    The primary structure of a grapevine viroid (GVs) isolated in Spain was determined. The sequence consisted of 369 nucleotide residues forming a circular molecule. GVs presented extensive homology with viroids of the potato spindle tuber viroid (PSTV) group, that was specially high in the case of citrus exocortis viroid (CEV) both with variants found in isolates inducing severe (92% with CEV-A) and mild (89% with CEV-DE26) symptoms on tomato. The secondary structure proposed for GVs showed that the changes in the sequence in relation to CEV-A generated modifications of the secondary structure particularly important in the left terminal (Tl), variable (V) and pathogenesis (P) viroid domains that have been postulated. Nevertheless it was noted in GVs a central core in the P domain that is conserved in the class A sequence variants characteristic of severe isolates, but not in the class B ones found in mild isolates of CEV. These observations indicate that GVs should be considered as a severe isolate of CEV from grapevine (CEV-g), a suggestion that correlates with the biological properties of CEV-g both in tomato and in Gynura aurantiaca. The presence of this central core in the P domain seems to characterize all the variants of CEV inducing severe symptoms in tomato. PMID:2438653

  11. Antigenic typing of Brazilian rabies virus samples isolated from animals and humans, 1989-2000.

    PubMed

    Favoretto, Silvana Regina; Carrieri, Maria Luiza; Cunha, Elenice Maria S; Aguiar, Elizabeth A C; Silva, Luzia Helena Q; Sodre, Miriam M; Souza, Maria Conceição A M; Kotait, Ivanete

    2002-01-01

    Animal and human rabies samples isolated between 1989 and 2000 were typified by means of a monoclonal antibody panel against the viral nucleoprotein. The panel had been previously established to study the molecular epidemiology of rabies virus in the Americas. Samples were isolated in the Diagnostic Laboratory of the Pasteur Institute and in other rabies diagnostic centers in Brazil. In addition to the fixed virus samples CVS-31/96-IP, preserved in mouse brain, and PV-BHK/97, preserved in cell culture, a total of 330 rabies virus samples were isolated from dogs, cats, cattle, horses, bats, sheep, goat, swine, foxes, marmosets, coati and humans. Six antigenic variants that were compatible with the pre-established monoclonal antibodies panel were defined: numbers 2 (dog), 3 (Desmodus rotundus), 4 (Tadarida brasiliensis), 5 (vampire bat from Venezuela), 6 (Lasiurus cinereus) and Lab (reacted to all used antibodies). Six unknown profiles, not compatible with the panel, were also found. Samples isolated from insectivore bats showed the greatest variability and the most commonly isolated variant was variant-3 (Desmodus rotundus). These findings may be related to the existence of multiple independent transmission cycles, involving different bat species. PMID:12048546

  12. Characterization of Virulence Plasmids and Serotyping of Rhodococcus equi Isolates from Submaxillary Lymph Nodes of Pigs in Hungary

    PubMed Central

    Makrai, László; Takayama, Saki; Dénes, Béla; Hajtós, István; Sasaki, Yukako; Kakuda, Tsutomu; Tsubaki, Shiro; Major, Andrea; Fodor, László; Varga, János; Takai, Shinji

    2005-01-01

    The plasmid types and serotypes of 164 Rhodococcus equi strains obtained from submaxillary lymph nodes of swine from different piggeries in 28 villages and towns located throughout the country were examined. The strains were tested by PCR for the presence of 15- to 17-kDa virulence-associated protein antigen (VapA) and 20-kDa virulence-associated protein antigen (VapB) genes. Plasmid DNAs were isolated and analyzed by digestion with restriction endonucleases to estimate size and compare their polymorphism characteristics. None of the 164 isolates contained the vapA gene, and 44 (26.8%) isolates were positive for the vapB gene, showing a product of the expected 827-bp size in the PCR amplification. The 44 isolates of intermediate virulence contained virulence plasmids that were identified as types 1 (3 isolates), 4 (1 isolate), 5 (36 isolates), 6 (1 isolate), and 7 (2 isolates) and as a new variant (1 isolate). On the basis of restriction digestion patterns of plasmid DNAs, we tentatively designated the variant as type 17. Use of the serotyping method of Prescott showed that 110 (67.1%) out of the 164 isolates were typeable and that serotype 2 predominated (83 isolates [50.6%]), followed by serotype 1 (26 strains [15.9%]). Only one isolate belonged to serotype 3. A total of 54 (32.9%) isolates were untypeable in Prescott's system. The prevalence of R. equi strains of intermediate virulence among the isolates that came from the submaxillary lymph nodes of swine in Hungary was lower than that seen with isolates obtained elsewhere. PMID:15750091

  13. Atypical face shape and genomic structural variants in epilepsy

    PubMed Central

    Chinthapalli, Krishna; Bartolini, Emanuele; Novy, Jan; Suttie, Michael; Marini, Carla; Falchi, Melania; Fox, Zoe; Clayton, Lisa M. S.; Sander, Josemir W.; Guerrini, Renzo; Depondt, Chantal; Hennekam, Raoul; Hammond, Peter

    2012-01-01

    Many pathogenic structural variants of the human genome are known to cause facial dysmorphism. During the past decade, pathogenic structural variants have also been found to be an important class of genetic risk factor for epilepsy. In other fields, face shape has been assessed objectively using 3D stereophotogrammetry and dense surface models. We hypothesized that computer-based analysis of 3D face images would detect subtle facial abnormality in people with epilepsy who carry pathogenic structural variants as determined by chromosome microarray. In 118 children and adults attending three European epilepsy clinics, we used an objective measure called Face Shape Difference to show that those with pathogenic structural variants have a significantly more atypical face shape than those without such variants. This is true when analysing the whole face, or the periorbital region or the perinasal region alone. We then tested the predictive accuracy of our measure in a second group of 63 patients. Using a minimum threshold to detect face shape abnormalities with pathogenic structural variants, we found high sensitivity (4/5, 80% for whole face; 3/5, 60% for periorbital and perinasal regions) and specificity (45/58, 78% for whole face and perinasal regions; 40/58, 69% for periorbital region). We show that the results do not seem to be affected by facial injury, facial expression, intellectual disability, drug history or demographic differences. Finally, we use bioinformatics tools to explore relationships between facial shape and gene expression within the developing forebrain. Stereophotogrammetry and dense surface models are powerful, objective, non-contact methods of detecting relevant face shape abnormalities. We demonstrate that they are useful in identifying atypical face shape in adults or children with structural variants, and they may give insights into the molecular genetics of facial development. PMID:22975390

  14. Mendelian Randomization Analysis With Multiple Genetic Variants Using Summarized Data

    PubMed Central

    Burgess, Stephen; Butterworth, Adam; Thompson, Simon G

    2013-01-01

    Genome-wide association studies, which typically report regression coefficients summarizing the associations of many genetic variants with various traits, are potentially a powerful source of data for Mendelian randomization investigations. We demonstrate how such coefficients from multiple variants can be combined in a Mendelian randomization analysis to estimate the causal effect of a risk factor on an outcome. The bias and efficiency of estimates based on summarized data are compared to those based on individual-level data in simulation studies. We investigate the impact of gene–gene interactions, linkage disequilibrium, and ‘weak instruments’ on these estimates. Both an inverse-variance weighted average of variant-specific associations and a likelihood-based approach for summarized data give similar estimates and precision to the two-stage least squares method for individual-level data, even when there are gene–gene interactions. However, these summarized data methods overstate precision when variants are in linkage disequilibrium. If the P-value in a linear regression of the risk factor for each variant is less than , then weak instrument bias will be small. We use these methods to estimate the causal association of low-density lipoprotein cholesterol (LDL-C) on coronary artery disease using published data on five genetic variants. A 30% reduction in LDL-C is estimated to reduce coronary artery disease risk by 67% (95% CI: 54% to 76%). We conclude that Mendelian randomization investigations using summarized data from uncorrelated variants are similarly efficient to those using individual-level data, although the necessary assumptions cannot be so fully assessed. PMID:24114802

  15. Functionally Significant, Rare Transcription Factor Variants in Tetralogy of Fallot

    PubMed Central

    Töpf, Ana; Griffin, Helen R.; Glen, Elise; Soemedi, Rachel; Brown, Danielle L.; Hall, Darroch; Rahman, Thahira J.; Eloranta, Jyrki J.; Jüngst, Christoph; Stuart, A. Graham; O'Sullivan, John; Keavney, Bernard D.; Goodship, Judith A.

    2014-01-01

    Objective Rare variants in certain transcription factors involved in cardiac development cause Mendelian forms of congenital heart disease. The purpose of this study was to systematically assess the frequency of rare transcription factor variants in sporadic patients with the cardiac outflow tract malformation tetralogy of Fallot (TOF). Methods and Results We sequenced the coding, 5?UTR, and 3?UTR regions of twelve transcription factor genes implicated in cardiac outflow tract development (NKX2.5, GATA4, ISL1, TBX20, MEF2C, BOP/SMYD1, HAND2, FOXC1, FOXC2, FOXH, FOXA2 and TBX1) in 93 non-syndromic, non-Mendelian TOF cases. We also analysed Illumina Human 660W-Quad SNP Array data for copy number variants in these genes; none were detected. Four of the rare variants detected have previously been shown to affect transactivation in in vitro reporter assays: FOXC1 p.P297S, FOXC2 p.Q444R, FOXH1 p.S113T and TBX1 p.P43_G61del PPPPRYDPCAAAAPGAPGP. Two further rare variants, HAND2 p.A25_A26insAA and FOXC1 p.G378_G380delGGG, A488_491delAAAA, affected transactivation in in vitro reporter assays. Each of these six functionally significant variants was present in a single patient in the heterozygous state; each of the four for which parental samples were available were maternally inherited. Thus in the 93 TOF cases we identified six functionally significant mutations in the secondary heart field transcriptional network. Significance This study indicates that rare genetic variants in the secondary heart field transcriptional network with functional effects on protein function occur in 3–13% of patients with TOF. This is the first report of a functionally significant HAND2 mutation in a patient with congenital heart disease. PMID:25093829

  16. Epidemiology and molecular characterization of co-circulating influenza A/H3N2 virus variants in children: Houston, Texas, 1997-8.

    PubMed Central

    O'Donnell, F. T.; Munoz, F. M.; Atmar, R. L.; Hwang, L. Y.; Demmler, G. J.; Glezen, W. P.

    2003-01-01

    Co-circulating variants of influenza A/H3N2 viruses in children were studied in Houston, Texas between October 1997 and March 1998 to assess the effects of a new variant strain on the severity of clinical illness. Influenza A virus was isolated from the nasal wash or nasal aspirate specimens collected from children at two tertiary care hospitals, and 271 isolates were available for variant-specific subtyping using RT-PCR and restriction fragment length polymorphism (RFLP) analysis. We classified 124 (46%) influenza viruses as A/H3N2/Wuhan/359/95-like and 137 (50%) as A/H3N2/Sydney/05/97-like. Ten (4%) virus isolates could not be classified. Ill contacts in the household were reported more frequently in patients infected with A/Sydney-like viruses than in those infected with A/Wuhan-like viruses (85% vs. 71%, respectively, P=0.02). There were no differences in other demographic variables among children infected with these strains. This study found no increase in illness severity in children infected with a newly emerging strain. PMID:12825738

  17. Variant G57E of Mannose Binding Lectin Associated with Protection against Tuberculosis Caused by Mycobacterium africanum but not by M. tuberculosis

    PubMed Central

    Walter, Kerstin; Homolka, Susanne; Intemann, Christopher D.; Chinbuah, Margaret Amanua; Enimil, Anthony; Gyapong, John; Osei, Ivy; Owusu-Dabo, Ellis; Rüsch-Gerdes, Sabine; Horstmann, Rolf D.; Ehlers, Stefan; Meyer, Christian G.

    2011-01-01

    Structural variants of the Mannose Binding Lectin (MBL) cause quantitative and qualitative functional deficiencies, which are associated with various patterns of susceptibility to infectious diseases and other disorders. We determined genetic MBL variants in 2010 Ghanaian patients with pulmonary tuberculosis (TB) and 2346 controls and characterized the mycobacterial isolates of the patients. Assuming a recessive mode of inheritance, we found a protective association between TB and the MBL2 G57E variant (odds ratio 0.60, confidence interval 0.4–0.9, P 0.008) and the corresponding LYQC haplotype (Pcorrected 0.007) which applied, however, only to TB caused by M. africanum but not to TB caused by M. tuberculosis. In vitro, M. africanum isolates bound recombinant human MBL more efficiently than did isolates of M. tuberculosis. We conclude that MBL binding may facilitate the uptake of M. africanum by macrophages, thereby promoting infection and that selection by TB may have favoured the spread of functional MBL deficiencies in regions endemic for M. africanum. PMID:21695215

  18. Adenosquamous Variant of Metaplastic Carcinoma of Breast – An Unusual Histological Variant

    PubMed Central

    Arunalatha, P.; Chandramouleeswari, K.; Lily, S. Mary; Ramya, S.

    2015-01-01

    Metaplastic carcinoma of breast refers to a heterogeneous group of neoplasms characterized by intimate admixture of adenocarcinoma with dominant areas of spindle cell, squamous cell and/ or mesenchymal differentiation. They constitute the rarest histological variant of invasive ductal carcinoma. These carcinomas have aggressive clinical behaviour and show suboptimal response to standard treatment. A 49-year-old female presented with lump in the left breast for one year. She was diagnosed as infiltrating ductal carcinoma breast with triple negative hormone status by trucut biopsy. She completed four cycles of neoadjuvant chemotherapy. Postchemotherapy, axillary nodes decreased in size but the size of the primary tumour remained the same. Hence, she underwent modified radical mastectomy and the specimen sent for histopathological examination. Grossly, there was a solitary cyst measuring 4x3cm. Histologically, cyst enclosing malignant cells which resemble mature squamous epithelial cells. Also, seen are malignant cells in glandular pattern.

  19. Mutation and premating isolation

    NASA Technical Reports Server (NTRS)

    Woodruff, R. C.; Thompson, J. N. Jr

    2002-01-01

    While premating isolation might be traceable to different genetic mechanisms in different species, evidence supports the idea that as few as one or two genes may often be sufficient to initiate isolation. Thus, new mutation can theoretically play a key role in the process. But it has long been thought that a new isolation mutation would fail, because there would be no other individuals for the isolation-mutation-carrier to mate with. We now realize that premeiotic mutations are very common and will yield a cluster of progeny carrying the same new mutant allele. In this paper, we discuss the evidence for genetically simple premating isolation barriers and the role that clusters of an isolation mutation may play in initiating allopatric, and even sympatric, species divisions.

  20. Enterobacter cloacae with a novel variant of ACT AmpC beta-lactamase originating from glaucous gull (Larus hyperboreus) in Svalbard.

    PubMed

    Literak, Ivan; Manga, Ivan; Wojczulanis-Jakubas, Katarzyna; Chroma, Magdalena; Jamborova, Ivana; Dobiasova, Hana; Sedlakova, Miroslava Htoutou; Cizek, Alois

    2014-07-16

    We aimed at Escherichia coli and Enterobacter cloacae isolates resistant to cephalosporins and fluoroquinolones and Salmonella isolates in wild birds in Arctic Svalbard, Norway. Cloacal swabs of little auks (Alle alle, n=215) and samples of faeces of glaucous gulls (Larus hyperboreus, n=15) were examined. Inducible production of AmpC enzyme was detected in E. cloacae KW218 isolate. Sequence analysis of the 1146 bp PCR product of the ampC gene from this isolate revealed 99% sequence homology with the blaACT-14 and blaACT-5 AmpC beta-lactamase genes. Four, respectively six of the identified single nucleotide polymorphisms generated amino acid substitutions in the amino acid chain. As the ampC sequence polymorphism in the investigated E. cloacae strain was identified as unique, we revealed a novel variant of the ampC beta-lactamase gene blaACT-23. PMID:24629772

  1. Solitary liver metastasis from follicular variant papillary thyroid carcinoma: A case report and literature review

    PubMed Central

    Djenic, Brano; Duick, Daniel; Newell, James O.; Demeure, Michael J.

    2014-01-01

    Introduction Papillary (PTC) and follicular (FTC) thyroid carcinomas, together known as differentiated thyroid carcinomas (DTC), are among the most curable of cancers. Sites of metastases from FTC are usually osseous and those from PTC are in regional nodal basins and the lungs. Visceral metastases are rare and when they do occur, they tend do so in multiple sites. We present the case of a patient with a follicular variant of PTC and a solitary metastasis to the liver then review the relevant literature. Presentation of case An otherwise healthy 68-year-old woman was diagnosed with follicular variant papillary thyroid cancer in 2003 and subsequently underwent thyroidectomy. The patient’s endocrinologist conducted surveillance of her thyroid cancer. In 2012, due to rise in thyroglobulin, a whole body radioiodine scan was obtained which revealed an iodine-avid left liver lobe mass. Three cycles of radioiodine ablation therapy were unsuccessful and eventually the patient was referred for surgical resection. Metastatic evaluation including a PET scan was negative with the exception of an isolated enhancing 4 cm mass in segment 4B of the liver. Anatomic segmental resection of liver was performed without complications. Intraoperative ultrasonography was used to guide resection of the liver mass. Pathology reports confirmed metastatic follicular variant of PTC. Surgical margins were free of tumor. Patient was discharged home and is doing well one year after surgery. The latest thyroglobulin level was undetectable. Discussion Post-operative surveillance by PCP, endocrinologist or surgeon for patients with thyroid carcinoma should be performed routinely. If identified, a solitary liver metastasis from primary thyroid carcinoma should be considered for surgical resection. Due to sparse data available in literature, collecting more data to establish algorithms for treatment of such rare metastatic cancers may be able to aid physicians to achieve better outcomes. Conclusion Rare distant sites of metastases from DTC include eyes, pharynx, skin, muscle, ovaries, adrenal glands, kidneys, esophagus, pancreas and liver. Isolated, resectable liver metastases from PTC are exceedingly rare. Literature review revealed only 10 reported cases of liver metastases from DTC. As in our patient, solitary liver metastasis from PTC should be considered for surgical resection which offers the best chance for prolonged survival. PMID:25536153

  2. VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing

    PubMed Central

    Medina, Ignacio; De Maria, Alejandro; Bleda, Marta; Salavert, Francisco; Alonso, Roberto; Gonzalez, Cristina Y.; Dopazo, Joaquin

    2012-01-01

    The massive use of Next-Generation Sequencing (NGS) technologies is uncovering an unexpected amount of variability. The functional characterization of such variability, particularly in the most common form of variation found, the Single Nucleotide Variants (SNVs), has become a priority that needs to be addressed in a systematic way. VARIANT (VARIant ANalyis Tool) reports information on the variants found that include consequence type and annotations taken from different databases and repositories (SNPs and variants from dbSNP and 1000 genomes, and disease-related variants from the Genome-Wide Association Study (GWAS) catalog, Online Mendelian Inheritance in Man (OMIM), Catalog of Somatic Mutations in Cancer (COSMIC) mutations, etc). VARIANT also produces a rich variety of annotations that include information on the regulatory (transcription factor or miRNA-binding sites, etc.) or structural roles, or on the selective pressures on the sites affected by the variation. This information allows extending the conventional reports beyond the coding regions and expands the knowledge on the contribution of non-coding or synonymous variants to the phenotype studied. Contrarily to other tools, VARIANT uses a remote database and operates through efficient RESTful Web Services that optimize search and transaction operations. In this way, local problems of installation, update or disk size limitations are overcome without the need of sacrifice speed (thousands of variants are processed per minute). VARIANT is available at: http://variant.bioinfo.cipf.es. PMID:22693211

  3. Hemoglobin Cranston, an unstable variant having an elongated beta chain due to nonhomologous crossover between two normal beta chain genes.

    PubMed Central

    Bunn, H F; Schmidt, G J; Haney, D N; Dluhy, R G

    1975-01-01

    An asymptomatic woman was found to have a compensated hemolytic state due to an unstable hemoglobin variant, comprising 35% of the total. Peptide maps of tryptic digests of the abnormal beta chain were identical to those of beta A except that tryptic peptide 15 (Tyr-His-COOH) was absent and a new peptide was detected, containing equivalent amounts of Ser, Ile, Thr, and Lys. Its sequence was determined by manual Edman degradation. An additional hydrophobic peptide isolated by counter-current distribution contained: Asx, Ser, Ala, Tyr, 2 Phe, and 3 Leu. Its sequence was determined on an automatic solid phase sequencer. Digestion with carboxypeptidase A confirmed the C-terminal sequence. Hemoglobin Cranston has an elongated beta chain with the following structure: (see article). This variant is the first "adult" human hemoglobin known to contain isoleucine. It is likely that hemoglobin Cranston arose because of a nonhomologous crossover of two normal beta chain genes, probably during meiosis, with the insertion of two nucleotides (AG) at position 144, resulting in a frame shift. Hemoglobin Cranston provides new information on the structure of the beta chain gene as well as an explanation of both the structure and genetic basis of hemoglobin Tak, the only other elongated beta chain variant that has been described. Images PMID:1059149

  4. [Specificities of the logopenic variant of primary progressive aphasia].

    PubMed

    Magnin, E; Teichmann, M; Martinaud, O; Moreaud, O; Ryff, I; Belliard, S; Pariente, J; Moulin, T; Vandel, P; Démonet, J-F

    2015-01-01

    The logopenic variant of primary progressive aphasia is a syndrome with neuropsychological and linguistic specificities, including phonological loop impairment for which diagnosis is currently mainly based on the exclusion of the two other variants, semantic and nonfluent/agrammatic primary progressive aphasia. The syndrome may be underdiagnosed due (1) to mild language difficulties during the early stages of the disease or (2) to being mistaken for mild cognitive impairment or Alzheimer's disease when the evaluation of episodic memory is based on verbal material and (3) finally, it is not uncommon that the disorders are attributed to psychiatric co-morbidities such as, for example, anxiety. Moreover, compared to other variants of primary progressive aphasia, brain abnormalities are different. The left temporoparietal junction is initially affected. Neuropathology and biomarkers (cerebrospinal fluid, molecular amyloid nuclear imaging) frequently reveal Alzheimer's disease. Consequently this variant of primary progressive aphasia does not fall under the traditional concept of frontotemporal lobar degeneration. These distinctive features highlight the utility of correct diagnosis, classification, and use of biomarkers to show the neuropathological processes underlying logopenic primary progressive aphasia. The logopenic variant of primary progressive aphasia is a specific form of Alzheimer's disease frequently presenting a rapid decline; specific linguistic therapies are needed. Further investigation of this syndrome is needed to refine screening, improve diagnostic criteria and better understand the epidemiology and the biological mechanisms involved. PMID:25444173

  5. Assessment of Functional Effects of Unclassified Genetic Variants

    PubMed Central

    Couch, Fergus J.; Rasmussen, Lene Juel; Hofstra, Robert; Monteiro, Alvaro N.A.; Greenblatt, Marc S.; de Wind, Niels

    2009-01-01

    Inherited predisposition to disease is often linked to reduced activity of a disease associated gene product. Thus, quantitation of the influence of inherited variants on gene function can potentially be used to predict the disease relevance of these variants. While many disease genes have been extensively characterized at the functional level, few assays based on functional properties of the encoded proteins have been established for the purpose of predicting the contribution of rare inherited variants to disease. Much of the difficulty in establishing predictive functional assays stems from the technical complexity of the assays. However, perhaps the most challenging aspect of functional assay development for clinical testing purposes is the absolute requirement for validation of the sensitivity and specificity of the assays and the determination of positive predictive and negative predictive values of the assays relative to a “gold standard” measure of disease predisposition. In this commentary we provide examples of some of the functional assays under development for several cancer predisposition genes [BRCA1, BRCA2, CDKN2A, and mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2] and present a detailed review of the issues associated with functional assay development. We conclude that validation is paramount for all assays that will be used for clinical interpretation of inherited variants of any gene, but note that in certain circumstances information derived from incompletely validated assays may be valuable for classification of variants for clinical purposes when used to supplement data derived from other sources. PMID:18951449

  6. Common genetic variants influence human subcortical brain structures

    PubMed Central

    Hibar, Derrek P.; Stein, Jason L.; Renteria, Miguel E.; Arias-Vasquez, Alejandro; Desrivières, Sylvane; Jahanshad, Neda; Toro, Roberto; Wittfeld, Katharina; Abramovic, Lucija; Andersson, Micael; Aribisala, Benjamin S.; Armstrong, Nicola J.; Bernard, Manon; Bohlken, Marc M.; Boks, Marco P.; Bralten, Janita; Brown, Andrew A.; Chakravarty, M. Mallar; Chen, Qiang; Ching, Christopher R. K.; Cuellar-Partida, Gabriel; den Braber, Anouk; Giddaluru, Sudheer; Goldman, Aaron L.; Grimm, Oliver; Guadalupe, Tulio; Hass, Johanna; Woldehawariat, Girma; Holmes, Avram J.; Hoogman, Martine; Janowitz, Deborah; Jia, Tianye; Kim, Sungeun; Klein, Marieke; Kraemer, Bernd; Lee, Phil H.; Olde Loohuis, Loes M.; Luciano, Michelle; Macare, Christine; Mather, Karen A.; Mattheisen, Manuel; Milaneschi, Yuri; Nho, Kwangsik; Papmeyer, Martina; Ramasamy, Adaikalavan; Risacher, Shannon L.; Roiz-Santiañez, Roberto; Rose, Emma J.; Salami, Alireza; Sämann, Philipp G.; Schmaal, Lianne; Schork, Andrew J.; Shin, Jean; Strike, Lachlan T.; Teumer, Alexander; van Donkelaar, Marjolein M. J.; van Eijk, Kristel R.; Walters, Raymond K.; Westlye, Lars T.; Whelan, Christopher D.; Winkler, Anderson M.; Zwiers, Marcel P.; Alhusaini, Saud; Athanasiu, Lavinia; Ehrlich, Stefan; Hakobjan, Marina M. H.; Hartberg, Cecilie B.; Haukvik, Unn K.; Heister, Angelien J. G. A. M.; Hoehn, David; Kasperaviciute, Dalia; Liewald, David C. M.; Lopez, Lorna M.; Makkinje, Remco R. R.; Matarin, Mar; Naber, Marlies A. M.; McKay, D. Reese; Needham, Margaret; Nugent, Allison C.; Pütz, Benno; Royle, Natalie A.; Shen, Li; Sprooten, Emma; Trabzuni, Daniah; van der Marel, Saskia S. L.; van Hulzen, Kimm J. E.; Walton, Esther; Wolf, Christiane; Almasy, Laura; Ames, David; Arepalli, Sampath; Assareh, Amelia A.; Bastin, Mark E.; Brodaty, Henry; Bulayeva, Kazima B.; Carless, Melanie A.; Cichon, Sven; Corvin, Aiden; Curran, Joanne E.; Czisch, Michael; de Zubicaray, Greig I.; Dillman, Allissa; Duggirala, Ravi; Dyer, Thomas D.; Erk, Susanne; Fedko, Iryna O.; Ferrucci, Luigi; Foroud, Tatiana M.; Fox, Peter T.; Fukunaga, Masaki; Gibbs, J. Raphael; Göring, Harald H. H.; Green, Robert C.; Guelfi, Sebastian; Hansell, Narelle K.; Hartman, Catharina A.; Hegenscheid, Katrin; Heinz, Andreas; Hernandez, Dena G.; Heslenfeld, Dirk J.; Hoekstra, Pieter J.; Holsboer, Florian; Homuth, Georg; Hottenga, Jouke-Jan; Ikeda, Masashi; Jack, Clifford R.; Jenkinson, Mark; Johnson, Robert; Kanai, Ryota; Keil, Maria; Kent, Jack W.; Kochunov, Peter; Kwok, John B.; Lawrie, Stephen M.; Liu, Xinmin; Longo, Dan L.; McMahon, Katie L.; Meisenzahl, Eva; Melle, Ingrid; Mohnke, Sebastian; Montgomery, Grant W.; Mostert, Jeanette C.; Mühleisen, Thomas W.; Nalls, Michael A.; Nichols, Thomas E.; Nilsson, Lars G.; Nöthen, Markus M.; Ohi, Kazutaka; Olvera, Rene L.; Perez-Iglesias, Rocio; Pike, G. Bruce; Potkin, Steven G.; Reinvang, Ivar; Reppermund, Simone; Rietschel, Marcella; Romanczuk-Seiferth, Nina; Rosen, Glenn D.; Rujescu, Dan; Schnell, Knut; Schofield, Peter R.; Smith, Colin; Steen, Vidar M.; Sussmann, Jessika E.; Thalamuthu, Anbupalam; Toga, Arthur W.; Traynor, Bryan J.; Troncoso, Juan; Turner, Jessica A.; Valdés Hernández, Maria C.; van ’t Ent, Dennis; van der Brug, Marcel; van der Wee, Nic J. A.; van Tol, Marie-Jose; Veltman, Dick J.; Wassink, Thomas H.; Westman, Eric; Zielke, Ronald H.; Zonderman, Alan B.; Ashbrook, David G.; Hager, Reinmar; Lu, Lu; McMahon, Francis J.; Morris, Derek W.; Williams, Robert W.; Brunner, Han G.; Buckner, Randy L.; Buitelaar, Jan K.; Cahn, Wiepke; Calhoun, Vince D.; Cavalleri, Gianpiero L.; Crespo-Facorro, Benedicto; Dale, Anders M.; Davies, Gareth E.; Delanty, Norman; Depondt, Chantal; Djurovic, Srdjan; Drevets, Wayne C.; Espeseth, Thomas; Gollub, Randy L.; Ho, Beng-Choon; Hoffmann, Wolfgang; Hosten, Norbert; Kahn, René S.; Le Hellard, Stephanie; Meyer-Lindenberg, Andreas; Müller-Myhsok, Bertram; Nauck, Matthias; Nyberg, Lars; Pandolfo, Massimo; Penninx, Brenda W. J. H.; Roffman, Joshua L.; Sisodiya, Sanjay M.; Smoller, Jordan W.; van Bokhoven, Hans; van Haren, Neeltje E. M.; Völzke, Henry; Walter, Henrik; Weiner, Michael W.; Wen, Wei; White, Tonya; Agartz, Ingrid; Andreassen, Ole A.; Blangero, John; Boomsma, Dorret I.; Brouwer, Rachel M.; Cannon, Dara M.; Cookson, Mark R.; de Geus, Eco J. C.; Deary, Ian J.; Donohoe, Gary; Fernández, Guillén; Fisher, Simon E.; Francks, Clyde; Glahn, David C.; Grabe, Hans J.; Gruber, Oliver; Hardy, John; Hashimoto, Ryota; Hulshoff Pol, Hilleke E.; Jönsson, Erik G.

    2015-01-01

    The highly complex structure of the human brain is strongly shaped by genetic influences1. Subcortical brain regions form circuits with cortical areas to coordinate movement2, learning, memory3 and motivation4, and altered circuits can lead to abnormal behaviour and disease2. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume5 and intracranial volume6. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10?33; 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability inhuman brain development, and may help to determine mechanisms of neuropsychiatric dysfunction. PMID:25607358

  7. Reliable identification of genomic variants from RNA-seq data.

    PubMed

    Piskol, Robert; Ramaswami, Gokul; Li, Jin Billy

    2013-10-01

    Identifying genomic variation is a crucial step for unraveling the relationship between genotype and phenotype and can yield important insights into human diseases. Prevailing methods rely on cost-intensive whole-genome sequencing (WGS) or whole-exome sequencing (WES) approaches while the identification of genomic variants from often existing RNA sequencing (RNA-seq) data remains a challenge because of the intrinsic complexity in the transcriptome. Here, we present a highly accurate approach termed SNPiR to identify SNPs in RNA-seq data. We applied SNPiR to RNA-seq data of samples for which WGS and WES data are also available and achieved high specificity and sensitivity. Of the SNPs called from the RNA-seq data, >98% were also identified by WGS or WES. Over 70% of all expressed coding variants were identified from RNA-seq, and comparable numbers of exonic variants were identified in RNA-seq and WES. Despite our method's limitation in detecting variants in expressed regions only, our results demonstrate that SNPiR outperforms current state-of-the-art approaches for variant detection from RNA-seq data and offers a cost-effective and reliable alternative for SNP discovery. PMID:24075185

  8. Dynamic histone variant exchange accompanies gene induction in T cells.

    PubMed

    Sutcliffe, Elissa L; Parish, Ian A; He, Yi Qing; Juelich, Torsten; Tierney, M Louise; Rangasamy, Danny; Milburn, Peter J; Parish, Christopher R; Tremethick, David J; Rao, Sudha

    2009-04-01

    Changes in chromatin composition are often a prerequisite for gene induction. Nonallelic histone variants have recently emerged as key players in transcriptional control and chromatin modulation. While the changes in chromatin accessibility and histone posttranslational modification (PTM) distribution that accompany gene induction are well documented, the dynamics of histone variant exchange that parallel these events are still poorly defined. In this study, we have examined the changes in histone variant distribution that accompany activation of the inducible CD69 and heparanase genes in T cells. We demonstrate that the chromatin accessibility increases that accompany the induction of both of these genes are not associated with nucleosome loss but instead are paralleled by changes in histone variant distribution. Specifically, induction of these genes was paralleled by depletion of the H2A.Z histone variant and concomitant deposition of H3.3. Furthermore, H3.3 deposition was accompanied by changes in PTM patterns consistent with H3.3 enriching or depleting different PTMs upon incorporation into chromatin. Nevertheless, we present evidence that these H3.3-borne PTMs can be negated by recruited enzymatic activities. From these observations, we propose that H3.3 deposition may both facilitate chromatin accessibility increases by destabilizing nucleosomes and compete with recruited histone modifiers to alter PTM patterns upon gene induction. PMID:19158270

  9. Common genetic variants influence human subcortical brain structures.

    PubMed

    Hibar, Derrek P; Stein, Jason L; Renteria, Miguel E; Arias-Vasquez, Alejandro; Desrivières, Sylvane; Jahanshad, Neda; Toro, Roberto; Wittfeld, Katharina; Abramovic, Lucija; Andersson, Micael; Aribisala, Benjamin S; Armstrong, Nicola J; Bernard, Manon; Bohlken, Marc M; Boks, Marco P; Bralten, Janita; Brown, Andrew A; Chakravarty, M Mallar; Chen, Qiang; Ching, Christopher R K; Cuellar-Partida, Gabriel; den Braber, Anouk; Giddaluru, Sudheer; Goldman, Aaron L; Grimm, Oliver; Guadalupe, Tulio; Hass, Johanna; Woldehawariat, Girma; Holmes, Avram J; Hoogman, Martine; Janowitz, Deborah; Jia, Tianye; Kim, Sungeun; Klein, Marieke; Kraemer, Bernd; Lee, Phil H; Olde Loohuis, Loes M; Luciano, Michelle; Macare, Christine; Mather, Karen A; Mattheisen, Manuel; Milaneschi, Yuri; Nho, Kwangsik; Papmeyer, Martina; Ramasamy, Adaikalavan; Risacher, Shannon L; Roiz-Santiañez, Roberto; Rose, Emma J; Salami, Alireza; Sämann, Philipp G; Schmaal, Lianne; Schork, Andrew J; Shin, Jean; Strike, Lachlan T; Teumer, Alexander; van Donkelaar, Marjolein M J; van Eijk, Kristel R; Walters, Raymond K; Westlye, Lars T; Whelan, Christopher D; Winkler, Anderson M; Zwiers, Marcel P; Alhusaini, Saud; Athanasiu, Lavinia; Ehrlich, Stefan; Hakobjan, Marina M H; Hartberg, Cecilie B; Haukvik, Unn K; Heister, Angelien J G A M; Hoehn, David; Kasperaviciute, Dalia; Liewald, David C M; Lopez, Lorna M; Makkinje, Remco R R; Matarin, Mar; Naber, Marlies A M; McKay, D Reese; Needham, Margaret; Nugent, Allison C; Pütz, Benno; Royle, Natalie A; Shen, Li; Sprooten, Emma; Trabzuni, Daniah; van der Marel, Saskia S L; van Hulzen, Kimm J E; Walton, Esther; Wolf, Christiane; Almasy, Laura; Ames, David; Arepalli, Sampath; Assareh, Amelia A; Bastin, Mark E; Brodaty, Henry; Bulayeva, Kazima B; Carless, Melanie A; Cichon, Sven; Corvin, Aiden; Curran, Joanne E; Czisch, Michael; de Zubicaray, Greig I; Dillman, Allissa; Duggirala, Ravi; Dyer, Thomas D; Erk, Susanne; Fedko, Iryna O; Ferrucci, Luigi; Foroud, Tatiana M; Fox, Peter T; Fukunaga, Masaki; Gibbs, J Raphael; Göring, Harald H H; Green, Robert C; Guelfi, Sebastian; Hansell, Narelle K; Hartman, Catharina A; Hegenscheid, Katrin; Heinz, Andreas; Hernandez, Dena G; Heslenfeld, Dirk J; Hoekstra, Pieter J; Holsboer, Florian; Homuth, Georg; Hottenga, Jouke-Jan; Ikeda, Masashi; Jack, Clifford R; Jenkinson, Mark; Johnson, Robert; Kanai, Ryota; Keil, Maria; Kent, Jack W; Kochunov, Peter; Kwok, John B; Lawrie, Stephen M; Liu, Xinmin; Longo, Dan L; McMahon, Katie L; Meisenzahl, Eva; Melle, Ingrid; Mohnke, Sebastian; Montgomery, Grant W; Mostert, Jeanette C; Mühleisen, Thomas W; Nalls, Michael A; Nichols, Thomas E; Nilsson, Lars G; Nöthen, Markus M; Ohi, Kazutaka; Olvera, Rene L; Perez-Iglesias, Rocio; Pike, G Bruce; Potkin, Steven G; Reinvang, Ivar; Reppermund, Simone; Rietschel, Marcella; Romanczuk-Seiferth, Nina; Rosen, Glenn D; Rujescu, Dan; Schnell, Knut; Schofield, Peter R; Smith, Colin; Steen, Vidar M; Sussmann, Jessika E; Thalamuthu, Anbupalam; Toga, Arthur W; Traynor, Bryan J; Troncoso, Juan; Turner, Jessica A; Valdés Hernández, Maria C; van 't Ent, Dennis; van der Brug, Marcel; van der Wee, Nic J A; van Tol, Marie-Jose; Veltman, Dick J; Wassink, Thomas H; Westman, Eric; Zielke, Ronald H; Zonderman, Alan B; Ashbrook, David G; Hager, Reinmar; Lu, Lu; McMahon, Francis J; Morris, Derek W; Williams, Robert W; Brunner, Han G; Buckner, Randy L; Buitelaar, Jan K; Cahn, Wiepke; Calhoun, Vince D; Cavalleri, Gianpiero L; Crespo-Facorro, Benedicto; Dale, Anders M; Davies, Gareth E; Delanty, Norman; Depondt, Chantal; Djurovic, Srdjan; Drevets, Wayne C; Espeseth, Thomas; Gollub, Randy L; Ho, Beng-Choon; Hoffmann, Wolfgang; Hosten, Norbert; Kahn, René S; Le Hellard, Stephanie; Meyer-Lindenberg, Andreas; Müller-Myhsok, Bertram; Nauck, Matthias; Nyberg, Lars; Pandolfo, Massimo; Penninx, Brenda W J H; Roffman, Joshua L; Sisodiya, Sanjay M; Smoller, Jordan W; van Bokhoven, Hans; van Haren, Neeltje E M; Völzke, Henry; Walter, Henrik; Weiner, Michael W; Wen, Wei; White, Tonya; Agartz, Ingrid; Andreassen, Ole A; Blangero, John; Boomsma, Dorret I; Brouwer, Rachel M; Cannon, Dara M; Cookson, Mark R; de Geus, Eco J C; Deary, Ian J; Donohoe, Gary; Fernández, Guillén; Fisher, Simon E; Francks, Clyde; Glahn, David C; Grabe, Hans J; Gruber, Oliver; Hardy, John; Hashimoto, Ryota; Hulshoff Pol, Hilleke E; Jönsson, Erik G; Kloszewska, Iwona; Lovestone, Simon; Mattay, Venkata S; Mecocci, Patrizia; McDonald, Colm; McIntosh, Andrew M; Ophoff, Roel A; Paus, Tomas; Pausova, Zdenka; Ryten, Mina; Sachdev, Perminder S; Saykin, Andrew J; Simmons, Andy

    2015-04-01

    The highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume and intracranial volume. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08?×?10(-33); 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability in human brain development, and may help to determine mechanisms of neuropsychiatric dysfunction. PMID:25607358

  10. Testing optimally weighted combination of variants for hypertension

    PubMed Central

    2014-01-01

    Testing rare variants directly is possible with next-generation sequencing technology. In this article, we propose a sliding-window-based optimal-weighted approach to test for the effects of both rare and common variants across the whole genome. We measured the genetic association between a disease and a combination of variants of a single-nucleotide polymorphism window using the newly developed tests TOW and VW-TOW and performed a sliding-window technique to detect disease-susceptible windows. By applying the new approach to unrelated individuals of Genetic Analysis Workshop 18 on replicate 1 chromosome 3, we detected 3 highly susceptible windows across chromosome 3 for diastolic blood pressure and identified 10 of 48,176 windows as the most promising for both diastolic and systolic blood pressure. Seven of 9 top variants influencing diastolic blood pressure and 8 of 9 top variants influencing systolic blood pressure were found in or close to our top 10 windows. PMID:25519394

  11. A magnetic non-reciprocal isolator for broadband terahertz operation

    NASA Astrophysics Data System (ADS)

    Shalaby, Mostafa; Peccianti, Marco; Ozturk, Yavuz; Morandotti, Roberto

    2013-03-01

    A Faraday isolator is an electromagnetic non-reciprocal device, a key element in photonics. It is required to shield electromagnetic sources against the effect of back-reflected light, as well as to limit the detrimental effect of back-propagating spontaneous emissions. A common isolator variant, the circulator, is widely used to obtain a complete separation between forward- and backward-propagating waves, thus enabling the realization of a desired transfer function in reflection only. Here we demonstrate a non-reciprocal terahertz Faraday isolator, operating on a bandwidth exceeding one decade of frequency, a necessary requirement to achieve isolation with the (few-cycle) pulses generated by broadband sources. The exploited medium allows a broadband rotation, up to 194°/T, obtained using a SrFe12O19 terahertz-transparent permanent magnet. This in turn enables the design of a stand-alone complete terahertz isolator without resorting to an external magnetic field bias, as opposed to all the optical isolators realized so far.

  12. A magnetic non-reciprocal isolator for broadband terahertz operation

    PubMed Central

    Shalaby, Mostafa; Peccianti, Marco; Ozturk, Yavuz; Morandotti, Roberto

    2013-01-01

    A Faraday isolator is an electromagnetic non-reciprocal device, a key element in photonics. It is required to shield electromagnetic sources against the effect of back-reflected light, as well as to limit the detrimental effect of back-propagating spontaneous emissions. A common isolator variant, the circulator, is widely used to obtain a complete separation between forward- and backward-propagating waves, thus enabling the realization of a desired transfer function in reflection only. Here we demonstrate a non-reciprocal terahertz Faraday isolator, operating on a bandwidth exceeding one decade of frequency, a necessary requirement to achieve isolation with the (few-cycle) pulses generated by broadband sources. The exploited medium allows a broadband rotation, up to 194°/T, obtained using a SrFe12O19 terahertz-transparent permanent magnet. This in turn enables the design of a stand-alone complete terahertz isolator without resorting to an external magnetic field bias, as opposed to all the optical isolators realized so far. PMID:23463001

  13. In vitro digestion of purified ?-casein variants A(1), A(2), B, and I: effects on antioxidant and angiotensin-converting enzyme inhibitory capacity.

    PubMed

    Petrat-Melin, B; Andersen, P; Rasmussen, J T; Poulsen, N A; Larsen, L B; Young, J F

    2015-01-01

    Genetic polymorphisms of bovine milk proteins affect the protein profile of the milk and, hence, certain technological properties, such as casein (CN) number and cheese yield. However, reports show that such polymorphisms may also affect the health-related properties of milk. Therefore, to gain insight into their digestion pattern and bioactive potential, ?-CN was purified from bovine milk originating from cows homozygous for the variants A(1), A(2), B, and I by a combination of cold storage, ultracentrifugation, and acid precipitation. The purity of the isolated ?-CN was determined by HPLC, variants were verified by mass spectrometry, and molar extinction coefficients at ?=280nm were determined. ?-Casein from each of the variants was subjected to in vitro digestion using pepsin and pancreatic enzymes. Antioxidant and angiotensin-converting enzyme (ACE) inhibitory capacities of the hydrolysates were assessed at 3 stages of digestion and related to that of the undigested samples. Neither molar extinction coefficients nor overall digestibility varied significantly between these 4 variants; however, clear differences in digestion pattern were indicated by gel electrophoresis. In particular, after 60min of pepsin followed by 5min of pancreatic enzyme digestion, one ?4kDa peptide with the N-terminal sequence (106)H-K-E-M-P-F-P-K- was absent from ?-CN variant B. This is likely a result of the (122)Ser to (122)Arg substitution in variant B introducing a novel trypsin cleavage site, leading to the changed digestion pattern. All investigated ?-CN variants exhibited a significant increase in antioxidant capacity upon digestion, as measured by the Trolox-equivalent antioxidant capacity assay. After 60min of pepsin + 120min of pancreatic enzyme digestion, the accumulated increase in antioxidant capacity was ?1.7-fold for the 4 ?-CN variants. The ACE inhibitory capacity was also significantly increased by digestion, with the B variant reaching the highest inhibitory capacity at the end of digestion (60min of pepsin + 120min of pancreatic enzymes), possibly because of the observed alternative digestion pattern. These results demonstrate that genetic polymorphisms affect the digestion pattern and bioactivity of milk proteins. Moreover, their capacity for radical scavenging and ACE inhibition is affected by digestion. PMID:25465543

  14. HIV-1 Replication Fitness of HLA-B*57/58:01 CTL Escape Variants Is Restored by the Accumulation of Compensatory Mutations in Gag

    PubMed Central

    Gijsbers, Esther F.; Feenstra, K. Anton; van Nuenen, Ad C.; Navis, Marjon; Heringa, Jaap; Schuitemaker, Hanneke; Kootstra, Neeltje A.

    2013-01-01

    Expression of HLA-B*57 and the closely related HLA-B*58:01 are associated with prolonged survival after HIV-1 infection. However, large differences in disease course are observed among HLA-B*57/58:01 patients. Escape mutations in CTL epitopes restricted by these HLA alleles come at a fitness cost and particularly the T242N mutation in the TW10 CTL epitope in Gag has been demonstrated to decrease the viral replication capacity. Additional mutations within or flanking this CTL epitope can partially restore replication fitness of CTL escape variants. Five HLA-B*57/58:01 progressors and 5 HLA-B*57/58:01 long-term nonprogressors (LTNPs) were followed longitudinally and we studied which compensatory mutations were involved in the restoration of the viral fitness of variants that escaped from HLA-B*57/58:01-restricted CTL pressure. The Sequence Harmony algorithm was used to detect homology in amino acid composition by comparing longitudinal Gag sequences obtained from HIV-1 patients positive and negative for HLA-B*57/58:01 and from HLA-B*57/58:01 progressors and LTNPs. Although virus isolates from HLA-B*57/58:01 individuals contained multiple CTL escape mutations, these escape mutations were not associated with disease progression. In sequences from HLA-B*57/58:01 progressors, 5 additional mutations in Gag were observed: S126N, L215T, H219Q, M228I and N252H. The combination of these mutations restored the replication fitness of CTL escape HIV-1 variants. Furthermore, we observed a positive correlation between the number of escape and compensatory mutations in Gag and the replication fitness of biological HIV-1 variants isolated from HLA-B*57/58:01 patients, suggesting that the replication fitness of HLA-B*57/58:01 escape variants is restored by accumulation of compensatory mutations. PMID:24339913

  15. HIV-1 replication fitness of HLA-B*57/58:01 CTL escape variants is restored by the accumulation of compensatory mutations in gag.

    PubMed

    Gijsbers, Esther F; Feenstra, K Anton; van Nuenen, Ad C; Navis, Marjon; Heringa, Jaap; Schuitemaker, Hanneke; Kootstra, Neeltje A

    2013-01-01

    Expression of HLA-B*57 and the closely related HLA-B*58:01 are associated with prolonged survival after HIV-1 infection. However, large differences in disease course are observed among HLA-B*57/58:01 patients. Escape mutations in CTL epitopes restricted by these HLA alleles come at a fitness cost and particularly the T242N mutation in the TW10 CTL epitope in Gag has been demonstrated to decrease the viral replication capacity. Additional mutations within or flanking this CTL epitope can partially restore replication fitness of CTL escape variants. Five HLA-B*57/58:01 progressors and 5 HLA-B*57/58:01 long-term nonprogressors (LTNPs) were followed longitudinally and we studied which compensatory mutations were involved in the restoration of the viral fitness of variants that escaped from HLA-B*57/58:01-restricted CTL pressure. The Sequence Harmony algorithm was used to detect homology in amino acid composition by comparing longitudinal Gag sequences obtained from HIV-1 patients positive and negative for HLA-B*57/58:01 and from HLA-B*57/58:01 progressors and LTNPs. Although virus isolates from HLA-B*57/58:01 individuals contained multiple CTL escape mutations, these escape mutations were not associated with disease progression. In sequences from HLA-B*57/58:01 progressors, 5 additional mutations in Gag were observed: S126N, L215T, H219Q, M228I and N252H. The combination of these mutations restored the replication fitness of CTL escape HIV-1 variants. Furthermore, we observed a positive correlation between the number of escape and compensatory mutations in Gag and the replication fitness of biological HIV-1 variants isolated from HLA-B*57/58:01 patients, suggesting that the replication fitness of HLA-B*57/58:01 escape variants is restored by accumulation of compensatory mutations. PMID:24339913

  16. 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

    ABSTRACT 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